def run(self):
try:
result = "0"
# grise
self.disalbledButtonsCalibration()
self.ui.resetCalibrationPushButton.setDisabled(True)
self.actualizeOutFiles()
with open("fonctions_apprentissage.r", "r", encoding="utf-8") as apprentissageRopen:
apprentissage = "".join(apprentissageRopen.readlines())
apprentissage = SignatureTranslatedAnonymousPackage(apprentissage, "apprentissage")
if args.debug: print("{}\n{}".format(apprentissage, dir(apprentissage)))
# test if Rdata file already exist, if yes remove file if user say yes, or stop analyse
if os.path.exists(self.calibrationFilesOut["RData"]):
reply = QMessageBox.question(self, 'WARNING', 'File will be overwritten.\nDo you still want to proceed?', QMessageBox.Yes | QMessageBox.No, QMessageBox.No)
if reply == QMessageBox.Yes:
for key, path in self.calibrationFilesOut.items():
os.remove(path)
reloadCalibration = True
elif reply == QMessageBox.No:
reloadCalibration = False
else:
reloadCalibration = True
if reloadCalibration:
self.ui.statusbar.showMessage(str("Running calibration, please waiting ...."),9600)
#doivent être (dans cet ordre) le nom (relatif) des sous-répertoires fond, limbe, lésions
result , good = apprentissage.apprentissage(self.calibrationInOutPath,"background", "leaf", "lesion").r_repr().replace('"','').replace("c(","").replace(")","").split(",")
self.calibrationFileOpenLineEdit.setText(self.calibrationFilesOut["RData"])
#print(result, good)
if result == "1" and os.path.exists(self.calibrationFilesOut["RData"]):
print(result, self.calibrationFilesOut["RData"])
self.infoDialogue(status = "new")
self.ui.statusbar.showMessage(str("FINISH, files were product on : %s" % self.calibrationInOutPath),9600)
self.ui.resetCalibrationPushButton.setEnabled(True)
elif result == "0" and os.path.exists(self.calibrationFilesOut["RData"]):
self.infoDialogue(status = "already")
print(result, self.calibrationFilesOut["RData"])
self.calibrationFileOpenLineEdit.setText("")
self.ui.resetCalibrationPushButton.setEnabled(True)
self.resetLoadFolder()
self.enableButtonsCalibration()
elif result == "0" and not os.path.exists(self.calibrationFilesOut["RData"]):
self.displayError(typeError = "ERROR:", message = "Error when running R code....")
self.resetLoadFolder()
except Exception as e:
self.displayError(typeError = "ERROR:", message = "Error when running R code....\n"+e)
self.resetLoadFolder()
self.ui.resetCalibrationPushButton.setEnabled(True)
def run(self):
try:
result = "0"
# grise
self.disalbledButtonsCalibration()
self.ui.resetCalibrationPushButton.setDisabled(True)
with open("fonctions_apprentissage.r", "r", encoding="utf-8") as apprentissageRopen:
apprentissage = "".join(apprentissageRopen.readlines())
apprentissage = SignatureTranslatedAnonymousPackage(apprentissage, "apprentissage")
self.CalibrationOutPath = "/".join(str(self.dicoFoldersCalibration["leaf"]).split("/")[:-1])
self.CalibrationBasename = self.CalibrationOutPath.split("/")[-1]
self.actualizeOutFiles()
if debug: print("{}\n{}".format(apprentissage, dir(apprentissage)))
# test if Rdata file already exist, if yes remove file if user say yes, or stop analyse
if os.path.exists(self.CalibrationFilesOut["RData"]):
reply = QMessageBox.question(self, 'Warning', 'File will be overwritten.\nDo you still want to proceed?', QMessageBox.Yes | QMessageBox.No, QMessageBox.No)
if reply == QMessageBox.Yes:
for key, path in self.CalibrationFilesOut.items():
os.remove(path)
reloadCalibration = True
elif reply == QMessageBox.No:
reloadCalibration = False
else:
reloadCalibration = True
if reloadCalibration:
self.ui.statusbar.showMessage(str("Running Calibration, please waiting ...."),9600)
#result , self.CalibrationFilesOut["RData"] = apprentissage.apprentissage(self.dicoObjectOpenLineEditCalibration["leaf"],self.dicoObjectOpenLineEditCalibration["symptom"],self.dicoObjectOpenLineEditCalibration["background"]).r_repr().replace('"','').replace("c(","").replace(")","").split(",")
result , good = apprentissage.apprentissage(self.CalibrationOutPath).r_repr().replace('"','').replace("c(","").replace(")","").split(",")
self.calibrationFileOpenLineEdit.setText(self.CalibrationFilesOut["RData"])
if result == "1" and os.path.exists(self.CalibrationFilesOut["RData"]):
print(result, self.CalibrationFilesOut["RData"])
self.infoDialogue(status = "new")
self.ui.statusbar.showMessage(str("FINISH, files were product on : %s" % self.CalibrationOutPath),9600)
self.ui.resetCalibrationPushButton.setEnabled(True)
elif result == "0" and os.path.exists(self.CalibrationFilesOut["RData"]):
self.infoDialogue(status = "already")
print(result, self.CalibrationFilesOut["RData"])
self.calibrationFileOpenLineEdit.setText("")
self.ui.resetCalibrationPushButton.setEnabled(True)
self.resetLoadFolder()
self.enableButtonsCalibration()
elif result == "0" and not os.path.exists(self.CalibrationFilesOut["RData"]):
self.displayError(error = "Error when running R code....")
