From 7eeaedfe8fdc835e1bfc9b83ace1b540faf15597 Mon Sep 17 00:00:00 2001
From: David Manthey <david.manthey@kitware.com>
Date: Wed, 29 Jul 2020 16:02:54 -0400
Subject: [PATCH] Read more OME Tiff files.

---
 .../large_image_source_ometiff/__init__.py    | 24 +++++++++++++------
 .../large_image_source_tiff/tiff_reader.py    |  3 ++-
 2 files changed, 19 insertions(+), 8 deletions(-)

diff --git a/sources/ometiff/large_image_source_ometiff/__init__.py b/sources/ometiff/large_image_source_ometiff/__init__.py
index 1e1e29333..d93eff6f7 100644
--- 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:
@@ -182,7 +182,7 @@ def _checkForOMEZLoop(self, largeImagePath):
         info['Image']['Pixels']['PlanesFromZloop'] = 'true'
         info['Image']['Pixels']['SizeZ'] = str(zloop)
 
-    def _parseOMEInfo(self):
+    def _parseOMEInfo(self):  # noqa
         if isinstance(self._omeinfo['Image'], dict):
             self._omeinfo['Image'] = [self._omeinfo['Image']]
         for img in self._omeinfo['Image']:
@@ -190,20 +190,28 @@ 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 isinstance(self._omebase.get('Plane'), dict):
+                self._omebase['Plane'] = [self._omebase['Plane']]
             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)
                     self._omebase['TiffData'] = planes
+            if isinstance(self._omebase['TiffData'], dict):
+                self._omebase['TiffData'] = [self._omebase['TiffData']]
             if len({entry.get('UUID', {}).get('FileName', '')
                     for entry in self._omebase['TiffData']}) > 1:
                 raise TileSourceException('OME Tiff references multiple files')
@@ -211,8 +219,10 @@ def _parseOMEInfo(self):
                     int(self._omebase['SizeT']) * int(self._omebase['SizeZ']) or
                     len(self._omebase['TiffData']) != len(
                         self._omebase.get('Plane', self._omebase['TiffData']))):
-                raise TileSourceException('OME Tiff contains frames that contain multiple planes')
+                raise TileSourceException(
+                    'OME Tiff contains frames that contain multiple planes')
         except (KeyError, ValueError, IndexError):
+            print('B')
             raise TileSourceException('OME Tiff does not contain an expected record')
 
     def getMetadata(self):
diff --git a/sources/tiff/large_image_source_tiff/tiff_reader.py b/sources/tiff/large_image_source_tiff/tiff_reader.py
index f11231571..2fbc3d747 100644
--- 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()