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 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 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
