Read BIDS datasets using pydra-bids tasks (#791)

* Add pydra-bids to dependencies

* Fix invalid escape sequence in regexp

* Remove erroneous return

* Read BIDS datasets with BIDSDataReader

* Remove datatype attribute from BIDS queries

It is not supported by `pydra-bids` and could be computed from the suffix
anyway.

* Ugrade pydra-bids to version 0.0.3

* Fix name of BIDS dataset reader task

* Run formatter

clinica/pydra/engine_utils.py

@@ -72,10 +72,10 @@ def run(wf: Workflow) -> Result:
         with Submitter(plugin="cf") as submitter:
             submitter(wf)
     except Exception as e:
-        path = re.search("\/.*\.pklz", str(e))
+        path = re.search(r"/.*\.pklz", str(e))
         if path:
             print(read_error(path.group(0)))
-        return print(str(e))
+        print(str(e))
 
     return wf.result(return_inputs=False)
 

clinica/pydra/interfaces.py

@@ -116,7 +116,7 @@ def bids_reader(query: BIDSQuery, input_dir: PathLike):
     Parameters
     ----------
     query : BIDSQuery
-        Input to BIDSDataGrabber (c.f https://nipype.readthedocs.io/en/latest/api/generated/nipype.interfaces.io.html#bidsdatagrabber)
+        BIDS dataset reader query.
     input_dir :  PathLike
         The BIDS input directory.
 
@@ -125,14 +125,11 @@ def bids_reader(query: BIDSQuery, input_dir: PathLike):
     Nipype1Task
         The task used for reading files from BIDS.
     """
-    bids_data_grabber = nio.BIDSDataGrabber(output_query=query.query)
-    bids_reader_task = Nipype1Task(
-        name="bids_reader_task",
-        interface=bids_data_grabber,
-        base_dir=input_dir,
-        output_query=query.query,
+    from pydra.tasks.bids import BIDSDatasetReader
+
+    return BIDSDatasetReader(output_query=query.query).to_task(
+        name="bids_reader_task", dataset_path=input_dir
     )
-    return bids_reader_task
 
 
 def caps_reader(query: CAPSQuery, input_dir: PathLike):

clinica/pydra/query.py

@@ -69,7 +69,7 @@ def format_query(self, input_query: Optional[Dict] = None) -> Dict:
 
             {"label" : {query dict} or list of query dicts}
 
-            example: {"T1w": {"datatype": "anat", "suffix": "T1w", "extension": [".nii.gz"]}}
+            example: {"T1w": {"suffix": "T1w", "extension": [".nii.gz"]}}
 
         Parameters
         ----------
@@ -150,12 +150,12 @@ class BIDSQuery(Query):
     >>> len(q)
     1
     >>> q.query
-    {'T1w': {'datatype': 'anat', 'suffix': 'T1w', 'extension': ['.nii.gz']}}
+    {'T1w': {'suffix': 'T1w', 'extension': ['.nii.gz']}}
     """
 
     _default_queries = {
-        "T1w": {"datatype": "anat", "suffix": "T1w", "extension": [".nii.gz"]},
-        "pet": {"datatype": "pet", "suffix": "pet", "extension": [".nii.gz"]},
+        "T1w": {"suffix": "T1w", "extension": [".nii.gz"]},
+        "pet": {"suffix": "pet", "extension": [".nii.gz"]},
     }
 
     def parse_query(self, query: Dict) -> Dict:

pyproject.toml

@@ -57,6 +57,7 @@ joblib = "^1.2.0"
 attrs = ">=20.1.0"
 cattrs = "^1.9.0"
 brainstat = "^0.3.6"
+pydra-bids = "^0.0.3"
 
 [tool.poetry.group.dev.dependencies]
 black = "*"

test/unittests/pydra/test_engine.py

@@ -25,9 +25,7 @@ def smooth_image(input_image: PathLike) -> PurePath:
 def bids_query():
     from clinica.pydra.query import BIDSQuery
 
-    return BIDSQuery(
-        {"T1w": {"datatype": "anat", "suffix": "T1w", "extension": [".nii.gz"]}}
-    )
+    return BIDSQuery({"T1w": {"suffix": "T1w", "extension": [".nii.gz"]}})
 
 
 @pytest.fixture

test/unittests/pydra/test_interfaces.py

@@ -13,15 +13,14 @@
 
 
 def test_bids_reader_instantiation(tmp_path):
-    from nipype.interfaces.io import BIDSDataGrabber
+    from pydra.engine.task import FunctionTask
 
     from clinica.pydra.interfaces import bids_reader
 
     task = bids_reader(BIDSQuery(), tmp_path)
-    assert isinstance(task, Nipype1Task)
+    assert isinstance(task, FunctionTask)
     assert task.name == "bids_reader_task"
-    assert task.inputs.base_dir == tmp_path
-    assert isinstance(task._interface, BIDSDataGrabber)
+    assert task.inputs.dataset_path == tmp_path
 
 
 def test_bids_reader(tmp_path):

test/unittests/pydra/test_query.py

@@ -15,15 +15,12 @@ def test_bids_query():
     assert len(q) == 0
 
     q = BIDSQuery({"T1w": {}})
-    assert q.query == {
-        "T1w": {"datatype": "anat", "suffix": "T1w", "extension": [".nii.gz"]}
-    }
+    assert q.query == {"T1w": {"suffix": "T1w", "extension": [".nii.gz"]}}
     assert len(q) == 1
 
     q = BIDSQuery({"T1w": {"foo": "bar"}})
     assert q.query == {
         "T1w": {
-            "datatype": "anat",
             "suffix": "T1w",
             "extension": [".nii.gz"],
             "foo": "bar",
@@ -32,9 +29,7 @@ def test_bids_query():
     assert len(q) == 1
 
     q = BIDSQuery({"T1w": {}, "foo": {"bar": "baz"}})
-    assert q.query == {
-        "T1w": {"datatype": "anat", "suffix": "T1w", "extension": [".nii.gz"]}
-    }
+    assert q.query == {"T1w": {"suffix": "T1w", "extension": [".nii.gz"]}}
     assert len(q) == 1