def initializeSettings(self):
     AlgorithmProvider.initializeSettings(self)
     if SextanteUtils.isWindows() or SextanteUtils.isMac():
         SextanteConfig.addSetting(Setting(self.getDescription(), GrassUtils.GRASS_FOLDER, "GRASS folder", GrassUtils.grassPath()))
         SextanteConfig.addSetting(Setting(self.getDescription(), GrassUtils.GRASS_WIN_SHELL, "Msys folder", GrassUtils.grassWinShell()))
     SextanteConfig.addSetting(Setting(self.getDescription(), GrassUtils.GRASS_LOG_COMMANDS, "Log execution commands", False))
     SextanteConfig.addSetting(Setting(self.getDescription(), GrassUtils.GRASS_LOG_CONSOLE, "Log console output", False))

 def unload(self):
     AlgorithmProvider.unload(self)
     if SextanteUtils.isWindows() or SextanteUtils.isMac():
         SextanteConfig.removeSetting(GrassUtils.GRASS_FOLDER)
         SextanteConfig.removeSetting(GrassUtils.GRASS_WIN_SHELL)
     SextanteConfig.removeSetting(GrassUtils.GRASS_LOG_COMMANDS)
     SextanteConfig.removeSetting(GrassUtils.GRASS_LOG_CONSOLE)

 def executeGrass(commands, progress):
     if SextanteUtils.isWindows():
         GrassUtils.createGrassScript(commands)
         command = ["cmd.exe", "/C ", GrassUtils.grassScriptFilename()]
     else:
         gisrc =  SextanteUtils.userFolder() + os.sep + "sextante.gisrc"
         os.putenv("GISRC", gisrc)
         os.putenv("GRASS_MESSAGE_FORMAT", "gui")
         os.putenv("GRASS_BATCH_JOB", GrassUtils.grassBatchJobFilename())
         GrassUtils.createGrassBatchJobFileFromGrassCommands(commands)
         os.chmod(GrassUtils.grassBatchJobFilename(), stat.S_IEXEC | stat.S_IREAD | stat.S_IWRITE)
         if SextanteUtils.isMac():
             command = GrassUtils.grassPath() + os.sep + "grass.sh " + GrassUtils.grassMapsetFolder() + "/user"
         else:
             command = "grass64 " + GrassUtils.grassMapsetFolder() + "/user"
     loglines = []
     loglines.append("GRASS execution console output")
     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 "GRASS_INFO_PERCENT" in line:
             try:
                 progress.setPercentage(int(line[len("GRASS_INFO_PERCENT")+ 2:]))
             except:
                 pass
         else:
             loglines.append(line)
             progress.setConsoleInfo(line)
     if SextanteConfig.getSetting(GrassUtils.GRASS_LOG_CONSOLE):
         SextanteLog.addToLog(SextanteLog.LOG_INFO, loglines)
     shutil.rmtree(GrassUtils.grassMapsetFolder(), True)

 def exportRasterLayer(self, layer):
     destFilename = SextanteUtils.getTempFilename("sgrd")
     self.exportedLayers[layer]= destFilename
     if SextanteUtils.isWindows():
         return "io_gdal 0 -GRIDS \"" + destFilename + "\" -FILES \"" + layer+"\""
     else:
         return "libio_gdal 0 -GRIDS \"" + destFilename + "\" -FILES \"" + layer + "\""

 def otbPath():
     folder = SextanteConfig.getSetting(OTBUtils.OTB_FOLDER)
     if folder == None:
         folder = ""
         #try to configure the path automatically
         if SextanteUtils.isMac():
             testfolder = os.path.join(str(QgsApplication.prefixPath()), "bin")
             if os.path.exists(os.path.join(testfolder, "otbcli")):
                 folder = testfolder
             else:
                 testfolder = "/usr/local/bin"
                 if os.path.exists(os.path.join(testfolder, "otbcli")):
                     folder = testfolder
         elif SextanteUtils.isWindows():
             testfolder = os.path.dirname(str(QgsApplication.prefixPath()))
             testfolder = os.path.dirname(testfolder)
             testfolder = os.path.join(testfolder,  "bin")
             path = os.path.join(testfolder, "otbcli.bat")
             if os.path.exists(path):
                 folder = testfolder
         else:
             testfolder = "/usr/bin"
             if os.path.exists(os.path.join(testfolder, "otbcli")):
                 folder = testfolder
     return folder

