# -*- coding: utf-8 -*- """ *************************************************************************** RAlgorithm.py --------------------- Date : August 2012 Copyright : (C) 2012 by Victor Olaya Email : volayaf at gmail dot com *************************************************************************** * * * This program is free software; you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation; either version 2 of the License, or * * (at your option) any later version. * * * *************************************************************************** """ __author__ = 'Victor Olaya' __date__ = 'August 2012' __copyright__ = '(C) 2012, Victor Olaya' # This will get replaced with a git SHA1 when you do a git archive __revision__ = '$Format:%H$' import os from PyQt4.QtCore import * from PyQt4.QtGui import * from PyQt4 import QtGui, QtCore from sextante.core.GeoAlgorithm import GeoAlgorithm from sextante.parameters.ParameterRaster import ParameterRaster from sextante.parameters.ParameterTable import ParameterTable from sextante.parameters.ParameterVector import ParameterVector from sextante.parameters.ParameterMultipleInput import ParameterMultipleInput from sextante.script.WrongScriptException import WrongScriptException from sextante.outputs.OutputTable import OutputTable from sextante.outputs.OutputVector import OutputVector from sextante.outputs.OutputRaster import OutputRaster from sextante.parameters.ParameterString import ParameterString from sextante.parameters.ParameterNumber import ParameterNumber from sextante.parameters.ParameterBoolean import ParameterBoolean from sextante.parameters.ParameterSelection import ParameterSelection from sextante.parameters.ParameterTableField import ParameterTableField from sextante.outputs.OutputHTML import OutputHTML from sextante.r.RUtils import RUtils from sextante.core.GeoAlgorithmExecutionException import GeoAlgorithmExecutionException from sextante.core.SextanteLog import SextanteLog from sextante.core.SextanteUtils import SextanteUtils import subprocess from sextante.parameters.ParameterExtent import ParameterExtent from sextante.parameters.ParameterFile import ParameterFile from sextante.outputs.OutputFile import OutputFile from sextante.gui.Help2Html import Help2Html class RAlgorithm(GeoAlgorithm): R_CONSOLE_OUTPUT = "R_CONSOLE_OUTPUT" RPLOTS = "RPLOTS" def getCopy(self): newone = RAlgorithm(self.descriptionFile) newone.provider = self.provider return newone def __init__(self, descriptionFile, script=None): GeoAlgorithm.__init__(self) self.script = script self.descriptionFile = descriptionFile if script is not None: self.defineCharacteristicsFromScript() if descriptionFile is not None: self.defineCharacteristicsFromFile() def getIcon(self): return QtGui.QIcon(os.path.dirname(__file__) + "/../images/r.png") def defineCharacteristicsFromScript(self): lines = self.script.split("\n") self.silentOutputs = [] self.name = "[Unnamed algorithm]" self.group = "User R scripts" for line in lines: if line.startswith("##"): try: self.processParameterLine(line.strip("\n")) except: pass def defineCharacteristicsFromFile(self): self.script = "" self.commands=[] self.showPlots = False self.showConsoleOutput = False self.verboseCommands = [] filename = os.path.basename(self.descriptionFile) self.name = filename[:filename.rfind(".")].replace("_", " ") self.group = "User R scripts" lines = open(self.descriptionFile) line = lines.readline().strip("\n").strip("\r") while line != "": if line.startswith("##"): try: self.processParameterLine(line) except Exception: raise WrongScriptException("Could not load R script:" + self.descriptionFile + ".\n Problem with line \"" + line + "\"") elif line.startswith(">"): self.commands.append(line[1:]) self.verboseCommands.append(line[1:]) if not self.showConsoleOutput: self.addOutput(OutputHTML(RAlgorithm.R_CONSOLE_OUTPUT, "R Console Output")) self.showConsoleOutput = True else: self.commands.append(line) self.script += line + "\n" line = lines.readline().strip("\n").strip("\r") lines.close() def getVerboseCommands(self): return self.verboseCommands def createDescriptiveName(self, s): return s.replace("_", " ") def processParameterLine(self,line): param = None out = None line = line.replace("#", ""); if line.lower().strip().startswith("showplots"): self.showPlots = True self.addOutput(OutputHTML(RAlgorithm.RPLOTS, "R Plots")); return tokens = line.split("="); desc = self.createDescriptiveName(tokens[0]) if tokens[1].lower().strip() == "group": self.group = tokens[0] return if tokens[1].lower().strip() == "raster": param = ParameterRaster(tokens[0], desc, False) elif tokens[1].lower().strip() == "vector": param = ParameterVector(tokens[0], desc,ParameterVector.VECTOR_TYPE_ANY) elif tokens[1].lower().strip() == "table": param = ParameterTable(tokens[0], desc, False) elif tokens[1].lower().strip() == "multiple raster": param = ParameterMultipleInput(tokens[0], desc, ParameterMultipleInput.TYPE_RASTER) param.optional = False elif tokens[1].lower().strip() == "multiple vector": param = ParameterMultipleInput(tokens[0], desc, ParameterMultipleInput.TYPE_VECTOR_ANY) param.optional = False elif tokens[1].lower().strip().startswith("selection"): options = tokens[1].strip()[len("selection"):].split(";") param = ParameterSelection(tokens[0], desc, options); elif tokens[1].lower().strip().startswith("boolean"): default = tokens[1].strip()[len("boolean")+1:] param = ParameterBoolean(tokens[0], desc, default) elif tokens[1].lower().strip().startswith("number"): try: default = float(tokens[1].strip()[len("number")+1:]) param = ParameterNumber(tokens[0], desc, default=default) except: raise WrongScriptException("Could not load R script:" + self.descriptionFile + ".