def checkBeforeOpeningParametersDialog(self):
if SextanteUtils.isWindows():
path = RUtils.RFolder()
if path == "":
return "R folder is not configured.\nPlease configure it before running R scripts."
R_INSTALLED = "R_INSTALLED"
settings = QSettings()
if settings.contains(R_INSTALLED):
return
if SextanteUtils.isWindows():
if SextanteConfig.getSetting(RUtils.R_USE64):
execDir = "x64"
else:
execDir = "i386"
command = [
RUtils.RFolder() + os.sep + "bin" + os.sep + execDir + os.sep +
"R.exe --version"
]
else:
command = ["R --version"]
proc = subprocess.Popen(command,
shell=True,
stdout=subprocess.PIPE,
stdin=subprocess.PIPE,
stderr=subprocess.STDOUT,
universal_newlines=True).stdout
for line in iter(proc.readline, ""):
if "R version" in line:
settings.setValue(R_INSTALLED, True)
return
return "It seems that R is not correctly installed in your system.\nPlease install it before running R Scripts."
def initializeSettings(self):
AlgorithmProvider.initializeSettings(self)
SextanteConfig.addSetting(
Setting(self.getDescription(), RUtils.RSCRIPTS_FOLDER,
"R Scripts folder", RUtils.RScriptsFolder()))
if SextanteUtils.isWindows():
SextanteConfig.addSetting(
Setting(self.getDescription(), RUtils.R_FOLDER, "R folder",
RUtils.RFolder()))
def _loadAlgorithms(self):
folder = RUtils.RScriptsFolder()
for descriptionFile in os.listdir(folder):
if descriptionFile.endswith("rsx"):
try:
fullpath = os.path.join(RUtils.RScriptsFolder(), descriptionFile)
alg = RAlgorithm(fullpath)
if alg.name.strip() != "":
self.algs.append(alg)
except WrongScriptException,e:
SextanteLog.addToLog(SextanteLog.LOG_ERROR,e.msg)
except Exception, e:
SextanteLog.addToLog(SextanteLog.LOG_ERROR,"Could not load R script:" + descriptionFile)
def checkBeforeOpeningParametersDialog(self):
msg = RUtils.checkRIsInstalled()
if msg is not None:
html = ("<p>This algorithm requires R to be run."
"Unfortunately, it seems that R is not installed in your system, or it is not correctly configured to be used from QGIS</p>")
html += '<p><a href= "http://docs.qgis.org/2.0/html/en/docs/user_manual/sextante/3rdParty.html">Click here</a> to know more about how to install and configure R to be used with SEXTANTE</p>'
return html
def saveAlgorithm(self):
if self.filename is None:
self.filename = str(
QtGui.QFileDialog.getSaveFileName(self, "Save Script",
RUtils.RScriptsFolder(),
"SEXTANTE R script (*.rsx)"))
if self.filename:
if not self.filename.endswith(".rsx"):
self.filename += ".rsx"
text = str(self.text.toPlainText())
if self.alg is not None:
self.alg.script = text
try:
fout = open(self.filename, "w")
fout.write(text)
fout.close()
except IOError:
QMessageBox.warning(
self, self.tr("I/O error"),
self.tr("Unable to save edits. Reason:\n %1").arg(
unicode(sys.exc_info()[1])))
return
self.update = True
#if help strings were defined before saving the model for the first time, we do it here
if self.help:
f = open(self.filename + ".help", "wb")
pickle.dump(self.help, f)
f.close()
self.help = None
QtGui.QMessageBox.information(self, "Script saving",
"Script was correctly saved.")
else:
self.filename = None
def getPostProcessingErrorMessage(self, wrongLayers):
html = GeoAlgorithm.getPostProcessingErrorMessage(self, wrongLayers)
msg = RUtils.checkRIsInstalled(True)
html += ("<p>This algorithm requires R to be run. A test to check if R is correctly installed "
"and configured in your system has been performed, with the following result:</p><ul><i>")
if msg is None:
html += "GRASS seems to be correctly installed and configured</i></li></ul>"
html += "<p>The script you have executed needs the following packages:</p><ul>"
packages = RUtils.getRequiredPackages(self.script)
for p in packages:
html += '<li>' + p + '</li>'
html += "</ul><p>Make sure they are installed in your R environment before trying to execute this script.</p>"
else:
html += msg + "</i></li></ul>"
html += '<p><a href= "http://docs.qgis.org/2.0/html/en/docs/user_manual/sextante/3rdParty.html">Click here</a> to know more about how to install and configure R to be used with SEXTANTE</p>'
return html
def checkBeforeOpeningParametersDialog(self):
msg = RUtils.checkRIsInstalled()
if msg is not None:
html = (
"<p>This algorithm requires R to be run."
