Mercurial > repos > gregor.m > spyboat

annotate output_report.py @ 2:c59d1373230e draft

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"planemo upload commit eeba34c94465f41d13c2f5bcf68177d23c92d971-dirty"
author gregor.m
date Mon, 23 Nov 2020 14:38:37 +0000
parents 1d62de03829d
children 4d7f30a7e2f6
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1 ''' Produces plots and a summary html 'headless' '''
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2
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3 import os
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4 import matplotlib
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5 # headless plotting and disable latex
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6 matplotlib.use('Agg')
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7 matplotlib.rcParams['text.usetex'] = False
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8 import matplotlib.pyplot as ppl
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9
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10 import logging
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11
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12 import spyboat.plotting as spyplot
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13
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14 logger = logging.getLogger(__name__)
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15
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16 # figure resolution
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17 DPI=250
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18
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19 def produce_snapshots(input_movie, results, frame, Wkwargs,
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20 img_path='.'):
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21
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22 '''
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23 Takes the *input_movie* and the
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24 *results* dictionary from spyboat.processing.run_parallel
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25 and produces phase, period and amplitude snapshot png's.
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26
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27 For the period snapshot also the period range is needed,
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28 hence the analysis dictionary 'Wkwargs' also gets passed.
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29
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30 The output files name pattern is:
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31 [input, phase, period, amplitude]_frame{frame}.png
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32 and the storage location in *img_path*.
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33
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34 These get picked up by 'create_html'
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35 '''
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36
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37
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38 spyplot.input_snapshot(input_movie[frame])
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39 fig = ppl.gcf()
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40 out_path = os.path.join(img_path, f'input_frame{frame}.png')
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41 fig.savefig(out_path, dpi=DPI)
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42
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43 spyplot.phase_snapshot(results['phase'][frame])
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44 fig = ppl.gcf()
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45 out_path = os.path.join(img_path, f'phase_frame{frame}.png')
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46 fig.savefig(out_path, dpi=DPI)
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47
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48 spyplot.period_snapshot(results['period'][frame],
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49 Wkwargs,
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50 time_unit = 'a.u.')
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51
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52 fig = ppl.gcf()
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53 out_path = os.path.join(img_path, f'period_frame{frame}.png')
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54 fig.savefig(out_path, dpi=DPI)
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55
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56 spyplot.amplitude_snapshot(results['amplitude'][frame])
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57 fig = ppl.gcf()
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58 out_path = os.path.join(img_path, f'amplitude_frame{frame}.png')
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59 fig.savefig(out_path, dpi=DPI)
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60
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61
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62 logger.info(f'Produced 4 snapshots for frame {frame}..')
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63
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64 def produce_distr_plots(results, Wkwargs, img_path='.'):
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65
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66 '''
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67 Output file names are:
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68
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69 period_distr.png, power_distr.png and phase_distr.png
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70 '''
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71
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72 spyplot.period_distr_dynamics(results['period'], Wkwargs)
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73 fig = ppl.gcf()
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74 out_path = os.path.join(img_path, f'period_distr.png')
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75 fig.savefig(out_path, dpi=DPI)
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76
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77 spyplot.power_distr_dynamics(results['power'], Wkwargs)
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78 fig = ppl.gcf()
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79 out_path = os.path.join(img_path, f'power_distr.png')
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80 fig.savefig(out_path, dpi=DPI)
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81
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82 spyplot.phase_coherence_dynamics(results['phase'], Wkwargs)
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83 fig = ppl.gcf()
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84 out_path = os.path.join(img_path, f'phase_distr.png')
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85 fig.savefig(out_path, dpi=DPI)
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86
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87 logger.info(f'Produced 3 distribution plots..')
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88
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89
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90 def create_html(frame_num, html_fname='OutputReport.html'):
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91
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92 '''
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93 The html generated assumes the respective png's (7 in total)
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94 have been created with 'produce_snapshots' and 'produce_distr_plots'
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95 and can be found at the cwd (that's how Galaxy works..)
