# -*- coding: utf-8 -*-
#Author: Pierre Ratinaud
#Copyright (c) 2010 Pierre Ratinaud
-#Lisense: GNU/GPL
+#License: GNU/GPL
import HTML
import os
from time import sleep
from functions import exec_rcode, check_Rresult
from dialog import ChiDialog, PrefChi
+from analysematrix import AnalyseMatrix
def make_res(line) :
if float(line[5]) <= 0.05 and line[6] != 'warning':
return ['<a name=%i></a><br><font color=%s>%s</font><br><a href=#back_%i>retour</a><br>' % (i, val[-1], text[i], i) for i, val in enumerate(res)]
-
+chioption = { 'valobs' : True,
+ 'valtheo' : True,
+ 'resi' : False,
+ 'contrib' : True,
+ 'pourcent' : False,
+ 'pourcentl' : True,
+ 'pourcentc' : True,
+ 'graph' : True,
+ 'bw' : False,
+ }
class MakeChi2():
- def __init__(self, parent, select1, select2, chioption):
+ def __init__(self, parent, select1, select2, chioption, tableau):
+ self.tableau = tableau
self.OutFrame=tempfile.mktemp(dir=parent.TEMPDIR)
print self.OutFrame
self.parent=parent
self.TextCroise=[]
for i in select1 :
for j in select2 :
- self.TextCroise.append(parent.tableau.colnames[i] + ' / ' + parent.tableau.colnames[j])
+ self.TextCroise.append(self.tableau.colnames[i] + ' / ' + self.tableau.colnames[j])
rchioption = {}
for val in chioption :
if chioption[val]:
bw <- %s
""" % (rchioption['valobs'], rchioption['valtheo'], rchioption['contrib'], rchioption['resi'], rchioption['pourcent'], rchioption['pourcentl'], rchioption['pourcentc'], rchioption['graph'], rchioption['bw'])
txt+="""
- datadm <- ReadData("%s", encoding="%s", header = TRUE, sep = "%s",quote = '%s', na.strings = "%s",rownames= 1)
+ datadm <- read.csv2("%s", encoding="%s", header = TRUE, row.names = 1, sep='\\t', quote = '"', na.string = '')
listres<-list()
listcol<-list()
cont<-1
- """%(ffr(parent.tableau.parametre['csvfile']),self.parent.encode, parent.tableau.parametre['colsep'], parent.tableau.parametre['txtsep'], self.parent.nastrings)
+ """%(ffr(self.tableau.parametres['csvfile']), self.tableau.parametres['syscoding'])
if len(select1)==1:
strsel1=str(select1).replace(',','')
else:
chi$prl <- round((chi$observed/sr)*100,2)
chi$prc <- t(round((t(chi$observed)/sc)*100,2))
}
- fileout<-paste('histo',%i,sep='')
- fileout<-paste(fileout,'_',sep='')
- fileout<-paste(fileout,count,sep='')
+ fileout<-paste('histo_',count,sep='')
fileout<-paste(fileout,'.png',sep='')
count<-count+1
fileout<-file.path("%s",fileout)
li<-matrix('fin_analyse',1,maxcol)
frameout<-rbind(frameout,li)
write.csv2(frameout,file="%s")
- """%(parent.FreqNum,ffr(parent.TEMPDIR),ffr(self.OutFrame))
+ """ % (ffr(parent.TEMPDIR),ffr(self.OutFrame))
tmpfile=tempfile.mktemp(dir=self.TEMPDIR)
print tmpfile
tmpscript=open(tmpfile,'w')
txt = '<br><hr><br>\n'.join(['<br><br>'.join([tab[i] for tab in allhtml]) for i,val in enumerate(res)])
txt = header + pretxt + txt + '\n</body></html>'
- fileout=os.path.join(self.TEMPDIR,'resultats-chi2_%s.html'%str(self.parent.FreqNum))
- file=open(fileout,'w')
- file.write(txt)
- file.close()
