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MNE: Magnetoencephalography (MEG) and Electroencephalography (EEG) in Python
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MNE-Python failing test_io_set from mne.io.eeglab.tests.test_eeglab #4855

Closed smgutstein closed 6 years ago

smgutstein commented 6 years ago

I have just downloaded the most recent (?) version of mne-python

commit 79959786786311aedd20da272fb4de94a20f16ef
Author: Eric Larson <larson.eric.d@gmail.com>
Date:   Wed Dec 27 05:56:13 2017 -0500

but it is failing the following test:

>>> from mne.io.eeglab.tests.test_eeglab import test_io_set
>>> test_io_set()
/usr/local/lib/python2.7/dist-packages/scipy/special/__init__.py:627: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from ._ufuncs import *
/usr/local/lib/python2.7/dist-packages/scipy/special/__init__.py:627: RuntimeWarning: numpy.ufunc size changed, may indicate binary incompatibility. Expected 192, got 176
  from ._ufuncs import *
/usr/local/lib/python2.7/dist-packages/scipy/special/__init__.py:627: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from ._ufuncs import *
/usr/local/lib/python2.7/dist-packages/scipy/special/__init__.py:627: RuntimeWarning: numpy.ufunc size changed, may indicate binary incompatibility. Expected 192, got 176
  from ._ufuncs import *
/usr/local/lib/python2.7/dist-packages/scipy/special/_ellip_harm.py:7: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from ._ellip_harm_2 import _ellipsoid, _ellipsoid_norm
/usr/local/lib/python2.7/dist-packages/scipy/special/_ellip_harm.py:7: RuntimeWarning: numpy.ufunc size changed, may indicate binary incompatibility. Expected 192, got 176
  from ._ellip_harm_2 import _ellipsoid, _ellipsoid_norm
/usr/local/lib/python2.7/dist-packages/scipy/io/matlab/mio4.py:18: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from .mio_utils import squeeze_element, chars_to_strings
/usr/local/lib/python2.7/dist-packages/scipy/io/matlab/mio4.py:18: RuntimeWarning: numpy.ufunc size changed, may indicate binary incompatibility. Expected 192, got 176
  from .mio_utils import squeeze_element, chars_to_strings
/usr/local/lib/python2.7/dist-packages/scipy/io/matlab/mio5.py:98: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  from .mio5_utils import VarReader5
/usr/local/lib/python2.7/dist-packages/scipy/io/matlab/mio5.py:98: RuntimeWarning: numpy.ufunc size changed, may indicate binary incompatibility. Expected 192, got 176
  from .mio5_utils import VarReader5
Events like the following will be dropped entirely: ['rt', 'square'], 2 in total
154/154 event codes could not be mapped to integers. Use the 'event_id' parameter to map such events manually.
As is, the trigger channel will consist entirely of zeros.
Reading /home/smgutstein/mne_data/MNE-testing-data/EEGLAB/test_raw.fdt
Reading 0 ... 30503  =      0.000 ...   238.305 secs...
Events like the following will be dropped entirely: ['rt', 'square'], 2 in total
154/154 event codes could not be mapped to integers. Use the 'event_id' parameter to map such events manually.
As is, the trigger channel will consist entirely of zeros.
Reading /home/smgutstein/mne_data/MNE-testing-data/EEGLAB/test_raw.fdt
Reading 0 ... 30503  =      0.000 ...   238.305 secs...
Events like the following will be dropped entirely: ['rt', 'square'], 2 in total
154/154 event codes could not be mapped to integers. Use the 'event_id' parameter to map such events manually.
As is, the trigger channel will consist entirely of zeros.
Reading /home/smgutstein/mne_data/MNE-testing-data/EEGLAB/test_raw.fdt
Writing /tmp/tmp_mne_tempdir_3X7w0m/test_raw.fif
Closing /tmp/tmp_mne_tempdir_3X7w0m/test_raw.fif [done]
Opening raw data file /tmp/tmp_mne_tempdir_3X7w0m/test_raw.fif...
    Range : 0 ... 30503 =      0.000 ...   238.305 secs
Ready.
Events like the following will be dropped entirely: ['rt', 'square'], 2 in total
154/154 event codes could not be mapped to integers. Use the 'event_id' parameter to map such events manually.
As is, the trigger channel will consist entirely of zeros.
Events like the following will be dropped entirely: ['rt', 'square'], 2 in total
154/154 event codes could not be mapped to integers. Use the 'event_id' parameter to map such events manually.
As is, the trigger channel will consist entirely of zeros.
Data will be preloaded. preload=False or a string preload is not supported when the data is stored in the .set file
Events like the following will be dropped entirely: ['rt', 'square'], 2 in total
154/154 event codes could not be mapped to integers. Use the 'event_id' parameter to map such events manually.
As is, the trigger channel will consist entirely of zeros.
Data will be preloaded. preload=False or a string preload is not supported when the data is stored in the .set file
Writing /tmp/tmp_mne_tempdir_uwBxz0/test_raw.fif
Closing /tmp/tmp_mne_tempdir_uwBxz0/test_raw.fif [done]
Opening raw data file /tmp/tmp_mne_tempdir_uwBxz0/test_raw.fif...