    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 processAlgorithm(self, progress):
        #TODO:check correct num of bands
        input = self.getParameterValue(SplitRGBBands.INPUT)
        temp = SextanteUtils.getTempFilename(None).replace('.','');
        basename = os.path.basename(temp)
        validChars = "abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789"
        safeBasename = ''.join(c for c in basename if c in validChars)
        temp = os.path.join(os.path.dirname(temp), safeBasename)

        r = self.getOutputValue(SplitRGBBands.R)
        g = self.getOutputValue(SplitRGBBands.G)
        b = self.getOutputValue(SplitRGBBands.B)
        commands = []
        if SextanteUtils.isWindows():
            commands.append("io_gdal 0 -GRIDS \"" + temp + "\" -FILES \"" + input+"\"")
            commands.append("io_gdal 1 -GRIDS \"" + temp + "_0001.sgrd\" -FORMAT 1 -TYPE 0 -FILE \"" + r + "\"");
            commands.append("io_gdal 1 -GRIDS \"" + temp + "_0002.sgrd\" -FORMAT 1 -TYPE 0 -FILE \"" + g + "\"");
            commands.append("io_gdal 1 -GRIDS \"" + temp + "_0003.sgrd\" -FORMAT 1 -TYPE 0 -FILE \"" + b + "\"");
        else:
            commands.append("libio_gdal 0 -GRIDS \"" + temp + "\" -FILES \"" + input + "\"")
            commands.append("libio_gdal 1 -GRIDS \"" + temp + "_0001.sgrd\" -FORMAT 1 -TYPE 0 -FILE \"" + r + "\"");
            commands.append("libio_gdal 1 -GRIDS \"" + temp + "_0002.sgrd\" -FORMAT 1 -TYPE 0 -FILE \"" + g + "\"");
            commands.append("libio_gdal 1 -GRIDS \"" + temp + "_0003.sgrd\" -FORMAT 1 -TYPE 0 -FILE \"" + b + "\"");

        SagaUtils.createSagaBatchJobFileFromSagaCommands(commands)
        SagaUtils.executeSaga(progress);

    def checkRIsInstalled(ignoreRegistrySettings=False):
        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 not ignoreRegistrySettings:
            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
        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>"
            '<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 sagaBatchJobFilename():

        if SextanteUtils.isWindows():
            filename = "saga_batch_job.bat";
        else:
            filename = "saga_batch_job.sh";

        batchfile = SextanteUtils.userFolder() + os.sep + filename

        return batchfile

 def initializeSettings(self):
     AlgorithmProvider.initializeSettings(self)
     if SextanteUtils.isWindows():
         SextanteConfig.addSetting(
             Setting(self.getDescription(), SagaUtils.SAGA_FOLDER, "SAGA folder", SagaUtils.sagaPath())
         )
     SextanteConfig.addSetting(
         Setting(
             self.getDescription(),
             SagaUtils.SAGA_AUTO_RESAMPLING,
             "Use min covering grid system for resampling",
             True,
         )
     )
     SextanteConfig.addSetting(
         Setting(self.getDescription(), SagaUtils.SAGA_LOG_COMMANDS, "Log execution commands", False)
     )
     SextanteConfig.addSetting(
         Setting(self.getDescription(), SagaUtils.SAGA_LOG_CONSOLE, "Log console output", False)
     )
     SextanteConfig.addSetting(
         Setting(self.getDescription(), SagaUtils.SAGA_RESAMPLING_REGION_XMIN, "Resampling region min x", 0)
     )
     SextanteConfig.addSetting(
         Setting(self.getDescription(), SagaUtils.SAGA_RESAMPLING_REGION_YMIN, "Resampling region min y", 0)
     )
     SextanteConfig.addSetting(
         Setting(self.getDescription(), SagaUtils.SAGA_RESAMPLING_REGION_XMAX, "Resampling region max x", 1000)
     )
     SextanteConfig.addSetting(
         Setting(self.getDescription(), SagaUtils.SAGA_RESAMPLING_REGION_YMAX, "Resampling region max y", 1000)
     )
     SextanteConfig.addSetting(
         Setting(self.getDescription(), SagaUtils.SAGA_RESAMPLING_REGION_CELLSIZE, "Resampling region cellsize", 1)
     )