"Unfortunately, it seems that R is not installed in your system, or it is not correctly configured to be used from QGIS</p>"
)
html += '<p><a href= "http://docs.qgis.org/2.0/html/en/docs/user_manual/sextante/3rdParty.html">Click here</a> to know more about how to install and configure R to be used with SEXTANTE</p>'
return html
def getPostProcessingErrorMessage(self, wrongLayers):
html = GeoAlgorithm.getPostProcessingErrorMessage(self, wrongLayers)
msg = RUtils.checkRIsInstalled(True)
html += (
"<p>This algorithm requires R to be run. A test to check if R is correctly installed "
"and configured in your system has been performed, with the following result:</p><ul><i>"
)
if msg is None:
html += "GRASS seems to be correctly installed and configured</i></li></ul>"
html += "<p>The script you have executed needs the following packages:</p><ul>"
packages = RUtils.getRequiredPackages(self.script)
for p in packages:
html += '<li>' + p + '</li>'
html += "</ul><p>Make sure they are installed in your R environment before trying to execute this script.</p>"
else:
html += msg + "</i></li></ul>"
html += '<p><a href= "http://docs.qgis.org/2.0/html/en/docs/user_manual/sextante/3rdParty.html">Click here</a> to know more about how to install and configure R to be used with SEXTANTE</p>'
return html
def processAlgorithm(self, progress):
if SextanteUtils.isWindows():
path = RUtils.RFolder()
if path == "":
raise GeoAlgorithmExecutionException("R folder is not configured.\nPlease configure it before running R scripts.")
loglines = []
loglines.append("R execution commands")
loglines += self.getFullSetOfRCommands()
for line in loglines:
progress.setCommand(line)
SextanteLog.addToLog(SextanteLog.LOG_INFO, loglines)
RUtils.executeRAlgorithm(self, progress)
if self.showPlots:
htmlfilename = self.getOutputValue(RAlgorithm.RPLOTS)
f = open(htmlfilename, "w")
f.write("<img src=\"" + self.plotsFilename + "\"/>")
f.close()
if self.showConsoleOutput:
htmlfilename = self.getOutputValue(RAlgorithm.R_CONSOLE_OUTPUT)
f = open(htmlfilename, "w")
f.write(RUtils.getConsoleOutput())
f.close()
def processAlgorithm(self, progress):
if SextanteUtils.isWindows():
path = RUtils.RFolder()
if path == "":
raise GeoAlgorithmExecutionException(
"R folder is not configured.\nPlease configure it before running R scripts."
)
loglines = []
loglines.append("R execution commands")
loglines += self.getFullSetOfRCommands()
for line in loglines:
progress.setCommand(line)
SextanteLog.addToLog(SextanteLog.LOG_INFO, loglines)
RUtils.executeRAlgorithm(self, progress)
if self.showPlots:
htmlfilename = self.getOutputValue(RAlgorithm.RPLOTS)
f = open(htmlfilename, "w")
f.write("<img src=\"" + self.plotsFilename + "\"/>")
f.close()
if self.showConsoleOutput:
htmlfilename = self.getOutputValue(RAlgorithm.R_CONSOLE_OUTPUT)
f = open(htmlfilename, "w")
f.write(RUtils.getConsoleOutput())
f.close()
def saveAlgorithm(self):
if self.filename is None:
self.filename = QtGui.QFileDialog.getSaveFileName(
self, "Save Script", RUtils.RScriptsFolder(),
"SEXTANTE R script (*.rsx)")
if self.filename:
text = str(self.text.toPlainText())
if self.alg is not None:
self.alg.script = text
fout = open(self.filename, "w")
fout.write(text)
fout.close()
self.update = True
#if help strings were defined before saving the model for the first time, we do it here
if self.help:
f = open(self.filename + ".help", "wb")
pickle.dump(self.help, f)
f.close()
self.help = None
QtGui.QMessageBox.information(self, "Script saving",
"Script was correctly saved.")
