Source code for girder_large_image.girder_tilesource

from girder.constants import AccessType
from girder.exceptions import FilePathException, ValidationException
from girder.models.file import File
from girder.models.item import Item
from large_image import tilesource
from large_image.constants import SourcePriority
from large_image.exceptions import TileSourceAssetstoreError, TileSourceError

AvailableGirderTileSources = {}
KnownMimeTypes = set()
KnownExtensions = set()
KnownMimeTypesWithAdjacentFiles = set()
KnownExtensionsWithAdjacentFiles = set()

[docs]class GirderTileSource(tilesource.FileTileSource): girderSource = True # If the large image file has one of these extensions or mimetypes, it will # always be treated as if there are possible adjacent files. extensionsWithAdjacentFiles = set() mimeTypesWithAdjacentFiles = set() def __init__(self, item, *args, **kwargs): """ Initialize the tile class. See the base class for other available parameters. :param item: a Girder item document which contains ['largeImage']['fileId'] identifying the Girder file to be used for the tile source. """ super().__init__(item, *args, **kwargs) self.item = item
[docs] @staticmethod def getLRUHash(*args, **kwargs): return '%s,%s,%s,%s,%s,%s,%s,__STYLESTART__,%s,__STYLEEND__' % ( args[0]['largeImage']['fileId'], args[0]['updated'], kwargs.get('encoding', 'JPEG'), kwargs.get('jpegQuality', 95), kwargs.get('jpegSubsampling', 0), kwargs.get('tiffCompression', 'raw'), kwargs.get('edge', False), kwargs.get('style', None))
[docs] def getState(self): if hasattr(self, '_classkey'): return self._classkey return '%s,%s,%s,%s,%s,%s,%s,__STYLESTART__,%s,__STYLEEND__' % ( self.item['largeImage']['fileId'], self.item['updated'], self.encoding, self.jpegQuality, self.jpegSubsampling, self.tiffCompression, self.edge, self._jsonstyle)
[docs] def mayHaveAdjacentFiles(self, largeImageFile): if not hasattr(self, '_mayHaveAdjacentFiles'): largeImageFileId = self.item['largeImage']['fileId'] # The item has adjacent files if there are any files that are not # the large image file or an original file it was derived from. # This is always the case if there are 3 or more files. fileIds = [str(file['_id']) for file in Item().childFiles(self.item, limit=3)] knownIds = [str(largeImageFileId)] if 'originalId' in self.item['largeImage']: knownIds.append(str(self.item['largeImage']['originalId'])) self._mayHaveAdjacentFiles = ( len(fileIds) >= 3 or fileIds[0] not in knownIds or fileIds[-1] not in knownIds) if (any(ext in KnownExtensionsWithAdjacentFiles for ext in largeImageFile['exts']) or largeImageFile.get('mimeType') in KnownMimeTypesWithAdjacentFiles): self._mayHaveAdjacentFiles = True return self._mayHaveAdjacentFiles
def _getLargeImagePath(self): # If self.mayHaveAdjacentFiles is True, we try to use the girder # mount where companion files appear next to each other. largeImageFileId = self.item['largeImage']['fileId'] largeImageFile = File().load(largeImageFileId, force=True) try: largeImagePath = None if (self.mayHaveAdjacentFiles(largeImageFile) and hasattr(File(), 'getGirderMountFilePath')): try: if (largeImageFile.get('imported') and File().getLocalFilePath(largeImageFile) == largeImageFile['path']): largeImagePath = largeImageFile['path'] except Exception: pass if not largeImagePath: try: largeImagePath = File().getGirderMountFilePath(largeImageFile) except FilePathException: pass if not largeImagePath: try: largeImagePath = File().getLocalFilePath(largeImageFile) except AttributeError as e: raise TileSourceError( 'No local file path for this file: %s' % e.args[0]) return largeImagePath except (TileSourceAssetstoreError, FilePathException): raise except (KeyError, ValidationException, TileSourceError) as e: raise TileSourceError( 'No large image file in this item: %s' % e.args[0])
[docs]def loadGirderTileSources(): """ Load all Girder tilesources from entrypoints and add them to the AvailableGiderTileSources dictionary. """ tilesource.loadTileSources('girder_large_image.source', AvailableGirderTileSources) for sourceName in AvailableGirderTileSources: if getattr(AvailableGirderTileSources[sourceName], 'girderSource', False): KnownExtensions.update({ key for key in AvailableGirderTileSources[sourceName].extensions if key is not None}) KnownExtensionsWithAdjacentFiles.update({ key for key in AvailableGirderTileSources[sourceName].extensionsWithAdjacentFiles if key is not None}) if getattr(AvailableGirderTileSources[sourceName], 'girderSource', False): KnownMimeTypes.update({ key for key in AvailableGirderTileSources[sourceName].mimeTypes if key is not None}) KnownMimeTypesWithAdjacentFiles.update({ key for key in AvailableGirderTileSources[sourceName].mimeTypesWithAdjacentFiles if key is not None})
[docs]def getGirderTileSourceName(item, file=None, *args, **kwargs): """ Get a Girder tilesource name using the known sources. If tile sources have not yet been loaded, load them. :param item: a Girder item. :param file: if specified, the Girder file object to use as the large image file; used here only to check extensions. :returns: The name of a tilesource that can read the Girder item. """ if not len(AvailableGirderTileSources): loadGirderTileSources() if not file: file = File().load(item['largeImage']['fileId'], force=True) try: localPath = File().getLocalFilePath(file) except (FilePathException, AttributeError): localPath = None extensions = [entry.lower().split()[0] for entry in file['exts'] if entry] properties = {} if localPath: properties['_geospatial_source'] = tilesource.isGeospatial(localPath) sourceList = [] for sourceName in AvailableGirderTileSources: if not getattr(AvailableGirderTileSources[sourceName], 'girderSource', False): continue sourceExtensions = AvailableGirderTileSources[sourceName].extensions priority = sourceExtensions.get(None, SourcePriority.MANUAL) for ext in extensions: if ext in sourceExtensions: priority = min(priority, sourceExtensions[ext]) if priority >= SourcePriority.MANUAL: continue propertiesClash = any( getattr(AvailableGirderTileSources[sourceName], k, False) != v for k, v in properties.items()) sourceList.append((propertiesClash, priority, sourceName)) for _clash, _priority, sourceName in sorted(sourceList): if AvailableGirderTileSources[sourceName].canRead(item): return sourceName
[docs]def getGirderTileSource(item, file=None, *args, **kwargs): """ Get a Girder tilesource using the known sources. :param item: a Girder item or an item id. :param file: if specified, the Girder file object to use as the large image file; used here only to check extensions. :returns: A girder tilesource for the item. """ if not isinstance(item, dict): item = Item().load(item, user=kwargs.get('user', None), level=AccessType.READ) sourceName = getGirderTileSourceName(item, file, *args, **kwargs) if sourceName: return AvailableGirderTileSources[sourceName](item, *args, **kwargs)