From d053d02b63f5b7607b0765436d4d21d0b9e5d5fe Mon Sep 17 00:00:00 2001 From: github-actions-bot Date: Thu, 9 May 2024 19:08:01 +0000 Subject: [PATCH] Updates --- asset-manifest.json | 14 +++++++------- config/preview.js | 7 ++++++- index.html | 2 +- static/js/565.0856c1ff.chunk.js | 2 -- static/js/565.0856c1ff.chunk.js.map | 1 - static/js/565.0cd6df73.chunk.js | 2 ++ static/js/565.0cd6df73.chunk.js.map | 1 + static/js/745.e10b3c15.chunk.js | 3 --- static/js/745.f88f3252.chunk.js | 3 +++ ...CENSE.txt => 745.f88f3252.chunk.js.LICENSE.txt} | 0 ...3c15.chunk.js.map => 745.f88f3252.chunk.js.map} | 2 +- static/js/main.321ceb08.js.map | 1 - static/js/{main.321ceb08.js => main.5eaa645c.js} | 6 +++--- ...js.LICENSE.txt => main.5eaa645c.js.LICENSE.txt} | 0 static/js/main.5eaa645c.js.map | 1 + 15 files changed, 25 insertions(+), 20 deletions(-) delete mode 100644 static/js/565.0856c1ff.chunk.js delete mode 100644 static/js/565.0856c1ff.chunk.js.map create mode 100644 static/js/565.0cd6df73.chunk.js create mode 100644 static/js/565.0cd6df73.chunk.js.map delete mode 100644 static/js/745.e10b3c15.chunk.js create mode 100644 static/js/745.f88f3252.chunk.js rename static/js/{745.e10b3c15.chunk.js.LICENSE.txt => 745.f88f3252.chunk.js.LICENSE.txt} (100%) rename static/js/{745.e10b3c15.chunk.js.map => 745.f88f3252.chunk.js.map} (62%) delete mode 100644 static/js/main.321ceb08.js.map rename static/js/{main.321ceb08.js => main.5eaa645c.js} (99%) rename static/js/{main.321ceb08.js.LICENSE.txt => main.5eaa645c.js.LICENSE.txt} (100%) create mode 100644 static/js/main.5eaa645c.js.map diff --git a/asset-manifest.json b/asset-manifest.json index 5955512e..c14586a1 100644 --- a/asset-manifest.json +++ b/asset-manifest.json @@ -1,13 +1,13 @@ { "files": { "main.css": "https://imagingdatacommons.github.io/slim/static/css/main.e6c13ad2.css", - "main.js": "https://imagingdatacommons.github.io/slim/static/js/main.321ceb08.js", + "main.js": "https://imagingdatacommons.github.io/slim/static/js/main.5eaa645c.js", "static/css/455.b37fdaf9.chunk.css": "https://imagingdatacommons.github.io/slim/static/css/455.b37fdaf9.chunk.css", "static/js/455.46becc8e.chunk.js": "https://imagingdatacommons.github.io/slim/static/js/455.46becc8e.chunk.js", "static/css/267.ca42ab60.chunk.css": "https://imagingdatacommons.github.io/slim/static/css/267.ca42ab60.chunk.css", "static/js/267.9beeab82.chunk.js": "https://imagingdatacommons.github.io/slim/static/js/267.9beeab82.chunk.js", - "static/js/745.e10b3c15.chunk.js": "https://imagingdatacommons.github.io/slim/static/js/745.e10b3c15.chunk.js", - "static/js/565.0856c1ff.chunk.js": "https://imagingdatacommons.github.io/slim/static/js/565.0856c1ff.chunk.js", + "static/js/745.f88f3252.chunk.js": "https://imagingdatacommons.github.io/slim/static/js/745.f88f3252.chunk.js", + "static/js/565.0cd6df73.chunk.js": "https://imagingdatacommons.github.io/slim/static/js/565.0cd6df73.chunk.js", "static/js/dicomMicroscopyViewer.min.js.map": "https://imagingdatacommons.github.io/slim/static/js/dicomMicroscopyViewer.min.js.map", "static/js/dicomMicroscopyViewer.min.js": "https://imagingdatacommons.github.io/slim/static/js/dicomMicroscopyViewer.min.js", "static/js/index.worker.min.worker.js.map": "https://imagingdatacommons.github.io/slim/static/js/index.worker.min.worker.js.map", @@ -15,16 +15,16 @@ "static/js/index.worker.min.worker.js": "https://imagingdatacommons.github.io/slim/static/js/index.worker.min.worker.js", "index.html": "https://imagingdatacommons.github.io/slim/index.html", "main.e6c13ad2.css.map": "https://imagingdatacommons.github.io/slim/static/css/main.e6c13ad2.css.map", - 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"static/js/main.321ceb08.js" + "static/js/main.5eaa645c.js" ] } \ No newline at end of file diff --git a/config/preview.js b/config/preview.js index 0ac792bf..86ad1953 100644 --- a/config/preview.js +++ b/config/preview.js @@ -7,6 +7,11 @@ window.config = { write: false } ], + disableWorklist: false, + disableAnnotationTools: false, + enableServerSelection: true, + mode: "light", + preload: true, annotations: [ { finding: { value: '85756007', schemeDesignator: 'SCT', meaning: 'Tissue' }, @@ -19,6 +24,6 @@ window.config = { color: [255, 255, 255, 0.2] } } - }, + } ] } diff --git a/index.html b/index.html index cfd347f5..ae3ab968 100644 --- a/index.html +++ b/index.html @@ -1 +1 @@ -Slim
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0})}if(null!=e.SoftcopyVOILUTSequence){var l=e.SoftcopyVOILUTSequence[0],c=l.WindowCenter,d=l.WindowWidth;r=[c-.5*d,c+.5*d]}n[i]={opacity:1,paletteColorLookupTable:o,limitValues:r}}}))}))}));var i=new Set;Object.keys(n).forEach((function(e){var t=n[e];null!=t?(a.volumeViewer.setOpticalPathStyle(e,t),a.volumeViewer.activateOpticalPath(e),a.volumeViewer.showOpticalPath(e),i.add(e)):(a.volumeViewer.hideOpticalPath(e),a.volumeViewer.deactivateOpticalPath(e))}));var o=new URLSearchParams(a.props.location.search);o.set("state",e.SOPInstanceUID),a.props.navigate({pathname:a.props.location.pathname,search:o.toString()},{replace:!0}),a.setState((function(t){return{activeOpticalPathIdentifiers:i,visibleOpticalPathIdentifiers:i,selectedPresentationStateUID:e.SOPInstanceUID}}))},a.getRoiStyle=function(e){return null==e?a.defaultRoiStyle:void 0!==a.roiStyles[e]?a.roiStyles[e]:a.defaultRoiStyle},a.addAnnotations=function(){console.info("search for Comprehensive 3D SR instances");var e=a.props.clients[M.COMPREHENSIVE_3D_SR];e.searchForInstances({studyInstanceUID:a.props.studyInstanceUID,queryParams:{Modality:"SR"}}).then((function(t){null==t&&(t=[]),t.forEach((function(t){var n=g.metadata.formatMetadata(t).dataset;n.SOPClassUID===M.COMPREHENSIVE_3D_SR&&(console.info('retrieve SR instance "'.concat(n.SOPInstanceUID,'"')),e.retrieveInstance({studyInstanceUID:a.props.studyInstanceUID,seriesInstanceUID:n.SeriesInstanceUID,sopInstanceUID:n.SOPInstanceUID}).then((function(e){var t=fe.aT.DicomMessage.readFile(e),n=g.metadata.formatMetadata(t.dict).dataset;(function(e){var t=e.ContentTemplateSequence;return t.length>0&&"1500"===t[0].TemplateIdentifier})(n)?!function(e){var t=je({content:e.ContentSequence,name:new fe.sr.coding.CodedConcept({value:"121024",schemeDesignator:"DCM",meaning:"Subject Class"})});if(0===t.length)return!1;var n=t[0].ConceptCodeSequence[0],i=new fe.sr.coding.CodedConcept({value:n.CodeValue,meaning:n.CodeMeaning,schemeDesignator:n.CodingSchemeDesignator}),a=new fe.sr.coding.CodedConcept({value:"121027",meaning:"Specimen",schemeDesignator:"DCM"});return!!i.equals(a)}(n)?console.debug('ignore SR document "'.concat(n.SOPInstanceUID,'" ')+"because it does not describe a specimen subject"):!function(e){var t=je({content:e.ContentSequence,name:new fe.sr.coding.CodedConcept({value:"126010",schemeDesignator:"DCM",meaning:"Imaging Measurements"})});if(0===t.length)return!1;var n=t[0],i=je({content:n.ContentSequence,name:new fe.sr.coding.CodedConcept({value:"125007",schemeDesignator:"DCM",meaning:"Measurement Group"})}),a=!1;return i.forEach((function(e){var t=je({content:e.ContentSequence,name:new fe.sr.coding.CodedConcept({value:"111030",schemeDesignator:"DCM",meaning:"Image Region"})});t.length>0&&t[0].ValueType===fe.sr.valueTypes.ValueTypes.SCOORD3D&&(a=!0)})),a}(n)?console.debug('ignore SR document "'.concat(n.SOPInstanceUID,'" ')+"because it does not contain any suitable ROI annotations"):new Te(n).ROIs.forEach((function(e){console.info('add ROI "'.concat(e.uid,'"'));var t=e.scoord3d,i=a.props.slide.volumeImages[0];if(t.frameOfReferenceUID===i.FrameOfReferenceUID){var o=a.volumeViewer.getAllROIs().some((function(t){return function(e,t){if(e.scoord3d.graphicType!==t.scoord3d.graphicType)return!1;if(e.scoord3d.frameOfReferenceUID!==t.scoord3d.frameOfReferenceUID)return!1;if(e.scoord3d.graphicData.length!==t.scoord3d.graphicData.length)return!1;for(var n=0;n0){try{a.volumeViewer.addSegments(t)}catch(n){$.onError(H,new q(G,"Segmentations cannot be displayed")),console.error("failed to add segments: ",n)}a.forceUpdate()}})).catch((function(e){console.error(e),$.onError(H,new q(G,"Retrieval of metadata of Segmentation instances failed."))}))}))})).catch((function(e){console.error(e),$.onError(H,new q(G,"Search for Segmentation instances failed."))}))},a.addParametricMaps=function(){console.info("search for Parametric Map instances");var e=a.props.clients[M.PARAMETRIC_MAP];e.searchForSeries({studyInstanceUID:a.props.studyInstanceUID,queryParams:{Modality:"OT"}}).then((function(t){null==t&&(t=[]),t.forEach((function(t){var n=g.metadata.formatMetadata(t).dataset;e.retrieveSeriesMetadata({studyInstanceUID:a.props.studyInstanceUID,seriesInstanceUID:n.SeriesInstanceUID}).then((function(e){var t=[];if(e.forEach((function(e){var n=new g.metadata.ParametricMap({metadata:e}),i=a.props.slide.volumeImages[0];n.FrameOfReferenceUID===i.FrameOfReferenceUID&&n.ContainerIdentifier===i.ContainerIdentifier?t.push(n):console.warn('skip Parametric Map instance "'.concat(n.SOPInstanceUID,'"'))})),t.length>0){try{a.volumeViewer.addParameterMappings(t)}catch(n){$.onError(H,new q(G,"Parametric Map cannot be displayed")),console.error("failed to add mappings: ",n)}a.forceUpdate()}})).catch((function(e){console.error(e),$.onError(H,new q(G,"Retrieval of metadata of Parametric Map instances failed."))}))}))})).catch((function(e){console.error(e),$.onError(H,new q(G,"Search for Parametric Map instances failed."))}))},a.populateViewports=function(){console.info("populate viewports..."),a.setState({isLoading:!0,presentationStates:[]}),null!=a.volumeViewportRef.current&&a.volumeViewer.render({container:a.volumeViewportRef.current}),null!=a.labelViewportRef.current&&null!=a.labelViewer&&a.labelViewer.render({container:a.labelViewportRef.current}),a.setState({isLoading:!1}),a.setDefaultPresentationState(),a.loadPresentationStates(),a.addAnnotations(),a.addAnnotationGroups(),a.addSegmentations(),a.addParametricMaps()},a.onRoiModified=function(e){a.setState((function(e){return{visibleRoiUIDs:new Set(e.visibleRoiUIDs)}}))},a.onWindowResize=function(e){console.info("resize viewports"),a.volumeViewer.resize(),null!=a.labelViewer&&a.labelViewer.resize()},a.onRoiDrawn=function(e){var t=e.detail.payload,n=a.state.selectedFinding,i=a.state.selectedEvaluations;if(void 0!==t&&void 0!==n){console.debug('add ROI "'.concat(t.uid,'"'));var o=new fe.sr.valueTypes.CodeContentItem({name:new fe.sr.coding.CodedConcept({value:"121071",meaning:"Finding",schemeDesignator:"DCM"}),value:n,relationshipType:"CONTAINS"});t.addEvaluation(o),i.forEach((function(e){var n=new fe.sr.valueTypes.CodeContentItem({name:e.name,value:e.value,relationshipType:"CONTAINS"});t.addEvaluation(n)}));var r=rt(n),s=a.getRoiStyle(r);a.volumeViewer.addROI(t,s),a.setState((function(e){var n=e.visibleRoiUIDs;return n.add(t.uid),{visibleRoiUIDs:n}}))}else console.debug('could not add ROI "'.concat(t.uid,'"'))},a.onRoiDoubleClicked=function(e){null!=e.detail.payload?a.setState({isSelectedRoiModalVisible:!0}):a.setState({isSelectedRoiModalVisible:!1})},a.onRoiSelected=function(e){var t=e.detail.payload;if(null!=t){console.debug('selected ROI "'.concat(t.uid,'"')),a.volumeViewer.setROIStyle(t.uid,a.selectedRoiStyle);var n=st(t);a.volumeViewer.getAllROIs().forEach((function(e){e.uid!==t.uid&&a.volumeViewer.setROIStyle(e.uid,a.getRoiStyle(n))})),a.setState({selectedRoiUIDs:new Set([t.uid]),selectedRoi:t})}else a.setState({selectedRoiUIDs:new Set,selectedRoi:void 0})},a.onLoadingStarted=function(e){a.setState({isLoading:!0})},a.onLoadingEnded=function(e){a.setState({isLoading:!1})},a.onFrameLoadingStarted=function(e){var t=e.detail.payload,n="".concat(t.sopInstanceUID,"-").concat(t.frameNumber);a.setState((function(e){return e.loadingFrames.add(n),e}))},a.onFrameLoadingError=function(e){console.error("Failed to load frame")},a.onLoadingError=function(e){console.error("Failed to load data"),$.onError(H,new q(G,e.detail.payload&&e.detail.payload.message?e.detail.payload.message:"Failed to load data"))},a.onFrameLoadingEnded=function(e){var t=e.detail.payload,n="".concat(t.sopInstanceUID,"-").concat(t.frameNumber);if(a.setState((function(e){e.loadingFrames.delete(n);var t=!1;return e.loadingFrames.size>0&&(t=!0),{isLoading:t,loadingFrames:e.loadingFrames}})),t.sopClassUID===M.VL_WHOLE_SLIDE_MICROSCOPY_IMAGE&&a.props.slide.areVolumeImagesMonochrome){var i=t.channelIdentifier;if(!(i in a.state.pixelDataStatistics)&&null!=t.pixelArray){for(var o=Math.pow(2,16),r=Math.ceil(t.pixelArray.length/o),s=0,l=[],c=[],d=0;d=n&&t<=i)return void this.setState({selectedXCoordinate:t,isSelectedXCoordinateValid:!0})}this.setState({selectedXCoordinate:void 0,isSelectedXCoordinateValid:!1})}},{key:"handleYCoordinateSelection",value:function(e){if(null!=e){var t=Number(e),n=this.state.validYCoordinateRange[0],i=this.state.validYCoordinateRange[1];if(t>=n&&t<=i)return void this.setState({selectedYCoordinate:t,isSelectedYCoordinateValid:!0})}this.setState({selectedYCoordinate:void 0,isSelectedYCoordinateValid:!1})}},{key:"handleMagnificationSelection",value:function(e){null!=e&&e>0&&e<=40?this.setState({selectedMagnification:Number(e),isSelectedMagnificationValid:!0}):this.setState({selectedMagnification:void 0,isSelectedMagnificationValid:!1})}},{key:"handleSlidePositionSelection",value:function(){if(this.state.isSelectedXCoordinateValid&&this.state.isSelectedYCoordinateValid&&this.state.isSelectedMagnificationValid&&null!=this.state.selectedXCoordinate&&null!=this.state.selectedYCoordinate&&null!=this.state.selectedMagnification){console.info("select slide position "+"(".concat(this.state.selectedXCoordinate,", ")+"".concat(this.state.selectedYCoordinate,") ")+"at ".concat(this.state.selectedMagnification,"x magnification"));for(var e=.01/this.state.selectedMagnification,t=[],n=0;n1&&$.onError(H,new q(G,"More than one specimen has been described for the slide"));var a,o=i.SpecimenDescriptionSequence[0];console.debug("create Observation Context"),void 0!==this.props.user?a=new fe.sr.templates.PersonObserverIdentifyingAttributes({name:this.props.user.name,loginName:this.props.user.email}):(console.warn("no user information available"),a=new fe.sr.templates.PersonObserverIdentifyingAttributes({name:"ANONYMOUS"}));var r=new fe.sr.templates.ObservationContext({observerPersonContext:new fe.sr.templates.ObserverContext({observerType:new fe.sr.coding.CodedConcept({value:"121006",schemeDesignator:"DCM",meaning:"Person"}),observerIdentifyingAttributes:a}),observerDeviceContext:new fe.sr.templates.ObserverContext({observerType:new fe.sr.coding.CodedConcept({value:"121007",schemeDesignator:"DCM",meaning:"Device"}),observerIdentifyingAttributes:new fe.sr.templates.DeviceObserverIdentifyingAttributes({uid:this.props.app.uid,manufacturerName:"MGH Computational Pathology",modelName:this.props.app.name})}),subjectContext:new fe.sr.templates.SubjectContext({subjectClass:new fe.sr.coding.CodedConcept({value:"121027",schemeDesignator:"DCM",meaning:"Specimen"}),subjectClassSpecificContext:new fe.sr.templates.SubjectContextSpecimen({uid:o.SpecimenUID,identifier:o.SpecimenIdentifier,containerIdentifier:i.ContainerIdentifier})})});console.debug("encode Imaging Measurements");for(var s=[],l=0;l0?(this.state.selectedRoiUIDs.forEach((function(t){void 0!==t?(console.info('remove ROI "'.concat(t,'"')),e.volumeViewer.removeROI(t),u.ZP.info("Annotation was removed")):u.ZP.warning("No annotation was selected for removal")})),this.setState({selectedRoiUIDs:new Set,isRoiTranslationActive:!1,isRoiDrawingActive:!1,isRoiModificationActive:!1})):(this.state.visibleRoiUIDs.forEach((function(t){console.info('remove ROI "'.concat(t,'"')),e.volumeViewer.removeROI(t)})),this.setState({visibleRoiUIDs:new 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e=this,t=[],n=[],i=[],a=[];t.push.apply(t,(0,ie.Z)(this.volumeViewer.getAllROIs())),n.push.apply(n,(0,ie.Z)(this.volumeViewer.getAllSegments())),i.push.apply(i,(0,ie.Z)(this.volumeViewer.getAllParameterMappings())),a.push.apply(a,(0,ie.Z)(this.volumeViewer.getAllAnnotationGroups()));var o,r,s=["specimens","optical-paths","annotations","presentation-states"],c=this.state.generatedReport;void 0!==c&&(o=(0,I.jsx)(Ae,{dataset:c})),t.length>0&&(r=(0,I.jsx)(Ie,{rois:t,selectedRoiUIDs:this.state.selectedRoiUIDs,visibleRoiUIDs:this.state.visibleRoiUIDs,onSelection:this.handleAnnotationSelection,onVisibilityChange:this.handleAnnotationVisibilityChange}));var d=this.findingOptions.map((function(e){return(0,I.jsx)(ae.Z.Option,{value:e.CodeValue,children:e.CodeMeaning},e.CodeValue)})),u={point:(0,I.jsx)(ae.Z.Option,{value:"point",children:"Point"},"point"),circle:(0,I.jsx)(ae.Z.Option,{value:"circle",children:"Circle"},"circle"),box:(0,I.jsx)(ae.Z.Option,{value:"box",children:"Box"},"box"),polygon:(0,I.jsx)(ae.Z.Option,{value:"polygon",children:"Polygon"},"polygon"),line:(0,I.jsx)(ae.Z.Option,{value:"line",children:"Line"},"line"),freehandpolygon:(0,I.jsx)(ae.Z.Option,{value:"freehandpolygon",children:"Polygon (freehand)"},"freehandpolygon"),freehandline:(0,I.jsx)(ae.Z.Option,{value:"freehandline",children:"Line (freehand)"},"freehandline")},m=[(0,I.jsx)(ae.Z,{style:{minWidth:130},onSelect:this.handleAnnotationFindingSelection,defaultActiveFirstOption:!0,children:d},"annotation-finding")],v=this.state.selectedFinding;if(void 0!==v){var g=rt(v);this.evaluationOptions[g].forEach((function(t){var n=t.values.map((function(e){return(0,I.jsx)(ae.Z.Option,{value:e.CodeValue,label:t.name,children:e.CodeMeaning},e.CodeValue)}));m.push((0,I.jsxs)(I.Fragment,{children:[t.name.CodeMeaning,(0,I.jsx)(ae.Z,{style:{minWidth:130},onSelect:e.handleAnnotationEvaluationSelection,allowClear:!0,onClear:e.handleAnnotationEvaluationClearance,defaultActiveFirstOption:!1,children:n})]}))}));var S=this.geometryTypeOptions[g].map((function(e){return u[e]}));m.push((0,I.jsxs)(I.Fragment,{children:["ROI geometry type",(0,I.jsx)(ae.Z,{style:{minWidth:130},onSelect:this.handleAnnotationGeometryTypeSelection,children:S},"annotation-geometry-type")]})),m.push((0,I.jsx)(oe.Z,{onChange:this.handleAnnotationMeasurementActivation,children:"measure"},"annotation-measurement"))}var C=(0,I.jsx)(f.Z.SubMenu,{title:"Specimens",children:(0,I.jsx)(qe,{metadata:this.props.slide.volumeImages[0],showstain:!1})},"specimens"),b=(0,I.jsx)(f.Z.SubMenu,{title:"Equipment",children:(0,I.jsx)(Me,{metadata:this.props.slide.volumeImages[0]})},"equipment"),w=this.volumeViewer.getAllOpticalPaths();w.sort((function(e,t){return 1===e.identifier.localeCompare(t.identifier)?1:1===t.identifier.localeCompare(e.identifier)?-1:0}));var D={},x={};w.forEach((function(t){var n=t.identifier,i=e.volumeViewer.getOpticalPathMetadata(n);x[n]=i;var a=(0,j.Z)({},e.volumeViewer.getOpticalPathStyle(n));D[n]=a}));var V,Z,R,O,P,M=(0,I.jsx)(f.Z.SubMenu,{title:"Optical 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k={},L={};i.forEach((function(t){k[t.uid]=e.volumeViewer.getParameterMappingStyle(t.uid),L[t.uid]=e.volumeViewer.getParameterMappingMetadata(t.uid)})),R=(0,I.jsx)(f.Z.SubMenu,{title:"Parametric Maps",children:(0,I.jsx)($e,{mappings:i,metadata:L,defaultMappingStyles:k,visibleMappingUIDs:this.state.visibleMappingUIDs,onMappingVisibilityChange:this.handleMappingVisibilityChange,onMappingStyleChange:this.handleMappingStyleChange})},"parmetric-maps"),s.push("parametric-maps")}if(a.length>0){var _={},N={},G=this.volumeViewer.getAllAnnotationGroups();G.forEach((function(t){_[t.uid]=e.volumeViewer.getAnnotationGroupStyle(t.uid),N[t.uid]=e.volumeViewer.getAnnotationGroupMetadata(t.uid)})),O=(0,I.jsx)(f.Z.SubMenu,{title:"Annotation 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React from 'react'\nimport { v4 as generateUUID } from 'uuid'\nimport { Card, Descriptions } from 'antd'\n\nexport interface Attribute {\n name: string\n value: any\n}\n\nexport interface AttributeGroup {\n name: string\n attributes: Attribute[]\n}\n\ninterface DescriptionProps {\n header?: string\n icon?: any\n attributes: Attribute[]\n selectable?: boolean\n hasLongValues?: boolean\n methods?: React.ReactNode[]\n children?: React.ReactNode\n}\n\n/**\n * React component for a description consisting of a header containing a\n * header and a body containing a list of name-value pairs.\n */\nclass Description extends React.Component {\n render (): React.ReactNode {\n let layout: 'horizontal' | 'vertical' = 'horizontal'\n let labelLineHeight = '14px'\n const contentLineHeight = '14px'\n if (this.props.hasLongValues !== undefined && this.props.hasLongValues) {\n layout = 'vertical'\n labelLineHeight = '20px'\n }\n const items = this.props.attributes.map((item: Attribute, index: number) => {\n const uid = generateUUID()\n return (\n \n {item.value}\n \n )\n })\n let icon = null\n if (this.props.icon !== undefined) {\n icon = \n }\n return (\n \n \n {items}\n \n {this.props.children}\n \n )\n }\n}\n\nexport default Description\n","import React from 'react'\nimport * as dmv from 'dicom-microscopy-viewer'\n\nimport Description from './Description'\n\ninterface ClinicalTrialProps {\n metadata: dmv.metadata.SOPClass\n}\n\n/**\n * React component representing a DICOM ClinicalTrial Information Entity that displays\n * common study-level attributes of contained DICOM Slide Microscopy images.\n */\nclass ClinicalTrial extends React.Component {\n render (): React.ReactNode {\n const attributes = []\n if (this.props.metadata.ClinicalTrialSponsorName != null) {\n // Attributes of Clinical Trial Subject module\n attributes.push(\n ...[\n {\n name: 'Sponsor Name',\n value: this.props.metadata.ClinicalTrialSponsorName\n },\n {\n name: 'Protocol ID',\n value: this.props.metadata.ClinicalTrialProtocolID\n },\n {\n name: 'Protocol Name',\n value: this.props.metadata.ClinicalTrialProtocolName\n },\n {\n name: 'Site Name',\n value: this.props.metadata.ClinicalTrialSiteName\n }\n ]\n )\n }\n if (this.props.metadata.ClinicalTrialTimePointID != null) {\n // Attributes of Clinical Trial Study module\n attributes.push(\n {\n name: 'Time Point ID',\n value: this.props.metadata.ClinicalTrialTimePointID\n }\n )\n }\n // Attributes of Clinical Trial Subject module\n return \n }\n}\n\nexport default ClinicalTrial\n","import * as dmv from 'dicom-microscopy-viewer'\n\nfunction parseName (value: dmv.metadata.PersonName|null|undefined): string {\n if (typeof value === 'object' && value !== null && value !== undefined) {\n if (value.Alphabetic !== undefined) {\n return value.Alphabetic.split('^').join(' ')\n }\n return ''\n }\n return ''\n}\n\nfunction parseDate (value: string|null|undefined): string {\n if (value !== null && value !== undefined) {\n const year = value.substring(0, 4)\n const month = value.substring(4, 6)\n const day = value.substring(6, 8)\n return `${year}-${month}-${day}`\n }\n return ''\n}\n\nfunction parseTime (value: string|null|undefined): string {\n if (value !== null && value !== undefined) {\n const hours = value.substring(0, 2)\n const minutes = value.substring(2, 4)\n const seconds = value.substring(4, 6)\n return `${hours}:${minutes}:${seconds}`\n }\n return ''\n}\n\nfunction parseDateTime (value: string|null|undefined): string {\n if (value !== null && value !== undefined) {\n const year = value.substring(0, 4)\n const month = value.substring(4, 6)\n const day = value.substring(6, 8)\n const hours = value.substring(8, 10)\n const minutes = value.substring(10, 12)\n const seconds = value.substring(12, 14)\n return `${year}-${month}-${day} ${hours}:${minutes}:${seconds}`\n }\n return ''\n}\n\nfunction parseSex (value: string|null|undefined): string {\n const lut: { [key: string]: string } = {\n F: 'Female',\n M: 'Male',\n O: 'Other'\n }\n if (value !== null && value !== undefined) {\n return lut[value]\n }\n return ''\n}\n\nexport { parseDate, parseDateTime, parseName, parseSex, parseTime }\n","import React from 'react'\nimport * as dmv from 'dicom-microscopy-viewer'\n\nimport Description from './Description'\nimport { parseName, parseSex, parseDate } from '../utils/values'\n\ninterface PatientProps {\n metadata: dmv.metadata.Study|dmv.metadata.SOPClass\n}\n\n/**\n * React component representing a DICOM Patient Information Entity that\n * displays common study-level, patient-related attributes of contained\n * DICOM Slide Microscopy images.\n */\nclass Patient extends React.Component {\n render (): React.ReactNode {\n const attributes = [\n {\n name: 'ID',\n value: this.props.metadata.PatientID\n },\n {\n name: 'Name',\n value: parseName(this.props.metadata.PatientName)\n },\n {\n name: 'Gender',\n value: parseSex(this.props.metadata.PatientSex)\n },\n {\n name: 'Birthdate',\n value: parseDate(this.props.metadata.PatientBirthDate)\n }\n ]\n return (\n \n )\n }\n}\n\nexport default Patient\n","import React from 'react'\nimport * as dmv from 'dicom-microscopy-viewer'\n\nimport Description from './Description'\nimport { parseDate, parseTime } from '../utils/values'\n\ninterface StudyProps {\n metadata: dmv.metadata.Study|dmv.metadata.SOPClass\n}\n\n/**\n * React component representing a DICOM Study Information Entity that displays\n * common study-level attributes of contained DICOM Slide Microscopy images.\n */\nclass Study extends React.Component {\n render (): React.ReactNode {\n const attributes = [\n {\n name: 'Accession #',\n value: this.props.metadata.AccessionNumber\n },\n {\n name: 'ID',\n value: this.props.metadata.StudyID\n },\n {\n name: 'Date',\n value: parseDate(this.props.metadata.StudyDate)\n },\n {\n name: 'Time',\n value: parseTime(this.props.metadata.StudyTime)\n }\n ]\n return \n }\n}\n\nexport default Study\n","export enum StorageClasses {\n VL_WHOLE_SLIDE_MICROSCOPY_IMAGE = '1.2.840.10008.5.1.4.1.1.77.1.6',\n COMPREHENSIVE_SR = '1.2.840.10008.5.1.4.1.1.88.33',\n COMPREHENSIVE_3D_SR = '1.2.840.10008.5.1.4.1.1.88.34',\n SEGMENTATION = '1.2.840.10008.5.1.4.1.1.66.4',\n MICROSCOPY_BULK_SIMPLE_ANNOTATION = '1.2.840.10008.5.1.4.1.1.91.1',\n PARAMETRIC_MAP = '1.2.840.10008.5.1.4.1.1.30',\n ADVANCED_BLENDING_PRESENTATION_STATE = '1.2.840.10008.5.1.4.1.1.11.8',\n COLOR_SOFTCOPY_PRESENTATION_STATE = '1.2.840.10008.5.1.4.1.1.11.2',\n GRAYSCALE_SOFTCOPY_PRESENTATION_STATE = '1.2.840.10008.5.1.4.1.1.11.1',\n PSEUDOCOLOR_SOFTCOPY_PRESENTATION_STATE = '1.2.840.10008.5.1.4.1.1.11.3'\n}\n","// Use symbols to prevent exposing private attributes\nconst _subscriptions = Symbol('subscriptions')\nconst _lastSubscriptionId = Symbol('lastSubscriptionId')\n\n/**\n * Class to enable implementation of publish/subscribe pattern\n * @class\n * @classdesc Enables publishing/subscribing\n */\nexport default class PubSub {\n constructor () {\n this[_subscriptions] = {}\n this[_lastSubscriptionId] = 0\n }\n\n /**\n * Adds a subscription callback to the provided event name\n * @param {string} eventName Event name that will trigger the callback\n * @param {Function} callback Function to be executed when event is published\n * @returns {void}\n */\n subscribe (eventName, callback) {\n if (eventName === undefined) {\n throw new Error('Trying to subscribe to an inexistent event')\n }\n\n if (typeof callback !== 'function') {\n throw new Error('The provided callback must be a function')\n }\n\n if (!this[_subscriptions].hasOwnProperty(eventName)) {\n this[_subscriptions][eventName] = {}\n }\n\n const subscriptionId = `sub${this[_lastSubscriptionId]++}`\n this[_subscriptions][eventName][subscriptionId] = callback\n }\n\n /**\n * Removes a subscription callback for the provided event name\n * @param {string} eventName Event name for the registerd callback\n * @param {Function} [callback] Function to have its subscription removed\n * @returns {void}\n */\n unsubscribe (eventName, callback) {\n const callbacks = this[_subscriptions][eventName] || {}\n for (const subscriptionId in callbacks) {\n if (!callback) {\n delete callbacks[subscriptionId]\n } else if (callbacks[subscriptionId] === callback) {\n delete callbacks[subscriptionId]\n }\n }\n }\n\n /**\n * Trigger all registered subscription callbacks for a specific event name\n * @param {String} eventName Event name to trigger subscriptions from\n * @param {any} [payload] Payload that will be passed to the callback fuction\n * @returns {void}\n */\n publish (eventName, ...payload) {\n if (eventName === undefined) {\n throw new Error('Trying to publish an inexistent event')\n }\n\n const callbacks = this[_subscriptions][eventName] || {}\n for (const subscriptionId in callbacks) {\n callbacks[subscriptionId](...payload)\n }\n }\n\n /**\n * Cleares all subscriptions for current instance\n * @returns {void}\n */\n unsubscribeFromAll () {\n for (const eventName in this[_subscriptions]) {\n const callbacks = this[_subscriptions][eventName]\n for (const subscriptionId in callbacks) {\n delete callbacks[subscriptionId]\n }\n }\n }\n}\n","const errorTypes = {\n AUTHENTICATION: 'Authentication',\n COMMUNICATION: 'Communication',\n ENCODINGANDDECODING: 'EncodingDecoding',\n VISUALIZATION: 'Visualization'\n}\n\nclass CustomError extends Error {\n constructor (type, message) {\n super()\n this.message = message\n this.stack = new Error().stack\n this.type = type\n }\n}\n\nexport { errorTypes, CustomError }\n","import PubSub from '../utils/PubSub'\nimport { notification } from 'antd'\nimport { CustomError, errorTypes } from '../utils/CustomError'\n\nexport const NotificationMiddlewareEvents = {\n OnError: 'onError',\n OnWarning: 'onWarning'\n}\n\nexport const NotificationMiddlewareContext = {\n DICOMWEB: 'dicomweb-client',\n DMV: 'dicom-microscopy-viewer',\n DCMJS: 'dcmjs',\n SLIM: 'slim',\n AUTH: 'authentication'\n}\n\nconst NotificationType = {\n TOAST: 'toast',\n CONSOLE: 'console'\n}\n\n/* Sources of Error:\n 1. 'dicomweb-client': Error while requesting/fetching data, tagged as 'Communication'\n 2. 'slim' and 'dicom-microscopy-viewer' library: Error related to dicom data encoding/decoding,\n could directly/indirectly impact image-related visualization, tagged as 'Visualization' or\n 'Encoding/Decoding' accordingly\n 3. 'dcmjs' library: Data parsing error, tagged as 'DICOMError'\n 4. 'authentication': Error during user authentication, tagged as 'Authentication'\n */\nconst NotificationSourceDefinition = {\n sources: [\n {\n category: errorTypes.AUTHENTICATION,\n notificationType: NotificationType.TOAST\n },\n {\n category: errorTypes.COMMUNICATION,\n notificationType: NotificationType.TOAST\n },\n {\n category: errorTypes.VISUALIZATION,\n notificationType: NotificationType.TOAST\n },\n {\n category: errorTypes.ENCODINGANDDECODING,\n notificationType: NotificationType.CONSOLE\n },\n {\n category: 'Warning',\n notificationType: NotificationType.TOAST\n }\n ]\n}\n\nclass NotificationMiddleware extends PubSub {\n constructor() {\n super()\n\n const outerContext = (args) => {\n this.publish(NotificationMiddlewareEvents.OnWarning, Array.from(args).join(' '))\n }\n\n (function () {\n var warn = console.warn;\n console.warn = function () {\n if (!JSON.stringify(arguments).includes('request')) {\n outerContext(arguments)\n }\n warn.apply(this, Array.prototype.slice.call(arguments))\n }\n }())\n }\n\n /**\n * Error handling middleware function\n *\n * @param source - source of error - dicomweb-client, dmv, dcmjs or slim itself\n * @param error - error object\n */\n onError (source, error) {\n const errorCategory = error.type\n const sourceConfig = NotificationSourceDefinition.sources.find(\n s => s.category === errorCategory\n )\n const { notificationType } = sourceConfig\n\n this.publish(NotificationMiddlewareEvents.OnError, {\n source,\n error\n })\n\n let notificationMsg\n if (error instanceof CustomError) {\n notificationMsg = error.message\n } else {\n notificationMsg = String(error)\n }\n\n switch (notificationType) {\n case NotificationType.TOAST:\n console.error(`A ${errorCategory} error occurred: `, error)\n return notification.error({\n message: `${errorCategory} error`,\n description: notificationMsg,\n duration: 3\n })\n\n case NotificationType.CONSOLE:\n console.error(`A ${errorCategory} error occurred: `, error)\n break\n\n default:\n }\n }\n}\n\nexport default new NotificationMiddleware()\n","import React from 'react'\nimport { FaSpinner } from 'react-icons/fa'\nimport * as dmv from 'dicom-microscopy-viewer'\nimport { Menu } from 'antd'\n\nimport DicomWebManager from '../DicomWebManager'\nimport Description from './Description'\nimport { Slide } from '../data/slides'\nimport { StorageClasses } from '../data/uids'\nimport NotificationMiddleware, {\n NotificationMiddlewareContext\n} from '../services/NotificationMiddleware'\nimport { CustomError } from '../utils/CustomError'\n\ninterface SlideItemProps {\n clients: { [key: string]: DicomWebManager }\n slide: Slide\n}\n\ninterface SlideItemState {\n isLoading: boolean\n}\n\n/**\n * React component representing a DICOM Series Information Entity that displays\n * common series-level attributes of contained DICOM Slide Microscopy images\n * as well as the OVERVIEW image (if available).\n * When selected a Slide Viewer instance is created for the display of the\n * contained images.\n */\nclass SlideItem extends React.Component {\n state = { isLoading: false }\n\n private readonly overviewViewportRef = React.createRef()\n\n private overviewViewer?: dmv.viewer.OverviewImageViewer\n\n constructor (props: SlideItemProps) {\n super(props)\n this.overviewViewer = undefined\n }\n\n componentDidMount (): void {\n this.setState({ isLoading: true })\n if (this.props.slide.overviewImages.length > 0) {\n const metadata = this.props.slide.overviewImages[0]\n if (this.overviewViewportRef.current !== null) {\n this.overviewViewportRef.current.innerHTML = ''\n console.info(\n 'instantiate viewer for OVERVIEW image of slide ' +\n `\"${metadata.ContainerIdentifier}\"`\n )\n this.overviewViewer = new dmv.viewer.OverviewImageViewer({\n client: this.props.clients[\n StorageClasses.VL_WHOLE_SLIDE_MICROSCOPY_IMAGE\n ],\n metadata: metadata,\n resizeFactor: 1,\n errorInterceptor: (error: CustomError) =>\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.DMV,\n error\n )\n })\n this.overviewViewer.render({\n container: this.overviewViewportRef.current\n })\n }\n }\n\n this.setState({ isLoading: false })\n }\n\n render (): React.ReactNode {\n if (this.overviewViewer !== undefined) {\n this.overviewViewer.resize()\n }\n const attributes = []\n const description = this.props.slide.description\n if (description != null && description !== '') {\n attributes.push({\n name: 'Description',\n value: description\n })\n }\n if (this.state.isLoading) {\n return ()\n }\n\n /* Properties need to be propagated down to Menu.Item:\n * https://github.com/react-component/menu/issues/142\n */\n return (\n \n \n
\n \n \n )\n }\n}\n\nexport default SlideItem\n","import React from 'react'\nimport { Menu } from 'antd'\n\nimport DicomWebManager from '../DicomWebManager'\nimport SlideItem from './SlideItem'\nimport { Slide } from '../data/slides'\n\ninterface SlideListProps {\n metadata: Slide[]\n clients: { [key: string]: DicomWebManager }\n selectedSeriesInstanceUID: string\n onSeriesSelection: (\n { seriesInstanceUID }: { seriesInstanceUID: string }\n ) => void\n}\n\ninterface SlideListState {\n selectedSeriesInstanceUID: string\n}\n\n/**\n * React component representing a list of DICOM Series Information Entities.\n */\nclass SlideList extends React.Component {\n state = {\n selectedSeriesInstanceUID: this.props.selectedSeriesInstanceUID\n }\n\n componentDidMount (): void {\n this.props.onSeriesSelection({\n seriesInstanceUID: this.state.selectedSeriesInstanceUID\n })\n }\n\n render (): React.ReactNode {\n const slideList = this.props.metadata\n const slideItemList = []\n for (let i = 0; i < slideList.length; ++i) {\n const slide = slideList[i]\n const slideItem = (\n \n )\n\n slideItemList.push(slideItem)\n }\n\n const handleMenuItemSelection = ({ key, keyPath, domEvent, selectedKeys }: {\n key: React.ReactText\n keyPath: React.ReactText[]\n domEvent: React.MouseEvent | React.KeyboardEvent\n selectedKeys?: React.ReactText[]\n }): void => {\n console.info(`select slide \"${key}\"`)\n this.setState({ selectedSeriesInstanceUID: key.toString() })\n this.props.onSeriesSelection({ seriesInstanceUID: key.toString() })\n }\n\n let selectedKeys\n if (this.state.selectedSeriesInstanceUID !== undefined &&\n this.state.selectedSeriesInstanceUID !== null) {\n selectedKeys = [this.state.selectedSeriesInstanceUID]\n }\n\n return (\n \n {slideItemList}\n \n )\n }\n}\n\nexport default SlideList\n","import React from 'react'\nimport * as dmv from 'dicom-microscopy-viewer'\nimport * as dcmjs from 'dcmjs'\nimport { Menu, Space, Switch } from 'antd'\nimport { FaEye, FaEyeSlash } from 'react-icons/fa'\n\nimport Description from './Description'\n\ninterface AnnotationItemProps {\n roi: dmv.roi.ROI\n index: number\n isVisible: boolean\n onVisibilityChange: ({ roiUID, isVisible }: {\n roiUID: string\n isVisible: boolean\n }) => void\n}\n\n/**\n * React component representing a Region of Interest (ROI) annotation.\n */\nclass AnnotationItem extends React.Component {\n constructor (props: AnnotationItemProps) {\n super(props)\n this.handleVisibilityChange = this.handleVisibilityChange.bind(this)\n }\n\n handleVisibilityChange (\n checked: boolean,\n event: React.MouseEvent\n ): void {\n this.props.onVisibilityChange({\n roiUID: this.props.roi.uid,\n isVisible: checked\n })\n }\n\n render (): React.ReactNode {\n const identifier = `ROI ${this.props.index + 1}`\n const attributes: Array<{ name: string, value: string }> = []\n /**\n * This hack is required for Menu.Item to work properly:\n * https://github.com/react-component/menu/issues/142\n */\n const { isVisible, onVisibilityChange, ...otherProps } = this.props\n this.props.roi.evaluations.forEach((\n item: (\n dcmjs.sr.valueTypes.TextContentItem |\n dcmjs.sr.valueTypes.CodeContentItem\n )\n ) => {\n const nameValue = item.ConceptNameCodeSequence[0].CodeValue\n const nameMeaning = item.ConceptNameCodeSequence[0].CodeMeaning\n const name = `${nameMeaning}`\n if (item.ValueType === dcmjs.sr.valueTypes.ValueTypes.CODE) {\n const codeContentItem = item as dcmjs.sr.valueTypes.CodeContentItem\n const valueMeaning = codeContentItem.ConceptCodeSequence[0].CodeMeaning\n // For consistency with Segment and Annotation Group\n if (nameValue === '276214006') {\n attributes.push({\n name: 'Property category',\n value: `${valueMeaning}`\n })\n } else if (nameValue === '121071') {\n attributes.push({\n name: 'Property type',\n value: `${valueMeaning}`\n })\n } else if (nameValue === '111001') {\n attributes.push({\n name: 'Algorithm Name',\n value: `${valueMeaning}`\n })\n } else {\n attributes.push({\n name: name,\n value: `${valueMeaning}`\n })\n }\n } else if (item.ValueType === dcmjs.sr.valueTypes.ValueTypes.TEXT) {\n const textContentItem = item as dcmjs.sr.valueTypes.TextContentItem\n attributes.push({\n name: name,\n value: textContentItem.TextValue\n })\n }\n })\n this.props.roi.measurements.forEach(item => {\n const nameMeaning = item.ConceptNameCodeSequence[0].CodeMeaning\n const name = `${nameMeaning}`\n const seq = item.MeasuredValueSequence[0]\n const value = seq.NumericValue.toPrecision(6)\n const unit = seq.MeasurementUnitsCodeSequence[0].CodeValue\n attributes.push({\n name: name,\n value: `${value} ${unit}`\n })\n })\n return (\n \n
\n }\n unCheckedChildren={}\n />\n
\n \n \n \n \n )\n }\n}\n\nexport default AnnotationItem\n","import React from 'react'\nimport * as dmv from 'dicom-microscopy-viewer'\nimport { Menu, Switch } from 'antd'\nimport { FaEye, FaEyeSlash } from 'react-icons/fa'\n\nimport AnnotationItem from './AnnotationItem'\n\ninterface AnnotationListProps {\n rois: dmv.roi.ROI[]\n selectedRoiUIDs: Set\n visibleRoiUIDs: Set\n onVisibilityChange: ({ roiUID, isVisible }: {\n roiUID: string\n isVisible: boolean\n }) => void\n onSelection: ({ roiUID }: { roiUID: string }) => void\n}\n\n/**\n * React component representing a list of Region of Interest (ROI)\n * annotations.\n */\nclass AnnotationList extends React.Component {\n constructor (props: AnnotationListProps) {\n super(props)\n this.handleMenuItemSelection = this.handleMenuItemSelection.bind(this)\n this.handleVisibilityChange = this.handleVisibilityChange.bind(this)\n }\n\n handleVisibilityChange (\n checked: boolean,\n event: React.MouseEvent\n ): void {\n if (checked) {\n this.props.rois.forEach(roi => {\n this.props.onVisibilityChange({ roiUID: roi.uid, isVisible: checked })\n })\n } else {\n this.props.visibleRoiUIDs.forEach(roiUID => {\n this.props.onVisibilityChange({ roiUID, isVisible: checked })\n })\n }\n }\n\n handleMenuItemSelection (object: any): void {\n this.props.onSelection({ roiUID: object.key })\n }\n\n render (): React.ReactNode {\n const items = this.props.rois.map((roi, index) => (\n \n ))\n\n return (\n <>\n
\n 0}\n checkedChildren={}\n unCheckedChildren={}\n />\n
\n \n {items}\n \n \n )\n }\n}\n\nexport default AnnotationList\n","import React from 'react'\nimport {\n Badge,\n Button,\n Col,\n Divider,\n InputNumber,\n Menu,\n Popover,\n Row,\n Select,\n Slider,\n Space,\n Switch\n} from 'antd'\nimport { SettingOutlined } from '@ant-design/icons'\nimport { FaEye, FaEyeSlash } from 'react-icons/fa'\nimport * as dmv from 'dicom-microscopy-viewer'\nimport * as dcmjs from 'dcmjs'\n\nimport Description from './Description'\n\ninterface AnnotationGroupItemProps {\n annotationGroup: dmv.annotation.AnnotationGroup\n isVisible: boolean\n metadata: dmv.metadata.MicroscopyBulkSimpleAnnotations\n defaultStyle: {\n opacity: number\n color: number[]\n }\n onVisibilityChange: ({ annotationGroupUID, isVisible }: {\n annotationGroupUID: string\n isVisible: boolean\n }) => void\n onStyleChange: ({ annotationGroupUID, styleOptions }: {\n annotationGroupUID: string\n styleOptions: {\n opacity?: number\n color?: number[]\n limitValues?: number[]\n measurement?: dcmjs.sr.coding.CodedConcept\n }\n }) => void\n}\n\ninterface AnnotationGroupItemState {\n isVisible: boolean\n currentStyle: {\n opacity: number\n color?: number[]\n limitValues?: number[]\n measurement?: dcmjs.sr.coding.CodedConcept\n }\n}\n\n/**\n * React component representing an Annotation Group.\n */\nclass AnnotationGroupItem extends React.Component {\n constructor (props: AnnotationGroupItemProps) {\n super(props)\n this.handleVisibilityChange = this.handleVisibilityChange.bind(this)\n this.handleMeasurementSelection = this.handleMeasurementSelection.bind(this)\n this.handleOpacityChange = this.handleOpacityChange.bind(this)\n this.handleColorRChange = this.handleColorRChange.bind(this)\n this.handleColorGChange = this.handleColorGChange.bind(this)\n this.handleColorBChange = this.handleColorBChange.bind(this)\n this.getCurrentColor = this.getCurrentColor.bind(this)\n this.state = {\n isVisible: this.props.isVisible,\n currentStyle: {\n opacity: this.props.defaultStyle.opacity,\n color: this.props.defaultStyle.color\n }\n }\n }\n\n handleVisibilityChange (\n checked: boolean,\n event: React.MouseEvent\n ): void {\n this.props.onVisibilityChange({\n annotationGroupUID: this.props.annotationGroup.uid,\n isVisible: checked\n })\n this.setState({ isVisible: checked })\n }\n\n handleOpacityChange (value: number | null): void {\n if (value != null) {\n this.props.onStyleChange({\n annotationGroupUID: this.props.annotationGroup.uid,\n styleOptions: {\n opacity: value\n }\n })\n this.setState({\n currentStyle: {\n opacity: value,\n color: this.state.currentStyle.color,\n limitValues: this.state.currentStyle.limitValues\n }\n })\n }\n }\n\n handleColorRChange (\n value: number | number[] | null\n ): void {\n if (value != null && this.state.currentStyle.color !== undefined) {\n const color = [\n Array.isArray(value) ? value[0] : value,\n this.state.currentStyle.color[1],\n this.state.currentStyle.color[2]\n ]\n this.setState(state => ({\n currentStyle: {\n color: color,\n opacity: state.currentStyle.opacity,\n limitValues: state.currentStyle.limitValues\n }\n }))\n this.props.onStyleChange({\n annotationGroupUID: this.props.annotationGroup.uid,\n styleOptions: { color: color }\n })\n }\n }\n\n handleColorGChange (\n value: number | number[] | null\n ): void {\n if (value != null && this.state.currentStyle.color !== undefined) {\n const color = [\n this.state.currentStyle.color[0],\n Array.isArray(value) ? value[0] : value,\n this.state.currentStyle.color[2]\n ]\n this.setState(state => ({\n currentStyle: {\n color: color,\n opacity: state.currentStyle.opacity,\n limitValues: state.currentStyle.limitValues\n }\n }))\n this.props.onStyleChange({\n annotationGroupUID: this.props.annotationGroup.uid,\n styleOptions: { color: color }\n })\n }\n }\n\n handleColorBChange (\n value: number | number[] | null\n ): void {\n if (value != null && this.state.currentStyle.color !== undefined) {\n const color = [\n this.state.currentStyle.color[0],\n this.state.currentStyle.color[1],\n Array.isArray(value) ? value[0] : value\n ]\n this.setState(state => ({\n currentStyle: {\n color: color,\n opacity: state.currentStyle.opacity,\n limitValues: state.currentStyle.limitValues\n }\n }))\n this.props.onStyleChange({\n annotationGroupUID: this.props.annotationGroup.uid,\n styleOptions: { color: color }\n })\n }\n }\n\n getCurrentColor (): string {\n const rgb2hex = (values: number[]): string => {\n const r = values[0]\n const g = values[1]\n const b = values[2]\n return '#' + (0x1000000 + (r << 16) + (g << 8) + b).toString(16).slice(1)\n }\n\n if (this.state.currentStyle.color != null) {\n return rgb2hex(this.state.currentStyle.color)\n } else {\n return 'white'\n }\n }\n\n handleLowerLimitChange (\n value: number | null\n ): void {\n if (value != null && this.state.currentStyle.limitValues !== undefined) {\n this.setState(state => {\n if (state.currentStyle.limitValues !== undefined) {\n return {\n currentStyle: {\n color: state.currentStyle.color,\n opacity: state.currentStyle.opacity,\n limitValues: [value, state.currentStyle.limitValues[1]]\n }\n }\n } else {\n return {\n currentStyle: {\n color: state.currentStyle.color,\n opacity: state.currentStyle.opacity,\n limitValues: state.currentStyle.limitValues\n }\n }\n }\n })\n this.props.onStyleChange({\n annotationGroupUID: this.props.annotationGroup.uid,\n styleOptions: {\n limitValues: [\n value,\n this.state.currentStyle.limitValues[1]\n ]\n }\n })\n }\n }\n\n handleUpperLimitChange (\n value: number | null\n ): void {\n if (value != null && this.state.currentStyle.limitValues !== undefined) {\n this.setState(state => {\n if (state.currentStyle.limitValues !== undefined) {\n return {\n currentStyle: {\n color: state.currentStyle.color,\n opacity: state.currentStyle.opacity,\n limitValues: [state.currentStyle.limitValues[0], value]\n }\n }\n } else {\n return {\n currentStyle: {\n color: state.currentStyle.color,\n opacity: state.currentStyle.opacity,\n limitValues: state.currentStyle.limitValues\n }\n }\n }\n })\n this.props.onStyleChange({\n annotationGroupUID: this.props.annotationGroup.uid,\n styleOptions: {\n limitValues: [\n this.state.currentStyle.limitValues[0],\n value\n ]\n }\n })\n }\n }\n\n handleLimitChange (\n values: number[]\n ): void {\n this.setState(state => ({\n currentStyle: {\n color: state.currentStyle.color,\n opacity: state.currentStyle.opacity,\n limitValues: values\n }\n }))\n this.props.onStyleChange({\n annotationGroupUID: this.props.annotationGroup.uid,\n styleOptions: { limitValues: values }\n })\n }\n\n handleMeasurementSelection (value?: string, option?: any): void {\n if (value != null && option.children != null) {\n const codeComponents = value.split('-')\n const measurement = new dcmjs.sr.coding.CodedConcept({\n value: codeComponents[1],\n schemeDesignator: codeComponents[0],\n meaning: option.children\n })\n this.props.onStyleChange({\n annotationGroupUID: this.props.annotationGroup.uid,\n styleOptions: { measurement }\n })\n this.setState(state => ({\n currentStyle: {\n opacity: state.currentStyle.opacity,\n measurement\n }\n }))\n } else {\n this.props.onStyleChange({\n annotationGroupUID: this.props.annotationGroup.uid,\n styleOptions: {\n color: this.props.defaultStyle.color\n }\n })\n this.setState(state => ({\n currentStyle: {\n opacity: state.currentStyle.opacity,\n color: this.props.defaultStyle.color,\n limitValues: undefined\n }\n }))\n }\n }\n\n render (): React.ReactNode {\n const index = this.props.metadata.AnnotationGroupSequence.findIndex(\n item => (item.AnnotationGroupUID === this.props.annotationGroup.uid)\n )\n const item = this.props.metadata.AnnotationGroupSequence[index]\n const attributes: Array<{ name: string, value: string }> = [\n {\n name: 'Property type',\n value: this.props.annotationGroup.propertyType.CodeMeaning\n },\n {\n name: 'Property category',\n value: this.props.annotationGroup.propertyCategory.CodeMeaning\n },\n // {\n // name: 'Algorithm Name',\n // value: this.props.annotationGroup.algorithmName\n // },\n {\n name: 'Graphic type',\n value: item.GraphicType\n },\n {\n name: 'Annotation coordinate type',\n value: this.props.metadata.AnnotationCoordinateType\n }\n ]\n\n const measurementsSequence = item.MeasurementsSequence ?? []\n const measurementOptions = measurementsSequence.map((measurementItem, i) => {\n const name = measurementItem.ConceptNameCodeSequence[0]\n return (\n \n {name.CodeMeaning}\n \n )\n })\n measurementOptions.push(\n \n {}\n \n )\n\n let colorSettings\n if (this.state.currentStyle.color != null) {\n colorSettings = (\n <>\n \n Color\n \n \n \n Red\n \n \n \n \n \n \n \n \n\n \n \n Green\n \n \n \n \n \n \n \n \n\n \n \n Blue\n \n \n \n \n \n \n \n \n \n \n )\n }\n\n let windowSettings\n let explorationSettings\n if (measurementsSequence.length > 0) {\n if (this.state.currentStyle.limitValues != null) {\n // TODO: need to get default min/max values from viewer first\n const minValue = 0\n const maxValue = 1000\n windowSettings = (\n <>\n \n Values of interest\n \n \n \n \n \n \n \n \n \n \n \n \n \n )\n }\n explorationSettings = (\n <>\n \n Exploration\n \n \n \n Measurement\n \n \n \n {measurementOptions}\n \n \n \n \n )\n }\n\n const settings = (\n
\n {colorSettings}\n {windowSettings}\n \n \n Opacity\n \n \n \n \n \n \n \n \n {explorationSettings}\n
\n )\n\n const color = this.getCurrentColor()\n const isBadgeVisible = (\n this.state.isVisible && this.state.currentStyle.measurement == null\n )\n const {\n annotationGroup,\n defaultStyle,\n isVisible,\n metadata,\n onVisibilityChange,\n onStyleChange,\n ...otherProps\n } = this.props\n return (\n \n \n
\n \n }\n unCheckedChildren={}\n />\n \n }\n />\n \n \n
\n \n \n \n \n \n )\n }\n}\n\nexport default AnnotationGroupItem\n","import React from 'react'\nimport { Menu } from 'antd'\nimport * as dmv from 'dicom-microscopy-viewer'\nimport * as dcmjs from 'dcmjs'\n\nimport AnnotationGroupItem from './AnnotationGroupItem'\n\ninterface AnnotationGroupListProps {\n annotationGroups: dmv.annotation.AnnotationGroup[]\n visibleAnnotationGroupUIDs: Set\n metadata: {\n [annotationGroupUID: string]: dmv.metadata.MicroscopyBulkSimpleAnnotations\n }\n defaultAnnotationGroupStyles: {\n [annotationGroupUID: string]: {\n opacity: number\n color: number[]\n }\n }\n onAnnotationGroupVisibilityChange: ({ annotationGroupUID, isVisible }: {\n annotationGroupUID: string\n isVisible: boolean\n }) => void\n onAnnotationGroupStyleChange: ({ annotationGroupUID, styleOptions }: {\n annotationGroupUID: string\n styleOptions: {\n opacity?: number\n color?: number[]\n measurement?: dcmjs.sr.coding.CodedConcept\n }\n }) => void\n}\n\n/**\n * React component representing a list of Annotation Groups.\n */\nclass AnnotationGroupList extends React.Component {\n render (): React.ReactNode {\n const items = this.props.annotationGroups.map((annotationGroup, index) => {\n const uid = annotationGroup.uid\n return (\n \n )\n })\n\n return (\n \n {items}\n \n )\n }\n}\n\nexport default AnnotationGroupList\n","import React from 'react'\nimport { Button as Btn, Divider, Tooltip } from 'antd'\n\ninterface ButtonProps {\n icon: any\n tooltip?: string\n label?: string\n onClick?: (options: any) => void\n isSelected?: boolean\n}\n\n/**\n * React component for a button.\n */\nclass Button extends React.Component {\n constructor (props: ButtonProps) {\n super(props)\n this.handleClick = this.handleClick.bind(this)\n }\n\n handleClick (event: React.SyntheticEvent): void {\n if (this.props.onClick !== undefined) {\n this.props.onClick(event)\n }\n }\n\n render (): React.ReactNode {\n const Icon = this.props.icon\n if (Icon === undefined) {\n return null\n }\n\n let text\n if (this.props.label != null) {\n text = (\n <>\n \n {this.props.label}\n \n )\n }\n\n let button\n if (this.props.isSelected ?? false) {\n button = (\n }\n type='primary'\n style={{ lineHeight: '1.0' }}\n >\n {text}\n \n )\n } else {\n button = (\n }\n type='default'\n style={{ lineHeight: '1.0' }}\n >\n {text}\n \n )\n }\n\n if (this.props.tooltip !== undefined) {\n return (\n \n {button}\n \n )\n } else {\n return button\n }\n }\n}\n\nexport default Button\n","import React from 'react'\nimport * as dmv from 'dicom-microscopy-viewer'\n\nimport Description from './Description'\n\ninterface EquipmentProps {\n metadata?: dmv.metadata.VLWholeSlideMicroscopyImage\n}\n\n/**\n * React component representing a list of DICOM Equipment Entities.\n */\nclass Equipment extends React.Component {\n render (): React.ReactNode {\n if (this.props.metadata === undefined) {\n return null\n }\n const attributes = [\n {\n name: 'Manufacturer',\n value: this.props.metadata.Manufacturer\n },\n {\n name: 'Model Name',\n value: this.props.metadata.ManufacturerModelName\n },\n {\n name: 'Device Serial Number',\n value: this.props.metadata.DeviceSerialNumber\n },\n {\n name: 'Software Versions',\n value: this.props.metadata.SoftwareVersions\n }\n ]\n if (this.props.metadata.InstitutionName != null) {\n attributes.push({\n name: 'Institution Name',\n value: this.props.metadata.InstitutionName\n })\n }\n return \n }\n}\n\nexport default Equipment\n","import * as dcmjs from 'dcmjs'\n\n/**\n * Check whether a DICOM SR content item has a given name.\n *\n * @param item - Content item\n * @param name - Coded name that should be compared\n * @returns Whether the content item has the given name\n */\nconst hasName = (\n item: dcmjs.sr.valueTypes.ContentItem,\n name: dcmjs.sr.coding.CodedConcept\n): boolean => {\n const concept = item.ConceptNameCodeSequence[0]\n return (\n concept.CodeValue === name.CodeValue &&\n concept.CodingSchemeDesignator === name.CodingSchemeDesignator\n )\n}\n\n/**\n * Check whether a DICOM SR content item has a given value type.\n *\n * @param item - Content item\n * @param valueType - Value Type\n * @returns Whether the content item has the given value type\n */\nconst hasValueType = (\n item: dcmjs.sr.valueTypes.ContentItem,\n valueType: dcmjs.sr.valueTypes.ValueTypes\n): boolean => {\n console.log(item.ValueType, valueType)\n return item.ValueType === valueType\n}\n\n/**\n * Find content items in a DICOM SR document given their name.\n *\n * Only finds content items at the root level, but not any nested content items.\n *\n * @param content - Document content, i.e., sequence of content items\n * @param name - Coded name that should be compared\n * @returns Matched content items\n */\nexport const findContentItemsByName = (\n { content, name }: {\n content: dcmjs.sr.valueTypes.ContentItem[]\n name: dcmjs.sr.coding.CodedConcept\n }\n): dcmjs.sr.valueTypes.ContentItem[] => {\n const items: dcmjs.sr.valueTypes.ContentItem[] = []\n content.forEach(i => {\n if (hasName(i, name)) {\n items.push(i)\n }\n })\n return items\n}\n\n/**\n * Find content items in a DICOM SR document given their value type.\n *\n * Only finds content items at the root level, but not any nested content items.\n *\n * @param content - Document content, i.e., sequence of content items\n * @param valueType - Value Type\n * @returns Matched content items\n */\nexport const findContentItemsByValueType = (\n { content, valueType }: {\n content: dcmjs.sr.valueTypes.ContentItem[]\n valueType: dcmjs.sr.valueTypes.ValueTypes\n }\n): dcmjs.sr.valueTypes.ContentItem[] => {\n const items: dcmjs.sr.valueTypes.ContentItem[] = []\n content.forEach(i => {\n if (hasValueType(i, valueType)) {\n items.push(i)\n }\n })\n return items\n}\n","import React from 'react'\nimport * as dmv from 'dicom-microscopy-viewer'\nimport * as dcmjs from 'dcmjs'\nimport { Divider } from 'antd'\nimport { v4 as generateUUID } from 'uuid'\n\nimport Description from './Description'\nimport Patient from './Patient'\nimport Study from './Study'\nimport { findContentItemsByName } from '../utils/sr'\nimport { CustomError, errorTypes } from '../utils/CustomError'\nimport NotificationMiddleware, {\n NotificationMiddlewareContext\n} from '../services/NotificationMiddleware'\n\nexport const hasValueType = (\n item: dcmjs.sr.valueTypes.ContentItem,\n valueType: string\n): boolean => {\n return item.ValueType === valueType\n}\n\nconst findMeasurementItems = (\n { content }: { content: dcmjs.sr.valueTypes.ContentItem[] }\n): dcmjs.sr.valueTypes.NumContentItem[] => {\n const items: dcmjs.sr.valueTypes.NumContentItem[] = []\n content.forEach(i => {\n if (hasValueType(i, dcmjs.sr.valueTypes.ValueTypes.NUM)) {\n const measurement = i as dcmjs.sr.valueTypes.NumContentItem\n items.push(measurement)\n }\n })\n return items\n}\n\nconst findEvaluationItems = (\n { content }: { content: dcmjs.sr.valueTypes.ContentItem[] }\n): dcmjs.sr.valueTypes.CodeContentItem[] => {\n const items: dcmjs.sr.valueTypes.CodeContentItem[] = []\n content.forEach(i => {\n if (hasValueType(i, dcmjs.sr.valueTypes.ValueTypes.CODE)) {\n const evaluation = i as dcmjs.sr.valueTypes.CodeContentItem\n items.push(evaluation)\n }\n })\n return items\n}\n\nconst getROIs = (report: dmv.metadata.Comprehensive3DSR): dmv.roi.ROI[] => {\n // TID 1500 Measurement Report\n const matches = findContentItemsByName({\n content: report.ContentSequence,\n name: new dcmjs.sr.coding.CodedConcept({\n value: '126010',\n schemeDesignator: 'DCM',\n meaning: 'Imaging Measurements'\n })\n })\n if (matches.length !== 1) {\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.SLIM,\n new CustomError(\n errorTypes.ENCODINGANDDECODING,\n 'Content item \"Imaging Measurements\" not found.' +\n 'Content of Comprehensive 3D SR document is not structured based on ' +\n 'TID 1500 \"Measurement Report\".'\n )\n )\n }\n const measurementsItem = matches[0] as dcmjs.sr.valueTypes.ContainerContentItem\n // TID 1410 Planar ROI Measurements and Qualitative Evaluations\n const measurementGroupItems = findContentItemsByName({\n content: measurementsItem.ContentSequence,\n name: new dcmjs.sr.coding.CodedConcept({\n value: '125007',\n schemeDesignator: 'DCM',\n meaning: 'Measurement Group'\n })\n })\n\n const rois: dmv.roi.ROI[] = []\n measurementGroupItems.forEach((item) => {\n const evaluations = []\n let observerType: string\n const group = item as dcmjs.sr.valueTypes.ContainerContentItem\n let items = findContentItemsByName({\n content: group.ContentSequence,\n name: new dcmjs.sr.coding.CodedConcept({\n value: '112040',\n schemeDesignator: 'DCM',\n meaning: 'Tracking Unique Identifier'\n })\n })\n if (items.length === 0) {\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.SLIM,\n new CustomError(\n errorTypes.ENCODINGANDDECODING,\n 'Content item \"Tracking Unique Identifier\" not found. ' +\n 'Content of Comprehensive 3D SR document is not structured ' +\n 'based on TID 1500 \"Measurement Report\" -> ' +\n 'TID 1410 \"Planar ROI Measurements and Qualitative Evaluations\".'\n )\n )\n }\n const trackingUIDItem = items[0] as dcmjs.sr.valueTypes.UIDRefContentItem\n\n items = findContentItemsByName({\n content: group.ContentSequence,\n name: new dcmjs.sr.coding.CodedConcept({\n value: '121071',\n schemeDesignator: 'DCM',\n meaning: 'Finding'\n })\n })\n if (items.length === 0) {\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.SLIM,\n new CustomError(\n errorTypes.ENCODINGANDDECODING,\n 'Content item \"Finding\" not found. ' +\n 'Content of Comprehensive 3D SR document is not structured ' +\n 'based on TID 1500 \"Measurement Report\" -> ' +\n 'TID 1410 \"Planar ROI Measurements and Qualitative Evaluations\".'\n )\n )\n }\n\n items = findContentItemsByName({\n content: group.ContentSequence,\n name: new dcmjs.sr.coding.CodedConcept({\n value: '111001',\n schemeDesignator: 'DCM',\n meaning: 'Algorithm Name'\n })\n })\n if (items.length !== 0) {\n const algorithmNameItem = items[0] as dcmjs.sr.valueTypes.CodeContentItem\n evaluations.push(algorithmNameItem)\n observerType = 'Device'\n } else {\n observerType = 'Person'\n }\n\n items = findContentItemsByName({\n content: group.ContentSequence,\n name: new dcmjs.sr.coding.CodedConcept({\n value: '111003',\n schemeDesignator: 'DCM',\n meaning: 'Algorithm Version'\n })\n })\n if (items.length !== 0) {\n const algorithmVersionItem = items[0] as dcmjs.sr.valueTypes.CodeContentItem\n evaluations.push(algorithmVersionItem)\n }\n\n items = findContentItemsByName({\n content: group.ContentSequence,\n name: new dcmjs.sr.coding.CodedConcept({\n value: '111030',\n schemeDesignator: 'DCM',\n meaning: 'Image Region'\n })\n })\n if (items.length === 0) {\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.SLIM,\n new CustomError(\n errorTypes.ENCODINGANDDECODING,\n 'Content item \"Image Region\" not found. ' +\n 'Content of Comprehensive 3D SR document is not structured ' +\n 'based on TID 1500 \"Measurement Report\" -> ' +\n 'TID 1410 \"Planar ROI Measurements and Qualitative Evaluations\".'\n )\n )\n }\n const regionItem = items[0] as dcmjs.sr.valueTypes.Scoord3DContentItem\n let scoord3d: any\n if (regionItem.GraphicType === 'POINT') {\n scoord3d = new dmv.scoord3d.Point({\n frameOfReferenceUID: regionItem.ReferencedFrameOfReferenceUID,\n coordinates: regionItem.GraphicData\n })\n } else {\n const coordinates: number[][] = []\n for (let i = 0; i < regionItem.GraphicData.length; i += 3) {\n coordinates.push(regionItem.GraphicData.slice(i, i + 3))\n }\n if (regionItem.GraphicType === 'POLYGON') {\n scoord3d = new dmv.scoord3d.Polygon({\n frameOfReferenceUID: regionItem.ReferencedFrameOfReferenceUID,\n coordinates: coordinates\n })\n } else if (regionItem.GraphicType === 'MULTIPOINT') {\n scoord3d = new dmv.scoord3d.MultiPoint({\n frameOfReferenceUID: regionItem.ReferencedFrameOfReferenceUID,\n coordinates: coordinates\n })\n } else if (regionItem.GraphicType === 'POLYLINE') {\n scoord3d = new dmv.scoord3d.Polyline({\n frameOfReferenceUID: regionItem.ReferencedFrameOfReferenceUID,\n coordinates: coordinates\n })\n } else if (regionItem.GraphicType === 'ELLIPSE') {\n scoord3d = new dmv.scoord3d.Ellipse({\n frameOfReferenceUID: regionItem.ReferencedFrameOfReferenceUID,\n coordinates: coordinates\n })\n } else if (regionItem.GraphicType === 'ELLIPSOID') {\n scoord3d = new dmv.scoord3d.Ellipsoid({\n frameOfReferenceUID: regionItem.ReferencedFrameOfReferenceUID,\n coordinates: coordinates\n })\n } else {\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.SLIM,\n new CustomError(\n errorTypes.ENCODINGANDDECODING,\n 'Content item \"Image Region\" has unknown graphic type ' +\n `\"${regionItem.GraphicType}\". ` +\n 'Content of Comprehensive 3D SR document is not structured ' +\n 'based on TID 1500 \"Measurement Report\" -> ' +\n 'TID 1410 \"Planar ROI Measurements and Qualitative Evaluations\".'\n )\n )\n }\n }\n\n evaluations.push(\n ...findEvaluationItems({ content: group.ContentSequence })\n )\n const measurements = findMeasurementItems({\n content: group.ContentSequence\n })\n\n const roi = new dmv.roi.ROI({\n scoord3d: scoord3d,\n uid: generateUUID(),\n properties: {\n trackingUID: trackingUIDItem.UID,\n observerType: observerType,\n evaluations: evaluations,\n measurements: measurements\n }\n })\n rois.push(roi)\n })\n return rois\n}\n\nclass MeasurementReport {\n public PersonObserverName?: string\n\n public PersonObserverLoginName?: string\n\n public DeviceObserverUID?: string\n\n public DeviceObserverName?: string\n\n public SpecimenUID: string\n\n public SpecimenIdentifier: string\n\n public ContainerIdentifier: string\n\n public ROIs: dmv.roi.ROI[] = []\n\n constructor (report: dmv.metadata.Comprehensive3DSR) {\n let items = findContentItemsByName({\n content: report.ContentSequence,\n name: new dcmjs.sr.coding.CodedConcept({\n value: '121039',\n schemeDesignator: 'DCM',\n meaning: 'Specimen UID'\n })\n })\n if (items.length === 0) {\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.SLIM,\n new CustomError(\n errorTypes.ENCODINGANDDECODING,\n 'Content item \"Specimen UID\" not found. ' +\n 'Content of Comprehensive 3D SR document is not structured based on ' +\n 'TID 1500 \"Measurement Report\" -> TID 1001 \"Observation Context\" -> ' +\n 'TID 1006 \"Subject Context\" -> TID 1009 \"Subject Context, Specimen\".'\n )\n )\n }\n const specimenUIDItem = (\n items[0] as unknown as dcmjs.sr.valueTypes.UIDRefContentItem\n )\n this.SpecimenUID = specimenUIDItem.UID\n\n items = findContentItemsByName({\n content: report.ContentSequence,\n name: new dcmjs.sr.coding.CodedConcept({\n value: '121041',\n schemeDesignator: 'DCM',\n meaning: 'Specimen Identifier'\n })\n })\n if (items.length === 0) {\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.SLIM,\n new CustomError(\n errorTypes.ENCODINGANDDECODING,\n 'Content item \"Specimen Identifier\" not found. ' +\n 'Content of Comprehensive 3D SR document is not structured based on ' +\n 'TID 1500 \"Measurement Report\" -> TID 1001 \"Observation Context\" -> ' +\n 'TID 1006 \"Subject Context\" -> TID 1009 \"Subject Context, Specimen\".'\n )\n )\n }\n const specimenIdItem = (\n items[0] as unknown as dcmjs.sr.valueTypes.TextContentItem\n )\n this.SpecimenIdentifier = specimenIdItem.TextValue\n\n items = findContentItemsByName({\n content: report.ContentSequence,\n name: new dcmjs.sr.coding.CodedConcept({\n value: '111700',\n schemeDesignator: 'DCM',\n meaning: 'Specimen Container Identifier'\n })\n })\n if (items.length === 0) {\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.SLIM,\n new CustomError(\n errorTypes.ENCODINGANDDECODING,\n 'Content item \"Specimen Container Identifier\" not found. ' +\n 'Content of Comprehensive 3D SR document is not structured based on ' +\n 'TID 1500 \"Measurement Report\" -> TID 1001 \"Observation Context\" -> ' +\n 'TID 1006 \"Subject Context\" -> TID 1009 \"Subject Context, Specimen\".'\n )\n )\n }\n const containerIdItem = (\n items[0] as unknown as dcmjs.sr.valueTypes.TextContentItem\n )\n this.ContainerIdentifier = containerIdItem.TextValue\n\n items = findContentItemsByName({\n content: report.ContentSequence,\n name: new dcmjs.sr.coding.CodedConcept({\n value: '121008',\n schemeDesignator: 'DCM',\n meaning: 'Person Observer Name'\n })\n })\n if (items.length !== 0) {\n const personNameItem = (\n items[0] as unknown as dcmjs.sr.valueTypes.PNameContentItem\n )\n this.PersonObserverName = personNameItem.PersonName\n }\n\n items = findContentItemsByName({\n content: report.ContentSequence,\n name: new dcmjs.sr.coding.CodedConcept({\n value: '128774',\n schemeDesignator: 'DCM',\n meaning: \"Person Observer's Login Name\"\n })\n })\n if (items.length !== 0) {\n const personLoginNameItem = (\n items[0] as unknown as dcmjs.sr.valueTypes.TextContentItem\n )\n this.PersonObserverLoginName = personLoginNameItem.TextValue\n }\n\n items = findContentItemsByName({\n content: report.ContentSequence,\n name: new dcmjs.sr.coding.CodedConcept({\n value: '121012',\n schemeDesignator: 'DCM',\n meaning: 'Device Observer UID'\n })\n })\n if (items.length > 0) {\n const deviceUIDItem = (\n items[0] as unknown as dcmjs.sr.valueTypes.UIDRefContentItem\n )\n this.DeviceObserverUID = deviceUIDItem.UID\n }\n\n items = findContentItemsByName({\n content: report.ContentSequence,\n name: new dcmjs.sr.coding.CodedConcept({\n value: '121013',\n schemeDesignator: 'DCM',\n meaning: 'Device Observer Name'\n })\n })\n if (items.length !== 0) {\n const deviceNameItem = (\n items[0] as unknown as dcmjs.sr.valueTypes.TextContentItem\n )\n this.DeviceObserverName = deviceNameItem.TextValue\n }\n\n this.ROIs = getROIs(report)\n }\n}\n\ninterface ReportProps {\n dataset: dmv.metadata.Comprehensive3DSR\n}\n\n/**\n * React component representing a DICOM SR document that displays the\n * document content (a selected subset of content items).\n */\nclass Report extends React.Component {\n render (): React.ReactNode {\n const report = new MeasurementReport(this.props.dataset)\n const containerAttrs = [\n {\n name: 'ID',\n value: report.ContainerIdentifier\n }\n ]\n const specimenAttrs = [\n {\n name: 'ID',\n value: report.SpecimenIdentifier\n }\n ]\n const observerAttrs = [\n {\n name: 'Name',\n value: report.PersonObserverName\n }\n ]\n const annotations = report.ROIs.map(\n (roi, index): React.ReactNode => {\n const id = `Region ${index + 1}`\n const attrs: Array<{ name: string, value: string }> = []\n roi.evaluations.forEach((\n item: (\n dcmjs.sr.valueTypes.CodeContentItem |\n dcmjs.sr.valueTypes.TextContentItem\n )\n ) => {\n if (item.ValueType === dcmjs.sr.valueTypes.ValueTypes.CODE) {\n item = item as dcmjs.sr.valueTypes.CodeContentItem\n attrs.push({\n name: item.ConceptNameCodeSequence[0].CodeMeaning,\n value: item.ConceptCodeSequence[0].CodeMeaning\n })\n } else if (item.ValueType === dcmjs.sr.valueTypes.ValueTypes.TEXT) {\n item = item as dcmjs.sr.valueTypes.TextContentItem\n attrs.push({\n name: item.ConceptNameCodeSequence[0].CodeMeaning,\n value: item.TextValue\n })\n }\n })\n return \n }\n )\n\n return (\n
\n Patient\n \n Case\n \n Slide\n \n Specimen\n \n Observer\n \n Annotations\n {annotations}\n
