def scrap(data, axis=0):
originalOrder = data.getOrder(ids=True)
if axis not in ['x', 'y', 'z', 't'] and not isinstance(axis, int):
order = "({})...".format(axis)
else:
order = "{}...".format(axis)
new = data(order=order)
axes = new.getAxisList() # Save for later
new = MV2.array(new.asma()) # lose dims
for i in range(new.shape[0] - 1, -1, -1):
tmp = new[i]
if not isinstance(tmp, (float, numpy.float)) and tmp.mask.all():
a = new[:i]
b = new[i + 1:]
if b.shape[0] == 0:
new = a
else:
new = MV2.concatenate((a, b))
newAxis = []
for v in new.getAxis(0):
newAxis.append(axes[0][int(v)])
ax = cdms2.createAxis(newAxis, id=axes[0].id)
axes[0] = ax
new.setAxisList(axes)
return new(order=originalOrder)
def post(self,fetched,slab,axes,specifications,confined_by,aux,axismap):
''' Post processing retouches the bounds and later will deal with the mask'''
import cdms2 as cdms
fetched=cdms.createVariable(fetched,copy=1)
faxes=fetched.getAxisList()
a=None
for i in range(len(faxes)):
if confined_by[i] is self:
newaxvals=[]
bounds=[]
a=None
sh=list(fetched.shape)
sh[i]=1
for l in self.aux[i]:
try:
tmp=fetched(**{faxes[i].id:(l,l)})
ax=tmp.getAxis(i)
#print ax
newaxvals.append(ax[0])
if ax.getBounds()!=None:
bounds.append(ax.getBounds()[0])
else:
bounds=None
except Exception,err:
#print 'err:',err,'match:',self.match
if self.match==1:
raise Exception,'Error axis value :'+str(l)+' was requested but is not present in slab\n(more missing might exists)'
elif self.match==0:
tmp=MV2.ones(sh,typecode=MV2.float)
tmp=MV2.masked_equal(tmp,1)
if type(l)==type(cdtime.comptime(1999)) or type(l)==type(cdtime.reltime(0,'days since 1999')) or type(l)==type(''):
if type(l)!=type(''):
newaxvals.append(l.torel(faxes[i].units).value)
else:
newaxvals.append(cdtime.s2r(l,faxes[i].units).value)
else:
newaxvals.append(l)
if bounds is not None:
bounds.append([ax[-1]-1.,ax[-1]+1])
else:
tmp=None
if not tmp is None:
if a is None:
a=tmp
elif not tmp is None:
a=MV2.concatenate((a,tmp),i)
if bounds is not None:
newax=cdms.createAxis(numpy.array(newaxvals),bounds=numpy.array(bounds),id=ax.id)
else:
newax=cdms.createAxis(numpy.array(newaxvals),id=ax.id)
for att in faxes[i].attributes.keys():
setattr(newax,att,faxes[i].attributes.get(att))
for j in range(len(fetched.shape)):
if j==i:
a.setAxis(i,newax)
else:
a.setAxis(j,faxes[j])
fetched=a.astype(fetched.dtype.char)
faxes=fetched.getAxisList()
def _get(self):
if 'relative' in self.portrait_types.keys():
d=self.portrait_types['relative']
vals=d[1]
real_value=getattr(self,d[0])
real=self.__get()
setattr(self,d[0],vals[0])
a0=self.__get()
sh=list(a0.shape)
sh.insert(0,1)
a0=MV2.reshape(a0,sh)
for v in vals[1:]:
setattr(self,d[0],v)
tmp=self.__get()
tmp=MV2.reshape(tmp,sh)
a0=MV2.concatenate((a0,tmp))
a0=MV2.sort(a0,0).filled()
real2=real.filled()
a0=MV2.reshape(a0,(a0.shape[0],sh[1]*sh[2]))
real2=MV2.reshape(real2,(sh[1]*sh[2],))
a0=MV2.transpose(a0)
indices=[]
for i in range(len(real2)):
indices.append(MV2.searchsorted(a0[i],real2[i]))
indices=MV2.array(indices)
indices=MV2.reshape(indices,(sh[1],sh[2]))
if not ((real.mask is None) or (real.mask is MV2.nomask)):
indices=MV2.masked_where(real.mask,indices)
a=MV2.masked_equal(a0,1.e20)
a=MV2.count(a,1)
