Merge branch 'main' into test/hotfix-file-type

bids-apps · May 31, 2024 · 541e0fd · 541e0fd
2 parents 6af3eea + 8e8be89
commit 541e0fd
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Showing 4 changed files with 86 additions and 7 deletions.
diff --git a/giga_connectome/mask.py b/giga_connectome/mask.py
@@ -76,13 +76,20 @@ def generate_gm_mask_atlas(
             subject_mask_dir / target_subject_mask_file_name
         )
 
-    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
@@ -59,11 +59,14 @@ 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",
         ]
     )
+    # check outputs
     assert "has been deprecated" in caplog.text.splitlines()[0]
 
     output_folder = output_dir / "sub-1" / "ses-timepoint1" / "func"
@@ -94,3 +97,53 @@ def test_smoke(tmp_path, caplog):
     assert timeseries_file.exists()
     timeseries = pd.read_csv(timeseries_file, sep="\t")
     assert len(timeseries.columns) == 100
+
+    # immediately rerun should cover the case where the output already exists
+    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",
+        ]
+    )
+
+    # deleate gm mask to trigger rerun the atlas generation
+
+    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",
+        ]
+    )
diff --git a/giga_connectome/tests/test_utils.py b/giga_connectome/tests/test_utils.py
@@ -100,14 +100,32 @@ def test_output_filename(suffix, extension, target):
 
 
 @pytest.mark.parametrize(
-    "atlas,atlas_desc,suffix,target",
+    "source_file,atlas,atlas_desc,suffix,target",
     [
-        ("fake", "100", "dseg", "sub-01_seg-fake100_dseg.nii.gz"),
-        ("", "", "mask", "sub-01_space-MNIfake_res-2_label-GM_mask.nii.gz"),
+        (
+            "sub-01_ses-ah_task-rest_run-1_space-MNIfake_res-2_desc-brain_mask.nii.gz",
+            "fake",
+            "100",
+            "dseg",
+            "sub-01_seg-fake100_dseg.nii.gz",
+        ),
+        (
+            "sub-01_ses-ah_task-rest_run-1_space-MNIfake_res-2_desc-brain_mask.nii.gz",
+            "",
+            "",
+            "mask",
+            "sub-01_space-MNIfake_res-2_label-GM_mask.nii.gz",
+        ),
+        (
+            "sub-01_ses-ah_task-rest_run-1_space-MNIfake_desc-brain_mask.nii.gz",
+            "",
+            "",
+            "mask",
+            "sub-01_space-MNIfake_label-GM_mask.nii.gz",
+        ),
     ],
 )
-def test_output_filename_seg(atlas, atlas_desc, suffix, target):
-    source_file = "sub-01_ses-ah_task-rest_run-1_space-MNIfake_res-2_desc-brain_mask.nii.gz"
+def test_output_filename_seg(source_file, atlas, atlas_desc, suffix, target):
     generated_target = utils.output_filename(
         source_file=source_file,
         atlas=atlas,

diff --git a/giga_connectome/utils.py b/giga_connectome/utils.py
@@ -278,7 +278,8 @@ def output_filename(
 
     elif suffix == "mask":
         reference = parse_bids_filename(source_file)
-        tpl: str = f"space-{reference['space']}_res-{reference['res']}"
+        tpl: str = f"space-{reference['space']}"
+        tpl += f"_res-{reference['res']}" if "res" in reference else ""
         return f"{subject}_{tpl}_label-GM_{suffix}.{extension}"
     else:
         return f"{subject}_{seg}_{suffix}.{extension}"