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))
#~ pcr.aguila(basin_map)
# - extend/extrapolate the basin
basin_map = pcr.cover(basin_map, pcr.windowmajority(basin_map, 0.5))
basin_map = pcr.cover(basin_map, pcr.windowmajority(basin_map, 0.5))
basin_map = pcr.cover(basin_map, pcr.windowmajority(basin_map, 0.5))
basin_map = pcr.cover(basin_map, pcr.windowmajority(basin_map, 1.0))
basin_map = pcr.cover(basin_map, pcr.windowmajority(basin_map, 1.5))
basin_map = pcr.ifthen(landmask, basin_map)
#~ pcr.aguila(basin_map)
msg = "Redefining the basin map (so that it is consistent with the ldd map used in PCR-GLOBWB):"
logger.info(msg)
# - calculate the upstream area of every pixel:
upstream_area = pcr.catchmenttotal(cell_area, ldd)
# - calculate the catchment area of every basin:
upstream_area_maximum = pcr.areamaximum(upstream_area, basin_map)
# - identify the outlet of every basin (in order to rederive the basin so that it is consistent with the ldd)
outlet = pcr.nominal(pcr.uniqueid(pcr.ifthen(upstream_area == upstream_area_maximum, pcr.boolean(1.0))))
def identifyModelPixel(self,tmpDir,\
catchmentAreaAll,\
landMaskClass,\
xCoordinate,yCoordinate,id):
# TODO: Include an option to consider average discharge.
logger.info("Identify model pixel for the grdc station "+str(id)+".")
# make a temporary directory:
randomDir = self.makeRandomDir(tmpDir)
# coordinate of grdc station
xCoord = float(self.attributeGRDC["grdc_longitude_in_arc_degree"][str(id)])
yCoord = float(self.attributeGRDC["grdc_latitude_in_arc_degree"][str(id)])
# identify the point at pcraster model
point = pcr.ifthen((pcr.abs(xCoordinate - xCoord) == pcr.mapminimum(pcr.abs(xCoordinate - xCoord))) &\
(pcr.abs(yCoordinate - yCoord) == pcr.mapminimum(pcr.abs(yCoordinate - yCoord))), \
pcr.boolean(1))
# expanding the point
point = pcr.windowmajority(point, self.cell_size_in_arc_degree * 5.0)
point = pcr.ifthen(catchmentAreaAll > 0, point)
point = pcr.boolean(point)
# values based on the model;
modelCatchmentArea = pcr.ifthen(point, catchmentAreaAll) # unit: km2
model_x_ccordinate = pcr.ifthen(point, xCoordinate) # unit: arc degree
model_y_ccordinate = pcr.ifthen(point, yCoordinate) # unit: arc degree
# calculate (absolute) difference with GRDC data
# - initiating all of them with the values of MV
diffCatchArea = pcr.abs(pcr.scalar(vos.MV)) # difference between the model and grdc catchment area (unit: km2)
diffDistance = pcr.abs(pcr.scalar(vos.MV)) # distance between the model pixel and grdc catchment station (unit: arc degree)
diffLongitude = pcr.abs(pcr.scalar(vos.MV)) # longitude difference (unit: arc degree)
diffLatitude = pcr.abs(pcr.scalar(vos.MV)) # latitude difference (unit: arc degree)
#
# - calculate (absolute) difference with GRDC data
try:
diffCatchArea = pcr.abs(modelCatchmentArea-\
float(self.attributeGRDC["grdc_catchment_area_in_km2"][str(id)]))
except:
logger.info("The difference in the model and grdc catchment area cannot be calculated.")
try:
diffLongitude = pcr.abs(model_x_ccordinate - xCoord)
except:
logger.info("The difference in longitude cannot be calculated.")
try:
diffLatitude = pcr.abs(model_y_ccordinate - yCoord)
except:
logger.info("The difference in latitude cannot be calculated.")
try:
diffDistance = (diffLongitude**(2) + \
diffLatitude**(2))**(0.5) # TODO: calculate distance in meter
except:
logger.info("Distance cannot be calculated.")