a=MV2.reshape(a,indices.shape)
indices=indices/a*100
setattr(self,d[0],real_value)
indices.setAxisList(real.getAxisList())
## print indices.shape
return indices
else:
return self.__get()
cdutil.setTimeBoundsMonthly(th)
#ref = cdutil.YEAR.climatology(th(time=('1951-1-1','1980-12-31')))
#dep_h = cdutil.YEAR.departures(th,ref=ref)(time=(truestart,'2005-12-31'))
dep_h = cdutil.YEAR(th)(time=(truestart, '2005-12-31'))
tr = cdutil.averager(fr("tas"), axis='xy')
start_r = cmip5.start_time(tr)
stop_r = cmip5.stop_time(tr)
cdutil.setTimeBoundsMonthly(tr)
#dep_r = cdutil.YEAR.departures(tr,ref=ref)(time=(start_r,'2099-12-31'))
dep_r = cdutil.YEAR(tr)(time=(start_r, '2099-12-31'))
try:
BIG[i] = MV.concatenate((dep_h, dep_r))
except:
print rip
print MV.concatenate((dep_h, dep_r)).shape
continue
i += 1
T = np.arange(1900, 2100)
tax = cdms.createAxis(T)
tax.units = 'years since 0001-1-1'
tax.designateTime()
BIG2 = MV.masked_where(np.abs(BIG) > 1.e10, BIG)
modax = cdms.createAxis(np.arange(L))
modax.models = str(overlap.tolist())
temporary[region] = d_sub_aave(time=(start_t,
end_t))
continue
else:
# n-1 year 7/1~12/31
part1 = copy.copy(temporary[region])
# n year 1/1~6/30
part2 = d_sub_aave(time=(
cdtime.comptime(year),
cdtime.comptime(year, 6, 30, 23, 59, 59)))
start_t = cdtime.comptime(year, 7, 1)
end_t = cdtime.comptime(
year, 12, 31, 23, 59, 59)
temporary[region] = d_sub_aave(time=(start_t,
end_t))
d_sub_aave = MV2.concatenate([part1, part2],
axis=0)
if debug:
print(
'debug: ', region, year,
d_sub_aave.getTime().asComponentTime())
# get pentad time series
list_d_sub_aave_chunks = list(
divide_chunks_advanced(d_sub_aave, n, debug=debug))
pentad_time_series = []
for d_sub_aave_chunk in list_d_sub_aave_chunks:
# ignore when chunk length is shorter than defined
if d_sub_aave_chunk.shape[0] >= n:
ave_chunk = MV2.average(d_sub_aave_chunk,
axis=0)
pentad_time_series.append(float(ave_chunk))
idi = "i"
idj = "j"
lat_units = 'degrees_north'
lon_units = 'degrees_east'
iaxis = TransientVirtualAxis(idi,ni)
jaxis = TransientVirtualAxis(idj,nj)
lataxis = TransientAxis2D(lat, axes=(iaxis, jaxis),
attributes={'units':lat_units}, id="latitude")
lonaxis = TransientAxis2D(lon, axes=(iaxis, jaxis),
attributes={'units':lon_units}, id="longitude")
curvegrid = TransientGenericGrid(lataxis, lonaxis, tempmask=None)
attributs = None ; vid = None
if hasattr(v,'attributes') : attributs= v.attributes
if hasattr(v,'id') : vid= v.id
axis0 = v.getAxis(0)
return cdms2.createVariable(v, axes=[axis0,iaxis,jaxis], grid=curvegrid, \
attributes=attributs, id=v.id)
lat = MV2.array([[-20,-10,0,-15,-5]],'f')
lon = MV2.array([[0,10,20,50,60]],'f')
data1 = MV2.array([[[2,3,1,6,2]]],'f')
data2 = MV2.array([[[2,3,1,6,2]]],'f')
data1 = CurveGrid(data1, lat, lon)
data2 = CurveGrid(data2, lat, lon)
result = MV2.concatenate([data1,data2],axis=0)
def read(self, cfg=None):
""" Lecture des fichiers NetCDF de NAR SST """
import cdms2, sys, os, glob
import numpy, MV2
import cdtime
from vacumm.misc.axes import create_lon
from vacumm.misc.grid import create_grid, set_grid
from vacumm.misc.atime import create_time
from vacumm.misc.phys.units import kel2degc
if self.ctdeb >= cdtime.comptime(2012, 01, 01, 0, 0, 0):