+ fileout=os.path.join(self.parametres['pathout'],'resultats-chi2.html')
+ with open(fileout, 'w') as f :
+ f.write(txt)
ListFile.append(fileout)
return ListFile
-class ChiSquare():
- def __init__(self,parent):
- chioption = { 'valobs' : True,
- 'valtheo' : True,
- 'resi' : False,
- 'contrib' : True,
- 'pourcent' : False,
- 'pourcentl' : True,
- 'pourcentc' : True,
- 'graph' : True,
- 'bw' : False,
- }
- dlg = ChiDialog(parent, -1, u"Chi2", chioption, size=(400, 350),
+class ChiSquare(AnalyseMatrix):
+ def doparametres(self, dlg = None):
+ if dlg is None :
+ return
+ dial = ChiDialog(self.parent, -1, u"Chi2", chioption, self.tableau, size=(400, 350),
style = wx.DEFAULT_DIALOG_STYLE
)
- dlg.CenterOnParent()
- val = dlg.ShowModal()
- if val==wx.ID_OK :
- self.dlg=wx.ProgressDialog("Traitements",
- "Veuillez patienter...",
- maximum = 4,
- parent=parent,
- style = wx.PD_APP_MODAL|wx.PD_AUTO_HIDE|wx.PD_ELAPSED_TIME
- )
- self.dlg.Center()
+ dial.CenterOnParent()
+ val = dial.ShowModal()
+ if val==wx.ID_OK :
+ dlg.Center()
self.count = 1
- keepGoing = self.dlg.Update(self.count)
+ keepGoing = dlg.Update(self.count)
- ColSel1 = dlg.list_box_1.GetSelections()
- ColSel2 = dlg.list_box_2.GetSelections()
- if dlg.chiopt :
- chioption['valobs'] = dlg.dial.check1.GetValue()
- chioption['valtheo'] = dlg.dial.check2.GetValue()
- chioption['resi'] = dlg.dial.check3.GetValue()
- chioption['contrib'] = dlg.dial.check4.GetValue()
- chioption['pourcent'] = dlg.dial.check5.GetValue()
- chioption['pourcentl'] = dlg.dial.check6.GetValue()
- chioption['pourcentc'] = dlg.dial.check7.GetValue()
- chioption['graph'] = dlg.dial.check8.GetValue()
- chioption['bw'] = dlg.dial.checkbw.GetValue()
- dlg.dial.Destroy()
+ self.colsel1 = dial.list_box_1.GetSelections()
+ self.colsel2 = dial.list_box_2.GetSelections()
+ if dial.chiopt :
+ chioption['valobs'] = dial.dial.check1.GetValue()
+ chioption['valtheo'] = dial.dial.check2.GetValue()
+ chioption['resi'] = dial.dial.check3.GetValue()
+ chioption['contrib'] = dial.dial.check4.GetValue()
+ chioption['pourcent'] = dial.dial.check5.GetValue()
+ chioption['pourcentl'] = dial.dial.check6.GetValue()
+ chioption['pourcentc'] = dial.dial.check7.GetValue()
+ chioption['graph'] = dial.dial.check8.GetValue()
+ chioption['bw'] = dial.dial.checkbw.GetValue()
+ dial.dial.Destroy()
+ dial.Destroy()
+ self.parametres.update(chioption)
+ self.chioption = chioption
+ else :
+ if dial.chiopt :
+ dial.dial.Destroy()
+ dial.Destroy()
+ self.parametres = None
- self.count += 1
- keepGoing = self.dlg.Update(self.count,u"Analyse dans R...")
- analyse=MakeChi2(parent,ColSel1,ColSel2, chioption)
+ def doanalyse(self):
+
+
+ #self.dlg=wx.ProgressDialog("Traitements",
+ # "Veuillez patienter...",
+ # maximum = 4,
+ # parent=parent,
+ # style = wx.PD_APP_MODAL|wx.PD_AUTO_HIDE|wx.PD_ELAPSED_TIME
+ # )
+
+
- self.count += 1
- keepGoing = self.dlg.Update(self.count,u"Ecriture des résultats")
+ self.count += 1
+ keepGoing = self.dlg.Update(self.count,u"Analyse dans R...")