# identify masks
masks = pcr.ifthen(pcr.boolean(point), landMaskClass)
# export the difference to temporary files: maps and txt
catchmentAreaMap = randomDir+"/"+vos.get_random_word()+".area.map"
diffCatchAreaMap = randomDir+"/"+vos.get_random_word()+".dare.map"
diffDistanceMap = randomDir+"/"+vos.get_random_word()+".dist.map"
diffLatitudeMap = randomDir+"/"+vos.get_random_word()+".dlat.map"
diffLongitudeMap = randomDir+"/"+vos.get_random_word()+".dlon.map"
diffLatitudeMap = randomDir+"/"+vos.get_random_word()+".dlat.map"
#
maskMap = randomDir+"/"+vos.get_random_word()+".mask.map"
diffColumnFile = randomDir+"/"+vos.get_random_word()+".cols.txt" # output
#
pcr.report(pcr.ifthen(point,modelCatchmentArea), catchmentAreaMap)
pcr.report(pcr.ifthen(point,diffCatchArea ), diffCatchAreaMap)
pcr.report(pcr.ifthen(point,diffDistance ), diffDistanceMap )
pcr.report(pcr.ifthen(point,diffLatitude ), diffLongitudeMap)
pcr.report(pcr.ifthen(point,diffLongitude ), diffLatitudeMap )
pcr.report(pcr.ifthen(point,masks ), maskMap)
#
cmd = 'map2col '+catchmentAreaMap +' '+\
diffCatchAreaMap +' '+\
diffDistanceMap +' '+\
diffLongitudeMap +' '+\
diffLatitudeMap +' '+\
maskMap+' '+diffColumnFile
print(cmd); os.system(cmd)
# use R to sort the file
cmd = 'R -f saveIdentifiedPixels.R '+diffColumnFile
print(cmd); os.system(cmd)
try:
# read the output file (from R)
f = open(diffColumnFile+".sel") ; allLines = f.read() ; f.close()
# split the content of the file into several lines
allLines = allLines.replace("\r",""); allLines = allLines.split("\n")
selectedPixel = allLines[0].split(";")
model_longitude_in_arc_degree = float(selectedPixel[0])
model_latitude_in_arc_degree = float(selectedPixel[1])
model_catchment_area_in_km2 = float(selectedPixel[2])
model_landmask = str(selectedPixel[7])
log_message = "Model pixel for grdc station "+str(id)+" is identified (lat/lon in arc degree): "
log_message += str(model_latitude_in_arc_degree) + " ; " + str(model_longitude_in_arc_degree)
logger.info(log_message)
self.attributeGRDC["model_longitude_in_arc_degree"][str(id)] = model_longitude_in_arc_degree
self.attributeGRDC["model_latitude_in_arc_degree"][str(id)] = model_latitude_in_arc_degree
self.attributeGRDC["model_catchment_area_in_km2"][str(id)] = model_catchment_area_in_km2
self.attributeGRDC["model_landmask"][str(id)] = model_landmask
except:
logger.info("Model pixel for grdc station "+str(id)+" can NOT be identified.")
