add data and bids tests

Author: bpinsard

heudiconv/convert.py

@@ -533,7 +533,7 @@ def update_multiorient_name(
         )
         return filename
     iop = metadata.get("ImageOrientationPatientDICOM")
-    iop = [round(x) for x in iop]
+    # iop = [round(x) for x in iop]
     cross_prod = [
         iop[1] * iop[5] - iop[2] * iop[4],
         iop[2] * iop[3] - iop[0] * iop[5],
@@ -1002,8 +1002,6 @@ def save_converted_files(
             except KeyError:
                 pass
 
-        print(iops)
-
         is_multiecho = (
             len(set(filter(bool, echo_times))) > 1
         )  # Check for varying echo times

heudiconv/heuristics/bids_ME.py renamed to heudiconv/heuristics/bids_localizer.py

@@ -33,21 +33,12 @@ def infotodict(
     seqitem: run number during scanning
     subindex: sub index within group
     """
-    bold = create_key("sub-{subject}/func/sub-{subject}_task-test_run-{item}_bold")
-    megre_mag = create_key("sub-{subject}/anat/sub-{subject}_part-mag_MEGRE")
-    megre_phase = create_key("sub-{subject}/anat/sub-{subject}_part-phase_MEGRE")
+    localizer = create_key("sub-{subject}/anat/sub-{subject}_localizer")
 
     info: dict[tuple[str, tuple[str, ...], None], list[str]] = {
-        bold: [],
-        megre_mag: [],
-        megre_phase: [],
+        localizer: [],
     }
     for s in seqinfo:
-        if "_ME_" in s.series_description:
-            info[bold].append(s.series_id)
-        if "GRE_QSM" in s.series_description:
-            if s.image_type[2] == "M":
-                info[megre_mag].append(s.series_id)
-            elif s.image_type[2] == "P":
-                info[megre_phase].append(s.series_id)
+        if "localizer" in s.series_description:
+            info[localizer].append(s.series_id)
     return info

heudiconv/tests/data/01-localizer_64ch/MR.1.3.12.2.1107.5.2.43.167006.2018113015350928736278242

@@ -1369,6 +1369,31 @@ def test_BIDSFile() -> None:
     assert my_bids_file["echo"] == "2"
 
 
+@pytest.mark.skipif(not have_datalad, reason="no datalad")
+def test_convert_multiorient(
+    tmp_path: Path,
+    heuristic: str = "bids_localizer.py",
+    subID: str = "loc",
+) -> None:
+    """Unit test for the case of multi-orient localizer data.
+    The different orientations should be labeled in `acq` entity.
+    """
+    datadir = op.join(TESTS_DATA_PATH, "01-localizer_64ch")
+    outdir = tmp_path / "out"
+    outdir.mkdir()
+    args = gen_heudiconv_args(datadir, str(outdir), subID, heuristic)
+    runner(args)
+
+    # Check that the expected files have been extracted.
+    # This also checks that the "echo" entity comes before "part":
+    for orient in ["sagittal", "coronal", "axial"]:
+        for ext in ["nii.gz", "json"]:
+            assert op.exists(
+                op.join(outdir, "sub-%s", "anat", "sub-%s_acq-%s_localizer.%s")
+                % (subID, subID, orient, ext)
+            )
+
+
 @pytest.mark.skipif(not have_datalad, reason="no datalad")
 def test_ME_mag_phase_conversion(
     monkeypatch: pytest.MonkeyPatch,