# -- Creation d'un objet cdms nomme self.data et d'un tableau cumt pour les dates extraites des noms de fichiers
self.data = () # Initialise un tuple
# =============== ATTENTION ====================
# Initialiser self.data pour ne pas dupliquer en memoire !!!!!!!!!
# ============================================
# -- Methode amelioree
# Cree une liste
files = []
# Cree la liste des fichiers correspondants a la periode consideree
ctest = self.ctdeb
while ctest <= self.ctfin:
for iH in numpy.arange(24):
flnme_only = "%04d%02d%02d%02d*.nc" % (ctest.year, ctest.month, ctest.day, iH)
files.extend(glob.glob(os.path.join(self.OBSDIR, flnme_only)))
ctest = ctest.add(1, cdtime.Days)
# --
if cfg is None:
config = ConfigParser.RawConfigParser()
config.read(os.path.join(self.SCRIPT_DIR, "config.cfg"))
lomin = float(config.get("Domain", "lomin"))
lomax = float(config.get("Domain", "lomax"))
lamin = float(config.get("Domain", "lamin"))
lamax = float(config.get("Domain", "lamax"))
else:
lomin = cfg["Domain"]["lomin"]
lomax = cfg["Domain"]["lomax"]
lamin = cfg["Domain"]["lamin"]
lamax = cfg["Domain"]["lamax"]
if cfg is None:
try:
timerange = config.get("Seviri SST", "timerange")
# timerange = 'midnight' pour donnees a minuit seulement
# timerange = 'all' pour donnees a minuit seulement
except ConfigParser.NoOptionError:
# print 'No Time Range'
timerange = "all" # Par defaut, lecture de toutes les heures
else:
timerange = cfg["Seviri SST"]["timerange"]
if files == []:
print "No data file to read ..."
else:
for ifile, filename in enumerate(files):
# -- Lecture du fichier filename
f = cdms2.open(filename)
temp = f("sea_surface_temperature", lon=(lomin, lomax), lat=(lamin, lamax))
f.close()
# -- Transfert de temp dans l'objet cdat self.data (concatenation)
self.data += (temp,)
# -- Creation de l'axe temporel
# taxis = create_time(cumt)
# -- MV2.concatenate pour concatener les informations dans self.data (entre autre construit l'axe temporel)
self.data = MV2.concatenate(self.data)
# -- Informations sur le dataset
# self.data.name = "SEVIRI_SST"
self.data.units = "degree_Celsius"
self.data.standard_name = "satellite_sea_surface_temperature"
self.data.long_name = "Satellite Sea Surface Temperature - SEVIRI"
# -- Change unit
self.data = kel2degc(self.data)
s=f("clt")
cdutil.setTimeBoundsMonthly(s)
print 'Getting JJA, which should be inexistant in data'
try:
cdutil.JJA(s[:5])
raise RuntimeError( "data w/o season did not fail")
except:
pass
## Create a year worth of data w/o JJA
s1 = s[:5]
s2 = s[8:12]
s3 = MV2.concatenate((s1,s2))
t = MV2.concatenate((s1.getTime()[:],s2.getTime()[:]))
t = cdms2.createAxis(t,id='time')
t.units=s.getTime().units
t.designateTime()
s3.setAxis(0,t)
cdutil.setTimeBoundsMonthly(s3)
try:
cdutil.JJA(s3)
raise RuntimeError, "data w/o season did not return None"
except:
pass
try:
cdutil.JJA.departures(s3)
raise RuntimeError, "data w/o season did not return None for dep"
# Deal with plev17 to plev19 conversion
plev19 = np.append(plev17, [500., 100.])
