From 44d57f0cb135cb32d61e5c1b814be358b87a3826 Mon Sep 17 00:00:00 2001 From: Ian Dryg Date: Thu, 17 Oct 2024 15:19:02 -0700 Subject: [PATCH 1/2] Updated SizeC and plane_count in halo_mif_tiff.py --- omeify/inputs/halo_mif_tiff.py | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/omeify/inputs/halo_mif_tiff.py b/omeify/inputs/halo_mif_tiff.py index 4d2a00b..51b5eda 100644 --- a/omeify/inputs/halo_mif_tiff.py +++ b/omeify/inputs/halo_mif_tiff.py @@ -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 @@ -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 \ No newline at end of file + return channel_features From 188585776e0592bb37d77f96cf57ba24ec550173 Mon Sep 17 00:00:00 2001 From: Ian Dryg Date: Thu, 17 Oct 2024 15:27:01 -0700 Subject: [PATCH 2/2] Update raw2ometiff_converter.py --- omeify/converters/raw2ometiff_converter.py | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/omeify/converters/raw2ometiff_converter.py b/omeify/converters/raw2ometiff_converter.py index ec46bab..3b323e5 100644 --- a/omeify/converters/raw2ometiff_converter.py +++ b/omeify/converters/raw2ometiff_converter.py @@ -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"))