def getRowColPoint(in_map, xcor, ycor):
"""
returns the row and col in a map at the point given.
Works but is rather slow.
Input:
- in_map - map to determine coordinates from
- xcor - x coordinate
- ycor - y coordinate
Output:
- row, column
"""
x = pcr.pcr2numpy(pcr.xcoordinate(pcr.boolean(pcr.scalar(in_map) + 1.0)), np.nan)
y = pcr.pcr2numpy(pcr.ycoordinate(pcr.boolean(pcr.scalar(in_map) + 1.0)), np.nan)
XX = pcr.pcr2numpy(pcr.celllength(), 0.0)
tolerance = 0.5 # takes a single point
diffx = x - xcor
diffy = y - ycor
col_ = np.absolute(diffx) <= (XX[0, 0] * tolerance) # cellsize
row_ = np.absolute(diffy) <= (XX[0, 0] * tolerance) # cellsize
point = col_ * row_
return point.argmax(0).max(), point.argmax(1).max()
def getRowColPoint(in_map, xcor, ycor):
"""
returns the row and col in a map at the point given.
Works but is rather slow.
Input:
- in_map - map to determine coordinates from
- xcor - x coordinate
- ycor - y coordinate
Output:
- row, column
"""
x = pcr.pcr2numpy(pcr.xcoordinate(pcr.boolean(pcr.scalar(in_map) + 1.0)), np.nan)
y = pcr.pcr2numpy(pcr.ycoordinate(pcr.boolean(pcr.scalar(in_map) + 1.0)), np.nan)
XX = pcr.pcr2numpy(pcr.celllength(), 0.0)
tolerance = 0.5 # takes a single point
diffx = x - xcor
diffy = y - ycor
col_ = np.absolute(diffx) <= (XX[0, 0] * tolerance) # cellsize
row_ = np.absolute(diffy) <= (XX[0, 0] * tolerance) # cellsize
point = col_ * row_
return point.argmax(0).max(), point.argmax(1).max()
def __init__(self, netcdffile, logging):
"""
First try to setup a class read netcdf files
(converted with pcr2netcdf.py)
netcdffile: file to read the forcing data from
logging: python logging object
vars: list of variables to get from file
"""
if os.path.exists(netcdffile):
self.dataset = netCDF4.Dataset(netcdffile, mode="r")
else:
msg = os.path.abspath(netcdffile) + " not found!"
logging.error(msg)
raise ValueError(msg)
try:
self.x = self.dataset.variables["x"][:]
except:
self.x = self.dataset.variables["lon"][:]
# Now check Y values to see if we must flip the data
try:
self.y = self.dataset.variables["y"][:]
except:
self.y = self.dataset.variables["lat"][:]
x = pcr.pcr2numpy(pcr.xcoordinate(pcr.boolean(pcr.cover(1.0))), np.nan)[0, :]
y = pcr.pcr2numpy(pcr.ycoordinate(pcr.boolean(pcr.cover(1.0))), np.nan)[:, 0]
(self.latidx,) = np.logical_and(self.x >= x.min(), self.x < x.max()).nonzero()
(self.lonidx,) = np.logical_and(self.y >= x.min(), self.y < y.max()).nonzero()
logging.info("Reading static input from netCDF file: " + netcdffile)
def set_latlon_based_on_cloneMapFileName(self, cloneMapFileName):
# cloneMap
cloneMap = pcr.boolean(pcr.readmap(cloneMapFileName))
cloneMap = pcr.boolean(pcr.scalar(1.0))
# properties of the clone maps
# - numbers of rows and colums
rows = pcr.clone().nrRows()
cols = pcr.clone().nrCols()
# - cell size in arc minutes rounded to one value behind the decimal
cellSizeInArcMin = round(pcr.clone().cellSize() * 60.0, 1)
# - cell sizes in ar degrees for longitude and langitude direction
deltaLon = cellSizeInArcMin / 60.
deltaLat = deltaLon
# - coordinates of the upper left corner - rounded to two values behind the decimal in order to avoid rounding errors during (future) resampling process
x_min = round(pcr.clone().west(), 2)
y_max = round(pcr.clone().north(), 2)
# - coordinates of the lower right corner - rounded to two values behind the decimal in order to avoid rounding errors during (future) resampling process
x_max = round(x_min + cols*deltaLon, 2)
y_min = round(y_max - rows*deltaLat, 2)
# cell centres coordinates
longitudes = np.arange(x_min + deltaLon/2., x_max, deltaLon)
latitudes = np.arange(y_max - deltaLat/2., y_min,-deltaLat)
#~ # cell centres coordinates
#~ longitudes = np.linspace(x_min + deltaLon/2., x_max - deltaLon/2., cols)
#~ latitudes = np.linspace(y_max - deltaLat/2., y_min + deltaLat/2., rows)
#~ # cell centres coordinates (latitudes and longitudes, directly from the clone maps)
#~ longitudes = np.unique(pcr.pcr2numpy(pcr.xcoordinate(cloneMap), vos.MV))
#~ latitudes = np.unique(pcr.pcr2numpy(pcr.ycoordinate(cloneMap), vos.MV))[::-1]
return longitudes, latitudes, cellSizeInArcMin
def __init__(self,
cloneMapFileName,
resetClone=None,
attributeDictionary=None):
# cloneMap
if resetClone != None: pcr.setclone(cloneMapFileName)
cloneMap = pcr.boolean(pcr.readmap(cloneMapFileName))
cloneMap = pcr.boolean(pcr.scalar(1.0))
# latitudes and longitudes
self.latitudes = np.unique(
pcr.pcr2numpy(pcr.ycoordinate(cloneMap), vos.MV))[::-1]
self.longitudes = np.unique(
pcr.pcr2numpy(pcr.xcoordinate(cloneMap), vos.MV))
# reset clone (if necessary)
if resetClone != None: pcr.setclone(resetClone)
# netcdf format:
self.format = 'NETCDF3_CLASSIC'
self.attributeDictionary = {}
if attributeDictionary == None:
self.attributeDictionary['institution'] = "None"
self.attributeDictionary['title'] = "None"
self.attributeDictionary['source'] = "None"
self.attributeDictionary['history'] = "None"
self.attributeDictionary['references'] = "None"
self.attributeDictionary['description'] = "None"
self.attributeDictionary['comment'] = "None"
else:
self.attributeDictionary = attributeDictionary
def upscale_riverlength(ldd, order, factor):
"""
Upscales the riverlength using 'factor'
The resulting maps can be resampled (e.g. using resample.exe) by factor and should
include the accurate length as determined with the original higher
resolution maps. This function is **depricated**,
use are_riverlength instead as this version
is very slow for large maps
Input:
- ldd
- minimum streamorder to include
Output:
- distance per factor cells
"""
strorder = pcr.streamorder(ldd)
strorder = pcr.ifthen(strorder >= order, strorder)
dist = pcr.cover(
pcr.max(pcr.celllength(),
pcr.ifthen(pcr.boolean(strorder), pcr.downstreamdist(ldd))),
0,
)
totdist = pcr.max(
pcr.ifthen(
pcr.boolean(strorder),
pcr.windowtotal(pcr.ifthen(pcr.boolean(strorder), dist),
pcr.celllength() * factor),
),
dist,
)
return totdist
def subcatch_order_a(ldd, oorder):
"""
Determines subcatchments using the catchment order
This version uses the last cell BELOW order to derive the
catchments. In general you want the _b version
Input:
- ldd
- order - order to use
Output:
- map with catchment for the given streamorder
"""
outl = find_outlet(ldd)
large = pcr.subcatchment(ldd, pcr.boolean(outl))
stt = pcr.streamorder(ldd)
sttd = pcr.downstream(ldd, stt)
pts = pcr.ifthen((pcr.scalar(sttd) - pcr.scalar(stt)) > 0.0, sttd)
dif = pcr.upstream(
ldd,
pcr.cover(
pcr.ifthen(
large,
pcr.uniqueid(pcr.boolean(pcr.ifthen(stt == pcr.ordinal(oorder), pts))),
),
0,
),
)
dif = pcr.cover(pcr.scalar(outl), dif) # Add catchment outlet
dif = pcr.ordinal(pcr.uniqueid(pcr.boolean(dif)))
sc = pcr.subcatchment(ldd, dif)
return sc, dif, stt
def subcatch_stream(ldd, stream, threshold):
"""
Derive catchments based upon strahler threshold
Input:
ldd -- pcraster object direction, local drain directions
stream -- pcraster object direction, streamorder
threshold -- integer, strahler threshold, subcatchments ge threshold are
derived
output:
stream_ge -- pcraster object, streams of strahler order ge threshold
subcatch -- pcraster object, subcatchments of strahler order ge threshold
"""
# derive stream order
# stream = pcr.streamorder(ldd)
stream_ge = pcr.ifthen(stream >= threshold, stream)
stream_up_sum = pcr.ordinal(
pcr.upstream(ldd, pcr.cover(pcr.scalar(stream_ge), 0)))
# detect any transfer of strahler order, to a higher strahler order.
transition_strahler = pcr.ifthenelse(
pcr.downstream(ldd, stream_ge) != stream_ge, pcr.boolean(1),
pcr.ifthenelse(
pcr.nominal(ldd) == 5, pcr.boolean(1),
pcr.ifthenelse(
pcr.downstream(ldd, pcr.scalar(stream_up_sum)) >
pcr.scalar(stream_ge), pcr.boolean(1), pcr.boolean(0))))
# make unique ids (write to file)
transition_unique = pcr.ordinal(pcr.uniqueid(transition_strahler))
# derive upstream catchment areas (write to file)
subcatch = pcr.nominal(pcr.subcatchment(ldd, transition_unique))
return stream_ge, subcatch
def set_latlon_based_on_cloneMapFileName(
self, cloneMapFileName, netcdf_y_orientation_from_top_bottom=True):
# cloneMap
cloneMap = pcr.boolean(pcr.readmap(cloneMapFileName))
cloneMap = pcr.boolean(pcr.scalar(1.0))
# properties of the clone maps
# - numbers of rows and colums
rows = pcr.clone().nrRows()
cols = pcr.clone().nrCols()
# - cell size in arc minutes rounded to one value behind the decimal
cellSizeInArcMin = round(pcr.clone().cellSize() * 60.0, 1)
# - cell sizes in ar degrees for longitude and langitude direction
deltaLon = cellSizeInArcMin / 60.
