Merge pull request #256 from vinferrer/file_restruct

Create folder code/conversion to store trigger and channel plots, yaml and heuristic files and the call.sh file

phys2bids/phys2bids.py

@@ -26,10 +26,12 @@
 
 """
 
-import os
 import datetime
 import logging
+import os
+import sys
 from copy import deepcopy
+from shutil import copy as cp
 
 from numpy import savetxt
 
@@ -145,14 +147,17 @@ def phys2bids(filename, info=False, indir='.', outdir='.', heur_file=None,
     # #!# This can probably be done while parsing?
     outdir = utils.check_input_dir(outdir)
     utils.path_exists_or_make_it(outdir)
+    utils.path_exists_or_make_it(os.path.join(outdir, 'code'))
+    conversion_path = os.path.join(outdir, 'code/conversion')
+    utils.path_exists_or_make_it(conversion_path)
     # generate extra path
     extra_dir = os.path.join(outdir, 'bids_ignore')
     utils.path_exists_or_make_it(extra_dir)
     # Create logfile name
     basename = 'phys2bids_'
     extension = 'tsv'
     isotime = datetime.datetime.now().strftime('%Y-%m-%dT%H%M%S')
-    logname = os.path.join(extra_dir, (basename + isotime + '.' + extension))
+    logname = os.path.join(conversion_path, (basename + isotime + '.' + extension))
 
     # Set logging format
     log_formatter = logging.Formatter(
@@ -178,6 +183,13 @@ def phys2bids(filename, info=False, indir='.', outdir='.', heur_file=None,
     LGR.info(f'Currently running phys2bids version {version_number}')
     LGR.info(f'Input file is {filename}')
 
+    # Save call.sh
+    arg_str = ' '.join(sys.argv[1:])
+    call_str = f'phys2bids {arg_str}'
+    f = open(os.path.join(conversion_path, 'call.sh'), "a")
+    f.write(f'#!bin/bash \n{call_str}')
+    f.close()
+
     # Check options to make them internally coherent pt. II
     # #!# This can probably be done while parsing?
     indir = utils.check_input_dir(indir)
@@ -208,7 +220,7 @@ def phys2bids(filename, info=False, indir='.', outdir='.', heur_file=None,
     phys_in.print_info(filename)
     # #!# Here the function viz.plot_channel should be called
     viz.plot_all(phys_in.ch_name, phys_in.timeseries, phys_in.units,
-                 phys_in.freq, infile, extra_dir)
+                 phys_in.freq, infile, conversion_path)
     # If only info were asked, end here.
     if info:
         return
@@ -220,7 +232,7 @@ def phys2bids(filename, info=False, indir='.', outdir='.', heur_file=None,
         # #!# Get option of no trigger! (which is wrong practice or Respiract)
         phys_in.check_trigger_amount(thr, num_timepoints_expected, tr)
         LGR.info('Plot trigger')
-        plot_path = os.path.join(extra_dir,
+        plot_path = os.path.join(conversion_path,
                                  os.path.splitext(os.path.basename(filename))[0])
         if sub:
             plot_path += f'_sub-{sub}'
@@ -286,6 +298,8 @@ def phys2bids(filename, info=False, indir='.', outdir='.', heur_file=None,
         bids.dataset_description_file(outdir)
         # Generate README file if it doesn't exist already.
         bids.readme_file(outdir)
+        cp(heur_file, os.path.join(conversion_path,
+           os.path.splitext(os.path.basename(heur_file))[0] + '.py'))
     elif heur_file and not sub:
         LGR.warning('While "-heur" was specified, option "-sub" was not.\n'
                     'Skipping BIDS formatting.')
@@ -317,7 +331,8 @@ def phys2bids(filename, info=False, indir='.', outdir='.', heur_file=None,
         print_summary(filename, num_timepoints_expected,
                       phys_in.num_timepoints_found, uniq_freq,
                       phys_out[uniq_freq].start_time,
-                      os.path.join(extra_dir, os.path.splitext(os.path.basename(outfile))[0]))
+                      os.path.join(conversion_path,
+                                   os.path.splitext(os.path.basename(outfile))[0]))
 
 
 def _main(argv=None):
@@ -326,7 +341,7 @@ def _main(argv=None):
 
 
 if __name__ == '__main__':
-    _main()
+    _main(sys.argv[1:])
 
