Mercurial > repos > iuc > spyboat
view output_report.py @ 3:9c53c7da9cbe draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 169dbae234162ed1e7167e62a3e54de8f89b0268
author | iuc |
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date | Thu, 23 Jun 2022 17:28:14 +0000 |
parents | 639d2031d998 |
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""" Produces plots and a summary html 'headless' """ import logging import os import matplotlib import matplotlib.pyplot as ppl import spyboat.plotting as spyplot ppl.switch_backend('Agg') matplotlib.rcParams["text.usetex"] = False 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) ppl.close(fig) 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) ppl.close(fig) spyplot.period_snapshot( results["period"][frame], Wkwargs["Tmin"], Wkwargs["Tmax"], 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) ppl.close(fig) 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) ppl.close(fig) 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, "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, "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, "phase_distr.png") fig.savefig(out_path, dpi=DPI) logger.info("Produced 3 distribution plots..") def create_html(frame_nums, par_str, html_fname="OutputReport.html"): """ The html generated assumes the respective png's have been created with 'produce_snapshots' and 'produce_distr_plots' and can be found at the cwd (that's how Galaxy works..) """ # -- create a gallery for every frame in frame_nums -- galleries = "" for frame_num in frame_nums: new_gal = f""" <div class="FrameSlides"> <h3 style="text-align:center; color=#363333"> Frame Nr. {frame_num} </h3> <div class="snapshot_gallery"> <figure class=”snapshot_gallery__item snapshot_gallery__item--1" style="margin: 0 0"> <img src="input_frame{frame_num}.png" alt="The Input" class="snapshot_gallery__img"> </figure> <figure class=”snapshot_gallery__item snapshot_gallery__item--2" style="margin: 0 0"> <img src="phase_frame{frame_num}.png" alt="Phase" class="snapshot_gallery__img"> </figure> <figure class=”snapshot_gallery__item snapshot_gallery__item--3" style="margin: 0 0"> <img src="period_frame{frame_num}.png" alt="Period" class="snapshot_gallery__img"> </figure> <figure class=”snapshot_gallery__item snapshot_gallery__item--4" style="margin: 0 0"> <img src="amplitude_frame{frame_num}.png" alt="Amplitude" class="snapshot_gallery__img"> </figure> </div> </div> """ galleries += new_gal parameter_cells = '' for line in par_str.split('\n'): # last str is empty.. if not line: break par_name, par_val = line.split('->') parameter_cells += f''' <tr> <td>{par_name}</td> <td>{par_val}</td> </tr>''' html_string = f""" <html> <!-- this file got automatically created by 'output_report.py' --> <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; }} p{{ text-align: center; margin-top: 0.05cm; margin-bottom: .05cm; color:#2c2e2e; }} .center{{ text-align: center; display: block; margin-left: auto; margin-right: auto; width: 100%;}} /* matplotlib output at 1600x1200 */ .snapshot_gallery {{ margin: 0 0; text-align: center; display: grid; grid-template-columns: repeat(2,1fr); grid-template-rows: repeat(2,27vw); grid-gap: 5px; }} .snapshot_gallery__img {{ width: 100%; height: 100%; object-fit: contain; margin-top: 5px; margin-bottom: 15px; }} .subheader{{ text-align:center; font-size: 160%; color:#363333;}} .centerimg{{ text-align: center; width: 65%; max-width: 400px; display: block; padding: 10px; margin-left: auto; margin-right: auto; }} .div_distr{{ text-align: center; border-radius: 25px; margin-top: 1cm; margin: auto; margin-bottom: 0.5cm; background-color: #cce1e3; max-width: 550px; }} .partable{{ width: 70%; margin-left: auto; margin-right: auto; }} tr, td{{ color:#2c2e2e; font-size: 110%; }} </style> </head> <body> <h1 style="text-align:center; color:#363333">SpyBOAT Results Report</h1> <hr style="width:70%"> <h1 class="subheader"> Spatial Summary Statistics </h1> <div class="div_distr"> <img src="period_distr.png" alt="Period" class="centerimg"> <p> Median and quartiles of the estimated periods for each frame </p> </div> <div class="div_distr"> <img src="power_distr.png" alt="Period" class="centerimg"> <p> Median and quartiles of the ridge wavelet power for each frame </p> </div> <div class="div_distr"> <img src="phase_distr.png" alt="Period" class="centerimg"> <p> Kuramoto order parameter for the phases estimated for each frame </p> </div> <h1 class="subheader"> Output Movie Snapshots </h1> <!-- trigger the javascript at the end---> <div class="center"> <button class="w3-button" onclick="plusDivs(-1)">❮ Prev</button> <button class="w3-button" onclick="plusDivs(1)">Next ❯</button> </div> <!-- defines all elements of the "FrameSlides" class ---> {galleries} </div> <h1 class="subheader"> Parameters </h1> <div class="div_distr"> <table border = "1" class="partable"> <tr> <th>Name</th> <th>Value</th> </tr> {parameter_cells} </table> </div> <!-- javascript with escaped '{{'---> <script> var slideIndex = 1; showDivs(slideIndex); function plusDivs(n) {{ showDivs(slideIndex += n); }} function showDivs(n) {{ var i; var x = document.getElementsByClassName("FrameSlides"); if (n > x.length) {{slideIndex = 1}} if (n < 1) {{slideIndex = x.length}} ; for (i = 0; i < x.length; i++) {{ x[i].style.display = "none"; }} x[slideIndex-1].style.display = "block"; }} </script> </body> </html> """ with open(html_fname, "w") as OUT: OUT.write(html_string) logger.info("Created html report") return html_string # for local testing # create_html([0,20], 'par1 -> val1\n verylongpar2 -> val2')