# -*- 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.SextanteConfig import SextanteConfig
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.name = "[Unnamed algorithm]"
self.group = "User R scripts"
self.parseDescription(iter(lines))
def defineCharacteristicsFromFile(self):
filename = os.path.basename(self.descriptionFile)
self.name = filename[:filename.rfind(".")].replace("_", " ")
self.group = "User R scripts"
with open(self.descriptionFile, 'r') as f:
lines = [line.strip() for line in f]
self.parseDescription(iter(lines))
def parseDescription(self, lines):
self.script = ""
self.commands=[]
self.showPlots = False
self.showConsoleOutput = False
self.useRasterPackage = True
self.passFileNames = False
self.verboseCommands = []
ender = 0
line = lines.next().strip("\n").strip("\r")
while ender < 10:
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:
if line == '':
ender += 1
else:
ender=0
self.commands.append(line)
self.script += line + "\n"
try:
line = lines.next().strip("\n").strip("\r")
except:
break
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
if line.lower().strip().startswith("dontuserasterpackage"):
self.useRasterPackage = False
return
if line.lower().strip().startswith("passfilenames"):
self.passFileNames = True
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().startswith("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().startswith("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
value = value.replace("\\", "/")
if self.useRasterPackage or self.passFileNames:
commands.append("writeRaster(" + out.name + ",\"" + value + "\", overwrite=TRUE)")
else:
if not value.endswith("tif"):
value = value + ".tif"
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 = []
# 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 getRCommands(self):
return self.commands
def helpFile(self):
helpfile = unicode(self.descriptionFile) + ".help"
if os.path.exists(helpfile):
h2h = Help2Html()
return h2h.getHtmlFile(self, helpfile)
else:
return None
def checkBeforeOpeningParametersDialog(self):
msg = RUtils.checkRIsInstalled()
if msg is not None:
html = ("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
")
html += 'Click here to know more about how to install and configure R to be used with SEXTANTE
'
return html
def getPostProcessingErrorMessage(self, wrongLayers):
html = GeoAlgorithm.getPostProcessingErrorMessage(self, wrongLayers)
msg = RUtils.checkRIsInstalled(True)
html += ("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:
")
if msg is None:
html += "GRASS seems to be correctly installed and configured
"
html += "The script you have executed needs the following packages:
"
packages = RUtils.getRequiredPackages(self.script)
for p in packages:
html += '- ' + p + '
'
html += "
Make sure they are installed in your R environment before trying to execute this script.
"
else:
html += msg + ""
html += 'Click here to know more about how to install and configure R to be used with SEXTANTE
'
return html