self.cleanRandomDir(randomDir)
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))
#~ pcr.aguila(basin_map)
# - extend/extrapolate the basin
basin_map = pcr.cover(basin_map, pcr.windowmajority(basin_map, 0.5))
basin_map = pcr.cover(basin_map, pcr.windowmajority(basin_map, 0.5))
basin_map = pcr.cover(basin_map, pcr.windowmajority(basin_map, 0.5))
basin_map = pcr.cover(basin_map, pcr.windowmajority(basin_map, 1.0))
basin_map = pcr.cover(basin_map, pcr.windowmajority(basin_map, 1.5))
basin_map = pcr.ifthen(landmask, basin_map)
#~ pcr.aguila(basin_map)
msg = "Redefining the basin map (so that it is consistent with the ldd map used in PCR-GLOBWB):"
logger.info(msg)
# - calculate the upstream area of every pixel:
upstream_area = pcr.catchmenttotal(cell_area, ldd)
# - calculate the catchment area of every basin:
upstream_area_maximum = pcr.areamaximum(upstream_area, basin_map)
# - identify the outlet of every basin (in order to rederive the basin so that it is consistent with the ldd)
outlet = pcr.nominal(
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 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")
None, False, None, True))
uniqueIDs = pcr.readmap(uniqueIDsFile)
uniqueIDs = pcr.ifthen(pcr.scalar(uniqueIDs) >= 0.0, uniqueIDs)
# landmask
landmask = pcr.defined(pcr.readmap(landmask05minFile))
landmask = pcr.ifthen(landmask, landmask)
# - extending landmask with uniqueIDs
landmask = pcr.cover(landmask, pcr.defined(uniqueIDs))
# extending class (country) ids
max_step = 5
for i in range(1, max_step+1, 1):
cmd = "Extending class: step "+str(i)+" from " + str(max_step)
print(cmd)
uniqueIDs = pcr.cover(uniqueIDs, pcr.windowmajority(uniqueIDs, 0.5))
# - use only cells within the landmask
uniqueIDs = pcr.ifthen(landmask, uniqueIDs)
pcr.report(uniqueIDs, "class_ids.map")
# cell area at 5 arc min resolution
cellArea = vos.readPCRmapClone(cellArea05minFile,
cloneMapFileName, tmp_directory)
cellArea = pcr.ifthen(landmask, cellArea)
# get a sample cell for every id
x_min_for_each_id = pcr.areaminimum(pcr.xcoordinate(pcr.boolean(1.0)), uniqueIDs)
sample_cells = pcr.xcoordinate(pcr.boolean(1.0)) == x_min_for_each_id
y_min_for_each_id = pcr.areaminimum(pcr.ycoordinate(sample_cells), uniqueIDs)
sample_cells = pcr.ycoordinate(sample_cells) == y_min_for_each_id
uniqueIDs_sample = pcr.ifthen(sample_cells, uniqueIDs)
pcr.defined(edwin_code), pcrglobwb_catchment_area_km2)
# calculate the absolute difference
abs_diff = pcr.abs(usgs_drain_area_km2 -
edwin_code_pcrglobwb_catchment_area_km2)
# make correction if required
abs_diff_value = pcr.cellvalue(pcr.mapmaximum(abs_diff), 1)[0]
usgs_drain_area_km2 = pcr.cellvalue(pcr.mapmaximum(usgs_drain_area_km2),
1)[0]
if (usgs_drain_area_km2 > 1000.0) and \
(abs_diff_value > 0.10 * usgs_drain_area_km2):
# class within 0.1 arc degree windows
edwin_code = pcr.windowmajority(edwin_code, 0.1)
# find the most accurate cell:
areaorder = pcr.areaorder(
pcr.windowmaximum(pcr.spatial(pcr.scalar(usgs_drain_area_km2)),
0.1) - pcrglobwb_catchment_area_km2, edwin_code)
# select pixel
edwin_code = pcr.ifthen(areaorder == 1., edwin_code)
# pcrglobwb catchment area
edwin_code_pcrglobwb_catchment_area_km2 = pcr.ifthen(
areaorder == 1., pcrglobwb_catchment_area_km2)
# save using map2col
pcr.report(edwin_code, "edwin_code.map")
def __init__(self, clone_map_file,\
input_thickness_netcdf_file,\
input_thickness_var_name ,\
margat_aquifers,\
tmp_directory,
landmask = None,
arcdegree = True):
object.__init__(self)
# aquifer table from Margat and van der Gun
self.margat_aquifers = margat_aquifers
# clone map
self.clone_map_file = clone_map_file
self.clone_map_attr = vos.getMapAttributesALL(self.clone_map_file)
if arcdegree == True:
self.clone_map_attr['cellsize'] = round(self.clone_map_attr['cellsize'] * 360000.)/360000.