\n )\n }\n}\n\nexport default Report\nexport { MeasurementReport }\n","import React from 'react'\nimport { List } from 'antd'\n\nimport Description, { Attribute, AttributeGroup } from './Description'\n\ninterface ItemProps {\n uid: string\n identifier: string\n attributes: Attribute[]\n groups?: AttributeGroup[]\n children?: React.ReactElement[]\n type?: string\n hasLongValues?: boolean\n}\n\n/**\n * React component for a list item that consists of a header element\n * containing an identifier and a body element containing a description list\n * of attributes rendered as name-value pairs.\n */\nclass Item extends React.Component {\n render (): React.ReactNode {\n let groups = null\n if (this.props.groups !== undefined) {\n groups = this.props.groups.map((item, index: number) => (\n \n ))\n }\n let title\n if (this.props.type !== undefined) {\n title = `${this.props.type}: ${this.props.identifier}`\n } else {\n title = this.props.identifier\n }\n return (\n \n \n {groups}\n \n {this.props.children}\n \n )\n }\n}\n\nexport default Item\n","import * as dcmjs from 'dcmjs'\n\nexport const SpecimenPreparationTypes: {\n [key: string]: dcmjs.sr.coding.CodedConcept\n} = {\n COLLECTION: new dcmjs.sr.coding.CodedConcept({\n value: '17636008',\n schemeDesignator: 'SCT',\n meaning: 'Specimen collection'\n }),\n SAMPLING: new dcmjs.sr.coding.CodedConcept({\n value: '433465004',\n schemeDesignator: 'SCT',\n meaning: 'Sampling of tissue specimen'\n }),\n STAINING: new dcmjs.sr.coding.CodedConcept({\n value: '127790008',\n schemeDesignator: 'SCT',\n meaning: 'Specimen staining'\n }),\n PROCESSING: new dcmjs.sr.coding.CodedConcept({\n value: '9265001',\n schemeDesignator: 'SCT',\n meaning: 'Specimen processing'\n })\n}\n\nexport const SpecimenPreparationAdditives: {\n [key: string]: dcmjs.sr.coding.CodedConcept\n} = {\n FIXATIVE: new dcmjs.sr.coding.CodedConcept({\n value: '430864009',\n schemeDesignator: 'SCT',\n meaning: 'Tissue fixative'\n }),\n EMBEDDING_MEDIUM: new dcmjs.sr.coding.CodedConcept({\n value: '430863003',\n schemeDesignator: 'SCT',\n meaning: 'Embedding medium'\n })\n}\n\nexport const SpecimenPreparationStepItems: {\n [key: string]: dcmjs.sr.coding.CodedConcept\n} = {\n SPECIMEN_IDENTIFIER: new dcmjs.sr.coding.CodedConcept({\n value: '121041',\n schemeDesignator: 'DCM',\n meaning: 'Specimen identifier'\n }),\n PARENT_SPECIMEN_IDENTIFIER: new dcmjs.sr.coding.CodedConcept({\n value: '111705',\n schemeDesignator: 'DCM',\n meaning: 'Parent specimen identifier'\n }),\n PROCESSING_TYPE: new dcmjs.sr.coding.CodedConcept({\n value: '111701',\n schemeDesignator: 'DCM',\n meaning: 'Processing type'\n }),\n DATETIME_OF_PROCESSING: new dcmjs.sr.coding.CodedConcept({\n value: '111702',\n schemeDesignator: 'DCM',\n meaning: 'Datetime of processing'\n }),\n PROCESSING_STEP_DESCRIPTION: new dcmjs.sr.coding.CodedConcept({\n value: '111703',\n schemeDesignator: 'DCM',\n meaning: 'Processing step description'\n }),\n COLLECTION_METHOD: new dcmjs.sr.coding.CodedConcept({\n value: '17636008',\n schemeDesignator: 'SCT',\n meaning: 'Specimen collection'\n }),\n SAMPLING_METHOD: new dcmjs.sr.coding.CodedConcept({\n value: '111704',\n schemeDesignator: 'DCM',\n meaning: 'Sampling method'\n }),\n STAIN: new dcmjs.sr.coding.CodedConcept({\n value: '424361007',\n schemeDesignator: 'SCT',\n meaning: 'Using substance'\n }),\n ...SpecimenPreparationAdditives\n}\n","import React from 'react'\nimport * as dmv from 'dicom-microscopy-viewer'\nimport * as dcmjs from 'dcmjs'\n\nimport Item from './Item'\nimport { Attribute } from './Description'\nimport { SpecimenPreparationStepItems } from '../data/specimens'\n\ninterface SpecimenItemProps {\n index: number\n metadata?: dmv.metadata.VLWholeSlideMicroscopyImage\n showstain: boolean\n}\n\n/**\n * React component representing a DICOM Specimen Information Entity and\n * displays specimen-related attributes of a DICOM Slide Microscopy image.\n */\nclass SpecimenItem extends React.Component {\n render (): React.ReactNode {\n if (this.props.metadata === undefined) {\n return null\n }\n const specimenDescription = this.props.metadata.SpecimenDescriptionSequence[\n this.props.index\n ]\n const attributes: Attribute[] = []\n if (specimenDescription.SpecimenShortDescription !== undefined) {\n attributes.push({\n name: 'Description',\n value: specimenDescription.SpecimenShortDescription\n })\n }\n if (specimenDescription.PrimaryAnatomicStructureSequence !== undefined) {\n if (specimenDescription.PrimaryAnatomicStructureSequence.length > 0) {\n const structures = specimenDescription.PrimaryAnatomicStructureSequence\n attributes.push({\n name: 'Anatomical structure',\n value: structures.map(item => item.CodeMeaning).join(', ')\n })\n }\n }\n\n // TID 8001 \"Specimen Preparation\"\n const preparationSteps: dmv.metadata.SpecimenPreparation[] = (\n specimenDescription.SpecimenPreparationSequence ?? []\n )\n preparationSteps.forEach(\n (step: dmv.metadata.SpecimenPreparation, index: number): void => {\n step.SpecimenPreparationStepContentItemSequence.forEach((\n item: (\n dcmjs.sr.valueTypes.CodeContentItem |\n dcmjs.sr.valueTypes.TextContentItem |\n dcmjs.sr.valueTypes.UIDRefContentItem |\n dcmjs.sr.valueTypes.PNameContentItem |\n dcmjs.sr.valueTypes.DateTimeContentItem\n ),\n index: number\n ) => {\n const name = new dcmjs.sr.coding.CodedConcept({\n value: item.ConceptNameCodeSequence[0].CodeValue,\n schemeDesignator:\n item.ConceptNameCodeSequence[0].CodingSchemeDesignator,\n meaning: item.ConceptNameCodeSequence[0].CodeMeaning\n })\n if (item.ValueType === dcmjs.sr.valueTypes.ValueTypes.CODE) {\n item = item as dcmjs.sr.valueTypes.CodeContentItem\n const value = new dcmjs.sr.coding.CodedConcept({\n value: item.ConceptCodeSequence[0].CodeValue,\n schemeDesignator:\n item.ConceptCodeSequence[0].CodingSchemeDesignator,\n meaning: item.ConceptCodeSequence[0].CodeMeaning\n })\n if (!name.equals(SpecimenPreparationStepItems.PROCESSING_TYPE)) {\n if (\n name.equals(SpecimenPreparationStepItems.COLLECTION_METHOD)\n ) {\n attributes.push({\n name: 'Collection method',\n value: value.CodeMeaning\n })\n } else if (\n name.equals(SpecimenPreparationStepItems.FIXATIVE)\n ) {\n attributes.push({\n name: 'Tissue fixative',\n value: value.CodeMeaning\n })\n } else if (\n name.equals(SpecimenPreparationStepItems.EMBEDDING_MEDIUM)\n ) {\n attributes.push({\n name: 'Tissue embedding medium',\n value: value.CodeMeaning\n })\n } else if (\n name.equals(SpecimenPreparationStepItems.STAIN) &&\n this.props.showstain\n ) {\n attributes.push({\n name: 'Tissue stain',\n value: value.CodeMeaning\n })\n }\n }\n } else if (item.ValueType === dcmjs.sr.valueTypes.ValueTypes.TEXT) {\n item = item as dcmjs.sr.valueTypes.TextContentItem\n if (\n name.equals(SpecimenPreparationStepItems.STAIN) &&\n this.props.showstain\n ) {\n attributes.push({\n name: 'Tissue stain',\n value: item.TextValue\n })\n } else if (\n name.equals(SpecimenPreparationStepItems.PARENT_SPECIMEN_IDENTIFIER)\n ) {\n attributes.push({\n name: 'Parent specimen',\n value: item.TextValue\n })\n }\n }\n })\n }\n )\n const uid = specimenDescription.SpecimenUID\n const identifier = specimenDescription.SpecimenIdentifier\n return (\n \n )\n }\n}\n\nexport default SpecimenItem\n","import React from 'react'\nimport * as dmv from 'dicom-microscopy-viewer'\nimport { List } from 'antd'\n\nimport SpecimenItem from './SpecimenItem'\n\ninterface SpecimenListProps {\n metadata?: dmv.metadata.VLWholeSlideMicroscopyImage\n showstain: boolean\n}\n\n/**\n * React component representing a list of DICOM Specimen Information Entities.\n */\nclass SpecimenList extends React.Component {\n render (): React.ReactNode {\n if (this.props.metadata === undefined) {\n return null\n }\n /*\n * Specimen Description Sequence is a type 1 attribute. However, it is\n * nevertheless missing in some data sets. This is a violation of the\n * standard, but it may be better to facilitate display of the data.\n */\n const descriptions = this.props.metadata.SpecimenDescriptionSequence ?? []\n const items = descriptions.map(\n (item: dmv.metadata.SpecimenDescription, index: number) => {\n return (\n \n )\n }\n )\n return (\n \n {items}\n \n )\n }\n}\n\nexport default SpecimenList\n","import React from 'react'\nimport {\n Badge,\n Button,\n Col,\n Divider,\n InputNumber,\n Menu,\n Popover,\n Row,\n Slider,\n Space,\n Switch,\n Tooltip\n} from 'antd'\nimport {\n DeleteOutlined,\n EyeOutlined,\n EyeInvisibleOutlined,\n SettingOutlined\n} from '@ant-design/icons'\nimport Description from './Description'\nimport * as dmv from 'dicom-microscopy-viewer'\nimport * as dcmjs from 'dcmjs'\n\nimport { SpecimenPreparationStepItems } from '../data/specimens'\nimport NotificationMiddleware, {\n NotificationMiddlewareContext\n} from '../services/NotificationMiddleware'\nimport { CustomError, errorTypes } from '../utils/CustomError'\n\ninterface OpticalPathItemProps {\n opticalPath: dmv.opticalPath.OpticalPath\n metadata: dmv.metadata.VLWholeSlideMicroscopyImage[]\n isVisible: boolean\n isRemovable: boolean\n defaultStyle: {\n opacity: number\n color?: number[]\n paletteColorLookupTable?: dmv.color.PaletteColorLookupTable\n limitValues?: number[]\n }\n onVisibilityChange: ({ opticalPathIdentifier, isVisible }: {\n opticalPathIdentifier: string\n isVisible: boolean\n }) => void\n onStyleChange: ({ opticalPathIdentifier, styleOptions }: {\n opticalPathIdentifier: string\n styleOptions: {\n opacity?: number\n color?: number[]\n paletteColorLookupTable?: dmv.color.PaletteColorLookupTable\n limitValues?: number[]\n }\n }) => void\n onRemoval: (opticalPathIdentifier: string) => void\n}\n\ninterface OpticalPathItemState {\n isVisible: boolean\n currentStyle: {\n opacity: number\n color?: number[]\n paletteColorLookupTable?: dmv.color.PaletteColorLookupTable\n limitValues?: number[]\n }\n}\n\n/**\n * React component representing an optical path of a\n * multi-channel acquistion with control of visualization parameters.\n */\nclass OpticalPathItem extends React.Component {\n constructor (props: OpticalPathItemProps) {\n super(props)\n this.handleVisibilityChange = this.handleVisibilityChange.bind(this)\n this.handleOpacityChange = this.handleOpacityChange.bind(this)\n this.handleLimitChange = this.handleLimitChange.bind(this)\n this.handleLowerLimitChange = this.handleLowerLimitChange.bind(this)\n this.handleUpperLimitChange = this.handleUpperLimitChange.bind(this)\n this.handleColorRChange = this.handleColorRChange.bind(this)\n this.handleColorGChange = this.handleColorGChange.bind(this)\n this.handleColorBChange = this.handleColorBChange.bind(this)\n this.handleRemoval = this.handleRemoval.bind(this)\n this.getCurrentColors = this.getCurrentColors.bind(this)\n this.state = {\n isVisible: this.props.isVisible,\n currentStyle: {\n opacity: this.props.defaultStyle.opacity,\n color: this.props.defaultStyle.color,\n paletteColorLookupTable: this.props.defaultStyle.paletteColorLookupTable,\n limitValues: this.props.defaultStyle.limitValues\n }\n }\n }\n\n componentDidUpdate (\n previousProps: OpticalPathItemProps,\n previousState: OpticalPathItemState\n ): void {\n if (this.props.defaultStyle !== previousProps.defaultStyle) {\n this.setState({\n currentStyle: this.props.defaultStyle\n })\n }\n }\n\n handleVisibilityChange (\n checked: boolean,\n event: React.MouseEvent\n ): void {\n const identifier = this.props.opticalPath.identifier\n this.setState({\n isVisible: checked\n })\n this.props.onVisibilityChange({\n opticalPathIdentifier: identifier,\n isVisible: checked\n })\n }\n\n handleOpacityChange (\n value: number | null\n ): void {\n if (value != null) {\n const identifier = this.props.opticalPath.identifier\n this.props.onStyleChange({\n opticalPathIdentifier: identifier,\n styleOptions: { opacity: value }\n })\n this.setState(state => ({\n currentStyle: {\n color: state.currentStyle.color,\n paletteColorLookupTable: state.currentStyle.paletteColorLookupTable,\n opacity: value,\n limitValues: state.currentStyle.limitValues\n }\n }))\n }\n }\n\n handleColorRChange (\n value: number | number[] | null\n ): void {\n const identifier = this.props.opticalPath.identifier\n if (value != null && this.state.currentStyle.color !== undefined) {\n const color = [\n Array.isArray(value) ? value[0] : value,\n this.state.currentStyle.color[1],\n this.state.currentStyle.color[2]\n ]\n this.setState(state => ({\n currentStyle: {\n color: color,\n paletteColorLookupTable: state.currentStyle.paletteColorLookupTable,\n opacity: state.currentStyle.opacity,\n limitValues: state.currentStyle.limitValues\n }\n }))\n this.props.onStyleChange({\n opticalPathIdentifier: identifier,\n styleOptions: { color: color }\n })\n }\n }\n\n handleColorGChange (\n value: number | number[] | null\n ): void {\n const identifier = this.props.opticalPath.identifier\n if (value != null && this.state.currentStyle.color !== undefined) {\n const color = [\n this.state.currentStyle.color[0],\n Array.isArray(value) ? value[0] : value,\n this.state.currentStyle.color[2]\n ]\n this.setState(state => ({\n currentStyle: {\n color: color,\n paletteColorLookupTable: state.currentStyle.paletteColorLookupTable,\n opacity: state.currentStyle.opacity,\n limitValues: state.currentStyle.limitValues\n }\n }))\n this.props.onStyleChange({\n opticalPathIdentifier: identifier,\n styleOptions: { color: color }\n })\n }\n }\n\n handleColorBChange (\n value: number | number[] | null\n ): void {\n const identifier = this.props.opticalPath.identifier\n if (value != null && this.state.currentStyle.color !== undefined) {\n const color = [\n this.state.currentStyle.color[0],\n this.state.currentStyle.color[1],\n Array.isArray(value) ? value[0] : value\n ]\n this.setState(state => ({\n currentStyle: {\n color: color,\n paletteColorLookupTable: state.currentStyle.paletteColorLookupTable,\n opacity: state.currentStyle.opacity,\n limitValues: state.currentStyle.limitValues\n }\n }))\n this.props.onStyleChange({\n opticalPathIdentifier: identifier,\n styleOptions: { color: color }\n })\n }\n }\n\n getCurrentColors (): string[] {\n const rgb2hex = (values: number[]): string => {\n const r = values[0]\n const g = values[1]\n const b = values[2]\n return '#' + (0x1000000 + (r << 16) + (g << 8) + b).toString(16).slice(1)\n }\n\n if (this.props.defaultStyle.paletteColorLookupTable != null) {\n const colormap = this.props.defaultStyle.paletteColorLookupTable.data\n return colormap.map(values => rgb2hex(values))\n } else if (this.state.currentStyle.color != null) {\n return [\n '#000000',\n rgb2hex(this.state.currentStyle.color)\n ]\n } else {\n return ['white', 'white']\n }\n }\n\n handleLowerLimitChange (\n value: number | null\n ): void {\n const identifier = this.props.opticalPath.identifier\n if (value != null && this.state.currentStyle.limitValues !== undefined) {\n this.setState(state => {\n if (state.currentStyle.limitValues !== undefined) {\n return {\n currentStyle: {\n color: state.currentStyle.color,\n paletteColorLookupTable: state.currentStyle.paletteColorLookupTable,\n opacity: state.currentStyle.opacity,\n limitValues: [value, state.currentStyle.limitValues[1]]\n }\n }\n } else {\n return {\n currentStyle: {\n color: state.currentStyle.color,\n paletteColorLookupTable: state.currentStyle.paletteColorLookupTable,\n opacity: state.currentStyle.opacity,\n limitValues: state.currentStyle.limitValues\n }\n }\n }\n })\n this.props.onStyleChange({\n opticalPathIdentifier: identifier,\n styleOptions: {\n limitValues: [\n value,\n this.state.currentStyle.limitValues[1]\n ]\n }\n })\n }\n }\n\n handleUpperLimitChange (\n value: number | null\n ): void {\n const identifier = this.props.opticalPath.identifier\n if (value != null && this.state.currentStyle.limitValues !== undefined) {\n this.setState(state => {\n if (state.currentStyle.limitValues !== undefined) {\n return {\n currentStyle: {\n color: state.currentStyle.color,\n paletteColorLookupTable: state.currentStyle.paletteColorLookupTable,\n opacity: state.currentStyle.opacity,\n limitValues: [state.currentStyle.limitValues[0], value]\n }\n }\n } else {\n return {\n currentStyle: {\n color: state.currentStyle.color,\n paletteColorLookupTable: state.currentStyle.paletteColorLookupTable,\n opacity: state.currentStyle.opacity,\n limitValues: state.currentStyle.limitValues\n }\n }\n }\n })\n this.props.onStyleChange({\n opticalPathIdentifier: identifier,\n styleOptions: {\n limitValues: [\n this.state.currentStyle.limitValues[0],\n value\n ]\n }\n })\n }\n }\n\n handleLimitChange (\n values: number[]\n ): void {\n const identifier = this.props.opticalPath.identifier\n this.setState(state => ({\n currentStyle: {\n color: state.currentStyle.color,\n paletteColorLookupTable: state.currentStyle.paletteColorLookupTable,\n opacity: state.currentStyle.opacity,\n limitValues: values\n }\n }))\n this.props.onStyleChange({\n opticalPathIdentifier: identifier,\n styleOptions: { limitValues: values }\n })\n }\n\n handleRemoval (): void {\n const identifier = this.props.opticalPath.identifier\n this.props.onRemoval(identifier)\n }\n\n render (): React.ReactNode {\n const identifier = this.props.opticalPath.identifier\n const description = this.props.opticalPath.description\n const attributes: Array<{ name: string, value: string }> = []\n if (this.props.opticalPath.illuminationWaveLength !== undefined) {\n attributes.push(\n {\n name: 'Illumination wavelength',\n value: `${this.props.opticalPath.illuminationWaveLength} nm`\n }\n )\n }\n if (this.props.opticalPath.illuminationColor !== undefined) {\n attributes.push(\n {\n name: 'Illumination color',\n value: this.props.opticalPath.illuminationColor.CodeMeaning\n }\n )\n }\n\n // TID 8001 \"Specimen Preparation\"\n const specimenDescriptions: dmv.metadata.SpecimenDescription[] = (\n this.props.metadata[0].SpecimenDescriptionSequence ?? []\n )\n try {\n specimenDescriptions.forEach(description => {\n const specimenPreparationSteps: dmv.metadata.SpecimenPreparation[] =\n description.SpecimenPreparationSequence ?? []\n specimenPreparationSteps.forEach(\n (step: dmv.metadata.SpecimenPreparation, index: number): void => {\n step.SpecimenPreparationStepContentItemSequence.forEach((\n item: (\n dcmjs.sr.valueTypes.CodeContentItem |\n dcmjs.sr.valueTypes.TextContentItem |\n dcmjs.sr.valueTypes.UIDRefContentItem |\n dcmjs.sr.valueTypes.PNameContentItem |\n dcmjs.sr.valueTypes.DateTimeContentItem\n ),\n index: number\n ) => {\n const name = new dcmjs.sr.coding.CodedConcept({\n value: item.ConceptNameCodeSequence[0].CodeValue,\n schemeDesignator:\n item.ConceptNameCodeSequence[0].CodingSchemeDesignator,\n meaning: item.ConceptNameCodeSequence[0].CodeMeaning\n })\n if (item.ValueType === dcmjs.sr.valueTypes.ValueTypes.CODE) {\n item = item as dcmjs.sr.valueTypes.CodeContentItem\n const value = new dcmjs.sr.coding.CodedConcept({\n value: item.ConceptCodeSequence[0].CodeValue,\n schemeDesignator:\n item.ConceptCodeSequence[0].CodingSchemeDesignator,\n meaning: item.ConceptCodeSequence[0].CodeMeaning\n })\n if (!name.equals(SpecimenPreparationStepItems.PROCESSING_TYPE)) {\n if (name.equals(SpecimenPreparationStepItems.STAIN)) {\n attributes.push({\n name: 'Tissue stain',\n value: value.CodeMeaning\n })\n }\n }\n } else if (item.ValueType === dcmjs.sr.valueTypes.ValueTypes.TEXT) {\n item = item as dcmjs.sr.valueTypes.TextContentItem\n if (!name.equals(SpecimenPreparationStepItems.PROCESSING_TYPE)) {\n if (name.equals(SpecimenPreparationStepItems.STAIN)) {\n attributes.push({\n name: 'Tissue stain',\n value: item.TextValue\n })\n }\n }\n }\n })\n }\n )\n })\n } catch (error: any) {\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.DCMJS,\n new CustomError(\n errorTypes.ENCODINGANDDECODING,\n error.message\n )\n )\n }\n\n const maxValue = Math.pow(2, this.props.metadata[0].BitsAllocated) - 1\n\n const title = (\n description != null ? `${identifier}: ${description}` : identifier\n )\n let settings\n let item\n if (this.props.opticalPath.isMonochromatic) {\n // monochrome images that can be pseudo-colored\n let colorSettings\n if (this.state.currentStyle.color != null) {\n colorSettings = (\n <>\n \n Color\n \n \n \n Red\n \n \n \n \n \n \n \n \n\n \n \n Green\n \n \n \n \n \n \n \n \n\n \n \n Blue\n \n \n \n \n \n \n \n \n \n )\n } else {\n colorSettings = (\n <>\n \n Color\n \n Custom pseudo-coloring is disabled because pixels are colorized via\n a provided palette color lookup table.\n \n )\n }\n\n let windowSettings\n if (this.state.currentStyle.limitValues != null) {\n windowSettings = (\n <>\n \n Values of interest\n \n \n \n \n \n \n \n \n \n \n \n \n \n )\n }\n settings = (\n
\n {windowSettings}\n {colorSettings}\n \n \n \n Opacity\n \n \n \n \n \n \n \n \n
\n )\n const colors = this.getCurrentColors()\n item = (\n \n \n \n )\n } else {\n // color images\n settings = (\n
\n \n \n Opacity\n \n \n \n \n \n \n \n \n
\n )\n item = (\n \n )\n }\n\n const buttons = []\n if (this.props.isRemovable) {\n buttons.push(\n \n }\n onClick={this.handleRemoval}\n />\n \n )\n }\n\n const {\n defaultStyle,\n isRemovable,\n isVisible,\n metadata,\n onVisibilityChange,\n onStyleChange,\n onRemoval,\n opticalPath,\n ...otherProps\n } = this.props\n return (\n \n \n
\n \n }\n unCheckedChildren={}\n />\n \n }\n />\n \n {buttons}\n \n
\n {item}\n \n \n )\n }\n}\n\nexport default OpticalPathItem\n","import React from 'react'\nimport * as dmv from 'dicom-microscopy-viewer'\nimport { Button as Btn, Menu, Select, Space, Tooltip } from 'antd'\nimport { AppstoreAddOutlined } from '@ant-design/icons'\n\nimport OpticalPathItem from './OpticalPathItem'\n\nconst { Option } = Select\n\ninterface OpticalPathListProps {\n opticalPaths: dmv.opticalPath.OpticalPath[]\n metadata: {\n [opticalPathIdentifier: string]: dmv.metadata.VLWholeSlideMicroscopyImage[]\n }\n visibleOpticalPathIdentifiers: Set\n activeOpticalPathIdentifiers: Set\n defaultOpticalPathStyles: {\n [opticalPathIdentifier: string]: {\n opacity: number\n color?: number[]\n limitValues?: number[]\n paletteColorLookupTable?: dmv.color.PaletteColorLookupTable\n }\n }\n onOpticalPathVisibilityChange: ({ opticalPathIdentifier, isVisible }: {\n opticalPathIdentifier: string\n isVisible: boolean\n }) => void\n onOpticalPathStyleChange: ({ opticalPathIdentifier, styleOptions }: {\n opticalPathIdentifier: string\n styleOptions: {\n opacity?: number\n color?: number[]\n limitValues?: number[]\n }\n }) => void\n onOpticalPathActivityChange: ({ opticalPathIdentifier, isActive }: {\n opticalPathIdentifier: string\n isActive: boolean\n }) => void\n selectedPresentationStateUID?: string\n}\n\ninterface OpticalPathListState {\n selectedOpticalPathIdentifier?: string\n}\n\n/**\n * React component representing a list of optical paths.\n */\nclass OpticalPathList extends React.Component {\n state = {\n selectedOpticalPathIdentifier: undefined\n }\n\n constructor (props: OpticalPathListProps) {\n super(props)\n this.handleItemAddition = this.handleItemAddition.bind(this)\n this.handleItemRemoval = this.handleItemRemoval.bind(this)\n this.handleItemSelectionChange = this.handleItemSelectionChange.bind(this)\n }\n\n /**\n * Handler that gets called when an optical path should be removed.\n */\n handleItemRemoval (opticalPathIdentifier: string): void {\n this.props.onOpticalPathActivityChange({\n opticalPathIdentifier,\n isActive: false\n })\n }\n\n /**\n * Handler that gets called when the selection of an optical path should change.\n */\n handleItemSelectionChange (\n value: string\n ): void {\n this.setState({ selectedOpticalPathIdentifier: value })\n }\n\n /**\n * Handler that gets called when an optical path should be added.\n */\n handleItemAddition (): void {\n const identifier = this.state.selectedOpticalPathIdentifier\n if (identifier !== undefined) {\n this.props.onOpticalPathActivityChange({\n opticalPathIdentifier: identifier,\n isActive: true\n })\n this.setState({ selectedOpticalPathIdentifier: undefined })\n }\n }\n\n render (): React.ReactNode {\n if (this.props.metadata === undefined) {\n return null\n }\n\n const isSelectable = this.props.opticalPaths.length > 1\n const opticalPathItems: React.ReactNode[] = []\n const optionItems: React.ReactNode[] = []\n this.props.opticalPaths.forEach(opticalPath => {\n const opticalPathIdentifier = opticalPath.identifier\n const images = this.props.metadata[opticalPathIdentifier]\n const seriesInstanceUID = images[0].SeriesInstanceUID\n images[0].OpticalPathSequence.forEach(opticalPathItem => {\n const id = opticalPathItem.OpticalPathIdentifier\n const description = opticalPathItem.OpticalPathDescription\n if (opticalPath.identifier === id) {\n if (this.props.activeOpticalPathIdentifiers.has(id)) {\n opticalPathItems.push(\n \n )\n } else {\n let title\n if (description !== '') {\n title = `${id} - ${description}`\n } else {\n title = `${id}`\n }\n optionItems.push(\n \n )\n }\n }\n })\n })\n\n let opticalPathSelector\n if (isSelectable) {\n opticalPathSelector = (\n \n \n {optionItems}\n \n \n }\n type='primary'\n onClick={this.handleItemAddition}\n />\n \n \n )\n }\n\n return (\n \n {opticalPathItems}\n {opticalPathSelector}\n \n )\n }\n}\n\nexport default OpticalPathList\n","import React from 'react'\nimport * as dmv from 'dicom-microscopy-viewer'\nimport {\n Button,\n Col,\n InputNumber,\n Menu,\n Popover,\n Row,\n Slider,\n Space,\n Switch\n} from 'antd'\nimport { SettingOutlined } from '@ant-design/icons'\nimport { FaEye, FaEyeSlash } from 'react-icons/fa'\n\nimport Description from './Description'\n\ninterface MappingItemProps {\n mapping: dmv.mapping.ParameterMapping\n metadata: dmv.metadata.ParametricMap[]\n isVisible: boolean\n defaultStyle: {\n opacity: number\n }\n onVisibilityChange: ({ mappingUID, isVisible }: {\n mappingUID: string\n isVisible: boolean\n }) => void\n onStyleChange: ({ mappingUID, styleOptions }: {\n mappingUID: string\n styleOptions: {\n opacity?: number\n }\n }) => void\n}\n\ninterface MappingItemState {\n isVisible: boolean\n currentStyle: {\n opacity: number\n }\n}\n\n/**\n * React component representing a Real World Value Mapping.\n */\nclass MappingItem extends React.Component {\n constructor (props: MappingItemProps) {\n super(props)\n this.handleVisibilityChange = this.handleVisibilityChange.bind(this)\n this.handleOpacityChange = this.handleOpacityChange.bind(this)\n this.state = {\n isVisible: this.props.isVisible,\n currentStyle: {\n opacity: this.props.defaultStyle.opacity\n }\n }\n }\n\n handleVisibilityChange (\n checked: boolean,\n event: React.MouseEvent\n ): void {\n this.props.onVisibilityChange({\n mappingUID: this.props.mapping.uid,\n isVisible: checked\n })\n this.setState({ isVisible: checked })\n }\n\n handleOpacityChange (value: number | null): void {\n if (value != null) {\n this.props.onStyleChange({\n mappingUID: this.props.mapping.uid,\n styleOptions: {\n opacity: value\n }\n })\n this.setState(state => ({\n currentStyle: {\n opacity: value\n }\n }))\n }\n }\n\n render (): React.ReactNode {\n const attributes: Array<{ name: string, value: string }> = [\n {\n name: 'Description',\n value: this.props.mapping.description\n }\n ]\n\n const settings = (\n
\n \n \n Opacity\n \n \n \n \n \n \n \n \n
\n )\n\n /**\n * This hack is required for Menu.Item to work properly:\n * https://github.com/react-component/menu/issues/142\n */\n const {\n defaultStyle,\n isVisible,\n mapping,\n metadata,\n onVisibilityChange,\n onStyleChange,\n ...otherProps\n } = this.props\n return (\n \n \n
\n \n \n }\n unCheckedChildren={}\n />\n \n }\n />\n \n \n \n
\n \n \n \n )\n }\n}\n\nexport default MappingItem\n","import React from 'react'\nimport * as dmv from 'dicom-microscopy-viewer'\nimport { Menu } from 'antd'\n\nimport MappingItem from './MappingItem'\n\ninterface MappingListProps {\n mappings: dmv.mapping.ParameterMapping[]\n metadata: {\n [mappingUID: string]: dmv.metadata.ParametricMap[]\n }\n visibleMappingUIDs: Set\n defaultMappingStyles: {\n [mappingUID: string]: { opacity: number }\n }\n onMappingVisibilityChange: ({ mappingUID, isVisible }: {\n mappingUID: string\n isVisible: boolean\n }) => void\n onMappingStyleChange: ({ mappingUID, styleOptions }: {\n mappingUID: string\n styleOptions: {\n opacity?: number\n }\n }) => void\n}\n\n/**\n * React component representing a list of Real World Value Mappings.\n */\nclass MappingList extends React.Component {\n render (): React.ReactNode {\n const items = this.props.mappings.map((mapping, index) => {\n const uid = mapping.uid\n return (\n \n )\n })\n\n return (\n \n {items}\n \n )\n }\n}\n\nexport default MappingList\n","import React from 'react'\nimport * as dmv from 'dicom-microscopy-viewer'\nimport {\n Button,\n Col,\n InputNumber,\n Menu,\n Popover,\n Row,\n Slider,\n Space,\n Switch\n} from 'antd'\nimport { SettingOutlined } from '@ant-design/icons'\nimport { FaEye, FaEyeSlash } from 'react-icons/fa'\n\nimport Description from './Description'\n\ninterface SegmentItemProps {\n segment: dmv.segment.Segment\n isVisible: boolean\n metadata: dmv.metadata.Segmentation[]\n defaultStyle: {\n opacity: number\n }\n onVisibilityChange: ({ segmentUID, isVisible }: {\n segmentUID: string\n isVisible: boolean\n }) => void\n onStyleChange: ({ segmentUID, styleOptions }: {\n segmentUID: string\n styleOptions: {\n opacity: number\n }\n }) => void\n}\n\ninterface SegmentItemState {\n isVisible: boolean\n currentStyle: {\n opacity: number\n }\n}\n\n/**\n * React component representing a Segment.\n */\nclass SegmentItem extends React.Component {\n constructor (props: SegmentItemProps) {\n super(props)\n this.handleVisibilityChange = this.handleVisibilityChange.bind(this)\n this.handleOpacityChange = this.handleOpacityChange.bind(this)\n this.state = {\n isVisible: this.props.isVisible,\n currentStyle: { opacity: this.props.defaultStyle.opacity }\n }\n }\n\n handleVisibilityChange (\n checked: boolean,\n event: React.MouseEvent\n ): void {\n this.props.onVisibilityChange({\n segmentUID: this.props.segment.uid,\n isVisible: checked\n })\n this.setState({ isVisible: checked })\n }\n\n handleOpacityChange (value: number | null): void {\n if (value != null) {\n this.props.onStyleChange({\n segmentUID: this.props.segment.uid,\n styleOptions: {\n opacity: value\n }\n })\n this.setState({ currentStyle: { opacity: value } })\n }\n }\n\n render (): React.ReactNode {\n const attributes: Array<{ name: string, value: string }> = [\n {\n name: 'Property Type',\n value: this.props.segment.propertyType.CodeMeaning\n },\n {\n name: 'Property Category',\n value: this.props.segment.propertyCategory.CodeMeaning\n },\n {\n name: 'Algorithm Name',\n value: this.props.segment.algorithmName\n }\n ]\n\n const settings = (\n
\n \n \n Opacity\n \n \n \n \n \n \n \n \n
\n )\n\n /**\n * This hack is required for Menu.Item to work properly:\n * https://github.com/react-component/menu/issues/142\n */\n const {\n defaultStyle,\n isVisible,\n segment,\n metadata,\n onVisibilityChange,\n onStyleChange,\n ...otherProps\n } = this.props\n return (\n \n \n
\n \n }\n unCheckedChildren={}\n />\n \n }\n />\n \n \n
\n \n \n \n )\n }\n}\n\nexport default SegmentItem\n","import React from 'react'\nimport * as dmv from 'dicom-microscopy-viewer'\nimport { Menu } from 'antd'\n\nimport SegmentItem from './SegmentItem'\n\ninterface SegmentListProps {\n segments: dmv.segment.Segment[]\n visibleSegmentUIDs: Set\n metadata: {\n [segmentUID: string]: dmv.metadata.Segmentation[]\n }\n defaultSegmentStyles: {\n [segmentUID: string]: {\n opacity: number\n }\n }\n onSegmentVisibilityChange: ({ segmentUID, isVisible }: {\n segmentUID: string\n isVisible: boolean\n }) => void\n onSegmentStyleChange: ({ segmentUID, styleOptions }: {\n segmentUID: string\n styleOptions: {\n opacity: number\n }\n }) => void\n}\n\n/**\n * React component representing a list of Segments.\n */\nclass SegmentList extends React.Component {\n render (): React.ReactNode {\n const items = this.props.segments.map((segment, index) => {\n const uid = segment.uid\n return (\n \n )\n })\n\n return (\n \n {items}\n \n )\n }\n}\n\nexport default SegmentList\n","import React from 'react'\nimport {\n NavigateFunction,\n Params,\n useLocation,\n useNavigate,\n useParams,\n Location\n} from 'react-router-dom'\n\nexport interface RouteComponentProps {\n location: Location\n navigate: NavigateFunction\n params: Params\n}\n\nexport function withRouter (Component: React.ComponentType): Function {\n function ComponentWithRouterProp (props: any): JSX.Element {\n const location = useLocation()\n const navigate = useNavigate()\n const params = useParams()\n return (\n \n )\n }\n return ComponentWithRouterProp\n}\n","import React from 'react'\nimport {\n FaCrosshairs,\n FaDrawPolygon,\n FaEye,\n FaEyeSlash,\n FaHandPaper,\n FaHandPointer,\n FaTrash,\n FaSave\n} from 'react-icons/fa'\nimport {\n Button as Btn,\n Checkbox,\n Descriptions,\n Divider,\n InputNumber,\n message,\n Menu,\n Modal,\n Layout,\n Row,\n Select,\n Space,\n Tooltip\n} from 'antd'\nimport { UndoOutlined, CheckOutlined, StopOutlined } from '@ant-design/icons'\nimport * as dmv from 'dicom-microscopy-viewer'\nimport * as dcmjs from 'dcmjs'\nimport * as dwc from 'dicomweb-client'\n\nimport DicomWebManager from '../DicomWebManager'\nimport AnnotationList from './AnnotationList'\nimport AnnotationGroupList from './AnnotationGroupList'\nimport Button from './Button'\nimport Equipment from './Equipment'\nimport Report, { MeasurementReport } from './Report'\nimport SpecimenList from './SpecimenList'\nimport OpticalPathList from './OpticalPathList'\nimport MappingList from './MappingList'\nimport SegmentList from './SegmentList'\nimport { AnnotationSettings } from '../AppConfig'\nimport { Slide } from '../data/slides'\nimport { StorageClasses } from '../data/uids'\nimport { findContentItemsByName } from '../utils/sr'\nimport { RouteComponentProps, withRouter } from '../utils/router'\nimport { CustomError, errorTypes } from '../utils/CustomError'\nimport NotificationMiddleware, {\n NotificationMiddlewareContext\n} from '../services/NotificationMiddleware'\n\nconst DEFAULT_ROI_STROKE_COLOR: number[] = [255, 234, 0] // [0, 126, 163]\nconst DEFAULT_ROI_FILL_COLOR: number[] = [255, 234, 0, 0.2] // [0, 126, 163, 0.2]\nconst DEFAULT_ROI_STROKE_WIDTH: number = 2\nconst DEFAULT_ROI_RADIUS: number = 5\n\nconst _buildKey = (concept: {\n CodeValue: string\n CodeMeaning: string\n CodingSchemeDesignator: string\n CodingSchemeVersion?: string\n}): string => {\n const codingScheme = concept.CodingSchemeDesignator\n const codeValue = concept.CodeValue\n return `${codingScheme}-${codeValue}`\n}\n\nconst _getRoiKey = (roi: dmv.roi.ROI): string | undefined => {\n const matches = findContentItemsByName({\n content: roi.evaluations,\n name: new dcmjs.sr.coding.CodedConcept({\n value: '121071',\n meaning: 'Finding',\n schemeDesignator: 'DCM'\n })\n })\n if (matches.length === 0) {\n console.warn(`no finding found for ROI ${roi.uid}`)\n return\n }\n const finding = matches[0] as dcmjs.sr.valueTypes.CodeContentItem\n const findingName = finding.ConceptCodeSequence[0]\n return _buildKey(findingName)\n}\n\nconst _areROIsEqual = (a: dmv.roi.ROI, b: dmv.roi.ROI): boolean => {\n if (a.scoord3d.graphicType !== b.scoord3d.graphicType) {\n return false\n }\n if (a.scoord3d.frameOfReferenceUID !== b.scoord3d.frameOfReferenceUID) {\n return false\n }\n if (a.scoord3d.graphicData.length !== b.scoord3d.graphicData.length) {\n return false\n }\n\n const decimals = 6\n for (let i = 0; i < a.scoord3d.graphicData.length; ++i) {\n if (a.scoord3d.graphicType === 'POINT') {\n const s1 = a.scoord3d as dmv.scoord3d.Point\n const s2 = b.scoord3d as dmv.scoord3d.Point\n const c1 = s1.graphicData[i].toPrecision(decimals)\n const c2 = s2.graphicData[i].toPrecision(decimals)\n if (c1 !== c2) {\n return false\n }\n } else {\n const s1 = a.scoord3d as dmv.scoord3d.Polygon\n const s2 = b.scoord3d as dmv.scoord3d.Polygon\n for (let j = 0; j < s1.graphicData[i].length; ++j) {\n const c1 = s1.graphicData[i][j].toPrecision(decimals)\n const c2 = s2.graphicData[i][j].toPrecision(decimals)\n if (c1 !== c2) {\n return false\n }\n }\n }\n }\n return true\n}\n\nconst _formatRoiStyle = (style: {\n stroke?: {\n color?: number[]\n width?: number\n }\n fill?: {\n color?: number[]\n }\n radius?: number\n}): dmv.viewer.ROIStyleOptions => {\n const stroke = {\n color: DEFAULT_ROI_STROKE_COLOR,\n width: DEFAULT_ROI_STROKE_WIDTH\n }\n if (style.stroke != null) {\n if (style.stroke.color != null) {\n stroke.color = style.stroke.color\n }\n if (style.stroke.width != null) {\n stroke.width = style.stroke.width\n }\n }\n const fill = {\n color: DEFAULT_ROI_FILL_COLOR\n }\n if (style.fill != null) {\n if (style.fill.color != null) {\n fill.color = style.fill.color\n }\n }\n return {\n stroke,\n fill,\n image: {\n circle: {\n radius: style.radius != null\n ? style.radius\n : Math.max(5 - stroke.width, 1),\n stroke,\n fill\n }\n }\n }\n}\n\nconst _constructViewers = ({ clients, slide, preload }: {\n clients: { [key: string]: dwc.api.DICOMwebClient }\n slide: Slide\n preload?: boolean\n}): {\n volumeViewer: dmv.viewer.VolumeImageViewer\n labelViewer?: dmv.viewer.LabelImageViewer\n} => {\n console.info(\n 'instantiate viewer for VOLUME images of slide ' +\n `\"${slide.volumeImages[0].ContainerIdentifier}\"`\n )\n try {\n const volumeViewer = new dmv.viewer.VolumeImageViewer({\n clientMapping: clients,\n metadata: slide.volumeImages,\n controls: ['overview', 'position'],\n preload: preload,\n errorInterceptor: (error: CustomError) =>\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.DMV, error\n )\n })\n volumeViewer.activateSelectInteraction({})\n\n let labelViewer\n if (slide.labelImages.length > 0) {\n console.info(\n 'instantiate viewer for LABEL image of slide ' +\n `\"${slide.labelImages[0].ContainerIdentifier}\"`\n )\n labelViewer = new dmv.viewer.LabelImageViewer({\n client: clients[StorageClasses.VL_WHOLE_SLIDE_MICROSCOPY_IMAGE],\n metadata: slide.labelImages[0],\n resizeFactor: 1,\n orientation: 'vertical',\n errorInterceptor: (error: CustomError) =>\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.DMV,\n error\n )\n })\n }\n\n return { volumeViewer, labelViewer }\n } catch (error) {\n // eslint-disable-next-line @typescript-eslint/no-floating-promises\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.SLIM,\n new CustomError(\n errorTypes.VISUALIZATION,\n 'Failed to instantiate viewer'\n )\n )\n throw error\n }\n}\n\n/*\n * Check whether the report is structured according to template\n * TID 1500 \"MeasurementReport\".\n */\nconst _implementsTID1500 = (\n report: dmv.metadata.Comprehensive3DSR\n): boolean => {\n const templateSeq = report.ContentTemplateSequence\n if (templateSeq.length > 0) {\n const tid = templateSeq[0].TemplateIdentifier\n if (tid === '1500') {\n return true\n }\n }\n return false\n}\n\n/*\n * Check whether the subject described in the report is a specimen as compared\n * to a patient, fetus, or device.\n */\nconst _describesSpecimenSubject = (\n report: dmv.metadata.Comprehensive3DSR\n): boolean => {\n const items = findContentItemsByName({\n content: report.ContentSequence,\n name: new dcmjs.sr.coding.CodedConcept({\n value: '121024',\n schemeDesignator: 'DCM',\n meaning: 'Subject Class'\n })\n })\n if (items.length === 0) {\n return false\n }\n const subjectClassItem = items[0] as dcmjs.sr.valueTypes.CodeContentItem\n const subjectClassValue = subjectClassItem.ConceptCodeSequence[0]\n const retrievedConcept = new dcmjs.sr.coding.CodedConcept({\n value: subjectClassValue.CodeValue,\n meaning: subjectClassValue.CodeMeaning,\n schemeDesignator: subjectClassValue.CodingSchemeDesignator\n })\n const expectedConcept = new dcmjs.sr.coding.CodedConcept({\n value: '121027',\n meaning: 'Specimen',\n schemeDesignator: 'DCM'\n })\n if (retrievedConcept.equals(expectedConcept)) {\n return true\n }\n return false\n}\n\n/*\n * Check whether the report contains appropriate graphic ROI annotations.\n */\nconst _containsROIAnnotations = (\n report: dmv.metadata.Comprehensive3DSR\n): boolean => {\n const measurements = findContentItemsByName({\n content: report.ContentSequence,\n name: new dcmjs.sr.coding.CodedConcept({\n value: '126010',\n schemeDesignator: 'DCM',\n meaning: 'Imaging Measurements'\n })\n })\n if (measurements.length === 0) {\n return false\n }\n const container = measurements[0] as dcmjs.sr.valueTypes.ContainerContentItem\n const measurementGroups = findContentItemsByName({\n content: container.ContentSequence,\n name: new dcmjs.sr.coding.CodedConcept({\n value: '125007',\n schemeDesignator: 'DCM',\n meaning: 'Measurement Group'\n })\n })\n\n let foundRegion = false\n measurementGroups.forEach((group) => {\n const container = group as dcmjs.sr.valueTypes.ContainerContentItem\n const regions = findContentItemsByName({\n content: container.ContentSequence,\n name: new dcmjs.sr.coding.CodedConcept({\n value: '111030',\n schemeDesignator: 'DCM',\n meaning: 'Image Region'\n })\n })\n if (regions.length > 0) {\n if (regions[0].ValueType === dcmjs.sr.valueTypes.ValueTypes.SCOORD3D) {\n foundRegion = true\n }\n }\n })\n\n return foundRegion\n}\n\ninterface EvaluationOptions {\n name: dcmjs.sr.coding.CodedConcept\n values: dcmjs.sr.coding.CodedConcept[]\n}\n\ninterface Evaluation {\n name: dcmjs.sr.coding.CodedConcept\n value: dcmjs.sr.coding.CodedConcept\n}\n\ninterface Measurement {\n name: dcmjs.sr.coding.CodedConcept\n value?: number\n unit: dcmjs.sr.coding.CodedConcept\n}\n\ninterface SlideViewerProps extends RouteComponentProps {\n slide: Slide\n clients: { [key: string]: DicomWebManager }\n studyInstanceUID: string\n seriesInstanceUID: string\n app: {\n name: string\n version: string\n uid: string\n organization?: string\n }\n preload?: boolean\n annotations: AnnotationSettings[]\n enableAnnotationTools: boolean\n user?: {\n name: string\n email: string\n }\n selectedPresentationStateUID?: string\n}\n\ninterface SlideViewerState {\n visibleRoiUIDs: Set\n visibleSegmentUIDs: Set\n visibleMappingUIDs: Set\n visibleAnnotationGroupUIDs: Set\n visibleOpticalPathIdentifiers: Set\n activeOpticalPathIdentifiers: Set\n presentationStates: dmv.metadata.AdvancedBlendingPresentationState[]\n selectedPresentationStateUID?: string\n selectedFinding?: dcmjs.sr.coding.CodedConcept\n selectedEvaluations: Evaluation[]\n selectedGeometryType?: string\n selectedMarkup?: string\n selectedRoi?: dmv.roi.ROI\n selectedRoiUIDs: Set\n generatedReport?: dmv.metadata.Comprehensive3DSR\n isLoading: boolean\n isAnnotationModalVisible: boolean\n isSelectedRoiModalVisible: boolean\n isReportModalVisible: boolean\n isRoiDrawingActive: boolean\n isRoiModificationActive: boolean\n isRoiTranslationActive: boolean\n isGoToModalVisible: boolean\n isSelectedMagnificationValid: boolean\n isSelectedXCoordinateValid: boolean\n isSelectedYCoordinateValid: boolean\n selectedXCoordinate?: number\n validXCoordinateRange: number[]\n selectedYCoordinate?: number\n validYCoordinateRange: number[]\n selectedMagnification?: number\n areRoisHidden: boolean\n pixelDataStatistics: {\n [opticalPathIdentifier: string]: {\n min: number\n max: number\n numFramesSampled: number\n }\n }\n loadingFrames: Set\n}\n\n/**\n * React component for interactive viewing of an individual digital slide,\n * which corresponds to one DICOM Series of DICOM Slide Microscopy images and\n * potentially one or more associated DICOM Series of DICOM SR documents.\n */\nclass SlideViewer extends React.Component {\n private readonly findingOptions: dcmjs.sr.coding.CodedConcept[] = []\n\n private readonly evaluationOptions: { [key: string]: EvaluationOptions[] } = {}\n\n private readonly measurements: Measurement[] = []\n\n private readonly geometryTypeOptions: { [key: string]: string[] } = {}\n\n private readonly volumeViewportRef: React.RefObject\n\n private readonly labelViewportRef: React.RefObject\n\n private volumeViewer: dmv.viewer.VolumeImageViewer\n\n private labelViewer?: dmv.viewer.LabelImageViewer\n\n private readonly defaultRoiStyle: dmv.viewer.ROIStyleOptions = {\n stroke: {\n color: DEFAULT_ROI_STROKE_COLOR,\n width: DEFAULT_ROI_STROKE_WIDTH\n },\n fill: {\n color: DEFAULT_ROI_FILL_COLOR\n },\n image: {\n circle: {\n fill: {\n color: DEFAULT_ROI_STROKE_COLOR\n },\n radius: DEFAULT_ROI_RADIUS\n }\n }\n }\n\n private roiStyles: {[key: string]: dmv.viewer.ROIStyleOptions} = {}\n\n private readonly selectionColor: number[] = [140, 184, 198]\n\n private readonly selectedRoiStyle: dmv.viewer.ROIStyleOptions = {\n stroke: { color: [...this.selectionColor, 1], width: 3 },\n fill: { color: [...this.selectionColor, 0.2] },\n image: {\n circle: {\n radius: 5,\n fill: { color: [...this.selectionColor, 1] }\n }\n }\n }\n\n constructor (props: SlideViewerProps) {\n super(props)\n console.info(\n `view slide \"${this.props.slide.containerIdentifier}\": `,\n this.props.slide\n )\n const geometryTypeOptions = [\n 'point',\n 'circle',\n 'box',\n 'polygon',\n 'line',\n 'freehandpolygon',\n 'freehandline'\n ]\n props.annotations.forEach((annotation: AnnotationSettings) => {\n const finding = new dcmjs.sr.coding.CodedConcept(annotation.finding)\n this.findingOptions.push(finding)\n const key = _buildKey(finding)\n if (annotation.geometryTypes !== undefined) {\n this.geometryTypeOptions[key] = annotation.geometryTypes\n } else {\n this.geometryTypeOptions[key] = geometryTypeOptions\n }\n this.evaluationOptions[key] = []\n if (annotation.evaluations !== undefined) {\n annotation.evaluations.forEach(evaluation => {\n this.evaluationOptions[key].push({\n name: new dcmjs.sr.coding.CodedConcept(evaluation.name),\n values: evaluation.values.map(value => {\n return new dcmjs.sr.coding.CodedConcept(value)\n })\n })\n })\n }\n if (annotation.measurements !== undefined) {\n annotation.measurements.forEach(measurement => {\n this.measurements.push({\n name: new dcmjs.sr.coding.CodedConcept(measurement.name),\n value: undefined,\n unit: new dcmjs.sr.coding.CodedConcept(measurement.unit)\n })\n })\n }\n if (annotation.style != null) {\n this.roiStyles[key] = _formatRoiStyle(annotation.style)\n } else {\n this.roiStyles[key] = this.defaultRoiStyle\n }\n })\n\n this.componentSetup = this.componentSetup.bind(this)\n this.componentCleanup = this.componentCleanup.bind(this)\n\n this.onWindowResize = this.onWindowResize.bind(this)\n this.handleRoiDrawing = this.handleRoiDrawing.bind(this)\n this.handleRoiTranslation = this.handleRoiTranslation.bind(this)\n this.handleRoiModification = this.handleRoiModification.bind(this)\n this.handleRoiVisibilityChange = this.handleRoiVisibilityChange.bind(this)\n this.handleRoiRemoval = this.handleRoiRemoval.bind(this)\n this.handleRoiSelectionCancellation = this.handleRoiSelectionCancellation.bind(this)\n this.handleAnnotationConfigurationCancellation = this.handleAnnotationConfigurationCancellation.bind(this)\n this.handleAnnotationGeometryTypeSelection = this.handleAnnotationGeometryTypeSelection.bind(this)\n this.handleAnnotationMeasurementActivation = this.handleAnnotationMeasurementActivation.bind(this)\n this.handleAnnotationFindingSelection = this.handleAnnotationFindingSelection.bind(this)\n this.handleAnnotationEvaluationSelection = this.handleAnnotationEvaluationSelection.bind(this)\n this.handleAnnotationEvaluationClearance = this.handleAnnotationEvaluationClearance.bind(this)\n this.handleAnnotationConfigurationCompletion = this.handleAnnotationConfigurationCompletion.bind(this)\n this.handleAnnotationSelection = this.handleAnnotationSelection.bind(this)\n this.handleAnnotationVisibilityChange = this.handleAnnotationVisibilityChange.bind(this)\n this.handleAnnotationGroupVisibilityChange = this.handleAnnotationGroupVisibilityChange.bind(this)\n this.handleAnnotationGroupStyleChange = this.handleAnnotationGroupStyleChange.bind(this)\n this.handleGoTo = this.handleGoTo.bind(this)\n this.handleXCoordinateSelection = this.handleXCoordinateSelection.bind(this)\n this.handleYCoordinateSelection = this.handleYCoordinateSelection.bind(this)\n this.handleMagnificationSelection = this.handleMagnificationSelection.bind(this)\n this.handleSlidePositionSelection = this.handleSlidePositionSelection.bind(this)\n this.handleSlidePositionSelectionCancellation = this.handleSlidePositionSelectionCancellation.bind(this)\n this.handleReportGeneration = this.handleReportGeneration.bind(this)\n this.handleReportVerification = this.handleReportVerification.bind(this)\n this.handleReportCancellation = this.handleReportCancellation.bind(this)\n this.handleSegmentVisibilityChange = this.handleSegmentVisibilityChange.bind(this)\n this.handleSegmentStyleChange = this.handleSegmentStyleChange.bind(this)\n this.handleMappingVisibilityChange = this.handleMappingVisibilityChange.bind(this)\n this.handleMappingStyleChange = this.handleMappingStyleChange.bind(this)\n this.handleOpticalPathVisibilityChange = this.handleOpticalPathVisibilityChange.bind(this)\n this.handleOpticalPathStyleChange = this.handleOpticalPathStyleChange.bind(this)\n this.handleOpticalPathActivityChange = this.handleOpticalPathActivityChange.bind(this)\n this.handlePresentationStateSelection = this.handlePresentationStateSelection.bind(this)\n this.handlePresentationStateReset = this.handlePresentationStateReset.bind(this)\n\n const { volumeViewer, labelViewer } = _constructViewers({\n clients: this.props.clients,\n slide: this.props.slide,\n preload: this.props.preload\n })\n this.volumeViewer = volumeViewer\n this.labelViewer = labelViewer\n this.volumeViewportRef = React.createRef()\n this.labelViewportRef = React.createRef()\n\n /**\n * Deactivate all optical paths. Visibility will be set later, potentially\n * using based on available presentation state instances.\n */\n this.volumeViewer.getAllOpticalPaths().forEach(opticalPath => {\n this.volumeViewer.deactivateOpticalPath(opticalPath.identifier)\n })\n\n const [offset, size] = this.volumeViewer.boundingBox\n\n this.state = {\n selectedRoiUIDs: new Set(),\n visibleRoiUIDs: new Set(),\n visibleSegmentUIDs: new Set(),\n visibleMappingUIDs: new Set(),\n visibleAnnotationGroupUIDs: new Set(),\n visibleOpticalPathIdentifiers: new Set(),\n activeOpticalPathIdentifiers: new Set(),\n presentationStates: [],\n selectedFinding: undefined,\n selectedEvaluations: [],\n generatedReport: undefined,\n isLoading: false,\n isAnnotationModalVisible: false,\n isSelectedRoiModalVisible: false,\n isSelectedMagnificationValid: false,\n isReportModalVisible: false,\n isRoiDrawingActive: false,\n isRoiTranslationActive: false,\n isRoiModificationActive: false,\n isGoToModalVisible: false,\n isSelectedXCoordinateValid: false,\n isSelectedYCoordinateValid: false,\n selectedXCoordinate: undefined,\n validXCoordinateRange: [offset[0], offset[0] + size[0]],\n selectedYCoordinate: undefined,\n validYCoordinateRange: [offset[1], offset[1] + size[1]],\n selectedMagnification: undefined,\n areRoisHidden: false,\n pixelDataStatistics: {},\n selectedPresentationStateUID: this.props.selectedPresentationStateUID,\n loadingFrames: new Set()\n }\n }\n\n componentDidUpdate (\n previousProps: SlideViewerProps,\n previousState: SlideViewerState\n ): void {\n /** Fetch data and update the viewports if the route has changed (\n * i.e., if another series has been selected) or if the client has changed.\n */\n if (\n this.props.location.pathname !== previousProps.location.pathname ||\n this.props.studyInstanceUID !== previousProps.studyInstanceUID ||\n this.props.seriesInstanceUID !== previousProps.seriesInstanceUID ||\n this.props.slide !== previousProps.slide ||\n this.props.clients !== previousProps.clients\n ) {\n if (this.volumeViewportRef.current != null) {\n this.volumeViewportRef.current.innerHTML = ''\n }\n this.volumeViewer.cleanup()\n if (this.labelViewer != null) {\n if (this.labelViewportRef.current != null) {\n this.labelViewportRef.current.innerHTML = ''\n }\n this.labelViewer.cleanup()\n }\n const { volumeViewer, labelViewer } = _constructViewers({\n clients: this.props.clients,\n slide: this.props.slide,\n preload: this.props.preload\n })\n this.volumeViewer = volumeViewer\n this.labelViewer = labelViewer\n\n const activeOpticalPathIdentifiers: Set = new Set()\n const visibleOpticalPathIdentifiers: Set = new Set()\n this.volumeViewer.getAllOpticalPaths().forEach(opticalPath => {\n const identifier = opticalPath.identifier\n if (this.volumeViewer.isOpticalPathVisible(identifier)) {\n visibleOpticalPathIdentifiers.add(identifier)\n }\n if (this.volumeViewer.isOpticalPathActive(identifier)) {\n activeOpticalPathIdentifiers.add(identifier)\n }\n })\n\n const [offset, size] = this.volumeViewer.boundingBox\n\n this.setState({\n visibleRoiUIDs: new Set(),\n visibleSegmentUIDs: new Set(),\n visibleMappingUIDs: new Set(),\n visibleAnnotationGroupUIDs: new Set(),\n visibleOpticalPathIdentifiers,\n activeOpticalPathIdentifiers,\n presentationStates: [],\n loadingFrames: new Set(),\n validXCoordinateRange: [offset[0], offset[0] + size[0]],\n validYCoordinateRange: [offset[1], offset[1] + size[1]]\n })\n this.populateViewports()\n }\n }\n\n /**\n * Retrieve Presentation State instances that reference the any images of\n * the currently selected series.\n */\n loadPresentationStates = (): void => {\n console.info('search for Presentation State instances')\n const client = this.props.clients[\n StorageClasses.ADVANCED_BLENDING_PRESENTATION_STATE\n ]\n client.searchForInstances({\n studyInstanceUID: this.props.studyInstanceUID,\n queryParams: {\n Modality: 'PR'\n }\n }).then((matchedInstances): void => {\n if (matchedInstances == null) {\n matchedInstances = []\n }\n matchedInstances.forEach((rawInstance, index) => {\n const { dataset } = dmv.metadata.formatMetadata(rawInstance)\n const instance = dataset as dmv.metadata.Instance\n console.info(`retrieve PR instance \"${instance.SOPInstanceUID}\"`)\n client.retrieveInstance({\n studyInstanceUID: this.props.studyInstanceUID,\n seriesInstanceUID: instance.SeriesInstanceUID,\n sopInstanceUID: instance.SOPInstanceUID\n }).then((retrievedInstance): void => {\n const data = dcmjs.data.DicomMessage.readFile(retrievedInstance)\n const { dataset } = dmv.metadata.formatMetadata(data.dict)\n if (this.props.slide.areVolumeImagesMonochrome) {\n const presentationState = (\n dataset as\n unknown as\n dmv.metadata.AdvancedBlendingPresentationState\n )\n let doesMatch = false\n presentationState.AdvancedBlendingSequence.forEach(blendingItem => {\n doesMatch = this.props.slide.seriesInstanceUIDs.includes(\n blendingItem.SeriesInstanceUID\n )\n }\n )\n if (doesMatch) {\n console.info(\n 'include Advanced Blending Presentation State instance ' +\n `\"${presentationState.SOPInstanceUID}\"`\n )\n if (\n index === 0 &&\n this.props.selectedPresentationStateUID == null\n ) {\n this.setPresentationState(presentationState)\n } else {\n if (\n presentationState.SOPInstanceUID ===\n this.props.selectedPresentationStateUID\n ) {\n this.setPresentationState(presentationState)\n }\n }\n this.setState(state => {\n const mapping: {\n [sopInstanceUID: string]:\n dmv.metadata.AdvancedBlendingPresentationState\n } = {}\n state.presentationStates.forEach(instance => {\n mapping[instance.SOPInstanceUID] = instance\n })\n mapping[presentationState.SOPInstanceUID] = presentationState\n return { presentationStates: Object.values(mapping) }\n })\n }\n } else {\n console.info(\n `ignore presentation state \"${instance.SOPInstanceUID}\", ` +\n 'application of presentation states for color images ' +\n 'has not (yet) been implemented'\n )\n }\n }).catch((error) => {\n // eslint-disable-next-line @typescript-eslint/no-floating-promises\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.SLIM,\n new CustomError(\n errorTypes.VISUALIZATION,\n 'Presentation State could not be loaded'\n )\n )\n console.error(\n 'failed to load presentation state ' +\n `of SOP instance \"${instance.SOPInstanceUID}\" ` +\n `of series \"${instance.SeriesInstanceUID}\" ` +\n `of study \"${this.props.studyInstanceUID}\": `,\n error\n )\n })\n })\n }).catch((error) => {\n console.error(error)\n // eslint-disable-next-line @typescript-eslint/no-floating-promises\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.SLIM,\n new CustomError(\n errorTypes.VISUALIZATION,\n 'Presentation State could not be loaded'\n )\n )\n })\n }\n\n /**\n * Set presentation state as specified by a DICOM Presentation State instance.\n */\n setPresentationState = (\n presentationState: dmv.metadata.AdvancedBlendingPresentationState\n ): void => {\n const opticalPaths = this.volumeViewer.getAllOpticalPaths()\n console.info(\n `apply Presentation State instance \"${presentationState.SOPInstanceUID}\"`\n )\n const opticalPathStyles: {\n [opticalPathIdentifier: string]: {\n opacity: number\n paletteColorLookupTable?: dmv.color.PaletteColorLookupTable\n limitValues?: number[]\n } | null\n } = {}\n opticalPaths.forEach(opticalPath => {\n // First, deactivate and hide all optical paths and reset style\n const identifier = opticalPath.identifier\n this.volumeViewer.hideOpticalPath(identifier)\n this.volumeViewer.deactivateOpticalPath(identifier)\n const style = this.volumeViewer.getOpticalPathDefaultStyle(identifier)\n this.volumeViewer.setOpticalPathStyle(identifier, style)\n\n presentationState.AdvancedBlendingSequence.forEach(blendingItem => {\n /**\n * Referenced Instance Sequence should be used instead of Referenced\n * Image Sequence, but that's easy to mix up and we have encountered\n * implementations that get it wrong.\n */\n let refInstanceItems = blendingItem.ReferencedInstanceSequence\n if (refInstanceItems === undefined) {\n refInstanceItems = blendingItem.ReferencedImageSequence\n }\n if (refInstanceItems === undefined) {\n return\n }\n refInstanceItems.forEach(imageItem => {\n const isReferenced = opticalPath.sopInstanceUIDs.includes(\n imageItem.ReferencedSOPInstanceUID\n ) as boolean\n if (isReferenced) {\n let paletteColorLUT\n if (blendingItem.PaletteColorLookupTableSequence != null) {\n const cpLUTItem = blendingItem.PaletteColorLookupTableSequence[0]\n paletteColorLUT = new dmv.color.PaletteColorLookupTable({\n uid: (\n cpLUTItem.PaletteColorLookupTableUID != null\n ? cpLUTItem.PaletteColorLookupTableUID\n : ''\n ),\n redDescriptor:\n cpLUTItem.RedPaletteColorLookupTableDescriptor,\n greenDescriptor:\n cpLUTItem.GreenPaletteColorLookupTableDescriptor,\n blueDescriptor:\n cpLUTItem.BluePaletteColorLookupTableDescriptor,\n redData: (\n (cpLUTItem.RedPaletteColorLookupTableData != null)\n ? new Uint16Array(\n cpLUTItem.RedPaletteColorLookupTableData\n )\n : undefined\n ),\n greenData: (\n (cpLUTItem.GreenPaletteColorLookupTableData != null)\n ? new Uint16Array(\n cpLUTItem.GreenPaletteColorLookupTableData\n )\n : undefined\n ),\n blueData: (\n (cpLUTItem.BluePaletteColorLookupTableData != null)\n ? new Uint16Array(\n cpLUTItem.BluePaletteColorLookupTableData\n )\n : undefined\n ),\n redSegmentedData: (\n (cpLUTItem.SegmentedRedPaletteColorLookupTableData != null)\n ? new Uint16Array(\n cpLUTItem.SegmentedRedPaletteColorLookupTableData\n )\n : undefined\n ),\n greenSegmentedData: (\n (cpLUTItem.SegmentedGreenPaletteColorLookupTableData != null)\n ? new Uint16Array(\n cpLUTItem.SegmentedGreenPaletteColorLookupTableData\n )\n : undefined\n ),\n blueSegmentedData: (\n (cpLUTItem.SegmentedBluePaletteColorLookupTableData != null)\n ? new Uint16Array(\n cpLUTItem.SegmentedBluePaletteColorLookupTableData\n )\n : undefined\n )\n })\n }\n\n let limitValues\n if (blendingItem.SoftcopyVOILUTSequence != null) {\n const voiLUTItem = blendingItem.SoftcopyVOILUTSequence[0]\n const windowCenter = voiLUTItem.WindowCenter\n const windowWidth = voiLUTItem.WindowWidth\n limitValues = [\n windowCenter - windowWidth * 0.5,\n windowCenter + windowWidth * 0.5\n ]\n }\n\n opticalPathStyles[identifier] = {\n opacity: 1,\n paletteColorLookupTable: paletteColorLUT,\n limitValues: limitValues\n }\n }\n })\n })\n })\n\n const selectedOpticalPathIdentifiers: Set = new Set()\n Object.keys(opticalPathStyles).forEach(identifier => {\n const styleOptions = opticalPathStyles[identifier]\n if (styleOptions != null) {\n this.volumeViewer.setOpticalPathStyle(identifier, styleOptions)\n this.volumeViewer.activateOpticalPath(identifier)\n this.volumeViewer.showOpticalPath(identifier)\n selectedOpticalPathIdentifiers.add(identifier)\n } else {\n this.volumeViewer.hideOpticalPath(identifier)\n this.volumeViewer.deactivateOpticalPath(identifier)\n }\n })\n const searchParams = new URLSearchParams(this.props.location.search)\n searchParams.set('state', presentationState.SOPInstanceUID)\n this.props.navigate(\n {\n pathname: this.props.location.pathname,\n search: searchParams.toString()\n },\n { replace: true }\n )\n this.setState(state => ({\n activeOpticalPathIdentifiers: selectedOpticalPathIdentifiers,\n visibleOpticalPathIdentifiers: selectedOpticalPathIdentifiers,\n selectedPresentationStateUID: presentationState.SOPInstanceUID\n }))\n }\n\n getRoiStyle = (key?: string): dmv.viewer.ROIStyleOptions => {\n if (key == null) {\n return this.defaultRoiStyle\n }\n if (this.roiStyles[key] !== undefined) {\n return this.roiStyles[key]\n }\n return this.defaultRoiStyle\n }\n\n /**\n * Retrieve Structured Report instances that contain regions of interests\n * with 3D spatial coordinates defined in the same frame of reference as the\n * currently selected series and add them to the VOLUME image viewer.\n */\n addAnnotations = (): void => {\n console.info('search for Comprehensive 3D SR instances')\n const client = this.props.clients[StorageClasses.COMPREHENSIVE_3D_SR]\n client.searchForInstances({\n studyInstanceUID: this.props.studyInstanceUID,\n queryParams: {\n Modality: 'SR'\n }\n }).then((matchedInstances): void => {\n if (matchedInstances == null) {\n matchedInstances = []\n }\n matchedInstances.forEach(i => {\n const { dataset } = dmv.metadata.formatMetadata(i)\n const instance = dataset as dmv.metadata.Instance\n if (instance.SOPClassUID === StorageClasses.COMPREHENSIVE_3D_SR) {\n console.info(`retrieve SR instance \"${instance.SOPInstanceUID}\"`)\n client.retrieveInstance({\n studyInstanceUID: this.props.studyInstanceUID,\n seriesInstanceUID: instance.SeriesInstanceUID,\n sopInstanceUID: instance.SOPInstanceUID\n }).then((retrievedInstance): void => {\n const data = dcmjs.data.DicomMessage.readFile(retrievedInstance)\n const { dataset } = dmv.metadata.formatMetadata(data.dict)\n const report = dataset as unknown as dmv.metadata.Comprehensive3DSR\n /*\n * Perform a couple of checks to ensure the document content of the\n * report fullfils the requirements of the application.\n */\n if (!_implementsTID1500(report)) {\n console.debug(\n `ignore SR document \"${report.SOPInstanceUID}\" ` +\n 'because it is not structured according to template ' +\n 'TID 1500 \"MeasurementReport\"'\n )\n return\n }\n if (!_describesSpecimenSubject(report)) {\n console.debug(\n `ignore SR document \"${report.SOPInstanceUID}\" ` +\n 'because it does not describe a specimen subject'\n )\n return\n }\n if (!_containsROIAnnotations(report)) {\n console.debug(\n `ignore SR document \"${report.SOPInstanceUID}\" ` +\n 'because it does not contain any suitable ROI annotations'\n )\n return\n }\n\n const content = new MeasurementReport(report)\n content.ROIs.forEach(roi => {\n console.info(`add ROI \"${roi.uid}\"`)\n const scoord3d = roi.scoord3d\n const image = this.props.slide.volumeImages[0]\n if (scoord3d.frameOfReferenceUID === image.FrameOfReferenceUID) {\n /*\n * ROIs may get assigned new UIDs upon re-rendering of the\n * page and we need to ensure that we don't add them twice.\n * The same ROI may be stored in multiple SR documents and\n * we don't want them to show up twice.\n * TODO: We should probably either \"merge\" measurements and\n * quantitative evaluations or pick the ROI from the \"best\"\n * available report (COMPLETE and VERIFIED).\n */\n const doesROIExist = this.volumeViewer.getAllROIs().some(\n (otherROI: dmv.roi.ROI): boolean => {\n return _areROIsEqual(otherROI, roi)\n }\n )\n if (!doesROIExist) {\n try {\n // Add ROI without style such that it won't be visible.\n this.volumeViewer.addROI(roi, {})\n } catch {\n console.error(`could not add ROI \"${roi.uid}\"`)\n }\n } else {\n console.debug(`skip already existing ROI \"${roi.uid}\"`)\n }\n } else {\n console.debug(\n `skip ROI \"${roi.uid}\" ` +\n `of SR document \"${report.SOPInstanceUID}\"` +\n 'because it is defined in another frame of reference'\n )\n }\n })\n }).catch((error) => {\n // eslint-disable-next-line @typescript-eslint/no-floating-promises\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.SLIM,\n new CustomError(\n errorTypes.VISUALIZATION,\n 'Annotations could not be loaded'\n )\n )\n console.error(\n 'failed to load ROIs ' +\n `of SOP instance \"${instance.SOPInstanceUID}\" ` +\n `of series \"${instance.SeriesInstanceUID}\" ` +\n `of study \"${this.props.studyInstanceUID}\": `,\n error\n )\n })\n /*\n * React is not aware of the fact that ROIs have been added via the\n * viewer (the viewport is a ref object) and won't show the\n * annotations in the user interface unless an update is forced.\n */\n this.forceUpdate()\n }\n })\n }).catch((error) => {\n console.error(error)\n // eslint-disable-next-line @typescript-eslint/no-floating-promises\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.SLIM,\n new CustomError(\n errorTypes.VISUALIZATION,\n 'Annotations could not be loaded'\n )\n )\n })\n }\n\n /**\n * Retrieve Microscopy Bulk Simple Annotations instances that contain\n * annotation groups defined in the same frame of reference as the currently\n * selected series and add them to the VOLUME image viewer.\n */\n addAnnotationGroups = (): void => {\n console.info('search for Microscopy Bulk Simple Annotations instances')\n const client = this.props.clients[\n StorageClasses.MICROSCOPY_BULK_SIMPLE_ANNOTATION\n ]\n client.searchForSeries({\n studyInstanceUID: this.props.studyInstanceUID,\n queryParams: {\n Modality: 'ANN'\n }\n }).then((matchedSeries): void => {\n if (matchedSeries == null) {\n matchedSeries = []\n }\n matchedSeries.forEach(s => {\n const { dataset } = dmv.metadata.formatMetadata(s)\n const series = dataset as dmv.metadata.Series\n client.retrieveSeriesMetadata({\n studyInstanceUID: this.props.studyInstanceUID,\n seriesInstanceUID: series.SeriesInstanceUID\n }).then((retrievedMetadata): void => {\n let annotations: dmv.metadata.MicroscopyBulkSimpleAnnotations[]\n annotations = retrievedMetadata.map(metadata => {\n return new dmv.metadata.MicroscopyBulkSimpleAnnotations({\n metadata\n })\n })\n // annotations = annotations.filter(ann => {\n // const refImage = this.props.slide.volumeImages[0]\n // return (\n // ann.FrameOfReferenceUID === refImage.FrameOfReferenceUID &&\n // ann.ContainerIdentifier === refImage.ContainerIdentifier\n // )\n // })\n annotations.forEach(ann => {\n try {\n this.volumeViewer.addAnnotationGroups(ann)\n } catch (error: any) {\n // eslint-disable-next-line @typescript-eslint/no-floating-promises\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.SLIM,\n new CustomError(\n errorTypes.VISUALIZATION,\n 'Microscopy Bulk Simple Annotations cannot be displayed.'\n )\n )\n // eslint-disable-next-line @typescript-eslint/no-floating-promises\n console.error('failed to add annotation groups:', error)\n }\n ann.AnnotationGroupSequence.forEach(item => {\n const annotationGroupUID = item.AnnotationGroupUID\n const finding = item.AnnotationPropertyTypeCodeSequence[0]\n const key = _buildKey(finding)\n const style = this.roiStyles[key]\n // eslint-disable-next-line @typescript-eslint/prefer-optional-chain\n if (style != null && style.fill != null) {\n this.volumeViewer.setAnnotationGroupStyle(\n annotationGroupUID,\n { color: style.fill.color }\n )\n }\n })\n })\n /*\n * React is not aware of the fact that annotation groups have been\n * added via the viewer (the underlying HTML viewport element is a\n * ref object) and won't show the annotation groups in the user\n * interface unless an update is forced.\n */\n this.forceUpdate()\n }).catch((error) => {\n console.error(error)\n // eslint-disable-next-line @typescript-eslint/no-floating-promises\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.SLIM,\n new CustomError(\n errorTypes.VISUALIZATION,\n 'Retrieval of metadata of Microscopy Bulk Simple Annotations ' +\n 'instances failed.'\n )\n )\n })\n })\n }).catch((error) => {\n console.error(error)\n // eslint-disable-next-line @typescript-eslint/no-floating-promises\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.SLIM,\n new CustomError(\n errorTypes.VISUALIZATION,\n 'Search for Microscopy Bulk Simple Annotations instances failed.'\n )\n )\n })\n }\n\n /**\n * Retrieve Segmentation instances that contain segments defined in the same\n * frame of reference as the currently selected series and add them to the\n * VOLUME image viewer.