def __init__(self, configuration, currTimeStep, initialState = None):
self._configuration = configuration
self._modelTime = currTimeStep
pcr.setclone(configuration.cloneMap)
# Read the ldd map.
self.lddMap = vos.readPCRmapClone(\
configuration.routingOptions['lddMap'],
configuration.cloneMap,configuration.tmpDir,configuration.globalOptions['inputDir'],True)
#ensure ldd map is correct, and actually of type "ldd"
self.lddMap = pcr.lddrepair(pcr.ldd(self.lddMap))
if configuration.globalOptions['landmask'] != "None":
self.landmask = vos.readPCRmapClone(\
configuration.globalOptions['landmask'],
configuration.cloneMap,configuration.tmpDir,configuration.globalOptions['inputDir'])
else:
self.landmask = pcr.defined(self.lddMap)
# ADDED: variables necessary for 2-way coupling functions
# ----------------------------------------------------------------------------------------------------------------
# variable to control activation of 2-way coupling functions (can be changed through BMI)
self.ActivateCoupling = self._configuration.globalOptions['ActivateCoupling']
# ----------------------------------------------------------------------------------------------------------------
# defining catchment areas
self.catchment_class = 1.0
# number of upperSoilLayers:
self.numberOfSoilLayers = int(configuration.landSurfaceOptions['numberOfUpperSoilLayers'])
self.createSubmodels(initialState)
def readPCRmapClone(v,cloneMapFileName,tmpDir,absolutePath=None,isLddMap=False,cover=None,isNomMap=False):
# v: inputMapFileName or floating values
# cloneMapFileName: If the inputMap and cloneMap have different clones,
# resampling will be done.
#logger.info('read file/values: '+str(v))
if v == "None":
PCRmap = str("None")
elif not re.match(r"[0-9.-]*$",v):
if absolutePath != None: v = getFullPath(v,absolutePath)
# print(v)
sameClone = isSameClone(v,cloneMapFileName)
if sameClone == True:
PCRmap = pcr.readmap(v)
else:
# resample using GDAL:
output = tmpDir+'temp.map'
warp = gdalwarpPCR(v,output,cloneMapFileName,tmpDir,isLddMap,isNomMap)
# read from temporary file and delete the temporary file:
PCRmap = pcr.readmap(output)
if isLddMap == True: PCRmap = pcr.ifthen(pcr.scalar(PCRmap) < 10., PCRmap)
if isLddMap == True: PCRmap = pcr.ldd(PCRmap)
if isNomMap == True: PCRmap = pcr.ifthen(pcr.scalar(PCRmap) > 0., PCRmap)
if isNomMap == True: PCRmap = pcr.nominal(PCRmap)
co = 'rm '+str(tmpDir)+'*.*'
cOut,err = subprocess.Popen(co, stdout=subprocess.PIPE,stderr=open('/dev/null'),shell=True).communicate()
else:
PCRmap = pcr.scalar(float(v))
if cover != None:
PCRmap = pcr.cover(PCRmap, cover)
co = None; cOut = None; err = None; warp = None
del co; del cOut; del err; del warp
stdout = None; del stdout
stderr = None; del stderr
return PCRmap
def __init__(self, configuration, currTimeStep, initialState = None):
self._configuration = configuration
self._modelTime = currTimeStep
pcr.setclone(configuration.cloneMap)
# Read the ldd map.
self.lddMap = vos.readPCRmapClone(\
configuration.routingOptions['lddMap'],
configuration.cloneMap,configuration.tmpDir,configuration.globalOptions['inputDir'],True)
#ensure ldd map is correct, and actually of type "ldd"
self.lddMap = pcr.lddrepair(pcr.ldd(self.lddMap))
if configuration.globalOptions['landmask'] != "None":
self.landmask = vos.readPCRmapClone(\
configuration.globalOptions['landmask'],
configuration.cloneMap,configuration.tmpDir,configuration.globalOptions['inputDir'])
else:
self.landmask = pcr.defined(self.lddMap)
# defining catchment areas
self.catchment_class = 1.0
# number of upperSoilLayers:
self.numberOfSoilLayers = int(configuration.landSurfaceOptions['numberOfUpperSoilLayers'])
self.createSubmodels(initialState)
def readPCRmapClone(v,cloneMapFileName,tmpDir,absolutePath=None,isLddMap=False,cover=None,isNomMap=False):
# v: inputMapFileName or floating values
# cloneMapFileName: If the inputMap and cloneMap have different clones,
# resampling will be done.
print(v)
if v == "None":
PCRmap = str("None")
elif not re.match(r"[0-9.-]*$",v):
if absolutePath != None: v = getFullPath(v,absolutePath)
# print(v)
sameClone = isSameClone(v,cloneMapFileName)
if sameClone == True:
PCRmap = pcr.readmap(v)
else:
# resample using GDAL:
output = tmpDir+'temp.map'
warp = gdalwarpPCR(v,output,cloneMapFileName,tmpDir,isLddMap,isNomMap)
# read from temporary file and delete the temporary file:
PCRmap = pcr.readmap(output)
if isLddMap == True: PCRmap = pcr.ifthen(pcr.scalar(PCRmap) < 10., PCRmap)
if isLddMap == True: PCRmap = pcr.ldd(PCRmap)
if isNomMap == True: PCRmap = pcr.ifthen(pcr.scalar(PCRmap) > 0., PCRmap)
if isNomMap == True: PCRmap = pcr.nominal(PCRmap)
co = 'rm '+str(tmpDir)+'*.*'
cOut,err = subprocess.Popen(co, stdout=subprocess.PIPE,stderr=open('/dev/null'),shell=True).communicate()
else:
PCRmap = pcr.scalar(float(v))
if cover != None:
PCRmap = pcr.cover(PCRmap, cover)
co = None; cOut = None; err = None; warp = None
del co; del cOut; del err; del warp
stdout = None; del stdout
stderr = None; del stderr
return PCRmap
def _parseLine(self, line, lineNumber, nrColumns, externalNames, keyDict):
line = re.sub("\n", "", line)
line = re.sub("\t", " ", line)
result = None
# read until first comment
content = ""
content, sep, comment = line.partition("#")
if len(content) > 1:
collectionVariableName, sep, tail = content.partition(" ")
if collectionVariableName == self._varName:
tail = tail.strip()
key, sep, variableValue = tail.rpartition(" ")
if len(key.split()) != nrColumns:
tmp = re.sub("\(|\)|,", "", str(key))
msg = "Error reading %s line %d, order of columns given (%s columns) does not match expected order of %s columns" % (
self._fileName, lineNumber, len(key.split()) + 2,
int(nrColumns) + 2)
raise ValueError(msg)
variableValue = re.sub('\"', "", variableValue)
tmp = None
try:
tmp = int(variableValue)
if self._dataType == pcraster.Boolean:
tmp = pcraster.boolean(tmp)
elif self._dataType == pcraster.Nominal:
tmp = pcraster.nominal(tmp)
elif self._dataType == pcraster.Ordinal:
tmp = pcraster.ordinal(tmp)
elif self._dataType == pcraster.Ldd:
tmp = pcraster.ldd(tmp)
else:
msg = "Conversion to %s failed" % (self._dataType)
raise Exception(msg)
except ValueError, e:
try:
tmp = float(variableValue)
if self._dataType == pcraster.Scalar:
tmp = pcraster.scalar(tmp)
elif self._dataType == pcraster.Directional:
tmp = pcraster.directional(tmp)
else:
msg = "Conversion to %s failed" % (self._dataType)
raise Exception(msg)
except ValueError, e:
variableValue = re.sub("\\\\", "/", variableValue)
variableValue = variableValue.strip()
path = os.path.normpath(variableValue)
try:
tmp = pcraster.readmap(path)
except RuntimeError, e:
msg = "Error reading %s line %d, %s" % (
self._fileName, lineNumber, e)
raise ValueError(msg)
def readPCRmapClone(v,
cloneMapFileName,
tmpDir,
absolutePath=None,
isLddMap=False,
cover=None,
isNomMap=False):
# v: inputMapFileName or floating values
# cloneMapFileName: If the inputMap and cloneMap have different clones,
# resampling will be done.
logger.debug('read file/values: ' + str(v))
if v == "None":
#~ PCRmap = str("None")
PCRmap = None # 29 July: I made an experiment by changing the type of this object.
elif not re.match(r"[0-9.-]*$", v):
if absolutePath != None: v = getFullPath(v, absolutePath)
# print v
# print cloneMapFileName
sameClone = isSameClone(v, cloneMapFileName)
if sameClone == True:
PCRmap = pcr.readmap(v)
else:
# resample using GDAL:
output = tmpDir + 'temp.map'
warp = gdalwarpPCR(v, output, cloneMapFileName, tmpDir, isLddMap,
isNomMap)
# read from temporary file and delete the temporary file:
PCRmap = pcr.readmap(output)
if isLddMap == True:
PCRmap = pcr.ifthen(pcr.scalar(PCRmap) < 10., PCRmap)
if isLddMap == True: PCRmap = pcr.ldd(PCRmap)
if isNomMap == True:
PCRmap = pcr.ifthen(pcr.scalar(PCRmap) > 0., PCRmap)
if isNomMap == True: PCRmap = pcr.nominal(PCRmap)
if os.path.isdir(tmpDir):
shutil.rmtree(tmpDir)
os.makedirs(tmpDir)
else:
PCRmap = pcr.spatial(pcr.scalar(float(v)))
if cover != None:
PCRmap = pcr.cover(PCRmap, cover)
co = None
cOut = None
err = None
warp = None
del co
del cOut
del err
del warp
stdout = None
del stdout
stderr = None
del stderr
# SM: revisit this
PCRmap = pcr.pcr2numpy(PCRmap, np.nan)
return PCRmap
def __init__(self, iniItems, landmask, Dir, cloneMap, tmpDir):
object.__init__(self)
# clone map file names, temporary directory and global/absolute path of input directory
self.cloneMap = cloneMap #iniItems.cloneMap
self.tmpDir = tmpDir #iniItems.tmpDir
self.inputDir = Dir #iniItems.globalOptions['inputDir']
self.landmask = landmask
# local drainage direction:
self.lddMap = vos.readPCRmapClone(
iniItems.get("routingOptions", "lddMap"), self.cloneMap,
self.tmpDir, self.inputDir, True)
self.lddMap = pcr.lddrepair(pcr.ldd(self.lddMap))
self.lddMap = pcr.lddrepair(self.lddMap)
# option to activate water balance check
self.debugWaterBalance = True
if configget(iniItems, "routingOptions", "debugWaterBalance",
"True") == "False":
self.debugWaterBalance = False
# option to perform a run with only natural lakes (without reservoirs)
self.onlyNaturalWaterBodies = False
if "onlyNaturalWaterBodies" in iniItems._sections[
'routingOptions'] and configget(iniItems, "routingOptions",
"onlyNaturalWaterBodies",
"False") == "True":
logger.info(
"Using only natural water bodies identified in the year 1900. All reservoirs in 1900 are assumed as lakes."
)
self.onlyNaturalWaterBodies = True
self.dateForNaturalCondition = "1900-01-01" # The run for a natural condition should access only this date.
# names of files containing water bodies parameters
if configget(iniItems, "routingOptions", "waterBodyInputNC",
"None") == str(None):
self.useNetCDF = False
self.fracWaterInp = iniItems.get("routingOptions", "fracWaterInp")
self.waterBodyIdsInp = iniItems.get("routingOptions",
"waterBodyIds")
self.waterBodyTypInp = iniItems.get("routingOptions",
"waterBodyTyp")
self.resMaxCapInp = iniItems.get("routingOptions", "resMaxCapInp")
self.resSfAreaInp = iniItems.get("routingOptions", "resSfAreaInp")
else:
self.useNetCDF = True
self.ncFileInp = vos.getFullPath(\
iniItems.get("routingOptions","waterBodyInputNC"),\
self.inputDir)
# minimum width (m) used in the weir formula # TODO: define minWeirWidth based on the GLWD, GRanD database and/or bankfull discharge formula
self.minWeirWidth = 10.
# lower and upper limits at which reservoir release is terminated and
# at which reservoir release is equal to long-term average outflow
self.minResvrFrac = 0.10
self.maxResvrFrac = 0.75
def initial(self):
#####################
# * initial section #
#####################
#-constants
# betaQ [-]: constant of kinematic wave momentum equation
self.betaQ = 0.6
#-channel LDD
self.channelLDD= pcr.ifthenelse(self.waterBodies.distribution != 0,\
pcr.ldd(5),self.LDD)
#-channel area and storage
self.channelArea = self.channelWidth * self.channelLength
self.channelStorageCapacity= pcr.ifthenelse(self.waterBodies.distribution == 0,\
self.channelArea*self.channelDepth,pcr.scalar(0.))
#-basin outlets
self.basinOutlet = pcr.pit(self.LDD) != 0
#-read initial conditions
self.Q = clippedRead.get(self.QIniMap)
self.actualStorage = clippedRead.get(self.actualStorageIniMap)
self.actualStorage= pcr.ifthenelse(self.waterBodies.distribution != 0,\
pcr.ifthenelse(self.waterBodies.location != 0,\
pcr.areatotal(self.actualStorage,self.waterBodies.distribution),0),\
self.actualStorage)
self.waterBodies.actualStorage = self.waterBodies.retrieveMapValue(
self.actualStorage)
#-update targets of average and bankful discharge
self.waterBodies.averageQ = self.waterBodies.retrieveMapValue(
self.averageQ)
self.waterBodies.bankfulQ = self.waterBodies.retrieveMapValue(
self.bankfulQ)
#-return the parameters for the kinematic wave,
# including alpha, wetted area, flood fraction, flood volume and depth
# and the corresponding land area
floodedFraction,floodedDepth,\
self.wettedArea,self.alphaQ= self.kinAlphaComposite(self.actualStorage,self.floodplainMask)
self.wettedArea= self.waterBodies.returnMapValue(self.wettedArea,\
self.waterBodies.channelWidth+2.*self.waterBodies.updateWaterHeight())
self.waterFraction= pcr.ifthenelse(self.waterBodies.distribution == 0,\
pcr.max(self.waterFractionMask,floodedFraction),self.waterFractionMask)
self.landFraction = pcr.max(0., 1. - self.waterFraction)
#-update on velocity and check on Q - NOTE: does not work in case of reservoirs!
self.flowVelocity = pcr.ifthenelse(self.wettedArea > 0,
self.Q / self.wettedArea, 0.)
pcr.report(
self.flowVelocity,
pcrm.generateNameT(flowVelocityFileName,
0).replace('.000', '.ini'))
#-setting initial values for specific runoff and surface water extraction
self.landSurfaceQ = pcr.scalar(0.)
self.potWaterSurfaceQ = pcr.scalar(0.)
self.surfaceWaterExtraction = pcr.scalar(0.)
#-budget check: setting initial values for cumulative discharge and
# net cumulative input, including initial storage [m3]
self.totalDischarge = pcr.scalar(0.)
self.cumulativeDeltaStorage = pcr.catchmenttotal(
self.actualStorage, self.LDD)
def _parseLine(self, line, lineNumber, nrColumns, externalNames, keyDict):
line = re.sub("\n","",line)
line = re.sub("\t"," ",line)
result = None
# read until first comment
content = ""
content,sep,comment = line.partition("#")
if len(content) > 1:
collectionVariableName, sep, tail = content.partition(" ")
if collectionVariableName == self._varName:
tail = tail.strip()
key, sep, variableValue = tail.rpartition(" ")
if len(key.split()) != nrColumns:
tmp = re.sub("\(|\)|,","",str(key))
msg = "Error reading %s line %d, order of columns given (%s columns) does not match expected order of %s columns" %(self._fileName, lineNumber, len(key.split()) + 2, int(nrColumns) + 2)
raise ValueError(msg)
variableValue = re.sub('\"', "", variableValue)
tmp = None
try:
tmp = int(variableValue)
if self._dataType == pcraster.Boolean:
tmp = pcraster.boolean(tmp)
elif self._dataType == pcraster.Nominal:
tmp = pcraster.nominal(tmp)
elif self._dataType == pcraster.Ordinal:
tmp = pcraster.ordinal(tmp)
elif self._dataType == pcraster.Ldd:
tmp = pcraster.ldd(tmp)
else:
msg = "Conversion to %s failed" % (self._dataType)
raise Exception(msg)
except ValueError, e:
try:
tmp = float(variableValue)
if self._dataType == pcraster.Scalar:
tmp = pcraster.scalar(tmp)
elif self._dataType == pcraster.Directional:
tmp = pcraster.directional(tmp)
else:
msg = "Conversion to %s failed" % (self._dataType)
raise Exception(msg)
except ValueError,e:
variableValue = re.sub("\\\\","/",variableValue)
variableValue = variableValue.strip()
path = os.path.normpath(variableValue)
try:
tmp = pcraster.readmap(path)
except RuntimeError, e:
msg = "Error reading %s line %d, %s" %(self._fileName, lineNumber, e)
raise ValueError(msg)
def initial(self):
#####################
# * initial section #
#####################
#-constants
# betaQ [-]: constant of kinematic wave momentum equation
self.betaQ= 0.6
#-channel LDD
self.channelLDD= pcr.ifthenelse(self.waterBodies.distribution != 0,\
pcr.ldd(5),self.LDD)
#-channel area and storage
self.channelArea= self.channelWidth*self.channelLength
self.channelStorageCapacity= pcr.ifthenelse(self.waterBodies.distribution == 0,\
self.channelArea*self.channelDepth,pcr.scalar(0.))
#-basin outlets
self.basinOutlet= pcr.pit(self.LDD) != 0
#-read initial conditions
self.Q= clippedRead.get(self.QIniMap)
self.actualStorage= clippedRead.get(self.actualStorageIniMap)
self.actualStorage= pcr.ifthenelse(self.waterBodies.distribution != 0,\
pcr.ifthenelse(self.waterBodies.location != 0,\
pcr.areatotal(self.actualStorage,self.waterBodies.distribution),0),\
self.actualStorage)
self.waterBodies.actualStorage= self.waterBodies.retrieveMapValue(self.actualStorage)
#-update targets of average and bankful discharge
self.waterBodies.averageQ= self.waterBodies.retrieveMapValue(self.averageQ)
self.waterBodies.bankfulQ= self.waterBodies.retrieveMapValue(self.bankfulQ)
#-return the parameters for the kinematic wave,
# including alpha, wetted area, flood fraction, flood volume and depth
# and the corresponding land area
floodedFraction,floodedDepth,\
self.wettedArea,self.alphaQ= self.kinAlphaComposite(self.actualStorage,self.floodplainMask)
self.wettedArea= self.waterBodies.returnMapValue(self.wettedArea,\
self.waterBodies.channelWidth+2.*self.waterBodies.updateWaterHeight())
self.waterFraction= pcr.ifthenelse(self.waterBodies.distribution == 0,\
pcr.max(self.waterFractionMask,floodedFraction),self.waterFractionMask)
self.landFraction= pcr.max(0.,1.-self.waterFraction)
#-update on velocity and check on Q - NOTE: does not work in case of reservoirs!
self.flowVelocity= pcr.ifthenelse(self.wettedArea > 0,self.Q/self.wettedArea,0.)
pcr.report(self.flowVelocity,pcrm.generateNameT(flowVelocityFileName,0).replace('.000','.ini'))
#-setting initial values for specific runoff and surface water extraction
self.landSurfaceQ= pcr.scalar(0.)
self.potWaterSurfaceQ= pcr.scalar(0.)
self.surfaceWaterExtraction= pcr.scalar(0.)
#-budget check: setting initial values for cumulative discharge and
# net cumulative input, including initial storage [m3]
self.totalDischarge= pcr.scalar(0.)
self.cumulativeDeltaStorage= pcr.catchmenttotal(self.actualStorage,self.LDD)
def testNotEqualsLdd(self):
pcraster.setclone("accu_Ldd.map")
ldd = pcraster.readmap("accu_Ldd.map")
nonSpatial = pcraster._pcraster._newNonSpatialField(5)
# we need to explicitly cast PODs to ldd (or directional)
# when using the multicore module
#raster = mcop.pcrmcNE("accu_Ldd.map", 5)
raster = mcop.pcrmcNE("accu_Ldd.map", pcraster.ldd(5))
warnings.warn("Difference between pcraster and multicore module...")
value, isValid = pcraster.cellvalue(raster, 1)
self.assertEqual(isValid, True)
self.assertEqual(value, True)
value, isValid = pcraster.cellvalue(raster, 22)
self.assertEqual(isValid, True)
self.assertEqual(value, False)
value, isValid = pcraster.cellvalue(raster, 25)
self.assertEqual(isValid, True)
self.assertEqual(value, True)
def testNotEqualsLdd(self):
pcraster.setclone("accu_Ldd.map")
ldd = pcraster.readmap("accu_Ldd.map")
nonSpatial = pcraster._pcraster._newNonSpatialField(5)
# we need to explicitly cast PODs to ldd (or directional)
# when using the multicore module
#raster = mcop.pcrmcNE("accu_Ldd.map", 5)
raster = mcop.pcrmcNE("accu_Ldd.map", pcraster.ldd(5))
warnings.warn("Difference between pcraster and multicore module...")
value, isValid = pcraster.cellvalue(raster, 1)
self.assertEqual(isValid, True)
self.assertEqual(value, True)
value, isValid = pcraster.cellvalue(raster, 22)
self.assertEqual(isValid, True)
self.assertEqual(value, False)
value, isValid = pcraster.cellvalue(raster, 25)
self.assertEqual(isValid, True)
self.assertEqual(value, True)
def __init__(self, configuration, currTimeStep, initialState=None):
self._configuration = configuration
self._modelTime = currTimeStep
pcr.setclone(configuration.cloneMap)
# Read the ldd map.
self.lddMap = vos.readPCRmapClone(\
configuration.routingOptions['lddMap'],
configuration.cloneMap,configuration.tmpDir,configuration.globalOptions['inputDir'],True)
#ensure ldd map is correct, and actually of type "ldd"
self.lddMap = pcr.lddrepair(pcr.ldd(self.lddMap))
if configuration.globalOptions['landmask'] != "None":
self.landmask = vos.readPCRmapClone(\
configuration.globalOptions['landmask'],
configuration.cloneMap,configuration.tmpDir,configuration.globalOptions['inputDir'])
else:
self.landmask = pcr.defined(self.lddMap)
# defining catchment areas
self.catchment_class = 1.0
# number of upperSoilLayers:
self.numberOfSoilLayers = int(
configuration.landSurfaceOptions['numberOfUpperSoilLayers'])
# preparing sub-modules
self.createSubmodels(initialState)
# option for debugging to PCR-GLOBWB version 1.0
self.debug_to_version_one = False
if configuration.debug_to_version_one: self.debug_to_version_one = True
if self.debug_to_version_one:
# preparing initial folder directory
self.directory_for_initial_maps = vos.getFullPath(
"initials/", self.configuration.mapsDir)
if os.path.exists(self.directory_for_initial_maps):
shutil.rmtree(self.directory_for_initial_maps)
os.makedirs(self.directory_for_initial_maps)
# dump the initial state
self.dumpState(self.directory_for_initial_maps, "initial")
def testDeepCopyRasterNonSpatial(self):
pcraster.setclone("validated/boolean_Result.map")
raster = pcraster.boolean(1)
tmp = copy.deepcopy(raster)
self.assertEqual(True, self.arbitraryMapEquals(raster, tmp))
raster1 = pcraster.nominal(1)
tmp1 = copy.deepcopy(raster1)
self.assertEqual(True, self.arbitraryMapEquals(raster1, tmp1))
raster2 = pcraster.ordinal(1)
tmp2 = copy.deepcopy(raster2)
self.assertEqual(True, self.arbitraryMapEquals(raster2, tmp2))
raster3 = pcraster.scalar(1)
tmp3 = copy.deepcopy(raster3)
self.assertEqual(True, self.arbitraryMapEquals(raster3, tmp3))
raster4 = pcraster.directional(1)
tmp4 = copy.deepcopy(raster4)
self.assertEqual(True, self.arbitraryMapEquals(raster4, tmp4))
raster5 = pcraster.ldd(1)
tmp5 = copy.deepcopy(raster5)
self.assertEqual(True, self.arbitraryMapEquals(raster5, tmp5))
def testDeepCopyRasterNonSpatial(self):
pcraster.setclone("validated/boolean_Result.map")
raster = pcraster.boolean(1)
tmp = copy.deepcopy(raster)
self.assertEqual(True, self.arbitraryMapEquals(raster, tmp))
raster1 = pcraster.nominal(1)
tmp1 = copy.deepcopy(raster1)
self.assertEqual(True, self.arbitraryMapEquals(raster1, tmp1))
raster2 = pcraster.ordinal(1)
tmp2 = copy.deepcopy(raster2)
self.assertEqual(True, self.arbitraryMapEquals(raster2, tmp2))
raster3 = pcraster.scalar(1)
tmp3 = copy.deepcopy(raster3)
self.assertEqual(True, self.arbitraryMapEquals(raster3, tmp3))
raster4 = pcraster.directional(1)
tmp4 = copy.deepcopy(raster4)
self.assertEqual(True, self.arbitraryMapEquals(raster4, tmp4))
raster5 = pcraster.ldd(1)
tmp5 = copy.deepcopy(raster5)
self.assertEqual(True, self.arbitraryMapEquals(raster5, tmp5))
def pcr_preprocess(dem_in, x, y, itile, tempdir, ldd_in=None,
test=False, create_ldd=True):
"""
function to set pcr clone and translate DEM (terrain) and ldd numpy 2d arrays to pcr maps
:param terrain: masked numpy 2d array with elevation data
:param x: numpy 1d array with x coordinates of elevation grid
:param y: numpy 1d array with Y coordinates of elevation grid
:param tempdir: string with directory to temporary save clone pcrmap
:param ldd: numpy 2d array with ldd grid, make sure it uses the pcrmap definition of ldd
:param test: if True do not remove clone maps
:return: pcr maps for dem and ldd
"""
# create clone in temp_dir
fn_clone = os.path.join(tempdir, '_{:03d}_dem.map'.format(itile))
cl.makeDir(tempdir) # make dir if not exist
# DEM
gdal_writemap(fn_clone, 'PCRaster', x, y, dem_in, -9999) # note: missing value needs conversion in python item
pcr.setclone(fn_clone)
pcr.setglobaloption("unitcell")
dem = pcr.readmap(fn_clone)
# cleanup
if not test:
os.unlink(fn_clone) # cleanup clone file
os.unlink(fn_clone+'.aux.xml')
# LDD
if create_ldd:
if ldd_in is None:
print('Calculating LDD')
ldd = pcr.lddcreate(dem, 1E31, 1E31, 1E31, 1E31)
else:
