Peakdet workflow pipeline

peakdet/blocks.py

@@ -0,0 +1,39 @@
+from peakdet import load_physio, save_physio
+from peakdet.operations import edit_physio, interpolate_physio, filter_physio, peakfind_physio
+
+FUNCTION_MAPPINGS = {
+    "interpolate_physio": interpolate_physio,
+    "filter_physio": filter_physio,
+    "peakfind_physio": peakfind_physio
+}
+
+def process_signals(data, steps):
+    """
+    Parameters
+    ----------
+    data : :class:`peakdet.Physio`
+    steps : list
+
+    Return
+    ------
+    data : :class:`peakdet.Physio` (w/ features from peakfind_physio)
+    """
+    for step in steps:
+        func = list(step.keys())[0]
+        data = FUNCTION_MAPPINGS[func](data, **step[func])
+    return data
+
+
+def manual_peaks(data, fname):
+    """
+    data : str or array_like or Physio_like
+        Input physiological data. If array_like, should be one-dimensional
+    fname : str
+        Path to output file; .phys will be appended if necessary
+    """
+    # Load signals
+    phys = load_physio(data, allow_pickle=True)
+    # Edit peaks
+    phys = edit_physio(data)
+    # Save edits
+    save_physio(fname, phys)

peakdet/cli/run.py

@@ -8,8 +8,6 @@
 from gooey import Gooey, GooeyParser
 import peakdet
 
-TARGET = 'pythonw' if sys.platform == 'darwin' else 'python'
-TARGET += ' -u ' + os.path.abspath(__file__)
 
 LOADERS = dict(
     rtpeaks=peakdet.load_rtpeaks,
@@ -45,9 +43,8 @@
 
 @Gooey(program_name='Physio pipeline',
        program_description='Physiological processing pipeline',
-       default_size=(800, 600),
-       target=TARGET)
-def get_parser():
+       default_size=(800, 600))
+def _get_parser():
     """ Parser for GUI and command-line arguments """
     parser = GooeyParser()
     parser.add_argument('file_template', metavar='Filename template',
@@ -224,10 +221,10 @@ def workflow(*, file_template, modality, fs, source='MRI', channel=1,
             dest.write(','.join([fname] + outputs) + '\n')
 
 
-def main():
-    opts = get_parser().parse_args()
-    workflow(**vars(opts))
-
-
 if __name__ == '__main__':
-    main()
+    raise RuntimeError(
+        "peakdet/cli/run.py should not be run directly;\n"
+        "Please `pip install` peakdet and use the "
+        "`peakdet` command"
+    )
+

peakdet/configs/config_ppg_example.json

@@ -0,0 +1,16 @@
+{
+    "PPG": [
+        {
+            "filter_physio": {
+                "cutoffs": 1.0,
+                "method": "lowpass"
+            }
+        },
+        {
+            "filter_physio": {
+                "cutoffs": 40,
+                "method": "highpass"
+            }
+        }
+    ]
+}