diff --git a/QMRITools/Kernel/MaskingTools.wl b/QMRITools/Kernel/MaskingTools.wl index 3c67830b..28725ae9 100644 --- a/QMRITools/Kernel/MaskingTools.wl +++ b/QMRITools/Kernel/MaskingTools.wl @@ -49,6 +49,10 @@ SmoothMask::usage = MaskData::usage = "MaskData[data, mask] applies a mask to data. mask can be 2D or 3D, data can be 2D, 3D or 4D." +MaskSegmentation::usage = +"MaskSegmentation[seg, mask] applies a mask to a splited segmentation seg from SplitSegmentations. +The mask is 3D, seg is 4D." + GetMaskData::usage = "GetMaskData[data, mask] retruns the data selected by the mask." @@ -107,7 +111,8 @@ maskdim is the dimensions of the output {zout,xout,yout}." NormalizeMethod::usage = -"NormalizeMethod is an option for NormalizeData. Can be \"Set\" or \"Volumes\" wichi normalizes to the firs volume or normalizes each volume individually, respectively." +"NormalizeMethod is an option for NormalizeData. Can be \"Set\" or \"Volumes\" wich normalizes to the first volume or normalizes each volume individually, respectively. +If \"Uniform\" normalizes the histogram of the data to have a uniform distribution between 0 and 1 where 0 is treated as background of the data." FitOrder::usage = "FitOrder is an option for HomogenizeData. It specifies the order of harmonics to be used for the homogenization." @@ -177,9 +182,13 @@ Options[NormalizeData] = {NormalizeMethod -> "Set"} SyntaxInformation[NormalizeData] = {"ArgumentsPattern" -> {_, _., OptionsPattern[]}}; NormalizeData[data_, opts : OptionsPattern[]] := Block[{ndat, mask}, - ndat = Switch[ArrayDepth[data], 3, data, 4, Mean@Transpose@data]; - mask = Mask[NormDat[ndat - Min@ndat, 0.]]; - NormalizeData[data, mask, opts] + If[OptionValue[NormalizeMethod]=!="Uniform", + ndat = Switch[ArrayDepth[data], 3, data, 4, Mean@Transpose@data]; + mask = Mask[NormDat[ndat - Min@ndat, 0.]]; + NormalizeData[data, mask, opts] + , + NormDatC[data] + ] ] NormalizeData[data_, msk_, opts : OptionsPattern[]] := Block[{dat, mn, min, dato, mask}, @@ -196,6 +205,19 @@ NormalizeData[data_, msk_, opts : OptionsPattern[]] := Block[{dat, mn, min, dato ] +(*normalization towards uniform distribution*) +NormDatC = Compile[{{dat, _Real, 3}}, Block[{fl, flp, min, max, bins, cdf, n}, + n = 512; + fl = Flatten[dat]; + flp = Pick[fl, Unitize[fl], 1]; + {min, max} = MinMax[flp]; + bins = BinCounts[flp, {min, max, (max - min)/n}]; + cdf = Prepend[N[Accumulate[bins]/Total[bins]], 0.]; + Map[cdf[[# + 1]] &, Clip[Floor[(dat - min)/(max - min) n], {0, n}, {0, n}], {-2}] +], RuntimeAttributes -> {Listable}, RuntimeOptions -> "Speed", Parallelization -> True]; + + +(*normalization towards median of given valueue*) NormDat[dat_, mn_] := ToPackedArray[100. Which[ mn===0., dat/MedianNoZero[Flatten@dat], ListQ[mn],Transpose[Transpose[dat]/mn], @@ -330,23 +352,26 @@ SmoothMask[msk_, OptionsPattern[]] := Block[{itt, dil, pad, close, obj, filt, ma SyntaxInformation[DilateMask] = {"ArgumentsPattern" -> {_, _}}; -DilateMask[seg_, size_] := Which[ - (*dilation*) - size > 0, - If[ArrayDepth[seg]>3, - Transpose[SparseArray[SparseArray[ImageData@Dilation[Image3D[#], Round[size]]] & /@ Transpose[seg]]], - SparseArray[Dilation[Normal[seg], Round[size]]] - ], - (*erosion*) - size < 0, - If[ArrayDepth[seg]>3, - Transpose[SparseArray[SparseArray[ImageData@Erosion[Image3D[#], Round[Abs[size]]]] & /@ Transpose[seg]]], - SparseArray[Erosion[Normal[seg], Round[Abs[size]]]] - ], - True, - SparseArray[seg] +DilateMask[seg_, size_] := Block[{sz, fun}, + sz = Abs[Round[size]]; + + If[sz =!= 0, + (*see if dilation of erosion*) + fun = If[size > 0, Dilation, Erosion]; + + (*3D or 4D data*) + SparseArray@Switch[ArrayDepth[seg], + 3, DilateMaskI[seg, fun, sz], + 4, Transpose[DilateMaskI[#, fun, sz] & /@ Transpose[seg]] + ] + , + (*if size is 0 dont do anything*) + SparseArray@seg + ] ] +DilateMaskI[seg_, fun_, size_] := Round[SparseArray[ReverseCrop[fun[#[[1]], size], Dimensions[seg], #[[2]]]] &[AutoCropData[seg]]] + (* ::Subsubsection::Closed:: *) (*MaskData*) @@ -366,19 +391,34 @@ MaskData[data_, mask_]:=Block[{dataD, maskD,dimD,dimM,out}, {2,2}, If[dimD == dimM, mask data, 1], {3,3}, If[dimD == dimM, mask data, 1], {3,2}, If[dimD[[2;;]] == dimM, mask # &/@ data, 1], - {4,3}, Which[dimD[[2;;]] == dimM, mask # & /@ data, dimD[[{1,3,4}]] == dimM, Transpose[mask # & /@ Transpose[data]], True, 1], - _, 2 + {4,3}, Which[ + dimD[[2;;]] == dimM, mask # & /@ data, + dimD[[{1,3,4}]] == dimM, Transpose[mask # & /@ Transpose[data]], + True, Return[Message[MaskData::dim, dimD, dimM];$Failed]], + _, Return[Message[MaskData::dep, dataD, maskD];,$Failed] ]; - (*check