xmin = self.clone_map_attr['xUL']
xmax = xmin + self.clone_map_attr['cols'] * self.clone_map_attr['cellsize']
ymax = self.clone_map_attr['yUL']
ymin = ymax - self.clone_map_attr['rows'] * self.clone_map_attr['cellsize']
pcr.setclone(self.clone_map_file)
# temporary directory
self.tmp_directory = tmp_directory
# thickness approximation (unit: m, file in netcdf with variable name = average
self.approx_thick = vos.netcdf2PCRobjCloneWithoutTime(input_thickness_netcdf_file,\
input_thickness_var_name,\
self.clone_map_file)
# set minimum value to 0.1 mm
self.approx_thick = pcr.max(0.0001, self.approx_thick)
# rasterize the shape file
# -
# save current directory and move to temporary directory
current_dir = str(os.getcwd()+"/")
os.chdir(str(self.tmp_directory))
#
cmd_line = 'gdal_rasterize -a MARGAT ' # layer name = MARGAT
cmd_line += '-te '+str(xmin)+' '+str(ymin)+' '+str(xmax)+' '+str(ymax)+ ' '
cmd_line += '-tr '+str(self.clone_map_attr['cellsize'])+' '+str(self.clone_map_attr['cellsize'])+' '
cmd_line += str(margat_aquifers['shapefile'])+' '
cmd_line += 'tmp.tif'
print(cmd_line); os.system(cmd_line)
#
# make it nomial
cmd_line = 'pcrcalc tmp.map = "nominal(tmp.tif)"'
print(cmd_line); os.system(cmd_line)
#
# make sure that the clone map is correct
cmd_line = 'mapattr -c '+str(self.clone_map_file)+' tmp.map'
print(cmd_line); os.system(cmd_line)
#
# read the map
self.margat_aquifer_map = pcr.nominal(pcr.readmap("tmp.map"))
#
# clean temporary directory and return to the original directory
vos.clean_tmp_dir(self.tmp_directory)
os.chdir(current_dir)
# extend the extent of each aquifer
self.margat_aquifer_map = pcr.cover(self.margat_aquifer_map,
pcr.windowmajority(self.margat_aquifer_map, 1.25))
# assign aquifer thickness, unit: m (lookuptable operation)
self.margat_aquifer_thickness = pcr.lookupscalar(margat_aquifers['txt_table'], self.margat_aquifer_map)
self.margat_aquifer_thickness = pcr.ifthen(self.margat_aquifer_thickness > 0., \
self.margat_aquifer_thickness)
#~ pcr.report(self.margat_aquifer_thickness,"thick.map"); os.system("aguila thick.map")
# aquifer map
self.margat_aquifer_map = pcr.ifthen(self.margat_aquifer_thickness > 0., self.margat_aquifer_map)
# looping per aquifer: cirrecting or rescaling
aquifer_ids = np.unique(pcr.pcr2numpy(pcr.scalar(self.margat_aquifer_map), vos.MV))
aquifer_ids = aquifer_ids[aquifer_ids > 0]
aquifer_ids = aquifer_ids[aquifer_ids < 10000]
self.rescaled_thickness = None
for id in aquifer_ids:
rescaled_thickness = self.correction_per_aquifer(id)
try:
self.rescaled_thickness = pcr.cover(self.rescaled_thickness, rescaled_thickness)
except:
self.rescaled_thickness = rescaled_thickness
# integrating
ln_aquifer_thickness = self.mapFilling( pcr.ln(self.rescaled_thickness), pcr.ln(self.approx_thick) )
self.aquifer_thickness = pcr.exp(ln_aquifer_thickness)
#~ pcr.report(self.aquifer_thickness,"thick.map"); os.system("aguila thick.map")
# cropping only in the landmask region
if landmask == None: landmask = self.clone_map_file
self.landmask = pcr.defined(vos.readPCRmapClone(landmask,self.clone_map_file,self.tmp_directory))
#~ pcr.report(self.landmask,"test.map"); os.system("aguila test.map")
self.aquifer_thickness = pcr.ifthen(self.landmask, self.aquifer_thickness)
def __init__(self, clone_map_file, \
dem_average_netcdf, dem_floodplain_netcdf, ldd_netcdf, \
lookup_table_average_thickness, lookup_table_zscore, \
number_of_samples, include_percentile = True,\
threshold_sedimentary_basin = 50.0, elevation_F_min = 0.0, elevation_F_max = 50.0): # values defined in de Graaf et al. (2014)
DynamicModel.__init__(self)
MonteCarloModel.__init__(self)
msg = "\n"
msg += "\n"
msg += 'For each step, please refer to de Graaf et al. (2014).'