# Add missing upper two values
plev19 = cdm.createAxis(plev19, id='plev')
plev19.designateLevel()
plev19.axis = 'Z'
plev19.long_name = 'pressure'
plev19.positive = 'down'
plev19.realtopology = 'linear'
plev19.standard_name = 'air_pressure'
plev19.units = 'Pa'
# Pad data array with missing values
d2 = np.ma.array(np.ma.ones([d1.shape[0], 2, d1.shape[2], d1.shape[3]]),
mask=True) * 1e20
d = mv.concatenate((d1, d2), axis=1)
del (d1, d2, plev17)
# Cleanup
#%% Initialize and run CMOR
# For more information see https://cmor.llnl.gov/mydoc_cmor3_api/
cmor.setup(inpath='./',
netcdf_file_action=cmor.CMOR_REPLACE_4) #,logfile='cmorLog.txt')
cmor.dataset_json(inputJson)
cmor.load_table(cmorTable)
#cmor.set_cur_dataset_attribute('history',f.history) ; # Force input file attribute as history
axes = [
{
'table_entry': 'time',
'units': time.units, # 'days since 1870-01-01',
ct1 = MV2.TransientVariable([1,1,2,0,1])
ctr = MV2.choose(ct1, [numpy.ma.masked, 10,20,30,40])
if not MV2.allclose(ctr, [10, 10, 20, 100, 10]): markError('choose error 1')
ctx = MV2.TransientVariable([1,2,3,150,4])
cty = -MV2.TransientVariable([1,2,3,150,4])
ctr = MV2.choose(MV2.greater(ctx,100), (ctx, 100))
if not MV2.allclose(ctr, [1,2,3,100,4]): markError('choose error 2')
ctr = MV2.choose(MV2.greater(ctx,100), (ctx, cty))
if not MV2.allclose(ctr, [1,2,3,-150,4]): markError('choose error 3')
## concatenate(arrays, axis=0, axisid=None, axisattributes=None)
## Concatenate the arrays along the given axis. Give the extended axis the id and
## attributes provided - by default, those of the first array.
try:
xcon = MV2.concatenate((ud,vd))
except:
markError('Concatenate error')
## isMaskedVariable(x)
## Is x a masked variable, that is, an instance of AbstractVariable?
im1 = MV2.isMaskedVariable(xones)
im2 = MV2.isMaskedVariable(xmasked)
## outerproduct(a, b)
## outerproduct(a,b) = {a[i]*b[j]}, has shape (len(a),len(b))
xouter = MV2.outerproduct(MV2.arange(16.),MV2.arange(32.))
lat = uf.getLatitude()
lon = uf.getLongitude()
xouter.setAxis(0,lat)
xouter.setAxis(1,lon)
def read(self):
""" Lecture des fichiers NetCDF de NAR SST """
import cdms2,sys,os, glob
import numpy,MV2
import cdtime
from vacumm.misc.axes import create_lon
from vacumm.misc.grid import create_grid, set_grid
from vacumm.misc.atime import create_time
from vacumm.misc.phys.units import kel2degc
# -- Dans le cas d'un NAR SST on lit la grille lon lat dans le fichier grid
# -- Lecture de la grille
znar=self.ZONE_NAR
gridfile="grid_%(znar)s.nc"%vars()
f=cdms2.open(gridfile)
la = f('latitude')
lo = f('longitude')
f.close()
# -- Creation des axes longitude et latitude
lat_axis = create_lon(la,id='latitude')
lon_axis = create_lon(lo,id='longitude')
# -- Creation de la grille
grid = create_grid(lon_axis, lat_axis)
# -- Creation d'un objet cdms nomme self.data et d'un tableau cumt pour les dates extraites des noms de fichiers
self.data = () #Initialise un tuple
# =============== ATTENTION ====================
# Initialiser self.data pour ne pas dupliquer en memoire !!!!!!!!!
# ============================================
#cumt = [] # Initialise un array
# -- Boucle sur les fichiers presents dans le WORKDIR
#url_file_def="%(YYYY)s%(MM)s%(DD)s%(HH)s%(ext)s"%vars()
#self.ctdeb
# -- Ancienne methode
#files = glob.glob(os.path.join(self.WORKDIR, '2*.nc'))
#files.sort()
# --
# -- Methode amelioree
# Cree une liste
files = []
# Cree la liste des fichiers correspondants a la periode consideree
ctest = self.ctdeb
while ctest <= self.ctfin:
flnme_only = '%(#)04d%(##)02d%(###)02d*.nc'%{'#':ctest.year, '##':ctest.month, '###':ctest.day}
files.extend(glob.glob(os.path.join(self.WORKDIR, flnme_only)))
ctest=ctest.add(1,cdtime.Days)
# --
for filename in files:
# -- Lecture du fichier filename
f = cdms2.open(filename)
temp = f('sea_surface_temperature')
# =============== ATTENTION ==================================
# Verifier que temp utilise tout le temps le meme espace memoire ... voir du cote de cdms
# ==========================================================
f.close()
# -- Extraction de la date et heure du nom du fichier
#ty = numpy.int(filename[-15:-11])
#tm = numpy.int(filename[-11:-9])
#tj = numpy.int(filename[-9:-7])
#th = numpy.int(filename[-7:-5])
#tt = cdtime.comptime(ty,tm,tj,th)
#cumt.append(tt)