\n */\n addSegmentations = (): void => {\n console.info('search for Segmentation instances')\n const client = this.props.clients[StorageClasses.SEGMENTATION]\n client.searchForSeries({\n studyInstanceUID: this.props.studyInstanceUID,\n queryParams: {\n Modality: 'SEG'\n }\n }).then((matchedSeries): void => {\n if (matchedSeries == null) {\n matchedSeries = []\n }\n matchedSeries.forEach((s, i) => {\n const { dataset } = dmv.metadata.formatMetadata(s)\n const series = dataset as dmv.metadata.Series\n client.retrieveSeriesMetadata({\n studyInstanceUID: this.props.studyInstanceUID,\n seriesInstanceUID: series.SeriesInstanceUID\n }).then((retrievedMetadata): void => {\n const segmentations: dmv.metadata.Segmentation[] = []\n retrievedMetadata.forEach(metadata => {\n const seg = new dmv.metadata.Segmentation({ metadata })\n const refImage = this.props.slide.volumeImages[0]\n if (\n seg.FrameOfReferenceUID === refImage.FrameOfReferenceUID &&\n seg.ContainerIdentifier === refImage.ContainerIdentifier\n ) {\n segmentations.push(seg)\n }\n })\n if (segmentations.length > 0) {\n try {\n this.volumeViewer.addSegments(segmentations)\n } catch (error: any) {\n // eslint-disable-next-line @typescript-eslint/no-floating-promises\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.SLIM,\n new CustomError(\n errorTypes.VISUALIZATION,\n 'Segmentations cannot be displayed'\n )\n )\n console.error('failed to add segments: ', error)\n }\n /*\n * React is not aware of the fact that segments have been added via\n * the viewer (the underlying HTML viewport element is a ref object)\n * and won't show the segments in the user interface unless an update\n * is forced.\n */\n this.forceUpdate()\n }\n }).catch((error) => {\n console.error(error)\n // eslint-disable-next-line @typescript-eslint/no-floating-promises\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.SLIM,\n new CustomError(\n errorTypes.VISUALIZATION,\n 'Retrieval of metadata of Segmentation instances failed.'\n )\n )\n })\n })\n }).catch((error) => {\n console.error(error)\n // eslint-disable-next-line @typescript-eslint/no-floating-promises\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.SLIM,\n new CustomError(\n errorTypes.VISUALIZATION,\n 'Search for Segmentation instances failed.'\n )\n )\n })\n }\n\n /**\n * Retrieve Parametric Map instances that contain mappings defined in the same\n * frame of reference as the currently selected series and add them to the\n * VOLUME image viewer.\n */\n addParametricMaps = (): void => {\n console.info('search for Parametric Map instances')\n const client = this.props.clients[StorageClasses.PARAMETRIC_MAP]\n client.searchForSeries({\n studyInstanceUID: this.props.studyInstanceUID,\n queryParams: {\n Modality: 'OT'\n }\n }).then((matchedSeries): void => {\n if (matchedSeries == null) {\n matchedSeries = []\n }\n matchedSeries.forEach(s => {\n const { dataset } = dmv.metadata.formatMetadata(s)\n const series = dataset as dmv.metadata.Series\n client.retrieveSeriesMetadata({\n studyInstanceUID: this.props.studyInstanceUID,\n seriesInstanceUID: series.SeriesInstanceUID\n }).then((retrievedMetadata): void => {\n const parametricMaps: dmv.metadata.ParametricMap[] = []\n retrievedMetadata.forEach(metadata => {\n const pm = new dmv.metadata.ParametricMap({ metadata })\n const refImage = this.props.slide.volumeImages[0]\n if (\n pm.FrameOfReferenceUID === refImage.FrameOfReferenceUID &&\n pm.ContainerIdentifier === refImage.ContainerIdentifier\n ) {\n parametricMaps.push(pm)\n } else {\n console.warn(\n `skip Parametric Map instance \"${pm.SOPInstanceUID}\"`\n )\n }\n })\n if (parametricMaps.length > 0) {\n try {\n this.volumeViewer.addParameterMappings(parametricMaps)\n } catch (error: any) {\n // eslint-disable-next-line @typescript-eslint/no-floating-promises\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.SLIM,\n new CustomError(\n errorTypes.VISUALIZATION,\n 'Parametric Map cannot be displayed'\n )\n )\n console.error('failed to add mappings: ', error)\n }\n /*\n * React is not aware of the fact that mappings have been added via\n * the viewer (the underlying HTML viewport element is a ref object)\n * and won't show the mappings in the user interface unless an update\n * is forced.\n */\n this.forceUpdate()\n }\n }).catch((error) => {\n console.error(error)\n // eslint-disable-next-line @typescript-eslint/no-floating-promises\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.SLIM,\n new CustomError(\n errorTypes.VISUALIZATION,\n 'Retrieval of metadata of Parametric Map instances failed.'\n )\n )\n })\n })\n }).catch((error) => {\n console.error(error)\n // eslint-disable-next-line @typescript-eslint/no-floating-promises\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.SLIM,\n new CustomError(\n errorTypes.VISUALIZATION,\n 'Search for Parametric Map instances failed.'\n )\n )\n })\n }\n\n /**\n * Populate viewports of the VOLUME and LABEL image viewers.\n */\n populateViewports = (): void => {\n console.info('populate viewports...')\n this.setState({\n isLoading: true,\n presentationStates: []\n })\n\n if (this.volumeViewportRef.current != null) {\n this.volumeViewer.render({ container: this.volumeViewportRef.current })\n }\n if (\n this.labelViewportRef.current != null &&\n this.labelViewer != null\n ) {\n this.labelViewer.render({ container: this.labelViewportRef.current })\n }\n\n // State update will also ensure that the component is re-rendered.\n this.setState({ isLoading: false })\n\n this.setDefaultPresentationState()\n this.loadPresentationStates()\n\n this.addAnnotations()\n this.addAnnotationGroups()\n this.addSegmentations()\n this.addParametricMaps()\n }\n\n onRoiModified = (event: CustomEventInit): void => {\n // Update state to trigger rendering\n this.setState(state => ({\n visibleRoiUIDs: new Set(state.visibleRoiUIDs)\n }))\n }\n\n onWindowResize = (event: Event): void => {\n console.info('resize viewports')\n this.volumeViewer.resize()\n if (this.labelViewer != null) {\n this.labelViewer.resize()\n }\n }\n\n onRoiDrawn = (event: CustomEventInit): void => {\n const roi = event.detail.payload as dmv.roi.ROI\n const selectedFinding = this.state.selectedFinding\n const selectedEvaluations = this.state.selectedEvaluations\n if (roi !== undefined && selectedFinding !== undefined) {\n console.debug(`add ROI \"${roi.uid}\"`)\n const findingItem = new dcmjs.sr.valueTypes.CodeContentItem({\n name: new dcmjs.sr.coding.CodedConcept({\n value: '121071',\n meaning: 'Finding',\n schemeDesignator: 'DCM'\n }),\n value: selectedFinding,\n relationshipType: 'CONTAINS'\n })\n roi.addEvaluation(findingItem)\n selectedEvaluations.forEach((evaluation: Evaluation) => {\n const item = new dcmjs.sr.valueTypes.CodeContentItem({\n name: evaluation.name,\n value: evaluation.value,\n relationshipType: 'CONTAINS'\n })\n roi.addEvaluation(item)\n })\n const key = _buildKey(selectedFinding)\n const style = this.getRoiStyle(key)\n this.volumeViewer.addROI(roi, style)\n this.setState(state => {\n const visibleRoiUIDs = state.visibleRoiUIDs\n visibleRoiUIDs.add(roi.uid)\n return { visibleRoiUIDs }\n })\n } else {\n console.debug(`could not add ROI \"${roi.uid}\"`)\n }\n }\n\n onRoiDoubleClicked = (event: CustomEventInit): void => {\n const selectedRoi = event.detail.payload as dmv.roi.ROI\n if (selectedRoi != null) {\n this.setState({\n isSelectedRoiModalVisible: true\n })\n } else {\n this.setState({\n isSelectedRoiModalVisible: false\n })\n }\n }\n\n onRoiSelected = (event: CustomEventInit): void => {\n const selectedRoi = event.detail.payload as dmv.roi.ROI\n if (selectedRoi != null) {\n console.debug(`selected ROI \"${selectedRoi.uid}\"`)\n this.volumeViewer.setROIStyle(selectedRoi.uid, this.selectedRoiStyle)\n const key = _getRoiKey(selectedRoi)\n this.volumeViewer.getAllROIs().forEach((roi) => {\n if (roi.uid !== selectedRoi.uid) {\n this.volumeViewer.setROIStyle(roi.uid, this.getRoiStyle(key))\n }\n })\n this.setState({\n selectedRoiUIDs: new Set([selectedRoi.uid]),\n selectedRoi: selectedRoi\n })\n } else {\n this.setState({\n selectedRoiUIDs: new Set(),\n selectedRoi: undefined\n })\n }\n }\n\n handleRoiSelectionCancellation (): void {\n this.setState({\n isSelectedRoiModalVisible: false\n })\n }\n\n onLoadingStarted = (event: CustomEventInit): void => {\n this.setState({ isLoading: true })\n }\n\n onLoadingEnded = (event: CustomEventInit): void => {\n this.setState({ isLoading: false })\n }\n\n onFrameLoadingStarted = (event: CustomEventInit): void => {\n const frameInfo: {\n studyInstanceUID: string\n seriesInstanceUID: string\n sopInstanceUID: string\n sopClassUID: string\n frameNumber: string\n channelIdentifier: string\n } = event.detail.payload\n const key: string = `${frameInfo.sopInstanceUID}-${frameInfo.frameNumber}`\n this.setState(state => {\n state.loadingFrames.add(key)\n return state\n })\n }\n\n onFrameLoadingError = (event: CustomEventInit): void => { \n console.error('Failed to load frame')\n }\n\n onLoadingError = (event: CustomEventInit): void => { \n console.error('Failed to load data')\n // eslint-disable-next-line @typescript-eslint/no-floating-promises\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.SLIM,\n new CustomError(\n errorTypes.VISUALIZATION,\n event.detail.payload && event.detail.payload.message ? event.detail.payload.message : 'Failed to load data'\n )\n )\n }\n\n onFrameLoadingEnded = (event: CustomEventInit): void => {\n const frameInfo: {\n studyInstanceUID: string\n seriesInstanceUID: string\n sopInstanceUID: string\n sopClassUID: string\n frameNumber: string\n channelIdentifier: string\n pixelArray: Uint8Array|Uint16Array|Float32Array|null\n } = event.detail.payload\n const key = `${frameInfo.sopInstanceUID}-${frameInfo.frameNumber}`\n this.setState(state => {\n state.loadingFrames.delete(key)\n let isLoading: boolean = false\n if (state.loadingFrames.size > 0) {\n isLoading = true\n }\n return {\n isLoading,\n loadingFrames: state.loadingFrames\n }\n })\n if (\n frameInfo.sopClassUID === StorageClasses.VL_WHOLE_SLIDE_MICROSCOPY_IMAGE &&\n this.props.slide.areVolumeImagesMonochrome\n ) {\n const opticalPathIdentifier = frameInfo.channelIdentifier\n if (\n !(opticalPathIdentifier in this.state.pixelDataStatistics) &&\n frameInfo.pixelArray != null\n ) {\n /*\n * There are limits on the number of arguments Math.min and Math.max\n * functions can accept. Therefore, we compute values in smaller chunks.\n */\n const size = 2 ** 16\n const chunks = Math.ceil(frameInfo.pixelArray.length / size)\n let offset = 0\n const minValues: number[] = []\n const maxValues: number[] = []\n for (let i = 0; i < chunks; i++) {\n offset = i * size\n const pixels = frameInfo.pixelArray.slice(offset, offset + size)\n minValues.push(Math.min(...pixels))\n maxValues.push(Math.max(...pixels))\n }\n const min = Math.min(...minValues)\n const max = Math.max(...maxValues)\n this.setState(state => {\n const stats = state.pixelDataStatistics\n if (stats[opticalPathIdentifier] != null) {\n stats[opticalPathIdentifier] = {\n min: Math.min(stats[opticalPathIdentifier].min, min),\n max: Math.max(stats[opticalPathIdentifier].max, max),\n numFramesSampled: stats[opticalPathIdentifier].numFramesSampled + 1\n }\n } else {\n stats[opticalPathIdentifier] = {\n min: min,\n max: max,\n numFramesSampled: 1\n }\n }\n if (state.selectedPresentationStateUID == null) {\n const style = {\n ...this.volumeViewer.getOpticalPathStyle(opticalPathIdentifier)\n }\n style.limitValues = [\n stats[opticalPathIdentifier].min,\n stats[opticalPathIdentifier].max\n ]\n this.volumeViewer.setOpticalPathStyle(opticalPathIdentifier, style)\n }\n return state\n })\n }\n }\n }\n\n onRoiRemoved = (event: CustomEventInit): void => {\n const roi = event.detail.payload as dmv.roi.ROI\n console.debug(`removed ROI \"${roi.uid}\"`)\n }\n\n componentCleanup (): void {\n document.body.removeEventListener(\n 'dicommicroscopyviewer_roi_drawn',\n this.onRoiDrawn\n )\n document.body.removeEventListener(\n 'dicommicroscopyviewer_roi_selected',\n this.onRoiSelected\n )\n document.body.removeEventListener(\n 'dicommicroscopyviewer_roi_double_clicked',\n this.onRoiDoubleClicked\n )\n document.body.removeEventListener(\n 'dicommicroscopyviewer_roi_removed',\n this.onRoiRemoved\n )\n document.body.removeEventListener(\n 'dicommicroscopyviewer_roi_modified',\n this.onRoiModified\n )\n document.body.removeEventListener(\n 'dicommicroscopyviewer_loading_started',\n this.onLoadingStarted\n )\n document.body.removeEventListener(\n 'dicommicroscopyviewer_loading_ended',\n this.onLoadingEnded\n )\n document.body.removeEventListener(\n 'dicommicroscopyviewer_frame_loading_started',\n this.onFrameLoadingStarted\n )\n document.body.removeEventListener(\n 'dicommicroscopyviewer_frame_loading_ended',\n this.onFrameLoadingEnded\n )\n document.body.removeEventListener(\n 'keyup',\n this.onKeyUp\n )\n window.removeEventListener('resize', this.onWindowResize)\n\n this.volumeViewer.cleanup()\n if (this.labelViewer != null) {\n this.labelViewer.cleanup()\n }\n /*\n * FIXME: React appears to not clean the content of referenced\n * HTMLDivElement objects when the page is reloaded. As a consequence,\n * optical paths and other display items cannot be toggled or updated after\n * a manual page reload. I have tried using ref callbacks and passing the\n * ref objects from the parent component via the props. Both didn't work\n * either.\n */\n }\n\n onKeyUp = (event: KeyboardEvent): void => {\n if (event.key === 'Escape') {\n if (this.state.isRoiDrawingActive) {\n console.info('deactivate drawing of ROIs')\n this.volumeViewer.deactivateDrawInteraction()\n this.volumeViewer.activateSelectInteraction({})\n } else if (this.state.isRoiModificationActive) {\n console.info('deactivate modification of ROIs')\n this.volumeViewer.deactivateModifyInteraction()\n this.volumeViewer.activateSelectInteraction({})\n } else if (this.state.isRoiTranslationActive) {\n console.info('deactivate modification of ROIs')\n this.volumeViewer.deactivateTranslateInteraction()\n this.volumeViewer.activateSelectInteraction({})\n }\n this.setState({\n isAnnotationModalVisible: false,\n isSelectedRoiModalVisible: false,\n isRoiTranslationActive: false,\n isRoiDrawingActive: false,\n isRoiModificationActive: false,\n isGoToModalVisible: false\n })\n } else if (event.altKey) {\n if (event.code === 'KeyD') {\n this.handleRoiDrawing()\n } else if (event.code === 'KeyM') {\n this.handleRoiModification()\n } else if (event.code === 'KeyT') {\n this.handleRoiTranslation()\n } else if (event.code === 'KeyR') {\n this.handleRoiRemoval()\n } else if (event.code === 'KeyV') {\n this.handleRoiVisibilityChange()\n } else if (event.code === 'KeyS') {\n this.handleReportGeneration()\n } else if (event.code === 'KeyG') {\n this.handleGoTo()\n }\n }\n }\n\n componentWillUnmount (): void {\n this.volumeViewer.cleanup()\n if (this.labelViewer != null) {\n this.labelViewer.cleanup()\n }\n window.removeEventListener('beforeunload', this.componentCleanup)\n }\n\n componentSetup (): void {\n document.body.addEventListener(\n 'dicommicroscopyviewer_roi_drawn',\n this.onRoiDrawn\n )\n document.body.addEventListener(\n 'dicommicroscopyviewer_roi_selected',\n this.onRoiSelected\n )\n document.body.addEventListener(\n 'dicommicroscopyviewer_roi_double_clicked',\n this.onRoiDoubleClicked\n )\n document.body.addEventListener(\n 'dicommicroscopyviewer_roi_removed',\n this.onRoiRemoved\n )\n document.body.addEventListener(\n 'dicommicroscopyviewer_roi_modified',\n this.onRoiModified\n )\n document.body.addEventListener(\n 'dicommicroscopyviewer_loading_started',\n this.onLoadingStarted\n )\n document.body.addEventListener(\n 'dicommicroscopyviewer_loading_ended',\n this.onLoadingEnded\n )\n document.body.addEventListener(\n 'dicommicroscopyviewer_loading_error',\n this.onLoadingError\n )\n document.body.addEventListener(\n 'dicommicroscopyviewer_frame_loading_started',\n this.onFrameLoadingStarted\n )\n document.body.addEventListener(\n 'dicommicroscopyviewer_frame_loading_ended',\n this.onFrameLoadingEnded\n )\n document.body.addEventListener(\n 'dicommicroscopyviewer_frame_loading_error',\n this.onFrameLoadingError\n )\n document.body.addEventListener(\n 'keyup',\n this.onKeyUp\n )\n window.addEventListener('beforeunload', this.componentCleanup)\n window.addEventListener('resize', this.onWindowResize)\n }\n\n componentDidMount (): void {\n this.componentSetup()\n this.populateViewports()\n\n if (!this.props.slide.areVolumeImagesMonochrome) {\n let hasICCProfile = false\n const image = this.props.slide.volumeImages[0]\n const metadataItem = image.OpticalPathSequence[0]\n if (metadataItem.ICCProfile == null) {\n if ('OpticalPathSequence' in image.bulkdataReferences) {\n // @ts-expect-error\n const bulkdataItem = image.bulkdataReferences.OpticalPathSequence[0]\n if ('ICCProfile' in bulkdataItem) {\n hasICCProfile = true\n }\n }\n } else {\n hasICCProfile = true\n }\n if (!hasICCProfile) {\n // eslint-disable-next-line @typescript-eslint/no-floating-promises\n message.warning('No ICC Profile was found for color images')\n }\n }\n }\n\n /**\n * Handler that gets called when a finding has been selected for annotation.\n *\n * @param value - Code value of the coded finding that got selected\n * @param option - Option that got selected\n */\n handleAnnotationFindingSelection (\n value: string,\n option: any\n ): void {\n this.findingOptions.forEach(finding => {\n if (finding.CodeValue === value) {\n console.info(`selected finding \"${finding.CodeMeaning}\"`)\n this.setState({\n selectedFinding: finding,\n selectedEvaluations: []\n })\n }\n })\n }\n\n /**\n * Handler that gets called when a geometry type has been selected for\n * annotation.\n *\n * @param value - Code value of the coded finding that got selected\n * @param option - Option that got selected\n */\n handleAnnotationGeometryTypeSelection (value: string, option: any): void {\n this.setState({ selectedGeometryType: value })\n }\n\n /**\n * Handler that gets called when measurements have been selected for\n * annotation.\n */\n handleAnnotationMeasurementActivation (event: any): void {\n const active: boolean = event.target.checked\n if (active) {\n this.setState({ selectedMarkup: 'measurement' })\n } else {\n this.setState({ selectedMarkup: undefined })\n }\n }\n\n /**\n * Handler that gets called when an evaluation has been selected for an\n * annotation.\n *\n * @param value - Code value of the coded evaluation that got selected\n * @param option - Option that got selected\n */\n handleAnnotationEvaluationSelection (\n value: string,\n option: any\n ): void {\n const selectedFinding = this.state.selectedFinding\n if (selectedFinding !== undefined) {\n const key = _buildKey(selectedFinding)\n const name = option.label\n this.evaluationOptions[key].forEach(evaluation => {\n if (\n evaluation.name.CodeValue === name.CodeValue &&\n evaluation.name.CodingSchemeDesignator === name.CodingSchemeDesignator\n ) {\n evaluation.values.forEach(code => {\n if (code.CodeValue === value) {\n const filteredEvaluations = this.state.selectedEvaluations.filter(\n (item: Evaluation) => item.name !== evaluation.name\n )\n this.setState({\n selectedEvaluations: [\n ...filteredEvaluations,\n { name: name, value: code }\n ]\n })\n }\n })\n }\n })\n }\n }\n\n /**\n * Handler that gets called when an evaluation has been cleared for an\n * annotation.\n */\n handleAnnotationEvaluationClearance (): void {\n this.setState({\n selectedEvaluations: []\n })\n }\n\n handleXCoordinateSelection (value: any): void {\n if (value != null) {\n const x = Number(value)\n const start = this.state.validXCoordinateRange[0]\n const end = this.state.validXCoordinateRange[1]\n if (x >= start && x <= end) {\n this.setState({\n selectedXCoordinate: x,\n isSelectedXCoordinateValid: true\n })\n return\n }\n }\n this.setState({\n selectedXCoordinate: undefined,\n isSelectedXCoordinateValid: false\n })\n }\n\n handleYCoordinateSelection (value: any): void {\n if (value != null) {\n const y = Number(value)\n const start = this.state.validYCoordinateRange[0]\n const end = this.state.validYCoordinateRange[1]\n if (y >= start && y <= end) {\n this.setState({\n selectedYCoordinate: y,\n isSelectedYCoordinateValid: true\n })\n return\n }\n }\n this.setState({\n selectedYCoordinate: undefined,\n isSelectedYCoordinateValid: false\n })\n }\n\n handleMagnificationSelection (value: any): void {\n if (value != null) {\n if (value > 0 && value <= 40) {\n this.setState({\n selectedMagnification: Number(value),\n isSelectedMagnificationValid: true\n })\n return\n }\n }\n this.setState({\n selectedMagnification: undefined,\n isSelectedMagnificationValid: false\n })\n }\n\n /**\n * Handler that gets called when the selection of slide position was\n * completed.\n */\n handleSlidePositionSelection (): void {\n if (\n this.state.isSelectedXCoordinateValid &&\n this.state.isSelectedYCoordinateValid &&\n this.state.isSelectedMagnificationValid &&\n this.state.selectedXCoordinate != null &&\n this.state.selectedYCoordinate != null &&\n this.state.selectedMagnification != null\n ) {\n console.info(\n 'select slide position ' +\n `(${this.state.selectedXCoordinate}, ` +\n `${this.state.selectedYCoordinate}) ` +\n `at ${this.state.selectedMagnification}x magnification`\n )\n\n const factor = this.state.selectedMagnification\n /**\n * On an optical microscope an objective with 1x magnification\n * corresponds to approximately 10 micrometer pixel spacing\n * (due to the ocular).\n */\n const targetPixelSpacing = 0.01 / factor\n const diffs = []\n for (let i = 0; i < this.volumeViewer.numLevels; i++) {\n const actualPixelSpacing = this.volumeViewer.getPixelSpacing(i)[0]\n diffs.push(Math.abs(targetPixelSpacing - actualPixelSpacing))\n }\n const level = diffs.indexOf(Math.min(...diffs))\n this.volumeViewer.navigate({\n position: [\n this.state.selectedXCoordinate,\n this.state.selectedYCoordinate\n ],\n level: level\n })\n const point = new dmv.scoord3d.Point({\n coordinates: [\n this.state.selectedXCoordinate,\n this.state.selectedYCoordinate,\n 0\n ],\n frameOfReferenceUID: this.volumeViewer.frameOfReferenceUID\n })\n const roi = new dmv.roi.ROI({ scoord3d: point })\n this.volumeViewer.addROI(roi, this.defaultRoiStyle)\n this.setState(state => {\n const visibleRoiUIDs = state.visibleRoiUIDs\n visibleRoiUIDs.add(roi.uid)\n return {\n visibleRoiUIDs,\n isGoToModalVisible: false\n }\n })\n }\n }\n\n /**\n * Handler that gets called when the selection of a slide position was\n * canceled.\n */\n handleSlidePositionSelectionCancellation (): void {\n console.log('cancel slide position selection')\n this.setState({\n isGoToModalVisible: false,\n isSelectedXCoordinateValid: false,\n isSelectedYCoordinateValid: false,\n isSelectedMagnificationValid: false,\n selectedXCoordinate: undefined,\n selectedYCoordinate: undefined,\n selectedMagnification: undefined\n })\n }\n\n /**\n * Handler that gets called when annotation configuration has been completed.\n */\n handleAnnotationConfigurationCompletion (): void {\n console.debug('complete annotation configuration')\n const finding = this.state.selectedFinding\n const geometryType = this.state.selectedGeometryType\n const markup = this.state.selectedMarkup\n if (geometryType !== undefined && finding !== undefined) {\n this.volumeViewer.activateDrawInteraction({ geometryType, markup })\n this.setState({\n isAnnotationModalVisible: false,\n isRoiDrawingActive: true\n })\n } else {\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.SLIM,\n new CustomError(\n errorTypes.VISUALIZATION,\n 'Could not complete annotation configuration'\n )\n )\n }\n }\n\n /**\n * Handler that gets called when annotation configuration has been cancelled.\n */\n handleAnnotationConfigurationCancellation (): void {\n console.debug('cancel annotation configuration')\n this.setState({\n isAnnotationModalVisible: false,\n isRoiDrawingActive: false\n })\n }\n\n /**\n * Handler that gets called when a report should be generated for the current\n * set of annotations.\n */\n handleReportGeneration (): void {\n console.info('save ROIs')\n const rois = this.volumeViewer.getAllROIs()\n const opticalPaths = this.volumeViewer.getAllOpticalPaths()\n const metadata = this.volumeViewer.getOpticalPathMetadata(\n opticalPaths[0].identifier\n )\n // Metadata should be sorted such that the image with the highest\n // resolution is the last item in the array.\n const refImage = metadata[metadata.length - 1]\n // We assume that there is only one specimen (tissue section) per\n // ontainer (slide). Only the tissue section is tracked with a unique\n // identifier, even if the section may be composed of different biological\n // samples.\n if (refImage.SpecimenDescriptionSequence.length > 1) {\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.SLIM,\n new CustomError(\n errorTypes.VISUALIZATION,\n 'More than one specimen has been described for the slide'\n )\n )\n }\n const refSpecimen = refImage.SpecimenDescriptionSequence[0]\n\n console.debug('create Observation Context')\n let observer\n if (this.props.user !== undefined) {\n observer = new dcmjs.sr.templates.PersonObserverIdentifyingAttributes({\n name: this.props.user.name,\n loginName: this.props.user.email\n })\n } else {\n console.warn('no user information available')\n observer = new dcmjs.sr.templates.PersonObserverIdentifyingAttributes({\n name: 'ANONYMOUS'\n })\n }\n const observationContext = new dcmjs.sr.templates.ObservationContext({\n observerPersonContext: new dcmjs.sr.templates.ObserverContext({\n observerType: new dcmjs.sr.coding.CodedConcept({\n value: '121006',\n schemeDesignator: 'DCM',\n meaning: 'Person'\n }),\n observerIdentifyingAttributes: observer\n }),\n observerDeviceContext: new dcmjs.sr.templates.ObserverContext({\n observerType: new dcmjs.sr.coding.CodedConcept({\n value: '121007',\n schemeDesignator: 'DCM',\n meaning: 'Device'\n }),\n observerIdentifyingAttributes:\n new dcmjs.sr.templates.DeviceObserverIdentifyingAttributes({\n uid: this.props.app.uid,\n manufacturerName: 'MGH Computational Pathology',\n modelName: this.props.app.name\n })\n }),\n subjectContext: new dcmjs.sr.templates.SubjectContext({\n subjectClass: new dcmjs.sr.coding.CodedConcept({\n value: '121027',\n schemeDesignator: 'DCM',\n meaning: 'Specimen'\n }),\n subjectClassSpecificContext:\n new dcmjs.sr.templates.SubjectContextSpecimen({\n uid: refSpecimen.SpecimenUID,\n identifier: refSpecimen.SpecimenIdentifier,\n containerIdentifier: refImage.ContainerIdentifier\n })\n })\n })\n\n console.debug('encode Imaging Measurements')\n const imagingMeasurements: dcmjs.sr.valueTypes.ContainerContentItem[] = []\n for (let i = 0; i < rois.length; i++) {\n const roi = rois[i]\n if (!this.state.visibleRoiUIDs.has(roi.uid)) {\n continue\n }\n let findingType = roi.evaluations.find(\n (item: dcmjs.sr.valueTypes.ContentItem) => {\n return item.ConceptNameCodeSequence[0].CodeValue === '121071'\n }\n )\n if (findingType === undefined) {\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.SLIM,\n new CustomError(\n errorTypes.ENCODINGANDDECODING,\n `No finding type was specified for ROI \"${roi.uid}\"`\n )\n )\n }\n findingType = findingType as dcmjs.sr.valueTypes.CodeContentItem\n const group = new dcmjs.sr.templates.PlanarROIMeasurementsAndQualitativeEvaluations({\n trackingIdentifier: new dcmjs.sr.templates.TrackingIdentifier({\n uid: roi.properties.trackingUID ?? roi.uid,\n identifier: `ROI #${i + 1}`\n }),\n referencedRegion: new dcmjs.sr.contentItems.ImageRegion3D({\n graphicType: roi.scoord3d.graphicType,\n graphicData: roi.scoord3d.graphicData,\n frameOfReferenceUID: roi.scoord3d.frameOfReferenceUID\n }),\n findingType: new dcmjs.sr.coding.CodedConcept({\n value: findingType.ConceptCodeSequence[0].CodeValue,\n schemeDesignator:\n findingType.ConceptCodeSequence[0].CodingSchemeDesignator,\n meaning: findingType.ConceptCodeSequence[0].CodeMeaning\n }),\n qualitativeEvaluations: roi.evaluations.filter(\n (item: dcmjs.sr.valueTypes.ContentItem) => {\n return item.ConceptNameCodeSequence[0].CodeValue !== '121071'\n }\n ),\n measurements: roi.measurements\n })\n const measurements = group as dcmjs.sr.valueTypes.ContainerContentItem[]\n measurements[0].ContentTemplateSequence = [{\n MappingResource: 'DCMR',\n TemplateIdentifier: '1410'\n }]\n imagingMeasurements.push(...measurements)\n }\n\n console.debug('create Measurement Report document content')\n const measurementReport = new dcmjs.sr.templates.MeasurementReport({\n languageOfContentItemAndDescendants: new dcmjs.sr.templates.LanguageOfContentItemAndDescendants({}),\n observationContext: observationContext,\n procedureReported: new dcmjs.sr.coding.CodedConcept({\n value: '112703',\n schemeDesignator: 'DCM',\n meaning: 'Whole Slide Imaging'\n }),\n imagingMeasurements: imagingMeasurements\n })\n\n console.info('create Comprehensive 3D SR document')\n const dataset = new dcmjs.sr.documents.Comprehensive3DSR({\n content: measurementReport[0],\n evidence: [refImage],\n seriesInstanceUID: dcmjs.data.DicomMetaDictionary.uid(),\n seriesNumber: 1,\n seriesDescription: 'Annotation',\n sopInstanceUID: dcmjs.data.DicomMetaDictionary.uid(),\n instanceNumber: 1,\n manufacturer: 'MGH Computational Pathology',\n previousVersions: undefined // TODO\n })\n\n this.setState({\n isReportModalVisible: true,\n generatedReport: dataset as dmv.metadata.Comprehensive3DSR\n })\n }\n\n /**\n * Handler that gets called when a report should be verified. The current\n * list of annotations will be presented to the user together with other\n * pertinent metadata about the patient, study, and specimen.\n */\n handleReportVerification (): void {\n console.info('verfied report')\n\n const report = this.state.generatedReport\n if (report !== undefined) {\n const dataset = report as unknown as dmv.metadata.Comprehensive3DSR\n console.debug('create File Meta Information')\n const fileMetaInformationVersionArray = new Uint8Array(2)\n fileMetaInformationVersionArray[1] = 1\n const fileMeta = {\n // FileMetaInformationVersion\n '00020001': {\n Value: [fileMetaInformationVersionArray.buffer],\n vr: 'OB'\n },\n // MediaStorageSOPClassUID\n '00020002': {\n Value: [dataset.SOPClassUID],\n vr: 'UI'\n },\n // MediaStorageSOPInstanceUID\n '00020003': {\n Value: [dataset.SOPInstanceUID],\n vr: 'UI'\n },\n // TransferSyntaxUID\n '00020010': {\n Value: ['1.2.840.10008.1.2.1'],\n vr: 'UI'\n },\n // ImplementationClassUID\n '00020012': {\n Value: [this.props.app.uid],\n vr: 'UI'\n }\n }\n\n console.info('store Comprehensive 3D SR document')\n const writer = new dcmjs.data.DicomDict(fileMeta)\n writer.dict = dcmjs.data.DicomMetaDictionary.denaturalizeDataset(dataset)\n const buffer = writer.write()\n const client = this.props.clients[StorageClasses.COMPREHENSIVE_3D_SR]\n client.storeInstances({ datasets: [buffer] }).then(\n (response: any) => message.info('Annotations were saved.')\n ).catch((error) => {\n console.error(error)\n // eslint-disable-next-line @typescript-eslint/no-floating-promises\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.SLIM,\n new CustomError(\n errorTypes.ENCODINGANDDECODING,\n 'Annotations could not be saved'\n )\n )\n })\n }\n this.setState({\n isReportModalVisible: false,\n generatedReport: undefined\n })\n }\n\n /**\n * Handler that gets called when report generation has been cancelled.\n */\n handleReportCancellation (): void {\n this.setState({\n isReportModalVisible: false,\n generatedReport: undefined\n })\n }\n\n /**\n * Handler that gets called when an annotation has been selected from the\n * current list of annotations.\n */\n handleAnnotationSelection ({ roiUID }: { roiUID: string }): void {\n console.log(`selected ROI ${roiUID}`)\n this.setState({ selectedRoiUIDs: new Set([roiUID]) })\n this.volumeViewer.getAllROIs().forEach((roi) => {\n let style = {}\n if (roi.uid === roiUID) {\n style = this.selectedRoiStyle\n this.setState(state => {\n const visibleRoiUIDs = state.visibleRoiUIDs\n visibleRoiUIDs.add(roi.uid)\n return { visibleRoiUIDs }\n })\n } else {\n if (this.state.visibleRoiUIDs.has(roi.uid)) {\n const key = _getRoiKey(roi)\n style = this.getRoiStyle(key)\n }\n }\n this.volumeViewer.setROIStyle(roi.uid, style)\n })\n }\n\n /**\n * Handle toggling of annotation visibility, i.e., whether a given\n * annotation should be either displayed or hidden by the viewer.\n */\n handleAnnotationVisibilityChange ({ roiUID, isVisible }: {\n roiUID: string\n isVisible: boolean\n }): void {\n if (isVisible) {\n console.info(`show ROI ${roiUID}`)\n const roi = this.volumeViewer.getROI(roiUID)\n const key = _getRoiKey(roi)\n this.volumeViewer.setROIStyle(roi.uid, this.getRoiStyle(key))\n this.setState(state => {\n const visibleRoiUIDs = state.visibleRoiUIDs\n visibleRoiUIDs.add(roi.uid)\n return { visibleRoiUIDs }\n })\n } else {\n console.info(`hide ROI ${roiUID}`)\n this.setState(state => {\n const selectedRoiUIDs = state.selectedRoiUIDs\n selectedRoiUIDs.delete(roiUID)\n const visibleRoiUIDs = state.visibleRoiUIDs\n visibleRoiUIDs.delete(roiUID)\n return { visibleRoiUIDs, selectedRoiUIDs }\n })\n this.volumeViewer.setROIStyle(roiUID, {})\n }\n }\n\n /**\n * Handle toggling of annotation group visibility, i.e., whether a given\n * annotation group should be either displayed or hidden by the viewer.\n */\n handleAnnotationGroupVisibilityChange ({ annotationGroupUID, isVisible }: {\n annotationGroupUID: string\n isVisible: boolean\n }): void {\n console.log(`change visibility of annotation group ${annotationGroupUID}`)\n if (isVisible) {\n console.info(`show annotation group ${annotationGroupUID}`)\n try {\n this.volumeViewer.showAnnotationGroup(annotationGroupUID)\n } catch (error) {\n // eslint-disable-next-line @typescript-eslint/no-floating-promises\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.SLIM,\n new CustomError(\n errorTypes.VISUALIZATION,\n 'Failed to show annotation group.'\n )\n )\n throw error\n }\n this.setState(state => {\n const visibleAnnotationGroupUIDs = new Set(\n state.visibleAnnotationGroupUIDs\n )\n visibleAnnotationGroupUIDs.add(annotationGroupUID)\n return { visibleAnnotationGroupUIDs }\n })\n } else {\n console.info(`hide annotation group ${annotationGroupUID}`)\n this.volumeViewer.hideAnnotationGroup(annotationGroupUID)\n this.setState(state => {\n const visibleAnnotationGroupUIDs = new Set(\n state.visibleAnnotationGroupUIDs\n )\n visibleAnnotationGroupUIDs.delete(annotationGroupUID)\n return { visibleAnnotationGroupUIDs }\n })\n }\n }\n\n /**\n * Handle change of annotation group style.\n */\n handleAnnotationGroupStyleChange ({ annotationGroupUID, styleOptions }: {\n annotationGroupUID: string\n styleOptions: {\n opacity?: number\n color?: number[]\n measurement?: dcmjs.sr.coding.CodedConcept\n }\n }): void {\n console.log(`change style of annotation group ${annotationGroupUID}`)\n try {\n this.volumeViewer.setAnnotationGroupStyle(\n annotationGroupUID,\n styleOptions\n )\n } catch (error) {\n // eslint-disable-next-line @typescript-eslint/no-floating-promises\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.SLIM,\n new CustomError(\n errorTypes.VISUALIZATION,\n 'Failed to change style of annotation group.'\n )\n )\n throw error\n }\n }\n\n /**\n * Handle toggling of segment visibility, i.e., whether a given\n * segment should be either displayed or hidden by the viewer.\n */\n handleSegmentVisibilityChange ({ segmentUID, isVisible }: {\n segmentUID: string\n isVisible: boolean\n }): void {\n console.log(`change visibility of segment ${segmentUID}`)\n if (isVisible) {\n console.info(`show segment ${segmentUID}`)\n this.volumeViewer.showSegment(segmentUID)\n this.setState(state => {\n const visibleSegmentUIDs = new Set(state.visibleSegmentUIDs)\n visibleSegmentUIDs.add(segmentUID)\n return { visibleSegmentUIDs }\n })\n } else {\n console.info(`hide segment ${segmentUID}`)\n this.volumeViewer.hideSegment(segmentUID)\n this.setState(state => {\n const visibleSegmentUIDs = new Set(state.visibleSegmentUIDs)\n visibleSegmentUIDs.delete(segmentUID)\n return { visibleSegmentUIDs }\n })\n }\n }\n\n /**\n * Handle change of segment style.\n */\n handleSegmentStyleChange ({ segmentUID, styleOptions }: {\n segmentUID: string\n styleOptions: {\n opacity?: number\n }\n }): void {\n console.log(`change style of segment ${segmentUID}`)\n this.volumeViewer.setSegmentStyle(segmentUID, styleOptions)\n }\n\n /**\n * Handle toggling of mapping visibility, i.e., whether a given\n * mapping should be either displayed or hidden by the viewer.\n */\n handleMappingVisibilityChange ({ mappingUID, isVisible }: {\n mappingUID: string\n isVisible: boolean\n }): void {\n console.log(`change visibility of mapping ${mappingUID}`)\n if (isVisible) {\n console.info(`show mapping ${mappingUID}`)\n this.volumeViewer.showParameterMapping(mappingUID)\n this.setState(state => {\n const visibleMappingUIDs = new Set(state.visibleMappingUIDs)\n visibleMappingUIDs.add(mappingUID)\n return { visibleMappingUIDs }\n })\n } else {\n console.info(`hide mapping ${mappingUID}`)\n this.volumeViewer.hideParameterMapping(mappingUID)\n this.setState(state => {\n const visibleMappingUIDs = new Set(state.visibleMappingUIDs)\n visibleMappingUIDs.delete(mappingUID)\n return { visibleMappingUIDs }\n })\n }\n }\n\n /**\n * Handle change of mapping style.\n */\n handleMappingStyleChange ({ mappingUID, styleOptions }: {\n mappingUID: string\n styleOptions: {\n opacity?: number\n }\n }): void {\n console.log(`change style of mapping ${mappingUID}`)\n this.volumeViewer.setParameterMappingStyle(mappingUID, styleOptions)\n }\n\n /**\n * Handle toggling of optical path visibility, i.e., whether a given\n * optical path should be either displayed or hidden by the viewer.\n */\n handleOpticalPathVisibilityChange ({ opticalPathIdentifier, isVisible }: {\n opticalPathIdentifier: string\n isVisible: boolean\n }): void {\n console.log(`change visibility of optical path ${opticalPathIdentifier}`)\n if (isVisible) {\n console.info(`show optical path ${opticalPathIdentifier}`)\n this.volumeViewer.showOpticalPath(opticalPathIdentifier)\n this.setState(state => {\n const visibleOpticalPathIdentifiers = new Set(\n state.visibleOpticalPathIdentifiers\n )\n visibleOpticalPathIdentifiers.add(opticalPathIdentifier)\n return { visibleOpticalPathIdentifiers }\n })\n } else {\n console.info(`hide optical path ${opticalPathIdentifier}`)\n this.volumeViewer.hideOpticalPath(opticalPathIdentifier)\n this.setState(state => {\n const visibleOpticalPathIdentifiers = new Set(\n state.visibleOpticalPathIdentifiers\n )\n visibleOpticalPathIdentifiers.delete(opticalPathIdentifier)\n return { visibleOpticalPathIdentifiers }\n })\n }\n }\n\n /**\n * Handle change of optical path style.\n */\n handleOpticalPathStyleChange ({ opticalPathIdentifier, styleOptions }: {\n opticalPathIdentifier: string\n styleOptions: {\n opacity?: number\n color?: number[]\n limitValues?: number[]\n }\n }): void {\n console.log(`change style of optical path ${opticalPathIdentifier}`)\n this.volumeViewer.setOpticalPathStyle(opticalPathIdentifier, styleOptions)\n }\n\n /**\n * Handle toggling of optical path activity, i.e., whether a given\n * optical path should be either added or removed from the viewport.\n */\n handleOpticalPathActivityChange ({ opticalPathIdentifier, isActive }: {\n opticalPathIdentifier: string\n isActive: boolean\n }): void {\n console.log(`change activity of optical path ${opticalPathIdentifier}`)\n if (isActive) {\n console.info(`activate optical path ${opticalPathIdentifier}`)\n this.volumeViewer.activateOpticalPath(opticalPathIdentifier)\n this.setState(state => {\n const activeOpticalPathIdentifiers = new Set(\n state.activeOpticalPathIdentifiers\n )\n activeOpticalPathIdentifiers.add(opticalPathIdentifier)\n return { activeOpticalPathIdentifiers }\n })\n } else {\n console.info(`deactivate optical path ${opticalPathIdentifier}`)\n this.volumeViewer.deactivateOpticalPath(opticalPathIdentifier)\n this.setState(state => {\n const activeOpticalPathIdentifiers = new Set(\n state.activeOpticalPathIdentifiers\n )\n activeOpticalPathIdentifiers.delete(opticalPathIdentifier)\n return { activeOpticalPathIdentifiers }\n })\n }\n }\n\n /**\n * Set default presentation state that is either defined by metadata included\n * in the DICOM Slide Microscopy instance or by the viewer.\n */\n setDefaultPresentationState (): void {\n const visibleOpticalPathIdentifiers: Set = new Set()\n const opticalPaths = this.volumeViewer.getAllOpticalPaths()\n opticalPaths.sort((a, b) => {\n if (a.identifier.localeCompare(b.identifier) === 1) {\n return 1\n } else if (b.identifier.localeCompare(a.identifier) === 1) {\n return -1\n }\n return 0\n })\n opticalPaths.forEach((item: dmv.opticalPath.OpticalPath) => {\n const identifier = item.identifier\n const style = this.volumeViewer.getOpticalPathDefaultStyle(identifier)\n this.volumeViewer.setOpticalPathStyle(identifier, style)\n this.volumeViewer.hideOpticalPath(identifier)\n this.volumeViewer.deactivateOpticalPath(identifier)\n if (item.isMonochromatic) {\n /*\n * If the image metadata contains a palette color lookup table for the\n * optical path, then it will be displayed by default.\n */\n if (item.paletteColorLookupTableUID != null) {\n visibleOpticalPathIdentifiers.add(identifier)\n }\n } else {\n /* Color images will always be displayed by default. */\n visibleOpticalPathIdentifiers.add(identifier)\n }\n })\n\n /*\n * If no optical paths have been selected for visualization so far, select\n * first n optical paths and set a default value of interest (VOI) window\n * (using pre-computed pixel data statistics) and a default color.\n */\n if (visibleOpticalPathIdentifiers.size === 0) {\n const defaultColors = [\n [255, 255, 255]\n ]\n opticalPaths.forEach((item: dmv.opticalPath.OpticalPath) => {\n const identifier = item.identifier\n if (item.isMonochromatic) {\n const numVisible = visibleOpticalPathIdentifiers.size\n if (numVisible < defaultColors.length) {\n const style = {\n ...this.volumeViewer.getOpticalPathStyle(identifier)\n }\n const index = numVisible\n style.color = defaultColors[index]\n const stats = this.state.pixelDataStatistics[item.identifier]\n if (stats != null) {\n style.limitValues = [stats.min, stats.max]\n }\n this.volumeViewer.setOpticalPathStyle(item.identifier, style)\n visibleOpticalPathIdentifiers.add(item.identifier)\n }\n }\n })\n }\n\n console.info(\n `selected n=${visibleOpticalPathIdentifiers.size} optical paths ` +\n 'for visualization'\n )\n visibleOpticalPathIdentifiers.forEach(identifier => {\n this.volumeViewer.showOpticalPath(identifier)\n })\n this.setState(state => ({\n activeOpticalPathIdentifiers: new Set(visibleOpticalPathIdentifiers),\n visibleOpticalPathIdentifiers: new Set(visibleOpticalPathIdentifiers)\n }))\n }\n\n /**\n * Handler that gets called when a presentation state has been selected from\n * the current list of available presentation states.\n */\n handlePresentationStateReset (): void {\n this.setState({ selectedPresentationStateUID: undefined })\n const urlPath = this.props.location.pathname\n this.props.navigate(urlPath)\n this.setDefaultPresentationState()\n }\n\n /**\n * Handler that gets called when a presentation state has been selected from\n * the current list of available presentation states.\n */\n handlePresentationStateSelection (\n value?: string,\n option?: any\n ): void {\n if (value != null) {\n console.info(`select Presentation State instance \"${value}\"`)\n let presentationState\n this.state.presentationStates.forEach(instance => {\n if (instance.SOPInstanceUID === value) {\n presentationState = instance\n }\n })\n if (presentationState != null) {\n let urlPath = this.props.location.pathname\n urlPath += `?state=${value}`\n this.props.navigate(urlPath)\n this.setPresentationState(presentationState)\n } else {\n // eslint-disable-next-line @typescript-eslint/no-floating-promises\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.SLIM,\n new CustomError(\n errorTypes.VISUALIZATION,\n 'Presentation State could not be found'\n )\n )\n console.log(\n 'failed to handle section of presentation state: ' +\n `could not find instance \"${value}\"`\n )\n }\n } else {\n this.handlePresentationStateReset()\n }\n this.setState({ selectedPresentationStateUID: value })\n }\n\n /**\n * Handler that will toggle the ROI drawing tool, i.e., either activate or\n * de-activate it, depending on its current state.\n */\n handleRoiDrawing (): void {\n if (this.state.isRoiDrawingActive) {\n console.info('deactivate drawing of ROIs')\n this.volumeViewer.deactivateDrawInteraction()\n this.volumeViewer.activateSelectInteraction({})\n this.setState({\n isAnnotationModalVisible: false,\n isSelectedRoiModalVisible: false,\n isRoiTranslationActive: false,\n isRoiDrawingActive: false,\n isRoiModificationActive: false,\n isGoToModalVisible: false\n })\n } else {\n console.info('activate drawing of ROIs')\n this.setState({\n isAnnotationModalVisible: true,\n isSelectedRoiModalVisible: false,\n isRoiDrawingActive: true,\n isRoiModificationActive: false,\n isRoiTranslationActive: false,\n isGoToModalVisible: false\n })\n this.volumeViewer.deactivateSelectInteraction()\n this.volumeViewer.deactivateSnapInteraction()\n this.volumeViewer.deactivateTranslateInteraction()\n this.volumeViewer.deactivateModifyInteraction()\n }\n }\n\n /**\n * Handler that will toggle the ROI modification tool, i.e., either activate\n * or de-activate it, depending on its current state.\n */\n handleRoiModification (): void {\n console.info('toggle modification of ROIs')\n if (this.volumeViewer.isModifyInteractionActive) {\n this.volumeViewer.deactivateModifyInteraction()\n this.volumeViewer.deactivateSnapInteraction()\n this.volumeViewer.activateSelectInteraction({})\n this.setState({\n isRoiTranslationActive: false,\n isRoiDrawingActive: false,\n isRoiModificationActive: false\n })\n } else {\n this.setState({\n isRoiModificationActive: true,\n isRoiDrawingActive: false,\n isRoiTranslationActive: false\n })\n this.volumeViewer.deactivateDrawInteraction()\n this.volumeViewer.deactivateTranslateInteraction()\n this.volumeViewer.deactivateSelectInteraction()\n this.volumeViewer.activateSnapInteraction({})\n this.volumeViewer.activateModifyInteraction({})\n }\n }\n\n /**\n * Handler that will toggle the ROI translation tool, i.e., either activate\n * or de-activate it, depending on its current state.\n */\n handleRoiTranslation (): void {\n console.info('toggle translation of ROIs')\n if (this.volumeViewer.isTranslateInteractionActive) {\n this.volumeViewer.deactivateTranslateInteraction()\n this.setState({\n isRoiTranslationActive: false,\n isRoiDrawingActive: false,\n isRoiModificationActive: false\n })\n } else {\n this.setState({\n isRoiTranslationActive: true,\n isRoiDrawingActive: false,\n isRoiModificationActive: false\n })\n this.volumeViewer.deactivateModifyInteraction()\n this.volumeViewer.deactivateSnapInteraction()\n this.volumeViewer.deactivateDrawInteraction()\n this.volumeViewer.deactivateSelectInteraction()\n this.volumeViewer.activateTranslateInteraction({})\n }\n }\n\n handleGoTo (): void {\n this.volumeViewer.deactivateDrawInteraction()\n this.volumeViewer.deactivateModifyInteraction()\n this.volumeViewer.deactivateSnapInteraction()\n this.volumeViewer.deactivateTranslateInteraction()\n this.volumeViewer.deactivateSelectInteraction()\n this.setState({\n isGoToModalVisible: true,\n isAnnotationModalVisible: false,\n isSelectedRoiModalVisible: false,\n isReportModalVisible: false,\n isRoiTranslationActive: false,\n isRoiModificationActive: false,\n isRoiDrawingActive: false\n })\n }\n\n /**\n * Handler that will toggle the ROI removal tool, i.e., either activate\n * or de-activate it, depending on its current state.\n */\n handleRoiRemoval (): void {\n this.volumeViewer.deactivateDrawInteraction()\n this.volumeViewer.deactivateSnapInteraction()\n this.volumeViewer.deactivateTranslateInteraction()\n this.volumeViewer.deactivateModifyInteraction()\n if (this.state.selectedRoiUIDs.size > 0) {\n this.state.selectedRoiUIDs.forEach(uid => {\n if (uid === undefined) {\n // eslint-disable-next-line @typescript-eslint/no-floating-promises\n message.warning('No annotation was selected for removal')\n return\n }\n console.info(`remove ROI \"${uid}\"`)\n this.volumeViewer.removeROI(uid)\n // eslint-disable-next-line @typescript-eslint/no-floating-promises\n message.info('Annotation was removed')\n })\n this.setState({\n selectedRoiUIDs: new Set(),\n isRoiTranslationActive: false,\n isRoiDrawingActive: false,\n isRoiModificationActive: false\n })\n } else {\n this.state.visibleRoiUIDs.forEach(uid => {\n console.info(`remove ROI \"${uid}\"`)\n this.volumeViewer.removeROI(uid)\n })\n this.setState({\n visibleRoiUIDs: new Set(),\n isRoiTranslationActive: false,\n isRoiDrawingActive: false,\n isRoiModificationActive: false\n })\n }\n this.volumeViewer.activateSelectInteraction({})\n }\n\n /**\n * Handler that will toggle the ROI visibility tool, i.e., either activate\n * or de-activate it, depending on its current state.\n */\n handleRoiVisibilityChange (): void {\n console.info('toggle visibility of ROIs')\n if (this.volumeViewer.areROIsVisible) {\n this.volumeViewer.deactivateDrawInteraction()\n this.volumeViewer.deactivateSnapInteraction()\n this.volumeViewer.deactivateTranslateInteraction()\n this.volumeViewer.deactivateSelectInteraction()\n this.volumeViewer.deactivateModifyInteraction()\n this.volumeViewer.hideROIs()\n this.setState({\n areRoisHidden: true,\n isRoiDrawingActive: false,\n isRoiModificationActive: false,\n isRoiTranslationActive: false\n })\n } else {\n this.volumeViewer.showROIs()\n this.volumeViewer.activateSelectInteraction({})\n this.state.selectedRoiUIDs.forEach(uid => {\n if (uid !== undefined) {\n this.volumeViewer.setROIStyle(uid, this.selectedRoiStyle)\n }\n })\n this.setState({ areRoisHidden: false })\n }\n }\n\n render (): React.ReactNode {\n const rois: dmv.roi.ROI[] = []\n const segments: dmv.segment.Segment[] = []\n const mappings: dmv.mapping.ParameterMapping[] = []\n const annotationGroups: dmv.annotation.AnnotationGroup[] = []\n rois.push(...this.volumeViewer.getAllROIs())\n segments.push(...this.volumeViewer.getAllSegments())\n mappings.push(...this.volumeViewer.getAllParameterMappings())\n annotationGroups.push(...this.volumeViewer.getAllAnnotationGroups())\n\n const openSubMenuItems = [\n 'specimens', 'optical-paths', 'annotations', 'presentation-states'\n ]\n\n let report: React.ReactNode\n const dataset = this.state.generatedReport\n if (dataset !== undefined) {\n report = \n }\n\n let annotationMenuItems: React.ReactNode\n if (rois.length > 0) {\n annotationMenuItems = (\n \n )\n }\n\n const findingOptions = this.findingOptions.map(finding => {\n return (\n \n {finding.CodeMeaning}\n \n )\n })\n\n const geometryTypeOptionsMapping: { [key: string]: React.ReactNode } = {\n point: Point,\n circle: Circle,\n box: Box,\n polygon: Polygon,\n line: Line,\n freehandpolygon: (\n \n Polygon (freehand)\n \n ),\n freehandline: (\n \n Line (freehand)\n \n )\n }\n\n const annotationConfigurations: React.ReactNode[] = [\n (\n \n {findingOptions}\n \n )\n ]\n\n const selectedFinding = this.state.selectedFinding\n if (selectedFinding !== undefined) {\n const key = _buildKey(selectedFinding)\n this.evaluationOptions[key].forEach(evaluation => {\n const evaluationOptions = evaluation.values.map(code => {\n return (\n \n {code.CodeMeaning}\n \n )\n })\n annotationConfigurations.push(\n <>\n {evaluation.name.CodeMeaning}\n \n {evaluationOptions}\n \n \n )\n })\n const geometryTypeOptions = this.geometryTypeOptions[key].map(name => {\n return geometryTypeOptionsMapping[name]\n })\n annotationConfigurations.push(\n <>\n ROI geometry type\n \n {geometryTypeOptions}\n \n \n )\n annotationConfigurations.push(\n \n measure\n \n )\n }\n\n const specimenMenu = (\n \n \n \n )\n\n const equipmentMenu = (\n \n \n \n )\n\n const opticalPaths = this.volumeViewer.getAllOpticalPaths()\n opticalPaths.sort((a, b) => {\n if (a.identifier.localeCompare(b.identifier) === 1) {\n return 1\n } else if (b.identifier.localeCompare(a.identifier) === 1) {\n return -1\n }\n return 0\n })\n const opticalPathStyles: {\n [identifier: string]: {\n opacity: number\n color?: number[]\n limitValues?: number[]\n paletteColorLookupTable?: dmv.color.PaletteColorLookupTable\n }\n } = {}\n const opticalPathMetadata: {\n [identifier: string]: dmv.metadata.VLWholeSlideMicroscopyImage[]\n } = {}\n opticalPaths.forEach(opticalPath => {\n const identifier = opticalPath.identifier\n const metadata = this.volumeViewer.getOpticalPathMetadata(identifier)\n opticalPathMetadata[identifier] = metadata\n const style = {\n ...this.volumeViewer.getOpticalPathStyle(identifier)\n }\n opticalPathStyles[identifier] = style\n })\n const opticalPathMenu = (\n \n \n \n )\n\n let presentationStateMenu\n if (this.state.presentationStates.length > 0) {\n const presentationStateOptions = []\n this.state.presentationStates.forEach(instance => {\n presentationStateOptions.push(\n \n {instance.ContentDescription}\n \n )\n })\n presentationStateOptions.push(\n \n {}\n \n )\n presentationStateMenu = (\n \n \n \n {presentationStateOptions}\n \n \n }\n type='primary'\n onClick={this.handlePresentationStateReset}\n />\n \n \n \n )\n }\n\n let segmentationMenu\n if (segments.length > 0) {\n const defaultSegmentStyles: {\n [segmentUID: string]: {\n opacity: number\n }\n } = {}\n const segmentMetadata: {\n [segmentUID: string]: dmv.metadata.Segmentation[]\n } = {}\n const segments = this.volumeViewer.getAllSegments()\n segments.forEach(segment => {\n defaultSegmentStyles[segment.uid] = this.volumeViewer.getSegmentStyle(\n segment.uid\n )\n segmentMetadata[segment.uid] = this.volumeViewer.getSegmentMetadata(\n segment.uid\n )\n })\n segmentationMenu = (\n \n \n \n )\n openSubMenuItems.push('segmentations')\n }\n\n let parametricMapMenu\n if (mappings.length > 0) {\n const defaultMappingStyles: {\n [mappingUID: string]: {\n opacity: number\n }\n } = {}\n const mappingMetadata: {\n [mappingUID: string]: dmv.metadata.ParametricMap[]\n } = {}\n mappings.forEach(mapping => {\n defaultMappingStyles[mapping.uid] = this.volumeViewer.getParameterMappingStyle(\n mapping.uid\n )\n mappingMetadata[mapping.uid] = this.volumeViewer.getParameterMappingMetadata(\n mapping.uid\n )\n })\n parametricMapMenu = (\n \n \n \n )\n openSubMenuItems.push('parametric-maps')\n }\n\n let annotationGroupMenu\n if (annotationGroups.length > 0) {\n const defaultAnnotationGroupStyles: {\n [annotationGroupUID: string]: {\n opacity: number\n color: number[]\n }\n } = {}\n const annotationGroupMetadata: {\n [annotationGroupUID: string]: dmv.metadata.MicroscopyBulkSimpleAnnotations\n } = {}\n const annotationGroups = this.volumeViewer.getAllAnnotationGroups()\n annotationGroups.forEach(annotationGroup => {\n defaultAnnotationGroupStyles[annotationGroup.uid] = this.volumeViewer.getAnnotationGroupStyle(\n annotationGroup.uid\n )\n annotationGroupMetadata[annotationGroup.uid] = this.volumeViewer.getAnnotationGroupMetadata(\n annotationGroup.uid\n )\n })\n annotationGroupMenu = (\n \n \n \n )\n openSubMenuItems.push('annotationGroups')\n }\n\n let toolbar\n let toolbarHeight = '0px'\n const annotationTools = [\n ,\n ,\n ,\n ,\n ,\n \n ]\n const controlTools = [\n \n ]\n if (this.props.enableAnnotationTools) {\n toolbar = (\n \n {annotationTools.map((item, i) => {\n return {item}\n })}\n {controlTools.map((item, i) => {\n return {item}\n })}\n \n )\n toolbarHeight = '50px'\n }\n\n let cursor = 'default'\n if (this.state.isLoading) {\n cursor = 'progress'\n }\n\n let selectedRoiInformation\n if (this.state.selectedRoi != null) {\n const roiAttributes: Array<{\n name: string\n value: string\n unit?: string\n }> = [\n {\n name: 'UID',\n value: this.state.selectedRoi.uid\n }\n ]\n const roiScoordAttributes: Array<{\n name: string\n value: string\n }> = [\n {\n name: 'Graphic type',\n value: this.state.selectedRoi.scoord3d.graphicType\n }\n ]\n const roiEvaluationAttributes: Array<{\n name: string\n value: string\n }> = []\n this.state.selectedRoi.evaluations.forEach(item => {\n if (item.ValueType === 'CODE') {\n const codeItem = item as dcmjs.sr.valueTypes.CodeContentItem\n roiEvaluationAttributes.push({\n name: codeItem.ConceptNameCodeSequence[0].CodeMeaning,\n value: codeItem.ConceptCodeSequence[0].CodeMeaning\n })\n } else {\n const textItem = item as dcmjs.sr.valueTypes.TextContentItem\n roiEvaluationAttributes.push({\n name: textItem.ConceptNameCodeSequence[0].CodeMeaning,\n value: textItem.TextValue\n })\n }\n })\n const roiMeasurmentAttributesPerOpticalPath: {\n [identifier: string]: Array<{\n name: string\n value: string\n unit?: string\n }>\n } = {}\n this.state.selectedRoi.measurements.forEach(item => {\n let identifier = 'default'\n if (item.ContentSequence != null) {\n const refItems = findContentItemsByName({\n content: item.ContentSequence,\n name: new dcmjs.sr.coding.CodedConcept({\n value: '121112',\n meaning: 'Source of Measurement',\n schemeDesignator: 'DCM'\n })\n })\n if (refItems.length > 0) {\n identifier = (\n refItems[0]\n // @ts-expect-error\n .ReferencedSOPSequence[0]\n .ReferencedOpticalPathIdentifier\n )\n }\n }\n if (!(identifier in roiMeasurmentAttributesPerOpticalPath)) {\n roiMeasurmentAttributesPerOpticalPath[identifier] = []\n }\n const measuredValueItem = item.MeasuredValueSequence[0]\n roiMeasurmentAttributesPerOpticalPath[identifier].push({\n name: item.ConceptNameCodeSequence[0].CodeMeaning,\n value: measuredValueItem.NumericValue.toString(),\n unit: measuredValueItem.MeasurementUnitsCodeSequence[0].CodeMeaning\n })\n })\n const createRoiDescription = (\n attributes: Array<{ name: string, value: string, unit?: string }>\n ): React.ReactNode[] => {\n return attributes.map(item => {\n let value\n if (item.unit != null) {\n value = `${item.value} [${item.unit}]`\n } else {\n value = item.value\n }\n return (\n \n {value}\n \n )\n })\n }\n const roiDescriptions = createRoiDescription(roiAttributes)\n const roiScoordDescriptions = createRoiDescription(\n roiScoordAttributes\n )\n const roiEvaluationDescriptions = createRoiDescription(\n roiEvaluationAttributes\n )\n const roiMeasurementDescriptions = []\n for (const identifier in roiMeasurmentAttributesPerOpticalPath) {\n const descriptions = createRoiDescription(\n roiMeasurmentAttributesPerOpticalPath[identifier]\n )\n if (identifier === 'default') {\n roiMeasurementDescriptions.push(descriptions)\n } else {\n roiMeasurementDescriptions.push(\n <>\n \n {identifier}\n \n {descriptions}\n \n )\n }\n }\n selectedRoiInformation = (\n <>\n \n {roiDescriptions}\n \n \n Spatial coordinates\n \n \n {roiScoordDescriptions}\n \n \n Evaluations\n \n \n {roiEvaluationDescriptions}\n \n \n Measurements\n \n \n {roiMeasurementDescriptions}\n \n \n )\n }\n\n return (\n \n \n {toolbar}\n\n \n\n \n \n {annotationConfigurations}\n \n \n\n \n \n {selectedRoiInformation}\n \n \n\n \n \n \n : \n }\n />\n \n : \n }\n />\n \n : \n }\n />\n \n \n\n \n {report}\n \n \n\n \n {\n // Give menu item time to render before updating viewer size\n setTimeout(\n () => {\n if (this.labelViewer != null) {\n this.labelViewer.resize()\n }\n },\n 100\n )\n }}\n >\n \n \n \n \n \n {specimenMenu}\n {equipmentMenu}\n {opticalPathMenu}\n {presentationStateMenu}\n \n {annotationMenuItems}\n \n {annotationGroupMenu}\n {segmentationMenu}\n {parametricMapMenu}\n \n \n \n )\n }\n}\n\nexport default withRouter(SlideViewer)\n","import * as dmv from 'dicom-microscopy-viewer'\nimport { CustomError, errorTypes } from '../utils/CustomError'\nimport NotificationMiddleware, {\n NotificationMiddlewareContext\n} from '../services/NotificationMiddleware'\n\nenum ImageFlavors {\n VOLUME = 'VOLUME',\n LABEL = 'LABEL',\n OVERVIEW = 'OVERVIEW',\n THUMBNAIL = 'THUMBNAIL'\n}\n\nconst hasImageFlavor = (\n image: dmv.metadata.VLWholeSlideMicroscopyImage,\n imageFlavor: ImageFlavors\n): boolean => {\n return image.ImageType[2] === imageFlavor\n}\n\nconst areSameAcquisition = (\n image: dmv.metadata.VLWholeSlideMicroscopyImage,\n refImage: dmv.metadata.VLWholeSlideMicroscopyImage\n): boolean => {\n if (image.AcquisitionUID != null) {\n return image.AcquisitionUID === refImage.AcquisitionUID\n }\n return false\n}\n\ninterface SlideImageCollection {\n acquisitionUID?: string\n frameOfReferenceUID: string\n containerIdentifier: string\n volumeImages: dmv.metadata.VLWholeSlideMicroscopyImage[]\n labelImages: dmv.metadata.VLWholeSlideMicroscopyImage[]\n overviewImages: dmv.metadata.VLWholeSlideMicroscopyImage[]\n}\n\ninterface SlideOptions {\n images: dmv.metadata.VLWholeSlideMicroscopyImage[]\n description?: string\n}\n\n/**\n * Slide - collection of images with the same Frame of Reference UID and\n * Container Identifier.\n */\nclass Slide {\n readonly description: string\n readonly acquisitionUID: string | null | undefined\n readonly frameOfReferenceUID: string\n readonly containerIdentifier: string\n readonly seriesInstanceUIDs: string[]\n readonly opticalPathIdentifiers: string[]\n readonly pyramidUIDs: string[] = []\n readonly areVolumeImagesMonochrome: boolean\n readonly volumeImages: dmv.metadata.VLWholeSlideMicroscopyImage[]\n readonly labelImages: dmv.metadata.VLWholeSlideMicroscopyImage[]\n readonly overviewImages: dmv.metadata.VLWholeSlideMicroscopyImage[]\n\n /**\n * @param options\n * @param options.images - Metadata of images associated with the slide\n * @param options.description - Description of the slide\n */\n constructor (\n options: SlideOptions\n ) {\n if (options.images.length === 0) {\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.SLIM,\n new CustomError(\n errorTypes.ENCODINGANDDECODING,\n 'Value of option \"images\" have been non-zero length.'\n )\n )\n }\n\n const seriesInstanceUIDs = new Set([] as string[])\n const acquisitionUIDs = new Set([] as string[])\n const opticalPathIdentifiers = new Set([] as string[])\n const containerIdentifiers = new Set([] as string[])\n const frameOfReferenceUIDs = {\n VOLUME: new Set([] as string[]),\n LABEL: new Set([] as string[]),\n OVERVIEW: new Set([] as string[])\n }\n const pyramidUIDs: {\n [key: string]: { [opticalPathIdentifier: string]: Set }\n } = {\n VOLUME: {}\n }\n const volumeImages: dmv.metadata.VLWholeSlideMicroscopyImage[] = []\n const labelImages: dmv.metadata.VLWholeSlideMicroscopyImage[] = []\n const overviewImages: dmv.metadata.VLWholeSlideMicroscopyImage[] = []\n options.images.forEach((image) => {\n containerIdentifiers.add(image.ContainerIdentifier)\n seriesInstanceUIDs.add(image.SeriesInstanceUID)\n image.OpticalPathSequence.forEach(item => {\n opticalPathIdentifiers.add(item.OpticalPathIdentifier)\n })\n if (image.AcquisitionUID != null) {\n acquisitionUIDs.add(image.AcquisitionUID)\n }\n if (\n hasImageFlavor(image, ImageFlavors.VOLUME) ||\n hasImageFlavor(image, ImageFlavors.THUMBNAIL)\n ) {\n frameOfReferenceUIDs.VOLUME.add(image.FrameOfReferenceUID)\n if (image.PyramidUID != null) {\n for (const identifier in opticalPathIdentifiers) {\n pyramidUIDs.VOLUME[identifier].add(image.PyramidUID)\n }\n }\n volumeImages.push(image)\n } else if (hasImageFlavor(image, ImageFlavors.LABEL)) {\n frameOfReferenceUIDs.LABEL.add(image.FrameOfReferenceUID)\n labelImages.push(image)\n } else if (hasImageFlavor(image, ImageFlavors.OVERVIEW)) {\n frameOfReferenceUIDs.OVERVIEW.add(image.FrameOfReferenceUID)\n overviewImages.push(image)\n }\n })\n if (volumeImages.length === 0) {\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.SLIM,\n new CustomError(\n errorTypes.ENCODINGANDDECODING,\n 'At least one VOLUME image must be provided for a slide.'\n )\n )\n } else {\n if (acquisitionUIDs.size > 1) {\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.SLIM,\n new CustomError(\n errorTypes.ENCODINGANDDECODING,\n 'All VOLUME images of a slide must have the same number of ' +\n 'Samples per Pixel.'\n )\n )\n }\n const samplesPerPixel = new Set([] as number[])\n volumeImages.forEach((image) => {\n samplesPerPixel.add(image.SamplesPerPixel)\n })\n if (samplesPerPixel.size > 1) {\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.SLIM,\n new CustomError(\n errorTypes.ENCODINGANDDECODING,\n 'All VOLUME images of a slide must have the same number of ' +\n 'Samples per Pixel.'\n )\n )\n }\n const isNotResampled = volumeImages.filter(image => {\n return image.ImageType[3] !== 'RESAMPLED'\n })\n if (isNotResampled.length > opticalPathIdentifiers.size) {\n console.warn(\n 'the set of VOLUME images of a slide must contain only a single ' +\n 'image that has not been resampled per optical path'\n )\n }\n }\n this.volumeImages = volumeImages\n this.labelImages = labelImages\n this.overviewImages = overviewImages\n\n this.seriesInstanceUIDs = [...seriesInstanceUIDs]\n this.opticalPathIdentifiers = [...opticalPathIdentifiers]\n\n if (containerIdentifiers.size !== 1) {\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.SLIM,\n new CustomError(\n errorTypes.ENCODINGANDDECODING,\n 'All images of a slide must have the same Container Identifier.'\n )\n )\n }\n this.containerIdentifier = [...containerIdentifiers][0]\n\n if (frameOfReferenceUIDs.VOLUME.size !== 1) {\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.SLIM,\n new CustomError(\n errorTypes.ENCODINGANDDECODING,\n 'All VOLUME images of a slide must have ' +\n 'the same Frame of Reference UID.'\n )\n )\n }\n this.frameOfReferenceUID = [...frameOfReferenceUIDs.VOLUME][0]\n\n let requirePyramidUID = false\n if (Object.keys(pyramidUIDs.VOLUME).length > 0) {\n requirePyramidUID = true\n }\n this.opticalPathIdentifiers.forEach(identifier => {\n if (pyramidUIDs.VOLUME[identifier] != null) {\n if (pyramidUIDs.VOLUME[identifier].size > 1) {\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.SLIM,\n new CustomError(\n errorTypes.ENCODINGANDDECODING,\n `All VOLUME images for optical path \"${identifier}\"` +\n 'must be part of the same multi-resolution pyramid.'\n )\n )\n } else if (pyramidUIDs.VOLUME[identifier].size === 1) {\n this.pyramidUIDs.push([...pyramidUIDs.VOLUME[identifier]][0])\n } else {\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.SLIM,\n new CustomError(\n errorTypes.ENCODINGANDDECODING,\n `The VOLUME images for optical path \"${identifier}\" ` +\n 'lack the Pyramid UID, while the images for other optical paths ' +\n 'contain it.'\n )\n )\n }\n } else {\n if (requirePyramidUID) {\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.SLIM,\n new CustomError(\n errorTypes.ENCODINGANDDECODING,\n `The VOLUME images for optical path \"${identifier}\" ` +\n 'lack the Pyramid UID, while the images for other optical paths ' +\n 'contain it.'\n )\n )\n }\n }\n })\n\n if (acquisitionUIDs.size > 1) {\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.SLIM,\n new CustomError(\n errorTypes.ENCODINGANDDECODING,\n 'All VOLUME images of a slide must be part of the same ' +\n 'acquisition and have the same Acquisition UID.'\n )\n )\n } else if (acquisitionUIDs.size === 1) {\n this.acquisitionUID = [...acquisitionUIDs][0]\n } else {\n this.acquisitionUID = null\n }\n\n this.areVolumeImagesMonochrome = (\n this.volumeImages[0].SamplesPerPixel === 1 &&\n this.volumeImages[0].PhotometricInterpretation === 'MONOCHROME2'\n )\n\n this.description = (\n options.description !== undefined ? options.description : ''\n )\n }\n}\n\n/**\n * Create slides.\n *\n * @param imagesPerSeries - Image instances grouped per series\n * @param referenceSeriesInstanceUID - Unique identifier of the series that serves as a reference for the slide\n * @returns Slides\n */\nconst createSlides = (\n images: dmv.metadata.VLWholeSlideMicroscopyImage[][]\n): Slide[] => {\n const slideMetadata: SlideImageCollection[] = []\n images.forEach((series) => {\n if (series.length > 0) {\n const volumeImages = series.filter((image) => {\n return (\n hasImageFlavor(image, ImageFlavors.VOLUME) ||\n hasImageFlavor(image, ImageFlavors.THUMBNAIL)\n )\n })\n if (volumeImages.length > 0) {\n const refImage = volumeImages[0]\n const filteredVolumeImages = volumeImages.filter((image) => {\n return refImage.SamplesPerPixel === image.SamplesPerPixel\n })\n const slideMetadataIndex = slideMetadata.findIndex((slide) => {\n return _doesImageBelongToSlide(slide, refImage)\n })\n\n const labelImages = series.filter((image) => {\n return hasImageFlavor(image, ImageFlavors.LABEL)\n })\n let filteredLabelImages: dmv.metadata.VLWholeSlideMicroscopyImage[]\n if (labelImages.length > 1) {\n filteredLabelImages = labelImages.filter((image) => {\n return areSameAcquisition(image, refImage)\n })\n } else {\n filteredLabelImages = labelImages\n }\n const overviewImages = series.filter((image) => {\n return hasImageFlavor(image, ImageFlavors.OVERVIEW)\n })\n let filteredOverviewImages: dmv.metadata.VLWholeSlideMicroscopyImage[]\n if (overviewImages.length > 1) {\n filteredOverviewImages = overviewImages.filter((image) => {\n return areSameAcquisition(image, refImage)\n })\n } else {\n filteredOverviewImages = overviewImages\n }\n\n if (slideMetadataIndex === -1) {\n const slideMetadataItem: SlideImageCollection = {\n acquisitionUID: refImage.AcquisitionUID,\n frameOfReferenceUID: refImage.FrameOfReferenceUID,\n containerIdentifier: refImage.ContainerIdentifier,\n volumeImages: filteredVolumeImages,\n labelImages: filteredLabelImages,\n overviewImages: filteredOverviewImages\n }\n slideMetadata.push(slideMetadataItem)\n } else {\n const slideMetadataItem = slideMetadata[slideMetadataIndex]\n slideMetadataItem.volumeImages.push(...filteredVolumeImages)\n slideMetadataItem.labelImages.push(...filteredLabelImages)\n slideMetadataItem.overviewImages.push(...filteredOverviewImages)\n }\n }\n }\n })\n\n let slides: Slide[] = slideMetadata.map((item) => {\n return new Slide({\n images: [\n ...item.volumeImages,\n ...item.labelImages,\n ...item.overviewImages\n ]\n })\n })\n slides = slides.sort((a, b) => {\n const imgA = a.volumeImages[0]\n const imgB = b.volumeImages[0]\n if (imgA.ContainerIdentifier != null && imgB.ContainerIdentifier != null) {\n return Number(imgA.ContainerIdentifier) - Number(imgB.ContainerIdentifier)\n } else {\n return 0\n }\n })\n\n return slides\n}\n\n/**\n * Check if instance belongs to the slide.