Implemented a --force option to automatically ignore previous RABIES …

…outputs.
CoBrALab · Sep 25, 2023 · a7262d7 · a7262d7
1 parent 32f3461
commit a7262d7
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Showing 3 changed files with 40 additions and 6 deletions.
diff --git a/rabies/parser.py b/rabies/parser.py
@@ -156,6 +156,14 @@ def get_parser():
             "(default: %(default)s)\n"
             "\n"
         )
+    g_execution.add_argument(
+        "-f", "--force", dest='force', action='store_true',
+        help=
+            "The pipeline will not stop if previous outputs are encountered. \n"
+            "Previous outputs will be overwritten.\n"
+            "(default: %(default)s)\n"
+            "\n"
+        )
 
 
     ####Preprocessing

diff --git a/rabies/run_main.py b/rabies/run_main.py
@@ -79,12 +79,13 @@ def execute_workflow(args=None):
 
 def prep_logging(opts, output_folder):
     cli_file = f'{output_folder}/rabies_{opts.rabies_stage}.pkl'
-    if os.path.isfile(cli_file):
+    if os.path.isfile(cli_file) and not opts.force:
         raise ValueError(f"""
             A previous run was indicated by the presence of {cli_file}.
             This can lead to inconsistencies between previous outputs and the log files.
-            To prevent this, you are required to manually remove {cli_file}, and we 
-            recommend also removing previous datasinks from the {opts.rabies_stage} RABIES step.
+            To prevent this, we recommend removing previous datasinks from the {opts.rabies_stage} 
+            RABIES stage. To continue with your execution, the {cli_file} file must be  
+            removed (use --force to automatically do so).
             """)
 
     # remove old versions of the log if already existing

diff --git a/scripts/debug_workflow.py b/scripts/debug_workflow.py
@@ -1,24 +1,27 @@
 #! /usr/bin/env python
 
 from rabies.utils import generate_token_data
+from rabies.run_main import execute_workflow
 
 import tempfile
 tmppath = tempfile.mkdtemp()
 
 #### increase the number of scans generated to 3 if running group analysis
-generate_token_data(tmppath, number_scans=1)
+generate_token_data(tmppath, number_scans=3)
 
 output_folder = f'{tmppath}/outputs'
 
 #### HERE ARE SET THE DESIRED PARAMETERS FOR PREPROCESSING
 args = [
+        f'--exclusion_ids',f'{tmppath}/inputs/sub-token1_bold.nii.gz',
+        '-f',
         #'--debug',
         'preprocess', f'{tmppath}/inputs', output_folder,
         '--anat_inho_cor', 'method=disable,otsu_thresh=2,multiotsu=false', 
         '--bold_inho_cor', 'method=disable,otsu_thresh=2,multiotsu=false',
         '--bold2anat_coreg', 'registration=no_reg,masking=false,brain_extraction=false', 
         '--commonspace_reg', 'masking=false,brain_extraction=false,fast_commonspace=true,template_registration=no_reg', 
-        '--data_type', 'int16', '--bold_only',
+        '--data_type', 'int16', 
         '--anat_template', f'{tmppath}/inputs/sub-token1_T1w.nii.gz',
         '--brain_mask', f'{tmppath}/inputs/token_mask.nii.gz', 
         '--WM_mask', f'{tmppath}/inputs/token_mask.nii.gz',
@@ -27,5 +30,27 @@
         '--labels', f'{tmppath}/inputs/token_mask.nii.gz',
         ]
 
-from rabies.run_main import execute_workflow
 execute_workflow(args=args)
+
+
+
+'''
+
+args = [
+        f'--exclusion_ids',f'{tmppath}/inputs/sub-token1_bold.nii.gz',f'{tmppath}/inputs/sub-token2_bold.nii.gz',
+        '-f',
+        'confound_correction', output_folder, output_folder,
+        '--nativespace_analysis',
+        ]
+execute_workflow(args=args)
+
+
+args = [
+        f'--exclusion_ids',f'{tmppath}/inputs/sub-token3_bold.nii.gz',
+        '-f',
+        'analysis', output_folder, output_folder,
+        '--data_diagnosis'
+        ]
+execute_workflow(args=args)
+
+'''