def test_plot_trigger(samefreq_full_acq_file):
chtrig = 3
test_path, test_filename = os.path.split(samefreq_full_acq_file)
out = os.path.join(test_path, 'Test_belt_pulse_samefreq')
phys_obj = io.load_acq(samefreq_full_acq_file, chtrig)
viz.plot_trigger(phys_obj.timeseries[0], phys_obj.timeseries[chtrig], out,
1.5, 1.6, 60, test_filename)
assert os.path.isfile(out + '_trigger_time.png')
def phys2bids(filename,
info=False,
indir='.',
outdir='.',
heur_file=None,
sub=None,
ses=None,
chtrig=0,
chsel=None,
num_timepoints_expected=0,
tr=1,
thr=None,
ch_name=[],
chplot='',
debug=False,
quiet=False):
"""
Main workflow of phys2bids.
Runs the parser, does some checks on input, then imports
the right interface file to read the input. If only info is required,
it returns a summary onscreen.
Otherwise, it operates on the input to return a .tsv.gz file, possibily
in BIDS format.
Raises
------
NotImplementedError
If the file extension is not supported yet.
"""
# Check options to make them internally coherent pt. I
# #!# This can probably be done while parsing?
outdir = utils.check_input_dir(outdir)
utils.path_exists_or_make_it(outdir)
# Create logfile name
basename = 'phys2bids_'
extension = 'tsv'
isotime = datetime.datetime.now().strftime('%Y-%m-%dT%H%M%S')
logname = os.path.join(outdir, (basename + isotime + '.' + extension))
# Set logging format
log_formatter = logging.Formatter(
'%(asctime)s\t%(name)-12s\t%(levelname)-8s\t%(message)s',
datefmt='%Y-%m-%dT%H:%M:%S')
# Set up logging file and open it for writing
log_handler = logging.FileHandler(logname)
log_handler.setFormatter(log_formatter)
sh = logging.StreamHandler()
if quiet:
logging.basicConfig(level=logging.WARNING, handlers=[log_handler, sh])
elif debug:
logging.basicConfig(level=logging.DEBUG, handlers=[log_handler, sh])
else:
logging.basicConfig(level=logging.INFO, handlers=[log_handler, sh])
version_number = _version.get_versions()['version']
LGR.info(f'Currently running phys2bids version {version_number}')
LGR.info(f'Input file is {filename}')
# Check options to make them internally coherent pt. II
# #!# This can probably be done while parsing?
indir = utils.check_input_dir(indir)
filename, ftype = utils.check_input_type(filename, indir)
if heur_file:
heur_file = utils.check_input_ext(heur_file, '.py')
utils.check_file_exists(heur_file)
infile = os.path.join(indir, filename)
utils.check_file_exists(infile)
# Read file!
if ftype == 'acq':
from phys2bids.interfaces.acq import populate_phys_input
elif ftype == 'txt':
from phys2bids.interfaces.txt import populate_phys_input
else:
# #!# We should add a logger here.
raise NotImplementedError('Currently unsupported file type.')
LGR.info(f'Reading the file {infile}')
phys_in = populate_phys_input(infile, chtrig)
LGR.info('Reading infos')
phys_in.print_info(filename)
# #!# Here the function viz.plot_channel should be called
if chplot != '' or info:
viz.plot_all(phys_in.ch_name, phys_in.timeseries, phys_in.units,
phys_in.freq, infile, chplot)
# If only info were asked, end here.
if info:
return
# Create trigger plot. If possible, to have multiple outputs in the same
# place, adds sub and ses label.
if tr != 0 and num_timepoints_expected != 0:
