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Add an openjpeg source using the glymur library.
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| # -*- coding: utf-8 -*- | ||
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| ############################################################################## | ||
| # Copyright Kitware Inc. | ||
| # | ||
| # Licensed under the Apache License, Version 2.0 ( the "License" ); | ||
| # you may not use this file except in compliance with the License. | ||
| # You may obtain a copy of the License at | ||
| # | ||
| # http://www.apache.org/licenses/LICENSE-2.0 | ||
| # | ||
| # Unless required by applicable law or agreed to in writing, software | ||
| # distributed under the License is distributed on an "AS IS" BASIS, | ||
| # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. | ||
| # See the License for the specific language governing permissions and | ||
| # limitations under the License. | ||
| ############################################################################## | ||
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| import glymur | ||
| import math | ||
| import PIL.Image | ||
| import six | ||
| import threading | ||
| import warnings | ||
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| from six import BytesIO | ||
| from xml.etree import cElementTree | ||
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| from ..cache_util import LruCacheMetaclass, methodcache | ||
| from ..constants import SourcePriority | ||
| from .base import TileSourceException, FileTileSource, etreeToDict, TILE_FORMAT_PIL | ||
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| try: | ||
| import girder | ||
| from girder import logger | ||
| from .base import GirderTileSource | ||
| except ImportError: | ||
| girder = None | ||
| import logging as logger | ||
| logger.getLogger().setLevel(logger.INFO) | ||
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| warnings.filterwarnings('ignore', category=UserWarning, module='glymur') | ||
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| @six.add_metaclass(LruCacheMetaclass) | ||
| class OpenjpegFileTileSource(FileTileSource): | ||
| """ | ||
| Provides tile access to SVS files and other files the openjpeg library can | ||
| read. | ||
| """ | ||
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| cacheName = 'tilesource' | ||
| name = 'openjpegfile' | ||
| extensions = { | ||
| None: SourcePriority.MEDIUM, | ||
| 'jp2': SourcePriority.PREFERRED, | ||
| 'jpf': SourcePriority.PREFERRED, | ||
| 'j2k': SourcePriority.PREFERRED, | ||
| 'jpx': SourcePriority.PREFERRED, | ||
| } | ||
| mimeTypes = { | ||
| None: SourcePriority.FALLBACK, | ||
| 'image/jp2': SourcePriority.PREFERRED, | ||
| 'image/jpx': SourcePriority.PREFERRED, | ||
| } | ||
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| _boxToTag = { | ||
| # In the few samples I've seen, both of these appear to be macro images | ||
| b'mig ': 'macro', | ||
| b'mag ': 'label', | ||
| # This contains a largish image | ||
| # b'psi ': 'other', | ||
| } | ||
| _xmlTag = b'mxl ' | ||
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| def __init__(self, path, **kwargs): | ||
| """ | ||
| Initialize the tile class. See the base class for other available | ||
| parameters. | ||
| :param path: a filesystem path for the tile source. | ||
| """ | ||
| super(OpenjpegFileTileSource, self).__init__(path, **kwargs) | ||
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| largeImagePath = self._getLargeImagePath() | ||
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| self._largeImagePath = largeImagePath | ||
| self._pixelInfo = {} | ||
| self._openjpegLock = threading.RLock() | ||
| try: | ||
| self._openjpeg = glymur.Jp2k(largeImagePath) | ||
| except glymur.jp2box.InvalidJp2kError: | ||
| raise TileSourceException('File cannot be opened via Glymur and OpenJPEG.') | ||
| try: | ||
| self.sizeY, self.sizeX = self._openjpeg.shape[:2] | ||
| except IndexError: | ||
| raise TileSourceException('File cannot be opened via Glymur and OpenJPEG.') | ||
| self.levels = self._openjpeg.codestream.segment[2].num_res + 1 | ||
| self.tileWidth = self.tileHeight = 2 ** int(math.ceil(max( | ||
| math.log(float(self.sizeX)) / math.log(2) - self.levels + 1, | ||
| math.log(float(self.sizeY)) / math.log(2) - self.levels + 1))) | ||
| # read associated images and metadata from boxes | ||
| self._associatedImages = {} | ||
| for box in self._openjpeg.box: | ||
