Пример #1
0
    def processAlgorithm(self, progress):
        if system.isWindows():
            path = CircuitscapeUtils.circuitscapePath()
            if path == '':
                raise GeoAlgorithmExecutionException(
                    'Circuitscape folder is not configured.\nPlease '
                    'configure it before running Circuitscape algorithms.')

        resistance = self.getParameterValue(self.RESISTANCE_MAP)
        useConductance = str(not self.getParameterValue(self.IS_CONDUCTANCES))
        currentSources = self.getParameterValue(self.CURRENT_SOURCE)
        groundPoints = self.getParameterValue(self.GROUND_POINT)
        gpConductance = str(not self.getParameterValue(self.GP_CONDUCTANCES))

        writeCurrent = str(self.getParameterValue(self.WRITE_CURRENT_MAP))
        writeVoltage = str(self.getParameterValue(self.WRITE_VOLTAGE_MAP))

        # advanced parameters
        mode = self.MODES_DICT[self.getParameterValue(self.MODE)]
        unitCurrents = str(self.getParameterValue(self.UNIT_CURRENTS))
        directConnections = str(self.getParameterValue(
            self.DIRECT_CONNECTIONS))
        mask = self.getParameterValue(self.MASK)
        shortCircuit = self.getParameterValue(self.SHORT_CIRCUIT)

        baseName = self.getParameterValue(self.BASENAME)
        directory = self.getOutputValue(self.DIRECTORY)
        progress.setInfo('basename: %s' % baseName)
        progress.setInfo('directory: %s' % directory)

        basePath = os.path.join(directory, baseName)

        iniPath = CircuitscapeUtils.writeConfiguration()
        cfg = ConfigParser.SafeConfigParser()
        cfg.read(iniPath)

        commands = self.prepareInputs()

        # set parameters
        cfg.set('Circuitscape mode', 'scenario', 'advanced')

        cfg.set('Habitat raster or graph', 'habitat_map_is_resistances',
                useConductance)
        if resistance in self.exportedLayers.keys():
            resistance = self.exportedLayers[resistance]
        cfg.set('Habitat raster or graph', 'habitat_file', resistance)

        if currentSources in self.exportedLayers.keys():
            currentSources = self.exportedLayers[currentSources]
        cfg.set('Options for advanced mode', 'source_file', currentSources)
        if groundPoints in self.exportedLayers.keys():
            groundPoints = self.exportedLayers[groundPoints]
        cfg.set('Options for advanced mode', 'ground_file', groundPoints)
        cfg.set('Options for advanced mode', 'ground_file_is_resistances',
                gpConductance)
        cfg.set('Options for advanced mode', 'remove_src_or_gnd', unitCurrents)
        cfg.set('Options for advanced mode', 'use_direct_grounds',
                directConnections)

        if mask is not None:
            if mask in self.exportedLayers.keys():
                mask = self.exportedLayers[mask]
            cfg.set('Mask file', 'mask_file', mask)
            cfg.set('Mask file', 'use_mask', 'True')

        if shortCircuit is not None:
            if shortCircuit in self.exportedLayers.keys():
                shortCircuit = self.exportedLayers[shortCircuit]
            cfg.set('Short circuit regions (aka polygons)', 'polygon_file',
                    shortCircuit)
            cfg.set('Short circuit regions (aka polygons)', 'use_polygons',
                    'True')

        cfg.set('Output options', 'write_cur_maps', writeCurrent)
        cfg.set('Output options', 'write_volt_maps', writeVoltage)
        cfg.set('Output options', 'output_file', basePath)

        # write configuration back to file
        with open(iniPath, 'wb') as f:
            cfg.write(f)

        if system.isWindows():
            commands.append('"' + os.path.join(path, 'cs_run.exe') + '" ' +
                            iniPath)
        else:
            commands.append('csrun.py ' + iniPath)

        CircuitscapeUtils.createBatchJobFileFromCommands(commands)
        loglines = []
        loglines.append('Circuitscape execution commands')
        for line in commands:
            progress.setCommand(line)
            loglines.append(line)

        if ProcessingConfig.getSetting(CircuitscapeUtils.LOG_COMMANDS):
            ProcessingLog.addToLog(ProcessingLog.LOG_INFO, loglines)

