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MNE: Magnetoencephalography (MEG) and Electroencephalography (EEG) in Python
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RuntimeError: info channel name inconsistency detected, please notify mne-python developers #2470

Closed devadidev closed 9 years ago

devadidev commented 9 years ago

Hi, I'm new to MNE and Python and I've been trying to run the example plot_decoding_csp_eeg.py on my Ubuntu 14.04, Anaconda with conda 3.17.0 and MNE: 0.10.dev0 . I'm getting the following error and wondering if Im missing something trivial! Thanks

(mnemeeg)➜ programs : python plot_decoding_csp_eeg.py

Motor imagery decoding from EEG data using the Common Spatial Pattern (CSP)

Decoding of motor imagery applied to EEG data decomposed using CSP. Here the classifier is applied to features extracted on CSP filtered signals.

See http://en.wikipedia.org/wiki/Common_spatial_pattern and [1]

The EEGBCI dataset is documented in [2] The data set is available at PhysioNet [3]

[1] Zoltan J. Koles. The quantitative extraction and topographic mapping of the abnormal components in the clinical EEG. Electroencephalography and Clinical Neurophysiology, 79(6):440--447, December 1991.

[2] Schalk, G., McFarland, D.J., Hinterberger, T., Birbaumer, N., Wolpaw, J.R. (2004) BCI2000: A General-Purpose Brain-Computer Interface (BCI) System. IEEE TBME 51(6):1034-1043

[3] Goldberger AL, Amaral LAN, Glass L, Hausdorff JM, Ivanov PCh, Mark RG, Mietus JE, Moody GB, Peng C-K, Stanley HE. (2000) PhysioBank, PhysioToolkit, and PhysioNet: Components of a New Research Resource for Complex Physiologic Signals. Circulation 101(23):e215-e220

Extracting edf Parameters from /home/devanka/src/examples/MNE-eegbci-data/physiobank/database/eegmmidb/S001/S001R06.edf... Setting channel info structure... Creating Raw.info structure... Reading 0 ... 19999 = 0.000 ... 124.994 secs... [done] Ready. Extracting edf Parameters from /home/devanka/src/examples/MNE-eegbci-data/physiobank/database/eegmmidb/S001/S001R10.edf... Setting channel info structure... Creating Raw.info structure... Reading 0 ... 19999 = 0.000 ... 124.994 secs... [done] Ready. Extracting edf Parameters from /home/devanka/src/examples/MNE-eegbci-data/physiobank/database/eegmmidb/S001/S001R14.edf... Setting channel info structure... Creating Raw.info structure... Reading 0 ... 19999 = 0.000 ... 124.994 secs... [done] Ready. Traceback (most recent call last): File "plot_decoding_csp_eeg.py", line 62, in raw.filter(7., 30., method='iir') File "", line 2, in filter File "/home/devanka/projects/mneruns/programs/src/mne/mne/utils.py", line 540, in verbose return function(_args, *_kwargs) File "/home/devanka/projects/mneruns/programs/src/mne/mne/io/base.py", line 804, in filter picks = pick_types(self.info, exclude=[], **pick_parameters) File "/home/devanka/projects/mneruns/programs/src/mne/mne/io/pick.py", line 205, in pick_types info._check_consistency() File "/home/devanka/projects/mneruns/programs/src/mne/mne/io/meas_info.py", line 219, in _check_consistency raise RuntimeError('info channel name inconsistency detected, ' RuntimeError: info channel name inconsistency detected, please notify mne-python developers (mnemeeg)➜ programs python plot_decoding_csp_eeg.py

Motor imagery decoding from EEG data using the Common Spatial Pattern (CSP)

Decoding of motor imagery applied to EEG data decomposed using CSP. Here the classifier is applied to features extracted on CSP filtered signals.

See http://en.wikipedia.org/wiki/Common_spatial_pattern and [1]

The EEGBCI dataset is documented in [2] The data set is available at PhysioNet [3]

[1] Zoltan J. Koles. The quantitative extraction and topographic mapping of the abnormal components in the clinical EEG. Electroencephalography and Clinical Neurophysiology, 79(6):440--447, December 1991.