# Run analysis on trigger channel to get first timepoint and the time offset.
# #!# Get option of no trigger! (which is wrong practice or Respiract)
phys_in.check_trigger_amount(chtrig, thr, num_timepoints_expected, tr)
LGR.info('Plot trigger')
plot_path = os.path.join(
outdir,
os.path.splitext(os.path.basename(filename))[0])
if sub:
plot_path += f'_sub-{sub}'
if ses:
plot_path += f'_ses-{ses}'
viz.plot_trigger(phys_in.timeseries[0], phys_in.timeseries[chtrig],
plot_path, tr, phys_in.thr, num_timepoints_expected,
filename)
else:
LGR.warning('Skipping trigger pulse count. If you want to run it, '
'call phys2bids using "-ntp" and "-tr" arguments')
# The next few lines remove the undesired channels from phys_in.
if chsel:
LGR.info('Dropping unselected channels')
for i in reversed(range(0, phys_in.ch_amount)):
if i not in chsel:
phys_in.delete_at_index(i)
# If requested, change channel names.
if ch_name:
LGR.info('Renaming channels with given names')
phys_in.rename_channels(ch_name)
# The next few lines create a dictionary of different BlueprintInput
# objects, one for each unique frequency in phys_in
uniq_freq_list = set(phys_in.freq)
output_amount = len(uniq_freq_list)
if output_amount > 1:
LGR.warning(f'Found {output_amount} different frequencies in input!')
LGR.info(f'Preparing {output_amount} output files.')
phys_out = {} # create phys_out dict that will have a
# blueprint object per frequency
# for each different frequency
for uniq_freq in uniq_freq_list:
# copy the phys_in object to the new dict entry
phys_out[uniq_freq] = deepcopy(phys_in)
# this counter will take into account how many channels are eliminated
count = 0
# for each channel in the original phys_in object
# take the frequency
for idx, i in enumerate(phys_in.freq):
# if that frequency is different than the frequency of the phys_obj entry
if i != uniq_freq:
# eliminate that channel from the dict since we only want channels
# with the same frequency
phys_out[uniq_freq].delete_at_index(idx - count)
# take into acount the elimination so in the next eliminated channel we
# eliminate correctly
count += 1
# Also create a BlueprintOutput object for each unique frequency found.
# Populate it with the corresponding blueprint input and replace it
# in the dictionary.
phys_out[uniq_freq] = BlueprintOutput.init_from_blueprint(
phys_out[uniq_freq])
if heur_file and sub:
LGR.info(f'Preparing BIDS output using {heur_file}')
elif heur_file and not sub:
LGR.warning(f'While "-heur" was specified, option "-sub" was not.\n'
f'Skipping BIDS formatting.')
# Preparing output parameters: name and folder.
for uniq_freq in uniq_freq_list:
# If possible, prepare bids renaming.
if heur_file and sub:
if output_amount > 1:
# Add "recording-freq" to filename if more than one freq
outfile = use_heuristic(heur_file, sub, ses, filename, outdir,
uniq_freq)
else:
outfile = use_heuristic(heur_file, sub, ses, filename, outdir)
else:
outfile = os.path.join(
outdir,
os.path.splitext(os.path.basename(filename))[0])
if output_amount > 1:
# Append "freq" to filename if more than one freq
outfile = f'{outfile}_{uniq_freq}'
LGR.info(f'Exporting files for freq {uniq_freq}')
savetxt(outfile + '.tsv.gz',
phys_out[uniq_freq].timeseries,
fmt='%.8e',
delimiter='\t')
print_json(outfile, phys_out[uniq_freq].freq,
phys_out[uniq_freq].start_time, phys_out[uniq_freq].ch_name)
print_summary(filename, num_timepoints_expected,
phys_in.num_timepoints_found, uniq_freq,
phys_out[uniq_freq].start_time, outfile)
def _main(argv=None):
"""
Main workflow of phys2bids.
Runs the parser, does some checks on input, then imports
the right interface file to read the input. If only info is required,
it returns a summary onscreen.
Otherwise, it operates on the input to return a .tsv.gz file, possibily
in BIDS format.
