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reportsmanager.py
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reportsmanager.py
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import cellprocessing as cp
import tkFileDialog
import os
from skimage.util import img_as_float, img_as_int
from skimage.io import imsave
class ReportsManager(object):
def __init__(self, parameters):
self.keys = cp.stats_format(parameters.cellprocessingparams)
def generate_report_experiment(self, image_manager, cells_manager, fret_manager, path):
cells = cells_manager.cells
g_value = fret_manager.fret_G
cell_e = fret_manager.cell_E
membrane_e = fret_manager.membrane_E
cyto_e = fret_manager.cyto_E
membsept_e = fret_manager.membsept_E
septum_e = fret_manager.septum_E
auto_d = fret_manager.autofluorescence_donor
auto_a = fret_manager.autofluorescence_acceptor
auto_f = fret_manager.autofluorescence_fret
cf_a = fret_manager.fret_a
cf_b = fret_manager.fret_b
cf_c = fret_manager.fret_c
cf_d = fret_manager.fret_d
HTML_HEADER = """<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01//EN"
"http://www.w3.org/TR/html4/strict.dtd">
<html lang="en">
<head>
<meta http-equiv="content-type" content="text/html; charset=utf-8">
<title>title</title>
<link rel="stylesheet" type="text/css" href="style.css">
<script type="text/javascript" src="script.js"></script>
</head>
<body>\n"""
report = [HTML_HEADER]
g_report = "<h2>Average G value: " + str(g_value) + "</h2>"
report.extend(g_report)
cell_e_report = "<h2>Average Cell E value: " + str(cell_e) + "</h2>"
report.extend(cell_e_report)
membrane_e_report = "<h2>Average Membrane E value: " + str(membrane_e) + "</h2>"
report.extend(membrane_e_report)
cyto_e_report = "<h2>Average Cytoplasm E value: " + str(cyto_e) + "</h2>"
report.extend(cyto_e_report)
septum_e_report = "<h2>Average Septum E value: " + str(septum_e) + "</h2>"
report.extend(septum_e_report)
membsept_e_report = "<h2>Average MembSept E value: " + str(membsept_e) + "</h2>"
report.extend(membsept_e_report)
auto_d_report = "<h2>Average Donor Autofluorescence value: " + str(auto_d) + "</h2>"
report.extend(auto_d_report)
auto_a_report = "<h2>Average Acceptor Autofluorescence value: " + str(auto_a) + "</h2>"
report.extend(auto_a_report)
auto_f_report = "<h2>Average FRET Autofluorescence value: " + str(auto_f) + "</h2>"
report.extend(auto_f_report)
cf_a_report = "<h2>Average a value: " + str(cf_a) + "</h2>"
report.extend(cf_a_report)
cf_b_report = "<h2>Average b value: " + str(cf_b) + "</h2>"
report.extend(cf_b_report)
cf_c_report = "<h2>Average c value: " + str(cf_c) + "</h2>"
report.extend(cf_c_report)
cf_d_report = "<h2>Average d value: " + str(cf_d) + "</h2>"
report.extend(cf_d_report)
if len(cells) > 0:
header = '<table border=1>\n<th>Cell ID</th><th>Images'
for k in self.keys:
label, digits = k
header = header + '</th><th>' + label
header += '</th>\n'
fret = ['\n<h1>FRET cells:</h1>\n' + header + '\n']
donor = ['\n<h1>Donor cells:</h1>\n' + header + '\n']
acceptor = ['\n<h1>Acceptor Cells:</h1>\n' + header + '\n']
control = ['\n<h1>Control Cells:</h1>\n' + header + '\n']
wt = ['\n<h1>wt Cells:</h1>\n' + header + '\n']
discarded = ['\n<h1>Discarded Cells:</h1>\n' + header + '\n']
sorted_keys = []
for k in sorted(cells.keys()):
sorted_keys.append(int(k))
sorted_keys = sorted(sorted_keys)
for k in sorted_keys:
cell = cells[str(k)]
if cell.channel == "both":
cellid = str(int(cell.label))
img = img_as_float(cell.image[:, 0:1+cell.image.shape[1]/2])
imsave(path + "/_fret_images" +
os.sep + cellid + '.png', img)
lin = '<tr><td>' + cellid + '</td><td><img src="./' + '_fret_images/' + \
cellid + '.png" alt="pic" width="200"/></td>'
for stat in self.keys:
lbl, digits = stat
lin = lin + '</td><td>' + \
("{0:." + str(digits) +
"f}").format(cell.stats[lbl])
lin += '</td></tr>\n'
fret.append(lin)
