Working transform_to_physio pydra task and tests

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

@@ -1,15 +1,26 @@
+import logging
+
 import pydra
 
-from physutils.io import load_from_bids, load_history, load_physio
+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") -> Physio:
+def transform_to_physio(input_file: str, mode="physio", fs=None) -> Physio:
+    LGR.debug(f"Loading physio object from {input_file}")
+    if not fs:
+        fs = None
+
     if mode == "physio":
-        physio_obj = load_physio(input_file)
-    elif mode == "history":
-        physio_obj = load_history(input_file)
+        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":
         physio_obj = load_from_bids(input_file)
     else:

physutils/tests/test_tasks.py

@@ -0,0 +1,22 @@
+"""Tests for physutils.tasks and their integration."""
+
+import os
+
+import physutils.tasks as tasks
+from physutils import physio
+
+
+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,)