FIX: Montage Index error when importing CNT files

[massich]

Fixes #5493

[codecov]

Codecov Report

Merging #6025 into master will increase coverage by 6.03%.
The diff coverage is 100%.

@@            Coverage Diff             @@
##           master    #6025      +/-   ##
==========================================
+ Coverage    81.3%   87.34%   +6.03%     
==========================================
  Files         402      402              
  Lines       73181    73162      -19     
  Branches    12163    12159       -4     
==========================================
+ Hits        59503    63904    +4401     
+ Misses      11021     6411    -4610     
- Partials     2657     2847     +190

[massich]

Just for the record, testing with some confidential files + some files on the web running the following

import mne
import pytest
import os.path as op
from datetime import datetime
from mne import __file__ as _mne_file
from mne.tests.test_annotations import _assert_annotations_equal

regular_path = op.join(op.dirname(_mne_file), '..', 'sandbox', 'data')
confidential_path = op.join(regular_path, 'confidential', 'cnt')

flankers_path = op.join(regular_path, '914flankers.cnt')

cnt_files_with_eeglab_pair = [
    op.join(confidential_path, 'BoyoAEpic1_16bit.cnt'),
    op.join(confidential_path, 'cont_67chan_resp_32bit.cnt'),
    op.join(confidential_path, 'SampleCNTFile_16bit.cnt')
]


def test_ensure_meas_date(recwarn):
    raw = mne.io.read_raw_cnt(flankers_path, montage=None,
                              date_format='dd/mm/yy')
    meas_date = (datetime
                 .fromtimestamp(raw.info['meas_date'][0])
                 .strftime('%d/%m/%y %H:%M:%S'))

    assert meas_date == '23/09/07 12:22:15'


@pytest.mark.parametrize('fname', cnt_files_with_eeglab_pair, ids=op.basename)
def test_check_cnt_eeglab_pairs(fname, recwarn):
    raw_eeglab = mne.io.read_raw_eeglab(fname.replace('.cnt', '.set'),
                                        montage=None)
    raw_cnt = mne.io.read_raw_cnt(fname, montage=None)

    assert raw_cnt.info.keys() == raw_eeglab.info.keys()
    xx = object_diff(raw_cnt.info, raw_eeglab.info)
    print(xx)

I get:

• The date work properly,
• the info difference between cnt and its transformed eeglab version are
  • the subject_info anonymization (eeglab is none cnt has empty fields)
  • digitization mismatch (but this is beeing addressed somwhere else)
  • for one file cnt has a trigger channel marked as bad that does not appear in the eeglab version of the file.

['chs'][63]['cal'] type mismatch (<class 'numpy.ndarray'>, <class 'float'>)
['chs'][63]['coord_frame'] value mismatch (4, 0)
['chs'][63]['loc'] array mismatch
['chs'][63]['unit_mul'] type mismatch (<class 'float'>, <class 'int'>)
['subject_info'] type mismatch (<class 'dict'>, <class 'NoneType'>)

[massich]

Most probably I'm breaking something here.

[massich]

reading 914flankers.cnt in master:

>               stim_channel[event_time - 1] = event_id
E               IndexError: index 583988 is out of bounds for axis 0 with size 582560

in this PR:

 sandbox/mwe/5493_montage_index_error.py ✓                                                100% ██████████
-------------------- generated xml file: /home/sik/code/mne-python/junit-results.xml --------------------
======================================= slowest 20 test durations =======================================
1.34s setup    sandbox/mwe/5493_montage_index_error.py::test_foo
0.02s call     sandbox/mwe/5493_montage_index_error.py::test_foo

(0.00 durations hidden.  Use -vv to show these durations.)

Results (1.55s):
       1 passed

[massich]

This PR goes after #6047 and misses whatsnew

[massich]

rootdir: /home/sik/code/mne-python, inifile: setup.cfg
plugins: timeout-1.3.3, sugar-0.9.2, mock-1.10.1, faulthandler-1.5.0, cov-2.6.1
timeout: 30.0s
timeout method: signal
timeout func_only: False
collecting ... 1526

 sandbox/mwe/5493_montage_index_error.py ✓                                       100% ██████████
--------------- generated xml file: /home/sik/code/mne-python/junit-results.xml ----------------
================================== slowest 20 test durations ===================================
1.29s setup    sandbox/mwe/5493_montage_index_error.py::test_foo
0.01s call     sandbox/mwe/5493_montage_index_error.py::test_foo

(0.00 durations hidden.  Use -vv to show these durations.)

Results (1.62s):
       1 passed

Compilation finished at Mon Mar 18 15:10:42

It reads without error and recovers 1526 events

[agramfort]

thx @massich