elif cell.channel == "donor":
cellid = str(int(cell.label))
img = img_as_float(cell.image[:, 0:1+cell.image.shape[1]/2])
imsave(path + "/_donor_images" +
os.sep + cellid + '.png', img)
lin = '<tr><td>' + cellid + '</td><td><img src="./' + '_donor_images/' + \
cellid + '.png" alt="pic" width="200"/></td>'
for stat in self.keys:
lbl, digits = stat
lin = lin + '</td><td>' + \
("{0:." + str(digits) +
"f}").format(cell.stats[lbl])
lin += '</td></tr>\n'
donor.append(lin)
elif cell.channel == "acceptor":
cellid = str(int(cell.label))
img = img_as_float(cell.image[:, 0:1+cell.image.shape[1]/2])
imsave(path + "/_acceptor_images" +
os.sep + cellid + '.png', img)
lin = '<tr><td>' + cellid + '</td><td><img src="./' + '_acceptor_images/' + \
cellid + '.png" alt="pic" width="200"/></td>'
for stat in self.keys:
lbl, digits = stat
lin = lin + '</td><td>' + \
("{0:." + str(digits) +
"f}").format(cell.stats[lbl])
lin += '</td></tr>\n'
acceptor.append(lin)
elif cell.channel == "control":
cellid = str(int(cell.label))
img = img_as_float(cell.image[:, 0:1+cell.image.shape[1]/2])
imsave(path + "/_control_images" +
os.sep + cellid + '.png', img)
lin = '<tr><td>' + cellid + '</td><td><img src="./' + '_control_images/' + \
cellid + '.png" alt="pic" width="200"/></td>'
for stat in self.keys:
lbl, digits = stat
lin = lin + '</td><td>' + \
("{0:." + str(digits) +
"f}").format(cell.stats[lbl])
lin += '</td></tr>\n'
control.append(lin)
elif cell.channel == "wt":
cellid = str(int(cell.label))
img = img_as_float(cell.image[:, 0:1+cell.image.shape[1]/2])
imsave(path + "/_wt_images" +
os.sep + cellid + '.png', img)
lin = '<tr><td>' + cellid + '</td><td><img src="./' + '_wt_images/' + \
cellid + '.png" alt="pic" width="200"/></td>'
for stat in self.keys:
lbl, digits = stat
lin = lin + '</td><td>' + \
("{0:." + str(digits) +
"f}").format(cell.stats[lbl])
lin += '</td></tr>\n'
wt.append(lin)
elif cell.channel == "discard":
cellid = str(int(cell.label))
img = img_as_float(cell.image[:, 0:1+cell.image.shape[1]/2])
imsave(path + "/_discarded_images" +
os.sep + cellid + '.png', img)
lin = '<tr><td>' + cellid + '</td><td><img src="./' + '_discarded_images/' + \
cellid + '.png" alt="pic" width="200"/></td>'
for stat in self.keys:
lbl, digits = stat
lin = lin + '</td><td>' + \
("{0:." + str(digits) +
"f}").format(cell.stats[lbl])
lin += '</td></tr>\n'
discarded.append(lin)
if len(fret) > 1:
report.extend(fret)
report.append("</table>\n")
if len(donor) > 1:
report.extend(donor)
report.append("</table>\n")
if len(acceptor) > 1:
report.extend(acceptor)
report.append("</table>\n")
if len(control) > 1:
report.extend(control)
report.append("</table>\n")
if len(wt) > 1:
report.extend(wt)
report.append("</table>\n")
if len(discarded) > 1:
report.extend(discarded)
report.append("</table>\n")
report.append('</body>\n</html>')
open(path + os.sep + "html_report.html", "w").writelines(report)
def generate_report(self, image_manager, cells_manager, fret_manager, path=None):
if path is None:
path = tkFileDialog.askdirectory()
path = path + os.sep + "Report Experiment"
if not os.path.exists(path + os.sep + "_fret_images"):
os.makedirs(path + os.sep + "_fret_images")
if not os.path.exists(path + os.sep + "_donor_images"):
os.makedirs(path + os.sep + "_donor_images")
if not os.path.exists(path + os.sep + "_acceptor_images"):
os.makedirs(path + os.sep + "_acceptor_images")
if not os.path.exists(path + os.sep + "_control_images"):
os.makedirs(path + os.sep + "_control_images")
if not os.path.exists(path + os.sep + "_wt_images"):
os.makedirs(path + os.sep + "_wt_images")
if not os.path.exists(path + os.sep + "_discarded_images"):
os.makedirs(path + os.sep + "_discarded_images")
self.generate_report_experiment(image_manager, cells_manager, fret_manager, path)
imsave(path + os.sep + "heatmap.png", img_as_int(fret_manager.fret_heatmap))