for errors*) - If[out === 1, Message[MaskData::dim, dimD, dimM]]; - If[out === 2, Message[MaskData::dep, dataD, maskD]]; - (*make the output*) ToPackedArray@N@Normal@out ] +(* ::Subsubsection::Closed:: *) +(*MaskSegmentation*) + + +SyntaxInformation[MaskSegmentation] = {"ArgumentsPattern" -> {_, _}}; + +MaskSegmentation[seg_, mask_] := Block[{dim, sc, cr}, + msk = Normal@mask; + dim = Dimensions[seg[[All, 1]]]; + Transpose[( + {sc, cr} = AutoCropData[#]; + Round@SparseArray@ReverseCrop[ApplyCrop[msk, cr] sc, dim, cr] + ) & /@ Transpose[seg]] +] + + (* ::Subsubsection::Closed:: *) (*GetMaskData*) @@ -390,19 +430,26 @@ SyntaxInformation[GetMaskData] = {"ArgumentsPattern" -> {_, _, OptionsPattern[]} GetMaskData[data_?ArrayQ, mask_, opts:OptionsPattern[]] := Block[{out}, Which[ ArrayDepth[data]===4&&ArrayDepth[mask]===3, - GetMaskData[#,mask, opts]&/@Transpose[data] + GetMaskData[#, mask, opts]&/@Transpose[data] , ArrayDepth[data]===3&&ArrayDepth[mask]===4, - GetMaskData[data,#, opts]&/@Transpose[mask] + GetMaskData[data, #, opts]&/@Transpose[mask] , True, If[!(Dimensions[data]=!=Dimensions[mask] || Drop[Dimensions[data], {2}]=!=Dimensions[mask]), - Message[GetMaskData::dim,Dimensions[data],Dimensions[mask]], + Retrun[Message[GetMaskData::dim,Dimensions[data],Dimensions[mask]];$Failed] + , out = Switch[OptionValue[GetMaskOutput], "Slices", MapThread[Pick[Chop[Flatten[N[#1]]], Unitize[Flatten[Normal@#2]], 1]&, {data, mask}, ArrayDepth[data]-2], "Sparse", (data mask)["ExplicitValues"], _, Pick[Flatten[N[data]], Unitize[Flatten[Normal@mask]], 1] ]; + + out = Switch[OptionValue[GetMaskOutput], + "Mean", Mean[out], + "Median", Median[out], + _, out + ]; (*select only non zero values if mask only to false*) If[OptionValue[GetMaskOnly],out,Pick[out, Unitize[out], 1]] ] @@ -445,10 +492,16 @@ SyntaxInformation[SplitSegmentations] = {"ArgumentsPattern" -> {_}}; SplitSegmentations[segI_]:=SplitSegmentations[segI, True] -SplitSegmentations[segI_, sparse_] := Block[{vals, seg}, +SplitSegmentations[segI_, sparse_] := Block[{seg, dim, exVals, exPos, vals}, seg = SparseArray[Round[segI]]; - vals = Sort[DeleteDuplicates[seg["ExplicitValues"]]]; - seg = Transpose[1 - SparseArray[(Unitize[seg - #] & /@ vals)]]; + dim = Dimensions[seg]; + + exVals = seg["ExplicitValues"]; + exPos = seg["ExplicitPositions"]; + vals = Sort@DeleteDuplicates@exVals; + + seg = Transpose[SparseArray[Pick[exPos, Unitize[exVals - #], 0] -> 1, dim] & /@ vals]; + {If[sparse, seg, Normal@seg], vals} ] @@ -457,7 +510,7 @@ SplitSegmentations[segI_, sparse_] := Block[{vals, seg}, (*GetSegmentationLabels*) -GetSegmentationLabels[seg_]:= DeleteCases[Sort@Round[DeleteDuplicates[Flatten[seg]]],0]; +GetSegmentationLabels[segI_]:= Sort[DeleteDuplicates[SparseArray[Round[segI]]["ExplicitValues"]]]; (* ::Subsubsection::Closed:: *) @@ -466,9 +519,12 @@ GetSegmentationLabels[seg_]:= DeleteCases[Sort@Round[DeleteDuplicates[Flatten[se SyntaxInformation[MergeSegmentations] = {"ArgumentsPattern" -> {_,_}}; -MergeSegmentations[seg_, lab_] := Block[{mt}, - mt = Transpose[SparseArray[seg]]; - Normal[Total[lab mt](1 - UnitStep[Total[mt] - 2])] +MergeSegmentations[seg_, lab_] := Block[{mt,nv}, + mt = Transpose[SparseArray[Round[seg]]]; + nv = Range[Length@lab]; + + (*mapping over sparce is quicker than direct multiplication and total*) + Normal[Total[mt[[#]] lab[[#]] & /@ nv] (1 - UnitStep[Total[mt[[#]] & /@ nv] - 2])] ] @@ -494,13 +550,17 @@ ReplaceSegmentations[segm_, labSel_, labNew_] := SelectReplaceSegmentations[segm (*SelectReplaceSegmentations*) -SelectReplaceSegmentations[segm_, labSel_, labNew_] := Block[{seg, lab, sel}, - {seg, lab} = SplitSegmentations[segm]; +SelectReplaceSegmentations[segm_, labSel_, labNew_] := Block[{split, seg, lab, sel}, + split = If[Length[segm] == 2, False, True]; + + {seg, lab} = If[split, SplitSegmentations[segm], segm]; + sel = MemberQ[labSel, #] & /@ lab; - MergeSegmentations[ - Transpose[Pick[Transpose[seg], sel, True]], - Pick[lab /. Thread[labSel->labNew], sel, True] - ] + seg = Transpose[Pick[Transpose[seg], sel, True]]; + lab = Pick[lab /. Thread[labSel->labNew], sel, True]; + or = Ordering[lab]; + + If[split, MergeSegmentations[seg, lab], {seg[[All,or]], lab[[or]]}] ] diff --git a/QMRITools/Kernel/SegmentationTools.wl b/QMRITools/Kernel/SegmentationTools.wl index 3835f910..2fa1acba 100644 --- a/QMRITools/Kernel/SegmentationTools.wl +++ b/QMRITools/Kernel/SegmentationTools.wl @@ -60,10 +60,16 @@ ChangeNetDimensions::usage = AddLossLayer::usage = -"AddLossLayer[net] adds three loss layers to a NetGraph, a SoftDiceLossLayer, BrierLossLayer and a CrossEntropyLossLayer." +"AddLossLayer[net] adds three loss layers to a NetGraph, a DiceLossLayer, JaccardLossLayer, TverskyLossLayer, MeanSqyaredLossLayer and a CrossEntropyLossLayer are added." -SoftDiceLossLayer::usage = -"SoftDiceLossLayer[dim] represents a net layer that computes the SoftDice loss by comparing input class probability vectors with the target class vector." +DiceLossLayer::usage = +"DiceLossLayer[dim] represents a net layer that computes the Dice loss by comparing input class probability vectors with the target class vector." + +JaccardLossLayer::usage = +"JaccardLossLayer[dim] represents a net layer that computes the Jaccard loss by comparing input class probability vectors with the target class vector." + +TverskyLossLayer::usage = +"TverskyLossLayer[dim] represents a net layer that computes the Tversky loss by comparing input class probability vectors with the target class vector." ClassEncoder::usage = @@ -80,12 +86,17 @@ DiceSimilarity::usage = DiceSimilarity[x, y, class] gives the Dice Similarity of segmentations ref and pred for class. DiceSimilarity[x, y, {class, ..}] gives the Dice Similarity of segmentations ref and pred for the list of gives classes." -MeanSurfaceDistance::usage = -"MeanSurfaceDistance[ref, pred] gives the mean surface distance of segmentations ref and pred for class equals 1 in voxels. -MeanSurfaceDistance[x, y, class] gives the mean surface distance of segmentations ref and pred for class in voxels. -MeanSurfaceDistance[x, y, {class, ..}] gives the mean surface distance of segmentations ref and pred for the list of gives classes in voxels. -MeanSurfaceDistance[x, y, class , vox] gives the mean surface distance of segmentations ref and pred for class in milimeter. -MeanSurfaceDistance[x, y, {class, ..}, vox] gives the mean surface distance of segmentations ref and pred for the list of gives classes in milimeters." +JaccardSimilarity::usage = +"JaccardSimilarity[ref, pred] gives the Jaccard Similarity between 1 and 0 of segmentations ref and pred for class equals 1. +JaccardSimilarity[x, y, class] gives the Jaccard Similarity of segmentations ref and pred for class. +JaccardSimilarity[x, y, {class, ..}] gives the Jaccard Similarity of segmentations ref and pred for the list of gives classes." + +SurfaceDistance::usage = +"SurfaceDistance[ref, pred] gives the mean surface distance of segmentations ref and pred for class equals 1 in voxels. +SurfaceDistance[x, y, class] gives the mean surface distance of segmentations ref and pred for class in voxels. +SurfaceDistance[x, y, {class, ..}] gives the mean surface distance of segmentations ref and pred for the list of gives classes in voxels. +SurfaceDistance[x, y, class , vox] gives the mean surface distance of segmentations ref and pred for class in milimeter. +SurfaceDistance[x, y, {class, ..}, vox] gives the mean surface distance of segmentations ref and pred for the list of gives classes in milimeters." SegmentData::usage = @@ -185,6 +196,9 @@ It prompts the user to enter the paths for the input and output files, and allow FindPatchDim::usage = "FindPatchDim[net, data] finds the optimal patch size for the network net and the data data." +AnalyseNetworkFeatures::usage = +"AnalyseNetworkFeatures[net, data] gives overview of the information density of the network features by analysing them with SVD." + (* ::Subsection::Closed:: *) (*Options*) @@ -282,6 +296,10 @@ MakeUnet::sett = "The setting input is not valid. It can be a number or a list o MakeUnet::feat = "The feature input is not valid. It can be a number or a list of numbers that will be applied to the Layers."; + +SurfaceDistance::met = "Method `1` not recognized"; + + (*ConvBlock::usage = "";MakeNode::usage ="";*) (* ::Section:: *) @@ -662,15 +680,17 @@ AddLossLayer[net_]:=Block[{dim}, dim = Length[Information[net,"OutputPorts"][[1]]]-1; NetGraph[<| "net"->net, - "SoftDice" -> SoftDiceLossLayer[dim, 2], - "Jaccard" -> SofJaccardLossLayer[dim], + "Dice" -> DiceLossLayer[dim, 2], + "Jaccard" -> JaccardLossLayer[dim], "Tversky" -> TverskyLossLayer[dim, 0.7], + "Focal" -> FocalLossLayer[1 ,1], "SquaredDiff" -> {MeanSquaredLossLayer[], ElementwiseLayer[50 #&]}, "CrossEntropy" -> {CrossEntropyLossLayer["Probabilities"]} |>,{ - {"net", NetPort["Target"]}->"SoftDice"->NetPort["SoftDice"],(*using squared dice*) + {"net", NetPort["Target"]}->"Dice"->NetPort["Dice"],(*using squared dice, F1score*) {"net", NetPort["Target"]}->"Jaccard"->NetPort["Jaccard"], {"net", NetPort["Target"]}->"Tversky"->NetPort["Tversky"], + {"net", NetPort["Target"]}->"Focal"->NetPort["Focal"],(*not weighted for size, alpha=1,gamma=1*) {"net", NetPort["Target"]}->"SquaredDiff"->NetPort["SquaredDiff"],(*Brier Score*) {"net", NetPort["Target"]}->"CrossEntropy"->NetPort["CrossEntropy"] }] @@ -678,14 +698,14 @@ AddLossLayer[net_]:=Block[{dim}, (* ::Subsubsection::Closed:: *) -(*SoftDiceLossLayer*) +(*DiceLossLayer*) -SyntaxInformation[SoftDiceLossLayer] = {"ArgumentsPattern" -> {_, _.