From 63c4cea10085c049661e611cf24bbeb9c54fd3e1 Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Wed, 24 Jul 2024 09:26:07 +0200
Subject: [PATCH] fix output ROI

---
 src/bidspm/bidspm.py                | 12 ------------
 src/bidspm/parsers.py               | 22 ++++++++--------------
 src/cli/getOptionsFromCliArgument.m |  6 +++++-
 src/cli/inputParserForCreateRoi.m   |  1 -
 tests/test_bidspm.py                |  3 ---
 5 files changed, 13 insertions(+), 31 deletions(-)

diff --git a/src/bidspm/bidspm.py b/src/bidspm/bidspm.py
index 06f5d8a12..035c9588a 100755
--- a/src/bidspm/bidspm.py
+++ b/src/bidspm/bidspm.py
@@ -194,7 +194,6 @@ def create_roi(
     preproc_dir: Path | None = None,
     verbosity: str | int = 2,
     participant_label: list[str] | None = None,
-    roi_dir: Path | None = None,
     roi_atlas: str | None = "neuromorphometrics",
     roi_name: str | list[str] | None = None,
     space: list[str] | None = None,
@@ -202,8 +201,6 @@ def create_roi(
     options: Path | None = None,
 ) -> str:
     roi_name = _cellify(roi_name) if roi_name is not None else None
-    if roi_dir is None:
-        roi_dir = output_dir
 
     cmd = generate_cmd(
         bids_dir=bids_dir,
@@ -222,8 +219,6 @@ def create_roi(
     )
     cmd += f"{new_line}'roi_atlas', '{roi_atlas}'"
     cmd += f"{new_line}'roi_name', {roi_name}"
-    if roi_dir:
-        cmd += f"{new_line}'roi_dir', '{roi_dir}'"
     if preproc_dir:
         cmd += f"{new_line}'preproc_dir', '{preproc_dir}'"
     cmd = end_cmd(cmd)
@@ -393,12 +388,6 @@ def generate_command_create_roi(argv: Any) -> str:
     parser = sub_command_parser()
     args = parser.parse_args(argv[1:])
 
-    if args.roi_dir is None or args.roi_dir[0] is None:
-        roi_dir = args.output_dir[0]
-    else:
-        roi_dir = args.roi_dir[0]
-    roi_dir = Path(roi_dir).absolute()
-
     cmd = create_roi(
         bids_dir=Path(args.bids_dir[0]).absolute(),
         output_dir=Path(args.output_dir[0]).absolute(),
@@ -406,7 +395,6 @@ def generate_command_create_roi(argv: Any) -> str:
         preproc_dir=_get_preproc_dir(args),
         verbosity=_get_verbosity(args),
         participant_label=args.participant_label,
-        roi_dir=roi_dir,
         roi_atlas=_get_roi_atlas(args),
         roi_name=args.roi_name,
         space=args.space,
diff --git a/src/bidspm/parsers.py b/src/bidspm/parsers.py
index c66be9227..3fd0b3939 100644
--- a/src/bidspm/parsers.py
+++ b/src/bidspm/parsers.py
@@ -234,7 +234,6 @@ def sub_command_parser() -> ArgumentParser:
     roi_parser = _add_common_arguments(roi_parser)
     roi_parser = _add_boilerplate_only(roi_parser)
     roi_parser = _add_space(roi_parser)
-    roi_parser = _add_roi_dir(roi_parser)
     roi_parser.add_argument(
         "--roi_name",
         help="""
@@ -290,7 +289,14 @@ def sub_command_parser() -> ArgumentParser:
         action="store_true",
         default=False,
     )
-    stats_parser = _add_roi_dir(stats_parser)
+    stats_parser.add_argument(
+        "--roi_dir",
+        help="""
+        Fullpath to the directory with the regions of interest.
+        """,
+        type=str,
+        nargs=1,
+    )
     stats_parser.add_argument(
         "--roi_name",
         help="""
@@ -419,18 +425,6 @@ def _add_skip_validation(parser: ArgumentParser) -> ArgumentParser:
     return parser
 
 
-def _add_roi_dir(parser: ArgumentParser) -> ArgumentParser:
-    parser.add_argument(
-        "--roi_dir",
-        help="""
-        Fullpath to the directory with the regions of interest.
-        """,
-        type=str,
-        nargs=1,
-    )
-    return parser
-
-
 def _add_task(parser: ArgumentParser) -> ArgumentParser:
     parser.add_argument(
         "--task",
diff --git a/src/cli/getOptionsFromCliArgument.m b/src/cli/getOptionsFromCliArgument.m
index 27b55f387..b47089237 100644
--- a/src/cli/getOptionsFromCliArgument.m
+++ b/src/cli/getOptionsFromCliArgument.m
@@ -150,8 +150,12 @@
 end
 
 function opt = roiOptions(opt, args)
+
   if isfield(args.Results, 'roi_dir')
-    opt.dir.roi = args.Results.roi_dir;
+    opt.dir.roi = args.Results.output_dir;
+  end
+  if ismember(lower(args.Results.action), {'create_roi'})
+    opt.dir.roi = fullfile(args.Results.output_dir, 'derivatives', 'bidspm-roi');
   end
   if isfield(args.Results, 'roi_atlas')
     opt.roi.atlas = args.Results.roi_atlas;
diff --git a/src/cli/inputParserForCreateRoi.m b/src/cli/inputParserForCreateRoi.m
index 597a75697..efd748465 100644
--- a/src/cli/inputParserForCreateRoi.m
+++ b/src/cli/inputParserForCreateRoi.m
@@ -17,7 +17,6 @@
   isLogical = @(x) islogical(x) && numel(x) == 1;
 
   addParameter(args, 'space', {}, isCellStr);
-  addParameter(args, 'roi_dir', '', isDir);
   addParameter(args, 'preproc_dir', '', isDir);
   addParameter(args, 'hemisphere', {'L', 'R'}, isCellStr);
   addParameter(args, 'roi_atlas', 'neuromorphometrics', isInAvailableAtlas);
diff --git a/tests/test_bidspm.py b/tests/test_bidspm.py
index 378ac4c31..50b3b3e2f 100644
--- a/tests/test_bidspm.py
+++ b/tests/test_bidspm.py
@@ -180,7 +180,6 @@ def test_create_roi():
         preproc_dir=Path(),
         verbosity=2,
         participant_label=["01"],
-        roi_dir=Path(),
         roi_atlas="neuromorphometrics",
         roi_name=["foo", "bar"],
         space=["MNI"],
@@ -263,8 +262,6 @@ def test_generate_command_create_roi(analysis_level):
             "--space",
             "IXI549Space",
             "--boilerplate_only",
-            "--roi_dir",
-            str(Path().absolute()),
             "--preproc_dir",
             str(Path().absolute()),
             "--hemisphere",