Verify transform_to_physio for BIDS files

physutils/tasks.py

@@ -10,7 +10,9 @@
 
 
 @pydra.mark.task
-def transform_to_physio(input_file: str, mode="physio", fs=None) -> Physio:
+def transform_to_physio(
+    input_file: str, mode="physio", fs=None, bids_parameters=dict(), bids_channel=None
+) -> Physio:
     LGR.debug(f"Loading physio object from {input_file}")
     if not fs:
         fs = None
@@ -22,7 +24,11 @@ def transform_to_physio(input_file: str, mode="physio", fs=None) -> Physio:
             physio_obj = load_physio(input_file, allow_pickle=True)
 
     elif mode == "bids":
-        physio_obj = load_from_bids(input_file)
+        if bids_parameters is {}:
+            raise ValueError("BIDS parameters must be provided when loading from BIDS")
+        else:
+            physio_array = load_from_bids(input_file, **bids_parameters)
+            physio_obj = physio_array[bids_channel]
     else:
         raise ValueError(f"Invalid transform_to_physio mode: {mode}")
     return physio_obj

physutils/tests/test_tasks.py

@@ -4,6 +4,7 @@
 
 import physutils.tasks as tasks
 from physutils import physio
+from physutils.tests.utils import create_random_bids_structure
 
 
 def test_transform_to_physio_phys_file():
@@ -20,3 +21,33 @@ def test_transform_to_physio_phys_file():
     assert isinstance(physio_obj, physio.Physio)
     assert physio_obj.fs == 1000
     assert physio_obj.data.shape == (44611,)
+
+
+def test_transform_to_physio_bids_file():
+    """Test transform_to_physio task."""
+    create_random_bids_structure("physutils/tests/data", recording_id="cardiac")
+    bids_parameters = {
+        "subject": "01",
+        "session": "01",
+        "task": "rest",
+        "run": "01",
+        "recording": "cardiac",
+    }
+    bids_dir = os.path.abspath("physutils/tests/data/bids-dir")
+    task = tasks.transform_to_physio(
+        input_file=bids_dir,
+        mode="bids",
+        bids_parameters=bids_parameters,
+        bids_channel="cardiac",
+    )
+
+    assert task.inputs.input_file == bids_dir
+    assert task.inputs.mode == "bids"
+    assert task.inputs.fs is None
+    assert task.inputs.bids_parameters == bids_parameters
+    assert task.inputs.bids_channel == "cardiac"
+
+    task()
+
+    physio_obj = task.result().output.out
+    assert isinstance(physio_obj, physio.Physio)