except Exception as e:
self.displayError(error = e)
from rpy2.robjects.packages import importr
from rpy2.robjects.packages import SignatureTranslatedAnonymousPackage
# import R's "base" package
base = importr('base')
with open("fonctions_apprentissage.r", "r", encoding="utf-8") as apprentissageRopen:
apprentissage = "".join(apprentissageRopen.readlines())
print(apprentissage)
apprentissage = SignatureTranslatedAnonymousPackage(apprentissage, "apprentissage")
path_sample = "/media/sebastien/Bayer/ScriptsSEB/scripts/GUI/EBimage/AnalyseImagesV2/Samples/5583"
print(dir(apprentissage))
print(apprentissage.apprentissage(path_sample))
def run(self):
print("RUN")
try:
warning = "" # initialise le nombre d'erreur
val = 0 # initialise le nombre d'erreur
txtInfo = ""
# import R's "base" package
base = importr('base')
with open("fonctions_apprentissage.r", "r", encoding="utf-8") as apprentissageRopen:
apprentissage = "".join(apprentissageRopen.readlines())
print(apprentissage)
apprentissage = SignatureTranslatedAnonymousPackage(apprentissage, "apprentissage")
#path_sample = "/media/sebastien/Bayer/ScriptsSEB/scripts/GUI/EBimage/AnalyseImagesV2/Samples/5583"
path_sample = "/".join(str(self.dicoFoldersCallibration["leaf"]).split("/")[:-1])
print(path_sample)
print(dir(apprentissage))
result , pathRdataFile= apprentissage.apprentissage(path_sample).r_repr().replace('"','').replace("c(","").replace(")","").split(",")
print(result, pathRdataFile)
if result == "1":
reply = QMessageBox.question(parent=self, title='Attention', text='File will be overwritten.\nDo you still want to proceed?', buttons=QMessageBox.Yes | QMessageBox.No, defaultButton=QMessageBox.No)
if reply == QMessageBox.Yes:
print("OK")
self.callibrationFileOpenLineEdit.setText(pathRdataFile)
else:
print("BAD")
##grise les boutons pour pas relancer job
#self.ui.frameRun.show()
#self.ui.runPushButton.setDisabled(True)
#self.ui.loadMatriceFilePushButton.setDisabled(True)
#self.ui.loadOrderFilePushButton.setDisabled(True)
#self.ui.PCAlineEdit.setDisabled(True)
#self.ui.DAlineEdit.setDisabled(True)
#self.ui.popMinLineEdit.setDisabled(True)
#self.ui.popMaxLineEdit.setDisabled(True)
#self.ui.rmOldCheckBox.setDisabled(True)
#self.ui.expertCheckBox.setDisabled(True)
#self.ui.expertFrame.setDisabled(True)
#self.ui.graphTypeComboBox.setDisabled(True)
#if self.expertMode == "True":
#self.EBimagefix = str(self.ui.EBimagefixPlainTextEdit.toPlainText().toUtf8())
#self.EBimagechange = str(self.ui.EBimagechangePlainTextEdit.toPlainText().toUtf8())
#"""to run programme"""
## création du pathout
#if os.path.isdir(self.pathFileOut):
#if self.rmOld == "True":
#shutil.rmtree(str(self.pathFileOut))
#os.mkdir(self.pathFileOut)
#else:
#warning += "Warnnig folder "+self.pathFileOut+" already exist,\nPlease remove/rename before run new analysis or use checkbox"
#raise Exception(warning)
#else:
#os.mkdir(self.pathFileOut)
################################################
## code commun mode graphique ou interface
################################################
## charge l'ordre a refaire
#self.orderList = loadInListCol(self.orderPathFile, 0)
## copie de la matrice dans un dico
#self.dicoMatrice = loadInDictLine(self.matricePathFile)
## Comptage du nombre d'individus, de markers et ncode:
#self.nbindParam = len(self.dicoMatrice.keys())-1
#if self.nbindParam != len(self.orderList):
#txtInfo += "WARNING: More individu in Matrice file (%s) than Order label file (%s)!!!\n" % (self.nbindParam, len(self.orderList))
#fileMat = open(self.matricePathFile,"r")
#header = fileMat.readline()
#self.nbmarkParam = len(header.split("\t"))
#header = " \t"+"\t".join(header.split("\t")[1:])
#nbcode = fileMat.readline().split("\t")[1]