# TODO note that np.nan is default NoDataValue for ldd file. check this when reading data
# TODO: x and y axis got mixed up when translating with numpy2pcr. check if it works here!
# in process_tile function in coastal_inun.py
ldd = pcr.lddrepair(pcr.ldd(pcr.numpy2pcr(pcr.Ldd, ldd_in, np.nan)))
else:
ldd = None
return dem, ldd
def __init__(self, configuration, currTimeStep):
self._configuration = configuration
self._modelTime = currTimeStep
pcr.setclone(configuration.cloneMap)
# read the ldd map
self.lddMap = vos.netcdf2PCRobjCloneWithoutTime(configuration.modflowParameterOptions['channelNC'],'lddMap',\
configuration.cloneMap)
# ensure ldd map is correct, and actually of type "ldd"
self.lddMap = pcr.lddrepair(pcr.ldd(self.lddMap))
# defining the landmask map
if configuration.globalOptions['landmask'] != "None":
self.landmask = vos.readPCRmapClone(\
configuration.globalOptions['landmask'],
configuration.cloneMap,configuration.tmpDir,configuration.globalOptions['inputDir'])
else:
self.landmask = pcr.defined(self.lddMap)
# preparing the sub-model(s) - Currently, there is only one sub-model.
self.createSubmodels()
def readPCRmapClone(v,cloneMapFileName,tmpDir,absolutePath=None,isLddMap=False,cover=None,isNomMap=False,inputEPSG="EPSG:4326",outputEPSG="EPSG:4326",method="near"):
# v: inputMapFileName or floating values
# cloneMapFileName: If the inputMap and cloneMap have different clones,
# resampling will be done.
logger.debug('read file/values: '+str(v))
if v == "None":
PCRmap = str("None")
elif not re.match(r"[0-9.-]*$",v):
if absolutePath != None: v = getFullPath(v,absolutePath)
# print(v)
sameClone = isSameClone(v,cloneMapFileName)
if sameClone == True:
PCRmap = pcr.readmap(v)
else:
# resample using GDAL:
output = tmpDir+'temp.map'
# if no re-projection needed:
if inputEPSG == outputEPSG or outputEPSG == None:
warp = gdalwarpPCR(v,output,cloneMapFileName,tmpDir,isLddMap,isNomMap)
else:
warp = gdalwarpPCR(v,output,cloneMapFileName,tmpDir,isLddMap,isNomMap,inputEPSG,outputEPSG,method)
# read from temporary file and delete the temporary file:
PCRmap = pcr.readmap(output)
if isLddMap == True: PCRmap = pcr.ifthen(pcr.scalar(PCRmap) < 10., PCRmap)
if isLddMap == True: PCRmap = pcr.ldd(PCRmap)
if isNomMap == True: PCRmap = pcr.ifthen(pcr.scalar(PCRmap) > 0., PCRmap)
if isNomMap == True: PCRmap = pcr.nominal(PCRmap)
if os.path.isdir(tmpDir):
shutil.rmtree(tmpDir)
os.makedirs(tmpDir)
else:
PCRmap = pcr.scalar(float(v))
if cover != None:
PCRmap = pcr.cover(PCRmap, cover)
co = None; cOut = None; err = None; warp = None
del co; del cOut; del err; del warp
stdout = None; del stdout
stderr = None; del stderr
return PCRmap
def readPCRmapClone(v,cloneMapFileName,tmpDir,absolutePath=None,isLddMap=False,cover=None,isNomMap=False,inputEPSG="EPSG:4326",outputEPSG="EPSG:4326",method="near"):
# v: inputMapFileName or floating values
# cloneMapFileName: If the inputMap and cloneMap have different clones,
# resampling will be done.
logger.debug('read file/values: '+str(v))
if v == "None":
PCRmap = str("None")
elif not re.match(r"[0-9.-]*$",v):
if absolutePath != None: v = getFullPath(v,absolutePath)
# print(v)
sameClone = isSameClone(v,cloneMapFileName)
if sameClone == True:
PCRmap = pcr.readmap(v)
else:
# resample using GDAL:
output = tmpDir+'temp.map'
# if no re-projection needed:
if inputEPSG == outputEPSG or outputEPSG == None:
warp = gdalwarpPCR(v,output,cloneMapFileName,tmpDir,isLddMap,isNomMap)
else:
warp = gdalwarpPCR(v,output,cloneMapFileName,tmpDir,isLddMap,isNomMap,inputEPSG,outputEPSG,method)
# read from temporary file and delete the temporary file:
PCRmap = pcr.readmap(output)
if isLddMap == True: PCRmap = pcr.ifthen(pcr.scalar(PCRmap) < 10., PCRmap)
if isLddMap == True: PCRmap = pcr.ldd(PCRmap)
if isNomMap == True: PCRmap = pcr.ifthen(pcr.scalar(PCRmap) > 0., PCRmap)
if isNomMap == True: PCRmap = pcr.nominal(PCRmap)
if os.path.isdir(tmpDir):
shutil.rmtree(tmpDir)
os.makedirs(tmpDir)
else:
PCRmap = pcr.scalar(float(v))
if cover != None:
PCRmap = pcr.cover(PCRmap, cover)
co = None; cOut = None; err = None; warp = None
del co; del cOut; del err; del warp
stdout = None; del stdout
stderr = None; del stderr
return PCRmap
def main():
### Read input arguments #####
parser = OptionParser()
usage = "usage: %prog [options]"
parser = OptionParser(usage=usage)
parser.add_option('-q', '--quiet',
dest='verbose', default=True, action='store_false',
help='do not print status messages to stdout')
parser.add_option('-i', '--ini', dest='inifile',
default='hand_contour_inun.ini', nargs=1,
help='ini configuration file')
parser.add_option('-f', '--flood_map',
nargs=1, dest='flood_map',
help='Flood map file (NetCDF point time series file')
parser.add_option('-v', '--flood_variable',
nargs=1, dest='flood_variable',
default='water_level',
help='variable name of flood water level')
parser.add_option('-b', '--bankfull_map',
dest='bankfull_map', default='',
help='Map containing bank full level (is subtracted from flood map, in NetCDF)')
parser.add_option('-c', '--catchment',
dest='catchment_strahler', default=7, type='int',
help='Strahler order threshold >= are selected as catchment boundaries')
parser.add_option('-s', '--hand_strahler',
dest='hand_strahler', default=7, type='int',
help='Strahler order threshold >= selected as riverine')
parser.add_option('-d', '--destination',
dest='dest_path', default='inun',
help='Destination path')
(options, args) = parser.parse_args()
if not os.path.exists(options.inifile):
print 'path to ini file cannot be found'
sys.exit(1)
options.dest_path = os.path.abspath(options.dest_path)
if not(os.path.isdir(options.dest_path)):
os.makedirs(options.dest_path)
# set up the logger
flood_name = os.path.split(options.flood_map)[1].split('.')[0]
case_name = 'inun_{:s}_hand_{:02d}_catch_{:02d}'.format(flood_name, options.hand_strahler, options.catchment_strahler)
logfilename = os.path.join(options.dest_path, 'hand_contour_inun.log')
logger, ch = inun_lib.setlogger(logfilename, 'HAND_INUN', options.verbose)
logger.info('$Id: $')
logger.info('Flood map: {:s}'.format(options.flood_map))
logger.info('Bank full map: {:s}'.format(options.bankfull_map))
logger.info('Destination path: {:s}'.format(options.dest_path))
# read out ini file
### READ CONFIG FILE
# open config-file
config = inun_lib.open_conf(options.inifile)
# read settings
options.dem_file = inun_lib.configget(config, 'maps',
'dem_file',
True)
options.ldd_file = inun_lib.configget(config, 'maps',
'ldd_file',
True)
options.stream_file = inun_lib.configget(config, 'maps',
'stream_file',
True)
options.riv_length_file = inun_lib.configget(config, 'maps',
'riv_length_file',
True)
options.riv_width_file = inun_lib.configget(config, 'maps',
'riv_width_file',
True)
options.file_format = inun_lib.configget(config, 'maps',
'file_format', 0, datatype='int')
options.x_tile = inun_lib.configget(config, 'tiling',
'x_tile', 10000, datatype='int')
options.y_tile = inun_lib.configget(config, 'tiling',
'y_tile', 10000, datatype='int')
options.x_overlap = inun_lib.configget(config, 'tiling',
'x_overlap', 1000, datatype='int')
options.y_overlap = inun_lib.configget(config, 'tiling',
'y_overlap', 1000, datatype='int')
options.iterations = inun_lib.configget(config, 'inundation',
'iterations', 20, datatype='int')
options.initial_level = inun_lib.configget(config, 'inundation',
'initial_level', 32., datatype='float')
options.area_multiplier = inun_lib.configget(config, 'inundation',
'area_multiplier', 1., datatype='float')
logger.info('DEM file: {:s}'.format(options.dem_file))
logger.info('LDD file: {:s}'.format(options.ldd_file))
logger.info('Columns per tile: {:d}'.format(options.x_tile))
logger.info('Rows per tile: {:d}'.format(options.y_tile))
logger.info('Columns overlap: {:d}'.format(options.x_overlap))
logger.info('Rows overlap: {:d}'.format(options.y_overlap))
metadata_global = {}
# add metadata from the section [metadata]
meta_keys = config.options('metadata_global')
for key in meta_keys:
metadata_global[key] = config.get('metadata_global', key)
# add a number of metadata variables that are mandatory
metadata_global['config_file'] = os.path.abspath(options.inifile)
metadata_var = {}
metadata_var['units'] = 'm'
metadata_var['standard_name'] = 'water_surface_height_above_reference_datum'
metadata_var['long_name'] = 'Coastal flooding'
metadata_var['comment'] = 'water_surface_reference_datum_altitude is given in file {:s}'.format(options.dem_file)
if not os.path.exists(options.dem_file):
logger.error('path to dem file {:s} cannot be found'.format(options.dem_file))
sys.exit(1)
if not os.path.exists(options.ldd_file):
logger.error('path to ldd file {:s} cannot be found'.format(options.ldd_file))
sys.exit(1)
# Read extent from a GDAL compatible file
try:
extent = inun_lib.get_gdal_extent(options.dem_file)
except:
msg = 'Input file {:s} not a gdal compatible file'.format(options.dem_file)
inun_lib.close_with_error(logger, ch, msg)
sys.exit(1)
try:
x, y = inun_lib.get_gdal_axes(options.dem_file, logging=logger)
srs = inun_lib.get_gdal_projection(options.dem_file, logging=logger)
except:
msg = 'Input file {:s} not a gdal compatible file'.format(options.dem_file)
inun_lib.close_with_error(logger, ch, msg)
sys.exit(1)
# read history from flood file
if options.file_format == 0:
a = nc.Dataset(options.flood_map, 'r')
metadata_global['history'] = 'Created by: $Id: $, boundary conditions from {:s},\nhistory: {:s}'.format(os.path.abspath(options.flood_map), a.history)
a.close()
else:
metadata_global['history'] = 'Created by: $Id: $, boundary conditions from {:s},\nhistory: {:s}'.format(os.path.abspath(options.flood_map), 'PCRaster file, no history')
# first write subcatch maps and hand maps
############### TODO ######
# setup a HAND file
dem_name = os.path.split(options.dem_file)[1].split('.')[0]
hand_file = os.path.join(options.dest_path, '{:s}_hand_strahler_{:02d}.tif'.format(dem_name, options.hand_strahler))
if not(os.path.isfile(hand_file)):
# hand file does not exist yet! Generate it, otherwise skip!
logger.info('HAND file {:s} setting up...please wait...'.format(hand_file))
hand_file_tmp = os.path.join(options.dest_path, '{:s}_hand_strahler_{:02d}.tif.tmp'.format(dem_name, options.hand_strahler))
ds_hand = inun_lib.prepare_gdal(hand_file_tmp, x, y, logging=logger, srs=srs)
band_hand = ds_hand.GetRasterBand(1)
# Open terrain data for reading
ds_dem, rasterband_dem = inun_lib.get_gdal_rasterband(options.dem_file)
ds_ldd, rasterband_ldd = inun_lib.get_gdal_rasterband(options.ldd_file)
ds_stream, rasterband_stream = inun_lib.get_gdal_rasterband(options.stream_file)
n = 0
for x_loop in range(0, len(x), options.x_tile):
x_start = np.maximum(x_loop, 0)
x_end = np.minimum(x_loop + options.x_tile, len(x))
# determine actual overlap for cutting
for y_loop in range(0, len(y), options.y_tile):
x_overlap_min = x_start - np.maximum(x_start - options.x_overlap, 0)
x_overlap_max = np.minimum(x_end + options.x_overlap, len(x)) - x_end
n += 1
# print('tile {:001d}:'.format(n))
y_start = np.maximum(y_loop, 0)
y_end = np.minimum(y_loop + options.y_tile, len(y))
y_overlap_min = y_start - np.maximum(y_start - options.y_overlap, 0)
y_overlap_max = np.minimum(y_end + options.y_overlap, len(y)) - y_end
# cut out DEM
logger.debug('Computing HAND for xmin: {:d} xmax: {:d} ymin {:d} ymax {:d}'.format(x_start, x_end,y_start, y_end))
terrain = rasterband_dem.ReadAsArray(x_start - x_overlap_min,
y_start - y_overlap_min,
(x_end + x_overlap_max) - (x_start - x_overlap_min),
(y_end + y_overlap_max) - (y_start - y_overlap_min)
)
drainage = rasterband_ldd.ReadAsArray(x_start - x_overlap_min,
y_start - y_overlap_min,
(x_end + x_overlap_max) - (x_start - x_overlap_min),
(y_end + y_overlap_max) - (y_start - y_overlap_min)
)
stream = rasterband_stream.ReadAsArray(x_start - x_overlap_min,
y_start - y_overlap_min,
(x_end + x_overlap_max) - (x_start - x_overlap_min),
(y_end + y_overlap_max) - (y_start - y_overlap_min)
)
# write to temporary file
terrain_temp_file = os.path.join(options.dest_path, 'terrain_temp.map')
drainage_temp_file = os.path.join(options.dest_path, 'drainage_temp.map')
stream_temp_file = os.path.join(options.dest_path, 'stream_temp.map')
if rasterband_dem.GetNoDataValue() is not None:
inun_lib.gdal_writemap(terrain_temp_file, 'PCRaster',
np.arange(0, terrain.shape[1]),
np.arange(0, terrain.shape[0]),
terrain, rasterband_dem.GetNoDataValue(),
gdal_type=gdal.GDT_Float32,
logging=logger)
else:
# in case no nodata value is found
logger.warning('No nodata value found in {:s}. assuming -9999'.format(options.dem_file))
inun_lib.gdal_writemap(terrain_temp_file, 'PCRaster',
np.arange(0, terrain.shape[1]),
np.arange(0, terrain.shape[0]),
terrain, -9999.,
gdal_type=gdal.GDT_Float32,
logging=logger)
inun_lib.gdal_writemap(drainage_temp_file, 'PCRaster',
np.arange(0, terrain.shape[1]),
np.arange(0, terrain.shape[0]),
drainage, rasterband_ldd.GetNoDataValue(),
gdal_type=gdal.GDT_Int32,
logging=logger)
inun_lib.gdal_writemap(stream_temp_file, 'PCRaster',
np.arange(0, terrain.shape[1]),
np.arange(0, terrain.shape[0]),
stream, rasterband_ldd.GetNoDataValue(),
gdal_type=gdal.GDT_Int32,
logging=logger)
# read as pcr objects
pcr.setclone(terrain_temp_file)
terrain_pcr = pcr.readmap(terrain_temp_file)
drainage_pcr = pcr.lddrepair(pcr.ldd(pcr.readmap(drainage_temp_file))) # convert to ldd type map
stream_pcr = pcr.scalar(pcr.readmap(stream_temp_file)) # convert to ldd type map
# compute streams
stream_ge, subcatch = inun_lib.subcatch_stream(drainage_pcr, stream_pcr, options.hand_strahler) # generate streams
basin = pcr.boolean(subcatch)
hand_pcr, dist_pcr = inun_lib.derive_HAND(terrain_pcr, drainage_pcr, 3000, rivers=pcr.boolean(stream_ge), basin=basin)
# convert to numpy
hand = pcr.pcr2numpy(hand_pcr, -9999.)
# cut relevant part
if y_overlap_max == 0:
y_overlap_max = -hand.shape[0]
if x_overlap_max == 0:
x_overlap_max = -hand.shape[1]
hand_cut = hand[0+y_overlap_min:-y_overlap_max, 0+x_overlap_min:-x_overlap_max]
band_hand.WriteArray(hand_cut, x_start, y_start)
os.unlink(terrain_temp_file)
os.unlink(drainage_temp_file)
band_hand.FlushCache()
ds_dem = None
ds_ldd = None
ds_stream = None
band_hand.SetNoDataValue(-9999.)
ds_hand = None
logger.info('Finalizing {:s}'.format(hand_file))
# rename temporary file to final hand file
os.rename(hand_file_tmp, hand_file)
else:
logger.info('HAND file {:s} already exists...skipping...'.format(hand_file))
#####################################################################################
# HAND file has now been prepared, moving to flood mapping part #
#####################################################################################
# load the staticmaps needed to estimate volumes across all
xax, yax, riv_length, fill_value = inun_lib.gdal_readmap(options.riv_length_file, 'GTiff')
riv_length = np.ma.masked_where(riv_length==fill_value, riv_length)
xax, yax, riv_width, fill_value = inun_lib.gdal_readmap(options.riv_width_file, 'GTiff')
riv_width[riv_width == fill_value] = 0
x_res = np.abs((xax[-1]-xax[0])/(len(xax)-1))
y_res = np.abs((yax[-1]-yax[0])/(len(yax)-1))
flood_folder = os.path.join(options.dest_path, case_name)
flood_vol_map = os.path.join(flood_folder, '{:s}_vol.tif'.format(os.path.split(options.flood_map)[1].split('.')[0]))
if not(os.path.isdir(flood_folder)):
os.makedirs(flood_folder)
inun_file_tmp = os.path.join(flood_folder, '{:s}.tif.tmp'.format(case_name))
inun_file = os.path.join(flood_folder, '{:s}.tif'.format(case_name))
hand_temp_file = os.path.join(flood_folder, 'hand_temp.map')
drainage_temp_file = os.path.join(flood_folder, 'drainage_temp.map')
stream_temp_file = os.path.join(flood_folder, 'stream_temp.map')
flood_vol_temp_file = os.path.join(flood_folder, 'flood_warp_temp.tif')
# load the data with river levels and compute the volumes
if options.file_format == 0:
# assume we need the maximum value in a NetCDF time series grid
a = nc.Dataset(options.flood_map, 'r')
xax = a.variables['x'][:]
yax = a.variables['y'][:]
flood_series = a.variables[options.flood_variable][:]
flood_data = flood_series.max(axis=0)
if np.ma.is_masked(flood_data):
flood = flood_data.data
flood[flood_data.mask] = 0
if yax[-1] > yax[0]:
yax = np.flipud(yax)
flood = np.flipud(flood)
a.close()
elif options.file_format == 1:
xax, yax, flood, flood_fill_value = inun_lib.gdal_readmap(options.flood_map, 'PCRaster')
flood[flood==flood_fill_value] = 0.
#res_x = x[1]-x[0]
#res_y = y[1]-y[0]
# load the bankfull depths
if options.bankfull_map == '':
bankfull = np.zeros(flood.shape)
else:
if options.file_format == 0:
a = nc.Dataset(options.bankfull_map, 'r')
xax = a.variables['x'][:]
yax = a.variables['y'][:]
bankfull = a.variables[options.flood_variable][0, :, :]
if yax[-1] > yax[0]:
yax = np.flipud(yax)
bankfull = np.flipud(bankful)
a.close()
elif options.file_format == 1:
xax, yax, bankfull, bankfull_fill_value = inun_lib.gdal_readmap(options.bankfull_map, 'PCRaster')
# flood = bankfull*2
# res_x = 2000
# res_y = 2000
# subtract the bankfull water level to get flood levels (above bankfull)
flood_vol = np.maximum(flood-bankfull, 0)
flood_vol_m = riv_length*riv_width*flood_vol/(x_res * y_res) # volume expressed in meters water disc (1e6 is the surface area of one wflow grid cell)
flood_vol_m_data = flood_vol_m.data
flood_vol_m_data[flood_vol_m.mask] = -999.
print('Saving water layer map to {:s}'.format(flood_vol_map))
# write to a tiff file
inun_lib.gdal_writemap(flood_vol_map, 'GTiff', xax, yax, np.maximum(flood_vol_m_data, 0), -999.)
ds_hand, rasterband_hand = inun_lib.get_gdal_rasterband(hand_file)
ds_ldd, rasterband_ldd = inun_lib.get_gdal_rasterband(options.ldd_file)
ds_stream, rasterband_stream = inun_lib.get_gdal_rasterband(options.stream_file)
logger.info('Preparing flood map in {:s} ...please wait...'.format(inun_file))
ds_inun = inun_lib.prepare_gdal(inun_file_tmp, x, y, logging=logger, srs=srs)
band_inun = ds_inun.GetRasterBand(1)
# loop over all the tiles
n = 0
for x_loop in range(0, len(x), options.x_tile):
x_start = np.maximum(x_loop, 0)
x_end = np.minimum(x_loop + options.x_tile, len(x))
# determine actual overlap for cutting
for y_loop in range(0, len(y), options.y_tile):
x_overlap_min = x_start - np.maximum(x_start - options.x_overlap, 0)
x_overlap_max = np.minimum(x_end + options.x_overlap, len(x)) - x_end
n += 1
# print('tile {:001d}:'.format(n))
y_start = np.maximum(y_loop, 0)
y_end = np.minimum(y_loop + options.y_tile, len(y))
y_overlap_min = y_start - np.maximum(y_start - options.y_overlap, 0)
y_overlap_max = np.minimum(y_end + options.y_overlap, len(y)) - y_end
x_tile_ax = x[x_start - x_overlap_min:x_end + x_overlap_max]
y_tile_ax = y[y_start - y_overlap_min:y_end + y_overlap_max]
# cut out DEM
logger.debug('handling xmin: {:d} xmax: {:d} ymin {:d} ymax {:d}'.format(x_start, x_end, y_start, y_end))
hand = rasterband_hand.ReadAsArray(x_start - x_overlap_min,
y_start - y_overlap_min,
(x_end + x_overlap_max) - (x_start - x_overlap_min),
(y_end + y_overlap_max) - (y_start - y_overlap_min)
)
drainage = rasterband_ldd.ReadAsArray(x_start - x_overlap_min,
y_start - y_overlap_min,
(x_end + x_overlap_max) - (x_start - x_overlap_min),
(y_end + y_overlap_max) - (y_start - y_overlap_min)
)
stream = rasterband_stream.ReadAsArray(x_start - x_overlap_min,
y_start - y_overlap_min,
(x_end + x_overlap_max) - (x_start - x_overlap_min),
(y_end + y_overlap_max) - (y_start - y_overlap_min)
)
print('len x-ax: {:d} len y-ax {:d} x-shape {:d} y-shape {:d}'.format(len(x_tile_ax), len(y_tile_ax), hand.shape[1], hand.shape[0]))
inun_lib.gdal_writemap(hand_temp_file, 'PCRaster',
x_tile_ax,
y_tile_ax,
hand, rasterband_hand.GetNoDataValue(),
gdal_type=gdal.GDT_Float32,
logging=logger)
inun_lib.gdal_writemap(drainage_temp_file, 'PCRaster',
x_tile_ax,
y_tile_ax,
drainage, rasterband_ldd.GetNoDataValue(),
gdal_type=gdal.GDT_Int32,
logging=logger)
inun_lib.gdal_writemap(stream_temp_file, 'PCRaster',
x_tile_ax,
y_tile_ax,
stream, rasterband_stream.GetNoDataValue(),
gdal_type=gdal.GDT_Int32,
logging=logger)
# read as pcr objects
pcr.setclone(hand_temp_file)
hand_pcr = pcr.readmap(hand_temp_file)
drainage_pcr = pcr.lddrepair(pcr.ldd(pcr.readmap(drainage_temp_file))) # convert to ldd type map
stream_pcr = pcr.scalar(pcr.readmap(drainage_temp_file)) # convert to ldd type map
# prepare a subcatchment map
stream_ge, subcatch = inun_lib.subcatch_stream(drainage_pcr, stream_pcr, options.catchment_strahler) # generate subcatchments
drainage_surf = pcr.ifthen(stream_ge > 0, pcr.accuflux(drainage_pcr, 1)) # proxy of drainage surface inaccurate at tile edges
# compute weights for spreadzone (1/drainage_surf)
subcatch = pcr.spreadzone(subcatch, 0, 0)
# TODO check weighting scheme, perhaps not necessary
# weight = 1./pcr.scalar(pcr.spreadzone(pcr.cover(pcr.ordinal(drainage_surf), 0), 0, 0))
# subcatch_fill = pcr.scalar(pcr.spreadzone(subcatch, 0, weight))
# # cover subcatch with subcatch_fill
# pcr.report(weight, 'weight_{:02d}.map'.format(n))
# pcr.report(subcatch, 'subcatch_{:02d}.map'.format(n))
# pcr.report(pcr.nominal(subcatch_fill), 'subcatch_fill_{:02d}.map'.format(n))
inun_lib.gdal_warp(flood_vol_map, hand_temp_file, flood_vol_temp_file, gdal_interp=gdalconst.GRA_NearestNeighbour) # ,
x_tile_ax, y_tile_ax, flood_meter, fill_value = inun_lib.gdal_readmap(flood_vol_temp_file, 'GTiff')
# convert meter depth to volume [m3]
flood_vol = pcr.numpy2pcr(pcr.Scalar, flood_meter, fill_value)*((x_tile_ax[1] - x_tile_ax[0]) * (y_tile_ax[0] - y_tile_ax[1])) # resolution of SRTM *1166400000.
## now we have some nice volume. Now we need to redistribute!
inundation_pcr = inun_lib.volume_spread(drainage_pcr, hand_pcr, subcatch, flood_vol,
volume_thres=0., iterations=options.iterations,
area_multiplier=options.area_multiplier) # 1166400000.
inundation = pcr.pcr2numpy(inundation_pcr, -9999.)
