def readgridV6(H, **kwargs):
"""
Accepts a header object as input, and selects appropriate readgrid function
to use for reading in data from the flexpart binary Fortran files.
See the :func:`read_grid` for more information on keyword arguments
This is the 'V6' version of the function.
"""
# set up the return dictionary (FLEXDATA updates fd, fd is returned)
FLEXDATA = {}
fd = reflexible.conv2netcdf4.Structure()
# OPS is the options Structure, sets defaults, then update w/ kwargs
fd.options = OPS = reflexible.conv2netcdf4.Structure()
OPS.unit = 'time'
OPS.nspec_ret = 0
OPS.pspec_ret = 0
OPS.age_ret = 0
OPS.time_ret = 0
OPS.scaledepo = 1.0
OPS.scaleconc = 1.0
OPS.decayconstant = 9e6
OPS.date = None
OPS.calcfoot = False
OPS.verbose = False
OPS.BinaryFile = False
# add keyword overrides and options to header
OPS.update(kwargs)
# What direction is the run?
unit = OPS.unit
if H['loutstep'] > 0:
forward = True
if unit == 'time':
# default forward unit
unit = 'conc'
else:
forward = False
# What species to return?
nspec_ret = OPS.nspec_ret
if isinstance(nspec_ret, int):
nspec_ret = [nspec_ret]
assert iter(nspec_ret), "nspec_ret must be iterable."
# get times to return
get_dates = None
if OPS.time_ret is not None:
get_dates = []
time_ret = OPS.time_ret
if isinstance(time_ret, int) == True:
time_ret = [time_ret]
if time_ret[0] < 0:
if forward == False:
# get all dates for calculating footprint.
time_ret = np.arange(len(H.available_dates))
else:
raise ValueError(
"Must enter a positive time_ret for forward runs")
for t in time_ret:
get_dates.append(H.available_dates[t])
# define what dates to extract if user has explicitly defined a 'date'
if OPS.date is not None:
date = OPS.date
if time_ret is not None:
Warning("overwriting time_ret variable, date was requested")
get_dates = []
if not isinstance(date, list):
date = date.strip().split(',')
for d in date:
try:
get_dates.append(H.available_dates[H.available_dates.index(d)])
time_ret = None
except:
_shout("Cannot find date: %s in H['available_dates']\n" % d)
if get_dates is None:
raise ValueError("Must provide either time_ret or date value.")
else:
# assign grid dates for indexing fd
fd.grid_dates = get_dates[:]
print('getting grid for: ', get_dates)
# Some pre-definitions
fail = 0
# set filename prefix
prefix = ['grid_conc_', 'grid_pptv_',
'grid_time_', 'footprint_', 'footprint_total',
'grid_conc_nest_', 'grid_pptv_nest_',
'grid_time_nest_', 'footprint_nest_', 'footprint_total_nest'
]
units = ['conc', 'pptv', 'time', 'footprint', 'footprint_total']
unit_i = units.index(unit)
# Determine what module to read, try to use FortFlex, then dumpgrid, lastly pure Python
# import the FortFlex / Fortran module
try:
from .FortFlex import readgrid_v6 as readgrid
from .FortFlex import sumgrid
useFortFlex = True
OPS.useFortFlex = useFortFlex
print('using FortFlex VERSION 6')
except:
# get the original module (no memory allocation)
useFortFlex = False
raise Warning('Cannot import FortFlex trying to use BinaryFile')
if not useFortFlex:
readgrid = _readgridBF
OPS.BinaryFile = True
# cheat: use key2var function to get values from header dict, H
# need to change this to using H.xxxxx
# headervars = ['nested','nspec','numxgrid','numygrid','numzgrid','nageclass',\
# 'dates','pathname','decayconstant','numpoint','numpointspec',
# 'area','Heightnn','lage']
# for k in headervars:
# key2var(H,k)
# reserve output fields
print(H.numxgrid, H.numygrid, H.numzgrid, OPS.nspec_ret, OPS.pspec_ret, OPS.age_ret, len(get_dates), H.numpoint)
# -------------------------------------------------
# if forward:
# numpointspec = 1
# else:
# numpointspec = numpoint
# numpointspec = H['numpointspec']
# if unit_i == 4:
# grid=np.empty((numxgrid,numygrid,1,nspec_ret,pspec_ret,age_ret,len(get_dates)))
# else:
# grid=np.empty((numxgrid,numygrid,numzgrid,nspec_ret,pspec_ret,age_ret,len(get_dates)))
# zplot=np.empty((numxgrid,numygrid,numzgrid,numpointspec))
# --------------------------------------------------
# Loop over all times, given in field H['available_dates']
# --------------------------------------------------
for date_i in range(len(get_dates)):
datestring = get_dates[date_i]
print(datestring)
for s in nspec_ret: # range(OPS.nspec_ret,OPS.nspec_ret+1):
FLEXDATA[(s, datestring)] = fdc = reflexible.conv2netcdf4.FDC()
# spec_fid = '_'+str(s+1).zfill(3)
if unit_i != 4:
filename = os.path.join(H['pathname'],
prefix[(unit_i) + (H.nested * 5)] + datestring)
H.zdims = H.numzgrid
else:
# grid total footprint
print("Total footprint")
filename = os.path.join(H['pathname'],
prefix[(unit_i) + (H.nested * 5)])
H.zdims = 1
