def function(params):
common.runSystemChecks(
) # Run to ensure config.xml is copied across to user_settings.xml if needed. This line can be removed after 31/10/18.
# Get inputs
p = common.paramsAsText(params)
scratchPath = p[1]
developerMode = common.strToBool(p[2])
if developerMode == True:
developerMode = 'Yes'
else:
developerMode = 'No'
# Override the default values from user settings file (if they exist in the file)
try:
configValues = [('scratchPath', scratchPath),
('developerMode', developerMode)]
common.writeXML(configuration.userSettingsFile, configValues)
log.info('Scratch path updated: ' + scratchPath)
log.info('Developer mode updated: ' + developerMode)
except Exception:
raise
def function(params):
try:
pText = common.paramsAsText(params)
# Get inputs
runSystemChecks = common.strToBool(pText[1])
outputFolder = pText[5]
yearAFolder = pText[6]
yearBFolder = pText[7]
slopeOption = pText[8]
slopeAngle = pText[9]
yearARain = pText[10]
yearBRain = pText[11]
yearASupport = pText[12]
yearBSupport = pText[13]
# Set option for LS-factor
if slopeOption == 'Calculate based on slope and length only':
lsOption = 'SlopeLength'
elif slopeOption == 'Include upslope contributing area':
lsOption = 'UpslopeArea'
else:
log.error('Invalid LS-factor option')
sys.exit()
# System checks and setup
if runSystemChecks:
common.runSystemChecks()
# Create output folder
if not os.path.exists(outputFolder):
os.mkdir(outputFolder)
# Set up logging output to file
log.setupLogging(outputFolder)
# Call RUSLE_scen_acc function
RUSLE_scen_acc.function(outputFolder, yearAFolder, yearBFolder,
lsOption, slopeAngle, yearARain, yearBRain,
yearASupport, yearBSupport)
# Set up filenames for display purposes
soilLossA = os.path.join(outputFolder, "soillossA")
soilLossB = os.path.join(outputFolder, "soillossB")
soilLossDiff = os.path.join(outputFolder, "soillossDiff")
arcpy.SetParameter(2, soilLossA)
arcpy.SetParameter(3, soilLossB)
arcpy.SetParameter(4, soilLossDiff)
log.info("RUSLE accounts operations completed successfully")
except Exception:
log.exception("RUSLE accounts tool failed")
raise
def function(params):
try:
pText = common.paramsAsText(params)
runSystemChecks = common.strToBool(pText[1])
if params[2].name == 'Output_folder':
outputFolder = pText[2]
elif params[2].name == 'Land_extent_accounts':
outputFolder = os.path.join(arcpy.env.scratchFolder, 'LCaccounts')
LCaccounts = pText[2]
lcOption = pText[3]
inputLC = pText[4]
openingLC = pText[5]
closingLC = pText[6]
openingField = pText[7]
closingField = pText[8]
lcTable = pText[9]
lcCodeField = pText[10]
lcNameField = pText[11]
# System checks and setup
if runSystemChecks:
common.runSystemChecks()
# Create output folder
if not os.path.exists(outputFolder):
os.mkdir(outputFolder)
# Set up logging output to file
log.setupLogging(outputFolder)
# Call aggregation function
lcOutputs = land_accounts.function(outputFolder, lcOption, inputLC,
openingLC, closingLC, openingField,
closingField, lcTable, lcCodeField,
lcNameField)
# Set up filenames for display purposes
lcOpening = lcOutputs[0]
lcClosing = lcOutputs[1]
lcOpeningWithAccounts = lcOutputs[2]
outCSV = lcOutputs[3]
