X-Git-Url: http://www.iramuteq.org/git?a=blobdiff_plain;f=PrintRScript.py;h=27c4d272baa6bfd0f84ae4157f73aeeab1f6c6aa;hb=eaa044d1147e26b82942ce56d5965c83fdddf069;hp=e334a87660cc74ed61e6e8ed3abd6c3cbee34935;hpb=10d67a5cd48583c060b6a0e77e87c41f80671027;p=iramuteq diff --git a/PrintRScript.py b/PrintRScript.py index e334a87..27c4d27 100755 --- a/PrintRScript.py +++ b/PrintRScript.py @@ -1,68 +1,83 @@ # -*- coding: utf-8 -*- #Author: Pierre Ratinaud -#Copyright (c) 2008-2011 Pierre Ratinaud +#Copyright (c) 2008-2020 Pierre Ratinaud +#modification pour python 3 : Laurent Mérat, 6x7 - mai 2020 #License: GNU/GPL +#------------------------------------ +# import des modules python +#------------------------------------ import tempfile -from chemins import ffr, PathOut import os import locale from datetime import datetime import logging +#------------------------------------ +# import des fichiers du projet +#------------------------------------ +from chemins import ffr, PathOut + + log = logging.getLogger('iramuteq.printRscript') -class PrintRScript : + +class PrintRScript: + def __init__ (self, analyse, parametres = None): log.info('Rscript') self.pathout = analyse.pathout self.analyse = analyse - if parametres is None : + if parametres is None: self.parametres = analyse.parametres - else : + else: self.parametres = parametres #self.scriptout = ffr(self.pathout['lastRscript.R']) self.scriptout = self.pathout['temp'] - self.script = u"#Script genere par IRaMuTeQ - %s\n" % datetime.now().ctime() + self.script = "#Script genere par IRaMuTeQ - %s\n" % datetime.now().ctime() - def add(self, txt) : + def add(self, txt): self.script = '\n'.join([self.script, txt]) - def defvar(self, name, value) : + def defvar(self, name, value): self.add(' <- '.join([name, value])) - def defvars(self, lvars) : - for val in lvars : + def defvars(self, lvars): + for val in lvars: self.defvar(val[0],val[1]) - def sources(self, lsources) : - for source in lsources : + def sources(self, lsources): + for source in lsources: self.add('source("%s", encoding = \'utf8\')' % ffr(source)) - def packages(self, lpks) : - for pk in lpks : + def packages(self, lpks): + for pk in lpks: self.add('library(%s)' % pk) - def load(self, l) : - for val in l : + def load(self, l): + for val in l: self.add('load("%s")' % ffr(val)) - def write(self) : - with open(self.scriptout, 'w') as f : + def write(self): + with open(self.scriptout, 'w') as f: f.write(self.script) -class chdtxt(PrintRScript) : +# ??? +class chdtxt(PrintRScript): pass -def Rcolor(color) : + +def Rcolor(color): return str(color).replace(')', ', max=255)') -class Alceste2(PrintRScript) : - def doscript(self) : + +class Alceste2(PrintRScript): + + def doscript(self): self.sources(['chdfunct']) self.load(['Rdata']) - lvars = [['clnb', `self.analyse.clnb`], + lvars = [['clnb', repr(self.analyse.clnb)], ['Contout', '"%s"' % self.pathout['Contout']], ['ContSupOut', '"%s"' % self.pathout['ContSupOut']], ['ContEtOut', '"%s"' % self.pathout['ContEtOut']], @@ -73,8 +88,6 @@ class Alceste2(PrintRScript) : self.defvars(lvars) - - # txt = "clnb<-%i\n" % clnb # txt += """ #source("%s") @@ -120,35 +133,34 @@ def RchdTxt(DicoPath, RscriptPath, mincl, classif_mode, nbt = 9, svdmethod = 'sv source("%s") source("%s") """ % (ffr(RscriptPath['CHD']), ffr(RscriptPath['chdtxt']), ffr(RscriptPath['anacor']), ffr(RscriptPath['Rgraph'])) - if R_max_mem : + if R_max_mem: txt += """ memory.limit(%i) """ % R_max_mem - txt += """ nbt <- %i """ % nbt - if svdmethod == 'svdlibc' and libsvdc : + if svdmethod == 'svdlibc' and libsvdc: txt += """ svd.method <- 'svdlibc' libsvdc.path <- "%s" """ % ffr(libsvdc_path) - elif svdmethod == 'irlba' : + elif svdmethod == 'irlba': txt += """ library(irlba) svd.method <- 'irlba' libsvdc.path <- NULL """ - else : + else: txt += """ svd.method = 'svdR' libsvdc.path <- NULL """ - if mode_patate : + if mode_patate: txt += """ mode.patate = TRUE """ - else : + else: txt += """ mode.patate = FALSE """ @@ -158,7 +170,6 @@ def RchdTxt(DicoPath, RscriptPath, mincl, classif_mode, nbt = 9, svdmethod = 'sv data1 <- as(data1, "dgCMatrix") row.names(data1) <- 1:nrow(data1) """ % ffr(DicoPath['TableUc1']) - if classif_mode == 0: txt += """ data2 <- readMM("%s") @@ -173,28 +184,23 @@ def RchdTxt(DicoPath, RscriptPath, mincl, classif_mode, nbt = 9, svdmethod = 'sv #chd1<-CHD(data1, x = nbt, mode.patate = mode.patate, svd.method = svd.method, libsvdc.path = libsvdc.path, find='matrix', select.next='size', sample=20, amp=500, proc.nb=nbproc) chd1<-CHD(data1, x = nbt, mode.patate = mode.patate, svd.method = svd.method, libsvdc.path = libsvdc.path)#, log.file = log1) """ % (ffr(DicoPath['log-chd1.txt']), nbproc) - if classif_mode == 0: txt += """ log2 <- "%s" chd2<-CHD(data2, x = nbt, mode.patate = mode.patate, svd.method = svd.method, libsvdc.path = libsvdc.path)#, log.file = log2) """ % ffr(DicoPath['log-chd2.txt']) - txt += """ #lecture des uce listuce1<-read.csv2("%s") """ % ffr(DicoPath['listeuce1']) - if classif_mode == 0: txt += """ listuce2<-read.csv2("%s") """ % ffr(DicoPath['listeuce2']) - txt += """ rm(data1) """ - if classif_mode == 0: txt += """ rm(data2) @@ -210,7 +216,6 @@ def RchdTxt(DicoPath, RscriptPath, mincl, classif_mode, nbt = 9, svdmethod = 'sv classeuce1 <- chd.result$cuce1 tree.tot1 <- make_tree_tot(chd1) tree.cut1 <- make_dendro_cut_tuple(tree.tot1$dendro_tuple, chd.result$coord_ok, classeuce1, 1, nbt) - } else { #chd.result <- Rchdtxt(uceout, chd1, chd2 = chd1, mincl = mincl,classif_mode = classif_mode, nbt = nbt) tree.tot1 <- make_tree_tot(chd1) @@ -222,14 +227,12 @@ def RchdTxt(DicoPath, RscriptPath, mincl, classif_mode, nbt = 9, svdmethod = 'sv classes<-chd.result$n1[,ncol(chd.result$n1)] write.csv2(chd.result$n1, file="%s") """ % (classif_mode, mincl, ffr(DicoPath['uce']), ffr(DicoPath['n1-1.csv']), ffr(DicoPath['n1.csv'])) - txt += """ # tree.tot1 <- make_tree_tot(chd1) # open_file_graph("%s", widt = 600, height=400) # plot(tree.tot1$tree.cl) # dev.off() """ % ffr(DicoPath['arbre1']) - if classif_mode == 0: txt += """ classeuce2 <- chd.result$cuce2 @@ -238,7 +241,6 @@ def RchdTxt(DicoPath, RscriptPath, mincl, classif_mode, nbt = 9, svdmethod = 'sv # plot(tree.tot2$tree.cl) # dev.off() """ % ffr(DicoPath['arbre2'] ) - txt += """ save(tree.cut1, file="%s") @@ -248,7 +250,6 @@ def RchdTxt(DicoPath, RscriptPath, mincl, classif_mode, nbt = 9, svdmethod = 'sv plot(tree.cut1$dendro_tot_cl) dev.off() """ % (ffr(DicoPath['Rdendro']), ffr(DicoPath['dendro1']), ffr(DicoPath['arbre1'])) - if classif_mode == 0: txt += """ tree.cut2 <- make_dendro_cut_tuple(tree.tot2$dendro_tuple, chd.result$coord_ok, classeuce2, 2, nbt) @@ -259,12 +260,9 @@ def RchdTxt(DicoPath, RscriptPath, mincl, classif_mode, nbt = 9, svdmethod = 'sv plot(tree.cut2$dendro_tot_cl) dev.off() """ % (ffr(DicoPath['dendro2']), ffr(DicoPath['arbre2'])) - txt += """ - #save.image(file="%s") """ % (ffr(DicoPath['RData'])) - fileout = open(DicoPath['Rchdtxt'], 'w') fileout.write(txt) fileout.close() @@ -293,7 +291,6 @@ def RPamTxt(corpus, RscriptPath): fileout = open(DicoPath['Rchdtxt'], 'w') fileout.write(txt) fileout.close() - def RchdQuest(DicoPath, RscriptPath, nbcl = 10, mincl = 10): txt = """ @@ -302,25 +299,21 @@ def RchdQuest(DicoPath, RscriptPath, nbcl = 10, mincl = 10): source("%s") source("%s") """ % (ffr(RscriptPath['CHD']), ffr(RscriptPath['chdquest']), ffr(RscriptPath['anacor']),ffr(RscriptPath['Rgraph'])) - txt += """ nbt <- %i - 1 mincl <- %i """ % (nbcl, mincl) - txt += """ chd.result<-Rchdquest("%s","%s","%s", nbt = nbt, mincl = mincl) n1 <- chd.result$n1 classeuce1 <- chd.result$cuce1 """ % (ffr(DicoPath['mat01.csv']), ffr(DicoPath['listeuce1']), ffr(DicoPath['uce'])) - txt += """ tree_tot1 <- make_tree_tot(chd.result$chd) open_file_graph("%s", width = 600, height=400) plot(tree_tot1$tree.cl) dev.off() """ % ffr(DicoPath['arbre1']) - txt += """ tree_cut1 <- make_dendro_cut_tuple(tree_tot1$dendro_tuple, chd.result$coord_ok, classeuce1, 1, nbt) tree.cut1 <- tree_cut1 @@ -329,7 +322,6 @@ def RchdQuest(DicoPath, RscriptPath, nbcl = 10, mincl = 10): classes<-n1[,ncol(n1)] plot.dendropr(tree_cut1$tree.cl,classes, histo = TRUE) """ % (ffr(DicoPath['Rdendro']), ffr(DicoPath['dendro1'])) - txt += """ save.image(file="%s") """ % ffr(DicoPath['RData']) @@ -357,7 +349,6 @@ print('ATTENTION NEW BUILD PROF') tablesqrpact<-new.build.prof(as.matrix(dataact),n1,clnb) tablesqrpsup<-new.build.prof(as.matrix(datasup),n1,clnb) tablesqrpet<-new.build.prof(as.matrix(dataet),n1,clnb) - """ txt += """ PrintProfile(n1,tablesqrpact[4],tablesqrpet[4],tablesqrpact[5],tablesqrpet[5],clnb,"%s","%s",tablesqrpsup[4],tablesqrpsup[5]) @@ -379,7 +370,7 @@ write.csv2(ptabletot,file="%s") gbcluster<-n1 write.csv2(gbcluster,file="%s") """ % (ffr(DictChdTxtOut['chisqtable']), ffr(DictChdTxtOut['ptable']), ffr(DictChdTxtOut['SbyClasseOut'])) - if clnb > 2 : + if clnb > 2: txt += """ library(ca) colnames(dataact)<-paste('classe',1:clnb,sep=' ') @@ -399,7 +390,6 @@ write.csv2(gbcluster,file="%s") txt += """ source("%s") """ % ffr(RscriptsPath['Rgraph']) - txt += """ afc <- summary.ca.dm(afc) afc_table <- create_afc_table(afc) @@ -407,7 +397,6 @@ write.csv2(gbcluster,file="%s") write.csv2(afc_table$colonne, file = "%s") write.csv2(afc_table$ligne, file = "%s") """ % (ffr(DictChdTxtOut['afc_facteur']), ffr(DictChdTxtOut['afc_col']), ffr(DictChdTxtOut['afc_row'])) - txt += """ PARCEX<-%s """ % taillecar @@ -426,12 +415,11 @@ write.csv2(gbcluster,file="%s") PlotAfc2dCoul(afc, as.data.frame(chistabletot), "%s", col=TRUE, what='coord', xlab = xlab, ylab = ylab, xmin = xyminmax$xminmax[1], xmax = xyminmax$xminmax[2], ymin = xyminmax$yminmax[1], ymax = xyminmax$yminmax[2], active=FALSE) """ % (ffr(DictChdTxtOut['AFC2DCL_OUT'])) # txt += """ - # PlotAfc2dCoul(afc, as.data.frame(chistabletot), "%s", what='crl', deb=1, fin=(debsup-1), xlab = xlab, ylab = ylab) - # PlotAfc2dCoul(afc, as.data.frame(chistabletot), "%s", what='crl', deb=debsup, fin=(debet-1), xlab = xlab, ylab = ylab) - # PlotAfc2dCoul(afc, as.data.frame(chistabletot), "%s", what='crl', deb=debet, fin=fin, xlab = xlab, ylab = ylab) - # PlotAfc2dCoul(afc, as.data.frame(chistabletot), "%s", col=TRUE, what='crl', xlab = xlab, ylab = ylab) - # """ % (DictChdTxtOut['AFC2DCoul'], DictChdTxtOut['AFC2DCoulSup'], DictChdTxtOut['AFC2DCoulEt'], DictChdTxtOut['AFC2DCoulCl']) - +# PlotAfc2dCoul(afc, as.data.frame(chistabletot), "%s", what='crl', deb=1, fin=(debsup-1), xlab = xlab, ylab = ylab) +# PlotAfc2dCoul(afc, as.data.frame(chistabletot), "%s", what='crl', deb=debsup, fin=(debet-1), xlab = xlab, ylab = ylab) +# PlotAfc2dCoul(afc, as.data.frame(chistabletot), "%s", what='crl', deb=debet, fin=fin, xlab = xlab, ylab = ylab) +# PlotAfc2dCoul(afc, as.data.frame(chistabletot), "%s", col=TRUE, what='crl', xlab = xlab, ylab = ylab) +# """ % (DictChdTxtOut['AFC2DCoul'], DictChdTxtOut['AFC2DCoulSup'], DictChdTxtOut['AFC2DCoulEt'], DictChdTxtOut['AFC2DCoulCl']) txt += """ #rm(dataact) #rm(datasup) @@ -445,39 +433,43 @@ save.image(file="%s") file.write(txt) file.close() - def write_afc_graph(self): - if self.param['over'] : over = 'TRUE' - else : over = 'FALSE' - - if self.param['do_select_nb'] : do_select_nb = 'TRUE' - else : do_select_nb = 'FALSE' - - if self.param['do_select_chi'] : do_select_chi = 'TRUE' - else : do_select_chi = 'FALSE' - - if self.param['do_select_chi_classe'] : do_select_chi_classe = 'TRUE' - else : do_select_chi_classe = 'FALSE' - - if self.param['cex_txt'] : cex_txt = 'TRUE' - else : cex_txt = 'FALSE' - - if self.param['tchi'] : tchi = 'TRUE' - else : tchi = 'FALSE' - - if self.param['svg'] : svg = 'TRUE' - else : svg = 'FALSE' - - if self.param['typegraph'] == 4 : + if self.param['over']: + over = 'TRUE' + else: + over = 'FALSE' + if self.param['do_select_nb']: + do_select_nb = 'TRUE' + else: + do_select_nb = 'FALSE' + if self.param['do_select_chi']: + do_select_chi = 'TRUE' + else: + do_select_chi = 'FALSE' + if self.param['do_select_chi_classe']: + do_select_chi_classe = 'TRUE' + else: + do_select_chi_classe = 'FALSE' + if self.param['cex_txt']: + cex_txt = 'TRUE' + else: + cex_txt = 'FALSE' + if self.param['tchi']: + tchi = 'TRUE' + else: + tchi = 'FALSE' + if self.param['svg']: + svg = 'TRUE' + else: + svg = 'FALSE' + if self.param['typegraph'] == 4: nodesfile = os.path.join(os.path.dirname(self.fileout),'nodes.csv') edgesfile = os.path.join(os.path.dirname(self.fileout),'edges.csv') - else : + else: nodesfile = 'NULL' edgesfile = 'NULL' - with open(self.RscriptsPath['afc_graph'], 'r') as f: txt = f.read() - # self.DictPathOut['RData'], \ scripts = txt % (ffr(self.RscriptsPath['Rgraph']),\ self.param['typegraph'], \ @@ -508,30 +500,26 @@ def write_afc_graph(self): ffr(os.path.dirname(self.fileout)),\ svg) return scripts - + def print_simi3d(self): simi3d = self.parent.simi3dpanel txt = '#Fichier genere par Iramuteq' - if simi3d.movie.GetValue() : + if simi3d.movie.GetValue(): movie = "'" + ffr(os.path.dirname(self.DictPathOut['RData'])) + "'" - else : + else: movie = 'NULL' - - #if self.corpus.parametres['type'] == 'corpus' : + #if self.corpus.parametres['type'] == 'corpus': # header = 'TRUE' - #else : + #else: # header = 'FALSE' header = 'FALSE' txt += """ dm<-read.csv2("%s",row.names=1,header = %s) load("%s") """ % (self.DictPathOut['Contout'], header, self.DictPathOut['RData']) - txt += """ source("%s") """ % self.parent.RscriptsPath['Rgraph'] - - txt += """ make.simi.afc(dm,chistabletot, lim=%i, alpha = %.2f, movie = %s) """ % (simi3d.spin_1.GetValue(), float(simi3d.slider_1.GetValue())/100, movie) @@ -541,20 +529,20 @@ def print_simi3d(self): tmp.close() return tmpfile -def dendroandbarplot(table, rownames, colnames, rgraph, tmpgraph, intxt = False, dendro=False) : - if not intxt : +def dendroandbarplot(table, rownames, colnames, rgraph, tmpgraph, intxt = False, dendro=False): + if not intxt: txttable = 'c(' + ','.join([','.join(line) for line in table]) + ')' rownb = len(rownames) rownames = 'c("' + '","'.join(rownames) + '")' colnames = 'c("' + '","'.join(colnames) + '")' - if not intxt : + if not intxt: #FIXME txt = """ di <- matrix(data=%s, nrow=%i, byrow = TRUE) rownames(di)<- %s colnames(di) <- %s """ % (txttable, rownb, rownames, colnames) - else : + else: txt = intxt txt += """ load("%s") @@ -568,18 +556,17 @@ def dendroandbarplot(table, rownames, colnames, rgraph, tmpgraph, intxt = False, """ % (ffr(dendro),ffr(rgraph), ffr(tmpgraph)) return txt -def barplot(table, parametres, intxt = False) : - if not intxt : +def barplot(table, parametres, intxt = False): + if not intxt: txttable = 'c(' + ','.join([','.join(line) for line in table]) + ')' #width = 100 + (15 * len(rownames)) + (100 * len(colnames)) #height = len(rownames) * 15 rownb = len(parametres['rownames']) - #if height < 400 : + #if height < 400: # height = 400 rownames = 'c("' + '","'.join(parametres['rownames']) + '")' colnames = 'c("' + '","'.join(parametres['colnames']) + '")' - - if not intxt : + if not intxt: #FIXME txt = """ di <- matrix(data=%s, nrow=%i, byrow = TRUE) @@ -608,17 +595,17 @@ def barplot(table, parametres, intxt = False) : rownames(di)<- %s colnames(di) <- %s """ % (txttable, rownb, rownames, colnames) - else : + else: txt = intxt - if not 'tree' in parametres : + if not 'tree' in parametres: txt += """ source("%s") color = rainbow(nrow(di)) width <- %i height <- %i open_file_graph("%s",width = width, height = height, svg = %s) - par(mar=c(0,0,0,0)) - layout(matrix(c(1,2),1,2, byrow=TRUE),widths=c(3,lcm(12))) + par(mar=c(0,0,0,0)) + layout(matrix(c(1,2),1,2, byrow=TRUE),widths=c(3,lcm(12))) par(mar=c(8,4,1,0)) yp = ifelse(length(toinf), 0.2, 0) ym = ifelse(length(tominf), 0.2, 0) @@ -662,7 +649,7 @@ def barplot(table, parametres, intxt = False) : legend(x = 'center' , rownames(di), fill = color) dev.off() """ % (ffr(parametres['rgraph']), parametres['width'], parametres['height'], ffr(parametres['tmpgraph']), parametres['svg']) - else : + else: txt += """ load("%s") library(ape) @@ -729,24 +716,26 @@ def barplot(table, parametres, intxt = False) : # f.write(txt) # f.close() -class PrintSimiScript(PrintRScript) : - def make_script(self) : + +class PrintSimiScript(PrintRScript): + + def make_script(self): self.txtgraph = '' self.packages(['igraph', 'proxy', 'Matrix']) self.sources([self.analyse.parent.RscriptsPath['simi'], self.analyse.parent.RscriptsPath['Rgraph']]) txt = '' - if not self.parametres['keep_coord'] and not (self.parametres['type'] == 'simimatrix' or self.parametres['type'] == 'simiclustermatrix') : + if not self.parametres['keep_coord'] and not (self.parametres['type'] == 'simimatrix' or self.parametres['type'] == 'simiclustermatrix'): txt += """ dm.path <- "%s" cn.path <- "%s" selected.col <- "%s" """ % (ffr(self.pathout['mat01.csv']), ffr(self.pathout['actives.csv']), ffr(self.pathout['selected.csv'])) - if 'word' in self.parametres : + if 'word' in self.parametres: txt += """ word <- TRUE index <- %i + 1 """ % self.parametres['word'] - else : + else: txt += """ word <- FALSE index <- NULL @@ -777,12 +766,12 @@ class PrintSimiScript(PrintRScript) : dm.path <- "%s" selected.col <- "%s" """ % (ffr(self.pathout['mat01.csv']), ffr(self.pathout['selected.csv'])) - if 'word' in self.parametres : + if 'word' in self.parametres: txt += """ word <- TRUE index <- %i + 1 """ % self.parametres['word'] - else : + else: txt += """ word <- FALSE """ @@ -806,51 +795,50 @@ class PrintSimiScript(PrintRScript) : index <- which(colnames(dm) == forme) } """ - else : + else: txt += """ load("%s") """ % ffr(self.pathout['RData.RData']) - - if self.parametres['coeff'] == 0 : + if self.parametres['coeff'] == 0: method = 'cooc' - if not self.parametres['keep_coord'] : + if not self.parametres['keep_coord']: txt += """ method <- 'cooc' mat <- make.a(dm) """ - elif self.analyse.indices[self.parametres['coeff']] == 'Jaccard' : + elif self.analyse.indices[self.parametres['coeff']] == 'Jaccard': method = 'Jaccard' - if not self.parametres['keep_coord'] : + if not self.parametres['keep_coord']: txt += """ method <- 'Jaccard' mat <- sparse.jaccard(dm) """ - else : - if not self.parametres['keep_coord'] : + else: + if not self.parametres['keep_coord']: txt += """ dm <- as.matrix(dm) """ - if self.parametres['coeff'] == 1 : + if self.parametres['coeff'] == 1: method = 'prcooc' txt += """ method <- 'Russel' mat <- simil(dm, method = 'Russel', diag = TRUE, upper = TRUE, by_rows = FALSE) """ - elif self.analyse.indices[self.parametres['coeff']] == 'binomial' : + elif self.analyse.indices[self.parametres['coeff']] == 'binomial': method = 'binomial' - if not self.parametres['keep_coord'] : + if not self.parametres['keep_coord']: txt += """ method <- 