[Mne_analysis] How to create report using MNE Report module?

[Mainak Jas]

        External Email - Use Caution        

Hi,

I am not sure why you expect figs.append to suppress the figure from
popping out. What you want is controlled by the "show" parameter of our
plotting functions.

Mainak

On Fri, Aug 7, 2020 at 9:51 AM <balandongiv at gmail.com> wrote:

>         External Email - Use Caution
>
> Hi All,
>
> It is a great thing that mne has a feature for creating an HTML report.
> However, I am having difficulty in applying the information provided from
> the Getting started with mne.Report tutorial onto my real-life
> application.
>
> In the tutorial, it seems that any figure generated needs to be appended.
> But, upon completion, a figure of the plot_properties is outputted
> despite it is enclosed within the figs.append(). Also, there is no HTML
> report generated upon completion.
>
> Also, may I know how to append additional information into the report.
>
> The full code to reproduce the above scenario is given below.
>
> Appreciate for any insight.
>
> def generate_report(raw,filename, ica, ch_not_considered):
>
>     report = Report(image_format='png', subject='try_sample_subject',
>
>                     raw_psd=True)  # use False for speed here
>
>     report.parse_folder(filename, on_error='ignore')
>
>     figs = list()
>
>     figs.append(ica.plot_components())
>
>     figs.append(ica.plot_properties(raw, picks=[0]))
>
>     # How to include additional text? say channel that ch_not_considered
>
>     report.add_slider_to_section(figs, image_format='png')  # can also use
> 'svg'
>
>     report.save('my_reportxx.html', overwrite=True)
>
>
>
>
>
> def all_procedure():
>
>     filename = r'S17_3.mff' # Accessible via:
> https://drive.google.com/drive/folders/14R_2A-ceqOFvRkDZH6Skm4CqF5B-K7Co?usp=sharing
>
>     ch_not_considered = ['E128', 'E127', 'E126', 'E126', 'E48', 'E119',
> 'E17']
>
>     raw = mne.io.read_raw_egi(filename, preload=True)
>
>     raw.crop(0, 300)  # crop huge artifact at the end
>
>     all_bad_ch = ['E128', 'E127', 'E126', 'E126', 'E48', 'E119', 'E17']
>
>     raw.info['bads'] = all_bad_ch  # mark bad channels
>
>     filt_raw = raw.copy()
>
>     ica = ICA(n_components=5, random_state=97)
>
>     ica.fit(filt_raw)
>
>
>
>     generate_report(raw,filename, ica, ch_not_considered)
>
>
>
>
>
> all_procedure()
>
>
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