[2] Schalk, G., McFarland, D.J., Hinterberger, T., Birbaumer, N., Wolpaw, J.R. (2004) BCI2000: A General-Purpose Brain-Computer Interface (BCI) System. IEEE TBME 51(6):1034-1043

[3] Goldberger AL, Amaral LAN, Glass L, Hausdorff JM, Ivanov PCh, Mark RG, Mietus JE, Moody GB, Peng C-K, Stanley HE. (2000) PhysioBank, PhysioToolkit, and PhysioNet: Components of a New Research Resource for Complex Physiologic Signals. Circulation 101(23):e215-e220

Extracting edf Parameters from /home/devanka/src/examples/MNE-eegbci-data/physiobank/database/eegmmidb/S001/S001R06.edf... Setting channel info structure... Creating Raw.info structure... Reading 0 ... 19999 = 0.000 ... 124.994 secs... [done] Ready. Extracting edf Parameters from /home/devanka/src/examples/MNE-eegbci-data/physiobank/database/eegmmidb/S001/S001R10.edf... Setting channel info structure... Creating Raw.info structure... Reading 0 ... 19999 = 0.000 ... 124.994 secs... [done] Ready. Extracting edf Parameters from /home/devanka/src/examples/MNE-eegbci-data/physiobank/database/eegmmidb/S001/S001R14.edf... Setting channel info structure... Creating Raw.info structure... Reading 0 ... 19999 = 0.000 ... 124.994 secs... [done] Ready. Traceback (most recent call last): File "plot_decoding_csp_eeg.py", line 62, in raw.filter(7., 30., method='iir') File "", line 2, in filter File "/home/devanka/projects/mneruns/programs/src/mne/mne/utils.py", line 540, in verbose return function(_args, *_kwargs) File "/home/devanka/projects/mneruns/programs/src/mne/mne/io/base.py", line 804, in filter picks = pick_types(self.info, exclude=[], **pick_parameters) File "/home/devanka/projects/mneruns/programs/src/mne/mne/io/pick.py", line 205, in pick_types info._check_consistency() File "/home/devanka/projects/mneruns/programs/src/mne/mne/io/meas_info.py", line 219, in _check_consistency raise RuntimeError('info channel name inconsistency detected, ' RuntimeError: info channel name inconsistency detected, please notify mne-python developers

kingjr commented 9 years ago

Have you tried with ipython instead of python? Check your mne version inside ipython:

import mne
print mne.__version__
mainakjas commented 9 years ago

looks related to changes in PR https://github.com/mne-tools/mne-python/pull/2452

devadidev commented 9 years ago

@kingjr, the version returned is as I quoted in the original, I tried with iPython and got a different (qt related?) error. I'll explore this further and update here if I'm able to configure and run it successfully also @mainakjas thanks for linking the issue, I'll go through that update here if it's related to that.

iPython Error: computing connectivity for epoch 58 computing connectivity for epoch 59 computing connectivity for epoch 60 [Connectivity computation done] Computing PSI from estimated Coherency

[PSI Estimation Done]

ValueError Traceback (most recent call last) /home/devanka/projects/mneruns/programs/plot_mne_inverse_psi_visual.py in () 110 time_label='Phase Slope Index (PSI)', 111 subjects_dir=subjects_dir, --> 112 clim=dict(kind='percent', pos_lims=(95, 97.5, 100))) 113 brain.show_view('medial') 114 brain.add_label(fname_label, color='green', alpha=0.7)

/home/devanka/projects/mneruns/programs/src/mne/mne/source_estimate.pyc in plot(self, subject, surface, hemi, colormap, time_label, smoothing_steps, transparent, alpha, time_viewer, config_opts, subjects_dir, figure, views, colorbar, clim) 1362 subjects_dir=subjects_dir, figure=figure, 1363 views=views, colorbar=colorbar, -> 1364 clim=clim) 1365 return brain 1366

/home/devanka/projects/mneruns/programs/src/mne/mne/viz/_3d.pyc in plot_source_estimates(stc, subject, surface, hemi, colormap, time_label, smoothing_steps, transparent, alpha, time_viewer, config_opts, subjects_dir, figure, views, colorbar, clim) 519 A instance of surfer.viz.Brain from PySurfer. 520 """ --> 521 from surfer import Brain, TimeViewer 522 config_opts = _handle_default('config_opts', config_opts) 523

