def htmlSummaryPP(self):
"""
Create HTML/php files for Labelit.precession_photo output results.
"""
if self.verbose:
self.logger.debug('LabelitPP::htmlSummaryPP')
try:
l = ['0KL','H0L','HK0']
if self.gui:
sl = 'jon_summary_pp.php'
else:
sl = 'jon_summary_pp.html'
jon_summary = open(sl,'w')
jon_summary.write(Utils.getHTMLHeader(self))
jon_summary.write("%4s$(function() {\n%6s$('.tabs').tabs();\n%4s});\n"%(3*('',)))
jon_summary.write("%4s</script>\n%2s</head>\n%2s<body>\n%4s<table>\n%6s<tr>\n"%(5*('',)))
jon_summary.write('%8s<td width="100%%">\n%10s<div class="tabs">\n%12s<ul>\n'%(3*('',)))
for i in range(len(l)):
jon_summary.write('%14s<li><a href="#tabs-54%s">%s</a></li>\n'%('',i,l[i]))
jon_summary.write("%12s</ul>\n"%'')
for i in range(len(l)):
jon_summary.write('%12s<div id="tabs-54%s">\n'%('',i))
if self.labelitpp_results.get('LabelitPP results').get('%s jpg'%l[i]) == None:
jon_summary.write('%14s<p>The precession photo for this plane did not work.</p>\n'%'')
else:
if self.gui:
jon_summary.write("%14s<div id='pp%s_jpg' style='text-align:center'></div>\n"%('',i))
else:
jon_summary.write('%14s<IMG SRC="%s">\n'%('',self.labelitpp_results.get('LabelitPP results').get('%s jpg'%l[i])))
jon_summary.write("%12s</div>\n"%'')
jon_summary.write("%10s</div>\n%8s</td>\n%6s</tr>\n%4s</table>\n%2s</body>\n</html>\n"%(5*('',)))
jon_summary.close()
except:
self.logger.exception('**ERROR in LabelitPP.htmlSummaryPP**')
def htmlSummaryPP(self):
"""
Create HTML/php files for Labelit.precession_photo output results.
"""
if self.verbose:
self.logger.debug('LabelitPP::htmlSummaryPP')
try:
l = ['0KL', 'H0L', 'HK0']
if self.gui:
sl = 'jon_summary_pp.php'
else:
sl = 'jon_summary_pp.html'
jon_summary = open(sl, 'w')
jon_summary.write(Utils.getHTMLHeader(self))
jon_summary.write(
"%4s$(function() {\n%6s$('.tabs').tabs();\n%4s});\n" %
(3 * ('', )))
jon_summary.write(
"%4s</script>\n%2s</head>\n%2s<body>\n%4s<table>\n%6s<tr>\n" %
(5 * ('', )))
jon_summary.write(
'%8s<td width="100%%">\n%10s<div class="tabs">\n%12s<ul>\n' %
(3 * ('', )))
for i in range(len(l)):
jon_summary.write(
'%14s<li><a href="#tabs-54%s">%s</a></li>\n' %
('', i, l[i]))
jon_summary.write("%12s</ul>\n" % '')
for i in range(len(l)):
jon_summary.write('%12s<div id="tabs-54%s">\n' % ('', i))
if self.labelitpp_results.get('LabelitPP results').get(
'%s jpg' % l[i]) == None:
jon_summary.write(
'%14s<p>The precession photo for this plane did not work.</p>\n'
% '')
else:
if self.gui:
jon_summary.write(
"%14s<div id='pp%s_jpg' style='text-align:center'></div>\n"
% ('', i))
else:
jon_summary.write(
'%14s<IMG SRC="%s">\n' %
('', self.labelitpp_results.get(
'LabelitPP results').get('%s jpg' % l[i])))
jon_summary.write("%12s</div>\n" % '')
jon_summary.write(
"%10s</div>\n%8s</td>\n%6s</tr>\n%4s</table>\n%2s</body>\n</html>\n"
% (5 * ('', )))
jon_summary.close()
except:
self.logger.exception('**ERROR in LabelitPP.htmlSummaryPP**')
def htmlSummaryXtriage(self):
"""
Create HTML/php files for xtriage output results.
