Read more OME Tiff files.

girder · Jul 30, 2020 · c8b84c1 · c8b84c1
1 parent 31bfb29
commit c8b84c1
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Showing 2 changed files with 11 additions and 6 deletions.
diff --git a/sources/ometiff/large_image_source_ometiff/__init__.py b/sources/ometiff/large_image_source_ometiff/__init__.py
@@ -114,7 +114,7 @@ def __init__(self, path, **kwargs):
         self._omeLevels = [omebylevel.get(key) for key in range(max(omebylevel.keys()) + 1)]
         if base._tiffInfo.get('istiled'):
             self._tiffDirectories = [
-                TiledTiffDirectory(largeImagePath, int(entry['TiffData'][0]['IFD']))
+                TiledTiffDirectory(largeImagePath, int(entry['TiffData'][0].get('IFD', 0)))
                 if entry else None
                 for entry in self._omeLevels]
         else:
@@ -190,16 +190,20 @@ def _parseOMEInfo(self):
                 img['Pixels']['TiffData'] = [img['Pixels']['TiffData']]
             if isinstance(img['Pixels'].get('Plane'), dict):
                 img['Pixels']['Plane'] = [img['Pixels']['Plane']]
+            if isinstance(img['Pixels'].get('Channels'), dict):
+                img['Pixels']['Channels'] = [img['Pixels']['Channels']]
         try:
             self._omebase = self._omeinfo['Image'][0]['Pixels']
             if ((not len(self._omebase['TiffData']) or
                     len(self._omebase['TiffData']) == 1) and
-                    len(self._omebase['Plane'])):
+                    (len(self._omebase.get('Plane', [])) or
+                     len(self._omebase.get('Channel', [])))):
                 if not len(self._omebase['TiffData']) or self._omebase['TiffData'][0] == {}:
-                    self._omebase['TiffData'] = self._omebase['Plane']
+                    self._omebase['TiffData'] = self._omebase.get(
+                        'Plane', self._omebase.get('Channel'))
                 elif (int(self._omebase['TiffData'][0].get('PlaneCount', 0)) ==
-                        len(self._omebase['Plane'])):
-                    planes = copy.deepcopy(self._omebase['Plane'])
+                        len(self._omebase.get('Plane', self._omebase.get('Channel', [])))):
+                    planes = copy.deepcopy(self._omebase.get('Plane', self._omebase.get('Channel')))
                     for idx, plane in enumerate(planes):
                         plane['IFD'] = plane.get(
                             'IFD', int(self._omebase['TiffData'][0].get('IFD', 0)) + idx)

diff --git a/sources/tiff/large_image_source_tiff/tiff_reader.py b/sources/tiff/large_image_source_tiff/tiff_reader.py
@@ -133,7 +133,8 @@ def __init__(self, filePath, directoryNum, mustBeTiled=True, subDirectoryNum=0,
         self._open(filePath, directoryNum, subDirectoryNum)
         self._loadMetadata()
         config.getConfig('logger').debug(
-            'TiffDirectory %d:%d Information %r', directoryNum, subDirectoryNum, self._tiffInfo)
+            'TiffDirectory %d:%d Information %r',
+            directoryNum, subDirectoryNum or 0, self._tiffInfo)
         try:
             if validate:
                 self._validate()