| if box.box_id == self._xmlTag or box.box_id in self._boxToTag: | ||
| data = self._readbox(box) | ||
| if data is None: | ||
| continue | ||
| if box.box_id == self._xmlTag: | ||
| self._parseMetadataXml(data) | ||
| continue | ||
| try: | ||
| self._associatedImages[self._boxToTag[box.box_id]] = PIL.Image.open( | ||
| BytesIO(data)) | ||
| except Exception: | ||
| pass | ||
| if box.box_id == 'jp2c': | ||
| for segment in box.codestream.segment: | ||
| if segment.marker_id == 'CME' and hasattr(segment, 'ccme'): | ||
| self._parseMetadataXml(segment.ccme) | ||
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| def getNativeMagnification(self): | ||
| """ | ||
| Get the magnification at a particular level. | ||
| :return: magnification, width of a pixel in mm, height of a pixel in mm. | ||
| """ | ||
| mm_x = self._pixelInfo.get('mm_x') | ||
| mm_y = self._pixelInfo.get('mm_y') | ||
| # Estimate the magnification if we don't have a direct value | ||
| mag = self._pixelInfo.get('magnification') or 0.01 / mm_x if mm_x else None | ||
| return { | ||
| 'magnification': mag, | ||
| 'mm_x': mm_x, | ||
| 'mm_y': mm_y, | ||
| } | ||
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| def _parseMetadataXml(self, meta): | ||
| if not isinstance(meta, six.string_types): | ||
| meta = meta.decode('utf8', 'ignore') | ||
| try: | ||
| xml = cElementTree.fromstring(meta) | ||
| except Exception: | ||
| return | ||
| self._description_xml = etreeToDict(xml) | ||
| try: | ||
| # Optrascan metadata | ||
| scanDetails = self._description_xml['ScanInfo']['ScanDetails'] | ||
| mag = float(scanDetails['Magnification']) | ||
| # In microns; convert to mm | ||
| scale = float(scanDetails['PixelResolution']) * 1e-3 | ||
| self._pixelInfo = { | ||
| 'magnification': mag, | ||
| 'mm_x': scale, | ||
| 'mm_y': scale, | ||
| } | ||
| except Exception: | ||
| pass | ||
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| def _getAssociatedImage(self, imageKey): | ||
| """ | ||
| Get an associated image in PIL format. | ||
| :param imageKey: the key of the associated image. | ||
| :return: the image in PIL format or None. | ||
| """ | ||
| return self._associatedImages.get(imageKey) | ||
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| def getAssociatedImagesList(self): | ||
| """ | ||
| Return a list of associated images. | ||
| :return: the list of image keys. | ||
| """ | ||
| return list(self._associatedImages.keys()) | ||
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| def _readbox(self, box): | ||
| if box.length > 16 * 1024 * 1024: | ||
| return | ||
| try: | ||
| fp = open(self._largeImagePath, 'rb') | ||
| headerLength = 16 | ||
| fp.seek(box.offset + headerLength) | ||
| data = fp.read(box.length - headerLength) | ||
| return data | ||
| except Exception: | ||
| pass | ||
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| @methodcache() | ||
| def getTile(self, x, y, z, pilImageAllowed=False, **kwargs): | ||
| if z < 0 or z >= self.levels: | ||
| raise TileSourceException('z layer does not exist') | ||
| step = 2 ** (self.levels - 1 - z) | ||
| x0 = x * step * self.tileWidth | ||
| x1 = min((x + 1) * step * self.tileWidth, self.sizeX) | ||
| y0 = y * step * self.tileHeight | ||
| y1 = min((y + 1) * step * self.tileHeight, self.sizeY) | ||
| if x < 0 or x0 >= self.sizeX: | ||
| raise TileSourceException('x is outside layer') | ||
| if y < 0 or y0 >= self.sizeY: | ||
| raise TileSourceException('y is outside layer') | ||
| with self._openjpegLock: | ||
| tile = self._openjpeg[y0:y1:step, x0:x1:step] | ||
| mode = 'L' | ||
| if len(tile.shape) == 3: | ||
| mode = ['L', 'LA', 'RGB', 'RGBA'][tile.shape[2] - 1] | ||
| tile = PIL.Image.frombytes(mode, (tile.shape[1], tile.shape[0]), tile) | ||
| if tile.size != (self.tileWidth, self.tileHeight): | ||
| wrap = PIL.Image.new(mode, (self.tileWidth, self.tileHeight)) | ||
| wrap.paste(tile, (0, 0)) | ||
| tile = wrap | ||
| return self._outputTile(tile, TILE_FORMAT_PIL, x, y, z, pilImageAllowed, **kwargs) | ||
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| if girder: | ||
| class OpenjpegGirderTileSource(OpenjpegFileTileSource, GirderTileSource): | ||
| """ | ||
| Provides tile access to Girder items with an SVS file or other files that | ||
| the openslide library can read. | ||
| """ | ||
|
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| cacheName = 'tilesource' | ||
| name = 'openjpeg' |
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