Merge pull request #1473 from girder/ndpi-test-file

Add a synthetic ndpi test file
girder · Mar 8, 2024 · dad17a8 · dad17a8
2 parents 8730233 + 8037060
commit dad17a8
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Showing 2 changed files with 8 additions and 6 deletions.
diff --git a/test/datastore.py b/test/datastore.py
@@ -112,6 +112,8 @@
     'd4db7ae6-1344-467e-8380-4ce13cc3f59e.dcm': 'sha512:48cb562b94d0daf4060abd9eef150c851d3509d9abbff4bea11d00832955720bf1941073a51e6fb68fb5cc23704dec2659fc0c02360a8ac753dc523dca2c8c36',  # noqa
     '18f6378f-433c-42bf-9373-1ff9c808c118.dcm': 'sha512:36432183380eb7d44417a2210a19d550527abd1181255e19ed5c1d17695d8bb8ca42f5b426a63fa73b84e0e17b770401a377ae0c705d0ed7fdf30d571ef60e2d',  # noqa
     'a131592c-a069-4aa7-8031-398654aa8a3d.dcm': 'sha512:99bd3da4b8e11ce7b4f7ed8a294ed0c37437320667a06c40c383f4b29be85fe8e6094043e0600bee0ba879f2401de4c57285800a4a23da2caf2eb94e5b847ee0',  # noqa
+    # Synthetic newer ndpi with binary data and nonblank image labelled as RGB
+    'synthetic_ndpi_2024.ndpi': 'sha512:192cdcf551a824277ef70358b8ed6225dca0c5b5d0817fe0d800b72638e0ad9416cd5bc40cb186219da60fd324b676d1b32cc05a276a33b71b485d665a31e42e',  # noqa
 }
 
 

diff --git a/test/test_source_base.py b/test/test_source_base.py
@@ -23,7 +23,7 @@
 # a download order.
 SourceAndFiles = {
     'bioformats': {
-        'read': r'(\.(czi|jp2|svs|scn|dcm|qptiff)|[0-9a-f].*\.dcm)$',
+        'read': r'(\.(czi|jp2|svs|scn|dcm|qptiff|ndppi)|[0-9a-f].*\.dcm)$',
         'noread': r'JK-kidney_B',
         'skip': r'TCGA-AA-A02O.*\.svs',
         # We need to modify the bioformats reader similar to tiff's
@@ -36,13 +36,13 @@
     },
     'dummy': {'any': True, 'skipTiles': r''},
     'gdal': {
-        'read': r'(\.(jpg|jpeg|jp2|ptif|scn|svs|tif.*|qptiff)|18[-0-9a-f]{34}\.dcm)$',
+        'read': r'(\.(jpg|jpeg|jp2|ptif|scn|svs|ndpi|tif.*|qptiff)|18[-0-9a-f]{34}\.dcm)$',
         'noread': r'(huron\.image2_jpeg2k|sample_jp2k_33003|TCGA-DU-6399|\.(ome.tiff|nc)$)',
         'skip': r'nokeyframe\.ome\.tiff$',
         'skipTiles': r'\.*nc$',
     },
     'mapnik': {
-        'read': r'(\.(jpg|jpeg|jp2|ptif|nc|scn|svs|tif.*|qptiff)|18[-0-9a-f]{34}\.dcm)$',
+        'read': r'(\.(jpg|jpeg|jp2|ptif|nc|scn|svs|ndpi|tif.*|qptiff)|18[-0-9a-f]{34}\.dcm)$',
         'noread': r'(huron\.image2_jpeg2k|sample_jp2k_33003|TCGA-DU-6399|\.(ome.tiff)$)',
         'skip': r'nokeyframe\.ome\.tiff$',
         # we should only test this with a projection
@@ -61,7 +61,7 @@
     },
     'openjpeg': {'read': r'\.(jp2)$'},
     'openslide': {
-        'read': r'\.(ptif|svs|tif.*|qptiff|dcm)$',
+        'read': r'\.(ptif|svs|ndpi|tif.*|qptiff|dcm)$',
         'noread': r'(oahu|DDX58_AXL|huron\.image2_jpeg2k|landcover_sample|d042-353\.crop|US_Geo\.|extraoverview|imagej|bad_axes)',  # noqa
         'skip': r'nokeyframe\.ome\.tiff$',
         'skipTiles': r'one_layer_missing',
@@ -71,7 +71,7 @@
         'noread': r'(G10-3|JK-kidney|d042-353.*tif|huron|one_layer_missing|US_Geo|extraoverview)',  # noqa
     },
     'rasterio': {
-        'read': r'(\.(jpg|jpeg|jp2|ptif|scn|svs|tif.*|qptiff)|18[-0-9a-f]{34}\.dcm)$',
+        'read': r'(\.(jpg|jpeg|jp2|ptif|scn|svs|ndpi|tif.*|qptiff)|18[-0-9a-f]{34}\.dcm)$',
         'noread': r'(huron\.image2_jpeg2k|sample_jp2k_33003|TCGA-DU-6399|\.(ome.tiff|nc)$)',
         'skip': r'nokeyframe\.ome\.tiff$',
     },
@@ -84,7 +84,7 @@
         'skipTiles': r'(sample_image\.ptif|one_layer_missing_tiles)'},
     'tifffile': {
         'read': r'',
-        'noread': r'((\.(nc|nd2|yml|yaml|json|czi|png|jpg|jpeg|jp2|zarr\.db|zarr\.zip)|(nokeyframe\.ome\.tiff|XY01\.ome\.tif|level.*\.dcm)$)' +  # noqa
+        'noread': r'((\.(nc|nd2|yml|yaml|json|czi|png|jpg|jpeg|jp2|ndpi|zarr\.db|zarr\.zip)|(nokeyframe\.ome\.tiff|XY01\.ome\.tif|level.*\.dcm)$)' +  # noqa
                   (r'|bad_axes' if sys.version_info < (3, 9) else '') +
                   r')',
     },