-
Notifications
You must be signed in to change notification settings - Fork 43
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
This uses wsidicom to read dicom files. So far it has only been tested with files that were generated with the wsi2dcm docker from the 1.0.3 deb from https://github.com/GoogleCloudPlatform/wsi-to-dicom-converter, which seems to have issues with some files. This may be refactored to use a different base library, and internal details should be considered provisional. It needs to have internal metadata exposed.
- Loading branch information
Showing
14 changed files
with
361 additions
and
5 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,5 +1,6 @@ | ||
| -e sources/bioformats | ||
| -e sources/deepzoom | ||
| -e sources/dicom | ||
| -e sources/dummy | ||
| -e sources/gdal | ||
| -e sources/multi | ||
|
|
||
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,224 @@ | ||
| import math | ||
| import os | ||
| import warnings | ||
|
|
||
| import numpy | ||
|
|
||
| from large_image.cache_util import LruCacheMetaclass, methodcache | ||
| from large_image.constants import TILE_FORMAT_PIL, SourcePriority | ||
| from large_image.exceptions import TileSourceError, TileSourceFileNotFoundError | ||
| from large_image.tilesource import FileTileSource | ||
| from large_image.tilesource.utilities import _imageToNumpy, _imageToPIL | ||
|
|
||
| wsidicom = None | ||
|
|
||
| try: | ||
| from importlib.metadata import PackageNotFoundError | ||
| from importlib.metadata import version as _importlib_version | ||
| except ImportError: | ||
| from importlib_metadata import PackageNotFoundError | ||
| from importlib_metadata import version as _importlib_version | ||
| try: | ||
| __version__ = _importlib_version(__name__) | ||
| except PackageNotFoundError: | ||
| # package is not installed | ||
| pass | ||
|
|
||
|
|
||
| def _lazyImport(): | ||
| """ | ||
| Import the wsidicom module. This is done when needed rather than in the | ||
| module initialization because it is slow. | ||
| """ | ||
| global wsidicom | ||
|
|
||
| if wsidicom is None: | ||
| try: | ||
| import wsidicom | ||
| except ImportError: | ||
| raise TileSourceError('nd2 module not found.') | ||
| warnings.filterwarnings('ignore', category=UserWarning, module='wsidicom') | ||
| warnings.filterwarnings('ignore', category=UserWarning, module='pydicom') | ||
|
|
||
|
|
||
| class DICOMFileTileSource(FileTileSource, metaclass=LruCacheMetaclass): | ||
| """ | ||
| Provides tile access to dicom files the dicom or dicomreader library can read. | ||
| """ | ||
|
|
||
| cacheName = 'tilesource' | ||
| name = 'dicom' | ||
| extensions = { | ||
| None: SourcePriority.LOW, | ||
| 'dcm': SourcePriority.PREFERRED, | ||
| 'dic': SourcePriority.PREFERRED, | ||
| 'dicom': SourcePriority.PREFERRED, | ||
| } | ||
| mimeTypes = { | ||
| None: SourcePriority.FALLBACK, | ||
| 'application/dicom': SourcePriority.PREFERRED, | ||
| } | ||
|
|
||
| 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().__init__(path, **kwargs) | ||
|
|
||
| # We want to make a list of paths of files in this item, if multiple, | ||
| # or adjacent items in the folder if the item is a single file. We | ||
| # filter files with names that have a preferred extension. | ||
| path = self._getLargeImagePath() | ||
| if not isinstance(path, list): | ||
| path = str(path) | ||
| if not os.path.isfile(path): | ||
| raise TileSourceFileNotFoundError(path) from None | ||
| root = os.path.dirname(path) | ||
| self._largeImagePath = [ | ||
| os.path.join(root, entry) for entry in os.listdir(root) | ||
| if os.path.isfile(os.path.join(root, entry)) and | ||
| os.path.splitext(entry)[-1][1:] in self.extensions] | ||
| if path not in self._largeImagePath: | ||
| self._largeImagePath = [path] | ||
| # TODO: fail if this file is level-(n) and a file that is | ||
| # level-(n-1) exists | ||
| else: | ||
| self._largeImagePath = path | ||
| _lazyImport() | ||
| try: | ||
| self._dicom = wsidicom.WsiDicom.open(self._largeImagePath) | ||
| except Exception: | ||
| raise TileSourceError('File cannot be opened via dicom tile source.') | ||
| self.sizeX = int(self._dicom.image_size.width) | ||
| self.sizeY = int(self._dicom.image_size.height) | ||
| self.tileWidth = int(self._dicom.tile_size.width) | ||
| self.tileHeight = int(self._dicom.tile_size.height) | ||
| self.levels = int(max(1, math.ceil(math.log( | ||
| float(max(self.sizeX, self.sizeY)) / self.tileWidth) / math.log(2)) + 1)) | ||
|
|
||
| def __del__(self): | ||
| if getattr(self, '_dicom', None) is not None: | ||
| try: | ||
| self._dicom.close() | ||
| finally: | ||
| self._dicom = None | ||
|
|
||
| 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 = mm_y = None | ||
| try: | ||
| mm_x = self._dicom.base_level.pixel_spacing.width or None | ||
| mm_y = self._dicom.base_level.pixel_spacing.height or None | ||