# -- Transfert de temp dans l'objet cdat self.data (concatenation)
# =============== ATTENTION ====================
# Faire une variable intermediaire qui sera au prealable allouee en memoire pour eviter
# trop de copies en memoire !!!!!!!!!!!!!!!!
# ============================================
self.data += temp,
# -- Creation de l'axe temporel
#taxis = create_time(cumt)
# -- MV2.concatenate pour concatener les informations dans self.data (entre autre construit l'axe temporel)
self.data = MV2.concatenate(self.data)
# -- Attribution de la grille a l'objet self.data
set_grid(self.data, grid, axes=True)
# -- Informations sur le dataset
self.data.name = "NAR_SST"
self.data.units = "degree_Celsius"
self.data.standard_name = "satellite_sea_surface_temperature"
self.data.long_name = "Satellite Sea Surface Temperature - NAR"
# -- Change unit
self.data = kel2degc(self.data)
plev19 = np.append(plev19, plev3)
plev19 = np.append(plev19, plev4)
# Add missing upper two values
plev19[:] = plev19[:] * 100.
plev19 = cdm.createAxis(plev19, id='plev')
plev19.designateLevel()
plev19.axis = 'Z'
plev19.long_name = 'pressure'
plev19.positive = 'down'
plev19.realtopology = 'linear'
plev19.standard_name = 'air_pressure'
plev19.units = 'Pa'
# Pad data array with missing values
# d2 = np.ma.array(np.ma.ones([d1.shape[0],2,d1.shape[2],d1.shape[3]]),mask=True)*1e20
d = mv.concatenate((d1, d2, d3, d4), axis=1)
#del(d1,d2,d3,d4,plev1,plev2,plev3,plev4) ; # Cleanup
#%% Initialize and run CMOR
# For more information see https://cmor.llnl.gov/mydoc_cmor3_api/
cmor.setup(
inpath='./',
netcdf_file_action=cmor.CMOR_REPLACE_4) #,logfile='cmorLog.txt')
cmor.dataset_json(inputJson)
cmor.load_table(cmorTable)
#cmor.set_cur_dataset_attribute('history',f.history) ; # Force input file attribute as history
axes = [
{
'table_entry': 'time',
'units':
def read(self, verbose=False, cfg=None):
""" Lecture des fichiers NetCDF de NAR SST """
import cdms2, sys, os, glob
import numpy, MV2
import cdtime
from vacumm.misc.axes import create_lon, set_order
from vacumm.misc.grid import create_grid, set_grid
from vacumm.misc.atime import create_time
from vacumm.misc.phys.units import kel2degc
import gc
# Get the configuration file information
#cfg = self.get_config()
#print cfg
# -- Creation d'un objet cdms nomme self.data et d'un tableau cumt pour les dates extraites des noms de fichiers
self.data = () #Initialise un tuple
# =============== ATTENTION ====================
# Initialiser self.data pour ne pas dupliquer en memoire !!!!!!!!!
# ============================================
# -- Methode amelioree
# Cree une liste
files = []
# Cree la liste des fichiers correspondants a la periode consideree
if cfg is None:
config = ConfigParser.RawConfigParser()
config.read(os.path.join(self.SCRIPT_DIR, 'config.cfg'))
hr_satellites = config.get('Nar SST', 'hr_satellites')
else:
hr_satellites = cfg['Nar SST']['hr_satellites']
hr_satellites = hr_satellites.split(',')
#hr_satellites = cfg['hr_satellites']
#print hr_satellites
ctest = self.ctdeb
while ctest <= self.ctfin:
for isat, s_name in enumerate(hr_satellites):
flnme_only = '%04d%02d%02d*%s*.nc' % (ctest.year, ctest.month,
ctest.day, s_name)
files.extend(glob.glob(os.path.join(flnme_only)))
ctest = ctest.add(1, cdtime.Days)
# --
if cfg is None:
lomin = float(config.get('Domain', 'lomin'))
lomax = float(config.get('Domain', 'lomax'))
lamin = float(config.get('Domain', 'lamin'))
lamax = float(config.get('Domain', 'lamax'))
else:
lomin = cfg['Domain']['lomin']
lomax = cfg['Domain']['lomax']
lamin = cfg['Domain']['lamin']
lamax = cfg['Domain']['lamax']
#print files
if files == []:
print 'No data file to read ...'