"""
if self.verbose:
self.logger.debug('AutoStats::htmlSummaryXtriage')
try:
if self.xtriage_summary:
if self.gui:
sl = 'jon_summary_xtriage.php'
else:
sl = 'jon_summary_xtriage.html'
jon_summary = open(sl,'w')
jon_summary.write(Utils.getHTMLHeader(self,'xtriage'))
jon_summary.write('%6s$(document).ready(function() {\n'%'')
jon_summary.write("%8s$('#accordion-xtriage').accordion({\n%11scollapsible: true,\n%11sactive: false });\n"%(3*('',)))
jon_summary.write("%8s$('#xtriage-auto2').dataTable({\n"%'')
jon_summary.write('%11s"bPaginate": false,\n%11s"bFilter": false,\n%11s"bInfo": false,\n%11s"bSort": false,\n%11s"bAutoWidth": false });\n'%(5*('',)))
jon_summary.write("%8s$('#xtriage_pat').dataTable({\n"%'')
jon_summary.write('%11s"bPaginate": false,\n%11s"bFilter": false,\n%11s"bInfo": false,\n%11s"bSort": false,\n%11s"bAutoWidth": false });\n'%(5*('',)))
if self.pts:
jon_summary.write("%8s$('#xtriage_pts').dataTable({\n"%'')
jon_summary.write('%11s"bPaginate": false,\n%11s"bFilter": false,\n%11s"bInfo": false,\n%11s"bSort": false,\n%11s"bAutoWidth": false });\n'%(5*('',)))
if self.twin:
jon_summary.write("%8s$('#xtriage_twin').dataTable({\n"%'')
jon_summary.write('%11s"bPaginate": false,\n%11s"bFilter": false,\n%11s"bInfo": false,\n%11s"bSort": false,\n%11s"bAutoWidth": false });\n'%(5*('',)))
jon_summary.write('%6s});\n%4s</script>\n%2s</head>\n%2s<body id="dt_example">\n'%(4*('',)))
jon_summary.writelines(self.xtriage_summary)
jon_summary.write('%4s<div id="container">\n%5s<div class="full_width big">\n%6s<div id="demo">\n'%(3*('',)))
jon_summary.write("%7s<h1 class='Results'>Xtriage Output</h1>\n%6s</div>\n%5s</div>\n"%(3*('',)))
jon_summary.write('%5s<div id="accordion-xtriage">\n'%'')
jon_summary.write('%6s<h3><a href="#">Click to view Xtriage log</a></h3>\n%6s<div>\n%7s<pre>\n'%(3*('',)))
if self.xtriage_log:
for line in self.xtriage_log:
jon_summary.write(line)
else:
jon_summary.write('---------------Xtriage FAILED---------------\n')
jon_summary.write('%7s</pre>\n%6s</div>\n%5s</div>\n%4s</div>\n%2s</body>\n</html>\n'%(5*('',)))
jon_summary.close()
else:
Utils.failedHTML(self,('jon_summary_xtriage','Input data could not be analysed, probably because resolution was too low.'))
except:
self.logger.exception('**ERROR in AutoStats.htmlSummaryXtriage**')
def htmlSummaryPhaser(self):
"""
Create HTML/php files for autoindex/strategy output results.