 def unload(self):
     self.toolbox.setVisible(False)
     self.menu.deleteLater()
     #delete temporary output files
     folder = SextanteUtils.tempFolder()
     if QDir(folder).exists():
         shutil.rmtree(folder, True)

    def scriptsFolder():
        folder = SextanteConfig.getSetting(ScriptUtils.SCRIPTS_FOLDER)
        if folder == None:
            folder = SextanteUtils.userFolder() + os.sep + "scripts"
        mkdir(folder)

        return folder

 def executeSaga(progress):
     if SextanteUtils.isWindows():
         command = ["cmd.exe", "/C ", SagaUtils.sagaBatchJobFilename()]
     else:
         os.chmod(SagaUtils.sagaBatchJobFilename(), stat.S_IEXEC | stat.S_IREAD | stat.S_IWRITE)
         command = [SagaUtils.sagaBatchJobFilename()]
     loglines = []
     loglines.append("SAGA execution console output")
     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 "%" in line:
             s = "".join([x for x in line if x.isdigit()])
             try:
                 progress.setPercentage(int(s))
             except:
                 pass
         else:
             line = line.strip()
             if line != "/" and line != "-" and line != "\\" and line != "|":
                 loglines.append(line)
                 progress.setConsoleInfo(line)
     if SextanteConfig.getSetting(SagaUtils.SAGA_LOG_CONSOLE):
         SextanteLog.addToLog(SextanteLog.LOG_INFO, loglines)

    def modelsFolder():
        folder = SextanteConfig.getSetting(ModelerUtils.MODELS_FOLDER)
        if folder == None:
            folder = unicode(os.path.join(SextanteUtils.userFolder(), "models"))
        mkdir(folder)

        return os.path.abspath(folder)

 def exportVectorLayer(layer):
     '''Takes a QgsVectorLayer and returns the filename to refer to it, which allows external
     apps which support only file-based layers to use it. It performs the necessary export
     in case the input layer is not in a standard format suitable for most applications, it is
     a remote one or db-based (non-file based) one, or if there is a selection and it should be
     used, exporting just the selected features.
     Currently, the output is restricted to shapefiles, so anything that is not in a shapefile
     will get exported.
     It also export to a new file if the original one contains non-ascii characters'''
     settings = QSettings()
     systemEncoding = settings.value( "/UI/encoding", "System" ).toString()
     output = SextanteUtils.getTempFilename("shp")
     provider = layer.dataProvider()
     useSelection = SextanteConfig.getSetting(SextanteConfig.USE_SELECTED)
     if useSelection and layer.selectedFeatureCount() != 0:
         writer = QgsVectorFileWriter(output, systemEncoding, layer.pendingFields(), provider.geometryType(), layer.crs())
         selection = layer.selectedFeatures()
         for feat in selection:
             writer.addFeature(feat)
         del writer
         return output
     else:
         isASCII=True
         try:
             unicode(layer.source()).decode("ascii")
         except UnicodeEncodeError:
             isASCII=False
         if (not unicode(layer.source()).endswith("shp") or not isASCII):
             writer = QgsVectorFileWriter( output, systemEncoding, layer.pendingFields(), provider.geometryType(), layer.crs() )
             for feat in layer.getFeatures():
                 writer.addFeature(feat)
             del writer
             return output
         else:
             return unicode(layer.source())

 def exportTable( table):
     '''Takes a QgsVectorLayer and returns the filename to refer to its attributes table,
     which allows external apps which support only file-based layers to use it.
     It performs the necessary export in case the input layer is not in a standard format
     suitable for most applications, it isa remote one or db-based (non-file based) one
     Currently, the output is restricted to dbf.
     It also export to a new file if the original one contains non-ascii characters'''
     settings = QSettings()
     systemEncoding = settings.value( "/UI/encoding", "System" )
     output = SextanteUtils.getTempFilename("dbf")
     provider = table.dataProvider()
     isASCII=True
     try:
         unicode(table.source()).decode("ascii")
     except UnicodeEncodeError:
         isASCII=False
     isDbf = unicode(table.source()).endswith("dbf") or unicode(table.source()).endswith("shp")
     if (not isDbf or not isASCII):
         writer = QgsVectorFileWriter( output, systemEncoding, provider.fields(), QGis.WKBNoGeometry, layer.crs() )
         for feat in table.getFeatures():
             writer.addFeature(feat)
         del writer
         return output
     else:
         filename = unicode(table.source())
         if unicode(table.source()).endswith("shp"):
             return filename[:-3] + "dbf"
         else:
             return filename