arcpy.SetParameter(12, lcOpening)
arcpy.SetParameter(13, lcClosing)
arcpy.SetParameter(14, outCSV)
return lcOpeningWithAccounts, lcClosing, outCSV
log.info("Land extent accounting operations completed successfully")
except Exception:
log.exception("Land extent accounting tool failed")
raise
def function(params):
try:
pText = common.paramsAsText(params)
runSystemChecks = common.strToBool(pText[1])
# Get inputs
if params[2].name == 'Output_folder':
outputFolder = pText[2]
elif params[2].name == 'Species_richness':
outputFolder = os.path.join(arcpy.env.scratchFolder,
'Species_richness')
speciesRichness = pText[2]
IUCN_rl_data = pText[4]
studymask = pText[5]
speciesdisplayname = pText[6]
#aggregateMask = pText[7] # will add optional mask if want to calculate over aggregrate spatial units
# System checks and setup
if runSystemChecks:
common.runSystemChecks()
# Create output folder
if not os.path.exists(outputFolder):
os.mkdir(outputFolder)
# Set up logging output to file
log.setupLogging(outputFolder)
# Call aggregation function
outputStats = PAspeciesRIchness.function(outputFolder,
dataSetsToAggregate,
aggregateMask,
maskFullyWithinSAM,
dataToAggregate)
# Set up filenames for display purposes
RareSpeciesRichness = os.path.join(outputFolder,
"RareSpeciesRichness.shp")
arcpy.CopyFeatures_management(outputStats[0], RareSpeciesRichness)
arcpy.SetParameter(3, SpeciesRichness)
return outputStats[0], PAspeciesRIchness
log.info("Rare species richness operations completed successfully")
except Exception:
log.exception("Rare species richness tool failed")
raise
def function(params):
try:
pText = common.paramsAsText(params)
# Get inputs
runSystemChecks = common.strToBool(pText[1])
outputFolder = pText[2]
inputRaster = pText[5]
aggregationZones = pText[6]
aggregationColumn = pText[7]
rerun = False
# Create output folder
if not os.path.exists(outputFolder):
os.mkdir(outputFolder)
# System checks and setup
if runSystemChecks:
common.runSystemChecks(outputFolder, rerun)
# Set up logging output to file
log.setupLogging(outputFolder)
# Set up progress log file
progress.initProgress(outputFolder, rerun)
# Write input params to XML
common.writeParamsToXML(params, outputFolder)
# Call zonal statistics function
CalcZonal.function(outputFolder, inputRaster, aggregationZones,
aggregationColumn)
# Set up filenames for display purposes
outRaster = os.path.join(outputFolder, 'statRaster')
outTable = os.path.join(outputFolder, 'statTable.dbf')
# Set up outputs
arcpy.SetParameter(3, outRaster)
arcpy.SetParameter(4, outTable)
log.info("Zonal statistics operations completed successfully")
except Exception:
log.exception("Zonal statistics tool failed")
raise
def function(params):
try:
pText = common.paramsAsText(params)
# Get inputs
runSystemChecks = common.strToBool(pText[1])
outputFolder = pText[2]
preprocessFolder = pText[4]
# R-factor
rData = pText[5]
# LS-factor
slopeOption = pText[6]
slopeAngle = pText[7]
# K-factor
kOption = pText[8]
soilData = pText[9]
soilCode = pText[10]
# C-factor
cOption = pText[11]
landCoverData = pText[12]
landCoverCode = pText[13]
# P-factor
supportData = pText[14]
saveFactors = common.strToBool(pText[15])
