Fix/generate physio

physutils/io.py

@@ -224,6 +224,52 @@ def load_physio(data, *, fs=None, dtype=None, history=None, allow_pickle=False):
     return phys
 
 
+def load_misc(data, *, fs=None):
+    """
+    Returns `Physio` object with provided data
+
+    Parameters
+    ----------
+    data : str, os.path.PathLike or array_like
+        Input physiological data. If array_like, should be one-dimensional
+    fs : float, optional
+        Sampling rate of `data`. Default: None
+
+    Returns
+    -------
+    phys: :class:`physutils.Physio`
+        Loaded physiological data
+
+    Raises
+    ------
+    TypeError
+        If provided `data` is unable to be loaded
+    """
+    # load data
+    if isinstance(data, str) or isinstance(data, os.PathLike):
+        if os.path.exists(data):
+            ext = os.path.splitext(data)[-1]
+
+            if ext == '.gz':
+                ext == os.path.splitext(os.path.splitext(data)[0])[-1]
+
+            if ext == '.tsv':
+                data = np.genfromtxt(data, delimiter='\t')
+            elif ext == '.csv':
+                data = np.genfromtxt(data, delimiter=',')
+            else:
+                data = np.genfromtxt(data)
+        else:
+            raise IOError(f'Cannot find {data}')
+    else:
+        raise TypeError(f'{type(data)} is not a supported type')
+
+    # instantiate physio object
+    phys = physio.Physio(data, fs=fs)
+
+    return phys
+
+
 def save_physio(fname, data):
     """
     Saves `data` to `fname`

physutils/tasks.py

@@ -5,7 +5,7 @@
 
 import logging
 
-from .io import load_from_bids, load_physio
+from .io import load_from_bids, load_physio, load_misc
 from .physio import Physio
 from .utils import is_bids_directory
 
@@ -45,16 +45,18 @@ def generate_physio(
     LGR.info(f"Loading physio object from {input_file}")
 
     if mode == "auto":
-        if input_file.endswith((".phys", ".physio", ".1D", ".txt", ".tsv", ".csv")):
+        if input_file.endswith((".phys")):
             mode = "physio"
         elif is_bids_directory(input_file):
             mode = "bids"
+        elif input_file.endswith((".txt", ".tsv", ".csv")):
+            mode = "misc"
         else:
             raise ValueError(
                 "Could not determine input mode automatically. Please specify it manually."
             )
     if mode == "physio":
-        physio_obj = load_physio(input_file, fs=fs, allow_pickle=True)
+        physio_obj = load_physio(input_file, allow_pickle=True)
 
     elif mode == "bids":
         if bids_parameters is {}:
@@ -64,6 +66,8 @@ def generate_physio(
             physio_obj = (
                 physio_array[col_physio_type] if col_physio_type else physio_array
             )
+    elif mode == "misc":
+        physio_obj = load_misc(input_file, fs=fs)
     else:
         raise ValueError(f"Invalid generate_physio mode: {mode}")
 

physutils/tests/test_io.py

@@ -87,6 +87,12 @@ def test_load_from_bids_no_rec():
         assert phys_array[col].history[0][0] == "physutils.io.load_from_bids"
 
 
+def test_load_misc():
+    csv = io.load_physio(get_test_data_path("ECG.csv"))
+    assert isinstance(csv, physio.Physio)
+    assert np.isnan(csv.fs)
+
+
 def test_save_physio(tmpdir):
     pckl = io.load_physio(get_test_data_path("ECG.phys"), allow_pickle=True)
     out = io.save_physio(tmpdir.join("tmp").purebasename, pckl)