/home/devanka/anaconda/envs/mnemeeg/lib/python2.7/site-packages/surfer/init.py in () ----> 1 from .viz import Brain, TimeViewer # noqa 2 from .utils import Surface, verbose, set_log_level, set_log_file # noqa 3 from .io import project_volume_data # noqa 4 5 version = "0.6"

/home/devanka/anaconda/envs/mnemeeg/lib/python2.7/site-packages/surfer/viz.py in () 12 import nibabel as nib 13 ---> 14 from mayavi import mlab 15 from mayavi.tools.mlab_scene_model import MlabSceneModel 16 from mayavi.core import lut_manager

/home/devanka/anaconda/envs/mnemeeg/lib/python2.7/site-packages/mayavi/mlab.py in () 25 26 # Mayavi imports ---> 27 from mayavi.tools.camera import view, roll, yaw, pitch, move 28 from mayavi.tools.figure import figure, clf, gcf, savefig, \ 29 draw, sync_camera, close, screenshot

/home/devanka/anaconda/envs/mnemeeg/lib/python2.7/site-packages/mayavi/tools/camera.py in () 23 # We can't use gcf, as it creates a circular import in camera management 24 # routines. ---> 25 from engine_manager import get_engine 26 27

/home/devanka/anaconda/envs/mnemeeg/lib/python2.7/site-packages/mayavi/tools/engine_manager.py in () 10 11 # Local imports ---> 12 from mayavi.preferences.api import preference_manager 13 from mayavi.core.registry import registry 14 from mayavi.core.engine import Engine

/home/devanka/anaconda/envs/mnemeeg/lib/python2.7/site-packages/mayavi/preferences/api.py in () 2 3 # The global PreferenceManager instance ----> 4 from preference_manager import preference_manager 5 from bindings import set_scene_preferences, get_scene_preferences

/home/devanka/anaconda/envs/mnemeeg/lib/python2.7/site-packages/mayavi/preferences/preference_manager.py in () 27 from traits.etsconfig.api import ETSConfig 28 from traits.api import HasTraits, Instance ---> 29 from traitsui.api import View, Group, Item 30 from apptools.preferences.api import (ScopedPreferences, IPreferences, 31 PreferencesHelper)

/home/devanka/anaconda/envs/mnemeeg/lib/python2.7/site-packages/traitsui/api.py in () 33 from .editor_factory import EditorFactory 34 ---> 35 from .editors.api import (ArrayEditor, BooleanEditor, ButtonEditor, 36 CheckListEditor, CodeEditor, ColorEditor, CompoundEditor, CustomEditor, 37 CSVListEditor,

/home/devanka/anaconda/envs/mnemeeg/lib/python2.7/site-packages/traitsui/editors/init.py in () 20 from future import absolute_import 21 ---> 22 from .api import (toolkit, ArrayEditor, BooleanEditor, ButtonEditor, 23 CheckListEditor, CodeEditor, ColorEditor, CompoundEditor, CustomEditor, 24 DateEditor, DefaultOverride, DirectoryEditor, DNDEditor, DropEditor,

/home/devanka/anaconda/envs/mnemeeg/lib/python2.7/site-packages/traitsui/editors/api.py in () 8 from .button_editor import ButtonEditor 9 from .check_list_editor import CheckListEditor ---> 10 from .code_editor import CodeEditor 11 from .color_editor import ColorEditor 12 from .compound_editor import CompoundEditor

/home/devanka/anaconda/envs/mnemeeg/lib/python2.7/site-packages/traitsui/editors/code_editor.py in () 34 #------------------------------------------------------------------------------- 35 ---> 36 class ToolkitEditorFactory ( EditorFactory ): 37 """ Editor factory for code editors. 38 """

/home/devanka/anaconda/envs/mnemeeg/lib/python2.7/site-packages/traitsui/editors/code_editor.py in ToolkitEditorFactory() 46 47 # Background color for marking lines ---> 48 mark_color = Color( 0xECE9D8 ) 49 50 # Object trait containing the currently selected line (optional)

/home/devanka/anaconda/envs/mnemeeg/lib/python2.7/site-packages/traits/traits.pyc in call(self, _args, _metadata) 485 486 def call ( self, _args, _metadata ): --> 487 return self.maker_function( _args, *_metadata ) 488 489 class TraitImportError ( TraitFactory ):