}}; +SyntaxInformation[DiceLossLayer] = {"ArgumentsPattern" -> {_, _.}}; -SoftDiceLossLayer[dim_ ] := SoftDiceLossLayer[dim, 1] +DiceLossLayer[dim_ ] := DiceLossLayer[dim, 1] -SoftDiceLossLayer[dim_, n_] := Block[{smooth}, +DiceLossLayer[dim_, n_] := Block[{smooth}, (*10.48550/arXiv.1911.02855 and 10.48550/arXiv.1606.04797 for scquared dice loss look at v-net*) smooth =1; NetGraph[<| @@ -706,14 +726,14 @@ SoftDiceLossLayer[dim_, n_] := Block[{smooth}, (* ::Subsubsection::Closed:: *) -(*SofJaccardLossLayer*) +(*JaccardLossLayer*) -SyntaxInformation[SofJaccardLossLayer] = {"ArgumentsPattern" -> {_}}; +SyntaxInformation[JaccardLossLayer] = {"ArgumentsPattern" -> {_}}; -SofJaccardLossLayer[dim_ ] := SofJaccardLossLayer[dim, 1] +JaccardLossLayer[dim_ ] := JaccardLossLayer[dim, 1] -SofJaccardLossLayer[dim_, n_]:= Block[{smooth}, +JaccardLossLayer[dim_, n_]:= Block[{smooth}, smooth = 1; NetGraph[<| (*flatten input and target; function layer allows to switch to L2 norm if #^2*) @@ -732,6 +752,30 @@ SofJaccardLossLayer[dim_, n_]:= Block[{smooth}, ] +(* ::Subsubsection::Closed:: *) +(*JaccardLossLayer*) + + +FocalLossLayer[] := FocalLossLayer[1, 1] + +FocalLossLayer[g_] := FocalLossLayer[g, 1] + +FocalLossLayer[g_, a_] := NetGraph[{ + "flatPr" -> {ThreadingLayer[#1 #2 &], AggregationLayer[Total, {-1}], FlattenLayer[]}, + "focal" -> {ThreadingLayer[-a Log[#1 + 10^-20](*#2*) (1 - #1)^g &], AggregationLayer[Mean, 1], FunctionLayer[# &]} + (* + "alph"->{AggregationLayer[Total,1;;-2],FunctionLayer[1. / ((# + 1) Total[1. / (# + 1)])&]}, + "trans"->TransposeLayer[4->1], + "alphGt"->{DotLayer[],FlattenLayer[]}, + *) + }, { + {NetPort["Input"], NetPort["Target"]} -> "flatPr" -> "focal" -> NetPort["Loss"] + (*,NetPort["Target"]->{"alph","trans"}->"alphGt", + {"flatPr","alphGt"}->"focal"*) +}, "Loss" -> "Real"] + + + (* ::Subsubsection::Closed:: *) (*TwerskyLossLayer*) @@ -1028,9 +1072,11 @@ ReplaceLabels[seg_, loc_, type_] := Block[{what, side, labNam, labIn, labOut, fi Options[ApplySegmentationNetwork]={TargetDevice->"GPU", DataPadding->0, MaxPatchSize->Automatic, Monitor->False} -SyntaxInformation[ApplySegmentationNetwork] = {"ArgumentsPattern" -> {_, _, OptionsPattern[]}}; +SyntaxInformation[ApplySegmentationNetwork] = {"ArgumentsPattern" -> {_, _, _., OptionsPattern[]}}; -ApplySegmentationNetwork[dat_, netI_, OptionsPattern[]]:=Block[{ +ApplySegmentationNetwork[dat_, netI_, opt:OptionsPattern[]]:=ApplySegmentationNetwork[dat, netI, "", opt] + +ApplySegmentationNetwork[dat_, netI_, node_, OptionsPattern[]]:=Block[{ dev, pad , lim, data, crp, net, dim, ptch, patch, pts, seg, mon, dimi, dimc, lab, class }, @@ -1058,45 +1104,45 @@ ApplySegmentationNetwork[dat_, netI_, OptionsPattern[]]:=Block[{ {patch, pts} = DataToPatches[data, ptch, PatchNumber -> 0, PatchPadding->pad]; If[mon, Echo[{ptch, Length@patch}, "Patch size and created number of patches is:"]]; - (*actualy perform the segmentation with the NN*) + (*create the network*) net = ChangeNetDimensions[net, "Dimensions" ->ptch]; - seg = ToPackedArray[Round[ClassDecoder[net[{NormDatH[#]}, TargetDevice->dev]]&/@patch]]; - - (*reverse all the padding and cropping and merged the patches if needed*) - class = NetDimensions[net,"Output"][[-1]]; - If[mon, Echo[{Dimensions[seg], Sort@Round@DeleteDuplicates[Flatten[seg]]}, - "Segmentations dimensions and labels:"]]; - seg = ArrayPad[PatchesToData[ArrayPad[#, -pad] & /@ seg, Map[# + {pad, -pad} &, pts, {2}], - dim, Range[class]], -pad]; - seg = Ramp[seg - 1]; (*set background to zero*) - seg = ToPackedArray@Round@ReverseCrop[seg, dimi, crp]; - If[mon, Echo[{Dimensions[seg], Sort@Round@DeleteDuplicates[Flatten[seg]]}, - "Output segmentations dimensions and labels:"]]; + + (*perform the segmentation*) + If[node==="", + (*actualy perform the segmentation with the NN*) + seg = ToPackedArray[Round[ClassDecoder[net[{NormalizeData[#, NormalizeMethod -> "Uniform"]}, TargetDevice->dev]]&/@patch]]; + + (*reverse all the padding and cropping and merged the patches