 def exportVectorLayer(layer):
     '''Takes a QgsVectorLayer and returns the filename to refer to it, which allows external
     apps which support only file-based layers to use it. It performs the necessary export
     in case the input layer is not in a standard format suitable for most applications, it is
     a remote one or db-based (non-file based) one, or if there is a selection and it should be
     used, exporting just the selected features.
     Currently, the output is restricted to shapefiles, so anything that is not in a shapefile
     will get exported'''
     settings = QSettings()
     systemEncoding = settings.value( "/UI/encoding", "System" ).toString()
     output = SextanteUtils.getTempFilename("shp")
     provider = layer.dataProvider()
     allAttrs = provider.attributeIndexes()
     provider.select( allAttrs )
     useSelection = SextanteConfig.getSetting(SextanteConfig.USE_SELECTED)
     if useSelection and layer.selectedFeatureCount() != 0:
         writer = QgsVectorFileWriter( output, systemEncoding,provider.fields(), provider.geometryType(), provider.crs() )
         selection = layer.selectedFeatures()
         for feat in selection:
             writer.addFeature(feat)
         del writer
         return output
     else:
         if (not unicode(layer.source()).endswith("shp")):
             writer = QgsVectorFileWriter( output, systemEncoding,provider.fields(), provider.geometryType(), provider.crs() )
             feat = QgsFeature()
             while provider.nextFeature(feat):
                 writer.addFeature(feat)
             del writer
             return output
         else:
             return unicode(layer.source())

 def test_SagaVectorAlgorithWithUnsupportedInputAndOutputFormat(self):
     '''this tests both the exporting to shp and then the format change in the output layer'''
     layer = sextante.getobject(polygonsGeoJson());
     feature = layer.getFeatures().next()
     selected = [feature.id()]
     layer.setSelectedFeatures(selected)
     outputs=sextante.runalg("saga:polygoncentroids",polygonsGeoJson(),True, SextanteUtils.getTempFilename("geojson"))
     layer.setSelectedFeatures([])
     output=outputs['CENTROIDS']
     layer=QGisLayers.getObjectFromUri(output, True)
     fields=layer.pendingFields()
     expectednames=['ID','POLY_NUM_A','POLY_ST_A']
     expectedtypes=['Real','Real','String']
     names=[str(f.name()) for f in fields]
     types=[str(f.typeName()) for f in fields]
     self.assertEqual(expectednames, names)
     self.assertEqual(expectedtypes, types)
     features=sextante.getfeatures(layer)
     self.assertEqual(1, len(features))
     feature=features.next()
     attrs=feature.attributes()
     expectedvalues=["0","1.1","string a"]
     values=[str(attr.toString()) for attr in attrs]
     self.assertEqual(expectedvalues, values)
     wkt='POINT(270787.49991451 4458955.46775295)'
     self.assertEqual(wkt, str(feature.geometry().exportToWkt()))

 def test_SagaRasterAlgorithmWithUnsupportedOutputFormat(self):
     outputs=sextante.runalg("saga:convergenceindex",raster(),0,0,SextanteUtils.getTempFilename("img"))
     output=outputs['RESULT']
     self.assertTrue(os.path.isfile(output))
     dataset=gdal.Open(output, GA_ReadOnly)
     strhash=hash(str(dataset.ReadAsArray(0).tolist()))
     self.assertEqual(strhash, 485390137)

    def modelsFolder():
        folder = SextanteConfig.getSetting(ModelerUtils.MODELS_FOLDER)
        if folder == None:
            folder = SextanteUtils.userFolder() + os.sep + "models"
        mkdir(folder)

        return folder