Fix an issue when tifffile reports no key frame

CHANGELOG.md

@@ -1,5 +1,10 @@
 # Change Log
 
+## 1.26.3
+
+### Bug Fixes
+- Fix an issue when tifffile reports no key frame ([#1396](../../pull/1396))
+
 ## 1.26.2
 
 ### Improvements
@@ -436,6 +441,7 @@
 ### Bug Fixes
 - Use open.read rather than download to access files in Girder ([#989](../../pull/989))
 - Fix nd2 source scale ([#990](../../pull/990))
+- Do not raise a login request when checking if the user can write annotations ([#991](../../pull/991))
 
 ## 1.17.3
 

sources/tifffile/large_image_source_tifffile/__init__.py

@@ -238,10 +238,10 @@ def _findAssociatedImages(self):
         Find associated images from unused pages and series.
         """
         pagesInSeries = [p for s in self._tf.series for ll in s.pages.levels for p in ll.pages]
-        hashes = [p.hash for p in pagesInSeries if p.keyframe is not None]
+        hashes = [p.hash for p in pagesInSeries if getattr(p, 'keyframe', None) is not None]
         self._associatedImages = {}
         for p in self._tf.pages:
-            if (p not in pagesInSeries and p.keyframe is not None and
+            if (p not in pagesInSeries and getattr(p, 'keyframe', None) is not None and
                     p.hash not in hashes and not len(set(p.axes) - set('YXS'))):
                 id = 'image_%s' % p.index
                 entry = {'page': p.index}

test/datastore.py

@@ -106,6 +106,8 @@
     'synthetic_multiaxis.zarr.zip': 'sha512:95da53061bd09deaf4357e745404780d78a0949935f82c10ee75237e775345caace18fad3f05c3452ba36efca6b3ed58d815d041f33197497ab53d2c80b9e2ac',  # noqa
     # Single flat array zarr
     'flat2.zarr.zip': 'sha512:c49ff5fbfa73615da4c2a7c8602723297d604892b848860a068ab200245eec6c4f638f35d0b40cde0233c55faa6dc4e46351a841b481211f36dc5fb43765d818',  # noqa
+    # OME tiff where tifffile reports no keyframe
+    'test_nokeyframe.ome.tiff': 'sha512:e810420ece0688bf4e1c347ef7e172a303a9cb3f0d56efc3d0068ec40decf05d2588b01a3f5ac9857ccf8f3d088819e532148488f30ad693d6d79c1aa66115d7',  # noqa
 }
 
 

test/test_source_base.py

@@ -38,11 +38,13 @@
     'gdal': {
         'read': r'\.(jpg|jpeg|jp2|ptif|scn|svs|tif.*|qptiff)$',
         'noread': r'(huron\.image2_jpeg2k|sample_jp2k_33003|TCGA-DU-6399|\.(ome.tiff|nc)$)',
+        'skip': r'nokeyframe\.ome\.tiff$',
         'skipTiles': r'\.*nc$',
     },
     'mapnik': {
         'read': r'\.(jpg|jpeg|jp2|ptif|nc|scn|svs|tif.*|qptiff)$',
         'noread': r'(huron\.image2_jpeg2k|sample_jp2k_33003|TCGA-DU-6399|\.(ome.tiff)$)',
+        'skip': r'nokeyframe\.ome\.tiff$',
         # we should only test this with a projection
         'skipTiles': r'',
     },
@@ -53,11 +55,15 @@
     'nd2': {
         'read': r'\.(nd2)$',
     },
-    'ometiff': {'read': r'\.(ome\.tif.*)$'},
+    'ometiff': {
+        'read': r'\.(ome\.tif.*)$',
+        'noread': r'nokeyframe\.ome\.tiff$',
+    },
     'openjpeg': {'read': r'\.(jp2)$'},
     'openslide': {
         'read': r'\.(ptif|svs|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',
     },
     'pil': {
@@ -67,13 +73,14 @@
     'rasterio': {
         'read': r'\.(jpg|jpeg|jp2|ptif|scn|svs|tif.*|qptiff)$',
         'noread': r'(huron\.image2_jpeg2k|sample_jp2k_33003|TCGA-DU-6399|\.(ome.tiff|nc)$)',
+        'skip': r'nokeyframe\.ome\.tiff$',
     },
     'test': {'any': True, 'skipTiles': r''},
     'tiff': {
         'read': r'\.(ptif|scn|svs|tif.*|qptiff)$',
         'noread': r'(oahu|DDX58_AXL|G10-3_pelvis_crop|'
                   r'd042-353\.crop\.small\.float|landcover_sample|US_Geo\.|'
-                  r'imagej|bad_axes)',
+                  r'imagej|bad_axes|nokeyframe\.ome\.tiff$)',
         'skipTiles': r'(sample_image\.ptif|one_layer_missing_tiles)'},
     'tifffile': {
         'read': r'',