if os.path.exists(filename):
H.filename = filename
# print('reading: ' + filename)
if OPS.verbose:
print('with values:')
inputvars = ['filename', 'numxgrid', 'numygrid',
'zdims', 'numpoint', 'nageclass',
'scaledepo', 'scaleconc',
'decayconstant', 'numpointspec']
for v in inputvars:
print(v, " ==> ", H[v])
if OPS.BinaryFile:
# print('Using BinaryFile')
gridT, wetgrid, drygrid, itime = _readgridBF(H, filename)
else:
gridT, wetgrid, drygrid, itime = readgrid(
filename, H.numxgrid, H.numygrid, H.zdims,
H.numpointspec, H.nageclass, OPS.scaledepo,
OPS.scaleconc, H.decayconstant)
# XXX zplot is the name below. needs some more name consistency
zplot = gridT
if OPS.calcfoot:
zplot = sumgrid(zplot, gridT,
H.area, H.Heightnn)
# get the total column and prep the grid
if H.direction == 'forward':
# not trying to do anything here... must be done
# after retrieving the grid
# D = get_slabs(H,np.squeeze(zplot))
# rel_i = H.available_dates.index(datestring)
D = zplot
rel_i = 'k'
else:
D = zplot
rel_i = 'k'
# NOTE:
# If you're changing things here, you might want to change
# them in fill_backward as well, yes I know... something is
# poorly designed ;(
fdc.grid = D # zplot
fdc.itime = itime
fdc.timestamp = datetime.datetime.strptime(
datestring, '%Y%m%d%H%M%S')
fdc.species = H['species'][s]
fdc.gridfile = filename
fdc.rel_i = rel_i
fdc.spec_i = s
else:
_shout('***ERROR: file %s not found! \n' % filename)
fail = 1
fd.set_with_dict(FLEXDATA)
try:
# just for testing, set the first available grid as a shortcut
# this will be removed.
qind = (0, fd.grid_dates[0])
fd.grid = fd[qind][fd[qind].keys()[0]].grid
except:
pass
return fd
def _readgrid_noFF(H, **kwargs):
""" accepts a header dictionary as input, returns dictionary of Grid values
%===========================================
%
%-------------------------------------------
% input
% - H: required header dictionary
%
% optional (most is obtained from header dict)
% - date: which yyyymmddhhmmss from dates
% - unit: 'conc', 'pptv', ['time'], 'footprint'
% - nspec_ret: numspecies
% - pspec_ret:
% - age_ret:
% - time_ret:
% - nested: nested = True
%
%
% output
% - grid dictionary object
% - fail indicator (-1=fail, 0=success)
%-------------------------------------------
% FLEXPART python import routines
%-------------------------------------------
% last changes: JFB, 10.10.2008
%===========================================
"""
# if os.sys.platform != 'win32':
# try:
# from FortFlex import readgrid, sumgrid
# useFortFlex = 1
# print('using FortFlex')
# except:
# useFortFlex = 0
# print('Cannot find FortFlex.so')
useFortFlex = 0
if 'date' in kwargs.keys():
date = kwargs['date']
# else: date = H['ibtime']
else:
date = None
if 'unit' in kwargs.keys():
unitname = kwargs['unit']
else:
unitname = 'time'
units = ['conc', 'pptv', 'time', 'footprint']
unit = units.index(unitname)
if 'nspec_ret' in kwargs.keys():
nspec_ret = kwargs['nspec_ret']
else:
nspec_ret = 1
if 'pspec_ret' in kwargs.keys():
pspec_ret = kwargs['ppsec_ret']
else:
pspec_ret = 1
if 'age_ret' in kwargs.keys():
age_ret = kwargs['age_ret']
else:
age_ret = 1
if 'nested' in kwargs.keys():
nested = kwargs['nested']
else:
nested = False
if 'time_ret' in kwargs.keys():
time_ret = kwargs['time_ret']
else:
time_ret = range(len(H['available_dates']))
if 'scaledepo' in kwargs.keys():
scaledepo = kwargs['scaledepo']
else:
scaledepo = 1.0
if 'scaleconc' in kwargs.keys():
scaleconc = kwargs['scaleconc']
else:
scaleconc = 1.0
if 'decaycons' in kwargs.keys():
decaycons = kwargs['decaycons']
else:
decaycons = 99999999990
fail = -1
# set filenames
prefix = ['grid_conc_', 'grid_pptv_',
'grid_time_', 'footprint_total',
'grid_conc_nest_', 'grid_pptv_nest_',
'grid_time_nest_', 'footprint_total_nest']
# local functions for reading binary data and creating grid dump
# skip = lambda n=8 : f.read(n)
# getbin = lambda fmt,n=1 : struct.unpack(fmt*n,f.read(struct.calcsize(fmt)))[0]
# Utility functions
skip = lambda n=8: f2.seek(n, 1)
getbin = lambda dtype, n=1: f2.read(dtype, (n,))
def getdump(n, fmt='f'):
""" function to get the dump values for the sparse format """
# print(n)
skip()
# Dfmt=[fmt]*n
# a=[struct.unpack(ft,f.read(struct.calcsize(ft))) for ft in Dfmt]
a = f2.read(fmt, n)
# dumplist=[a[j][0] for j in range(len(a))]
# dumplist=[a[j] for j in range(len(a))]
return a # dumplist
def key2var(D, key):
cmd = "global %s; %s = D['%s'];" % (key, key, key)
exec(cmd)
def dumpgrid(dmp_i, cnt_r, dmp_r, grd, k, nage):
""" function to dump sparse elements into grid """
ii = 0
fact = 1
for ir in range(cnt_r):
if dmp_r[ir] * fact > 0:
n = dmp_i[ii]
ii = ii + 1
fact = fact * -1.