msg += "\n"
logger.info(msg)
# set clone
self.clone_map_file = clone_map_file
pcr.setclone(clone_map_file)
# an option to include_percentile or not
self.include_percentile = include_percentile
# number of samples
self.number_of_samples = pcr.scalar(number_of_samples)
logger.info(
"Step 1: Identify the cells belonging to the sedimentary basin region."
)
dem_average = vos.netcdf2PCRobjCloneWithoutTime(dem_average_netcdf['file_name'],\
dem_average_netcdf['variable_name'],\
clone_map_file)
dem_average = pcr.max(0.0, dem_average)
self.dem_average = pcr.cover(dem_average, 0.0)
dem_floodplain = vos.netcdf2PCRobjCloneWithoutTime(
dem_floodplain_netcdf['file_name'],
dem_floodplain_netcdf['variable_name'], clone_map_file)
dem_floodplain = pcr.max(0.0, dem_floodplain)
lddMap = vos.netcdf2PCRobjCloneWithoutTime(ldd_netcdf['file_name'],
ldd_netcdf['variable_name'],
clone_map_file)
self.lddMap = pcr.lddrepair(pcr.lddrepair(pcr.ldd(lddMap)))
self.landmask = pcr.defined(self.lddMap)
elevation_F = dem_average - dem_floodplain
sedimentary_basin_extent = pcr.ifthen(
elevation_F < pcr.scalar(threshold_sedimentary_basin),
pcr.boolean(1))
# include the continuity along the river network
sedimentary_basin_extent = pcr.windowmajority(
sedimentary_basin_extent,
3.00 * vos.getMapAttributes(clone_map_file, "cellsize"))
sedimentary_basin_extent = pcr.cover(sedimentary_basin_extent, \
pcr.path(self.lddMap, pcr.defined(sedimentary_basin_extent)))
# TODO: We should also include the extent of major aquifer basins and unconsolidated sediments in the GLiM map.
elevation_F = pcr.ifthen(sedimentary_basin_extent, elevation_F)
elevation_F = pcr.max(0.0, elevation_F)
elevation_F = pcr.min(50., elevation_F)
logger.info(
"Step 2: Calculate relative difference and associate z_score.")
relative_elevation_F = pcr.scalar(
1.0) - (elevation_F - elevation_F_min) / (elevation_F_max -
elevation_F_min)
z_score_relat_elev_F = pcr.lookupscalar(lookup_table_zscore,
relative_elevation_F)
self.F = z_score_relat_elev_F # zscore (varying over the map)
# maximum and minimum z_score
self.F = pcr.min(3.75, self.F)
self.F = pcr.max(-10.00, self.F)
logger.info(
"Step 3: Assign average and variation of aquifer thickness.")
self.lookup_table_average_thickness = lookup_table_average_thickness
self.lnCV = pcr.scalar(
0.1
) # According to Inge, this lnCV value corresponds to the table "lookup_table_average_thickness".
def identifyModelPixel(self,tmpDir,\
catchmentAreaAll,\
landMaskClass,\
xCoordinate,yCoordinate,id):
# TODO: Include an option to consider average discharge.
logger.info("Identify model pixel for the grdc station "+str(id)+".")
