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Create folder code/conversion to store trigger and channel plots, yaml and heuristic files and the call.sh file #256

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merged 17 commits into from
Jun 18, 2020
Merged

Create folder code/conversion to store trigger and channel plots, yaml and heuristic files and the call.sh file #256

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c0d4b85
initial commit add the create path check
vinferrer Jun 18, 2020
b21cc7b
change log file path
vinferrer Jun 18, 2020
98feed7
add conversion path to the integration test for later
vinferrer Jun 18, 2020
258ed59
change log file dirs
vinferrer Jun 18, 2020
60bc494
change plot_all path
vinferrer Jun 18, 2020
ac645e1
change channel plot path
vinferrer Jun 18, 2020
79cd7c5
Merge branch 'master' of https://github.com/physiopy/phys2bids into f…
vinferrer Jun 18, 2020
87dede0
copy heur to conversion folder
vinferrer Jun 18, 2020
02fe0c2
change trigger path
vinferrer Jun 18, 2020
5f4a750
change summary log dir
vinferrer Jun 18, 2020
ce6325c
solve test_integrations path problems
vinferrer Jun 18, 2020
848a555
linting
vinferrer Jun 18, 2020
b58b76e
linting problems
vinferrer Jun 18, 2020
ea7660b
Add call string
eurunuela Jun 18, 2020
b496730
Merge branch 'file_restruct' of https://github.com/vinferrer/phys2bid…
eurunuela Jun 18, 2020
85e3a01
Save call.sh into code/conversion folder
eurunuela Jun 18, 2020
3bd02ff
Add test to check call.sh is generated
eurunuela Jun 18, 2020
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27 changes: 21 additions & 6 deletions phys2bids/phys2bids.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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

Expand Down Expand Up @@ -131,14 +133,17 @@ 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(
Expand All @@ -164,6 +169,13 @@ 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)
Expand Down Expand Up @@ -194,7 +206,7 @@ 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
Expand All @@ -206,7 +218,7 @@ 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}'
Expand Down Expand Up @@ -272,6 +284,8 @@ 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.')
Expand Down Expand Up @@ -303,7 +317,8 @@ 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):
Expand All @@ -312,7 +327,7 @@ def _main(argv=None):


if __name__ == '__main__':
_main()
_main(sys.argv[1:])

"""
Copyright 2019, The Phys2BIDS community.
Expand Down
67 changes: 36 additions & 31 deletions phys2bids/tests/test_integration.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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()

Expand All @@ -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):
Expand All @@ -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)
Expand All @@ -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
Expand Down Expand Up @@ -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):
Expand All @@ -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)
Expand All @@ -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
Expand All @@ -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):
Expand All @@ -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)
Expand All @@ -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
Expand All @@ -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
Expand All @@ -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
Expand All @@ -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
Expand All @@ -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):
Expand All @@ -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
Expand All @@ -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
Expand Down Expand Up @@ -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):
Expand All @@ -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
Expand All @@ -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()

Expand All @@ -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)