deltaLat = deltaLon
# - coordinates of the upper left corner - rounded to two values behind the decimal in order to avoid rounding errors during (future) resampling process
x_min = round(pcr.clone().west(), 2)
y_max = round(pcr.clone().north(), 2)
# - coordinates of the lower right corner - rounded to two values behind the decimal in order to avoid rounding errors during (future) resampling process
x_max = round(x_min + cols * deltaLon, 2)
y_min = round(y_max - rows * deltaLat, 2)
# cell centres coordinates
longitudes = np.arange(x_min + deltaLon / 2., x_max, deltaLon)
latitudes = np.arange(y_max - deltaLat / 2., y_min, -deltaLat)
if netcdf_y_orientation_from_top_bottom == False:
latitudes = latitudes[::-1]
return longitudes, latitudes, cellSizeInArcMin
def test_03(self):
""" nonspatial condition in ifthen """
nr_rows = 2
nr_cols = 3
nr_cells = nr_rows * nr_cols
pcraster.setclone(nr_rows, nr_cols, 5, 1, 1)
raster = pcraster.ifthen(pcraster.boolean(1), pcraster.scalar(4.567))
for idx in range(1, nr_cells + 1):
value, isValid = pcraster.cellvalue(raster, idx)
self.assertEqual(isValid, True)
self.assertAlmostEqual(value, 4.567, 6)
raster = pcraster.ifthen(pcraster.boolean(0), pcraster.scalar(4.567))
for idx in range(1, nr_cells + 1):
value, isValid = pcraster.cellvalue(raster, idx)
self.assertEqual(isValid, False)
raster = pcraster.ifthen(pcraster.scalar(1), pcraster.scalar(4.567))
for idx in range(1, nr_cells + 1):
value, isValid = pcraster.cellvalue(raster, idx)
self.assertEqual(isValid, True)
self.assertAlmostEqual(value, 4.567, 6)
raster = pcraster.ifthen(pcraster.scalar(0), pcraster.scalar(4.567))
for idx in range(1, nr_cells + 1):
value, isValid = pcraster.cellvalue(raster, idx)
self.assertEqual(isValid, False)
def subcatch_order_a(ldd, oorder):
"""
Determines subcatchments using the catchment order
This version uses the last cell BELOW order to derive the
catchments. In general you want the _b version
Input:
- ldd
- order - order to use
Output:
- map with catchment for the given streamorder
"""
outl = find_outlet(ldd)
large = pcr.subcatchment(ldd, pcr.boolean(outl))
stt = pcr.streamorder(ldd)
sttd = pcr.downstream(ldd, stt)
pts = pcr.ifthen((pcr.scalar(sttd) - pcr.scalar(stt)) > 0.0, sttd)
dif = pcr.upstream(
ldd,
pcr.cover(
pcr.ifthen(
large,
pcr.uniqueid(pcr.boolean(pcr.ifthen(stt == pcr.ordinal(oorder), pts))),
),
0,
),
)
dif = pcr.cover(pcr.scalar(outl), dif) # Add catchment outlet
dif = pcr.ordinal(pcr.uniqueid(pcr.boolean(dif)))
sc = pcr.subcatchment(ldd, dif)
return sc, dif, stt
def getCoordinates(cloneMap, MV=-9999):
'''returns cell centre coordinates for a clone map as numpy array
return longitudes, latitudes '''
cln = pcr.cover(pcr.boolean(cloneMap), pcr.boolean(1))
xMap = pcr.xcoordinate(cln)
yMap = pcr.ycoordinate(cln)
return pcr.pcr2numpy(xMap, MV)[1, :], pcr.pcr2numpy(yMap, MV)[:, 1]
def set_latlon_based_on_cloneMapFileName(self, cloneMapFileName):
# cloneMap
cloneMap = pcr.boolean(pcr.readmap(cloneMapFileName))
cloneMap = pcr.boolean(pcr.scalar(1.0))
# properties of the clone maps
# - numbers of rows and colums
rows = pcr.clone().nrRows()
cols = pcr.clone().nrCols()
# - cell size in arc minutes rounded to one value behind the decimal
cellSizeInArcMin = round(pcr.clone().cellSize() * 60.0, 1)
# - cell sizes in ar degrees for longitude and langitude direction
deltaLon = cellSizeInArcMin / 60.0
deltaLat = deltaLon
# - coordinates of the upper left corner - rounded to two values behind the decimal in order to avoid rounding errors during (future) resampling process
x_min = round(pcr.clone().west(), 2)
y_max = round(pcr.clone().north(), 2)
# - coordinates of the lower right corner - rounded to two values behind the decimal in order to avoid rounding errors during (future) resampling process
x_max = round(x_min + cols * deltaLon, 2)
y_min = round(y_max - rows * deltaLat, 2)
# cell centres coordinates
longitudes = np.arange(x_min + deltaLon / 2.0, x_max, deltaLon)
latitudes = np.arange(y_max - deltaLat / 2.0, y_min, -deltaLat)
# ~ # cell centres coordinates
# ~ longitudes = np.linspace(x_min + deltaLon/2., x_max - deltaLon/2., cols)
# ~ latitudes = np.linspace(y_max - deltaLat/2., y_min + deltaLat/2., rows)
# ~ # cell centres coordinates (latitudes and longitudes, directly from the clone maps)
# ~ longitudes = np.unique(pcr.pcr2numpy(pcr.xcoordinate(cloneMap), vos.MV))
# ~ latitudes = np.unique(pcr.pcr2numpy(pcr.ycoordinate(cloneMap), vos.MV))[::-1]
return longitudes, latitudes, cellSizeInArcMin
def __init__(self, cloneMapFileName, netcdf_attribute_description):
# cloneMap
cloneMap = pcr.boolean(pcr.readmap(cloneMapFileName))
cloneMap = pcr.boolean(pcr.scalar(1.0))
# latitudes and longitudes
self.latitudes = np.unique(
pcr.pcr2numpy(pcr.ycoordinate(cloneMap), vos.MV))[::-1]
self.longitudes = np.unique(
pcr.pcr2numpy(pcr.xcoordinate(cloneMap), vos.MV))
# netCDF format and attributes:
self.format = 'NETCDF3_CLASSIC'
self.attributeDictionary = {}
self.attributeDictionary['institution'] = "European Commission - JRC"
self.attributeDictionary[
'title'] = "EFAS-Meteo 5km for the Rhine-Meuse basin"
self.attributeDictionary[
'source'] = "5km Gridded Meteo Database (C) European Commission - JRDC, 2014"
self.attributeDictionary[
'history'] = "The data were provided by Ad de Roo ([email protected]) on 19 November 2014 and then converted by Edwin H. Sutanudjaja ([email protected]) to netcdf files on 27 November 2014."
self.attributeDictionary[
'references'] = "Ntegeka et al., 2013. EFAS-Meteo: A European daily high-resolution gridded meteorological data set. JRC Technical Reports. doi: 10.2788/51262"
self.attributeDictionary[
'comment'] = "Please use this dataset only for Hyper-Hydro test bed experiments. "
self.attributeDictionary[
'comment'] += "For using it and publishing it, please acknowledge its source: 5km Gridded Meteo Database (C) European Commission - JRDC, 2014 and its reference: Ntegeka et al., 2013 (doi: 10.2788/51262). "
self.attributeDictionary[
'comment'] += "The data are in European ETRS projection, 5km grid; http://en.wikipedia.org/wiki/European_grid. "
self.attributeDictionary['description'] = netcdf_attribute_description
def overview(self, msr, pollution_threshold=2):
"""Give the overview of costs and st.dev for dem and minor embankments.
