Source code for large_image_source_dicom

import math
import os
import re
import warnings
from importlib.metadata import PackageNotFoundError
from importlib.metadata import version as _importlib_version

import numpy as np

from large_image import config
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

from .dicom_tags import dicom_key_to_tag

dicomweb_client = None
pydicom = None
wsidicom = None

    __version__ = _importlib_version(__name__)
except PackageNotFoundError:
    # package is not installed

def _lazyImport():
    Import the wsidicom module.  This is done when needed rather than in the
    module initialization because it is slow.
    global wsidicom
    global dicomweb_client
    global pydicom

    if wsidicom is None:
            import dicomweb_client
            import pydicom
            import wsidicom
        except ImportError:
            msg = 'dicom modules not found.'
            raise TileSourceError(msg)
        warnings.filterwarnings('ignore', category=UserWarning, module='wsidicom')
        warnings.filterwarnings('ignore', category=UserWarning, module='dicomweb_client')
        warnings.filterwarnings('ignore', category=UserWarning, module='pydicom')

[docs] def dicom_to_dict(ds, base=None): """ Convert a pydicom dataset to a fairly flat python dictionary for purposes of reporting. This is not invertable without extra work. :param ds: a pydicom dataset. :param base: a base dataset entry within the dataset. :returns: a dictionary of values. """ if base is None: base = ds.to_json_dict( bulk_data_threshold=0, bulk_data_element_handler=lambda x: '<%s bytes>' % len(x.value)) info = {} for k, v in base.items(): key = k try: key = pydicom.datadict.keyword_for_tag(k) except Exception: pass if isinstance(v, str): val = v else: if v.get('vr') in {None, 'OB'}: continue if not len(v.get('Value', [])): continue if isinstance(v['Value'][0], dict): val = [dicom_to_dict(ds, entry) for entry in v['Value']] elif len(v['Value']) == 1: val = v['Value'][0] else: val = v['Value'] info[key] = val return info
[docs] 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, } nameMatches = { r'DCM_\d+$': SourcePriority.MEDIUM, r'\d+(\.\d+){3,20}$': SourcePriority.MEDIUM, } _minTileSize = 64 _maxTileSize = 4096 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) self.logger = config.getConfig('logger') # 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. # If the path is a dict, that likely means it is a DICOMweb asset. path = self._getLargeImagePath() if not isinstance(path, (dict, list)): path = str(path) if not os.path.isfile(path): raise TileSourceFileNotFoundError(path) from None root = os.path.dirname(path) or '.' self._largeImagePath = [ os.path.join(root, entry) for entry in os.listdir(root) if os.path.isfile(os.path.join(root, entry)) and self._pathMightBeDicom(entry)] if (path not in self._largeImagePath and os.path.join(root, os.path.basename(path)) not in self._largeImagePath): self._largeImagePath = [path] else: self._largeImagePath = path _lazyImport() try: self._dicom = self._open_wsi_dicom(self._largeImagePath) except Exception as exc: msg = f'File cannot be opened via dicom tile source ({exc}).' raise TileSourceError(msg) self.sizeX = int(self._dicom.size.width) self.sizeY = int(self._dicom.size.height) self.tileWidth = int(self._dicom.tile_size.width) self.tileHeight = int(self._dicom.tile_size.height) self.tileWidth = min(max(self.tileWidth, self._minTileSize), self._maxTileSize) self.tileHeight = min(max(self.tileHeight, self._minTileSize), self._maxTileSize) self.levels = int(max(1, math.ceil(math.log( max(self.sizeX / self.tileWidth, self.sizeY / self.tileHeight)) / math.log(2)) + 1)) self._populatedLevels = len(self._dicom.levels) # We need to detect which levels are functionally present if we want to # return a sensible _nonemptyLevelsList def _open_wsi_dicom(self, path): if isinstance(path, dict): # Use the DICOMweb open method return self._open_wsi_dicomweb(path) else: # Use the regular open method return def _open_wsi_dicomweb(self, info): # These are the required keys in the info dict url = info['url'] study_uid = info['study_uid'] series_uid = info['series_uid'] # Create the web client client = dicomweb_client.DICOMwebClient( url, # The following are optional keys qido_url_prefix=info.get('qido_prefix'), wado_url_prefix=info.get('wado_prefix'), session=info.get('session'), ) wsidicom_client = wsidicom.WsiDicomWebClient(client) # Identify the transfer syntax transfer_syntax = self._identify_dicomweb_transfer_syntax(client, study_uid, series_uid) # Open the WSI DICOMweb file return wsidicom.WsiDicom.open_web(wsidicom_client, study_uid, series_uid, requested_transfer_syntax=transfer_syntax) def _identify_dicomweb_transfer_syntax(self, client, study_uid, series_uid): # "client" is a dicomweb_client.DICOMwebClient # This is how we select the JPEG type to return # The available transfer syntaxes used by wsidicom may be found here: # # (we may need to update this if they add more options) # FIXME: maybe this function better belongs upstream in `wsidicom`? from pydicom.uid import JPEG2000, JPEG2000Lossless, JPEGBaseline8Bit, JPEGExtended12Bit # Prefer the transfer syntaxes in this order. transfer_syntax_preferred_order = [ JPEGBaseline8Bit, JPEGExtended12Bit, JPEG2000, JPEG2000Lossless, ] available_transfer_syntax_tag = dicom_key_to_tag('AvailableTransferSyntaxUID') # Access the dicom web client, and search for one instance for the given # study and series. Check the available transfer syntaxes. result, = client.search_for_instances( study_uid, series_uid, fields=[available_transfer_syntax_tag], limit=1) if available_transfer_syntax_tag in result: available_transfer_syntaxes = result[available_transfer_syntax_tag]['Value'] for syntax in transfer_syntax_preferred_order: if syntax in available_transfer_syntaxes: return syntax else: # The server is not telling us which transfer syntaxes are available. # Print a warning, default to JPEG2000, and hope for the best. self.logger.warning( 'DICOMweb server is not communicating the available ' 'transfer syntaxes. Assuming JPEG2000...', ) return JPEG2000 msg = ( 'Could not find an appropriate transfer syntax. ' f'Available transfer syntaxes are: {available_transfer_syntaxes}' ) raise TileSourceError(msg) def __del__(self): # If we have an _unstyledInstance attribute, this is not the owner of # the _docim handle, so we can't close it. Otherwise, we need to close # it or the _dicom library may prevent shutting down. if getattr(self, '_dicom', None) is not None and not hasattr(self, '_derivedSource'): try: self._dicom.close() finally: self._dicom = None def _pathMightBeDicom(self, path): """ Return True if the path looks like it might be a dicom file based on its name or extension. :param path: the path to check. :returns: True if this might be a dicom, False otherwise. """ path = os.path.basename(path) if os.path.splitext(path)[-1][1:] in self.extensions: return True if re.match(r'^([1-9][0-9]*|0)(\.([1-9][0-9]*|0))+$', path) and len(path) <= 64: return True if re.match(r'^DCM_\d+$', path): return True return False
[docs] 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.levels[0].pixel_spacing.width or None mm_y = self._dicom.levels[0].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, }
[docs] 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
[docs] 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 = {} idx = 0 for level in self._dicom.levels: for ds in level.datasets: result.setdefault('dicom', {}) info = dicom_to_dict(ds) if not idx: result['dicom'] = info else: for k, v in info.items(): if k not in result['dicom'] or v != result['dicom'][k]: result['dicom']['%s:%d' % (k, idx)] = v idx += 1 return result
[docs] @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.levels[0].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 = np.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)
[docs] 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
[docs] def open(*args, **kwargs): """ Create an instance of the module class. """ return DICOMFileTileSource(*args, **kwargs)
[docs] def canRead(*args, **kwargs): """ Check if an input can be read by the module class. """ return DICOMFileTileSource.canRead(*args, **kwargs)