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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