X-Git-Url: http://iramuteq.org/git?a=blobdiff_plain;ds=sidebyside;f=PrintRScript.py;h=f8aaa961ee6bd3eefe99570aee34014c6ef82a7c;hb=refs%2Fheads%2F3.0;hp=26947e1459f3428e699a70e57ee3267c2b4c919b;hpb=f7dde4ccc7e71af9d76431785031b55df6a80f60;p=iramuteq

diff --git a/PrintRScript.py b/PrintRScript.py
index 26947e1..e005361 100755
--- a/PrintRScript.py
+++ b/PrintRScript.py
@@ -1,7 +1,6 @@
 # -*- coding: utf-8 -*-
 #Author: Pierre Ratinaud
-#Copyright (c) 2008-2020 Pierre Ratinaud
-#modification pour python 3 : Laurent Mérat, 6x7 - mai 2020
+#Copyright (c) 2008-2011 Pierre Ratinaud
 #License: GNU/GPL
 
 #------------------------------------
@@ -59,7 +58,7 @@ class PrintRScript:
             self.add('load("%s")' % ffr(val))
 
     def write(self):
-        with open(self.scriptout, 'w') as f:
+        with open(self.scriptout, 'w', encoding='utf8') as f:
             f.write(self.script)
 
 
@@ -126,7 +125,7 @@ class Alceste2(PrintRScript):
 #
 
 
-def RchdTxt(DicoPath, RscriptPath, mincl, classif_mode, nbt = 9, svdmethod = 'svdR', libsvdc = False, libsvdc_path = None, R_max_mem = False, mode_patate = False, nbproc=1):
+def RchdTxt(DicoPath, RscriptPath, mincl, classif_mode, nbt = 9, svdmethod = 'svdR', libsvdc = False, libsvdc_path = None, R_max_mem = False, mode_patate = False, nbproc=10):
     txt = """
     source("%s")
     source("%s")
@@ -177,7 +176,7 @@ def RchdTxt(DicoPath, RscriptPath, mincl, classif_mode, nbt = 9, svdmethod = 'sv
         row.names(data2) <- 1:nrow(data2)
         """ % ffr(DicoPath['TableUc2'])
     txt += """
-    log1 <- "%s"
+    #log1 <- "%s"
     #print('FIXME : source newCHD')
     #source('/home/pierre/workspace/iramuteq/Rscripts/newCHD.R')
     #nbproc <- %s
@@ -263,7 +262,7 @@ def RchdTxt(DicoPath, RscriptPath, mincl, classif_mode, nbt = 9, svdmethod = 'sv
     txt += """
     #save.image(file="%s")
     """ % (ffr(DicoPath['RData']))
-    fileout = open(DicoPath['Rchdtxt'], 'w')
+    fileout = open(DicoPath['Rchdtxt'], 'w', encoding='utf8')
     fileout.write(txt)
     fileout.close()
 
@@ -288,7 +287,7 @@ def RPamTxt(corpus, RscriptPath):
     txt += """
     save.image(file="%s")
     """ % DicoPath['RData']
-    fileout = open(DicoPath['Rchdtxt'], 'w')
+    fileout = open(DicoPath['Rchdtxt'], 'w', encoding='utf8')
     fileout.write(txt)
     fileout.close()
 
@@ -325,7 +324,7 @@ def RchdQuest(DicoPath, RscriptPath, nbcl = 10, mincl = 10):
     txt += """
     save.image(file="%s")
     """ % ffr(DicoPath['RData'])
-    fileout = open(DicoPath['Rchdquest'], 'w')
+    fileout = open(DicoPath['Rchdquest'], 'w', encoding='utf8')
     fileout.write(txt)
     fileout.close()
     
@@ -429,7 +428,7 @@ rm(tablesqrpsup)
 rm(tablesqrpet)
 save.image(file="%s")
 """ % ffr(DictChdTxtOut['RData'])
-    file = open(DictChdTxtOut['RTxtProfGraph'], 'w')
+    file = open(DictChdTxtOut['RTxtProfGraph'], 'w', encoding='utf8')
     file.write(txt)
     file.close()
 
@@ -468,7 +467,7 @@ def write_afc_graph(self):
     else:
         nodesfile = 'NULL'
         edgesfile = 'NULL'
-    with open(self.RscriptsPath['afc_graph'], 'r') as f:
+    with open(self.RscriptsPath['afc_graph'], 'r', encoding='utf8') as f:
         txt = f.read()
 #    self.DictPathOut['RData'], \
     scripts = txt % (ffr(self.RscriptsPath['Rgraph']),\
@@ -524,7 +523,7 @@ def print_simi3d(self):
     make.simi.afc(dm,chistabletot, lim=%i, alpha = %.2f, movie = %s)
     """ % (simi3d.spin_1.GetValue(), float(simi3d.slider_1.GetValue())/100, movie)
     tmpfile = tempfile.mktemp(dir=self.parent.TEMPDIR)
-    tmp = open(tmpfile,'w')
+    tmp = open(tmpfile,'w', encoding='utf8')
     tmp.write(txt)
     tmp.close()
     return tmpfile
@@ -742,7 +741,7 @@ class PrintSimiScript(PrintRScript):
                 """
             txt += """
             dm <-readMM(dm.path)
-            cn <- read.table(cn.path, sep="\t", quote='"')
+            cn <- read.table(cn.path, sep="\t", quote='"', comment.char="")
             colnames(dm) <- cn[,1]
             if (file.exists(selected.col)) {
                 sel.col <- read.csv2(selected.col, header = FALSE)
@@ -1244,7 +1243,7 @@ class ProtoScript(PrintRScript):
         }
         mat <- read.csv2("%s", header = FALSE, row.names=1, sep='\t', quote='"', dec='.')
         open_file_graph("%s",height=800, width=1000)
-        prototypical(mat, mfreq = %s, mrank = %s, cloud = FALSE, cexrange=c(1,2.4), cexalpha= c(0.4, 1), type = '%s', mat.col.path='/tmp/matcol.csv')
+        prototypical(mat, mfreq = %s, mrank = %s, cloud = FALSE, cexrange=c(1,2.4), cexalpha= c(0.4, 1), type = '%s')#, mat.col.path='/tmp/matcol.csv')
         dev.off()
         """ % (ffr(self.analyse.pathout['table.csv']), ffr(self.analyse.pathout['proto.png']), self.parametres['limfreq'], self.parametres['limrang'], self.parametres['typegraph'])
         self.add(txt)
@@ -1385,6 +1384,17 @@ class LabbeScript(PrintRScript):
         tab <- read.csv2("%s", header=TRUE, sep=';', row.names=1)
         """ % (ffr(self.pathout['tableafcm.csv']))
         txt += """
+        cs <- colSums(tab)
+        if (min(cs) == 0) {
+            print('empty columns !!')
+            vide <- which(cs==0)
+            print(vide)
+            tab <- tab[,-vide]
+        }
+        #print('#### RcppIramuteq for C++ Labbe ####')
+        #library(RcppIramuteq)
+        #dist.mat <- labbe(as.matrix(tab))
+        #rownames(dist.mat) <- colnames(tab)
         dist.mat <- dist.labbe(tab)
         dist.mat <- as.dist(dist.mat, upper=F, diag=F)
         write.table(as.matrix(dist.mat), "%s", sep='\t')