# cut relevant part
if y_overlap_max == 0:
y_overlap_max = -inundation.shape[0]
if x_overlap_max == 0:
x_overlap_max = -inundation.shape[1]
inundation_cut = inundation[0+y_overlap_min:-y_overlap_max, 0+x_overlap_min:-x_overlap_max]
# inundation_cut
band_inun.WriteArray(inundation_cut, x_start, y_start)
band_inun.FlushCache()
# clean up
os.unlink(flood_vol_temp_file)
os.unlink(drainage_temp_file)
os.unlink(hand_temp_file)
# if n == 35:
# band_inun.SetNoDataValue(-9999.)
# ds_inun = None
# sys.exit(0)
os.unlink(flood_vol_map)
logger.info('Finalizing {:s}'.format(inun_file))
# add the metadata to the file and band
band_inun.SetNoDataValue(-9999.)
ds_inun.SetMetadata(metadata_global)
band_inun.SetMetadata(metadata_var)
ds_inun = None
ds_hand = None
ds_ldd = None
# rename temporary file to final hand file
if os.path.isfile(inun_file):
# remove an old result if available
os.unlink(inun_file)
os.rename(inun_file_tmp, inun_file)
logger.info('Done! Thank you for using hand_contour_inun.py')
logger, ch = inun_lib.closeLogger(logger, ch)
del logger, ch
sys.exit(0)
print("")
print(cmd)
os.system(cmd)
print("")
input_files['averageClimatologyDischargeMonthAvg'] = out_file
# set the pcraster clone, ldd, landmask, and cell area map
msg = "Setting the clone, ldd, landmask, and cell area maps" + ":"
logger.info(msg)
# - clone
clone_map_file = input_files['clone_map_05min']
pcr.setclone(clone_map_file)
# - ldd
ldd = vos.readPCRmapClone(input_files['ldd_map_05min'], clone_map_file,
output_files['tmp_folder'], None, True)
ldd = pcr.lddrepair(pcr.ldd(ldd))
ldd = pcr.lddrepair(ldd)
# - landmask
landmask = pcr.ifthen(pcr.defined(ldd), pcr.boolean(1.0))
# - cell area
cell_area = vos.readPCRmapClone(input_files['cell_area_05min'], clone_map_file,
output_files['tmp_folder'])
# set the basin map
msg = "Setting the basin map" + ":"
logger.info(msg)
basin_map = pcr.nominal(\
vos.readPCRmapClone(input_files['basin_map_05min'],
input_files['clone_map_05min'],
output_files['tmp_folder'],
None, False, None, True))
# - set the landmask
landmask_map_file = "/projects/0/dfguu/data/hydroworld/others/05ArcMinCloneMaps/new_masks_from_top/mask_" + str(mask_code) + ".map"
msg = "Set the landmask to : " + str(landmask_map_file)
logger.info(msg)
landmask = pcr.readmap(landmask_map_file)
# resampling low resolution ldd map
msg = "Resample the low resolution ldd map."
logger.info(msg)
ldd_map_low_resolution_file_name = "/projects/0/dfguu/data/hydroworld/PCRGLOBWB20/input5min/routing/lddsound_05min.map"
ldd_map_low_resolution = vos.readPCRmapClone(ldd_map_low_resolution_file_name, \
clone_map_file, \
tmp_folder, \
None, True, None, False)
ldd_map_low_resolution = pcr.ifthen(landmask, ldd_map_low_resolution) # NOTE THAT YOU MAY NOT HAVE TO MASK-OUT THE LDD.
ldd_map_low_resolution = pcr.lddrepair(pcr.ldd(ldd_map_low_resolution))
ldd_map_low_resolution = pcr.lddrepair(ldd_map_low_resolution)
pcr.report(ldd_map_low_resolution, "resampled_low_resolution_ldd.map")
# permanent water bodies files (at 5 arc-minute resolution)
reservoir_capacity_file = "/projects/0/dfguu/data/hydroworld/PCRGLOBWB20/input5min/routing/reservoirs/waterBodiesFinal_version15Sept2013/maps/reservoircapacity_2010.map"
fracwat_file = "/projects/0/dfguu/data/hydroworld/PCRGLOBWB20/input5min/routing/reservoirs/waterBodiesFinal_version15Sept2013/maps/fracwat_2010.map"
water_body_id_file = "/projects/0/dfguu/data/hydroworld/PCRGLOBWB20/input5min/routing/reservoirs/waterBodiesFinal_version15Sept2013/maps/waterbodyid_2010.map"
# cell_area_file
cell_area_file = "/projects/0/dfguu/data/hydroworld/PCRGLOBWB20/input5min/routing/cellsize05min.correct.map"
# bankfull capacity (5 arcmin, volume: m3)
def main():
### Read input arguments #####
parser = OptionParser()
usage = "usage: %prog [options]"
parser = OptionParser(usage=usage)
parser.add_option(
"-q",
"--quiet",
dest="verbose",
default=True,
action="store_false",
help="do not print status messages to stdout",
)
parser.add_option(
"-i",
"--ini",
dest="inifile",
default="hand_contour_inun.ini",
nargs=1,
help="ini configuration file",
)
parser.add_option(
"-f",
"--flood_map",
nargs=1,
dest="flood_map",
help="Flood map file (NetCDF point time series file",
)
parser.add_option(
"-v",
"--flood_variable",
nargs=1,
dest="flood_variable",
default="water_level",
help="variable name of flood water level",
)
parser.add_option(
"-b",
"--bankfull_map",
dest="bankfull_map",
default="",
help="Map containing bank full level (is subtracted from flood map, in NetCDF)",
)
parser.add_option(
"-c",
"--catchment",
dest="catchment_strahler",
default=7,
type="int",
help="Strahler order threshold >= are selected as catchment boundaries",
)
parser.add_option(
"-t",
"--time",
dest="time",
default="",
help="time in YYYYMMDDHHMMSS, overrides time in NetCDF input if set",
)
# parser.add_option('-s', '--hand_strahler',
# dest='hand_strahler', default=7, type='int',
# help='Strahler order threshold >= selected as riverine')
parser.add_option(
"-m",
"--max_strahler",
dest="max_strahler",
default=1000,
type="int",
help="Maximum Strahler order to loop over",
)
parser.add_option(
"-d", "--destination", dest="dest_path", default="inun", help="Destination path"
)
parser.add_option(
"-H",
"--hand_file_prefix",
dest="hand_file_prefix",
default="",
help="optional HAND file prefix of already generated HAND files",
)
parser.add_option(
"-n",
"--neg_HAND",
dest="neg_HAND",
default=0,
type="int",
help="if set to 1, allow for negative HAND values in HAND maps",
)
(options, args) = parser.parse_args()
if not os.path.exists(options.inifile):
print "path to ini file cannot be found"
sys.exit(1)
options.dest_path = os.path.abspath(options.dest_path)
if not (os.path.isdir(options.dest_path)):
os.makedirs(options.dest_path)
# set up the logger
flood_name = os.path.split(options.flood_map)[1].split(".")[0]
# case_name = 'inun_{:s}_hand_{:02d}_catch_{:02d}'.format(flood_name, options.hand_strahler, options.catchment_strahler)
case_name = "inun_{:s}_catch_{:02d}".format(flood_name, options.catchment_strahler)
logfilename = os.path.join(options.dest_path, "hand_contour_inun.log")
logger, ch = inun_lib.setlogger(logfilename, "HAND_INUN", options.verbose)
logger.info("$Id: $")
logger.info("Flood map: {:s}".format(options.flood_map))
logger.info("Bank full map: {:s}".format(options.bankfull_map))
logger.info("Destination path: {:s}".format(options.dest_path))
# read out ini file
### READ CONFIG FILE
# open config-file
config = inun_lib.open_conf(options.inifile)
# read settings
options.dem_file = inun_lib.configget(config, "HighResMaps", "dem_file", True)
options.ldd_file = inun_lib.configget(config, "HighResMaps", "ldd_file", True)
options.stream_file = inun_lib.configget(config, "HighResMaps", "stream_file", True)
options.riv_length_fact_file = inun_lib.configget(
config, "wflowResMaps", "riv_length_fact_file", True
)
options.ldd_wflow = inun_lib.configget(config, "wflowResMaps", "ldd_wflow", True)
options.riv_width_file = inun_lib.configget(
config, "wflowResMaps", "riv_width_file", True
)
options.file_format = inun_lib.configget(
config, "file_settings", "file_format", 0, datatype="int"
)
options.out_format = inun_lib.configget(
config, "file_settings", "out_format", 0, datatype="int"
)
options.latlon = inun_lib.configget(
config, "file_settings", "latlon", 0, datatype="int"
)
options.x_tile = inun_lib.configget(
config, "tiling", "x_tile", 10000, datatype="int"
)
options.y_tile = inun_lib.configget(
config, "tiling", "y_tile", 10000, datatype="int"
)
options.x_overlap = inun_lib.configget(
config, "tiling", "x_overlap", 1000, datatype="int"
)
options.y_overlap = inun_lib.configget(
config, "tiling", "y_overlap", 1000, datatype="int"
)
options.iterations = inun_lib.configget(
config, "inundation", "iterations", 20, datatype="int"
)
options.initial_level = inun_lib.configget(
config, "inundation", "initial_level", 32., datatype="float"
)
options.flood_volume_type = inun_lib.configget(
config, "inundation", "flood_volume_type", 0, datatype="int"
)
# options.area_multiplier = inun_lib.configget(config, 'inundation',
# 'area_multiplier', 1., datatype='float')
logger.info("DEM file: {:s}".format(options.dem_file))
logger.info("LDD file: {:s}".format(options.ldd_file))
logger.info("streamfile: {:s}".format(options.stream_file))
logger.info("Columns per tile: {:d}".format(options.x_tile))
logger.info("Rows per tile: {:d}".format(options.y_tile))
logger.info("Columns overlap: {:d}".format(options.x_overlap))
logger.info("Rows overlap: {:d}".format(options.y_overlap))
metadata_global = {}
# add metadata from the section [metadata]
meta_keys = config.options("metadata_global")
for key in meta_keys:
metadata_global[key] = config.get("metadata_global", key)
# add a number of metadata variables that are mandatory
metadata_global["config_file"] = os.path.abspath(options.inifile)
metadata_var = {}
metadata_var["units"] = "m"
metadata_var["standard_name"] = "water_surface_height_above_reference_datum"
metadata_var["long_name"] = "flooding"
metadata_var[
"comment"
] = "water_surface_reference_datum_altitude is given in file {:s}".format(
options.dem_file
)
if not os.path.exists(options.dem_file):
logger.error("path to dem file {:s} cannot be found".format(options.dem_file))
sys.exit(1)
if not os.path.exists(options.ldd_file):
logger.error("path to ldd file {:s} cannot be found".format(options.ldd_file))
sys.exit(1)
# Read extent from a GDAL compatible file
try:
extent = inun_lib.get_gdal_extent(options.dem_file)
except:
msg = "Input file {:s} not a gdal compatible file".format(options.dem_file)
inun_lib.close_with_error(logger, ch, msg)
sys.exit(1)
try:
x, y = inun_lib.get_gdal_axes(options.dem_file, logging=logger)
srs = inun_lib.get_gdal_projection(options.dem_file, logging=logger)
except:
msg = "Input file {:s} not a gdal compatible file".format(options.dem_file)
inun_lib.close_with_error(logger, ch, msg)
sys.exit(1)
# read history from flood file
if options.file_format == 0:
a = nc.Dataset(options.flood_map, "r")
metadata_global[
"history"
] = "Created by: $Id: $, boundary conditions from {:s},\nhistory: {:s}".format(
os.path.abspath(options.flood_map), a.history
)
a.close()
else:
metadata_global[
"history"
] = "Created by: $Id: $, boundary conditions from {:s},\nhistory: {:s}".format(
os.path.abspath(options.flood_map), "PCRaster file, no history"
)
# first write subcatch maps and hand maps
############### TODO ######
# setup a HAND file for each strahler order
max_s = inun_lib.define_max_strahler(options.stream_file, logging=logger)
stream_max = np.minimum(max_s, options.max_strahler)
for hand_strahler in range(options.catchment_strahler, stream_max + 1, 1):
dem_name = os.path.split(options.dem_file)[1].split(".")[0]
if os.path.isfile(
"{:s}_{:02d}.tif".format(options.hand_file_prefix, hand_strahler)
):
hand_file = "{:s}_{:02d}.tif".format(
options.hand_file_prefix, hand_strahler
)
else:
logger.info(
"No HAND files with HAND prefix were found, checking {:s}_hand_strahler_{:02d}.tif".format(
dem_name, hand_strahler
)
)
hand_file = os.path.join(
options.dest_path,
"{:s}_hand_strahler_{:02d}.tif".format(dem_name, hand_strahler),
)
if not (os.path.isfile(hand_file)):
# hand file does not exist yet! Generate it, otherwise skip!
logger.info(
"HAND file {:s} not found, start setting up...please wait...".format(
hand_file
)
)
hand_file_tmp = os.path.join(
options.dest_path,
"{:s}_hand_strahler_{:02d}.tif.tmp".format(dem_name, hand_strahler),
)
ds_hand, band_hand = inun_lib.prepare_gdal(
hand_file_tmp, x, y, logging=logger, srs=srs
)
# band_hand = ds_hand.GetRasterBand(1)
# Open terrain data for reading
ds_dem, rasterband_dem = inun_lib.get_gdal_rasterband(options.dem_file)
ds_ldd, rasterband_ldd = inun_lib.get_gdal_rasterband(options.ldd_file)
ds_stream, rasterband_stream = inun_lib.get_gdal_rasterband(
options.stream_file
)
n = 0
for x_loop in range(0, len(x), options.x_tile):
x_start = np.maximum(x_loop, 0)
x_end = np.minimum(x_loop + options.x_tile, len(x))
# determine actual overlap for cutting
for y_loop in range(0, len(y), options.y_tile):
x_overlap_min = x_start - np.maximum(x_start - options.x_overlap, 0)
x_overlap_max = (
np.minimum(x_end + options.x_overlap, len(x)) - x_end
)
n += 1
# print('tile {:001d}:'.format(n))
y_start = np.maximum(y_loop, 0)
y_end = np.minimum(y_loop + options.y_tile, len(y))
y_overlap_min = y_start - np.maximum(y_start - options.y_overlap, 0)
y_overlap_max = (
np.minimum(y_end + options.y_overlap, len(y)) - y_end
)
# cut out DEM
logger.debug(
"Computing HAND for xmin: {:d} xmax: {:d} ymin {:d} ymax {:d}".format(
x_start, x_end, y_start, y_end
)
)
terrain = rasterband_dem.ReadAsArray(
x_start - x_overlap_min,
y_start - y_overlap_min,
(x_end + x_overlap_max) - (x_start - x_overlap_min),
(y_end + y_overlap_max) - (y_start - y_overlap_min),
)
drainage = rasterband_ldd.ReadAsArray(
x_start - x_overlap_min,
y_start - y_overlap_min,
(x_end + x_overlap_max) - (x_start - x_overlap_min),
(y_end + y_overlap_max) - (y_start - y_overlap_min),
)
stream = rasterband_stream.ReadAsArray(
x_start - x_overlap_min,
y_start - y_overlap_min,
(x_end + x_overlap_max) - (x_start - x_overlap_min),
(y_end + y_overlap_max) - (y_start - y_overlap_min),
)
# write to temporary file
terrain_temp_file = os.path.join(
options.dest_path, "terrain_temp.map"
)
drainage_temp_file = os.path.join(
options.dest_path, "drainage_temp.map"
)
stream_temp_file = os.path.join(
options.dest_path, "stream_temp.map"
)
if rasterband_dem.GetNoDataValue() is not None:
inun_lib.gdal_writemap(
terrain_temp_file,
"PCRaster",
np.arange(0, terrain.shape[1]),
np.arange(0, terrain.shape[0]),
terrain,
rasterband_dem.GetNoDataValue(),
gdal_type=gdal.GDT_Float32,
logging=logger,
)
else:
# in case no nodata value is found
logger.warning(
"No nodata value found in {:s}. assuming -9999".format(
options.dem_file
)
)
inun_lib.gdal_writemap(
terrain_temp_file,
"PCRaster",
np.arange(0, terrain.shape[1]),
np.arange(0, terrain.shape[0]),
terrain,
-9999.,
gdal_type=gdal.GDT_Float32,
logging=logger,
)
inun_lib.gdal_writemap(
drainage_temp_file,
"PCRaster",
np.arange(0, terrain.shape[1]),
np.arange(0, terrain.shape[0]),
drainage,
rasterband_ldd.GetNoDataValue(),
gdal_type=gdal.GDT_Int32,
logging=logger,
)
inun_lib.gdal_writemap(
stream_temp_file,
"PCRaster",
np.arange(0, terrain.shape[1]),
np.arange(0, terrain.shape[0]),
stream,
rasterband_ldd.GetNoDataValue(),
gdal_type=gdal.GDT_Int32,
logging=logger,
)
# read as pcr objects
pcr.setclone(terrain_temp_file)
terrain_pcr = pcr.readmap(terrain_temp_file)
drainage_pcr = pcr.lddrepair(
pcr.ldd(pcr.readmap(drainage_temp_file))
) # convert to ldd type map
stream_pcr = pcr.scalar(
pcr.readmap(stream_temp_file)
) # convert to ldd type map
# check if the highest stream order of the tile is below the hand_strahler
# if the highest stream order of the tile is smaller than hand_strahler, than DEM values are taken instead of HAND values.
max_stream_tile = inun_lib.define_max_strahler(
stream_temp_file, logging=logger
)
if max_stream_tile < hand_strahler:
hand_pcr = terrain_pcr
logger.info(
"For this tile, DEM values are used instead of HAND because there is no stream order larger than {:02d}".format(
hand_strahler
)
)
else:
# compute streams
stream_ge, subcatch = inun_lib.subcatch_stream(
drainage_pcr, hand_strahler, stream=stream_pcr
) # generate streams
# compute basins
stream_ge_dummy, subcatch = inun_lib.subcatch_stream(
drainage_pcr, options.catchment_strahler, stream=stream_pcr
) # generate streams
basin = pcr.boolean(subcatch)
hand_pcr, dist_pcr = inun_lib.derive_HAND(
terrain_pcr,
drainage_pcr,
3000,
rivers=pcr.boolean(stream_ge),
basin=basin,
neg_HAND=options.neg_HAND,
)
# convert to numpy
hand = pcr.pcr2numpy(hand_pcr, -9999.)
# cut relevant part
if y_overlap_max == 0:
y_overlap_max = -hand.shape[0]
if x_overlap_max == 0:
x_overlap_max = -hand.shape[1]
hand_cut = hand[
0 + y_overlap_min : -y_overlap_max,
0 + x_overlap_min : -x_overlap_max,
]
band_hand.WriteArray(hand_cut, x_start, y_start)
os.unlink(terrain_temp_file)
os.unlink(drainage_temp_file)
os.unlink(stream_temp_file)
band_hand.FlushCache()
ds_dem = None
ds_ldd = None
ds_stream = None
band_hand.SetNoDataValue(-9999.)
ds_hand = None
logger.info("Finalizing {:s}".format(hand_file))
# rename temporary file to final hand file
os.rename(hand_file_tmp, hand_file)
else:
logger.info("HAND file {:s} already exists...skipping...".format(hand_file))
#####################################################################################
# HAND file has now been prepared, moving to flood mapping part #
#####################################################################################
# set the clone
pcr.setclone(options.ldd_wflow)
# read wflow ldd as pcraster object
ldd_pcr = pcr.readmap(options.ldd_wflow)
xax, yax, riv_width, fill_value = inun_lib.gdal_readmap(
options.riv_width_file, "GTiff", logging=logger
)
# determine cell length in meters using ldd_pcr as clone (if latlon=True, values are converted to m2
x_res, y_res, reallength_wflow = pcrut.detRealCellLength(
pcr.scalar(ldd_pcr), not (bool(options.latlon))
)
cell_surface_wflow = pcr.pcr2numpy(x_res * y_res, 0)
if options.flood_volume_type == 0:
# load the staticmaps needed to estimate volumes across all
# xax, yax, riv_length, fill_value = inun_lib.gdal_readmap(options.riv_length_file, 'GTiff', logging=logger)
# riv_length = np.ma.masked_where(riv_length==fill_value, riv_length)
xax, yax, riv_width, fill_value = inun_lib.gdal_readmap(
options.riv_width_file, "GTiff", logging=logger
)
riv_width[riv_width == fill_value] = 0
# read river length factor file (multiplier)
xax, yax, riv_length_fact, fill_value = inun_lib.gdal_readmap(
options.riv_length_fact_file, "GTiff", logging=logger
)
riv_length_fact = np.ma.masked_where(
riv_length_fact == fill_value, riv_length_fact
)
drain_length = wflow_lib.detdrainlength(ldd_pcr, x_res, y_res)
# compute river length in each cell
riv_length = pcr.pcr2numpy(drain_length, 0) * riv_length_fact
# riv_length_pcr = pcr.numpy2pcr(pcr.Scalar, riv_length, 0)
flood_folder = os.path.join(options.dest_path, case_name)
flood_vol_map = os.path.join(
flood_folder,
"{:s}_vol.tif".format(os.path.split(options.flood_map)[1].split(".")[0]),
)
if not (os.path.isdir(flood_folder)):
os.makedirs(flood_folder)
if options.out_format == 0:
inun_file_tmp = os.path.join(flood_folder, "{:s}.tif.tmp".format(case_name))
inun_file = os.path.join(flood_folder, "{:s}.tif".format(case_name))
else:
inun_file_tmp = os.path.join(flood_folder, "{:s}.nc.tmp".format(case_name))
inun_file = os.path.join(flood_folder, "{:s}.nc".format(case_name))
hand_temp_file = os.path.join(flood_folder, "hand_temp.map")
drainage_temp_file = os.path.join(flood_folder, "drainage_temp.map")
stream_temp_file = os.path.join(flood_folder, "stream_temp.map")
flood_vol_temp_file = os.path.join(flood_folder, "flood_warp_temp.tif")
# load the data with river levels and compute the volumes
if options.file_format == 0:
# assume we need the maximum value in a NetCDF time series grid
logger.info("Reading flood from {:s} NetCDF file".format(options.flood_map))
a = nc.Dataset(options.flood_map, "r")
if options.latlon == 0:
xax = a.variables["x"][:]
yax = a.variables["y"][:]
else:
try:
xax = a.variables["lon"][:]
yax = a.variables["lat"][:]
except:
xax = a.variables["x"][:]
yax = a.variables["y"][:]
if options.time == "":
time_list = nc.num2date(
a.variables["time"][:],
units=a.variables["time"].units,
calendar=a.variables["time"].calendar,
)
time = [time_list[len(time_list) / 2]]
else:
time = [dt.datetime.strptime(options.time, "%Y%m%d%H%M%S")]
flood_series = a.variables[options.flood_variable][:]
flood_data = flood_series.max(axis=0)
if np.ma.is_masked(flood_data):
flood = flood_data.data
flood[flood_data.mask] = 0
if yax[-1] > yax[0]:
yax = np.flipud(yax)
flood = np.flipud(flood)
a.close()
elif options.file_format == 1:
logger.info("Reading flood from {:s} PCRaster file".format(options.flood_map))
xax, yax, flood, flood_fill_value = inun_lib.gdal_readmap(
options.flood_map, "PCRaster", logging=logger
)
flood = np.ma.masked_equal(flood, flood_fill_value)
if options.time == "":
options.time = "20000101000000"
time = [dt.datetime.strptime(options.time, "%Y%m%d%H%M%S")]
flood[flood == flood_fill_value] = 0.
# load the bankfull depths
if options.bankfull_map == "":
bankfull = np.zeros(flood.shape)
else:
if options.file_format == 0:
logger.info(
"Reading bankfull from {:s} NetCDF file".format(options.bankfull_map)
)
a = nc.Dataset(options.bankfull_map, "r")
xax = a.variables["x"][:]
yax = a.variables["y"][:]
# xax = a.variables['lon'][:]
# yax = a.variables['lat'][:]
bankfull_series = a.variables[options.flood_variable][:]
bankfull_data = bankfull_series.max(axis=0)
if np.ma.is_masked(bankfull_data):
bankfull = bankfull_data.data
bankfull[bankfull_data.mask] = 0
if yax[-1] > yax[0]:
yax = np.flipud(yax)
bankfull = np.flipud(bankfull)
a.close()
elif options.file_format == 1:
logger.info(
"Reading bankfull from {:s} PCRaster file".format(options.bankfull_map)
)
xax, yax, bankfull, bankfull_fill_value = inun_lib.gdal_readmap(
options.bankfull_map, "PCRaster", logging=logger
)
bankfull = np.ma.masked_equal(bankfull, bankfull_fill_value)
# flood = bankfull*2
# res_x = 2000
# res_y = 2000
# subtract the bankfull water level to get flood levels (above bankfull)
flood_vol = np.maximum(flood - bankfull, 0)
if options.flood_volume_type == 0:
flood_vol_m = (
riv_length * riv_width * flood_vol / cell_surface_wflow
) # volume expressed in meters water disc
flood_vol_m_pcr = pcr.numpy2pcr(pcr.Scalar, flood_vol_m, 0)
else:
flood_vol_m = flood_vol / cell_surface_wflow
flood_vol_m_data = flood_vol_m.data
flood_vol_m_data[flood_vol_m.mask] = -999.
