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Adding txt support for labchart #54

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merged 18 commits into from
Dec 2, 2019
Merged

Adding txt support for labchart #54

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e03ba6c
add labchart testing file from chicago
vinferrer Nov 29, 2019
a2b0fc7
Merge branch 'master' of https://github.com/smoia/phys2bids into txt
vinferrer Nov 29, 2019
b41cea1
add interface for reading txt files from labchart
vinferrer Nov 29, 2019
862c42a
correct bug on line 140 so 0.0 is a float
vinferrer Nov 29, 2019
d3c1369
change first comment to say that the interface is for txt
vinferrer Nov 29, 2019
179a5bf
add function identation and eliminate remains from acq.py
vinferrer Nov 29, 2019
6274b39
add txt to supported files
vinferrer Nov 29, 2019
305848f
eliminate raise error for txt and make proper import
vinferrer Nov 29, 2019
459f52f
Update phys2bids/interfaces/txt.py
vinferrer Nov 30, 2019
66abb3d
Update phys2bids/interfaces/txt.py
vinferrer Nov 30, 2019
8a3ce1c
Update phys2bids/interfaces/txt.py
vinferrer Nov 30, 2019
0cdaa65
Update phys2bids/interfaces/txt.py
vinferrer Nov 30, 2019
2fb361c
reformulate phrase
vinferrer Nov 30, 2019
49f74a1
Merge branch 'txt' of github.com:vinferrer/phys2bids into txt
vinferrer Nov 30, 2019
2d13556
reoder imports and add channel ordering functionality
vinferrer Nov 30, 2019
10d7a18
add docstring
vinferrer Nov 30, 2019
2618250
call trigger channel 'trigger' hardcoding and revise docstring identa…
vinferrer Dec 2, 2019
d91682a
change output description
vinferrer Dec 2, 2019
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14 changes: 10 additions & 4 deletions phys2bids/interfaces/txt.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,9 +5,9 @@
phys2bids interface for txt files.
"""

import numpy as np
from phys2bids.physio_obj import BlueprintInput

import numpy as np
def populate_phys_input(filename, chtrig):
"""
Populate object phys_input
Expand Down Expand Up @@ -54,10 +54,16 @@ def populate_phys_input(filename, chtrig):
for item in range_list:
units.append(item.split(' ')[1])
# get names
header[4][1:]
names = ['time']+header[4][1:]
orig_names=header[4][1:]
names = ['time',orig_names[chtrig]]
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orig_names.pop(chtrig)
names=names+orig_names
# get channels
timeseries = np.matrix(channel_list).T.tolist()
freq = [1/interval[0]]*len(timeseries)
timeseries=[np.array(darray) for darray in timeseries]
return BlueprintInput(timeseries, freq, names, units)
ordered_timeseries=[timeseries[0],timeseries[chtrig]]
timeseries.pop(chtrig)
timeseries.pop(0)
ordered_timeseries=ordered_timeseries+timeseries
return BlueprintInput(ordered_timeseries, freq, names, units)