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Updated HaloMIFTiff to work with newer version of HALO #2

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Updated HaloMIFTiff to work with newer version of HALO #2

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44d57f0
Updated SizeC and plane_count in halo_mif_tiff.py
iddryg Oct 17, 2024
1885857
Update raw2ometiff_converter.py
iddryg Oct 17, 2024
a09ab68
Merge branch 'jason-weirather:master' into master
iddryg Oct 17, 2024
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7 changes: 6 additions & 1 deletion omeify/converters/raw2ometiff_converter.py
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Original file line number Diff line number Diff line change
Expand Up @@ -62,7 +62,12 @@ def _run_raw2ometiff(self,output_path,rgb,compression):

if self.logger.isEnabledFor(logging.INFO):
self.logger.info("Executing raw2ometiff conversion...")
process = subprocess.run(cmd, check=True, stdout=stdout_setting, stderr=stderr_setting)

#process = subprocess.run(cmd, check=True, stdout=stdout_setting, stderr=stderr_setting)
try:
process = subprocess.run(cmd, check=True, stdout=stdout_setting, stderr=stderr_setting)
except subprocess.CalledProcessError as e:
print(f"Command failed with exit code {e.returncode}: {e.stderr}")

if self.logger.isEnabledFor(logging.WARNING) and process.stderr:
self.logger.error(process.stderr.decode("utf-8"))
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10 changes: 7 additions & 3 deletions omeify/inputs/halo_mif_tiff.py
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Expand Up @@ -60,11 +60,15 @@ def size_y(self):
@property
def size_c(self):
# Implement the platform-specific logic for retrieving the size_c here
return len(self.report['series'][self.series]['levels'][0]['pages'])
#return len(self.report['series'][self.series]['levels'][0]['pages'])
return self.image_description['OME']\
['Image']['Pixels']['@SizeC']

@property
def plane_count(self):
return len(self.report['series'][self.series]['levels'][0]['pages'])
#return len(self.report['series'][self.series]['levels'][0]['pages'])
return self.image_description['OME']\
['Image']['Pixels']['@SizeZ']

# Override the channels property
@property
Expand All @@ -84,4 +88,4 @@ def channels(self):
for k, v in list(d.items()):
d[replacement.get(k, k)] = d.pop(k)

return channel_features
return channel_features