 """
 Copyright 2019, The Phys2BIDS community.

phys2bids/tests/test_integration.py

@@ -34,14 +34,16 @@ def test_logger(multifreq_lab_file):
     test_chtrig = 3
     test_ntp = 1
     test_outdir = test_path
-    extra_dir = os.path.join(test_path, 'bids_ignore')
+    conversion_path = os.path.join(test_path, 'code/conversion')
     # Phys2bids call through terminal
     subprocess.run(f'phys2bids -in {test_filename} -indir {test_path} '
                    f'-chtrig {test_chtrig} -ntp {test_ntp} -outdir {test_outdir}',
                    shell=True, check=True)
 
+    assert os.path.isfile(os.path.join(conversion_path, 'call.sh'))
+
     # Read logger file
-    logger_file = glob.glob(os.path.join(extra_dir, '*phys2bids*'))[0]
+    logger_file = glob.glob(os.path.join(conversion_path, '*phys2bids*'))[0]
     with open(logger_file) as logger_info:
         logger_info = logger_info.readlines()
 
@@ -51,6 +53,7 @@ def test_logger(multifreq_lab_file):
 
     # Removes generated files
     os.remove(os.path.join(test_path, logger_file))
+    shutil.rmtree(conversion_path)
 
 
 def test_integration_txt(samefreq_short_txt_file):
@@ -60,7 +63,7 @@ def test_integration_txt(samefreq_short_txt_file):
 
     test_path, test_filename = os.path.split(samefreq_short_txt_file)
     test_chtrig = 2
-    extra_dir = os.path.join(test_path, 'bids_ignore')
+    conversion_path = os.path.join(test_path, 'code/conversion')
 
     phys2bids(filename=test_filename, indir=test_path, outdir=test_path,
               chtrig=test_chtrig, num_timepoints_expected=1)
@@ -71,10 +74,11 @@ def test_integration_txt(samefreq_short_txt_file):
 
     # Check files in extra are generated
     for suffix in ['.log', '_trigger_time.png']:
-        assert os.path.isfile(os.path.join(extra_dir, 'Test_belt_pulse_samefreq_short' + suffix))
+        assert os.path.isfile(os.path.join(conversion_path,
+                                           'Test_belt_pulse_samefreq_short' + suffix))
 
     # Read log file (note that this file is not the logger file)
-    with open(os.path.join(extra_dir, 'Test_belt_pulse_samefreq_short.log')) as log_info:
+    with open(os.path.join(conversion_path, 'Test_belt_pulse_samefreq_short.log')) as log_info:
         log_info = log_info.readlines()
 
     # Check timepoints expected
@@ -102,7 +106,7 @@ def test_integration_txt(samefreq_short_txt_file):
         os.remove(filename)
     for filename in glob.glob(os.path.join(test_path, 'Test_belt_pulse_samefreq_short*')):
         os.remove(filename)
-    shutil.rmtree(extra_dir)
+    shutil.rmtree(conversion_path)
 
 
 def test_integration_acq(samefreq_full_acq_file):
@@ -112,7 +116,7 @@ def test_integration_acq(samefreq_full_acq_file):
 
     test_path, test_filename = os.path.split(samefreq_full_acq_file)
     test_chtrig = 3
-    extra_dir = os.path.join(test_path, 'bids_ignore')
+    conversion_path = os.path.join(test_path, 'code/conversion')
 
     phys2bids(filename=test_filename, indir=test_path, outdir=test_path,
               chtrig=test_chtrig, num_timepoints_expected=1)
@@ -123,10 +127,10 @@ def test_integration_acq(samefreq_full_acq_file):
 
     # Check files in extra are generated
     for suffix in ['.log', '_trigger_time.png']:
-        assert os.path.isfile(os.path.join(extra_dir, 'Test_belt_pulse_samefreq' + suffix))
+        assert os.path.isfile(os.path.join(conversion_path, 'Test_belt_pulse_samefreq' + suffix))
 