else:
n = n + 1 # XXX n is actually set before this?
kz = n / (numxgrid * numygrid)
jy = (n - kz * numxgrid * numygrid) / numxgrid
ix = n - numxgrid * numygrid * kz - numxgrid * jy
# print("n ==> ix,jy,kz,k,nage")
# print("%s ==> %s,%s,%s,%s,%s") % (n,ix,jy,kz,k,nage)
# print(grd.shape)
# print(grd[0,0,0,0,0])
grd[ix, jy, kz - 1, k, nage] = abs(dmp_r[ir])
return grd # flipud(grd.transpose())
G = {}
# get values from header file
H['nageclass'] = H['numageclasses']
headervars = ['nested', 'nspec', 'numxgrid', 'numygrid', 'numzgrid',
'nageclass', 'available_dates', 'pathname', 'decayconstant',
'numpoint', 'Area', 'Heightnn']
for k in headervars:
key2var(H, k)
# create zero arrays for datagrid and zplot
datagrid = np.zeros((numxgrid, numygrid, numzgrid, numpoint),
dtype=np.float32)
zplot = np.empty((numxgrid, numygrid, numzgrid, numpoint, nageclass))
# --------------------------------------------------
# Loop over all times, given in field H['dates']
# --------------------------------------------------
for ks in range(nspec_ret, nspec_ret + 1):
# print('processing: ' + str(H['dates'][date_i]) + ' ' + str(ks))
# print('processing: ' + str(date) + ' ' + str(ks))
specs = '_' + str(ks).zfill(3)
fpmax = -999.
if date is None and time_ret is None:
get_dates = [available_dates[0]]
elif time_ret is None:
get_dates = []
date = date.strip().split(',')
for d in date:
try:
get_dates.append(available_dates.index(d))
except:
shout("Cannot find date: %s in H['dates']\n" % d)
else:
get_dates = available_dates
print('getting grid for: ', get_dates)
for date_i in range(len(get_dates)):
if unit != 4:
datestring = H['available_dates'][date_i]
# datestring = date
filename = os.path.join(H['pathname'],
prefix[(unit) + (nested * 4)] + datestring + specs)
else:
filename = os.path.join(H['pathname'],
prefix[(unit) + (nested * 4)])
# print('reading: ' + filename)
if os.path.exists(filename):
# print(nspec,numxgrid,numygrid,numzgrid,nageclass,scaledepo,scaleconc,decaycons)
# print(ks)
# print(date)
if useFortFlex == 1:
# print('Using FortFLEX')
###########################################################
# FORTRAN WRAPPER CODE - only works on linux
# #
# USAGE: grid = readgrid(filegrid,numxgrid,numygrid,numzgrid,\
# nspec,nageclass,scaleconc,decayconstant)
# #
# zplot = sumgrid(zplot, grid, area, heightnn,
# [numxgrid,numygrid,numzgrid,numpoint,nageclass])
# #
# #
# NOTE: numpoint = number of releases, ageclass always 1 for backward
# #
# RETURN: grid(numxgrid,numygrid,numzgrid,numpoint,nageclass)
###########################################################
concgrid = readgrid(filename, numxgrid, numygrid, numzgrid,
numpoint, nageclass,
scaleconc, decayconstant)
# contribution[:,:,:] = concgrid[:,:,:,:,0]
print(np.min(concgrid))
print(np.max(concgrid))
# altitude = 50000
zplot = sumgrid(zplot, concgrid,
H.area, H.Heightnn)
else:
dat_cnt = 0
nage = 0
# read data:
# datagrid=np.zeros((numxgrid,numygrid,numzgrid[nspec-1],
# nspec,nageclass),np.float)
datagrid = np.zeros(
(numxgrid, numygrid, numzgrid, 1, 1), np.float)
# f = open(filename, 'rb')
# print(filename)
f2 = reflexible.conv2netcdf4.BinaryFile(filename, order='fortran')
skip(4)
G['itime'] = getbin('i')
print(H['available_dates'][date_i])
# Read Wet Depostion
skip()
cnt_i = getbin('i')
dmp_i = getdump(cnt_i, 'i')
skip()
cnt_r = getbin('i')
dmp_r = getdump(cnt_r)
# wet=dumpgrid(dmp_i, cnt_r, dmp_r, datagrid, ks-1, nage)
# Read Dry Deposition
skip()
cnt_i = getbin('i')
dmp_i = getdump(cnt_i, 'i')
skip()
cnt_r = getbin('i')
dmp_r = getdump(cnt_r)
# dry=dumpgrid(dmp_i, cnt_r, dmp_r, datagrid, ks-1, nage)
# Read Concentrations
skip()
cnt_i = getbin('i')
dmp_i = getdump(cnt_i, 'i')
skip()
cnt_r = getbin('i')
dmp_r = getdump(cnt_r)
# print(dmp_i, cnt_r, dmp_r, datagrid, ks-1, nage)
concgrid = dumpgrid(dmp_i, cnt_r, dmp_r, datagrid,
ks - 1, nage)
# G[H['ibtime']].append(concgrid) G[H['ibtime']] = concgrid
f2.close()
fail = 0
else:
print("\n\n INPUT ERROR: Could not find file: %s" % filename)
raise IOError('No file: %s' % filename)
if useFortFlex == 1:
G = zplot
return G
def readgridV6(H, **kwargs):
"""
Accepts a header object as input, and selects appropriate readgrid function
to use for reading in data from the flexpart binary Fortran files.
