Mercurial > repos > gregor.m > spyboat
diff output_report.py @ 0:1d62de03829d draft
"planemo upload commit c6cd06d44dce1eef9136017289d362f144687dc1"
| author | gregor.m |
|---|---|
| date | Mon, 23 Nov 2020 13:31:47 +0000 |
| parents | |
| children | 4d7f30a7e2f6 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/output_report.py Mon Nov 23 13:31:47 2020 +0000 @@ -0,0 +1,199 @@ +''' Produces plots and a summary html 'headless' ''' + +import os +import matplotlib +# headless plotting and disable latex +matplotlib.use('Agg') +matplotlib.rcParams['text.usetex'] = False +import matplotlib.pyplot as ppl + +import logging + +import spyboat.plotting as spyplot + +logger = logging.getLogger(__name__) + +# figure resolution +DPI=250 + +def produce_snapshots(input_movie, results, frame, Wkwargs, + img_path='.'): + + ''' + Takes the *input_movie* and the + *results* dictionary from spyboat.processing.run_parallel + and produces phase, period and amplitude snapshot png's. + + For the period snapshot also the period range is needed, + hence the analysis dictionary 'Wkwargs' also gets passed. + + The output files name pattern is: + [input, phase, period, amplitude]_frame{frame}.png + and the storage location in *img_path*. + + These get picked up by 'create_html' + ''' + + + spyplot.input_snapshot(input_movie[frame]) + fig = ppl.gcf() + out_path = os.path.join(img_path, f'input_frame{frame}.png') + fig.savefig(out_path, dpi=DPI) + + spyplot.phase_snapshot(results['phase'][frame]) + fig = ppl.gcf() + out_path = os.path.join(img_path, f'phase_frame{frame}.png') + fig.savefig(out_path, dpi=DPI) + + spyplot.period_snapshot(results['period'][frame], + Wkwargs, + time_unit = 'a.u.') + + fig = ppl.gcf() + out_path = os.path.join(img_path, f'period_frame{frame}.png') + fig.savefig(out_path, dpi=DPI) + + spyplot.amplitude_snapshot(results['amplitude'][frame]) + fig = ppl.gcf() + out_path = os.path.join(img_path, f'amplitude_frame{frame}.png') + fig.savefig(out_path, dpi=DPI) + + + logger.info(f'Produced 4 snapshots for frame {frame}..') + +def produce_distr_plots(results, Wkwargs, img_path='.'): + + ''' + Output file names are: + + period_distr.png, power_distr.png and phase_distr.png + ''' + + spyplot.period_distr_dynamics(results['period'], Wkwargs) + fig = ppl.gcf() + out_path = os.path.join(img_path, f'period_distr.png') + fig.savefig(out_path, dpi=DPI) + + spyplot.power_distr_dynamics(results['power'], Wkwargs) + fig = ppl.gcf() + out_path = os.path.join(img_path, f'power_distr.png') + fig.savefig(out_path, dpi=DPI) + + spyplot.phase_coherence_dynamics(results['phase'], Wkwargs) + fig = ppl.gcf() + out_path = os.path.join(img_path, f'phase_distr.png') + fig.savefig(out_path, dpi=DPI) + + logger.info(f'Produced 3 distribution plots..') + + +def create_html(frame_num, html_fname='OutputReport.html'): + + ''' + The html generated assumes the respective png's (7 in total) + have been created with 'produce_snapshots' and 'produce_distr_plots' + and can be found at the cwd (that's how Galaxy works..) + ''' + + html_string =f''' + <html> + <title>SpyBOAT Output Report</title> + <head> + <!-- that doesn't work with galaxy.. --> + <!--link rel="stylesheet" href="styles.css"--> + <style type="text/css"> + body{{ margin:10 100; background:whitesmoke; }} + /*body{{ margin:10 100; background:darkslategrey; }}*/ + .center{{ + display: block; + margin-left: auto; + margin-right: auto; + width: 40%;}} + + /* matplotlib output at 1600x1200 */ + .distr_gallery {{ + display: grid; + margin: 0 auto; + text-align: center; + /* border: 1px dashed rgba(4, 4, 4, 0.35); */ + grid-template-columns: repeat(3,1fr); + grid-template-rows: 25vw; + grid-gap: 0px; + column-gap: 0px + }} + .distr_gallery__img {{ + width: 100%; + height: 100%; + object-fit: contain; + }} + + + /* matplotlib output at 1600x1200 */ + .snapshot_gallery {{ + display: grid; + margin: 0 auto; + border: 1px dashed rgba(4, 4, 4, 0.35); + text-align: center; + grid-template-columns: repeat(2,1fr); + grid-template-rows: repeat(2,20vw); + grid-gap: 5px; + }} + .snapshot_gallery__img {{ + width: 100%; + height: 100%; + object-fit: contain; + }} + </style> + </head> + <body> + <h1 style="text-align:center">SpyBOAT Results Report</h1> + <hr style="width:50%"> + <div class="distr_gallery"> + <figure class=”distr_gallery__item distr_gallery__item--1"> + <img src="period_distr.png" alt="Period" class="distr_gallery__img"> + </figure> + + <figure class=”distr_gallery__item distr_gallery__item--2"> + <img src="power_distr.png" alt="Power" class="distr_gallery__img"> + </figure> + + <figure class=”distr_gallery__item distr_gallery__item--3"> + <img src="phase_distr.png" alt="Phase" class="distr_gallery__img"> + </figure> + + </div> + + <h2 style="text-align:center"> Snapshots - Frame {frame_num}</h2> + <div class="snapshot_gallery"> + <figure class=”snapshot_gallery__item snapshot_gallery__item--1"> + <img src="input_frame{frame_num}.png" alt="The Input" class="snapshot_gallery__img"> + </figure> + + <figure class=”snapshot_gallery__item snapshot_gallery__item--2"> + <img src="phase_frame{frame_num}.png" alt="Phase" class="snapshot_gallery__img"> + </figure> + + <figure class=”snapshot_gallery__item snapshot_gallery__item--3"> + <img src="period_frame{frame_num}.png" alt="Period" class="snapshot_gallery__img"> + </figure> + + <figure class=”snapshot_gallery__item snapshot_gallery__item--4"> + <img src="amplitude_frame{frame_num}.png" alt="Amplitude" class="snapshot_gallery__img"> + </figure> + </div> + + + <!-- *** Section 1 *** ---> + </body> + </html> + ''' + + with open(html_fname, 'w') as OUT: + + OUT.write(html_string) + + logger.info(f'Created html report') + return html_string + +# for local testing +# create_html(125)