        CircuitscapeUtils.executeCircuitscape(commands, progress)
Пример #2
0
    def processAlgorithm(self, progress):
        if system.isWindows():
            path = CircuitscapeUtils.circuitscapePath()
            if path == '':
                raise GeoAlgorithmExecutionException(
                    'Circuitscape folder is not configured.\nPlease '
                    'configure it before running Circuitscape algorithms.')

        resistance = self.getParameterValue(self.RESISTANCE_MAP)
        useConductance = str(not self.getParameterValue(self.IS_CONDUCTANCES))
        focal = self.getParameterValue(self.FOCAL_NODE)
        writeCurrent = str(self.getParameterValue(self.WRITE_CURRENT_MAP))
        writeVoltage = str(self.getParameterValue(self.WRITE_VOLTAGE_MAP))

        # advanced parameters
        mask = self.getParameterValue(self.MASK)
        shortCircuit = self.getParameterValue(self.SHORT_CIRCUIT)
        focalPairs = self.getParameterValue(self.EXCLUDE_INCLUDE)
        lowMemory = str(self.getParameterValue(self.LOW_MEMORY))

        baseName = self.getParameterValue(self.BASENAME)
        directory = self.getOutputValue(self.DIRECTORY)
        progress.setInfo('basename: %s' % baseName)
        progress.setInfo('directory: %s' % directory)

        basePath = os.path.join(directory, baseName)

        iniPath = CircuitscapeUtils.writeConfiguration()
        cfg = ConfigParser.SafeConfigParser()
        cfg.read(iniPath)

        commands = self.prepareInputs()

        # set parameters
        cfg.set('Circuitscape mode', 'scenario', 'pairwise')

        cfg.set('Habitat raster or graph', 'habitat_map_is_resistances',
                useConductance)
        if resistance in self.exportedLayers.keys():
            resistance = self.exportedLayers[resistance]
        cfg.set('Habitat raster or graph', 'habitat_file', resistance)

        if focal in self.exportedLayers.keys():
            focal = self.exportedLayers[focal]
        cfg.set('Options for pairwise and one-to-all and all-to-one modes',
                'point_file', focal)
        if focalPairs is not None:
            cfg.set('Options for pairwise and one-to-all and all-to-one modes',
                    'included_pairs_file', focalPairs)
            cfg.set('Options for pairwise and one-to-all and all-to-one modes',
                    'use_included_pairs', 'True')

        if mask is not None:
            if mask in self.exportedLayers.keys():
                mask = self.exportedLayers[mask]
            cfg.set('Mask file', 'mask_file', mask)
            cfg.set('Mask file', 'use_mask', 'True')

        if shortCircuit is not None:
            if shortCircuit in self.exportedLayers.keys():
                shortCircuit = self.exportedLayers[shortCircuit]
            cfg.set('Short circuit regions (aka polygons)', 'polygon_file',
                    shortCircuit)
            cfg.set('Short circuit regions (aka polygons)', 'use_polygons',
                    'True')

        cfg.set('Calculation options', 'low_memory_mode', lowMemory)

        cfg.set('Output options', 'write_cur_maps', writeCurrent)
        cfg.set('Output options', 'write_volt_maps', writeVoltage)
        cfg.set('Output options', 'output_file', basePath)

        # write configuration back to file
        with open(iniPath, 'wb') as f:
            cfg.write(f)

        if system.isWindows():
            commands.append('"' + os.path.join(path, 'cs_run.exe') + '" ' +
                            iniPath)
        else:
            commands.append('csrun.py ' + iniPath)

        CircuitscapeUtils.createBatchJobFileFromCommands(commands)
        loglines = []
        loglines.append('Circuitscape execution commands')
        for line in commands:
            progress.setCommand(line)
            loglines.append(line)

        if ProcessingConfig.getSetting(CircuitscapeUtils.LOG_COMMANDS):
            ProcessingLog.addToLog(ProcessingLog.LOG_INFO, loglines)