See the :func:`read_grid` for more information on keyword arguments
This is the 'V6' version of the function.
"""
# set up the return dictionary (FLEXDATA updates fd, fd is returned)
FLEXDATA = {}
fd = reflexible.conv2netcdf4.Structure()
# OPS is the options Structure, sets defaults, then update w/ kwargs
fd.options = OPS = reflexible.conv2netcdf4.Structure()
OPS.unit = 'time'
OPS.nspec_ret = 0
OPS.pspec_ret = 0
OPS.age_ret = 0
OPS.time_ret = 0
OPS.scaledepo = 1.0
OPS.scaleconc = 1.0
OPS.decayconstant = 9e6
OPS.date = None
OPS.calcfoot = False
OPS.verbose = False
OPS.BinaryFile = False
# add keyword overrides and options to header
OPS.update(kwargs)
# What direction is the run?
unit = OPS.unit
if H['loutstep'] > 0:
forward = True
if unit == 'time':
# default forward unit
unit = 'conc'
else:
forward = False
# What species to return?
nspec_ret = OPS.nspec_ret
if isinstance(nspec_ret, int):
nspec_ret = [nspec_ret]
assert iter(nspec_ret), "nspec_ret must be iterable."
# get times to return
get_dates = None
if OPS.time_ret is not None:
get_dates = []
time_ret = OPS.time_ret
if isinstance(time_ret, int) == True:
time_ret = [time_ret]
if time_ret[0] < 0:
if forward == False:
# get all dates for calculating footprint.
time_ret = np.arange(len(H.available_dates))
else:
raise ValueError(
"Must enter a positive time_ret for forward runs")
for t in time_ret:
get_dates.append(H.available_dates[t])
# define what dates to extract if user has explicitly defined a 'date'
if OPS.date is not None:
date = OPS.date
if time_ret is not None:
Warning("overwriting time_ret variable, date was requested")
get_dates = []
if not isinstance(date, list):
date = date.strip().split(',')
for d in date:
try:
get_dates.append(H.available_dates[H.available_dates.index(d)])
time_ret = None
except:
_shout("Cannot find date: %s in H['available_dates']\n" % d)
if get_dates is None:
raise ValueError("Must provide either time_ret or date value.")
