[BUG] multiple space chars causing wrong entities for FSL parser

bclenet · Oct 3, 2024 · 5b9d420 · 5b9d420
1 parent 7bcf386
commit 5b9d420
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Showing 2 changed files with 4 additions and 1 deletion.
diff --git a/bids_prov/fsl/description_functions.json b/bids_prov/fsl/description_functions.json
@@ -8,7 +8,7 @@
     "Name": "fslmaths",
     "Used": [0, "-add","-sub","-mul","-div","-rem","-mas","-max","-min","-seed","-restart","-save"],
     "GeneratedBy": [1], 
-    "ParametersValue" : ["-dt", "-odt","-thr","-thrp","-thrP","-uthr","-uthrp","-uthrP", 
+    "ParametersValue" : ["-dt", "-odt","-thr","-thrp","-thrP","-uthr","-uthrp","-uthrP", "-bptf",
     {
       "Name": "-grid",
       "Index": ["0:2"]

diff --git a/bids_prov/fsl/fsl_parser.py b/bids_prov/fsl/fsl_parser.py
@@ -423,6 +423,9 @@ def build_records(groups: Mapping[str, List[str]], agent_id: str, verbose: bool
         for cmd in v:
             # process to remove + and - in pngappend command
             cmd = cmd.replace(" + ", " ").replace(" - ", " ")
+            # remove multiple spaces
+            cmd = ' '.join(cmd.split())
+            # split according to the following chars " ", "|", and "="
             cmd_s = re.split(" |=", cmd)
             activity_name = cmd_s[0]