# Rerun parameter may not present when tool run as part of a batch run tool. If it is not, set rerun to False.
try:
rerun = common.strToBool(pText[16])
except IndexError:
rerun = False
except Exception:
raise
# Create output folder
if not os.path.exists(outputFolder):
os.mkdir(outputFolder)
# System checks and setup
if runSystemChecks:
common.runSystemChecks(outputFolder, rerun)
# Set up logging output to file
log.setupLogging(outputFolder)
# Set up progress log file
progress.initProgress(outputFolder, rerun)
# Write input params to XML
common.writeParamsToXML(params, outputFolder)
# Set option for LS-factor
if slopeOption == 'Calculate based on slope and length only':
lsOption = 'SlopeLength'
elif slopeOption == 'Include upslope contributing area':
lsOption = 'UpslopeArea'
else:
log.error('Invalid LS-factor option')
sys.exit()
# Set soilOption for K-factor
if kOption == 'Use preprocessed soil data':
soilOption = 'PreprocessSoil'
elif kOption == 'Use local K-factor dataset':
soilOption = 'LocalSoil'
else:
log.error('Invalid soil erodibility option')
sys.exit()
# Set lcOption for C-factor
if cOption == 'Use preprocessed land cover data':
lcOption = 'PrerocessLC'
elif cOption == 'Use local C-factor dataset':
lcOption = 'LocalCfactor'
else:
log.error('Invalid C-factor option')
sys.exit()
# Call RUSLE function
soilLoss = RUSLE.function(outputFolder, preprocessFolder, lsOption,
slopeAngle, soilOption, soilData, soilCode,
lcOption, landCoverData, landCoverCode,
rData, saveFactors, supportData, rerun)
# Set up filenames for display purposes
soilLoss = os.path.join(outputFolder, "soilloss")
arcpy.SetParameter(3, soilLoss)
return soilLoss
log.info("RUSLE operations completed successfully")
except Exception:
log.exception("RUSLE tool failed")
raise
def function(params):
try:
###################
### Read inputs ###
###################
pText = common.paramsAsText(params)
outputFolder = pText[1]
inputDEM = common.fullPath(pText[2])
inputStudyAreaMask = pText[3]
inputLC = pText[4]
lcCode = pText[5]
inputSoil = pText[6]
soilCode = pText[7]
reconDEM = common.strToBool(pText[8])
inputStreamNetwork = pText[9]
streamAccThresh = pText[10]
riverAccThresh = pText[11]
smoothDropBuffer = pText[12]
smoothDrop = pText[13]
streamDrop = pText[14]
rerun = common.strToBool(pText[15])
log.info('Inputs read in')
###########################
### Tool initialisation ###
###########################
# Create Baseline folder
if not os.path.exists(outputFolder):
os.mkdir(outputFolder)
# Set up logging output to file
log.setupLogging(outputFolder)
# Run system checks
common.runSystemChecks(outputFolder, rerun)
# Set up progress log file
progress.initProgress(outputFolder, rerun)
# Write input params to XML
common.writeParamsToXML(params, outputFolder, 'PreprocessDEM')
log.info('Tool initialised')
########################
### Define filenames ###
########################
files = common.getFilenames('preprocess', outputFolder)
studyAreaMask = files.studyareamask
outputLCras = files.lc_ras
outputLCvec = files.lc_vec
outputSoilras = files.soil_ras
outputSoilvec = files.soil_vec
###############################
### Set temporary variables ###
###############################
prefix = os.path.join(arcpy.env.scratchGDB, 'base_')
DEMTemp = prefix + 'DEMTemp'
clippedDEM = prefix + 'clippedDEM'
clippedLC = prefix + 'clippedLC'
clippedSoil = prefix + 'clippedSoil'
clippedStreamNetwork = prefix + 'clippedStreamNetwork'
studyAreaMaskTemp = prefix + "studyAreaMaskTemp"
studyAreaMaskBuff = prefix + "studyAreaMaskBuff"
studyAreaMaskDiss = prefix + "studyAreaMaskDiss"
log.info('Temporary variables set')
