Merge pull request #13 from filippocastelli/pyproject

omexml.py refactor, Channel bugfix in OMETIFFReader
filippocastelli · Feb 3, 2024 · b473d43 · b473d43
2 parents a24c5f9 + 924d095
commit b473d43
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Showing 3 changed files with 398 additions and 404 deletions.
diff --git a/pyometiff/omereader.py b/pyometiff/omereader.py
@@ -163,7 +163,11 @@ def parse_metadata(self, omexml_string):
             metadata["ObjMag"] = None
 
         # get channel names
-        metadata["Channels"] = self._parse_channels(metadata["SizeC"], self.ox, self.imageseries)
+        try:
+            metadata["Channels"] = self._parse_channels(metadata["SizeC"], self.ox, self.imageseries)
+        except (KeyError, AttributeError, IndexError) as e:
+            metadata["Channels"] = None
+
         # for c in range(metadata["SizeC"]):
         #     channel_names.append(
         #         self.ox.image(self.imageseries).Pixels.Channel(c).Name

diff --git a/pyometiff/omewriter.py b/pyometiff/omewriter.py
@@ -121,7 +121,7 @@ def write_stack(self, array, xml_meta):
             logging.warning("array size is larger than 4GB, using BigTIFF")
 
         with tifffile.TiffWriter(str(self.fpath), bigtiff=use_bigtiff) as tif:
-            tif.save(
+            tif.write(
                 array, description=xml_meta, photometric=self.photometric, metadata=None, compression=self.compression
             )