\n *\n * Compares values of Frame of Reference UID and Container Identifier attributes.\n *\n * @param slide - Slide metadata object\n * @param image - Metadata of VOLUME, LABEL or OVERVIEW image instance\n */\nfunction _doesImageBelongToSlide (\n slide: SlideImageCollection,\n image: dmv.metadata.VLWholeSlideMicroscopyImage\n): boolean {\n if (\n slide.frameOfReferenceUID === image.FrameOfReferenceUID &&\n slide.containerIdentifier === image.ContainerIdentifier &&\n slide.acquisitionUID === image.AcquisitionUID\n ) {\n return true\n }\n return false\n}\n\nexport { Slide, createSlides }\n","import React from 'react'\nimport { Routes, Route, useLocation, useParams } from 'react-router-dom'\nimport { Layout, Menu } from 'antd'\n\nimport * as dmv from 'dicom-microscopy-viewer'\n\nimport { AnnotationSettings } from '../AppConfig'\nimport ClinicalTrial from './ClinicalTrial'\nimport DicomWebManager from '../DicomWebManager'\nimport Patient from './Patient'\nimport Study from './Study'\nimport SlideList from './SlideList'\nimport SlideViewer from './SlideViewer'\n\nimport { User } from '../auth'\nimport { Slide, createSlides } from '../data/slides'\nimport { StorageClasses } from '../data/uids'\nimport { RouteComponentProps, withRouter } from '../utils/router'\nimport { CustomError, errorTypes } from '../utils/CustomError'\nimport NotificationMiddleware, {\n NotificationMiddlewareContext\n} from '../services/NotificationMiddleware'\n\nfunction ParametrizedSlideViewer ({\n clients,\n slides,\n user,\n app,\n preload,\n enableAnnotationTools,\n annotations\n}: {\n clients: { [key: string]: DicomWebManager }\n slides: Slide[]\n user?: User\n app: {\n name: string\n version: string\n uid: string\n organization?: string\n }\n preload: boolean\n enableAnnotationTools: boolean\n annotations: AnnotationSettings[]\n}): JSX.Element | null {\n const { studyInstanceUID, seriesInstanceUID } = useParams()\n const location = useLocation()\n\n const selectedSlide = slides.find((slide: Slide) => {\n return slide.seriesInstanceUIDs.find((uid: string) => {\n return uid === seriesInstanceUID\n })\n })\n const searchParams = new URLSearchParams(location.search)\n let presentationStateUID: string | null | undefined\n if (!searchParams.has('access_token')) {\n presentationStateUID = searchParams.get('state')\n if (presentationStateUID === null) {\n presentationStateUID = undefined\n }\n }\n let viewer = null\n if (selectedSlide != null) {\n viewer = (\n \n )\n }\n return viewer\n}\n\ninterface ViewerProps extends RouteComponentProps {\n clients: { [key: string]: DicomWebManager }\n studyInstanceUID: string\n app: {\n name: string\n version: string\n uid: string\n organization?: string\n }\n annotations: AnnotationSettings[]\n enableAnnotationTools: boolean\n preload: boolean\n user?: {\n name: string\n email: string\n }\n}\n\ninterface ViewerState {\n slides: Slide[]\n isLoading: boolean\n}\n\nclass Viewer extends React.Component {\n state = {\n slides: [],\n isLoading: true\n }\n\n constructor (props: ViewerProps) {\n super(props)\n this.handleSeriesSelection = this.handleSeriesSelection.bind(this)\n }\n\n componentDidMount (): void {\n this.fetchImageMetadata().then(\n (metadata: dmv.metadata.VLWholeSlideMicroscopyImage[][]) => {\n this.setState({\n slides: createSlides(metadata),\n isLoading: false\n })\n }\n ).catch((error) => {\n console.error(error)\n // eslint-disable-next-line @typescript-eslint/no-floating-promises\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.SLIM,\n new CustomError(\n errorTypes.ENCODINGANDDECODING,\n 'Image metadata could not be retrieved or decoded.')\n )\n this.setState({ isLoading: false })\n })\n }\n\n /**\n * Fetch metadata for VL Whole Slide Microscopy Image instances of the study.\n *\n * @returns Metadata of image instances of the study grouped per series\n */\n async fetchImageMetadata (): Promise {\n const images: dmv.metadata.VLWholeSlideMicroscopyImage[][] = []\n const studyInstanceUID = this.props.studyInstanceUID\n console.info(`search for series of study \"${studyInstanceUID}\"...`)\n const client = this.props.clients[\n StorageClasses.VL_WHOLE_SLIDE_MICROSCOPY_IMAGE\n ]\n const matchedSeries = await client.searchForSeries({\n queryParams: {\n Modality: 'SM',\n StudyInstanceUID: studyInstanceUID\n }\n })\n\n await Promise.all(matchedSeries.map(async (s) => {\n const { dataset } = dmv.metadata.formatMetadata(s)\n const loadingSeries = dataset as dmv.metadata.Series\n console.info(\n `retrieve metadata of series \"${loadingSeries.SeriesInstanceUID}\"`\n )\n const retrievedMetadata = await client.retrieveSeriesMetadata({\n studyInstanceUID: this.props.studyInstanceUID,\n seriesInstanceUID: loadingSeries.SeriesInstanceUID\n })\n\n const seriesImages: dmv.metadata.VLWholeSlideMicroscopyImage[] = []\n retrievedMetadata.forEach((item, index) => {\n if (item['00080016'] != null) {\n const values = item['00080016'].Value\n if (values != null) {\n const sopClassUID = values[0]\n if (sopClassUID === StorageClasses.VL_WHOLE_SLIDE_MICROSCOPY_IMAGE) {\n const image = new dmv.metadata.VLWholeSlideMicroscopyImage({\n metadata: item\n })\n seriesImages.push(image)\n }\n }\n }\n })\n\n if (seriesImages.length > 0) {\n images.push(seriesImages)\n }\n }))\n\n return images\n }\n\n handleSeriesSelection (\n { seriesInstanceUID }: { seriesInstanceUID: string }\n ): void {\n console.info(`switch to series \"${seriesInstanceUID}\"`)\n let urlPath = (\n `/studies/${this.props.studyInstanceUID}` +\n `/series/${seriesInstanceUID}`\n )\n if (\n this.props.location.pathname.includes('/series/') &&\n this.props.location.search != null\n ) {\n urlPath += this.props.location.search\n }\n this.props.navigate(urlPath, { replace: true })\n }\n\n render (): React.ReactNode {\n if (this.state.isLoading) {\n return null\n }\n\n if (this.state.slides.length === 0) {\n return null\n }\n const firstSlide = this.state.slides[0] as Slide\n const volumeInstances = firstSlide.volumeImages\n if (volumeInstances.length === 0) {\n return null\n }\n const refImage = volumeInstances[0]\n\n /* If a series is encoded in the path, route the viewer to this series.\n * Otherwise select the first series correspondent to\n * the first slide contained in the study.\n */\n let selectedSeriesInstanceUID: string\n if (this.props.location.pathname.includes('series/')) {\n const fragments = this.props.location.pathname.split('/')\n selectedSeriesInstanceUID = fragments[4]\n } else {\n selectedSeriesInstanceUID = volumeInstances[0].SeriesInstanceUID\n }\n\n let clinicalTrialMenu\n if (refImage.ClinicalTrialSponsorName != null) {\n clinicalTrialMenu = (\n \n \n \n )\n }\n\n return (\n \n \n \n \n \n \n \n \n \n {clinicalTrialMenu}\n \n \n \n \n \n\n \n \n }\n />\n \n \n )\n }\n}\n\nexport default withRouter(Viewer)\n","import React from 'react'\nimport { NavLink } from 'react-router-dom'\nimport {\n Col,\n Descriptions,\n Dropdown,\n Input,\n Layout,\n Menu,\n Modal,\n Row,\n Space,\n Badge,\n Collapse\n} from 'antd'\nimport {\n ApiOutlined,\n CheckOutlined,\n InfoOutlined,\n StopOutlined,\n UnorderedListOutlined,\n UserOutlined,\n SettingOutlined\n} from '@ant-design/icons'\nimport { detect } from 'detect-browser'\n\nimport Button from './Button'\nimport { RouteComponentProps, withRouter } from '../utils/router'\nimport NotificationMiddleware, { NotificationMiddlewareEvents } from '../services/NotificationMiddleware'\nimport { CustomError } from '../utils/CustomError'\nimport { v4 as uuidv4 } from 'uuid'\n\ninterface HeaderProps extends RouteComponentProps {\n app: {\n name: string\n version: string\n homepage: string\n uid: string\n organization?: string\n }\n user?: {\n name: string\n email: string\n }\n showWorklistButton: boolean\n onServerSelection: ({ url }: { url: string }) => void\n onUserLogout?: () => void\n showServerSelectionButton: boolean\n}\n\ninterface HeaderState {\n selectedServerUrl?: string\n isServerSelectionModalVisible: boolean\n isServerSelectionDisabled: boolean\n errorObj: CustomError[]\n errorCategory: string[]\n warnings: string[]\n}\n\n/**\n * React component for the application header.\n */\nclass Header extends React.Component {\n constructor (props: HeaderProps) {\n super(props)\n this.state = {\n isServerSelectionModalVisible: false,\n isServerSelectionDisabled: true,\n errorObj: [],\n errorCategory: [],\n warnings: [],\n }\n\n const onErrorHandler = ({ error }: {\n category: string\n error: CustomError\n }): void => {\n this.setState(state => ({\n ...state,\n errorObj: [...state.errorObj, error],\n errorCategory: [...state.errorCategory, error.type]\n }))\n }\n\n const onWarningHandler = (warning: string): void => {\n this.setState(state => ({\n ...state,\n warnings: [...state.warnings, warning]\n }))\n }\n\n NotificationMiddleware.subscribe(\n NotificationMiddlewareEvents.OnError,\n onErrorHandler\n )\n\n NotificationMiddleware.subscribe(\n NotificationMiddlewareEvents.OnWarning,\n onWarningHandler\n )\n }\n\n componentDidUpdate(prevProps: Readonly, prevState: Readonly): void {\n if ((prevState.warnings.length || prevState.errorObj.length) && this.props.location.pathname !== prevProps.location.pathname) {\n this.setState({\n isServerSelectionModalVisible: false,\n isServerSelectionDisabled: true,\n errorObj: [],\n errorCategory: [],\n warnings: [],\n })\n }\n }\n\n handleInfoButtonClick = (): void => {\n const browser = detect()\n const environment: {\n browser: {\n name?: string\n version?: string\n }\n os: {\n name?: string\n }\n } = {\n browser: {},\n os: {}\n }\n if (browser != null) {\n environment.browser = {\n name: browser.name != null ? browser.name : undefined,\n version: browser.version != null ? browser.version : undefined\n }\n environment.os = {\n name: browser.os != null ? browser.os : undefined\n }\n }\n\n Modal.info({\n title: 'About',\n width: 600,\n content: (\n <>\n \n \n {this.props.app.name}\n \n \n {this.props.app.version}\n \n \n {this.props.app.homepage}\n \n \n \n \n {environment.browser.name}\n \n \n {environment.browser.version}\n \n \n \n \n {environment.os.name}\n \n \n \n ),\n onOk (): void {}\n })\n }\n\n handleDebugButtonClick = (): void => {\n const errorMsgs: {\n Authentication: string[]\n Communication: string[]\n EncodingDecoding: string[]\n Visualization: string[]\n } = {\n Authentication: [],\n Communication: [],\n EncodingDecoding: [],\n Visualization: []\n }\n\n type ObjectKey = keyof typeof errorMsgs\n const errorNum = this.state.errorObj.length\n\n if (errorNum > 0) {\n for (let i = 0; i < errorNum; i++) {\n const category = this.state.errorCategory[i] as ObjectKey\n errorMsgs[category].push(this.state.errorObj[i].message)\n }\n }\n\n const { Panel } = Collapse\n\n const showErrorCount = (errcount: number): JSX.Element => (\n \n )\n\n const showWarningCount = (warncount: number): JSX.Element => (\n \n )\n\n Modal.info({\n title: 'Debug Information\\n (Check console for more information)',\n width: 800,\n content: (\n \n \n
    \n {errorMsgs.Communication.map(e => (\n
  1. {e}
    2. \n ))}\n
\n \n \n
    \n {errorMsgs.EncodingDecoding.map(e => (\n
  1. {e}
    2. \n ))}\n
\n \n \n
    \n {errorMsgs.Visualization.map(e => (\n
  1. {e}
    2. \n ))}\n
\n \n \n
    \n {errorMsgs.Authentication.map(e => (\n
  1. {e}
    2. \n ))}\n
\n \n \n
    \n {this.state.warnings.map(warning => (\n
  1. {warning}
    2. \n ))}\n
\n \n \n ),\n onOk (): void {}\n })\n }\n\n handleServerSelectionButtonClick = (): void => {\n this.setState({ isServerSelectionModalVisible: true })\n }\n\n render (): React.ReactNode {\n let user = null\n if (this.props.user !== undefined) {\n const userMenuItems = []\n if (this.props.onUserLogout !== undefined) {\n userMenuItems.push(\n {\n label: 'Logout',\n key: 'user-logout',\n onClick: () => {\n if (this.props.onUserLogout !== undefined) {\n this.props.onUserLogout()\n }\n }\n }\n )\n }\n const userMenu = \n user = (\n \n e.preventDefault()}\n label={`${this.props.user.name} (${this.props.user.email})`}\n />\n \n )\n }\n\n let worklistButton\n if (this.props.showWorklistButton) {\n worklistButton = (\n \n \n this.handleReset(clearFilters)}\n size='small'\n style={{ width: 90 }}\n >\n Reset\n \n \n
\n ),\n filterIcon: (filtered: boolean) => (\n \n )\n })\n}\n\nexport default withRouter(Worklist)\n","/**\n * Join a URI with a path to form a full URL.\n *\n * @param path - Path component\n * @param uri - Base URI to which the path component should be added\n */\nexport const joinUrl = (path: string, uri: string): string => {\n let baseUri = uri\n if (!baseUri.endsWith('/')) {\n baseUri += '/'\n }\n const url = new URL(path, baseUri)\n return url.toString()\n}\n\n/**\n * Check whether a URL contains an OAuth 2.0 authorization code.\n *\n * @param location - URL components (JavaScript location object)\n * @returns Whether the URL contains a code\n */\nexport const isAuthorizationCodeInUrl = (location: {\n search: string\n hash: string\n}): boolean => {\n const searchParams = new URLSearchParams(location.search)\n const hashParams = new URLSearchParams(location.hash.replace('#', '?'))\n\n return Boolean(\n searchParams.get('code') ??\n searchParams.get('id_token') ??\n searchParams.get('session_state') ??\n hashParams.get('code') ??\n hashParams.get('id_token') ??\n hashParams.get('session_state')\n )\n}\n","import { UserManager, User as UserData } from 'oidc-client'\n\nimport { OidcSettings } from '../AppConfig'\nimport { isAuthorizationCodeInUrl } from '../utils/url'\nimport { User, AuthManager, SignInCallback } from './'\nimport NotificationMiddleware,\n{ NotificationMiddlewareContext } from '../services/NotificationMiddleware'\nimport { CustomError, errorTypes } from '../utils/CustomError'\n\nconst createUser = (userData: UserData | null): User => {\n let profile\n if (userData !== null) {\n profile = userData.profile\n }\n\n if (profile !== undefined) {\n if (profile.name === undefined || profile.email === undefined) {\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.AUTH,\n new CustomError(\n errorTypes.AUTHENTICATION,\n 'Failed to obtain user \"name\" and \"email\".'\n )\n )\n } else {\n return {\n name: profile.name,\n email: profile.email\n }\n }\n } else {\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.AUTH,\n new CustomError(\n errorTypes.AUTHENTICATION,\n 'Failed to obtain user profile.'\n )\n )\n }\n return {\n name: undefined,\n email: undefined\n }\n}\n\nexport default class OidcManager implements AuthManager {\n private _oidc: UserManager\n\n constructor (baseUri: string, settings: OidcSettings) {\n let responseType = 'code'\n if (settings.grantType !== undefined) {\n if (settings.grantType === 'implicit') {\n responseType = 'id_token token'\n }\n }\n this._oidc = new UserManager({\n authority: settings.authority,\n client_id: settings.clientId,\n redirect_uri: baseUri,\n scope: settings.scope,\n response_type: responseType,\n loadUserInfo: true,\n automaticSilentRenew: true,\n revokeAccessTokenOnSignout: true,\n post_logout_redirect_uri: `${baseUri}/logout`\n })\n if (settings.endSessionEndpoint != null) {\n /*\n * Unfortunately, the end session endpoint alone cannot be provided to\n * the construction of UserManager and the other metadata parameters\n * would need to be provided as well. However, configuring all of them\n * individually would not be desirable and they will be automatically\n * determined anyways. Therefore, we first construct an object, get the\n * metadata, update the metadata, and then reconstruct an object with the\n * updated metadata.\n */\n this._oidc.metadataService.getMetadata().then(metadata => {\n if (settings.endSessionEndpoint != null) {\n metadata.end_session_endpoint = settings.endSessionEndpoint\n this._oidc = new UserManager({\n authority: settings.authority,\n client_id: settings.clientId,\n redirect_uri: baseUri,\n scope: settings.scope,\n response_type: responseType,\n loadUserInfo: true,\n automaticSilentRenew: true,\n revokeAccessTokenOnSignout: true,\n post_logout_redirect_uri: `${baseUri}/logout`,\n metadata\n })\n }\n }).catch((error) => {\n console.error(\n 'failed to get metadata from authorization server: ',\n error\n )\n })\n }\n }\n\n /**\n * Sign-in to authenticate the user and obtain authorization.\n */\n signIn = async ({ onSignIn }: {\n onSignIn?: SignInCallback\n }): Promise => {\n const handleSignIn = (userData: UserData): void => {\n const user = createUser(userData)\n const authorization = `${userData.token_type} ${userData.access_token}`\n if (onSignIn != null) {\n console.info('handling sign-in using provided callback function')\n onSignIn({ user: user, authorization: authorization })\n } else {\n console.warn('no callback function was provided to handle sign-in')\n }\n }\n\n if (isAuthorizationCodeInUrl(window.location)) {\n /* Handle the callback from the authorization server: extract the code\n * from the callback URL, obtain user information and the access token\n * for the DICOMweb server.\n */\n console.info('obtaining authorization')\n const userData = await this._oidc.signinCallback()\n if (userData != null) {\n console.info('obtained user data: ', userData)\n handleSignIn(userData)\n }\n } else {\n /* Redirect to the authorization server to authenticate the user\n * and authorize the application to obtain user information and access\n * the DICOMweb server.\n */\n const userData = await this._oidc.getUser()\n if (userData === null || userData.expired) {\n console.info('authenticating user')\n await this._oidc.signinRedirect()\n } else {\n console.info('user has already been authenticated')\n handleSignIn(userData)\n }\n }\n }\n\n /**\n * Sign-out to revoke authorization.\n */\n signOut = async (): Promise => {\n console.log('signing out user and revoking authorization')\n return await this._oidc.signoutRedirect()\n }\n\n /**\n * Get authorization. Requires prior sign-in.\n */\n getAuthorization = async (): Promise => {\n return await this._oidc.getUser().then((userData) => {\n if (userData !== null) {\n return userData.access_token\n } else {\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.AUTH,\n new CustomError(\n errorTypes.AUTHENTICATION,\n 'Failed to obtain user profile.'\n )\n )\n }\n })\n }\n\n /**\n * Get user information. Requires prior sign-in.\n */\n getUser = async (): Promise => {\n return await this._oidc.getUser().then((userData) => {\n if (userData === null) {\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.AUTH,\n new CustomError(\n errorTypes.AUTHENTICATION,\n 'Failed to obtain user information.'\n )\n )\n }\n return createUser(userData)\n })\n }\n}\n","import retry from 'retry'\n\nimport {\n RetryRequestSettings,\n DICOMwebClientRequestHookMetadata\n} from '../AppConfig'\n\ntype RequestHook = (\n request: XMLHttpRequest,\n metadata: DICOMwebClientRequestHookMetadata\n) => XMLHttpRequest\n\n/**\n * Returns a configured retry request hook function\n * that can be used to add retry functionality to XHR request.\n *\n * Default options:\n * retries: 5\n * factor: 3\n * minTimeout: 1 * 1000\n * maxTimeout: 60 * 1000\n * randomize: true\n *\n * @param options\n * @param options.retires - Number of retries\n * @param options.factor - Factor\n * @param options.minTimeout - Min number of seconds to wait before next retry\n * @param options.maxTimeout - Max number of seconds to wait before next retry\n * @param options.randomize - Whether randomization should be applied\n * @param options.retryableStatusCodes HTTP status codes that can trigger a retry\n * @returns Configured retry request function\n */\nexport const getXHRRetryHook = (options: RetryRequestSettings = {\n retries: 5,\n factor: 3,\n minTimeout: 1 * 1000,\n maxTimeout: 60 * 1000,\n randomize: true,\n retryableStatusCodes: [429, 500]\n}): RequestHook => {\n const retryOptions = options\n\n if (options.retries != null) {\n retryOptions.retries = options.retries\n }\n\n if (options.factor != null) {\n retryOptions.factor = options.factor\n }\n\n if (options.minTimeout != null) {\n retryOptions.minTimeout = options.minTimeout\n }\n\n if (options.maxTimeout != null) {\n retryOptions.maxTimeout = options.maxTimeout\n }\n\n if (options.randomize != null) {\n retryOptions.randomize = options.randomize\n }\n\n if (options.retryableStatusCodes != null) {\n retryOptions.retryableStatusCodes = options.retryableStatusCodes\n }\n\n /**\n * Request hook used to add retry functionality to XHR requests.\n *\n * @param request - XHR request instance\n * @param metadata - Metadata about the request\n * @param metadata.url - URL\n * @param metadata.method - HTTP method\n * @returns - XHR request instance (potentially modified)\n */\n const xhrRetryHook = (\n request: XMLHttpRequest,\n metadata: DICOMwebClientRequestHookMetadata\n ): XMLHttpRequest => {\n const { url, method } = metadata\n\n function faultTolerantRequestSend (...args: any): void {\n const operation = retry.operation(retryOptions)\n\n operation.attempt(function operationAttempt (currentAttempt) {\n const originalOnReadyStateChange = request.onreadystatechange\n\n /** Overriding/extending XHR function */\n request.onreadystatechange = function onReadyStateChange (...args: any): void {\n if (originalOnReadyStateChange != null) {\n originalOnReadyStateChange.apply(request, args)\n }\n\n if (retryOptions.retryableStatusCodes.includes(request.status)) {\n const errorMessage = `Attempt to request ${url} failed.`\n const attemptFailedError = new Error(errorMessage)\n operation.retry(attemptFailedError)\n }\n }\n\n /** Call open only on retry (after headers and other things were set in the xhr instance) */\n if (currentAttempt > 1) {\n console.warn(`Requesting ${url}... (attempt: ${currentAttempt})`)\n request.open(method, url, true)\n }\n })\n\n originalRequestSend.apply(request, args)\n }\n\n /** Overriding/extending XHR function */\n const originalRequestSend = request.send\n request.send = faultTolerantRequestSend\n\n return request\n }\n\n return xhrRetryHook\n}\n\nexport default getXHRRetryHook\n","import * as dwc from 'dicomweb-client'\n\nimport { ServerSettings, DicomWebManagerErrorHandler } from './AppConfig'\nimport { joinUrl } from './utils/url'\nimport getXHRRetryHook from './utils/xhrRetryHook'\nimport { CustomError, errorTypes } from './utils/CustomError'\nimport NotificationMiddleware, {\n NotificationMiddlewareContext\n} from './services/NotificationMiddleware'\n\ninterface Store {\n id: string\n read: boolean\n write: boolean\n client: dwc.api.DICOMwebClient\n}\n\nexport default class DicomWebManager implements dwc.api.DICOMwebClient {\n private readonly stores: Store[] = []\n\n private readonly handleError: DicomWebManagerErrorHandler\n\n constructor ({ baseUri, settings, onError }: {\n baseUri: string\n settings: ServerSettings[]\n onError?: DicomWebManagerErrorHandler\n }) {\n if (onError != null) {\n this.handleError = onError\n } else {\n this.handleError = (error, serverSettings) => {\n console.error(error, serverSettings)\n }\n }\n\n settings.forEach(serverSettings => {\n if (serverSettings === undefined) {\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.SLIM,\n new CustomError(\n errorTypes.COMMUNICATION,\n 'At least one server needs to be configured.'\n )\n )\n }\n\n let serviceUrl\n if (serverSettings.url !== undefined) {\n serviceUrl = serverSettings.url\n } else if (serverSettings.path !== undefined) {\n serviceUrl = joinUrl(serverSettings.path, baseUri)\n } else {\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.SLIM,\n new CustomError(\n errorTypes.COMMUNICATION,\n 'Either path or full URL needs to be configured for server.'\n )\n )\n }\n const clientSettings: dwc.api.DICOMwebClientOptions = {\n url: serviceUrl\n }\n if (serverSettings.qidoPathPrefix !== undefined) {\n clientSettings.qidoURLPrefix = serverSettings.qidoPathPrefix\n }\n if (serverSettings.wadoPathPrefix !== undefined) {\n clientSettings.wadoURLPrefix = serverSettings.wadoPathPrefix\n }\n if (serverSettings.stowPathPrefix !== undefined) {\n clientSettings.stowURLPrefix = serverSettings.stowPathPrefix\n }\n if (serverSettings.retry !== undefined) {\n clientSettings.requestHooks = [getXHRRetryHook(serverSettings.retry)]\n }\n\n clientSettings.errorInterceptor = (error: dwc.api.DICOMwebClientError) => {\n this.handleError(error, serverSettings)\n }\n\n this.stores.push({\n id: serverSettings.id,\n write: serverSettings.write ?? false,\n read: serverSettings.read ?? true,\n client: new dwc.api.DICOMwebClient(clientSettings)\n })\n })\n\n if (this.stores.length > 1) {\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.SLIM,\n new CustomError(\n errorTypes.COMMUNICATION,\n 'Only one store is supported for now.'\n )\n )\n }\n }\n\n get baseURL (): string {\n return this.stores[0].client.baseURL\n }\n\n updateHeaders = (fields: { [name: string]: string }): void => {\n for (const f in fields) {\n this.stores[0].client.headers[f] = fields[f]\n }\n }\n\n get headers (): { [name: string]: string } {\n return this.stores[0].client.headers\n }\n\n storeInstances = async (\n options: dwc.api.StoreInstancesOptions\n ): Promise => {\n if (this.stores[0].write) {\n return await this.stores[0].client.storeInstances(options)\n } else {\n return await Promise.reject(\n new Error('Store is not writable.')\n )\n }\n }\n\n searchForStudies = async (\n options: dwc.api.SearchForStudiesOptions\n ): Promise => {\n return await this.stores[0].client.searchForStudies(options)\n }\n\n searchForSeries = async (\n options: dwc.api.SearchForSeriesOptions\n ): Promise => {\n return await this.stores[0].client.searchForSeries(options)\n }\n\n searchForInstances = async (\n options: dwc.api.SearchForInstancesOptions\n ): Promise => {\n return await this.stores[0].client.searchForInstances(options)\n }\n\n retrieveStudyMetadata = async (\n options: dwc.api.RetrieveStudyMetadataOptions\n ): Promise => {\n return await this.stores[0].client.retrieveStudyMetadata(options)\n }\n\n retrieveSeriesMetadata = async (\n options: dwc.api.RetrieveSeriesMetadataOptions\n ): Promise => {\n return await this.stores[0].client.retrieveSeriesMetadata(options)\n }\n\n retrieveInstanceMetadata = async (\n options: dwc.api.RetrieveInstanceMetadataOptions\n ): Promise => {\n return await this.stores[0].client.retrieveInstanceMetadata(options)\n }\n\n retrieveInstance = async (\n options: dwc.api.RetrieveInstanceOptions\n ): Promise => {\n return await this.stores[0].client.retrieveInstance(options)\n }\n\n retrieveInstanceFrames = async (\n options: dwc.api.RetrieveInstanceFramesOptions\n ): Promise => {\n return await this.stores[0].client.retrieveInstanceFrames(options)\n }\n\n retrieveInstanceRendered = async (\n options: dwc.api.RetrieveInstanceRenderedOptions\n ): Promise => {\n return await this.stores[0].client.retrieveInstanceRendered(options)\n }\n\n retrieveInstanceFramesRendered = async (\n options: dwc.api.RetrieveInstanceFramesRenderedOptions\n ): Promise => {\n return await this.stores[0].client.retrieveInstanceFramesRendered(options)\n }\n\n retrieveBulkData = async (\n options: dwc.api.RetrieveBulkDataOptions\n ): Promise => {\n return await this.stores[0].client.retrieveBulkData(options)\n }\n}\n","import React from 'react'\nimport {\n BrowserRouter,\n Navigate,\n Route,\n Routes,\n useParams\n} from 'react-router-dom'\nimport { Layout, message } from 'antd'\nimport { FaSpinner } from 'react-icons/fa'\nimport * as dwc from 'dicomweb-client'\n\nimport AppConfig, { ServerSettings, ErrorMessageSettings } from './AppConfig'\nimport CaseViewer from './components/CaseViewer'\nimport Header from './components/Header'\nimport InfoPage from './components/InfoPage'\nimport Worklist from './components/Worklist'\n\nimport { User, AuthManager } from './auth'\nimport OidcManager from './auth/OidcManager'\nimport { StorageClasses } from './data/uids'\nimport DicomWebManager from './DicomWebManager'\nimport { joinUrl } from './utils/url'\nimport { CustomError, errorTypes } from './utils/CustomError'\nimport NotificationMiddleware, {\n NotificationMiddlewareContext\n} from './services/NotificationMiddleware'\n\nfunction ParametrizedCaseViewer ({ clients, user, app, config }: {\n clients: { [key: string]: DicomWebManager }\n user?: User\n app: {\n name: string\n version: string\n uid: string\n organization?: string\n }\n config: AppConfig\n}): JSX.Element {\n const { studyInstanceUID } = useParams()\n\n const enableAnnotationTools = !(config.disableAnnotationTools ?? false)\n const preload = config.preload ?? false\n return (\n \n )\n}\n\nfunction _createClientMapping ({ baseUri, settings, onError }: {\n baseUri: string\n settings: ServerSettings[]\n onError: (\n error: dwc.api.DICOMwebClientError,\n serverSettings: ServerSettings\n ) => void\n}): { [sopClassUID: string]: DicomWebManager } {\n const storageClassMapping: { [key: string]: number } = { default: 0 }\n const clientMapping: { [sopClassUID: string]: DicomWebManager } = {}\n\n settings.forEach(serverSettings => {\n if (serverSettings.storageClasses != null) {\n serverSettings.storageClasses.forEach(sopClassUID => {\n if (Object.values(StorageClasses).includes(sopClassUID)) {\n if (sopClassUID in storageClassMapping) {\n storageClassMapping[sopClassUID] += 1\n } else {\n storageClassMapping[sopClassUID] = 1\n }\n } else {\n console.warn(\n `unknown storage class \"${sopClassUID}\" specified ` +\n `for configured server \"${serverSettings.id}\"`\n )\n }\n })\n } else {\n storageClassMapping.default += 1\n clientMapping.default = new DicomWebManager({\n baseUri,\n settings: [serverSettings],\n onError\n })\n }\n })\n\n if (storageClassMapping.default > 1) {\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.SLIM,\n new CustomError(\n errorTypes.COMMUNICATION,\n 'Only one default server can be configured without specification ' +\n 'of storage classes.'\n )\n )\n }\n\n for (const key in storageClassMapping) {\n if (key === 'default') {\n continue\n }\n if (storageClassMapping[key] > 1) {\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.SLIM,\n new CustomError(\n errorTypes.COMMUNICATION,\n 'Only one configured server can specify a given storage class. ' +\n `Storage class \"${key}\" is specified by more than one ` +\n 'of the configured servers.'\n )\n )\n }\n }\n\n if (Object.keys(storageClassMapping).length > 1) {\n settings.forEach(server => {\n const client = new DicomWebManager({\n baseUri,\n settings: [server],\n onError\n })\n if (server.storageClasses != null) {\n server.storageClasses.forEach(sopClassUID => {\n clientMapping[sopClassUID] = client\n })\n }\n })\n }\n\n Object.values(StorageClasses).forEach(sopClassUID => {\n if (!(sopClassUID in clientMapping)) {\n clientMapping[sopClassUID] = clientMapping.default\n }\n })\n return clientMapping\n}\n\ninterface AppProps {\n name: string\n homepage: string\n version: string\n config: AppConfig\n}\n\ninterface AppState {\n clients: { [sopClassUID: string]: DicomWebManager }\n user?: User\n isLoading: boolean\n redirectTo?: string\n wasAuthSuccessful: boolean\n error?: ErrorMessageSettings\n}\n\nclass App extends React.Component {\n private readonly auth?: AuthManager\n\n private readonly handleDICOMwebError = (\n error: dwc.api.DICOMwebClientError,\n serverSettings: ServerSettings\n ): void => {\n if (error.status === 401) {\n this.signIn()\n } else if (error.status === 403) {\n // eslint-disable-next-line @typescript-eslint/no-floating-promises\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.DICOMWEB,\n new CustomError(\n errorTypes.COMMUNICATION,\n 'User is not authorized to access DICOMweb resources.')\n )\n }\n\n const logServerError = () => {\n // eslint-disable-next-line @typescript-eslint/no-floating-promises\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.DICOMWEB,\n new CustomError(\n errorTypes.COMMUNICATION,\n 'An unexpected server error occured.')\n )\n }\n\n if (serverSettings.errorMessages !== undefined) {\n serverSettings.errorMessages.forEach((setting: ErrorMessageSettings) => {\n if (error.status === setting.status) {\n this.setState({\n error: {\n status: error.status,\n message: setting.message\n }\n })\n } else if (error.status === 500) {\n logServerError()\n }\n })\n } else if (error.status === 500) {\n logServerError()\n }\n }\n\n constructor (props: AppProps) {\n super(props)\n\n console.info('instatiate app')\n console.info(`app is located at \"${props.config.path}\"`)\n const { protocol, host } = window.location\n const baseUri = `${protocol}//${host}`\n const appUri = joinUrl(props.config.path, baseUri)\n\n const oidcSettings = props.config.oidc\n if (oidcSettings !== undefined) {\n console.info(\n 'app uses the following OIDC configuration: ',\n props.config.oidc\n )\n this.auth = new OidcManager(appUri, oidcSettings)\n }\n\n if (props.config.servers.length === 0) {\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.SLIM,\n new CustomError(\n errorTypes.COMMUNICATION,\n 'One server needs to be configured.')\n )\n }\n console.info(\n 'app uses the following DICOMweb server configuration: ',\n props.config.servers\n )\n\n this.handleServerSelection = this.handleServerSelection.bind(this)\n\n message.config({ duration: 5 })\n this.addGcpSecondaryAnnotationServer(props.config)\n\n this.state = {\n clients: _createClientMapping({\n baseUri,\n settings: props.config.servers,\n onError: this.handleDICOMwebError\n }),\n isLoading: true,\n wasAuthSuccessful: false\n }\n }\n\n addGcpSecondaryAnnotationServer (config: AppProps['config']): void {\n const serverId = 'gcp_secondary_annotation_server'\n const urlParams = new URLSearchParams(window.location.search)\n const url = urlParams.get('gcp')\n const gcpSecondaryAnnotationServer = config.servers.find(\n (server) => server.id === serverId\n )\n if (gcpSecondaryAnnotationServer === undefined && typeof url === 'string') {\n config.servers.push({\n id: serverId,\n write: true,\n url,\n storageClasses: [\n StorageClasses.COMPREHENSIVE_SR,\n StorageClasses.COMPREHENSIVE_3D_SR,\n StorageClasses.SEGMENTATION,\n StorageClasses.MICROSCOPY_BULK_SIMPLE_ANNOTATION,\n StorageClasses.PARAMETRIC_MAP,\n StorageClasses.ADVANCED_BLENDING_PRESENTATION_STATE,\n StorageClasses.COLOR_SOFTCOPY_PRESENTATION_STATE,\n StorageClasses.GRAYSCALE_SOFTCOPY_PRESENTATION_STATE,\n StorageClasses.PSEUDOCOLOR_SOFTCOPY_PRESENTATION_STATE\n ]\n })\n }\n }\n\n handleServerSelection ({ url }: { url: string }): void {\n console.info('select DICOMweb server: ', url)\n const tmpClient = new DicomWebManager({\n baseUri: '',\n settings: [{\n id: 'tmp',\n url,\n read: true,\n write: false\n }],\n onError: this.handleDICOMwebError\n })\n tmpClient.updateHeaders(this.state.clients.default.headers)\n /**\n * Use the newly created client for all storage classes. We may want to\n * make this more sophisticated in the future to allow users to override\n * the entire server configuration.\n */\n this.setState(state => {\n const clients: { [key: string]: DicomWebManager } = {}\n for (const key in state.clients) {\n clients[key] = tmpClient\n }\n return { clients }\n })\n }\n\n /**\n * Handle successful authentication event.\n *\n * Authorizes the DICOMweb client to access the DICOMweb server and directs\n * the user back to the App.\n *\n * @param user - Information about the user\n * @param authorization - Value of the \"Authorization\" HTTP header field\n */\n handleSignIn = ({ user, authorization }: {\n user: User\n authorization: string\n }): void => {\n for (const key in this.state.clients) {\n const client = this.state.clients[key]\n client.updateHeaders({ Authorization: authorization })\n }\n const storedPath = window.localStorage.getItem('slim_path')\n const storedSearch = window.localStorage.getItem('slim_search')\n if (storedPath != null) {\n const currentPath = window.location.pathname\n if (storedPath !== currentPath) {\n let path = storedPath\n if (storedSearch != null) {\n path += storedSearch\n }\n window.location.href = path\n }\n }\n window.localStorage.removeItem('slim_path')\n window.localStorage.removeItem('slim_search')\n this.setState({ user: user })\n }\n\n signIn (): void {\n if (this.auth !== undefined) {\n console.info('try to sign in user')\n this.auth.signIn({ onSignIn: this.handleSignIn }).then(() => {\n console.info('sign-in was successful')\n this.setState({\n isLoading: false,\n wasAuthSuccessful: true\n })\n }).catch((error) => {\n console.error(error)\n // eslint-disable-next-line @typescript-eslint/no-floating-promises\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.AUTH,\n new CustomError(\n errorTypes.AUTHENTICATION,\n 'Could not sign-in user.')\n )\n this.setState({\n isLoading: false,\n redirectTo: undefined,\n wasAuthSuccessful: false\n })\n })\n } else {\n this.setState({\n isLoading: false,\n redirectTo: undefined,\n wasAuthSuccessful: true\n })\n }\n }\n\n componentDidMount (): void {\n const path = window.localStorage.getItem('slim_path')\n if (path == null) {\n window.localStorage.setItem('slim_path', window.location.pathname)\n window.localStorage.setItem('slim_search', window.location.search)\n }\n this.signIn()\n }\n\n render (): React.ReactNode {\n const appInfo = {\n name: this.props.name,\n version: this.props.version,\n homepage: this.props.homepage,\n uid: '1.2.826.0.1.3680043.9.7433.1.5',\n organization: this.props.config.organization\n }\n\n const enableWorklist = !(\n this.props.config.disableWorklist ?? false\n )\n const enableServerSelection = (\n this.props.config.enableServerSelection ?? false\n )\n\n let worklist\n if (enableWorklist) {\n worklist = \n } else {\n worklist =
Worklist has been disabled.
\n }\n\n let isLogoutPossible = false\n let onLogout: () => void\n if (\n // eslint-disable-next-line @typescript-eslint/prefer-optional-chain\n this.props.config.oidc != null &&\n this.props.config.oidc.endSessionEndpoint != null\n ) {\n onLogout = (): void => {\n if (this.auth != null) {\n // eslint-disable-next-line @typescript-eslint/no-floating-promises\n this.auth.signOut()\n }\n }\n isLogoutPossible = true\n } else {\n onLogout = () => {}\n isLogoutPossible = false\n }\n\n const layoutStyle = { height: '100vh' }\n const layoutContentStyle = { height: '100%' }\n\n if (this.state.redirectTo !== undefined) {\n return (\n \n \n \n )\n } else if (this.state.isLoading) {\n return (\n \n \n \n \n \n \n \n \n )\n } else if (!this.state.wasAuthSuccessful) {\n return (\n \n )\n } else if (this.state.error != null) {\n return (\n \n )\n } else {\n return (\n \n \n \n \n \n {worklist}\n \n \n }\n />\n \n \n \n \n \n \n }\n />\n \n \n Logged out\n \n }\n />\n \n \n )\n }\n }\n}\n\nexport 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t=e.CodingSchemeDesignator,n=e.CodeValue;return"".concat(t,"-").concat(n)},rt=function(e){var t=Me({content:e.evaluations,name:new ve.sr.coding.CodedConcept({value:"121071",meaning:"Finding",schemeDesignator:"DCM"})});if(0!==t.length){var n=t[0].ConceptCodeSequence[0];return ot(n)}console.warn("no finding found for ROI ".concat(e.uid))},st=function(e){var t=e.clients,n=e.slide,i=e.preload;console.info("instantiate viewer for VOLUME images of slide "+'"'.concat(n.volumeImages[0].ContainerIdentifier,'"'));try{var a,o=new g.viewer.VolumeImageViewer({clientMapping:t,metadata:n.volumeImages,controls:["overview","position"],preload:i,errorInterceptor:function(e){return J.onError(B,e)}});return o.activateSelectInteraction({}),n.labelImages.length>0&&(console.info("instantiate viewer for LABEL image of slide "+'"'.concat(n.labelImages[0].ContainerIdentifier,'"')),a=new 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0,a.defaultRoiStyle={stroke:{color:it,width:2},fill:{color:at},image:{circle:{fill:{color:it},radius:5}}},a.roiStyles={},a.selectionColor=[140,184,198],a.selectedRoiStyle={stroke:{color:[].concat((0,ne.Z)(a.selectionColor),[1]),width:3},fill:{color:[].concat((0,ne.Z)(a.selectionColor),[.2])},image:{circle:{radius:5,fill:{color:[].concat((0,ne.Z)(a.selectionColor),[1])}}}},a.loadPresentationStates=function(){console.info("search for Presentation State instances");var e=a.props.clients[M.ADVANCED_BLENDING_PRESENTATION_STATE];e.searchForInstances({studyInstanceUID:a.props.studyInstanceUID,queryParams:{Modality:"PR"}}).then((function(t){null==t&&(t=[]),t.forEach((function(t,n){var i=g.metadata.formatMetadata(t).dataset;console.info('retrieve PR instance "'.concat(i.SOPInstanceUID,'"')),e.retrieveInstance({studyInstanceUID:a.props.studyInstanceUID,seriesInstanceUID:i.SeriesInstanceUID,sopInstanceUID:i.SOPInstanceUID}).then((function(e){var t=ve.aT.DicomMessage.readFile(e),o=g.metadata.formatMetadata(t.dict).dataset;if(a.props.slide.areVolumeImagesMonochrome){var r=o,s=!1;r.AdvancedBlendingSequence.forEach((function(e){s=a.props.slide.seriesInstanceUIDs.includes(e.SeriesInstanceUID)})),s&&(console.info("include Advanced Blending Presentation State instance "+'"'.concat(r.SOPInstanceUID,'"')),(0===n&&null==a.props.selectedPresentationStateUID||r.SOPInstanceUID===a.props.selectedPresentationStateUID)&&a.setPresentationState(r),a.setState((function(e){var t={};return e.presentationStates.forEach((function(e){t[e.SOPInstanceUID]=e})),t[r.SOPInstanceUID]=r,{presentationStates:Object.values(t)}})))}else console.info('ignore presentation state "'.concat(i.SOPInstanceUID,'", ')+"application of presentation states for color images has not (yet) been implemented")})).catch((function(e){J.onError(Y,new q(G,"Presentation State could not be loaded")),console.error("failed to load presentation state "+'of SOP instance 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g.color.PaletteColorLookupTable({uid:null!=s.PaletteColorLookupTableUID?s.PaletteColorLookupTableUID:"",redDescriptor:s.RedPaletteColorLookupTableDescriptor,greenDescriptor:s.GreenPaletteColorLookupTableDescriptor,blueDescriptor:s.BluePaletteColorLookupTableDescriptor,redData:null!=s.RedPaletteColorLookupTableData?new Uint16Array(s.RedPaletteColorLookupTableData):void 0,greenData:null!=s.GreenPaletteColorLookupTableData?new Uint16Array(s.GreenPaletteColorLookupTableData):void 0,blueData:null!=s.BluePaletteColorLookupTableData?new Uint16Array(s.BluePaletteColorLookupTableData):void 0,redSegmentedData:null!=s.SegmentedRedPaletteColorLookupTableData?new Uint16Array(s.SegmentedRedPaletteColorLookupTableData):void 0,greenSegmentedData:null!=s.SegmentedGreenPaletteColorLookupTableData?new Uint16Array(s.SegmentedGreenPaletteColorLookupTableData):void 0,blueSegmentedData:null!=s.SegmentedBluePaletteColorLookupTableData?new Uint16Array(s.SegmentedBluePaletteColorLookupTableData):void 0})}if(null!=e.SoftcopyVOILUTSequence){var l=e.SoftcopyVOILUTSequence[0],c=l.WindowCenter,d=l.WindowWidth;r=[c-.5*d,c+.5*d]}n[i]={opacity:1,paletteColorLookupTable:o,limitValues:r}}}))}))}));var i=new Set;Object.keys(n).forEach((function(e){var t=n[e];null!=t?(a.volumeViewer.setOpticalPathStyle(e,t),a.volumeViewer.activateOpticalPath(e),a.volumeViewer.showOpticalPath(e),i.add(e)):(a.volumeViewer.hideOpticalPath(e),a.volumeViewer.deactivateOpticalPath(e))}));var o=new URLSearchParams(a.props.location.search);o.set("state",e.SOPInstanceUID),a.props.navigate({pathname:a.props.location.pathname,search:o.toString()},{replace:!0}),a.setState((function(t){return{activeOpticalPathIdentifiers:i,visibleOpticalPathIdentifiers:i,selectedPresentationStateUID:e.SOPInstanceUID}}))},a.getRoiStyle=function(e){return null==e?a.defaultRoiStyle:void 0!==a.roiStyles[e]?a.roiStyles[e]:a.defaultRoiStyle},a.addAnnotations=function(){console.info("search for Comprehensive 3D SR instances");var e=a.props.clients[M.COMPREHENSIVE_3D_SR];e.searchForInstances({studyInstanceUID:a.props.studyInstanceUID,queryParams:{Modality:"SR"}}).then((function(t){null==t&&(t=[]),t.forEach((function(t){var n=g.metadata.formatMetadata(t).dataset;n.SOPClassUID===M.COMPREHENSIVE_3D_SR&&(console.info('retrieve SR instance "'.concat(n.SOPInstanceUID,'"')),e.retrieveInstance({studyInstanceUID:a.props.studyInstanceUID,seriesInstanceUID:n.SeriesInstanceUID,sopInstanceUID:n.SOPInstanceUID}).then((function(e){var t=ve.aT.DicomMessage.readFile(e),n=g.metadata.formatMetadata(t.dict).dataset;(function(e){var t=e.ContentTemplateSequence;return t.length>0&&"1500"===t[0].TemplateIdentifier})(n)?!function(e){var t=Me({content:e.ContentSequence,name:new ve.sr.coding.CodedConcept({value:"121024",schemeDesignator:"DCM",meaning:"Subject Class"})});if(0===t.length)return!1;var n=t[0].ConceptCodeSequence[0],i=new ve.sr.coding.CodedConcept({value:n.CodeValue,meaning:n.CodeMeaning,schemeDesignator:n.CodingSchemeDesignator}),a=new ve.sr.coding.CodedConcept({value:"121027",meaning:"Specimen",schemeDesignator:"DCM"});return!!i.equals(a)}(n)?console.debug('ignore SR document "'.concat(n.SOPInstanceUID,'" ')+"because it does not describe a specimen subject"):!function(e){var t=Me({content:e.ContentSequence,name:new ve.sr.coding.CodedConcept({value:"126010",schemeDesignator:"DCM",meaning:"Imaging Measurements"})});if(0===t.length)return!1;var n=t[0],i=Me({content:n.ContentSequence,name:new ve.sr.coding.CodedConcept({value:"125007",schemeDesignator:"DCM",meaning:"Measurement Group"})}),a=!1;return i.forEach((function(e){var t=Me({content:e.ContentSequence,name:new ve.sr.coding.CodedConcept({value:"111030",schemeDesignator:"DCM",meaning:"Image Region"})});t.length>0&&t[0].ValueType===ve.sr.valueTypes.ValueTypes.SCOORD3D&&(a=!0)})),a}(n)?console.debug('ignore SR document "'.concat(n.SOPInstanceUID,'" ')+"because it does not contain any suitable ROI annotations"):new Ue(n).ROIs.forEach((function(e){console.info('add ROI "'.concat(e.uid,'"'));var t=e.scoord3d,i=a.props.slide.volumeImages[0];if(t.frameOfReferenceUID===i.FrameOfReferenceUID){var o=a.volumeViewer.getAllROIs().some((function(t){return function(e,t){if(e.scoord3d.graphicType!==t.scoord3d.graphicType)return!1;if(e.scoord3d.frameOfReferenceUID!==t.scoord3d.frameOfReferenceUID)return!1;if(e.scoord3d.graphicData.length!==t.scoord3d.graphicData.length)return!1;for(var n=0;n0){try{a.volumeViewer.addSegments(t)}catch(n){J.onError(Y,new q(G,"Segmentations cannot be displayed")),console.error("failed to add segments: ",n)}a.forceUpdate()}})).catch((function(){J.onError(Y,new q(G,"Retrieval of metadata of Segmentation instances failed."))}))}))})).catch((function(){J.onError(Y,new q(G,"Search for Segmentation instances failed."))}))},a.addParametricMaps=function(){console.info("search for Parametric Map instances");var e=a.props.clients[M.PARAMETRIC_MAP];e.searchForSeries({studyInstanceUID:a.props.studyInstanceUID,queryParams:{Modality:"OT"}}).then((function(t){null==t&&(t=[]),t.forEach((function(t){var n=g.metadata.formatMetadata(t).dataset;e.retrieveSeriesMetadata({studyInstanceUID:a.props.studyInstanceUID,seriesInstanceUID:n.SeriesInstanceUID}).then((function(e){var t=[];if(e.forEach((function(e){var n=new g.metadata.ParametricMap({metadata:e}),i=a.props.slide.volumeImages[0];n.FrameOfReferenceUID===i.FrameOfReferenceUID&&n.ContainerIdentifier===i.ContainerIdentifier?t.push(n):console.warn('skip Parametric Map instance "'.concat(n.SOPInstanceUID,'"'))})),t.length>0){try{a.volumeViewer.addParameterMappings(t)}catch(n){J.onError(Y,new q(G,"Parametric Map cannot be displayed")),console.error("failed to add mappings: ",n)}a.forceUpdate()}})).catch((function(){J.onError(Y,new q(G,"Retrieval of metadata of Parametric Map instances failed."))}))}))})).catch((function(){J.onError(Y,new q(G,"Search for Parametric Map instances failed."))}))},a.populateViewports=function(){console.info("populate viewports..."),a.setState({isLoading:!0,presentationStates:[]}),null!=a.volumeViewportRef.current&&a.volumeViewer.render({container:a.volumeViewportRef.current}),null!=a.labelViewportRef.current&&null!=a.labelViewer&&a.labelViewer.render({container:a.labelViewportRef.current}),a.setState({isLoading:!1}),a.setDefaultPresentationState(),a.loadPresentationStates(),a.addAnnotations(),a.addAnnotationGroups(),a.addSegmentations(),a.addParametricMaps()},a.onRoiModified=function(e){a.setState((function(e){return{visibleRoiUIDs:new Set(e.visibleRoiUIDs)}}))},a.onWindowResize=function(e){console.info("resize viewports"),a.volumeViewer.resize(),null!=a.labelViewer&&a.labelViewer.resize()},a.onRoiDrawn=function(e){var t=e.detail.payload,n=a.state.selectedFinding,i=a.state.selectedEvaluations;if(void 0!==t&&void 0!==n){console.debug('add ROI "'.concat(t.uid,'"'));var o=new ve.sr.valueTypes.CodeContentItem({name:new ve.sr.coding.CodedConcept({value:"121071",meaning:"Finding",schemeDesignator:"DCM"}),value:n,relationshipType:"CONTAINS"});t.addEvaluation(o),i.forEach((function(e){var n=new ve.sr.valueTypes.CodeContentItem({name:e.name,value:e.value,relationshipType:"CONTAINS"});t.addEvaluation(n)}));var r=ot(n),s=a.getRoiStyle(r);a.volumeViewer.addROI(t,s),a.setState((function(e){var n=e.visibleRoiUIDs;return n.add(t.uid),{visibleRoiUIDs:n}}))}else console.debug('could not add ROI "'.concat(t.uid,'"'))},a.onRoiDoubleClicked=function(e){null!=e.detail.payload?a.setState({isSelectedRoiModalVisible:!0}):a.setState({isSelectedRoiModalVisible:!1})},a.onRoiSelected=function(e){var t=e.detail.payload;if(null!=t){console.debug('selected ROI "'.concat(t.uid,'"')),a.volumeViewer.setROIStyle(t.uid,a.selectedRoiStyle);var n=rt(t);a.volumeViewer.getAllROIs().forEach((function(e){e.uid!==t.uid&&a.volumeViewer.setROIStyle(e.uid,a.getRoiStyle(n))})),a.setState({selectedRoiUIDs:new Set([t.uid]),selectedRoi:t})}else a.setState({selectedRoiUIDs:new Set,selectedRoi:void 0})},a.onLoadingStarted=function(e){a.setState({isLoading:!0})},a.onLoadingEnded=function(e){a.setState({isLoading:!1})},a.onFrameLoadingStarted=function(e){var t=e.detail.payload,n="".concat(t.sopInstanceUID,"-").concat(t.frameNumber);a.setState((function(e){return e.loadingFrames.add(n),e}))},a.onFrameLoadingEnded=function(e){var t=e.detail.payload,n="".concat(t.sopInstanceUID,"-").concat(t.frameNumber);if(a.setState((function(e){e.loadingFrames.delete(n);var t=!1;return e.loadingFrames.size>0&&(t=!0),{isLoading:t,loadingFrames:e.loadingFrames}})),t.sopClassUID===M.VL_WHOLE_SLIDE_MICROSCOPY_IMAGE&&a.props.slide.areVolumeImagesMonochrome){var i=t.channelIdentifier;if(!(i in a.state.pixelDataStatistics)&&null!=t.pixelArray){for(var o=Math.pow(2,16),r=Math.ceil(t.pixelArray.length/o),s=0,l=[],c=[],d=0;d=n&&t<=i)return void this.setState({selectedXCoordinate:t,isSelectedXCoordinateValid:!0})}this.setState({selectedXCoordinate:void 0,isSelectedXCoordinateValid:!1})}},{key:"handleYCoordinateSelection",value:function(e){if(null!=e){var t=Number(e),n=this.state.validYCoordinateRange[0],i=this.state.validYCoordinateRange[1];if(t>=n&&t<=i)return void this.setState({selectedYCoordinate:t,isSelectedYCoordinateValid:!0})}this.setState({selectedYCoordinate:void 0,isSelectedYCoordinateValid:!1})}},{key:"handleMagnificationSelection",value:function(e){null!=e&&e>0&&e<=40?this.setState({selectedMagnification:Number(e),isSelectedMagnificationValid:!0}):this.setState({selectedMagnification:void 0,isSelectedMagnificationValid:!1})}},{key:"handleSlidePositionSelection",value:function(){if(this.state.isSelectedXCoordinateValid&&this.state.isSelectedYCoordinateValid&&this.state.isSelectedMagnificationValid&&null!=this.state.selectedXCoordinate&&null!=this.state.selectedYCoordinate&&null!=this.state.selectedMagnification){console.info("select slide position "+"(".concat(this.state.selectedXCoordinate,", ")+"".concat(this.state.selectedYCoordinate,") ")+"at ".concat(this.state.selectedMagnification,"x magnification"));for(var e=.01/this.state.selectedMagnification,t=[],n=0;n1&&J.onError(Y,new q(G,"More than one specimen has been described for the slide"));var a,o=i.SpecimenDescriptionSequence[0];console.debug("create Observation Context"),void 0!==this.props.user?a=new ve.sr.templates.PersonObserverIdentifyingAttributes({name:this.props.user.name,loginName:this.props.user.email}):(console.warn("no user information available"),a=new ve.sr.templates.PersonObserverIdentifyingAttributes({name:"ANONYMOUS"}));var r=new ve.sr.templates.ObservationContext({observerPersonContext:new ve.sr.templates.ObserverContext({observerType:new ve.sr.coding.CodedConcept({value:"121006",schemeDesignator:"DCM",meaning:"Person"}),observerIdentifyingAttributes:a}),observerDeviceContext:new ve.sr.templates.ObserverContext({observerType:new ve.sr.coding.CodedConcept({value:"121007",schemeDesignator:"DCM",meaning:"Device"}),observerIdentifyingAttributes:new ve.sr.templates.DeviceObserverIdentifyingAttributes({uid:this.props.app.uid,manufacturerName:"MGH Computational Pathology",modelName:this.props.app.name})}),subjectContext:new ve.sr.templates.SubjectContext({subjectClass:new ve.sr.coding.CodedConcept({value:"121027",schemeDesignator:"DCM",meaning:"Specimen"}),subjectClassSpecificContext:new ve.sr.templates.SubjectContextSpecimen({uid:o.SpecimenUID,identifier:o.SpecimenIdentifier,containerIdentifier:i.ContainerIdentifier})})});console.debug("encode Imaging Measurements");for(var s=[],l=0;l0?(this.state.selectedRoiUIDs.forEach((function(t){void 0!==t?(console.info('remove ROI "'.concat(t,'"')),e.volumeViewer.removeROI(t),u.ZP.info("Annotation was removed")):u.ZP.warning("No annotation was selected for removal")})),this.setState({selectedRoiUIDs:new Set,isRoiTranslationActive:!1,isRoiDrawingActive:!1,isRoiModificationActive:!1})):(this.state.visibleRoiUIDs.forEach((function(t){console.info('remove ROI "'.concat(t,'"')),e.volumeViewer.removeROI(t)})),this.setState({visibleRoiUIDs:new Set,isRoiTranslationActive:!1,isRoiDrawingActive:!1,isRoiModificationActive:!1})),this.volumeViewer.activateSelectInteraction({})}},{key:"handleRoiVisibilityChange",value:function(){var e=this;console.info("toggle visibility of 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nts/SpecimenList.tsx","components/OpticalPathItem.tsx","components/OpticalPathList.tsx","components/MappingItem.tsx","components/MappingList.tsx","components/SegmentItem.tsx","components/SegmentList.tsx","utils/router.tsx","components/SlideViewer.tsx","data/slides.tsx","components/CaseViewer.tsx","components/Header.tsx","components/InfoPage.tsx","components/Worklist.tsx","utils/url.tsx","auth/OidcManager.tsx","utils/xhrRetryHook.ts","DicomWebManager.ts","App.tsx"],"sourcesContent":["import React from 'react'\nimport { v4 as generateUUID } from 'uuid'\nimport { Card, Descriptions } from 'antd'\n\nexport interface Attribute {\n name: string\n value: any\n}\n\nexport interface AttributeGroup {\n name: string\n attributes: Attribute[]\n}\n\ninterface DescriptionProps {\n header?: string\n icon?: any\n attributes: Attribute[]\n selectable?: boolean\n hasLongValues?: boolean\n methods?: React.ReactNode[]\n children?: React.ReactNode\n}\n\n/**\n * React component for a description consisting of a header containing a\n * header and a body containing a list of name-value pairs.\n */\nclass Description extends React.Component {\n render (): React.ReactNode {\n let layout: 'horizontal' | 'vertical' = 'horizontal'\n let labelLineHeight = '14px'\n const contentLineHeight = '14px'\n if (this.props.hasLongValues !== undefined && this.props.hasLongValues) {\n layout = 'vertical'\n labelLineHeight = '20px'\n }\n const items = this.props.attributes.map((item: Attribute, index: number) => {\n const uid = generateUUID()\n return (\n \n {item.value}\n \n )\n })\n let icon = null\n if (this.props.icon !== undefined) {\n icon = \n }\n return (\n \n \n {items}\n \n {this.props.children}\n \n )\n }\n}\n\nexport default Description\n","import React from 'react'\nimport * as dmv from 'dicom-microscopy-viewer'\n\nimport Description from './Description'\n\ninterface ClinicalTrialProps {\n metadata: dmv.metadata.SOPClass\n}\n\n/**\n * React component representing a DICOM ClinicalTrial Information Entity that displays\n * common study-level attributes of contained DICOM Slide Microscopy images.\n */\nclass ClinicalTrial extends React.Component {\n render (): React.ReactNode {\n const attributes = []\n if (this.props.metadata.ClinicalTrialSponsorName != null) {\n // Attributes of Clinical Trial Subject module\n attributes.push(\n ...[\n {\n name: 'Sponsor Name',\n value: this.props.metadata.ClinicalTrialSponsorName\n },\n {\n name: 'Protocol ID',\n value: this.props.metadata.ClinicalTrialProtocolID\n },\n {\n name: 'Protocol Name',\n value: this.props.metadata.ClinicalTrialProtocolName\n },\n {\n name: 'Site Name',\n value: this.props.metadata.ClinicalTrialSiteName\n }\n ]\n )\n }\n if (this.props.metadata.ClinicalTrialTimePointID != null) {\n // Attributes of Clinical Trial Study module\n attributes.push(\n {\n name: 'Time Point ID',\n value: this.props.metadata.ClinicalTrialTimePointID\n }\n )\n }\n // Attributes of Clinical Trial Subject module\n return \n }\n}\n\nexport default ClinicalTrial\n","import * as dmv from 'dicom-microscopy-viewer'\n\nfunction parseName (value: dmv.metadata.PersonName|null|undefined): string {\n if (typeof value === 'object' && value !== null && value !== undefined) {\n if (value.Alphabetic !== undefined) {\n return value.Alphabetic.split('^').join(' ')\n }\n return ''\n }\n return ''\n}\n\nfunction parseDate (value: string|null|undefined): string {\n if (value !== null && value !== undefined) {\n const year = value.substring(0, 4)\n const month = value.substring(4, 6)\n const day = value.substring(6, 8)\n return `${year}-${month}-${day}`\n }\n return ''\n}\n\nfunction parseTime (value: string|null|undefined): string {\n if (value !== null && value !== undefined) {\n const hours = value.substring(0, 2)\n const minutes = value.substring(2, 4)\n const seconds = value.substring(4, 6)\n return `${hours}:${minutes}:${seconds}`\n }\n return ''\n}\n\nfunction parseDateTime (value: string|null|undefined): string {\n if (value !== null && value !== undefined) {\n const year = value.substring(0, 4)\n const month = value.substring(4, 6)\n const day = value.substring(6, 8)\n const hours = value.substring(8, 10)\n const minutes = value.substring(10, 12)\n const seconds = value.substring(12, 14)\n return `${year}-${month}-${day} ${hours}:${minutes}:${seconds}`\n }\n return ''\n}\n\nfunction parseSex (value: string|null|undefined): string {\n const lut: { [key: string]: string } = {\n F: 'Female',\n M: 'Male',\n O: 'Other'\n }\n if (value !== null && value !== undefined) {\n return lut[value]\n }\n return ''\n}\n\nexport { parseDate, parseDateTime, parseName, parseSex, parseTime }\n","import React from 'react'\nimport * as dmv from 'dicom-microscopy-viewer'\n\nimport Description from './Description'\nimport { parseName, parseSex, parseDate } from '../utils/values'\n\ninterface PatientProps {\n metadata: dmv.metadata.Study|dmv.metadata.SOPClass\n}\n\n/**\n * React component representing a DICOM Patient Information Entity that\n * displays common study-level, patient-related attributes of contained\n * DICOM Slide Microscopy images.\n */\nclass Patient extends React.Component {\n render (): React.ReactNode {\n const attributes = [\n {\n name: 'ID',\n value: this.props.metadata.PatientID\n },\n {\n name: 'Name',\n value: parseName(this.props.metadata.PatientName)\n },\n {\n name: 'Gender',\n value: parseSex(this.props.metadata.PatientSex)\n },\n {\n name: 'Birthdate',\n value: parseDate(this.props.metadata.PatientBirthDate)\n }\n ]\n return (\n \n )\n }\n}\n\nexport default Patient\n","import React from 'react'\nimport * as dmv from 'dicom-microscopy-viewer'\n\nimport Description from './Description'\nimport { parseDate, parseTime } from '../utils/values'\n\ninterface StudyProps {\n metadata: dmv.metadata.Study|dmv.metadata.SOPClass\n}\n\n/**\n * React component representing a DICOM Study Information Entity that displays\n * common study-level attributes of contained DICOM Slide Microscopy images.\n */\nclass Study extends React.Component {\n render (): React.ReactNode {\n const attributes = [\n {\n name: 'Accession #',\n value: this.props.metadata.AccessionNumber\n },\n {\n name: 'ID',\n value: this.props.metadata.StudyID\n },\n {\n name: 'Date',\n value: parseDate(this.props.metadata.StudyDate)\n },\n {\n name: 'Time',\n value: parseTime(this.props.metadata.StudyTime)\n }\n ]\n return \n }\n}\n\nexport default Study\n","export enum StorageClasses {\n VL_WHOLE_SLIDE_MICROSCOPY_IMAGE = '1.2.840.10008.5.1.4.1.1.77.1.6',\n COMPREHENSIVE_SR = '1.2.840.10008.5.1.4.1.1.88.33',\n COMPREHENSIVE_3D_SR = '1.2.840.10008.5.1.4.1.1.88.34',\n SEGMENTATION = '1.2.840.10008.5.1.4.1.1.66.4',\n MICROSCOPY_BULK_SIMPLE_ANNOTATION = '1.2.840.10008.5.1.4.1.1.91.1',\n PARAMETRIC_MAP = '1.2.840.10008.5.1.4.1.1.30',\n ADVANCED_BLENDING_PRESENTATION_STATE = '1.2.840.10008.5.1.4.1.1.11.8',\n COLOR_SOFTCOPY_PRESENTATION_STATE = '1.2.840.10008.5.1.4.1.1.11.2',\n GRAYSCALE_SOFTCOPY_PRESENTATION_STATE = '1.2.840.10008.5.1.4.1.1.11.1',\n PSEUDOCOLOR_SOFTCOPY_PRESENTATION_STATE = '1.2.840.10008.5.1.4.1.1.11.3'\n}\n","// Use symbols to prevent exposing private attributes\nconst _subscriptions = Symbol('subscriptions')\nconst _lastSubscriptionId = Symbol('lastSubscriptionId')\n\n/**\n * Class to enable implementation of publish/subscribe pattern\n * @class\n * @classdesc Enables publishing/subscribing\n */\nexport default class PubSub {\n constructor () {\n this[_subscriptions] = {}\n this[_lastSubscriptionId] = 0\n }\n\n /**\n * Adds a subscription callback to the provided event name\n * @param {string} eventName Event name that will trigger the callback\n * @param {Function} callback Function to be executed when event is published\n * @returns {void}\n */\n subscribe (eventName, callback) {\n if (eventName === undefined) {\n throw new Error('Trying to subscribe to an inexistent event')\n }\n\n if (typeof callback !== 'function') {\n throw new Error('The provided callback must be a function')\n }\n\n if (!this[_subscriptions].hasOwnProperty(eventName)) {\n this[_subscriptions][eventName] = {}\n }\n\n const subscriptionId = `sub${this[_lastSubscriptionId]++}`\n this[_subscriptions][eventName][subscriptionId] = callback\n }\n\n /**\n * Removes a subscription callback for the provided event name\n * @param {string} eventName Event name for the registerd callback\n * @param {Function} [callback] Function to have its subscription removed\n * @returns {void}\n */\n unsubscribe (eventName, callback) {\n const callbacks = this[_subscriptions][eventName] || {}\n for (const subscriptionId in callbacks) {\n if (!callback) {\n delete callbacks[subscriptionId]\n } else if (callbacks[subscriptionId] === callback) {\n delete callbacks[subscriptionId]\n }\n }\n }\n\n /**\n * Trigger all registered subscription callbacks for a specific event name\n * @param {String} eventName Event name to trigger subscriptions from\n * @param {any} [payload] Payload that will be passed to the callback fuction\n * @returns {void}\n */\n publish (eventName, ...payload) {\n if (eventName === undefined) {\n throw new Error('Trying to publish an inexistent event')\n }\n\n const callbacks = this[_subscriptions][eventName] || {}\n for (const subscriptionId in callbacks) {\n callbacks[subscriptionId](...payload)\n }\n }\n\n /**\n * Cleares all subscriptions for current instance\n * @returns {void}\n */\n unsubscribeFromAll () {\n for (const eventName in this[_subscriptions]) {\n const callbacks = this[_subscriptions][eventName]\n for (const subscriptionId in callbacks) {\n delete callbacks[subscriptionId]\n }\n }\n }\n}\n","const errorTypes = {\n AUTHENTICATION: 'Authentication',\n COMMUNICATION: 'Communication',\n ENCODINGANDDECODING: 'EncodingDecoding',\n VISUALIZATION: 'Visualization'\n}\n\nclass CustomError extends Error {\n constructor (type, message) {\n super()\n this.message = message\n this.stack = new Error().stack\n this.type = type\n }\n}\n\nexport { errorTypes, CustomError }\n","import PubSub from '../utils/PubSub'\nimport { notification } from 'antd'\nimport { CustomError, errorTypes } from '../utils/CustomError'\n\nexport const NotificationMiddlewareEvents = {\n OnError: 'onError'\n}\n\nexport const NotificationMiddlewareContext = {\n DICOMWEB: 'dicomweb-client',\n DMV: 'dicom-microscopy-viewer',\n DCMJS: 'dcmjs',\n SLIM: 'slim',\n AUTH: 'authentication'\n}\n\nconst NotificationType = {\n TOAST: 'toast',\n CONSOLE: 'console'\n}\n\n/* Sources of Error:\n 1. 'dicomweb-client': Error while requesting/fetching data, tagged as 'Communication'\n 2. 'slim' and 'dicom-microscopy-viewer' library: Error related to dicom data encoding/decoding,\n could directly/indirectly impact image-related visualization, tagged as 'Visualization' or\n 'Encoding/Decoding' accordingly\n 3. 'dcmjs' library: Data parsing error, tagged as 'DICOMError'\n 4. 'authentication': Error during user authentication, tagged as 'Authentication'\n */\nconst NotificationSourceDefinition = {\n sources: [\n {\n category: errorTypes.AUTHENTICATION,\n notificationType: NotificationType.TOAST\n },\n {\n category: errorTypes.COMMUNICATION,\n notificationType: NotificationType.TOAST\n },\n {\n category: errorTypes.VISUALIZATION,\n notificationType: NotificationType.TOAST\n },\n {\n category: errorTypes.ENCODINGANDDECODING,\n notificationType: NotificationType.CONSOLE\n }\n ]\n}\n\nclass NotificationMiddleware extends PubSub {\n /**\n * Error handling middleware function\n *\n * @param source - source of error - dicomweb-client, dmv, dcmjs or slim itself\n * @param error - error object\n */\n onError (source, error) {\n const errorCategory = error.type\n const sourceConfig = NotificationSourceDefinition.sources.find(\n s => s.category === errorCategory\n )\n const { notificationType } = sourceConfig\n\n this.publish(NotificationMiddlewareEvents.OnError, {\n source,\n error\n })\n\n let notificationMsg\n if (error instanceof CustomError) {\n notificationMsg = error.message\n } else {\n notificationMsg = String(error)\n }\n\n switch (notificationType) {\n case NotificationType.TOAST:\n console.error(`A ${errorCategory} error occurred: `, error)\n return notification.error({\n message: `${errorCategory} error`,\n description: notificationMsg,\n duration: 3\n })\n\n case NotificationType.CONSOLE:\n console.error(`A ${errorCategory} error occurred: `, error)\n break\n\n default:\n }\n }\n}\n\nexport default new NotificationMiddleware()\n","import React from 'react'\nimport { FaSpinner } from 'react-icons/fa'\nimport * as dmv from 'dicom-microscopy-viewer'\nimport { Menu } from 'antd'\n\nimport DicomWebManager from '../DicomWebManager'\nimport Description from './Description'\nimport { Slide } from '../data/slides'\nimport { StorageClasses } from '../data/uids'\nimport NotificationMiddleware, {\n NotificationMiddlewareContext\n} from '../services/NotificationMiddleware'\nimport { CustomError } from '../utils/CustomError'\n\ninterface SlideItemProps {\n clients: { [key: string]: DicomWebManager }\n slide: Slide\n}\n\ninterface SlideItemState {\n isLoading: boolean\n}\n\n/**\n * React component representing a DICOM Series Information Entity that displays\n * common series-level attributes of contained DICOM Slide Microscopy images\n * as well as the OVERVIEW image (if available).\n * When selected a Slide Viewer instance is created for the display of the\n * contained images.\n */\nclass SlideItem extends React.Component {\n state = { isLoading: false }\n\n private readonly overviewViewportRef = React.createRef()\n\n private overviewViewer?: dmv.viewer.OverviewImageViewer\n\n constructor (props: SlideItemProps) {\n super(props)\n this.overviewViewer = undefined\n }\n\n componentDidMount (): void {\n this.setState({ isLoading: true })\n if (this.props.slide.overviewImages.length > 0) {\n const metadata = this.props.slide.overviewImages[0]\n if (this.overviewViewportRef.current !== null) {\n this.overviewViewportRef.current.innerHTML = ''\n console.info(\n 'instantiate viewer for OVERVIEW image of slide ' +\n `\"${metadata.ContainerIdentifier}\"`\n )\n this.overviewViewer = new dmv.viewer.OverviewImageViewer({\n client: this.props.clients[\n StorageClasses.VL_WHOLE_SLIDE_MICROSCOPY_IMAGE\n ],\n metadata: metadata,\n resizeFactor: 1,\n errorInterceptor: (error: CustomError) =>\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.DMV,\n error\n )\n })\n this.overviewViewer.render({\n container: this.overviewViewportRef.current\n })\n }\n }\n\n this.setState({ isLoading: false })\n }\n\n render (): React.ReactNode {\n if (this.overviewViewer !== undefined) {\n this.overviewViewer.resize()\n }\n const attributes = []\n const description = this.props.slide.description\n if (description != null && description !== '') {\n attributes.push({\n name: 'Description',\n value: description\n })\n }\n if (this.state.isLoading) {\n return ()\n }\n\n /* Properties need to be propagated down to Menu.Item:\n * https://github.com/react-component/menu/issues/142\n */\n return (\n \n \n