+ #analyse=MakeChi2(self.parent, self.colsel1, self.colsel2, self.chioption, self.tableau)
+ #self.tableau = tableau
+ self.OutFrame=tempfile.mktemp(dir=self.parent.TEMPDIR)
+ print self.OutFrame
+ #self.parent=parent
+ self.encode=self.parent.encode
+ self.TEMPDIR=self.parent.TEMPDIR
+ self.RPath=self.parent.PathPath.get('PATHS','rpath')
+ self.TextCroise=[]
+ for i in self.colsel1 :
+ for j in self.colsel2 :
+ self.TextCroise.append(self.tableau.colnames[i] + ' / ' + self.tableau.colnames[j])
+ rchioption = {}
+ for val in self.chioption :
+ if self.chioption[val]:
+ rchioption[val] = 'TRUE'
+ else :
+ rchioption[val] = 'FALSE'
+ txt="""
+ source("%s")
+ """%self.parent.RscriptsPath['Rfunct']
+# if parent.tableau.: rownames=1
+# else : rownames='NULL'
+# if parent.g_header : header = 'TRUE'
+# else : header = 'FALSE'
+ txt += """
+ source("%s")
+ """ % ffr(self.parent.RscriptsPath['Rgraph'])
+ txt += """
+ doobs <- %s
+ doexp <- %s
+ docontrib <- %s
+ doresi <- %s
+ dopr <- %s
+ doprl <- %s
+ doprc <- %s
+ dograph <- %s
+ bw <- %s
+ """ % (rchioption['valobs'], rchioption['valtheo'], rchioption['contrib'], rchioption['resi'], rchioption['pourcent'], rchioption['pourcentl'], rchioption['pourcentc'], rchioption['graph'], rchioption['bw'])
+ txt+="""
+ datadm <- read.csv2("%s", encoding="%s", header = TRUE, row.names = 1, sep='\\t', quote = '"', na.string = '')
+ listres<-list()
+ listcol<-list()
+ cont<-1
+ """%(ffr(self.tableau.parametres['csvfile']), self.tableau.parametres['syscoding'])
+ if len(self.colsel1)==1:
+ strsel1=str(self.colsel1).replace(',','')
+ else:
+ strsel1=str(self.colsel1)
+ if len(self.colsel2)==1:
+ strsel2=str(self.colsel2).replace(',','')
+ else:
+ strsel2=str(self.colsel2)
+ txt+="""
+ for (i in c%s) {""" % strsel1
+ txt+="""
+ for (j in c%s) {""" % strsel2
+ txt+="""
+ tab<-table(datadm[,i+1],datadm[,j+1])
+ if (min(dim(tab)) != 1) {
+ chi<-chisq.test(tab)
+ CS<-colSums(tab)
+ RS<-rowSums(tab)
+ GT<-sum(tab)
+ chi$contrib<-(tab-chi$expected)/sqrt(chi$expected * ((1 - RS/GT) %%*%% t(1 - CS/GT)))
+ listres[[cont]]<-chi
+ listcol[[cont]]<-ncol(tab)
+ cont<-cont+1
+ } else {
+ chi <- list(observed = tab, residuals = tab, contrib = tab, statistic = 0, p.value = 1, expected = tab, message = 'pas de calcul')
+ listres[[cont]] <- chi
+ listcol[[cont]]<-ncol(tab)
+ cont <- cont + 1
+ }
+ }
+ }
+ maxcol<-max(unlist(listcol))+1
+ if (maxcol<7) {maxcol<-7}
+ frameout<-matrix('*',1,maxcol)
+ count<-0
+ for (chi in listres) {
+ if (min(chi$expected)<5) {
+ att<-"warning"
+ } else {
+ att<-""
+ }
+ if ('message' %%in%% attributes(chi)$names) {
+ att <- "Ce chi2 n\'a pas été calculé"
+ nom_colresi<-colnames(chi$observed)
+ chi$prl <- chi$expected
+ chi$prc <- chi$expected
+ st <- sum(chi$observed)
+ } else {
