def _main(argv=None):
options = _get_parser().parse_args(argv)
phys2bids(**vars(options))
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)