"""
if self.verbose:
self.logger.debug('AutoMolRep::htmlSummaryPhaser')
try:
sl = 'jon_summary_cell.html'
if self.gui:
sl = sl.replace('html','php')
jon_summary = open(sl,'w')
jon_summary.write(Utils.getHTMLHeader(self,'phaser'))
jon_summary.write('%6s$(document).ready(function() {\n'%'')
#jon_summary.write("%8s$('#accordion').accordion({\n"%'')
#jon_summary.write('%11scollapsible: true,\n%11sactive: false });\n'%('',''))
if self.cell_summary:
jon_summary.write("%8s$('#phaser-cell').dataTable({\n"%'')
jon_summary.write('%11s"bPaginate": false,\n%11s"bFilter": false,\n%11s"bInfo": false,\n%11s"bSort": false,\n%11s"bAutoWidth": false});\n'%(5*('',)))
if self.pdb_summary:
jon_summary.write("%8s$('#phaser-pdb').dataTable({\n"%'')
jon_summary.write('%11s"bPaginate": false,\n%11s"bFilter": false,\n%11s"bInfo": false,\n%11s"bSort": false,\n%11s"bAutoWidth": false});\n'%(5*('',)))
#Style the button
jon_summary.write('%8s$("button").button();\n'%'')
if self.tooltips:
jon_summary.writelines(self.tooltips)
jon_summary.write('%6s});\n%4s</script>\n%2s</head>\n%2s<body id="dt_example">\n'%(4*('',)))
if self.cell_summary:
jon_summary.writelines(self.cell_summary)
if self.pdb_summary:
jon_summary.writelines(self.pdb_summary)
"""
jon_summary.write('%4s<div id="container">\n%5s<div class="full_width big">\n%6s<div id="demo">\n'%(3*('',)))
jon_summary.write("%7s<h1 class='Results'>RAPD Logfile</h1>\n%6s</div>\n%5s</div>\n"%(3*('',)))
jon_summary.write('%5s<div id="accordion">\n%6s<h3><a href="#">Click to view log</a></h3>\n%6s<div>\n%7s<pre>\n'%(4*('',)))
jon_summary.write('%7s</pre>\n%6s</div>\n%5s</div>\n%4s</div>\n%2s</body>\n</html>\n'%(5*('',)))
"""
jon_summary.write('%2s</body>\n</html>\n'%'')
jon_summary.close()
#copy html file to working dir
shutil.copy(sl,self.working_dir)
except:
self.logger.exception('**ERROR in AutoMolRep.htmlSummaryPhaser**')
def htmlSummaryMolrep(self):
"""
Create HTML/php files for Molrep output results.
"""
if self.verbose:
self.logger.debug('AutoStats::htmlSummaryMolrep')
try:
if self.molrep_summary:
molrep_log = self.molrep_results.get('Molrep results').get('Molrep log')
if self.gui:
sl = 'jon_summary_molrep.php'
else:
sl = 'jon_summary_molrep.html'
jon_summary = open(sl,'w')
jon_summary.write(Utils.getHTMLHeader(self))
jon_summary.write('%6s$(document).ready(function() {\n'%'')
jon_summary.write("%8s$('#accordion-molrep').accordion({\n"%'')
jon_summary.write('%11scollapsible: true,\n%11sactive: false });\n'%('',''))
if self.molrep_summary:
jon_summary.write("%8s$('#molrep').dataTable({\n"%'')
jon_summary.write('%11s"bPaginate": false,\n%11s"bFilter": false,\n%11s"bInfo": false,\n%11s"bSort": false,\n%11s"bAutoWidth": false});\n'%(5*('',)))
jon_summary.write('%6s});\n%4s</script>\n%2s</head>\n%2s<body id="dt_example">\n'%(4*('',)))
if self.molrep_summary:
jon_summary.writelines(self.molrep_summary)
else:
jon_summary.write("%7s<h2 class='Results'>Error in molrep analysis</h1>\n"%'')
jon_summary.write('%4s<div id="container">\n%5s<div class="full_width big">\n%6s<div id="demo">\n'%(3*('',)))