'binomial' mat <- binom.sim(dm) """ elif self.parametres['coeff'] != 0 and self.analyse.indices[self.parametres['coeff']] != 'Jaccard': method = self.analyse.indices[self.parametres['coeff']] - if not self.parametres['keep_coord'] : + if not self.parametres['keep_coord']: txt += """ method <-"%s" mat <- simil(dm, method = method, diag = TRUE, upper = TRUE, by_rows = FALSE) """ % self.analyse.indices[self.parametres['coeff']] - if not self.parametres['keep_coord'] : + if not self.parametres['keep_coord']: txt += """ mat <- as.matrix(stats::as.dist(mat,diag=TRUE,upper=TRUE)) mat[is.na(mat)] <- 0 @@ -877,7 +865,7 @@ class PrintSimiScript(PrintRScript) : mat[infm] <- minmat } """ - if 'word' in self.parametres and not self.parametres['keep_coord'] : + if 'word' in self.parametres and not self.parametres['keep_coord']: txt += """ mat <- graph.word(mat, index) cs <- colSums(mat) @@ -889,27 +877,33 @@ class PrintSimiScript(PrintRScript) : index <- which(colnames(mat)==forme) } """ - - if self.parametres['layout'] == 0 : layout = 'random' - if self.parametres['layout'] == 1 : layout = 'circle' - if self.parametres['layout'] == 2 : layout = 'frutch' - if self.parametres['layout'] == 3 : layout = 'kawa' - if self.parametres['layout'] == 4 : layout = 'graphopt' - if self.parametres['layout'] == 5 : layout = 'spirale' - if self.parametres['layout'] == 6 : layout = 'spirale3D' - - + if self.parametres['layout'] == 0: + layout = 'random' + if self.parametres['layout'] == 1: + layout = 'circle' + if self.parametres['layout'] == 2: + layout = 'frutch' + if self.parametres['layout'] == 3: + layout = 'kawa' + if self.parametres['layout'] == 4: + layout = 'graphopt' + if self.parametres['layout'] == 5: + layout = 'spirale' + if self.parametres['layout'] == 6: + layout = 'spirale3D' self.filename='' - if self.parametres['type_graph'] == 0 : type = 'tkplot' - if self.parametres['type_graph'] == 1 : + if self.parametres['type_graph'] == 0: + type = 'tkplot' + if self.parametres['type_graph'] == 1: graphnb = 1 type = 'nplot' dirout = os.path.dirname(self.pathout['mat01.csv']) while os.path.exists(os.path.join(dirout,'graph_simi_'+str(graphnb)+'.png')): graphnb +=1 self.filename = ffr(os.path.join(dirout,'graph_simi_'+str(graphnb)+'.png')) - if self.parametres['type_graph'] == 2 : type = 'rgl' - if self.parametres['type_graph'] == 3 : + if self.parametres['type_graph'] == 2: + type = 'rgl' + if self.parametres['type_graph'] == 3: graphnb = 1 type = 'web' dirout = os.path.dirname(self.pathout['mat01.csv']) @@ -918,7 +912,7 @@ class PrintSimiScript(PrintRScript) : self.filename = ffr(os.path.join(dirout,'web_'+str(graphnb))) os.mkdir(self.filename) self.filename = os.path.join(self.filename, 'gexf.gexf') - if self.parametres['type_graph'] == 4 : + if self.parametres['type_graph'] == 4: graphnb = 1 type = 'rglweb' dirout = os.path.dirname(self.pathout['mat01.csv']) @@ -926,46 +920,47 @@ class PrintSimiScript(PrintRScript) : graphnb +=1 self.filename = ffr(os.path.join(dirout,'webrgl_'+str(graphnb))) os.mkdir(self.filename) - - if self.parametres['arbremax'] : + if self.parametres['arbremax']: arbremax = 'TRUE' self.txtgraph += ' - arbre maximum' - else : arbremax = 'FALSE' - - if self.parametres['coeff_tv'] : + else: + arbremax = 'FALSE' + + if self.parametres['coeff_tv']: coeff_tv = self.parametres['coeff_tv_nb'] tvminmax = 'c(NULL,NULL)' - elif not self.parametres['coeff_tv'] or self.parametres.get('sformchi', False) : + elif not self.parametres['coeff_tv'] or self.parametres.get('sformchi', False): coeff_tv = 'NULL' tvminmax = 'c(%i, %i)' %(self.parametres['tvmin'], self.parametres['tvmax']) - if self.parametres['coeff_te'] : coeff_te = 'c(%i,%i)' % (self.parametres['coeff_temin'], self.parametres['coeff_temax']) - else : coeff_te = 'NULL' - - if self.parametres['vcex'] or self.parametres.get('cexfromchi', False) : + if self.parametres['coeff_te']: + coeff_te = 'c(%i,%i)' % (self.parametres['coeff_temin'], self.parametres['coeff_temax']) + else: + coeff_te = 'NULL' + if self.parametres['vcex'] or self.parametres.get('cexfromchi', False): vcexminmax = 'c(%i/10,%i/10)' % (self.parametres['vcexmin'],self.parametres['vcexmax']) - else : + else: vcexminmax = 'c(NULL,NULL)' - if not self.parametres['label_v'] : label_v = 'FALSE' - else : label_v = 'TRUE' - - if not self.parametres['label_e'] : label_e = 'FALSE' - else : label_e = 'TRUE' - - if self.parametres['seuil_ok'] : seuil = str(self.parametres['seuil']) - else : seuil = 'NULL' - - if not self.parametres.get('edgecurved', False) : + if not self.parametres['label_v']: + label_v = 'FALSE' + else: + label_v = 'TRUE' + if not self.parametres['label_e']: + label_e = 