else:
# assign grid dates for indexing fd
fd.grid_dates = get_dates[:]
print('getting grid for: ', get_dates)
# Some pre-definitions
fail = 0
# set filename prefix
prefix = [
'grid_conc_', 'grid_pptv_', 'grid_time_', 'footprint_',
'footprint_total', 'grid_conc_nest_', 'grid_pptv_nest_',
'grid_time_nest_', 'footprint_nest_', 'footprint_total_nest'
]
units = ['conc', 'pptv', 'time', 'footprint', 'footprint_total']
unit_i = units.index(unit)
# Determine what module to read, try to use FortFlex, then dumpgrid, lastly pure Python
# import the FortFlex / Fortran module
try:
from .FortFlex import readgrid_v6 as readgrid
from .FortFlex import sumgrid
useFortFlex = True
OPS.useFortFlex = useFortFlex
print('using FortFlex VERSION 6')
except:
# get the original module (no memory allocation)
useFortFlex = False
raise Warning('Cannot import FortFlex trying to use BinaryFile')
if not useFortFlex:
readgrid = _readgridBF
OPS.BinaryFile = True
# cheat: use key2var function to get values from header dict, H
# need to change this to using H.xxxxx
# headervars = ['nested','nspec','numxgrid','numygrid','numzgrid','nageclass',\
# 'dates','pathname','decayconstant','numpoint','numpointspec',
# 'area','Heightnn','lage']
# for k in headervars:
# key2var(H,k)
# reserve output fields
print(H.numxgrid, H.numygrid, H.numzgrid, OPS.nspec_ret, OPS.pspec_ret,
OPS.age_ret, len(get_dates), H.numpoint)
# -------------------------------------------------
# if forward:
# numpointspec = 1
# else:
# numpointspec = numpoint
# numpointspec = H['numpointspec']
# if unit_i == 4:
# grid=np.empty((numxgrid,numygrid,1,nspec_ret,pspec_ret,age_ret,len(get_dates)))
# else:
# grid=np.empty((numxgrid,numygrid,numzgrid,nspec_ret,pspec_ret,age_ret,len(get_dates)))
# zplot=np.empty((numxgrid,numygrid,numzgrid,numpointspec))
# --------------------------------------------------
# Loop over all times, given in field H['available_dates']
# --------------------------------------------------
for date_i in range(len(get_dates)):
datestring = get_dates[date_i]
print(datestring)
for s in nspec_ret: # range(OPS.nspec_ret,OPS.nspec_ret+1):
FLEXDATA[(s, datestring)] = fdc = reflexible.conv2netcdf4.FDC()
# spec_fid = '_'+str(s+1).zfill(3)
if unit_i != 4:
filename = os.path.join(
H['pathname'],
prefix[(unit_i) + (H.nested * 5)] + datestring)
H.zdims = H.numzgrid
else:
# grid total footprint
print("Total footprint")
filename = os.path.join(H['pathname'],
prefix[(unit_i) + (H.nested * 5)])
H.zdims = 1
if os.path.exists(filename):
H.filename = filename
# print('reading: ' + filename)
if OPS.verbose:
print('with values:')
inputvars = [
'filename', 'numxgrid', 'numygrid', 'zdims',
'numpoint', 'nageclass', 'scaledepo', 'scaleconc',
'decayconstant', 'numpointspec'
]
for v in inputvars:
print(v, " ==> ", H[v])
if OPS.BinaryFile:
# print('Using BinaryFile')
gridT, wetgrid, drygrid, itime = _readgridBF(H, filename)
else:
gridT, wetgrid, drygrid, itime = readgrid(
filename, H.numxgrid, H.numygrid, H.zdims,
H.numpointspec, H.nageclass, OPS.scaledepo,
OPS.scaleconc, H.decayconstant)
# XXX zplot is the name below. needs some more name consistency
zplot = gridT
if OPS.calcfoot:
zplot = sumgrid(zplot, gridT, H.area, H.Heightnn)
# get the total column and prep the grid
if H.direction == 'forward':
# not trying to do anything here... must be done
# after retrieving the grid
# D = get_slabs(H,np.squeeze(zplot))
# rel_i = H.available_dates.index(datestring)
D = zplot
rel_i = 'k'
else:
D = zplot
rel_i = 'k'
# NOTE:
# If you're changing things here, you might want to change
# them in fill_backward as well, yes I know... something is
# poorly designed ;(
fdc.grid = D # zplot
fdc.itime = itime
fdc.timestamp = datetime.datetime.strptime(
datestring, '%Y%m%d%H%M%S')
fdc.species = H['species'][s]
fdc.gridfile = filename
fdc.rel_i = rel_i
fdc.spec_i = s
else:
_shout('***ERROR: file %s not found! \n' % filename)
fail = 1
fd.set_with_dict(FLEXDATA)
try:
# just for testing, set the first available grid as a shortcut
# this will be removed.
qind = (0, fd.grid_dates[0])
fd.grid = fd[qind][fd[qind].keys()[0]].grid
except:
pass
return fd
def readgridV8(H, **kwargs):
"""
Accepts a header object as input, and selects appropriate readgrid function
to use for reading in data from the flexpart binary Fortran files.
See the :func:`read_grid` for more information on keyword arguments
This is the 'V8' version of the function.
"""
# set up the return dictionary (FLEXDATA updates fd, fd is returned)
FLEXDATA = {}
fd = reflexible.conv2netcdf4.Structure()
# OPS is the options Structure, sets defaults, then update w/ kwargs
fd.options = OPS = reflexible.conv2netcdf4.Structure()
OPS.unit = H.unit
OPS.getwet = False
OPS.getdry = False
OPS.nspec_ret = 0
# allows to select an index of npsec when calling readgrid
OPS.npspec_int = False
OPS.pspec_ret = 0
OPS.age_ret = 0
OPS.time_ret = 0
OPS.scaledepo = 1.0
OPS.scaleconc = 1.0
OPS.decayconstant = 9e6
OPS.date = None
OPS.calcfoot = False
OPS.verbose = False
OPS.BinaryFile = False
OPS.version = 'V8'
# add keyword overrides and options to header
OPS.update(kwargs)
# H.update(OPS)
# What direction is the run?
unit = OPS.unit
if H['loutstep'] > 0:
forward = True
if unit == 'time':
# default forward unit
unit = 'conc'
OPS.unit = unit
else:
forward = False
# What species to return?
nspec_ret = OPS.nspec_ret
if isinstance(nspec_ret, int):
nspec_ret = [nspec_ret]
assert iter(nspec_ret), "nspec_ret must be iterable."
