<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 dir="ltr"><div>Hi,</div><div><br></div><div>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.</div><div><br></div><div>Mainak<br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Fri, Aug 7, 2020 at 9:51 AM <<a href="mailto:balandongiv@gmail.com">balandongiv@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div lang="EN-MY"><p><span style="padding:3px 10px;border-radius:5px;color:rgb(255,255,255);font-weight:bold;display:inline-block;background-color:rgb(255,0,0)"> External Email - Use Caution </span></p><p></p><div class="gmail-m_-673165308618418795WordSection1"><p class="MsoNormal"><span>Hi All,<u></u><u></u></span></p><p class="MsoNormal"><span>It is a great thing that </span><span style="font-size:10pt;font-family:"Courier New"">mne</span><span> 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:10pt;font-family:"Courier New"">Getting started with mne.Report</span><span> tutorial onto my real-life application.<u></u><u></u></span></p><p class="MsoNormal"><span>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:10pt;font-family:"Courier New"">plot_properties</span><span> is outputted despite it is enclosed within the </span><span style="font-size:10pt;font-family:"Courier New"">figs.append()</span><span>. Also, there is no </span><span style="font-size:10pt;font-family:"Courier New"">HTML report</span><span> generated upon completion.<u></u><u></u></span></p><p class="MsoNormal"><span>Also, may I know how to append additional information into the report.<u></u><u></u></span></p><p class="MsoNormal"><span>The full code to reproduce the above scenario is given below.<u></u><u></u></span></p><p class="MsoNormal"><span>Appreciate for any insight.<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:10pt;font-family:"Courier New"">def generate_report(raw,filename, ica, ch_not_considered):<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:10pt;font-family:"Courier New""> report = Report(image_format='png', subject='try_sample_subject',<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:10pt;font-family:"Courier New""> raw_psd=True) # use False for speed here<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:10pt;font-family:"Courier New""> report.parse_folder(filename, on_error='ignore')<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:10pt;font-family:"Courier New""> figs = list()<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:10pt;font-family:"Courier New""> figs.append(ica.plot_components())<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:10pt;font-family:"Courier New""> figs.append(ica.plot_properties(raw, picks=[0]))<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:10pt;font-family:"Courier New""> # How to include additional text? say channel that ch_not_considered<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:10pt;font-family:"Courier New""> report.add_slider_to_section(figs, image_format='png') # can also use 'svg'<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:10pt;font-family:"Courier New""> report.save('my_reportxx.html', overwrite=True)<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:10pt;font-family:"Courier New""><u></u> <u></u></span></p><p class="MsoNormal"><span style="font-size:10pt;font-family:"Courier New""><u></u> <u></u></span></p><p class="MsoNormal"><span style="font-size:10pt;font-family:"Courier New"">def all_procedure():<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:10pt;font-family:"Courier New""> filename = r'S17_3.mff' # Accessible via: <a href="https://drive.google.com/drive/folders/14R_2A-ceqOFvRkDZH6Skm4CqF5B-K7Co?usp=sharing" target="_blank">https://drive.google.com/drive/folders/14R_2A-ceqOFvRkDZH6Skm4CqF5B-K7Co?usp=sharing</a><u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:10pt;font-family:"Courier New""> ch_not_considered = ['E128', 'E127', 'E126', 'E126', 'E48', 'E119', 'E17']<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:10pt;font-family:"Courier New""> raw = mne.io.read_raw_egi(filename, preload=True)<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:10pt;font-family:"Courier New""> raw.crop(0, 300) # crop huge artifact at the end<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:10pt;font-family:"Courier New""> all_bad_ch = ['E128', 'E127', 'E126', 'E126', 'E48', 'E119', 'E17']<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:10pt;font-family:"Courier New""> <a href="http://raw.info" target="_blank">raw.info</a>['bads'] = all_bad_ch # mark bad channels<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:10pt;font-family:"Courier New""> filt_raw = raw.copy()<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:10pt;font-family:"Courier New""> ica = ICA(n_components=5, random_state=97)<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:10pt;font-family:"Courier New""> ica.fit(filt_raw)<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:10pt;font-family:"Courier New""><u></u> <u></u></span></p><p class="MsoNormal"><span style="font-size:10pt;font-family:"Courier New""> generate_report(raw,filename, ica, ch_not_considered)<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:10pt;font-family:"Courier New""><u></u> <u></u></span></p><p class="MsoNormal"><span style="font-size:10pt;font-family:"Courier New""><u></u> <u></u></span></p><p class="MsoNormal"><span style="font-size:10pt;font-family:"Courier New"">all_procedure()<u></u><u></u></span></p><p class="MsoNormal"><u></u> <u></u></p></div></div>_______________________________________________<br>
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