\n \n \n )\n }\n}\n\nexport default SlideItem\n","import React from 'react'\nimport { Menu } from 'antd'\n\nimport DicomWebManager from '../DicomWebManager'\nimport SlideItem from './SlideItem'\nimport { Slide } from '../data/slides'\n\ninterface SlideListProps {\n metadata: Slide[]\n clients: { [key: string]: DicomWebManager }\n selectedSeriesInstanceUID: string\n onSeriesSelection: (\n { seriesInstanceUID }: { seriesInstanceUID: string }\n ) => void\n}\n\ninterface SlideListState {\n selectedSeriesInstanceUID: string\n}\n\n/**\n * React component representing a list of DICOM Series Information Entities.\n */\nclass SlideList extends React.Component {\n state = {\n selectedSeriesInstanceUID: this.props.selectedSeriesInstanceUID\n }\n\n componentDidMount (): void {\n this.props.onSeriesSelection({\n seriesInstanceUID: this.state.selectedSeriesInstanceUID\n })\n }\n\n render (): React.ReactNode {\n const slideList = this.props.metadata\n const slideItemList = []\n for (let i = 0; i < slideList.length; ++i) {\n const slide = slideList[i]\n const slideItem = (\n \n )\n\n slideItemList.push(slideItem)\n }\n\n const handleMenuItemSelection = ({ key, keyPath, domEvent, selectedKeys }: {\n key: React.ReactText\n keyPath: React.ReactText[]\n domEvent: React.MouseEvent | React.KeyboardEvent\n selectedKeys?: React.ReactText[]\n }): void => {\n console.info(`select slide \"${key}\"`)\n this.setState({ selectedSeriesInstanceUID: key.toString() })\n this.props.onSeriesSelection({ seriesInstanceUID: key.toString() })\n }\n\n let selectedKeys\n if (this.state.selectedSeriesInstanceUID !== undefined &&\n this.state.selectedSeriesInstanceUID !== null) {\n selectedKeys = [this.state.selectedSeriesInstanceUID]\n }\n\n return (\n \n {slideItemList}\n \n )\n }\n}\n\nexport default SlideList\n","import React from 'react'\nimport * as dmv from 'dicom-microscopy-viewer'\nimport * as dcmjs from 'dcmjs'\nimport { Menu, Space, Switch } from 'antd'\nimport { FaEye, FaEyeSlash } from 'react-icons/fa'\n\nimport Description from './Description'\n\ninterface AnnotationItemProps {\n roi: dmv.roi.ROI\n index: number\n isVisible: boolean\n onVisibilityChange: ({ roiUID, isVisible }: {\n roiUID: string\n isVisible: boolean\n }) => void\n}\n\n/**\n * React component representing a Region of Interest (ROI) annotation.\n */\nclass AnnotationItem extends React.Component {\n constructor (props: AnnotationItemProps) {\n super(props)\n this.handleVisibilityChange = this.handleVisibilityChange.bind(this)\n }\n\n handleVisibilityChange (\n checked: boolean,\n event: React.MouseEvent\n ): void {\n this.props.onVisibilityChange({\n roiUID: this.props.roi.uid,\n isVisible: checked\n })\n }\n\n render (): React.ReactNode {\n const identifier = `ROI ${this.props.index + 1}`\n const attributes: Array<{ name: string, value: string }> = []\n /**\n * This hack is required for Menu.Item to work properly:\n * https://github.com/react-component/menu/issues/142\n */\n const { isVisible, onVisibilityChange, ...otherProps } = this.props\n this.props.roi.evaluations.forEach((\n item: (\n dcmjs.sr.valueTypes.TextContentItem |\n dcmjs.sr.valueTypes.CodeContentItem\n )\n ) => {\n const nameValue = item.ConceptNameCodeSequence[0].CodeValue\n const nameMeaning = item.ConceptNameCodeSequence[0].CodeMeaning\n const name = `${nameMeaning}`\n if (item.ValueType === dcmjs.sr.valueTypes.ValueTypes.CODE) {\n const codeContentItem = item as dcmjs.sr.valueTypes.CodeContentItem\n const valueMeaning = codeContentItem.ConceptCodeSequence[0].CodeMeaning\n // For consistency with Segment and Annotation Group\n if (nameValue === '276214006') {\n attributes.push({\n name: 'Property category',\n value: `${valueMeaning}`\n })\n } else if (nameValue === '121071') {\n attributes.push({\n name: 'Property type',\n value: `${valueMeaning}`\n })\n } else if (nameValue === '111001') {\n attributes.push({\n name: 'Algorithm Name',\n value: `${valueMeaning}`\n })\n } else {\n attributes.push({\n name: name,\n value: `${valueMeaning}`\n })\n }\n } else if (item.ValueType === dcmjs.sr.valueTypes.ValueTypes.TEXT) {\n const textContentItem = item as dcmjs.sr.valueTypes.TextContentItem\n attributes.push({\n name: name,\n value: textContentItem.TextValue\n })\n }\n })\n this.props.roi.measurements.forEach(item => {\n const nameMeaning = item.ConceptNameCodeSequence[0].CodeMeaning\n const name = `${nameMeaning}`\n const seq = item.MeasuredValueSequence[0]\n const value = seq.NumericValue.toPrecision(6)\n const unit = seq.MeasurementUnitsCodeSequence[0].CodeValue\n attributes.push({\n name: name,\n value: `${value} ${unit}`\n })\n })\n return (\n \n
\n }\n unCheckedChildren={}\n />\n
\n \n \n \n \n )\n }\n}\n\nexport default AnnotationItem\n","import React from 'react'\nimport * as dmv from 'dicom-microscopy-viewer'\nimport { Menu, Switch } from 'antd'\nimport { FaEye, FaEyeSlash } from 'react-icons/fa'\n\nimport AnnotationItem from './AnnotationItem'\n\ninterface AnnotationListProps {\n rois: dmv.roi.ROI[]\n selectedRoiUIDs: Set\n visibleRoiUIDs: Set\n onVisibilityChange: ({ roiUID, isVisible }: {\n roiUID: string\n isVisible: boolean\n }) => void\n onSelection: ({ roiUID }: { roiUID: string }) => void\n}\n\n/**\n * React component representing a list of Region of Interest (ROI)\n * annotations.\n */\nclass AnnotationList extends React.Component {\n constructor (props: AnnotationListProps) {\n super(props)\n this.handleMenuItemSelection = this.handleMenuItemSelection.bind(this)\n this.handleVisibilityChange = this.handleVisibilityChange.bind(this)\n }\n\n handleVisibilityChange (\n checked: boolean,\n event: React.MouseEvent\n ): void {\n if (checked) {\n this.props.rois.forEach(roi => {\n this.props.onVisibilityChange({ roiUID: roi.uid, isVisible: checked })\n })\n } else {\n this.props.visibleRoiUIDs.forEach(roiUID => {\n this.props.onVisibilityChange({ roiUID, isVisible: checked })\n })\n }\n }\n\n handleMenuItemSelection (object: any): void {\n this.props.onSelection({ roiUID: object.key })\n }\n\n render (): React.ReactNode {\n const items = this.props.rois.map((roi, index) => (\n \n ))\n\n return (\n <>\n
\n 0}\n checkedChildren={}\n unCheckedChildren={}\n />\n
\n \n {items}\n \n \n )\n }\n}\n\nexport default AnnotationList\n","import React from 'react'\nimport {\n Badge,\n Button,\n Col,\n Divider,\n InputNumber,\n Menu,\n Popover,\n Row,\n Select,\n Slider,\n Space,\n Switch\n} from 'antd'\nimport { SettingOutlined } from '@ant-design/icons'\nimport { FaEye, FaEyeSlash } from 'react-icons/fa'\nimport * as dmv from 'dicom-microscopy-viewer'\nimport * as dcmjs from 'dcmjs'\n\nimport Description from './Description'\n\ninterface AnnotationGroupItemProps {\n annotationGroup: dmv.annotation.AnnotationGroup\n isVisible: boolean\n metadata: dmv.metadata.MicroscopyBulkSimpleAnnotations\n defaultStyle: {\n opacity: number\n color: number[]\n }\n onVisibilityChange: ({ annotationGroupUID, isVisible }: {\n annotationGroupUID: string\n isVisible: boolean\n }) => void\n onStyleChange: ({ annotationGroupUID, styleOptions }: {\n annotationGroupUID: string\n styleOptions: {\n opacity?: number\n color?: number[]\n limitValues?: number[]\n measurement?: dcmjs.sr.coding.CodedConcept\n }\n }) => void\n}\n\ninterface AnnotationGroupItemState {\n isVisible: boolean\n currentStyle: {\n opacity: number\n color?: number[]\n limitValues?: number[]\n measurement?: dcmjs.sr.coding.CodedConcept\n }\n}\n\n/**\n * React component representing an Annotation Group.\n */\nclass AnnotationGroupItem extends React.Component {\n constructor (props: AnnotationGroupItemProps) {\n super(props)\n this.handleVisibilityChange = this.handleVisibilityChange.bind(this)\n this.handleMeasurementSelection = this.handleMeasurementSelection.bind(this)\n this.handleOpacityChange = this.handleOpacityChange.bind(this)\n this.handleColorRChange = this.handleColorRChange.bind(this)\n this.handleColorGChange = this.handleColorGChange.bind(this)\n this.handleColorBChange = this.handleColorBChange.bind(this)\n this.getCurrentColor = this.getCurrentColor.bind(this)\n this.state = {\n isVisible: this.props.isVisible,\n currentStyle: {\n opacity: this.props.defaultStyle.opacity,\n color: this.props.defaultStyle.color\n }\n }\n }\n\n handleVisibilityChange (\n checked: boolean,\n event: React.MouseEvent\n ): void {\n this.props.onVisibilityChange({\n annotationGroupUID: this.props.annotationGroup.uid,\n isVisible: checked\n })\n this.setState({ isVisible: checked })\n }\n\n handleOpacityChange (value: number | null): void {\n if (value != null) {\n this.props.onStyleChange({\n annotationGroupUID: this.props.annotationGroup.uid,\n styleOptions: {\n opacity: value\n }\n })\n this.setState({\n currentStyle: {\n opacity: value,\n color: this.state.currentStyle.color,\n limitValues: this.state.currentStyle.limitValues\n }\n })\n }\n }\n\n handleColorRChange (\n value: number | number[] | null\n ): void {\n if (value != null && this.state.currentStyle.color !== undefined) {\n const color = [\n Array.isArray(value) ? value[0] : value,\n this.state.currentStyle.color[1],\n this.state.currentStyle.color[2]\n ]\n this.setState(state => ({\n currentStyle: {\n color: color,\n opacity: state.currentStyle.opacity,\n limitValues: state.currentStyle.limitValues\n }\n }))\n this.props.onStyleChange({\n annotationGroupUID: this.props.annotationGroup.uid,\n styleOptions: { color: color }\n })\n }\n }\n\n handleColorGChange (\n value: number | number[] | null\n ): void {\n if (value != null && this.state.currentStyle.color !== undefined) {\n const color = [\n this.state.currentStyle.color[0],\n Array.isArray(value) ? value[0] : value,\n this.state.currentStyle.color[2]\n ]\n this.setState(state => ({\n currentStyle: {\n color: color,\n opacity: state.currentStyle.opacity,\n limitValues: state.currentStyle.limitValues\n }\n }))\n this.props.onStyleChange({\n annotationGroupUID: this.props.annotationGroup.uid,\n styleOptions: { color: color }\n })\n }\n }\n\n handleColorBChange (\n value: number | number[] | null\n ): void {\n if (value != null && this.state.currentStyle.color !== undefined) {\n const color = [\n this.state.currentStyle.color[0],\n this.state.currentStyle.color[1],\n Array.isArray(value) ? value[0] : value\n ]\n this.setState(state => ({\n currentStyle: {\n color: color,\n opacity: state.currentStyle.opacity,\n limitValues: state.currentStyle.limitValues\n }\n }))\n this.props.onStyleChange({\n annotationGroupUID: this.props.annotationGroup.uid,\n styleOptions: { color: color }\n })\n }\n }\n\n getCurrentColor (): string {\n const rgb2hex = (values: number[]): string => {\n const r = values[0]\n const g = values[1]\n const b = values[2]\n return '#' + (0x1000000 + (r << 16) + (g << 8) + b).toString(16).slice(1)\n }\n\n if (this.state.currentStyle.color != null) {\n return rgb2hex(this.state.currentStyle.color)\n } else {\n return 'white'\n }\n }\n\n handleLowerLimitChange (\n value: number | null\n ): void {\n if (value != null && this.state.currentStyle.limitValues !== undefined) {\n this.setState(state => {\n if (state.currentStyle.limitValues !== undefined) {\n return {\n currentStyle: {\n color: state.currentStyle.color,\n opacity: state.currentStyle.opacity,\n limitValues: [value, state.currentStyle.limitValues[1]]\n }\n }\n } else {\n return {\n currentStyle: {\n color: state.currentStyle.color,\n opacity: state.currentStyle.opacity,\n limitValues: state.currentStyle.limitValues\n }\n }\n }\n })\n this.props.onStyleChange({\n annotationGroupUID: this.props.annotationGroup.uid,\n styleOptions: {\n limitValues: [\n value,\n this.state.currentStyle.limitValues[1]\n ]\n }\n })\n }\n }\n\n handleUpperLimitChange (\n value: number | null\n ): void {\n if (value != null && this.state.currentStyle.limitValues !== undefined) {\n this.setState(state => {\n if (state.currentStyle.limitValues !== undefined) {\n return {\n currentStyle: {\n color: state.currentStyle.color,\n opacity: state.currentStyle.opacity,\n limitValues: [state.currentStyle.limitValues[0], value]\n }\n }\n } else {\n return {\n currentStyle: {\n color: state.currentStyle.color,\n opacity: state.currentStyle.opacity,\n limitValues: state.currentStyle.limitValues\n }\n }\n }\n })\n this.props.onStyleChange({\n annotationGroupUID: this.props.annotationGroup.uid,\n styleOptions: {\n limitValues: [\n this.state.currentStyle.limitValues[0],\n value\n ]\n }\n })\n }\n }\n\n handleLimitChange (\n values: number[]\n ): void {\n this.setState(state => ({\n currentStyle: {\n color: state.currentStyle.color,\n opacity: state.currentStyle.opacity,\n limitValues: values\n }\n }))\n this.props.onStyleChange({\n annotationGroupUID: this.props.annotationGroup.uid,\n styleOptions: { limitValues: values }\n })\n }\n\n handleMeasurementSelection (value?: string, option?: any): void {\n if (value != null && option.children != null) {\n const codeComponents = value.split('-')\n const measurement = new dcmjs.sr.coding.CodedConcept({\n value: codeComponents[1],\n schemeDesignator: codeComponents[0],\n meaning: option.children\n })\n this.props.onStyleChange({\n annotationGroupUID: this.props.annotationGroup.uid,\n styleOptions: { measurement }\n })\n this.setState(state => ({\n currentStyle: {\n opacity: state.currentStyle.opacity,\n measurement\n }\n }))\n } else {\n this.props.onStyleChange({\n annotationGroupUID: this.props.annotationGroup.uid,\n styleOptions: {\n color: this.props.defaultStyle.color\n }\n })\n this.setState(state => ({\n currentStyle: {\n opacity: state.currentStyle.opacity,\n color: this.props.defaultStyle.color,\n limitValues: undefined\n }\n }))\n }\n }\n\n render (): React.ReactNode {\n const index = this.props.metadata.AnnotationGroupSequence.findIndex(\n item => (item.AnnotationGroupUID === this.props.annotationGroup.uid)\n )\n const item = this.props.metadata.AnnotationGroupSequence[index]\n const attributes: Array<{ name: string, value: string }> = [\n {\n name: 'Property type',\n value: this.props.annotationGroup.propertyType.CodeMeaning\n },\n {\n name: 'Property category',\n value: this.props.annotationGroup.propertyCategory.CodeMeaning\n },\n // {\n // name: 'Algorithm Name',\n // value: this.props.annotationGroup.algorithmName\n // },\n {\n name: 'Graphic type',\n value: item.GraphicType\n }\n ]\n\n const measurementsSequence = item.MeasurementsSequence ?? []\n const measurementOptions = measurementsSequence.map((measurementItem, i) => {\n const name = measurementItem.ConceptNameCodeSequence[0]\n return (\n \n {name.CodeMeaning}\n \n )\n })\n measurementOptions.push(\n \n {}\n \n )\n\n let colorSettings\n if (this.state.currentStyle.color != null) {\n colorSettings = (\n <>\n \n Color\n \n \n \n Red\n \n \n \n \n \n \n \n \n\n \n \n Green\n \n \n \n \n \n \n \n \n\n \n \n Blue\n \n \n \n \n \n \n \n \n \n \n )\n }\n\n let windowSettings\n let explorationSettings\n if (measurementsSequence.length > 0) {\n if (this.state.currentStyle.limitValues != null) {\n // TODO: need to get default min/max values from viewer first\n const minValue = 0\n const maxValue = 1000\n windowSettings = (\n <>\n \n Values of interest\n \n \n \n \n \n \n \n \n \n \n \n \n \n )\n }\n explorationSettings = (\n <>\n \n Exploration\n \n \n \n Measurement\n \n \n \n {measurementOptions}\n \n \n \n \n )\n }\n\n const settings = (\n
\n {colorSettings}\n {windowSettings}\n \n \n Opacity\n \n \n \n \n \n \n \n \n {explorationSettings}\n
\n )\n\n const color = this.getCurrentColor()\n const isBadgeVisible = (\n this.state.isVisible && this.state.currentStyle.measurement == null\n )\n const {\n annotationGroup,\n defaultStyle,\n isVisible,\n metadata,\n onVisibilityChange,\n onStyleChange,\n ...otherProps\n } = this.props\n return (\n \n \n
\n \n }\n unCheckedChildren={}\n />\n \n }\n />\n \n \n
\n \n \n \n \n \n )\n }\n}\n\nexport default AnnotationGroupItem\n","import React from 'react'\nimport { Menu } from 'antd'\nimport * as dmv from 'dicom-microscopy-viewer'\nimport * as dcmjs from 'dcmjs'\n\nimport AnnotationGroupItem from './AnnotationGroupItem'\n\ninterface AnnotationGroupListProps {\n annotationGroups: dmv.annotation.AnnotationGroup[]\n visibleAnnotationGroupUIDs: Set\n metadata: {\n [annotationGroupUID: string]: dmv.metadata.MicroscopyBulkSimpleAnnotations\n }\n defaultAnnotationGroupStyles: {\n [annotationGroupUID: string]: {\n opacity: number\n color: number[]\n }\n }\n onAnnotationGroupVisibilityChange: ({ annotationGroupUID, isVisible }: {\n annotationGroupUID: string\n isVisible: boolean\n }) => void\n onAnnotationGroupStyleChange: ({ annotationGroupUID, styleOptions }: {\n annotationGroupUID: string\n styleOptions: {\n opacity?: number\n color?: number[]\n measurement?: dcmjs.sr.coding.CodedConcept\n }\n }) => void\n}\n\n/**\n * React component representing a list of Annotation Groups.\n */\nclass AnnotationGroupList extends React.Component {\n render (): React.ReactNode {\n const items = this.props.annotationGroups.map((annotationGroup, index) => {\n const uid = annotationGroup.uid\n return (\n \n )\n })\n\n return (\n \n {items}\n \n )\n }\n}\n\nexport default AnnotationGroupList\n","import React from 'react'\nimport { Button as Btn, Divider, Tooltip } from 'antd'\n\ninterface ButtonProps {\n icon: any\n tooltip?: string\n label?: string\n onClick?: (options: any) => void\n isSelected?: boolean\n}\n\n/**\n * React component for a button.\n */\nclass Button extends React.Component {\n constructor (props: ButtonProps) {\n super(props)\n this.handleClick = this.handleClick.bind(this)\n }\n\n handleClick (event: React.SyntheticEvent): void {\n if (this.props.onClick !== undefined) {\n this.props.onClick(event)\n }\n }\n\n render (): React.ReactNode {\n const Icon = this.props.icon\n if (Icon === undefined) {\n return null\n }\n\n let text\n if (this.props.label != null) {\n text = (\n <>\n \n {this.props.label}\n \n )\n }\n\n let button\n if (this.props.isSelected ?? false) {\n button = (\n }\n type='primary'\n style={{ lineHeight: '1.0' }}\n >\n {text}\n \n )\n } else {\n button = (\n }\n type='default'\n style={{ lineHeight: '1.0' }}\n >\n {text}\n \n )\n }\n\n if (this.props.tooltip !== undefined) {\n return (\n \n {button}\n \n )\n } else {\n return button\n }\n }\n}\n\nexport default Button\n","import React from 'react'\nimport * as dmv from 'dicom-microscopy-viewer'\n\nimport Description from './Description'\n\ninterface EquipmentProps {\n metadata?: dmv.metadata.VLWholeSlideMicroscopyImage\n}\n\n/**\n * React component representing a list of DICOM Equipment Entities.\n */\nclass Equipment extends React.Component {\n render (): React.ReactNode {\n if (this.props.metadata === undefined) {\n return null\n }\n const attributes = [\n {\n name: 'Manufacturer',\n value: this.props.metadata.Manufacturer\n },\n {\n name: 'Model Name',\n value: this.props.metadata.ManufacturerModelName\n },\n {\n name: 'Device Serial Number',\n value: this.props.metadata.DeviceSerialNumber\n },\n {\n name: 'Software Versions',\n value: this.props.metadata.SoftwareVersions\n }\n ]\n if (this.props.metadata.InstitutionName != null) {\n attributes.push({\n name: 'Institution Name',\n value: this.props.metadata.InstitutionName\n })\n }\n return \n }\n}\n\nexport default Equipment\n","import * as dcmjs from 'dcmjs'\n\n/**\n * Check whether a DICOM SR content item has a given name.\n *\n * @param item - Content item\n * @param name - Coded name that should be compared\n * @returns Whether the content item has the given name\n */\nconst hasName = (\n item: dcmjs.sr.valueTypes.ContentItem,\n name: dcmjs.sr.coding.CodedConcept\n): boolean => {\n const concept = item.ConceptNameCodeSequence[0]\n return (\n concept.CodeValue === name.CodeValue &&\n concept.CodingSchemeDesignator === name.CodingSchemeDesignator\n )\n}\n\n/**\n * Check whether a DICOM SR content item has a given value type.\n *\n * @param item - Content item\n * @param valueType - Value Type\n * @returns Whether the content item has the given value type\n */\nconst hasValueType = (\n item: dcmjs.sr.valueTypes.ContentItem,\n valueType: dcmjs.sr.valueTypes.ValueTypes\n): boolean => {\n console.log(item.ValueType, valueType)\n return item.ValueType === valueType\n}\n\n/**\n * Find content items in a DICOM SR document given their name.\n *\n * Only finds content items at the root level, but not any nested content items.\n *\n * @param content - Document content, i.e., sequence of content items\n * @param name - Coded name that should be compared\n * @returns Matched content items\n */\nexport const findContentItemsByName = (\n { content, name }: {\n content: dcmjs.sr.valueTypes.ContentItem[]\n name: dcmjs.sr.coding.CodedConcept\n }\n): dcmjs.sr.valueTypes.ContentItem[] => {\n const items: dcmjs.sr.valueTypes.ContentItem[] = []\n content.forEach(i => {\n if (hasName(i, name)) {\n items.push(i)\n }\n })\n return items\n}\n\n/**\n * Find content items in a DICOM SR document given their value type.\n *\n * Only finds content items at the root level, but not any nested content items.\n *\n * @param content - Document content, i.e., sequence of content items\n * @param valueType - Value Type\n * @returns Matched content items\n */\nexport const findContentItemsByValueType = (\n { content, valueType }: {\n content: dcmjs.sr.valueTypes.ContentItem[]\n valueType: dcmjs.sr.valueTypes.ValueTypes\n }\n): dcmjs.sr.valueTypes.ContentItem[] => {\n const items: dcmjs.sr.valueTypes.ContentItem[] = []\n content.forEach(i => {\n if (hasValueType(i, valueType)) {\n items.push(i)\n }\n })\n return items\n}\n","import React from 'react'\nimport * as dmv from 'dicom-microscopy-viewer'\nimport * as dcmjs from 'dcmjs'\nimport { Divider } from 'antd'\nimport { v4 as generateUUID } from 'uuid'\n\nimport Description from './Description'\nimport Patient from './Patient'\nimport Study from './Study'\nimport { findContentItemsByName } from '../utils/sr'\nimport { CustomError, errorTypes } from '../utils/CustomError'\nimport NotificationMiddleware, {\n NotificationMiddlewareContext\n} from '../services/NotificationMiddleware'\n\nexport const hasValueType = (\n item: dcmjs.sr.valueTypes.ContentItem,\n valueType: string\n): boolean => {\n return item.ValueType === valueType\n}\n\nconst findMeasurementItems = (\n { content }: { content: dcmjs.sr.valueTypes.ContentItem[] }\n): dcmjs.sr.valueTypes.NumContentItem[] => {\n const items: dcmjs.sr.valueTypes.NumContentItem[] = []\n content.forEach(i => {\n if (hasValueType(i, dcmjs.sr.valueTypes.ValueTypes.NUM)) {\n const measurement = i as dcmjs.sr.valueTypes.NumContentItem\n items.push(measurement)\n }\n })\n return items\n}\n\nconst findEvaluationItems = (\n { content }: { content: dcmjs.sr.valueTypes.ContentItem[] }\n): dcmjs.sr.valueTypes.CodeContentItem[] => {\n const items: dcmjs.sr.valueTypes.CodeContentItem[] = []\n content.forEach(i => {\n if (hasValueType(i, dcmjs.sr.valueTypes.ValueTypes.CODE)) {\n const evaluation = i as dcmjs.sr.valueTypes.CodeContentItem\n items.push(evaluation)\n }\n })\n return items\n}\n\nconst getROIs = (report: dmv.metadata.Comprehensive3DSR): dmv.roi.ROI[] => {\n // TID 1500 Measurement Report\n const matches = findContentItemsByName({\n content: report.ContentSequence,\n name: new dcmjs.sr.coding.CodedConcept({\n value: '126010',\n schemeDesignator: 'DCM',\n meaning: 'Imaging Measurements'\n })\n })\n if (matches.length !== 1) {\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.SLIM,\n new CustomError(\n errorTypes.ENCODINGANDDECODING,\n 'Content item \"Imaging Measurements\" not found.' +\n 'Content of Comprehensive 3D SR document is not structured based on ' +\n 'TID 1500 \"Measurement Report\".'\n )\n )\n }\n const measurementsItem = matches[0] as dcmjs.sr.valueTypes.ContainerContentItem\n // TID 1410 Planar ROI Measurements and Qualitative Evaluations\n const measurementGroupItems = findContentItemsByName({\n content: measurementsItem.ContentSequence,\n name: new dcmjs.sr.coding.CodedConcept({\n value: '125007',\n schemeDesignator: 'DCM',\n meaning: 'Measurement Group'\n })\n })\n\n const rois: dmv.roi.ROI[] = []\n measurementGroupItems.forEach((item) => {\n const evaluations = []\n let observerType: string\n const group = item as dcmjs.sr.valueTypes.ContainerContentItem\n let items = findContentItemsByName({\n content: group.ContentSequence,\n name: new dcmjs.sr.coding.CodedConcept({\n value: '112040',\n schemeDesignator: 'DCM',\n meaning: 'Tracking Unique Identifier'\n })\n })\n if (items.length === 0) {\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.SLIM,\n new CustomError(\n errorTypes.ENCODINGANDDECODING,\n 'Content item \"Tracking Unique Identifier\" not found. ' +\n 'Content of Comprehensive 3D SR document is not structured ' +\n 'based on TID 1500 \"Measurement Report\" -> ' +\n 'TID 1410 \"Planar ROI Measurements and Qualitative Evaluations\".'\n )\n )\n }\n const trackingUIDItem = items[0] as dcmjs.sr.valueTypes.UIDRefContentItem\n\n items = findContentItemsByName({\n content: group.ContentSequence,\n name: new dcmjs.sr.coding.CodedConcept({\n value: '121071',\n schemeDesignator: 'DCM',\n meaning: 'Finding'\n })\n })\n if (items.length === 0) {\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.SLIM,\n new CustomError(\n errorTypes.ENCODINGANDDECODING,\n 'Content item \"Finding\" not found. ' +\n 'Content of Comprehensive 3D SR document is not structured ' +\n 'based on TID 1500 \"Measurement Report\" -> ' +\n 'TID 1410 \"Planar ROI Measurements and Qualitative Evaluations\".'\n )\n )\n }\n\n items = findContentItemsByName({\n content: group.ContentSequence,\n name: new dcmjs.sr.coding.CodedConcept({\n value: '111001',\n schemeDesignator: 'DCM',\n meaning: 'Algorithm Name'\n })\n })\n if (items.length !== 0) {\n const algorithmNameItem = items[0] as dcmjs.sr.valueTypes.CodeContentItem\n evaluations.push(algorithmNameItem)\n observerType = 'Device'\n } else {\n observerType = 'Person'\n }\n\n items = findContentItemsByName({\n content: group.ContentSequence,\n name: new dcmjs.sr.coding.CodedConcept({\n value: '111003',\n schemeDesignator: 'DCM',\n meaning: 'Algorithm Version'\n })\n })\n if (items.length !== 0) {\n const algorithmVersionItem = items[0] as dcmjs.sr.valueTypes.CodeContentItem\n evaluations.push(algorithmVersionItem)\n }\n\n items = findContentItemsByName({\n content: group.ContentSequence,\n name: new dcmjs.sr.coding.CodedConcept({\n value: '111030',\n schemeDesignator: 'DCM',\n meaning: 'Image Region'\n })\n })\n if (items.length === 0) {\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.SLIM,\n new CustomError(\n errorTypes.ENCODINGANDDECODING,\n 'Content item \"Image Region\" not found. ' +\n 'Content of Comprehensive 3D SR document is not structured ' +\n 'based on TID 1500 \"Measurement Report\" -> ' +\n 'TID 1410 \"Planar ROI Measurements and Qualitative Evaluations\".'\n )\n )\n }\n const regionItem = items[0] as dcmjs.sr.valueTypes.Scoord3DContentItem\n let scoord3d: any\n if (regionItem.GraphicType === 'POINT') {\n scoord3d = new dmv.scoord3d.Point({\n frameOfReferenceUID: regionItem.ReferencedFrameOfReferenceUID,\n coordinates: regionItem.GraphicData\n })\n } else {\n const coordinates: number[][] = []\n for (let i = 0; i < regionItem.GraphicData.length; i += 3) {\n coordinates.push(regionItem.GraphicData.slice(i, i + 3))\n }\n if (regionItem.GraphicType === 'POLYGON') {\n scoord3d = new dmv.scoord3d.Polygon({\n frameOfReferenceUID: regionItem.ReferencedFrameOfReferenceUID,\n coordinates: coordinates\n })\n } else if (regionItem.GraphicType === 'MULTIPOINT') {\n scoord3d = new dmv.scoord3d.MultiPoint({\n frameOfReferenceUID: regionItem.ReferencedFrameOfReferenceUID,\n coordinates: coordinates\n })\n } else if (regionItem.GraphicType === 'POLYLINE') {\n scoord3d = new dmv.scoord3d.Polyline({\n frameOfReferenceUID: regionItem.ReferencedFrameOfReferenceUID,\n coordinates: coordinates\n })\n } else if (regionItem.GraphicType === 'ELLIPSE') {\n scoord3d = new dmv.scoord3d.Ellipse({\n frameOfReferenceUID: regionItem.ReferencedFrameOfReferenceUID,\n coordinates: coordinates\n })\n } else if (regionItem.GraphicType === 'ELLIPSOID') {\n scoord3d = new dmv.scoord3d.Ellipsoid({\n frameOfReferenceUID: regionItem.ReferencedFrameOfReferenceUID,\n coordinates: coordinates\n })\n } else {\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.SLIM,\n new CustomError(\n errorTypes.ENCODINGANDDECODING,\n 'Content item \"Image Region\" has unknown graphic type ' +\n `\"${regionItem.GraphicType}\". ` +\n 'Content of Comprehensive 3D SR document is not structured ' +\n 'based on TID 1500 \"Measurement Report\" -> ' +\n 'TID 1410 \"Planar ROI Measurements and Qualitative Evaluations\".'\n )\n )\n }\n }\n\n evaluations.push(\n ...findEvaluationItems({ content: group.ContentSequence })\n )\n const measurements = findMeasurementItems({\n content: group.ContentSequence\n })\n\n const roi = new dmv.roi.ROI({\n scoord3d: scoord3d,\n uid: generateUUID(),\n properties: {\n trackingUID: trackingUIDItem.UID,\n observerType: observerType,\n evaluations: evaluations,\n measurements: measurements\n }\n })\n rois.push(roi)\n })\n return rois\n}\n\nclass MeasurementReport {\n public PersonObserverName?: string\n\n public PersonObserverLoginName?: string\n\n public DeviceObserverUID?: string\n\n public DeviceObserverName?: string\n\n public SpecimenUID: string\n\n public SpecimenIdentifier: string\n\n public ContainerIdentifier: string\n\n public ROIs: dmv.roi.ROI[] = []\n\n constructor (report: dmv.metadata.Comprehensive3DSR) {\n let items = findContentItemsByName({\n content: report.ContentSequence,\n name: new dcmjs.sr.coding.CodedConcept({\n value: '121039',\n schemeDesignator: 'DCM',\n meaning: 'Specimen UID'\n })\n })\n if (items.length === 0) {\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.SLIM,\n new CustomError(\n errorTypes.ENCODINGANDDECODING,\n 'Content item \"Specimen UID\" not found. ' +\n 'Content of Comprehensive 3D SR document is not structured based on ' +\n 'TID 1500 \"Measurement Report\" -> TID 1001 \"Observation Context\" -> ' +\n 'TID 1006 \"Subject Context\" -> TID 1009 \"Subject Context, Specimen\".'\n )\n )\n }\n const specimenUIDItem = (\n items[0] as unknown as dcmjs.sr.valueTypes.UIDRefContentItem\n )\n this.SpecimenUID = specimenUIDItem.UID\n\n items = findContentItemsByName({\n content: report.ContentSequence,\n name: new dcmjs.sr.coding.CodedConcept({\n value: '121041',\n schemeDesignator: 'DCM',\n meaning: 'Specimen Identifier'\n })\n })\n if (items.length === 0) {\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.SLIM,\n new CustomError(\n errorTypes.ENCODINGANDDECODING,\n 'Content item \"Specimen Identifier\" not found. ' +\n 'Content of Comprehensive 3D SR document is not structured based on ' +\n 'TID 1500 \"Measurement Report\" -> TID 1001 \"Observation Context\" -> ' +\n 'TID 1006 \"Subject Context\" -> TID 1009 \"Subject Context, Specimen\".'\n )\n )\n }\n const specimenIdItem = (\n items[0] as unknown as dcmjs.sr.valueTypes.TextContentItem\n )\n this.SpecimenIdentifier = specimenIdItem.TextValue\n\n items = findContentItemsByName({\n content: report.ContentSequence,\n name: new dcmjs.sr.coding.CodedConcept({\n value: '111700',\n schemeDesignator: 'DCM',\n meaning: 'Specimen Container Identifier'\n })\n })\n if (items.length === 0) {\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.SLIM,\n new CustomError(\n errorTypes.ENCODINGANDDECODING,\n 'Content item \"Specimen Container Identifier\" not found. ' +\n 'Content of Comprehensive 3D SR document is not structured based on ' +\n 'TID 1500 \"Measurement Report\" -> TID 1001 \"Observation Context\" -> ' +\n 'TID 1006 \"Subject Context\" -> TID 1009 \"Subject Context, Specimen\".'\n )\n )\n }\n const containerIdItem = (\n items[0] as unknown as dcmjs.sr.valueTypes.TextContentItem\n )\n this.ContainerIdentifier = containerIdItem.TextValue\n\n items = findContentItemsByName({\n content: report.ContentSequence,\n name: new dcmjs.sr.coding.CodedConcept({\n value: '121008',\n schemeDesignator: 'DCM',\n meaning: 'Person Observer Name'\n })\n })\n if (items.length !== 0) {\n const personNameItem = (\n items[0] as unknown as dcmjs.sr.valueTypes.PNameContentItem\n )\n this.PersonObserverName = personNameItem.PersonName\n }\n\n items = findContentItemsByName({\n content: report.ContentSequence,\n name: new dcmjs.sr.coding.CodedConcept({\n value: '128774',\n schemeDesignator: 'DCM',\n meaning: \"Person Observer's Login Name\"\n })\n })\n if (items.length !== 0) {\n const personLoginNameItem = (\n items[0] as unknown as dcmjs.sr.valueTypes.TextContentItem\n )\n this.PersonObserverLoginName = personLoginNameItem.TextValue\n }\n\n items = findContentItemsByName({\n content: report.ContentSequence,\n name: new dcmjs.sr.coding.CodedConcept({\n value: '121012',\n schemeDesignator: 'DCM',\n meaning: 'Device Observer UID'\n })\n })\n if (items.length > 0) {\n const deviceUIDItem = (\n items[0] as unknown as dcmjs.sr.valueTypes.UIDRefContentItem\n )\n this.DeviceObserverUID = deviceUIDItem.UID\n }\n\n items = findContentItemsByName({\n content: report.ContentSequence,\n name: new dcmjs.sr.coding.CodedConcept({\n value: '121013',\n schemeDesignator: 'DCM',\n meaning: 'Device Observer Name'\n })\n })\n if (items.length !== 0) {\n const deviceNameItem = (\n items[0] as unknown as dcmjs.sr.valueTypes.TextContentItem\n )\n this.DeviceObserverName = deviceNameItem.TextValue\n }\n\n this.ROIs = getROIs(report)\n }\n}\n\ninterface ReportProps {\n dataset: dmv.metadata.Comprehensive3DSR\n}\n\n/**\n * React component representing a DICOM SR document that displays the\n * document content (a selected subset of content items).\n */\nclass Report extends React.Component {\n render (): React.ReactNode {\n const report = new MeasurementReport(this.props.dataset)\n const containerAttrs = [\n {\n name: 'ID',\n value: report.ContainerIdentifier\n }\n ]\n const specimenAttrs = [\n {\n name: 'ID',\n value: report.SpecimenIdentifier\n }\n ]\n const observerAttrs = [\n {\n name: 'Name',\n value: report.PersonObserverName\n }\n ]\n const annotations = report.ROIs.map(\n (roi, index): React.ReactNode => {\n const id = `Region ${index + 1}`\n const attrs: Array<{ name: string, value: string }> = []\n roi.evaluations.forEach((\n item: (\n dcmjs.sr.valueTypes.CodeContentItem |\n dcmjs.sr.valueTypes.TextContentItem\n )\n ) => {\n if (item.ValueType === dcmjs.sr.valueTypes.ValueTypes.CODE) {\n item = item as dcmjs.sr.valueTypes.CodeContentItem\n attrs.push({\n name: item.ConceptNameCodeSequence[0].CodeMeaning,\n value: item.ConceptCodeSequence[0].CodeMeaning\n })\n } else if (item.ValueType === dcmjs.sr.valueTypes.ValueTypes.TEXT) {\n item = item as dcmjs.sr.valueTypes.TextContentItem\n attrs.push({\n name: item.ConceptNameCodeSequence[0].CodeMeaning,\n value: item.TextValue\n })\n }\n })\n return \n }\n )\n\n return (\n
\n Patient\n \n Case\n \n Slide\n \n Specimen\n \n Observer\n \n Annotations\n {annotations}\n
\n )\n }\n}\n\nexport default Report\nexport { MeasurementReport }\n","import React from 'react'\nimport { List } from 'antd'\n\nimport Description, { Attribute, AttributeGroup } from './Description'\n\ninterface ItemProps {\n uid: string\n identifier: string\n attributes: Attribute[]\n groups?: AttributeGroup[]\n children?: React.ReactElement[]\n type?: string\n hasLongValues?: boolean\n}\n\n/**\n * React component for a list item that consists of a header element\n * containing an identifier and a body element containing a description list\n * of attributes rendered as name-value pairs.\n */\nclass Item extends React.Component {\n render (): React.ReactNode {\n let groups = null\n if (this.props.groups !== undefined) {\n groups = this.props.groups.map((item, index: number) => (\n \n ))\n }\n let title\n if (this.props.type !== undefined) {\n title = `${this.props.type}: ${this.props.identifier}`\n } else {\n title = this.props.identifier\n }\n return (\n \n \n {groups}\n \n {this.props.children}\n \n )\n }\n}\n\nexport default Item\n","import * as dcmjs from 'dcmjs'\n\nexport const SpecimenPreparationTypes: {\n [key: string]: dcmjs.sr.coding.CodedConcept\n} = {\n COLLECTION: new dcmjs.sr.coding.CodedConcept({\n value: '17636008',\n schemeDesignator: 'SCT',\n meaning: 'Specimen collection'\n }),\n SAMPLING: new dcmjs.sr.coding.CodedConcept({\n value: '433465004',\n schemeDesignator: 'SCT',\n meaning: 'Sampling of tissue specimen'\n }),\n STAINING: new dcmjs.sr.coding.CodedConcept({\n value: '127790008',\n schemeDesignator: 'SCT',\n meaning: 'Specimen staining'\n }),\n PROCESSING: new dcmjs.sr.coding.CodedConcept({\n value: '9265001',\n schemeDesignator: 'SCT',\n meaning: 'Specimen processing'\n })\n}\n\nexport const SpecimenPreparationAdditives: {\n [key: string]: dcmjs.sr.coding.CodedConcept\n} = {\n FIXATIVE: new dcmjs.sr.coding.CodedConcept({\n value: '430864009',\n schemeDesignator: 'SCT',\n meaning: 'Tissue fixative'\n }),\n EMBEDDING_MEDIUM: new dcmjs.sr.coding.CodedConcept({\n value: '430863003',\n schemeDesignator: 'SCT',\n meaning: 'Embedding medium'\n })\n}\n\nexport const SpecimenPreparationStepItems: {\n [key: string]: dcmjs.sr.coding.CodedConcept\n} = {\n SPECIMEN_IDENTIFIER: new dcmjs.sr.coding.CodedConcept({\n value: '121041',\n schemeDesignator: 'DCM',\n meaning: 'Specimen identifier'\n }),\n PARENT_SPECIMEN_IDENTIFIER: new dcmjs.sr.coding.CodedConcept({\n value: '111705',\n schemeDesignator: 'DCM',\n meaning: 'Parent specimen identifier'\n }),\n PROCESSING_TYPE: new dcmjs.sr.coding.CodedConcept({\n value: '111701',\n schemeDesignator: 'DCM',\n meaning: 'Processing type'\n }),\n DATETIME_OF_PROCESSING: new dcmjs.sr.coding.CodedConcept({\n value: '111702',\n schemeDesignator: 'DCM',\n meaning: 'Datetime of processing'\n }),\n PROCESSING_STEP_DESCRIPTION: new dcmjs.sr.coding.CodedConcept({\n value: '111703',\n schemeDesignator: 'DCM',\n meaning: 'Processing step description'\n }),\n COLLECTION_METHOD: new dcmjs.sr.coding.CodedConcept({\n value: '17636008',\n schemeDesignator: 'SCT',\n meaning: 'Specimen collection'\n }),\n SAMPLING_METHOD: new dcmjs.sr.coding.CodedConcept({\n value: '111704',\n schemeDesignator: 'DCM',\n meaning: 'Sampling method'\n }),\n STAIN: new dcmjs.sr.coding.CodedConcept({\n value: '424361007',\n schemeDesignator: 'SCT',\n meaning: 'Using substance'\n }),\n ...SpecimenPreparationAdditives\n}\n","import React from 'react'\nimport * as dmv from 'dicom-microscopy-viewer'\nimport * as dcmjs from 'dcmjs'\n\nimport Item from './Item'\nimport { Attribute } from './Description'\nimport { SpecimenPreparationStepItems } from '../data/specimens'\n\ninterface SpecimenItemProps {\n index: number\n metadata?: dmv.metadata.VLWholeSlideMicroscopyImage\n showstain: boolean\n}\n\n/**\n * React component representing a DICOM Specimen Information Entity and\n * displays specimen-related attributes of a DICOM Slide Microscopy image.\n */\nclass SpecimenItem extends React.Component {\n render (): React.ReactNode {\n if (this.props.metadata === undefined) {\n return null\n }\n const specimenDescription = this.props.metadata.SpecimenDescriptionSequence[\n this.props.index\n ]\n const attributes: Attribute[] = []\n if (specimenDescription.SpecimenShortDescription !== undefined) {\n attributes.push({\n name: 'Description',\n value: specimenDescription.SpecimenShortDescription\n })\n }\n if (specimenDescription.PrimaryAnatomicStructureSequence !== undefined) {\n if (specimenDescription.PrimaryAnatomicStructureSequence.length > 0) {\n const structures = specimenDescription.PrimaryAnatomicStructureSequence\n attributes.push({\n name: 'Anatomical structure',\n value: structures.map(item => item.CodeMeaning).join(', ')\n })\n }\n }\n\n // TID 8001 \"Specimen Preparation\"\n const preparationSteps: dmv.metadata.SpecimenPreparation[] = (\n specimenDescription.SpecimenPreparationSequence ?? []\n )\n preparationSteps.forEach(\n (step: dmv.metadata.SpecimenPreparation, index: number): void => {\n step.SpecimenPreparationStepContentItemSequence.forEach((\n item: (\n dcmjs.sr.valueTypes.CodeContentItem |\n dcmjs.sr.valueTypes.TextContentItem |\n dcmjs.sr.valueTypes.UIDRefContentItem |\n dcmjs.sr.valueTypes.PNameContentItem |\n dcmjs.sr.valueTypes.DateTimeContentItem\n ),\n index: number\n ) => {\n const name = new dcmjs.sr.coding.CodedConcept({\n value: item.ConceptNameCodeSequence[0].CodeValue,\n schemeDesignator:\n item.ConceptNameCodeSequence[0].CodingSchemeDesignator,\n meaning: item.ConceptNameCodeSequence[0].CodeMeaning\n })\n if (item.ValueType === dcmjs.sr.valueTypes.ValueTypes.CODE) {\n item = item as dcmjs.sr.valueTypes.CodeContentItem\n const value = new dcmjs.sr.coding.CodedConcept({\n value: item.ConceptCodeSequence[0].CodeValue,\n schemeDesignator:\n item.ConceptCodeSequence[0].CodingSchemeDesignator,\n meaning: item.ConceptCodeSequence[0].CodeMeaning\n })\n if (!name.equals(SpecimenPreparationStepItems.PROCESSING_TYPE)) {\n if (\n name.equals(SpecimenPreparationStepItems.COLLECTION_METHOD)\n ) {\n attributes.push({\n name: 'Collection method',\n value: value.CodeMeaning\n })\n } else if (\n name.equals(SpecimenPreparationStepItems.FIXATIVE)\n ) {\n attributes.push({\n name: 'Tissue fixative',\n value: value.CodeMeaning\n })\n } else if (\n name.equals(SpecimenPreparationStepItems.EMBEDDING_MEDIUM)\n ) {\n attributes.push({\n name: 'Tissue embedding medium',\n value: value.CodeMeaning\n })\n } else if (\n name.equals(SpecimenPreparationStepItems.STAIN) &&\n this.props.showstain\n ) {\n attributes.push({\n name: 'Tissue stain',\n value: value.CodeMeaning\n })\n }\n }\n } else if (item.ValueType === dcmjs.sr.valueTypes.ValueTypes.TEXT) {\n item = item as dcmjs.sr.valueTypes.TextContentItem\n if (\n name.equals(SpecimenPreparationStepItems.STAIN) &&\n this.props.showstain\n ) {\n attributes.push({\n name: 'Tissue stain',\n value: item.TextValue\n })\n } else if (\n name.equals(SpecimenPreparationStepItems.PARENT_SPECIMEN_IDENTIFIER)\n ) {\n attributes.push({\n name: 'Parent specimen',\n value: item.TextValue\n })\n }\n }\n })\n }\n )\n const uid = specimenDescription.SpecimenUID\n const identifier = specimenDescription.SpecimenIdentifier\n return (\n \n )\n }\n}\n\nexport default SpecimenItem\n","import React from 'react'\nimport * as dmv from 'dicom-microscopy-viewer'\nimport { List } from 'antd'\n\nimport SpecimenItem from './SpecimenItem'\n\ninterface SpecimenListProps {\n metadata?: dmv.metadata.VLWholeSlideMicroscopyImage\n showstain: boolean\n}\n\n/**\n * React component representing a list of DICOM Specimen Information Entities.\n */\nclass SpecimenList extends React.Component {\n render (): React.ReactNode {\n if (this.props.metadata === undefined) {\n return null\n }\n /*\n * Specimen Description Sequence is a type 1 attribute. However, it is\n * nevertheless missing in some data sets. This is a violation of the\n * standard, but it may be better to facilitate display of the data.\n */\n const descriptions = this.props.metadata.SpecimenDescriptionSequence ?? []\n const items = descriptions.map(\n (item: dmv.metadata.SpecimenDescription, index: number) => {\n return (\n \n )\n }\n )\n return (\n \n {items}\n \n )\n }\n}\n\nexport default SpecimenList\n","import React from 'react'\nimport {\n Badge,\n Button,\n Col,\n Divider,\n InputNumber,\n Menu,\n Popover,\n Row,\n Slider,\n Space,\n Switch,\n Tooltip\n} from 'antd'\nimport {\n DeleteOutlined,\n EyeOutlined,\n EyeInvisibleOutlined,\n SettingOutlined\n} from '@ant-design/icons'\nimport Description from './Description'\nimport * as dmv from 'dicom-microscopy-viewer'\nimport * as dcmjs from 'dcmjs'\n\nimport { SpecimenPreparationStepItems } from '../data/specimens'\nimport NotificationMiddleware, {\n NotificationMiddlewareContext\n} from '../services/NotificationMiddleware'\nimport { CustomError, errorTypes } from '../utils/CustomError'\n\ninterface OpticalPathItemProps {\n opticalPath: dmv.opticalPath.OpticalPath\n metadata: dmv.metadata.VLWholeSlideMicroscopyImage[]\n isVisible: boolean\n isRemovable: boolean\n defaultStyle: {\n opacity: number\n color?: number[]\n paletteColorLookupTable?: dmv.color.PaletteColorLookupTable\n limitValues?: number[]\n }\n onVisibilityChange: ({ opticalPathIdentifier, isVisible }: {\n opticalPathIdentifier: string\n isVisible: boolean\n }) => void\n onStyleChange: ({ opticalPathIdentifier, styleOptions }: {\n opticalPathIdentifier: string\n styleOptions: {\n opacity?: number\n color?: number[]\n paletteColorLookupTable?: dmv.color.PaletteColorLookupTable\n limitValues?: number[]\n }\n }) => void\n onRemoval: (opticalPathIdentifier: string) => void\n}\n\ninterface OpticalPathItemState {\n isVisible: boolean\n currentStyle: {\n opacity: number\n color?: number[]\n paletteColorLookupTable?: dmv.color.PaletteColorLookupTable\n limitValues?: number[]\n }\n}\n\n/**\n * React component representing an optical path of a\n * multi-channel acquistion with control of visualization parameters.\n */\nclass OpticalPathItem extends React.Component {\n constructor (props: OpticalPathItemProps) {\n super(props)\n this.handleVisibilityChange = this.handleVisibilityChange.bind(this)\n this.handleOpacityChange = this.handleOpacityChange.bind(this)\n this.handleLimitChange = this.handleLimitChange.bind(this)\n this.handleLowerLimitChange = this.handleLowerLimitChange.bind(this)\n this.handleUpperLimitChange = this.handleUpperLimitChange.bind(this)\n this.handleColorRChange = this.handleColorRChange.bind(this)\n this.handleColorGChange = this.handleColorGChange.bind(this)\n this.handleColorBChange = this.handleColorBChange.bind(this)\n this.handleRemoval = this.handleRemoval.bind(this)\n this.getCurrentColors = this.getCurrentColors.bind(this)\n this.state = {\n isVisible: this.props.isVisible,\n currentStyle: {\n opacity: this.props.defaultStyle.opacity,\n color: this.props.defaultStyle.color,\n paletteColorLookupTable: this.props.defaultStyle.paletteColorLookupTable,\n limitValues: this.props.defaultStyle.limitValues\n }\n }\n }\n\n componentDidUpdate (\n previousProps: OpticalPathItemProps,\n previousState: OpticalPathItemState\n ): void {\n if (this.props.defaultStyle !== previousProps.defaultStyle) {\n this.setState({\n currentStyle: this.props.defaultStyle\n })\n }\n }\n\n handleVisibilityChange (\n checked: boolean,\n event: React.MouseEvent\n ): void {\n const identifier = this.props.opticalPath.identifier\n this.setState({\n isVisible: checked\n })\n this.props.onVisibilityChange({\n opticalPathIdentifier: identifier,\n isVisible: checked\n })\n }\n\n handleOpacityChange (\n value: number | null\n ): void {\n if (value != null) {\n const identifier = this.props.opticalPath.identifier\n this.props.onStyleChange({\n opticalPathIdentifier: identifier,\n styleOptions: { opacity: value }\n })\n this.setState(state => ({\n currentStyle: {\n color: state.currentStyle.color,\n paletteColorLookupTable: state.currentStyle.paletteColorLookupTable,\n opacity: value,\n limitValues: state.currentStyle.limitValues\n }\n }))\n }\n }\n\n handleColorRChange (\n value: number | number[] | null\n ): void {\n const identifier = this.props.opticalPath.identifier\n if (value != null && this.state.currentStyle.color !== undefined) {\n const color = [\n Array.isArray(value) ? value[0] : value,\n this.state.currentStyle.color[1],\n this.state.currentStyle.color[2]\n ]\n this.setState(state => ({\n currentStyle: {\n color: color,\n paletteColorLookupTable: state.currentStyle.paletteColorLookupTable,\n opacity: state.currentStyle.opacity,\n limitValues: state.currentStyle.limitValues\n }\n }))\n this.props.onStyleChange({\n opticalPathIdentifier: identifier,\n styleOptions: { color: color }\n })\n }\n }\n\n handleColorGChange (\n value: number | number[] | null\n ): void {\n const identifier = this.props.opticalPath.identifier\n if (value != null && this.state.currentStyle.color !== undefined) {\n const color = [\n this.state.currentStyle.color[0],\n Array.isArray(value) ? value[0] : value,\n this.state.currentStyle.color[2]\n ]\n this.setState(state => ({\n currentStyle: {\n color: color,\n paletteColorLookupTable: state.currentStyle.paletteColorLookupTable,\n opacity: state.currentStyle.opacity,\n limitValues: state.currentStyle.limitValues\n }\n }))\n this.props.onStyleChange({\n opticalPathIdentifier: identifier,\n styleOptions: { color: color }\n })\n }\n }\n\n handleColorBChange (\n value: number | number[] | null\n ): void {\n const identifier = this.props.opticalPath.identifier\n if (value != null && this.state.currentStyle.color !== undefined) {\n const color = [\n this.state.currentStyle.color[0],\n this.state.currentStyle.color[1],\n Array.isArray(value) ? value[0] : value\n ]\n this.setState(state => ({\n currentStyle: {\n color: color,\n paletteColorLookupTable: state.currentStyle.paletteColorLookupTable,\n opacity: state.currentStyle.opacity,\n limitValues: state.currentStyle.limitValues\n }\n }))\n this.props.onStyleChange({\n opticalPathIdentifier: identifier,\n styleOptions: { color: color }\n })\n }\n }\n\n getCurrentColors (): string[] {\n const rgb2hex = (values: number[]): string => {\n const r = values[0]\n const g = values[1]\n const b = values[2]\n return '#' + (0x1000000 + (r << 16) + (g << 8) + b).toString(16).slice(1)\n }\n\n if (this.props.defaultStyle.paletteColorLookupTable != null) {\n const colormap = this.props.defaultStyle.paletteColorLookupTable.data\n return colormap.map(values => rgb2hex(values))\n } else if (this.state.currentStyle.color != null) {\n return [\n '#000000',\n rgb2hex(this.state.currentStyle.color)\n ]\n } else {\n return ['white', 'white']\n }\n }\n\n handleLowerLimitChange (\n value: number | null\n ): void {\n const identifier = this.props.opticalPath.identifier\n if (value != null && this.state.currentStyle.limitValues !== undefined) {\n this.setState(state => {\n if (state.currentStyle.limitValues !== undefined) {\n return {\n currentStyle: {\n color: state.currentStyle.color,\n paletteColorLookupTable: state.currentStyle.paletteColorLookupTable,\n opacity: state.currentStyle.opacity,\n limitValues: [value, state.currentStyle.limitValues[1]]\n }\n }\n } else {\n return {\n currentStyle: {\n color: state.currentStyle.color,\n paletteColorLookupTable: state.currentStyle.paletteColorLookupTable,\n opacity: state.currentStyle.opacity,\n limitValues: state.currentStyle.limitValues\n }\n }\n }\n })\n this.props.onStyleChange({\n opticalPathIdentifier: identifier,\n styleOptions: {\n limitValues: [\n value,\n this.state.currentStyle.limitValues[1]\n ]\n }\n })\n }\n }\n\n handleUpperLimitChange (\n value: number | null\n ): void {\n const identifier = this.props.opticalPath.identifier\n if (value != null && this.state.currentStyle.limitValues !== undefined) {\n this.setState(state => {\n if (state.currentStyle.limitValues !== undefined) {\n return {\n currentStyle: {\n color: state.currentStyle.color,\n paletteColorLookupTable: state.currentStyle.paletteColorLookupTable,\n opacity: state.currentStyle.opacity,\n limitValues: [state.currentStyle.limitValues[0], value]\n }\n }\n } else {\n return {\n currentStyle: {\n color: state.currentStyle.color,\n paletteColorLookupTable: state.currentStyle.paletteColorLookupTable,\n opacity: state.currentStyle.opacity,\n limitValues: state.currentStyle.limitValues\n }\n }\n }\n })\n this.props.onStyleChange({\n opticalPathIdentifier: identifier,\n styleOptions: {\n limitValues: [\n this.state.currentStyle.limitValues[0],\n value\n ]\n }\n })\n }\n }\n\n handleLimitChange (\n values: number[]\n ): void {\n const identifier = this.props.opticalPath.identifier\n this.setState(state => ({\n currentStyle: {\n color: state.currentStyle.color,\n paletteColorLookupTable: state.currentStyle.paletteColorLookupTable,\n opacity: state.currentStyle.opacity,\n limitValues: values\n }\n }))\n this.props.onStyleChange({\n opticalPathIdentifier: identifier,\n styleOptions: { limitValues: values }\n })\n }\n\n handleRemoval (): void {\n const identifier = this.props.opticalPath.identifier\n this.props.onRemoval(identifier)\n }\n\n render (): React.ReactNode {\n const identifier = this.props.opticalPath.identifier\n const description = this.props.opticalPath.description\n const attributes: Array<{ name: string, value: string }> = []\n if (this.props.opticalPath.illuminationWaveLength !== undefined) {\n attributes.push(\n {\n name: 'Illumination wavelength',\n value: `${this.props.opticalPath.illuminationWaveLength} nm`\n }\n )\n }\n if (this.props.opticalPath.illuminationColor !== undefined) {\n attributes.push(\n {\n name: 'Illumination color',\n value: this.props.opticalPath.illuminationColor.CodeMeaning\n }\n )\n }\n\n // TID 8001 \"Specimen Preparation\"\n const specimenDescriptions: dmv.metadata.SpecimenDescription[] = (\n this.props.metadata[0].SpecimenDescriptionSequence ?? []\n )\n try {\n specimenDescriptions.forEach(description => {\n const specimenPreparationSteps: dmv.metadata.SpecimenPreparation[] =\n description.SpecimenPreparationSequence ?? []\n specimenPreparationSteps.forEach(\n (step: dmv.metadata.SpecimenPreparation, index: number): void => {\n step.SpecimenPreparationStepContentItemSequence.forEach((\n item: (\n dcmjs.sr.valueTypes.CodeContentItem |\n dcmjs.sr.valueTypes.TextContentItem |\n dcmjs.sr.valueTypes.UIDRefContentItem |\n dcmjs.sr.valueTypes.PNameContentItem |\n dcmjs.sr.valueTypes.DateTimeContentItem\n ),\n index: number\n ) => {\n const name = new dcmjs.sr.coding.CodedConcept({\n value: item.ConceptNameCodeSequence[0].CodeValue,\n schemeDesignator:\n item.ConceptNameCodeSequence[0].CodingSchemeDesignator,\n meaning: item.ConceptNameCodeSequence[0].CodeMeaning\n })\n if (item.ValueType === dcmjs.sr.valueTypes.ValueTypes.CODE) {\n item = item as dcmjs.sr.valueTypes.CodeContentItem\n const value = new dcmjs.sr.coding.CodedConcept({\n value: item.ConceptCodeSequence[0].CodeValue,\n schemeDesignator:\n item.ConceptCodeSequence[0].CodingSchemeDesignator,\n meaning: item.ConceptCodeSequence[0].CodeMeaning\n })\n if (!name.equals(SpecimenPreparationStepItems.PROCESSING_TYPE)) {\n if (name.equals(SpecimenPreparationStepItems.STAIN)) {\n attributes.push({\n name: 'Tissue stain',\n value: value.CodeMeaning\n })\n }\n }\n } else if (item.ValueType === dcmjs.sr.valueTypes.ValueTypes.TEXT) {\n item = item as dcmjs.sr.valueTypes.TextContentItem\n if (!name.equals(SpecimenPreparationStepItems.PROCESSING_TYPE)) {\n if (name.equals(SpecimenPreparationStepItems.STAIN)) {\n attributes.push({\n name: 'Tissue stain',\n value: item.TextValue\n })\n }\n }\n }\n })\n }\n )\n })\n } catch (error: any) {\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.DCMJS,\n new CustomError(\n errorTypes.ENCODINGANDDECODING,\n error.message\n )\n )\n }\n\n const maxValue = Math.pow(2, this.props.metadata[0].BitsAllocated) - 1\n\n const title = (\n description != null ? `${identifier}: ${description}` : identifier\n )\n let settings\n let item\n if (this.props.opticalPath.isMonochromatic) {\n // monochrome images that can be pseudo-colored\n let colorSettings\n if (this.state.currentStyle.color != null) {\n colorSettings = (\n <>\n \n Color\n \n \n \n Red\n \n \n \n \n \n \n \n \n\n \n \n Green\n \n \n \n \n \n \n \n \n\n \n \n Blue\n \n \n \n \n \n \n \n \n \n )\n } else {\n colorSettings = (\n <>\n \n Color\n \n Custom pseudo-coloring is disabled because pixels are colorized via\n a provided palette color lookup table.\n \n )\n }\n\n let windowSettings\n if (this.state.currentStyle.limitValues != null) {\n windowSettings = (\n <>\n \n Values of interest\n \n \n \n \n \n \n \n \n \n \n \n \n \n )\n }\n settings = (\n
\n {windowSettings}\n {colorSettings}\n \n \n \n Opacity\n \n \n \n \n \n \n \n \n
\n )\n const colors = this.getCurrentColors()\n item = (\n \n \n \n )\n } else {\n // color images\n settings = (\n
\n \n \n Opacity\n \n \n \n \n \n \n \n \n
\n )\n item = (\n \n )\n }\n\n const buttons = []\n if (this.props.isRemovable) {\n buttons.push(\n \n }\n onClick={this.handleRemoval}\n />\n \n )\n }\n\n const {\n defaultStyle,\n isRemovable,\n isVisible,\n metadata,\n onVisibilityChange,\n onStyleChange,\n onRemoval,\n opticalPath,\n ...otherProps\n } = this.props\n return (\n \n \n
\n \n }\n unCheckedChildren={}\n />\n \n }\n />\n \n {buttons}\n \n
\n {item}\n \n \n )\n }\n}\n\nexport default OpticalPathItem\n","import React from 'react'\nimport * as dmv from 'dicom-microscopy-viewer'\nimport { Button as Btn, Menu, Select, Space, Tooltip } from 'antd'\nimport { AppstoreAddOutlined } from '@ant-design/icons'\n\nimport OpticalPathItem from './OpticalPathItem'\n\nconst { Option } = Select\n\ninterface OpticalPathListProps {\n opticalPaths: dmv.opticalPath.OpticalPath[]\n metadata: {\n [opticalPathIdentifier: string]: dmv.metadata.VLWholeSlideMicroscopyImage[]\n }\n visibleOpticalPathIdentifiers: Set\n activeOpticalPathIdentifiers: Set\n defaultOpticalPathStyles: {\n [opticalPathIdentifier: string]: {\n opacity: number\n color?: number[]\n limitValues?: number[]\n paletteColorLookupTable?: dmv.color.PaletteColorLookupTable\n }\n }\n onOpticalPathVisibilityChange: ({ opticalPathIdentifier, isVisible }: {\n opticalPathIdentifier: string\n isVisible: boolean\n }) => void\n onOpticalPathStyleChange: ({ opticalPathIdentifier, styleOptions }: {\n opticalPathIdentifier: string\n styleOptions: {\n opacity?: number\n color?: number[]\n limitValues?: number[]\n }\n }) => void\n onOpticalPathActivityChange: ({ opticalPathIdentifier, isActive }: {\n opticalPathIdentifier: string\n isActive: boolean\n }) => void\n selectedPresentationStateUID?: string\n}\n\ninterface OpticalPathListState {\n selectedOpticalPathIdentifier?: string\n}\n\n/**\n * React component representing a list of optical paths.\n */\nclass OpticalPathList extends React.Component {\n state = {\n selectedOpticalPathIdentifier: undefined\n }\n\n constructor (props: OpticalPathListProps) {\n super(props)\n this.handleItemAddition = this.handleItemAddition.bind(this)\n this.handleItemRemoval = this.handleItemRemoval.bind(this)\n this.handleItemSelectionChange = this.handleItemSelectionChange.bind(this)\n }\n\n /**\n * Handler that gets called when an optical path should be removed.\n */\n handleItemRemoval (opticalPathIdentifier: string): void {\n this.props.onOpticalPathActivityChange({\n opticalPathIdentifier,\n isActive: false\n })\n }\n\n /**\n * Handler that gets called when the selection of an optical path should change.\n */\n handleItemSelectionChange (\n value: string\n ): void {\n this.setState({ selectedOpticalPathIdentifier: value })\n }\n\n /**\n * Handler that gets called when an optical path should be added.\n */\n handleItemAddition (): void {\n const identifier = this.state.selectedOpticalPathIdentifier\n if (identifier !== undefined) {\n this.props.onOpticalPathActivityChange({\n opticalPathIdentifier: identifier,\n isActive: true\n })\n this.setState({ selectedOpticalPathIdentifier: undefined })\n }\n }\n\n render (): React.ReactNode {\n if (this.props.metadata === undefined) {\n return null\n }\n\n const isSelectable = this.props.opticalPaths.length > 1\n const opticalPathItems: React.ReactNode[] = []\n const optionItems: React.ReactNode[] = []\n this.props.opticalPaths.forEach(opticalPath => {\n const opticalPathIdentifier = opticalPath.identifier\n const images = this.props.metadata[opticalPathIdentifier]\n const seriesInstanceUID = images[0].SeriesInstanceUID\n images[0].OpticalPathSequence.forEach(opticalPathItem => {\n const id = opticalPathItem.OpticalPathIdentifier\n const description = opticalPathItem.OpticalPathDescription\n if (opticalPath.identifier === id) {\n if (this.props.activeOpticalPathIdentifiers.has(id)) {\n opticalPathItems.push(\n \n )\n } else {\n let title\n if (description !== '') {\n title = `${id} - ${description}`\n } else {\n title = `${id}`\n }\n optionItems.push(\n \n )\n }\n }\n })\n })\n\n let opticalPathSelector\n if (isSelectable) {\n opticalPathSelector = (\n \n \n {optionItems}\n \n \n }\n type='primary'\n onClick={this.handleItemAddition}\n />\n \n \n )\n }\n\n return (\n \n {opticalPathItems}\n {opticalPathSelector}\n \n )\n }\n}\n\nexport default OpticalPathList\n","import React from 'react'\nimport * as dmv from 'dicom-microscopy-viewer'\nimport {\n Button,\n Col,\n InputNumber,\n Menu,\n Popover,\n Row,\n Slider,\n Space,\n Switch\n} from 'antd'\nimport { SettingOutlined } from '@ant-design/icons'\nimport { FaEye, FaEyeSlash } from 'react-icons/fa'\n\nimport Description from './Description'\n\ninterface MappingItemProps {\n mapping: dmv.mapping.ParameterMapping\n metadata: dmv.metadata.ParametricMap[]\n isVisible: boolean\n defaultStyle: {\n opacity: number\n }\n onVisibilityChange: ({ mappingUID, isVisible }: {\n mappingUID: string\n isVisible: boolean\n }) => void\n onStyleChange: ({ mappingUID, styleOptions }: {\n mappingUID: string\n styleOptions: {\n opacity?: number\n }\n }) => void\n}\n\ninterface MappingItemState {\n isVisible: boolean\n currentStyle: {\n opacity: number\n }\n}\n\n/**\n * React component representing a Real World Value Mapping.\n */\nclass MappingItem extends React.Component {\n constructor (props: MappingItemProps) {\n super(props)\n this.handleVisibilityChange = this.handleVisibilityChange.bind(this)\n this.handleOpacityChange = this.handleOpacityChange.bind(this)\n this.state = {\n isVisible: this.props.isVisible,\n currentStyle: {\n opacity: this.props.defaultStyle.opacity\n }\n }\n }\n\n handleVisibilityChange (\n checked: boolean,\n event: React.MouseEvent\n ): void {\n this.props.onVisibilityChange({\n mappingUID: this.props.mapping.uid,\n isVisible: checked\n })\n this.setState({ isVisible: checked })\n }\n\n handleOpacityChange (value: number | null): void {\n if (value != null) {\n this.props.onStyleChange({\n mappingUID: this.props.mapping.uid,\n styleOptions: {\n opacity: value\n }\n })\n this.setState(state => ({\n currentStyle: {\n opacity: value\n }\n }))\n }\n }\n\n render (): React.ReactNode {\n const attributes: Array<{ name: string, value: string }> = [\n {\n name: 'Description',\n value: this.props.mapping.description\n }\n ]\n\n const settings = (\n
\n \n \n Opacity\n \n \n \n \n \n \n \n \n
\n )\n\n /**\n * This hack is required for Menu.Item to work properly:\n * https://github.com/react-component/menu/issues/142\n */\n const {\n defaultStyle,\n isVisible,\n mapping,\n metadata,\n onVisibilityChange,\n onStyleChange,\n ...otherProps\n } = this.props\n return (\n \n \n
\n \n \n }\n unCheckedChildren={}\n />\n \n }\n />\n \n \n \n
\n \n \n \n )\n }\n}\n\nexport default MappingItem\n","import React from 'react'\nimport * as dmv from 'dicom-microscopy-viewer'\nimport { Menu } from 'antd'\n\nimport MappingItem from './MappingItem'\n\ninterface MappingListProps {\n mappings: dmv.mapping.ParameterMapping[]\n metadata: {\n [mappingUID: string]: dmv.metadata.ParametricMap[]\n }\n visibleMappingUIDs: Set\n defaultMappingStyles: {\n [mappingUID: string]: { opacity: number }\n }\n onMappingVisibilityChange: ({ mappingUID, isVisible }: {\n mappingUID: string\n isVisible: boolean\n }) => void\n onMappingStyleChange: ({ mappingUID, styleOptions }: {\n mappingUID: string\n styleOptions: {\n opacity?: number\n }\n }) => void\n}\n\n/**\n * React component representing a list of Real World Value Mappings.\n */\nclass MappingList extends React.Component {\n render (): React.ReactNode {\n const items = this.props.mappings.map((mapping, index) => {\n const uid = mapping.uid\n return (\n \n )\n })\n\n return (\n \n {items}\n \n )\n }\n}\n\nexport default MappingList\n","import React from 'react'\nimport * as dmv from 'dicom-microscopy-viewer'\nimport {\n Button,\n Col,\n InputNumber,\n Menu,\n Popover,\n Row,\n Slider,\n Space,\n Switch\n} from 'antd'\nimport { SettingOutlined } from '@ant-design/icons'\nimport { FaEye, FaEyeSlash } from 'react-icons/fa'\n\nimport Description from './Description'\n\ninterface SegmentItemProps {\n segment: dmv.segment.Segment\n isVisible: boolean\n metadata: dmv.metadata.Segmentation[]\n defaultStyle: {\n opacity: number\n }\n onVisibilityChange: ({ segmentUID, isVisible }: {\n segmentUID: string\n isVisible: boolean\n }) => void\n onStyleChange: ({ segmentUID, styleOptions }: {\n segmentUID: string\n styleOptions: {\n opacity: number\n }\n }) => void\n}\n\ninterface SegmentItemState {\n isVisible: boolean\n currentStyle: {\n opacity: number\n }\n}\n\n/**\n * React component representing a Segment.\n */\nclass SegmentItem extends React.Component {\n constructor (props: SegmentItemProps) {\n super(props)\n this.handleVisibilityChange = this.handleVisibilityChange.bind(this)\n this.handleOpacityChange = this.handleOpacityChange.bind(this)\n this.state = {\n isVisible: this.props.isVisible,\n currentStyle: { opacity: this.props.defaultStyle.opacity }\n }\n }\n\n handleVisibilityChange (\n checked: boolean,\n event: React.MouseEvent\n ): void {\n this.props.onVisibilityChange({\n segmentUID: this.props.segment.uid,\n isVisible: checked\n })\n this.setState({ isVisible: checked })\n }\n\n handleOpacityChange (value: number | null): void {\n if (value != null) {\n this.props.onStyleChange({\n segmentUID: this.props.segment.uid,\n styleOptions: {\n opacity: value\n }\n })\n this.setState({ currentStyle: { opacity: value } })\n }\n }\n\n render (): React.ReactNode {\n const attributes: Array<{ name: string, value: string }> = [\n {\n name: 'Property Type',\n value: this.props.segment.propertyType.CodeMeaning\n },\n {\n name: 'Property Category',\n value: this.props.segment.propertyCategory.CodeMeaning\n },\n {\n name: 'Algorithm Name',\n value: this.props.segment.algorithmName\n }\n ]\n\n const settings = (\n
\n \n \n Opacity\n \n \n \n \n \n \n \n \n
\n )\n\n /**\n * This hack is required for Menu.Item to work properly:\n * https://github.com/react-component/menu/issues/142\n */\n const {\n defaultStyle,\n isVisible,\n segment,\n metadata,\n onVisibilityChange,\n onStyleChange,\n ...otherProps\n } = this.props\n return (\n \n \n
\n \n }\n unCheckedChildren={}\n />\n \n }\n />\n \n \n