"""
msr_type = msr.settings.loc['msr_type', 1]
name = msr_type + '_' + msr.settings.loc['ID']
# Separate between clean and polluted areas
area_clean = pcr.ifthen(self.pollution_zones >= pollution_threshold,\
pcr.nominal(1))
area_polluted = pcr.ifthen(self.pollution_zones < pollution_threshold,\
pcr.nominal(1))
area_clean = pcr.defined(msr.area) & pcr.defined(area_clean)
area_clean = pcr.ifthen(area_clean, pcr.boolean(1))
area_polluted = pcr.defined(msr.area) &\
pcr.defined(area_polluted)
area_polluted = pcr.ifthen(area_polluted, pcr.boolean(1))
# Calculate costs and stddev for all earthwork types.
flpl_low_values = self.dem_lowering(msr, area_polluted)
minemb_low_values = self.minemb_lowering(msr, area_polluted)
groyne_lowering_values = self.groyne_lowering(msr)
cost_ew = pd.concat(
[flpl_low_values, groyne_lowering_values, minemb_low_values])
cost_df = cost_ew.iloc[:, 0:1].T
cost_df.index = [name]
std_df = cost_ew.iloc[:, 1:2].T
std_df.index = [name]
return cost_df, std_df
def create_city_map(ESA_CCI_land_use_map_filename, city_class_id):
#Create cities map from land use map
land_use_map = pcr.readmap(ESA_CCI_land_use_map_filename)
cities = pcr.ifthenelse(land_use_map == city_class_id, pcr.boolean(1),
pcr.boolean(0))
pcr.report(
cities,
os.path.join(os_output_folder, "cities_" + CASE_STUDY_NAME + ".map"))
return
def derive_HAND(dem,
ldd,
accuThreshold,
rivers=None,
basin=None,
up_area=None):
"""
Function derives Height-Above-Nearest-Drain.
See http://www.sciencedirect.com/science/article/pii/S003442570800120X
Input:
dem -- pcraster object float32, elevation data
ldd -- pcraster object direction, local drain directions
accuThreshold -- upstream amount of cells as threshold for river
delineation
rivers=None -- you can provide a rivers layer here. Pixels that are
identified as river should have a value > 0, other
pixels a value of zero.
basin=None -- set a boolean pcraster map where areas with True are estimated using the nearest drain in ldd distance
and areas with False by means of the nearest friction distance. Friction distance estimated using the
upstream area as weight (i.e. drains with a bigger upstream area have a lower friction)
the spreadzone operator is used in this case.
up_area=None -- provide the upstream area (if not assigned a guesstimate is prepared, assuming the LDD covers a
full catchment area)
Output:
hand -- pcraster bject float32, height, normalised to nearest stream
dist -- distance to nearest stream measured in cell lengths
according to D8 directions
"""
if rivers is None:
# prepare stream from a strahler threshold
stream = pcr.ifthenelse(
pcr.accuflux(ldd, 1) >= accuThreshold, pcr.boolean(1),
pcr.boolean(0))
else:
# convert stream network to boolean
stream = pcr.boolean(pcr.cover(rivers, 0))
# determine height in river (in DEM*100 unit as ordinal)
height_river = pcr.ifthenelse(stream, pcr.ordinal(dem * 100), 0)
if basin is None:
up_elevation = pcr.scalar(pcr.subcatchment(ldd, height_river))
else:
# use basin to allocate areas outside basin to the nearest stream. Nearest is weighted by upstream area
if up_area is None:
up_area = pcr.accuflux(ldd, 1)
up_area = pcr.ifthen(stream, up_area) # mask areas outside streams
friction = 1. / pcr.scalar(
pcr.spreadzone(pcr.cover(pcr.ordinal(up_area), 0), 0, 0))
# if basin, use nearest river within subcatchment, if outside basin, use weighted-nearest river
up_elevation = pcr.ifthenelse(
basin, pcr.scalar(pcr.subcatchment(ldd, height_river)),
pcr.scalar(pcr.spreadzone(height_river, 0, friction)))
# replace areas outside of basin by a spread zone calculation.
hand = pcr.max(pcr.scalar(pcr.ordinal(dem * 100)) - up_elevation,
0) / 100 # convert back to float in DEM units
# hand = (pcr.scalar(pcr.ordinal(dem*100))-up_elevation)/100 # convert back to float in DEM units
dist = pcr.ldddist(ldd, stream, 1) # compute horizontal distance estimate
return hand, dist
def create_pcr_clone_and_nullmask(land_use_map_filename):
land_use_map = pcr.readmap(land_use_map_filename)
clone_map = pcr.boolean(1)
pcr.report(
clone_map,
os.path.join(os_output_folder, "clone_" + CASE_STUDY_NAME + ".map"))
nullmask_map = pcr.ifthen(pcr.boolean(land_use_map), pcr.boolean(0))
pcr.report(
nullmask_map,
os.path.join(os_output_folder, "nullMask_" + CASE_STUDY_NAME + ".map"))
return clone_map, nullmask_map
def finalize_prot_area_maps(protected_areas_map, nullmask_map):
#Finalizing protected areas
protected_areas_map_country = pcr.cover(protected_areas_map, 0)
protected_areas_map_country_cut = pcr.ifthen(nullmask_map == 0,
protected_areas_map_country)
protected_areas_map_country_bool = pcr.ifthenelse(
pcr.scalar(protected_areas_map_country_cut) > 0, pcr.boolean(1),
pcr.boolean(0))
pcr.report(
protected_areas_map_country_bool,
os.path.join(os_output_folder,
"protected_areas_map_" + CASE_STUDY_NAME + "_bool.map"))
def selectCatchments(ldd, pitsMap, pitsDict, continentList, cloneMap):
catchments = pcr.ifthen(pcr.boolean(pcr.readmap(cloneMap)) == 0, pcr.scalar(1))
for continent in pitsDict.iterkeys():
continentNr = pitsDict[continent][0]
pitsContinent = pitsDict[continent][1:]
print 'updating catchments for ', continent
for pitNr in pitsContinent:
pitMap = pcr.ifthen(pitsMap == pitNr, pcr.scalar(continentNr))
catchment = pcr.catchment(ldd, pcr.nominal(pitMap))
catchment = pcr.ifthen(pcr.boolean(catchment) == 1, catchment)
catchments = pcr.cover(catchments, pcr.scalar(catchment))
return catchments
def derive_HAND(dem, ldd, accuThreshold, rivers=None, basin=None, up_area=None, neg_HAND=None):
"""
Function derives Height-Above-Nearest-Drain.
See http://www.sciencedirect.com/science/article/pii/S003442570800120X
Input:
dem -- pcraster object float32, elevation data
ldd -- pcraster object direction, local drain directions
accuThreshold -- upstream amount of cells as threshold for river
delineation
rivers=None -- you can provide a rivers layer here. Pixels that are
identified as river should have a value > 0, other
pixels a value of zero.
basin=None -- set a boolean pcraster map where areas with True are estimated using the nearest drain in ldd distance
and areas with False by means of the nearest friction distance. Friction distance estimated using the
upstream area as weight (i.e. drains with a bigger upstream area have a lower friction)
the spreadzone operator is used in this case.
up_area=None -- provide the upstream area (if not assigned a guesstimate is prepared, assuming the LDD covers a
full catchment area)
neg_HAND=None -- if set to 1, HAND maps can have negative values when elevation outside of stream is lower than
stream (for example when there are natural embankments)
Output:
hand -- pcraster bject float32, height, normalised to nearest stream
dist -- distance to nearest stream measured in cell lengths
according to D8 directions
"""
if rivers is None:
# prepare stream from a strahler threshold
stream = pcr.ifthenelse(pcr.accuflux(ldd, 1) >= accuThreshold,
pcr.boolean(1), pcr.boolean(0))
else:
# convert stream network to boolean
stream = pcr.boolean(pcr.cover(rivers, 0))
# determine height in river (in DEM*100 unit as ordinal)
height_river = pcr.ifthenelse(stream, pcr.ordinal(dem*100), 0)
if basin is None:
up_elevation = pcr.scalar(pcr.subcatchment(ldd, height_river))
else:
# use basin to allocate areas outside basin to the nearest stream. Nearest is weighted by upstream area
if up_area is None:
up_area = pcr.accuflux(ldd, 1)
up_area = pcr.ifthen(stream, up_area) # mask areas outside streams
friction = 1./pcr.scalar(pcr.spreadzone(pcr.cover(pcr.ordinal(up_area), 0), 0, 0))
# if basin, use nearest river within subcatchment, if outside basin, use weighted-nearest river
up_elevation = pcr.ifthenelse(basin, pcr.scalar(pcr.subcatchment(ldd, height_river)), pcr.scalar(pcr.spreadzone(height_river, 0, friction)))
# replace areas outside of basin by a spread zone calculation.
# make negative HANDS also possible
if neg_HAND == 1:
hand = (pcr.scalar(pcr.ordinal(dem*100))-up_elevation)/100 # convert back to float in DEM units
else:
hand = pcr.max(pcr.scalar(pcr.ordinal(dem*100))-up_elevation, 0)/100 # convert back to float in DEM units
dist = pcr.ldddist(ldd, stream, 1) # compute horizontal distance estimate
return hand, dist
def pointPerClass(classMap):
""" Select a single random point from each class in classMap"""
rand1 = 100 * pcr.uniform(pcr.boolean(classMap))
rand2 = 100 * pcr.uniform(pcr.boolean(classMap))
rand3 = 100 * pcr.uniform(pcr.boolean(classMap))
randomMap = pcr.scalar(classMap) * rand1 * rand2 * rand3
pointMap = pcr.ifthen(randomMap == pcr.areaminimum(randomMap, classMap),
classMap)
nrPointsPerClass = pcr.areatotal(pcr.scalar(pcr.boolean(pointMap)),
classMap)
assert pcr.cellvalue(pcr.mapmaximum(nrPointsPerClass), 0)[0] == 1
return pointMap
def __init__(self,cloneMapFileName,netcdf_attribute_description):
# cloneMap
cloneMap = pcr.boolean(pcr.readmap(cloneMapFileName))
cloneMap = pcr.boolean(pcr.scalar(1.0))
# properties of the clone maps
# - numbers of rows and colums
rows = pcr.clone().nrRows()
cols = pcr.clone().nrCols()
# - cell size in arc minutes rounded to one value behind the decimal
cellSizeInArcMin = round(pcr.clone().cellSize() * 60.0, 1)
# - cell sizes in ar degrees for longitude and langitude direction
deltaLon = cellSizeInArcMin / 60.
