Add test for the dataset that raised nipy#541

heudiconv/heuristics/bids_ME.py

@@ -21,9 +21,16 @@ def infotodict(seqinfo):
     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')
 
-    info = {bold: []}
+    info = {bold: [], megre_mag: [], megre_phase: []}
     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)
     return info

heudiconv/tests/test_bids.py

@@ -5,6 +5,13 @@
     maybe_na,
     treat_age,
 )
+from heudiconv.cli.run import main as runner
+from .utils import TESTS_DATA_PATH
+
+from os.path import (
+    join as pjoin,
+    exists as pexists,
+)
 
 
 def test_maybe_na():
@@ -23,4 +30,28 @@ def test_treat_age():
     assert treat_age('1M') == '0.08'
     assert treat_age('12M') == '1'
     assert treat_age('0000.1') == '0.1'
-    assert treat_age(0000.1) == '0.1'
+    assert treat_age(0000.1) == '0.1'
+
+
+def test_ME_mag_phase_conversion(tmpdir):
+    """ Unit test for the case of multi-echo GRE data with
+    magnitude and phase.
+    The different echoes should be labeled automatically.
+    """
+    tmppath = tmpdir.strpath
+    subID = 'MEGRE'
+    args = (
+        "-c dcm2niix -o %s -b -f bids_ME --files %s -s %s"
+        % (tmpdir, pjoin(TESTS_DATA_PATH, subID), subID)
+    ).split(' ')
+    runner(args)
+
+    # Check that the expected files have been extracted.
+    # This also checks that the "echo" entity comes before "part":
+    for part in ['mag', 'phase']:
+        for e in range(1,4):
+            for ext in ['nii.gz', 'json']:
+                assert pexists(
+                    pjoin(tmppath, 'sub-%s', 'anat', 'sub-%s_echo-%s_part-%s_MEGRE.%s')
+                    % (subID, subID, e, part, ext)
+                )