logger.info("Saving water layer map to {:s}".format(flood_vol_map))
# write to a tiff file
inun_lib.gdal_writemap(
flood_vol_map,
"GTiff",
xax,
yax,
np.maximum(flood_vol_m_data, 0),
-999.,
logging=logger,
)
# this is placed later in the hand loop
# ds_hand, rasterband_hand = inun_lib.get_gdal_rasterband(hand_file)
ds_ldd, rasterband_ldd = inun_lib.get_gdal_rasterband(options.ldd_file)
ds_stream, rasterband_stream = inun_lib.get_gdal_rasterband(options.stream_file)
logger.info("Preparing flood map in {:s} ...please wait...".format(inun_file))
if options.out_format == 0:
ds_inun, band_inun = inun_lib.prepare_gdal(
inun_file_tmp, x, y, logging=logger, srs=srs
)
# band_inun = ds_inun.GetRasterBand(1)
else:
ds_inun, band_inun = inun_lib.prepare_nc(
inun_file_tmp,
time,
x,
np.flipud(y),
metadata=metadata_global,
metadata_var=metadata_var,
logging=logger,
)
# loop over all the tiles
n = 0
for x_loop in range(0, len(x), options.x_tile):
x_start = np.maximum(x_loop, 0)
x_end = np.minimum(x_loop + options.x_tile, len(x))
# determine actual overlap for cutting
for y_loop in range(0, len(y), options.y_tile):
x_overlap_min = x_start - np.maximum(x_start - options.x_overlap, 0)
x_overlap_max = np.minimum(x_end + options.x_overlap, len(x)) - x_end
n += 1
# print('tile {:001d}:'.format(n))
y_start = np.maximum(y_loop, 0)
y_end = np.minimum(y_loop + options.y_tile, len(y))
y_overlap_min = y_start - np.maximum(y_start - options.y_overlap, 0)
y_overlap_max = np.minimum(y_end + options.y_overlap, len(y)) - y_end
x_tile_ax = x[x_start - x_overlap_min : x_end + x_overlap_max]
y_tile_ax = y[y_start - y_overlap_min : y_end + y_overlap_max]
# cut out DEM
logger.debug(
"handling xmin: {:d} xmax: {:d} ymin {:d} ymax {:d}".format(
x_start, x_end, y_start, y_end
)
)
drainage = rasterband_ldd.ReadAsArray(
x_start - x_overlap_min,
y_start - y_overlap_min,
(x_end + x_overlap_max) - (x_start - x_overlap_min),
(y_end + y_overlap_max) - (y_start - y_overlap_min),
)
stream = rasterband_stream.ReadAsArray(
x_start - x_overlap_min,
y_start - y_overlap_min,
(x_end + x_overlap_max) - (x_start - x_overlap_min),
(y_end + y_overlap_max) - (y_start - y_overlap_min),
)
# stream_max = np.minimum(stream.max(), options.max_strahler)
inun_lib.gdal_writemap(
drainage_temp_file,
"PCRaster",
x_tile_ax,
y_tile_ax,
drainage,
rasterband_ldd.GetNoDataValue(),
gdal_type=gdal.GDT_Int32,
logging=logger,
)
inun_lib.gdal_writemap(
stream_temp_file,
"PCRaster",
x_tile_ax,
y_tile_ax,
stream,
rasterband_stream.GetNoDataValue(),
gdal_type=gdal.GDT_Int32,
logging=logger,
)
# read as pcr objects
pcr.setclone(stream_temp_file)
drainage_pcr = pcr.lddrepair(
pcr.ldd(pcr.readmap(drainage_temp_file))
) # convert to ldd type map
stream_pcr = pcr.scalar(
pcr.readmap(stream_temp_file)
) # convert to ldd type map
# warp of flood volume to inundation resolution
inun_lib.gdal_warp(
flood_vol_map,
stream_temp_file,
flood_vol_temp_file,
gdal_interp=gdalconst.GRA_NearestNeighbour,
) # ,
x_tile_ax, y_tile_ax, flood_meter, fill_value = inun_lib.gdal_readmap(
flood_vol_temp_file, "GTiff", logging=logger
)
# make sure that the option unittrue is on !! (if unitcell was is used in another function)
x_res_tile, y_res_tile, reallength = pcrut.detRealCellLength(
pcr.scalar(stream_pcr), not (bool(options.latlon))
)
cell_surface_tile = pcr.pcr2numpy(x_res_tile * y_res_tile, 0)
# convert meter depth to volume [m3]
flood_vol = pcr.numpy2pcr(
pcr.Scalar, flood_meter * cell_surface_tile, fill_value
)
# first prepare a basin map, belonging to the lowest order we are looking at
inundation_pcr = pcr.scalar(stream_pcr) * 0
for hand_strahler in range(options.catchment_strahler, stream_max + 1, 1):
# hand_temp_file = os.path.join(flood_folder, 'hand_temp.map')
if os.path.isfile(
os.path.join(
options.dest_path,
"{:s}_hand_strahler_{:02d}.tif".format(dem_name, hand_strahler),
)
):
hand_file = os.path.join(
options.dest_path,
"{:s}_hand_strahler_{:02d}.tif".format(dem_name, hand_strahler),
)
else:
hand_file = "{:s}_{:02d}.tif".format(
options.hand_file_prefix, hand_strahler
)
ds_hand, rasterband_hand = inun_lib.get_gdal_rasterband(hand_file)
hand = rasterband_hand.ReadAsArray(
x_start - x_overlap_min,
y_start - y_overlap_min,
(x_end + x_overlap_max) - (x_start - x_overlap_min),
(y_end + y_overlap_max) - (y_start - y_overlap_min),
)
print (
"len x-ax: {:d} len y-ax {:d} x-shape {:d} y-shape {:d}".format(
len(x_tile_ax), len(y_tile_ax), hand.shape[1], hand.shape[0]
)
)
inun_lib.gdal_writemap(
hand_temp_file,
"PCRaster",
x_tile_ax,
y_tile_ax,
hand,
rasterband_hand.GetNoDataValue(),
gdal_type=gdal.GDT_Float32,
logging=logger,
)
hand_pcr = pcr.readmap(hand_temp_file)
stream_ge_hand, subcatch_hand = inun_lib.subcatch_stream(
drainage_pcr, options.catchment_strahler, stream=stream_pcr
)
# stream_ge_hand, subcatch_hand = inun_lib.subcatch_stream(drainage_pcr, hand_strahler, stream=stream_pcr)
stream_ge, subcatch = inun_lib.subcatch_stream(
drainage_pcr,
options.catchment_strahler,
stream=stream_pcr,
basin=pcr.boolean(pcr.cover(subcatch_hand, 0)),
assign_existing=True,
min_strahler=hand_strahler,
max_strahler=hand_strahler,
) # generate subcatchments, only within basin for HAND
flood_vol_strahler = pcr.ifthenelse(
pcr.boolean(pcr.cover(subcatch, 0)), flood_vol, 0
) # mask the flood volume map with the created subcatch map for strahler order = hand_strahler
inundation_pcr_step = inun_lib.volume_spread(
drainage_pcr,
hand_pcr,
pcr.subcatchment(
drainage_pcr, subcatch
), # to make sure backwater effects can occur from higher order rivers to lower order rivers
flood_vol_strahler,
volume_thres=0.,
iterations=options.iterations,
cell_surface=pcr.numpy2pcr(pcr.Scalar, cell_surface_tile, -9999),
logging=logger,
order=hand_strahler,
neg_HAND=options.neg_HAND,
) # 1166400000.
# use maximum value of inundation_pcr_step and new inundation for higher strahler order
inundation_pcr = pcr.max(inundation_pcr, inundation_pcr_step)
inundation = pcr.pcr2numpy(inundation_pcr, -9999.)
# cut relevant part
if y_overlap_max == 0:
y_overlap_max = -inundation.shape[0]
if x_overlap_max == 0:
x_overlap_max = -inundation.shape[1]
inundation_cut = inundation[
0 + y_overlap_min : -y_overlap_max, 0 + x_overlap_min : -x_overlap_max
]
# inundation_cut
if options.out_format == 0:
band_inun.WriteArray(inundation_cut, x_start, y_start)
band_inun.FlushCache()
else:
# with netCDF, data is up-side-down.
inun_lib.write_tile_nc(band_inun, inundation_cut, x_start, y_start)
# clean up
os.unlink(flood_vol_temp_file)
os.unlink(drainage_temp_file)
os.unlink(hand_temp_file)
os.unlink(
stream_temp_file
) # also remove temp stream file from output folder
# if n == 35:
# band_inun.SetNoDataValue(-9999.)
# ds_inun = None
# sys.exit(0)
# os.unlink(flood_vol_map)
logger.info("Finalizing {:s}".format(inun_file))
# add the metadata to the file and band
# band_inun.SetNoDataValue(-9999.)
# ds_inun.SetMetadata(metadata_global)
# band_inun.SetMetadata(metadata_var)
if options.out_format == 0:
ds_inun = None
ds_hand = None
else:
ds_inun.close()
ds_ldd = None
# rename temporary file to final hand file
if os.path.isfile(inun_file):
# remove an old result if available
os.unlink(inun_file)
os.rename(inun_file_tmp, inun_file)
logger.info("Done! Thank you for using hand_contour_inun.py")
logger, ch = inun_lib.closeLogger(logger, ch)
del logger, ch
sys.exit(0)
def __init__(self, iniItems, landmask):
object.__init__(self)
# cloneMap, temporary directory for the resample process, temporary directory for the modflow process, absolute path for input directory, landmask
self.cloneMap = iniItems.cloneMap
self.tmpDir = iniItems.tmpDir
self.tmp_modflow_dir = iniItems.tmp_modflow_dir
self.inputDir = iniItems.globalOptions['inputDir']
self.landmask = landmask
# configuration from the ini file
self.iniItems = iniItems
# topography properties: read several variables from the netcdf file
for var in ['dem_minimum','dem_maximum','dem_average','dem_standard_deviation',\
'slopeLength','orographyBeta','tanslope',\
'dzRel0000','dzRel0001','dzRel0005',\
'dzRel0010','dzRel0020','dzRel0030','dzRel0040','dzRel0050',\
'dzRel0060','dzRel0070','dzRel0080','dzRel0090','dzRel0100']:
vars(self)[var] = vos.netcdf2PCRobjCloneWithoutTime(self.iniItems.modflowParameterOptions['topographyNC'], \
var, self.cloneMap)
vars(self)[var] = pcr.cover(vars(self)[var], 0.0)
# channel properties: read several variables from the netcdf file
for var in ['lddMap','cellAreaMap','gradient','bankfull_width',
'bankfull_depth','dem_floodplain','dem_riverbed']:
vars(self)[var] = vos.netcdf2PCRobjCloneWithoutTime(self.iniItems.modflowParameterOptions['channelNC'], \
var, self.cloneMap)
vars(self)[var] = pcr.cover(vars(self)[var], 0.0)
# minimum channel width
minimum_channel_width = 0.5 # TODO: Define this one in the configuration file
self.bankfull_width = pcr.max(minimum_channel_width, self.bankfull_width)
#~ # cell fraction if channel water reaching the flood plan # NOT USED YET
#~ self.flood_plain_fraction = self.return_innundation_fraction(pcr.max(0.0, self.dem_floodplain - self.dem_minimum))
# coefficient of Manning
self.manningsN = vos.readPCRmapClone(self.iniItems.modflowParameterOptions['manningsN'],\
self.cloneMap,self.tmpDir,self.inputDir)
# minimum channel gradient
minGradient = 0.00005 # TODO: Define this one in the configuration file
self.gradient = pcr.max(minGradient, pcr.cover(self.gradient, minGradient))
# correcting lddMap
self.lddMap = pcr.ifthen(pcr.scalar(self.lddMap) > 0.0, self.lddMap)
self.lddMap = pcr.lddrepair(pcr.ldd(self.lddMap))
# channelLength = approximation of channel length (unit: m) # This is approximated by cell diagonal.
cellSizeInArcMin = np.round(pcr.clone().cellSize()*60.) # FIXME: This one will not work if you use the resolution: 0.5, 1.5, 2.5 arc-min
verticalSizeInMeter = cellSizeInArcMin*1852.
horizontalSizeInMeter = self.cellAreaMap/verticalSizeInMeter
self.channelLength = ((horizontalSizeInMeter)**(2)+\
(verticalSizeInMeter)**(2))**(0.5)
# option for lakes and reservoir
self.onlyNaturalWaterBodies = False
if self.iniItems.modflowParameterOptions['onlyNaturalWaterBodies'] == "True": self.onlyNaturalWaterBodies = True
# groundwater linear recession coefficient (day-1) ; the linear reservoir concept is still being used to represent fast response flow
# particularly from karstic aquifer in mountainous regions
self.recessionCoeff = vos.netcdf2PCRobjCloneWithoutTime(self.iniItems.modflowParameterOptions['groundwaterPropertiesNC'],\
'recessionCoeff', self.cloneMap)
self.recessionCoeff = pcr.cover(self.recessionCoeff,0.00)
self.recessionCoeff = pcr.min(1.0000,self.recessionCoeff)
#
if 'minRecessionCoeff' in iniItems.modflowParameterOptions.keys():
minRecessionCoeff = float(iniItems.modflowParameterOptions['minRecessionCoeff'])
else:
minRecessionCoeff = 1.0e-4 # This is the minimum value used in Van Beek et al. (2011).
self.recessionCoeff = pcr.max(minRecessionCoeff,self.recessionCoeff)
# aquifer saturated conductivity (m/day)
self.kSatAquifer = vos.netcdf2PCRobjCloneWithoutTime(self.iniItems.modflowParameterOptions['groundwaterPropertiesNC'],\
'kSatAquifer', self.cloneMap)
self.kSatAquifer = pcr.cover(self.kSatAquifer,pcr.mapmaximum(self.kSatAquifer))
self.kSatAquifer = pcr.max(0.001,self.kSatAquifer)
# TODO: Define the minimum value as part of the configuration file
# aquifer specific yield (dimensionless)
self.specificYield = vos.netcdf2PCRobjCloneWithoutTime(self.iniItems.modflowParameterOptions['groundwaterPropertiesNC'],\
'specificYield', self.cloneMap)
self.specificYield = pcr.cover(self.specificYield,pcr.mapmaximum(self.specificYield))
self.specificYield = pcr.max(0.010,self.specificYield) # TODO: TO BE CHECKED: The resample process of specificYield
self.specificYield = pcr.min(1.000,self.specificYield)
# TODO: Define the minimum value as part of the configuration file
# estimate of thickness (unit: m) of accesible groundwater
totalGroundwaterThickness = vos.netcdf2PCRobjCloneWithoutTime(self.iniItems.modflowParameterOptions['estimateOfTotalGroundwaterThicknessNC'],\
'thickness', self.cloneMap)
# extrapolation
totalGroundwaterThickness = pcr.cover(totalGroundwaterThickness,\
pcr.windowaverage(totalGroundwaterThickness, 1.0))
totalGroundwaterThickness = pcr.cover(totalGroundwaterThickness,\
pcr.windowaverage(totalGroundwaterThickness, 1.5))
totalGroundwaterThickness = pcr.cover(totalGroundwaterThickness, 0.0)
#
# set minimum thickness
minimumThickness = pcr.scalar(float(\
self.iniItems.modflowParameterOptions['minimumTotalGroundwaterThickness']))
totalGroundwaterThickness = pcr.max(minimumThickness, totalGroundwaterThickness)
#
# set maximum thickness: 250 m. # TODO: Define this one as part of the ini file
maximumThickness = 250.
self.totalGroundwaterThickness = pcr.min(maximumThickness, totalGroundwaterThickness)
# TODO: Define the maximum value as part of the configuration file
# surface water bed thickness (unit: m)
bed_thickness = 0.1 # TODO: Define this as part of the configuration file
# surface water bed resistance (unit: day)
bed_resistance = bed_thickness / (self.kSatAquifer)
minimum_bed_resistance = 1.0 # TODO: Define this as part of the configuration file
self.bed_resistance = pcr.max(minimum_bed_resistance,\
bed_resistance,)
# option to ignore capillary rise
self.ignoreCapRise = True
if self.iniItems.modflowParameterOptions['ignoreCapRise'] == "False": self.ignoreCapRise = False
# a variable to indicate if the modflow has been called or not
self.modflow_has_been_called = False
# list of the convergence criteria for HCLOSE (unit: m)
# - Deltares default's value is 0.001 m # check this value with Jarno
self.criteria_HCLOSE = [0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0]
self.criteria_HCLOSE = sorted(self.criteria_HCLOSE)
# list of the convergence criteria for RCLOSE (unit: m3)
# - Deltares default's value for their 25 and 250 m resolution models is 10 m3 # check this value with Jarno
cell_area_assumption = verticalSizeInMeter * float(pcr.cellvalue(pcr.mapmaximum(horizontalSizeInMeter),1)[0])
self.criteria_RCLOSE = [10., 10.* cell_area_assumption/(250.*250.), 10.* cell_area_assumption/(25.*25.)]
self.criteria_RCLOSE = sorted(self.criteria_RCLOSE)
# initiate the index for HCLOSE and RCLOSE
self.iteration_HCLOSE = 0
self.iteration_RCLOSE = 0
# initiate old style reporting # TODO: remove this!
self.initiate_old_style_groundwater_reporting(iniItems)
def __init__(self, iniItems, landmask, Dir, cloneMap, tmpDir):
object.__init__(self)
# clone map file names, temporary directory and global/absolute path of input directory
self.cloneMap = cloneMap # iniItems.cloneMap
self.tmpDir = tmpDir # iniItems.tmpDir
self.inputDir = Dir # iniItems.globalOptions['inputDir']
self.landmask = landmask
# local drainage direction:
self.lddMap = vos.readPCRmapClone(
iniItems.get("routingOptions", "lddMap"),
self.cloneMap,
self.tmpDir,
self.inputDir,
True,
)
self.lddMap = pcr.lddrepair(pcr.ldd(self.lddMap))
self.lddMap = pcr.lddrepair(self.lddMap)
# option to activate water balance check
self.debugWaterBalance = True
if (
configget(iniItems, "routingOptions", "debugWaterBalance", "True")
== "False"
):
self.debugWaterBalance = False
# option to perform a run with only natural lakes (without reservoirs)
self.onlyNaturalWaterBodies = False
if (
"onlyNaturalWaterBodies" in iniItems._sections["routingOptions"]
and configget(iniItems, "routingOptions", "onlyNaturalWaterBodies", "False")
== "True"
):
logger.info(
"Using only natural water bodies identified in the year 1900. All reservoirs in 1900 are assumed as lakes."
)
self.onlyNaturalWaterBodies = True
self.dateForNaturalCondition = (
"1900-01-01"
) # The run for a natural condition should access only this date.
# names of files containing water bodies parameters
if configget(iniItems, "routingOptions", "waterBodyInputNC", "None") == str(
None
):
self.useNetCDF = False
self.fracWaterInp = iniItems.get("routingOptions", "fracWaterInp")
self.waterBodyIdsInp = iniItems.get("routingOptions", "waterBodyIds")
self.waterBodyTypInp = iniItems.get("routingOptions", "waterBodyTyp")
self.resMaxCapInp = iniItems.get("routingOptions", "resMaxCapInp")
self.resSfAreaInp = iniItems.get("routingOptions", "resSfAreaInp")
else:
self.useNetCDF = True
self.ncFileInp = vos.getFullPath(
iniItems.get("routingOptions", "waterBodyInputNC"), self.inputDir
)
# minimum width (m) used in the weir formula # TODO: define minWeirWidth based on the GLWD, GRanD database and/or bankfull discharge formula
self.minWeirWidth = 10.0
# lower and upper limits at which reservoir release is terminated and
# at which reservoir release is equal to long-term average outflow
self.minResvrFrac = 0.10
self.maxResvrFrac = 0.75
call(('gdal_translate', '-of', 'PCRaster', '-a_srs', clone_EPSG, '-ot',
'Float32', rivers_tif, rivers_map))
call(('gdal_translate', '-of', 'PCRaster', '-a_srs', clone_EPSG, '-ot',
'Float32', outlets_tif, outlets_map))
# burn the layers in DEM
outletsburn = pcr.scalar(pcr.readmap(outlets_map)) * pcr.scalar(burn_outlets)
connectionsburn = pcr.scalar(
pcr.readmap(connections_map)) * pcr.scalar(burn_connections)
riverburn = pcr.scalar(pcr.readmap(rivers_map)) * pcr.scalar(burn_rivers)
ldddem = pcr.cover(dem_resample_map, pcr.ifthen(riverburn > 0, pcr.scalar(0)))
ldddem = ldddem - outletsburn - connectionsburn - riverburn
ldddem = pcr.cover(ldddem, pcr.scalar(0))
pcr.report(ldddem, workdir + "dem_burn.map")
''' create ldd for multi-catchments '''
ldd = pcr.ldd(empty)
# reproject catchment shape-file
ds = ogr.Open(catchshp)
file_att = os.path.splitext(os.path.basename(catchshp))[0]
lyr = ds.GetLayerByName(file_att)
spatialref = lyr.GetSpatialRef()
# if not spatialref == None:
# srs = osr.SpatialReference()
# srs.ImportFromWkt(spatialref.ExportToWkt())
# srs.AutoIdentifyEPSG()
# catchshp_EPSG = 'EPSG:'+srs.GetAttrValue("AUTHORITY",1)
# spatialref == None
# else:
catchshp_EPSG = clone_EPSG
print 'No projection defined for ' + file_att + '.shp'
print 'Assumed to be the same as model projection (' + clone_EPSG + ')'
def main():
# output folder
clean_out_folder = True
if os.path.exists(out_folder):
if clean_out_folder:
shutil.rmtree(out_folder)
os.makedirs(out_folder)
else:
os.makedirs(out_folder)
os.chdir(out_folder)
os.system("pwd")
# tmp folder
tmp_folder = out_folder + "/tmp/"
if os.path.exists(tmp_folder): shutil.rmtree(tmp_folder)
os.makedirs(tmp_folder)
# set the clone map
print("set the clone map")
pcr.setclone(global_clone_map_file)
# read ldd map
print("define the ldd")
# ~ ldd_map = pcr.readmap(global_ldd_inp_file)
ldd_map = pcr.lddrepair(pcr.lddrepair(pcr.ldd(vos.readPCRmapClone(v = global_ldd_inp_file, \
cloneMapFileName = global_clone_map_file, \
tmpDir = tmp_folder, \
absolutePath = None, \
isLddMap = True, \
cover = None, \
isNomMap = False))))
# define the landmask
if landmask_map_file == None:
print("define the landmask based on the ldd input")
# ~ landmask = pcr.defined(pcr.readmap(global_ldd_inp_file))
landmask = pcr.defined(ldd_map)
landmask = pcr.ifthen(landmask, landmask)
else:
print("define the landmask based on the input landmask_map_file")
landmask = pcr.readmap(landmask_map_file)
ldd_map = pcr.ifthen(landmask, pcr.cover(ldd_map, pcr.ldd(5)))
ldd_map = pcr.lddrepair(pcr.lddrepair(pcr.ldd(ldd_map)))
landmask = pcr.defined(ldd_map)
landmask = pcr.ifthen(landmask, landmask)
# save ldd files used
# - global ldd
cmd = "cp " + str(global_ldd_inp_file) + " ."
print(cmd)
os.system(cmd)
# - ldd map that is used
pcr.report(ldd_map, "lddmap_used.map")
# make catchment map
print("make catchment map")
catchment_map = pcr.catchment(ldd_map, pcr.pit(ldd_map))
# read global subdomain file
print("read global subdomain file")
global_subdomain_map = vos.readPCRmapClone(
v=global_subdomain_file,
cloneMapFileName=global_clone_map_file,
tmpDir=tmp_folder,
absolutePath=None,
isLddMap=False,
cover=None,
isNomMap=True)
# set initial subdomain
print("assign subdomains to all catchments")
subdomains_initial = pcr.areamajority(global_subdomain_map, catchment_map)
subdomains_initial = pcr.ifthen(landmask, subdomains_initial)
pcr.aguila(subdomains_initial)
pcr.report(subdomains_initial, "global_subdomains_initial.map")
print(str(int(vos.getMinMaxMean(pcr.scalar(subdomains_initial))[0])))
print(str(int(vos.getMinMaxMean(pcr.scalar(subdomains_initial))[1])))
print("Checking all subdomains, avoid too large subdomains")
num_of_masks = int(vos.getMinMaxMean(pcr.scalar(subdomains_initial))[1])
# clone code that will be assigned
assigned_number = 0
subdomains_final = pcr.ifthen(
pcr.scalar(subdomains_initial) < -7777, pcr.nominal(0))
for nr in range(1, num_of_masks + 1, 1):
msg = "Processing the landmask %s" % (str(nr))
print(msg)
mask_selected_boolean = pcr.ifthen(subdomains_initial == nr,
pcr.boolean(1.0))
process_this_clone = False
if pcr.cellvalue(pcr.mapmaximum(pcr.scalar(mask_selected_boolean)), 1,
1)[0] > 0:
process_this_clone = True
# ~ if nr == 1: pcr.aguila(mask_selected_boolean)
# - initial check value
check_ok = True
if process_this_clone:
xmin, ymin, xmax, ymax = boundingBox(mask_selected_boolean)
area_in_degree2 = (xmax - xmin) * (ymax - ymin)
# ~ print(str(area_in_degree2))
# check whether the size of bounding box is ok
reference_area_in_degree2 = 2500.
if area_in_degree2 > 1.50 * reference_area_in_degree2:
check_ok = False
if (xmax - xmin) > 10 * (ymax - ymin): check_ok = False
# ~ # ignore checking
# ~ check_ok = True
if check_ok == True and process_this_clone == True:
msg = "Clump is not needed."
msg = "\n\n" + str(msg) + "\n\n"
print(msg)
# assign the clone code
assigned_number = assigned_number + 1
# update global landmask for river and land
mask_selected_nominal = pcr.ifthen(mask_selected_boolean,
pcr.nominal(assigned_number))
subdomains_final = pcr.cover(subdomains_final,
mask_selected_nominal)
if check_ok == False and process_this_clone == True:
msg = "Clump is needed."
msg = "\n\n" + str(msg) + "\n\n"
print(msg)
# make clump
clump_ids = pcr.nominal(pcr.clump(mask_selected_boolean))
# merge clumps that are close together
clump_ids_window_majority = pcr.windowmajority(clump_ids, 10.0)
clump_ids = pcr.areamajority(clump_ids_window_majority, clump_ids)
# ~ pcr.aguila(clump_ids)
# minimimum and maximum values
min_clump_id = int(
pcr.cellvalue(pcr.mapminimum(pcr.scalar(clump_ids)), 1)[0])
max_clump_id = int(
pcr.cellvalue(pcr.mapmaximum(pcr.scalar(clump_ids)), 1)[0])
for clump_id in range(min_clump_id, max_clump_id + 1, 1):
msg = "Processing the clump %s of %s from the landmask %s" % (
str(clump_id), str(max_clump_id), str(nr))
msg = "\n\n" + str(msg) + "\n\n"
print(msg)
# identify mask based on the clump
mask_selected_boolean_from_clump = pcr.ifthen(
clump_ids == pcr.nominal(clump_id), mask_selected_boolean)
mask_selected_boolean_from_clump = pcr.ifthen(
mask_selected_boolean_from_clump,
mask_selected_boolean_from_clump)
# check whether the clump is empty
check_mask_selected_boolean_from_clump = pcr.ifthen(
mask_selected_boolean, mask_selected_boolean_from_clump)
check_if_empty = float(
pcr.cellvalue(
pcr.mapmaximum(
pcr.scalar(
pcr.defined(
check_mask_selected_boolean_from_clump))),
1)[0])
if check_if_empty == 0.0:
msg = "Map is empty !"
msg = "\n\n" + str(msg) + "\n\n"
print(msg)
else:
msg = "Map is NOT empty !"
msg = "\n\n" + str(msg) + "\n\n"
print(msg)
# assign the clone code
assigned_number = assigned_number + 1
# update global landmask for river and land
mask_selected_nominal = pcr.ifthen(
mask_selected_boolean_from_clump,
pcr.nominal(assigned_number))
subdomains_final = pcr.cover(subdomains_final,
mask_selected_nominal)
# ~ # kill all aguila processes if exist
# ~ os.system('killall aguila')
pcr.aguila(subdomains_final)
print("")
print("")
print("")
print("The subdomain map is READY.")
pcr.report(subdomains_final, "global_subdomains_final.map")
num_of_masks = int(vos.getMinMaxMean(pcr.scalar(subdomains_final))[1])
print(num_of_masks)
print("")
print("")
print("")
print("Making the clone and landmask maps for all subdomains")
num_of_masks = int(vos.getMinMaxMean(pcr.scalar(subdomains_final))[1])
# clone and mask folders
clone_folder = out_folder + "/clone/"
if os.path.exists(clone_folder): shutil.rmtree(clone_folder)
os.makedirs(clone_folder)
mask_folder = out_folder + "/mask/"
if os.path.exists(mask_folder): shutil.rmtree(mask_folder)
os.makedirs(mask_folder)
print("")
print("")
for nr in range(1, num_of_masks + 1, 1):
msg = "Processing the subdomain %s" % (str(nr))
print(msg)
# set the global clone
pcr.setclone(global_clone_map_file)
mask_selected_boolean = pcr.ifthen(subdomains_final == nr,
pcr.boolean(1.0))
mask_selected_nominal = pcr.ifthen(subdomains_final == nr,
pcr.nominal(nr))
mask_file = "mask/mask_%s.map" % (str(nr))
pcr.report(mask_selected_nominal, mask_file)
xmin, ymin, xmax, ymax = boundingBox(mask_selected_boolean)
area_in_degree2 = (xmax - xmin) * (ymax - ymin)
print(
str(nr) + " ; " + str(area_in_degree2) + " ; " +
str((xmax - xmin)) + " ; " + str((ymax - ymin)))
# cellsize in arcdegree
cellsize = cellsize_in_arcmin / 60.
