from girder_large_image.girder_tilesource import GirderTileSource
from girder.constants import AssetstoreType
from girder.models.file import File
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)
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)
filepath = filelist[0]
for file in Item().collection.aggregate([
{'$match': {'folderId': self.item['folderId']}},
{'$lookup': {
'from': 'file', 'localField': '_id', 'foreignField': 'itemId', 'as': 'files',
}},
{'$addFields': {'fileCount': {'$size': '$files'}}},
{'$match': {'fileCount': 1}},
{'$unwind': '$files'},
{'$replaceRoot': {'newRoot': '$files'}},
]):
if self._pathMightBeDicom(File().getLocalFilePath(file), filepath):
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()