deltaLat = deltaLon
# - coordinates of the upper left corner - rounded to two values behind the decimal in order to avoid rounding errors during (future) resampling process
x_min = round(pcr.clone().west(), 2)
y_max = round(pcr.clone().north(), 2)
# - coordinates of the lower right corner - rounded to two values behind the decimal in order to avoid rounding errors during (future) resampling process
x_max = round(x_min + cols*deltaLon, 2)
y_min = round(y_max - rows*deltaLat, 2)
# cell centres coordinates
self.longitudes = np.arange(x_min + deltaLon/2., x_max, deltaLon)
self.latitudes = np.arange(y_max - deltaLat/2., y_min,-deltaLat)
#~ # cell centres coordinates
#~ self.longitudes = np.linspace(x_min + deltaLon/2., x_max - deltaLon/2., cols)
#~ self.latitudes = np.linspace(y_max - deltaLat/2., y_min + deltaLat/2., rows)
#~ # cell centres coordinates (latitudes and longitudes, directly from the clone maps)
#~ self.latitudes = np.unique(pcr.pcr2numpy(pcr.ycoordinate(cloneMap), vos.MV))[::-1]
#~ self.longitudes = np.unique(pcr.pcr2numpy(pcr.xcoordinate(cloneMap), vos.MV))
# netCDF format and attributes:
important_information = "The dataset was resampled to "+str(cellSizeInArcMin)+" arc minute resolution. "
self.format = 'NETCDF3_CLASSIC'
self.attributeDictionary = {}
self.attributeDictionary['institution'] = "European Commission - JRC and Department of Physical Geography, Utrecht University"
self.attributeDictionary['title' ] = "EFAS-Meteo 5km for Rhine-Meuse - resampled to "+str(cellSizeInArcMin)+" arc minute resolution. "
self.attributeDictionary['source' ] = "5km Gridded Meteo Database (C) European Commission - JRDC, 2014"
self.attributeDictionary['history' ] = "The data were provided by Ad de Roo ([email protected]) on 19 November 2014 and then converted by Edwin H. Sutanudjaja ([email protected]) to netcdf. "
self.attributeDictionary['history' ] += important_information
self.attributeDictionary['references' ] = "Ntegeka et al., 2013. EFAS-Meteo: A European daily high-resolution gridded meteorological data set. JRC Technical Reports. doi: 10.2788/51262"
self.attributeDictionary['comment' ] = "Please use this dataset only for Hyper-Hydro test bed experiments. "
self.attributeDictionary['comment' ] += "For using it and publishing it, please acknowledge its source: 5km Gridded Meteo Database (C) European Commission - JRDC, 2014 and its reference: Ntegeka et al., 2013 (doi: 10.2788/51262). "
self.attributeDictionary['comment' ] += "The original data provided by JRC are in European ETRS projection, 5km grid; http://en.wikipedia.org/wiki/European_grid. "
self.attributeDictionary['comment' ] += important_information
self.attributeDictionary['description'] = netcdf_attribute_description
def map_edges(clone):
"""Boolean map true map edges, false elsewhere"""
pcr.setglobaloption('unittrue')
xmin, xmax, ymin, ymax, nr_rows, nr_cols, cell_size = clone_attributes()
clone = pcr.ifthenelse(pcr.defined(clone), pcr.boolean(1), pcr.boolean(1))
x_coor = pcr.xcoordinate(clone)
y_coor = pcr.ycoordinate(clone)
north = y_coor > (ymax - cell_size)
south = y_coor < (ymin + cell_size)
west = x_coor < (xmin + cell_size)
east = x_coor > (xmax - cell_size)
edges = north | south | west | east
return edges
def relocation(self, reloc_area):
"""Sum up the cost and st.dev of dike relocation."""
reloc_area = pcr.cover(pcr.boolean(reloc_area), pcr.boolean(0))
buffer_m = 1.5 * pcr.clone().cellSize(
) # buffer 1 cell in 8 directions
reloc_buffered = pcr.spreadmaxzone(reloc_area, 0, 1, buffer_m)
reloc_length = pcr.ifthen(reloc_buffered, self.dike_length)
cost_spatial = 0.001 * reloc_length * self.dike_reloc_distr.mean
std_spatial = 0.001 * reloc_length * self.dike_reloc_distr.stddev
area = pcr.ifthen(reloc_area, pcr.boolean(1))
cost = area_total_value(cost_spatial, area)
std = area_total_value(std_spatial, area)
return cost, std
def subcatch_stream(ldd, stream, threshold):
"""
Derive catchments based upon strahler threshold
Input:
ldd -- pcraster object direction, local drain directions
stream -- pcraster object direction, streamorder
threshold -- integer, strahler threshold, subcatchments ge threshold are
derived
output:
stream_ge -- pcraster object, streams of strahler order ge threshold
subcatch -- pcraster object, subcatchments of strahler order ge threshold
"""
# derive stream order
# stream = pcr.streamorder(ldd)
stream_ge = pcr.ifthen(stream >= threshold, stream)
stream_up_sum = pcr.ordinal(pcr.upstream(ldd, pcr.cover(pcr.scalar(stream_ge), 0)))
# detect any transfer of strahler order, to a higher strahler order.
transition_strahler = pcr.ifthenelse(pcr.downstream(ldd, stream_ge) != stream_ge, pcr.boolean(1),
pcr.ifthenelse(pcr.nominal(ldd) == 5, pcr.boolean(1), pcr.ifthenelse(pcr.downstream(ldd, pcr.scalar(stream_up_sum)) > pcr.scalar(stream_ge), pcr.boolean(1),
pcr.boolean(0))))
# make unique ids (write to file)
transition_unique = pcr.ordinal(pcr.uniqueid(transition_strahler))
# derive upstream catchment areas (write to file)
subcatch = pcr.nominal(pcr.subcatchment(ldd, transition_unique))
return stream_ge, subcatch
def mapEllipse(r_a, r_b, azimuth, latC, lonC, lat, lon, numberStepsArc= 360): '''Maps an ellipse for the given spatial attributes using a predefined number \ of steps along the arc: r_a: length of semi_major axis r_b: length of semi_major axis azimuth: angle of semi_major axis with the centroid to north latC: latitude of centroid lonC: longitude of centroid lat: map of latitude lon: map of longitude numberStepsArc= 360 (default) where r= r_a*r_b/(r_a**2*sin(theta)**2+r_b**2*cos(theta)**2)**0.5 \n''' #-compute theta as the azimuth and rotated towards the semi-major axis theta= np.linspace(0.,360.-360./numberStepsArc,numberStepsArc) radius= (r_a*r_b)/(r_a**2*(np.sin(theta*deg2Rad))**2+r_b**2*(np.cos(theta*deg2Rad))**2)**0.5 theta= (theta+azimuth) % 360. lat1, lon1= getDestinationPoint(latC, lonC, radius, theta) ellipse= pcr.boolean(0) for iCnt in xrange(lat1.size): ellipse= ellipse | \ (pcr.abs(lat-lat1[iCnt]) == pcr.mapminimum(pcr.abs(lat-lat1[iCnt]))) & \ (pcr.abs(lon-lon1[iCnt]) == pcr.mapminimum(pcr.abs(lon-lon1[iCnt]))) ellipse= pcr.ifthen(ellipse, ellipse) #-return ellipse return ellipse
def test_001(self):
""" nonspatial and pcr2numpy """
nrRows, nrCols, cellSize = 5, 8, 1.0
west, north = 0.0, 0.0
pcraster.setclone(nrRows, nrCols, cellSize, west, north)
value = 1.23456
nonspatial = pcraster.scalar(value)
array = pcraster.pcr2numpy(nonspatial, numpy.nan)
for row in range(0, nrRows):
for col in range(0, nrCols):
self.assertAlmostEqual(array[row][col], value)
value = 3
nonspatial = pcraster.nominal(value)
array = pcraster.pcr2numpy(nonspatial, numpy.nan)
for row in range(0, nrRows):
for col in range(0, nrCols):
self.assertAlmostEqual(array[row][col], value)
value = True
nonspatial = pcraster.boolean(value)
array = pcraster.pcr2numpy(nonspatial, numpy.nan)
for row in range(0, nrRows):
for col in range(0, nrCols):
self.assertAlmostEqual(array[row][col], value)
def testNonSpatialConversions(self):
nonSpatialValue = pcraster.mapmaximum(pcraster.readmap("map2asc_PCRmap.map"))
# Ordinal.
nonSpatial = pcraster.ordinal(nonSpatialValue)
self.assertEqual(bool(nonSpatial), True)
self.assertEqual(int(nonSpatial), 124)
self.assertEqual(float(nonSpatial), 124.0)