# number of rows and cols
num_rows = int(round(ymax - ymin) / cellsize)
num_cols = int(round(xmax - xmin) / cellsize)
# make the clone map using mapattr
clonemap_mask_file = "clone/clonemap_mask_%s.map" % (str(nr))
cmd = "mapattr -s -R %s -C %s -B -P yb2t -x %s -y %s -l %s %s" % (
str(num_rows), str(num_cols), str(xmin), str(ymax), str(cellsize),
clonemap_mask_file)
print(cmd)
os.system(cmd)
# set the local landmask for the clump
pcr.setclone(clonemap_mask_file)
local_mask = vos.readPCRmapClone(v = mask_file, \
cloneMapFileName = clonemap_mask_file,
tmpDir = tmp_folder, \
absolutePath = None, isLddMap = False, cover = None, isNomMap = True)
local_mask_boolean = pcr.defined(local_mask)
local_mask_boolean = pcr.ifthen(local_mask_boolean, local_mask_boolean)
pcr.report(local_mask_boolean, mask_file)
print("")
print("")
print("")
print(num_of_masks)
def loadmap(name,
pcr=False,
lddflag=False,
timestampflag='exact',
averageyearflag=False):
""" Load a static map either value or pcraster map or netcdf (single or stack)
Load a static map either value or pcraster map or netcdf (single or stack)
If a netCDF stack is loaded, map is read according to timestepInit date (i.e. model time step). If timestepInit is a
step number, step number is converted to date (referred to CalendarDayStart in settings.xml). Then date is used to
read time step from netCDF file.
if timestampflag = 'closest' and loadmap is reading a NetCDF stack, the timestep with the closest timestamp will be
loaded if the exact one is not available.
:param name: name of key in Settings.xml input file containing path and name of the map file (as string)
:param pcr: flag for output maps in pcraster format
:param lddflag: flag for local drain direction map (CM??)
:param timestampflag: look for exact time stamp in netcdf file ('exact') or for the closest (left) time stamp available ('closest')
:param averageyearflag: if True, use "average year" netcdf file over the entire model simulation period
:return: map or mapC
:except: pcr: maps must have the same size of clone.map
netCDF: time step timestepInit must be included into the stack
"""
# name of the key in Settimgs.xml file containing path and name of the map file
settings = LisSettings.instance()
binding = settings.binding
flags = settings.flags
value = binding[name]
# path and name of the map file
filename = value
load = False
pcrmap = False
# try reading in PCRaster map format
try:
# try reading constant value
mapC = float(value)
flagmap = False
load = True
if pcr: map = mapC
except ValueError:
try:
# try reading pcraster map exploiting the iterAccess class
map = iterReadPCRasterMap(value)
flagmap = True
load = True
pcrmap = True
except:
load = False
if load and pcrmap:
#map is loaded and it is in pcraster format
try:
# test if map is same size as clone map, if not it will make an error
test = pcraster.scalar(map) + pcraster.scalar(map)
except:
raise LisfloodError(
"{} might be of a different size than clone size".format(
value))
# if failed before try reading from netCDF map format
if not load:
# read a netcdf (single one not a stack)
filename = os.path.splitext(value)[0] + '.nc'
# get mapextend of netcdf map and calculate the cutting
cut0, cut1, cut2, cut3 = mapattrNetCDF(filename)
# load netcdf map but only the rectangle needed
nf1 = iterOpenNetcdf(filename, "", 'r')
value = listitems(nf1.variables)[-1][0]
# get the last variable name (it must be the variable to be read by Lisflood)
if not settings.timestep_init:
# if timestep_init is missing, read netcdf as single static map
mapnp = nf1.variables[value][cut2:cut3, cut0:cut1]
else:
if 'time' in nf1.variables:
# read a netcdf (stack) - state files
# get information from netCDF stack
t_steps = nf1.variables[
'time'][:] # get values for timesteps ([ 0., 24., 48., 72., 96.])
t_unit = nf1.variables[
'time'].units # get unit (u'hours since 2015-01-01 06:00:00')
t_cal = get_calendar_type(nf1)
# get year from time unit in case average year is used
if averageyearflag:
# get date of the first step in netCDF file containing average year values
first_date = num2date(t_steps[0], t_unit, t_cal)
# get year of the first step in netCDF file containing average year values
t_ref_year = first_date.year
# select timestep to use for reading from netCDF stack based on timestep_init (state file time step)
timestepI = calendar(settings.timestep_init,
binding['calendar_type'])
if isinstance(timestepI, datetime.datetime):
#reading dates in XML settings file
# get step id number in netCDF stack for timestepInit date
if averageyearflag:
#if using an average year don't care about the year in timestepIDate and change it to the netCDF first time step year
try:
timestepI = timestepI.replace(year=t_ref_year)
except:
timestepI = timestepI.replace(day=28)
timestepI = timestepI.replace(year=t_ref_year)
timestepI = date2num(timestepI,
nf1.variables['time'].units)
else:
# reading step numbers in XML file
# timestepI = int(timestepI) -1
begin = calendar(binding['CalendarDayStart'])
DtSec = float(binding['DtSec'])
DtDay = DtSec / 86400.
# Time step, expressed as fraction of day (same as self.var.DtSec and self.var.DtDay)
# get date for step number timestepI (referred to CalendarDayStart)
timestepIDate = begin + datetime.timedelta(
days=(timestepI - 1) * DtDay)
# get step id number in netCDF stack for step timestepInit
# timestepInit refers to CalenradDayStart
# timestepI now refers to first date in netCDF stack
if averageyearflag:
#using an average year, don't care about the year in timestepIDate and change it to the netCDF time unit year
try:
timestepIDate = timestepIDate.replace(
year=t_ref_year)
except:
#if simulation year is leap and average year is not, switch 29/2 with 28/2
timestepIDate = timestepIDate.replace(day=28)
timestepIDate = timestepIDate.replace(
year=t_ref_year)
timestepI = date2num(timestepIDate,
units=t_unit,
calendar=t_cal)
if not (timestepI in nf1.variables['time'][:]):
if timestampflag == 'exact':
#look for exact time stamp when loading data
msg = "time step " + str(int(
timestepI) + 1) + " is not stored in " + filename
raise LisfloodError(msg)
elif timestampflag == 'closest':
#get the closest value
timestepInew = takeClosest(t_steps, timestepI)
#set timestepI to the closest available time step in netCDF file
timestepI = timestepInew
itime = np.where(nf1.variables['time'][:] == timestepI)[0][0]
mapnp = nf1.variables[value][itime, cut2:cut3, cut0:cut1]
else:
# read a netcdf (single one)
mapnp = nf1.variables[value][cut2:cut3, cut0:cut1]
# masking
try:
maskinfo = MaskInfo.instance()
mapnp.mask = maskinfo.info.mask
except (KeyError, AttributeError):
pass
nf1.close()
# if a map should be pcraster
if pcr:
# check if integer map (like outlets, lakes etc
checkint = str(mapnp.dtype)
if checkint == "int16" or checkint == "int32":
mapnp[mapnp.mask] = -9999
map = numpy2pcr(Nominal, mapnp, -9999)
elif checkint == "int8":
mapnp[mapnp < 0] = -9999
map = numpy2pcr(Nominal, mapnp, -9999)
else:
mapnp[np.isnan(mapnp)] = -9999
map = numpy2pcr(Scalar, mapnp, -9999)
# if the map is a ldd
if lddflag:
map = pcraster.ldd(pcraster.nominal(map))
else:
mapC = compressArray(mapnp, pcr=False, name=filename)
flagmap = True
# pcraster map but it has to be an array
if pcrmap and not pcr:
mapC = compressArray(map, name=filename)
if flags['checkfiles']:
print(name, filename)
if flagmap == False:
checkmap(name, filename, mapC, flagmap, 0)
elif pcr:
checkmap(name, filename, map, flagmap, 0)
else:
print(name, mapC.size)
if mapC.size > 0:
map = decompress(mapC)
checkmap(name, filename, map, flagmap, 0)
if pcr:
if flags['nancheck'] and name != 'Ldd':
nanCheckMap(map, filename, name)
return map
elif isinstance(mapC, np.ndarray):
return mapC.astype(float)
else:
if flags['nancheck'] and name != 'Ldd':
nanCheckMap(mapC, filename, name)
return mapC
def __init__(self, iniItems, landmask):
object.__init__(self)
# cloneMap, temporary directory, absolute path for input directory, landmask
self.cloneMap = iniItems.cloneMap
self.tmpDir = iniItems.tmpDir
self.inputDir = iniItems.globalOptions['inputDir']
self.landmask = landmask
# configuration from the ini file
self.iniItems = iniItems
# topography properties: read several variables from the netcdf file
for var in ['dem_minimum','dem_maximum','dem_average','dem_standard_deviation',\
'slopeLength','orographyBeta','tanslope',\
'dzRel0000','dzRel0001','dzRel0005',\
'dzRel0010','dzRel0020','dzRel0030','dzRel0040','dzRel0050',\
'dzRel0060','dzRel0070','dzRel0080','dzRel0090','dzRel0100']:
vars(self)[var] = vos.netcdf2PCRobjCloneWithoutTime(self.iniItems.modflowParameterOptions['topographyNC'], \
var, self.cloneMap)
vars(self)[var] = pcr.cover(vars(self)[var], 0.0)
# channel properties: read several variables from the netcdf file
for var in [
'lddMap', 'cellAreaMap', 'gradient', 'bankfull_width',
'bankfull_depth', 'dem_floodplain', 'dem_riverbed'
]:
vars(self)[var] = vos.netcdf2PCRobjCloneWithoutTime(self.iniItems.modflowParameterOptions['channelNC'], \
var, self.cloneMap)
vars(self)[var] = pcr.cover(vars(self)[var], 0.0)
# minimum channel width
minimum_channel_width = 0.1
self.bankfull_width = pcr.max(minimum_channel_width,
self.bankfull_width)
#~ # cell fraction if channel water reaching the flood plan # NOT USED
#~ self.flood_plain_fraction = self.return_innundation_fraction(pcr.max(0.0, self.dem_floodplain - self.dem_minimum))
# coefficient of Manning
self.manningsN = vos.readPCRmapClone(self.iniItems.modflowParameterOptions['manningsN'],\
self.cloneMap,self.tmpDir,self.inputDir)
# minimum channel gradient
minGradient = 0.00005
self.gradient = pcr.max(minGradient,
pcr.cover(self.gradient, minGradient))
# correcting lddMap
self.lddMap = pcr.ifthen(pcr.scalar(self.lddMap) > 0.0, self.lddMap)
self.lddMap = pcr.lddrepair(pcr.ldd(self.lddMap))
# channelLength = approximation of channel length (unit: m) # This is approximated by cell diagonal.
cellSizeInArcMin = np.round(pcr.clone().cellSize() * 60.)
verticalSizeInMeter = cellSizeInArcMin * 1852.
self.channelLength = ((self.cellAreaMap/verticalSizeInMeter)**(2)+\
(verticalSizeInMeter)**(2))**(0.5)
# option for lakes and reservoir
self.onlyNaturalWaterBodies = False
if self.iniItems.modflowParameterOptions[
'onlyNaturalWaterBodies'] == "True":
self.onlyNaturalWaterBodies = True
# groundwater linear recession coefficient (day-1) ; the linear reservoir concept is still being used to represent fast response flow
# particularly from karstic aquifer in mountainous regions
self.recessionCoeff = vos.netcdf2PCRobjCloneWithoutTime(self.iniItems.modflowParameterOptions['groundwaterPropertiesNC'],\
'recessionCoeff', self.cloneMap)
self.recessionCoeff = pcr.cover(self.recessionCoeff, 0.00)
self.recessionCoeff = pcr.min(1.0000, self.recessionCoeff)
#
if 'minRecessionCoeff' in iniItems.modflowParameterOptions.keys():
minRecessionCoeff = float(
iniItems.modflowParameterOptions['minRecessionCoeff'])
else:
minRecessionCoeff = 1.0e-4 # This is the minimum value used in Van Beek et al. (2011).
self.recessionCoeff = pcr.max(minRecessionCoeff, self.recessionCoeff)
# aquifer saturated conductivity (m/day)
self.kSatAquifer = vos.netcdf2PCRobjCloneWithoutTime(self.iniItems.modflowParameterOptions['groundwaterPropertiesNC'],\
'kSatAquifer', self.cloneMap)
self.kSatAquifer = pcr.cover(self.kSatAquifer,
pcr.mapmaximum(self.kSatAquifer))
self.kSatAquifer = pcr.max(0.010, self.kSatAquifer)
self.kSatAquifer *= 0.001
# aquifer specific yield (dimensionless)
self.specificYield = vos.netcdf2PCRobjCloneWithoutTime(self.iniItems.modflowParameterOptions['groundwaterPropertiesNC'],\
'specificYield', self.cloneMap)
self.specificYield = pcr.cover(self.specificYield,
pcr.mapmaximum(self.specificYield))
self.specificYield = pcr.max(
0.010, self.specificYield
) # TODO: TO BE CHECKED: The resample process of specificYield
self.specificYield = pcr.min(1.000, self.specificYield)
# estimate of thickness (unit: m) of accesible groundwater
totalGroundwaterThickness = vos.netcdf2PCRobjCloneWithoutTime(self.iniItems.modflowParameterOptions['estimateOfTotalGroundwaterThicknessNC'],\
'thickness', self.cloneMap)
# extrapolation
totalGroundwaterThickness = pcr.cover(totalGroundwaterThickness,\
pcr.windowaverage(totalGroundwaterThickness, 1.0))
totalGroundwaterThickness = pcr.cover(totalGroundwaterThickness,\
pcr.windowaverage(totalGroundwaterThickness, 1.5))
totalGroundwaterThickness = pcr.cover(totalGroundwaterThickness, 0.0)
#
# set minimum thickness
minimumThickness = pcr.scalar(float(\
self.iniItems.modflowParameterOptions['minimumTotalGroundwaterThickness']))
totalGroundwaterThickness = pcr.max(minimumThickness,
totalGroundwaterThickness)
#
# set maximum thickness: 250 m.
maximumThickness = 250.
self.totalGroundwaterThickness = pcr.min(maximumThickness,
totalGroundwaterThickness)
# river bed resistance (unit: day)
self.bed_resistance = 1.0
# option to ignore capillary rise
self.ignoreCapRise = True
if self.iniItems.modflowParameterOptions['ignoreCapRise'] == "False":
self.ignoreCapRise = False
# initiate old style reporting # TODO: remove this!
self.initiate_old_style_groundwater_reporting(iniItems)
def __init__(self, modelTime, input_file, output_file, variable_name,
variable_unit):
DynamicModel.__init__(self)
self.modelTime = modelTime
# netcdf input file - based on PCR-GLOBWB output
self.input_file = "/projects/0/dfguu/users/edwin/pcr-globwb-aqueduct/historical/1951-2005/gfdl-esm2m/temperature_annuaAvg_output_%s-12-31_to_%s-12-31.nc"
self.input_file = input_file
# output file - in netcdf format
self.output_file = output_folder + "/mekong/basin_temperature_annuaAvg_output.nc"
self.output_file = output_file
# output variable name and unit
self.variable_name = variable_name
self.variable_unit = variable_unit
# preparing temporary directory
self.temporary_directory = output_folder + "/tmp/"
os.makedirs(self.temporary_directory)
# clone and landmask maps
logger.info("Set the clone and landmask maps.")
self.clonemap_file_name = "/projects/0/dfguu/users/edwinhs/data/mekong_etc_clone/version_2018-10-22/final/clone_mekong.map"
pcr.setclone(self.clonemap_file_name)
landmask_file_name = "/projects/0/dfguu/users/edwinhs/data/mekong_etc_clone/version_2018-10-22/final/mask_mekong.map"
self.landmask = vos.readPCRmapClone(landmask_file_name, \
self.clonemap_file_name, \
self.temporary_directory, \
None, False, None, True)
# pcraster input files
# - river network map and sub-catchment map
ldd_file_name = "/projects/0/dfguu/data/hydroworld/PCRGLOBWB20/input5min/routing/lddsound_05min.map"
# - cell area (unit: m2)
cell_area_file_name = "/projects/0/dfguu/data/hydroworld/PCRGLOBWB20/input5min/routing/cellsize05min.correct.map"
# loading pcraster input maps
self.ldd_network = vos.readPCRmapClone(ldd_file_name, \
self.clonemap_file_name, \
self.temporary_directory, \
None, \
True)
self.ldd_network = pcr.lddrepair(pcr.ldd(self.ldd_network))
self.ldd_network = pcr.lddrepair(self.ldd_network)
self.cell_area = vos.readPCRmapClone(cell_area_file_name, \
self.clonemap_file_name, \
self.temporary_directory, \
None)
# set/limit all input maps to the defined landmask
self.ldd_network = pcr.ifthen(self.landmask, self.ldd_network)
self.cell_area = pcr.ifthen(self.landmask, self.cell_area)
# calculate basin/catchment area
self.basin_area = pcr.catchmenttotal(self.cell_area, self.ldd_network)
self.basin_area = pcr.ifthen(self.landmask, self.basin_area)
# preparing an object for reporting netcdf files:
self.netcdf_report = netcdf_writer.PCR2netCDF(self.clonemap_file_name)
# preparing netcdf output files:
self.netcdf_report.createNetCDF(self.output_file, \
self.variable_name, \
self.variable_unit)
def main():
# output folder (and tmp folder)
clean_out_folder = True
if os.path.exists(out_folder):
if clean_out_folder:
shutil.rmtree(out_folder)
os.makedirs(out_folder)
else:
os.makedirs(out_folder)
os.chdir(out_folder)
os.system("pwd")
# set the clone map
print("set the clone")
pcr.setclone(global_ldd_30min_inp_file)
# define the landmask
print("define the landmask")
# - based on the 30min input
landmask_30min = define_landmask(input_file = global_landmask_30min_file,\
clone_map_file = global_ldd_30min_inp_file,\
output_map_file = "landmask_30min_only.map")
# - based on the 05min input
landmask_05min = define_landmask(input_file = global_landmask_05min_file,\
clone_map_file = global_ldd_30min_inp_file,\
output_map_file = "landmask_05min_only.map")
# - based on the 06min input
landmask_06min = define_landmask(input_file = global_landmask_06min_file,\
clone_map_file = global_ldd_30min_inp_file,\
output_map_file = "landmask_06min_only.map")
# - based on the 30sec input
landmask_30sec = define_landmask(input_file = global_landmask_30sec_file,\
clone_map_file = global_ldd_30min_inp_file,\
output_map_file = "landmask_30sec_only.map")
# - based on the 30sec input
landmask_03sec = define_landmask(input_file = global_landmask_03sec_file,\
clone_map_file = global_ldd_30min_inp_file,\
output_map_file = "landmask_03sec_only.map")
#
# - merge all landmasks
landmask = pcr.cover(landmask_30min, landmask_05min, landmask_06min,
landmask_30sec, landmask_03sec)
pcr.report(landmask, "global_landmask_extended_30min.map")
# ~ pcr.aguila(landmask)
# extend ldd
print("extend/define the ldd")
ldd_map = pcr.readmap(global_ldd_30min_inp_file)
ldd_map = pcr.ifthen(landmask, pcr.cover(ldd_map, pcr.ldd(5)))
pcr.report(ldd_map, "global_ldd_extended_30min.map")
# ~ pcr.aguila(ldd_map)
# catchment map and size
catchment_map = pcr.catchment(ldd_map, pcr.pit(ldd_map))
catchment_size = pcr.areatotal(pcr.spatial(pcr.scalar(1.0)), catchment_map)
# ~ pcr.aguila(catchment_size)
# identify small islands
print("identify small islands")
# - maps of islands smaller than 15000 cells (at half arc degree resolution)
island_map = pcr.ifthen(landmask, pcr.clump(pcr.defined(ldd_map)))
island_size = pcr.areatotal(pcr.spatial(pcr.scalar(1.0)), island_map)
island_map = pcr.ifthen(island_size < 15000., island_map)
# ~ # - use catchments (instead of islands)
# ~ island_map = catchment_map
# ~ island_size = catchment_size
# ~ island_map = pcr.ifthen(island_size < 10000., island_map)
# - sort from the largest island
# -- take one cell per island as a representative
island_map_rep_size = pcr.ifthen(
pcr.areaorder(island_size, island_map) == 1.0, island_size)
# -- sort from the largest island
island_map_rep_ids = pcr.areaorder(
island_map_rep_size * -1.00,
pcr.ifthen(pcr.defined(island_map_rep_size), pcr.nominal(1.0)))
# -- map of smaller islands, sorted from the largest one
island_map = pcr.areamajority(pcr.nominal(island_map_rep_ids), island_map)
# identify the biggest island for every group of small islands within a certain window (arcdeg cells)
print("the biggest island for every group of small islands")
large_island_map = pcr.ifthen(
pcr.scalar(island_map) == pcr.windowminimum(pcr.scalar(island_map),
15.), island_map)
# ~ pcr.aguila(large_island_map)
# identify big catchments
print("identify large catchments")
catchment_map = pcr.catchment(ldd_map, pcr.pit(ldd_map))
catchment_size = pcr.areatotal(pcr.spatial(pcr.scalar(1.0)), catchment_map)
# ~ # - identify all large catchments with size >= 50 cells (at the resolution of 30 arcmin) = 50 x (50^2) km2 = 125000 km2
# ~ large_catchment_map = pcr.ifthen(catchment_size >= 50, catchment_map)
# ~ # - identify all large catchments with size >= 10 cells (at the resolution of 30 arcmin)
# ~ large_catchment_map = pcr.ifthen(catchment_size >= 10, catchment_map)
# ~ # - identify all large catchments with size >= 5 cells (at the resolution of 30 arcmin)
# ~ large_catchment_map = pcr.ifthen(catchment_size >= 5, catchment_map)
# ~ # - identify all large catchments with size >= 20 cells (at the resolution of 30 arcmin)
# ~ large_catchment_map = pcr.ifthen(catchment_size >= 20, catchment_map)
# - identify all large catchments with size >= 25 cells (at the resolution of 30 arcmin)
large_catchment_map = pcr.ifthen(catchment_size >= 25, catchment_map)
# - give the codes that are different than islands
large_catchment_map = pcr.nominal(
pcr.scalar(large_catchment_map) +
10. * vos.getMinMaxMean(pcr.scalar(large_island_map))[1])
# merge biggest islands and big catchments
print("merge large catchments and islands")
large_catchment_and_island_map = pcr.cover(large_catchment_map,
large_island_map)
# ~ large_catchment_and_island_map = pcr.cover(large_island_map, large_catchment_map)
large_catchment_and_island_map_size = pcr.areatotal(
pcr.spatial(pcr.scalar(1.0)), large_catchment_and_island_map)
# - sort from the largest one
# -- take one cell per island as a representative
large_catchment_and_island_map_rep_size = pcr.ifthen(
pcr.areaorder(large_catchment_and_island_map_size,
large_catchment_and_island_map) == 1.0,
large_catchment_and_island_map_size)
# -- sort from the largest
large_catchment_and_island_map_rep_ids = pcr.areaorder(
large_catchment_and_island_map_rep_size * -1.00,
pcr.ifthen(pcr.defined(large_catchment_and_island_map_rep_size),
pcr.nominal(1.0)))
# -- map of largest catchments and islands, sorted from the largest one
large_catchment_and_island_map = pcr.areamajority(
pcr.nominal(large_catchment_and_island_map_rep_ids),
large_catchment_and_island_map)
# ~ pcr.report(large_catchment_and_island_map, "large_catchments_and_islands.map")
# ~ # perform cdo fillmiss2 in order to merge the small catchments to the nearest large catchments
# ~ print("spatial interpolation/extrapolation using cdo fillmiss2 to get initial subdomains")
# ~ cmd = "gdal_translate -of NETCDF large_catchments_and_islands.map large_catchments_and_islands.nc"
# ~ print(cmd); os.system(cmd)
# ~ cmd = "cdo fillmiss2 large_catchments_and_islands.nc large_catchments_and_islands_filled.nc"
# ~ print(cmd); os.system(cmd)
# ~ cmd = "gdal_translate -of PCRaster large_catchments_and_islands_filled.nc large_catchments_and_islands_filled.map"
# ~ print(cmd); os.system(cmd)
# ~ cmd = "mapattr -c " + global_ldd_30min_inp_file + " " + "large_catchments_and_islands_filled.map"
# ~ print(cmd); os.system(cmd)
# ~ # - initial subdomains
# ~ subdomains_initial = pcr.nominal(pcr.readmap("large_catchments_and_islands_filled.map"))
# ~ subdomains_initial = pcr.areamajority(subdomains_initial, catchment_map)
# ~ pcr.aguila(subdomains_initial)
# spatial interpolation/extrapolation in order to merge the small catchments to the nearest large catchments
print("spatial interpolation/extrapolation to get initial subdomains")
field = large_catchment_and_island_map
cellID = pcr.nominal(pcr.uniqueid(pcr.defined(field)))
zoneID = pcr.spreadzone(cellID, 0, 1)
field = pcr.areamajority(field, zoneID)
subdomains_initial = field
subdomains_initial = pcr.areamajority(subdomains_initial, catchment_map)
pcr.aguila(subdomains_initial)
pcr.report(subdomains_initial, "global_subdomains_30min_initial.map")
print(str(int(vos.getMinMaxMean(pcr.scalar(subdomains_initial))[0])))
print(str(int(vos.getMinMaxMean(pcr.scalar(subdomains_initial))[1])))
# ~ print(str(int(vos.getMinMaxMean(pcr.scalar(subdomains_initial_clump))[0])))
# ~ print(str(int(vos.getMinMaxMean(pcr.scalar(subdomains_initial_clump))[1])))
print("Checking all subdomains, avoid too large subdomains")
num_of_masks = int(vos.getMinMaxMean(pcr.scalar(subdomains_initial))[1])
# clone code that will be assigned
assigned_number = 0
subdomains_final = pcr.ifthen(
pcr.scalar(subdomains_initial) < -7777, pcr.nominal(0))
for nr in range(1, num_of_masks + 1, 1):
msg = "Processing the landmask %s" % (str(nr))
print(msg)
mask_selected_boolean = pcr.ifthen(subdomains_initial == nr,
pcr.boolean(1.0))
# ~ if nr == 1: pcr.aguila(mask_selected_boolean)
xmin, ymin, xmax, ymax = boundingBox(mask_selected_boolean)
area_in_degree2 = (xmax - xmin) * (ymax - ymin)
# ~ print(str(area_in_degree2))
# check whether the size of bounding box is ok
# - initial check value
check_ok = True
reference_area_in_degree2 = 2500.
if area_in_degree2 > 1.50 * reference_area_in_degree2: check_ok = False
if (xmax - xmin) > 10 * (ymax - ymin): check_ok = False
if check_ok == True:
msg = "Clump is not needed."