/home/devanka/anaconda/envs/mnemeeg/lib/python2.7/site-packages/traits/traits.pyc in Color(_args, _metadata) 1189 from traitsui.toolkit_traits import ColorTrait 1190 -> 1191 return ColorTrait( _args, _metadata ) 1192 1193 Color = TraitFactory( Color )

/home/devanka/anaconda/envs/mnemeeg/lib/python2.7/site-packages/traitsui/toolkit_traits.pyc in ColorTrait(_args, _traits) 5 6 def ColorTrait ( _args, _traits ): ----> 7 return toolkit().color_trait( _args, _traits ) 8 9 def RGBColorTrait ( _args, _traits ):

/home/devanka/anaconda/envs/mnemeeg/lib/python2.7/site-packages/traitsui/toolkit.pyc in toolkit(*toolkits) 115 for toolkit_name in toolkits: 116 try: --> 117 _toolkit = _import_toolkit( toolkit_name ) 118 119 # In case we have just decided on a toolkit, tell everybody else:

/home/devanka/anaconda/envs/mnemeeg/lib/python2.7/site-packages/traitsui/toolkit.pyc in _import_toolkit(name) 49 50 def _import_toolkit ( name ): ---> 51 return import( name, globals=globals(), level=1 ).toolkit 52 53

/home/devanka/anaconda/envs/mnemeeg/lib/python2.7/site-packages/traitsui/qt4/init.py in () 16 # import pyface.qt before anything else is done so the sipapi 17 # can be set correctly if needed ---> 18 import pyface.qt 19 20 #----------------------------------------------------------------------------

/home/devanka/anaconda/envs/mnemeeg/lib/python2.7/site-packages/pyface/qt/init.py in () 26 except ImportError: 27 try: ---> 28 prepare_pyqt4() 29 import PyQt4 30 qt_api = 'pyqt'

/home/devanka/anaconda/envs/mnemeeg/lib/python2.7/site-packages/pyface/qt/init.py in prepare_pyqt4() 15 # Set PySide compatible APIs. 16 import sip ---> 17 sip.setapi('QString', 2) 18 sip.setapi('QVariant', 2) 19

ValueError: API 'QString' has already been set to version 1

mainakjas commented 9 years ago

@devadidev for the error, have a look here: https://pysurfer.github.io/install.html. It should fix it

devadidev commented 9 years ago

@mainakjas, thanks that fixed the iPython qt error but back to the RunTime one:

/home/devanka/projects/mneruns/programs/src/mne/mne/io/meas_info.pyc in _check_consistency(self) 217 ch_1 != ch_2 for ch_1, ch_2 in zip(self['ch_names'], chs)) or \ 218 self['nchan'] != len(chs): --> 219 raise RuntimeError('info channel name inconsistency detected, ' 220 'please notify mne-python developers') 221 # make sure we have the proper datatypes

RuntimeError: info channel name inconsistency detected, please notify mne-python developers

agramfort commented 9 years ago

plot_decoding_csp_eeg.py runs fine for me in master. Are you using master?

what version of python are you using?

mainakjas commented 9 years ago

where did you get the example from? Did you download it from the website or github?

mainakjas commented 9 years ago

it runs fine for me too

devadidev commented 9 years ago

Ah ic now, I downloaded from the website (http://martinos.org/mne/stable/auto_examples/decoding/plot_decoding_csp_eeg.html) and there are some diff with GH version of the code, which runs fine for me in master now.

(mnemeeg)➜ programs diff plot_decoding_csp_eeg_old.py plot_decoding_csp_eeg_github.py 5d4 < 8d6 < 10d7 < 13d9 < 17d12 < 21d15 < 34,36c28,30 < from mne import Epochs, pick_types < from mne.io import concatenate_raws

< from mne.io.edf import read_raw_edf

from mne import Epochs, pick_types, find_events from mne.channels import read_layout from mne.io import concatenate_raws, read_raw_edf 38d31 < from mne.event import find_events 40d32 < from mne.channels import read_layout 58,59c50,51 < # strip channel names

< raw.info['ch_names'] = [chn.strip('.') for chn in raw.info['ch_names']]

strip channel names of "." characters

raw.rename_channels(lambda x: x.strip('.'))

agramfort commented 9 years ago

ok please close then.