"""
options = _get_parser().parse_args(argv)
# Check options to make them internally coherent
# #!# This can probably be done while parsing?
options.indir = utils.check_input_dir(options.indir)
options.outdir = utils.check_input_dir(options.outdir)
options.filename, ftype = utils.check_input_type(options.filename,
options.indir)
if options.heur_file:
options.heur_file = utils.check_input_ext(options.heur_file, '.py')
utils.check_file_exists(options.heur_file)
infile = os.path.join(options.indir, options.filename)
utils.check_file_exists(infile)
outfile = os.path.join(
options.outdir,
os.path.splitext(os.path.basename(options.filename))[0])
# Read file!
if ftype == 'acq':
from phys2bids.interfaces.acq import populate_phys_input
elif ftype == 'txt':
from phys2bids.interfaces.txt import populate_phys_input
else:
# #!# We should add a logger here.
raise NotImplementedError('Currently unsupported file type.')
print('Reading the file')
phys_in = populate_phys_input(infile, options.chtrig)
print('Reading infos')
phys_in.print_info(options.filename)
# #!# Here the function viz.plot_channel should be called
# for the desired channels.
# If only info were asked, end here.
if options.info:
return
# Run analysis on trigger channel to get first timepoint and the time offset.
# #!# Get option of no trigger! (which is wrong practice or Respiract)
phys_in.check_trigger_amount(options.thr, options.num_timepoints_expected,
options.tr)
# Create output folder if necessary
print('Checking that the output folder exists')
utils.path_exists_or_make_it(options.outdir)
# Create trigger plot. If possible, to have multiple outputs in the same
# place, adds sub and ses label.
print('Plot trigger')
plot_path = deepcopy(outfile)
if options.sub:
plot_path += f'_sub-{options.sub}'
if options.ses:
plot_path += f'_sub-{options.ses}'
viz.plot_trigger(phys_in.timeseries[0], phys_in.timeseries[1], plot_path,
options)
# The next few lines remove the undesired channels from phys_in.
if options.chsel:
print('Dropping unselected channels')
for i in reversed(range(0, phys_in.ch_amount)):
if i not in options.chsel:
phys_in.delete_at_index(i)
# If requested, change channel names.
if options.ch_name:
print('Renaming channels with given names')
phys_in.rename_channels(options.ch_name)
# The next few lines create a dictionary of different BlueprintInput
# objects, one for each unique frequency in phys_in
uniq_freq_list = set(phys_in.freq)
output_amount = len(uniq_freq_list)
if output_amount > 1:
print(f'Found {output_amount} different frequencies in input!')
print(f'Preparing {output_amount} output files.')
phys_out = {}
for uniq_freq in uniq_freq_list:
phys_out[uniq_freq] = deepcopy(phys_in)
for i in reversed(phys_in.freq):
if i != uniq_freq:
phys_out[uniq_freq].delete_at_index(phys_in.ch_amount - i - 1)
# Also create a BlueprintOutput object for each unique frequency found.
# Populate it with the corresponding blueprint input and replace it
# in the dictionary.
phys_out[uniq_freq] = BlueprintOutput.init_from_blueprint(
phys_out[uniq_freq])
if options.heur_file and options.sub:
print(f'Preparing BIDS output using {options.heur_file}')
elif options.heur_file and not options.sub:
print(f'While "-heur" was specified, option "-sub" was not.\n'
f'Skipping BIDS formatting.')
for uniq_freq in uniq_freq_list:
# If possible, prepare bids renaming.
if options.heur_file and options.sub:
if output_amount > 1:
# Add "recording-freq" to filename if more than one freq
outfile = use_heuristic(options.heur_file, options.sub,
options.ses, options.filename,
options.outdir, uniq_freq)
else:
outfile = use_heuristic(options.heur_file, options.sub,
options.ses, options.filename,
options.outdir)
elif output_amount > 1:
# Append "freq" to filename if more than one freq
outfile = f'outfile_{uniq_freq}'
print(f'Exporting files for freq {uniq_freq}')
savetxt(outfile + '.tsv.gz',
phys_out[uniq_freq].timeseries,
fmt='%.8e',
delimiter='\t')
print_json(outfile, phys_out[uniq_freq].freq,
phys_out[uniq_freq].start_time, phys_out[uniq_freq].ch_name)
print_summary(options.filename, options.num_timepoints_expected,
phys_in.num_timepoints_found, uniq_freq,
phys_out[uniq_freq].start_time, outfile)