\n \n \n \n )\n }\n}\n\nexport default SegmentItem\n","import React from 'react'\nimport * as dmv from 'dicom-microscopy-viewer'\nimport { Menu } from 'antd'\n\nimport SegmentItem from './SegmentItem'\n\ninterface SegmentListProps {\n segments: dmv.segment.Segment[]\n visibleSegmentUIDs: Set\n metadata: {\n [segmentUID: string]: dmv.metadata.Segmentation[]\n }\n defaultSegmentStyles: {\n [segmentUID: string]: {\n opacity: number\n }\n }\n onSegmentVisibilityChange: ({ segmentUID, isVisible }: {\n segmentUID: string\n isVisible: boolean\n }) => void\n onSegmentStyleChange: ({ segmentUID, styleOptions }: {\n segmentUID: string\n styleOptions: {\n opacity: number\n }\n }) => void\n}\n\n/**\n * React component representing a list of Segments.\n */\nclass SegmentList extends React.Component {\n render (): React.ReactNode {\n const items = this.props.segments.map((segment, index) => {\n const uid = segment.uid\n return (\n \n )\n })\n\n return (\n \n {items}\n \n )\n }\n}\n\nexport default SegmentList\n","import React from 'react'\nimport {\n NavigateFunction,\n Params,\n useLocation,\n useNavigate,\n useParams,\n Location\n} from 'react-router-dom'\n\nexport interface RouteComponentProps {\n location: Location\n navigate: NavigateFunction\n params: Params\n}\n\nexport function withRouter (Component: React.ComponentType): Function {\n function ComponentWithRouterProp (props: any): JSX.Element {\n const location = useLocation()\n const navigate = useNavigate()\n const params = useParams()\n return (\n \n )\n }\n return ComponentWithRouterProp\n}\n","import React from 'react'\nimport {\n FaCrosshairs,\n FaDrawPolygon,\n FaEye,\n FaEyeSlash,\n FaHandPaper,\n FaHandPointer,\n FaTrash,\n FaSave\n} from 'react-icons/fa'\nimport {\n Button as Btn,\n Checkbox,\n Descriptions,\n Divider,\n InputNumber,\n message,\n Menu,\n Modal,\n Layout,\n Row,\n Select,\n Space,\n Tooltip\n} from 'antd'\nimport { UndoOutlined, CheckOutlined, StopOutlined } from '@ant-design/icons'\nimport * as dmv from 'dicom-microscopy-viewer'\nimport * as dcmjs from 'dcmjs'\nimport * as dwc from 'dicomweb-client'\n\nimport DicomWebManager from '../DicomWebManager'\nimport AnnotationList from './AnnotationList'\nimport AnnotationGroupList from './AnnotationGroupList'\nimport Button from './Button'\nimport Equipment from './Equipment'\nimport Report, { MeasurementReport } from './Report'\nimport SpecimenList from './SpecimenList'\nimport OpticalPathList from './OpticalPathList'\nimport MappingList from './MappingList'\nimport SegmentList from './SegmentList'\nimport { AnnotationSettings } from '../AppConfig'\nimport { Slide } from '../data/slides'\nimport { StorageClasses } from '../data/uids'\nimport { findContentItemsByName } from '../utils/sr'\nimport { RouteComponentProps, withRouter } from '../utils/router'\nimport { CustomError, errorTypes } from '../utils/CustomError'\nimport NotificationMiddleware, {\n NotificationMiddlewareContext\n} from '../services/NotificationMiddleware'\n\nconst DEFAULT_ROI_STROKE_COLOR: number[] = [0, 126, 163]\nconst DEFAULT_ROI_FILL_COLOR: number[] = [0, 126, 163, 0.2]\nconst DEFAULT_ROI_STROKE_WIDTH: number = 2\nconst DEFAULT_ROI_RADIUS: number = 5\n\nconst _buildKey = (concept: {\n CodeValue: string\n CodeMeaning: string\n CodingSchemeDesignator: string\n CodingSchemeVersion?: string\n}): string => {\n const codingScheme = concept.CodingSchemeDesignator\n const codeValue = concept.CodeValue\n return `${codingScheme}-${codeValue}`\n}\n\nconst _getRoiKey = (roi: dmv.roi.ROI): string | undefined => {\n const matches = findContentItemsByName({\n content: roi.evaluations,\n name: new dcmjs.sr.coding.CodedConcept({\n value: '121071',\n meaning: 'Finding',\n schemeDesignator: 'DCM'\n })\n })\n if (matches.length === 0) {\n console.warn(`no finding found for ROI ${roi.uid}`)\n return\n }\n const finding = matches[0] as dcmjs.sr.valueTypes.CodeContentItem\n const findingName = finding.ConceptCodeSequence[0]\n return _buildKey(findingName)\n}\n\nconst _areROIsEqual = (a: dmv.roi.ROI, b: dmv.roi.ROI): boolean => {\n if (a.scoord3d.graphicType !== b.scoord3d.graphicType) {\n return false\n }\n if (a.scoord3d.frameOfReferenceUID !== b.scoord3d.frameOfReferenceUID) {\n return false\n }\n if (a.scoord3d.graphicData.length !== b.scoord3d.graphicData.length) {\n return false\n }\n\n const decimals = 6\n for (let i = 0; i < a.scoord3d.graphicData.length; ++i) {\n if (a.scoord3d.graphicType === 'POINT') {\n const s1 = a.scoord3d as dmv.scoord3d.Point\n const s2 = b.scoord3d as dmv.scoord3d.Point\n const c1 = s1.graphicData[i].toPrecision(decimals)\n const c2 = s2.graphicData[i].toPrecision(decimals)\n if (c1 !== c2) {\n return false\n }\n } else {\n const s1 = a.scoord3d as dmv.scoord3d.Polygon\n const s2 = b.scoord3d as dmv.scoord3d.Polygon\n for (let j = 0; j < s1.graphicData[i].length; ++j) {\n const c1 = s1.graphicData[i][j].toPrecision(decimals)\n const c2 = s2.graphicData[i][j].toPrecision(decimals)\n if (c1 !== c2) {\n return false\n }\n }\n }\n }\n return true\n}\n\nconst _formatRoiStyle = (style: {\n stroke?: {\n color?: number[]\n width?: number\n }\n fill?: {\n color?: number[]\n }\n radius?: number\n}): dmv.viewer.ROIStyleOptions => {\n const stroke = {\n color: DEFAULT_ROI_STROKE_COLOR,\n width: DEFAULT_ROI_STROKE_WIDTH\n }\n if (style.stroke != null) {\n if (style.stroke.color != null) {\n stroke.color = style.stroke.color\n }\n if (style.stroke.width != null) {\n stroke.width = style.stroke.width\n }\n }\n const fill = {\n color: DEFAULT_ROI_FILL_COLOR\n }\n if (style.fill != null) {\n if (style.fill.color != null) {\n fill.color = style.fill.color\n }\n }\n return {\n stroke,\n fill,\n image: {\n circle: {\n radius: style.radius != null\n ? style.radius\n : Math.max(5 - stroke.width, 1),\n stroke,\n fill\n }\n }\n }\n}\n\nconst _constructViewers = ({ clients, slide, preload }: {\n clients: { [key: string]: dwc.api.DICOMwebClient }\n slide: Slide\n preload?: boolean\n}): {\n volumeViewer: dmv.viewer.VolumeImageViewer\n labelViewer?: dmv.viewer.LabelImageViewer\n} => {\n console.info(\n 'instantiate viewer for VOLUME images of slide ' +\n `\"${slide.volumeImages[0].ContainerIdentifier}\"`\n )\n try {\n const volumeViewer = new dmv.viewer.VolumeImageViewer({\n clientMapping: clients,\n metadata: slide.volumeImages,\n controls: ['overview', 'position'],\n preload: preload,\n errorInterceptor: (error: CustomError) =>\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.DMV, error\n )\n })\n volumeViewer.activateSelectInteraction({})\n\n let labelViewer\n if (slide.labelImages.length > 0) {\n console.info(\n 'instantiate viewer for LABEL image of slide ' +\n `\"${slide.labelImages[0].ContainerIdentifier}\"`\n )\n labelViewer = new dmv.viewer.LabelImageViewer({\n client: clients[StorageClasses.VL_WHOLE_SLIDE_MICROSCOPY_IMAGE],\n metadata: slide.labelImages[0],\n resizeFactor: 1,\n orientation: 'vertical',\n errorInterceptor: (error: CustomError) =>\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.DMV,\n error\n )\n })\n }\n\n return { volumeViewer, labelViewer }\n } catch (error) {\n // eslint-disable-next-line @typescript-eslint/no-floating-promises\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.SLIM,\n new CustomError(\n errorTypes.VISUALIZATION,\n 'Failed to instantiate viewer'\n )\n )\n throw error\n }\n}\n\n/*\n * Check whether the report is structured according to template\n * TID 1500 \"MeasurementReport\".\n */\nconst _implementsTID1500 = (\n report: dmv.metadata.Comprehensive3DSR\n): boolean => {\n const templateSeq = report.ContentTemplateSequence\n if (templateSeq.length > 0) {\n const tid = templateSeq[0].TemplateIdentifier\n if (tid === '1500') {\n return true\n }\n }\n return false\n}\n\n/*\n * Check whether the subject described in the report is a specimen as compared\n * to a patient, fetus, or device.\n */\nconst _describesSpecimenSubject = (\n report: dmv.metadata.Comprehensive3DSR\n): boolean => {\n const items = findContentItemsByName({\n content: report.ContentSequence,\n name: new dcmjs.sr.coding.CodedConcept({\n value: '121024',\n schemeDesignator: 'DCM',\n meaning: 'Subject Class'\n })\n })\n if (items.length === 0) {\n return false\n }\n const subjectClassItem = items[0] as dcmjs.sr.valueTypes.CodeContentItem\n const subjectClassValue = subjectClassItem.ConceptCodeSequence[0]\n const retrievedConcept = new dcmjs.sr.coding.CodedConcept({\n value: subjectClassValue.CodeValue,\n meaning: subjectClassValue.CodeMeaning,\n schemeDesignator: subjectClassValue.CodingSchemeDesignator\n })\n const expectedConcept = new dcmjs.sr.coding.CodedConcept({\n value: '121027',\n meaning: 'Specimen',\n schemeDesignator: 'DCM'\n })\n if (retrievedConcept.equals(expectedConcept)) {\n return true\n }\n return false\n}\n\n/*\n * Check whether the report contains appropriate graphic ROI annotations.\n */\nconst _containsROIAnnotations = (\n report: dmv.metadata.Comprehensive3DSR\n): boolean => {\n const measurements = findContentItemsByName({\n content: report.ContentSequence,\n name: new dcmjs.sr.coding.CodedConcept({\n value: '126010',\n schemeDesignator: 'DCM',\n meaning: 'Imaging Measurements'\n })\n })\n if (measurements.length === 0) {\n return false\n }\n const container = measurements[0] as dcmjs.sr.valueTypes.ContainerContentItem\n const measurementGroups = findContentItemsByName({\n content: container.ContentSequence,\n name: new dcmjs.sr.coding.CodedConcept({\n value: '125007',\n schemeDesignator: 'DCM',\n meaning: 'Measurement Group'\n })\n })\n\n let foundRegion = false\n measurementGroups.forEach((group) => {\n const container = group as dcmjs.sr.valueTypes.ContainerContentItem\n const regions = findContentItemsByName({\n content: container.ContentSequence,\n name: new dcmjs.sr.coding.CodedConcept({\n value: '111030',\n schemeDesignator: 'DCM',\n meaning: 'Image Region'\n })\n })\n if (regions.length > 0) {\n if (regions[0].ValueType === dcmjs.sr.valueTypes.ValueTypes.SCOORD3D) {\n foundRegion = true\n }\n }\n })\n\n return foundRegion\n}\n\ninterface EvaluationOptions {\n name: dcmjs.sr.coding.CodedConcept\n values: dcmjs.sr.coding.CodedConcept[]\n}\n\ninterface Evaluation {\n name: dcmjs.sr.coding.CodedConcept\n value: dcmjs.sr.coding.CodedConcept\n}\n\ninterface Measurement {\n name: dcmjs.sr.coding.CodedConcept\n value?: number\n unit: dcmjs.sr.coding.CodedConcept\n}\n\ninterface SlideViewerProps extends RouteComponentProps {\n slide: Slide\n clients: { [key: string]: DicomWebManager }\n studyInstanceUID: string\n seriesInstanceUID: string\n app: {\n name: string\n version: string\n uid: string\n organization?: string\n }\n preload?: boolean\n annotations: AnnotationSettings[]\n enableAnnotationTools: boolean\n user?: {\n name: string\n email: string\n }\n selectedPresentationStateUID?: string\n}\n\ninterface SlideViewerState {\n visibleRoiUIDs: Set\n visibleSegmentUIDs: Set\n visibleMappingUIDs: Set\n visibleAnnotationGroupUIDs: Set\n visibleOpticalPathIdentifiers: Set\n activeOpticalPathIdentifiers: Set\n presentationStates: dmv.metadata.AdvancedBlendingPresentationState[]\n selectedPresentationStateUID?: string\n selectedFinding?: dcmjs.sr.coding.CodedConcept\n selectedEvaluations: Evaluation[]\n selectedGeometryType?: string\n selectedMarkup?: string\n selectedRoi?: dmv.roi.ROI\n selectedRoiUIDs: Set\n generatedReport?: dmv.metadata.Comprehensive3DSR\n isLoading: boolean\n isAnnotationModalVisible: boolean\n isSelectedRoiModalVisible: boolean\n isReportModalVisible: boolean\n isRoiDrawingActive: boolean\n isRoiModificationActive: boolean\n isRoiTranslationActive: boolean\n isGoToModalVisible: boolean\n isSelectedMagnificationValid: boolean\n isSelectedXCoordinateValid: boolean\n isSelectedYCoordinateValid: boolean\n selectedXCoordinate?: number\n validXCoordinateRange: number[]\n selectedYCoordinate?: number\n validYCoordinateRange: number[]\n selectedMagnification?: number\n areRoisHidden: boolean\n pixelDataStatistics: {\n [opticalPathIdentifier: string]: {\n min: number\n max: number\n numFramesSampled: number\n }\n }\n loadingFrames: Set\n}\n\n/**\n * React component for interactive viewing of an individual digital slide,\n * which corresponds to one DICOM Series of DICOM Slide Microscopy images and\n * potentially one or more associated DICOM Series of DICOM SR documents.\n */\nclass SlideViewer extends React.Component {\n private readonly findingOptions: dcmjs.sr.coding.CodedConcept[] = []\n\n private readonly evaluationOptions: { [key: string]: EvaluationOptions[] } = {}\n\n private readonly measurements: Measurement[] = []\n\n private readonly geometryTypeOptions: { [key: string]: string[] } = {}\n\n private readonly volumeViewportRef: React.RefObject\n\n private readonly labelViewportRef: React.RefObject\n\n private volumeViewer: dmv.viewer.VolumeImageViewer\n\n private labelViewer?: dmv.viewer.LabelImageViewer\n\n private readonly defaultRoiStyle: dmv.viewer.ROIStyleOptions = {\n stroke: {\n color: DEFAULT_ROI_STROKE_COLOR,\n width: DEFAULT_ROI_STROKE_WIDTH\n },\n fill: {\n color: DEFAULT_ROI_FILL_COLOR\n },\n image: {\n circle: {\n fill: {\n color: DEFAULT_ROI_STROKE_COLOR\n },\n radius: DEFAULT_ROI_RADIUS\n }\n }\n }\n\n private roiStyles: {[key: string]: dmv.viewer.ROIStyleOptions} = {}\n\n private readonly selectionColor: number[] = [140, 184, 198]\n\n private readonly selectedRoiStyle: dmv.viewer.ROIStyleOptions = {\n stroke: { color: [...this.selectionColor, 1], width: 3 },\n fill: { color: [...this.selectionColor, 0.2] },\n image: {\n circle: {\n radius: 5,\n fill: { color: [...this.selectionColor, 1] }\n }\n }\n }\n\n constructor (props: SlideViewerProps) {\n super(props)\n console.info(\n `view slide \"${this.props.slide.containerIdentifier}\": `,\n this.props.slide\n )\n const geometryTypeOptions = [\n 'point',\n 'circle',\n 'box',\n 'polygon',\n 'line',\n 'freehandpolygon',\n 'freehandline'\n ]\n props.annotations.forEach((annotation: AnnotationSettings) => {\n const finding = new dcmjs.sr.coding.CodedConcept(annotation.finding)\n this.findingOptions.push(finding)\n const key = _buildKey(finding)\n if (annotation.geometryTypes !== undefined) {\n this.geometryTypeOptions[key] = annotation.geometryTypes\n } else {\n this.geometryTypeOptions[key] = geometryTypeOptions\n }\n this.evaluationOptions[key] = []\n if (annotation.evaluations !== undefined) {\n annotation.evaluations.forEach(evaluation => {\n this.evaluationOptions[key].push({\n name: new dcmjs.sr.coding.CodedConcept(evaluation.name),\n values: evaluation.values.map(value => {\n return new dcmjs.sr.coding.CodedConcept(value)\n })\n })\n })\n }\n if (annotation.measurements !== undefined) {\n annotation.measurements.forEach(measurement => {\n this.measurements.push({\n name: new dcmjs.sr.coding.CodedConcept(measurement.name),\n value: undefined,\n unit: new dcmjs.sr.coding.CodedConcept(measurement.unit)\n })\n })\n }\n if (annotation.style != null) {\n this.roiStyles[key] = _formatRoiStyle(annotation.style)\n } else {\n this.roiStyles[key] = this.defaultRoiStyle\n }\n })\n\n this.componentSetup = this.componentSetup.bind(this)\n this.componentCleanup = this.componentCleanup.bind(this)\n\n this.onWindowResize = this.onWindowResize.bind(this)\n this.handleRoiDrawing = this.handleRoiDrawing.bind(this)\n this.handleRoiTranslation = this.handleRoiTranslation.bind(this)\n this.handleRoiModification = this.handleRoiModification.bind(this)\n this.handleRoiVisibilityChange = this.handleRoiVisibilityChange.bind(this)\n this.handleRoiRemoval = this.handleRoiRemoval.bind(this)\n this.handleRoiSelectionCancellation = this.handleRoiSelectionCancellation.bind(this)\n this.handleAnnotationConfigurationCancellation = this.handleAnnotationConfigurationCancellation.bind(this)\n this.handleAnnotationGeometryTypeSelection = this.handleAnnotationGeometryTypeSelection.bind(this)\n this.handleAnnotationMeasurementActivation = this.handleAnnotationMeasurementActivation.bind(this)\n this.handleAnnotationFindingSelection = this.handleAnnotationFindingSelection.bind(this)\n this.handleAnnotationEvaluationSelection = this.handleAnnotationEvaluationSelection.bind(this)\n this.handleAnnotationEvaluationClearance = this.handleAnnotationEvaluationClearance.bind(this)\n this.handleAnnotationConfigurationCompletion = this.handleAnnotationConfigurationCompletion.bind(this)\n this.handleAnnotationSelection = this.handleAnnotationSelection.bind(this)\n this.handleAnnotationVisibilityChange = this.handleAnnotationVisibilityChange.bind(this)\n this.handleAnnotationGroupVisibilityChange = this.handleAnnotationGroupVisibilityChange.bind(this)\n this.handleAnnotationGroupStyleChange = this.handleAnnotationGroupStyleChange.bind(this)\n this.handleGoTo = this.handleGoTo.bind(this)\n this.handleXCoordinateSelection = this.handleXCoordinateSelection.bind(this)\n this.handleYCoordinateSelection = this.handleYCoordinateSelection.bind(this)\n this.handleMagnificationSelection = this.handleMagnificationSelection.bind(this)\n this.handleSlidePositionSelection = this.handleSlidePositionSelection.bind(this)\n this.handleSlidePositionSelectionCancellation = this.handleSlidePositionSelectionCancellation.bind(this)\n this.handleReportGeneration = this.handleReportGeneration.bind(this)\n this.handleReportVerification = this.handleReportVerification.bind(this)\n this.handleReportCancellation = this.handleReportCancellation.bind(this)\n this.handleSegmentVisibilityChange = this.handleSegmentVisibilityChange.bind(this)\n this.handleSegmentStyleChange = this.handleSegmentStyleChange.bind(this)\n this.handleMappingVisibilityChange = this.handleMappingVisibilityChange.bind(this)\n this.handleMappingStyleChange = this.handleMappingStyleChange.bind(this)\n this.handleOpticalPathVisibilityChange = this.handleOpticalPathVisibilityChange.bind(this)\n this.handleOpticalPathStyleChange = this.handleOpticalPathStyleChange.bind(this)\n this.handleOpticalPathActivityChange = this.handleOpticalPathActivityChange.bind(this)\n this.handlePresentationStateSelection = this.handlePresentationStateSelection.bind(this)\n this.handlePresentationStateReset = this.handlePresentationStateReset.bind(this)\n\n const { volumeViewer, labelViewer } = _constructViewers({\n clients: this.props.clients,\n slide: this.props.slide,\n preload: this.props.preload\n })\n this.volumeViewer = volumeViewer\n this.labelViewer = labelViewer\n this.volumeViewportRef = React.createRef()\n this.labelViewportRef = React.createRef()\n\n /**\n * Deactivate all optical paths. Visibility will be set later, potentially\n * using based on available presentation state instances.\n */\n this.volumeViewer.getAllOpticalPaths().forEach(opticalPath => {\n this.volumeViewer.deactivateOpticalPath(opticalPath.identifier)\n })\n\n const [offset, size] = this.volumeViewer.boundingBox\n\n this.state = {\n selectedRoiUIDs: new Set(),\n visibleRoiUIDs: new Set(),\n visibleSegmentUIDs: new Set(),\n visibleMappingUIDs: new Set(),\n visibleAnnotationGroupUIDs: new Set(),\n visibleOpticalPathIdentifiers: new Set(),\n activeOpticalPathIdentifiers: new Set(),\n presentationStates: [],\n selectedFinding: undefined,\n selectedEvaluations: [],\n generatedReport: undefined,\n isLoading: false,\n isAnnotationModalVisible: false,\n isSelectedRoiModalVisible: false,\n isSelectedMagnificationValid: false,\n isReportModalVisible: false,\n isRoiDrawingActive: false,\n isRoiTranslationActive: false,\n isRoiModificationActive: false,\n isGoToModalVisible: false,\n isSelectedXCoordinateValid: false,\n isSelectedYCoordinateValid: false,\n selectedXCoordinate: undefined,\n validXCoordinateRange: [offset[0], offset[0] + size[0]],\n selectedYCoordinate: undefined,\n validYCoordinateRange: [offset[1], offset[1] + size[1]],\n selectedMagnification: undefined,\n areRoisHidden: false,\n pixelDataStatistics: {},\n selectedPresentationStateUID: this.props.selectedPresentationStateUID,\n loadingFrames: new Set()\n }\n }\n\n componentDidUpdate (\n previousProps: SlideViewerProps,\n previousState: SlideViewerState\n ): void {\n /** Fetch data and update the viewports if the route has changed (\n * i.e., if another series has been selected) or if the client has changed.\n */\n if (\n this.props.location.pathname !== previousProps.location.pathname ||\n this.props.studyInstanceUID !== previousProps.studyInstanceUID ||\n this.props.seriesInstanceUID !== previousProps.seriesInstanceUID ||\n this.props.slide !== previousProps.slide ||\n this.props.clients !== previousProps.clients\n ) {\n if (this.volumeViewportRef.current != null) {\n this.volumeViewportRef.current.innerHTML = ''\n }\n this.volumeViewer.cleanup()\n if (this.labelViewer != null) {\n if (this.labelViewportRef.current != null) {\n this.labelViewportRef.current.innerHTML = ''\n }\n this.labelViewer.cleanup()\n }\n const { volumeViewer, labelViewer } = _constructViewers({\n clients: this.props.clients,\n slide: this.props.slide,\n preload: this.props.preload\n })\n this.volumeViewer = volumeViewer\n this.labelViewer = labelViewer\n\n const activeOpticalPathIdentifiers: Set = new Set()\n const visibleOpticalPathIdentifiers: Set = new Set()\n this.volumeViewer.getAllOpticalPaths().forEach(opticalPath => {\n const identifier = opticalPath.identifier\n if (this.volumeViewer.isOpticalPathVisible(identifier)) {\n visibleOpticalPathIdentifiers.add(identifier)\n }\n if (this.volumeViewer.isOpticalPathActive(identifier)) {\n activeOpticalPathIdentifiers.add(identifier)\n }\n })\n\n const [offset, size] = this.volumeViewer.boundingBox\n\n this.setState({\n visibleRoiUIDs: new Set(),\n visibleSegmentUIDs: new Set(),\n visibleMappingUIDs: new Set(),\n visibleAnnotationGroupUIDs: new Set(),\n visibleOpticalPathIdentifiers,\n activeOpticalPathIdentifiers,\n presentationStates: [],\n loadingFrames: new Set(),\n validXCoordinateRange: [offset[0], offset[0] + size[0]],\n validYCoordinateRange: [offset[1], offset[1] + size[1]]\n })\n this.populateViewports()\n }\n }\n\n /**\n * Retrieve Presentation State instances that reference the any images of\n * the currently selected series.\n */\n loadPresentationStates = (): void => {\n console.info('search for Presentation State instances')\n const client = this.props.clients[\n StorageClasses.ADVANCED_BLENDING_PRESENTATION_STATE\n ]\n client.searchForInstances({\n studyInstanceUID: this.props.studyInstanceUID,\n queryParams: {\n Modality: 'PR'\n }\n }).then((matchedInstances): void => {\n if (matchedInstances == null) {\n matchedInstances = []\n }\n matchedInstances.forEach((rawInstance, index) => {\n const { dataset } = dmv.metadata.formatMetadata(rawInstance)\n const instance = dataset as dmv.metadata.Instance\n console.info(`retrieve PR instance \"${instance.SOPInstanceUID}\"`)\n client.retrieveInstance({\n studyInstanceUID: this.props.studyInstanceUID,\n seriesInstanceUID: instance.SeriesInstanceUID,\n sopInstanceUID: instance.SOPInstanceUID\n }).then((retrievedInstance): void => {\n const data = dcmjs.data.DicomMessage.readFile(retrievedInstance)\n const { dataset } = dmv.metadata.formatMetadata(data.dict)\n if (this.props.slide.areVolumeImagesMonochrome) {\n const presentationState = (\n dataset as\n unknown as\n dmv.metadata.AdvancedBlendingPresentationState\n )\n let doesMatch = false\n presentationState.AdvancedBlendingSequence.forEach(blendingItem => {\n doesMatch = this.props.slide.seriesInstanceUIDs.includes(\n blendingItem.SeriesInstanceUID\n )\n }\n )\n if (doesMatch) {\n console.info(\n 'include Advanced Blending Presentation State instance ' +\n `\"${presentationState.SOPInstanceUID}\"`\n )\n if (\n index === 0 &&\n this.props.selectedPresentationStateUID == null\n ) {\n this.setPresentationState(presentationState)\n } else {\n if (\n presentationState.SOPInstanceUID ===\n this.props.selectedPresentationStateUID\n ) {\n this.setPresentationState(presentationState)\n }\n }\n this.setState(state => {\n const mapping: {\n [sopInstanceUID: string]:\n dmv.metadata.AdvancedBlendingPresentationState\n } = {}\n state.presentationStates.forEach(instance => {\n mapping[instance.SOPInstanceUID] = instance\n })\n mapping[presentationState.SOPInstanceUID] = presentationState\n return { presentationStates: Object.values(mapping) }\n })\n }\n } else {\n console.info(\n `ignore presentation state \"${instance.SOPInstanceUID}\", ` +\n 'application of presentation states for color images ' +\n 'has not (yet) been implemented'\n )\n }\n }).catch((error) => {\n // eslint-disable-next-line @typescript-eslint/no-floating-promises\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.SLIM,\n new CustomError(\n errorTypes.VISUALIZATION,\n 'Presentation State could not be loaded'\n )\n )\n console.error(\n 'failed to load presentation state ' +\n `of SOP instance \"${instance.SOPInstanceUID}\" ` +\n `of series \"${instance.SeriesInstanceUID}\" ` +\n `of study \"${this.props.studyInstanceUID}\": `,\n error\n )\n })\n })\n }).catch(() => {\n // eslint-disable-next-line @typescript-eslint/no-floating-promises\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.SLIM,\n new CustomError(\n errorTypes.VISUALIZATION,\n 'Presentation State could not be loaded'\n )\n )\n })\n }\n\n /**\n * Set presentation state as specified by a DICOM Presentation State instance.\n */\n setPresentationState = (\n presentationState: dmv.metadata.AdvancedBlendingPresentationState\n ): void => {\n const opticalPaths = this.volumeViewer.getAllOpticalPaths()\n console.info(\n `apply Presentation State instance \"${presentationState.SOPInstanceUID}\"`\n )\n const opticalPathStyles: {\n [opticalPathIdentifier: string]: {\n opacity: number\n paletteColorLookupTable?: dmv.color.PaletteColorLookupTable\n limitValues?: number[]\n } | null\n } = {}\n opticalPaths.forEach(opticalPath => {\n // First, deactivate and hide all optical paths and reset style\n const identifier = opticalPath.identifier\n this.volumeViewer.hideOpticalPath(identifier)\n this.volumeViewer.deactivateOpticalPath(identifier)\n const style = this.volumeViewer.getOpticalPathDefaultStyle(identifier)\n this.volumeViewer.setOpticalPathStyle(identifier, style)\n\n presentationState.AdvancedBlendingSequence.forEach(blendingItem => {\n /**\n * Referenced Instance Sequence should be used instead of Referenced\n * Image Sequence, but that's easy to mix up and we have encountered\n * implementations that get it wrong.\n */\n let refInstanceItems = blendingItem.ReferencedInstanceSequence\n if (refInstanceItems === undefined) {\n refInstanceItems = blendingItem.ReferencedImageSequence\n }\n if (refInstanceItems === undefined) {\n return\n }\n refInstanceItems.forEach(imageItem => {\n const isReferenced = opticalPath.sopInstanceUIDs.includes(\n imageItem.ReferencedSOPInstanceUID\n ) as boolean\n if (isReferenced) {\n let paletteColorLUT\n if (blendingItem.PaletteColorLookupTableSequence != null) {\n const cpLUTItem = blendingItem.PaletteColorLookupTableSequence[0]\n paletteColorLUT = new dmv.color.PaletteColorLookupTable({\n uid: (\n cpLUTItem.PaletteColorLookupTableUID != null\n ? cpLUTItem.PaletteColorLookupTableUID\n : ''\n ),\n redDescriptor:\n cpLUTItem.RedPaletteColorLookupTableDescriptor,\n greenDescriptor:\n cpLUTItem.GreenPaletteColorLookupTableDescriptor,\n blueDescriptor:\n cpLUTItem.BluePaletteColorLookupTableDescriptor,\n redData: (\n (cpLUTItem.RedPaletteColorLookupTableData != null)\n ? new Uint16Array(\n cpLUTItem.RedPaletteColorLookupTableData\n )\n : undefined\n ),\n greenData: (\n (cpLUTItem.GreenPaletteColorLookupTableData != null)\n ? new Uint16Array(\n cpLUTItem.GreenPaletteColorLookupTableData\n )\n : undefined\n ),\n blueData: (\n (cpLUTItem.BluePaletteColorLookupTableData != null)\n ? new Uint16Array(\n cpLUTItem.BluePaletteColorLookupTableData\n )\n : undefined\n ),\n redSegmentedData: (\n (cpLUTItem.SegmentedRedPaletteColorLookupTableData != null)\n ? new Uint16Array(\n cpLUTItem.SegmentedRedPaletteColorLookupTableData\n )\n : undefined\n ),\n greenSegmentedData: (\n (cpLUTItem.SegmentedGreenPaletteColorLookupTableData != null)\n ? new Uint16Array(\n cpLUTItem.SegmentedGreenPaletteColorLookupTableData\n )\n : undefined\n ),\n blueSegmentedData: (\n (cpLUTItem.SegmentedBluePaletteColorLookupTableData != null)\n ? new Uint16Array(\n cpLUTItem.SegmentedBluePaletteColorLookupTableData\n )\n : undefined\n )\n })\n }\n\n let limitValues\n if (blendingItem.SoftcopyVOILUTSequence != null) {\n const voiLUTItem = blendingItem.SoftcopyVOILUTSequence[0]\n const windowCenter = voiLUTItem.WindowCenter\n const windowWidth = voiLUTItem.WindowWidth\n limitValues = [\n windowCenter - windowWidth * 0.5,\n windowCenter + windowWidth * 0.5\n ]\n }\n\n opticalPathStyles[identifier] = {\n opacity: 1,\n paletteColorLookupTable: paletteColorLUT,\n limitValues: limitValues\n }\n }\n })\n })\n })\n\n const selectedOpticalPathIdentifiers: Set = new Set()\n Object.keys(opticalPathStyles).forEach(identifier => {\n const styleOptions = opticalPathStyles[identifier]\n if (styleOptions != null) {\n this.volumeViewer.setOpticalPathStyle(identifier, styleOptions)\n this.volumeViewer.activateOpticalPath(identifier)\n this.volumeViewer.showOpticalPath(identifier)\n selectedOpticalPathIdentifiers.add(identifier)\n } else {\n this.volumeViewer.hideOpticalPath(identifier)\n this.volumeViewer.deactivateOpticalPath(identifier)\n }\n })\n const searchParams = new URLSearchParams(this.props.location.search)\n searchParams.set('state', presentationState.SOPInstanceUID)\n this.props.navigate(\n {\n pathname: this.props.location.pathname,\n search: searchParams.toString()\n },\n { replace: true }\n )\n this.setState(state => ({\n activeOpticalPathIdentifiers: selectedOpticalPathIdentifiers,\n visibleOpticalPathIdentifiers: selectedOpticalPathIdentifiers,\n selectedPresentationStateUID: presentationState.SOPInstanceUID\n }))\n }\n\n getRoiStyle = (key?: string): dmv.viewer.ROIStyleOptions => {\n if (key == null) {\n return this.defaultRoiStyle\n }\n if (this.roiStyles[key] !== undefined) {\n return this.roiStyles[key]\n }\n return this.defaultRoiStyle\n }\n\n /**\n * Retrieve Structured Report instances that contain regions of interests\n * with 3D spatial coordinates defined in the same frame of reference as the\n * currently selected series and add them to the VOLUME image viewer.\n */\n addAnnotations = (): void => {\n console.info('search for Comprehensive 3D SR instances')\n const client = this.props.clients[StorageClasses.COMPREHENSIVE_3D_SR]\n client.searchForInstances({\n studyInstanceUID: this.props.studyInstanceUID,\n queryParams: {\n Modality: 'SR'\n }\n }).then((matchedInstances): void => {\n if (matchedInstances == null) {\n matchedInstances = []\n }\n matchedInstances.forEach(i => {\n const { dataset } = dmv.metadata.formatMetadata(i)\n const instance = dataset as dmv.metadata.Instance\n if (instance.SOPClassUID === StorageClasses.COMPREHENSIVE_3D_SR) {\n console.info(`retrieve SR instance \"${instance.SOPInstanceUID}\"`)\n client.retrieveInstance({\n studyInstanceUID: this.props.studyInstanceUID,\n seriesInstanceUID: instance.SeriesInstanceUID,\n sopInstanceUID: instance.SOPInstanceUID\n }).then((retrievedInstance): void => {\n const data = dcmjs.data.DicomMessage.readFile(retrievedInstance)\n const { dataset } = dmv.metadata.formatMetadata(data.dict)\n const report = dataset as unknown as dmv.metadata.Comprehensive3DSR\n /*\n * Perform a couple of checks to ensure the document content of the\n * report fullfils the requirements of the application.\n */\n if (!_implementsTID1500(report)) {\n console.debug(\n `ignore SR document \"${report.SOPInstanceUID}\" ` +\n 'because it is not structured according to template ' +\n 'TID 1500 \"MeasurementReport\"'\n )\n return\n }\n if (!_describesSpecimenSubject(report)) {\n console.debug(\n `ignore SR document \"${report.SOPInstanceUID}\" ` +\n 'because it does not describe a specimen subject'\n )\n return\n }\n if (!_containsROIAnnotations(report)) {\n console.debug(\n `ignore SR document \"${report.SOPInstanceUID}\" ` +\n 'because it does not contain any suitable ROI annotations'\n )\n return\n }\n\n const content = new MeasurementReport(report)\n content.ROIs.forEach(roi => {\n console.info(`add ROI \"${roi.uid}\"`)\n const scoord3d = roi.scoord3d\n const image = this.props.slide.volumeImages[0]\n if (scoord3d.frameOfReferenceUID === image.FrameOfReferenceUID) {\n /*\n * ROIs may get assigned new UIDs upon re-rendering of the\n * page and we need to ensure that we don't add them twice.\n * The same ROI may be stored in multiple SR documents and\n * we don't want them to show up twice.\n * TODO: We should probably either \"merge\" measurements and\n * quantitative evaluations or pick the ROI from the \"best\"\n * available report (COMPLETE and VERIFIED).\n */\n const doesROIExist = this.volumeViewer.getAllROIs().some(\n (otherROI: dmv.roi.ROI): boolean => {\n return _areROIsEqual(otherROI, roi)\n }\n )\n if (!doesROIExist) {\n try {\n // Add ROI without style such that it won't be visible.\n this.volumeViewer.addROI(roi, {})\n } catch {\n console.error(`could not add ROI \"${roi.uid}\"`)\n }\n } else {\n console.debug(`skip already existing ROI \"${roi.uid}\"`)\n }\n } else {\n console.debug(\n `skip ROI \"${roi.uid}\" ` +\n `of SR document \"${report.SOPInstanceUID}\"` +\n 'because it is defined in another frame of reference'\n )\n }\n })\n }).catch((error) => {\n // eslint-disable-next-line @typescript-eslint/no-floating-promises\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.SLIM,\n new CustomError(\n errorTypes.VISUALIZATION,\n 'Annotations could not be loaded'\n )\n )\n console.error(\n 'failed to load ROIs ' +\n `of SOP instance \"${instance.SOPInstanceUID}\" ` +\n `of series \"${instance.SeriesInstanceUID}\" ` +\n `of study \"${this.props.studyInstanceUID}\": `,\n error\n )\n })\n /*\n * React is not aware of the fact that ROIs have been added via the\n * viewer (the viewport is a ref object) and won't show the\n * annotations in the user interface unless an update is forced.\n */\n this.forceUpdate()\n }\n })\n }).catch(() => {\n // eslint-disable-next-line @typescript-eslint/no-floating-promises\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.SLIM,\n new CustomError(\n errorTypes.VISUALIZATION,\n 'Annotations could not be loaded'\n )\n )\n })\n }\n\n /**\n * Retrieve Microscopy Bulk Simple Annotations instances that contain\n * annotation groups defined in the same frame of reference as the currently\n * selected series and add them to the VOLUME image viewer.\n */\n addAnnotationGroups = (): void => {\n console.info('search for Microscopy Bulk Simple Annotations instances')\n const client = this.props.clients[\n StorageClasses.MICROSCOPY_BULK_SIMPLE_ANNOTATION\n ]\n client.searchForSeries({\n studyInstanceUID: this.props.studyInstanceUID,\n queryParams: {\n Modality: 'ANN'\n }\n }).then((matchedSeries): void => {\n if (matchedSeries == null) {\n matchedSeries = []\n }\n matchedSeries.forEach(s => {\n const { dataset } = dmv.metadata.formatMetadata(s)\n const series = dataset as dmv.metadata.Series\n client.retrieveSeriesMetadata({\n studyInstanceUID: this.props.studyInstanceUID,\n seriesInstanceUID: series.SeriesInstanceUID\n }).then((retrievedMetadata): void => {\n let annotations: dmv.metadata.MicroscopyBulkSimpleAnnotations[]\n annotations = retrievedMetadata.map(metadata => {\n return new dmv.metadata.MicroscopyBulkSimpleAnnotations({\n metadata\n })\n })\n annotations = annotations.filter(ann => {\n const refImage = this.props.slide.volumeImages[0]\n return (\n ann.FrameOfReferenceUID === refImage.FrameOfReferenceUID &&\n ann.ContainerIdentifier === refImage.ContainerIdentifier\n )\n })\n annotations.forEach(ann => {\n try {\n this.volumeViewer.addAnnotationGroups(ann)\n } catch (error: any) {\n // eslint-disable-next-line @typescript-eslint/no-floating-promises\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.SLIM,\n new CustomError(\n errorTypes.VISUALIZATION,\n 'Microscopy Bulk Simple Annotations cannot be displayed.'\n )\n )\n // eslint-disable-next-line @typescript-eslint/no-floating-promises\n console.error('failed to add annotation groups: ', error)\n }\n ann.AnnotationGroupSequence.forEach(item => {\n const annotationGroupUID = item.AnnotationGroupUID\n const finding = item.AnnotationPropertyTypeCodeSequence[0]\n const key = _buildKey(finding)\n const style = this.roiStyles[key]\n // eslint-disable-next-line @typescript-eslint/prefer-optional-chain\n if (style != null && style.fill != null) {\n this.volumeViewer.setAnnotationGroupStyle(\n annotationGroupUID,\n { color: style.fill.color }\n )\n }\n })\n })\n /*\n * React is not aware of the fact that annotation groups have been\n * added via the viewer (the underlying HTML viewport element is a\n * ref object) and won't show the annotation groups in the user\n * interface unless an update is forced.\n */\n this.forceUpdate()\n }).catch(() => {\n // eslint-disable-next-line @typescript-eslint/no-floating-promises\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.SLIM,\n new CustomError(\n errorTypes.VISUALIZATION,\n 'Retrieval of metadata of Microscopy Bulk Simple Annotations ' +\n 'instances failed.'\n )\n )\n })\n })\n }).catch(() => {\n // eslint-disable-next-line @typescript-eslint/no-floating-promises\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.SLIM,\n new CustomError(\n errorTypes.VISUALIZATION,\n 'Search for Microscopy Bulk Simple Annotations instances failed.'\n )\n )\n })\n }\n\n /**\n * Retrieve Segmentation instances that contain segments defined in the same\n * frame of reference as the currently selected series and add them to the\n * VOLUME image viewer.\n */\n addSegmentations = (): void => {\n console.info('search for Segmentation instances')\n const client = this.props.clients[StorageClasses.SEGMENTATION]\n client.searchForSeries({\n studyInstanceUID: this.props.studyInstanceUID,\n queryParams: {\n Modality: 'SEG'\n }\n }).then((matchedSeries): void => {\n if (matchedSeries == null) {\n matchedSeries = []\n }\n matchedSeries.forEach((s, i) => {\n const { dataset } = dmv.metadata.formatMetadata(s)\n const series = dataset as dmv.metadata.Series\n client.retrieveSeriesMetadata({\n studyInstanceUID: this.props.studyInstanceUID,\n seriesInstanceUID: series.SeriesInstanceUID\n }).then((retrievedMetadata): void => {\n const segmentations: dmv.metadata.Segmentation[] = []\n retrievedMetadata.forEach(metadata => {\n const seg = new dmv.metadata.Segmentation({ metadata })\n const refImage = this.props.slide.volumeImages[0]\n if (\n seg.FrameOfReferenceUID === refImage.FrameOfReferenceUID &&\n seg.ContainerIdentifier === refImage.ContainerIdentifier\n ) {\n segmentations.push(seg)\n }\n })\n if (segmentations.length > 0) {\n try {\n this.volumeViewer.addSegments(segmentations)\n } catch (error: any) {\n // eslint-disable-next-line @typescript-eslint/no-floating-promises\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.SLIM,\n new CustomError(\n errorTypes.VISUALIZATION,\n 'Segmentations cannot be displayed'\n )\n )\n console.error('failed to add segments: ', error)\n }\n /*\n * React is not aware of the fact that segments have been added via\n * the viewer (the underlying HTML viewport element is a ref object)\n * and won't show the segments in the user interface unless an update\n * is forced.\n */\n this.forceUpdate()\n }\n }).catch(() => {\n // eslint-disable-next-line @typescript-eslint/no-floating-promises\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.SLIM,\n new CustomError(\n errorTypes.VISUALIZATION,\n 'Retrieval of metadata of Segmentation instances failed.'\n )\n )\n })\n })\n }).catch(() => {\n // eslint-disable-next-line @typescript-eslint/no-floating-promises\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.SLIM,\n new CustomError(\n errorTypes.VISUALIZATION,\n 'Search for Segmentation instances failed.'\n )\n )\n })\n }\n\n /**\n * Retrieve Parametric Map instances that contain mappings defined in the same\n * frame of reference as the currently selected series and add them to the\n * VOLUME image viewer.\n */\n addParametricMaps = (): void => {\n console.info('search for Parametric Map instances')\n const client = this.props.clients[StorageClasses.PARAMETRIC_MAP]\n client.searchForSeries({\n studyInstanceUID: this.props.studyInstanceUID,\n queryParams: {\n Modality: 'OT'\n }\n }).then((matchedSeries): void => {\n if (matchedSeries == null) {\n matchedSeries = []\n }\n matchedSeries.forEach(s => {\n const { dataset } = dmv.metadata.formatMetadata(s)\n const series = dataset as dmv.metadata.Series\n client.retrieveSeriesMetadata({\n studyInstanceUID: this.props.studyInstanceUID,\n seriesInstanceUID: series.SeriesInstanceUID\n }).then((retrievedMetadata): void => {\n const parametricMaps: dmv.metadata.ParametricMap[] = []\n retrievedMetadata.forEach(metadata => {\n const pm = new dmv.metadata.ParametricMap({ metadata })\n const refImage = this.props.slide.volumeImages[0]\n if (\n pm.FrameOfReferenceUID === refImage.FrameOfReferenceUID &&\n pm.ContainerIdentifier === refImage.ContainerIdentifier\n ) {\n parametricMaps.push(pm)\n } else {\n console.warn(\n `skip Parametric Map instance \"${pm.SOPInstanceUID}\"`\n )\n }\n })\n if (parametricMaps.length > 0) {\n try {\n this.volumeViewer.addParameterMappings(parametricMaps)\n } catch (error: any) {\n // eslint-disable-next-line @typescript-eslint/no-floating-promises\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.SLIM,\n new CustomError(\n errorTypes.VISUALIZATION,\n 'Parametric Map cannot be displayed'\n )\n )\n console.error('failed to add mappings: ', error)\n }\n /*\n * React is not aware of the fact that mappings have been added via\n * the viewer (the underlying HTML viewport element is a ref object)\n * and won't show the mappings in the user interface unless an update\n * is forced.\n */\n this.forceUpdate()\n }\n }).catch(() => {\n // eslint-disable-next-line @typescript-eslint/no-floating-promises\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.SLIM,\n new CustomError(\n errorTypes.VISUALIZATION,\n 'Retrieval of metadata of Parametric Map instances failed.'\n )\n )\n })\n })\n }).catch(() => {\n // eslint-disable-next-line @typescript-eslint/no-floating-promises\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.SLIM,\n new CustomError(\n errorTypes.VISUALIZATION,\n 'Search for Parametric Map instances failed.'\n )\n )\n })\n }\n\n /**\n * Populate viewports of the VOLUME and LABEL image viewers.\n */\n populateViewports = (): void => {\n console.info('populate viewports...')\n this.setState({\n isLoading: true,\n presentationStates: []\n })\n\n if (this.volumeViewportRef.current != null) {\n this.volumeViewer.render({ container: this.volumeViewportRef.current })\n }\n if (\n this.labelViewportRef.current != null &&\n this.labelViewer != null\n ) {\n this.labelViewer.render({ container: this.labelViewportRef.current })\n }\n\n // State update will also ensure that the component is re-rendered.\n this.setState({ isLoading: false })\n\n this.setDefaultPresentationState()\n this.loadPresentationStates()\n\n this.addAnnotations()\n this.addAnnotationGroups()\n this.addSegmentations()\n this.addParametricMaps()\n }\n\n onRoiModified = (event: CustomEventInit): void => {\n // Update state to trigger rendering\n this.setState(state => ({\n visibleRoiUIDs: new Set(state.visibleRoiUIDs)\n }))\n }\n\n onWindowResize = (event: Event): void => {\n console.info('resize viewports')\n this.volumeViewer.resize()\n if (this.labelViewer != null) {\n this.labelViewer.resize()\n }\n }\n\n onRoiDrawn = (event: CustomEventInit): void => {\n const roi = event.detail.payload as dmv.roi.ROI\n const selectedFinding = this.state.selectedFinding\n const selectedEvaluations = this.state.selectedEvaluations\n if (roi !== undefined && selectedFinding !== undefined) {\n console.debug(`add ROI \"${roi.uid}\"`)\n const findingItem = new dcmjs.sr.valueTypes.CodeContentItem({\n name: new dcmjs.sr.coding.CodedConcept({\n value: '121071',\n meaning: 'Finding',\n schemeDesignator: 'DCM'\n }),\n value: selectedFinding,\n relationshipType: 'CONTAINS'\n })\n roi.addEvaluation(findingItem)\n selectedEvaluations.forEach((evaluation: Evaluation) => {\n const item = new dcmjs.sr.valueTypes.CodeContentItem({\n name: evaluation.name,\n value: evaluation.value,\n relationshipType: 'CONTAINS'\n })\n roi.addEvaluation(item)\n })\n const key = _buildKey(selectedFinding)\n const style = this.getRoiStyle(key)\n this.volumeViewer.addROI(roi, style)\n this.setState(state => {\n const visibleRoiUIDs = state.visibleRoiUIDs\n visibleRoiUIDs.add(roi.uid)\n return { visibleRoiUIDs }\n })\n } else {\n console.debug(`could not add ROI \"${roi.uid}\"`)\n }\n }\n\n onRoiDoubleClicked = (event: CustomEventInit): void => {\n const selectedRoi = event.detail.payload as dmv.roi.ROI\n if (selectedRoi != null) {\n this.setState({\n isSelectedRoiModalVisible: true\n })\n } else {\n this.setState({\n isSelectedRoiModalVisible: false\n })\n }\n }\n\n onRoiSelected = (event: CustomEventInit): void => {\n const selectedRoi = event.detail.payload as dmv.roi.ROI\n if (selectedRoi != null) {\n console.debug(`selected ROI \"${selectedRoi.uid}\"`)\n this.volumeViewer.setROIStyle(selectedRoi.uid, this.selectedRoiStyle)\n const key = _getRoiKey(selectedRoi)\n this.volumeViewer.getAllROIs().forEach((roi) => {\n if (roi.uid !== selectedRoi.uid) {\n this.volumeViewer.setROIStyle(roi.uid, this.getRoiStyle(key))\n }\n })\n this.setState({\n selectedRoiUIDs: new Set([selectedRoi.uid]),\n selectedRoi: selectedRoi\n })\n } else {\n this.setState({\n selectedRoiUIDs: new Set(),\n selectedRoi: undefined\n })\n }\n }\n\n handleRoiSelectionCancellation (): void {\n this.setState({\n isSelectedRoiModalVisible: false\n })\n }\n\n onLoadingStarted = (event: CustomEventInit): void => {\n this.setState({ isLoading: true })\n }\n\n onLoadingEnded = (event: CustomEventInit): void => {\n this.setState({ isLoading: false })\n }\n\n onFrameLoadingStarted = (event: CustomEventInit): void => {\n const frameInfo: {\n studyInstanceUID: string\n seriesInstanceUID: string\n sopInstanceUID: string\n sopClassUID: string\n frameNumber: string\n channelIdentifier: string\n } = event.detail.payload\n const key: string = `${frameInfo.sopInstanceUID}-${frameInfo.frameNumber}`\n this.setState(state => {\n state.loadingFrames.add(key)\n return state\n })\n }\n\n onFrameLoadingEnded = (event: CustomEventInit): void => {\n const frameInfo: {\n studyInstanceUID: string\n seriesInstanceUID: string\n sopInstanceUID: string\n sopClassUID: string\n frameNumber: string\n channelIdentifier: string\n pixelArray: Uint8Array|Uint16Array|Float32Array|null\n } = event.detail.payload\n const key = `${frameInfo.sopInstanceUID}-${frameInfo.frameNumber}`\n this.setState(state => {\n state.loadingFrames.delete(key)\n let isLoading: boolean = false\n if (state.loadingFrames.size > 0) {\n isLoading = true\n }\n return {\n isLoading,\n loadingFrames: state.loadingFrames\n }\n })\n if (\n frameInfo.sopClassUID === StorageClasses.VL_WHOLE_SLIDE_MICROSCOPY_IMAGE &&\n this.props.slide.areVolumeImagesMonochrome\n ) {\n const opticalPathIdentifier = frameInfo.channelIdentifier\n if (\n !(opticalPathIdentifier in this.state.pixelDataStatistics) &&\n frameInfo.pixelArray != null\n ) {\n /*\n * There are limits on the number of arguments Math.min and Math.max\n * functions can accept. Therefore, we compute values in smaller chunks.\n */\n const size = 2 ** 16\n const chunks = Math.ceil(frameInfo.pixelArray.length / size)\n let offset = 0\n const minValues: number[] = []\n const maxValues: number[] = []\n for (let i = 0; i < chunks; i++) {\n offset = i * size\n const pixels = frameInfo.pixelArray.slice(offset, offset + size)\n minValues.push(Math.min(...pixels))\n maxValues.push(Math.max(...pixels))\n }\n const min = Math.min(...minValues)\n const max = Math.max(...maxValues)\n this.setState(state => {\n const stats = state.pixelDataStatistics\n if (stats[opticalPathIdentifier] != null) {\n stats[opticalPathIdentifier] = {\n min: Math.min(stats[opticalPathIdentifier].min, min),\n max: Math.max(stats[opticalPathIdentifier].max, max),\n numFramesSampled: stats[opticalPathIdentifier].numFramesSampled + 1\n }\n } else {\n stats[opticalPathIdentifier] = {\n min: min,\n max: max,\n numFramesSampled: 1\n }\n }\n if (state.selectedPresentationStateUID == null) {\n const style = {\n ...this.volumeViewer.getOpticalPathStyle(opticalPathIdentifier)\n }\n style.limitValues = [\n stats[opticalPathIdentifier].min,\n stats[opticalPathIdentifier].max\n ]\n this.volumeViewer.setOpticalPathStyle(opticalPathIdentifier, style)\n }\n return state\n })\n }\n }\n }\n\n onRoiRemoved = (event: CustomEventInit): void => {\n const roi = event.detail.payload as dmv.roi.ROI\n console.debug(`removed ROI \"${roi.uid}\"`)\n }\n\n componentCleanup (): void {\n document.body.removeEventListener(\n 'dicommicroscopyviewer_roi_drawn',\n this.onRoiDrawn\n )\n document.body.removeEventListener(\n 'dicommicroscopyviewer_roi_selected',\n this.onRoiSelected\n )\n document.body.removeEventListener(\n 'dicommicroscopyviewer_roi_double_clicked',\n this.onRoiDoubleClicked\n )\n document.body.removeEventListener(\n 'dicommicroscopyviewer_roi_removed',\n this.onRoiRemoved\n )\n document.body.removeEventListener(\n 'dicommicroscopyviewer_roi_modified',\n this.onRoiModified\n )\n document.body.removeEventListener(\n 'dicommicroscopyviewer_loading_started',\n this.onLoadingStarted\n )\n document.body.removeEventListener(\n 'dicommicroscopyviewer_loading_ended',\n this.onLoadingEnded\n )\n document.body.removeEventListener(\n 'dicommicroscopyviewer_frame_loading_started',\n this.onFrameLoadingStarted\n )\n document.body.removeEventListener(\n 'dicommicroscopyviewer_frame_loading_ended',\n this.onFrameLoadingEnded\n )\n document.body.removeEventListener(\n 'keyup',\n this.onKeyUp\n )\n window.removeEventListener('resize', this.onWindowResize)\n\n this.volumeViewer.cleanup()\n if (this.labelViewer != null) {\n this.labelViewer.cleanup()\n }\n /*\n * FIXME: React appears to not clean the content of referenced\n * HTMLDivElement objects when the page is reloaded. As a consequence,\n * optical paths and other display items cannot be toggled or updated after\n * a manual page reload. I have tried using ref callbacks and passing the\n * ref objects from the parent component via the props. Both didn't work\n * either.\n */\n }\n\n onKeyUp = (event: KeyboardEvent): void => {\n if (event.key === 'Escape') {\n if (this.state.isRoiDrawingActive) {\n console.info('deactivate drawing of ROIs')\n this.volumeViewer.deactivateDrawInteraction()\n this.volumeViewer.activateSelectInteraction({})\n } else if (this.state.isRoiModificationActive) {\n console.info('deactivate modification of ROIs')\n this.volumeViewer.deactivateModifyInteraction()\n this.volumeViewer.activateSelectInteraction({})\n } else if (this.state.isRoiTranslationActive) {\n console.info('deactivate modification of ROIs')\n this.volumeViewer.deactivateTranslateInteraction()\n this.volumeViewer.activateSelectInteraction({})\n }\n this.setState({\n isAnnotationModalVisible: false,\n isSelectedRoiModalVisible: false,\n isRoiTranslationActive: false,\n isRoiDrawingActive: false,\n isRoiModificationActive: false,\n isGoToModalVisible: false\n })\n } else if (event.altKey) {\n if (event.code === 'KeyD') {\n this.handleRoiDrawing()\n } else if (event.code === 'KeyM') {\n this.handleRoiModification()\n } else if (event.code === 'KeyT') {\n this.handleRoiTranslation()\n } else if (event.code === 'KeyR') {\n this.handleRoiRemoval()\n } else if (event.code === 'KeyV') {\n this.handleRoiVisibilityChange()\n } else if (event.code === 'KeyS') {\n this.handleReportGeneration()\n } else if (event.code === 'KeyG') {\n this.handleGoTo()\n }\n }\n }\n\n componentWillUnmount (): void {\n window.removeEventListener('beforeunload', this.componentCleanup)\n }\n\n componentSetup (): void {\n document.body.addEventListener(\n 'dicommicroscopyviewer_roi_drawn',\n this.onRoiDrawn\n )\n document.body.addEventListener(\n 'dicommicroscopyviewer_roi_selected',\n this.onRoiSelected\n )\n document.body.addEventListener(\n 'dicommicroscopyviewer_roi_double_clicked',\n this.onRoiDoubleClicked\n )\n document.body.addEventListener(\n 'dicommicroscopyviewer_roi_removed',\n this.onRoiRemoved\n )\n document.body.addEventListener(\n 'dicommicroscopyviewer_roi_modified',\n this.onRoiModified\n )\n document.body.addEventListener(\n 'dicommicroscopyviewer_loading_started',\n this.onLoadingStarted\n )\n document.body.addEventListener(\n 'dicommicroscopyviewer_loading_ended',\n this.onLoadingEnded\n )\n document.body.addEventListener(\n 'dicommicroscopyviewer_frame_loading_started',\n this.onFrameLoadingStarted\n )\n document.body.addEventListener(\n 'dicommicroscopyviewer_frame_loading_ended',\n this.onFrameLoadingEnded\n )\n document.body.addEventListener(\n 'keyup',\n this.onKeyUp\n )\n window.addEventListener('resize', this.onWindowResize)\n }\n\n componentDidMount (): void {\n window.addEventListener('beforeunload', this.componentCleanup)\n this.componentSetup()\n this.populateViewports()\n\n if (!this.props.slide.areVolumeImagesMonochrome) {\n let hasICCProfile = false\n const image = this.props.slide.volumeImages[0]\n const metadataItem = image.OpticalPathSequence[0]\n if (metadataItem.ICCProfile == null) {\n if ('OpticalPathSequence' in image.bulkdataReferences) {\n // @ts-expect-error\n const bulkdataItem = image.bulkdataReferences.OpticalPathSequence[0]\n if ('ICCProfile' in bulkdataItem) {\n hasICCProfile = true\n }\n }\n } else {\n hasICCProfile = true\n }\n if (!hasICCProfile) {\n // eslint-disable-next-line @typescript-eslint/no-floating-promises\n message.warning('No ICC Profile was found for color images')\n }\n }\n }\n\n /**\n * Handler that gets called when a finding has been selected for annotation.\n *\n * @param value - Code value of the coded finding that got selected\n * @param option - Option that got selected\n */\n handleAnnotationFindingSelection (\n value: string,\n option: any\n ): void {\n this.findingOptions.forEach(finding => {\n if (finding.CodeValue === value) {\n console.info(`selected finding \"${finding.CodeMeaning}\"`)\n this.setState({\n selectedFinding: finding,\n selectedEvaluations: []\n })\n }\n })\n }\n\n /**\n * Handler that gets called when a geometry type has been selected for\n * annotation.\n *\n * @param value - Code value of the coded finding that got selected\n * @param option - Option that got selected\n */\n handleAnnotationGeometryTypeSelection (value: string, option: any): void {\n this.setState({ selectedGeometryType: value })\n }\n\n /**\n * Handler that gets called when measurements have been selected for\n * annotation.\n */\n handleAnnotationMeasurementActivation (event: any): void {\n const active: boolean = event.target.checked\n if (active) {\n this.setState({ selectedMarkup: 'measurement' })\n } else {\n this.setState({ selectedMarkup: undefined })\n }\n }\n\n /**\n * Handler that gets called when an evaluation has been selected for an\n * annotation.\n *\n * @param value - Code value of the coded evaluation that got selected\n * @param option - Option that got selected\n */\n handleAnnotationEvaluationSelection (\n value: string,\n option: any\n ): void {\n const selectedFinding = this.state.selectedFinding\n if (selectedFinding !== undefined) {\n const key = _buildKey(selectedFinding)\n const name = option.label\n this.evaluationOptions[key].forEach(evaluation => {\n if (\n evaluation.name.CodeValue === name.CodeValue &&\n evaluation.name.CodingSchemeDesignator === name.CodingSchemeDesignator\n ) {\n evaluation.values.forEach(code => {\n if (code.CodeValue === value) {\n const filteredEvaluations = this.state.selectedEvaluations.filter(\n (item: Evaluation) => item.name !== evaluation.name\n )\n this.setState({\n selectedEvaluations: [\n ...filteredEvaluations,\n { name: name, value: code }\n ]\n })\n }\n })\n }\n })\n }\n }\n\n /**\n * Handler that gets called when an evaluation has been cleared for an\n * annotation.\n */\n handleAnnotationEvaluationClearance (): void {\n this.setState({\n selectedEvaluations: []\n })\n }\n\n handleXCoordinateSelection (value: any): void {\n if (value != null) {\n const x = Number(value)\n const start = this.state.validXCoordinateRange[0]\n const end = this.state.validXCoordinateRange[1]\n if (x >= start && x <= end) {\n this.setState({\n selectedXCoordinate: x,\n isSelectedXCoordinateValid: true\n })\n return\n }\n }\n this.setState({\n selectedXCoordinate: undefined,\n isSelectedXCoordinateValid: false\n })\n }\n\n handleYCoordinateSelection (value: any): void {\n if (value != null) {\n const y = Number(value)\n const start = this.state.validYCoordinateRange[0]\n const end = this.state.validYCoordinateRange[1]\n if (y >= start && y <= end) {\n this.setState({\n selectedYCoordinate: y,\n isSelectedYCoordinateValid: true\n })\n return\n }\n }\n this.setState({\n selectedYCoordinate: undefined,\n isSelectedYCoordinateValid: false\n })\n }\n\n handleMagnificationSelection (value: any): void {\n if (value != null) {\n if (value > 0 && value <= 40) {\n this.setState({\n selectedMagnification: Number(value),\n isSelectedMagnificationValid: true\n })\n return\n }\n }\n this.setState({\n selectedMagnification: undefined,\n isSelectedMagnificationValid: false\n })\n }\n\n /**\n * Handler that gets called when the selection of slide position was\n * completed.\n */\n handleSlidePositionSelection (): void {\n if (\n this.state.isSelectedXCoordinateValid &&\n this.state.isSelectedYCoordinateValid &&\n this.state.isSelectedMagnificationValid &&\n this.state.selectedXCoordinate != null &&\n this.state.selectedYCoordinate != null &&\n this.state.selectedMagnification != null\n ) {\n console.info(\n 'select slide position ' +\n `(${this.state.selectedXCoordinate}, ` +\n `${this.state.selectedYCoordinate}) ` +\n `at ${this.state.selectedMagnification}x magnification`\n )\n\n const factor = this.state.selectedMagnification\n /**\n * On an optical microscope an objective with 1x magnification\n * corresponds to approximately 10 micrometer pixel spacing\n * (due to the ocular).\n */\n const targetPixelSpacing = 0.01 / factor\n const diffs = []\n for (let i = 0; i < this.volumeViewer.numLevels; i++) {\n const actualPixelSpacing = this.volumeViewer.getPixelSpacing(i)[0]\n diffs.push(Math.abs(targetPixelSpacing - actualPixelSpacing))\n }\n const level = diffs.indexOf(Math.min(...diffs))\n this.volumeViewer.navigate({\n position: [\n this.state.selectedXCoordinate,\n this.state.selectedYCoordinate\n ],\n level: level\n })\n const point = new dmv.scoord3d.Point({\n coordinates: [\n this.state.selectedXCoordinate,\n this.state.selectedYCoordinate,\n 0\n ],\n frameOfReferenceUID: this.volumeViewer.frameOfReferenceUID\n })\n const roi = new dmv.roi.ROI({ scoord3d: point })\n this.volumeViewer.addROI(roi, this.defaultRoiStyle)\n this.setState(state => {\n const visibleRoiUIDs = state.visibleRoiUIDs\n visibleRoiUIDs.add(roi.uid)\n return {\n visibleRoiUIDs,\n isGoToModalVisible: false\n }\n })\n }\n }\n\n /**\n * Handler that gets called when the selection of a slide position was\n * canceled.\n */\n handleSlidePositionSelectionCancellation (): void {\n console.log('cancel slide position selection')\n this.setState({\n isGoToModalVisible: false,\n isSelectedXCoordinateValid: false,\n isSelectedYCoordinateValid: false,\n isSelectedMagnificationValid: false,\n selectedXCoordinate: undefined,\n selectedYCoordinate: undefined,\n selectedMagnification: undefined\n })\n }\n\n /**\n * Handler that gets called when annotation configuration has been completed.\n */\n handleAnnotationConfigurationCompletion (): void {\n console.debug('complete annotation configuration')\n const finding = this.state.selectedFinding\n const geometryType = this.state.selectedGeometryType\n const markup = this.state.selectedMarkup\n if (geometryType !== undefined && finding !== undefined) {\n this.volumeViewer.activateDrawInteraction({ geometryType, markup })\n this.setState({\n isAnnotationModalVisible: false,\n isRoiDrawingActive: true\n })\n } else {\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.SLIM,\n new CustomError(\n errorTypes.VISUALIZATION,\n 'Could not complete annotation configuration'\n )\n )\n }\n }\n\n /**\n * Handler that gets called when annotation configuration has been cancelled.\n */\n handleAnnotationConfigurationCancellation (): void {\n console.debug('cancel annotation configuration')\n this.setState({\n isAnnotationModalVisible: false,\n isRoiDrawingActive: false\n })\n }\n\n /**\n * Handler that gets called when a report should be generated for the current\n * set of annotations.\n */\n handleReportGeneration (): void {\n console.info('save ROIs')\n const rois = this.volumeViewer.getAllROIs()\n const opticalPaths = this.volumeViewer.getAllOpticalPaths()\n const metadata = this.volumeViewer.getOpticalPathMetadata(\n opticalPaths[0].identifier\n )\n // Metadata should be sorted such that the image with the highest\n // resolution is the last item in the array.\n const refImage = metadata[metadata.length - 1]\n // We assume that there is only one specimen (tissue section) per\n // ontainer (slide). Only the tissue section is tracked with a unique\n // identifier, even if the section may be composed of different biological\n // samples.\n if (refImage.SpecimenDescriptionSequence.length > 1) {\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.SLIM,\n new CustomError(\n errorTypes.VISUALIZATION,\n 'More than one specimen has been described for the slide'\n )\n )\n }\n const refSpecimen = refImage.SpecimenDescriptionSequence[0]\n\n console.debug('create Observation Context')\n let observer\n if (this.props.user !== undefined) {\n observer = new dcmjs.sr.templates.PersonObserverIdentifyingAttributes({\n name: this.props.user.name,\n loginName: this.props.user.email\n })\n } else {\n console.warn('no user information available')\n observer = new dcmjs.sr.templates.PersonObserverIdentifyingAttributes({\n name: 'ANONYMOUS'\n })\n }\n const observationContext = new dcmjs.sr.templates.ObservationContext({\n observerPersonContext: new dcmjs.sr.templates.ObserverContext({\n observerType: new dcmjs.sr.coding.CodedConcept({\n value: '121006',\n schemeDesignator: 'DCM',\n meaning: 'Person'\n }),\n observerIdentifyingAttributes: observer\n }),\n observerDeviceContext: new dcmjs.sr.templates.ObserverContext({\n observerType: new dcmjs.sr.coding.CodedConcept({\n value: '121007',\n schemeDesignator: 'DCM',\n meaning: 'Device'\n }),\n observerIdentifyingAttributes:\n new dcmjs.sr.templates.DeviceObserverIdentifyingAttributes({\n uid: this.props.app.uid,\n manufacturerName: 'MGH Computational Pathology',\n modelName: this.props.app.name\n })\n }),\n subjectContext: new dcmjs.sr.templates.SubjectContext({\n subjectClass: new dcmjs.sr.coding.CodedConcept({\n value: '121027',\n schemeDesignator: 'DCM',\n meaning: 'Specimen'\n }),\n subjectClassSpecificContext:\n new dcmjs.sr.templates.SubjectContextSpecimen({\n uid: refSpecimen.SpecimenUID,\n identifier: refSpecimen.SpecimenIdentifier,\n containerIdentifier: refImage.ContainerIdentifier\n })\n })\n })\n\n console.debug('encode Imaging Measurements')\n const imagingMeasurements: dcmjs.sr.valueTypes.ContainerContentItem[] = []\n for (let i = 0; i < rois.length; i++) {\n const roi = rois[i]\n if (!this.state.visibleRoiUIDs.has(roi.uid)) {\n continue\n }\n let findingType = roi.evaluations.find(\n (item: dcmjs.sr.valueTypes.ContentItem) => {\n return item.ConceptNameCodeSequence[0].CodeValue === '121071'\n }\n )\n if (findingType === undefined) {\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.SLIM,\n new CustomError(\n errorTypes.ENCODINGANDDECODING,\n `No finding type was specified for ROI \"${roi.uid}\"`\n )\n )\n }\n findingType = findingType as dcmjs.sr.valueTypes.CodeContentItem\n const group = new dcmjs.sr.templates.PlanarROIMeasurementsAndQualitativeEvaluations({\n trackingIdentifier: new dcmjs.sr.templates.TrackingIdentifier({\n uid: roi.properties.trackingUID ?? roi.uid,\n identifier: `ROI #${i + 1}`\n }),\n referencedRegion: new dcmjs.sr.contentItems.ImageRegion3D({\n graphicType: roi.scoord3d.graphicType,\n graphicData: roi.scoord3d.graphicData,\n frameOfReferenceUID: roi.scoord3d.frameOfReferenceUID\n }),\n findingType: new dcmjs.sr.coding.CodedConcept({\n value: findingType.ConceptCodeSequence[0].CodeValue,\n schemeDesignator:\n findingType.ConceptCodeSequence[0].CodingSchemeDesignator,\n meaning: findingType.ConceptCodeSequence[0].CodeMeaning\n }),\n qualitativeEvaluations: roi.evaluations.filter(\n (item: dcmjs.sr.valueTypes.ContentItem) => {\n return item.ConceptNameCodeSequence[0].CodeValue !== '121071'\n }\n ),\n measurements: roi.measurements\n })\n const measurements = group as dcmjs.sr.valueTypes.ContainerContentItem[]\n measurements[0].ContentTemplateSequence = [{\n MappingResource: 'DCMR',\n TemplateIdentifier: '1410'\n }]\n imagingMeasurements.push(...measurements)\n }\n\n console.debug('create Measurement Report document content')\n const measurementReport = new dcmjs.sr.templates.MeasurementReport({\n languageOfContentItemAndDescendants: new dcmjs.sr.templates.LanguageOfContentItemAndDescendants({}),\n observationContext: observationContext,\n procedureReported: new dcmjs.sr.coding.CodedConcept({\n value: '112703',\n schemeDesignator: 'DCM',\n meaning: 'Whole Slide Imaging'\n }),\n imagingMeasurements: imagingMeasurements\n })\n\n console.info('create Comprehensive 3D SR document')\n const dataset = new dcmjs.sr.documents.Comprehensive3DSR({\n content: measurementReport[0],\n evidence: [refImage],\n seriesInstanceUID: dcmjs.data.DicomMetaDictionary.uid(),\n seriesNumber: 1,\n seriesDescription: 'Annotation',\n sopInstanceUID: dcmjs.data.DicomMetaDictionary.uid(),\n instanceNumber: 1,\n manufacturer: 'MGH Computational Pathology',\n previousVersions: undefined // TODO\n })\n\n this.setState({\n isReportModalVisible: true,\n generatedReport: dataset as dmv.metadata.Comprehensive3DSR\n })\n }\n\n /**\n * Handler that gets called when a report should be verified. The current\n * list of annotations will be presented to the user together with other\n * pertinent metadata about the patient, study, and specimen.\n */\n handleReportVerification (): void {\n console.info('verfied report')\n\n const report = this.state.generatedReport\n if (report !== undefined) {\n const dataset = report as unknown as dmv.metadata.Comprehensive3DSR\n console.debug('create File Meta Information')\n const fileMetaInformationVersionArray = new Uint8Array(2)\n fileMetaInformationVersionArray[1] = 1\n const fileMeta = {\n // FileMetaInformationVersion\n '00020001': {\n Value: [fileMetaInformationVersionArray.buffer],\n vr: 'OB'\n },\n // MediaStorageSOPClassUID\n '00020002': {\n Value: [dataset.SOPClassUID],\n vr: 'UI'\n },\n // MediaStorageSOPInstanceUID\n '00020003': {\n Value: [dataset.SOPInstanceUID],\n vr: 'UI'\n },\n // TransferSyntaxUID\n '00020010': {\n Value: ['1.2.840.10008.1.2.1'],\n vr: 'UI'\n },\n // ImplementationClassUID\n '00020012': {\n Value: [this.props.app.uid],\n vr: 'UI'\n }\n }\n\n console.info('store Comprehensive 3D SR document')\n const writer = new dcmjs.data.DicomDict(fileMeta)\n writer.dict = dcmjs.data.DicomMetaDictionary.denaturalizeDataset(dataset)\n const buffer = writer.write()\n const client = this.props.clients[StorageClasses.COMPREHENSIVE_3D_SR]\n client.storeInstances({ datasets: [buffer] }).then(\n (response: any) => message.info('Annotations were saved.')\n ).catch(() => {\n // eslint-disable-next-line @typescript-eslint/no-floating-promises\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.SLIM,\n new CustomError(\n errorTypes.ENCODINGANDDECODING,\n 'Annotations could not be saved'\n )\n )\n })\n }\n this.setState({\n isReportModalVisible: false,\n generatedReport: undefined\n })\n }\n\n /**\n * Handler that gets called when report generation has been cancelled.\n */\n handleReportCancellation (): void {\n this.setState({\n isReportModalVisible: false,\n generatedReport: undefined\n })\n }\n\n /**\n * Handler that gets called when an annotation has been selected from the\n * current list of annotations.\n */\n handleAnnotationSelection ({ roiUID }: { roiUID: string }): void {\n console.log(`selected ROI ${roiUID}`)\n this.setState({ selectedRoiUIDs: new Set([roiUID]) })\n this.volumeViewer.getAllROIs().forEach((roi) => {\n let style = {}\n if (roi.uid === roiUID) {\n style = this.selectedRoiStyle\n this.setState(state => {\n const visibleRoiUIDs = state.visibleRoiUIDs\n visibleRoiUIDs.add(roi.uid)\n return { visibleRoiUIDs }\n })\n } else {\n if (this.state.visibleRoiUIDs.has(roi.uid)) {\n const key = _getRoiKey(roi)\n style = this.getRoiStyle(key)\n }\n }\n this.volumeViewer.setROIStyle(roi.uid, style)\n })\n }\n\n /**\n * Handle toggling of annotation visibility, i.e., whether a given\n * annotation should be either displayed or hidden by the viewer.\n */\n handleAnnotationVisibilityChange ({ roiUID, isVisible }: {\n roiUID: string\n isVisible: boolean\n }): void {\n if (isVisible) {\n console.info(`show ROI ${roiUID}`)\n const roi = this.volumeViewer.getROI(roiUID)\n const key = _getRoiKey(roi)\n this.volumeViewer.setROIStyle(roi.uid, this.getRoiStyle(key))\n this.setState(state => {\n const visibleRoiUIDs = state.visibleRoiUIDs\n visibleRoiUIDs.add(roi.uid)\n return { visibleRoiUIDs }\n })\n } else {\n console.info(`hide ROI ${roiUID}`)\n this.setState(state => {\n const selectedRoiUIDs = state.selectedRoiUIDs\n selectedRoiUIDs.delete(roiUID)\n const visibleRoiUIDs = state.visibleRoiUIDs\n visibleRoiUIDs.delete(roiUID)\n return { visibleRoiUIDs, selectedRoiUIDs }\n })\n this.volumeViewer.setROIStyle(roiUID, {})\n }\n }\n\n /**\n * Handle toggling of annotation group visibility, i.e., whether a given\n * annotation group should be either displayed or hidden by the viewer.\n */\n handleAnnotationGroupVisibilityChange ({ annotationGroupUID, isVisible }: {\n annotationGroupUID: string\n isVisible: boolean\n }): void {\n console.log(`change visibility of annotation group ${annotationGroupUID}`)\n if (isVisible) {\n console.info(`show annotation group ${annotationGroupUID}`)\n try {\n this.volumeViewer.showAnnotationGroup(annotationGroupUID)\n } catch (error) {\n // eslint-disable-next-line @typescript-eslint/no-floating-promises\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.SLIM,\n new CustomError(\n errorTypes.VISUALIZATION,\n 'Failed to show annotation group.'\n )\n )\n throw error\n }\n this.setState(state => {\n const visibleAnnotationGroupUIDs = new Set(\n state.visibleAnnotationGroupUIDs\n )\n visibleAnnotationGroupUIDs.add(annotationGroupUID)\n return { visibleAnnotationGroupUIDs }\n })\n } else {\n console.info(`hide annotation group ${annotationGroupUID}`)\n this.volumeViewer.hideAnnotationGroup(annotationGroupUID)\n this.setState(state => {\n const visibleAnnotationGroupUIDs = new Set(\n state.visibleAnnotationGroupUIDs\n )\n visibleAnnotationGroupUIDs.delete(annotationGroupUID)\n return { visibleAnnotationGroupUIDs }\n })\n }\n }\n\n /**\n * Handle change of annotation group style.\n */\n handleAnnotationGroupStyleChange ({ annotationGroupUID, styleOptions }: {\n annotationGroupUID: string\n styleOptions: {\n opacity?: number\n color?: number[]\n measurement?: dcmjs.sr.coding.CodedConcept\n }\n }): void {\n console.log(`change style of annotation group ${annotationGroupUID}`)\n try {\n this.volumeViewer.setAnnotationGroupStyle(\n annotationGroupUID,\n styleOptions\n )\n } catch (error) {\n // eslint-disable-next-line @typescript-eslint/no-floating-promises\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.SLIM,\n new CustomError(\n errorTypes.VISUALIZATION,\n 'Failed to change style of annotation group.'\n )\n )\n throw error\n }\n }\n\n /**\n * Handle toggling of segment visibility, i.e., whether a given\n * segment should be either displayed or hidden by the viewer.\n */\n handleSegmentVisibilityChange ({ segmentUID, isVisible }: {\n segmentUID: string\n isVisible: boolean\n }): void {\n console.log(`change visibility of segment ${segmentUID}`)\n if (isVisible) {\n console.info(`show segment ${segmentUID}`)\n this.volumeViewer.showSegment(segmentUID)\n this.setState(state => {\n const visibleSegmentUIDs = new Set(state.visibleSegmentUIDs)\n visibleSegmentUIDs.add(segmentUID)\n return { visibleSegmentUIDs }\n })\n } else {\n console.info(`hide segment ${segmentUID}`)\n this.volumeViewer.hideSegment(segmentUID)\n this.setState(state => {\n const visibleSegmentUIDs = new Set(state.visibleSegmentUIDs)\n visibleSegmentUIDs.delete(segmentUID)\n return { visibleSegmentUIDs }\n })\n }\n }\n\n /**\n * Handle change of segment style.\n */\n handleSegmentStyleChange ({ segmentUID, styleOptions }: {\n segmentUID: string\n styleOptions: {\n opacity?: number\n }\n }): void {\n console.log(`change style of segment ${segmentUID}`)\n this.volumeViewer.setSegmentStyle(segmentUID, styleOptions)\n }\n\n /**\n * Handle toggling of mapping visibility, i.e., whether a given\n * mapping should be either displayed or hidden by the viewer.\n */\n handleMappingVisibilityChange ({ mappingUID, isVisible }: {\n mappingUID: string\n isVisible: boolean\n }): void {\n console.log(`change visibility of mapping ${mappingUID}`)\n if (isVisible) {\n console.info(`show mapping ${mappingUID}`)\n this.volumeViewer.showParameterMapping(mappingUID)\n this.setState(state => {\n const visibleMappingUIDs = new Set(state.visibleMappingUIDs)\n visibleMappingUIDs.add(mappingUID)\n return { visibleMappingUIDs }\n })\n } else {\n console.info(`hide mapping ${mappingUID}`)\n this.volumeViewer.hideParameterMapping(mappingUID)\n this.setState(state => {\n const visibleMappingUIDs = new Set(state.visibleMappingUIDs)\n visibleMappingUIDs.delete(mappingUID)\n return { visibleMappingUIDs }\n })\n }\n }\n\n /**\n * Handle change of mapping style.