else:
self.filename = None
def _loadAlgorithms(self):
folder = RUtils.RScriptsFolder()
self.loadFromFolder(folder)
folder = os.path.join(os.path.dirname(__file__), "scripts")
self.loadFromFolder(folder)
def getImportCommands(self):
commands = []
# just use main mirror
commands.append('options("repos"="http://cran.at.r-project.org/")')
# try to install packages if needed
packages = RUtils.getRequiredPackages(self.script)
packages.extend(['rgdal', 'raster'])
for p in packages:
commands.append(
'tryCatch(find.package("' + p +
'"), error=function(e) install.packages("' + p +'", dependencies=TRUE))')
commands.append('library("raster")')
commands.append('library("rgdal")')
for param in self.parameters:
if isinstance(param, ParameterRaster):
value = param.value
value = value.replace("\\", "/")
if self.passFileNames:
commands.append(param.name + " = \"" + value + "\"")
elif self.useRasterPackage:
commands.append(param.name + " = " + "brick(\"" + value + "\")")
else:
commands.append(param.name + " = " + "readGDAL(\"" + value + "\")")
if isinstance(param, ParameterVector):
value = param.getSafeExportedLayer()
value = value.replace("\\", "/")
filename = os.path.basename(value)
filename = filename[:-4]
folder = os.path.dirname(value)
if self.passFileNames:
commands.append(param.name + " = \"" + value + "\"")
else:
commands.append(param.name + " = readOGR(\"" + folder + "\",layer=\"" + filename + "\")")
if isinstance(param, ParameterTable):
value = param.value
if not value.lower().endswith("csv"):
raise GeoAlgorithmExecutionException("Unsupported input file format.\n" + value)
if self.passFileNames:
commands.append(param.name + " = \"" + value + "\"")
else:
commands.append(param.name + " <- read.csv(\"" + value + "\", head=TRUE, sep=\",\")")
elif isinstance(param, (ParameterTableField, ParameterString, ParameterFile)):
commands.append(param.name + "=\"" + param.value + "\"")
elif isinstance(param, (ParameterNumber, ParameterSelection)):
commands.append(param.name + "=" + str(param.value))
elif isinstance(param, ParameterBoolean):
if param.value:
commands.append(param.name + "=TRUE")
else:
commands.append(param.name + "=FALSE")
elif isinstance(param, ParameterMultipleInput):
iLayer = 0;
if param.datatype == ParameterMultipleInput.TYPE_RASTER:
layers = param.value.split(";")
for layer in layers:
#if not layer.lower().endswith("asc") and not layer.lower().endswith("tif") and not self.passFileNames:
#raise GeoAlgorithmExecutionException("Unsupported input file format.\n" + layer)
layer = layer.replace("\\", "/")
if self.passFileNames:
commands.append("tempvar" + str(iLayer)+ " <- \"" + layer + "\"")
elif self.useRasterPackage:
commands.append("tempvar" + str(iLayer)+ " <- " + "brick(\"" + layer + "\")")
else:
commands.append("tempvar" + str(iLayer)+ " <- " + "readGDAL(\"" + layer + "\")")
iLayer+=1
else:
exported = param.getSafeExportedLayers()
layers = exported.split(";")
for layer in layers:
if not layer.lower().endswith("shp") and not self.passFileNames:
raise GeoAlgorithmExecutionException("Unsupported input file format.\n" + layer)
layer = layer.replace("\\", "/")
filename = os.path.basename(layer)
filename = filename[:-4]
if self.passFileNames:
commands.append("tempvar" + str(iLayer)+ " <- \"" + layer + "\"")
else:
commands.append("tempvar" + str(iLayer) + " <- " + "readOGR(\"" + layer + "\",layer=\"" + filename + "\")")
iLayer+=1
s = ""
s += param.name
s += (" = c(")
iLayer = 0
for layer in layers:
if iLayer != 0:
s +=","
s += "tempvar" + str(iLayer)
iLayer += 1
s+=")\n"
commands.append(s)
if self.showPlots:
htmlfilename = self.getOutputValue(RAlgorithm.RPLOTS)
self.plotsFilename = htmlfilename +".png"
self.plotsFilename = self.plotsFilename.replace("\\", "/");