# get times to return
get_dates = None
if OPS.time_ret is not None:
get_dates = []
time_ret = OPS.time_ret
if isinstance(time_ret, int) == True:
time_ret = [time_ret]
if time_ret[0] < 0:
# if forward == False:
# get all dates for calculating footprint.
time_ret = np.arange(len(H.available_dates))
# else:
# raise ValueError("Must enter a positive time_ret for forward runs")
for t in time_ret:
get_dates.append(H.available_dates[t])
# define what dates to extract if user has explicitly defined a 'date'
if OPS.date is not None:
date = OPS.date
if time_ret is not None:
Warning("overwriting time_ret variable, date was requested")
get_dates = []
if not isinstance(date, list):
date = date.strip().split(',')
for d in date:
try:
get_dates.append(H.available_dates[H.available_dates.index(d)])
time_ret = None
except:
_shout("Cannot find date: %s in H['available_dates']\n" % d)
if get_dates is None:
raise ValueError("Must provide either time_ret or date value.")
else:
# assign grid dates for indexing fd
fd.grid_dates = get_dates[:]
print 'getting grid for: ', get_dates
# Some pre-definitions
fail = 0
# set filename prefix
prefix = ['grid_conc_', 'grid_pptv_',
'grid_time_', 'footprint_', 'footprint_total',
'grid_conc_nest_', 'grid_pptv_nest_',
'grid_time_nest_', 'footprint_nest_', 'footprint_total_nest'
]
units = ['conc', 'pptv', 'time', 'footprint', 'footprint_total']
unit_i = units.index(unit)
# Determine what module to read, try to use FortFlex, then dumpgrid, lastly pure Python
# import the FortFlex / Fortran module
try:
print('Assumed V8 Flexpart')
from .FortFlex import readgrid, sumgrid
useFortFlex = True
print('Using readgrid from FortFlex')
except:
# get the original module (no memory allocation)
try:
from nilu.pflexpart.FortFlex import readgrid, sumgrid
useFortFlex = True
print('Using old nilu.pflexpart.FortFlex')
# print 'using nilu.pflexpart FortFlex'
except:
useFortFlex = False
print('Cannot load FortFlex, reverting to BinaryFile.')
if not useFortFlex:
readgrid = _readgridBF
OPS.BinaryFile = True
print('Using BinaryFile')
# reserve output fields
print H.numxgrid, H.numygrid, H.numzgrid, OPS.nspec_ret, OPS.pspec_ret, OPS.age_ret, len(get_dates), H.numpoint
# -------------------------------------------------
# add the requests to the fd object to be returned
OPS.unit = unit
#--------------------------------------------------
# Loop over all times, given in field H['available_dates']
#--------------------------------------------------
for date_i in range(len(get_dates)):
datestring = get_dates[date_i]
print datestring
for s in nspec_ret: # range(OPS.nspec_ret,OPS.nspec_ret+1):A
FLEXDATA[(s, datestring)] = fdc = reflexible.conv2netcdf4.FDC()
spec_fid = '_' + str(s + 1).zfill(3)
if unit_i != 4:
filename = os.path.join(
H['pathname'],
prefix[(unit_i) + (H.nested * 5)] + datestring + spec_fid)
H.zdims = H.numzgrid
else:
# grid total footprint
print "Total footprint"
filename = os.path.join(
H['pathname'],
prefix[(unit_i) + (H.nested * 5)] + spec_fid)
H.zdims = 1
if os.path.exists(filename):
H.filename = filename
# print 'reading: ' + filename
if OPS.verbose:
print 'with values:'
inputvars = ['filename', 'numxgrid', 'numygrid',
'zdims', 'numpoint', 'nageclass',
'scaledepo', 'scaleconc',
'decayconstant', 'numpointspec']
for v in inputvars:
print v, " ==> ", H[v]
if OPS.BinaryFile:
print("Reading {0} with BinaryFile".format(filename))
gridT, wetgrid, drygrid, itime = _readgridBF(H, filename)
else:
# Quick fix for Sabine's Ship releases, added nspec_int so that only one
# field of the nspec dimension is actually read
if OPS.npspec_int is not False:
npspec_int = OPS.npspec_int
numpointspec = 1
else:
npspec_int = 0
numpointspec = H.numpointspec
gridT, wetgrid, drygrid, itime = readgrid(
filename, H.numxgrid, H.numygrid, H.zdims,
numpointspec, H.nageclass, OPS.scaledepo,
OPS.scaleconc, H.decayconstant, npspec_int)
if OPS.getwet:
wet = wetgrid
if OPS.getdry:
dry = drygrid
# XXX zplot is the name below. needs some more name consistency
zplot = gridT
if OPS.calcfoot:
zplot = sumgrid(zplot, gridT, H.area, H.Heightnn)
# get the total column and prep the grid
if H.direction == 'forward':
# not trying to do anything here... must be done
# after retrieving the grid
# D = get_slabs(H,np.squeeze(zplot))
rel_i = 0 # H.available_dates.index(datestring)
D = zplot
else:
D = zplot
rel_i = 'k'
# NOTE:
# If you're changing things here, you might want to change
# them in fill_backward as well, yes I know... something is
# poorly designed ;(
fdc.grid = D # zplot
fdc.itime = itime
fdc.timestamp = \
datetime.datetime.strptime(datestring, '%Y%m%d%H%M%S')
fdc.species = H['species'][s]
fdc.gridfile = filename
fdc.rel_i = rel_i
fdc.spec_i = s
if OPS.getwet:
fdc.wet = wet
else:
fdc.wet = None
if OPS.getdry:
fdc.dry = dry
else:
fdc.dry = None
else:
_shout('***ERROR: file %s not found! \n' % filename)
fail = 1
fd.set_with_dict(FLEXDATA) # XXX keys are tuples, is this really intended?
