Source code for large_image_source_dicom.girder_source

from girder_large_image.girder_tilesource import GirderTileSource

from girder.constants import AssetstoreType
from girder.models.file import File
from girder.models.folder import Folder
from girder.models.item import Item
from girder.utility import assetstore_utilities
from large_image.exceptions import TileSourceError

from . import DICOMFileTileSource, _lazyImportPydicom
from .assetstore import DICOMWEB_META_KEY

[docs] 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 _getAssetstore(self): files = Item().childFiles(self.item, limit=1) if not files: return None assetstore_id = files[0].get('assetstoreId') if not assetstore_id: return None return File()._getAssetstoreModel(files[0]).load(assetstore_id) def _getLargeImagePath(self): # Look at a single file and see what type of assetstore it came from # If it came from a DICOMweb assetstore, then we will use that method. assetstore = self._getAssetstore() assetstore_type = assetstore['type'] if assetstore else None if assetstore_type == getattr(AssetstoreType, 'DICOMWEB', '__undefined__'): return self._getDICOMwebLargeImagePath(assetstore) else: return self._getFilesystemLargeImagePath() def _getFilesystemLargeImagePath(self): filelist = [ File().getLocalFilePath(file) for file in Item().childFiles(self.item) if self._pathMightBeDicom(file['name'])] if len(filelist) != 1: return filelist try: _lazyImportPydicom().filereader.dcmread(filelist[0], stop_before_pixels=True) except Exception as exc: msg = f'File cannot be opened via dicom tile source ({exc}).' raise TileSourceError(msg) 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 self._pathMightBeDicom(File().getLocalFilePath(file)): filelist.append(File().getLocalFilePath(file)) return filelist def _getDICOMwebLargeImagePath(self, assetstore): meta = assetstore[DICOMWEB_META_KEY] item_uids = self.item['dicom_uids'] adapter = assetstore_utilities.getAssetstoreAdapter(assetstore) return { 'url': meta['url'], 'study_uid': item_uids['study_uid'], 'series_uid': item_uids['series_uid'], # The following are optional 'qido_prefix': meta.get('qido_prefix'), 'wado_prefix': meta.get('wado_prefix'), 'session': adapter.auth_session, } def _getDicomMetadata(self): if self._isDicomWeb: # This should have already been saved in the item return self.item['dicomweb_meta'] # Return the parent result. This is a cached method. return super()._getDicomMetadata()