Merge branch 'report' into 'master'

Report See merge request !1

Merge branch 'report' into 'master'
Report See merge request !1
eb4d5877 · Sean Fitzgibbon · b235e4ad · cf4f1fd1 · eb4d5877 · eb4d5877
Commit eb4d5877 authored Jun 29, 2021 by Sean Fitzgibbon
--- a/slider/chart_reg.py
+++ b/slider/chart_reg.py
@@ -50,6 +50,10 @@ def register_chart_to_slide(chart, slide, slide_res, out, config=None):

    global OUTDIR
    OUTDIR = out
+
+    #  create output dir
+    if not op.exists(out):
+        os.makedirs(out)
        
    # load chart
    contour, cells = neurolucida.read(chart)
@@ -82,9 +86,6 @@ def register_chart_to_slide(chart, slide, slide_res, out, config=None):
        f'Rotation:\t{opt.rotation}\nTranslation:\t{opt.translation}\nScale:\t\t{list(opt.scale)}\nShear:\t\t{opt.shear}')

    # save opt transform
-    if not op.exists(out):
-        os.makedirs(out)
-
    np.savetxt(f'{out}/chart-to-image.xfm', opt.params)

    # apply opt-xfm to contours and cells and save
@@ -113,6 +114,19 @@ def register_chart_to_slide(chart, slide, slide_res, out, config=None):
        
        fig.savefig(f'{OUTDIR}/aligned_chart.png', bbox_inches='tight', dpi=300)

+        # fig, ax = plt.subplots(1, 5, figsize=(25, 5))    
+        # ax[0].imshow(plt.imread(f'{OUTDIR}/chart_bounding_box.png'))
+        # ax[1].imshow(plt.imread(f'{OUTDIR}/image_bounding_box.png'))
+        # ax[2].imshow(plt.imread(f'{OUTDIR}/normals.png'))
+        # ax[3].imshow(plt.imread(f'{OUTDIR}/refined_coords.png'))
+        # ax[4].imshow(plt.imread(f'{OUTDIR}/aligned_chart.png'))
+
+        # for a in ax:
+        #     a.axis('off')
+
+        # fig.savefig(f'{OUTDIR}/alignment.png', bbox_inches='tight', dpi=150)
+
+        

    with open(f'{out}/contour.json', 'w') as fp:
        json.dump(contour_xfm, fp, indent=4)

