This tests reading dicom wsi using the dicomslide library. For files generated with wsi2dcm, this augments and modifies some data to conform to what dicomslide expects. If invalid UIDs are present, it will still fail.

dstest.py

import logging
import sys

import dicomslide
import dicomweb_client
import pydicom

dslog = logging.getLogger('dicomslide')
# dslog.addHandler(logging.StreamHandler(sys.stderr))
# dslog.setLevel(logging.WARN)


root = '/mnt/data2/dicom/sample3' if len(sys.argv) < 2 else sys.argv[1]

c = dicomweb_client.DICOMfileClient(
    url='file://' + root,
    in_memory=True, recreate_db=True)
c_retrieve_instance_metadata = c.retrieve_instance_metadata


def ditag(key):
    return '%08X' % pydicom.datadict.tag_for_keyword(key)


defaultTags = {
    ditag('ContainerIdentifier'): {'vr': 'LO', 'Value': ['1']},
    ditag('OpticalPathSequence'): {
        'vr': 'SQ', 'Value': [{
            '00220016': {'vr': 'SQ', 'Value': [{
                '00080100': {'vr': 'SH', 'Value': ['111744']},
                '00080102': {'vr': 'SH', 'Value': ['DCM']},
                '00080104': {'vr': 'LO', 'Value': ['Brightfield illumination']}}]},
            '00480106': {'vr': 'SH', 'Value': ['1']},
            '00480108': {'vr': 'SQ', 'Value': [{
                '00080100': {'vr': 'SH', 'Value': ['414298005']},
                '00080102': {'vr': 'SH', 'Value': ['SCT']},
                '00080104': {'vr': 'LO', 'Value': ['Full spectrum']}}]},
        }]},
    ditag('TotalPixelMatrixOriginSequence'): {
        'vr': 'SQ', 'Value': [{
            '0040072A': {'vr': 'DS', 'Value': [0.0]},
            '0040073A': {'vr': 'DS', 'Value': [0.0]}
        }]},
    ditag('TotalPixelMatrixFocalPlanes'): {'vr': 'UL', 'Value': [1]},
}


def retrieve_instance_metadata(*args, **kwargs):
    metadata = c_retrieve_instance_metadata(*args, **kwargs)
    # print('>', metadata)
    anySet = False
    for tag, value in defaultTags.items():
        if tag not in metadata:
            metadata[tag] = value
            anySet = True
    if anySet:
        metadata[ditag('FrameOfReferenceUID')]['Value'][0] = metadata[
            ditag('FrameOfReferenceUID')]['Value'][0].rsplit('.', 1)[0]
    return metadata


c.retrieve_instance_metadata = retrieve_instance_metadata
try:
    for idx, slide in enumerate(dicomslide.find_slides(c)):
        print('-- Slide %d (%s):' % (idx, root))
        print(slide)
        print('Channels:', slide.num_channels)
        print('Focal planes:', slide.num_focal_planes)
        print('Levels:', slide.num_levels)
        print('Dimensions:', slide.total_pixel_matrix_dimensions)
        print('Downsampling:', slide.downsampling_factors)
        print('Label images:', slide.label_images)
        print('Volume image 0,0:', slide.get_volume_images(channel_index=0, focal_plane_index=0))
except Exception:
    print('XX Exception of %s' % root)