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#!/usr/bin/env python3
"""Create ROI overview report.
This report consists of plots of all metrics (y: metric, x: rank of value).
Each plot is written out as a PNG file and we also create one output HTML file
that shows all HTML files.
Plotting is done using the fine matplotlib.
"""
__author__ = 'Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>'
__copyright__ = 'Copyring 2013, Freie Universitaet Berlin'
__license__ = 'BSD 3-clause'
import sys
import os
import os.path
try:
import argparse
except ImportError:
import argparse26 as argparse
import Cheetah.Template
import matplotlib.pyplot as plt
import ngs_roi.io
import ngs_roi.app
import ngs_roi.argparse
# The HTML template to use for generating the HTML page.
REPORT_TPL = """
<html>
<head>
<title>ROI Report</title>
</head>
<body>
<h1>ROI Report</h1>
<h2>Table of Contents</h2>
<ul>
#for figure in $figures
<li><a href="#$figure.slug">$figure.title</a></li>
#end for
</ul>
<h2>Plots</h2>
#for figure in $figures
<h3 id="$figure.slug">$figure.title</h3>
<img src="$figure.file_name" title="$figure.title" />
#end for
</body>
</html>
"""
class ReportBuilder(ngs_roi.app.App):
"""This class is used for building the report."""
def __init__(self, args):
self.args = args
self.in_file = self.args.in_file
self.out_file = self.args.out_file
self.out_dir = self.args.out_dir
self.prepareOutDir()
def plotAndWrite(self, file_name, numbers, ylabel):
"""Create plot of numbers and write as PNG.
:param file_name:path to write plot to as image
:param numbers:list of numbers to plot
:param ylabel:label for y axis
"""
plt.figure()
plt.plot(numbers)
plt.ylabel(ylabel)
plt.savefig(file_name)
def run(self):
# Load ROI.
print('Loading ROI...', file=sys.stderr)
records = ngs_roi.io.load(self.in_file)
keys = records[0].data_keys
# Create ROI plots.
print('Creating plots...', file=sys.stderr)
METRICS = [('start position', 'start_pos', lambda x: x.start_pos),
('end position', 'end_pos', lambda x: x.end_pos),
('region length', 'region_length', lambda x: x.region_length),
('max count', 'max_count', lambda x: x.max_count)]
def getData(i):
def func(x):
try:
res = float(x.data[i])
except ValueError:
res = 0
return res
return func
for i, key in enumerate(keys):
slug = ''.join(x for x in key if x.isalnum())
METRICS.append((key, slug, getData(i)))
figure_infos = []
for title, slug, func in METRICS:
values = [func(x) for x in records]
file_name = 'report_%s.png' % slug
file_path = os.path.join(self.out_dir, file_name)
self.plotAndWrite(file_path, sorted(values), title)
figure_infos.append({'file_name': file_name, 'title': title, 'slug': slug})
# Create report HTML.
name_space = {'figures': figure_infos}
t = Cheetah.Template.Template(REPORT_TPL, searchList=name_space)
with open(os.path.join(self.out_dir, 'index.html'), 'wb') as f:
f.write(str(t))
with open(os.path.join(self.out_file), 'wb') as f:
f.write(str(t))
def main():
"""Program entry point."""
parser = argparse.ArgumentParser(description='Create ROI report.')
ngs_roi.argparse.addFileArguments(parser)
args = parser.parse_args()
ngs_roi.argparse.applyFileDefaults(args)
report_builder = ReportBuilder(args)
return report_builder.run()
if __name__ == '__main__':
sys.exit(main())
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