    Range : 0 ... 30503 =      0.000 ...   238.305 secs
Ready.
Reading /home/smgutstein/mne_data/MNE-testing-data/EEGLAB/test_raw.fdt
Reading 0 ... 30503  =      0.000 ...   238.305 secs...
Reading /home/smgutstein/mne_data/MNE-testing-data/EEGLAB/test_raw.fdt
Data will be preloaded. preload=False or a string preload is not supported when the data is stored in the .set file
Reading /home/smgutstein/mne_data/MNE-testing-data/EEGLAB/test_raw.fdt
Events like the following will be dropped entirely: ['rt', 'square'], 2 in total
154/154 event codes could not be mapped to integers. Use the 'event_id' parameter to map such events manually.
As is, the trigger channel will consist entirely of zeros.
Reading /home/smgutstein/mne_data/MNE-testing-data/EEGLAB/test_raw.fdt
154 events found
Event IDs: [1 2]
154 matching events found
Applying baseline correction (mode: mean)
Not setting metadata
0 projection items activated
154 events found
Event IDs: [1 2]
154 matching events found
Applying baseline correction (mode: mean)
Not setting metadata
0 projection items activated
Setting up high-pass filter at 1 Hz
l_trans_bandwidth chosen to be 1.0 Hz
Filter length of 423 samples (3.305 sec) selected
Reading /home/smgutstein/mne_data/MNE-testing-data/EEGLAB/test_raw.fdt
At least one epoch has multiple events. Only the latency of the first event will be retained.
Extracting parameters from /home/smgutstein/mne_data/MNE-testing-data/EEGLAB/test_epochs.set...
4 matching events found
No baseline correction applied
Not setting metadata
0 projection items activated
Ready.
At least one epoch has multiple events. Only the latency of the first event will be retained.
Extracting parameters from /home/smgutstein/mne_data/MNE-testing-data/EEGLAB/test_epochs_onefile.set...
4 matching events found
No baseline correction applied
Not setting metadata
0 projection items activated
Ready.
Extracting parameters from /home/smgutstein/mne_data/MNE-testing-data/EEGLAB/test_epochs.set...
4 matching events found
No baseline correction applied
Not setting metadata
0 projection items activated
Ready.
Extracting parameters from /home/smgutstein/mne_data/MNE-testing-data/EEGLAB/test_epochs.set...
4 matching events found
No baseline correction applied
Not setting metadata
0 projection items activated
Ready.
Reading /tmp/tmp_mne_tempdir_N5mvqG/test_one_event.fdt
Reading 0 ... 30503  =      0.000 ...   238.305 secs...
1 events will be dropped because they occur on the same time sample as another event. `mne.io.Raw` objects store events on an event channel, which cannot represent two events on the same sample. You can extract the original event structure using `mne.io.eeglab.read_events_eeglab`. Then, you can e.g. subset the extracted events for constructing epochs.
Reading /tmp/tmp_mne_tempdir_N5mvqG/test_overlap_event.fdt
Reading 0 ... 30503  =      0.000 ...   238.305 secs...
1 events found
Event IDs: [2]
No events found, returning empty stim channel ...
The following EEG sensors did not have a position specified in the selected montage: [u'FPz']. Their position has been left untouched.
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/usr/local/lib/python2.7/dist-packages/numpy/testing/decorators.py", line 147, in skipper_func
    return f(*args, **kwargs)
  File "mne/io/eeglab/tests/test_eeglab.py", line 180, in test_io_set
    raw = read_raw_eeglab(input_fname=one_chanpos_fname, preload=True)
  File "mne/io/eeglab/eeglab.py", line 194, in read_raw_eeglab
    verbose=verbose, uint16_codec=uint16_codec)
  File "<string>", line 2, in __init__
  File "mne/utils.py", line 728, in verbose
    return function(*args, **kwargs)
  File "mne/io/eeglab/eeglab.py", line 340, in __init__
    info = _get_info(eeg, montage, eog=eog)
  File "mne/io/eeglab/eeglab.py", line 109, in _get_info
    update_ch_names=update_ch_names)
  File "mne/io/base.py", line 2517, in _check_update_montage
    % str(missing_positions))
KeyError: "The following positions are missing from the montage definitions: [u'FPz']. If those channels lack positions because they are EOG channels use the eog parameter."

How should I fix this?

larsoner commented 6 years ago

I see this error, too, but I don't really get how it creeped into our code with CI testing (?!?).

Can you use git bisect to figure out which PR broke it?

larsoner commented 6 years ago

I found the error, the positions were never checked properly and a recent PR made it fix those checks

smgutstein commented 6 years ago

Cool. Thanks.

On Tue, Jan 9, 2018 at 3:46 PM, Eric Larson notifications@github.com wrote:

I found the error, the positions were never checked properly and a recent PR made it fix those checks

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/mne-tools/mne-python/issues/4855#issuecomment-356408800, or mute the thread https://github.com/notifications/unsubscribe-auth/AEfaJHwLMmz-CBbFsbBVQnfOUdXFu9fAks5tI9AYgaJpZM4RXWXE .