Removed --scan_list which was replaced by --inclusion_ids

CoBrALab · Oct 2, 2023 · 9a5bb00 · 9a5bb00
1 parent e9606e0
commit 9a5bb00
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diff --git a/rabies/analysis_pkg/main_wf.py b/rabies/analysis_pkg/main_wf.py
@@ -393,27 +393,6 @@ def read_confound_workflow(conf_output, nativespace=False):
     return split_dict, split_name, target_list
 
 
-def get_iterable_scan_list(scan_list, split_name):
-    # prep the subset of scans on which the analysis will be run
-    import numpy as np
-    import pandas as pd
-    if os.path.isfile(os.path.abspath(scan_list[0])):
-        updated_split_name=[]
-        if '.nii' in pathlib.Path(scan_list[0]).name:
-            for scan in scan_list:
-                updated_split_name.append(find_split(scan, split_name))
-        else:
-            # read the file as a .txt
-            scan_list = np.array(pd.read_csv(os.path.abspath(scan_list[0]), header=None)).flatten()
-            for scan in scan_list:
-                updated_split_name.append(find_split(scan, split_name))
-    elif scan_list[0]=='all':
-        updated_split_name = split_name
-    else:
-        raise ValueError(f"The --scan_list {scan_list} input had improper format. It must the full path to a .txt or .nii files, or 'all' to keep all scans.")
-    return updated_split_name
-
-
 def find_split(scan, split_name):
     for split in split_name:
         if split in scan:

diff --git a/rabies/parser.py b/rabies/parser.py
@@ -763,19 +763,6 @@ def get_parser():
             "path for analysis outputs.\n"
             "\n"
         )
-    analysis.add_argument(
-        '--scan_list', type=str,
-        nargs="*",  # 0 or more values expected => creates a list
-        default=['all'],
-        help=
-            "This option offers to run the analysis on a subset of the scans. The scans are selected by\n"
-            "providing the full path to the corresponding EPI file in the input BIDS folder. The list \n"
-            "of scan can be specified manually as a list of file name '--scan_list scan1.nii.gz \n"
-            "scan2.nii.gz ...' or the files can be imbedded into a .txt file with one filename per row.\n"
-            "By default, 'all' will use all the scans previously processed.\n"
-            "(default: %(default)s)\n"
-            "\n"
-        )
     analysis.add_argument(
         '--prior_maps', action='store', type=Path,
         default=f"{rabies_path}/melodic_IC.nii.gz",