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)
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)
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)
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)