Merge pull request #903 from girder/harden-tifffile

Harden tifffile source

CHANGELOG.md

@@ -3,8 +3,9 @@
 ## 1.16.0
 
 ### Features
-- Add a tifffile tile source ([885](../../pull/885), [896](../../pull/896))
+- Add a tifffile tile source ([885](../../pull/885), [896](../../pull/896), [903](../../pull/903))
 - Added a canReadList method to large_image to show which source can be used ([895](../../pull/895))
+- Optionally show metadata in item lists ([901](../../pull/901))
 
 ### Improvements
 - Pass options to the annotationLayer mode ([881](../../pull/881))

sources/tifffile/large_image_source_tifffile/__init__.py

@@ -95,17 +95,7 @@ def __init__(self, path, **kwargs):
             if not os.path.isfile(self._largeImagePath):
                 raise TileSourceFileNotFoundError(self._largeImagePath) from None
             raise TileSourceError('File cannot be opened via tifffile.')
-        # Find the series with the most pixels.  Use all series that have the
-        # same dimensionality and resolution.  They can differ in X, Y size.
-        maxseries = None
-        maxsamples = 0
-        for idx, s in enumerate(self._tf.series):
-            samples = numpy.prod(s.shape)
-            if samples > maxsamples and 'X' in s.axes and 'Y' in s.axes:
-                maxseries = idx
-                maxsamples = samples
-        if maxseries is None:
-            raise TileSourceError('File cannot be opened via tifffile source.')
+        maxseries, maxsamples = self._biggestSeries()
         self.tileWidth = self.tileHeight = self._tileSize
         s = self._tf.series[maxseries]
         self._baseSeries = s
@@ -136,6 +126,29 @@ def __init__(self, path, **kwargs):
                     getattr(self._tf, key)):
                 getattr(self, '_handle_' + key[3:])()
 
+    def _biggestSeries(self):
+        """
+        Find the series with the most pixels.  Use all series that have the
+        same dimensionality and resolution.  They can differ in X, Y size.
+
+        :returns: index of the largest series, number of pixels in a frame in
+            that series.
+        """
+        maxseries = None
+        maxsamples = 0
+        try:
+            for idx, s in enumerate(self._tf.series):
+                samples = numpy.prod(s.shape)
+                if samples > maxsamples and 'X' in s.axes and 'Y' in s.axes:
+                    maxseries = idx
+                    maxsamples = samples
+        except Exception as exc:
+            self.logger.debug('Cannot use tifffile: %r', exc)
+            maxseries = None
+        if maxseries is None:
+            raise TileSourceError('File cannot be opened via tifffile source.')
+        return maxseries, maxsamples
+
     def _findMatchingSeries(self):
         """
         Given a series in self._baseSeries, find other series that have the