jon_summary.write("%7s<h1 class='Results'>Molrep Output</h1>\n%6s</div>\n%5s</div>\n"%(3*('',)))
jon_summary.write('%5s<div id="accordion-molrep">\n'%'')
jon_summary.write('%6s<h3><a href="#">Click to view Molrep log</a></h3>\n%6s<div>\n%7s<pre>\n\n'%(3*('',)))
if molrep_log:
for line in open(molrep_log,'r').readlines():
jon_summary.write(line)
else:
jon_summary.write('---------------Molrep FAILED---------------\n')
jon_summary.write('%7s</pre>\n%6s</div>\n%5s</div>\n%4s</div>\n%2s</body>\n</html>\n'%(5*('',)))
jon_summary.close()
else:
Utils.failedHTML(self,'jon_summary_molrep')
except:
self.logger.exception('**ERROR in AutoStats.htmlSummaryMolrep**')
def plotXtriage(self):
"""
generate plots html/php file
"""
if self.verbose:
self.logger.debug('AutoStats::plotXtriage')
try:
cid0 = False
cid1 = False
anom = self.xtriage_results.get('Xtriage results').get('Xtriage anom plot')
intensity = self.xtriage_results.get('Xtriage results').get('Xtriage int plot')
#xtriage_i = self.xtriage_results.get('Xtriage results').get('Xtriage i plot')
nz = self.xtriage_results.get('Xtriage results').get('Xtriage nz plot')
l_test = self.xtriage_results.get('Xtriage results').get('Xtriage l-test plot')
#xtriage_z = self.xtriage_results.get('Xtriage results').get('Xtriage z plot')
if self.NCS_results:
cid0 = self.NCS_results.get('PhaserNCS results').get('CID').get('before')
cid1 = self.NCS_results.get('PhaserNCS results').get('CID').get('after')
#List of params for parsing later.
l = [['Intensity','Mean I vs. Resolution','Resolution(A)','M e a n   I',intensity,
("< I > smooth","< I > binning","< I > expected")],
#['Z scores','Data Sanity and Completeness check','Resolution(A)','Z   S c o r e','z',
#('Z_score','Completeness')],
['Anom_Signal','Anomalous Measurability','Resolution(A)','',anom,
('Obs_anom_meas','Smoothed')],
#['I/sigI','Signal to Noise vs. Resolution','Resolution(A)','I / S i g I','i',
#('Signal_to_Noise',)],
['NZ_Test','NZ Test','z','',nz,('Acen_obs','Acen_untwinned','Cen_obs','Cen_untwinned')],
['L_Test','L-Test','|I|','',l_test,('Obs','Acen_th_untwinned','Acen_th_perfect_twin')],
['CID0','CID before Anisotropic and tNCS correction','Z','',cid0,
('Acen_theo','Acen_twin','Acen_obs','Cen_theo','Cen_obs')],
['CID1','CID after Anisotropic and tNCS correction','Z','',cid1,
('Acen_theo','Acen_twin','Acen_obs','Cen_theo','Cen_obs')]
]
if self.NCS_results:
e = len(l)
else:
e = len(l) - 2
if nz != 'None':
xtriage_plot = ''
xtriage_plot += Utils.getHTMLHeader(self,'plots')
xtriage_plot +="%4s$(function() {\n%6s$('.tabs').tabs();\n%4s});\n"%(3*('',))
xtriage_plot +="%4s</script>\n%2s</head>\n%2s<body>\n%4s<table>\n%6s<tr>\n"%(5*('',))
xtriage_plot +='%8s<td width="100%%">\n%10s<div class="tabs">\n%12s<ul>\n'%(3*('',))
for i in range(e):
xtriage_plot += '%14s<li><a href="#tabs-44%s">%s</a></li>\n'%('',i,l[i][0])
xtriage_plot += "%12s</ul>\n"%''
for i in range(e):
xtriage_plot += '%12s<div id="tabs-44%s">\n%14s<div class=title><b>%s</b></div>\n'%('',i,'',l[i][1])
xtriage_plot += '%14s<div id="chart%s_div3" style="width:750px;height:550px;margin-left:20;"></div>\n'%('',i)