# Check formats of inputs
lcFormat = arcpy.Describe(inputLC).dataType
soilFormat = arcpy.Describe(inputSoil).dataType
###################
### Data checks ###
###################
codeBlock = 'Data checks 1'
if not progress.codeSuccessfullyRun(codeBlock, outputFolder, rerun):
inputFiles = [inputDEM, inputStudyAreaMask, inputLC, inputSoil]
if inputStreamNetwork is not None:
inputFiles.append(inputStreamNetwork)
for file in inputFiles:
common.checkSpatialRef(file)
# Set environment variables
arcpy.env.snapRaster = inputDEM
arcpy.env.cellSize = inputDEM
arcpy.env.compression = "None"
cellsizedem = float(
arcpy.GetRasterProperties_management(inputDEM,
"CELLSIZEX").getOutput(0))
# Get spatial references of DEM and study area mask
DEMSpatRef = arcpy.Describe(inputDEM).SpatialReference
maskSpatRef = arcpy.Describe(inputStudyAreaMask).SpatialReference
# Reproject study area mask if it does not have the same coordinate system as the DEM
if not common.equalProjections(DEMSpatRef, maskSpatRef):
warning = "Study area mask does not have the same coordinate system as the DEM"
log.warning(warning)
common.logWarnings(outputFolder, warning)
warning = "Mask coordinate system is " + maskSpatRef.Name + " while DEM coordinate system is " + DEMSpatRef.Name
log.warning(warning)
common.logWarnings(outputFolder, warning)
warning = "Reprojecting study area mask to DEM coordinate system"
log.warning(warning)
common.logWarnings(outputFolder, warning)
arcpy.Project_management(inputStudyAreaMask, studyAreaMaskTemp,
DEMSpatRef)
arcpy.CopyFeatures_management(studyAreaMaskTemp, studyAreaMask)
else:
arcpy.CopyFeatures_management(inputStudyAreaMask,
studyAreaMask)
# If DEM is large, clip it to a large buffer around the study area mask (~5km)
inputDEM = baseline.clipLargeDEM(inputDEM, studyAreaMask)
rasterInputFiles = []
fcInputFiles = []
# Sort land cover and soil into appropriate arrays based on data type
if lcFormat in ['RasterDataset', 'RasterLayer']:
rasterInputFiles.append(inputLC)
outputLC = os.path.join(outputFolder, 'landcover')
elif lcFormat in ['ShapeFile', 'FeatureClass']:
fcInputFiles.append(inputLC)
outputLC = os.path.join(outputFolder, 'landcover.shp')
if soilFormat in ['RasterDataset', 'RasterLayer']:
rasterInputFiles.append(inputSoil)
outputSoil = os.path.join(outputFolder, 'soil')
elif soilFormat in ['ShapeFile', 'FeatureClass']:
fcInputFiles.append(inputSoil)
outputSoil = os.path.join(outputFolder, 'soil.shp')
if reconDEM is True and inputStreamNetwork is None:
log.error(
'Cannot recondition the DEM without an input stream network'
)
log.error('Please provide an input stream network')
sys.exit()
# If the user has provided a stream network, add it to the list of inputs to check
if inputStreamNetwork is not None:
fcInputFiles.append(inputStreamNetwork)
# Check that the inputs contain data
for ras in rasterInputFiles:
if ras is not None:
# Check file size
fileSizeGB = baseline.checkRasterSizeGB(ras)
if fileSizeGB < 1.0:
baseline.checkInputRaster(ras, outputFolder)
else:
log.warning(
"Cannot check if raster is empty or all NoData because it is too large"
)
log.warning(
"Please ensure this raster is not empty or all NoData: "
+ str(ras))
for fc in fcInputFiles:
if fc is not None:
baseline.checkInputFC(fc, outputFolder)
# Check that the land cover and soil FCs have the linking codes specified by the user
if lcFormat in ['ShapeFile', 'FeatureClass']:
if len(arcpy.ListFields(inputLC, lcCode)) != 1:
log.error('Field ' + lcCode +
'does not exist in feature class ' + inputLC)
sys.exit()
if soilFormat in ['ShapeFile', 'FeatureClass']:
if len(arcpy.ListFields(inputSoil, soilCode)) != 1:
log.error('Field ' + soilCode +