| except Exception: | ||
| pass | ||
| # Estimate the magnification; we don't have a direct value | ||
| mag = 0.01 / mm_x if mm_x else None | ||
| return { | ||
| 'magnification': mag, | ||
| 'mm_x': mm_x, | ||
| 'mm_y': mm_y, | ||
| } | ||
|
|
||
| def getMetadata(self): | ||
| """ | ||
| Return a dictionary of metadata containing levels, sizeX, sizeY, | ||
| tileWidth, tileHeight, magnification, mm_x, mm_y, and frames. | ||
| :returns: metadata dictionary. | ||
| """ | ||
| result = super().getMetadata() | ||
| return result | ||
|
|
||
| def getInternalMetadata(self, **kwargs): | ||
| """ | ||
| Return additional known metadata about the tile source. Data returned | ||
| from this method is not guaranteed to be in any particular format or | ||
| have specific values. | ||
| :returns: a dictionary of data or None. | ||
| """ | ||
| result = {} | ||
| return result | ||
|
|
||
| @methodcache() | ||
| def getTile(self, x, y, z, pilImageAllowed=False, numpyAllowed=False, **kwargs): | ||
| frame = self._getFrame(**kwargs) | ||
| self._xyzInRange(x, y, z, frame) | ||
| x0, y0, x1, y1, step = self._xyzToCorners(x, y, z) | ||
| bw = self.tileWidth * step | ||
| bh = self.tileHeight * step | ||
| level = 0 | ||
| levelfactor = 1 | ||
| basefactor = self._dicom.base_level.pixel_spacing.width | ||
| for checklevel in range(1, len(self._dicom.levels)): | ||
| factor = round(self._dicom.levels[checklevel].pixel_spacing.width / basefactor) | ||
| if factor <= step: | ||
| level = checklevel | ||
| levelfactor = factor | ||
| else: | ||
| break | ||
| x0f = int(x0 // levelfactor) | ||
| y0f = int(y0 // levelfactor) | ||
| x1f = min(int(math.ceil(x1 / levelfactor)), self._dicom.levels[level].size.width) | ||
| y1f = min(int(math.ceil(y1 / levelfactor)), self._dicom.levels[level].size.height) | ||
| bw = int(bw // levelfactor) | ||
| bh = int(bh // levelfactor) | ||
| tile = self._dicom.read_region( | ||
| (x0f, y0f), self._dicom.levels[level].level, (x1f - x0f, y1f - y0f)) | ||
| format = TILE_FORMAT_PIL | ||
| if tile.width < bw or tile.height < bh: | ||
| tile = _imageToNumpy(tile)[0] | ||
| tile = numpy.pad( | ||
| tile, | ||
| ((0, bh - tile.shape[0]), (0, bw - tile.shape[1]), (0, 0)), | ||
| 'constant', constant_values=0) | ||
| tile = _imageToPIL(tile) | ||
| if bw > self.tileWidth or bh > self.tileHeight: | ||
| tile = tile.resize((self.tileWidth, self.tileHeight)) | ||
| return self._outputTile(tile, format, x, y, z, | ||
| pilImageAllowed, numpyAllowed, **kwargs) | ||
|
|
||
| def getAssociatedImagesList(self): | ||
| """ | ||
| Return a list of associated images. | ||
| :return: the list of image keys. | ||
| """ | ||
| return [key for key in ['label', 'macro'] if self._getAssociatedImage(key)] | ||
|
|
||
| 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. | ||
| """ | ||
| keyMap = { | ||
| 'label': 'read_label', | ||
| 'macro': 'read_overview', | ||
| } | ||
| try: | ||
| return getattr(self._dicom, keyMap[imageKey])() | ||
| except Exception: | ||
| return None | ||
|
|
||
|
|
||
| def open(*args, **kwargs): | ||
| """ | ||
| Create an instance of the module class. | ||
| """ | ||
| return DICOMFileTileSource(*args, **kwargs) | ||
|
|
||
|
|
||
| def canRead(*args, **kwargs): | ||
| """ | ||
| Check if an input can be read by the module class. | ||
| """ | ||
| return DICOMFileTileSource.canRead(*args, **kwargs) |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,38 @@ | ||
| import os | ||
|
|
||
| from girder_large_image.girder_tilesource import GirderTileSource | ||
|
|
||
| from girder.models.file import File | ||
| from girder.models.folder import Folder | ||
| from girder.models.item import Item | ||
|
|
||
| from . import DICOMFileTileSource | ||
|
|
||
|
|
||
| class DICOMGirderTileSource(DICOMFileTileSource, GirderTileSource): | ||
| """ | ||
| Provides tile access to Girder items with an DICOM file or other files that | ||
| the dicomreader library can read. | ||
| """ | ||
|
|
||
| cacheName = 'tilesource' | ||
| name = 'dicom' | ||
|
|
||
| _mayHaveAdjacentFiles = True | ||
|
|
||
| def _getLargeImagePath(self): | ||
| filelist = [ | ||
| File().getLocalFilePath(file) for file in Item().childFiles(self.item) | ||
| if os.path.splitext(file['name'])[-1][1:] in self.extensions] | ||
| if len(filelist) > 1: | ||
| return filelist | ||
| filelist = [] | ||
| folder = Folder().load(self.item['folderId'], force=True) | ||
| for item in Folder().childItems(folder): | ||
| if len(list(Item().childFiles(item, limit=2))) == 1: | ||
| file = next(Item().childFiles(item, limit=2)) | ||
| if os.path.splitext(file['name'])[-1][1:] in self.extensions: | ||
| filelist.append(File().getLocalFilePath(file)) | ||
| # TODO: fail if this file is level-(n) and a file that is | ||
| # level-(n-1) exists | ||
| return filelist |
Oops, something went wrong.