'FALSE' + else: + label_e = 'TRUE' + if self.parametres['seuil_ok']: + seuil = str(self.parametres['seuil']) + else: + seuil = 'NULL' + if not self.parametres.get('edgecurved', False): ec = 'FALSE' - else : + else: ec = 'TRUE' - txt += """ edge.curved <- %s """ % ec - cols = str(self.parametres['cols']).replace(')',', max=255)') cola = str(self.parametres['cola']).replace(')',',max=255)') - txt += """ minmaxeff <- %s """ % tvminmax @@ -975,12 +970,11 @@ class PrintSimiScript(PrintRScript) : txt += """ cex = %i/10 """ % self.parametres['cex'] - - if self.parametres['film'] : + if self.parametres['film']: txt += """ film <- "%s" """ % ffr(self.pathout['film']) - else : + else: txt += """ film <- NULL """ @@ -992,7 +986,6 @@ class PrintSimiScript(PrintRScript) : } } """ % seuil - txt += """ label.v <- %s label.e <- %s @@ -1005,14 +998,14 @@ class PrintSimiScript(PrintRScript) : width <- %i height <- %i """ % (self.parametres['width'], self.parametres['height']) - if self.parametres['keep_coord'] : + if self.parametres['keep_coord']: txt += """ coords <- try(coords, TRUE) if (!is.matrix(coords)) { coords<-NULL } """ - else : + else: txt += """ coords <- NULL """ @@ -1022,15 +1015,15 @@ class PrintSimiScript(PrintRScript) : txt += """ alpha <- %i/100 """ % self.parametres['alpha'] -############################################# - if self.parametres.get('bystar',False) : + ######### ??? ########## + if self.parametres.get('bystar',False): txt += """ et <- list() """ - for i, line in enumerate(self.parametres['listet']) : + for i, line in enumerate(self.parametres['listet']): txt+= """ et[[%i]] <- c(%s) - """ % (i+1, ','.join([`val + 1` for val in line])) + """ % (i+1, ','.join([repr(val + 1) for val in line])) txt+= """ unetoile <- c('%s') """ % ("','".join([val for val in self.parametres['selectedstars']])) @@ -1059,14 +1052,13 @@ class PrintSimiScript(PrintRScript) : chivertex.size <- norm.vec(toblack, vcexminmax[1], vcexminmax[2]) """ % (ffr(self.analyse.parent.RscriptsPath['chdfunct'])) - else : + else: txt += """ vertex.label.color <- 'black' chivertex.size <- 1 leg<-NULL """ -############################################# - + ######### ??? ########## # txt += """ # eff <- colSums(dm) # g.ori <- graph.adjacency(mat, mode='lower', weighted = TRUE) @@ -1088,13 +1080,13 @@ class PrintSimiScript(PrintRScript) : # g.toplot <- g.ori # } # """ - if self.parametres['com'] : - com = `self.parametres['communities']` - else : + if self.parametres['com']: + com = repr(self.parametres['communities']) + else: com = 'NULL' - if self.parametres['halo'] : + if self.parametres['halo']: halo = 'TRUE' - else : + else: halo = 'FALSE' txt += """ communities <- %s @@ -1105,25 +1097,24 @@ class PrintSimiScript(PrintRScript) : x <- list(mat = mat, eff = eff) graph.simi <- do.simi(x, method='%s', seuil = seuil, p.type = '%s', layout.type = '%s', max.tree = %s, coeff.vertex=%s, coeff.edge = %s, minmaxeff = minmaxeff, vcexminmax = vcexminmax, cex = cex, coords = coords, communities = communities, halo = halo, index.word=index) """ % (method, type, layout, arbremax, coeff_tv, coeff_te) - - if self.parametres.get('bystar',False) : - if self.parametres.get('cexfromchi', False) : + if self.parametres.get('bystar',False): + if self.parametres.get('cexfromchi', False): txt+=""" label.cex<-chivertex.size """ - else : + else: txt+=""" label.cex <- cex """ - if self.parametres.get('sfromchi', False) : + if self.parametres.get('sfromchi', False): txt += """ vertex.size <- norm.vec(toblack, minmaxeff[1], minmaxeff[2]) """ - else : + else: txt += """ vertex.size <- NULL """ - else : + else: #print self.parametres if (self.parametres['type'] == 'clustersimitxt' and self.parametres.get('tmpchi', False)) or (self.parametres['type'] in ['simimatrix','simiclustermatrix'] and 'tmpchi' in self.parametres): txt += """ @@ -1133,11 +1124,11 @@ class PrintSimiScript(PrintRScript) : txt += """ lchi <- lchi[sel.col] """ - if self.parametres['type'] in ['clustersimitxt', 'simimatrix', 'simiclustermatrix'] and self.parametres.get('cexfromchi', False) : + if self.parametres['type'] in ['clustersimitxt', 'simimatrix', 'simiclustermatrix'] and self.parametres.get('cexfromchi', False): txt += """ label.cex <- norm.vec(lchi, vcexminmax[1], vcexminmax[2]) """ - else : + else: txt += """ if (is.null(vcexminmax[1])) { label.cex <- cex @@ -1150,7 +1141,7 @@ class PrintSimiScript(PrintRScript) : vertex.size <- norm.vec(lchi, minmaxeff[1], minmaxeff[2]) if (!length(vertex.size)) vertex.size <- 0 """ - else : + else: txt += """ if (is.null(minmaxeff[1])) { vertex.size <- 0 @@ -1159,8 +1150,10 @@ class PrintSimiScript(PrintRScript) : } """ #txt += """ vertex.size <- NULL """ - if self.parametres['svg'] : svg = 'TRUE' - else : svg = 'FALSE' + if self.parametres['svg']: + svg = 'TRUE' + else: + svg = 'FALSE' txt += """ svg <- %s """ % svg @@ -1196,19 +1189,20 @@ class PrintSimiScript(PrintRScript) : coords <- plot.simi(graph.simi, p.type='%s',filename="%s", vertex.label = label.v, edge.label = label.e, vertex.col = vertex.col, vertex.label.color = vertex.label.color, vertex.label.cex=label.cex, vertex.size = vertex.size, edge.col = cola, leg=leg, width = width, height = height, alpha = alpha, movie = film, edge.curved = edge.curved, svg = svg) save.image(file="%s") """ % (type, self.filename, ffr(self.pathout['RData'])) - self.add(txt) self.write() -class WordCloudRScript(PrintRScript) : - def make_script(self) : + +class WordCloudRScript(PrintRScript): + + def make_script(self): self.sources([self.analyse.parent.RscriptsPath['Rgraph']]) self.packages(['wordcloud']) bg_col = Rcolor(self.parametres['col_bg']) txt_col = Rcolor(self.parametres['col_text']) - if self.parametres['svg'] : + if self.parametres['svg']: svg = 'TRUE' - else : + else: svg = 'FALSE' txt = """ svg <- %s @@ -1231,13 +1225,15 @@ class WordCloudRScript(PrintRScript) : self.add(txt) self.write() -class ProtoScript(PrintRScript) : - def make_script(self) : + +class ProtoScript(PrintRScript): + + def make_script(self): self.sources([self.analyse.parent.RscriptsPath['Rgraph'], self.analyse.parent.RscriptsPath['prototypical.R']]) self.packages(['wordcloud']) - if self.parametres.get('cloud', False) : + if self.parametres.get('cloud', False): cloud = 'TRUE' - else : + else: cloud = 'FALSE' txt = """ errorn <- function(x) { @@ -1255,24 +1251,26 @@ class ProtoScript(PrintRScript) : self.write() -class ExportAfc(PrintRScript) : - def make_script(self) : +class ExportAfc(PrintRScript): + + def make_script(self): self.source([self.analyse.parent.RscriptsPath['Rgraph']]) self.packages(['rgexf']) txt = """ """ -class MergeGraphes(PrintRScript) : + +class MergeGraphes(PrintRScript): + def __init__(self, analyse): - self.script = u"#Script genere par IRaMuTeQ - %s\n" % datetime.now().ctime() + self.script = "#Script genere par IRaMuTeQ - %s\n" % datetime.now().ctime() self.pathout = PathOut() self.parametres = analyse.parametres self.scriptout = self.pathout['temp'] self.analyse = analyse - def make_script(self) : + def make_script(self): #FIXME - txt = """ library(igraph) library(Matrix) @@ -1284,9 +1282,9 @@ class MergeGraphes(PrintRScript) : V(g)$weight <- (graph.simi$mat.eff/nrow(dm))*100 graphs[['%s']] <- g """ - for i, graph in enumerate(self.parametres['graphs']) : + for i, graph in enumerate(self.parametres['graphs']): path = os.path.dirname(graph) - gname = ''.join(['g', `i`]) + gname = ''.join(['g', repr(i)]) RData = os.path.join(path,'RData.RData') txt += load % (ffr(RData), gname) self.add(txt) @@ -1302,8 +1300,10 @@ class MergeGraphes(PrintRScript) : write.graph(ng, "%s", format = 'graphml') """ % ffr(self.parametres['grapheout']) self.add(txt) - + + class TgenSpecScript(PrintRScript): + def make_script(self): self.packages(['textometry']) txt = """ @@ -1323,8 +1323,10 @@ class TgenSpecScript(PrintRScript): write.table(result, file = "%s", sep='\\t', col.names = NA) """ % ffr(self.pathout['tgenspec.csv']) self.add(txt) - + + class TgenProfScript(PrintRScript): + def make_script(self): self.sources([self.analyse.ira.RscriptsPath['chdfunct']]) txt = """ @@ -1344,8 +1346,10 @@ class TgenProfScript(PrintRScript): write.table(reslem$pchi2, file = "%s", sep='\\t', col.names = NA) """ % (ffr(self.pathout['tgenlemchi2.csv']), ffr(self.pathout['tgenlempchi2.csv'])) self.add(txt) - + + class FreqMultiScript(PrintRScript): + def make_script(self): self.sources([self.analyse.parent.RscriptsPath['Rgraph']]) txt = """ @@ -1371,8 +1375,10 @@ class FreqMultiScript(PrintRScript): self.add(txt) self.write() -class LabbeScript(PrintRScript) : - def make_script(self) : + +class LabbeScript(PrintRScript): + + def make_script(self): self.sources([self.analyse.parent.RscriptsPath['distance-labbe.R'], self.analyse.parent.RscriptsPath['Rgraph']]) txt = """ @@ -1427,10 +1433,12 @@ class LabbeScript(PrintRScript) : self.add(txt) self.write() -class ChronoChi2Script(PrintRScript) : - def make_script(self) : + +class ChronoChi2Script(PrintRScript): + + def make_script(self): self.sources([self.analyse.parent.RscriptsPath['Rgraph']]) - print self.parametres + print(self.parametres) txt = """ inRData <- "%s" dendrof <- "%s" @@ -1450,7 +1458,7 @@ class ChronoChi2Script(PrintRScript) : ptc <- tcp/sum(tcp) dpt <- t(dpt) dd <- dpt - """ % self.parametres['var'].replace(u'*', u"\\\\*") + """ % self.parametres['var'].replace('*', "\\\\*") txt += """ classes <- n1[,ncol(n1)] tcl <- table(classes) @@ -1459,7 +1467,6 @@ class ChronoChi2Script(PrintRScript) : tcl <- tcl[-to.vire] } tclp <- tcl/sum(tcl) - #chi2 colors library(ape) k <- 1e-02 @@ -1511,7 +1518,6 @@ class ChronoChi2Script(PrintRScript) : last.col <- c(last.col, rgb(r=col2rgb(mcol)[1]/255, g=col2rgb(mcol)[2]/255, b=col2rgb(mcol)[3]/255, a=k)) } #print(last.col) - barplot(rep(1,ncol(dd)), width=ptc, names.arg=FALSE, axes=FALSE, col=last.col[lcol], border=rgb(r=0, g=0, b=0, a=0.3)) } plot(0,type='n',axes=FALSE,ann=FALSE) @@ -1522,10 +1528,12 @@ class ChronoChi2Script(PrintRScript) : self.add(txt) self.write() -class ChronoPropScript(PrintRScript) : - def make_script(self) : + +class ChronoPropScript(PrintRScript): + + def make_script(self): self.sources([self.analyse.parent.RscriptsPath['Rgraph']]) - print self.parametres + print(self.parametres) txt = """ inRData <- "%s" dendrof <- "%s" @@ -1545,7 +1553,7 @@ class ChronoPropScript(PrintRScript) : ptc <- tcp/sum(tcp) dpt <- t(dpt) dd <- dpt - """ % self.parametres['var'].replace(u'*', u"\\\\*") + """ % self.parametres['var'].replace('*', "\\\\*") txt += """ classes <- n1[,ncol(n1)] tcl <- table(classes) @@ -1567,10 +1575,12 @@ class ChronoPropScript(PrintRScript) : self.add(txt) self.write() -class ChronoggScript(PrintRScript) : - def make_script(self) : + +class ChronoggScript(PrintRScript): + + def make_script(self): self.sources([self.analyse.parent.RscriptsPath['Rgraph']]) - print self.parametres + print(self.parametres) txt = """ library(ggplot2) inRData <- "%s" @@ -1591,7 +1601,7 @@ class ChronoggScript(PrintRScript) : ptc <- tcp/sum(tcp) dpt <- t(dpt) dd <- dpt - """ % self.parametres['var'].replace(u'*', u"\\\\*") + """ % self.parametres['var'].replace('*', "\\\\*") txt += """ classes <- n1[,ncol(n1)] tcl <- table(classes) @@ -1619,31 +1629,33 @@ class ChronoggScript(PrintRScript) : self.add(txt) self.write() -class DendroScript(PrintRScript) : - def make_script(self) : - if self.parametres['svg'] : + +class DendroScript(PrintRScript): + + def make_script(self): + if self.parametres['svg']: typefile = '.svg' - else : + else: typefile = '.png' fileout = self.parametres['fileout'] width = self.parametres['width'] height = self.parametres['height'] type_dendro = self.parametres['dendro_type'] - if self.parametres['taille_classe'] : + if self.parametres['taille_classe']: tclasse = 'TRUE' - else : + else: tclasse = 'FALSE' - if self.parametres['color_nb'] == 0 : + if self.parametres['color_nb'] == 0: bw = 'FALSE' - else : + else: bw = 'TRUE' - if self.parametres['type_tclasse'] == 0 : + if self.parametres['type_tclasse'] == 0: histo='FALSE' - else : + else: histo = 'TRUE' - if self.parametres['svg'] : + if self.parametres['svg']: svg = 'TRUE' - else : + else: svg = 'FALSE' dendro_path = self.pathout['Rdendro'] classe_path = self.pathout['uce'] @@ -1654,12 +1666,12 @@ class DendroScript(PrintRScript) : classes <- read.csv2("%s", row.names=1) classes <- classes[,1] """ % (ffr(dendro_path), ffr(self.parametres['Rgraph']), ffr(classe_path)) - if self.parametres['dendro'] == 'simple' : + if self.parametres['dendro'] == 'simple': txt += """ open_file_graph("%s", width=%i, height=%i, svg=%s) plot.dendropr(tree.cut1$tree.cl, classes, type.dendro="%s", histo=%s, bw=%s, lab=NULL, tclasse=%s) """ % (ffr(fileout), width, height, svg, type_dendro, histo, bw, tclasse) - elif self.parametres['dendro'] == 'texte' : + elif self.parametres['dendro'] == 'texte': txt += """ load("%s") source("%s") @@ -1668,7 +1680,7 @@ class DendroScript(PrintRScript) : } chistable <- chistabletot[1:(debsup-1),] """ % (ffr(self.pathout['RData.RData']), ffr(self.parametres['Rgraph'])) - if self.parametres.get('translation', False) : + if self.parametres.get('translation', False): txt += """ rn <- read.csv2("%s", header=FALSE, sep='\t') rnchis <- row.names(chistable) @@ -1681,7 +1693,7 @@ class DendroScript(PrintRScript) : open_file_graph("%s", width=%i, height=%i, svg = %s) plot.dendro.prof(tree.cut1$tree.cl, classes, chistable, nbbycl = 60, type.dendro="%s", bw=%s, lab=NULL) """ % (ffr(fileout), width, height, svg, type_dendro, bw) - elif self.parametres['dendro'] == 'cloud' : + elif self.parametres['dendro'] == 'cloud': txt += """ load("%s") source("%s") @@ -1696,8 +1708,8 @@ class DendroScript(PrintRScript) : self.write() -class ReDoProfScript(PrintRScript) : - def make_script(self) : - self.sources([self.analyse.parent.RscriptsPath['chdfunct.R']]) - print self.parametres +class ReDoProfScript(PrintRScript): + def make_script(self): + self.sources([self.analyse.parent.RscriptsPath['chdfunct.R']]) + print(self.parametres)