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Correct trigger channel indexing while reading AcqKnowledge files. #275

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merged 7 commits into from
Jul 16, 2020
Merged

Correct trigger channel indexing while reading AcqKnowledge files. #275

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07ddced
Correct chtrig extraction, add explanation in the docstring
Jul 7, 2020
37673dc
Update phys2bids/interfaces/acq.py
Jul 7, 2020
542a271
Update phys2bids/interfaces/acq.py
Jul 7, 2020
be2a485
Revert docstring
Jul 7, 2020
2af654b
Set default chtrig as 1
Jul 7, 2020
d227c37
Change default chtrig to 1, add check.
Jul 7, 2020
528912b
Update phys2bids/phys2bids.py
Jul 9, 2020
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6 changes: 3 additions & 3 deletions phys2bids/cli/run.py
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Original file line number Diff line number Diff line change
Expand Up @@ -76,9 +76,9 @@ def _get_parser():
dest='chtrig',
type=int,
help='The column number of the trigger channel. '
'Channel numbering starts with 0. '
'Default is 0.',
default=0)
'Channel numbering starts with 1. '
'Default is 1.',
default=1)
optional.add_argument('-chsel', '--channel-selection',
dest='chsel',
nargs='*',
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14 changes: 10 additions & 4 deletions phys2bids/interfaces/acq.py
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Expand Up @@ -21,23 +21,29 @@ def populate_phys_input(filename, chtrig):
filename: str
path to the txt labchart file
chtrig : int
index of trigger channel
index of trigger channel.
!!! ATTENTION: IT'S MEANT TO REPRESENT AN INDEX STARTING FROM 1 !!!

Returns
-------
BlueprintInput

Note
----
chtrig is not a 0-based Python index - instead, it's human readable (i.e., 1-based).
This is handy because, when initialising the class, a new channel corresponding
to time is added at the beginning - that is already taken into account!

See Also
--------
physio_obj.BlueprintInput
"""

with warnings.catch_warnings():
warnings.filterwarnings('ignore', category=DeprecationWarning)
data = read_file(filename).channels

freq = [data[chtrig].samples_per_second, ]
timeseries = [data[chtrig].time_index, ]
freq = [data[chtrig - 1].samples_per_second, ]
timeseries = [data[chtrig - 1].time_index, ]
units = ['s', ]
names = ['time', ]

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5 changes: 4 additions & 1 deletion phys2bids/phys2bids.py
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Original file line number Diff line number Diff line change
Expand Up @@ -127,7 +127,7 @@ def print_json(outfile, samp_freq, time_offset, ch_name):
description='The BIDS specification',
cite_module=True)
def phys2bids(filename, info=False, indir='.', outdir='.', heur_file=None,
sub=None, ses=None, chtrig=0, chsel=None, num_timepoints_expected=None,
sub=None, ses=None, chtrig=1, chsel=None, num_timepoints_expected=None,
tr=None, thr=None, pad=9, ch_name=[], yml='', debug=False, quiet=False):
"""
Run main workflow of phys2bids.
Expand Down Expand Up @@ -191,6 +191,9 @@ def phys2bids(filename, info=False, indir='.', outdir='.', heur_file=None,
# Check options to make them internally coherent pt. II
# #!# This can probably be done while parsing?
indir = utils.check_input_dir(indir)
if chtrig < 1:
raise Exception('Wrong trigger channel. Channel indexing starts with 1!')

filename, ftype = utils.check_input_type(filename,
indir)

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