# Nominal.
nonSpatial = pcraster.nominal(nonSpatialValue)
self.assertEqual(bool(nonSpatial), True)
self.assertEqual(int(nonSpatial), 124)
self.assertEqual(float(nonSpatial), 124)
# Boolean.
nonSpatial = pcraster.boolean(nonSpatialValue)
self.assertEqual(bool(nonSpatial), True)
self.assertEqual(int(nonSpatial), 1)
self.assertEqual(float(nonSpatial), 1.0)
# Scalar.
nonSpatial = pcraster.scalar(pcraster.mapmaximum("abs_Expr.map"))
self.assertEqual(bool(nonSpatial), True)
self.assertEqual(int(nonSpatial), 14)
self.assertEqual(float(nonSpatial), 14.0)
def __init__(self,configuration,model,specificAttributeDictionary=None):
# Set clone map
pcr.setclone(configuration.cloneMap)
cloneMap = pcr.boolean(1.0) # map with all cell values equal to 1
# Retrieve latitudes and longitudes from clone map
self.latitudes = np.unique(pcr.pcr2numpy(pcr.ycoordinate(cloneMap), vos.MV))[::-1]
self.longitudes = np.unique(pcr.pcr2numpy(pcr.xcoordinate(cloneMap), vos.MV))
self.crops = np.arange(1, model.nCrop + 1)
self.depths = np.arange(1, model.nComp + 1)
# Let users decide what their preference regarding latitude order
self.netcdf_y_orientation_follow_cf_convention = False
if 'netcdf_y_orientation_follow_cf_convention' in configuration.reportingOptions.keys() and\
configuration.reportingOptions['netcdf_y_orientation_follow_cf_convention'] == "True":
msg = "Latitude (y) orientation for output netcdf files start from the bottom to top."
self.netcdf_y_orientation_follow_cf_convention = True
self.latitudes = np.unique(pcr.pcr2numpy(pcr.ycoordinate(cloneMap), vos.MV))
# Set general netcdf attributes (based on the information given in the ini/configuration file)
self.set_general_netcdf_attributes(configuration, specificAttributeDictionary)
# netcdf format and zlib setup
self.format = 'NETCDF3_CLASSIC'
self.zlib = False
if "formatNetCDF" in configuration.reportingOptions.keys():
self.format = str(configuration.reportingOptions['formatNetCDF'])
if "zlib" in configuration.reportingOptions.keys():
if configuration.reportingOptions['zlib'] == "True": self.zlib = True
def snaptomap(points, mmap):
"""
Snap the points in _points_ to nearest non missing
values in _mmap_. Can be used to move gauge locations
to the nearest rivers.
Input:
- points - map with points to move
- mmap - map with points to move to
Return:
- map with shifted points
"""
points = pcr.cover(points, 0)
# Create unique id map of mmap cells
unq = pcr.nominal(pcr.cover(pcr.uniqueid(pcr.defined(mmap)), pcr.scalar(0.0)))
# Now fill holes in mmap map with lues indicating the closes mmap cell.
dist_cellid = pcr.scalar(pcr.spreadzone(unq, 0, 1))
# Get map with values at location in points with closes mmap cell
dist_cellid = pcr.ifthenelse(points > 0, dist_cellid, 0)
# Spread this out
dist_fill = pcr.spreadzone(pcr.nominal(dist_cellid), 0, 1)
# Find the new (moved) locations
npt = pcr.uniqueid(pcr.boolean(pcr.ifthen(dist_fill == unq, unq)))
# Now recreate the original value in the points maps
ptcover = pcr.spreadzone(pcr.cover(points, 0), 0, 1)
# Now get the org point value in the pt map
nptorg = pcr.ifthen(npt > 0, ptcover)
return nptorg
def __init__(self, iniItems):
# cloneMap
pcr.setclone(iniItems.cloneMap)
cloneMap = pcr.boolean(1.0)
# latitudes and longitudes
self.latitudes = np.unique(pcr2numpy(pcr.ycoordinate(cloneMap),
vos.MV))[::-1]
self.longitudes = np.unique(
pcr2numpy(pcr.xcoordinate(cloneMap), vos.MV))
# TODO: Let users decide what their preference regarding latitude order.
# Consult with Stefanie regarding CF convention.
# netCDF format and attributes:
self.attributeDictionary = {}
self.attributeDictionary['institution'] = iniItems.globalOptions[
'institution']
self.attributeDictionary['title'] = iniItems.globalOptions['title']
self.attributeDictionary['description'] = iniItems.globalOptions[
'description']
# netcdf format and zlib setup
self.format = 'NETCDF3_CLASSIC'
self.zlib = False
if "formatNetCDF" in iniItems.reportingOptions.keys():
self.format = str(iniItems.reportingOptions['formatNetCDF'])
if "zlib" in iniItems.reportingOptions.keys():
if iniItems.reportingOptions['zlib'] == "True": self.zlib = True
def test_001(self):
""" nonspatial and pcr2numpy """
nrRows, nrCols, cellSize = 5, 8, 1.0
west, north = 0.0, 0.0
pcraster.setclone(nrRows, nrCols, cellSize, west, north)
value = 1.23456
nonspatial = pcraster.scalar(value)
array = pcraster.pcr2numpy(nonspatial, numpy.nan)
for row in range(0, nrRows):
for col in range(0, nrCols):
self.assertAlmostEqual(array[row][col], value)
value = 3
nonspatial = pcraster.nominal(value)
array = pcraster.pcr2numpy(nonspatial, numpy.nan)
for row in range(0, nrRows):
for col in range(0, nrCols):
self.assertAlmostEqual(array[row][col], value)
value = True
nonspatial = pcraster.boolean(value)
array = pcraster.pcr2numpy(nonspatial, numpy.nan)
for row in range(0, nrRows):
for col in range(0, nrCols):
self.assertAlmostEqual(array[row][col], value)
def testNonSpatialConversions(self):
nonSpatialValue = pcraster.mapmaximum(
pcraster.readmap("map2asc_PCRmap.map"))
# Ordinal.
nonSpatial = pcraster.ordinal(nonSpatialValue)
self.assertEqual(bool(nonSpatial), True)
self.assertEqual(int(nonSpatial), 124)
self.assertEqual(float(nonSpatial), 124.0)
# Nominal.
nonSpatial = pcraster.nominal(nonSpatialValue)
self.assertEqual(bool(nonSpatial), True)
self.assertEqual(int(nonSpatial), 124)
self.assertEqual(float(nonSpatial), 124)
# Boolean.
nonSpatial = pcraster.boolean(nonSpatialValue)
self.assertEqual(bool(nonSpatial), True)
self.assertEqual(int(nonSpatial), 1)
self.assertEqual(float(nonSpatial), 1.0)
# Scalar.
nonSpatial = pcraster.scalar(pcraster.mapmaximum("abs_Expr.map"))
self.assertEqual(bool(nonSpatial), True)
self.assertEqual(int(nonSpatial), 14)
self.assertEqual(float(nonSpatial), 14.0)
def snaptomap(points, mmap):
"""
Snap the points in _points_ to nearest non missing
values in _mmap_. Can be used to move gauge locations
to the nearest rivers.
Input:
- points - map with points to move
- mmap - map with points to move to
Return:
- map with shifted points
"""
points = pcr.cover(points, 0)
# Create unique id map of mmap cells
unq = pcr.nominal(pcr.cover(pcr.uniqueid(pcr.defined(mmap)), pcr.scalar(0.0)))
