add tests for B0Field cases

Author: bpinsard

sdcflows/utils/tests/test_wrangler.py

@@ -202,6 +202,146 @@ def gen_layout(bids_dir, database_dir=None):
 }
 
 
+pepolar_b0ids = {
+    "01": [
+        {
+            "session": "01",
+            "anat": [{"suffix": "T1w", "metadata": {"EchoTime": 1}}],
+            "func": [
+                {
+                    "task": "rest",
+                    "run": 1,
+                    "suffix": "bold",
+                    "metadata": {
+                        "RepetitionTime": 0.8,
+                        "TotalReadoutTime": 0.5,
+                        "PhaseEncodingDirection": "j",
+                        "B0FieldIdentifier": "b0_pepolar",
+                        "B0FieldSource": "b0_pepolar",
+                    },
+                },
+                {
+                    "task": "rest",
+                    "run": 2,
+                    "suffix": "bold",
+                    "metadata": {
+                        "RepetitionTime": 0.8,
+                        "TotalReadoutTime": 0.5,
+                        "PhaseEncodingDirection": "j-",
+                        "B0FieldIdentifier": "b0_pepolar",
+                        "B0FieldSource": "b0_pepolar",
+                    },
+                },
+            ],
+        },
+        {
+            "session": "02",
+            "anat": [{"suffix": "T1w", "metadata": {"EchoTime": 1}}],
+            "func": [
+                {
+                    "task": "rest",
+                    "run": 1,
+                    "suffix": "bold",
+                    "metadata": {
+                        "RepetitionTime": 0.8,
+                        "TotalReadoutTime": 0.5,
+                        "PhaseEncodingDirection": "j",
+                        "B0FieldSource": "b0_pepolar",
+                    },
+                },
+                {
+                    "task": "rest",
+                    "run": 2,
+                    "suffix": "bold",
+                    "metadata": {
+                        "RepetitionTime": 0.8,
+                        "TotalReadoutTime": 0.5,
+                        "PhaseEncodingDirection": "j-",
+                        "B0FieldSource": "b0_pepolar",
+                    },
+                },
+                {
+                    "task": "rest",
+                    "run": 1,
+                    "suffix": "sbref",
+                    "metadata": {
+                        "RepetitionTime": 0.8,
+                        "TotalReadoutTime": 0.5,
+                        "PhaseEncodingDirection": "j",
+                        "B0FieldIdentifier": "b0_pepolar",
+                        "B0FieldSource": "b0_pepolar",
+                    },
+                },
+                {
+                    "task": "rest",
+                    "run": 2,
+                    "suffix": "sbref",
+                    "metadata": {
+                        "RepetitionTime": 0.8,
+                        "TotalReadoutTime": 0.5,
+                        "PhaseEncodingDirection": "j-",
+                        "B0FieldIdentifier": "b0_pepolar",
+                        "B0FieldSource": "b0_pepolar",
+                    },
+                },
+            ],
+        },
+        {
+            "session": "03",
+            "anat": [{"suffix": "T1w", "metadata": {"EchoTime": 1}}],
+            "func": [
+                {
+                    "task": "rest",
+                    "run": 1,
+                    "suffix": "bold",
+                    "metadata": {
+                        "RepetitionTime": 0.8,
+                        "TotalReadoutTime": 0.5,
+                        "PhaseEncodingDirection": "j",
+                        "B0FieldSource": "b0_pepolar",
+                    },
+                },
+                {
+                    "task": "rest",
+                    "run": 2,
+                    "suffix": "bold",
+                    "metadata": {
+                        "RepetitionTime": 0.8,
+                        "TotalReadoutTime": 0.5,
+                        "PhaseEncodingDirection": "j-",
+                        "B0FieldSource": "b0_pepolar",
+                    },
+                },
+                {
+                    "task": "rest",
+                    "run": 1,
+                    "suffix": "sbref",
+                    "metadata": {
+                        "RepetitionTime": 0.8,
+                        "TotalReadoutTime": 0.5,
+                        "PhaseEncodingDirection": "j",
+                        "B0FieldIdentifier": ["b0_pepolar", "b0_pepolar_dup"],
+                        "B0FieldSource": "b0_pepolar",
+                    },
+                },
+                {
+                    "task": "rest",
+                    "run": 2,
+                    "suffix": "sbref",
+                    "metadata": {
+                        "RepetitionTime": 0.8,
+                        "TotalReadoutTime": 0.5,
+                        "PhaseEncodingDirection": "j-",
+                        "B0FieldIdentifier": ["b0_pepolar", "b0_pepolar_dup"],
+                        "B0FieldSource": "b0_pepolar",
+                    },
+                },
+            ],
+        },
+    ]
+}
+
+
 phasediff = {
     '01': [
         {
@@ -304,26 +444,28 @@ def gen_layout(bids_dir, database_dir=None):
 
 
 @pytest.mark.parametrize(
-    'name,skeleton,estimations',
+    'name,skeleton,estimations,bids_filters',
     [
-        ('pepolar', pepolar, 1),
-        ('phasediff', phasediff, 1),
+        ('pepolar', pepolar, 1 , "fmap"),
+        ('pepolar_b0ids', pepolar_b0ids, 1, "bold"),
+        ('phasediff', phasediff, 1, "fmap"),
     ],
 )
-def test_wrangler_filter(tmpdir, name, skeleton, estimations):
+def test_wrangler_filter(tmpdir, name, skeleton, estimations, bids_filters):
     bids_dir = str(tmpdir / name)
     generate_bids_skeleton(bids_dir, skeleton)
     layout = gen_layout(bids_dir)
-    est = find_estimators(layout=layout, subject='01', bids_filters=filters['fmap'])
+    est = find_estimators(layout=layout, subject='01', bids_filters=filters[bids_filters])
     assert len(est) == estimations
     clear_registry()
 
 
 @pytest.mark.parametrize(
-    'name,skeleton,total_estimations',
+    'name,skeleton,total_estimations,test_auto',
     [
-        ('pepolar', pepolar, 5),
-        ('phasediff', phasediff, 3),
+        ('pepolar', pepolar, 5, True),
+        ('pepolar_b0ids', pepolar_b0ids, 2, False),
+        ('phasediff', phasediff, 3, True),
     ],
 )
 @pytest.mark.parametrize(
@@ -345,8 +487,8 @@ def test_wrangler_URIs(tmpdir, name, skeleton, session, estimations, total_estim
         sessions=[session] if session else None,
     )
     assert len(est) == estimations or total_estimations
-    if session:
-        bold = layout.get(session=session, suffix='bold', extension='.nii.gz')[0]
+    if session and test_auto:
+        bold = layout.get(session=session, suffix="bold", extension=".nii.gz")[0]
         intended_rel = re.sub(r'^sub-[a-zA-Z0-9]*/', '', str(Path(bold).relative_to(layout.root)))
         b0_id = get_identifier(intended_rel)
         assert b0_id == ('auto_00000',)