\n Problem with line \"" + line + "\"") elif tokens[1].lower().strip().startswith("field"): field = tokens[1].strip()[len("field")+1:] found = False for p in self.parameters: if p.name == field: found = True break if found: param = ParameterTableField(tokens[0], tokens[0], field) elif tokens[1].lower().strip() == "extent": param = ParameterExtent(tokens[0], desc) elif tokens[1].lower().strip() == "file": param = ParameterFile(tokens[0], desc, False) elif tokens[1].lower().strip() == "folder": param = ParameterFile(tokens[0], desc, True) elif tokens[1].lower().strip().startswith("string"): default = tokens[1].strip()[len("string")+1:] param = ParameterString(tokens[0], desc, default) elif tokens[1].lower().strip().startswith("output raster"): out = OutputRaster() elif tokens[1].lower().strip().startswith("output vector"): out = OutputVector() elif tokens[1].lower().strip().startswith("output table"): out = OutputTable() elif tokens[1].lower().strip().startswith("output file"): out = OutputFile() if param != None: self.addParameter(param) elif out != None: out.name = tokens[0] out.description = tokens[0] self.addOutput(out) else: raise WrongScriptException("Could not load R script:" + self.descriptionFile + ".\n Problem with line \"" + line + "\"") 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("") f.close() if self.showConsoleOutput: htmlfilename = self.getOutputValue(RAlgorithm.R_CONSOLE_OUTPUT) f = open(htmlfilename, "w") f.write(RUtils.getConsoleOutput()) f.close() def getFullSetOfRCommands(self): commands = [] commands += self.getImportCommands() commands += self.getRCommands() commands += self.getExportCommands() return commands def getExportCommands(self): commands = [] for out in self.outputs: if isinstance(out, OutputRaster): value = out.value if not value.endswith("tif"): value = value + ".tif" value = value.replace("\\", "/") commands.append("writeGDAL(" + out.name + ",\"" + value + "\")") if isinstance(out, OutputVector): value = out.value if not value.endswith("shp"): value = value + ".shp" value = value.replace("\\", "/") filename = os.path.basename(value) filename = filename[:-4] commands.append("writeOGR(" + out.name + ",\"" + value + "\",\"" + filename + "\", driver=\"ESRI Shapefile\")"); if self.showPlots: commands.append("dev.off()"); return commands def getImportCommands(self): commands = [] # if rgdal is not available, try to install it # just use US mirror commands.append('options("repos"="http://cran.us.r-project.org")') rLibDir = "%s/rlibs" % SextanteUtils.userFolder().replace("\\","/") if not os.path.isdir(rLibDir): os.mkdir(rLibDir) commands.append( 'tryCatch(find.package("rgdal"), error=function(e) install.packages("rgdal", lib="%s"))' % rLibDir) commands.append("library(\"rgdal\")"); for param in self.parameters: if isinstance(param, ParameterRaster): value = param.value value = value.replace("\\", "/") 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) 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) commands.append(param.name + " <- read.csv(\"" + value + "\", head=TRUE, sep=\",\")") if isinstance(param, (ParameterTableField, ParameterString)): commands.append(param.name + "=\"" + param.value + "\"") if isinstance(param, (ParameterNumber, ParameterSelection)): commands.append(param.name + "=" + str(param.value)) if isinstance(param, ParameterBoolean): if param.value: commands.append(param.name + "=TRUE") else: commands.append(param.name + "=FALSE") if 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"): raise GeoAlgorithmExecutionException("Unsupported input file format.\n" + layer) layer = layer.replace("\\", "/") 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"): raise GeoAlgorithmExecutionException("Unsupported input file format.\n" + layer) layer = layer.replace("\\", "/") filename = os.path.basename(layer) filename = filename[:-4] 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 getRCommands(self): return self.commands def helpFile(self): helpfile = self.descriptionFile + ".help" if os.path.exists(helpfile): h2h = Help2Html() return h2h.getHtmlFile(self, helpfile) else: return None def checkBeforeOpeningParametersDialog(self): if SextanteUtils.isWindows(): path = RUtils.RFolder() if path == "": return "R folder is not configured.\nPlease configure it before running R scripts." else: R_INSTALLED = "R_INSTALLED" settings = QSettings() if settings.contains(R_INSTALLED): return 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."