# Now fill holes in mmap map with lues indicating the closes mmap cell.
dist_cellid = pcr.scalar(pcr.spreadzone(unq, 0, 1))
# Get map with values at location in points with closes mmap cell
dist_cellid = pcr.ifthenelse(points > 0, dist_cellid, 0)
# Spread this out
dist_fill = pcr.spreadzone(pcr.nominal(dist_cellid), 0, 1)
# Find the new (moved) locations
npt = pcr.uniqueid(pcr.boolean(pcr.ifthen(dist_fill == unq, unq)))
# Now recreate the original value in the points maps
ptcover = pcr.spreadzone(pcr.cover(points, 0), 0, 1)
# Now get the org point value in the pt map
nptorg = pcr.ifthen(npt > 0, ptcover)
return nptorg
def getCellValues(pointMap, mapList=[], columns=[]):
""" Get the cell values of the maps in mapList at the locations of pointMap
"""
#-determine where the indices are True
arr = pcr.pcr2numpy(pcr.boolean(pointMap), 0).astype('bool')
indices = np.where(arr == True)
#-loop over the points in pointMap
pcr.setglobaloption('unitcell')
ll = []
for rowIdx, colIdx in zip(indices[0], indices[1]):
line = []
line.append(rowIdx)
line.append(colIdx)
for pcrMap in mapList:
line.append(
pcr.cellvalue(pcrMap, np.int(rowIdx + 1),
np.int(colIdx + 1))[0])
ll.append(line)
#-optionally add column names
if len(columns) == len(mapList):
columnNames = ['rowIdx', 'colIdx'] + columns
else:
columnNames = ['rowIdx', 'colIdx'] + \
['map' + str(ii) for ii in range(1, 1 + len(mapList), 1)]
#-return as Pandas DataFrame
return pd.DataFrame(np.array(ll), columns=columnNames)
def pcr2col(listOfMaps, MV, selection='ONE_TRUE'):
"""converts a set of maps to a column array: X, Y, map values
selection can be set to ALL, ALL_TRUE, ONE_TRUE"""
#-intersect all maps and get X and Y coordinates
intersection = pcr.boolean(pcr.cover(listOfMaps[0], 0))
for mapX in listOfMaps[1:]:
intersection = intersection | pcr.boolean(pcr.cover(mapX, 0))
pcr.setglobaloption("unittrue")
xCoor = pcr.ifthen(intersection, pcr.xcoordinate(intersection))
yCoor = pcr.ifthen(intersection, pcr.ycoordinate(intersection))
pcr.setglobaloption("unitcell")
#-initiate outArray with xCoor and yCoor
xCoorArr = pcr.pcr2numpy(xCoor, MV)
yCoorArr = pcr.pcr2numpy(yCoor, MV)
nRows, nCols = xCoorArr.shape
nrCells = nRows * nCols
outArray = np.hstack((xCoorArr.reshape(nrCells,
1), yCoorArr.reshape(nrCells, 1)))
#-add subsequent maps
for mapX in listOfMaps:
arr = pcr.pcr2numpy(mapX, MV).reshape(nrCells, 1)
outArray = np.hstack((outArray, arr))
#-subset output based on selection criterium
ll = []
nrMaps = len(listOfMaps)
if selection == 'ONE_TRUE':
for line in outArray:
nrMV = len(line[line == MV])
if nrMV < nrMaps:
ll.append(line)
else:
pass
outArray = np.array(ll)
elif selection == 'ALL_TRUE':
for line in outArray:
if MV not in line:
ll.append(line)
else:
pass
outArray = np.array(ll)
elif selection == 'ALL':
pass
return outArray
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 __init__(self, iniItems, specificAttributeDictionary=None):
# cloneMap
pcr.setclone(iniItems.cloneMap)
cloneMap = pcr.boolean(1.0)
# latitudes and longitudes
self.latitudes = np.unique(pcr.pcr2numpy(pcr.ycoordinate(cloneMap), vos.MV))[
::-1
]
self.longitudes = np.unique(pcr.pcr2numpy(pcr.xcoordinate(cloneMap), vos.MV))
# Let users decide what their preference regarding latitude order.
self.netcdf_y_orientation_follow_cf_convention = False
if (
"netcdf_y_orientation_follow_cf_convention"
in list(iniItems.reportingOptions.keys())
and iniItems.reportingOptions["netcdf_y_orientation_follow_cf_convention"]
== "True"
):
msg = "Latitude (y) orientation for output netcdf files start from the bottom to top."
self.netcdf_y_orientation_follow_cf_convention = True
self.latitudes = np.unique(pcr.pcr2numpy(pcr.ycoordinate(cloneMap), vos.MV))
# set the general netcdf attributes (based on the information given in the ini/configuration file)
self.set_general_netcdf_attributes(iniItems, specificAttributeDictionary)
# netcdf format and zlib setup
self.format = "NETCDF3_CLASSIC"
self.zlib = False
if "formatNetCDF" in list(iniItems.reportingOptions.keys()):
self.format = str(iniItems.reportingOptions["formatNetCDF"])
if "zlib" in list(iniItems.reportingOptions.keys()):
if iniItems.reportingOptions["zlib"] == "True":
self.zlib = True
# if given in the ini file, use the netcdf as given in the section 'specific_attributes_for_netcdf_output_files'
if "specific_attributes_for_netcdf_output_files" in iniItems.allSections:
for key in list(
iniItems.specific_attributes_for_netcdf_output_files.keys()
):
self.attributeDictionary[
key
] = iniItems.specific_attributes_for_netcdf_output_files[key]
if self.attributeDictionary[key] == "None":
self.attributeDictionary[key] = ""
if key == "history" and self.attributeDictionary[key] == "Default":
self.attributeDictionary[
key
] = "created on " + datetime.datetime.today().isoformat(" ")
if self.attributeDictionary[key] == "Default" and (
key == "date_created" or key == "date_issued"
):
self.attributeDictionary[key] = datetime.datetime.today().isoformat(
" "
)
def derive_HAND(dem, ldd, accuThreshold, rivers=None, basin=None):
"""
Function derives Height-Above-Nearest-Drain.
See http://www.sciencedirect.com/science/article/pii/S003442570800120X
Input:
dem -- pcraster object float32, elevation data
ldd -- pcraster object direction, local drain directions
accuThreshold -- upstream amount of cells as threshold for river
delineation
rivers=None -- you can provide a rivers layer here. Pixels that are
identified as river should have a value > 0, other
pixels a value of zero.
basin=None -- set a boolean pcraster map where areas with True are estimated using the nearest drain in ldd distance
and areas with False by means of the nearest friction distance. Friction distance estimated using the
upstream area as weight (i.e. drains with a bigger upstream area have a lower friction)
the spreadzone operator is used in this case.
Output:
hand -- pcraster bject float32, height, normalised to nearest stream
dist -- distance to nearest stream measured in cell lengths
according to D8 directions
"""
if rivers is None:
stream = pcr.ifthenelse(
pcr.accuflux(ldd, 1) >= accuThreshold, pcr.boolean(1), pcr.boolean(0)
)
else:
stream = pcr.boolean(pcr.cover(rivers, 0))
height_river = pcr.ifthenelse(stream, pcr.ordinal(dem * 100), 0)
if basin is None:
up_elevation = pcr.scalar(pcr.subcatchment(ldd, height_river))
else:
drainage_surf = pcr.ifthen(rivers, pcr.accuflux(ldd, 1))
weight = 1.0 / pcr.scalar(
pcr.spreadzone(pcr.cover(pcr.ordinal(drainage_surf), 0), 0, 0)
)
up_elevation = pcr.ifthenelse(
basin,
pcr.scalar(pcr.subcatchment(ldd, height_river)),
pcr.scalar(pcr.spreadzone(height_river, 0, weight)),
)
# replace areas outside of basin by a spread zone calculation.
hand = pcr.max(pcr.scalar(pcr.ordinal(dem * 100)) - up_elevation, 0) / 100
dist = pcr.ldddist(ldd, stream, 1)
return hand, dist
def derive_HAND(dem, ldd, accuThreshold, rivers=None, basin=None):
"""
Function derives Height-Above-Nearest-Drain.
See http://www.sciencedirect.com/science/article/pii/S003442570800120X
Input:
dem -- pcraster object float32, elevation data
ldd -- pcraster object direction, local drain directions
accuThreshold -- upstream amount of cells as threshold for river
delineation
rivers=None -- you can provide a rivers layer here. Pixels that are
identified as river should have a value > 0, other
pixels a value of zero.
basin=None -- set a boolean pcraster map where areas with True are estimated using the nearest drain in ldd distance
and areas with False by means of the nearest friction distance. Friction distance estimated using the
upstream area as weight (i.e. drains with a bigger upstream area have a lower friction)
the spreadzone operator is used in this case.
Output:
hand -- pcraster bject float32, height, normalised to nearest stream
dist -- distance to nearest stream measured in cell lengths
according to D8 directions
"""
if rivers is None:
stream = pcr.ifthenelse(
pcr.accuflux(ldd, 1) >= accuThreshold, pcr.boolean(1), pcr.boolean(0)
)
else:
stream = pcr.boolean(pcr.cover(rivers, 0))
height_river = pcr.ifthenelse(stream, pcr.ordinal(dem * 100), 0)
if basin is None:
up_elevation = pcr.scalar(pcr.subcatchment(ldd, height_river))
else:
drainage_surf = pcr.ifthen(rivers, pcr.accuflux(ldd, 1))
weight = 1.0 / pcr.scalar(
pcr.spreadzone(pcr.cover(pcr.ordinal(drainage_surf), 0), 0, 0)
)
up_elevation = pcr.ifthenelse(
basin,
pcr.scalar(pcr.subcatchment(ldd, height_river)),
pcr.scalar(pcr.spreadzone(height_river, 0, weight)),
)
# replace areas outside of basin by a spread zone calculation.
hand = pcr.max(pcr.scalar(pcr.ordinal(dem * 100)) - up_elevation, 0) / 100
dist = pcr.ldddist(ldd, stream, 1)
return hand, dist
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 __init__(self,cloneMapFileName,netcdf_attribute_description):
# cloneMap
cloneMap = pcr.boolean(pcr.readmap(cloneMapFileName))
cloneMap = pcr.boolean(pcr.scalar(1.0))
# latitudes and longitudes
self.latitudes = np.unique(pcr.pcr2numpy(pcr.ycoordinate(cloneMap), vos.MV))[::-1]
self.longitudes = np.unique(pcr.pcr2numpy(pcr.xcoordinate(cloneMap), vos.MV))
# netCDF format and attributes:
self.format = 'NETCDF3_CLASSIC'
self.attributeDictionary = {}
self.attributeDictionary['institution'] = "European Commission - JRC"
self.attributeDictionary['title' ] = "EFAS-Meteo 5km for the Rhine-Meuse basin"
self.attributeDictionary['source' ] = "5km Gridded Meteo Database (C) European Commission - JRDC, 2014"
self.attributeDictionary['history' ] = "The data were provided by Ad de Roo ([email protected]) on 19 November 2014 and then converted by Edwin H. Sutanudjaja ([email protected]) to netcdf files on 27 November 2014."