if needed*) + class = NetDimensions[net,"Output"][[-1]]; + If[mon, Echo[{Dimensions[seg], Sort@Round@DeleteDuplicates[Flatten[seg]]}, + "Segmentations dimensions and labels:"]]; + seg = ArrayPad[PatchesToData[ArrayPad[#, -pad] & /@ seg, Map[# + {pad, -pad} &, pts, {2}], + dim, Range[class]], -pad]; + seg = Ramp[seg - 1]; (*set background to zero*) + seg = ToPackedArray@Round@ReverseCrop[seg, dimi, crp]; + If[mon, Echo[{Dimensions[seg], Sort@Round@DeleteDuplicates[Flatten[seg]]}, "Output segmentations dimensions and labels:"]]; + , + (*perform the segmentation on a specific node*) + (*check if node is part of the network*) + nodes = DeleteDuplicates[Keys[Information[net, "Layers"]][[All, 1]]]; + If[!MemberQ[nodes, node], + Echo["The node "<>node<>" is not part of the network"]; + Echo[nodes]; + Return[$Failed] + , + seg = NetTake[net, node][{First@patch}]; + If[Head[seg] === Association, seg = Last@seg]; + If[node == nodes[[-1]], seg = RotateDimensionsRight[seg]]; + ]; + ]; + (*give the output*) seg ] ] -(* ::Subsubsection::Closed:: *) -(*NormDat*) - - -NormDat[dat_] := Block[{q = Quantile[Flatten[dat], 0.9], m = Max[dat]}, If[q <= 0.5 m, If[m===0., dat, dat/m], If[q===0., dat, 0.75 dat/q]]] - - -NormDatH = Compile[{{dat, _Real, 3}}, Block[{fl, flp, min, max, bins, cdf, n}, - n = 512; - fl = Flatten[dat]; - flp = Pick[fl, Unitize[fl], 1]; - {min, max} = MinMax[flp]; - bins = BinCounts[flp, {min, max, (max - min)/n}]; - cdf = Prepend[N[Accumulate[bins]/Total[bins]], 0.]; - Map[cdf[[# + 1]] &, Clip[Floor[(dat - min)/(max - min) n], {0, n}, {0, n}], {-2}] -], RuntimeAttributes -> {Listable}, RuntimeOptions -> "Speed", Parallelization -> True]; - - (* ::Subsubsection::Closed:: *) (*FindPatchDim*) @@ -1151,20 +1197,26 @@ NetDimensions[net_]:=NetDimensions[net, ""] NetDimensions[net_, port_]:=Block[{block, neti},Switch[port, "Input", Information[net,"InputPorts"]["Input"], + "Output", Information[net,"OutputPorts"]["Output"], + "FirstEncodingIn", Last@Values@Information[ NetTake[net, {block = First[Select[Keys[net[[All, 1]]], StringContainsQ[#, "enc_"] &]], block}], "InputPorts"], + "FirstEncodingOut", Values@Information[ NetTake[net, {block = First[Select[Keys[net[[All, 1]]], StringContainsQ[#, "enc_"] &]], block}], "OutputPorts"], + "LastEncodingIn", Last@Values@Information[ NetTake[net, {block = Last[Select[Keys[net[[All, 1]]], StringContainsQ[#, "enc_"] &]], block}], "InputPorts"], + "LastEncodingOut", Last@Values@Information[ NetTake[net, {block = Last[Select[Keys[net[[All, 1]]], StringContainsQ[#, "enc_"] &]], block}], "OutputPorts"], + "U2Encoding", block = First@Select[Keys[net[[All, 1]]], StringContainsQ[#, "enc_"] &]; neti = NetFlatten[NetTake[net, {block, block}], 1]; @@ -1547,11 +1599,11 @@ TrainSegmentationNetwork[{inFol_?StringQ, outFol_?StringQ}, netCont_, opts : Opt (*define the training loss funciton*) loss = Which[ - loss === All, {"SoftDice", "SquaredDiff", "Tversky" , "CrossEntropy", "Jaccard"}, + loss === All, {"Dice", "SquaredDiff", "Tversky" , "CrossEntropy", "Jaccard", "Focal"}, StringQ[loss], {loss}, True, loss ]; - If[! And @@ (MemberQ[{"SoftDice", "SquaredDiff", "Tversky", "CrossEntropy", "Jaccard"}, #] & /@ loss), + If[! And @@ (MemberQ[{"Dice", "SquaredDiff", "Tversky", "CrossEntropy", "Jaccard", "Focal"}, #] & /@ loss), Return[Message[TrainSegmentationNetwork::loss]; $Failed]]; Echo[DateString[], "Starting training"]; @@ -1596,7 +1648,7 @@ MakeTestData[data_, n_, patch_] := Block[{testData, len, sel, testDat}, sel = Range @@ Clip[Round[(Clip[Round[len/3 - (0.5 n) First@patch], {0, Infinity}] + {1, n First@patch})], {1, len}, {1, len}]; testData = First@AutoCropData[testData[[sel]]] ]; - {{NormDatH@PadToDimensions[testData, patch]}, data[[3]]} + {{NormalizeData[PadToDimensions[testData, patch], NormalizeMethod -> "Uniform"]}, data[[3]]} ]; @@ -1610,14 +1662,25 @@ ShowTrainLog[fol_, max_] := Block[{files, log, keys, plots}, {keys, log} = LoadLog[fol, max]; (* Create a dynamic module to display the interactive plot *) - DynamicModule[{pdat = log, klist = keys, folder=fol, plot, ymaxv, xmin, xmax, key, ymax, temp}, + DynamicModule[{pdat = log, klist = keys, folder = fol, plot, ymaxv, xmin, xmax, key, ymax, temp}, + key1 = Select[klist, ! StringContainsQ[#, "Current"] &]; + key2 = Select[Select[key1, StringContainsQ[#, "Loss"] &], # =!= "RoundLoss" && # =!= "ValidationLoss" &]; + key1 = Select[Complement[key1, key2], # =!= "RoundLoss" && # =!