Restructure

phys2bids/cli/run.py

@@ -73,7 +73,7 @@ def _get_parser():
                           type=int,
                           help=('The number corresponding to the trigger channel.'
                                 ' Channel numbering starts with 0'),
-                          default=1)
+                          default=0)
     optional.add_argument('-chsel', '--channel-selection',
                           dest='chsel',
                           nargs='*',
@@ -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/heuristics/heur_test_acq.py

@@ -0,0 +1,54 @@
+import sys
+import fnmatch
+
+
+def heur(physinfo, name, task='', acq='', direct='', rec='', run=''):
+    # ############################## #
+    # ##       Modify here!       ## #
+    # ##                          ## #
+    # ##  Possible variables are: ## #
+    # ##    -task (required)      ## #
+    # ##    -run                  ## #
+    # ##    -rec                  ## #
+    # ##    -acq                  ## #
+    # ##    -direct               ## #
+    # ##                          ## #
+    # ##                          ## #
+    # ##    See example below     ## #
+    # ############################## #
+
+    if fnmatch.fnmatchcase(physinfo, '*samefreq*.acq'):
+        task = 'test'
+        run = '00'
+        rec = 'biopac'
+    elif physinfo == 'Example':
+        task = 'rest'
+        run = '01'
+        acq = 'resp'
+        # ############################## #
+        # ## Don't modify below this! ## #
+        # ############################## #
+    else:
+        # #!# Transform sys.exit in debug warnings or raiseexceptions!
+        # #!# Make all of the above a dictionary
+        sys.exit()
+
+    if not task:
+        sys.exit()
+
+    name = name + '_task-' + task
+
+    # filename spec: sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_ce-<label>][_dir-<label>][_rec-<label>][_run-<index>][_recording-<label>]_physio
+    if acq:
+        name = name + '_acq-' + acq
+
+    if direct:
+        name = name + '_dir-' + direct
+
+    if rec:
+        name = name + '_rec-' + rec
+
+    if run:
+        name = name + '_run-' + run
+
+    return name

phys2bids/interfaces/acq.py

@@ -0,0 +1,32 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+"""
+phys2bids interface for acqknowledge files.
+"""
+from bioread import read_file
+
+from phys2bids.physio_obj import BlueprintInput
+
+
+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']
+
+    for k, ch in enumerate(data):
+        if k != chtrig:
+            print(f'{k:02d}. {ch}')
+            timeseries.append(ch.data)
+            freq.append(ch.samples_per_second)
+            units.append(ch.units)
+            names.append(ch.name)
+
+    return BlueprintInput(timeseries, freq, names, units)