self.attributeDictionary['references' ] = "Ntegeka et al., 2013. EFAS-Meteo: A European daily high-resolution gridded meteorological data set. JRC Technical Reports. doi: 10.2788/51262"
self.attributeDictionary['comment' ] = "Please use this dataset only for Hyper-Hydro test bed experiments. "
self.attributeDictionary['comment' ] += "For using it and publishing it, please acknowledge its source: 5km Gridded Meteo Database (C) European Commission - JRDC, 2014 and its reference: Ntegeka et al., 2013 (doi: 10.2788/51262). "
self.attributeDictionary['comment' ] += "The data are in European ETRS projection, 5km grid; http://en.wikipedia.org/wiki/European_grid. "
self.attributeDictionary['description'] = netcdf_attribute_description
def testIfThenElse(self):
pcraster.setclone("and_Expr1.map")
exceptionThrown = False
try:
result = pcraster.ifthenelse(1.0 == 2.0, 3.0, 4.0)
except RuntimeError as exception:
message = str(exception)
self.assertTrue(message.find("conversion function to pick a data type") != -1)
exceptionThrown = True
self.assertTrue(exceptionThrown)
result = pcraster.ifthenelse(pcraster.boolean(1.0 == 2.0), \
pcraster.scalar(3.0), pcraster.scalar(4.0))
self.assertEqual(pcraster.cellvalue(result, 1)[0], 4.0)
def upscale_riverlength(ldd, order, factor):
"""
Upscales the riverlength using 'factor'
The resulting maps can be resampled (e.g. using resample.exe) by factor and should
include the accurate length as determined with the original higher
resolution maps. This function is **depricated**,
use are_riverlength instead as this version
is very slow for large maps
Input:
- ldd
- minimum streamorder to include
Output:
- distance per factor cells
"""
strorder = pcr.streamorder(ldd)
strorder = pcr.ifthen(strorder >= order, strorder)
dist = pcr.cover(
pcr.max(
pcr.celllength(), pcr.ifthen(pcr.boolean(strorder), pcr.downstreamdist(ldd))
),
0,
)
totdist = pcr.max(
pcr.ifthen(
pcr.boolean(strorder),
pcr.windowtotal(
pcr.ifthen(pcr.boolean(strorder), dist), pcr.celllength() * factor
),
),
dist,
)
return totdist
def interpolategauges(inputmap, method):
""""
Interpolate time series gauge data onto a grid using different methods
inputmap: map with points data for a single timestep
method: string indicating the method
inv
pol
input: inputmap, method
returns: interpolated map
"""
if method == "inv":
result = pcr.inversedistance(1, inputmap, 3, 0, 0)
elif method == "pol":
Unq = pcr.uniqueid(pcr.boolean(inputmap + 1))
result = pcr.spreadzone(pcr.ordinal(pcr.cover(Unq, 0)), 0, 1)
result = pcr.areaaverage(inputmap, result)
else:
Unq = pcr.uniqueid(pcr.boolean(inputmap + 1))
result = pcr.spreadzone(pcr.ordinal(pcr.cover(Unq, 0)), 0, 1)
result = pcr.areaaverage(inputmap, result)
return result
def test_003(self):
""" pcr2numpy should not run out of memory """
nrRows, nrCols, cellSize = 200, 200, 1.0
west, north = 0.0, 0.0
pcraster.setclone(nrRows, nrCols, cellSize, west, north)
raster = pcraster.uniform(1)
process = psutil.Process(os.getpid())
mem = process.memory_info()
init_mem = mem.rss / 2**10
nr_iterations = 50
mem_increase = False
# small memory increase can occur at runtime
# allow for, but less than iterations * size(raster)
max_diff = 400
for it in range(0, nr_iterations):
pcraster.pcr2numpy(raster, numpy.nan)
mem = process.memory_info()
curr_mem = mem.rss / 2**10
if curr_mem - init_mem > max_diff:
mem_increase = True
raster = pcraster.spatial(pcraster.boolean(1))
for it in range(0, nr_iterations):
pcraster.pcr2numpy(raster, numpy.nan)
mem = process.memory_info()
curr_mem = mem.rss / 2**10
if curr_mem - init_mem > max_diff:
mem_increase = True
raster = pcraster.nominal(pcraster.uniform(1) * 10)
for it in range(0, nr_iterations):
pcraster.pcr2numpy(raster, numpy.nan)
mem = process.memory_info()
curr_mem = mem.rss / 2**10
if curr_mem - init_mem > max_diff:
mem_increase = True
self.assertEqual(mem_increase, False)
def riverlength(ldd, order):
"""
Determines the length of a river using the ldd.
only determined for order and higher.
Input:
- ldd, order (streamorder)
Returns:
- totallength,lengthpercell, streamorder
"""
strorder = pcr.streamorder(ldd)
strorder = pcr.ifthen(strorder >= pcr.ordinal(order), strorder)
dist = pcr.max(
pcr.celllength(), pcr.ifthen(pcr.boolean(strorder), pcr.downstreamdist(ldd))
)
return pcr.catchmenttotal(pcr.cover(dist, 0), ldd), dist, strorder
def __init__(self, cloneMapFile, attribute=None, cellSizeInArcMinutes=None):
# cloneMap
# - the cloneMap must be at 5 arc min resolution
cloneMap = pcr.readmap(cloneMapFile)
cloneMap = pcr.boolean(1.0)
# latitudes and longitudes
self.latitudes = np.unique(pcr.pcr2numpy(pcr.ycoordinate(cloneMap), vos.MV))[::-1]
self.longitudes = np.unique(pcr.pcr2numpy(pcr.xcoordinate(cloneMap), vos.MV))
#~ # properties of the clone map
#~ # - number of rows and columns
#~ self.nrRows = np.round(pcr.clone().nrRows())
#~ self.nrCols = np.round(pcr.clone().nrCols())
#~ # - upper right coordinate, unit: arc degree ; must be integer (without decimals)
#~ self.minLongitude = np.round(pcr.clone().west() , 0)
#~ self.maxLatitude = np.round(pcr.clone().north(), 0)
#~ # - cell resolution, unit: arc degree
#~ self.cellSize = pcr.clone().cellSize()
#~ if cellSizeInArcMinutes != None: self.cellSize = cellSizeInArcMinutes / 60.0
#~ # - lower right coordinate, unit: arc degree ; must be integer (without decimals)
#~ self.maxLongitude = np.round(self.minLongitude + self.cellSize*self.nrCols, 0)
#~ self.minLatitude = np.round(self.maxLatitude - self.cellSize*self.nrRows, 0)
#~
#~ # latitudes and longitudes for netcdf files
#~ latMin = self.minLatitude + self.cellSize / 2
#~ latMax = self.maxLatitude - self.cellSize / 2
#~ lonMin = self.minLongitude + self.cellSize / 2
#~ lonMax = self.maxLongitude - self.cellSize / 2
#~ self.longitudes = np.arange(lonMin,lonMax+self.cellSize, self.cellSize)
#~ self.latitudes= np.arange(latMax,latMin-self.cellSize,-self.cellSize)
# netCDF format and attributes:
self.format = 'NETCDF4'
self.attributeDictionary = {}
if attribute == None:
self.attributeDictionary['institution'] = "None"
self.attributeDictionary['title' ] = "None"
self.attributeDictionary['description'] = "None"
else:
self.attributeDictionary = attribute
def area_river_burnin(ldd, dem, order, Area):
"""
Calculates the lowest values in as DEM for each erea in an area map for
river of order *order*
Input:
- ldd
- dem
- order
- Area map
Output:
- dem
"""
strorder = pcr.streamorder(ldd)
strordermax = pcr.areamaximum(strorder, Area)
maxordcell = pcr.ifthen(strordermax > order, strordermax)
riverdem = pcr.areaminimum(dem, Area)
return pcr.ifthen(pcr.boolean(maxordcell), riverdem)
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 detRealCellLength(ZeroMap, sizeinmetres):
"""
Determine cellength. Always returns the length
in meters.
"""
if sizeinmetres:
reallength = pcr.celllength()
xl = pcr.celllength()
yl = pcr.celllength()
else:
aa = pcr.ycoordinate(pcr.boolean(pcr.cover(ZeroMap + 1, 1)))
yl, xl = lattometres(aa)
xl = xl * pcr.celllength()
yl = yl * pcr.celllength()
# Average length for surface area calculations.
reallength = (xl + yl) * 0.5
return xl, yl, reallength
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)
def evaluateAllModelResults(self,globalCloneMapFileName,\
catchmentClassFileName,\
lddMapFileName,\
cellAreaMapFileName,\
pcrglobwb_output,\
analysisOutputDir="",\
tmpDir = None):
# temporary directory
if tmpDir == None: tmpDir = self.tmpDir+"/edwin_grdc_"
# output directory for all analyses for all stations
analysisOutputDir = str(analysisOutputDir)
self.chartOutputDir = analysisOutputDir+"/chart/"
self.tableOutputDir = analysisOutputDir+"/table/"
#
if analysisOutputDir == "": self.chartOutputDir = "chart/"
if analysisOutputDir == "": self.tableOutputDir = "table/"
#
# make the chart and table directories:
os.system('rm -r '+self.chartOutputDir+"*")
os.system('rm -r '+self.tableOutputDir+"*")
os.makedirs(self.chartOutputDir)
os.makedirs(self.tableOutputDir)
# cloneMap for all pcraster operations
pcr.setclone(globalCloneMapFileName)
cloneMap = pcr.boolean(1)
self.cell_size_in_arc_degree = vos.getMapAttributesALL(globalCloneMapFileName)['cellsize']
lddMap = pcr.lddrepair(pcr.readmap(lddMapFileName))
cellArea = pcr.scalar(pcr.readmap(cellAreaMapFileName))
# The landMaskClass map contains the nominal classes for all landmask regions.
landMaskClass = pcr.nominal(cloneMap) # default: if catchmentClassFileName is not given
if catchmentClassFileName != None:
landMaskClass = pcr.nominal(pcr.readmap(catchmentClassFileName))
# model catchment areas and cordinates
catchmentAreaAll = pcr.catchmenttotal(cellArea, lddMap) / (1000*1000) # unit: km2
xCoordinate = pcr.xcoordinate(cloneMap)
yCoordinate = pcr.ycoordinate(cloneMap)
for id in self.list_of_grdc_ids:
logger.info("Evaluating simulated discharge to the grdc observation at "+str(self.attributeGRDC["id_from_grdc"][str(id)])+".")