        CircuitscapeUtils.executeCircuitscape(commands, progress)
Пример #3
0
    def processAlgorithm(self, progress):
        if system.isWindows():
            path = CircuitscapeUtils.circuitscapePath()
            if path == '':
                raise GeoAlgorithmExecutionException(
                    'Circuitscape folder is not configured.\nPlease '
                    'configure it before running Circuitscape algorithms.')

        resistance = self.getParameterValue(self.RESISTANCE_MAP)
        useConductance = str(not self.getParameterValue(self.IS_CONDUCTANCES))
        focal = self.getParameterValue(self.FOCAL_NODE)
        writeCurrent = str(self.getParameterValue(self.WRITE_CURRENT_MAP))
        writeVoltage = str(self.getParameterValue(self.WRITE_VOLTAGE_MAP))

        # advanced parameters
        mask = self.getParameterValue(self.MASK)
        shortCircuit = self.getParameterValue(self.SHORT_CIRCUIT)
        focalPairs = self.getParameterValue(self.EXCLUDE_INCLUDE)
        lowMemory = str(self.getParameterValue(self.LOW_MEMORY))

        baseName = self.getParameterValue(self.BASENAME)
        directory = self.getOutputValue(self.DIRECTORY)
        progress.setInfo('basename: %s' % baseName)
        progress.setInfo('directory: %s' % directory)

        basePath = os.path.join(directory, baseName)

        iniPath = CircuitscapeUtils.writeConfiguration()
        cfg = ConfigParser.SafeConfigParser()
        cfg.read(iniPath)

        commands = self.prepareInputs()

        # set parameters
        cfg.set('Circuitscape mode', 'scenario', 'pairwise')

        cfg.set('Habitat raster or graph',
            'habitat_map_is_resistances', useConductance)
        if resistance in self.exportedLayers.keys():
            resistance = self.exportedLayers[resistance]
        cfg.set('Habitat raster or graph', 'habitat_file', resistance)

        if focal in self.exportedLayers.keys():
            focal = self.exportedLayers[focal]
        cfg.set('Options for pairwise and one-to-all and all-to-one modes',
            'point_file', focal)
        if focalPairs is not None:
            cfg.set('Options for pairwise and one-to-all and all-to-one modes',
                'included_pairs_file', focalPairs)
            cfg.set('Options for pairwise and one-to-all and all-to-one modes',
                'use_included_pairs', 'True')

        if mask is not None:
            if mask in self.exportedLayers.keys():
                mask = self.exportedLayers[mask]
            cfg.set('Mask file', 'mask_file', mask)
            cfg.set('Mask file', 'use_mask', 'True')

        if shortCircuit is not None:
            if shortCircuit in self.exportedLayers.keys():
                shortCircuit = self.exportedLayers[shortCircuit]
            cfg.set('Short circuit regions (aka polygons)',
                'polygon_file', shortCircuit)
            cfg.set('Short circuit regions (aka polygons)',
                'use_polygons', 'True')

        cfg.set('Calculation options', 'low_memory_mode', lowMemory)

        cfg.set('Output options', 'write_cur_maps', writeCurrent)
        cfg.set('Output options', 'write_volt_maps', writeVoltage)
        cfg.set('Output options', 'output_file', basePath)

        # write configuration back to file
        with open(iniPath, 'wb') as f:
            cfg.write(f)

        if system.isWindows():
            commands.append(
                '"' + os.path.join(path, 'cs_run.exe') + '" ' + iniPath)
        else:
            commands.append('csrun.py ' + iniPath)

        CircuitscapeUtils.createBatchJobFileFromCommands(commands)
        loglines = []
        loglines.append('Circuitscape execution commands')
        for line in commands:
            progress.setCommand(line)
            loglines.append(line)

        if ProcessingConfig.getSetting(CircuitscapeUtils.LOG_COMMANDS):
            ProcessingLog.addToLog(ProcessingLog.LOG_INFO, loglines)

        CircuitscapeUtils.executeCircuitscape(commands, progress)
Пример #4
0
    def processAlgorithm(self, progress):
        if system.isWindows():
            path = CircuitscapeUtils.circuitscapePath()
            if path == '':
                raise GeoAlgorithmExecutionException(
                    'Circuitscape folder is not configured.\nPlease '
                    'configure it before running Circuitscape algorithms.')

