PSF path only required for deconvolution

aicjanelia · Nov 5, 2024 · 63d136d · 63d136d
1 parent 5539ae9
commit 63d136d
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Showing 2 changed files with 4 additions and 4 deletions.
diff --git a/src/python/llsm-pipeline.py b/src/python/llsm-pipeline.py
@@ -17,7 +17,7 @@
 import settings2json
 
 def parse_args():
-    parser = argparse.ArgumentParser(description='Batch deskewing, deconvolution, and mip script for LLSM images.')
+    parser = argparse.ArgumentParser(description='Batch processing script for LLSM images.')
     parser.add_argument('input', type=Path, help='path to configuration JSON file')
     parser.add_argument('--dry-run', '-d', default=False, action='store_true', dest='dryrun',help='execute without submitting any bsub jobs')
     parser.add_argument('--verbose', '-v', default=False, action='store_true', dest='verbose',help='print details (including commands to bsub)')
@@ -571,7 +571,7 @@ def process(dirs, configs, dryrun=False, verbose=False):
 
     # get all directories containing a Settings files
     excludes = list(processed_json)
-    if configs['paths']['psf']['dir'] != None:
+    if 'psf' in configs['paths']:
         excludes.append(str(root_dir / configs['paths']['psf']['dir']))
 
     unprocessed_dirs = get_dirs(root_dir, excludes)

diff --git a/src/python/mosaic-pipeline.py b/src/python/mosaic-pipeline.py
@@ -17,7 +17,7 @@
 import mosaicsettings2json
 
 def parse_args():
-    parser = argparse.ArgumentParser(description='Batch deskewing, deconvolution, and mip script for MOSAIC images.')
+    parser = argparse.ArgumentParser(description='Batch processing script for MOSAIC images.')
     parser.add_argument('input', type=Path, help='path to configuration JSON file')
     parser.add_argument('--dry-run', '-d', default=False, action='store_true', dest='dryrun',help='execute without submitting any bsub jobs')
     parser.add_argument('--verbose', '-v', default=False, action='store_true', dest='verbose',help='print details (including commands to bsub)')
@@ -775,7 +775,7 @@ def process(dirs, configs, dryrun=False, verbose=False):
 
     # get all directories containing a Settings files
     excludes = list(processed_json)
-    if configs['paths']['psf']['dir'] != None:
+    if 'psf' in configs['paths']:
         excludes.append(str(root_dir / configs['paths']['psf']['dir']))
 
     unprocessed_dirs = get_dirs(root_dir, excludes)