[Mne_analysis] ImportError: cannot import name sigtools
Maria Hakonen
maria.hakonen at gmail.com
Tue Sep 2 02:06:20 EDT 2014
Hi Mainak,
Many thanks! This works.
Regards,
Maria
2014-09-01 12:37 GMT+03:00 Mainak Jas <mainakjas at gmail.com>:
> Hi Maria,
>
> I am forwarding this email to the mailing list since this is a new issue
> than the one you had previously posted. There are more people on the
> mailing list who can answer your questions and you can expect a faster
> response. In the future, can you try to share a small gist (
> https://gist.github.com/), not more than 15-20 lines to reproduce the
> problem using the sample dataset? Here is an example to reproduce this
> problem you had: https://gist.github.com/mainakjas/966714622a73eaeb9b6f.
>
> The issue is that picks is a numpy array but evoked.pick_channels expects
> a list of strings. You can do something like:
>
> evoked_clean.pick_channels([evoked_clean.info['ch_names'][p] for p in
> picks_good])
>
> to solve your problem. Does this work?
>
> Mainak
>
> On Sun, Aug 31, 2014 at 11:04 PM, Hakonen Maria <maria.hakonen at aalto.fi>
> wrote:
>
>> Hi again Mainak,
>>
>> I managed to solve that import error already by closing all terminals and
>> logging off. The figures are also saved correctly now and the events are
>> printed in a file. Many thanks for your advice!
>>
>> However, there is still one problem, I haven't managed to solve. I wonder
>> if you have any ideas how it could be solved? I get the following error:
>>
>> ValueError Traceback (most recent call
>> last)
>> /usr/lib/python2.7/dist-packages/IPython/utils/py3compat.pyc in
>> execfile(fname, *where)
>> 173 else:
>> 174 filename = fname
>> --> 175 __builtin__.execfile(filename, *where)
>>
>> /scratch/braindata/mhhakone/intell/scripts/evoke_and_do_ica.py in
>> <module>()
>> 141 filename =subject+session+file_end
>> 142 picks_good = mne.pick_types(evoked_clean.info, meg=True,
>> eeg=False, eog=True, ecg=False, stim=False, exclude='bads')
>> --> 143 evoked_clean.pick_channels(picks_good)
>> 144 evoked_clean.save(filename)
>> 145
>>
>> /home/mhhakone/env/src/mne/mne/channels.pyc in pick_channels(self,
>> ch_names, copy)
>> 147
>> 148 idx = [inst.ch_names.index(c) for c in ch_names if c in
>> inst.ch_names]
>> --> 149 inst._pick_drop_channels(idx)
>> 150
>> 151 return inst
>>
>> /home/mhhakone/env/src/mne/mne/channels.pyc in _pick_drop_channels(self,
>> idx)
>> 189 self.cals = self.cals[idx]
>> 190
>> --> 191 self.info = pick_info(self.info, idx, copy=False)
>> 192
>> 193 if inst_has('_projector'):
>>
>> /home/mhhakone/env/src/mne/mne/io/pick.pyc in pick_info(info, sel, copy)
>> 285
>> 286 if len(sel) == 0:
>> --> 287 raise ValueError('Warning : No channels match the
>> selection.')
>> 288
>> 289 info['chs'] = [info['chs'][k] for k in sel]
>>
>> ValueError: Warning : No channels match the selection.
>>
>> I don't really understand how it is possible that no channels match the
>> selection if picks_good are calculated from evoked_clean?