= "ValidationLoss" &]; + key0 = {"RoundLoss", "ValidationLoss"}; + Manipulate[ plot = Transpose[Values /@ Normal[pdat[All, key]][[All, All]]]; + + plotf = If[filt, GaussianFilter[#, fsize]&/@plot,plot]; + ymaxv = Max[{1.1, 1.1 If[plot==={}, 1, Max[Select[Flatten@plot,NumberQ]]]}]; ymax = Min[{ymax, ymaxv}]; + (* Plot the selected metrics *) - ListLinePlot[If[key === {}, {}, plot], - PlotLegends -> Placed[key, Right], ImageSize -> 600, PlotRange->{{xmin,xmax} ,{0,ymax}}], + ListLinePlot[If[key === {}, {}, plotf], + PlotLegends -> Placed[key, Right], ImageSize -> 600, PlotRange->{{xmin,xmax} ,{0,ymax}}, + If[grid, GridLines -> Automatic, GridLines -> None], PlotHighlighting -> "YSlice"], + (*the controls*) Row[{ InputField[Dynamic[folder], String, Enabled -> True, FieldSize -> 50], @@ -1628,8 +1691,24 @@ ShowTrainLog[fol_, max_] := Block[{files, log, keys, plots}, , ImageSize -> {60, Automatic}, Method->"Queued"]} ], Button["Reload", {klist, pdat} = LoadLog[folder, max]; xmax = Length[pdat];], - Control[{{key, {}, ""}, klist, ControlType -> TogglerBar, - Appearance -> "Vertical" -> {Automatic, 4}, BaseStyle -> Medium}], + + Delimiter, + {{filt, False, "Filter"}, {True, False}}, + {{fsize, 5, "FilterSize"}, 1, 10, 1}, + {{grid, False, "Grid"}, {True, False}}, + + Delimiter, + (*Control[{{key, {}, ""}, klist, ControlType -> TogglerBar, Appearance -> "Vertical" -> {Automatic, 4}, BaseStyle -> Medium}],*) + Control[{{key, {}, ""}, key0, ControlType -> TogglerBar, + Appearance -> "Vertical" -> {Automatic, 4}, BaseStyle -> Medium}], + Delimiter, + Control[{{key, {}, ""}, key2, ControlType -> TogglerBar, + Appearance -> "Vertical" -> {Automatic, 4}, BaseStyle -> Medium}], + Delimiter, + Control[{{key, {}, ""}, key1, ControlType -> TogglerBar, + Appearance -> "Vertical" -> {2, Automatic}, BaseStyle -> Medium}], + Delimiter, + Row[{ Control[{{xmin, 1,"X min"},1, Dynamic[xmax-1], 1}], " ", Control[{{xmax,Length[pdat],"X max"}, Dynamic[xmin+1], Dynamic[Length[pdat]], 1}] @@ -1712,7 +1791,7 @@ GetTrainData[datas_, nBatch_, patch_, nClass_, OptionsPattern[]] := Block[{ (*normalize the data and segmentations and pad to at least patch dimensions*) dim = Max /@ Transpose[{Dimensions@dat, patch}]; - dat = NormDatH@PadToDimensions[dat, dim]; + dat = NormalizeData[PadToDimensions[dat, dim], NormalizeMethod -> "Uniform"]; seg = PadToDimensions[seg, dim]; (*check if augmentation is a boolean or a list*) @@ -1836,7 +1915,7 @@ PrepTrainData[dat_, seg_, labi_?VectorQ]:= PrepTrainData[dat, seg, {labi, labi}] PrepTrainData[dat_, seg_, {labi_?VectorQ, labo_?VectorQ}] := Block[{cr}, cr = FindCrop[dat Mask[NormalizeData[dat], 5, MaskDilation -> 1]]; { - NormDat[ApplyCrop[dat, cr]], + NormalizeData[ApplyCrop[dat, cr], NormalizeMethod -> "Uniform"], If[labi==={0}, ApplyCrop[seg,cr], ReplaceSegmentations[ApplyCrop[seg, cr], labi, labo] @@ -1898,7 +1977,7 @@ SplitDataForSegementation[data_]:=Block[{dim,whatSide,side,whatPos,pos,dat,right CropPart[data_]:=Block[{dat,up,sid,upst,upend,sidst,sidend,crp}, {dat, {up, {upst, upend}}, {sid, {sidst, sidend}}} = data; - {dat, crp} = AutoCropData[Dilation[Normal[TakeLargestComponent[Mask[NormalizeData[dat],10]]],1] dat, CropPadding->0]; + {dat, crp} = AutoCropData[Dilation[Normal[TakeLargestComponent[Mask[NormalizeData[dat], 10]]],1] dat, CropPadding->0]; {dat, Partition[crp,2]+{upst-1,0,sidst-1}, {up,sid}} ] @@ -2024,54 +2103,202 @@ MuscleNameToLabel[num_, file_] := Block[{muscleNames, muscleLabels}, (*DiceSimilarity*) -SyntaxInformation[DiceSimilarity] = {"ArgumentsPattern" -> {_, _, _}}; +SyntaxInformation[DiceSimilarity] = {"ArgumentsPattern" -> {_, _, _.}}; -DiceSimilarity[ref_, pred_, nClasses_?ListQ] := Table[DiceSimilarity[ref, pred, c], {c, nClasses}] +DiceSimilarity[ref_, pred_, nClasses_?ListQ] := Block[{refF, predF}, + refF = Flatten@Round@ToPackedArray@ref; + predF = Flatten@Round@ToPackedArray@pred; + Table[DiceSimilarityC[refF, predF, c], {c, nClasses}] +] -DiceSimilarity[ref_, pred_] := DiceSimilarityC[Flatten[ref], Flatten[pred], 1] +DiceSimilarity[ref_, pred_] := DiceSimilarityC[Flatten@Round@ToPackedArray@ref, Flatten@Round@ToPackedArray@pred, 1] -DiceSimilarity[ref_, pred_, c_?IntegerQ] := DiceSimilarityC[Flatten[ref], Flatten[pred], c] +DiceSimilarity[ref_, pred_, c_?IntegerQ] := DiceSimilarityC[Flatten@Round@ToPackedArray@ref, Flatten@Round@ToPackedArray@pred, c] -DiceSimilarityC = Compile[{{ref, _Integer, 1}, {pred, _Integer, 1}, {class, _Integer, 0}}, Block[{refv, predv, denom}, - refv = Flatten[1 - Unitize[ref - class]]; - predv = Flatten[1 - Unitize[pred - class]]; - denom = (Total[refv] + Total[predv]); - (*If[denom === 0., 1., N[2 Total[refv predv] / denom]]*) - N[(2 Total[refv predv] + 1) / (denom + 1)] - ], RuntimeOptions -> "Speed"]; +DiceSimilarityC = Compile[{{ref, _Integer, 1}, {pred, _Integer, 1}, {class, _Integer, 0}}, Block[{refv, predv, inter}, + refv = 1 - Unitize[ref - class]; + predv = 1 - Unitize[pred - class]; + inter = Total[refv predv]; + N[(2 inter + 1) / (Total[refv] + Total[predv] + 1)]] +, RuntimeOptions -> "Speed"]; (* ::Subsubsection::Closed:: *) -(*MeanSurfaceDistance*) +(*JaccardSimilarity*) -SyntaxInformation[MeanSurfaceDistance] = {"ArgumentsPattern" -> {_, _, _, _.