+ nom_colresi<-colnames(chi$observed)
+ st <- sum(chi$observed)
+ sc <- colSums(chi$observed)
+ sr <- rowSums(chi$observed)
+ chi$prl <- round((chi$observed/sr)*100,2)
+ chi$prc <- t(round((t(chi$observed)/sc)*100,2))
+ }
+ fileout<-paste('histo_',count,sep='')
+ fileout<-paste(fileout,'.png',sep='')
+ count<-count+1
+ fileout<-file.path("%s",fileout)
+ if (max(nchar(colnames(chi$observed)))>15) {
+ leg <- 1:length(colnames(chi$observed))
+ } else {
+ leg <- colnames(chi$observed)
+ }
+ if (dograph) {
+ width<-ncol(chi$observed)*100
+ if (width < 350) {width <- 350}
+ open_file_graph(fileout,width = width, height = 300)
+ par(mar=c(0,0,0,0))
+ layout(matrix(c(1,2),1,2, byrow=TRUE),widths=c(3,1))
+ par(mar=c(2,2,1,0))
+ par(cex=0.8)
+ if (!bw) colors <- rainbow(length(rownames(chi$observed)))
+ else colors <- gray.colors(length(rownames(chi$observed)))
+ barplot(chi$prl,names.arg = leg, beside=TRUE,border=NA, col=colors)
+ par(mar=c(0,0,0,0))
+ par(cex=0.8)
+ plot(0, axes = FALSE, pch = '')
+ legend(x = 'center' , rownames(chi$observed), fill = colors)
+ dev.off()
+ }
+ chi$prl <- cbind(chi$prl, total = rowSums(chi$prl))
+ chi$prc <- rbind(chi$prc, total = colSums(chi$prc))
+ chi$observed<-rbind(chi$observed,total=colSums(chi$observed))
+ chi$observed<-cbind(chi$observed,total=rowSums(chi$observed))
+ chi$pr <- round((chi$observed/st)*100,2)
+ chi$expected<-rbind(chi$expected,total=colSums(chi$expected))
+ chi$expected<-cbind(chi$expected,total=rowSums(chi$expected))
+ chi$expected<-round(chi$expected,digits=2)
+ chi$residuals<-round(chi$residuals,digits=2)
+ chi$contrib<-round(chi$contrib, digits=2)
+ nom_col<-colnames(chi$observed)
+
+ if (ncol(chi$observed)<maxcol) {
+ for (i in 1:(maxcol-ncol(chi$observed))) {
+ chi$observed<-cbind(chi$observed,'**')
+ chi$pr<-cbind(chi$pr,'**')
+ chi$prl<-cbind(chi$prl,'**')
+ chi$prc<-cbind(chi$prc,'**')
+ chi$expected<-cbind(chi$expected,'**')
+ chi$residuals<-cbind(chi$residuals,'**')
+ chi$contrib<-cbind(chi$contrib,'**')
+ nom_col<-append(nom_col,'**')
+ nom_colresi<-append(nom_colresi,'**')
+ }
+ chi$residuals<-cbind(chi$residuals,'**')
+ chi$contrib<-cbind(chi$contrib,'**')
+ nom_colresi<-append(nom_colresi,'**')
+ chi$prc<-cbind(chi$prc,'**')
+ } else if (ncol(chi$observed)==maxcol) {
+ chi$residuals<-cbind(chi$residuals,'**')
+ chi$contrib<-cbind(chi$contrib,'**')
+ nom_colresi<-append(nom_colresi,'**')
+ chi$prc<-cbind(chi$prc,'**')
+ }
+ if (doobs) {
+ li<-matrix('*obs*',1,maxcol)
+ frameout<-rbind(frameout,li)
+ frameout<-rbind(frameout,nom_col)
+ frameout<-rbind(frameout,chi$observed)
+ }
+ if (doexp) {
+ li<-matrix('*exp*',1,maxcol)
+ frameout<-rbind(frameout,li)
+ frameout<-rbind(frameout,nom_col)
+ frameout<-rbind(frameout,chi$expected)
+ }
+ if (doresi) {
+ li<-matrix('*resi*',1,maxcol)
