Restructure

phys2bids/cli/run.py

@@ -89,20 +89,18 @@ def _get_parser():
                           dest='tr',
                           type=float,
                           help='TR of sequence in seconds.',
-                          default=1)
+                          default=0)
     optional.add_argument('-thr', '--threshold',
                           dest='thr',
                           type=float,
                           help='Threshold used for trigger detection.',
                           default=2.5)
-    optional.add_argument('-tbhd', '--table-header',
-                          dest='table_header',
+    optional.add_argument('-chnames', '--channel-names',
+                          dest='ch_name',
                           nargs='*',
                           type=str,
                           help='Columns header (for json file).',
-                          # #!# Has to go to empty list
-                          default=['time', 'respiratory_chest', 'trigger',
-                                   'cardiac', 'respiratory_CO2', 'respiratory_O2'])
+                          default=[''])
 
     optional.add_argument('-v', '--version', action='version',
                           version=('%(prog)s ' + __version__))

phys2bids/interfaces/acq.py

@@ -0,0 +1,33 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+"""
+phys2bids interface for acqknowledge files.
+"""
+from bioread import read_file
+
+from phys2bids.physio_obj import blueprint_input
+
+
+def populate_phys_input(filename, chtrig):
+    """
+    Populate object phys_input
+    """
+
+    data = read_file(filename).channels
+
+    freq = [data[chtrig].samples_per_second] * 2
+    timeseries = [data[chtrig].time_index, data[chtrig].data]
+    units = ['s', data[chtrig].units]
+    names = ['time', 'trigger']
+
+    k = 0
+    for ch in data:
+        if k != chtrig:
+            print(f'{k:02d}. {ch}')
+            timeseries.append(ch.data)
+            freq.append(ch.samples_per_second)
+            units.append(ch.units)
+        k += 1
+
+    return blueprint_input(timeseries, freq, names, units)