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')