xtriage_plot += '%14s<div class=x-label>%s</div>\n%14s<span class=y-label>%s</span>\n%12s</div>\n'%('',l[i][2],'',l[i][3],'')
xtriage_plot +="%10s</div>\n%8s</td>\n%6s</tr>\n%4s</table>\n"%(4*('',))
xtriage_plot += '%4s<script id="source" language="javascript" type="text/javascript">\n'%''
xtriage_plot += "%6s$(function () {\n"%''
s = '\n%8svar '%''
for i in range(e):
l1 = []
l2 = []
label = ['%10s[\n'%'']
s1 = s
for x in range(len(l[i][4][0])-1):
var = '%s%s'%(l[i][0].upper(),x)
s1 += '%s=[],'%var
label.append('%12s{ data: %s, label:"%s" },\n'%('',var,l[i][5][x]))
for y in range(len(l[i][4])):
if l[i][0] == 'Anom_Signal':
l2.append(float(l[i][4][y][0]))
if l[i][0] in ('Intensity','Anom_Signal'):
l1.append("%8s%s.push([-%s,%s]);\n"%('',var,l[i][4][y][0],l[i][4][y][x+1]))
else:
l1.append("%8s%s.push([%s,%s]);\n"%('',var,l[i][4][y][0],l[i][4][y][x+1]))
if l[i][0] == 'Anom_Signal':
xtriage_plot += '%s,mark=[];\n'%s1[:-1]
label.append('%12s{ data: mark, label:"min level for anom signal" },\n'%'')
else:
xtriage_plot += '%s;\n'%s1[:-1]
label.append('%10s],\n'%'')
l[i].append(label)
for line in l1:
xtriage_plot += line
if l[i][0] == 'Anom_Signal':
xtriage_plot += "%8sfor (var i = -%s; i < -%s; i +=0.25)\n%8smark.push([i,0.05]);\n"%('',max(l2),min(l2),'')
for i in range(e):
xtriage_plot += '%8svar plot%s = $.plot($("#chart%s_div3"),\n'%('',i,i)
for line in l[i][-1]:
xtriage_plot += line
xtriage_plot += "%10s{ lines: { show: true},\n%12spoints: { show: true },\n"%('','')
xtriage_plot += "%12sselection: { mode: 'xy' },\n%12sgrid: { hoverable: false, clickable: false },\n"%('','')
if l[i][0] in ('Intensity','Anom_Signal'):
xtriage_plot += "%12sxaxis: { transform: function (v) { return Math.log(-v); },\n"%''
xtriage_plot += "%21sinverseTransform: function (v) { return Math.exp(-v); },\n"%''
xtriage_plot += "%21stickFormatter: ( function negformat(val,axis){return -val.toFixed(axis.tickDecimals);} ) },\n"%''
else:
xtriage_plot += "%12sxaxis: {min:0},\n"%''
xtriage_plot += "%12syaxis: {min:0},\n%10s});\n\n"%('','')
"""
xtriage_plot += "%8sfunction showTooltip(x, y, contents) {\n"%''
xtriage_plot += "%10s$('<div id=\"tooltip\">' + contents + '</div>').css( {\n"%''
xtriage_plot += "%12sposition: 'absolute',\n%12sdisplay: 'none',\n"%('','')
xtriage_plot += "%12stop: y + 5,\n%12sleft: x + 5,\n%12sborder: '1px solid #fdd',\n"%(3*('',))
xtriage_plot += "%12spadding: '2px',\n%12s'background-color': '#fee',\n"%('','')
xtriage_plot += '%12sopacity: 0.80\n%10s}).appendTo("body").fadeIn(200);\n'%('','')
xtriage_plot += "%8s}\n%6s});\n%4s</script>\n%2s</body>\n</html>\n"%(4*('',))
"""
xtriage_plot += "%6s});\n%4s</script>\n%2s</body>\n</html>\n"%(3*('',))
if xtriage_plot:
if self.gui:
sp = 'plots_xtriage.php'
else:
sp = 'plots_xtriage.html'
xtriage_plot_file = open(sp,'w')
xtriage_plot_file.writelines(xtriage_plot)
xtriage_plot_file.close()
else:
Utils.failedHTML(self,'plots_xtriage')
except:
self.logger.exception('**ERROR in AutoStats.plotXtriage**')
Utils.failedHTML(self,'plots_xtriage')