# make a temporary directory:
randomDir = self.makeRandomDir(tmpDir)
# coordinate of grdc station
xCoord = float(self.attributeGRDC["grdc_longitude_in_arc_degree"][str(id)])
yCoord = float(self.attributeGRDC["grdc_latitude_in_arc_degree"][str(id)])
# identify the point at pcraster model
point = pcr.ifthen((pcr.abs(xCoordinate - xCoord) == pcr.mapminimum(pcr.abs(xCoordinate - xCoord))) &\
(pcr.abs(yCoordinate - yCoord) == pcr.mapminimum(pcr.abs(yCoordinate - yCoord))), \
pcr.boolean(1))
# expanding the point
point = pcr.windowmajority(point, self.cell_size_in_arc_degree * 5.0)
point = pcr.ifthen(catchmentAreaAll > 0, point)
point = pcr.boolean(point)
# values based on the model;
modelCatchmentArea = pcr.ifthen(point, catchmentAreaAll) # unit: km2
model_x_ccordinate = pcr.ifthen(point, xCoordinate) # unit: arc degree
model_y_ccordinate = pcr.ifthen(point, yCoordinate) # unit: arc degree
# calculate (absolute) difference with GRDC data
# - initiating all of them with the values of MV
diffCatchArea = pcr.abs(pcr.scalar(vos.MV)) # difference between the model and grdc catchment area (unit: km2)
diffDistance = pcr.abs(pcr.scalar(vos.MV)) # distance between the model pixel and grdc catchment station (unit: arc degree)
diffLongitude = pcr.abs(pcr.scalar(vos.MV)) # longitude difference (unit: arc degree)
diffLatitude = pcr.abs(pcr.scalar(vos.MV)) # latitude difference (unit: arc degree)
#
# - calculate (absolute) difference with GRDC data
try:
diffCatchArea = pcr.abs(modelCatchmentArea-\
float(self.attributeGRDC["grdc_catchment_area_in_km2"][str(id)]))
except:
logger.info("The difference in the model and grdc catchment area cannot be calculated.")
try:
diffLongitude = pcr.abs(model_x_ccordinate - xCoord)
except:
logger.info("The difference in longitude cannot be calculated.")
try:
diffLatitude = pcr.abs(model_y_ccordinate - yCoord)
except:
logger.info("The difference in latitude cannot be calculated.")
try:
diffDistance = (diffLongitude**(2) + \
diffLatitude**(2))**(0.5) # TODO: calculate distance in meter
except:
logger.info("Distance cannot be calculated.")