'does not exist in feature class ' + inputSoil)
sys.exit()
progress.logProgress(codeBlock, outputFolder)
###############################
### Tidy up study area mask ###
###############################
codeBlock = 'Tidy up study area mask'
if not progress.codeSuccessfullyRun(codeBlock, outputFolder, rerun):
# Check how many polygons are in the mask shapefile
numPolysInMask = int(
arcpy.GetCount_management(studyAreaMask).getOutput(0))
if numPolysInMask > 1:
# Reduce multiple features where possible
arcpy.Union_analysis(studyAreaMask, studyAreaMaskDiss,
"ONLY_FID", "", "NO_GAPS")
arcpy.Dissolve_management(studyAreaMaskDiss, studyAreaMask, "",
"", "SINGLE_PART", "DISSOLVE_LINES")
# Buffer study area mask
baseline.bufferMask(inputDEM,
studyAreaMask,
outputStudyAreaMaskBuff=studyAreaMaskBuff)
log.info('Study area mask buffered')
progress.logProgress(codeBlock, outputFolder)
#######################
### Clip input data ###
#######################
codeBlock = 'Clip inputs'
if not progress.codeSuccessfullyRun(codeBlock, outputFolder, rerun):
baseline.clipInputs(outputFolder,
studyAreaMaskBuff,
inputDEM,
inputLC,
inputSoil,
inputStreamNetwork,
outputDEM=clippedDEM,
outputLC=clippedLC,
outputSoil=clippedSoil,
outputStream=clippedStreamNetwork)
progress.logProgress(codeBlock, outputFolder)
##############################################
### Coverage checks on soil and land cover ###
##############################################
codeBlock = 'Do coverage checks on clipped land cover and soil'
if not progress.codeSuccessfullyRun(codeBlock, outputFolder, rerun):
# Do coverage checks on land cover and soil and copy to outputFolder
if lcFormat in ['RasterDataset', 'RasterLayer']:
lcMask = common.extractRasterMask(clippedLC)
common.checkCoverage(lcMask, studyAreaMaskBuff, inputLC)
arcpy.CopyRaster_management(clippedLC, outputLCras)
elif lcFormat in ['ShapeFile', 'FeatureClass']:
lcMask = common.dissolvePolygon(clippedLC)
common.checkCoverage(lcMask, studyAreaMaskBuff, inputLC)
arcpy.CopyFeatures_management(clippedLC, outputLCvec)
if soilFormat in ['RasterDataset', 'RasterLayer']:
soilMask = common.extractRasterMask(clippedSoil)
common.checkCoverage(soilMask, studyAreaMaskBuff, inputLC)
arcpy.CopyRaster_management(clippedSoil, outputSoilras)
elif soilFormat in ['ShapeFile', 'FeatureClass']:
soilMask = common.dissolvePolygon(clippedSoil)
common.checkCoverage(soilMask, studyAreaMaskBuff, inputSoil)
arcpy.CopyFeatures_management(clippedSoil, outputSoilvec)
progress.logProgress(codeBlock, outputFolder)
######################################
### Convert LC and soil to rasters ###
######################################
# For the RUSLE tool, the LC and soil must be in raster format
codeBlock = 'Convert land cover and soil to rasters'
if not progress.codeSuccessfullyRun(codeBlock, outputFolder, rerun):
if lcFormat in ['ShapeFile', 'FeatureClass']:
arcpy.PolygonToRaster_conversion(clippedLC, lcCode,
outputLCras, "CELL_CENTER",
"", cellsizedem)
log.info('Land cover raster produced')
if soilFormat in ['ShapeFile', 'FeatureClass']:
arcpy.PolygonToRaster_conversion(clippedSoil, soilCode,
outputSoilras, "CELL_CENTER",
"", cellsizedem)
log.info('Soil raster produced')
# Delete intermediate files
arcpy.Delete_management(clippedLC)
arcpy.Delete_management(clippedSoil)
progress.logProgress(codeBlock, outputFolder)
###########################
### Run HydTopo process ###
###########################
log.info("*** Preprocessing DEM ***")
preprocess_dem.function(outputFolder, clippedDEM, studyAreaMask,
clippedStreamNetwork, streamAccThresh,
riverAccThresh, smoothDropBuffer, smoothDrop,
streamDrop, reconDEM, rerun)
