[Mne_analysis] Could you help me find events from ".set" file?

Soan KIM cheukusi.kim at gmail.com
Thu May 23 07:04:11 EDT 2019
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        External Email - Use Caution        

I think mine is 3.1.0!

Requirement already satisfied: matplotlib in
/anaconda3/lib/python3.7/site-packages (3.1.0)

Requirement already satisfied: python-dateutil>=2.1 in
/anaconda3/lib/python3.7/site-packages (from matplotlib) (2.7.3)

Requirement already satisfied: kiwisolver>=1.0.1 in
/anaconda3/lib/python3.7/site-packages (from matplotlib) (1.0.1)

Requirement already satisfied: numpy>=1.11 in
/anaconda3/lib/python3.7/site-packages (from matplotlib) (1.15.1)

Requirement already satisfied: cycler>=0.10 in
/anaconda3/lib/python3.7/site-packages (from matplotlib) (0.10.0)

Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in
/anaconda3/lib/python3.7/site-packages (from matplotlib) (2.2.0)

Requirement already satisfied: six>=1.5 in
/anaconda3/lib/python3.7/site-packages (from
python-dateutil>=2.1->matplotlib) (1.11.0)

Requirement already satisfied: setuptools in
/anaconda3/lib/python3.7/site-packages (from kiwisolver>=1.0.1->matplotlib)
(40.6.3)

2019년 5월 23일 (목) 오후 8:00, Brunner, Clemens (clemens.brunner at uni-graz.at) <
clemens.brunner at uni-graz.at>님이 작성:

>         External Email - Use Caution
>
> What matplotlib version are you using? This was a regression introduced in
> 3.0.1, but it should be fixed in matplotlib 3.0.2 and later (I recommend
> that you use the latest release if possible, which is 3.1.0).
>
> Clemens
>
>
> > On 23.05.2019, at 12:47, Soan KIM <cheukusi.kim at gmail.com> wrote:
> >
> >         External Email - Use Caution
> >
> >
> > Thank you for your reply.
> > It worked perfectly and you saved my day!
> >
> > but could you take a look at another issue?
> > I get this error when I try to plot with the option, "spatial colors =
> True" on Jupyter notebook. :
> >
> > TypeError: get_tightbbox() got an unexpected keyword argument
> 'bbox_extra_artists'
> >
> > Thank you.
> > -------------
> > My code :
> > evoked = epochs.average()
> > evoked.plot(spatial_colors=True)
> >
> > Error :
> > TypeError                                 Traceback (most recent call
> last)
> >
> /anaconda3/envs/mne/lib/python3.6/site-packages/IPython/core/formatters.py
> in __call__(self, obj)
> >     339                 pass
> >     340             else:
> > --> 341                 return printer(obj)
> >     342             # Finally look for special method names
> >     343             method = get_real_method(obj, self.print_method)
> >
> >
> /anaconda3/envs/mne/lib/python3.6/site-packages/IPython/core/pylabtools.py
> in <lambda>(fig)
> >     242
> >     243     if 'png' in formats:
> > --> 244         png_formatter.for_type(Figure, lambda fig:
> print_figure(fig, 'png', **kwargs))
> >     245     if 'retina' in formats or 'png2x' in formats:
> >     246         png_formatter.for_type(Figure, lambda fig:
> retina_figure(fig, **kwargs))
> >
> >
> /anaconda3/envs/mne/lib/python3.6/site-packages/IPython/core/pylabtools.py
> in print_figure(fig, fmt, bbox_inches, **kwargs)
> >     126
> >     127     bytes_io = BytesIO()
> > --> 128     fig.canvas.print_figure(bytes_io, **kw)
> >     129     data = bytes_io.getvalue()
> >     130     if fmt == 'svg':
> >
> >
> /anaconda3/envs/mne/lib/python3.6/site-packages/matplotlib/backends/backend_qt5agg.py
> in print_figure(self, *args, **kwargs)
> >      86
> >      87     def print_figure(self, *args, **kwargs):
> > ---> 88         super().print_figure(*args, **kwargs)
> >      89         self.draw()
> >      90
> >
> >
> /anaconda3/envs/mne/lib/python3.6/site-packages/matplotlib/backend_bases.py
> in print_figure(self, filename, dpi, facecolor, edgecolor, orientation,
> format, bbox_inches, **kwargs)
> >    2051                     bbox_artists =
> kwargs.pop("bbox_extra_artists", None)
> >    2052                     bbox_inches =
> self.figure.get_tightbbox(renderer,
> > -> 2053                             bbox_extra_artists=bbox_artists)
> >    2054                     pad = kwargs.pop("pad_inches", None)
> >    2055                     if pad is None:
> >
> > /anaconda3/envs/mne/lib/python3.6/site-packages/matplotlib/figure.py in
> get_tightbbox(self, renderer, bbox_extra_artists)
> >    2274         bb.extend(
> >    2275             ax.get_tightbbox(renderer,
> bbox_extra_artists=bbox_extra_artists)
> > -> 2276             for ax in self.axes if ax.get_visible())
> >    2277
> >    2278         if len(bb) == 0:
> >
> > /anaconda3/envs/mne/lib/python3.6/site-packages/matplotlib/figure.py in
> <genexpr>(.0)
> >    2274         bb.extend(
> >    2275             ax.get_tightbbox(renderer,
> bbox_extra_artists=bbox_extra_artists)
> > -> 2276             for ax in self.axes if ax.get_visible())
> >    2277
> >    2278         if len(bb) == 0:
> >
> > TypeError: get_tightbbox() got an unexpected keyword argument
> 'bbox_extra_artists'
> >
> > <Figure size 921x432 with 2 Axes>
> >
> >
> > 2019년 5월 23일 (목) 오후 2:40, Brunner, Clemens (clemens.brunner at uni-graz.at)
> <clemens.brunner at uni-graz.at>님이 작성:
> >         External Email - Use Caution
> >
> > Could you try mne.read_epochs_eeglab again? It looks like your .set file
> already contains the epochs, so this function should do the job. You
> certainly shouldn't have to construct your own info object, because this
> information should already be present in raw.info.
> >
> > Without the data file it is difficult to tell what the exact problem is,
> so feel free to send it to me if my suggestion doesn't work.
> >
> > Clemens
> >
> >
> > > On 22.05.2019, at 17:59, Soan KIM <cheukusi.kim at gmail.com> wrote:
> > >
> > >         External Email - Use Caution
> > >
> > >
> > > Thank you so much!! It worked!
> > > but I've faced with another problem making custom epochs. Could you
> give me some advice?
> > >
> > > Thank you!!
> > >
> > >
> > > I see this error even though I picked 18 channels  :
> > >
> > > ValueError: All picks must be < n_channels (30), got 30
> > >
> > > This is my code :
> > >
> > > event_id = {'S  4':4, 'S  6':6, 'S  7':7, 'S  1':1, 'S  5':5, 'S
> 3':3, 'S  2':2}
> > > events= mne.events_from_annotations(raw)
> > > n_channels = 32
> > > sampling_rate = 500
> > > info = mne.create_info(n_channels, sampling_rate)
> > > channel_names = ['Fp1', 'Fp2', 'F3', 'F4', 'C3', 'C4', 'P3', 'P4',
> 'O1', 'O2', 'F7', 'F8', 'T7', 'T8', 'P7', 'P8', 'Fz', 'Cz', 'Pz', 'FC1',
> 'FC2', 'CP1', 'CP2', 'FC5', 'FC6', 'CP5', 'CP6', 'TP9', 'TP10', 'EOG',
> 'M1', 'M2']
> > > channel_types = ['eeg', 'eeg', 'eeg', 'eeg', 'eeg', 'eeg', 'eeg',