msg = "\n\n" + str(msg) + "\n\n"
print(msg)
# assign the clone code
assigned_number = assigned_number + 1
# update global landmask for river and land
mask_selected_nominal = pcr.ifthen(mask_selected_boolean,
pcr.nominal(assigned_number))
subdomains_final = pcr.cover(subdomains_final,
mask_selected_nominal)
if check_ok == False:
msg = "Clump is needed."
msg = "\n\n" + str(msg) + "\n\n"
print(msg)
# make clump
clump_ids = pcr.nominal(pcr.clump(mask_selected_boolean))
# merge clumps that are close together
clump_ids_window_majority = pcr.windowmajority(clump_ids, 10.0)
clump_ids = pcr.areamajority(clump_ids_window_majority, clump_ids)
# ~ pcr.aguila(clump_ids)
# minimimum and maximum values
min_clump_id = int(
pcr.cellvalue(pcr.mapminimum(pcr.scalar(clump_ids)), 1)[0])
max_clump_id = int(
pcr.cellvalue(pcr.mapmaximum(pcr.scalar(clump_ids)), 1)[0])
for clump_id in range(min_clump_id, max_clump_id + 1, 1):
msg = "Processing the clump %s of %s from the landmask %s" % (
str(clump_id), str(max_clump_id), str(nr))
msg = "\n\n" + str(msg) + "\n\n"
print(msg)
# identify mask based on the clump
mask_selected_boolean_from_clump = pcr.ifthen(
clump_ids == pcr.nominal(clump_id), mask_selected_boolean)
mask_selected_boolean_from_clump = pcr.ifthen(
mask_selected_boolean_from_clump,
mask_selected_boolean_from_clump)
# check whether the clump is empty
check_mask_selected_boolean_from_clump = pcr.ifthen(
mask_selected_boolean, mask_selected_boolean_from_clump)
check_if_empty = float(
pcr.cellvalue(
pcr.mapmaximum(
pcr.scalar(
pcr.defined(
check_mask_selected_boolean_from_clump))),
1)[0])
if check_if_empty == 0.0:
msg = "Map is empty !"
msg = "\n\n" + str(msg) + "\n\n"
print(msg)
else:
msg = "Map is NOT empty !"
msg = "\n\n" + str(msg) + "\n\n"
print(msg)
# assign the clone code
assigned_number = assigned_number + 1
# update global landmask for river and land
mask_selected_nominal = pcr.ifthen(
mask_selected_boolean_from_clump,
pcr.nominal(assigned_number))
subdomains_final = pcr.cover(subdomains_final,
mask_selected_nominal)
# ~ # kill all aguila processes if exist
# ~ os.system('killall aguila')
pcr.aguila(subdomains_final)
print("")
print("")
print("")
print("The subdomain map is READY.")
pcr.report(subdomains_final, "global_subdomains_30min_final.map")
num_of_masks = int(vos.getMinMaxMean(pcr.scalar(subdomains_final))[1])
print(num_of_masks)
print("")
print("")
print("")
for nr in range(1, num_of_masks + 1, 1):
mask_selected_boolean = pcr.ifthen(subdomains_final == nr,
pcr.boolean(1.0))
xmin, ymin, xmax, ymax = boundingBox(mask_selected_boolean)
area_in_degree2 = (xmax - xmin) * (ymax - ymin)
print(
str(nr) + " ; " + str(area_in_degree2) + " ; " +
str((xmax - xmin)) + " ; " + str((ymax - ymin)))
print("")
print("")
print("")
print("Number of subdomains: " + str(num_of_masks))
print("")
print("")
print("")
# spatial extrapolation in order to cover the entire map
print("spatial interpolation/extrapolation to cover the entire map")
field = subdomains_final
cellID = pcr.nominal(pcr.uniqueid(pcr.defined(field)))
zoneID = pcr.spreadzone(cellID, 0, 1)
field = pcr.areamajority(field, zoneID)
subdomains_final_filled = field
pcr.aguila(subdomains_final_filled)
pcr.report(subdomains_final_filled,
"global_subdomains_30min_final_filled.map")
def main():
### Read input arguments #####
parser = OptionParser()
usage = "usage: %prog [options]"
parser = OptionParser(usage=usage)
parser.add_option('-q', '--quiet',
dest='verbose', default=True, action='store_false',
help='do not print status messages to stdout')
parser.add_option('-i', '--ini', dest='inifile',
default='hand_contour_inun.ini', nargs=1,
help='ini configuration file')
parser.add_option('-f', '--flood_map',
nargs=1, dest='flood_map',
help='Flood map file (NetCDF point time series file')
parser.add_option('-v', '--flood_variable',
nargs=1, dest='flood_variable',
default='water_level',
help='variable name of flood water level')
parser.add_option('-b', '--bankfull_map',
dest='bankfull_map', default='',
help='Map containing bank full level (is subtracted from flood map, in NetCDF)')
parser.add_option('-c', '--catchment',
dest='catchment_strahler', default=7, type='int',
help='Strahler order threshold >= are selected as catchment boundaries')
parser.add_option('-t', '--time',
dest='time', default='',
help='time in YYYYMMDDHHMMSS, overrides time in NetCDF input if set')
# parser.add_option('-s', '--hand_strahler',
# dest='hand_strahler', default=7, type='int',
# help='Strahler order threshold >= selected as riverine')
parser.add_option('-m', '--max_strahler',
dest = 'max_strahler', default=1000, type='int',
help='Maximum Strahler order to loop over')
parser.add_option('-d', '--destination',
dest='dest_path', default='inun',
help='Destination path')
parser.add_option('-H', '--hand_file_prefix',
dest='hand_file_prefix', default='',
help='optional HAND file prefix of already generated HAND files')
parser.add_option('-n', '--neg_HAND',
dest='neg_HAND', default=0, type='int',
help='if set to 1, allow for negative HAND values in HAND maps')
(options, args) = parser.parse_args()
if not os.path.exists(options.inifile):
print 'path to ini file cannot be found'
sys.exit(1)
options.dest_path = os.path.abspath(options.dest_path)
if not(os.path.isdir(options.dest_path)):
os.makedirs(options.dest_path)
# set up the logger
flood_name = os.path.split(options.flood_map)[1].split('.')[0]
# case_name = 'inun_{:s}_hand_{:02d}_catch_{:02d}'.format(flood_name, options.hand_strahler, options.catchment_strahler)
case_name = 'inun_{:s}_catch_{:02d}'.format(flood_name, options.catchment_strahler)
logfilename = os.path.join(options.dest_path, 'hand_contour_inun.log')
logger, ch = inun_lib.setlogger(logfilename, 'HAND_INUN', options.verbose)
logger.info('$Id: $')
logger.info('Flood map: {:s}'.format(options.flood_map))
logger.info('Bank full map: {:s}'.format(options.bankfull_map))
logger.info('Destination path: {:s}'.format(options.dest_path))
# read out ini file
### READ CONFIG FILE
# open config-file
config = inun_lib.open_conf(options.inifile)
# read settings
options.dem_file = inun_lib.configget(config, 'HighResMaps',
'dem_file',
True)
options.ldd_file = inun_lib.configget(config, 'HighResMaps',
'ldd_file',
True)
options.stream_file = inun_lib.configget(config, 'HighResMaps',
'stream_file',
True)
options.riv_length_fact_file = inun_lib.configget(config, 'wflowResMaps',
'riv_length_fact_file',
True)
options.ldd_wflow = inun_lib.configget(config, 'wflowResMaps',
'ldd_wflow',
True)
options.riv_width_file = inun_lib.configget(config, 'wflowResMaps',
'riv_width_file',
True)
options.file_format = inun_lib.configget(config, 'file_settings',
'file_format', 0, datatype='int')
options.out_format = inun_lib.configget(config, 'file_settings',
'out_format', 0, datatype='int')
options.latlon = inun_lib.configget(config, 'file_settings',
'latlon', 0, datatype='int')
options.x_tile = inun_lib.configget(config, 'tiling',
'x_tile', 10000, datatype='int')
options.y_tile = inun_lib.configget(config, 'tiling',
'y_tile', 10000, datatype='int')
options.x_overlap = inun_lib.configget(config, 'tiling',
'x_overlap', 1000, datatype='int')
options.y_overlap = inun_lib.configget(config, 'tiling',
'y_overlap', 1000, datatype='int')
options.iterations = inun_lib.configget(config, 'inundation',
'iterations', 20, datatype='int')
options.initial_level = inun_lib.configget(config, 'inundation',
'initial_level', 32., datatype='float')
options.flood_volume_type = inun_lib.configget(config, 'inundation',
'flood_volume_type', 0, datatype='int')
# options.area_multiplier = inun_lib.configget(config, 'inundation',
# 'area_multiplier', 1., datatype='float')
logger.info('DEM file: {:s}'.format(options.dem_file))
logger.info('LDD file: {:s}'.format(options.ldd_file))
logger.info('Columns per tile: {:d}'.format(options.x_tile))
logger.info('Rows per tile: {:d}'.format(options.y_tile))
logger.info('Columns overlap: {:d}'.format(options.x_overlap))
logger.info('Rows overlap: {:d}'.format(options.y_overlap))
metadata_global = {}
# add metadata from the section [metadata]
meta_keys = config.options('metadata_global')
for key in meta_keys:
metadata_global[key] = config.get('metadata_global', key)
# add a number of metadata variables that are mandatory
metadata_global['config_file'] = os.path.abspath(options.inifile)
metadata_var = {}
metadata_var['units'] = 'm'
metadata_var['standard_name'] = 'water_surface_height_above_reference_datum'
metadata_var['long_name'] = 'flooding'
metadata_var['comment'] = 'water_surface_reference_datum_altitude is given in file {:s}'.format(options.dem_file)
if not os.path.exists(options.dem_file):
logger.error('path to dem file {:s} cannot be found'.format(options.dem_file))
sys.exit(1)
if not os.path.exists(options.ldd_file):
logger.error('path to ldd file {:s} cannot be found'.format(options.ldd_file))
sys.exit(1)
# Read extent from a GDAL compatible file
try:
extent = inun_lib.get_gdal_extent(options.dem_file)
except:
msg = 'Input file {:s} not a gdal compatible file'.format(options.dem_file)
inun_lib.close_with_error(logger, ch, msg)
sys.exit(1)
try:
x, y = inun_lib.get_gdal_axes(options.dem_file, logging=logger)
srs = inun_lib.get_gdal_projection(options.dem_file, logging=logger)
except:
msg = 'Input file {:s} not a gdal compatible file'.format(options.dem_file)
inun_lib.close_with_error(logger, ch, msg)
sys.exit(1)
# read history from flood file
if options.file_format == 0:
a = nc.Dataset(options.flood_map, 'r')
metadata_global['history'] = 'Created by: $Id: $, boundary conditions from {:s},\nhistory: {:s}'.format(os.path.abspath(options.flood_map), a.history)
a.close()
else:
metadata_global['history'] = 'Created by: $Id: $, boundary conditions from {:s},\nhistory: {:s}'.format(os.path.abspath(options.flood_map), 'PCRaster file, no history')
# first write subcatch maps and hand maps
############### TODO ######
# setup a HAND file for each strahler order
max_s = inun_lib.define_max_strahler(options.stream_file, logging=logger)
stream_max = np.minimum(max_s, options.max_strahler)
for hand_strahler in range(options.catchment_strahler, stream_max + 1, 1):
dem_name = os.path.split(options.dem_file)[1].split('.')[0]
if os.path.isfile('{:s}_{:02d}.tif'.format(options.hand_file_prefix, hand_strahler)):
hand_file = '{:s}_{:02d}.tif'.format(options.hand_file_prefix, hand_strahler)
else:
logger.info('No HAND files with HAND prefix were found, checking {:s}_hand_strahler_{:02d}.tif'.format(dem_name, hand_strahler))
hand_file = os.path.join(options.dest_path, '{:s}_hand_strahler_{:02d}.tif'.format(dem_name, hand_strahler))
if not(os.path.isfile(hand_file)):
# hand file does not exist yet! Generate it, otherwise skip!
logger.info('HAND file {:s} not found, start setting up...please wait...'.format(hand_file))
hand_file_tmp = os.path.join(options.dest_path, '{:s}_hand_strahler_{:02d}.tif.tmp'.format(dem_name, hand_strahler))
ds_hand, band_hand = inun_lib.prepare_gdal(hand_file_tmp, x, y, logging=logger, srs=srs)
# band_hand = ds_hand.GetRasterBand(1)
# Open terrain data for reading
ds_dem, rasterband_dem = inun_lib.get_gdal_rasterband(options.dem_file)
ds_ldd, rasterband_ldd = inun_lib.get_gdal_rasterband(options.ldd_file)
ds_stream, rasterband_stream = inun_lib.get_gdal_rasterband(options.stream_file)
n = 0
for x_loop in range(0, len(x), options.x_tile):
x_start = np.maximum(x_loop, 0)
x_end = np.minimum(x_loop + options.x_tile, len(x))
# determine actual overlap for cutting
for y_loop in range(0, len(y), options.y_tile):
x_overlap_min = x_start - np.maximum(x_start - options.x_overlap, 0)
x_overlap_max = np.minimum(x_end + options.x_overlap, len(x)) - x_end
n += 1
# print('tile {:001d}:'.format(n))
y_start = np.maximum(y_loop, 0)
y_end = np.minimum(y_loop + options.y_tile, len(y))
y_overlap_min = y_start - np.maximum(y_start - options.y_overlap, 0)
y_overlap_max = np.minimum(y_end + options.y_overlap, len(y)) - y_end
# cut out DEM
logger.debug('Computing HAND for xmin: {:d} xmax: {:d} ymin {:d} ymax {:d}'.format(x_start, x_end,y_start, y_end))
terrain = rasterband_dem.ReadAsArray(x_start - x_overlap_min,
y_start - y_overlap_min,
(x_end + x_overlap_max) - (x_start - x_overlap_min),
(y_end + y_overlap_max) - (y_start - y_overlap_min)
)
drainage = rasterband_ldd.ReadAsArray(x_start - x_overlap_min,
y_start - y_overlap_min,
(x_end + x_overlap_max) - (x_start - x_overlap_min),
(y_end + y_overlap_max) - (y_start - y_overlap_min)
)
stream = rasterband_stream.ReadAsArray(x_start - x_overlap_min,
y_start - y_overlap_min,
(x_end + x_overlap_max) - (x_start - x_overlap_min),
(y_end + y_overlap_max) - (y_start - y_overlap_min)
)
# write to temporary file
terrain_temp_file = os.path.join(options.dest_path, 'terrain_temp.map')
drainage_temp_file = os.path.join(options.dest_path, 'drainage_temp.map')
stream_temp_file = os.path.join(options.dest_path, 'stream_temp.map')
if rasterband_dem.GetNoDataValue() is not None:
inun_lib.gdal_writemap(terrain_temp_file, 'PCRaster',
np.arange(0, terrain.shape[1]),
np.arange(0, terrain.shape[0]),
terrain, rasterband_dem.GetNoDataValue(),
gdal_type=gdal.GDT_Float32,
logging=logger)
else:
# in case no nodata value is found
logger.warning('No nodata value found in {:s}. assuming -9999'.format(options.dem_file))
inun_lib.gdal_writemap(terrain_temp_file, 'PCRaster',
np.arange(0, terrain.shape[1]),
np.arange(0, terrain.shape[0]),
terrain, -9999.,
gdal_type=gdal.GDT_Float32,
logging=logger)
inun_lib.gdal_writemap(drainage_temp_file, 'PCRaster',
np.arange(0, terrain.shape[1]),
np.arange(0, terrain.shape[0]),
drainage, rasterband_ldd.GetNoDataValue(),
gdal_type=gdal.GDT_Int32,
logging=logger)
inun_lib.gdal_writemap(stream_temp_file, 'PCRaster',
np.arange(0, terrain.shape[1]),
np.arange(0, terrain.shape[0]),
stream, rasterband_ldd.GetNoDataValue(),
gdal_type=gdal.GDT_Int32,
logging=logger)
# read as pcr objects
pcr.setclone(terrain_temp_file)
terrain_pcr = pcr.readmap(terrain_temp_file)
drainage_pcr = pcr.lddrepair(pcr.ldd(pcr.readmap(drainage_temp_file))) # convert to ldd type map
stream_pcr = pcr.scalar(pcr.readmap(stream_temp_file)) # convert to ldd type map
#check if the highest stream order of the tile is below the hand_strahler
# if the highest stream order of the tile is smaller than hand_strahler, than DEM values are taken instead of HAND values.
max_stream_tile = inun_lib.define_max_strahler(stream_temp_file, logging=logger)
if max_stream_tile < hand_strahler:
hand_pcr = terrain_pcr
logger.info('For this tile, DEM values are used instead of HAND because there is no stream order larger than {:02d}'.format(hand_strahler))
else:
# compute streams
stream_ge, subcatch = inun_lib.subcatch_stream(drainage_pcr, hand_strahler, stream=stream_pcr) # generate streams
# compute basins
stream_ge_dummy, subcatch = inun_lib.subcatch_stream(drainage_pcr, options.catchment_strahler, stream=stream_pcr) # generate streams
basin = pcr.boolean(subcatch)
hand_pcr, dist_pcr = inun_lib.derive_HAND(terrain_pcr, drainage_pcr, 3000,
rivers=pcr.boolean(stream_ge), basin=basin, neg_HAND=options.neg_HAND)
# convert to numpy
hand = pcr.pcr2numpy(hand_pcr, -9999.)
# cut relevant part
if y_overlap_max == 0:
y_overlap_max = -hand.shape[0]
if x_overlap_max == 0:
x_overlap_max = -hand.shape[1]
hand_cut = hand[0+y_overlap_min:-y_overlap_max, 0+x_overlap_min:-x_overlap_max]
band_hand.WriteArray(hand_cut, x_start, y_start)
os.unlink(terrain_temp_file)
os.unlink(drainage_temp_file)
os.unlink(stream_temp_file)
band_hand.FlushCache()
ds_dem = None
ds_ldd = None
ds_stream = None
band_hand.SetNoDataValue(-9999.)
ds_hand = None
logger.info('Finalizing {:s}'.format(hand_file))
# rename temporary file to final hand file
os.rename(hand_file_tmp, hand_file)
else:
logger.info('HAND file {:s} already exists...skipping...'.format(hand_file))
#####################################################################################
# HAND file has now been prepared, moving to flood mapping part #
#####################################################################################
# set the clone
pcr.setclone(options.ldd_wflow)
# read wflow ldd as pcraster object
ldd_pcr = pcr.readmap(options.ldd_wflow)
xax, yax, riv_width, fill_value = inun_lib.gdal_readmap(options.riv_width_file, 'GTiff', logging=logger)
# determine cell length in meters using ldd_pcr as clone (if latlon=True, values are converted to m2
x_res, y_res, reallength_wflow = pcrut.detRealCellLength(pcr.scalar(ldd_pcr), not(bool(options.latlon)))
cell_surface_wflow = pcr.pcr2numpy(x_res * y_res, 0)
if options.flood_volume_type == 0:
# load the staticmaps needed to estimate volumes across all
# xax, yax, riv_length, fill_value = inun_lib.gdal_readmap(options.riv_length_file, 'GTiff', logging=logger)
# riv_length = np.ma.masked_where(riv_length==fill_value, riv_length)
xax, yax, riv_width, fill_value = inun_lib.gdal_readmap(options.riv_width_file, 'GTiff', logging=logger)
riv_width[riv_width == fill_value] = 0
# read river length factor file (multiplier)
xax, yax, riv_length_fact, fill_value = inun_lib.gdal_readmap(options.riv_length_fact_file, 'GTiff', logging=logger)
riv_length_fact = np.ma.masked_where(riv_length_fact==fill_value, riv_length_fact)
drain_length = wflow_lib.detdrainlength(ldd_pcr, x_res, y_res)
# compute river length in each cell
riv_length = pcr.pcr2numpy(drain_length, 0) * riv_length_fact
# riv_length_pcr = pcr.numpy2pcr(pcr.Scalar, riv_length, 0)
flood_folder = os.path.join(options.dest_path, case_name)
flood_vol_map = os.path.join(flood_folder, '{:s}_vol.tif'.format(os.path.split(options.flood_map)[1].split('.')[0]))
if not(os.path.isdir(flood_folder)):
os.makedirs(flood_folder)
if options.out_format == 0:
inun_file_tmp = os.path.join(flood_folder, '{:s}.tif.tmp'.format(case_name))
inun_file = os.path.join(flood_folder, '{:s}.tif'.format(case_name))
else:
inun_file_tmp = os.path.join(flood_folder, '{:s}.nc.tmp'.format(case_name))
inun_file = os.path.join(flood_folder, '{:s}.nc'.format(case_name))
hand_temp_file = os.path.join(flood_folder, 'hand_temp.map')
drainage_temp_file = os.path.join(flood_folder, 'drainage_temp.map')
stream_temp_file = os.path.join(flood_folder, 'stream_temp.map')
flood_vol_temp_file = os.path.join(flood_folder, 'flood_warp_temp.tif')
# load the data with river levels and compute the volumes
if options.file_format == 0:
# assume we need the maximum value in a NetCDF time series grid
logger.info('Reading flood from {:s} NetCDF file'.format(options.flood_map))
a = nc.Dataset(options.flood_map, 'r')
if options.latlon == 0:
xax = a.variables['x'][:]
yax = a.variables['y'][:]
else:
xax = a.variables['lon'][:]
yax = a.variables['lat'][:]
if options.time == '':
time_list = nc.num2date(a.variables['time'][:], units = a.variables['time'].units, calendar=a.variables['time'].calendar)
time = [time_list[len(time_list)/2]]
else:
time = [dt.datetime.strptime(options.time, '%Y%m%d%H%M%S')]
flood_series = a.variables[options.flood_variable][:]
flood_data = flood_series.max(axis=0)
if np.ma.is_masked(flood_data):
flood = flood_data.data
flood[flood_data.mask] = 0
if yax[-1] > yax[0]:
yax = np.flipud(yax)
flood = np.flipud(flood)
a.close()
elif options.file_format == 1:
logger.info('Reading flood from {:s} PCRaster file'.format(options.flood_map))
xax, yax, flood, flood_fill_value = inun_lib.gdal_readmap(options.flood_map, 'PCRaster', logging=logger)
flood = np.ma.masked_equal(flood, flood_fill_value)
if options.time == '':
options.time = '20000101000000'
time = [dt.datetime.strptime(options.time, '%Y%m%d%H%M%S')]
flood[flood==flood_fill_value] = 0.
# load the bankfull depths
if options.bankfull_map == '':
bankfull = np.zeros(flood.shape)
else:
if options.file_format == 0:
logger.info('Reading bankfull from {:s} NetCDF file'.format(options.bankfull_map))
a = nc.Dataset(options.bankfull_map, 'r')
xax = a.variables['x'][:]
yax = a.variables['y'][:]
bankfull_series = a.variables[options.flood_variable][:]
bankfull_data = bankfull_series.max(axis=0)
if np.ma.is_masked(bankfull_data):
bankfull = bankfull_data.data
bankfull[bankfull_data.mask] = 0
if yax[-1] > yax[0]:
yax = np.flipud(yax)
bankfull = np.flipud(bankfull)
a.close()
elif options.file_format == 1:
logger.info('Reading bankfull from {:s} PCRaster file'.format(options.bankfull_map))
xax, yax, bankfull, bankfull_fill_value = inun_lib.gdal_readmap(options.bankfull_map, 'PCRaster', logging=logger)
bankfull = np.ma.masked_equal(bankfull, bankfull_fill_value)
# flood = bankfull*2
# res_x = 2000
# res_y = 2000
# subtract the bankfull water level to get flood levels (above bankfull)
flood_vol = np.maximum(flood-bankfull, 0)
if options.flood_volume_type == 0:
flood_vol_m = riv_length*riv_width*flood_vol/cell_surface_wflow # volume expressed in meters water disc
flood_vol_m_pcr = pcr.numpy2pcr(pcr.Scalar, flood_vol_m, 0)
else:
flood_vol_m = flood_vol/cell_surface_wflow
flood_vol_m_data = flood_vol_m.data
flood_vol_m_data[flood_vol_m.mask] = -999.
