Harden reading with tifffile on images with bad axes information

CHANGELOG.md

@@ -6,6 +6,7 @@
 - Harden when the bioformats reader claims it has a zero sized image ([#1268](../../pull/1268))
 - Harden internal retiling.  This sometimes affected histograms ([#1269](../../pull/1269))
 - Set annotation update user in client so it appears faster ([#1270](../../pull/1270))
+- Harden reading with tifffile on images with bad axes information ([#1273](../../pull/1273))
 
 ### Changes
 - Adjust tifffile log level ([#1265](../../pull/1265))

sources/tifffile/large_image_source_tifffile/__init__.py

@@ -89,7 +89,7 @@ class TifffileFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
     _minAssociatedImageSize = 64
     _maxAssociatedImageSize = 8192
 
-    def __init__(self, path, **kwargs):
+    def __init__(self, path, **kwargs):  # noqa
         """
         Initialize the tile class.  See the base class for other available
         parameters.
@@ -146,6 +146,15 @@ def __init__(self, path, **kwargs):
                     getattr(self._tf, key)):
                 getattr(self, '_handle_' + key[3:])()
         self._populatedLevels = len(self._baseSeries.levels)
+        # Some files have their axes listed in the wrong order.  Try to access
+        # the lastmost pixel; if that fails, probably the axes and shape don't
+        # match the file (or the file is corrupted).
+        try:
+            self.getPixel(region={'left': self.sizeX - 1, 'top': self.sizeY - 1},
+                          frame=self.frames - 1)
+        except Exception:
+            msg = 'File cannot be opened via tifffile: axes and shape do not match access pattern.'
+            raise TileSourceError(msg)
 
     def _biggestSeries(self):
         """

test/datastore.py

@@ -96,6 +96,8 @@
     'synthetic_qptiff.qptiff': 'sha512:652e61c650bcc57beeb2f89b8fa9ac4ba44ce5c0b48c5d3c6fb40ca539b015e36fe831ea5abd95d5650ec342de6a4207a9c22d410f5e2d8bfafbf19e2a6d5d96',  # noqa
     # Blank imageJ file with multiple channels
     'synthetic_imagej.tiff': 'sha512:f4fcf9633b7fc8c819aace248352b3ef89364418d734aa8326096829d64956f11b961c24003bd5ca1f7e46462a8230b64177b37b1517a416d7c7123a0932d5dc',  # noqa
+    # Blank untiled tiff with bad tifffile axes information
+    'bad_axes_description.tif': 'sha512:cbe82614a83d315a2f22c32b14fd32560fadb3f263bfeffc75f42f88e535e8a11728f691499cb7f5714bbbc55938c472ee4a706d7281bdfefe6fdb965c0a2d6b',  # noqa
 }
 
 

test/test_source_base.py

@@ -60,7 +60,7 @@
     '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)',  # noqa
+        'noread': r'(oahu|DDX58_AXL|huron\.image2_jpeg2k|landcover_sample|d042-353\.crop|US_Geo\.|extraoverview|imagej|bad_axes)',  # noqa
         'skipTiles': r'one_layer_missing',
     },
     'pil': {
@@ -78,11 +78,11 @@
         'read': r'\.(ptif|scn|svs|tif.*|qptiff)$',
         'noread': r'(oahu|DDX58_AXL|G10-3_pelvis_crop|'
                   r'd042-353\.crop\.small\.float|landcover_sample|US_Geo\.|'
-                  r'imagej)',
+                  r'imagej|bad_axes)',
         'skipTiles': r'(sample_image\.ptif|one_layer_missing_tiles)'},
     'tifffile': {
         'read': r'',
-        'noread': r'\.(nc|nd2|yml|yaml|json|czi|png|jpg|jpeg|jp2|dcm)$',
+        'noread': r'((\.(nc|nd2|yml|yaml|json|czi|png|jpg|jpeg|jp2|dcm)$)|bad_axes)',
         'python': sys.version_info >= (3, 7),
     },
     'vips': {