     # Read log file (note that this file is not the logger file)
-    with open(os.path.join(extra_dir, 'Test_belt_pulse_samefreq.log')) as log_info:
+    with open(os.path.join(conversion_path, 'Test_belt_pulse_samefreq.log')) as log_info:
         log_info = log_info.readlines()
 
     # Check timepoints expected
@@ -151,11 +155,11 @@ def test_integration_acq(samefreq_full_acq_file):
                                     'MR TRIGGER - Custom, HLT100C - A 5', 'PPG100C', 'CO2', 'O2']
 
     # Remove generated files
-    for filename in glob.glob(os.path.join(extra_dir, 'phys2bids*')):
+    for filename in glob.glob(os.path.join(conversion_path, 'phys2bids*')):
         os.remove(filename)
     for filename in glob.glob(os.path.join(test_path, 'Test_belt_pulse_samefreq*')):
         os.remove(filename)
-    shutil.rmtree(extra_dir)
+    shutil.rmtree(conversion_path)
 
 
 def test_integration_multifreq(multifreq_lab_file):
@@ -165,7 +169,7 @@ def test_integration_multifreq(multifreq_lab_file):
 
     test_path, test_filename = os.path.split(multifreq_lab_file)
     test_chtrig = 3
-    extra_dir = os.path.join(test_path, 'bids_ignore')
+    conversion_path = os.path.join(test_path, 'code/conversion')
 
     phys2bids(filename=test_filename, indir=test_path, outdir=test_path,
               chtrig=test_chtrig, num_timepoints_expected=1)
@@ -184,15 +188,16 @@ def test_integration_multifreq(multifreq_lab_file):
         assert os.path.isfile(os.path.join(test_path,
                                            'Test1_multifreq_onescan_1000.0' + suffix))
     for freq in ['40', '100', '500', '1000']:
-        assert os.path.isfile(os.path.join(extra_dir,
+        assert os.path.isfile(os.path.join(conversion_path,
                                            'Test1_multifreq_onescan_' + freq + '.log'))
-    assert os.path.isfile(os.path.join(extra_dir, 'Test1_multifreq_onescan_trigger_time.png'))
+    assert os.path.isfile(os.path.join(conversion_path,
+                          'Test1_multifreq_onescan_trigger_time.png'))
 
     """
     Checks 40 Hz output
     """
     # Read log file of frequency 625 (note that this file is not the logger file)
-    with open(os.path.join(extra_dir, 'Test1_multifreq_onescan_40.log')) as log_info:
+    with open(os.path.join(conversion_path, 'Test1_multifreq_onescan_40.log')) as log_info:
         log_info = log_info.readlines()
 
     # Check timepoints expected
@@ -219,7 +224,7 @@ def test_integration_multifreq(multifreq_lab_file):
     Checks 100 Hz output
     """
     # Read log file of frequency 625 (note that this file is not the logger file)
-    with open(os.path.join(extra_dir, 'Test1_multifreq_onescan_100.log')) as log_info:
+    with open(os.path.join(conversion_path, 'Test1_multifreq_onescan_100.log')) as log_info:
         log_info = log_info.readlines()
 
     # Check timepoints expected
@@ -246,7 +251,7 @@ def test_integration_multifreq(multifreq_lab_file):
     Checks 500 Hz output
     """
     # Read log file of frequency 625 (note that this file is not the logger file)
-    with open(os.path.join(extra_dir, 'Test1_multifreq_onescan_500.log')) as log_info:
+    with open(os.path.join(conversion_path, 'Test1_multifreq_onescan_500.log')) as log_info:
         log_info = log_info.readlines()
 
     # Check timepoints expected
@@ -273,7 +278,7 @@ def test_integration_multifreq(multifreq_lab_file):
     Checks 1000 Hz output
     """
     # Read log file of frequency 625 (note that this file is not the logger file)
-    with open(os.path.join(extra_dir, 'Test1_multifreq_onescan_1000.log')) as log_info:
+    with open(os.path.join(conversion_path, 'Test1_multifreq_onescan_1000.log')) as log_info:
         log_info = log_info.readlines()
 
     # Check timepoints expected
@@ -297,11 +302,11 @@ def test_integration_multifreq(multifreq_lab_file):
     assert json_data['Columns'] == ['time', 'Trigger']
 