logger.info('Saving water layer map to {:s}'.format(flood_vol_map))
# write to a tiff file
inun_lib.gdal_writemap(flood_vol_map, 'GTiff', xax, yax, np.maximum(flood_vol_m_data, 0), -999., logging=logger)
# this is placed later in the hand loop
# ds_hand, rasterband_hand = inun_lib.get_gdal_rasterband(hand_file)
ds_ldd, rasterband_ldd = inun_lib.get_gdal_rasterband(options.ldd_file)
ds_stream, rasterband_stream = inun_lib.get_gdal_rasterband(options.stream_file)
logger.info('Preparing flood map in {:s} ...please wait...'.format(inun_file))
if options.out_format == 0:
ds_inun, band_inun = inun_lib.prepare_gdal(inun_file_tmp, x, y, logging=logger, srs=srs)
# band_inun = ds_inun.GetRasterBand(1)
else:
ds_inun, band_inun = inun_lib.prepare_nc(inun_file_tmp, time, x, np.flipud(y), metadata=metadata_global,
metadata_var=metadata_var, logging=logger)
# loop over all the tiles
n = 0
for x_loop in range(0, len(x), options.x_tile):
x_start = np.maximum(x_loop, 0)
x_end = np.minimum(x_loop + options.x_tile, len(x))
# determine actual overlap for cutting
for y_loop in range(0, len(y), options.y_tile):
x_overlap_min = x_start - np.maximum(x_start - options.x_overlap, 0)
x_overlap_max = np.minimum(x_end + options.x_overlap, len(x)) - x_end
n += 1
# print('tile {:001d}:'.format(n))
y_start = np.maximum(y_loop, 0)
y_end = np.minimum(y_loop + options.y_tile, len(y))
y_overlap_min = y_start - np.maximum(y_start - options.y_overlap, 0)
y_overlap_max = np.minimum(y_end + options.y_overlap, len(y)) - y_end
x_tile_ax = x[x_start - x_overlap_min:x_end + x_overlap_max]
y_tile_ax = y[y_start - y_overlap_min:y_end + y_overlap_max]
# cut out DEM
logger.debug('handling xmin: {:d} xmax: {:d} ymin {:d} ymax {:d}'.format(x_start, x_end, y_start, y_end))
drainage = rasterband_ldd.ReadAsArray(x_start - x_overlap_min,
y_start - y_overlap_min,
(x_end + x_overlap_max) - (x_start - x_overlap_min),
(y_end + y_overlap_max) - (y_start - y_overlap_min)
)
stream = rasterband_stream.ReadAsArray(x_start - x_overlap_min,
y_start - y_overlap_min,
(x_end + x_overlap_max) - (x_start - x_overlap_min),
(y_end + y_overlap_max) - (y_start - y_overlap_min)
)
# stream_max = np.minimum(stream.max(), options.max_strahler)
inun_lib.gdal_writemap(drainage_temp_file, 'PCRaster',
x_tile_ax,
y_tile_ax,
drainage, rasterband_ldd.GetNoDataValue(),
gdal_type=gdal.GDT_Int32,
logging=logger)
inun_lib.gdal_writemap(stream_temp_file, 'PCRaster',
x_tile_ax,
y_tile_ax,
stream, rasterband_stream.GetNoDataValue(),
gdal_type=gdal.GDT_Int32,
logging=logger)
# read as pcr objects
pcr.setclone(stream_temp_file)
drainage_pcr = pcr.lddrepair(pcr.ldd(pcr.readmap(drainage_temp_file))) # convert to ldd type map
stream_pcr = pcr.scalar(pcr.readmap(stream_temp_file)) # convert to ldd type map
# warp of flood volume to inundation resolution
inun_lib.gdal_warp(flood_vol_map, stream_temp_file, flood_vol_temp_file, gdal_interp=gdalconst.GRA_NearestNeighbour) # ,
x_tile_ax, y_tile_ax, flood_meter, fill_value = inun_lib.gdal_readmap(flood_vol_temp_file, 'GTiff', logging=logger)
# make sure that the option unittrue is on !! (if unitcell was is used in another function)
x_res_tile, y_res_tile, reallength = pcrut.detRealCellLength(pcr.scalar(stream_pcr), not(bool(options.latlon)))
cell_surface_tile = pcr.pcr2numpy(x_res_tile * y_res_tile, 0)
# convert meter depth to volume [m3]
flood_vol = pcr.numpy2pcr(pcr.Scalar, flood_meter*cell_surface_tile, fill_value)
# first prepare a basin map, belonging to the lowest order we are looking at
inundation_pcr = pcr.scalar(stream_pcr) * 0
for hand_strahler in range(options.catchment_strahler, stream_max + 1, 1):
# hand_temp_file = os.path.join(flood_folder, 'hand_temp.map')
if os.path.isfile(os.path.join(options.dest_path, '{:s}_hand_strahler_{:02d}.tif'.format(dem_name, hand_strahler))):
hand_file = os.path.join(options.dest_path, '{:s}_hand_strahler_{:02d}.tif'.format(dem_name, hand_strahler))
else:
hand_file = '{:s}_{:02d}.tif'.format(options.hand_file_prefix, hand_strahler)
ds_hand, rasterband_hand = inun_lib.get_gdal_rasterband(hand_file)
hand = rasterband_hand.ReadAsArray(x_start - x_overlap_min,
y_start - y_overlap_min,
(x_end + x_overlap_max) - (x_start - x_overlap_min),
(y_end + y_overlap_max) - (y_start - y_overlap_min)
)
print('len x-ax: {:d} len y-ax {:d} x-shape {:d} y-shape {:d}'.format(len(x_tile_ax), len(y_tile_ax), hand.shape[1], hand.shape[0]))
inun_lib.gdal_writemap(hand_temp_file, 'PCRaster',
x_tile_ax,
y_tile_ax,
hand, rasterband_hand.GetNoDataValue(),
gdal_type=gdal.GDT_Float32,
logging=logger)
hand_pcr = pcr.readmap(hand_temp_file)
stream_ge_hand, subcatch_hand = inun_lib.subcatch_stream(drainage_pcr, options.catchment_strahler, stream=stream_pcr)
# stream_ge_hand, subcatch_hand = inun_lib.subcatch_stream(drainage_pcr, hand_strahler, stream=stream_pcr)
stream_ge, subcatch = inun_lib.subcatch_stream(drainage_pcr,
options.catchment_strahler,
stream=stream_pcr,
basin=pcr.boolean(pcr.cover(subcatch_hand, 0)),
assign_existing=True,
min_strahler=hand_strahler,
max_strahler=hand_strahler) # generate subcatchments, only within basin for HAND
flood_vol_strahler = pcr.ifthenelse(pcr.boolean(pcr.cover(subcatch, 0)), flood_vol, 0) # mask the flood volume map with the created subcatch map for strahler order = hand_strahler
inundation_pcr_step = inun_lib.volume_spread(drainage_pcr, hand_pcr,
pcr.subcatchment(drainage_pcr, subcatch), # to make sure backwater effects can occur from higher order rivers to lower order rivers
flood_vol_strahler,
volume_thres=0.,
iterations=options.iterations,
cell_surface=pcr.numpy2pcr(pcr.Scalar, cell_surface_tile, -9999),
logging=logger,
order=hand_strahler,
neg_HAND=options.neg_HAND) # 1166400000.
# use maximum value of inundation_pcr_step and new inundation for higher strahler order
inundation_pcr = pcr.max(inundation_pcr, inundation_pcr_step)
inundation = pcr.pcr2numpy(inundation_pcr, -9999.)
# cut relevant part
if y_overlap_max == 0:
y_overlap_max = -inundation.shape[0]
if x_overlap_max == 0:
x_overlap_max = -inundation.shape[1]
inundation_cut = inundation[0+y_overlap_min:-y_overlap_max, 0+x_overlap_min:-x_overlap_max]
# inundation_cut
if options.out_format == 0:
band_inun.WriteArray(inundation_cut, x_start, y_start)
band_inun.FlushCache()
else:
# with netCDF, data is up-side-down.
inun_lib.write_tile_nc(band_inun, inundation_cut, x_start, y_start)
# clean up
os.unlink(flood_vol_temp_file)
os.unlink(drainage_temp_file)
os.unlink(hand_temp_file)
os.unlink(stream_temp_file) #also remove temp stream file from output folder
# if n == 35:
# band_inun.SetNoDataValue(-9999.)
# ds_inun = None
# sys.exit(0)
# os.unlink(flood_vol_map)
logger.info('Finalizing {:s}'.format(inun_file))
# add the metadata to the file and band
# band_inun.SetNoDataValue(-9999.)
# ds_inun.SetMetadata(metadata_global)
# band_inun.SetMetadata(metadata_var)
if options.out_format == 0:
ds_inun = None
ds_hand = None
else:
ds_inun.close()
ds_ldd = None
# rename temporary file to final hand file
if os.path.isfile(inun_file):
# remove an old result if available
os.unlink(inun_file)
os.rename(inun_file_tmp, inun_file)
logger.info('Done! Thank you for using hand_contour_inun.py')
logger, ch = inun_lib.closeLogger(logger, ch)
del logger, ch
sys.exit(0)
msg = "Set the landmask to : " + str(landmask_map_file)
logger.info(msg)
landmask = pcr.readmap(landmask_map_file)
# resampling low resolution ldd map
msg = "Resample the low resolution ldd map."
logger.info(msg)
ldd_map_low_resolution_file_name = "/projects/0/dfguu/data/hydroworld/PCRGLOBWB20/input5min/routing/lddsound_05min.map"
ldd_map_low_resolution = vos.readPCRmapClone(ldd_map_low_resolution_file_name, \
clone_map_file, \
tmp_folder, \
None, True, None, False)
ldd_map_low_resolution = pcr.ifthen(
landmask,
ldd_map_low_resolution) # NOTE THAT YOU MAY NOT HAVE TO MASK-OUT THE LDD.
ldd_map_low_resolution = pcr.lddrepair(pcr.ldd(ldd_map_low_resolution))
ldd_map_low_resolution = pcr.lddrepair(ldd_map_low_resolution)
pcr.report(ldd_map_low_resolution, "resampled_low_resolution_ldd.map")
# permanent water bodies files (at 5 arc-minutes resolution)
reservoir_capacity_file = "/projects/0/dfguu/data/hydroworld/PCRGLOBWB20/input5min/routing/reservoirs/waterBodiesFinal_version15Sept2013/maps/reservoircapacity_2010.map"
fracwat_file = "/projects/0/dfguu/data/hydroworld/PCRGLOBWB20/input5min/routing/reservoirs/waterBodiesFinal_version15Sept2013/maps/fracwat_2010.map"
water_body_id_file = "/projects/0/dfguu/data/hydroworld/PCRGLOBWB20/input5min/routing/reservoirs/waterBodiesFinal_version15Sept2013/maps/waterbodyid_2010.map"
# cell_area_file
cell_area_file = "/projects/0/dfguu/data/hydroworld/PCRGLOBWB20/input5min/routing/cellsize05min.correct.map"
# read all extreme value maps (low resolution maps), resample them, and save them to the output folder
msg = "Resampling extreme value maps."
logger.info(msg)
file_names = [
def _parseLine(self, line, lineNumber, nrColumns, externalNames, keyDict):
line = re.sub("\n", "", line)
line = re.sub("\t", " ", line)
result = None
# read until first comment
content = ""
content, sep, comment = line.partition("#")
if len(content) > 1:
collectionVariableName, sep, tail = content.partition(" ")
if collectionVariableName == self._varName:
tail = tail.strip()
key, sep, variableValue = tail.rpartition(" ")
if len(key.split()) != nrColumns:
tmp = re.sub("\(|\)|,", "", str(key))
msg = "Error reading %s line %d, order of columns given (%s columns) does not match expected order of %s columns" % (
self._fileName, lineNumber, len(key.split()) + 2,
int(nrColumns) + 2)
raise ValueError(msg)
variableValue = re.sub('\"', "", variableValue)
tmp = None
try:
tmp = int(variableValue)
if self._dataType == pcraster.Boolean:
tmp = pcraster.boolean(tmp)
elif self._dataType == pcraster.Nominal:
tmp = pcraster.nominal(tmp)
elif self._dataType == pcraster.Ordinal:
tmp = pcraster.ordinal(tmp)
elif self._dataType == pcraster.Ldd:
tmp = pcraster.ldd(tmp)
else:
msg = "Conversion to %s failed" % (self._dataType)
raise Exception(msg)
except ValueError as e:
try:
tmp = float(variableValue)
if self._dataType == pcraster.Scalar:
tmp = pcraster.scalar(tmp)
elif self._dataType == pcraster.Directional:
tmp = pcraster.directional(tmp)
else:
msg = "Conversion to %s failed" % (self._dataType)
raise Exception(msg)
except ValueError as e:
variableValue = re.sub("\\\\", "/", variableValue)
variableValue = variableValue.strip()
path = os.path.normpath(variableValue)
try:
tmp = pcraster.readmap(path)
except RuntimeError as e:
msg = "Error reading %s line %d, %s" % (
self._fileName, lineNumber, e)
raise ValueError(msg)
# test if key is an external name
transformedKeys = []
counter = 0
for k in key.split():
k = k.strip()
if externalNames[counter].get(k):
transformedKeys.append(externalNames[counter].get(k))
else:
transformedKeys.append(k)
counter += 1
key = tuple(transformedKeys)
if not key in keyDict:
tmp = re.sub("\(|\)|,", "", str(key))
msg = "Error reading %s line %d, %s unknown collection index" % (
self._fileName, lineNumber, tmp)
raise ValueError(msg)
if not keyDict[key] is None:
tmp = re.sub("\(|\)|,", "", str(key))
msg = "Error reading %s line %d, %s %s already initialised" % (
self._fileName, lineNumber, self._varName, tmp)
raise ValueError(msg)
keyDict[key] = tmp
if lddin:
pcr.setglobaloption("lddin")
ldd_map = workdir + 'ldd.map'
streamorder_map = workdir + 'streamorder.map'
river_map = workdir + 'river.map'
catchments_map = workdir + 'catchments.map'
catchments_tif = workdir + 'catchments.tif'
#catchments_shp = resultdir + 'catchments.shp'
generateldd = True
if skipldd:
print 'Option -S is set'
print 'ldd will be read from ' + ldd_map
if os.path.exists(ldd_map):
ldd = pcr.ldd(pcr.readmap(ldd_map))
generateldd = False
else:
print 'file ' + ldd_map + ' does not exist'
print 'new ldd will be generated'
if generateldd:
print 'Generating ldd...'
if burndem:
linescover = pcr.ifthen(lines==1,pcr.scalar(0))
pointscover = pcr.ifthen(pcr.scalar(points)==1,pcr.scalar(0))
#pcr.report(linescover,'lines.map')
#pcr.report(pointscover,'points.map')
dem = pcr.cover(dem,linescover,pointscover)
#pcr.report(dem,'dem1.map')
dem = dem + burn
def __init__(self,
iniItems,
landmask,
onlyNaturalWaterBodies=False,
lddMap=None):
object.__init__(self)
# clone map file names, temporary directory and global/absolute path of input directory
self.cloneMap = iniItems.cloneMap
self.tmpDir = iniItems.tmpDir
self.inputDir = iniItems.globalOptions['inputDir']
self.landmask = landmask
self.iniItems = iniItems
# local drainage direction:
if lddMap is None:
self.lddMap = vos.readPCRmapClone(
iniItems.routingOptions['lddMap'], self.cloneMap, self.tmpDir,
self.inputDir, True)
self.lddMap = pcr.lddrepair(pcr.ldd(self.lddMap))
self.lddMap = pcr.lddrepair(self.lddMap)
else:
self.lddMap = lddMap
# the following is needed for a modflowOfflineCoupling run
if 'modflowOfflineCoupling' in list(iniItems.globalOptions.keys(
)) and iniItems.globalOptions[
'modflowOfflineCoupling'] == "True" and 'routingOptions' not in iniItems.allSections:
logger.info(
"The 'routingOptions' are not defined in the configuration ini file. We will adopt them from the 'modflowParameterOptions'."
)
iniItems.routingOptions = iniItems.modflowParameterOptions
# option to activate water balance check
self.debugWaterBalance = True
if 'debugWaterBalance' in list(iniItems.routingOptions.keys(
)) and iniItems.routingOptions['debugWaterBalance'] == "False":
self.debugWaterBalance = False
# option to perform a run with only natural lakes (without reservoirs)
self.onlyNaturalWaterBodies = onlyNaturalWaterBodies
if "onlyNaturalWaterBodies" in list(iniItems.routingOptions.keys(
)) and iniItems.routingOptions['onlyNaturalWaterBodies'] == "True":
logger.info(
"Using only natural water bodies identified in the year 1900. All reservoirs in 1900 are assumed as lakes."
)
self.onlyNaturalWaterBodies = True
self.dateForNaturalCondition = "1900-01-01" # The run for a natural condition should access only this date.
# names of files containing water bodies parameters
if iniItems.routingOptions['waterBodyInputNC'] == str(None):
self.useNetCDF = False
self.fracWaterInp = iniItems.routingOptions['fracWaterInp']
self.waterBodyIdsInp = iniItems.routingOptions['waterBodyIds']
self.waterBodyTypInp = iniItems.routingOptions['waterBodyTyp']
self.resMaxCapInp = iniItems.routingOptions['resMaxCapInp']
self.resSfAreaInp = iniItems.routingOptions['resSfAreaInp']
else:
self.useNetCDF = True
self.ncFileInp = vos.getFullPath(\
iniItems.routingOptions['waterBodyInputNC'],\
self.inputDir)
# minimum width (m) used in the weir formula # TODO: define minWeirWidth based on the GLWD, GRanD database and/or bankfull discharge formula
self.minWeirWidth = 10.
# lower and upper limits at which reservoir release is terminated and
# at which reservoir release is equal to long-term average outflow
# - default values
self.minResvrFrac = 0.10
self.maxResvrFrac = 0.75
# - from the ini file
if "minResvrFrac" in list(iniItems.routingOptions.keys()):
minResvrFrac = iniItems.routingOptions['minResvrFrac']
self.minResvrFrac = vos.readPCRmapClone(minResvrFrac,
self.cloneMap, self.tmpDir,
self.inputDir)
if "maxResvrFrac" in list(iniItems.routingOptions.keys()):
maxResvrFrac = iniItems.routingOptions['maxResvrFrac']
self.maxResvrFrac = vos.readPCRmapClone(maxResvrFrac,
self.cloneMap, self.tmpDir,
self.inputDir)
def __init__(self, modelTime, output_folder, totat_runoff_input_file):
DynamicModel.__init__(self)
self.modelTime = modelTime
# netcdf input files - based on PCR-GLOBWB output
# - total runoff (m/month)
self.totat_runoff_input_file = "/scratch-shared/edwin/05min_runs_for_gmd_paper_30_oct_2017/05min_runs_4LCs_accutraveltime_cru-forcing_1958-2015/non-natural_starting_from_1958/merged_1958_to_2015/totalRunoff_monthTot_output_1958-01-31_to_2015-12-31.nc"
self.totat_runoff_input_file = totat_runoff_input_file
#
#~ # - discharge (m3/s) - NOT USED anymore
#~ self.discharge_input_file = "/scratch-shared/edwin/05min_runs_for_gmd_paper_30_oct_2017/05min_runs_4LCs_accutraveltime_cru-forcing_1958-2015/non-natural_starting_from_1958/merged_1958_to_2015/discharge_monthAvg_output_1958-01-31_to_2015-12-31.nc"
# output files - in netcdf format
self.total_flow_output_file = output_folder + "/total_flow.nc"
self.internal_flow_output_file = output_folder + "/internal_flow.nc"
# - all will have unit m3/s
# preparing temporary directory
self.temporary_directory = output_folder + "/tmp/"
os.makedirs(self.temporary_directory)
# clone map
logger.info("Set the clone map")
self.clonemap_file_name = "/home/edwinvua/github/edwinkost/estimate_discharge_from_local_runoff/making_subcatchment_map/version_20180202/clone_version_20180202.map"
pcr.setclone(self.clonemap_file_name)
# pcraster input files
landmask_file_name = None
# - river network map and sub-catchment map
ldd_file_name = "/projects/0/dfguu/data/hydroworld/PCRGLOBWB20/input5min/routing/lddsound_05min.map"
sub_catchment_file_name = "/home/edwinvua/github/edwinkost/estimate_discharge_from_local_runoff/making_subcatchment_map/version_20180202/subcatchments_of_station_pcraster_ids.nom.bigger_than_zero.map"
# - cell area (unit: m2)
cell_area_file_name = "/projects/0/dfguu/data/hydroworld/PCRGLOBWB20/input5min/routing/cellsize05min.correct.map"
# loading pcraster input maps
self.sub_catchment = vos.readPCRmapClone(sub_catchment_file_name, \
self.clonemap_file_name, \
self.temporary_directory, \
None, False, None, \
True)
self.ldd_network = vos.readPCRmapClone(ldd_file_name, \
self.clonemap_file_name, \
self.temporary_directory, \
None, \
True)
self.ldd_network = pcr.lddrepair(pcr.ldd(self.ldd_network))
self.ldd_network = pcr.lddrepair(self.ldd_network)
self.cell_area = vos.readPCRmapClone(cell_area_file_name, \
self.clonemap_file_name, \
self.temporary_directory, \
None)
# define the landmask
self.landmask = pcr.defined(self.ldd_network)
if landmask_file_name != None:
self.landmask = vos.readPCRmapClone(landmask_file_name, \
self.clonemap_file_name, \
self.temporary_directory, \
None)
self.landmask = pcr.ifthen(pcr.defined(self.ldd_network), self.landmask)
self.landmask = pcr.ifthen(self.landmask, self.landmask)
# set/limit all input maps to the defined landmask
self.sub_catchment = pcr.ifthen(self.landmask, self.sub_catchment)
self.ldd_network = pcr.ifthen(self.landmask, self.ldd_network)
self.cell_area = pcr.ifthen(self.landmask, self.cell_area)
# preparing an object for reporting netcdf files:
self.netcdf_report = netcdf_writer.PCR2netCDF(self.clonemap_file_name)
# preparing netcdf output files:
# - for total inflow
self.netcdf_report.createNetCDF(self.total_flow_output_file,\
"total_flow",\
"m3/s")
self.netcdf_report.createNetCDF(self.internal_flow_output_file,\
"internal_flow",\
"m3/s")
def main():
clone_map = "mask\mask.map"
clone_shp = "mask\mask.shp"
clone_prj = "mask\mask.prj"
workdir = "work\\"
resultdir = "staticmaps\\"
''' read commandline arguments '''
argv = sys.argv
clone_EPSG = False
try:
opts, args = getopt.getopt(argv[1:], 'i:g:p:r:c:d:l:s:CA')
except getopt.error:
print 'fout'
Usage()
sys.exit(1)
inifile = None
rivshp = None
catchshp = None
dem_in = None
landuse = None
soiltype = None
clean = False
gaugeshp = None
alltouching = False
for o, a in opts:
if o == '-i': inifile = a
if o == '-p': clone_EPSG = 'EPSG:' + a
if o == '-r': rivshp = a
if o == '-c': catchshp = a
if o == '-d': dem_in = a
if o == '-l': landuse = a
if o == '-s': soiltype = a
if o == '-C': clean = True
if o == '-g': gaugeshp = a
if o == '-A': alltouching = True
if inifile == None or rivshp == None or catchshp == None or dem_in == None:
print 'the following files are compulsory:'
print ' - ini-file'
print ' - DEM (raster)'
print ' - river (shape)'
print ' - catchment (shape)'
Usage()
sys.exit(1)
if landuse == None:
print 'no raster with landuse classifications is specified. 1 class will be applied for the entire domain'
if soiltype == None:
print 'no raster with soil classifications is specified. 1 class will be applied for the entire domain'
''' read mask '''
if not os.path.exists(clone_map):
print 'Mask not found. Make sure the file mask\mask.map exists'
print 'This file is usually created with the CreateGrid script'
sys.exit(1)
else:
pcr.setclone(clone_map)
ds = gdal.Open(clone_map, GA_ReadOnly)
clone_trans = ds.GetGeoTransform()
cellsize = clone_trans[1]
clone_rows = ds.RasterYSize
clone_columns = ds.RasterXSize
extent_mask = [
clone_trans[0], clone_trans[3] - ds.RasterYSize * cellsize,
clone_trans[0] + ds.RasterXSize * cellsize, clone_trans[3]
]
xmin, ymin, xmax, ymax = map(str, extent_mask)
ds = None
ones = pcr.scalar(pcr.readmap(clone_map))
zeros = ones * 0
empty = pcr.ifthen(ones == 0, pcr.scalar(0))
''' read projection from mask.shp '''
# TODO: check how to deal with projections (add .prj to mask.shp in creategrid)
if not os.path.exists(clone_prj):
print 'please add prj-file to mask.shp'
sys.exit(1)
if os.path.exists(clone_shp):
ds = ogr.Open(clone_shp)
file_att = os.path.splitext(os.path.basename(clone_shp))[0]
lyr = ds.GetLayerByName(file_att)
spatialref = lyr.GetSpatialRef()
if not spatialref == None:
srs_clone = osr.SpatialReference()
srs_clone.ImportFromWkt(spatialref.ExportToWkt())
srs_clone.AutoIdentifyEPSG()
unit_clone = False
unit_clone = srs_clone.GetAttrValue('UNIT').lower()
#clone_EPSG = 'EPSG:'+srs_clone.GetAttrValue("AUTHORITY",1)
# TODO: fix hard EPSG code below
clone_EPSG = 'EPSG:' + '4167'
print 'EPSG-code is read from mask.shp: ' + clone_EPSG
spatialref == None
if not clone_EPSG:
print 'EPSG-code cannot be read from mask.shp'
print 'please add prj-file to mask.shp or specify on command line'
print 'e.g. -p EPSG:4326 (for WGS84 lat lon projection)'
ds = None
clone_EPSG_int = int(clone_EPSG[5:len(clone_EPSG)])
''' open config-file '''
config = wt.OpenConf(inifile)
''' read settings '''
snapgaugestoriver = bool(
int(wt.configget(config, "settings", "snapgaugestoriver", "1")))
burnalltouching = bool(
int(wt.configget(config, "settings", "burncatchalltouching", "1")))
burninorder = bool(
int(wt.configget(config, "settings", "burncatchalltouching", "0")))
verticetollerance = float(
wt.configget(config, "settings", "vertice_tollerance", "0.0001"))
''' read parameters '''
burn_outlets = int(
wt.configget(config, "parameters", "burn_outlets", 10000))
burn_rivers = int(wt.configget(config, "parameters", "burn_rivers", 200))
burn_connections = int(
wt.configget(config, "parameters", "burn_connections", 100))
burn_gauges = int(wt.configget(config, "parameters", "burn_gauges", 100))
minorder = int(wt.configget(config, "parameters", "riverorder_min", 3))
exec "percentile=tr.array(" + wt.configget(config, "parameters",
"statisticmaps", [0, 100]) + ")"
if not unit_clone:
print 'failed to read unit (meter or degree) from mask projection'
unit_clone = str(wt.configget(config, "settings", "unit", 'meter'))
print 'unit read from settings: ' + unit_clone
if unit_clone == 'degree':
cellsize_hr = float(
wt.configget(config, "parameters", "highres_degree", 0.0005))
elif (unit_clone == 'metre') or (unit_clone == 'meter'):
cellsize_hr = float(
wt.configget(config, "parameters", "highres_metre", 50))
cols_hr = int((float(xmax) - float(xmin)) / cellsize_hr + 2)
rows_hr = int((float(ymax) - float(ymin)) / cellsize_hr + 2)
hr_trans = (float(xmin), cellsize_hr, float(0), float(ymax), 0,
-cellsize_hr)
''' read staticmap locations '''
catchment_map = wt.configget(config, "staticmaps", "catchment",
"wflow_catchment.map")
dem_map = wt.configget(config, "staticmaps", "dem", "wflow_dem.map")
demmax_map = wt.configget(config, "staticmaps", "demmax",
"wflow_demmax.map")
demmin_map = wt.configget(config, "staticmaps", "demmin",
"wflow_demmin.map")
gauges_map = wt.configget(config, "staticmaps", "gauges",
"wflow_gauges.map")
landuse_map = wt.configget(config, "staticmaps", "landuse",
"wflow_landuse.map")
ldd_map = wt.configget(config, "staticmaps", "ldd", "wflow_ldd.map")
river_map = wt.configget(config, "staticmaps", "river", "wflow_river.map")
outlet_map = wt.configget(config, "staticmaps", "outlet",
"wflow_outlet.map")
riverlength_fact_map = wt.configget(config, "staticmaps",
"riverlength_fact",
"wflow_riverlength_fact.map")
soil_map = wt.configget(config, "staticmaps", "soil", "wflow_soil.map")
streamorder_map = wt.configget(config, "staticmaps", "streamorder",
"wflow_streamorder.map")
subcatch_map = wt.configget(config, "staticmaps", "subcatch",
"wflow_subcatch.map")
''' read mask location (optional) '''
masklayer = wt.configget(config, "mask", "masklayer", catchshp)
''' create directories '''
if os.path.isdir(workdir):
shutil.rmtree(workdir)
os.makedirs(workdir)
if os.path.isdir(resultdir):
shutil.rmtree(resultdir)
os.makedirs(resultdir)
''' Preperation steps '''
zero_map = workdir + "zero.map"
zero_tif = workdir + "zero.tif"
pcr.report(zeros, zero_map)
# TODO: replace gdal_translate call
call(('gdal_translate', '-of', 'GTiff', '-a_srs', clone_EPSG, '-ot',
'Float32', zero_map, zero_tif))
pcr.setglobaloption("lddin")
''' resample DEM '''
dem_resample = workdir + "dem_resampled.tif"
ds = gdal.Open(dem_in, GA_ReadOnly)
band = ds.GetRasterBand(1)
nodata = band.GetNoDataValue()
proj = ds.GetGeoTransform()
cellsize_dem = proj[1]
''' read DEM projection '''
spatialref == None
spatialref = ds.GetProjection()
if not spatialref == None:
srs = osr.SpatialReference()
srs.ImportFromWkt(spatialref)
srs.AutoIdentifyEPSG()
dem_EPSG = 'EPSG:' + srs.GetAttrValue("AUTHORITY", 1)
print 'EPSG-code is read from ' + os.path.basename(
dem_in) + ': ' + dem_EPSG
spatialref == None
dem_EPSG_int = int(dem_EPSG[5:len(dem_EPSG)])
srs_DEM = osr.SpatialReference()
srs_DEM.ImportFromEPSG(dem_EPSG_int)
clone2dem_transform = osr.CoordinateTransformation(srs_clone, srs_DEM)
else:
dem_EPSG = clone_EPSG
print 'No projection defined for ' + os.path.basename(dem_in)
print 'Assumed to be the same as model projection (' + clone_EPSG + ')'
ds = None
print 'Resampling DEM...'