}}; +SyntaxInformation[JaccardSimilarity] = {"ArgumentsPattern" -> {_, _, _.}}; + +JaccardSimilarity[ref_, pred_, nClasses_?ListQ] := Block[{refF, predF}, + refF = Flatten@Round@ToPackedArray@ref; + predF = Flatten@Round@ToPackedArray@pred; + Table[JaccardSimilarityC[refF, predF, c], {c, nClasses}] +] + +JaccardSimilarity[ref_, pred_] := JaccardSimilarityC[Flatten@Round@ToPackedArray@ref, Flatten@Round@ToPackedArray@pred, 1] -MeanSurfaceDistance[ref_, pred_] := MeanSurfaceDistance[ref, pred, 1, {1, 1, 1}] +JaccardSimilarity[ref_, pred_, c_?IntegerQ] := JaccardSimilarityC[Flatten@Round@ToPackedArray@ref, Flatten@Round@ToPackedArray@pred, c] -MeanSurfaceDistance[ref_, pred_, class_?IntegerQ] := MeanSurfaceDistance[ref, pred, class, {1, 1, 1}] -MeanSurfaceDistance[ref_, pred_, nClasses_?ListQ] := MeanSurfaceDistance[ref, pred, nClasses, {1, 1, 1}] +JaccardSimilarityC = Compile[{{ref, _Integer, 1}, {pred, _Integer, 1}, {class, _Integer, 0}}, Block[{refv, predv, inter}, + refv = 1 - Unitize[ref - class]; + predv = 1 - Unitize[pred - class]; + inter = Total[refv predv]; + N[(inter + 1) / (Total[refv] + Total[predv] - inter + 1)]] +, RuntimeOptions -> "Speed"]; -MeanSurfaceDistance[ref_, pred_, nClasses_?ListQ, vox_] := Table[MeanSurfaceDistance[ref, pred, class, vox], {class, nClasses}] -MeanSurfaceDistance[ref_, pred_, class_?IntegerQ, vox_] := Block[{coorRef, coorPred, fun}, - coorRef = Transpose[vox Transpose[GetEdge[ref, class]["ExplicitPositions"]]]; - coorPred = Transpose[vox Transpose[GetEdge[pred, class]["ExplicitPositions"]]]; +(* ::Subsubsection::Closed:: *) +(*SurfaceDistance*) + + +Options[SurfaceDistance] = {Method->"HD95"}; + + +SyntaxInformation[SurfaceDistance] = {"ArgumentsPattern" -> {_, _, _, _., OptionsPattern[]}}; + +SurfaceDistance[ref_, pred_, opts : OptionsPattern[]] := SurfaceDistance[Round@ToPackedArray@ref, Round@ToPackedArray@pred, 1, {1, 1, 1}, opts] + +SurfaceDistance[ref_, pred_, class_?IntegerQ, opts : OptionsPattern[]] := SurfaceDistance[Round@ToPackedArray@ref, Round@ToPackedArray@pred, class, {1, 1, 1}, opts] + +SurfaceDistance[ref_, pred_, nClasses_?ListQ, opts : OptionsPattern[]] := SurfaceDistance[ref, pred, nClasses, {1, 1, 1}, opts] + +SurfaceDistance[ref_, pred_, nClasses_?ListQ, vox : {_?NumberQ, _?NumberQ, _?NumberQ}, opts : OptionsPattern[]] := Block[{refF, predF}, + refF = Round@ToPackedArray@ref; + predF = Round@ToPackedArray@pred; + Table[SurfaceDistance[refF, predF, class, vox, opts], {class, nClasses}] +] + + +SurfaceDistance[ref_, pred_, class_?IntegerQ, vox : {_?NumberQ, _?NumberQ, _?NumberQ}, opts :OptionsPattern[]] := Block[{ + coorRef, coorPred, funRef, funPred, met, dist + }, + + coorRef = GetEdge[ref, class, vox]; + coorPred = GetEdge[pred, class, vox]; If[coorRef==={}||coorPred==={}, "noSeg", - fun = Nearest[coorRef]; - Mean@Sqrt@Total[(fun[coorPred,1][[All,1]]-coorPred)^2,{2}] + met = OptionValue[Method]; + + funRef = Nearest[coorRef, DistanceFunction -> EuclideanDistance]; + funPred = Nearest[coorPred, DistanceFunction -> EuclideanDistance]; + dist = Sqrt@Total[Join[ + funRef[coorPred, 1][[All,1]] - coorPred, + funPred[coorRef, 1][[All,1]] - coorRef + ]^2, {2}]; + + If[ListQ[met], + SufDistFunc[dist, #]&/@met, + SufDistFunc[dist, met] + ] ] ] +(* ::Subsubsection::Closed:: *) +(*SufDistFunc*) + + +SufDistFunc[dist_, met_] := Switch[met, + "Mean", Mean@dist, + "Median", Median@dist, + "RootMeanSquare"|"RMS", Sqrt[Mean[dist^2]], + "Max"|"Hausdorff"|"HD", Max@dist, + "Hausdorff95"|"HD95", Quantile[dist,.95], + "Std"|"StandardDeviation", StandardDeviation@dist, + _ , Message[SurfaceDistance::met, met]; $Failed + ] + + (* ::Subsubsection::Closed:: *) (*GetEdge*) -GetEdge[lab_, class_]:= SparseArray[ImageData[MorphologicalPerimeter[Image3D[1 - Unitize[lab - class], "Bit"], CornerNeighbors -> False],"Bit"]] +GetEdge[lab_, class_] := GetEdge[lab, class, {1, 1, 1}] +GetEdge[lab_, class_, vox_] := Block[{out}, + out = SparseArray[ImageData[MorphologicalPerimeter[Image3D[1 - Unitize[lab - class], "Bit"], + CornerNeighbors -> False], "Bit"]]["ExplicitPositions"]; + If[out =!