     # Remove generated files
-    for filename in glob.glob(os.path.join(extra_dir, 'phys2bids*')):
+    for filename in glob.glob(os.path.join(conversion_path, 'phys2bids*')):
         os.remove(filename)
     for filename in glob.glob(os.path.join(test_path, 'Test_belt_pulse_multifreq*')):
         os.remove(filename)
-    shutil.rmtree(extra_dir)
+    shutil.rmtree(conversion_path)
 
 
 def test_integration_heuristic(samefreq_short_txt_file):
@@ -313,7 +318,7 @@ def test_integration_heuristic(samefreq_short_txt_file):
     test_full_path = os.path.join(test_path, test_filename)
     test_chtrig = 1
     test_outdir = test_path
-    extra_dir = os.path.join(test_path, 'bids_ignore')
+    conversion_path = os.path.join(test_path, 'code/conversion')
     test_ntp = 158
     test_tr = 1.2
     test_thr = 0.735
@@ -329,10 +334,10 @@ def test_integration_heuristic(samefreq_short_txt_file):
     base_filename = 'sub-006_ses-01_task-test_rec-biopac_run-01_physio'
     for suffix in ['.json', '.tsv.gz']:
         assert os.path.isfile(os.path.join(test_path_output, base_filename + suffix))
-    assert os.path.isfile(os.path.join(extra_dir, base_filename + '.log'))
+    assert os.path.isfile(os.path.join(conversion_path, base_filename + '.log'))
     # Read log file (note that this file is not the logger file)
     log_filename = 'sub-006_ses-01_task-test_rec-biopac_run-01_physio.log'
-    with open(os.path.join(extra_dir, log_filename)) as log_info:
+    with open(os.path.join(conversion_path, log_filename)) as log_info:
         log_info = log_info.readlines()
 
     # Check timepoints expected
@@ -370,13 +375,13 @@ def test_integration_heuristic(samefreq_short_txt_file):
             counter += 1
 
     # Remove generated files
-    for filename in glob.glob(os.path.join(extra_dir, 'phys2bids*')):
+    for filename in glob.glob(os.path.join(conversion_path, 'phys2bids*')):
         os.remove(filename)
     for filename in glob.glob(os.path.join(test_path, 'Test_belt_pulse_samefreq*')):
         os.remove(filename)
     for filename in glob.glob(os.path.join(test_path_output, '*')):
         os.remove(filename)
-    shutil.rmtree(extra_dir)
+    shutil.rmtree(conversion_path)
 
 
 def test_integration_info(samefreq_short_txt_file):
@@ -390,7 +395,7 @@ def test_integration_info(samefreq_short_txt_file):
     test_ntp = 158
     test_tr = 1.2
     test_thr = 0.735
-    extra_dir = os.path.join(test_path, 'bids_ignore')
+    conversion_path = os.path.join(test_path, 'code/conversion')
     # Move into folder
     subprocess.run(f'cd {test_path}', shell=True, check=True)
     # Phys2bids call through terminal
@@ -402,11 +407,11 @@ def test_integration_info(samefreq_short_txt_file):
     subprocess.run(command_str, shell=True, check=True)
 
     # Check that plot all file is generated
-    assert os.path.isfile(os.path.join(test_outdir,
-                                       'bids_ignore/Test_belt_pulse_samefreq_short.png'))
+    assert os.path.isfile(os.path.join(conversion_path,
+                                       'Test_belt_pulse_samefreq_short.png'))
 
     # Read logger file
-    logger_file = glob.glob(os.path.join(extra_dir, '*phys2bids*'))[0]
+    logger_file = glob.glob(os.path.join(conversion_path, '*phys2bids*'))[0]
     with open(logger_file) as logger_info:
         logger_info = logger_info.readlines()
 
@@ -415,6 +420,6 @@ def test_integration_info(samefreq_short_txt_file):
                         '02. MR TRIGGER - Custom, HLT100C - A 5; sampled at', '10000.0')
 
     # Remove generated files
-    for filename in glob.glob(os.path.join(extra_dir, 'phys2bids*')):
+    for filename in glob.glob(os.path.join(conversion_path, 'phys2bids*')):
         os.remove(filename)
-    shutil.rmtree(extra_dir)
+    shutil.rmtree(conversion_path)