added option in CLI to only calculate qc and skip staging

Author: VictorDidier

macsima2mc/CLI.py

@@ -63,6 +63,12 @@ def get_args():
                     help='measure features of contrast, intensity and sharpness of each image'
                     )
 
+    parser.add_argument('-oqc',
+                    '--only_qc_file',
+                    action='store_true',
+                    help='skips the stacking of the tiles and only calculates the qc table. Still flag -wt is required to write the table. '
+                    )
+    
     parser.add_argument('-wt',
                     '--write_table',
                     action='store_true',

macsima2mc/macsima2mc.py

@@ -21,32 +21,30 @@ def main():
     cycle_info = tools.append_metadata( cycle_info )
 
     # Create stack
-    output_dirs = tools.create_stack(cycle_info,
+    cycle_number=int(cycle_info['cycle'].unique()[0])
+    if args.only_qc_file:
+        pass
+    else:
+        output_dirs = tools.create_stack(cycle_info,
                                      output,
                                      ref_marker=ref,
                                      hi_exp=args.hi_exposure_only,
                                      ill_corr=basicpy_corr,
                                      out_folder=out_folder_name)
-    # Save markers file in each output directory
-    for path in output_dirs:
-        mc_tools.write_markers_file(path,args.remove_reference_marker)
+        # Save markers file in each output directory
+        for path in output_dirs:
+            mc_tools.write_markers_file(path,args.remove_reference_marker)
 
-    cycle_number=int(cycle_info['cycle'].unique()[0])
-    message_1='staging for cycle {c} is done'.format( c=f'{ cycle_number:03d}' )
-    print(message_1)
     # Calculate and append ome metadata info contained in each file
-    if args.qc_metrics:
+    if (args.qc_metrics or args.only_qc_file) :
         import qc
-        print("image qc is being calculated")
         cycle_info=qc.append_qc(cycle_info)
 
     if args.write_table:
         qc_output_dir=output / "cycle_info"
         qc_output_dir.mkdir(parents=True, exist_ok=True)
         cycle_info.to_csv( qc_output_dir / 'cycle_{c}.csv'.format( c=f'{ cycle_number:03d}' ), index=False )
 
-    
-        
 
 if __name__ == '__main__':
     main()

macsima2mc/mc_tools.py

@@ -103,7 +103,7 @@ def write_markers_file( data_path, rm_ref_marker,ref_marker='DAPI'):
     if rm_ref_marker:
         earliest_cycle=mks_file_df['cycle_number'].min()
         condition=( mks_file_df['marker_name']== ref_marker ) & ( mks_file_df['cycle_number']>earliest_cycle ) 
-        mks_file_df.loc[ condition , ['remove'] ]=True
+        mks_file_df.loc[ condition , ['remove'] ]='TRUE'
 
     mks_file_df.to_csv( data_path.parent.absolute() / 'markers.csv' , index=False )