= {}, Transpose[vox Transpose[out]], out] +] + + +(* ::Subsubsection::Closed:: *) +(*AnalyseNetworkFeatures*) + + +AnalyseNetworkFeatures[net_, data_] := AnalyseNetworkFeatures[net, data, ""] + +AnalyseNetworkFeatures[net_, data_, met_] := Block[{ + dim, dataP, netP, nodes, vals, cutoff, table, plot, feat, nfeat, ttt, n + }, + + (*find the patch dimensions and adjust data and network*) + dim = FindPatchDim[net, Dimensions@data]; + dataP = NormalizeData[PadToDimensions[data, dim], NormalizeMethod -> "Uniform"]; + netP = ChangeNetDimensions[net, "Dimensions" -> dim]; + + (*extract the network nodes*) + nodes = DeleteDuplicates[Keys[Information[net, "Layers"]][[All, 1]]]; + + (*calculate the singular values for plotting and reporting*) + {nfeat, table, plot} = Transpose[( + (*get the features*) + feat = NetTake[netP, #][{dataP}, TargetDevice -> "GPU"]; + If[Head[feat] === Association, feat = Last@feat]; + If[# == nodes[[-1]], feat = RotateDimensionsRight[feat]]; + feat = Map[Flatten, feat]; + + (*calculate the singular values of the features*) + nfeat = Length@feat; + vals = Diagonal[SingularValueDecomposition[feat, UpTo[nfeat]][[2]]]; + vals = 100 Rescale[Accumulate[vals]]; + + (*find cuoff index and percentage*) + cutoff = First[Position[UnitStep[vals - 99], 1]] - 1; + + (*give the output*) + { + nfeat, + Flatten[{Style[#, Bold], cutoff, Round[100 cutoff/nfeat, .1]}], + Transpose[{100 Rescale[Range[1., nfeat]], vals}] + } + ) & /@ nodes]; + + ttt = table[[2;;-2, 2]]; + n = Ceiling[(Length@ttt)/2]; + n = Max /@ Thread[{ttt[[ ;; n]], Reverse[ttt[[n ;; ]]]}]; + + (*output based on method*) + If[met === "", + Echo[n]; + + (*dynamic plot output*) + DynamicModule[{cols, tab = table, pl = plot, nods = nodes}, + + (*define colors for plotting*) + cols = Table[Directive[{GrayLevel[.5 + i/100], Dashed, Thick}], {i, Length@nodes}]; + cols[[1]] = Directive[{Red, Dashing[None], Thick}]; + + (*define the plots within a manipulate that allows to select the nodes of the network*) + Manipulate[Column[{ + Grid[Transpose@tab, Frame -> All, Background -> {{k -> Lighter@Red}, None}, Spacings -> {1.2, 1.2}], + Show[ + ListLinePlot[pl, PlotStyle -> RotateRight[cols, k - 1], GridLines -> {{tab[[k, 3]]}, {99}}, + ImageSize -> 500, AxesStyle -> Directive[{Black, Thick}], AspectRatio -> 1, + LabelStyle -> Directive[{Black, 14, Bold}] + ], + Plot[x, {x, 0, 100}, PlotStyle -> Directive[{Thick, Gray, Dotted}]] + ] + }, Alignment -> Center], + {{k, 1, ""}, Thread[Range@Length@nods -> (Style[#, Black, 14, Bold] & /@ nods)], ControlType -> SetterBar} + ] + ], + + (*value per node*) + table[[All, 3]] + ] +] (* ::Section:: *) diff --git a/QMRITools/PacletInfo.wl b/QMRITools/PacletInfo.wl index 5334cd76..47cfa61b 100644 --- a/QMRITools/PacletInfo.wl +++ b/QMRITools/PacletInfo.wl @@ -2,7 +2,7 @@ PacletObject[<| "Name" -> "QMRITools", - "Version" -> "3.22.0", + "Version" -> "3.24.0", "WolframVersion" -> "14.0+", "SystemID" -> All, diff --git a/README.md b/README.md index 385d81ed..1a9a0ccb 100644 --- a/README.md +++ b/README.md @@ -138,24 +138,22 @@ QMRITools contains the following [toolboxes](https://www.qmritools.com/tool/): - FasciculationTools - GeneralTools - GradientTools -- ImportTools - IVIMTools - JcouplingTools - LoggingTools - MaskingTools - MuscleBidsTools - NiftiTools -- PhysiologyTools - PlottingTools - ProcessingTools - ReconstructionTools - RelaxometryTools +- SegmentationTools - SimulationTools - SpectroTools - TaggingTools - TensorTools - TractographyTools -- VisteTools ------------------------------------------------------------------------ diff --git a/buildscripts.nb b/buildscripts.nb index fab3a25d..b4a28405 100644 --- a/buildscripts.nb +++ b/buildscripts.nb @@ -10,10 +10,10 @@ NotebookFileLineBreakTest NotebookFileLineBreakTest NotebookDataPosition[ 158, 7] -NotebookDataLength[ 1276948, 23273] -NotebookOptionsPosition[ 1270314, 23159] -NotebookOutlinePosition[ 1271103, 23182] -CellTagsIndexPosition[ 1271060, 23179] +NotebookDataLength[ 1603414, 28701] +NotebookOptionsPosition[ 1597581, 28597] +NotebookOutlinePosition[ 1598363, 28620] +CellTagsIndexPosition[ 1598320, 28617] WindowFrame->Normal*) (* Beginning of Notebook Content *) @@ -45,7 +45,7 @@ Cell[BoxData[{ InitializationCell->True, CellChangeTimes->{{3.899533951461589*^9, 3.89953395174713*^9}, 3.900061496481605*^9, 3.9007470254228354`*^9, 3.9007471177234387`*^9}, - 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