try:
# just for testing, set the first available grid as a shortcut
# this will be removed.
# TODO: this can be removed now?
qind = (nspec_ret[0], fd.grid_dates[0])
fd.grid = fd[qind][fd[qind].keys()[0]].grid
except:
pass
return fd
def _readgrid_noFF(H, **kwargs):
""" accepts a header dictionary as input, returns dictionary of Grid values
%===========================================
%
%-------------------------------------------
% input
% - H: required header dictionary
%
% optional (most is obtained from header dict)
% - date: which yyyymmddhhmmss from dates
% - unit: 'conc', 'pptv', ['time'], 'footprint'
% - nspec_ret: numspecies
% - pspec_ret:
% - age_ret:
% - time_ret:
% - nested: nested = True
%
%
% output
% - grid dictionary object
% - fail indicator (-1=fail, 0=success)
%-------------------------------------------
% FLEXPART python import routines
%-------------------------------------------
% last changes: JFB, 10.10.2008
%===========================================
"""
# if os.sys.platform != 'win32':
# try:
# from FortFlex import readgrid, sumgrid
# useFortFlex = 1
# print('using FortFlex')
# except:
# useFortFlex = 0
# print('Cannot find FortFlex.so')
useFortFlex = 0
if 'date' in kwargs.keys():
date = kwargs['date']
# else: date = H['ibtime']
else:
date = None
if 'unit' in kwargs.keys():
unitname = kwargs['unit']
else:
unitname = 'time'
units = ['conc', 'pptv', 'time', 'footprint']
unit = units.index(unitname)
if 'nspec_ret' in kwargs.keys():
nspec_ret = kwargs['nspec_ret']
else:
nspec_ret = 1
if 'pspec_ret' in kwargs.keys():
pspec_ret = kwargs['ppsec_ret']
else:
pspec_ret = 1
if 'age_ret' in kwargs.keys():
age_ret = kwargs['age_ret']
else:
age_ret = 1
if 'nested' in kwargs.keys():
nested = kwargs['nested']
else:
nested = False
if 'time_ret' in kwargs.keys():
time_ret = kwargs['time_ret']
else:
time_ret = range(len(H['available_dates']))
if 'scaledepo' in kwargs.keys():
scaledepo = kwargs['scaledepo']
else:
scaledepo = 1.0
if 'scaleconc' in kwargs.keys():
scaleconc = kwargs['scaleconc']
else:
scaleconc = 1.0
if 'decaycons' in kwargs.keys():
decaycons = kwargs['decaycons']
else:
decaycons = 99999999990
fail = -1
# set filenames
prefix = [
'grid_conc_', 'grid_pptv_', 'grid_time_', 'footprint_total',
'grid_conc_nest_', 'grid_pptv_nest_', 'grid_time_nest_',
'footprint_total_nest'
]
# local functions for reading binary data and creating grid dump
# skip = lambda n=8 : f.read(n)
# getbin = lambda fmt,n=1 : struct.unpack(fmt*n,f.read(struct.calcsize(fmt)))[0]
# Utility functions
skip = lambda n=8: f2.seek(n, 1)
getbin = lambda dtype, n=1: f2.read(dtype, (n, ))
def getdump(n, fmt='f'):
""" function to get the dump values for the sparse format """
# print(n)
skip()
# Dfmt=[fmt]*n
# a=[struct.unpack(ft,f.read(struct.calcsize(ft))) for ft in Dfmt]
a = f2.read(fmt, n)
# dumplist=[a[j][0] for j in range(len(a))]
# dumplist=[a[j] for j in range(len(a))]
return a # dumplist
def key2var(D, key):
cmd = "global %s; %s = D['%s'];" % (key, key, key)
exec(cmd)
def dumpgrid(dmp_i, cnt_r, dmp_r, grd, k, nage):
""" function to dump sparse elements into grid """
ii = 0
fact = 1
for ir in range(cnt_r):
if dmp_r[ir] * fact > 0:
n = dmp_i[ii]
ii = ii + 1
fact = fact * -1.
else:
n = n + 1 # XXX n is actually set before this?
