Merge pull request #547 from cbinyu/fix_echo_order_in_filename

Add test for the dataset that raised #541

Author: yarikoptic

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

@@ -43,13 +43,23 @@
     KeyInfoForForce,
     BIDSFile,
 )
+from heudiconv.cli.run import main as runner
 
 from .utils import (
+    fetch_data,
+    gen_heudiconv_args,
     TESTS_DATA_PATH,
 )
 
 import pytest
 
+have_datalad = True
+try:
+    from datalad.support.exceptions import IncompleteResultsError
+except ImportError:
+    have_datalad = False
+
+
 def gen_rand_label(label_size, label_seed, seed_stdout=True):
     seed(label_seed)
     rand_char = ''.join(choice(string.ascii_letters) for _ in range(label_size-1))
@@ -1116,3 +1126,32 @@ def test_BIDSFile():
     # -for an existing entity, you can overwrite it with "set":
     my_bids_file.set('echo', '2')
     assert my_bids_file['echo'] == '2'
+
+
+@pytest.mark.skipif(not have_datalad, reason="no datalad")
+def test_ME_mag_phase_conversion(tmpdir, subID='MEGRE', heuristic='bids_ME.py'):
+    """ Unit test for the case of multi-echo GRE data with
+    magnitude and phase.
+    The different echoes should be labeled automatically.
+    """
+    tmpdir.chdir()
+    tmppath = tmpdir.strpath
+    try:
+        datadir = fetch_data(tmppath, f"dicoms/velasco/{subID}")
+    except IncompleteResultsError as exc:
+        pytest.skip("Failed to fetch test data: %s" % str(exc))
+
+    outdir = tmpdir.mkdir('out').strpath
+    args = gen_heudiconv_args(datadir, outdir, subID, heuristic)
+    runner(args)  # run conversion
+
+    # 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 op.exists(
+                    op.join(outdir, 'sub-%s', 'anat', 'sub-%s_echo-%s_part-%s_MEGRE.%s')
+                    % (subID, subID, e, part, ext)
+                )
+