Refactored phys2bids code.

Restructure

phys2bids/cli/run.py

@@ -73,15 +73,15 @@ 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='*',
                           type=int,
                           help='The number corresponding to the channels to process.',
                           default=None)
     optional.add_argument('-ntp', '--numtps',
-                          dest='num_tps_expected',
+                          dest='num_timepoints_expected',
                           type=int,
                           help='Number of expected timepoints.',
                           default=0)
@@ -95,14 +95,12 @@ def _get_parser():
                           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.py

@@ -48,18 +48,14 @@ def heur(physinfo, name, task='', acq='', direct='', rec='', run=''):
     else:
         # #!# Transform sys.exit in debug warnings or raiseexceptions!
         # #!# Make all of the above a dictionary
-        print('File not found in heuristics!\nExiting')
-        sys.exit()
+        raise Warning(f'The heuristic {__file__} could not deal with {physinfo}')
 
     if not task:
-        print('No "task" specified for this file!\nExiting')
-        sys.exit()
+        raise KeyError(f'No "task" attribute found')
 
     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
+    # 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
 

phys2bids/heuristics/heur_ex.py

@@ -32,14 +32,16 @@ def heur(physinfo, name, task='', acq='', direct='', rec='', run=''):
     else:
         # #!# Transform sys.exit in debug warnings or raiseexceptions!
         # #!# Make all of the above a dictionary
-        sys.exit()
+        raise Warning(f'The heuristic {__file__} could not deal with {physinfo}')
 
     if not task:
-        sys.exit()
+        raise KeyError(f'No "task" attribute found')
 
     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
+    # 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
 

phys2bids/heuristics/heur_test_acq.py

@@ -0,0 +1,55 @@
+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*'):
+        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
+        raise Warning(f'The heuristic {__file__} could not deal with {physinfo}')
+
+    if not task:
+        raise KeyError(f'No "task" attribute found')
+
+    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)