Add BIDS reading support and prepare input loading for pydra workflow

physutils/physio.py

@@ -8,6 +8,7 @@
 
 import matplotlib.pyplot as plt
 import numpy as np
+import pandas as pd
 from loguru import logger
 
 
@@ -146,7 +147,7 @@ def check_physio(data, ensure_fs=True, copy=False):
 
     if not isinstance(data, Physio):
         data = load_physio(data)
-    if ensure_fs and np.isnan(data.fs):
+    if ensure_fs and pd.isna(data.fs):
         raise ValueError("Provided data does not have valid sampling rate.")
     if copy is True:
         return new_physio_like(

physutils/tasks.py

@@ -0,0 +1,34 @@
+import logging
+
+import pydra
+
+from physutils.io import load_from_bids, load_physio
+from physutils.physio import Physio
+
+LGR = logging.getLogger(__name__)
+LGR.setLevel(logging.DEBUG)
+
+
+@pydra.mark.task
+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
+
+    if mode == "physio":
+        if fs is not None:
+            physio_obj = load_physio(input_file, fs=fs, allow_pickle=True)
+        else:
+            physio_obj = load_physio(input_file, allow_pickle=True)
+
+    elif mode == "bids":
+        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

@@ -0,0 +1,53 @@
+"""Tests for physutils.tasks and their integration."""
+
+import os
+
+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():
+    """Test transform_to_physio task."""
+    physio_file = os.path.abspath("physutils/tests/data/ECG.phys")
+    task = tasks.transform_to_physio(input_file=physio_file, mode="physio")
+    assert task.inputs.input_file == physio_file
+    assert task.inputs.mode == "physio"
+    assert task.inputs.fs is None
+
+    task()
+
+    physio_obj = task.result().output.out
+    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)

setup.cfg

@@ -11,7 +11,7 @@ classifiers =
     License :: OSI Approved :: Apache Software License
     Programming Language :: Python :: 3
 license = Apache-2.0
-description = Set of utilities meant to be used with Physiopy's libraries
+description = Set of utilities meant to be used with Physiopy libraries
 long_description = file:README.md
 long_description_content_type = text/markdown; charset=UTF-8
 platforms = OS Independent
@@ -25,6 +25,7 @@ install_requires =
     numpy >=1.9.3
     scipy
     loguru
+    pydra
     pybids
 tests_require =
     pytest >=3.6