\n */\n handleMappingStyleChange ({ mappingUID, styleOptions }: {\n mappingUID: string\n styleOptions: {\n opacity?: number\n }\n }): void {\n console.log(`change style of mapping ${mappingUID}`)\n this.volumeViewer.setParameterMappingStyle(mappingUID, styleOptions)\n }\n\n /**\n * Handle toggling of optical path visibility, i.e., whether a given\n * optical path should be either displayed or hidden by the viewer.\n */\n handleOpticalPathVisibilityChange ({ opticalPathIdentifier, isVisible }: {\n opticalPathIdentifier: string\n isVisible: boolean\n }): void {\n console.log(`change visibility of optical path ${opticalPathIdentifier}`)\n if (isVisible) {\n console.info(`show optical path ${opticalPathIdentifier}`)\n this.volumeViewer.showOpticalPath(opticalPathIdentifier)\n this.setState(state => {\n const visibleOpticalPathIdentifiers = new Set(\n state.visibleOpticalPathIdentifiers\n )\n visibleOpticalPathIdentifiers.add(opticalPathIdentifier)\n return { visibleOpticalPathIdentifiers }\n })\n } else {\n console.info(`hide optical path ${opticalPathIdentifier}`)\n this.volumeViewer.hideOpticalPath(opticalPathIdentifier)\n this.setState(state => {\n const visibleOpticalPathIdentifiers = new Set(\n state.visibleOpticalPathIdentifiers\n )\n visibleOpticalPathIdentifiers.delete(opticalPathIdentifier)\n return { visibleOpticalPathIdentifiers }\n })\n }\n }\n\n /**\n * Handle change of optical path style.\n */\n handleOpticalPathStyleChange ({ opticalPathIdentifier, styleOptions }: {\n opticalPathIdentifier: string\n styleOptions: {\n opacity?: number\n color?: number[]\n limitValues?: number[]\n }\n }): void {\n console.log(`change style of optical path ${opticalPathIdentifier}`)\n this.volumeViewer.setOpticalPathStyle(opticalPathIdentifier, styleOptions)\n }\n\n /**\n * Handle toggling of optical path activity, i.e., whether a given\n * optical path should be either added or removed from the viewport.\n */\n handleOpticalPathActivityChange ({ opticalPathIdentifier, isActive }: {\n opticalPathIdentifier: string\n isActive: boolean\n }): void {\n console.log(`change activity of optical path ${opticalPathIdentifier}`)\n if (isActive) {\n console.info(`activate optical path ${opticalPathIdentifier}`)\n this.volumeViewer.activateOpticalPath(opticalPathIdentifier)\n this.setState(state => {\n const activeOpticalPathIdentifiers = new Set(\n state.activeOpticalPathIdentifiers\n )\n activeOpticalPathIdentifiers.add(opticalPathIdentifier)\n return { activeOpticalPathIdentifiers }\n })\n } else {\n console.info(`deactivate optical path ${opticalPathIdentifier}`)\n this.volumeViewer.deactivateOpticalPath(opticalPathIdentifier)\n this.setState(state => {\n const activeOpticalPathIdentifiers = new Set(\n state.activeOpticalPathIdentifiers\n )\n activeOpticalPathIdentifiers.delete(opticalPathIdentifier)\n return { activeOpticalPathIdentifiers }\n })\n }\n }\n\n /**\n * Set default presentation state that is either defined by metadata included\n * in the DICOM Slide Microscopy instance or by the viewer.\n */\n setDefaultPresentationState (): void {\n const visibleOpticalPathIdentifiers: Set = new Set()\n const opticalPaths = this.volumeViewer.getAllOpticalPaths()\n opticalPaths.sort((a, b) => {\n if (a.identifier.localeCompare(b.identifier) === 1) {\n return 1\n } else if (b.identifier.localeCompare(a.identifier) === 1) {\n return -1\n }\n return 0\n })\n opticalPaths.forEach((item: dmv.opticalPath.OpticalPath) => {\n const identifier = item.identifier\n const style = this.volumeViewer.getOpticalPathDefaultStyle(identifier)\n this.volumeViewer.setOpticalPathStyle(identifier, style)\n this.volumeViewer.hideOpticalPath(identifier)\n this.volumeViewer.deactivateOpticalPath(identifier)\n if (item.isMonochromatic) {\n /*\n * If the image metadata contains a palette color lookup table for the\n * optical path, then it will be displayed by default.\n */\n if (item.paletteColorLookupTableUID != null) {\n visibleOpticalPathIdentifiers.add(identifier)\n }\n } else {\n /* Color images will always be displayed by default. */\n visibleOpticalPathIdentifiers.add(identifier)\n }\n })\n\n /*\n * If no optical paths have been selected for visualization so far, select\n * first n optical paths and set a default value of interest (VOI) window\n * (using pre-computed pixel data statistics) and a default color.\n */\n if (visibleOpticalPathIdentifiers.size === 0) {\n const defaultColors = [\n [255, 255, 255]\n ]\n opticalPaths.forEach((item: dmv.opticalPath.OpticalPath) => {\n const identifier = item.identifier\n if (item.isMonochromatic) {\n const numVisible = visibleOpticalPathIdentifiers.size\n if (numVisible < defaultColors.length) {\n const style = {\n ...this.volumeViewer.getOpticalPathStyle(identifier)\n }\n const index = numVisible\n style.color = defaultColors[index]\n const stats = this.state.pixelDataStatistics[item.identifier]\n if (stats != null) {\n style.limitValues = [stats.min, stats.max]\n }\n this.volumeViewer.setOpticalPathStyle(item.identifier, style)\n visibleOpticalPathIdentifiers.add(item.identifier)\n }\n }\n })\n }\n\n console.info(\n `selected n=${visibleOpticalPathIdentifiers.size} optical paths ` +\n 'for visualization'\n )\n visibleOpticalPathIdentifiers.forEach(identifier => {\n this.volumeViewer.showOpticalPath(identifier)\n })\n this.setState(state => ({\n activeOpticalPathIdentifiers: new Set(visibleOpticalPathIdentifiers),\n visibleOpticalPathIdentifiers: new Set(visibleOpticalPathIdentifiers)\n }))\n }\n\n /**\n * Handler that gets called when a presentation state has been selected from\n * the current list of available presentation states.\n */\n handlePresentationStateReset (): void {\n this.setState({ selectedPresentationStateUID: undefined })\n const urlPath = this.props.location.pathname\n this.props.navigate(urlPath)\n this.setDefaultPresentationState()\n }\n\n /**\n * Handler that gets called when a presentation state has been selected from\n * the current list of available presentation states.\n */\n handlePresentationStateSelection (\n value?: string,\n option?: any\n ): void {\n if (value != null) {\n console.info(`select Presentation State instance \"${value}\"`)\n let presentationState\n this.state.presentationStates.forEach(instance => {\n if (instance.SOPInstanceUID === value) {\n presentationState = instance\n }\n })\n if (presentationState != null) {\n let urlPath = this.props.location.pathname\n urlPath += `?state=${value}`\n this.props.navigate(urlPath)\n this.setPresentationState(presentationState)\n } else {\n // eslint-disable-next-line @typescript-eslint/no-floating-promises\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.SLIM,\n new CustomError(\n errorTypes.VISUALIZATION,\n 'Presentation State could not be found'\n )\n )\n console.log(\n 'failed to handle section of presentation state: ' +\n `could not find instance \"${value}\"`\n )\n }\n } else {\n this.handlePresentationStateReset()\n }\n this.setState({ selectedPresentationStateUID: value })\n }\n\n /**\n * Handler that will toggle the ROI drawing tool, i.e., either activate or\n * de-activate it, depending on its current state.\n */\n handleRoiDrawing (): void {\n if (this.state.isRoiDrawingActive) {\n console.info('deactivate drawing of ROIs')\n this.volumeViewer.deactivateDrawInteraction()\n this.volumeViewer.activateSelectInteraction({})\n this.setState({\n isAnnotationModalVisible: false,\n isSelectedRoiModalVisible: false,\n isRoiTranslationActive: false,\n isRoiDrawingActive: false,\n isRoiModificationActive: false,\n isGoToModalVisible: false\n })\n } else {\n console.info('activate drawing of ROIs')\n this.setState({\n isAnnotationModalVisible: true,\n isSelectedRoiModalVisible: false,\n isRoiDrawingActive: true,\n isRoiModificationActive: false,\n isRoiTranslationActive: false,\n isGoToModalVisible: false\n })\n this.volumeViewer.deactivateSelectInteraction()\n this.volumeViewer.deactivateSnapInteraction()\n this.volumeViewer.deactivateTranslateInteraction()\n this.volumeViewer.deactivateModifyInteraction()\n }\n }\n\n /**\n * Handler that will toggle the ROI modification tool, i.e., either activate\n * or de-activate it, depending on its current state.\n */\n handleRoiModification (): void {\n console.info('toggle modification of ROIs')\n if (this.volumeViewer.isModifyInteractionActive) {\n this.volumeViewer.deactivateModifyInteraction()\n this.volumeViewer.deactivateSnapInteraction()\n this.volumeViewer.activateSelectInteraction({})\n this.setState({\n isRoiTranslationActive: false,\n isRoiDrawingActive: false,\n isRoiModificationActive: false\n })\n } else {\n this.setState({\n isRoiModificationActive: true,\n isRoiDrawingActive: false,\n isRoiTranslationActive: false\n })\n this.volumeViewer.deactivateDrawInteraction()\n this.volumeViewer.deactivateTranslateInteraction()\n this.volumeViewer.deactivateSelectInteraction()\n this.volumeViewer.activateSnapInteraction({})\n this.volumeViewer.activateModifyInteraction({})\n }\n }\n\n /**\n * Handler that will toggle the ROI translation tool, i.e., either activate\n * or de-activate it, depending on its current state.\n */\n handleRoiTranslation (): void {\n console.info('toggle translation of ROIs')\n if (this.volumeViewer.isTranslateInteractionActive) {\n this.volumeViewer.deactivateTranslateInteraction()\n this.setState({\n isRoiTranslationActive: false,\n isRoiDrawingActive: false,\n isRoiModificationActive: false\n })\n } else {\n this.setState({\n isRoiTranslationActive: true,\n isRoiDrawingActive: false,\n isRoiModificationActive: false\n })\n this.volumeViewer.deactivateModifyInteraction()\n this.volumeViewer.deactivateSnapInteraction()\n this.volumeViewer.deactivateDrawInteraction()\n this.volumeViewer.deactivateSelectInteraction()\n this.volumeViewer.activateTranslateInteraction({})\n }\n }\n\n handleGoTo (): void {\n this.volumeViewer.deactivateDrawInteraction()\n this.volumeViewer.deactivateModifyInteraction()\n this.volumeViewer.deactivateSnapInteraction()\n this.volumeViewer.deactivateTranslateInteraction()\n this.volumeViewer.deactivateSelectInteraction()\n this.setState({\n isGoToModalVisible: true,\n isAnnotationModalVisible: false,\n isSelectedRoiModalVisible: false,\n isReportModalVisible: false,\n isRoiTranslationActive: false,\n isRoiModificationActive: false,\n isRoiDrawingActive: false\n })\n }\n\n /**\n * Handler that will toggle the ROI removal tool, i.e., either activate\n * or de-activate it, depending on its current state.\n */\n handleRoiRemoval (): void {\n this.volumeViewer.deactivateDrawInteraction()\n this.volumeViewer.deactivateSnapInteraction()\n this.volumeViewer.deactivateTranslateInteraction()\n this.volumeViewer.deactivateModifyInteraction()\n if (this.state.selectedRoiUIDs.size > 0) {\n this.state.selectedRoiUIDs.forEach(uid => {\n if (uid === undefined) {\n // eslint-disable-next-line @typescript-eslint/no-floating-promises\n message.warning('No annotation was selected for removal')\n return\n }\n console.info(`remove ROI \"${uid}\"`)\n this.volumeViewer.removeROI(uid)\n // eslint-disable-next-line @typescript-eslint/no-floating-promises\n message.info('Annotation was removed')\n })\n this.setState({\n selectedRoiUIDs: new Set(),\n isRoiTranslationActive: false,\n isRoiDrawingActive: false,\n isRoiModificationActive: false\n })\n } else {\n this.state.visibleRoiUIDs.forEach(uid => {\n console.info(`remove ROI \"${uid}\"`)\n this.volumeViewer.removeROI(uid)\n })\n this.setState({\n visibleRoiUIDs: new Set(),\n isRoiTranslationActive: false,\n isRoiDrawingActive: false,\n isRoiModificationActive: false\n })\n }\n this.volumeViewer.activateSelectInteraction({})\n }\n\n /**\n * Handler that will toggle the ROI visibility tool, i.e., either activate\n * or de-activate it, depending on its current state.\n */\n handleRoiVisibilityChange (): void {\n console.info('toggle visibility of ROIs')\n if (this.volumeViewer.areROIsVisible) {\n this.volumeViewer.deactivateDrawInteraction()\n this.volumeViewer.deactivateSnapInteraction()\n this.volumeViewer.deactivateTranslateInteraction()\n this.volumeViewer.deactivateSelectInteraction()\n this.volumeViewer.deactivateModifyInteraction()\n this.volumeViewer.hideROIs()\n this.setState({\n areRoisHidden: true,\n isRoiDrawingActive: false,\n isRoiModificationActive: false,\n isRoiTranslationActive: false\n })\n } else {\n this.volumeViewer.showROIs()\n this.volumeViewer.activateSelectInteraction({})\n this.state.selectedRoiUIDs.forEach(uid => {\n if (uid !== undefined) {\n this.volumeViewer.setROIStyle(uid, this.selectedRoiStyle)\n }\n })\n this.setState({ areRoisHidden: false })\n }\n }\n\n render (): React.ReactNode {\n const rois: dmv.roi.ROI[] = []\n const segments: dmv.segment.Segment[] = []\n const mappings: dmv.mapping.ParameterMapping[] = []\n const annotationGroups: dmv.annotation.AnnotationGroup[] = []\n rois.push(...this.volumeViewer.getAllROIs())\n segments.push(...this.volumeViewer.getAllSegments())\n mappings.push(...this.volumeViewer.getAllParameterMappings())\n annotationGroups.push(...this.volumeViewer.getAllAnnotationGroups())\n\n const openSubMenuItems = [\n 'specimens', 'optical-paths', 'annotations', 'presentation-states'\n ]\n\n let report: React.ReactNode\n const dataset = this.state.generatedReport\n if (dataset !== undefined) {\n report = \n }\n\n let annotationMenuItems: React.ReactNode\n if (rois.length > 0) {\n annotationMenuItems = (\n \n )\n }\n\n const findingOptions = this.findingOptions.map(finding => {\n return (\n \n {finding.CodeMeaning}\n \n )\n })\n\n const geometryTypeOptionsMapping: { [key: string]: React.ReactNode } = {\n point: Point,\n circle: Circle,\n box: Box,\n polygon: Polygon,\n line: Line,\n freehandpolygon: (\n \n Polygon (freehand)\n \n ),\n freehandline: (\n \n Line (freehand)\n \n )\n }\n\n const annotationConfigurations: React.ReactNode[] = [\n (\n \n {findingOptions}\n \n )\n ]\n\n const selectedFinding = this.state.selectedFinding\n if (selectedFinding !== undefined) {\n const key = _buildKey(selectedFinding)\n this.evaluationOptions[key].forEach(evaluation => {\n const evaluationOptions = evaluation.values.map(code => {\n return (\n \n {code.CodeMeaning}\n \n )\n })\n annotationConfigurations.push(\n <>\n {evaluation.name.CodeMeaning}\n \n {evaluationOptions}\n \n \n )\n })\n const geometryTypeOptions = this.geometryTypeOptions[key].map(name => {\n return geometryTypeOptionsMapping[name]\n })\n annotationConfigurations.push(\n <>\n ROI geometry type\n \n {geometryTypeOptions}\n \n \n )\n annotationConfigurations.push(\n \n measure\n \n )\n }\n\n const specimenMenu = (\n \n \n \n )\n\n const equipmentMenu = (\n \n \n \n )\n\n const opticalPaths = this.volumeViewer.getAllOpticalPaths()\n opticalPaths.sort((a, b) => {\n if (a.identifier.localeCompare(b.identifier) === 1) {\n return 1\n } else if (b.identifier.localeCompare(a.identifier) === 1) {\n return -1\n }\n return 0\n })\n const opticalPathStyles: {\n [identifier: string]: {\n opacity: number\n color?: number[]\n limitValues?: number[]\n paletteColorLookupTable?: dmv.color.PaletteColorLookupTable\n }\n } = {}\n const opticalPathMetadata: {\n [identifier: string]: dmv.metadata.VLWholeSlideMicroscopyImage[]\n } = {}\n opticalPaths.forEach(opticalPath => {\n const identifier = opticalPath.identifier\n const metadata = this.volumeViewer.getOpticalPathMetadata(identifier)\n opticalPathMetadata[identifier] = metadata\n const style = {\n ...this.volumeViewer.getOpticalPathStyle(identifier)\n }\n opticalPathStyles[identifier] = style\n })\n const opticalPathMenu = (\n \n \n \n )\n\n let presentationStateMenu\n if (this.state.presentationStates.length > 0) {\n const presentationStateOptions = []\n this.state.presentationStates.forEach(instance => {\n presentationStateOptions.push(\n \n {instance.ContentDescription}\n \n )\n })\n presentationStateOptions.push(\n \n {}\n \n )\n presentationStateMenu = (\n \n \n \n {presentationStateOptions}\n \n \n }\n type='primary'\n onClick={this.handlePresentationStateReset}\n />\n \n \n \n )\n }\n\n let segmentationMenu\n if (segments.length > 0) {\n const defaultSegmentStyles: {\n [segmentUID: string]: {\n opacity: number\n }\n } = {}\n const segmentMetadata: {\n [segmentUID: string]: dmv.metadata.Segmentation[]\n } = {}\n const segments = this.volumeViewer.getAllSegments()\n segments.forEach(segment => {\n defaultSegmentStyles[segment.uid] = this.volumeViewer.getSegmentStyle(\n segment.uid\n )\n segmentMetadata[segment.uid] = this.volumeViewer.getSegmentMetadata(\n segment.uid\n )\n })\n segmentationMenu = (\n \n \n \n )\n openSubMenuItems.push('segmentations')\n }\n\n let parametricMapMenu\n if (mappings.length > 0) {\n const defaultMappingStyles: {\n [mappingUID: string]: {\n opacity: number\n }\n } = {}\n const mappingMetadata: {\n [mappingUID: string]: dmv.metadata.ParametricMap[]\n } = {}\n mappings.forEach(mapping => {\n defaultMappingStyles[mapping.uid] = this.volumeViewer.getParameterMappingStyle(\n mapping.uid\n )\n mappingMetadata[mapping.uid] = this.volumeViewer.getParameterMappingMetadata(\n mapping.uid\n )\n })\n parametricMapMenu = (\n \n \n \n )\n openSubMenuItems.push('parametric-maps')\n }\n\n let annotationGroupMenu\n if (annotationGroups.length > 0) {\n const defaultAnnotationGroupStyles: {\n [annotationGroupUID: string]: {\n opacity: number\n color: number[]\n }\n } = {}\n const annotationGroupMetadata: {\n [annotationGroupUID: string]: dmv.metadata.MicroscopyBulkSimpleAnnotations\n } = {}\n const annotationGroups = this.volumeViewer.getAllAnnotationGroups()\n annotationGroups.forEach(annotationGroup => {\n defaultAnnotationGroupStyles[annotationGroup.uid] = this.volumeViewer.getAnnotationGroupStyle(\n annotationGroup.uid\n )\n annotationGroupMetadata[annotationGroup.uid] = this.volumeViewer.getAnnotationGroupMetadata(\n annotationGroup.uid\n )\n })\n annotationGroupMenu = (\n \n \n \n )\n openSubMenuItems.push('annotationGroups')\n }\n\n let toolbar\n let toolbarHeight = '0px'\n const annotationTools = [\n ,\n ,\n ,\n ,\n ,\n \n ]\n const controlTools = [\n \n ]\n if (this.props.enableAnnotationTools) {\n toolbar = (\n \n {annotationTools.map((item, i) => {\n return {item}\n })}\n {controlTools.map((item, i) => {\n return {item}\n })}\n \n )\n toolbarHeight = '50px'\n }\n\n let cursor = 'default'\n if (this.state.isLoading) {\n cursor = 'progress'\n }\n\n let selectedRoiInformation\n if (this.state.selectedRoi != null) {\n const roiAttributes: Array<{\n name: string\n value: string\n unit?: string\n }> = [\n {\n name: 'UID',\n value: this.state.selectedRoi.uid\n }\n ]\n const roiScoordAttributes: Array<{\n name: string\n value: string\n }> = [\n {\n name: 'Graphic type',\n value: this.state.selectedRoi.scoord3d.graphicType\n }\n ]\n const roiEvaluationAttributes: Array<{\n name: string\n value: string\n }> = []\n this.state.selectedRoi.evaluations.forEach(item => {\n if (item.ValueType === 'CODE') {\n const codeItem = item as dcmjs.sr.valueTypes.CodeContentItem\n roiEvaluationAttributes.push({\n name: codeItem.ConceptNameCodeSequence[0].CodeMeaning,\n value: codeItem.ConceptCodeSequence[0].CodeMeaning\n })\n } else {\n const textItem = item as dcmjs.sr.valueTypes.TextContentItem\n roiEvaluationAttributes.push({\n name: textItem.ConceptNameCodeSequence[0].CodeMeaning,\n value: textItem.TextValue\n })\n }\n })\n const roiMeasurmentAttributesPerOpticalPath: {\n [identifier: string]: Array<{\n name: string\n value: string\n unit?: string\n }>\n } = {}\n this.state.selectedRoi.measurements.forEach(item => {\n let identifier = 'default'\n if (item.ContentSequence != null) {\n const refItems = findContentItemsByName({\n content: item.ContentSequence,\n name: new dcmjs.sr.coding.CodedConcept({\n value: '121112',\n meaning: 'Source of Measurement',\n schemeDesignator: 'DCM'\n })\n })\n if (refItems.length > 0) {\n identifier = (\n refItems[0]\n // @ts-expect-error\n .ReferencedSOPSequence[0]\n .ReferencedOpticalPathIdentifier\n )\n }\n }\n if (!(identifier in roiMeasurmentAttributesPerOpticalPath)) {\n roiMeasurmentAttributesPerOpticalPath[identifier] = []\n }\n const measuredValueItem = item.MeasuredValueSequence[0]\n roiMeasurmentAttributesPerOpticalPath[identifier].push({\n name: item.ConceptNameCodeSequence[0].CodeMeaning,\n value: measuredValueItem.NumericValue.toString(),\n unit: measuredValueItem.MeasurementUnitsCodeSequence[0].CodeMeaning\n })\n })\n const createRoiDescription = (\n attributes: Array<{ name: string, value: string, unit?: string }>\n ): React.ReactNode[] => {\n return attributes.map(item => {\n let value\n if (item.unit != null) {\n value = `${item.value} [${item.unit}]`\n } else {\n value = item.value\n }\n return (\n \n {value}\n \n )\n })\n }\n const roiDescriptions = createRoiDescription(roiAttributes)\n const roiScoordDescriptions = createRoiDescription(\n roiScoordAttributes\n )\n const roiEvaluationDescriptions = createRoiDescription(\n roiEvaluationAttributes\n )\n const roiMeasurementDescriptions = []\n for (const identifier in roiMeasurmentAttributesPerOpticalPath) {\n const descriptions = createRoiDescription(\n roiMeasurmentAttributesPerOpticalPath[identifier]\n )\n if (identifier === 'default') {\n roiMeasurementDescriptions.push(descriptions)\n } else {\n roiMeasurementDescriptions.push(\n <>\n \n {identifier}\n \n {descriptions}\n \n )\n }\n }\n selectedRoiInformation = (\n <>\n \n {roiDescriptions}\n \n \n Spatial coordinates\n \n \n {roiScoordDescriptions}\n \n \n Evaluations\n \n \n {roiEvaluationDescriptions}\n \n \n Measurements\n \n \n {roiMeasurementDescriptions}\n \n \n )\n }\n\n return (\n \n \n {toolbar}\n\n \n\n \n \n {annotationConfigurations}\n \n \n\n \n \n {selectedRoiInformation}\n \n \n\n \n \n \n : \n }\n />\n \n : \n }\n />\n \n : \n }\n />\n \n \n\n \n {report}\n \n \n\n \n {\n // Give menu item time to render before updating viewer size\n setTimeout(\n () => {\n if (this.labelViewer != null) {\n this.labelViewer.resize()\n }\n },\n 100\n )\n }}\n >\n \n \n \n \n \n {specimenMenu}\n {equipmentMenu}\n {opticalPathMenu}\n {presentationStateMenu}\n \n {annotationMenuItems}\n \n {annotationGroupMenu}\n {segmentationMenu}\n {parametricMapMenu}\n \n \n \n )\n }\n}\n\nexport default withRouter(SlideViewer)\n","import * as dmv from 'dicom-microscopy-viewer'\nimport { CustomError, errorTypes } from '../utils/CustomError'\nimport NotificationMiddleware, {\n NotificationMiddlewareContext\n} from '../services/NotificationMiddleware'\n\nenum ImageFlavors {\n VOLUME = 'VOLUME',\n LABEL = 'LABEL',\n OVERVIEW = 'OVERVIEW',\n THUMBNAIL = 'THUMBNAIL'\n}\n\nconst hasImageFlavor = (\n image: dmv.metadata.VLWholeSlideMicroscopyImage,\n imageFlavor: ImageFlavors\n): boolean => {\n return image.ImageType[2] === imageFlavor\n}\n\nconst areSameAcquisition = (\n image: dmv.metadata.VLWholeSlideMicroscopyImage,\n refImage: dmv.metadata.VLWholeSlideMicroscopyImage\n): boolean => {\n if (image.AcquisitionUID != null) {\n return image.AcquisitionUID === refImage.AcquisitionUID\n }\n return false\n}\n\ninterface SlideImageCollection {\n acquisitionUID?: string\n frameOfReferenceUID: string\n containerIdentifier: string\n volumeImages: dmv.metadata.VLWholeSlideMicroscopyImage[]\n labelImages: dmv.metadata.VLWholeSlideMicroscopyImage[]\n overviewImages: dmv.metadata.VLWholeSlideMicroscopyImage[]\n}\n\ninterface SlideOptions {\n images: dmv.metadata.VLWholeSlideMicroscopyImage[]\n description?: string\n}\n\n/**\n * Slide - collection of images with the same Frame of Reference UID and\n * Container Identifier.\n */\nclass Slide {\n readonly description: string\n readonly acquisitionUID: string | null | undefined\n readonly frameOfReferenceUID: string\n readonly containerIdentifier: string\n readonly seriesInstanceUIDs: string[]\n readonly opticalPathIdentifiers: string[]\n readonly pyramidUIDs: string[] = []\n readonly areVolumeImagesMonochrome: boolean\n readonly volumeImages: dmv.metadata.VLWholeSlideMicroscopyImage[]\n readonly labelImages: dmv.metadata.VLWholeSlideMicroscopyImage[]\n readonly overviewImages: dmv.metadata.VLWholeSlideMicroscopyImage[]\n\n /**\n * @param options\n * @param options.images - Metadata of images associated with the slide\n * @param options.description - Description of the slide\n */\n constructor (\n options: SlideOptions\n ) {\n if (options.images.length === 0) {\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.SLIM,\n new CustomError(\n errorTypes.ENCODINGANDDECODING,\n 'Value of option \"images\" have been non-zero length.'\n )\n )\n }\n\n const seriesInstanceUIDs = new Set([] as string[])\n const acquisitionUIDs = new Set([] as string[])\n const opticalPathIdentifiers = new Set([] as string[])\n const containerIdentifiers = new Set([] as string[])\n const frameOfReferenceUIDs = {\n VOLUME: new Set([] as string[]),\n LABEL: new Set([] as string[]),\n OVERVIEW: new Set([] as string[])\n }\n const pyramidUIDs: {\n [key: string]: { [opticalPathIdentifier: string]: Set }\n } = {\n VOLUME: {}\n }\n const volumeImages: dmv.metadata.VLWholeSlideMicroscopyImage[] = []\n const labelImages: dmv.metadata.VLWholeSlideMicroscopyImage[] = []\n const overviewImages: dmv.metadata.VLWholeSlideMicroscopyImage[] = []\n options.images.forEach((image) => {\n containerIdentifiers.add(image.ContainerIdentifier)\n seriesInstanceUIDs.add(image.SeriesInstanceUID)\n image.OpticalPathSequence.forEach(item => {\n opticalPathIdentifiers.add(item.OpticalPathIdentifier)\n })\n if (image.AcquisitionUID != null) {\n acquisitionUIDs.add(image.AcquisitionUID)\n }\n if (\n hasImageFlavor(image, ImageFlavors.VOLUME) ||\n hasImageFlavor(image, ImageFlavors.THUMBNAIL)\n ) {\n frameOfReferenceUIDs.VOLUME.add(image.FrameOfReferenceUID)\n if (image.PyramidUID != null) {\n for (const identifier in opticalPathIdentifiers) {\n pyramidUIDs.VOLUME[identifier].add(image.PyramidUID)\n }\n }\n volumeImages.push(image)\n } else if (hasImageFlavor(image, ImageFlavors.LABEL)) {\n frameOfReferenceUIDs.LABEL.add(image.FrameOfReferenceUID)\n labelImages.push(image)\n } else if (hasImageFlavor(image, ImageFlavors.OVERVIEW)) {\n frameOfReferenceUIDs.OVERVIEW.add(image.FrameOfReferenceUID)\n overviewImages.push(image)\n }\n })\n if (volumeImages.length === 0) {\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.SLIM,\n new CustomError(\n errorTypes.ENCODINGANDDECODING,\n 'At least one VOLUME image must be provided for a slide.'\n )\n )\n } else {\n if (acquisitionUIDs.size > 1) {\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.SLIM,\n new CustomError(\n errorTypes.ENCODINGANDDECODING,\n 'All VOLUME images of a slide must have the same number of ' +\n 'Samples per Pixel.'\n )\n )\n }\n const samplesPerPixel = new Set([] as number[])\n volumeImages.forEach((image) => {\n samplesPerPixel.add(image.SamplesPerPixel)\n })\n if (samplesPerPixel.size > 1) {\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.SLIM,\n new CustomError(\n errorTypes.ENCODINGANDDECODING,\n 'All VOLUME images of a slide must have the same number of ' +\n 'Samples per Pixel.'\n )\n )\n }\n const isNotResampled = volumeImages.filter(image => {\n return image.ImageType[3] !== 'RESAMPLED'\n })\n if (isNotResampled.length > opticalPathIdentifiers.size) {\n console.warn(\n 'the set of VOLUME images of a slide must contain only a single ' +\n 'image that has not been resampled per optical path'\n )\n }\n }\n this.volumeImages = volumeImages\n this.labelImages = labelImages\n this.overviewImages = overviewImages\n\n this.seriesInstanceUIDs = [...seriesInstanceUIDs]\n this.opticalPathIdentifiers = [...opticalPathIdentifiers]\n\n if (containerIdentifiers.size !== 1) {\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.SLIM,\n new CustomError(\n errorTypes.ENCODINGANDDECODING,\n 'All images of a slide must have the same Container Identifier.'\n )\n )\n }\n this.containerIdentifier = [...containerIdentifiers][0]\n\n if (frameOfReferenceUIDs.VOLUME.size !== 1) {\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.SLIM,\n new CustomError(\n errorTypes.ENCODINGANDDECODING,\n 'All VOLUME images of a slide must have ' +\n 'the same Frame of Reference UID.'\n )\n )\n }\n this.frameOfReferenceUID = [...frameOfReferenceUIDs.VOLUME][0]\n\n let requirePyramidUID = false\n if (Object.keys(pyramidUIDs.VOLUME).length > 0) {\n requirePyramidUID = true\n }\n this.opticalPathIdentifiers.forEach(identifier => {\n if (pyramidUIDs.VOLUME[identifier] != null) {\n if (pyramidUIDs.VOLUME[identifier].size > 1) {\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.SLIM,\n new CustomError(\n errorTypes.ENCODINGANDDECODING,\n `All VOLUME images for optical path \"${identifier}\"` +\n 'must be part of the same multi-resolution pyramid.'\n )\n )\n } else if (pyramidUIDs.VOLUME[identifier].size === 1) {\n this.pyramidUIDs.push([...pyramidUIDs.VOLUME[identifier]][0])\n } else {\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.SLIM,\n new CustomError(\n errorTypes.ENCODINGANDDECODING,\n `The VOLUME images for optical path \"${identifier}\" ` +\n 'lack the Pyramid UID, while the images for other optical paths ' +\n 'contain it.'\n )\n )\n }\n } else {\n if (requirePyramidUID) {\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.SLIM,\n new CustomError(\n errorTypes.ENCODINGANDDECODING,\n `The VOLUME images for optical path \"${identifier}\" ` +\n 'lack the Pyramid UID, while the images for other optical paths ' +\n 'contain it.'\n )\n )\n }\n }\n })\n\n if (acquisitionUIDs.size > 1) {\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.SLIM,\n new CustomError(\n errorTypes.ENCODINGANDDECODING,\n 'All VOLUME images of a slide must be part of the same ' +\n 'acquisition and have the same Acquisition UID.'\n )\n )\n } else if (acquisitionUIDs.size === 1) {\n this.acquisitionUID = [...acquisitionUIDs][0]\n } else {\n this.acquisitionUID = null\n }\n\n this.areVolumeImagesMonochrome = (\n this.volumeImages[0].SamplesPerPixel === 1 &&\n this.volumeImages[0].PhotometricInterpretation === 'MONOCHROME2'\n )\n\n this.description = (\n options.description !== undefined ? options.description : ''\n )\n }\n}\n\n/**\n * Create slides.\n *\n * @param imagesPerSeries - Image instances grouped per series\n * @param referenceSeriesInstanceUID - Unique identifier of the series that serves as a reference for the slide\n * @returns Slides\n */\nconst createSlides = (\n images: dmv.metadata.VLWholeSlideMicroscopyImage[][]\n): Slide[] => {\n const slideMetadata: SlideImageCollection[] = []\n images.forEach((series) => {\n if (series.length > 0) {\n const volumeImages = series.filter((image) => {\n return (\n hasImageFlavor(image, ImageFlavors.VOLUME) ||\n hasImageFlavor(image, ImageFlavors.THUMBNAIL)\n )\n })\n if (volumeImages.length > 0) {\n const refImage = volumeImages[0]\n const filteredVolumeImages = volumeImages.filter((image) => {\n return refImage.SamplesPerPixel === image.SamplesPerPixel\n })\n const slideMetadataIndex = slideMetadata.findIndex((slide) => {\n return _doesImageBelongToSlide(slide, refImage)\n })\n\n const labelImages = series.filter((image) => {\n return hasImageFlavor(image, ImageFlavors.LABEL)\n })\n let filteredLabelImages: dmv.metadata.VLWholeSlideMicroscopyImage[]\n if (labelImages.length > 1) {\n filteredLabelImages = labelImages.filter((image) => {\n return areSameAcquisition(image, refImage)\n })\n } else {\n filteredLabelImages = labelImages\n }\n const overviewImages = series.filter((image) => {\n return hasImageFlavor(image, ImageFlavors.OVERVIEW)\n })\n let filteredOverviewImages: dmv.metadata.VLWholeSlideMicroscopyImage[]\n if (overviewImages.length > 1) {\n filteredOverviewImages = overviewImages.filter((image) => {\n return areSameAcquisition(image, refImage)\n })\n } else {\n filteredOverviewImages = overviewImages\n }\n\n if (slideMetadataIndex === -1) {\n const slideMetadataItem: SlideImageCollection = {\n acquisitionUID: refImage.AcquisitionUID,\n frameOfReferenceUID: refImage.FrameOfReferenceUID,\n containerIdentifier: refImage.ContainerIdentifier,\n volumeImages: filteredVolumeImages,\n labelImages: filteredLabelImages,\n overviewImages: filteredOverviewImages\n }\n slideMetadata.push(slideMetadataItem)\n } else {\n const slideMetadataItem = slideMetadata[slideMetadataIndex]\n slideMetadataItem.volumeImages.push(...filteredVolumeImages)\n slideMetadataItem.labelImages.push(...filteredLabelImages)\n slideMetadataItem.overviewImages.push(...filteredOverviewImages)\n }\n }\n }\n })\n\n let slides: Slide[] = slideMetadata.map((item) => {\n return new Slide({\n images: [\n ...item.volumeImages,\n ...item.labelImages,\n ...item.overviewImages\n ]\n })\n })\n slides = slides.sort((a, b) => {\n const imgA = a.volumeImages[0]\n const imgB = b.volumeImages[0]\n if (imgA.ContainerIdentifier != null && imgB.ContainerIdentifier != null) {\n return Number(imgA.ContainerIdentifier) - Number(imgB.ContainerIdentifier)\n } else {\n return 0\n }\n })\n\n return slides\n}\n\n/**\n * Check if instance belongs to the slide.\n *\n * Compares values of Frame of Reference UID and Container Identifier attributes.\n *\n * @param slide - Slide metadata object\n * @param image - Metadata of VOLUME, LABEL or OVERVIEW image instance\n */\nfunction _doesImageBelongToSlide (\n slide: SlideImageCollection,\n image: dmv.metadata.VLWholeSlideMicroscopyImage\n): boolean {\n if (\n slide.frameOfReferenceUID === image.FrameOfReferenceUID &&\n slide.containerIdentifier === image.ContainerIdentifier &&\n slide.acquisitionUID === image.AcquisitionUID\n ) {\n return true\n }\n return false\n}\n\nexport { Slide, createSlides }\n","import React from 'react'\nimport { Routes, Route, useLocation, useParams } from 'react-router-dom'\nimport { Layout, Menu } from 'antd'\n\nimport * as dmv from 'dicom-microscopy-viewer'\n\nimport { AnnotationSettings } from '../AppConfig'\nimport ClinicalTrial from './ClinicalTrial'\nimport DicomWebManager from '../DicomWebManager'\nimport Patient from './Patient'\nimport Study from './Study'\nimport SlideList from './SlideList'\nimport SlideViewer from './SlideViewer'\n\nimport { User } from '../auth'\nimport { Slide, createSlides } from '../data/slides'\nimport { StorageClasses } from '../data/uids'\nimport { RouteComponentProps, withRouter } from '../utils/router'\nimport { CustomError, errorTypes } from '../utils/CustomError'\nimport NotificationMiddleware, {\n NotificationMiddlewareContext\n} from '../services/NotificationMiddleware'\n\nfunction ParametrizedSlideViewer ({\n clients,\n slides,\n user,\n app,\n preload,\n enableAnnotationTools,\n annotations\n}: {\n clients: { [key: string]: DicomWebManager }\n slides: Slide[]\n user?: User\n app: {\n name: string\n version: string\n uid: string\n organization?: string\n }\n preload: boolean\n enableAnnotationTools: boolean\n annotations: AnnotationSettings[]\n}): JSX.Element | null {\n const { studyInstanceUID, seriesInstanceUID } = useParams()\n const location = useLocation()\n\n const selectedSlide = slides.find((slide: Slide) => {\n return slide.seriesInstanceUIDs.find((uid: string) => {\n return uid === seriesInstanceUID\n })\n })\n const searchParams = new URLSearchParams(location.search)\n let presentationStateUID: string | null | undefined\n if (!searchParams.has('access_token')) {\n presentationStateUID = searchParams.get('state')\n if (presentationStateUID === null) {\n presentationStateUID = undefined\n }\n }\n let viewer = null\n if (selectedSlide != null) {\n viewer = (\n \n )\n }\n return viewer\n}\n\ninterface ViewerProps extends RouteComponentProps {\n clients: { [key: string]: DicomWebManager }\n studyInstanceUID: string\n app: {\n name: string\n version: string\n uid: string\n organization?: string\n }\n annotations: AnnotationSettings[]\n enableAnnotationTools: boolean\n preload: boolean\n user?: {\n name: string\n email: string\n }\n}\n\ninterface ViewerState {\n slides: Slide[]\n isLoading: boolean\n}\n\nclass Viewer extends React.Component {\n state = {\n slides: [],\n isLoading: true\n }\n\n constructor (props: ViewerProps) {\n super(props)\n this.handleSeriesSelection = this.handleSeriesSelection.bind(this)\n }\n\n componentDidMount (): void {\n this.fetchImageMetadata().then(\n (metadata: dmv.metadata.VLWholeSlideMicroscopyImage[][]) => {\n this.setState({\n slides: createSlides(metadata),\n isLoading: false\n })\n }\n ).catch(() => {\n // eslint-disable-next-line @typescript-eslint/no-floating-promises\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.SLIM,\n new CustomError(\n errorTypes.ENCODINGANDDECODING,\n 'Image metadata could not be retrieved or decoded.')\n )\n this.setState({ isLoading: false })\n })\n }\n\n /**\n * Fetch metadata for VL Whole Slide Microscopy Image instances of the study.\n *\n * @returns Metadata of image instances of the study grouped per series\n */\n async fetchImageMetadata (): Promise {\n const images: dmv.metadata.VLWholeSlideMicroscopyImage[][] = []\n const studyInstanceUID = this.props.studyInstanceUID\n console.info(`search for series of study \"${studyInstanceUID}\"...`)\n const client = this.props.clients[\n StorageClasses.VL_WHOLE_SLIDE_MICROSCOPY_IMAGE\n ]\n const matchedSeries = await client.searchForSeries({\n queryParams: {\n Modality: 'SM',\n StudyInstanceUID: studyInstanceUID\n }\n })\n\n await Promise.all(matchedSeries.map(async (s) => {\n const { dataset } = dmv.metadata.formatMetadata(s)\n const loadingSeries = dataset as dmv.metadata.Series\n console.info(\n `retrieve metadata of series \"${loadingSeries.SeriesInstanceUID}\"`\n )\n const retrievedMetadata = await client.retrieveSeriesMetadata({\n studyInstanceUID: this.props.studyInstanceUID,\n seriesInstanceUID: loadingSeries.SeriesInstanceUID\n })\n\n const seriesImages: dmv.metadata.VLWholeSlideMicroscopyImage[] = []\n retrievedMetadata.forEach((item, index) => {\n if (item['00080016'] != null) {\n const values = item['00080016'].Value\n if (values != null) {\n const sopClassUID = values[0]\n if (sopClassUID === StorageClasses.VL_WHOLE_SLIDE_MICROSCOPY_IMAGE) {\n const image = new dmv.metadata.VLWholeSlideMicroscopyImage({\n metadata: item\n })\n seriesImages.push(image)\n }\n }\n }\n })\n\n if (seriesImages.length > 0) {\n images.push(seriesImages)\n }\n }))\n\n return images\n }\n\n handleSeriesSelection (\n { seriesInstanceUID }: { seriesInstanceUID: string }\n ): void {\n console.info(`switch to series \"${seriesInstanceUID}\"`)\n let urlPath = (\n `/studies/${this.props.studyInstanceUID}` +\n `/series/${seriesInstanceUID}`\n )\n if (\n this.props.location.pathname.includes('/series/') &&\n this.props.location.search != null\n ) {\n urlPath += this.props.location.search\n }\n this.props.navigate(urlPath, { replace: true })\n }\n\n render (): React.ReactNode {\n if (this.state.isLoading) {\n return null\n }\n\n if (this.state.slides.length === 0) {\n return null\n }\n const firstSlide = this.state.slides[0] as Slide\n const volumeInstances = firstSlide.volumeImages\n if (volumeInstances.length === 0) {\n return null\n }\n const refImage = volumeInstances[0]\n\n /* If a series is encoded in the path, route the viewer to this series.\n * Otherwise select the first series correspondent to\n * the first slide contained in the study.\n */\n let selectedSeriesInstanceUID: string\n if (this.props.location.pathname.includes('series/')) {\n const fragments = this.props.location.pathname.split('/')\n selectedSeriesInstanceUID = fragments[4]\n } else {\n selectedSeriesInstanceUID = volumeInstances[0].SeriesInstanceUID\n }\n\n let clinicalTrialMenu\n if (refImage.ClinicalTrialSponsorName != null) {\n clinicalTrialMenu = (\n \n \n \n )\n }\n\n return (\n \n \n \n \n \n \n \n \n \n {clinicalTrialMenu}\n \n \n \n \n \n\n \n \n }\n />\n \n \n )\n }\n}\n\nexport default withRouter(Viewer)\n","import React from 'react'\nimport { NavLink } from 'react-router-dom'\nimport {\n Col,\n Descriptions,\n Dropdown,\n Input,\n Layout,\n Menu,\n Modal,\n Row,\n Space,\n Badge,\n Collapse\n} from 'antd'\nimport {\n ApiOutlined,\n CheckOutlined,\n InfoOutlined,\n StopOutlined,\n UnorderedListOutlined,\n UserOutlined,\n SettingOutlined\n} from '@ant-design/icons'\nimport { detect } from 'detect-browser'\n\nimport Button from './Button'\nimport { RouteComponentProps, withRouter } from '../utils/router'\nimport NotificationMiddleware, { NotificationMiddlewareEvents } from '../services/NotificationMiddleware'\nimport { CustomError } from '../utils/CustomError'\nimport { v4 as uuidv4 } from 'uuid'\n\ninterface HeaderProps extends RouteComponentProps {\n app: {\n name: string\n version: string\n homepage: string\n uid: string\n organization?: string\n }\n user?: {\n name: string\n email: string\n }\n showWorklistButton: boolean\n onServerSelection: ({ url }: { url: string }) => void\n onUserLogout?: () => void\n showServerSelectionButton: boolean\n}\n\ninterface HeaderState {\n selectedServerUrl?: string\n isServerSelectionModalVisible: boolean\n isServerSelectionDisabled: boolean\n errorObj: CustomError[]\n errorCategory: string[]\n}\n\n/**\n * React component for the application header.\n */\nclass Header extends React.Component {\n constructor (props: HeaderProps) {\n super(props)\n this.state = {\n isServerSelectionModalVisible: false,\n isServerSelectionDisabled: true,\n errorObj: [],\n errorCategory: []\n }\n\n const onErrorHandler = ({ error }: {\n category: string\n error: CustomError\n }): void => {\n this.setState({\n errorObj: [...this.state.errorObj, error],\n errorCategory: [...this.state.errorCategory, error.type]\n })\n }\n\n NotificationMiddleware.subscribe(\n NotificationMiddlewareEvents.OnError,\n onErrorHandler\n )\n }\n\n handleInfoButtonClick = (): void => {\n const browser = detect()\n const environment: {\n browser: {\n name?: string\n version?: string\n }\n os: {\n name?: string\n }\n } = {\n browser: {},\n os: {}\n }\n if (browser != null) {\n environment.browser = {\n name: browser.name != null ? browser.name : undefined,\n version: browser.version != null ? browser.version : undefined\n }\n environment.os = {\n name: browser.os != null ? browser.os : undefined\n }\n }\n\n Modal.info({\n title: 'About',\n width: 600,\n content: (\n <>\n \n \n {this.props.app.name}\n \n \n {this.props.app.version}\n \n \n {this.props.app.homepage}\n \n \n \n \n {environment.browser.name}\n \n \n {environment.browser.version}\n \n \n \n \n {environment.os.name}\n \n \n \n ),\n onOk (): void {}\n })\n }\n\n handleDebugButtonClick = (): void => {\n const errorMsgs: {\n Authentication: string[]\n Communication: string[]\n EncodingDecoding: string[]\n Visualization: string[]\n } = {\n Authentication: [],\n Communication: [],\n EncodingDecoding: [],\n Visualization: []\n }\n\n type ObjectKey = keyof typeof errorMsgs\n const errorNum = this.state.errorObj.length\n\n if (errorNum > 0) {\n for (let i = 0; i < errorNum; i++) {\n const category = this.state.errorCategory[i] as ObjectKey\n errorMsgs[category].push(this.state.errorObj[i].message)\n }\n }\n\n const { Panel } = Collapse\n\n const showErrorCount = (errcount: number): JSX.Element => (\n \n )\n\n Modal.info({\n title: 'Debug Information\\n (Check console for more information)',\n width: 800,\n content: (\n \n \n
    \n {errorMsgs.Communication.map(e => (\n
  1. {e}
    2. \n ))}\n
\n \n \n
    \n {errorMsgs.EncodingDecoding.map(e => (\n
  1. {e}
    2. \n ))}\n
\n \n \n
    \n {errorMsgs.Visualization.map(e => (\n
  1. {e}
    2. \n ))}\n
\n \n \n
    \n {errorMsgs.Authentication.map(e => (\n
  1. {e}
    2. \n ))}\n
\n \n \n ),\n onOk (): void {}\n })\n }\n\n handleServerSelectionButtonClick = (): void => {\n this.setState({ isServerSelectionModalVisible: true })\n }\n\n render (): React.ReactNode {\n let user = null\n if (this.props.user !== undefined) {\n const userMenuItems = []\n if (this.props.onUserLogout !== undefined) {\n userMenuItems.push(\n {\n label: 'Logout',\n key: 'user-logout',\n onClick: () => {\n if (this.props.onUserLogout !== undefined) {\n this.props.onUserLogout()\n }\n }\n }\n )\n }\n const userMenu = \n user = (\n \n e.preventDefault()}\n label={`${this.props.user.name} (${this.props.user.email})`}\n />\n \n )\n }\n\n let worklistButton\n if (this.props.showWorklistButton) {\n worklistButton = (\n \n \n this.handleReset(clearFilters)}\n size='small'\n style={{ width: 90 }}\n >\n Reset\n \n \n
\n ),\n filterIcon: (filtered: boolean) => (\n \n )\n })\n}\n\nexport default withRouter(Worklist)\n","/**\n * Join a URI with a path to form a full URL.\n *\n * @param path - Path component\n * @param uri - Base URI to which the path component should be added\n */\nexport const joinUrl = (path: string, uri: string): string => {\n let baseUri = uri\n if (!baseUri.endsWith('/')) {\n baseUri += '/'\n }\n const url = new URL(path, baseUri)\n return url.toString()\n}\n\n/**\n * Check whether a URL contains an OAuth 2.0 authorization code.\n *\n * @param location - URL components (JavaScript location object)\n * @returns Whether the URL contains a code\n */\nexport const isAuthorizationCodeInUrl = (location: {\n search: string\n hash: string\n}): boolean => {\n const searchParams = new URLSearchParams(location.search)\n const hashParams = new URLSearchParams(location.hash.replace('#', '?'))\n\n return Boolean(\n searchParams.get('code') ??\n searchParams.get('id_token') ??\n searchParams.get('session_state') ??\n hashParams.get('code') ??\n hashParams.get('id_token') ??\n hashParams.get('session_state')\n )\n}\n","import { UserManager, User as UserData } from 'oidc-client'\n\nimport { OidcSettings } from '../AppConfig'\nimport { isAuthorizationCodeInUrl } from '../utils/url'\nimport { User, AuthManager, SignInCallback } from './'\nimport NotificationMiddleware,\n{ NotificationMiddlewareContext } from '../services/NotificationMiddleware'\nimport { CustomError, errorTypes } from '../utils/CustomError'\n\nconst createUser = (userData: UserData | null): User => {\n let profile\n if (userData !== null) {\n profile = userData.profile\n }\n\n if (profile !== undefined) {\n if (profile.name === undefined || profile.email === undefined) {\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.AUTH,\n new CustomError(\n errorTypes.AUTHENTICATION,\n 'Failed to obtain user \"name\" and \"email\".'\n )\n )\n } else {\n return {\n name: profile.name,\n email: profile.email\n }\n }\n } else {\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.AUTH,\n new CustomError(\n errorTypes.AUTHENTICATION,\n 'Failed to obtain user profile.'\n )\n )\n }\n return {\n name: undefined,\n email: undefined\n }\n}\n\nexport default class OidcManager implements AuthManager {\n private _oidc: UserManager\n\n constructor (baseUri: string, settings: OidcSettings) {\n let responseType = 'code'\n if (settings.grantType !== undefined) {\n if (settings.grantType === 'implicit') {\n responseType = 'id_token token'\n }\n }\n this._oidc = new UserManager({\n authority: settings.authority,\n client_id: settings.clientId,\n redirect_uri: baseUri,\n scope: settings.scope,\n response_type: responseType,\n loadUserInfo: true,\n automaticSilentRenew: true,\n revokeAccessTokenOnSignout: true,\n post_logout_redirect_uri: `${baseUri}/logout`\n })\n if (settings.endSessionEndpoint != null) {\n /*\n * Unfortunately, the end session endpoint alone cannot be provided to\n * the construction of UserManager and the other metadata parameters\n * would need to be provided as well. However, configuring all of them\n * individually would not be desirable and they will be automatically\n * determined anyways. Therefore, we first construct an object, get the\n * metadata, update the metadata, and then reconstruct an object with the\n * updated metadata.\n */\n this._oidc.metadataService.getMetadata().then(metadata => {\n if (settings.endSessionEndpoint != null) {\n metadata.end_session_endpoint = settings.endSessionEndpoint\n this._oidc = new UserManager({\n authority: settings.authority,\n client_id: settings.clientId,\n redirect_uri: baseUri,\n scope: settings.scope,\n response_type: responseType,\n loadUserInfo: true,\n automaticSilentRenew: true,\n revokeAccessTokenOnSignout: true,\n post_logout_redirect_uri: `${baseUri}/logout`,\n metadata\n })\n }\n }).catch((error) => {\n console.error(\n 'failed to get metadata from authorization server: ',\n error\n )\n })\n }\n }\n\n /**\n * Sign-in to authenticate the user and obtain authorization.\n */\n signIn = async ({ onSignIn }: {\n onSignIn?: SignInCallback\n }): Promise => {\n const handleSignIn = (userData: UserData): void => {\n const user = createUser(userData)\n const authorization = `${userData.token_type} ${userData.access_token}`\n if (onSignIn != null) {\n console.info('handling sign-in using provided callback function')\n onSignIn({ user: user, authorization: authorization })\n } else {\n console.warn('no callback function was provided to handle sign-in')\n }\n }\n\n if (isAuthorizationCodeInUrl(window.location)) {\n /* Handle the callback from the authorization server: extract the code\n * from the callback URL, obtain user information and the access token\n * for the DICOMweb server.\n */\n console.info('obtaining authorization')\n const userData = await this._oidc.signinCallback()\n if (userData != null) {\n console.info('obtained user data: ', userData)\n handleSignIn(userData)\n }\n } else {\n /* Redirect to the authorization server to authenticate the user\n * and authorize the application to obtain user information and access\n * the DICOMweb server.\n */\n const userData = await this._oidc.getUser()\n if (userData === null || userData.expired) {\n console.info('authenticating user')\n await this._oidc.signinRedirect()\n } else {\n console.info('user has already been authenticated')\n handleSignIn(userData)\n }\n }\n }\n\n /**\n * Sign-out to revoke authorization.\n */\n signOut = async (): Promise => {\n console.log('signing out user and revoking authorization')\n return await this._oidc.signoutRedirect()\n }\n\n /**\n * Get authorization. Requires prior sign-in.\n */\n getAuthorization = async (): Promise => {\n return await this._oidc.getUser().then((userData) => {\n if (userData !== null) {\n return userData.access_token\n } else {\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.AUTH,\n new CustomError(\n errorTypes.AUTHENTICATION,\n 'Failed to obtain user profile.'\n )\n )\n }\n })\n }\n\n /**\n * Get user information. Requires prior sign-in.\n */\n getUser = async (): Promise => {\n return await this._oidc.getUser().then((userData) => {\n if (userData === null) {\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.AUTH,\n new CustomError(\n errorTypes.AUTHENTICATION,\n 'Failed to obtain user information.'\n )\n )\n }\n return createUser(userData)\n })\n }\n}\n","import retry from 'retry'\n\nimport {\n RetryRequestSettings,\n DICOMwebClientRequestHookMetadata\n} from '../AppConfig'\n\ntype RequestHook = (\n request: XMLHttpRequest,\n metadata: DICOMwebClientRequestHookMetadata\n) => XMLHttpRequest\n\n/**\n * Returns a configured retry request hook function\n * that can be used to add retry functionality to XHR request.\n *\n * Default options:\n * retries: 5\n * factor: 3\n * minTimeout: 1 * 1000\n * maxTimeout: 60 * 1000\n * randomize: true\n *\n * @param options\n * @param options.retires - Number of retries\n * @param options.factor - Factor\n * @param options.minTimeout - Min number of seconds to wait before next retry\n * @param options.maxTimeout - Max number of seconds to wait before next retry\n * @param options.randomize - Whether randomization should be applied\n * @param options.retryableStatusCodes HTTP status codes that can trigger a retry\n * @returns Configured retry request function\n */\nexport const getXHRRetryHook = (options: RetryRequestSettings = {\n retries: 5,\n factor: 3,\n minTimeout: 1 * 1000,\n maxTimeout: 60 * 1000,\n randomize: true,\n retryableStatusCodes: [429, 500]\n}): RequestHook => {\n const retryOptions = options\n\n if (options.retries != null) {\n retryOptions.retries = options.retries\n }\n\n if (options.factor != null) {\n retryOptions.factor = options.factor\n }\n\n if (options.minTimeout != null) {\n retryOptions.minTimeout = options.minTimeout\n }\n\n if (options.maxTimeout != null) {\n retryOptions.maxTimeout = options.maxTimeout\n }\n\n if (options.randomize != null) {\n retryOptions.randomize = options.randomize\n }\n\n if (options.retryableStatusCodes != null) {\n retryOptions.retryableStatusCodes = options.retryableStatusCodes\n }\n\n /**\n * Request hook used to add retry functionality to XHR requests.\n *\n * @param request - XHR request instance\n * @param metadata - Metadata about the request\n * @param metadata.url - URL\n * @param metadata.method - HTTP method\n * @returns - XHR request instance (potentially modified)\n */\n const xhrRetryHook = (\n request: XMLHttpRequest,\n metadata: DICOMwebClientRequestHookMetadata\n ): XMLHttpRequest => {\n const { url, method } = metadata\n\n function faultTolerantRequestSend (...args: any): void {\n const operation = retry.operation(retryOptions)\n\n operation.attempt(function operationAttempt (currentAttempt) {\n const originalOnReadyStateChange = request.onreadystatechange\n\n /** Overriding/extending XHR function */\n request.onreadystatechange = function onReadyStateChange (...args: any): void {\n if (originalOnReadyStateChange != null) {\n originalOnReadyStateChange.apply(request, args)\n }\n\n if (retryOptions.retryableStatusCodes.includes(request.status)) {\n const errorMessage = `Attempt to request ${url} failed.`\n const attemptFailedError = new Error(errorMessage)\n operation.retry(attemptFailedError)\n }\n }\n\n /** Call open only on retry (after headers and other things were set in the xhr instance) */\n if (currentAttempt > 1) {\n console.warn(`Requesting ${url}... (attempt: ${currentAttempt})`)\n request.open(method, url, true)\n }\n })\n\n originalRequestSend.apply(request, args)\n }\n\n /** Overriding/extending XHR function */\n const originalRequestSend = request.send\n request.send = faultTolerantRequestSend\n\n return request\n }\n\n return xhrRetryHook\n}\n\nexport default getXHRRetryHook\n","import * as dwc from 'dicomweb-client'\n\nimport { ServerSettings, DicomWebManagerErrorHandler } from './AppConfig'\nimport { joinUrl } from './utils/url'\nimport getXHRRetryHook from './utils/xhrRetryHook'\nimport { CustomError, errorTypes } from './utils/CustomError'\nimport NotificationMiddleware, {\n NotificationMiddlewareContext\n} from './services/NotificationMiddleware'\n\ninterface Store {\n id: string\n read: boolean\n write: boolean\n client: dwc.api.DICOMwebClient\n}\n\nexport default class DicomWebManager implements dwc.api.DICOMwebClient {\n private readonly stores: Store[] = []\n\n private readonly handleError: DicomWebManagerErrorHandler\n\n constructor ({ baseUri, settings, onError }: {\n baseUri: string\n settings: ServerSettings[]\n onError?: DicomWebManagerErrorHandler\n }) {\n if (onError != null) {\n this.handleError = onError\n } else {\n this.handleError = (error, serverSettings) => {\n console.error(error, serverSettings)\n }\n }\n\n settings.forEach(serverSettings => {\n if (serverSettings === undefined) {\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.SLIM,\n new CustomError(\n errorTypes.COMMUNICATION,\n 'At least one server needs to be configured.'\n )\n )\n }\n\n let serviceUrl\n if (serverSettings.url !== undefined) {\n serviceUrl = serverSettings.url\n } else if (serverSettings.path !== undefined) {\n serviceUrl = joinUrl(serverSettings.path, baseUri)\n } else {\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.SLIM,\n new CustomError(\n errorTypes.COMMUNICATION,\n 'Either path or full URL needs to be configured for server.'\n )\n )\n }\n const clientSettings: dwc.api.DICOMwebClientOptions = {\n url: serviceUrl\n }\n if (serverSettings.qidoPathPrefix !== undefined) {\n clientSettings.qidoURLPrefix = serverSettings.qidoPathPrefix\n }\n if (serverSettings.wadoPathPrefix !== undefined) {\n clientSettings.wadoURLPrefix = serverSettings.wadoPathPrefix\n }\n if (serverSettings.stowPathPrefix !== undefined) {\n clientSettings.stowURLPrefix = serverSettings.stowPathPrefix\n }\n if (serverSettings.retry !== undefined) {\n clientSettings.requestHooks = [getXHRRetryHook(serverSettings.retry)]\n }\n\n clientSettings.errorInterceptor = (error: dwc.api.DICOMwebClientError) => {\n this.handleError(error, serverSettings)\n }\n\n this.stores.push({\n id: serverSettings.id,\n write: serverSettings.write ?? false,\n read: serverSettings.read ?? true,\n client: new dwc.api.DICOMwebClient(clientSettings)\n })\n })\n\n if (this.stores.length > 1) {\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.SLIM,\n new CustomError(\n errorTypes.COMMUNICATION,\n 'Only one store is supported for now.'\n )\n )\n }\n }\n\n get baseURL (): string {\n return this.stores[0].client.baseURL\n }\n\n updateHeaders = (fields: { [name: string]: string }): void => {\n for (const f in fields) {\n this.stores[0].client.headers[f] = fields[f]\n }\n }\n\n get headers (): { [name: string]: string } {\n return this.stores[0].client.headers\n }\n\n storeInstances = async (\n options: dwc.api.StoreInstancesOptions\n ): Promise => {\n if (this.stores[0].write) {\n return await this.stores[0].client.storeInstances(options)\n } else {\n return await Promise.reject(\n new Error('Store is not writable.')\n )\n }\n }\n\n searchForStudies = async (\n options: dwc.api.SearchForStudiesOptions\n ): Promise => {\n return await this.stores[0].client.searchForStudies(options)\n }\n\n searchForSeries = async (\n options: dwc.api.SearchForSeriesOptions\n ): Promise => {\n return await this.stores[0].client.searchForSeries(options)\n }\n\n searchForInstances = async (\n options: dwc.api.SearchForInstancesOptions\n ): Promise => {\n return await this.stores[0].client.searchForInstances(options)\n }\n\n retrieveStudyMetadata = async (\n options: dwc.api.RetrieveStudyMetadataOptions\n ): Promise => {\n return await this.stores[0].client.retrieveStudyMetadata(options)\n }\n\n retrieveSeriesMetadata = async (\n options: dwc.api.RetrieveSeriesMetadataOptions\n ): Promise => {\n return await this.stores[0].client.retrieveSeriesMetadata(options)\n }\n\n retrieveInstanceMetadata = async (\n options: dwc.api.RetrieveInstanceMetadataOptions\n ): Promise => {\n return await this.stores[0].client.retrieveInstanceMetadata(options)\n }\n\n retrieveInstance = async (\n options: dwc.api.RetrieveInstanceOptions\n ): Promise => {\n return await this.stores[0].client.retrieveInstance(options)\n }\n\n retrieveInstanceFrames = async (\n options: dwc.api.RetrieveInstanceFramesOptions\n ): Promise => {\n return await this.stores[0].client.retrieveInstanceFrames(options)\n }\n\n retrieveInstanceRendered = async (\n options: dwc.api.RetrieveInstanceRenderedOptions\n ): Promise => {\n return await this.stores[0].client.retrieveInstanceRendered(options)\n }\n\n retrieveInstanceFramesRendered = async (\n options: dwc.api.RetrieveInstanceFramesRenderedOptions\n ): Promise => {\n return await this.stores[0].client.retrieveInstanceFramesRendered(options)\n }\n\n retrieveBulkData = async (\n options: dwc.api.RetrieveBulkDataOptions\n ): Promise => {\n return await this.stores[0].client.retrieveBulkData(options)\n }\n}\n","import React from 'react'\nimport {\n BrowserRouter,\n Navigate,\n Route,\n Routes,\n useParams\n} from 'react-router-dom'\nimport { Layout, message } from 'antd'\nimport { FaSpinner } from 'react-icons/fa'\nimport * as dwc from 'dicomweb-client'\n\nimport AppConfig, { ServerSettings, ErrorMessageSettings } from './AppConfig'\nimport CaseViewer from './components/CaseViewer'\nimport Header from './components/Header'\nimport InfoPage from './components/InfoPage'\nimport Worklist from './components/Worklist'\n\nimport { User, AuthManager } from './auth'\nimport OidcManager from './auth/OidcManager'\nimport { StorageClasses } from './data/uids'\nimport DicomWebManager from './DicomWebManager'\nimport { joinUrl } from './utils/url'\nimport { CustomError, errorTypes } from './utils/CustomError'\nimport NotificationMiddleware, {\n NotificationMiddlewareContext\n} from './services/NotificationMiddleware'\n\nfunction ParametrizedCaseViewer ({ clients, user, app, config }: {\n clients: { [key: string]: DicomWebManager }\n user?: User\n app: {\n name: string\n version: string\n uid: string\n organization?: string\n }\n config: AppConfig\n}): JSX.Element {\n const { studyInstanceUID } = useParams()\n\n const enableAnnotationTools = !(config.disableAnnotationTools ?? false)\n const preload = config.preload ?? false\n return (\n \n )\n}\n\nfunction _createClientMapping ({ baseUri, settings, onError }: {\n baseUri: string\n settings: ServerSettings[]\n onError: (\n error: dwc.api.DICOMwebClientError,\n serverSettings: ServerSettings\n ) => void\n}): { [sopClassUID: string]: DicomWebManager } {\n const storageClassMapping: { [key: string]: number } = { default: 0 }\n const clientMapping: { [sopClassUID: string]: DicomWebManager } = {}\n\n settings.forEach(serverSettings => {\n if (serverSettings.storageClasses != null) {\n serverSettings.storageClasses.forEach(sopClassUID => {\n if (Object.values(StorageClasses).includes(sopClassUID)) {\n if (sopClassUID in storageClassMapping) {\n storageClassMapping[sopClassUID] += 1\n } else {\n storageClassMapping[sopClassUID] = 1\n }\n } else {\n console.warn(\n `unknown storage class \"${sopClassUID}\" specified ` +\n `for configured server \"${serverSettings.id}\"`\n )\n }\n })\n } else {\n storageClassMapping.default += 1\n clientMapping.default = new DicomWebManager({\n baseUri,\n settings: [serverSettings],\n onError\n })\n }\n })\n\n if (storageClassMapping.default > 1) {\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.SLIM,\n new CustomError(\n errorTypes.COMMUNICATION,\n 'Only one default server can be configured without specification ' +\n 'of storage classes.'\n )\n )\n }\n\n for (const key in storageClassMapping) {\n if (key === 'default') {\n continue\n }\n if (storageClassMapping[key] > 1) {\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.SLIM,\n new CustomError(\n errorTypes.COMMUNICATION,\n 'Only one configured server can specify a given storage class. ' +\n `Storage class \"${key}\" is specified by more than one ` +\n 'of the configured servers.'\n )\n )\n }\n }\n\n if (Object.keys(storageClassMapping).length > 1) {\n settings.forEach(server => {\n const client = new DicomWebManager({\n baseUri,\n settings: [server],\n onError\n })\n if (server.storageClasses != null) {\n server.storageClasses.forEach(sopClassUID => {\n clientMapping[sopClassUID] = client\n })\n }\n })\n }\n\n Object.values(StorageClasses).forEach(sopClassUID => {\n if (!(sopClassUID in clientMapping)) {\n clientMapping[sopClassUID] = clientMapping.default\n }\n })\n return clientMapping\n}\n\ninterface AppProps {\n name: string\n homepage: string\n version: string\n config: AppConfig\n}\n\ninterface AppState {\n clients: { [sopClassUID: string]: DicomWebManager }\n user?: User\n isLoading: boolean\n redirectTo?: string\n wasAuthSuccessful: boolean\n error?: ErrorMessageSettings\n}\n\nclass App extends React.Component {\n private readonly auth?: AuthManager\n\n private readonly handleDICOMwebError = (\n error: dwc.api.DICOMwebClientError,\n serverSettings: ServerSettings\n ): void => {\n if (error.status === 401) {\n this.signIn()\n } else if (error.status === 403) {\n // eslint-disable-next-line @typescript-eslint/no-floating-promises\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.DICOMWEB,\n new CustomError(\n errorTypes.COMMUNICATION,\n 'User is not authorized to access DICOMweb resources.')\n )\n }\n if (serverSettings.errorMessages !== undefined) {\n serverSettings.errorMessages.forEach((setting: ErrorMessageSettings) => {\n if (error.status === setting.status) {\n this.setState({\n error: {\n status: error.status,\n message: setting.message\n }\n })\n } else if (error.status === 500) {\n // eslint-disable-next-line @typescript-eslint/no-floating-promises\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.DICOMWEB,\n new CustomError(\n errorTypes.COMMUNICATION,\n 'An unexpected server error occured.')\n )\n }\n })\n }\n }\n\n constructor (props: AppProps) {\n super(props)\n\n console.info('instatiate app')\n console.info(`app is located at \"${props.config.path}\"`)\n const { protocol, host } = window.location\n const baseUri = `${protocol}//${host}`\n const appUri = joinUrl(props.config.path, baseUri)\n\n const oidcSettings = props.config.oidc\n if (oidcSettings !== undefined) {\n console.info(\n 'app uses the following OIDC configuration: ',\n props.config.oidc\n )\n this.auth = new OidcManager(appUri, oidcSettings)\n }\n\n if (props.config.servers.length === 0) {\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.SLIM,\n new CustomError(\n errorTypes.COMMUNICATION,\n 'One server needs to be configured.')\n )\n }\n console.info(\n 'app uses the following DICOMweb server configuration: ',\n props.config.servers\n )\n\n this.handleServerSelection = this.handleServerSelection.bind(this)\n\n message.config({ duration: 5 })\n this.addGcpSecondaryAnnotationServer(props.config)\n\n this.state = {\n clients: _createClientMapping({\n baseUri,\n settings: props.config.servers,\n onError: this.handleDICOMwebError\n }),\n isLoading: true,\n wasAuthSuccessful: false\n }\n }\n\n addGcpSecondaryAnnotationServer (config: AppProps['config']): void {\n const serverId = 'gcp_secondary_annotation_server'\n const urlParams = new URLSearchParams(window.location.search)\n const url = urlParams.get('gcp')\n const gcpSecondaryAnnotationServer = config.servers.find(\n (server) => server.id === serverId\n )\n if (gcpSecondaryAnnotationServer === undefined && typeof url === 'string') {\n config.servers.push({\n id: serverId,\n write: true,\n url,\n storageClasses: [\n StorageClasses.COMPREHENSIVE_SR,\n StorageClasses.COMPREHENSIVE_3D_SR,\n StorageClasses.SEGMENTATION,\n StorageClasses.MICROSCOPY_BULK_SIMPLE_ANNOTATION,\n StorageClasses.PARAMETRIC_MAP,\n StorageClasses.ADVANCED_BLENDING_PRESENTATION_STATE,\n StorageClasses.COLOR_SOFTCOPY_PRESENTATION_STATE,\n StorageClasses.GRAYSCALE_SOFTCOPY_PRESENTATION_STATE,\n StorageClasses.PSEUDOCOLOR_SOFTCOPY_PRESENTATION_STATE\n ]\n })\n }\n }\n\n handleServerSelection ({ url }: { url: string }): void {\n console.info('select DICOMweb server: ', url)\n const tmpClient = new DicomWebManager({\n baseUri: '',\n settings: [{\n id: 'tmp',\n url,\n read: true,\n write: false\n }],\n onError: this.handleDICOMwebError\n })\n tmpClient.updateHeaders(this.state.clients.default.headers)\n /**\n * Use the newly created client for all storage classes. We may want to\n * make this more sophisticated in the future to allow users to override\n * the entire server configuration.\n */\n this.setState(state => {\n const clients: { [key: string]: DicomWebManager } = {}\n for (const key in state.clients) {\n clients[key] = tmpClient\n }\n return { clients }\n })\n }\n\n /**\n * Handle successful authentication event.\n *\n * Authorizes the DICOMweb client to access the DICOMweb server and directs\n * the user back to the App.\n *\n * @param user - Information about the user\n * @param authorization - Value of the \"Authorization\" HTTP header field\n */\n handleSignIn = ({ user, authorization }: {\n user: User\n authorization: string\n }): void => {\n for (const key in this.state.clients) {\n const client = this.state.clients[key]\n client.updateHeaders({ Authorization: authorization })\n }\n const storedPath = window.localStorage.getItem('slim_path')\n const storedSearch = window.localStorage.getItem('slim_search')\n if (storedPath != null) {\n const currentPath = window.location.pathname\n if (storedPath !== currentPath) {\n let path = storedPath\n if (storedSearch != null) {\n path += storedSearch\n }\n window.location.href = path\n }\n }\n window.localStorage.removeItem('slim_path')\n window.localStorage.removeItem('slim_search')\n this.setState({ user: user })\n }\n\n signIn (): void {\n if (this.auth !== undefined) {\n console.info('try to sign in user')\n this.auth.signIn({ onSignIn: this.handleSignIn }).then(() => {\n console.info('sign-in was successful')\n this.setState({\n isLoading: false,\n wasAuthSuccessful: true\n })\n }).catch(() => {\n // eslint-disable-next-line @typescript-eslint/no-floating-promises\n NotificationMiddleware.onError(\n NotificationMiddlewareContext.AUTH,\n new CustomError(\n errorTypes.AUTHENTICATION,\n 'Could not sign-in user.')\n )\n this.setState({\n isLoading: false,\n redirectTo: undefined,\n wasAuthSuccessful: false\n })\n })\n } else {\n this.setState({\n isLoading: false,\n redirectTo: undefined,\n wasAuthSuccessful: true\n })\n }\n }\n\n componentDidMount (): void {\n const path = window.localStorage.getItem('slim_path')\n if (path == null) {\n window.localStorage.setItem('slim_path', window.location.pathname)\n window.localStorage.setItem('slim_search', window.location.search)\n }\n this.signIn()\n }\n\n render (): React.ReactNode {\n const appInfo = {\n name: this.props.name,\n version: this.props.version,\n homepage: this.props.homepage,\n uid: '1.2.826.0.1.3680043.9.7433.1.5',\n organization: this.props.config.organization\n }\n\n const enableWorklist = !(\n this.props.config.disableWorklist ?? false\n )\n const enableServerSelection = (\n this.props.config.enableServerSelection ?? false\n )\n\n let worklist\n if (enableWorklist) {\n worklist = \n } else {\n worklist =
Worklist has been disabled.