#while nbcode == "-9":
#nbcode = fileMat.readline().split("\t")[1]
#self.ncodeParam = len(nbcode)
#fileMat.close()
## ouverture du nouveau fichier trier
#with open(self.pathFileOut+self.basename+"_Reorder.tab","w") as reorderMatriceFile:
#reorderMatriceFile.write(header)
#for ind in self.orderList:
#if ind not in self.dicoMatrice.keys():
#error = "ERROR: The individu %s define in label file was not in the matrice file !!! Exit programme" % ind
#raise Exception(error)
#line = self.dicoMatrice[ind].split("\t")[0]+"\t"+"\t".join(self.dicoMatrice[ind].split("\t")[1:]).replace("999","-9")
#reorderMatriceFile.write(line)
#txtInfo += "Nb individus: %i\tNb markers: %i\tncodeParam: %i\tGraph type: %s\n" % (self.nbindParam,int(self.nbmarkParam)-1,self.ncodeParam, self.graphType)
#if args.cmdMode:
#pass
#else:
#self.ui.runningPlainTextEdit.setPlainText(txtInfo)
##ouverture du script R
#Rscript = open(self.pathFileOut+self.basename+"_R_EBimage.R","w")
#Rscript.write(installPackageR)
## Ajout du path du fichier matrice dans EBimagefix
## modifie Script R pour adapter aux parametres rentrés
#dictToReplace = {
#"**MAKERS**" : str(self.nbmarkParam),
#"**NCODE**" : str(self.ncodeParam),
#"**INDIV**" : str(self.nbindParam),
#"**PATHTOFILE**": str(reorderMatriceFile.name),
#"**current_dir**" : str(self.pathFileOut),
#"**GRAPH**" : str(self.graphType)
#}
#EBimagefixModif = replace_all(dictToReplace, self.EBimagefix)
##print(EBimagefixModif)
#Rscript.write(EBimagefixModif)
#for pop in range(int(self.popMinValue),int(self.popMaxValue)+1):
##print(pop)
#popstr=str(pop)
#EBimagechange2 = self.EBimagechange.replace("**pop**",popstr).replace("**current_dir**",str(self.pathFileOut)).replace("**PCARETAIN**",str(self.PCAvalue)).replace("**DARETAIN**",str(self.DAvalue))
##print(EBimagechange2)
#Rscript.write(EBimagechange2)
#Rscript.close()
#self.ui.statusbar.showMessage(str("FINISH, script product on : %s" % self.pathFileOut),9600)
#txtInfo += "FINISH, script product on :\n %s" % (self.pathFileOut)
#if args.cmdMode:
#print(txtInfo)
#else:
#self.ui.runningPlainTextEdit.setPlainText(txtInfo)
## si des erreurs:
except Exception as e:
self.displayError(error = e)
def run(self):
print("RUN")
try:
warning = "" # initialise le nombre d'erreur
val = 0 # initialise le nombre d'erreur
txtInfo = ""
# import R's "base" package
base = importr('base')
with open("fonctions_apprentissage.r", "r",
encoding="utf-8") as apprentissageRopen:
apprentissage = "".join(apprentissageRopen.readlines())
print(apprentissage)
apprentissage = SignatureTranslatedAnonymousPackage(
apprentissage, "apprentissage")
#path_sample = "/media/sebastien/Bayer/ScriptsSEB/scripts/GUI/EBimage/AnalyseImagesV2/Samples/5583"
path_sample = "/".join(
str(self.dicoFoldersCallibration["leaf"]).split("/")[:-1])
print(path_sample)
print(dir(apprentissage))
result, pathRdataFile = apprentissage.apprentissage(
path_sample).r_repr().replace('"',
'').replace("c(", "").replace(
")", "").split(",")
print(result, pathRdataFile)
if result == "1":
reply = QMessageBox.question(
parent=self,
title='Attention',
text=
'File will be overwritten.\nDo you still want to proceed?',
buttons=QMessageBox.Yes | QMessageBox.No,
defaultButton=QMessageBox.No)
if reply == QMessageBox.Yes:
print("OK")
self.callibrationFileOpenLineEdit.setText(pathRdataFile)
else:
print("BAD")
##grise les boutons pour pas relancer job
#self.ui.frameRun.show()
#self.ui.runPushButton.setDisabled(True)
#self.ui.loadMatriceFilePushButton.setDisabled(True)
#self.ui.loadOrderFilePushButton.setDisabled(True)
#self.ui.PCAlineEdit.setDisabled(True)
#self.ui.DAlineEdit.setDisabled(True)
#self.ui.popMinLineEdit.setDisabled(True)
#self.ui.popMaxLineEdit.setDisabled(True)
