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_localizer.py

@@ -0,0 +1,44 @@
+"""Heuristic demonstrating conversion of the Multi-Echo sequences.
+
+It only cares about converting sequences which have _ME_ in their
+series_description and outputs to BIDS.
+"""
+
+from __future__ import annotations
+
+from typing import Optional
+
+from heudiconv.utils import SeqInfo
+
+
+def create_key(
+    template: Optional[str],
+    outtype: tuple[str, ...] = ("nii.gz",),
+    annotation_classes: None = None,
+) -> tuple[str, tuple[str, ...], None]:
+    if template is None or not template:
+        raise ValueError("Template must be a valid format string")
+    return (template, outtype, annotation_classes)
+
+
+def infotodict(
+    seqinfo: list[SeqInfo],
+) -> dict[tuple[str, tuple[str, ...], None], list[str]]:
+    """Heuristic evaluator for determining which runs belong where
+
+    allowed template fields - follow python string module:
+
+    item: index within category
+    subject: participant id
+    seqitem: run number during scanning
+    subindex: sub index within group
+    """
+    localizer = create_key("sub-{subject}/anat/sub-{subject}_localizer")
+
+    info: dict[tuple[str, tuple[str, ...], None], list[str]] = {
+        localizer: [],
+    }
+    for s in seqinfo:
+        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,