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96 '''
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97
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98 html_string =f'''
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99 <html>
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100 <title>SpyBOAT Output Report</title>
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101 <head>
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102 <!-- that doesn't work with galaxy.. -->
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103 <!--link rel="stylesheet" href="styles.css"-->
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104 <style type="text/css">
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105 body{{ margin:10 100; background:whitesmoke; }}
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106 /*body{{ margin:10 100; background:darkslategrey; }}*/
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107 .center{{
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108 display: block;
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109 margin-left: auto;
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110 margin-right: auto;
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111 width: 40%;}}
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112
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113 /* matplotlib output at 1600x1200 */
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114 .distr_gallery {{
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115 display: grid;
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116 margin: 0 auto;
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117 text-align: center;
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118 /* border: 1px dashed rgba(4, 4, 4, 0.35); */
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119 grid-template-columns: repeat(3,1fr);
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120 grid-template-rows: 25vw;
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121 grid-gap: 0px;
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122 column-gap: 0px
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123 }}
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124 .distr_gallery__img {{
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125 width: 100%;
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126 height: 100%;
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127 object-fit: contain;
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128 }}
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129
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130
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131 /* matplotlib output at 1600x1200 */
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132 .snapshot_gallery {{
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133 display: grid;
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134 margin: 0 auto;
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135 border: 1px dashed rgba(4, 4, 4, 0.35);
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136 text-align: center;
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137 grid-template-columns: repeat(2,1fr);
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138 grid-template-rows: repeat(2,20vw);
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139 grid-gap: 5px;
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140 }}
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141 .snapshot_gallery__img {{
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142 width: 100%;
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143 height: 100%;
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144 object-fit: contain;
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145 }}
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146 </style>
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147 </head>
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148 <body>
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149 <h1 style="text-align:center">SpyBOAT Results Report</h1>
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150 <hr style="width:50%">
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151 <div class="distr_gallery">
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152 <figure class=”distr_gallery__item distr_gallery__item--1">
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153 <img src="period_distr.png" alt="Period" class="distr_gallery__img">
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154 </figure>
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155
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156 <figure class=”distr_gallery__item distr_gallery__item--2">
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157 <img src="power_distr.png" alt="Power" class="distr_gallery__img">
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158 </figure>
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159
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160 <figure class=”distr_gallery__item distr_gallery__item--3">
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161 <img src="phase_distr.png" alt="Phase" class="distr_gallery__img">
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162 </figure>
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163
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164 </div>
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165
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166 <h2 style="text-align:center"> Snapshots - Frame {frame_num}</h2>
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167 <div class="snapshot_gallery">
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168 <figure class=”snapshot_gallery__item snapshot_gallery__item--1">
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169 <img src="input_frame{frame_num}.png" alt="The Input" class="snapshot_gallery__img">
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170 </figure>
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171
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172 <figure class=”snapshot_gallery__item snapshot_gallery__item--2">
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173 <img src="phase_frame{frame_num}.png" alt="Phase" class="snapshot_gallery__img">
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174 </figure>
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175
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176 <figure class=”snapshot_gallery__item snapshot_gallery__item--3">
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177 <img src="period_frame{frame_num}.png" alt="Period" class="snapshot_gallery__img">
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178 </figure>
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179
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180 <figure class=”snapshot_gallery__item snapshot_gallery__item--4">
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181 <img src="amplitude_frame{frame_num}.png" alt="Amplitude" class="snapshot_gallery__img">
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182 </figure>
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183 </div>
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184
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185
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186 <!-- *** Section 1 *** --->
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187 </body>
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188 </html>
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189 '''
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190
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191 with open(html_fname, 'w') as OUT:
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192
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193 OUT.write(html_string)
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194
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195 logger.info(f'Created html report')
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196 return html_string
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197
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198 # for local testing
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199 # create_html(125)