Merge pull request #123 from mehta-lab/zarr-converter-position-bug

Fix ome-tif to zarr converter for acquisitions with micromanager beta
mehta-lab · Jul 8, 2022 · 32edad9 · 32edad9
2 parents 3019357 + 031d577
commit 32edad9
Showing 1 changed file with 4 additions and 2 deletions.
diff --git a/recOrder/io/zarr_converter.py b/recOrder/io/zarr_converter.py
@@ -250,7 +250,10 @@ def _get_position_names(self):
 
  for p in range(self.p):
  if self.p > 1:
- name = self.summary_metadata['StagePositions'][p]['Label']
+ try:
+ name = self.summary_metadata['StagePositions'][p]['Label']
+ except KeyError:
+ name = ''
  else:
  name = ''
  self.pos_names.append(name)
@@ -331,7 +334,6 @@ def init_zarr_structure(self):
 
  chan_names = self._get_channel_names()
  self._get_position_names()
-
  for pos in range(self.p):
 
  clims = self.get_channel_clims(pos)