FIX reuse pregenerated subject segmentation or masks (#150)

* FIX reuse pregenerated subject segmentation or masks * FIX don't redefine subject_mask_nii * cover the mask reuse case in smoke test
bids-apps · May 31, 2024 · abb2407 · abb2407
1 parent 2349127
commit abb2407
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Showing 2 changed files with 40 additions and 1 deletion.
diff --git a/giga_connectome/mask.py b/giga_connectome/mask.py
@@ -71,14 +71,23 @@ def generate_gm_mask_atlas(
         nib.save(
             subject_mask_nii, subject_mask_dir / target_subject_mask_file_name
         )
+    else:
+        subject_mask_nii = load_img(target_subject_mask)
 
-    if not target_subject_seg:
+    if not target_subject_seg or not target_subject_mask:
+        # resample if the grey matter mask was not generated
+        # or the atlas was not present
         subject_seg_niis = resample_atlas_collection(
             target_subject_seg_file_names,
             atlas,
             subject_mask_dir,
             subject_mask_nii,
         )
+    else:
+        subject_seg_niis = [
+            load_img(subject_mask_dir / i)
+            for i in target_subject_seg_file_names
+        ]
 
     return subject_mask_nii, subject_seg_niis
 

diff --git a/giga_connectome/tests/test_cli.py b/giga_connectome/tests/test_cli.py
@@ -59,6 +59,8 @@ def test_smoke(tmp_path, caplog):
             "simple",
             "--reindex-bids",
             "--calculate-intranetwork-average-correlation",
+            "--bids-filter-file",
+            str(Path(bids_dir).parent / "bids_filter.json"),
             str(bids_dir),
             str(output_dir),
             "participant",
@@ -94,3 +96,31 @@ def test_smoke(tmp_path, caplog):
     assert timeseries_file.exists()
     timeseries = pd.read_csv(timeseries_file, sep="\t")
     assert len(timeseries.columns) == 100
+
+    gm_path = (
+        atlases_dir
+        / "sub-1"
+        / "func"
+        / "sub-1_space-MNI152NLin2009cAsym_res-2_label-GM_mask.nii.gz"
+    )
+    # delete gm_path
+    gm_path.unlink()
+    # rerun
+    main(
+        [
+            "--participant_label",
+            "1",
+            "-a",
+            str(atlases_dir),
+            "--atlas",
+            "Schaefer2018",
+            "--denoise-strategy",
+            "simple",
+            "--calculate-intranetwork-average-correlation",
+            "--bids-filter-file",
+            str(Path(bids_dir).parent / "bids_filter.json"),
+            str(bids_dir),
+            str(output_dir),
+            "participant",
+        ]
+    )