\n }\n\n let isLogoutPossible = false\n let onLogout: () => void\n if (\n // eslint-disable-next-line @typescript-eslint/prefer-optional-chain\n this.props.config.oidc != null &&\n this.props.config.oidc.endSessionEndpoint != null\n ) {\n onLogout = (): void => {\n if (this.auth != null) {\n // eslint-disable-next-line @typescript-eslint/no-floating-promises\n this.auth.signOut()\n }\n }\n isLogoutPossible = true\n } else {\n onLogout = () => {}\n isLogoutPossible = false\n }\n\n const layoutStyle = { height: '100vh' }\n const layoutContentStyle = { height: '100%' }\n\n if (this.state.redirectTo !== undefined) {\n return (\n \n \n \n )\n } else if (this.state.isLoading) {\n return (\n \n \n \n \n \n \n \n \n )\n } else if (!this.state.wasAuthSuccessful) {\n return (\n \n )\n } else if (this.state.error != null) {\n return (\n \n )\n } else {\n return (\n \n \n \n \n \n {worklist}\n \n \n }\n />\n \n \n \n \n \n \n }\n />\n \n \n Logged out\n \n }\n />\n \n \n )\n }\n }\n}\n\nexport default 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r=e.state;return t<0?(n=0,t=-t):(n=1+(t>>4),t<48&&(t&=15)),t&&(t<8||t>15)?In:(null!==r.window&&r.wbits!==t&&(r.window=null),r.wrap=n,r.wbits=t,Nn(e))},Ln=function(e,t){if(!e)return In;var n=new On;e.state=n,n.window=null;var r=bn(e,t);return r!==fn&&(e.state=null),r},wn=!0,xn=function(e){if(wn){yn=new Int32Array(512),Rn=new Int32Array(32);for(var t=0;t<144;)e.lens[t++]=8;for(;t<256;)e.lens[t++]=9;for(;t<280;)e.lens[t++]=7;for(;t<288;)e.lens[t++]=8;for(mn(1,e.lens,0,288,yn,0,e.work,{bits:9}),t=0;t<32;)e.lens[t++]=5;mn(2,e.lens,0,32,Rn,0,e.work,{bits:5}),wn=!1}e.lencode=yn,e.lenbits=9,e.distcode=Rn,e.distbits=5},Fn=function(e,t,n,r){var a,i=e.state;return null===i.window&&(i.wsize=1<=i.wsize?(i.window.set(t.subarray(n-i.wsize,n),0),i.wnext=0,i.whave=i.wsize):((a=i.wsize-i.wnext)>r&&(a=r),i.window.set(t.subarray(n-r,n-r+a),i.wnext),(r-=a)?(i.window.set(t.subarray(n-r,n),0),i.wnext=r,i.whave=i.wsize):(i.wnext+=a,i.wnext===i.wsize&&(i.wnext=0),i.whave>>8&255,n.check=ke(n.check,O,2,0),u=0,c=0,n.mode=2;break}if(n.flags=0,n.head&&(n.head.done=!1),!(1&n.wrap)||(((255&u)<<8)+(u>>8))%31){e.msg="incorrect header check",n.mode=Pn;break}if((15&u)!==Mn){e.msg="unknown compression method",n.mode=Pn;break}if(c-=4,E=8+(15&(u>>>=4)),0===n.wbits)n.wbits=E;else if(E>n.wbits){e.msg="invalid window size",n.mode=Pn;break}n.dmax=1<>8&1),512&n.flags&&(O[0]=255&u,O[1]=u>>>8&255,n.check=ke(n.check,O,2,0)),u=0,c=0,n.mode=3;case 3:for(;c<32;){if(0===s)break e;s--,u+=r[i++]<>>8&255,O[2]=u>>>16&255,O[3]=u>>>24&255,n.check=ke(n.check,O,4,0)),u=0,c=0,n.mode=4;case 4:for(;c<16;){if(0===s)break 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type",n.mode=Pn}u>>>=2,c-=2;break;case 14:for(u>>>=7&c,c-=7&c;c<32;){if(0===s)break e;s--,u+=r[i++]<>>16^65535)){e.msg="invalid stored block lengths",n.mode=Pn;break}if(n.length=65535&u,u=0,c=0,n.mode=15,t===dn)break e;case 15:n.mode=16;case 16:if(g=n.length){if(g>s&&(g=s),g>v&&(g=v),0===g)break e;a.set(r.subarray(i,i+g),o),s-=g,i+=g,v-=g,o+=g,n.length-=g;break}n.mode=An;break;case 17:for(;c<14;){if(0===s)break e;s--,u+=r[i++]<>>=5,c-=5,n.ndist=1+(31&u),u>>>=5,c-=5,n.ncode=4+(15&u),u>>>=4,c-=4,n.nlen>286||n.ndist>30){e.msg="too many length or distance symbols",n.mode=Pn;break}n.have=0,n.mode=18;case 18:for(;n.have>>=3,c-=3}for(;n.have<19;)n.lens[y[n.have++]]=0;if(n.lencode=n.lendyn,n.lenbits=7,A={bits:n.lenbits},M=mn(0,n.lens,0,19,n.lencode,0,n.work,A),n.lenbits=A.bits,M){e.msg="invalid code lengths set",n.mode=Pn;break}n.have=0,n.mode=19;case 19:for(;n.have>>16&255,p=65535&T,!((f=T>>>24)<=c);){if(0===s)break e;s--,u+=r[i++]<>>=f,c-=f,n.lens[n.have++]=p;else{if(16===p){for(P=f+2;c>>=f,c-=f,0===n.have){e.msg="invalid bit length repeat",n.mode=Pn;break}E=n.lens[n.have-1],g=3+(3&u),u>>>=2,c-=2}else if(17===p){for(P=f+3;c>>=f)),u>>>=3,c-=3}else{for(P=f+7;c>>=f)),u>>>=7,c-=7}if(n.have+g>n.nlen+n.ndist){e.msg="invalid bit length repeat",n.mode=Pn;break}for(;g--;)n.lens[n.have++]=E}}if(n.mode===Pn)break;if(0===n.lens[256]){e.msg="invalid code -- missing end-of-block",n.mode=Pn;break}if(n.lenbits=9,A={bits:n.lenbits},M=mn(1,n.lens,0,n.nlen,n.lencode,0,n.work,A),n.lenbits=A.bits,M){e.msg="invalid literal/lengths set",n.mode=Pn;break}if(n.distbits=6,n.distcode=n.distdyn,A={bits:n.distbits},M=mn(2,n.lens,n.nlen,n.ndist,n.distcode,0,n.work,A),n.distbits=A.bits,M){e.msg="invalid distances set",n.mode=Pn;break}if(n.mode=20,t===dn)break e;case 20:n.mode=21;case 21:if(s>=6&&v>=258){e.next_out=o,e.avail_out=v,e.next_in=i,e.avail_in=s,n.hold=u,n.bits=c,on(e,m),o=e.next_out,a=e.output,v=e.avail_out,i=e.next_in,r=e.input,s=e.avail_in,u=n.hold,c=n.bits,n.mode===An&&(n.back=-1);break}for(n.back=0;h=(T=n.lencode[u&(1<>>16&255,p=65535&T,!((f=T>>>24)<=c);){if(0===s)break e;s--,u+=r[i++]<>I)])>>>16&255,p=65535&T,!(I+(f=T>>>24)<=c);){if(0===s)break e;s--,u+=r[i++]<>>=I,c-=I,n.back+=I}if(u>>>=f,c-=f,n.back+=f,n.length=p,0===h){n.mode=26;break}if(32&h){n.back=-1,n.mode=An;break}if(64&h){e.msg="invalid literal/length code",n.mode=Pn;break}n.extra=15&h,n.mode=22;case 22:if(n.extra){for(P=n.extra;c>>=n.extra,c-=n.extra,n.back+=n.extra}n.was=n.length,n.mode=23;case 23:for(;h=(T=n.distcode[u&(1<>>16&255,p=65535&T,!((f=T>>>24)<=c);){if(0===s)break e;s--,u+=r[i++]<>I)])>>>16&255,p=65535&T,!(I+(f=T>>>24)<=c);){if(0===s)break e;s--,u+=r[i++]<>>=I,c-=I,n.back+=I}if(u>>>=f,c-=f,n.back+=f,64&h){e.msg="invalid distance code",n.mode=Pn;break}n.offset=p,n.extra=15&h,n.mode=24;case 24:if(n.extra){for(P=n.extra;c>>=n.extra,c-=n.extra,n.back+=n.extra}if(n.offset>n.dmax){e.msg="invalid distance too far back",n.mode=Pn;break}n.mode=25;case 25:if(0===v)break e;if(g=m-v,n.offset>g){if((g=n.offset-g)>n.whave&&n.sane){e.msg="invalid distance too far back",n.mode=Pn;break}g>n.wnext?(g-=n.wnext,S=n.wsize-g):S=n.wnext-g,g>n.length&&(g=n.length),d=n.window}else d=a,S=o-n.offset,g=n.length;g>v&&(g=v),v-=g,n.length-=g;do{a[o++]=d[S++]}while(--g);0===n.length&&(n.mode=21);break;case 26:if(0===v)break e;a[o++]=n.length,v--,n.mode=21;break;case 27:if(n.wrap){for(;c<32;){if(0===s)break e;s--,u|=r[i++]<=0&&t.windowBits<16&&(t.windowBits=-t.windowBits,0===t.windowBits&&(t.windowBits=-15)),!(t.windowBits>=0&&t.windowBits<16)||e&&e.windowBits||(t.windowBits+=32),t.windowBits>15&&t.windowBits<48&&0===(15&t.windowBits)&&(t.windowBits|=15),this.err=0,this.msg="",this.ended=!1,this.chunks=[],this.strm=new jt,this.strm.avail_out=0;var n=Gn.inflateInit2(this.strm,t.windowBits);if(n!==Hn)throw new Error(Ge[n]);if(this.header=new qn,Gn.inflateGetHeader(this.strm,this.header),t.dictionary&&("string"===typeof t.dictionary?t.dictionary=Bt(t.dictionary):"[object ArrayBuffer]"===Vn.call(t.dictionary)&&(t.dictionary=new Uint8Array(t.dictionary)),t.raw&&(n=Gn.inflateSetDictionary(this.strm,t.dictionary))!==Hn))throw new Error(Ge[n])}function Yn(e,t){var n=new Xn(t);if(n.push(e),n.err)throw n.msg||Ge[n.err];return n.result}Xn.prototype.push=function(e,t){var n,r,a,i=this.strm,o=this.options.chunkSize,s=this.options.dictionary;if(this.ended)return!1;for(r=t===~~t?t:!0===t?Qn:Bn,"[object ArrayBuffer]"===Vn.call(e)?i.input=new Uint8Array(e):i.input=e,i.next_in=0,i.avail_in=i.input.length;;){for(0===i.avail_out&&(i.output=new Uint8Array(o),i.next_out=0,i.avail_out=o),(n=Gn.inflate(i,r))===Wn&&s&&((n=Gn.inflateSetDictionary(i,s))===Hn?n=Gn.inflate(i,r):n===zn&&(n=Wn));i.avail_in>0&&n===jn&&i.state.wrap>0&&0!==e[i.next_in];)Gn.inflateReset(i),n=Gn.inflate(i,r);switch(n){case Zn:case zn:case Wn:case Kn:return this.onEnd(n),this.ended=!0,!1}if(a=i.avail_out,i.next_out&&(0===i.avail_out||n===jn))if("string"===this.options.to){var v=Ht(i.output,i.next_out),u=i.next_out-v,c=Qt(i.output,v);i.next_out=u,i.avail_out=o-u,u&&i.output.set(i.output.subarray(v,v+u),0),this.onData(c)}else this.onData(i.output.length===i.next_out?i.output:i.output.subarray(0,i.next_out));if(n!==Hn||0!==a){if(n===jn)return n=Gn.inflateEnd(this.strm),this.onEnd(n),this.ended=!0,!0;if(0===i.avail_in)break}}return!0},Xn.prototype.onData=function(e){this.chunks.push(e)},Xn.prototype.onEnd=function(e){e===Hn&&("string"===this.options.to?this.result=this.chunks.join(""):this.result=kt(this.chunks)),this.chunks=[],this.err=e,this.msg=this.strm.msg};var Jn={Inflate:Xn,inflate:Yn,inflateRaw:function(e,t){return(t=t||{}).raw=!0,Yn(e,t)},ungzip:Yn,constants:qe},$n={Deflate:an.Deflate,deflate:an.deflate,deflateRaw:an.deflateRaw,gzip:an.gzip,Inflate:Jn.Inflate,inflate:Jn.inflate,inflateRaw:Jn.inflateRaw,ungzip:Jn.ungzip,constants:qe};function er(e){if(isNaN(e))throw new Error("Not a number: "+e);return"string"==typeof e?parseInt(e):e}function tr(e){return"string"==typeof e?parseFloat(e):e}var nr=function(){function e(t,n){b(this,e),this.buffer="number"==typeof t?new ArrayBuffer(t):t,this.buffer||(this.buffer=new ArrayBuffer(0)),this.view=new 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t=this.offset+e+this.buffer.byteLength,n=new ArrayBuffer(t);new Uint8Array(n).set(new Uint8Array(this.buffer)),this.buffer=n,this.view=new DataView(this.buffer)}}},{key:"concat",value:function(e){var t=this.buffer.byteLength-this.offset;if(e.size>t){var n=new ArrayBuffer(this.offset+e.size),r=new Uint8Array(n);r.set(new Uint8Array(this.getBuffer(0,this.offset))),r.set(new Uint8Array(e.getBuffer(0,e.size)),this.offset),this.buffer=n,this.view=new DataView(this.buffer)}else{new Uint8Array(this.buffer).set(new Uint8Array(e.getBuffer(0,e.size)),this.offset)}return this.offset+=e.size,this.size=this.offset,this.buffer.byteLength}},{key:"increment",value:function(e){return this.offset+=e,this.offset>this.size&&(this.size=this.offset),e}},{key:"getBuffer",value:function(e,t){return e||t||(e=0,t=this.size),this.buffer.slice(e,t)}},{key:"more",value:function(e){if(this.offset+e>this.endOffset)throw new Error("Request more than currently allocated buffer");var t=new 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g=e.lookupTag(u);c=g?g.vr:4294967295==l?"SQ":u.isPixelDataTag()?"OW":"xs"==c?"US":u.isPrivateCreator()?"LO":"UN",m=hr.createByTypeString(c)}else c=t.readVR(),(m=hr.createByTypeString(c)).isExplicit()?(t.increment(2),l=t.readUint32()):l=t.readUint16();var S=[];if(m.isBinary()&&l>m.maxLength&&!m.noMultiple)for(var d=l/m.maxLength,f=0;f++0&&void 0!==arguments[0]?arguments[0]:{allowInvalidVRLength:!1},t=ra,n=new ir(4096,!0);n.writeUint8Repeat(0,128),n.writeAsciiString("DICM");var r=new ir(1024);this.meta["00020010"]||(this.meta["00020010"]={vr:"UI",Value:[ra]}),na.write(this.meta,r,t,e),na.writeTagObject(n,"00020000","UL",r.size,t,e),n.concat(r);var a=this.meta["00020010"].Value[0];return na.write(this.dict,n,a,e),n.getBuffer()}}]),e}(),ia=function(){function e(){b(this,e)}return w(e,null,[{key:"d65WhitePointXYZ",value:function(){return[.950456,1,1.088754]}},{key:"dicomlab2RGB",value:function(t){return e.lab2RGB(e.dicomlab2LAB(t))}},{key:"rgb2DICOMLAB",value:function(t){return e.lab2DICOMLAB(e.rgb2LAB(t))}},{key:"dicomlab2LAB",value:function(e){return[100*e[0]/65535,255*e[1]/65535-128,255*e[2]/65535-128]}},{key:"lab2DICOMLAB",value:function(e){return[65535*e[0]/100,65535*(e[1]+128)/255,65535*(e[2]+128)/255]}},{key:"rgb2LAB",value:function(t){return e.xyz2LAB(e.rgb2XYZ(t))}},{key:"gammaCorrection",value:function(e){return e<=.0031306684425005883?12.92*e:1.055*Math.pow(e,.4166666666666667)-.055}},{key:"invGammaCorrection",value:function(e){return e<=.0404482362771076?e/12.92:Math.pow((e+.055)/1.055,2.4)}},{key:"rgb2XYZ",value:function(t){var n=e.invGammaCorrection(t[0]),r=e.invGammaCorrection(t[1]),a=e.invGammaCorrection(t[2]);return[.41239558896741424*n+.3575834307637148*r+.18049264738170157*a,.21258623078559555*n+.7151703037034108*r+.07220049864333623*a,.019297215491746945*n+.11918386458084854*r+.9504971251315798*a]}},{key:"xyz2LAB",value:function(t){var n=e.d65WhitePointXYZ(),r=t[0]/n[0],a=t[1]/n[1],i=t[2]/n[2];return r=e.labf(r),[116*(a=e.labf(a))-16,500*(r-a),200*(a-(i=e.labf(i)))]}},{key:"lab2RGB",value:function(t){return e.xyz2RGB(e.lab2XYZ(t))}},{key:"lab2XYZ",value:function(t){var n=(t[0]+16)/116,r=n+t[1]/500,a=n-t[2]/200,i=e.d65WhitePointXYZ();return[i[0]*e.labfInv(r),i[1]*e.labfInv(n),i[2]*e.labfInv(a)]}},{key:"xyz2RGB",value:function(t){var n=3.2406*t[0]-1.5372*t[1]-.4986*t[2],r=-.9689*t[0]+1.8758*t[1]+.0415*t[2],a=.0557*t[0]-.204*t[1]+1.057*t[2],i=Math.min(n,r);return(i=Math.min(i,a))<0&&(n-=i,r-=i,a-=i),[e.gammaCorrection(n),e.gammaCorrection(r),e.gammaCorrection(a)]}},{key:"labf",value:function(e){return e>=.008856451679035631?Math.pow(e,.333333333333333):841/108*e+4/29}},{key:"labfInv",value:function(e){return e>=.20689655172413793?e*e*e:108/841*(e-4/29)}}]),e}();function oa(e){var t=new Uint8Array(2);t[1]=1;var n=e._meta.TransferSyntaxUID&&e._meta.TransferSyntaxUID.Value&&e._meta.TransferSyntaxUID.Value[0]?e._meta.TransferSyntaxUID.Value[0]:"1.2.840.10008.1.2.1";e._meta={MediaStorageSOPClassUID:e.SOPClassUID,MediaStorageSOPInstanceUID:e.SOPInstanceUID,ImplementationVersionName:"dcmjs-0.0",TransferSyntaxUID:n,ImplementationClassUID:"2.25.80302813137786398554742050926734630921603366648225212145404",FileMetaInformationVersion:t.buffer};var r=Jr.denaturalizeDataset(e._meta),a=new aa(r);return a.dict=Jr.denaturalizeDataset(e),a}function sa(e){return Buffer.from(oa(e).write())}function va(e){var t=sa(e);return new Blob([t],{type:"application/dicom"})}var ua=function(){function e(t){var n=arguments.length>1&&void 0!==arguments[1]?arguments[1]:{};b(this,e),this.options=JSON.parse(JSON.stringify(n));var r=this.options;r.Manufacturer=n.Manufacturer||"Unspecified",r.ManufacturerModelName=n.ManufacturerModelName||"Unspecified",r.SeriesDescription=n.SeriesDescription||"Research Derived series",r.SeriesNumber=n.SeriesNumber||"99",r.SoftwareVersions=n.SoftwareVersions||"0",r.DeviceSerialNumber=n.DeviceSerialNumber||"1";var a=Jr.date(),i=Jr.time();r.SeriesDate=n.SeriesDate||a,r.SeriesTime=n.SeriesTime||i,r.ContentDate=n.ContentDate||a,r.ContentTime=n.ContentTime||i,r.SOPInstanceUID=n.SOPInstanceUID||Jr.uid(),r.SeriesInstanceUID=n.SeriesInstanceUID||Jr.uid(),r.ClinicalTrialTimePointID=n.ClinicalTrialTimePointID||"",r.ClinicalTrialCoordinatingCenterName=n.ClinicalTrialCoordinatingCenterName||"",r.ClinicalTrialSeriesID=n.ClinicalTrialSeriesID||"",r.ImageComments=n.ImageComments||"NOT FOR CLINICAL USE",r.ContentQualification="RESEARCH",this.referencedDatasets=t,this.referencedDataset=this.referencedDatasets[0],this.dataset={_vrMap:this.referencedDataset._vrMap,_meta:this.referencedDataset._meta},this.derive()}return w(e,[{key:"assignToDataset",value:function(e){var t=this;Object.keys(e).forEach((function(n){return t.dataset[n]=e[n]}))}},{key:"assignFromReference",value:function(e){var t=this;e.forEach((function(e){return t.dataset[e]=t.referencedDataset[e]||""}))}},{key:"assignFromOptions",value:function(e){var t=this;e.forEach((function(e){return t.dataset[e]=t.options[e]||""}))}},{key:"derive",value:function(){this.assignFromReference(["AccessionNumber","ReferringPhysicianName","StudyDate","StudyID","StudyTime","PatientName","PatientID","PatientBirthDate","PatientSex","PatientAge","StudyInstanceUID","StudyID"]),this.assignFromOptions(["Manufacturer","SoftwareVersions","DeviceSerialNumber","ManufacturerModelName","SeriesDescription","SeriesNumber","ImageComments","SeriesDate","SeriesTime","ContentDate","ContentTime","ContentQualification","SOPInstanceUID","SeriesInstanceUID"])}}],[{key:"copyDataset",value:function(e){return JSON.parse(JSON.stringify(e))}}]),e}(),ca=function(e){F(n,e);var t=Q(n);function n(e){var r,a=arguments.length>1&&void 0!==arguments[1]?arguments[1]:{};b(this,n);var i=(r=t.call(this,e,a)).options;return i.ContentLabel=a.ContentLabel||"",i.ContentDescription=a.ContentDescription||"",i.ContentCreatorName=a.ContentCreatorName||"",r}return w(n,[{key:"derive",value:function(){j(U(n.prototype),"derive",this).call(this),this.assignToDataset({ImageType:["DERIVED","PRIMARY"],LossyImageCompression:"00",InstanceNumber:"1"}),this.assignFromReference(["SOPClassUID","Modality","FrameOfReferenceUID","PositionReferenceIndicator","NumberOfFrames","Rows","Columns","SamplesPerPixel","PhotometricInterpretation","BitsStored","HighBit"]),this.assignFromOptions(["ContentLabel","ContentDescription","ContentCreatorName"]),this.referencedDataset.SharedFunctionalGroupsSequence&&(this.dataset.SharedFunctionalGroupsSequence=ua.copyDataset(this.referencedDataset.SharedFunctionalGroupsSequence)),this.referencedDataset.PerFrameFunctionalGroupsSequence&&(this.dataset.PerFrameFunctionalGroupsSequence=ua.copyDataset(this.referencedDataset.PerFrameFunctionalGroupsSequence)),this.dataset.PixelData=new ArrayBuffer(this.referencedDataset.PixelData.byteLength)}}]),n}(ua),la=function(e){F(n,e);var t=Q(n);function n(e){var r=arguments.length>1&&void 0!==arguments[1]?arguments[1]:{};return b(this,n),t.call(this,e,r)}return w(n,[{key:"derive",value:function(){j(U(n.prototype),"derive",this).call(this),this.assignFromReference(["WindowCenter","WindowWidth","BitsAllocated","PixelRepresentation","BodyPartExamined","Laterality","PatientPosition","RescaleSlope","RescaleIntercept","PixelPresentation","VolumetricProperties","VolumeBasedCalculationTechnique","PresentationLUTShape"])}}]),n}(ca),ma=function(){function e(t){b(this,e),this.datasets=t,this.dataset=void 0}return w(e,[{key:"normalize",value:function(){return"No normalization defined"}}],[{key:"consistentSOPClassUIDs",value:function(e){var t;return e.forEach((function(e){e.SOPClassUID&&(t||(t=e.SOPClassUID),e.SOPClassUID===t||P.error("inconsistent sopClassUIDs: ",e.SOPClassUID,t))})),t}},{key:"normalizerForSOPClassUID",value:function(e){e=e.replace(/[^0-9.]/g,"");var t=Jr.sopClassUIDsByName,n={};return n[t.CTImage]=pa,n[t.ParametricMapStorage]=Da,n[t.MRImage]=Sa,n[t.EnhancedCTImage]=da,n[t.LegacyConvertedEnhancedCTImage]=da,n[t.EnhancedMRImage]=fa,n[t.LegacyConvertedEnhancedMRImage]=fa,n[t.EnhancedUSVolume]=ha,n[t.PETImage]=Ia,n[t.EnhancedPETImage]=Ia,n[t.LegacyConvertedEnhancedPETImage]=Ia,n[t.Segmentation]=Ca,n[t.DeformableSpatialRegistration]=Ea,n[e]}},{key:"isMultiframeSOPClassUID",value:function(e){var t=Jr.sopClassUIDsByName;return-1!==[t.EnhancedMRImage,t.LegacyConvertedEnhancedMRImage,t.EnhancedCTImage,t.LegacyConvertedEnhancedCTImage,t.EnhancedUSVolume,t.EnhancedPETImage,t.LegacyConvertedEnhancedPETImage,t.Segmentation,t.ParametricMapStorage].indexOf(e)}},{key:"isMultiframeDataset",value:function(){var t=arguments.length>0&&void 0!==arguments[0]?arguments[0]:this.dataset,n=t.SOPClassUID.replace(/[^0-9.]/g,"");return e.isMultiframeSOPClassUID(n)}},{key:"normalizeToDataset",value:function(t){var n=e.consistentSOPClassUIDs(t),r=e.normalizerForSOPClassUID(n);if(r){var a=new r(t);return a.normalize(),a.dataset}P.error("no normalizerClass for ",n)}}]),e}(),ga=function(e){F(n,e);var t=Q(n);function n(){return b(this,n),t.apply(this,arguments)}return w(n,[{key:"normalize",value:function(){this.convertToMultiframe(),this.normalizeMultiframe()}},{key:"convertToMultiframe",value:function(){if(1===this.datasets.length&&ma.isMultiframeDataset(this.datasets[0]))this.dataset=this.datasets[0];else{this.derivation=new la(this.datasets),this.dataset=this.derivation.dataset;var e=this.dataset,t=this.datasets[0];e.NumberOfFrames=this.datasets.length,e.SOPClassUID=t.SOPClassUID,e.Rows=t.Rows,e.Columns=t.Columns,e.BitsAllocated=t.BitsAllocated,e.PixelRepresentation=t.PixelRepresentation,e.RescaleSlope=t.RescaleSlope||"1",e.RescaleIntercept=t.RescaleIntercept||"0";var r=t.ImagePositionPatient,a=t.ImageOrientationPatient.slice(0,3),i=t.ImageOrientationPatient.slice(3,6),o=n.vec3CrossProduct(a,i),s=[];this.datasets.forEach((function(e){var t=e.ImagePositionPatient.slice(),a=n.vec3Subtract(t,r),i=n.vec3Dot(a,o);s.push([i,e])})),s.sort((function(e,t){return t[0]-e[0]})),16!==e.BitsAllocated&&P.error("Only works with 16 bit data, not "+String(this.dataset.BitsAllocated)),t._vrMap&&!t._vrMap.PixelData?(P.warn("No vr map given for pixel data, using OW"),e._vrMap={PixelData:"OW"}):e._vrMap={PixelData:t._vrMap.PixelData};var v=t.PixelData.byteLength;e.PixelData=new ArrayBuffer(e.NumberOfFrames*v);var u=0;s.forEach((function(t){var n=t[1],r=new Uint16Array(n.PixelData),a=new Uint16Array(e.PixelData,u*v,v/2);try{a.set(r)}catch(o){if(o instanceof RangeError){var i="Error inserting pixels in PixelData\n"+"frameSize ".concat(v,"\n")+"NumberOfFrames ".concat(e.NumberOfFrames,"\n")+"pair ".concat(t,"\n")+"dataset PixelData size ".concat(n.PixelData.length);P.error(i)}}u++})),e.NumberOfFrames<2&&P.error("Cannot populate shared groups uniquely without multiple frames");var c=W(s[0],2),l=c[0],m=c[1],g=s[1][0],S=Math.abs(g-l);e.SharedFunctionalGroupsSequence={PlaneOrientationSequence:{ImageOrientationPatient:m.ImageOrientationPatient},PixelMeasuresSequence:{PixelSpacing:m.PixelSpacing,SpacingBetweenSlices:S,SliceThickness:S}},e.ReferencedSeriesSequence={SeriesInstanceUID:m.SeriesInstanceUID,ReferencedInstanceSequence:[]},e.PerFrameFunctionalGroupsSequence=[],s.forEach((function(t){var n=t[1];e.PerFrameFunctionalGroupsSequence.push({PlanePositionSequence:{ImagePositionPatient:n.ImagePositionPatient},FrameVOILUTSequence:{WindowCenter:n.WindowCenter,WindowWidth:n.WindowWidth}}),e.ReferencedSeriesSequence.ReferencedInstanceSequence.push({ReferencedSOPClassUID:n.SOPClassUID,ReferencedSOPInstanceUID:n.SOPInstanceUID})}));var d=Jr.uid();this.dataset.DimensionOrganizationSequence={DimensionOrganizationUID:d},this.dataset.DimensionIndexSequence=[{DimensionOrganizationUID:d,DimensionIndexPointer:2097202,FunctionalGroupPointer:2134291,DimensionDescriptionLabel:"ImagePositionPatient"}]}}},{key:"normalizeMultiframe",value:function(){var e=this.dataset;if(e.NumberOfFrames){e.PixelRepresentation||(e.PixelRepresentation=1),e.StudyID&&""!==e.StudyID||(e.StudyID="No Study ID");-1===["R","L"].indexOf(e.Laterality)&&delete e.Laterality,e.PresentationLUTShape||(e.PresentationLUTShape="IDENTITY"),e.SharedFunctionalGroupsSequence||P.error("Can only process multiframe data with SharedFunctionalGroupsSequence"),"PROSTATE"===e.BodyPartExamined&&(e.SharedFunctionalGroupsSequence.FrameAnatomySequence={AnatomicRegionSequence:{CodeValue:"T-9200B",CodingSchemeDesignator:"SRT",CodeMeaning:"Prostate"},FrameLaterality:"U"});var t=e.RescaleIntercept||0,n=e.RescaleSlope||1;e.SharedFunctionalGroupsSequence.PixelValueTransformationSequence={RescaleIntercept:t,RescaleSlope:n,RescaleType:"US"};var r=1;if(this.datasets.forEach((function(t){1===e.NumberOfFrames&&(e.PerFrameFunctionalGroupsSequence=[e.PerFrameFunctionalGroupsSequence]),e.PerFrameFunctionalGroupsSequence[r-1].FrameContentSequence={FrameAcquisitionDuration:0,StackID:1,InStackPositionNumber:r,DimensionIndexValues:r};var n=t.AcquisitionDate+t.AcquisitionTime;if(!isNaN(n)){var a=e.PerFrameFunctionalGroupsSequence[r-1].FrameContentSequence;a.FrameAcquisitionDateTime=n,a.FrameReferenceDateTime=n}r++})),e.WindowCenter&&e.WindowWidth&&(Array.isArray(e.WindowCenter)||(e.WindowCenter=[e.WindowCenter]),Array.isArray(e.WindowWidth)||(e.WindowWidth=[e.WindowWidth])),(!e.WindowCenter||!e.WindowWidth)&&(e.WindowCenter=[],e.WindowWidth=[],e.PerFrameFunctionalGroupsSequence)){var a={center:0,width:0,count:0};e.PerFrameFunctionalGroupsSequence.forEach((function(e){if(e.FrameVOILUT){var t=e.FrameVOILUTSequence.WindowCenter,n=e.FrameVOILUTSequence.WindowWidth;e.FrameVOILUTSequence&&t&&n&&(Array.isArray(t)&&(t=t[0]),Array.isArray(n)&&(n=n[0]),a.center+=Number(t),a.width+=Number(n),a.count++)}})),a.count>0&&(e.WindowCenter.push(String(a.center/a.count)),e.WindowWidth.push(String(a.width/a.count)))}0===e.WindowCenter.length&&(e.WindowCenter=[300]),0===e.WindowWidth.length&&(e.WindowWidth=[500])}else P.error("Missing number or frames not supported")}}],[{key:"vec3CrossProduct",value:function(e,t){var n=e[0],r=e[1],a=e[2],i=t[0],o=t[1],s=t[2],v=[];return v[0]=r*s-a*o,v[1]=a*i-n*s,v[2]=n*o-r*i,v}},{key:"vec3Subtract",value:function(e,t){var n=[];return n[0]=e[0]-t[0],n[1]=e[1]-t[1],n[2]=e[2]-t[2],n}},{key:"vec3Dot",value:function(e,t){return e[0]*t[0]+e[1]*t[1]+e[2]*t[2]}}]),n}(ma),Sa=function(e){F(n,e);var t=Q(n);function n(){return b(this,n),t.apply(this,arguments)}return w(n,[{key:"normalize",value:function(){j(U(n.prototype),"normalize",this).call(this),this.dataset.SOPClassUID="LegacyConvertedEnhancedMRImage"}},{key:"normalizeMultiframe",value:function(){j(U(n.prototype),"normalizeMultiframe",this).call(this);var e=this.dataset;e.ImageType&&e.ImageType.constructor&&"Array"==e.ImageType.constructor.name&&4==e.ImageType.length||(e.ImageType=["ORIGINAL","PRIMARY","OTHER","NONE"]),e.SharedFunctionalGroupsSequence.MRImageFrameTypeSequence={FrameType:e.ImageType,PixelPresentation:"MONOCHROME",VolumetricProperties:"VOLUME",VolumeBasedCalculationTechnique:"NONE",ComplexImageComponent:"MAGNITUDE",AcquisitionContrast:"UNKNOWN"}}}]),n}(ga),da=function(e){F(n,e);var t=Q(n);function n(){return b(this,n),t.apply(this,arguments)}return w(n,[{key:"normalize",value:function(){j(U(n.prototype),"normalize",this).call(this)}}]),n}(ga),fa=function(e){F(n,e);var t=Q(n);function n(){return b(this,n),t.apply(this,arguments)}return w(n,[{key:"normalize",value:function(){j(U(n.prototype),"normalize",this).call(this)}}]),n}(ga),ha=function(e){F(n,e);var t=Q(n);function n(){return b(this,n),t.apply(this,arguments)}return w(n,[{key:"normalize",value:function(){j(U(n.prototype),"normalize",this).call(this)}}]),n}(ga),pa=function(e){F(n,e);var t=Q(n);function n(){return b(this,n),t.apply(this,arguments)}return w(n,[{key:"normalize",value:function(){j(U(n.prototype),"normalize",this).call(this);var e=Jr.sopClassUIDsByName;this.dataset.SOPClassUID=e.EnhancedCTImage}}]),n}(ga),Ia=function(e){F(n,e);var t=Q(n);function n(){return b(this,n),t.apply(this,arguments)}return w(n,[{key:"normalize",value:function(){j(U(n.prototype),"normalize",this).call(this);var e=Jr.sopClassUIDsByName;this.dataset.SOPClassUID=e.EnhancedPETImage}}]),n}(ga),Ca=function(e){F(n,e);var t=Q(n);function n(){return b(this,n),t.apply(this,arguments)}return w(n,[{key:"normalize",value:function(){j(U(n.prototype),"normalize",this).call(this)}}]),n}(ga),Da=function(e){F(n,e);var t=Q(n);function n(){return b(this,n),t.apply(this,arguments)}return w(n,[{key:"normalize",value:function(){j(U(n.prototype),"normalize",this).call(this);var e=this.datasets[0];32!==e.BitsAllocated&&P.error("Only works with 32 bit data, not "+String(e.BitsAllocated))}}]),n}(ga),Ea=function(e){F(n,e);var t=Q(n);function n(){return b(this,n),t.apply(this,arguments)}return w(n,[{key:"normalize",value:function(){this.dataset=this.datasets[0]}}]),n}(ma),Ma=function(e){F(n,e);var t=Q(n);function n(e){var r=arguments.length>1&&void 0!==arguments[1]?arguments[1]:{};return b(this,n),t.call(this,e,r)}return w(n,[{key:"derive",value:function(){j(U(n.prototype),"derive",this).call(this),this.assignToDataset({SOPClassUID:Jr.sopClassUIDsByName.EnhancedSR,Modality:"SR",ValueType:"CONTAINER"}),this.assignFromReference([])}}]),n}(ua),Aa=function(){function e(t){b(this,e),this.TIDIncludeGroups=t;var n=[],r=[];this.ImageLibraryContentSequence=n,this.CurrentRequestedProcedureEvidenceSequence=r,this.PersonObserverName={RelationshipType:"HAS OBS CONTEXT",ValueType:"PNAME",ConceptNameCodeSequence:{CodeValue:"121008",CodingSchemeDesignator:"DCM",CodeMeaning:"Person Observer Name"},PersonName:"unknown^unknown"},this.tid1500={ConceptNameCodeSequence:{CodeValue:"126000",CodingSchemeDesignator:"DCM",CodeMeaning:"Imaging Measurement Report"},ContinuityOfContent:"SEPARATE",PerformedProcedureCodeSequence:[],CompletionFlag:"COMPLETE",VerificationFlag:"UNVERIFIED",ReferencedPerformedProcedureStepSequence:[],InstanceNumber:1,CurrentRequestedProcedureEvidenceSequence:r,CodingSchemeIdentificationSequence:{CodingSchemeDesignator:"99dcmjs",CodingSchemeName:"Codes used for dcmjs",CodingSchemeVersion:"0",CodingSchemeResponsibleOrganization:"https://github.com/dcmjs-org/dcmjs"},ContentTemplateSequence:{MappingResource:"DCMR",TemplateIdentifier:"1500"},ContentSequence:[{RelationshipType:"HAS CONCEPT MOD",ValueType:"CODE",ConceptNameCodeSequence:cr({CodeValue:"121049",CodingSchemeDesignator:"DCM",CodeMeaning:"Language of Content Item and Descendants"}),ConceptCodeSequence:cr({CodeValue:"eng",CodingSchemeDesignator:"RFC5646",CodeMeaning:"English"}),ContentSequence:cr({RelationshipType:"HAS CONCEPT MOD",ValueType:"CODE",ConceptNameCodeSequence:cr({CodeValue:"121046",CodingSchemeDesignator:"DCM",CodeMeaning:"Country of Language"}),ConceptCodeSequence:cr({CodeValue:"US",CodingSchemeDesignator:"ISO3166_1",CodeMeaning:"United States"})})},this.PersonObserverName,{RelationshipType:"HAS CONCEPT MOD",ValueType:"CODE",ConceptNameCodeSequence:cr({CodeValue:"121058",CodingSchemeDesignator:"DCM",CodeMeaning:"Procedure reported"}),ConceptCodeSequence:cr({CodeValue:"1",CodingSchemeDesignator:"99dcmjs",CodeMeaning:"Unknown procedure"})},{RelationshipType:"CONTAINS",ValueType:"CONTAINER",ConceptNameCodeSequence:{CodeValue:"111028",CodingSchemeDesignator:"DCM",CodeMeaning:"Image Library"},ContinuityOfContent:"SEPARATE",ContentSequence:{RelationshipType:"CONTAINS",ValueType:"CONTAINER",ConceptNameCodeSequence:{CodeValue:"126200",CodingSchemeDesignator:"DCM",CodeMeaning:"Image Library Group"},ContinuityOfContent:"SEPARATE",ContentSequence:n}}]}}return w(e,[{key:"validate",value:function(){}},{key:"contentItem",value:function(e){var t=arguments.length>1&&void 0!==arguments[1]?arguments[1]:{};t.PersonName&&(this.PersonObserverName.PersonName=t.PersonName);var n=Array.isArray(e)?e:[e];return this.addTID1501MeasurementGroups(n,t),this.tid1500}},{key:"addTID1501MeasurementGroups",value:function(e){var t=arguments.length>1&&void 0!==arguments[1]?arguments[1]:{},n=this.CurrentRequestedProcedureEvidenceSequence,r=this.ImageLibraryContentSequence,a=t.sopInstanceUIDsToSeriesInstanceUIDMap;if(e.length>1&&void 0===a)throw new Error("addTID1501MeasurementGroups provided with ".concat(e.length," derivationSourceDatasets, with no sopInstanceUIDsToSeriesInstanceUIDMap in options."));var i=this.TIDIncludeGroups.TID1501MeasurementGroups;if(i){var o=[];i.forEach((function(e){o=o.concat(e.contentItem())}));var s=[];i.forEach((function(t){t.TID300Measurements.forEach((function(t){var i=t.ReferencedSOPSequence.ReferencedSOPInstanceUID;if(!s.includes(i)){var o;if(r.push({RelationshipType:"CONTAINS",ValueType:"IMAGE",ReferencedSOPSequence:t.ReferencedSOPSequence}),1===e.length)o=e[0];else{var v=a[i];o=e.find((function(e){return e.SeriesInstanceUID===v}))}n.push({StudyInstanceUID:o.StudyInstanceUID,ReferencedSeriesSequence:{SeriesInstanceUID:o.SeriesInstanceUID,ReferencedSOPSequence:t.ReferencedSOPSequence}}),s.push(i)}}))}));var v={RelationshipType:"CONTAINS",ValueType:"CONTAINER",ConceptNameCodeSequence:{CodeValue:"126010",CodingSchemeDesignator:"DCM",CodeMeaning:"Imaging Measurements"},ContinuityOfContent:"SEPARATE",ContentSequence:o};this.tid1500.ContentSequence.push(v)}}}]),e}(),Pa=function(){function e(t){b(this,e),this.TID300Measurements=t}return w(e,[{key:"contentItem",value:function(){var e=this,t=this.TID300Measurements,n=[];return t.forEach((function(t){n.push(e.getMeasurementGroup(t.contentItem()))})),n}},{key:"getMeasurementGroup",value:function(e){return{RelationshipType:"CONTAINS",ValueType:"CONTAINER",ConceptNameCodeSequence:{CodeValue:"125007",CodingSchemeDesignator:"DCM",CodeMeaning:"Measurement Group"},ContinuityOfContent:"SEPARATE",ContentSequence:Z(e)}}}]),e}(),Ta=function(e){return Array.isArray(e)?e:[e]},Oa=function(e){return function(t){return t.ConceptNameCodeSequence.CodeMeaning===e}},ya={CodingSchemeDesignator:"DCM",CodeValue:"121071"},Ra={CodingSchemeDesignator:"SCT",CodeValue:"363698007"},_a={CodingSchemeDesignator:"SRT",CodeValue:"G-C0E3"},Na=function(e,t,n){var r=e.ConceptNameCodeSequence;if(r){var a=r.CodingSchemeDesignator,i=r.CodeValue;return a==t.CodingSchemeDesignator&&i==t.CodeValue||n&&a==n.CodingSchemeDesignator&&i==n.CodeValue}};var ba=function(){function e(){b(this,e)}return w(e,null,[{key:"getSetupMeasurementData",value:function(e){var t=e.ContentSequence,n=Ta(t),r=n.find((function(e){return Na(e,ya)})),a=n.filter((function(e){return Na(e,Ra,_a)}))||[],i=n.find((function(e){return"NUM"===e.ValueType})),o=Ta(i.ContentSequence).find((function(e){return"SCOORD"===e.ValueType})),s=o.ContentSequence.ReferencedSOPSequence,v=s.ReferencedSOPInstanceUID,u=s.ReferencedFrameNumber,c={sopInstanceUid:v,frameIndex:u||1,complete:!0,finding:r?cr(r.ConceptCodeSequence):void 0,findingSites:a.map((function(e){return cr(e.ConceptCodeSequence)}))};c.finding&&(c.description=c.finding.CodeMeaning);var l=c.findingSites&&c.findingSites[0];return l&&(c.location=l[0]&&l[0].CodeMeaning||l.CodeMeaning),{defaultState:c,findingGroup:r,findingSiteGroups:a,NUMGroup:i,SCOORDGroup:o,ReferencedSOPSequence:s,ReferencedSOPInstanceUID:v,ReferencedFrameNumber:u}}},{key:"generateReport",value:function(e,t,n){var r=[],a=Object.keys(e)[0];if(!a)throw new Error("No measurements provided.");var i=t.get("generalSeriesModule",a),o=i.studyInstanceUID,s=i.seriesInstanceUID;Object.keys(e).forEach((function(n){var a=t.get("sopCommonModule",n),i=t.get("frameNumber",n),o=e[n],s=Object.keys(o),v={ReferencedSOPClassUID:a.sopClassUID,ReferencedSOPInstanceUID:a.sopInstanceUID};ma.isMultiframeSOPClassUID(a.sopClassUID)&&(v.ReferencedFrameNumber=i);var u=[];s.forEach((function(e){var t=function(e,t,n){var r=t[e],a=ba.CORNERSTONE_TOOL_CLASSES_BY_TOOL_TYPE[e];if(r&&r.data&&r.data.length&&a){var i=r.data.map((function(e){return function(e,t,n,r){var a=r.getTID300RepresentationArguments(e);return a.ReferencedSOPSequence=n,new r.TID300Representation(a)}(e,0,n,a)}));return new Pa(i)}}(e,o,v);t&&u.push(t)})),r=r.concat(u)}));var v=new Aa({TID1501MeasurementGroups:r},n),u=new Uint8Array(2);u[1]=1;var c={StudyInstanceUID:o,SeriesInstanceUID:s},l={FileMetaInformationVersion:{Value:[u.buffer],vr:"OB"},TransferSyntaxUID:{Value:["1.2.840.10008.1.2.1"],vr:"UI"},ImplementationClassUID:{Value:[Jr.uid()],vr:"UI"},ImplementationVersionName:{Value:["dcmjs"],vr:"SH"}};c._meta=l,c._vrMap={PixelData:"OW"};var m=new 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===")),console.log(o),v[a.toolType].push(o)}})),v}},{key:"registerTool",value:function(t){e.CORNERSTONE_TOOL_CLASSES_BY_UTILITY_TYPE[t.utilityToolType]=t,e.CORNERSTONE_TOOL_CLASSES_BY_TOOL_TYPE[t.toolType]=t,e.MEASUREMENT_BY_TOOLTYPE[t.toolType]=t.utilityToolType}}]),e}();ba.MEASUREMENT_BY_TOOLTYPE={},ba.CORNERSTONE_TOOL_CLASSES_BY_UTILITY_TYPE={},ba.CORNERSTONE_TOOL_CLASSES_BY_TOOL_TYPE={};var La=function(){function e(t){b(this,e),this.ReferencedSOPSequence=t.ReferencedSOPSequence,this.props=t}return w(e,[{key:"getMeasurement",value:function(e){return[].concat(Z(this.getTrackingGroups()),Z(this.getFindingGroup()),Z(this.getFindingSiteGroups()),Z(e))}},{key:"getTrackingGroups",value:function(){return[{RelationshipType:"HAS OBS CONTEXT",ValueType:"TEXT",ConceptNameCodeSequence:{CodeValue:"112039",CodingSchemeDesignator:"DCM",CodeMeaning:"Tracking Identifier"},TextValue:this.props.trackingIdentifierTextValue||"web annotation"},{RelationshipType:"HAS OBS CONTEXT",ValueType:"UIDREF",ConceptNameCodeSequence:{CodeValue:"112040",CodingSchemeDesignator:"DCM",CodeMeaning:"Tracking Unique Identifier"},UID:Jr.uid()}]}},{key:"getFindingGroup",value:function(){var e=this.props.finding;if(!e)return[];var t=e.CodeValue,n=e.CodingSchemeDesignator,r=e.CodeMeaning;return[{RelationshipType:"CONTAINS",ValueType:"CODE",ConceptNameCodeSequence:cr({CodeValue:"121071",CodingSchemeDesignator:"DCM",CodeMeaning:"Finding"}),ConceptCodeSequence:cr({CodeValue:t,CodingSchemeDesignator:n,CodeMeaning:r})}]}},{key:"getFindingSiteGroups",value:function(){return(this.props.findingSites||[]).map((function(e){var t=e.CodeValue,n=e.CodingSchemeDesignator,r=e.CodeMeaning;return{RelationshipType:"CONTAINS",ValueType:"CODE",ConceptNameCodeSequence:cr({CodeValue:"363698007",CodingSchemeDesignator:"SCT",CodeMeaning:"Finding 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this.getMeasurement([{RelationshipType:"CONTAINS",ValueType:"NUM",ConceptNameCodeSequence:{CodeValue:"G-D7FE",CodingSchemeDesignator:"SRT",CodeMeaning:"Length"},MeasuredValueSequence:{MeasurementUnitsCodeSequence:ka(a),NumericValue:i},ContentSequence:{RelationshipType:"INFERRED FROM",ValueType:"SCOORD",GraphicType:"POLYLINE",GraphicData:[t.x,t.y,n.x,n.y],ContentSequence:{RelationshipType:"SELECTED FROM",ValueType:"IMAGE",ReferencedSOPSequence:o}}}])}}]),n}(La),qa="cornerstoneTools@^4.0.0",Va="Length",Ba=function(){function e(){b(this,e)}return w(e,null,[{key:"getMeasurementData",value:function(t){var n=ba.getSetupMeasurementData(t),r=n.defaultState,a=n.NUMGroup,i=n.SCOORDGroup,o=_(_({},r),{},{length:a.MeasuredValueSequence.NumericValue,toolType:e.toolType,handles:{start:{},end:{},textBox:{hasMoved:!1,movesIndependently:!1,drawnIndependently:!0,allowedOutsideImage:!0,hasBoundingBox:!0}}}),s=W(i.GraphicData,4);return o.handles.start.x=s[0],o.handles.start.y=s[1],o.handles.end.x=s[2],o.handles.end.y=s[3],o}},{key:"getTID300RepresentationArguments",value:function(e){var t=e.handles,n=e.finding,r=e.findingSites;return{point1:t.start,point2:t.end,distance:e.length,trackingIdentifierTextValue:"cornerstoneTools@^4.0.0:Length",finding:n,findingSites:r||[]}}}]),e}();Ba.toolType=Va,Ba.utilityToolType=Va,Ba.TID300Representation=Ga,Ba.isValidCornerstoneTrackingIdentifier=function(e){if(!e.includes(":"))return!1;var t=W(e.split(":"),2),n=t[0],r=t[1];return n===qa&&r===Va},ba.registerTool(Ba);var Qa=function(e){F(n,e);var t=Q(n);function n(){return b(this,n),t.apply(this,arguments)}return w(n,[{key:"contentItem",value:function(){var e=this.props,t=e.points,n=e.area,r=e.areaUnit,a=void 0===r?"mm2":r,i=e.ReferencedSOPSequence,o=e.use3DSpatialCoordinates,s=void 0!==o&&o,v=e.perimeter,u=e.unit,c=void 0===u?"mm":u,l=function(e){var t=[];return e.forEach((function(e){t.push(e[0]||e.x),t.push(e[1]||e.y),void 0===e[2]&&void 0===e.z||t.push(e[2]||e.z)})),t}(t);return this.getMeasurement([{RelationshipType:"CONTAINS",ValueType:"NUM",ConceptNameCodeSequence:{CodeValue:"131191004",CodingSchemeDesignator:"SCT",CodeMeaning:"Perimeter"},MeasuredValueSequence:{MeasurementUnitsCodeSequence:ka(c),NumericValue:v},ContentSequence:{RelationshipType:"INFERRED FROM",ValueType:s?"SCOORD3D":"SCOORD",GraphicType:"POLYLINE",GraphicData:l,ContentSequence:s?void 0:{RelationshipType:"SELECTED FROM",ValueType:"IMAGE",ReferencedSOPSequence:i}}},{RelationshipType:"CONTAINS",ValueType:"NUM",ConceptNameCodeSequence:{CodeValue:"G-A166",CodingSchemeDesignator:"SRT",CodeMeaning:"Area"},MeasuredValueSequence:{MeasurementUnitsCodeSequence:ka(a),NumericValue:n},ContentSequence:{RelationshipType:"INFERRED FROM",ValueType:s?"SCOORD3D":"SCOORD",GraphicType:"POLYLINE",GraphicData:l,ContentSequence:s?void 0:{RelationshipType:"SELECTED FROM",ValueType:"IMAGE",ReferencedSOPSequence:i}}}])}}]),n}(La),Ha=function(){function e(){b(this,e)}return w(e,null,[{key:"getMeasurementData",value:function(t){for(var n=ba.getSetupMeasurementData(t),r=n.defaultState,a=n.SCOORDGroup,i=n.NUMGroup,o=_(_({},r),{},{toolType:e.toolType,handles:{points:[],textBox:{active:!1,hasMoved:!1,movesIndependently:!1,drawnIndependently:!0,allowedOutsideImage:!0,hasBoundingBox:!0}},cachedStats:{area:i?i.MeasuredValueSequence.NumericValue:0},color:void 0,invalidated:!0}),s=a.GraphicData,v=0;vc?(l.push({x:m.x-u,y:m.y}),l.push({x:m.x+u,y:m.y}),l.push({x:m.x,y:m.y-c}),l.push({x:m.x,y:m.y+c})):(l.push({x:m.x,y:m.y-c}),l.push({x:m.x,y:m.y+c}),l.push({x:m.x-u,y:m.y}),l.push({x:m.x+u,y:m.y}));return{area:v,points:l,trackingIdentifierTextValue:"cornerstoneTools@^4.0.0:EllipticalRoi",finding:a,findingSites:i||[]}}}]),e}();Xa.toolType=Ka,Xa.utilityToolType=Ka,Xa.TID300Representation=za,Xa.isValidCornerstoneTrackingIdentifier=function(e){if(!e.includes(":"))return!1;var t=W(e.split(":"),2),n=t[0],r=t[1];return n===qa&&r===Ka},ba.registerTool(Xa);var Ya=function(e){F(n,e);var t=Q(n);function n(){return b(this,n),t.apply(this,arguments)}return w(n,[{key:"contentItem",value:function(){var e=this.props,t=e.points,n=e.ReferencedSOPSequence,r=e.use3DSpatialCoordinates,a=void 0!==r&&r,i=e.perimeter,o=e.area,s=e.areaUnit,v=void 0===s?"mm2":s,u=e.unit,c=void 0===u?"mm":u,l=function(e){var t=[];return e.forEach((function(e){t.push(e.x),t.push(e.y)})),t}(t);return this.getMeasurement([{RelationshipType:"CONTAINS",ValueType:"NUM",ConceptNameCodeSequence:{CodeValue:"G-A197",CodingSchemeDesignator:"SRT",CodeMeaning:"Perimeter"},MeasuredValueSequence:{MeasurementUnitsCodeSequence:ka(c),NumericValue:i},ContentSequence:{RelationshipType:"INFERRED FROM",ValueType:a?"SCOORD3D":"SCOORD",GraphicType:"CIRCLE",GraphicData:l,ContentSequence:a?void 0:{RelationshipType:"SELECTED 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_(_({},r),{},{toolType:e.toolType,active:!1,cachedStats:{area:a?a.MeasuredValueSequence.NumericValue:0,radius:0,perimeter:0},handles:{end:_(_({},s),{},{highlight:!1,active:!1}),initialRotation:0,start:_(_({},o),{},{highlight:!1,active:!1}),textBox:{hasMoved:!1,movesIndependently:!1,drawnIndependently:!0,allowedOutsideImage:!0,hasBoundingBox:!0}},invalidated:!0,visible:!0})}},{key:"getTID300RepresentationArguments",value:function(e){var t=e.cachedStats,n=void 0===t?{}:t,r=e.handles,a=e.finding,i=e.findingSites,o=r.start,s=r.end,v=n.area,u=n.areaUnit,c=void 0===u?"mm2":u,l=n.unit,m=void 0===l?"mm":l,g=n.radius,S=2*Math.PI*g,d=[];d.push(o),d.push(s);return{area:v,areaUnit:c,perimeter:S,unit:m,radius:g,points:d,trackingIdentifierTextValue:"cornerstoneTools@^4.0.0:CircleRoi",finding:a,findingSites:i||[]}}}]),e}();$a.toolType=Ja,$a.utilityToolType=Ja,$a.TID300Representation=Ya,$a.isValidCornerstoneTrackingIdentifier=function(e){if(!e.includes(":"))return!1;var t=W(e.split(":"),2),n=t[0],r=t[1];return n===qa&&r===Ja},ba.registerTool($a);var ei=function(e){F(n,e);var t=Q(n);function n(){return b(this,n),t.apply(this,arguments)}return w(n,[{key:"contentItem",value:function(){var e=this.props,t=e.points,n=e.ReferencedSOPSequence,r=e.use3DSpatialCoordinates,a=void 0!==r&&r,i=a?[t[0].x,t[0].y,t[0].z]:[t[0].x,t[0].y];return 2==t.length&&(i.push(t[1].x),i.push(t[1].y),a&&i.push(t[1].z)),this.getMeasurement([{RelationshipType:"CONTAINS",ValueType:"NUM",ConceptNameCodeSequence:{CodeValue:"111010",CodingSchemeDesignator:"DCM",CodeMeaning:"Center"},ContentSequence:{RelationshipType:"INFERRED FROM",ValueType:a?"SCOORD3D":"SCOORD",GraphicType:"POINT",GraphicData:i,ContentSequence:a?void 0:{RelationshipType:"SELECTED FROM",ValueType:"IMAGE",ReferencedSOPSequence:n}}}])}}]),n}(La),ti="ArrowAnnotate",ni="CORNERSTONEFREETEXT",ri=function(){function e(){b(this,e)}return w(e,null,[{key:"getMeasurementData",value:function(t){var n=ba.getSetupMeasurementData(t),r=n.defaultState,a=n.SCOORDGroup,i=n.findingGroup.ConceptCodeSequence.CodeMeaning,o=a.GraphicData;return _(_({},r),{},{toolType:e.toolType,active:!1,handles:{start:{x:o[0],y:o[1],highlight:!0,active:!1},end:{x:4==o.length?o[2]:o[0]+20,y:4==o.length?o[3]:o[1]+20,highlight:!0,active:!1},textBox:{hasMoved:!1,movesIndependently:!1,drawnIndependently:!0,allowedOutsideImage:!0,hasBoundingBox:!0}},invalidated:!0,text:i,visible:!0})}},{key:"getTID300RepresentationArguments",value:function(e){var t=[e.handles.start,e.handles.end],n=e.finding,r={points:t,trackingIdentifierTextValue:"cornerstoneTools@^4.0.0:ArrowAnnotate",findingSites:e.findingSites||[]};return n&&n.CodeValue===ni||(n={CodeValue:ni,CodingSchemeDesignator:"CST4",CodeMeaning:e.text}),r.finding=n,r}}]),e}();ri.toolType=ti,ri.utilityToolType=ti,ri.TID300Representation=ei,ri.isValidCornerstoneTrackingIdentifier=function(e){if(!e.includes(":"))return!1;var t=W(e.split(":"),2),n=t[0],r=t[1];return 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this.getMeasurement([{RelationshipType:"CONTAINS",ValueType:"NUM",ConceptNameCodeSequence:{CodeValue:"285285000",CodingSchemeDesignator:"SCT",CodeMeaning:"Cobb angle"},MeasuredValueSequence:{MeasurementUnitsCodeSequence:{CodeValue:"deg",CodingSchemeDesignator:"UCUM",CodingSchemeVersion:"1.4",CodeMeaning:"\xb0"},NumericValue:i},ContentSequence:{RelationshipType:"INFERRED FROM",ValueType:"SCOORD",GraphicType:"POLYLINE",GraphicData:[t.x,t.y,n.x,n.y,r.x,r.y,a.x,a.y],ContentSequence:{RelationshipType:"SELECTED FROM",ValueType:"IMAGE",ReferencedSOPSequence:o}}}])}}]),n}(La),Ri="CobbAngle",_i=function(){function e(){b(this,e)}return w(e,null,[{key:"getMeasurementData",value:function(t){var n=ba.getSetupMeasurementData(t),r=n.defaultState,a=n.NUMGroup,i=n.SCOORDGroup,o=_(_({},r),{},{rAngle:a.MeasuredValueSequence.NumericValue,toolType:e.toolType,handles:{start:{},end:{},start2:{highlight:!0,drawnIndependently:!0},end2:{highlight:!0,drawnIndependently:!0},textBox:{hasMoved:!1,movesIndependently:!1,drawnIndependently:!0,allowedOutsideImage:!0,hasBoundingBox:!0}}}),s=W(i.GraphicData,8);return o.handles.start.x=s[0],o.handles.start.y=s[1],o.handles.end.x=s[2],o.handles.end.y=s[3],o.handles.start2.x=s[4],o.handles.start2.y=s[5],o.handles.end2.x=s[6],o.handles.end2.y=s[7],o}},{key:"getTID300RepresentationArguments",value:function(e){var t=e.handles,n=e.finding,r=e.findingSites;return{point1:t.start,point2:t.end,point3:t.start2,point4:t.end2,rAngle:e.rAngle,trackingIdentifierTextValue:"cornerstoneTools@^4.0.0:CobbAngle",finding:n,findingSites:r||[]}}}]),e}();_i.toolType=Ri,_i.utilityToolType=Ri,_i.TID300Representation=yi,_i.isValidCornerstoneTrackingIdentifier=function(e){if(!e.includes(":"))return!1;var t=W(e.split(":"),2),n=t[0],r=t[1];return n===qa&&r===Ri},ba.registerTool(_i);var Ni="Angle",bi=function(){function e(){b(this,e)}return w(e,null,[{key:"getMeasurementData",value:function(t){var n=ba.getSetupMeasurementData(t),r=n.defaultState,a=n.NUMGroup,i=n.SCOORDGroup,o=_(_({},r),{},{rAngle:a.MeasuredValueSequence.NumericValue,toolType:e.toolType,handles:{start:{},middle:{},end:{},textBox:{hasMoved:!1,movesIndependently:!1,drawnIndependently:!0,allowedOutsideImage:!0,hasBoundingBox:!0}}}),s=W(i.GraphicData,8);return o.handles.start.x=s[0],o.handles.start.y=s[1],o.handles.middle.x=s[2],o.handles.middle.y=s[3],o.handles.middle.x=s[4],o.handles.middle.y=s[5],o.handles.end.x=s[6],o.handles.end.y=s[7],o}},{key:"getTID300RepresentationArguments",value:function(e){var t=e.handles,n=e.finding,r=e.findingSites;return{point1:t.start,point2:t.middle,point3:t.middle,point4:t.end,rAngle:e.rAngle,trackingIdentifierTextValue:"cornerstoneTools@^4.0.0:Angle",finding:n,findingSites:r||[]}}}]),e}();bi.toolType=Ni,bi.utilityToolType=Ni,bi.TID300Representation=yi,bi.isValidCornerstoneTrackingIdentifier=function(e){if(!e.includes(":"))return!1;var t=W(e.split(":"),2),n=t[0],r=t[1];return n===qa&&r===Ni},ba.registerTool(bi);var Li=function(){function e(){b(this,e)}return w(e,null,[{key:"getMeasurementData",value:function(t){var n=ba.getSetupMeasurementData(t),r=n.defaultState,a=n.SCOORDGroup,i=n.NUMGroup,o=_(_({},r),{},{toolType:e.toolType,handles:{start:{},end:{},textBox:{active:!1,hasMoved:!1,movesIndependently:!1,drawnIndependently:!0,allowedOutsideImage:!0,hasBoundingBox:!0},initialRotation:0},cachedStats:{area:i?i.MeasuredValueSequence.NumericValue:0},color:void 0,invalidated:!0}),s=W(a.GraphicData,6);return o.handles.start.x=s[0],o.handles.start.y=s[1],s[2],s[3],o.handles.end.x=s[4],o.handles.end.y=s[5],o}},{key:"getTID300RepresentationArguments",value:function(e){var t=e.finding,n=e.findingSites,r=e.cachedStats,a=void 0===r?{}:r,i=e.handles;console.log("getTID300 Rectangle",e,a,i);var o=i.start,s=i.end,v=[o,{x:o.x,y:s.y},s,{x:s.x,y:o.y}],u=a.area,c=a.perimeter;console.log("Point=",v,"cachedStats=",a);return{points:v,area:u,perimeter:c,trackingIdentifierTextValue:"cornerstoneTools@^4.0.0:RectangleRoi",finding:t,findingSites:n||[]}}}]),e}();Li.toolType="RectangleRoi",Li.utilityToolType="RectangleRoi",Li.TID300Representation=Qa,Li.isValidCornerstoneTrackingIdentifier=function(e){if(!e.includes(":"))return!1;var t=W(e.split(":"),2),n=t[0],r=t[1];return n===qa&&r===Li.toolType},ba.registerTool(Li);var wi={CodingSchemeDesignator:"CORNERSTONEJS",codeValues:{CORNERSTONEFREETEXT:"CORNERSTONEFREETEXT"}},xi={CodingSchemeDesignator:"DCM",CodeValue:"121071"},Fi={CodingSchemeDesignator:"SCT",CodeValue:"363698007"},Ui={CodingSchemeDesignator:"SRT",CodeValue:"G-C0E3"},ki=function(e,t,n){var r=e.ConceptNameCodeSequence;if(r){var a=r.CodingSchemeDesignator,i=r.CodeValue;return a==t.CodingSchemeDesignator&&i==t.CodeValue||n&&a==n.CodingSchemeDesignator&&i==n.CodeValue}};var Gi=function(){function e(){b(this,e)}return w(e,null,[{key:"getCornerstoneLabelFromDefaultState",value:function(e){var t=e.findingSites,n=void 0===t?[]:t,r=e.finding,a=wi.codeValues.CORNERSTONEFREETEXT,i=n.find((function(e){return e.CodeValue===a}));return i?i.CodeMeaning:r&&r.CodeValue===a?r.CodeMeaning:void 0}},{key:"generateDatasetMeta",value:function(){var e=new Uint8Array(2);return e[1]=1,{FileMetaInformationVersion:{Value:[e.buffer],vr:"OB"},TransferSyntaxUID:{Value:["1.2.840.10008.1.2.1"],vr:"UI"},ImplementationClassUID:{Value:[Jr.uid()],vr:"UI"},ImplementationVersionName:{Value:["dcmjs"],vr:"SH"}}}},{key:"generateDerivationSourceDataset",value:function(t,n){return{StudyInstanceUID:t,SeriesInstanceUID:n,_meta:e.generateDatasetMeta(),_vrMap:{PixelData:"OW"}}}},{key:"getSetupMeasurementData",value:function(t,n,r,a){var i=t.ContentSequence,o=Ta(i),s=o.find((function(e){return ki(e,xi)})),v=o.filter((function(e){return ki(e,Fi,Ui)}))||[],u=o.find((function(e){return"NUM"===e.ValueType})),c=Ta(u.ContentSequence).find((function(e){return"SCOORD"===e.ValueType})),l=c.ContentSequence.ReferencedSOPSequence,m=l.ReferencedSOPInstanceUID,g=l.ReferencedFrameNumber,S=n[m],d=r.get("imagePlaneModule",S),f=s?cr(s.ConceptCodeSequence):void 0,h=v.map((function(e){return cr(e.ConceptCodeSequence)})),p={sopInstanceUid:m,annotation:{annotationUID:Jr.uid(),metadata:{toolName:a,referencedImageId:S,FrameOfReferenceUID:d.frameOfReferenceUID,label:""}},finding:f,findingSites:h};return p.finding&&(p.description=p.finding.CodeMeaning),p.annotation.metadata.label=e.getCornerstoneLabelFromDefaultState(p),{defaultState:p,NUMGroup:u,SCOORDGroup:c,ReferencedSOPSequence:l,ReferencedSOPInstanceUID:m,ReferencedFrameNumber:g}}},{key:"generateReport",value:function(t,n,r,a){var i=[],o={},s=[],v=e.generateDatasetMeta();Object.keys(t).forEach((function(a){var v=n.get("sopCommonModule",a),u=n.get("generalSeriesModule",a),c=v.sopInstanceUID,l=v.sopClassUID,m=u.studyInstanceUID,g=u.seriesInstanceUID;if(o[c]=g,!s.find((function(e){return e.SeriesInstanceUID===g}))){var S=e.generateDerivationSourceDataset(m,g);s.push(S)}var d=n.get("frameNumber",a),f=t[a],h=Object.keys(f),p={ReferencedSOPClassUID:l,ReferencedSOPInstanceUID:c},I=n.get("instance",a);(I&&I.NumberOfFrames&&I.NumberOfFrames>1||ma.isMultiframeSOPClassUID(l))&&(p.ReferencedFrameNumber=d);var C=[];h.forEach((function(e){var t=function(e,t,n,r){var a=t[e],i=Gi.CORNERSTONE_TOOL_CLASSES_BY_TOOL_TYPE[e];if(a&&a.data&&a.data.length&&i){var o=a.data.map((function(e){return function(e,t,n,r,a){var i=r.getTID300RepresentationArguments(e,a);return i.ReferencedSOPSequence=n,new r.TID300Representation(i)}(e,0,n,i,r)}));return new Pa(o)}}(e,f,p,r);t&&C.push(t)})),i=i.concat(C)}));var u=new Aa({TID1501MeasurementGroups:i},a),c=new Ma(s),l=u.contentItem(s,{sopInstanceUIDsToSeriesInstanceUIDMap:o});return c.dataset=Object.assign(c.dataset,l),c.dataset._meta=v,c}},{key:"generateToolState",value:function(t,n,r,a){var i=arguments.length>4&&void 0!==arguments[4]?arguments[4]:{};if("1500"!==t.ContentTemplateSequence.TemplateIdentifier)throw new Error("This package can currently only interpret DICOM SR TID 1500");var o="Imaging Measurements",s="Measurement Group",v="Tracking Identifier",u=Ta(t.ContentSequence).find(Oa(o)),c=Ta(u.ContentSequence).filter(Oa(s)),l={},m=e.CORNERSTONE_TOOL_CLASSES_BY_UTILITY_TYPE,g=[];return Object.keys(m).forEach((function(e){g.push(m[e]),l[e]=[]})),c.forEach((function(e,o){var s=Ta(e.ContentSequence).find((function(e){return e.ConceptNameCodeSequence.CodeMeaning===v})).TextValue,u=i.getToolClass?i.getToolClass(e,t,g):g.find((function(e){return e.isValidCornerstoneTrackingIdentifier(s)}));if(u){var c=u.getMeasurementData(e,n,r,a);console.log("=== ".concat(u.toolType," ===")),console.log(c),l[u.toolType].push(c)}})),l}},{key:"registerTool",value:function(t){e.CORNERSTONE_TOOL_CLASSES_BY_UTILITY_TYPE[t.utilityToolType]=t,e.CORNERSTONE_TOOL_CLASSES_BY_TOOL_TYPE[t.toolType]=t,e.MEASUREMENT_BY_TOOLTYPE[t.toolType]=t.utilityToolType}}]),e}();Gi.MEASUREMENT_BY_TOOLTYPE={},Gi.CORNERSTONE_TOOL_CLASSES_BY_UTILITY_TYPE={},Gi.CORNERSTONE_TOOL_CLASSES_BY_TOOL_TYPE={};var qi="Cornerstone3DTools@^0.1.0",Vi="Length",Bi="".concat(qi,":").concat(Vi),Qi=function(){function e(){b(this,e)}return w(e,null,[{key:"getMeasurementData",value:function(t,n,r,a){for(var i=Gi.getSetupMeasurementData(t,n,a,e.toolType),o=i.defaultState,s=i.NUMGroup,v=i.SCOORDGroup,u=i.ReferencedFrameNumber,c=o.annotation.metadata.referencedImageId,l=v.GraphicData,m=[],g=0;gMath.sqrt(Math.pow(h[0][0]-h[1][0],2)+Math.pow(h[0][1]-h[1][1],2)+Math.pow(h[0][2]-h[1][2],2))?(c=f,l=h):(c=h,l=f);var p=t(u,c[0]),I=t(u,c[1]),C=t(u,l[0]),D=t(u,l[1]);return{longAxis:{point1:{x:p[0],y:p[1]},point2:{x:I[0],y:I[1]}},shortAxis:{point1:{x:C[0],y:C[1]},point2:{x:D[0],y:D[1]}},longAxisLength:g,shortAxisLength:S,trackingIdentifierTextValue:ji,finding:r,findingSites:a||[]}}}]),e}();Wi.toolType=Hi,Wi.utilityToolType=Hi,Wi.TID300Representation=ja,Wi.isValidCornerstoneTrackingIdentifier=function(e){if(!e.includes(":"))return!1;var t=W(e.split(":"),2),n=t[0],r=t[1];return n===qi&&r===Hi},Gi.registerTool(Wi);var Zi="EllipticalROI",zi=1e-4,Ki="".concat(qi,":").concat(Zi),Xi=function(){function e(){b(this,e)}return w(e,null,[{key:"getMeasurementData",value:function(t,n,r,a){for(var i=Gi.getSetupMeasurementData(t,n,a,e.toolType),o=i.defaultState,s=i.NUMGroup,v=i.SCOORDGroup,u=i.ReferencedFrameNumber,c=o.annotation.metadata.referencedImageId,l=v.GraphicData,m=[],g=0;gMath.abs(m[0]-g[0])?(S.push({x:c[0],y:c[1]}),S.push({x:l[0],y:l[1]}),S.push({x:m[0],y:m[1]}),S.push({x:g[0],y:g[1]})):(S.push({x:m[0],y:m[1]}),S.push({x:g[0],y:g[1]}),S.push({x:c[0],y:c[1]}),S.push({x:l[0],y:l[1]})),{area:(s["imageId:".concat(u)]||{}).area,points:S,trackingIdentifierTextValue:Ki,finding:r,findingSites:a||[]}}}]),e}();Xi.toolType=Zi,Xi.utilityToolType=Zi,Xi.TID300Representation=za,Xi.isValidCornerstoneTrackingIdentifier=function(e){if(!e.includes(":"))return!1;var t=W(e.split(":"),2),n=t[0],r=t[1];return n===qi&&r.toLowerCase()===Zi.toLowerCase()},Gi.registerTool(Xi);var Yi="ArrowAnnotate",Ji="".concat(qi,":").concat(Yi),$i=wi.codeValues,eo=wi.CodingSchemeDesignator,to=function(){function e(){b(this,e)}return w(e,null,[{key:"getMeasurementData",value:function(t,n,r,a){for(var i=Gi.getSetupMeasurementData(t,n,a,e.toolType),o=i.defaultState,s=i.SCOORDGroup,v=i.ReferencedFrameNumber,u=o.annotation.metadata.referencedImageId,c=o.annotation.metadata.label,l=s.GraphicData,m=[],g=0;g9?"":"0")+e}function To(e){var t=e.getHours(),n=e.getMinutes(),r=e.getSeconds(),a=e.getMilliseconds();return Po(t)+Po(n)+Po(r)+a}function Oo(e){var t=e.getFullYear(),n=e.getMonth()+1,r=e.getDate();return t+Po(n)+Po(r)}Object.freeze(Mo);var yo=function(e){F(n,e);var t=Q(n);function n(){b(this,n);for(var e=arguments.length,r=new Array(e),a=0;a1)throw new Error("Only one of the following options should be provided: 'referencedRegions', 'referencedVolume', or 'referencedSegmentation'.");if(void 0!==e.referencedRegions){if(!("object"===N(e.referencedRegions)||e.referencedRegions instanceof Array))throw new Error("Option 'referencedRegions' must have type Array.");if(0===e.referencedRegions.length)throw new Error("Option 'referencedRegion' must have non-zero length.");e.referencedRegions.forEach((function(e){if(void 0===e||e.constructor!==Ko&&e.constructor!==Xo)throw new Error("Items of option 'referencedRegion' must have type ImageRegion or ImageRegion3D.");a.ContentSequence.push(e)}))}else if(void 0!==e.referencedVolume){if(e.referencedVolume.constructor!==Yo)throw new Error("Items of option 'referencedVolume' must have type VolumeSurface.");a.ContentSequence.push(referencedVolume)}else if(void 0!==e.referencedSegmentation){if(e.referencedSegmentation.constructor!==ts&&e.referencedSegmentation.constructor!==es)throw new Error("Option 'referencedSegmentation' must have type ReferencedSegmentation or ReferencedSegmentationFrame.");a.ContentSequence.push(referencedSegmentation)}return r[0]=a,r}return w(n)}(hs),Is=function(e){F(n,e);var t=Q(n);function n(e){b(this,n);var r=[void 0!==e.referencedRegion,void 0!==e.referencedSegmentation].reduce((function(e,t){return e+t}));if(0===r)throw new Error("One of the following options must be provided: 'referencedRegion', 'referencedSegmentation'.");if(r>1)throw new Error("Only one of the following options should be provided: 'referencedRegion', 'referencedSegmentation'.");return t.call(this,{trackingIdentifier:e.trackingIdentifier,referencedRegions:[e.referencedRegion],referencedSegmentation:e.referencedSegmentation,referencedRealWorldValueMap:e.referencedRealWorldValueMap,timePointContext:e.timePointContext,findingType:e.findingType,session:e.session,measurements:e.measurements,qualitativeEvaluations:e.qualitativeEvaluations})}return w(n)}(ps),Cs=function(e){F(n,e);var t=Q(n);function n(e){return b(this,n),t.call(this,{trackingIdentifier:e.trackingIdentifier,referencedRegions:e.referencedRegions,referencedSegmentation:e.referencedSegmentation,referencedRealWorldValueMap:e.referencedRealWorldValueMap,timePointContext:e.timePointContext,findingType:e.findingType,session:e.session,measurements:e.measurements,qualitativeEvaluations:e.qualitativeEvaluations})}return w(n)}(ps),Ds=function(e){function t(e){var n;if(b(this,t),void 0===e.derivation)throw new Error("Option 'derivation' is required for MeasurementsDerivedFromMultipleROIMeasurements.");var r=new Uo({name:e.derivation});if(r.ContentSequence=new yo,void 0===e.measurementGroups)throw new Error("Option 'measurementGroups' is required for MeasurementsDerivedFromMultipleROIMeasurements.");if(!("object"===N(e.measurementGroups)||e.measurementGroups instanceof Array))throw new Error("Option 'measurementGroups' must have type Array.");if(e.measurementGroups.forEach((function(e){var t;if(!e||e.constructor!==Is&&e.constructor!==Cs)throw new Error("Items of option 'measurementGroups' must have type PlanarROIMeasurementsAndQualitativeEvaluations or VolumetricROIMeasurementsAndQualitativeEvaluations.");e[0].RelationshipType="R-INFERRED FROM",(t=r.ContentSequence).push.apply(t,Z(e))})),void 0!==e.measurementProperties){var a;if(e.measurementProperties.constructor!==is)throw new Error("Option 'measurementProperties' must have type MeasurementProperties.");(a=r.ContentSequence).push.apply(a,Z(e.measurementProperties))}return n.push(r),B(n)}return F(t,e),Q(t),w(t)}(rs),Es=function(e){F(n,e);var t=Q(n);function n(e){return b(this,n),t.call(this,{trackingIdentifier:e.trackingIdentifier,referencedRealWorldValueMap:e.referencedRealWorldValueMap,timePointContext:e.timePointContext,findingType:e.findingType,session:e.session,measurements:e.measurements,qualitativeEvaluations:e.qualitativeEvaluations})}return w(n)}(hs),Ms=function(e){F(n,e);var t=Q(n);function n(e){var r;if(b(this,n),r=t.call(this),void 0!==e.method){var a=new _o({name:new ho({value:"370129005",meaning:"Measurement Method",schemeDesignator:"SCT"}),value:e.method,relationshipType:Mo.HAS_CONCEPT_MOD});r.push(a)}if(void 0!==e.findingSites){if(!("object"===N(e.findingSites)||e.findingSites instanceof Array))throw new Error("Option 'findingSites' must have type Array.");e.findingSites.forEach((function(e){if(!e||e.constructor!==$o)throw new Error("Items of option 'findingSites' must have type FindingSite.");r.push(e)}))}if(void 0===e.measurements)throw new Error("Options 'measurements' is required ROIMeasurements.");if(!("object"===N(e.measurements)||e.measurements instanceof Array))throw new Error("Option 'measurements' must have type Array.");if(0===e.measurements.length)throw new Error("Option 'measurements' must have non-zero length.");return e.measurements.forEach((function(e){if(!e||e.constructor!==as)throw new Error("Items of option 'measurements' must have type Measurement.");r.push(e)})),r}return w(n)}(rs),As=function(e){F(n,e);var t=Q(n);function n(e){var r,a,i,o;if(b(this,n),o=t.call(this),void 0===e.observationContext)throw new Error("Option 'observationContext' is required for MeasurementReport.");if(void 0===e.procedureReported)throw new Error("Option 'procedureReported' is required for MeasurementReport.");var s=new ko({name:new ho({value:"126000",schemeDesignator:"DCM",meaning:"Imaging Measurement Report"}),templateID:"1500"});if(s.ContentSequence=new yo,void 0===e.languageOfContentItemAndDescendants)throw new Error("Option 'languageOfContentItemAndDescendants' is required for MeasurementReport.");if(e.languageOfContentItemAndDescendants.constructor!==fs)throw new Error("Option 'languageOfContentItemAndDescendants' must have type LanguageOfContentItemAndDescendants.");if((r=s.ContentSequence).push.apply(r,Z(e.languageOfContentItemAndDescendants)),(a=s.ContentSequence).push.apply(a,Z(e.observationContext)),e.procedureReported.constructor!==ho&&e.procedureReported.constructor!==fo||(e.procedureReported=[e.procedureReported]),!("object"===N(e.procedureReported)||e.procedureReported instanceof Array))throw new Error("Option 'procedureReported' must have type Array.");e.procedureReported.forEach((function(e){var t=new _o({name:new ho({value:"121058",meaning:"Procedure reported",schemeDesignator:"DCM"}),value:e,relationshipType:Mo.HAS_CONCEPT_MOD});s.ContentSequence.push(t)}));var v=new Ts;if((i=s.ContentSequence).push.apply(i,Z(v)),[void 0!==e.imagingMeasurements,void 0!==e.derivedImagingMeasurements,void 0!==e.qualitativeEvaluations].reduce((function(e,t){return e+t}))>1)throw new Error("Only one of the following options should be provided: 'imagingMeasurements', 'derivedImagingMeasurement', 'qualitativeEvaluations'.");if(void 0!==e.imagingMeasurements){var u=new ko({name:new ho({value:"126010",meaning:"Imaging Measurements",schemeDesignator:"DCM"}),relationshipType:Mo.CONTAINS});u.ContentSequence=q(yo,Z(e.imagingMeasurements)),s.ContentSequence.push(u)}else if(void 0!==e.derivedImagingMeasurements){var c=new ko({name:new ho({value:"126011",meaning:"Derived Imaging Measurements",schemeDesignator:"DCM"}),relationshipType:Mo.CONTAINS});c.ContentSequence=q(yo,Z(e.derivedImagingMeasurements)),s.ContentSequence.push(c)}else if(void 0!==e.qualitativeEvaluations){var l=new ko({name:new ho({value:"C0034375",meaning:"Qualitative Evaluations",schemeDesignator:"UMLS"}),relationshipType:Mo.CONTAINS});l.ContentSequence=q(yo,Z(e.qualitativeEvaluations)),s.ContentSequence.push(l)}return o.push(s),o}return w(n)}(rs),Ps=function(e){function t(e){var n;if(b(this,t),void 0===e.timePoint)throw new Error("Option 'timePoint' is required for TimePointContext.");var r=new No({name:new ho({value:"C2348792",meaning:"Time Point",schemeDesignator:"UMLS"}),value:e.timePoint,relationshipType:Mo.HAS_OBS_CONTEXT});if(n.push(r),void 0!==e.timePointType){var a=new _o({name:new ho({value:"126072",meaning:"Time Point Type",schemeDesignator:"DCM"}),value:e.timePointType,relationshipType:Mo.HAS_OBS_CONTEXT});n.push(a)}if(void 0!==e.timePointOrder){var i=new Uo({name:new ho({value:"126073",meaning:"Time Point Order",schemeDesignator:"DCM"}),value:e.timePointOrder,relationshipType:Mo.HAS_OBS_CONTEXT});n.push(i)}if(void 0!==e.subjectTimePointIdentifier){var o=new Uo({name:new ho({value:"126070",meaning:"Subject Time Point Identifier",schemeDesignator:"DCM"}),value:e.subjectTimePointIdentifier,relationshipType:Mo.HAS_OBS_CONTEXT});n.push(o)}if(void 0!==e.protocolTimePointIdentifier){var s=new Uo({name:new ho({value:"126071",meaning:"Protocol Time Point Identifier",schemeDesignator:"DCM"}),value:e.protocolTimePointIdentifier,relationshipType:Mo.HAS_OBS_CONTEXT});n.push(s)}if(void 0!==e.temporalOffsetFromEvent){if(e.temporalOffsetFromEvent.constructor!==LongitudinalTemporalOffsetFromEventContentItem)throw new Error("Option 'temporalOffsetFromEvent' must have type LongitudinalTemporalOffsetFromEventContentItem.");n.push(temporalOffsetFromEvent)}return B(n)}return F(t,e),Q(t),w(t)}(rs),Ts=function(e){F(n,e);var t=Q(n);function n(e){var r;b(this,n),r=t.call(this);var a=new ko({name:new ho({value:"111028",meaning:"Image Library",schemeDesignator:"DCM"}),relationshipType:Mo.CONTAINS});return r.push(a),r}return w(n)}(rs),Os=function(e){F(n,e);var t=Q(n);function n(e){var r;if(b(this,n),r=t.call(this),void 0===e.name)throw new Error("Option 'name' is required for AlgorithmIdentification.");if(void 0===e.version)throw new Error("Option 'version' is required for AlgorithmIdentification.");var a=new No({name:new ho({value:"111001",meaning:"Algorithm Name",schemeDesignator:"DCM"}),value:e.name,relationshipType:Mo.HAS_CONCEPT_MOD});r.push(a);var i=new No({name:new ho({value:"111003",meaning:"Algorithm Version",schemeDesignator:"DCM"}),value:e.version,relationshipType:Mo.HAS_CONCEPT_MOD});if(r.push(i),void 0!==e.parameters){if(!("object"===N(e.parameters)||e.parameters instanceof Array))throw new Error("Option 'parameters' must have type Array.");e.parameters.forEach((function(e){var t=new No({name:new ho({value:"111002",meaning:"Algorithm Parameter",schemeDesignator:"DCM"}),value:param,relationshipType:Mo.HAS_CONCEPT_MOD});r.push(t)}))}return r}return 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