#self.ui.rmOldCheckBox.setDisabled(True)
#self.ui.expertCheckBox.setDisabled(True)
#self.ui.expertFrame.setDisabled(True)
#self.ui.graphTypeComboBox.setDisabled(True)
#if self.expertMode == "True":
#self.EBimagefix = str(self.ui.EBimagefixPlainTextEdit.toPlainText().toUtf8())
#self.EBimagechange = str(self.ui.EBimagechangePlainTextEdit.toPlainText().toUtf8())
#"""to run programme"""
## création du pathout
#if os.path.isdir(self.pathFileOut):
#if self.rmOld == "True":
#shutil.rmtree(str(self.pathFileOut))
#os.mkdir(self.pathFileOut)
#else:
#warning += "Warnnig folder "+self.pathFileOut+" already exist,\nPlease remove/rename before run new analysis or use checkbox"
#raise Exception(warning)
#else:
#os.mkdir(self.pathFileOut)
################################################
## code commun mode graphique ou interface
################################################
## charge l'ordre a refaire
#self.orderList = loadInListCol(self.orderPathFile, 0)
## copie de la matrice dans un dico
#self.dicoMatrice = loadInDictLine(self.matricePathFile)
## Comptage du nombre d'individus, de markers et ncode:
#self.nbindParam = len(self.dicoMatrice.keys())-1
#if self.nbindParam != len(self.orderList):
#txtInfo += "WARNING: More individu in Matrice file (%s) than Order label file (%s)!!!\n" % (self.nbindParam, len(self.orderList))
#fileMat = open(self.matricePathFile,"r")
#header = fileMat.readline()
#self.nbmarkParam = len(header.split("\t"))
#header = " \t"+"\t".join(header.split("\t")[1:])
#nbcode = fileMat.readline().split("\t")[1]
#while nbcode == "-9":
#nbcode = fileMat.readline().split("\t")[1]
#self.ncodeParam = len(nbcode)
#fileMat.close()
## ouverture du nouveau fichier trier
#with open(self.pathFileOut+self.basename+"_Reorder.tab","w") as reorderMatriceFile:
#reorderMatriceFile.write(header)
#for ind in self.orderList:
#if ind not in self.dicoMatrice.keys():
#error = "ERROR: The individu %s define in label file was not in the matrice file !!! Exit programme" % ind
#raise Exception(error)
#line = self.dicoMatrice[ind].split("\t")[0]+"\t"+"\t".join(self.dicoMatrice[ind].split("\t")[1:]).replace("999","-9")
#reorderMatriceFile.write(line)
#txtInfo += "Nb individus: %i\tNb markers: %i\tncodeParam: %i\tGraph type: %s\n" % (self.nbindParam,int(self.nbmarkParam)-1,self.ncodeParam, self.graphType)
#if args.cmdMode:
#pass
#else:
#self.ui.runningPlainTextEdit.setPlainText(txtInfo)
##ouverture du script R
#Rscript = open(self.pathFileOut+self.basename+"_R_EBimage.R","w")
#Rscript.write(installPackageR)
## Ajout du path du fichier matrice dans EBimagefix
## modifie Script R pour adapter aux parametres rentrés
#dictToReplace = {
#"**MAKERS**" : str(self.nbmarkParam),
#"**NCODE**" : str(self.ncodeParam),
#"**INDIV**" : str(self.nbindParam),
#"**PATHTOFILE**": str(reorderMatriceFile.name),
#"**current_dir**" : str(self.pathFileOut),
#"**GRAPH**" : str(self.graphType)
#}
#EBimagefixModif = replace_all(dictToReplace, self.EBimagefix)
##print(EBimagefixModif)
#Rscript.write(EBimagefixModif)
#for pop in range(int(self.popMinValue),int(self.popMaxValue)+1):
##print(pop)
#popstr=str(pop)
#EBimagechange2 = self.EBimagechange.replace("**pop**",popstr).replace("**current_dir**",str(self.pathFileOut)).replace("**PCARETAIN**",str(self.PCAvalue)).replace("**DARETAIN**",str(self.DAvalue))
##print(EBimagechange2)
#Rscript.write(EBimagechange2)
#Rscript.close()
#self.ui.statusbar.showMessage(str("FINISH, script product on : %s" % self.pathFileOut),9600)
#txtInfo += "FINISH, script product on :\n %s" % (self.pathFileOut)
#if args.cmdMode:
#print(txtInfo)
#else:
#self.ui.runningPlainTextEdit.setPlainText(txtInfo)
## si des erreurs:
except Exception as e:
self.displayError(error=e)