# identify masks
masks = pcr.ifthen(pcr.boolean(point), landMaskClass)
# export the difference to temporary files: maps and txt
catchmentAreaMap = randomDir+"/"+vos.get_random_word()+".area.map"
diffCatchAreaMap = randomDir+"/"+vos.get_random_word()+".dare.map"
diffDistanceMap = randomDir+"/"+vos.get_random_word()+".dist.map"
diffLatitudeMap = randomDir+"/"+vos.get_random_word()+".dlat.map"
diffLongitudeMap = randomDir+"/"+vos.get_random_word()+".dlon.map"
diffLatitudeMap = randomDir+"/"+vos.get_random_word()+".dlat.map"
#
maskMap = randomDir+"/"+vos.get_random_word()+".mask.map"
diffColumnFile = randomDir+"/"+vos.get_random_word()+".cols.txt" # output
#
pcr.report(pcr.ifthen(point,modelCatchmentArea), catchmentAreaMap)
pcr.report(pcr.ifthen(point,diffCatchArea ), diffCatchAreaMap)
pcr.report(pcr.ifthen(point,diffDistance ), diffDistanceMap )
pcr.report(pcr.ifthen(point,diffLatitude ), diffLongitudeMap)
pcr.report(pcr.ifthen(point,diffLongitude ), diffLatitudeMap )
pcr.report(pcr.ifthen(point,masks ), maskMap)
#
cmd = 'map2col '+catchmentAreaMap +' '+\
diffCatchAreaMap +' '+\
diffDistanceMap +' '+\
diffLongitudeMap +' '+\
diffLatitudeMap +' '+\
maskMap+' '+diffColumnFile
print(cmd); os.system(cmd)
# use R to sort the file
cmd = 'R -f saveIdentifiedPixels.R '+diffColumnFile
print(cmd); os.system(cmd)
try:
# read the output file (from R)
f = open(diffColumnFile+".sel") ; allLines = f.read() ; f.close()
# split the content of the file into several lines
allLines = allLines.replace("\r",""); allLines = allLines.split("\n")
selectedPixel = allLines[0].split(";")
model_longitude_in_arc_degree = float(selectedPixel[0])
model_latitude_in_arc_degree = float(selectedPixel[1])
model_catchment_area_in_km2 = float(selectedPixel[2])
model_landmask = str(selectedPixel[7])
log_message = "Model pixel for grdc station "+str(id)+" is identified (lat/lon in arc degree): "
log_message += str(model_latitude_in_arc_degree) + " ; " + str(model_longitude_in_arc_degree)
logger.info(log_message)
self.attributeGRDC["model_longitude_in_arc_degree"][str(id)] = model_longitude_in_arc_degree
self.attributeGRDC["model_latitude_in_arc_degree"][str(id)] = model_latitude_in_arc_degree
self.attributeGRDC["model_catchment_area_in_km2"][str(id)] = model_catchment_area_in_km2
self.attributeGRDC["model_landmask"][str(id)] = model_landmask
except:
logger.info("Model pixel for grdc station "+str(id)+" can NOT be identified.")
self.cleanRandomDir(randomDir)
lddDiff = pcr.scalar(ldd) - pcr.scalar(lddOld)
pcr.report(pcr.boolean(lddDiff), 'lddDiff.map')
p
############################### main ###################################
ldd = pcr.nominal(ldd)
ldd = fillMVBoundingBox(ldd, 1, 57, 76, 26, 47)
ldd = fillMVBoundingBox(ldd, 1, 58, 62, 51, 60)
ldd = fillMVBoundingBox(ldd, 1, -108, -101, 31, 40)
ldd = pcr.lddrepair(pcr.ldd(ldd))
pits = pcr.pit(ldd)
pcr.setglobaloption('unitcell')
continentMasks = pcr.cover(mask48, pcr.windowmajority(mask48,5))
#- adjust area masks with 5 min ldd
continentMasksNew = pcr.ifthen(pcr.boolean(pcr.readmap(cloneMap)) == 0, pcr.scalar(1))
for i in areas[0:]:
print 'area mask = ', i
mask = pcr.ifthen(continentMasks == i, pcr.boolean(1))
pitsContinent = pcr.pcrand(mask, pcr.boolean(pits))
pitsContinent = pcr.nominal(pcr.uniqueid(pcr.ifthen(pitsContinent == 1, pcr.boolean(1))))
catchments = pcr.catchment(ldd, pitsContinent)
newMask = pcr.ifthen(pcr.boolean(catchments) == 1, pcr.scalar(i))
continentMasksNew = pcr.cover(continentMasksNew, newMask)
updateCatchments = selectCatchments(ldd, pits, pitsDict, areas, cloneMap)
outMask = pcr.cover(updateCatchments, continentMasksNew)
pcr.report(pcr.nominal(outMask), 'mask5min.map')
pcr.report(ldd, 'ldd5min.map')