kz = n / (numxgrid * numygrid)
jy = (n - kz * numxgrid * numygrid) / numxgrid
ix = n - numxgrid * numygrid * kz - numxgrid * jy
# print("n ==> ix,jy,kz,k,nage")
# print("%s ==> %s,%s,%s,%s,%s") % (n,ix,jy,kz,k,nage)
# print(grd.shape)
# print(grd[0,0,0,0,0])
grd[ix, jy, kz - 1, k, nage] = abs(dmp_r[ir])
return grd # flipud(grd.transpose())
G = {}
# get values from header file
H['nageclass'] = H['numageclasses']
headervars = [
'nested', 'nspec', 'numxgrid', 'numygrid', 'numzgrid', 'nageclass',
'available_dates', 'pathname', 'decayconstant', 'numpoint', 'Area',
'Heightnn'
]
for k in headervars:
key2var(H, k)
# create zero arrays for datagrid and zplot
datagrid = np.zeros((numxgrid, numygrid, numzgrid, numpoint),
dtype=np.float32)
zplot = np.empty((numxgrid, numygrid, numzgrid, numpoint, nageclass))
# --------------------------------------------------
# Loop over all times, given in field H['dates']
# --------------------------------------------------
for ks in range(nspec_ret, nspec_ret + 1):
# print('processing: ' + str(H['dates'][date_i]) + ' ' + str(ks))
# print('processing: ' + str(date) + ' ' + str(ks))
specs = '_' + str(ks).zfill(3)
fpmax = -999.
if date is None and time_ret is None:
get_dates = [available_dates[0]]
elif time_ret is None:
get_dates = []
date = date.strip().split(',')
for d in date:
try:
get_dates.append(available_dates.index(d))
except:
shout("Cannot find date: %s in H['dates']\n" % d)
else:
get_dates = available_dates
print('getting grid for: ', get_dates)
for date_i in range(len(get_dates)):
if unit != 4:
datestring = H['available_dates'][date_i]
# datestring = date
filename = os.path.join(
H['pathname'],
prefix[(unit) + (nested * 4)] + datestring + specs)
else:
filename = os.path.join(H['pathname'],
prefix[(unit) + (nested * 4)])
# print('reading: ' + filename)
if os.path.exists(filename):
# print(nspec,numxgrid,numygrid,numzgrid,nageclass,scaledepo,scaleconc,decaycons)
# print(ks)
# print(date)
if useFortFlex == 1:
# print('Using FortFLEX')
###########################################################
# FORTRAN WRAPPER CODE - only works on linux
# #
# USAGE: grid = readgrid(filegrid,numxgrid,numygrid,numzgrid,\
# nspec,nageclass,scaleconc,decayconstant)
# #
# zplot = sumgrid(zplot, grid, area, heightnn,
# [numxgrid,numygrid,numzgrid,numpoint,nageclass])
# #
# #
# NOTE: numpoint = number of releases, ageclass always 1 for backward
# #
# RETURN: grid(numxgrid,numygrid,numzgrid,numpoint,nageclass)
###########################################################
concgrid = readgrid(filename, numxgrid, numygrid, numzgrid,
numpoint, nageclass, scaleconc,
decayconstant)
# contribution[:,:,:] = concgrid[:,:,:,:,0]
print(np.min(concgrid))
print(np.max(concgrid))
# altitude = 50000
zplot = sumgrid(zplot, concgrid, H.area, H.Heightnn)
else:
dat_cnt = 0
nage = 0
# read data:
# datagrid=np.zeros((numxgrid,numygrid,numzgrid[nspec-1],
# nspec,nageclass),np.float)
datagrid = np.zeros((numxgrid, numygrid, numzgrid, 1, 1),
np.float)
# f = open(filename, 'rb')
# print(filename)
f2 = reflexible.conv2netcdf4.BinaryFile(filename,
order='fortran')
skip(4)
G['itime'] = getbin('i')
print(H['available_dates'][date_i])
# Read Wet Depostion
skip()
cnt_i = getbin('i')
dmp_i = getdump(cnt_i, 'i')
skip()
cnt_r = getbin('i')
dmp_r = getdump(cnt_r)
# wet=dumpgrid(dmp_i, cnt_r, dmp_r, datagrid, ks-1, nage)
# Read Dry Deposition
skip()
cnt_i = getbin('i')
dmp_i = getdump(cnt_i, 'i')
skip()
cnt_r = getbin('i')
dmp_r = getdump(cnt_r)
# dry=dumpgrid(dmp_i, cnt_r, dmp_r, datagrid, ks-1, nage)
# Read Concentrations
skip()
cnt_i = getbin('i')
dmp_i = getdump(cnt_i, 'i')
skip()
cnt_r = getbin('i')
dmp_r = getdump(cnt_r)
# print(dmp_i, cnt_r, dmp_r, datagrid, ks-1, nage)
concgrid = dumpgrid(dmp_i, cnt_r, dmp_r, datagrid, ks - 1,
nage)
# G[H['ibtime']].append(concgrid) G[H['ibtime']] = concgrid
f2.close()
fail = 0
else:
print("\n\n INPUT ERROR: Could not find file: %s" % filename)
raise IOError('No file: %s' % filename)
if useFortFlex == 1:
G = zplot
return G