>>
>> picks_good and evoked_clean are as follows:
>>
>> In [4]: picks_good
>> Out[4]:
>> array([ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12,
>> 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25,
>> 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38,
>> 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51,
>> 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64,
>> 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77,
>> 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90,
>> 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103,
>> 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116,
>> 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129,
>> 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142,
>> 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155,
>> 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168,
>> 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181,
>> 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194,
>> 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207,
>> 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220,
>> 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233,
>> 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246,
>> 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259,
>> 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272,
>> 273, 274, 275, 276, 277, 278, 279, 280, 281, 282, 283, 284, 285,
>> 286, 287, 288, 289, 290, 291, 292, 293, 294, 295, 296, 297, 298,
>> 299, 300, 301, 302, 303, 304, 305])
>>
>> In [5]: evoked_clean
>> Out[5]: <Evoked | comment : 'Unknown', time : [-0.099994, 0.999936],
>> n_epochs : 148, n_channels x n_times : 306 x 1321>
>>
>> Thanks already in advance if you have yet time to help!
>>
>> Regards,
>> Maria
>> ________________________________________
>> Lähettäjä: Hakonen Maria
>> Lähetetty: 30. elokuuta 2014 10:02
>> Vastaanottaja: mainakjas at gmail.com
>> Aihe: ImportError: cannot import name sigtools
>>
>> Hi,
>>
>> I have tried to run the MEG preprocessing script but import mne gives the
>> error:
>>
>> ImportError Traceback (most recent call
>> last)
>> /scratch/braindata/mhhakone/intell/scripts/<ipython-input-12-39fc8b1a8697>
>> in <module>()
>> ----> 1 import mne
>>
>> /home/mhhakone/env/src/mne/mne/__init__.py in <module>()
>> 8 get_config, get_config_path, set_cache_dir,
>> 9 set_memmap_min_size)
>> ---> 10 from .io.pick import (pick_types, pick_channels,
>> pick_types_evoked,
>> 11 pick_channels_regexp, pick_channels_forward,
>> 12 pick_types_forward, pick_channels_cov,
>>
>> /home/mhhakone/env/src/mne/mne/io/__init__.py in <module>()
>> 6 # License: BSD (3-clause)
>>
>> 7
>> ----> 8 from .open import fiff_open, show_fiff, _fiff_get_fid
>> 9 from .meas_info import read_fiducials, write_fiducials,
>> read_info, write_info
>> 10
>>
>> /home/mhhakone/env/src/mne/mne/io/open.py in <module>()
>> 10
>> 11 from .tag import read_tag_info, read_tag, read_big, Tag
>> ---> 12 from .tree import make_dir_tree
>> 13 from .constants import FIFF
>> 14 from ..utils import logger, verbose
>>
>> /home/mhhakone/env/src/mne/mne/io/tree.py in <module>()
>> 10 from .tag import Tag
>> 11 from .tag import read_tag
>> ---> 12 from .write import write_id, start_block, end_block, _write
>> 13 from ..utils import logger, verbose
>> 14
>>
>> /home/mhhakone/env/src/mne/mne/io/write.py in <module>()
>> 15 from ..utils import logger
>> 16 from ..externals.jdcal import jcal2jd
>> ---> 17 from ..fixes import gzip_open
>> 18
>> 19
>>
>> /home/mhhakone/env/src/mne/mne/fixes.py in <module>()
>> 24 from numpy.fft import irfft
>> 25 from nose.tools import assert_true
>> ---> 26 from scipy.signal import filtfilt as sp_filtfilt
>> 27 from distutils.version import LooseVersion
>> 28 from functools import partial
>>
>> /home/mhhakone/env/local/lib/python2.7/site-packages/scipy/signal/__init__.py
>> in <module>()
>> 230 from __future__ import division, print_function, absolute_import
>> 231
>> --> 232 from . import sigtools
>> 233 from .waveforms import *
>> 234
>>
>> ImportError: cannot import name sigtools
>>
>> I wonder if you know what could cause this error? I haven't got it
>> before. Could it be relatrd to the Python version I have. Now I have the
>> following version:
>>
>> In [18]: sys.version
>> Out[18]: '2.7.3 (default, Feb 27 2014, 19:58:35) \n[GCC 4.6.3]'
>>
>> Thanks,
>> Maria
>>
>
>
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