+ frameout<-rbind(frameout,li)
+ frameout<-rbind(frameout,nom_colresi)
+ frameout<-rbind(frameout,chi$residuals)
+ }
+ if (docontrib) {
+ li<-matrix('*contrib*',1,maxcol)
+ frameout<-rbind(frameout,li)
+ frameout<-rbind(frameout,nom_colresi)
+ frameout<-rbind(frameout,chi$contrib)
+ }
+ if (dopr) {
+ li<-matrix('*pr*', 1, maxcol)
+ frameout<-rbind(frameout,li)
+ frameout<-rbind(frameout,nom_col)
+ frameout<-rbind(frameout,chi$pr)
+ }
+ if (doprl) {
+ li<-matrix('*prl*', 1, maxcol)
+ frameout<-rbind(frameout,li)
+ frameout<-rbind(frameout,nom_col)
+ frameout<-rbind(frameout,chi$prl)
+ }
+ if (doprc) {
+ li<-matrix('*prc*', 1, maxcol)
+ frameout<-rbind(frameout,li)
+ frameout<-rbind(frameout,nom_colresi)
+ frameout<-rbind(frameout,chi$prc)
+ }
+ res<-c('****','chi',chi$statistic,'p',chi$p.value,att,fileout)
+ frameout<-rbind(frameout,res)
+ }
+ li<-matrix('fin_analyse',1,maxcol)
+ frameout<-rbind(frameout,li)
+ write.csv2(frameout,file="%s")
+ """ % (ffr(self.parametres['pathout']),ffr(self.OutFrame))
+ tmpfile=tempfile.mktemp(dir=self.TEMPDIR)
+ print tmpfile
+ tmpscript=open(tmpfile,'w')
+ tmpscript.write(txt)
+ tmpscript.close()
+ pid = exec_rcode(self.RPath, tmpfile, wait = False)
+ while pid.poll() == None :
+ sleep(0.2)
+ check_Rresult(self.parent, pid)
+ self.count += 1
+ keepGoing = self.dlg.Update(self.count,u"Ecriture des résultats")
- listfileout = analyse.dolayout(chioption)
+ listfileout = self.dolayout(self.chioption)
#listfileout=dlg.ShowChi2(ColSel1,ColSel2)
- parent.FreqNum += 1
- parent.DictTab[u"Chi2_%s*"%parent.FreqNum]=listfileout
- parent.newtab = wx.html.HtmlWindow(parent.nb, -1)
- if "gtk2" in wx.PlatformInfo:
- parent.newtab.SetStandardFonts()
- parent.newtab.LoadPage(listfileout[len(listfileout)-1])
- parent.nb.AddPage(parent.newtab,u"Chi2_%s*"%parent.FreqNum)
- parent.nb.SetSelection(parent.nb.GetPageCount()-1)
- parent.ShowTab(wx.EVT_BUTTON)
- parent.DisEnSaveTabAs(True)
- self.count += 1
- keepGoing = self.dlg.Update(self.count,u"Fini")
- else :
- if dlg.chiopt :
- dlg.dial.Destroy()
- dlg.Destroy()
+ #parent.FreqNum += 1
+ #parent.DictTab[u"Chi2_%s*"%parent.FreqNum]=listfileout
+# parent.newtab = wx.html.HtmlWindow(parent.nb, -1)
+# if "gtk2" in wx.PlatformInfo:
+# parent.newtab.SetStandardFonts()
+# parent.newtab.LoadPage(listfileout[len(listfileout)-1])
+# parent.nb.AddPage(parent.newtab,u"Chi2_%s*"%parent.FreqNum)
+# parent.nb.SetSelection(parent.nb.GetPageCount()-1)
+# parent.ShowTab(wx.EVT_BUTTON)
+# parent.DisEnSaveTabAs(True)
+ self.count += 1
+ keepGoing = self.dlg.Update(self.count,u"Fini")
+
+ def dolayout(self, option):
+ ListFile=[False]
+ file=open(self.OutFrame,'rU')
+ content=file.readlines()
+ file.close()
+ lcont = [line.replace('"','').replace('\n','').split(';') for line in content]
+
+ lcont.pop(0)
