diff output_report.py @ 0:76733d05d8ef draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat commit 5c60a414c785246371beac23ce52d8bbab3602d1"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/output_report.py	Sat Nov 28 13:45:34 2020 +0000
@@ -0,0 +1,253 @@
+""" 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, 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">
+                 <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>
+        </div>
+        """
+        galleries += new_gal
+
+    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; }}
+        /*body{{ margin:10 100; background:darkslategrey; }}*/
+        .center{{
+            text-align: center;
+            display: block;
+            margin-left: auto;
+            margin-right: auto;
+            width: 100%;}}
+
+        /* 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: 20vw;
+            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;
+        }}
+        .subheader{{
+             text-align:center;
+             font-size: 160%;
+             color:#363333;}}
+     </style>
+    </head>
+    <body>
+    <h1 style="text-align:center; color:#363333">SpyBOAT Results Report</h1>
+    <hr style="width:50%">
+    <h1 class="subheader"> Distribution Dynamics </h1>
+    <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>
+
+    <h1 class="subheader"> Output Movie Snapshots </h1>
+
+    <!-- trigger the javascript at the end--->
+    <div class="center">
+        <button class="w3-button" onclick="plusDivs(-1)">&#10094; Prev</button>
+        <button class="w3-button" onclick="plusDivs(1)">Next &#10095;</button>
+    </div>
+
+    <!-- defines all elements of the "FrameSlides" class --->
+    {galleries}
+    </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([0,20,40,60,80])