commands.append("png(\"" + self.plotsFilename + "\")");
return commands
def getImportCommands(self):
commands = []
# just use main mirror
commands.append('options("repos"="http://cran.at.r-project.org/")')
# try to install packages if needed
packages = RUtils.getRequiredPackages(self.script)
packages.extend(['rgdal', 'raster'])
for p in packages:
commands.append('tryCatch(find.package("' + p +
'"), error=function(e) install.packages("' + p +
'", dependencies=TRUE))')
commands.append('library("raster")')
commands.append('library("rgdal")')
for param in self.parameters:
if isinstance(param, ParameterRaster):
value = param.value
value = value.replace("\\", "/")
if self.passFileNames:
commands.append(param.name + " = \"" + value + "\"")
elif self.useRasterPackage:
commands.append(param.name + " = " + "brick(\"" + value +
"\")")
else:
commands.append(param.name + " = " + "readGDAL(\"" +
value + "\")")
if isinstance(param, ParameterVector):
value = param.getSafeExportedLayer()
value = value.replace("\\", "/")
filename = os.path.basename(value)
filename = filename[:-4]
folder = os.path.dirname(value)
if self.passFileNames:
commands.append(param.name + " = \"" + value + "\"")
else:
commands.append(param.name + " = readOGR(\"" + folder +
"\",layer=\"" + filename + "\")")
if isinstance(param, ParameterTable):
value = param.value
if not value.lower().endswith("csv"):
raise GeoAlgorithmExecutionException(
"Unsupported input file format.\n" + value)
if self.passFileNames:
commands.append(param.name + " = \"" + value + "\"")
else:
commands.append(param.name + " <- read.csv(\"" + value +
"\", head=TRUE, sep=\",\")")
elif isinstance(
param,
(ParameterTableField, ParameterString, ParameterFile)):
commands.append(param.name + "=\"" + param.value + "\"")
elif isinstance(param, (ParameterNumber, ParameterSelection)):
commands.append(param.name + "=" + str(param.value))
elif isinstance(param, ParameterBoolean):
if param.value:
commands.append(param.name + "=TRUE")
else:
commands.append(param.name + "=FALSE")
elif isinstance(param, ParameterMultipleInput):
iLayer = 0
if param.datatype == ParameterMultipleInput.TYPE_RASTER:
layers = param.value.split(";")
for layer in layers:
#if not layer.lower().endswith("asc") and not layer.lower().endswith("tif") and not self.passFileNames:
#raise GeoAlgorithmExecutionException("Unsupported input file format.\n" + layer)
layer = layer.replace("\\", "/")
if self.passFileNames:
commands.append("tempvar" + str(iLayer) +
" <- \"" + layer + "\"")
elif self.useRasterPackage:
commands.append("tempvar" + str(iLayer) + " <- " +
"brick(\"" + layer + "\")")
else:
commands.append("tempvar" + str(iLayer) + " <- " +
"readGDAL(\"" + layer + "\")")
iLayer += 1
else:
exported = param.getSafeExportedLayers()
layers = exported.split(";")
for layer in layers:
if not layer.lower().endswith(
"shp") and not self.passFileNames:
raise GeoAlgorithmExecutionException(
"Unsupported input file format.\n" + layer)
layer = layer.replace("\\", "/")
filename = os.path.basename(layer)
filename = filename[:-4]
if self.passFileNames:
commands.append("tempvar" + str(iLayer) +
" <- \"" + layer + "\"")
else:
commands.append("tempvar" + str(iLayer) + " <- " +
"readOGR(\"" + layer +
"\",layer=\"" + filename + "\")")
iLayer += 1
s = ""
s += param.name
s += (" = c(")
iLayer = 0
for layer in layers:
if iLayer != 0:
s += ","
s += "tempvar" + str(iLayer)
iLayer += 1
s += ")\n"
commands.append(s)
if self.showPlots:
htmlfilename = self.getOutputValue(RAlgorithm.RPLOTS)
self.plotsFilename = htmlfilename + ".png"
self.plotsFilename = self.plotsFilename.replace("\\", "/")
commands.append("png(\"" + self.plotsFilename + "\")")
return commands