+ lcont.pop(0)
+
+ allcoord = []
+ names = []
+
+ res = [chi for chi in lcont if chi[0]=='res']
+ res = [make_res(line) for line in res]
+ coord_res = [i for i,chi in enumerate(lcont) if chi[0]=='res']
+ if option['valobs']:
+ allcoord.append([i for i,chi in enumerate(lcont) if chi[1]=='*obs*'])
+ names.append(u'Valeurs observées')
+ if option['valtheo'] :
+ allcoord.append([i for i,chi in enumerate(lcont) if chi[1]=='*exp*'])
+ names.append(u'Valeurs théoriques')
+ if option['resi'] :
+ allcoord.append([i for i,chi in enumerate(lcont) if chi[1]=='*resi*'])
+ names.append(u'Residuals')
+ if option['contrib'] :
+ allcoord.append([i for i,chi in enumerate(lcont) if chi[1]=='*contrib*'])
+ names.append(u'Contributions a posteriori')
+ if option['pourcent'] :
+ allcoord.append([i for i,chi in enumerate(lcont) if chi[1]=='*pr*'])
+ names.append(u'Pourcentages')
+ if option['pourcentl'] :
+ allcoord.append([i for i,chi in enumerate(lcont) if chi[1]=='*prl*'])
+ names.append(u'Pourcentages en ligne')
+ if option['pourcentc'] :
+ allcoord.append([i for i,chi in enumerate(lcont) if chi[1]=='*prc*'])
+ names.append(u'Pourcentages en colonne')
+
+ allcoord.append(coord_res)
+ allhtml = [[clean_line(lcont[allcoord[i][j]+1:allcoord[i+1][j]]) for j, line in enumerate(allcoord[i])] for i, tab in enumerate(allcoord) if i!=len(allcoord)-1]
+
+ allhtml = [make_table(val,names[i],res) for i,val in enumerate(allhtml)]
+
+ links = make_link_list(res, self.TextCroise)
+ #colors = [line[-1] for line in res]
+
+ # good = [i for i,chi in enumerate(res) if chi[-1] == 'green' or chi[-1] == 'blue']
+ #select_good = [[val[i] for i in good] for val in tout]
+
+
+ html_res = make_restab(res)
+ allhtml.insert(0,html_res)
+
+ titles = make_title(res, self.TextCroise)
+ allhtml.insert(0,titles)
+
+ if option['graph'] :
+ graphs = [line[7] for line in res]
+ ListFile += graphs
+ html_graphs = make_htmlgraphs(graphs)
+ allhtml.append(html_graphs)
+
+ header=u"""
+ <html>\n
+ <meta http-equiv="content-Type" content="text/html; charset=%s" />\n
+ <body>\n
+ <h1>Test du Chi2</h1>\n
+ <br>
+ <table border=1><tr><td>
+ Légende : <br>
+ <font color=green>p <= 0.05</font><br>
+ <font color=blue>p <= 0.05 mais il y a des valeurs théoriques < 5</font><br>
+ <font color=red>p > 0.05</font>
+ </td></tr></table><br><br>
+ """%self.parent.SysEncoding
+
+
+ pretxt = '<br>\n'.join(links)+'<br><hr><br>\n'
+ txt = '<br><hr><br>\n'.join(['<br><br>'.join([tab[i] for tab in allhtml]) for i,val in enumerate(res)])
+ txt = header + pretxt + txt + '\n</body></html>'
+
+ fileout=os.path.join(self.parametres['pathout'],'resultats-chi2.html')
+ with open(fileout, 'w') as f :
+ f.write(txt)
+ ListFile.append(fileout)
+ return ListFile
\ No newline at end of file
projects / iramuteq / blobdiff