--- a/slider/report.py
+++ b/slider/report.py
+#!/usr/bin/env python
+# 
+# Copyright 2021 Sean Fitzgibbon, University of Oxford
+# 
+#    Licensed under the Apache License, Version 2.0 (the "License");
+#    you may not use this file except in compliance with the License.
+#    You may obtain a copy of the License at
+# 
+#        http://www.apache.org/licenses/LICENSE-2.0
+# 
+#    Unless required by applicable law or agreed to in writing, software
+#    distributed under the License is distributed on an "AS IS" BASIS,
+#    WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+#    See the License for the specific language governing permissions and
+#    limitations under the License.
+# 
+import jinja2
+import os.path as op
+import os
+import base64
+
+def report_reg(dirs, out, embed=False):
+
+    images = [f'{d}/alignment.png' for d in dirs]
+    images = [d for d in images if op.exists(d)]
+
+    images = [(op.dirname(f), to_base64(f) if embed else f) for f in images]
+    
+    env = jinja2.Environment(
+        loader=jinja2.PackageLoader('slider', 'resources'),
+        autoescape=jinja2.select_autoescape(['html', 'xml']),
+        extensions=['jinja2.ext.do']
+    )
+
+    template = env.get_template('registration_report_template.html')
+    html = template.render(
+        images=images,
+    )
+
+    with open(out, 'w') as outfile:
+        outfile.write(html)
+
+
+def to_base64(fname):
+
+    with open(fname, 'rb') as tmp:
+        tmp.seek(0)
+        s = base64.b64encode(tmp.read()).decode("utf-8")
+
+    return 'data:image/{};base64,'.format(op.splitext(fname)[-1]) + s
--- a/slider/resources/registration_report_template.html
+++ b/slider/resources/registration_report_template.html
+<!doctype html>
+<html lang="en">
+
+{% set Nimages = images|length %}
+
+<head>
+    <!-- Required meta tags -->
+    <meta charset="utf-8">
+    <meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+
+    <!-- Bootstrap CSS -->
+    <link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/4.0.0/css/bootstrap.min.css"
+          integrity="sha384-Gn5384xqQ1aoWXA+058RXPxPg6fy4IWvTNh0E263XmFcJlSAwiGgFAW/dAiS6JXm"
+          crossorigin="anonymous">
+
+    <style type="text/css">
+        body {
+            background: whitesmoke !important;
+        }
+
+        .popover {
+            max-width: 100%;
+        }
+
+        @media (min-width: 34em) {
+            .card-columns {
+                -webkit-column-count: 1;
+                -moz-column-count: 1;
+                column-count: 1;
+            }
+        }
+
+        @media (min-width: 48em) {
+            .card-columns {
+                -webkit-column-count: 1;
+                -moz-column-count: 1;
+                column-count: 1;
+            }
+        }
+
+        @media (min-width: 62em) {
+            .card-columns {
+                -webkit-column-count: 1;
+                -moz-column-count: 1;
+                column-count: 1;
+            }
+        }
+
+        @media (min-width: 75em) {
+            .card-columns {
+                -webkit-column-count: 2;
+                -moz-column-count: 2;
+                column-count: 2;
+            }
+        }
+
+        /* Adding !important forces the browser to overwrite the default style applied by Bootstrap */
+    </style>
+
+    <title>SlideR Report</title>
+</head>
+
+<body>
+
+    <nav class="navbar sticky-top navbar-expand-lg navbar-dark bg-dark justify-content-between">
+        <span class="navbar-brand mb-0 h1">SlideR &#127828;: Registration Report</span>
+    </nav>
+    
+    <div class="container-fluid">
+    
+        <div class="row">
+    
+            <div class="col-xl-12">
+            {% for idx in range(Nimages) %}
+    
+                {% set img0 = images[idx] %}
+
+                <div class="card border-secondary mt-2" id="image-card">
+                    <div class="card-header">
+                        {{ img0[0] }}
+                    </div>
+
+                    <div class="card-body">
+                        
+                        <img src="{{ img0[1] }}" width="100%">
+    
+                        <div class="row justify-content-end">
+                            <div class="col-1"><small>Image {{ idx+1 }} of {{ Nimages }}</small></div>
+                        </div>
+    
+                    </div>
+    
+                </div>
+    
+            {% endfor %}
+            </div>
+
+    
+
+        </div>
+
+    <!-- Optional JavaScript -->
+    <!-- jQuery first, then Popper.js, then Bootstrap JS -->
+    <script src="https://code.jquery.com/jquery-3.3.1.slim.min.js"
+            integrity="sha384-q8i/X+965DzO0rT7abK41JStQIAqVgRVzpbzo5smXKp4YfRvH+8abtTE1Pi6jizo"
+            crossorigin="anonymous"></script>
+    <script src="https://cdnjs.cloudflare.com/ajax/libs/popper.js/1.14.7/umd/popper.min.js"
+            integrity="sha384-UO2eT0CpHqdSJQ6hJty5KVphtPhzWj9WO1clHTMGa3JDZwrnQq4sF86dIHNDz0W1"
+            crossorigin="anonymous"></script>
+    <script src="https://stackpath.bootstrapcdn.com/bootstrap/4.3.1/js/bootstrap.min.js"
+            integrity="sha384-JjSmVgyd0p3pXB1rRibZUAYoIIy6OrQ6VrjIEaFf/nJGzIxFDsf4x0xIM+B07jRM"
+            crossorigin="anonymous"></script>
+    <script>
+        $(document).ready(function () {
+            $('[data-toggle="popover"]').popover({container: 'body'});
+        });
+    </script>
+
+</body>
+
+</html>
--- a/slider_app.py
+++ b/slider_app.py
@@ -20,6 +20,7 @@ import sys
 from slider.slide_reg import register_slide_to_slide, apply_slide_xfm
 from slider.chart_reg import register_chart_to_slide
 from slider.batch import run_batch
+from slider.report import report_reg

 def add_slide_cli(subparsers):
    """
@@ -125,6 +126,24 @@ def add_batch_cli(subparsers):
    parser.set_defaults(method='batch')


+def add_report_cli(subparsers):
+    """
+    Set up report subparser instance.
+    """
+    parser = subparsers.add_parser(
+        'REPORT',
+        description='Generate report of SlideR registrations',
+        formatter_class=lambda prog: argparse.HelpFormatter(prog, max_help_position=55, width=100)
+    )
+    parser.add_argument("out", metavar="<dir>",
+                        help="Output directory", default=None, type=str)
+    parser.add_argument("dirs", metavar="<reg-dir>", nargs='+', 
+                        help="Registration directories to include in report")
+    parser.add_argument('--embed', dest='embed', action='store_true',
+                        help='Embed images into report to make it transportable as a single file (report will be much larger).')
+    parser.set_defaults(method='report')
+
+

 if __name__ == "__main__":
    """ Main program code. """
@@ -136,6 +155,7 @@ if __name__ == "__main__":
    add_chart_cli(subparsers)
    add_applyxfm_cli(subparsers)
    add_batch_cli(subparsers)
+    add_report_cli(subparsers)

    # ---

@@ -154,5 +174,7 @@ if __name__ == "__main__":
        apply_slide_xfm(**args)
    elif method == 'batch':
        run_batch(**args)
+    elif method == 'report':
+        report_reg(**args)
    else:
        raise RuntimeError(f'Unknown method: {method}')