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</o:shapelayout></xml><![endif]--></head><body lang=EN-MY link="#0563C1" vlink="#954F72"><p><span style="padding: 3px 10px; border-radius: 5px; color: #ffffff; font-weight: bold; display: inline-block; background-color: #ff0000;"> External Email - Use Caution </span></p><p></p><div class=WordSection1><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='mso-fareast-language:EN-MY'>Hi All,<o:p></o:p></span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='mso-fareast-language:EN-MY'>It is a great thing that </span><span style='font-size:10.0pt;font-family:"Courier New";mso-fareast-language:EN-MY'>mne</span><span style='mso-fareast-language:EN-MY'> has a feature for creating an HTML report.<br>However, I am having difficulty in applying the information provided from the </span><span style='font-size:10.0pt;font-family:"Courier New";mso-fareast-language:EN-MY'>Getting started with mne.Report</span><span style='mso-fareast-language:EN-MY'> tutorial onto my real-life application.<o:p></o:p></span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='mso-fareast-language:EN-MY'>In the tutorial, it seems that any figure generated needs to be appended. But, upon completion, a figure of the </span><span style='font-size:10.0pt;font-family:"Courier New";mso-fareast-language:EN-MY'>plot_properties</span><span style='mso-fareast-language:EN-MY'> is outputted despite it is enclosed within the </span><span style='font-size:10.0pt;font-family:"Courier New";mso-fareast-language:EN-MY'>figs.append()</span><span style='mso-fareast-language:EN-MY'>. Also, there is no </span><span style='font-size:10.0pt;font-family:"Courier New";mso-fareast-language:EN-MY'>HTML report</span><span style='mso-fareast-language:EN-MY'> generated upon completion.<o:p></o:p></span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='mso-fareast-language:EN-MY'>Also, may I know how to append additional information into the report.<o:p></o:p></span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='mso-fareast-language:EN-MY'>The full code to reproduce the above scenario is given below.<o:p></o:p></span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='mso-fareast-language:EN-MY'>Appreciate for any insight.<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New";mso-fareast-language:EN-MY'>def generate_report(raw,filename, ica, ch_not_considered):<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New";mso-fareast-language:EN-MY'> report = Report(image_format='png', subject='try_sample_subject',<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New";mso-fareast-language:EN-MY'> raw_psd=True) # use False for speed here<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New";mso-fareast-language:EN-MY'> report.parse_folder(filename, on_error='ignore')<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New";mso-fareast-language:EN-MY'> figs = list()<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New";mso-fareast-language:EN-MY'> figs.append(ica.plot_components())<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New";mso-fareast-language:EN-MY'> figs.append(ica.plot_properties(raw, picks=[0]))<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New";mso-fareast-language:EN-MY'> # How to include additional text? say channel that ch_not_considered<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New";mso-fareast-language:EN-MY'> report.add_slider_to_section(figs, image_format='png') # can also use 'svg'<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New";mso-fareast-language:EN-MY'> report.save('my_reportxx.html', overwrite=True)<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New";mso-fareast-language:EN-MY'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New";mso-fareast-language:EN-MY'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New";mso-fareast-language:EN-MY'>def all_procedure():<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New";mso-fareast-language:EN-MY'> filename = r'S17_3.mff' # Accessible via: <a href="https://drive.google.com/drive/folders/14R_2A-ceqOFvRkDZH6Skm4CqF5B-K7Co?usp=sharing">https://drive.google.com/drive/folders/14R_2A-ceqOFvRkDZH6Skm4CqF5B-K7Co?usp=sharing</a><o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New";mso-fareast-language:EN-MY'> ch_not_considered = ['E128', 'E127', 'E126', 'E126', 'E48', 'E119', 'E17']<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New";mso-fareast-language:EN-MY'> raw = mne.io.read_raw_egi(filename, preload=True)<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New";mso-fareast-language:EN-MY'> raw.crop(0, 300) # crop huge artifact at the end<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New";mso-fareast-language:EN-MY'> all_bad_ch = ['E128', 'E127', 'E126', 'E126', 'E48', 'E119', 'E17']<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New";mso-fareast-language:EN-MY'> raw.info['bads'] = all_bad_ch # mark bad channels<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New";mso-fareast-language:EN-MY'> filt_raw = raw.copy()<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New";mso-fareast-language:EN-MY'> ica = ICA(n_components=5, random_state=97)<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New";mso-fareast-language:EN-MY'> ica.fit(filt_raw)<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New";mso-fareast-language:EN-MY'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New";mso-fareast-language:EN-MY'> generate_report(raw,filename, ica, ch_not_considered)<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New";mso-fareast-language:EN-MY'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New";mso-fareast-language:EN-MY'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New";mso-fareast-language:EN-MY'>all_procedure()<o:p></o:p></span></p><p class=MsoNormal><o:p> </o:p></p></div></body></html>