if nodata == None:
call(('gdalwarp', '-overwrite', '-t_srs', clone_prj, '-te', xmin, ymin,
xmax, ymax, '-tr', str(cellsize), str(-cellsize), '-dstnodata',
str(-9999), '-r', 'cubic', dem_in, dem_resample))
else:
call(('gdalwarp', '-overwrite', '-t_srs', clone_prj,
'-te', xmin, ymin, xmax, ymax, '-tr', str(cellsize),
str(-cellsize), '-srcnodata', str(nodata), '-dstnodata',
str(nodata), '-r', 'cubic', dem_in, dem_resample))
''' create dem.map and statistic maps '''
dem_resample_map = resultdir + dem_map
call(('gdal_translate', '-of', 'PCRaster', '-a_srs', clone_EPSG, '-ot',
'Float32', dem_resample, dem_resample_map))
print 'Computing DEM statistics ....'
stats = wt.windowstats(dem_in, clone_rows, clone_columns, clone_trans,
srs_clone, resultdir, percentile)
''' burn DEM '''
ds = ogr.Open(rivshp)
file_att = os.path.splitext(os.path.basename(rivshp))[0]
lyr = ds.GetLayerByName(file_att)
spatialref = lyr.GetSpatialRef()
# if not spatialref == None:
# srs = osr.SpatialReference()
# srs.ImportFromWkt(spatialref.ExportToWkt())
# srs.AutoIdentifyEPSG()
# rivshp_EPSG = 'EPSG:'+srs.GetAttrValue("AUTHORITY",1)
# spatialref == None
# else:
rivshp_EPSG = clone_EPSG
print 'No projection defined for ' + file_att + '.shp'
print 'Assumed to be the same as model projection (' + clone_EPSG + ')'
# strip rivers to nodes
xminc = str(float(xmin) + 0.5 * cellsize)
yminc = str(float(ymin) + 0.5 * cellsize)
xmaxc = str(float(xmax) - 0.5 * cellsize)
ymaxc = str(float(ymax) - 0.5 * cellsize)
if rivshp_EPSG == clone_EPSG:
rivclipshp = workdir + 'rivshape_clip.shp'
call(('ogr2ogr', '-s_srs', clone_EPSG, '-t_srs', clone_EPSG, '-spat',
xmin, ymin, xmax, ymax, '-clipsrc', xminc, yminc, xmaxc, ymaxc,
rivclipshp, rivshp))
else:
rivprojshp = workdir + 'rivshape_proj.shp'
rivclipshp = workdir + 'rivshape_clip.shp'
call(('ogr2ogr', '-s_srs', rivshp_EPSG, '-t_srs', clone_EPSG, '-spat',
xmin, ymin, xmax, ymax, rivprojshp, rivshp))
call(('ogr2ogr', '-s_srs', clone_EPSG, '-t_srs', clone_EPSG, '-spat',
xmin, ymin, xmax, ymax, '-clipsrc', xminc, yminc, xmaxc, ymaxc,
rivclipshp, rivprojshp))
rivshp = rivclipshp
#### BURNING BELOW ####
# TODO: check if extraction can be done within memory and retun a burn layer
shapes = wt.Reach2Nodes(rivclipshp, clone_EPSG_int,
cellsize * verticetollerance, workdir)
outlets = shapes[1]
connections = shapes[2]
outlets_att = os.path.splitext(os.path.basename(outlets))[0]
connections_att = os.path.splitext(os.path.basename(connections))[0]
dem_resample_att = os.path.splitext(os.path.basename(dem_resample))[0]
connections_tif = workdir + connections_att + ".tif"
outlets_tif = workdir + outlets_att + ".tif"
# TODO: make the burning in memory
call(('gdal_translate', '-of', 'GTiff', '-a_srs', clone_EPSG, '-ot',
'Float32', zero_map, connections_tif))
call(('gdal_translate', '-of', 'GTiff', '-a_srs', clone_EPSG, '-ot',
'Float32', zero_map, outlets_tif))
call(('gdal_rasterize', '-burn', '1', '-l', outlets_att, outlets,
outlets_tif))
call(('gdal_rasterize', '-burn', '1', '-l', connections_att, connections,
connections_tif))
# convert rivers to order
rivshp_att = os.path.splitext(os.path.basename(rivshp))[0]
rivers_tif = workdir + rivshp_att + ".tif"
call(('gdal_translate', '-of', 'GTiff', '-a_srs', clone_EPSG, '-ot',
'Float32', zero_map, rivers_tif))
if burninorder: # make river shape with an order attribute
OrderSHPs = wt.ReachOrder(rivshp, clone_EPSG_int,
cellsize * verticetollerance, workdir)
wt.Burn2Tif(OrderSHPs, 'order', rivers_tif)
else:
call(('gdal_rasterize', '-burn', '1', '-l', rivshp_att, rivshp,
rivers_tif))
# convert 2 maps
connections_map = workdir + connections_att + ".map"
rivers_map = workdir + rivshp_att + ".map"
outlets_map = workdir + outlets_att + ".map"
call(('gdal_translate', '-of', 'PCRaster', '-a_srs', clone_EPSG, '-ot',
'Float32', connections_tif, connections_map))
call(('gdal_translate', '-of', 'PCRaster', '-a_srs', clone_EPSG, '-ot',
'Float32', rivers_tif, rivers_map))
call(('gdal_translate', '-of', 'PCRaster', '-a_srs', clone_EPSG, '-ot',
'Float32', outlets_tif, outlets_map))
# burn the layers in DEM
outletsburn = pcr.scalar(
pcr.readmap(outlets_map)) * pcr.scalar(burn_outlets)
connectionsburn = pcr.scalar(
pcr.readmap(connections_map)) * pcr.scalar(burn_connections)
riverburn = pcr.scalar(pcr.readmap(rivers_map)) * pcr.scalar(burn_rivers)
ldddem = pcr.cover(dem_resample_map,
pcr.ifthen(riverburn > 0, pcr.scalar(0)))
ldddem = ldddem - outletsburn - connectionsburn - riverburn
ldddem = pcr.cover(ldddem, pcr.scalar(0))
pcr.report(ldddem, workdir + "dem_burn.map")
''' create ldd for multi-catchments '''
ldd = pcr.ldd(empty)
# reproject catchment shape-file
ds = ogr.Open(catchshp)
file_att = os.path.splitext(os.path.basename(catchshp))[0]
lyr = ds.GetLayerByName(file_att)
spatialref = lyr.GetSpatialRef()
# if not spatialref == None:
# srs = osr.SpatialReference()
# srs.ImportFromWkt(spatialref.ExportToWkt())
# srs.AutoIdentifyEPSG()
# catchshp_EPSG = 'EPSG:'+srs.GetAttrValue("AUTHORITY",1)
# spatialref == None
# else:
catchshp_EPSG = clone_EPSG
print 'No projection defined for ' + file_att + '.shp'
print 'Assumed to be the same as model projection (' + clone_EPSG + ')'
if not rivshp_EPSG == clone_EPSG:
catchprojshp = workdir + 'catchshape_proj.shp'
call(('ogr2ogr', '-s_srs', catchshp_EPSG, '-t_srs', clone_ESPG,
catchprojshp, catchshp))
catchshp = catchprojshp
ds.Destroy()
ds = ogr.Open(catchshp)
file_att = os.path.splitext(os.path.basename(catchshp))[0]
lyr = ds.GetLayerByName(file_att)
fieldDef = ogr.FieldDefn("ID", ogr.OFTString)
fieldDef.SetWidth(12)
TEMP_out = Driver.CreateDataSource(workdir + "temp.shp")
if not srs == None:
TEMP_LYR = TEMP_out.CreateLayer("temp",
srs,
geom_type=ogr.wkbMultiPolygon)
else:
TEMP_LYR = TEMP_out.CreateLayer("temp", geom_type=ogr.wkbMultiPolygon)
TEMP_LYR.CreateField(fieldDef)
for i in range(lyr.GetFeatureCount()):
orgfeature = lyr.GetFeature(i)
geometry = orgfeature.geometry()
feature = ogr.Feature(TEMP_LYR.GetLayerDefn())
feature.SetGeometry(geometry)
feature.SetField("ID", str(i + 1))
TEMP_LYR.CreateFeature(feature)
TEMP_out.Destroy()
ds.Destroy
# rasterize catchment map
catchments_tif = workdir + "catchments.tif"
catchments_map = workdir + "catchments.map"
call(('gdal_translate', '-of', 'GTiff', '-a_srs', clone_EPSG, zero_map,
catchments_tif))
if alltouching:
call(('gdal_rasterize', '-at', '-a', 'ID', '-l', "temp",
workdir + 'temp.shp', catchments_tif))
else:
call(('gdal_rasterize', '-a', 'ID', '-l', "temp", workdir + 'temp.shp',
catchments_tif))
call(('gdal_translate', '-of', 'PCRaster', '-a_srs', clone_EPSG,
catchments_tif, catchments_map))
catchments = pcr.readmap(catchments_map)
riverunique = pcr.clump(pcr.nominal(pcr.ifthen(riverburn > 0, riverburn)))
rivercatch = pcr.areamajority(pcr.ordinal(catchments), riverunique)
#catchments = pcr.cover(pcr.ordinal(rivercatch),pcr.ordinal(pcr.ifthen(catchments > 0, catchments)),pcr.ordinal(0))
catchments = pcr.cover(
pcr.ifthen(catchments > 0, pcr.ordinal(catchments)),
pcr.ifthen(
riverburn > 0,
pcr.ordinal(
pcr.spreadzone(pcr.nominal(catchments),
pcr.ifthen(riverburn > 0, pcr.scalar(1)), 1))))
rivercatch_map = workdir + "catchments_river.map"
catchclip_map = workdir + "catchments_clip.map"
pcr.report(rivercatch, rivercatch_map)
pcr.report(catchments, catchclip_map)
ds = ogr.Open(workdir + "temp.shp")
lyr = ds.GetLayerByName("temp")
print 'calculating ldd'
for i in range(lyr.GetFeatureCount()):
feature = lyr.GetFeature(i)
catch = int(feature.GetField("ID"))
print "calculating ldd for catchment: " + str(i + 1) + "/" + str(
lyr.GetFeatureCount()) + "...."
ldddem_select = pcr.scalar(pcr.ifthen(catchments == catch,
catchments)) * 0 + 1 * ldddem
ldd_select = pcr.lddcreate(ldddem_select, float("1E35"), float("1E35"),
float("1E35"), float("1E35"))
ldd = pcr.cover(ldd, ldd_select)
pcr.report(ldd, resultdir + ldd_map)
ds.Destroy()
''' report stream order, river and dem '''
streamorder = pcr.ordinal(pcr.streamorder(ldd))
river = pcr.ifthen(streamorder >= pcr.ordinal(minorder), pcr.boolean(1))
mindem = int(np.min(pcr.pcr2numpy(pcr.ordinal(dem_resample_map), 9999999)))
dem_resample_map = pcr.cover(dem_resample_map,
pcr.scalar(river) * 0 + mindem)
pcr.report(dem_resample_map, resultdir + dem_map)
pcr.report(streamorder, resultdir + streamorder_map)
pcr.report(river, resultdir + river_map)
''' deal with your catchments '''
if gaugeshp == None:
print 'No gauges defined, using outlets instead'
gauges = pcr.ordinal(
pcr.uniqueid(
pcr.boolean(pcr.ifthen(pcr.scalar(ldd) == 5, pcr.boolean(1)))))
pcr.report(gauges, resultdir + gauges_map)
# ds = ogr.Open(gaugeshp)
# file_att = os.path.splitext(os.path.basename(gaugeshp))[0]
# lyr = ds.GetLayerByName(file_att)
# spatialref = lyr.GetSpatialRef()
## if not spatialref == None:
## srs = osr.SpatialReference()
## srs.ImportFromWkt(spatialref.ExportToWkt())
## srs.AutoIdentifyEPSG()
## gaugeshp_EPSG = 'EPSG:'+srs.GetAttrValue("AUTHORITY",1)
## spatialref == None
# #else:
# gaugeshp_EPSG = clone_EPSG
# print 'No projection defined for ' + file_att + '.shp'
# print 'Assumed to be the same as model projection (' + clone_EPSG + ')'
#
# # reproject gauge shape if necesarry
# if not gaugeshp_EPSG == clone_EPSG:
# gaugeprojshp = workdir + 'gaugeshape_proj.shp'
# call(('ogr2ogr','-s_srs',rivshp_EPSG,'-t_srs',clone_ESPG,gaugeprojshp,gaugeshp))
# gaugeshp = gaugeprojshp
#
# file_att = os.path.splitext(os.path.basename(gaugeshp))[0]
# gaugestif = workdir + file_att + '.tif'
# gaugesmap = workdir + file_att + '.map'
# call(('gdal_translate','-of','GTiff','-a_srs',clone_EPSG,zero_map,gaugestif))
# call(('gdal_rasterize','-burn','1','-l',file_att,gaugeshp,gaugestif))
# call(('gdal_translate','-of','PCRaster','-a_srs',clone_EPSG,gaugestif,gaugesmap))
# gaugelocs = pcr.readmap(gaugesmap)
# snapgaugestoriver = True
#
# if snapgaugestoriver:
# print "Snapping gauges to river"
# gauges = pcr.uniqueid(pcr.boolean(gaugelocs))
# gauges= wt.snaptomap(pcr.ordinal(gauges),river)
#
# gaugesmap = pcr.ifthen(gauges > 0, gauges)
''' report riverlengthfrac '''
riv_hr = workdir + 'river_highres.tif'
wt.CreateTif(riv_hr, rows_hr, cols_hr, hr_trans, srs_clone, 0)
file_att = os.path.splitext(os.path.basename(rivshp))[0]
call(('gdal_rasterize', '-burn', '1', '-l', file_att, rivshp, riv_hr))
print 'Computing river length...'
#riverlength = wt.windowstats(riv_hr,clone_rows,clone_columns,clone_trans,srs_clone,resultdir,'frac',clone2dem_transform)
riverlength = wt.windowstats(riv_hr, clone_rows, clone_columns,
clone_trans, srs_clone, resultdir, 'frac')
''' report outlet map '''
pcr.report(pcr.ifthen(pcr.ordinal(ldd) == 5, pcr.ordinal(1)),
resultdir + outlet_map)
''' report map '''
catchment = pcr.ifthen(catchments > 0, pcr.ordinal(1))
pcr.report(catchment, resultdir + catchment_map)
''' report subcatchment map '''
subcatchment = pcr.subcatchment(ldd, gauges)
pcr.report(pcr.ordinal(subcatchment), resultdir + subcatch_map)
''' report landuse map '''
if landuse == None:
pcr.report(pcr.nominal(ones), resultdir + landuse_map)
else:
landuse_resample = workdir + 'landuse.tif'
landuse_map = resultdir + landuse_map
transform = wt.GetRasterTranform(landuse, srs_clone)
if not transform[0]:
call(('gdalwarp', '-overwrite', '-s_srs', clone_EPSG, '-t_srs',
clone_EPSG, '-te', xmin, ymin, xmax, ymax, '-tr',
str(cellsize), str(-cellsize), '-r', 'mode', landuse,
landuse_resample))
else:
call(('gdalwarp', '-overwrite', '-s_srs', transform[1], '-t_srs',
clone_EPSG, '-te', xmin, ymin, xmax, ymax, '-tr',
str(cellsize), str(-cellsize), '-r', 'mode', landuse,
landuse_resample))
call(('gdal_translate', '-of', 'PCRaster', '-ot', 'Float32',
landuse_resample, landuse_map))
landuse_work = pcr.readmap(landuse_map)
pcr.report(pcr.nominal(landuse_work), landuse_map)
''' report soil map '''
if soiltype == None:
pcr.report(pcr.nominal(ones), resultdir + soil_map)
else:
soiltype_resample = workdir + 'soiltype.tif'
soil_map = resultdir + soil_map
#transform = wt.GetRasterTranform(soiltype,srs_clone)
# if not transform[0]:
call(('gdalwarp', '-overwrite', '-s_srs', clone_EPSG, '-t_srs',
clone_EPSG, '-te', xmin, ymin, xmax, ymax, '-tr', str(cellsize),
str(-cellsize), '-r', 'mode', soiltype, soiltype_resample))
# else:
# call(('gdalwarp','-overwrite','-s_srs',transform[1],'-t_srs',clone_EPSG,'-te', xmin, ymin, xmax, ymax,'-tr',str(cellsize),str(-cellsize),'-r','mode',soiltype, soiltype_resample))
call(('gdal_translate', '-of', 'PCRaster', '-ot', 'Float32',
soiltype_resample, soil_map))
soiltype_work = pcr.readmap(soil_map)
pcr.report(pcr.nominal(soiltype_work), soil_map)
if clean:
wt.DeleteList(glob.glob(os.getcwd() + '\\' + resultdir + '/*.xml'))
def _parseLine(self, line, lineNumber, nrColumns, externalNames, keyDict):
line = re.sub("\n","",line)
line = re.sub("\t"," ",line)
result = None
# read until first comment
content = ""
content,sep,comment = line.partition("#")
if len(content) > 1:
collectionVariableName, sep, tail = content.partition(" ")
if collectionVariableName == self._varName:
tail = tail.strip()
key, sep, variableValue = tail.rpartition(" ")
if len(key.split()) != nrColumns:
tmp = re.sub("\(|\)|,","",str(key))
msg = "Error reading %s line %d, order of columns given (%s columns) does not match expected order of %s columns" %(self._fileName, lineNumber, len(key.split()) + 2, int(nrColumns) + 2)
raise ValueError(msg)
variableValue = re.sub('\"', "", variableValue)
tmp = None
try:
tmp = int(variableValue)
if self._dataType == pcraster.Boolean:
tmp = pcraster.boolean(tmp)
elif self._dataType == pcraster.Nominal:
tmp = pcraster.nominal(tmp)
elif self._dataType == pcraster.Ordinal:
tmp = pcraster.ordinal(tmp)
elif self._dataType == pcraster.Ldd:
tmp = pcraster.ldd(tmp)
else:
msg = "Conversion to %s failed" % (self._dataType)
raise Exception(msg)
except ValueError as e:
try:
tmp = float(variableValue)
if self._dataType == pcraster.Scalar:
tmp = pcraster.scalar(tmp)
elif self._dataType == pcraster.Directional:
tmp = pcraster.directional(tmp)
else:
msg = "Conversion to %s failed" % (self._dataType)
raise Exception(msg)
except ValueError as e:
variableValue = re.sub("\\\\","/",variableValue)
variableValue = variableValue.strip()
path = os.path.normpath(variableValue)
try:
tmp = pcraster.readmap(path)
except RuntimeError as e:
msg = "Error reading %s line %d, %s" %(self._fileName, lineNumber, e)
raise ValueError(msg)
# test if key is an external name
transformedKeys = []
counter = 0
for k in key.split():
k = k.strip()
if externalNames[counter].get(k):
transformedKeys.append(externalNames[counter].get(k))
else:
transformedKeys.append(k)
counter += 1
key = tuple(transformedKeys)
if not key in keyDict:
tmp = re.sub("\(|\)|,","",str(key))
msg = "Error reading %s line %d, %s unknown collection index" %(self._fileName, lineNumber, tmp)
raise ValueError(msg)
if not keyDict[key] is None:
tmp = re.sub("\(|\)|,","",str(key))
msg = "Error reading %s line %d, %s %s already initialised" %(self._fileName, lineNumber, self._varName, tmp)
raise ValueError(msg)
keyDict[key] = tmp
def main():
try:
opts, args = getopt.getopt(sys.argv[1:], "fhC:N:I:s:M:", ['version'])
except getopt.error as msg:
usage(msg)
factor = 1
Verbose = 1
inmaps = True
force = False
caseName = "thecase"
caseNameNew = "thecase_resamp"
maxcpu = 4
for o, a in opts:
if o == "-C":
caseName = a
if o == "-N":
caseNameNew = a
if o == "-s":
subcatch = int(a)
if o == "-I":
inmaps = False
if o == "-h":
usage()
if o == "-f":
force = True
if o == "-M":
maxcpu = int(a)
if o == "--version":
import wflow
print("wflow version: ", wflow.__version__)
sys.exit(0)
dirs = [
"/intbl/",
"/staticmaps/",
"/intss/",
"/instate/",
"/outstate/",
"/inmaps/",
"/inmaps/clim/",
"/intbl/clim/",
]
ext_to_copy = ["*.tss", "*.tbl", "*.col", "*.xml"]
if os.path.isdir(caseNameNew) and not force:
print("Refusing to write into an existing directory:" + caseNameNew)
exit()
# ddir = []
dirs = []
for (path, thedirs, files) in os.walk(caseName):
print(path)
dirs.append(path)
if not os.path.isdir(caseNameNew):
for ddir in dirs:
os.makedirs(ddir.replace(caseName, caseNameNew))
for inifile in glob.glob(caseName + "/*.ini"):
shutil.copy(inifile, inifile.replace(caseName, caseNameNew))
# read subcatchment map
x, y, subcatchmap, FillVal = readMap(
os.path.join(caseName, "staticmaps", "wflow_subcatch.map"), "PCRaster")
for ddir in dirs:
print(ddir)
allcmd = []
for mfile in glob.glob(ddir + "/*.map"):
if not os.path.exists(mfile.replace(caseName, caseNameNew)):
x, y, data, FillVal = readMap(mfile, "PCRaster")
try:
good = 1
xn, yn, datan = cutMapById(data, subcatchmap, subcatch, x,
y, FillVal)
except Exception as e:
good = 0
print("Skipping: " + mfile + " exception: " + str(e))
if xn.size == 0:
good = 0
print("Skipping: " + mfile + " size does not match...")
if good:
ofile = mfile.replace(caseName, caseNameNew)
if data.dtype == np.int32 or data.dtype == np.uint8:
writeMap(ofile, "PCRaster", xn, yn,
datan.astype(np.int32), FillVal)
else:
writeMap(ofile, "PCRaster", xn, yn, datan, FillVal)
# Assume ldd and repair
if (data.dtype == np.uint8 and 'wflow_ldd.map' in mfile):
myldd = pcr.ldd(pcr.readmap(ofile))
myldd = pcr.lddrepair(myldd)
pcr.report(myldd, ofile)
for mfile in glob.glob(ddir + "/*.[0-9][0-9][0-9]"):
if not os.path.exists(mfile.replace(caseName, caseNameNew)):
x, y, data, FillVal = readMap(mfile, "PCRaster")
try:
good = 1
xn, yn, datan = cutMapById(data, subcatchmap, subcatch, x,
y, FillVal)
except Exception as e:
good = 0
print("Skipping: " + mfile + " exception: " + str(e))
if xn.size == 0:
good = 0
print("Skipping: " + mfile + " size does not match...")
if good:
ofile = mfile.replace(caseName, caseNameNew)
if data.dtype == np.int32 or data.dtype == np.uint8:
writeMap(ofile, "PCRaster", xn, yn,
datan.astype(np.int32), FillVal)
else:
writeMap(ofile, "PCRaster", xn, yn, datan, FillVal)
for ext in ext_to_copy:
for mfile in glob.glob(os.path.join(ddir, ext)):
shutil.copy(mfile, mfile.replace(caseName, caseNameNew))
# Copy ini files
for mfile in glob.glob(os.path.join(caseName, "*.ini")):
shutil.copy(mfile, mfile.replace(caseName, caseNameNew))
logger.info(msg)
# set the pcraster clone, ldd, landmask, and cell area map
msg = "Setting the clone, ldd, landmask, and cell area maps" + ":"
logger.info(msg)
# - clone
clone_map_file = input_files['clone_map_05min']
pcr.setclone(clone_map_file)
# - ldd
ldd = vos.readPCRmapClone(input_files['ldd_map_05min'],
clone_map_file,
output_files['tmp_folder'],
None,
True)
ldd = pcr.lddrepair(pcr.ldd(ldd))
ldd = pcr.lddrepair(ldd)
# - landmask
landmask = pcr.ifthen(pcr.defined(ldd), pcr.boolean(1.0))
# - cell area
cell_area = vos.readPCRmapClone(input_files['cell_area_05min'],
clone_map_file,
output_files['tmp_folder'])
# read the hydrological year
msg = "Reading the hydrological year types" + ":"
logger.info(msg)
hydro_year_type = pcr.nominal(\
vos.readPCRmapClone(input_files['hydro_year_05min'],
input_files['clone_map_05min'],
event_file_name = "channel_storage_" + chosen_date + ".map"
pcr.report(extreme_value_map, event_file_name)
#~ # - check it using aguila
#~ cmd = 'aguila ' + event_file_name
#~ os.system(cmd)
# resampling low resolution ldd map
msg = "Resample the low resolution ldd map."
logger.info(msg)
ldd_map_low_resolution_file_name = ldd_map_low_resolution_file_name
ldd_map_low_resolution = vos.readPCRmapClone(ldd_map_low_resolution_file_name, \
clone_map_file, \
tmp_folder, \
None, True, None, False)
#~ ldd_map_low_resolution = pcr.ifthen(landmask, ldd_map_low_resolution) # NOTE THAT YOU SHOULD NOT MASK-OUT THE LDD.
ldd_map_low_resolution = pcr.lddrepair(pcr.ldd(ldd_map_low_resolution))
ldd_map_low_resolution = pcr.lddrepair(ldd_map_low_resolution)
pcr.report(ldd_map_low_resolution, "resampled_low_resolution_ldd.map")
# resampling river length and width files (actually, we don't need these):
msg = "Resample the low resolution river length and width maps."
logger.info(msg)
# - river length
river_length_file_name = "/projects/0/dfguu/users/edwin/data/data_for_glofris_downscaling/input_data/maps_05min/celldiagonal05min.map"
river_length_low_resolution = vos.readPCRmapClone(river_length_file_name, \
clone_map_file, \
tmp_folder, \
None, False, None, False)
river_length_low_resolution = pcr.ifthen(landmask, river_length_low_resolution)
river_length_low_resolution = pcr.cover(river_length_low_resolution, 0.0)
pcr.report(river_length_low_resolution, "resampled_low_resolution_channel_length.map")