# identify model pixel
self.identifyModelPixel(tmpDir,catchmentAreaAll,landMaskClass,xCoordinate,yCoordinate,str(id))
# evaluate model results to GRDC data
self.evaluateModelResultsToGRDC(str(id),pcrglobwb_output,catchmentClassFileName,tmpDir)
# write the summary to a table
summary_file = analysisOutputDir+"summary.txt"
#
logger.info("Writing the summary for all stations to the file: "+str(summary_file)+".")
#
# prepare the file:
summary_file_handle = open(summary_file,"w")
#
# write the header
summary_file_handle.write( ";".join(self.grdc_dict_keys)+"\n")
#
# write the content
for id in self.list_of_grdc_ids:
rowLine = ""
for key in self.grdc_dict_keys: rowLine += str(self.attributeGRDC[key][str(id)]) + ";"
rowLine = rowLine[0:-1] + "\n"
summary_file_handle.write(rowLine)
summary_file_handle.close()
# 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'],
output_files['tmp_folder'],
None, False, None, True))
hydro_year_type = pcr.cover(hydro_year_type, pcr.nominal(1.0))
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
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)
# - save it to a pcraster map file
pcr.report(uniqueIDs_sample, "sample.ids")
# calculate the country values
index = 0 # for posCnt
for iYear in range(staYear,endYear+1):
# time stamp and index for netcdf files:
index = index + 1
timeStamp = datetime.datetime(int(iYear), int(12), int(31), int(0))
fulldate = '%4i-%02i-%02i' %(int(iYear), int(12), int(31))
# 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))
#~ pcr.aguila(basin_map)
def subcatch_stream(ldd, threshold, stream=None, min_strahler=-999, max_strahler=999, assign_edge=False, assign_existing=False, up_area=None, basin=None):
"""
Derive catchments based upon strahler threshold
Input:
ldd -- pcraster object direction, local drain directions
threshold -- integer, strahler threshold, subcatchments ge threshold
are derived
stream=None -- pcraster object ordinal, stream order map (made with pcr.streamorder), if provided, stream order
map is not generated on the fly but used from this map. Useful when a subdomain within a catchment is
provided, which would cause edge effects in the stream order map
min_strahler=-999 -- integer, minimum strahler threshold of river catchments
to return
max_strahler=999 -- integer, maximum strahler threshold of river catchments
to return
assign_unique=False -- if set to True, unassigned connected areas at
the edges of the domain are assigned a unique id as well. If set
to False, edges are not assigned
assign_existing=False == if set to True, unassigned edges are assigned
to existing basins with an upstream weighting. If set to False,
edges are assigned to unique IDs, or not assigned
output:
stream_ge -- pcraster object, streams of strahler order ge threshold
subcatch -- pcraster object, subcatchments of strahler order ge threshold
"""
# derive stream order
if stream is None:
stream = pcr.streamorder(ldd)
stream_ge = pcr.ifthen(stream >= threshold, stream)
stream_up_sum = pcr.ordinal(pcr.upstream(ldd, pcr.cover(pcr.scalar(stream_ge), 0)))
# detect any transfer of strahler order, to a higher strahler order.
transition_strahler = pcr.ifthenelse(pcr.downstream(ldd, stream_ge) != stream_ge, pcr.boolean(1),
pcr.ifthenelse(pcr.nominal(ldd) == 5, pcr.boolean(1), pcr.ifthenelse(pcr.downstream(ldd, pcr.scalar(stream_up_sum)) > pcr.scalar(stream_ge), pcr.boolean(1),
pcr.boolean(0))))
# make unique ids (write to file)
transition_unique = pcr.ordinal(pcr.uniqueid(transition_strahler))
# derive upstream catchment areas (write to file)
subcatch = pcr.nominal(pcr.subcatchment(ldd, transition_unique))
# mask out areas outside basin
if basin is not None:
subcatch = pcr.ifthen(basin, subcatch)
if assign_edge:
# fill unclassified areas (in pcraster equal to zero) with a unique id, above the maximum id assigned so far
unique_edge = pcr.clump(pcr.ifthen(subcatch==0, pcr.ordinal(0)))
subcatch = pcr.ifthenelse(subcatch==0, pcr.nominal(pcr.mapmaximum(pcr.scalar(subcatch)) + pcr.scalar(unique_edge)), pcr.nominal(subcatch))
elif assign_existing:
# unaccounted areas are added to largest nearest draining basin
if up_area is None:
up_area = pcr.ifthen(pcr.boolean(pcr.cover(stream_ge, 0)), pcr.accuflux(ldd, 1))
riverid = pcr.ifthen(pcr.boolean(pcr.cover(stream_ge, 0)), subcatch)
friction = 1./pcr.scalar(pcr.spreadzone(pcr.cover(pcr.ordinal(up_area), 0), 0, 0)) # *(pcr.scalar(ldd)*0+1)
delta = pcr.ifthen(pcr.scalar(ldd)>=0, pcr.ifthen(pcr.cover(subcatch, 0)==0, pcr.spreadzone(pcr.cover(riverid, 0), 0, friction)))
subcatch = pcr.ifthenelse(pcr.boolean(pcr.cover(subcatch, 0)),
subcatch,
delta)
# finally, only keep basins with minimum and maximum river order flowing through them
strahler_subcatch = pcr.areamaximum(stream, subcatch)
subcatch = pcr.ifthen(pcr.ordinal(strahler_subcatch) >= min_strahler, pcr.ifthen(pcr.ordinal(strahler_subcatch) <= max_strahler, subcatch))
return stream_ge, pcr.ordinal(subcatch)
def evaluateAllBaseflowResults(self,globalCloneMapFileName,\
catchmentClassFileName,\
lddMapFileName,\
cellAreaMapFileName,\
pcrglobwb_output,\
analysisOutputDir="",\
tmpDir = None):
# temporary directory
if tmpDir == None: tmpDir = self.tmpDir+"/edwin_iwmi_"
# output directory for all analyses for all stations
analysisOutputDir = str(analysisOutputDir)
self.chartOutputDir = analysisOutputDir+"/chart/"
self.tableOutputDir = analysisOutputDir+"/table/"
#
if analysisOutputDir == "": self.chartOutputDir = "chart/"
if analysisOutputDir == "": self.tableOutputDir = "table/"
#
# make the chart and table directories:
os.system('rm -r '+self.chartOutputDir+"*")
os.system('rm -r '+self.tableOutputDir+"*")
os.makedirs(self.chartOutputDir)
os.makedirs(self.tableOutputDir)
# cloneMap for all pcraster operations
pcr.setclone(globalCloneMapFileName)
cloneMap = pcr.boolean(1)
lddMap = pcr.lddrepair(pcr.readmap(lddMapFileName))
cellArea = pcr.scalar(pcr.readmap(cellAreaMapFileName))
# The landMaskClass map contains the nominal classes for all landmask regions.
landMaskClass = pcr.nominal(cloneMap) # default: if catchmentClassFileName is not given
if catchmentClassFileName != None:
landMaskClass = pcr.nominal(pcr.readmap(catchmentClassFileName))
for id in self.list_of_grdc_ids:
logger.info("Evaluating simulated annual baseflow time series to IWMI baseflow time series at "+str(self.attributeGRDC["id_from_grdc"][str(id)])+".")
# evaluate model results to GRDC data
self.evaluateBaseflowResult(str(id),pcrglobwb_output,catchmentClassFileName,tmpDir)
# write the summary to a table
summary_file = analysisOutputDir+"baseflow_summary.txt"
#
logger.info("Writing the summary for all stations to the file: "+str(summary_file)+".")
#
# prepare the file:
summary_file_handle = open(summary_file,"w")
#
# write the header
summary_file_handle.write( ";".join(self.grdc_dict_keys)+"\n")
#
# write the content
for id in self.list_of_grdc_ids:
rowLine = ""
for key in self.grdc_dict_keys: rowLine += str(self.attributeGRDC[key][str(id)]) + ";"
rowLine = rowLine[0:-1] + "\n"
summary_file_handle.write(rowLine)
summary_file_handle.close()