        resistance = self.getParameterValue(self.RESISTANCE_MAP)
        useConductance = str(not self.getParameterValue(self.IS_CONDUCTANCES))
        currentSources = self.getParameterValue(self.CURRENT_SOURCE)
        groundPoints = self.getParameterValue(self.GROUND_POINT)
        gpConductance = str(not self.getParameterValue(self.GP_CONDUCTANCES))

        writeCurrent = str(self.getParameterValue(self.WRITE_CURRENT_MAP))
        writeVoltage = str(self.getParameterValue(self.WRITE_VOLTAGE_MAP))

        # advanced parameters
        mode = self.MODES_DICT[self.getParameterValue(self.MODE)]
        unitCurrents = str(self.getParameterValue(self.UNIT_CURRENTS))
        directConnections = str(
            self.getParameterValue(self.DIRECT_CONNECTIONS))
        mask = self.getParameterValue(self.MASK)
        shortCircuit = self.getParameterValue(self.SHORT_CIRCUIT)

        baseName = self.getParameterValue(self.BASENAME)
        directory = self.getOutputValue(self.DIRECTORY)
        progress.setInfo('basename: %s' % baseName)
        progress.setInfo('directory: %s' % directory)

        basePath = os.path.join(directory, baseName)

        iniPath = CircuitscapeUtils.writeConfiguration()
        cfg = ConfigParser.SafeConfigParser()
        cfg.read(iniPath)

        commands = self.prepareInputs()

        # set parameters
        cfg.set('Circuitscape mode', 'scenario', 'advanced')

        cfg.set('Habitat raster or graph',
            'habitat_map_is_resistances', useConductance)
        if resistance in self.exportedLayers.keys():
            resistance = self.exportedLayers[resistance]
        cfg.set('Habitat raster or graph', 'habitat_file', resistance)

        if currentSources in self.exportedLayers.keys():
            currentSources = self.exportedLayers[currentSources]
        cfg.set('Options for advanced mode', 'source_file', currentSources)
        if groundPoints in self.exportedLayers.keys():
            groundPoints = self.exportedLayers[groundPoints]
        cfg.set('Options for advanced mode', 'ground_file', groundPoints)
        cfg.set('Options for advanced mode',
            'ground_file_is_resistances', gpConductance)
        cfg.set('Options for advanced mode', 'remove_src_or_gnd', unitCurrents)
        cfg.set('Options for advanced mode',
            'use_direct_grounds', directConnections)

        if mask is not None:
            if mask in self.exportedLayers.keys():
                mask = self.exportedLayers[mask]
            cfg.set('Mask file', 'mask_file', mask)
            cfg.set('Mask file', 'use_mask', 'True')

        if shortCircuit is not None:
            if shortCircuit in self.exportedLayers.keys():
                shortCircuit = self.exportedLayers[shortCircuit]
            cfg.set('Short circuit regions (aka polygons)',
                'polygon_file', shortCircuit)
            cfg.set('Short circuit regions (aka polygons)',
                'use_polygons', 'True')

        cfg.set('Output options', 'write_cur_maps', writeCurrent)
        cfg.set('Output options', 'write_volt_maps', writeVoltage)
        cfg.set('Output options', 'output_file', basePath)

        # write configuration back to file
        with open(iniPath, 'wb') as f:
            cfg.write(f)

        if system.isWindows():
            commands.append(
                '"' + os.path.join(path, 'cs_run.exe') + '" ' + iniPath)
        else:
            commands.append('csrun.py ' + iniPath)

        CircuitscapeUtils.createBatchJobFileFromCommands(commands)
        loglines = []
        loglines.append('Circuitscape execution commands')
        for line in commands:
            progress.setCommand(line)
            loglines.append(line)

        if ProcessingConfig.getSetting(CircuitscapeUtils.LOG_COMMANDS):
            ProcessingLog.addToLog(ProcessingLog.LOG_INFO, loglines)

        CircuitscapeUtils.executeCircuitscape(commands, progress)