except Exception:
arcpy.SetParameter(0, False)
log.exception("Preprocessing DEM functions did not complete")
raise
def function(params):
class DataToAggregate:
def __init__(self, dataSet, linkCode):
self.dataSet = dataSet
self.linkCode = linkCode
try:
pText = common.paramsAsText(params)
# Get inputs
if params[2].name == 'Output_folder':
outputFolder = pText[2]
elif params[2].name == 'Aggregated_data':
outputFolder = os.path.join(arcpy.env.scratchFolder, 'AggregatedData')
aggregatedData = pText[2]
runSystemChecks = common.strToBool(pText[1])
dataToAggregate = pText[7]
classificationColumn = pText[8]
aggregateMask = pText[9]
maskFullyWithinSAM = common.strToBool(pText[10])
# System checks and setup
if runSystemChecks:
common.runSystemChecks()
# Create output folder
if not os.path.exists(outputFolder):
os.mkdir(outputFolder)
# Set up logging output to file
log.setupLogging(outputFolder)
# Initialise variables
dataSetsToAggregate = [DataToAggregate(dataToAggregate, classificationColumn)]
# Call aggregation function
outputStats = aggregate_data.function(outputFolder, dataSetsToAggregate, aggregateMask, maskFullyWithinSAM, dataToAggregate)
# Set up filenames for display purposes
InvSimpson = os.path.join(outputFolder, "InverseSimpsonIndex.shp")
Shannon = os.path.join(outputFolder, "ShannonIndex.shp")
meanPatch = os.path.join(outputFolder, "MeanPatchSize.shp")
numCovers = os.path.join(outputFolder, "NumCovers.shp")
arcpy.CopyFeatures_management(outputStats[0], InvSimpson)
arcpy.CopyFeatures_management(outputStats[0], Shannon)
arcpy.CopyFeatures_management(outputStats[0], meanPatch)
arcpy.CopyFeatures_management(outputStats[0], numCovers)
arcpy.SetParameter(3, InvSimpson)
arcpy.SetParameter(4, Shannon)
arcpy.SetParameter(5, numCovers)
arcpy.SetParameter(6, meanPatch)
return outputStats[0], InvSimpson, Shannon, numCovers, meanPatch
log.info("Aggregation operations completed successfully")
except Exception:
log.exception("Aggregate data tool failed")
raise
def function(params):
try:
pText = common.paramsAsText(params)
# Get inputs
runSystemChecks = common.strToBool(pText[1])
outputFolder = pText[5]
yearAFolder = pText[6]
yearBFolder = pText[7]
# Inputs constant between the two years
slopeOption = pText[8]
slopeAngle = pText[9]
rData = pText[10]
soilData = pText[11]
soilCode = pText[12]
# Land covers
YearALCData = pText[13]
YearALCCode = pText[14]
YearBLCData = pText[15]
YearBLCCode = pText[16]
# Support factors
YearAPData = pText[17]
YearBPData = pText[18]
saveFactors = False
# Set option for LS-factor
if slopeOption == 'Calculate based on slope and length only':
lsOption = 'SlopeLength'
elif slopeOption == 'Include upslope contributing area':
lsOption = 'UpslopeArea'
else:
log.error('Invalid LS-factor option')
sys.exit()
# System checks and setup
if runSystemChecks:
common.runSystemChecks()
# Create output folder
if not os.path.exists(outputFolder):
os.mkdir(outputFolder)
# Set up logging output to file
log.setupLogging(outputFolder)
# Call RUSLE_accounts function
RUSLE_accounts.function(outputFolder, yearAFolder, yearBFolder,
lsOption, slopeAngle, rData, soilData,
soilCode, YearALCData, YearALCCode,
YearBLCData, YearBLCCode, YearAPData,
YearBPData, saveFactors)
# Set up filenames for display purposes
soilLossA = os.path.join(outputFolder, "soillossA")
soilLossB = os.path.join(outputFolder, "soillossB")
soilLossDiff = os.path.join(outputFolder, "soillossDiff")
arcpy.SetParameter(2, soilLossA)
arcpy.SetParameter(3, soilLossB)
arcpy.SetParameter(4, soilLossDiff)
log.info("RUSLE accounts operations completed successfully")
except Exception:
log.exception("RUSLE accounts tool failed")
raise