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Pragnya edited this page Jan 22, 2015 · 6 revisions

There is a feature "enable_detailed_results", which can be included in the competition YAML file. enable_detailed_results: True After enabling this feature, the scoring program should take care of the creation of an html file. If this file is created by the scoring program, CodaLab can access the file which is displayed in the leaderboard. There are a few important points to be able to use this module correctly

  • The images need to be embedded using base64 encoding in the html page rather than adding a html tag "img". This is needed because the images can't be accessed from the blob storage link (needs SAS key again for each image).
  • If you are using any javascript or CSS formatting in the html file, please make sure these files are publically accessible by the html file. Again the html file can't access any private blob storage in CodaLab.
  • If Linux compute worker is used, add these lines to the scoring program (only for python and matplotlib).

import matplotlib matplotlib.use('Agg') #very important to make it work on Linux

Example scoring program to create an html page with figures and tables:

import matplotlib
matplotlib.use('Agg')
import os, os.path, sys
import math
import matplotlib.pyplot as plt
import shutil
from pylab import *
import itertools
import numpy as np

def f(t):
    return np.exp(-t) * np.cos(2*np.pi*t)

def createHTML(outputDir):
htmlOutputDir = os.path.join(outputDir, "html")
imagesOutputDir = os.path.join(htmlOutputDir, "images")
if not os.path.exists(htmlOutputDir):
		os.makedirs(htmlOutputDir)
		os.makedirs(imagesOutputDir)
		
t1 = np.arange(0.0, 5.0, 0.1)
t2 = np.arange(0.0, 5.0, 0.02)
fig1 = plt.figure()
plt.plot(t1, f(t1), 'bo', t2, f(t2), 'k')
plt.savefig(os.path.join(outputDir,"testCurve.png"), bbox_inches=0, dpi=300)

#image 1
imageOrg = os.path.join(outputDir, "testCurve.png")
data_uri1 = open(imageOrg, 'rb').read().encode('base64').replace('\n', '')
img_tag1 = 'src="data:image/png;base64,{0}"'.format(data_uri1)

		
htmlString = '''<!DOCTYPE html>
<html>
<head>
    <title>Demo Html</title>
    <link href="theme.default.css" rel="stylesheet">  #Make sure this is a public location
    <script type="text/javascript" src="jquery.min.js"></script> #Make sure this is a public location
    <script type="text/javascript" src="jquery.tablesorter.min.js"></script> #Make sure this is a public location
    <script>
       $(function(){
          $("#table1").tablesorter({widgets: ['zebra']});
       });
    </script>
    <style>
		table.tablesorter td {
			text-align: center;
		}
		
		td.left-align {
			text-align: left !important;
		}
    </style>  
</head>
<body>
<p>
Results are plotted for all nodules and subsets of nodules. The subsets are small nodules (diameter smaller than 5 mm) and large nodules (diameter larger than 5mm) and isolated, juxtapleural, juxtavascular and peri-fissural nodules.</p>
<p>
The overal score of this system is given in the lower right cell of the table below. This is the average sensitivity at an average number of false positives per scan of 1/8, 1/4, 1/2, 1, 2, 4 and 8. The sensitivities at these false positive rates for all nodules and all subsets of nodules are tabulated below.</p>
<p>
<img border="0" %s alt="FROC" width="576pt" height="432pt">
<p>
The following table summarizes the results.</p>
<p>
<table border=1 class = "tablesorter" id="table1" style="width: auto; margin: 10px auto 0 auto;">
    <thead>
    <tr>
        <td class ="firstcol">FPs/scan</td><td align=center width='54'>1/8</td>
        <td align=center width='54'>1/4</td>
        <td align=center width='54'>1/2</td><td align=center width='54'>1</td>
        <td align=center width='54'>2</td><td align=center width='54'>4</td>
        <td align=center width='54'>8</td><td align=center width='54'>average</td>
    </tr>
    </thead>
    <tbody>
		<tr class = ""><td class="left-align">small nodules</td><td>0.470</td><td>0.491</td><td>0.573</td><td>0.658</td><td>0.711</td><td>0.761</td><td>0.778</td><td>0.634</td></tr>
		<tr class = ""><td class="left-align">large nodules</td><td>0.423</td><td>0.483</td><td>0.567</td><td>0.611</td><td>0.714</td><td>0.778</td><td>0.822</td><td>0.628</td></tr>
		<tr class = ""><td class="left-align">isolated nodules</td><td>0.548</td><td>0.595</td><td>0.595</td><td>0.619</td><td>0.619</td><td>0.643</td><td>0.643</td><td>0.609</td></tr>
		<tr class = ""><td class="left-align">vascular nodules</td><td>0.570</td><td>0.573</td><td>0.616</td><td>0.686</td><td>0.757</td><td>0.802</td><td>0.849</td><td>0.693</td></tr>
		<tr class = ""><td class="left-align">peri-fissural nodules</td><td>0.629</td><td>0.643</td><td>0.743</td><td>0.771</td><td>0.804</td><td>0.886</td><td>0.886</td><td>0.766</td></tr>
		<tr class = ""><td class="left-align">all nodules</td><td>0.450</td><td>0.488</td><td>0.570</td><td>0.638</td><td>0.712</td><td>0.768</td><td>0.797</td><td>0.632</td></tr></tbody>        
	</tbody>
</table>	
</div>	
</body>
</html>''' % (img_tag1)
	
htmlfile = open(htmlOutputDir+"\\detailed_results.html","w")
htmlfile.write(htmlString)
htmlfile.close()

### main 

if __name__ == "__main__":
##Stuff for CodaLab scoring program to work##
input_dir = sys.argv[1]
output_dir = sys.argv[2]
print sys.path[0] 
outputDir = output_dir+"/"

submit_dir = os.path.join(input_dir, 'res') + "/"
truth_dir = os.path.join(input_dir, 'ref') + "/"

if not os.path.isdir(submit_dir):
	print "%s doesn't exist" % submit_dir

if os.path.isdir(submit_dir) and os.path.isdir(truth_dir):
	if not os.path.exists(output_dir):
		os.makedirs(output_dir)
		
##writing codaLab scores.txt##
output_filename = os.path.join(output_dir, 'scores.txt')              
output_file = open(output_filename, 'wb')
output_file.write("SENSITIVITY: %.3f\n" % (float(88) / float(100)))
output_file.write("CANDIDATES: %.3f\n" % (float(120) / float(50)))
output_file.write("TP: 88\n")
output_file.write("FP: 20\n")
output_file.write("FN: 12\n")
output_file.write("TN: 32")
output_file.close()

##CodaLab stuff ends	
createHTML(outputDir)`
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