> 'eeg', 'eeg', 'eeg', 'eeg', 'eeg', 'eeg', 'eeg', 'eeg', 'eeg', 'eeg',
> 'eeg', 'eeg', 'eeg', 'eeg', 'eeg', 'eeg', 'eeg', 'eeg', 'eeg', 'eeg',
> 'eeg', 'eeg', 'eog', 'bio', 'bio']
> > > sfreq = 500
> > > info['description'] = 'My custom dataset'
> > > info['bads'] = ['Fp1', 'Fp2', 'F7', 'F8', 'T7', 'T8', 'TP9', 'TP10']
> > > include = ['F3', 'F4', 'C3', 'C4', 'P3', 'P4', 'O1', 'O2', 'P7', 'P8',
> 'FC1', 'FC2', 'CP1', 'CP2', 'FC5', 'FC6', 'CP5', 'CP6']
> > > picks = mne.pick_channels(channel_names, include=include,
> exclude=info['bads'], ordered=False)
> > > tmin= -0.2
> > > tmax = 0.8
> > > custom_epochs = mne.EpochsArray(raw, info, picks, events, event_id)
> > >
> > > 2019년 5월 22일 (수) 오후 10:26, Brunner, Clemens (
> clemens.brunner at uni-graz.at) <clemens.brunner at uni-graz.at>님이 작성:
> > >         External Email - Use Caution
> > >
> > >
> > > Hi!
> > >
> > >
> > >
> > > Your markers are probably in raw.annotations. If you want to convert
> them to events, use mne.events_from_annotations(raw).
> > >
> > >
> > >
> > > Clemens
> > >
> > >
> > >
> > >
> > >
> > > From: mne_analysis-bounces at nmr.mgh.harvard.edu <
> mne_analysis-bounces at nmr.mgh.harvard.edu> On Behalf Of Soan KIM
> > > Sent: Wednesday, 22 May 2019 14:04
> > > To: mne_analysis at nmr.mgh.harvard.edu
> > > Subject: [Mne_analysis] Could you help me find events from ".set" file?
> > >
> > >
> > >
> > >         External Email - Use Caution
> > >
> > > Hello, I am a student learning MNE-python.
> > > I have trouble finding events in my ".set" file. It appears empty.
> > > I've also tried mne.io.read_epochs_eeglab with my another epoched
> > > ".set" file, but the list of events is also empty.
> > > To be specific, my raw eeg file was '.vhdr', '.vmrk', and
> > > '.eeg.(BrainProduct)', with no stim_channel. And the data had no
> > > problem when I pre-processed and ran statistics with EEGLAB and
> > > ERPlab. Could you please help me?
> > >
> > > I attach my continuous eeg file('001.set' , '001.fdt'), and epoched
> one("001_sync.set", '001_sync.fdt")
> > >
> > >
> > > Thank you.
> > >
> > > -------
> > > This is how my file looks like.
> > >
> > > <Info | 17 non-empty fields
> > >     bads : list | 0 items
> > >     ch_names : list | Fp1, Fp2, F3, F4, C3, C4, P3, P4, O1, ...
> > >     chs : list | 30 items (EEG: 30)
> > >     comps : list | 0 items
> > >     custom_ref_applied : bool | False
> > >     dev_head_t : Transform | 3 items
> > >     dig : list | 29 items (29 EEG)
> > >     events : list | 0 items
> > >     highpass : float | 0.0 Hz
> > >     hpi_meas : list | 0 items
> > >     hpi_results : list | 0 items
> > >     lowpass : float | 125.0 Hz
> > >     meas_date : NoneType | unspecified
> > >     nchan : int | 30
> > >     proc_history : list | 0 items
> > >     projs : list | 0 items
> > >     sfreq : float | 250.0 Hz
> > >     acq_pars : NoneType
> > >     acq_stim : NoneType
> > >     ctf_head_t : NoneType
> > >     description : NoneType
> > >     dev_ctf_t : NoneType
> > >     experimenter : NoneType
> > >     file_id : NoneType
> > >     gantry_angle : NoneType
> > >     hpi_subsystem : NoneType
> > >     kit_system_id : NoneType
> > >     line_freq : NoneType
> > >     meas_id : NoneType
> > >     proj_id : NoneType
> > >     proj_name : NoneType
> > >     subject_info : NoneType
> > >     xplotter_layout : NoneType
> > >
> > > -----------
> > >
> > > This is my code :
> > >
> > > raw = mne.io.read_raw_eeglab('/001.set', preload=True)
> > > event_id = {'B1(1)': 1, 'B2(2)':2, 'B3(3)':3, 'B4(4)':4, 'B5(5)':5,
> > > 'B6(6)':6, 'B7(7)':7}
> > > events= mne.find_events(raw)
> > > data, times = raw[:, :]
> > > data.shape
> > > start, stop = raw.time_as_index([0, 503955])
> > > data, times = raw[:, start:stop]
> > > times.max()
> > > picks = mne.pick_types(raw.info
> ,meg=False,eeg=True,stim=False,eog=False,ecg=False,misc=False)
> > >
> > > events = mne.find_events(raw, stim_channel=None, verbose=True)
> > > events[:]
> > >
> > > array([], shape=(0, 3), dtype=int32)
> > >
> > > <~WRD000.jpg> 001.fdt<~WRD000.jpg>
> > >
> > > <~WRD000.jpg> 001.set<~WRD000.jpg>
> > >
> > > <~WRD000.jpg> 001_sync.fdt<~WRD000.jpg>
> > >
> > > <~WRD000.jpg> 001_sync.set<~WRD000.jpg>
> > >
> > >
> > >
> > > _______________________________________________
> > > Mne_analysis mailing list
> > > Mne_analysis at nmr.mgh.harvard.edu
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
> > >
> > >
> > > --
> > > 서울시 성북구 안암로 145 고려대학교 136-701
> > > Korea University, 145 Anam-ro, Seongbuk-gu, Seoul, Korea
> > > _______________________________________________
> > > Mne_analysis mailing list
> > > Mne_analysis at nmr.mgh.harvard.edu
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
> >
> >
> > _______________________________________________
> > Mne_analysis mailing list
> > Mne_analysis at nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
> >
> >
> > --
> > 서울시 성북구 안암로 145 고려대학교 136-701
> > Korea University, 145 Anam-ro, Seongbuk-gu, Seoul, Korea
> > _______________________________________________
> > Mne_analysis mailing list
> > Mne_analysis at nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>
>
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-- 
서울시 성북구 안암로 145 고려대학교 136-701
Korea University, 145 Anam-ro, Seongbuk-gu, Seoul, Korea
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