else:
# ---- Lecture et creation de la grille ----
#
# -- Lecture du fichier filename
f = cdms2.open(files[0])
lo = f.getVariable('lon')
la = f.getVariable('lat')
# -- Creation des axes longitude et latitude
# lat_axis = create_lon(la,id='latitude')
# lon_axis = create_lon(lo,id='longitude')
# -- Creation de la grille
grid = create_grid(lo, la)
del lo, la
for ifile, filename in enumerate(files):
# -- Lecture du fichier filename
f = cdms2.open(filename)
temp2 = f('sea_surface_temperature')
set_order(temp2, 'tyx') # pour que averager.py fontionne
# modif J.Gatti : utilisation de l'index de qualite (0:unprocessed 1:cloudy 2:bad 3:suspect 4:acceptable 5:excellent)
temp2.set_fill_value(temp2._FillValue)
conf = f('proximity_confidence')
MV2.putmask(temp2.data, conf.data < 3,
temp2._FillValue) # ne change que data
MV2.putmask(temp2.mask, conf.data < 3,
True) # ne change que mask
#autre methode
#--------------------
#temp2=MV2.masked_where(conf.data<3,temp2) # ne change que mask
#oldmask=temp2.mask
#temp2[:]=temp2.filled() # change data mais met mask a false partout
#temp2.mask=oldmask # remet le bon mask sans lien
del conf
# fin modif J.Gatti : utilisation de l'index de qualite
# -- Attribution de la grille a l'objet self.data
set_grid(temp2, grid, axes=True)
temp = temp2(lon=(lomin, lomax), lat=(lamin, lamax))
if verbose:
# == TEST OCCUPATION MEMOIRE ===
print ctest, 'Avant'
#print psutil.Process(os.getpid()).get_memory_percent()
#print psutil.Process(os.getpid()).get_memory_info()
#print 'CPU percent: ', psutil.cpu_percent(interval=0.1)
#print 'Used phymem: ', psutil.used_phymem()
#print 'Used virtmem: ', psutil.used_virtmem()
del temp2
if verbose:
# == TEST OCCUPATION MEMOIRE ===
print ctest, 'Apres del'
#print psutil.Process(os.getpid()).get_memory_percent()
#print psutil.Process(os.getpid()).get_memory_info()
#print 'CPU percent: ', psutil.cpu_percent(interval=0.1)
#print 'Used phymem: ', psutil.used_phymem()
#print 'Used virtmem: ', psutil.used_virtmem()
# =============== ATTENTION ==================================
# Verifier que temp utilise tout le temps le meme espace memoire ... voir du cote de cdms
# ==========================================================
f.close()
# -- Transfert de temp dans l'objet cdat self.data (concatenation)
# =============== ATTENTION ====================
# Faire une variable intermediaire qui sera au prealable allouee en memoire pour eviter
# trop de copies en memoire !!!!!!!!!!!!!!!!
# ============================================
#self.data += temp,
if ifile == 0:
self.data = temp
else:
self.data = MV2.concatenate((self.data, temp))
if verbose:
# == TEST OCCUPATION MEMOIRE ===
print ctest, 'Avant gccollect'
#print psutil.Process(os.getpid()).get_memory_percent()
#print psutil.Process(os.getpid()).get_memory_info()
#print 'CPU percent: ', psutil.cpu_percent(interval=0.1)
#print 'Used phymem: ', psutil.used_phymem()
#print 'Used virtmem: ', psutil.used_virtmem()
print gc.collect()
gc.collect()
if verbose:
# == TEST OCCUPATION MEMOIRE ===
print ctest, 'Apres gccollect'
#print psutil.Process(os.getpid()).get_memory_percent()
#print psutil.Process(os.getpid()).get_memory_info()
#print 'CPU percent: ', psutil.cpu_percent(interval=0.1)
#print 'Used phymem: ', psutil.used_phymem()
#print 'Used virtmem: ', psutil.used_virtmem()
# -- Creation de l'axe temporel
#taxis = create_time(cumt)
# -- MV2.concatenate pour concatener les informations dans self.data (entre autre construit l'axe temporel)
#self.data = MV2.concatenate(self.data)
# -- Informations sur le dataset
#self.data.name = "NAR_SST"
self.data.units = "degree_Celsius"
self.data.standard_name = "satellite_sea_surface_temperature"
self.data.long_name = "Satellite Sea Surface Temperature - NAR"
# -- Change unit
self.data = kel2degc(self.data)
def cat(var1,var2,axis=0,verbose=False):
'''Concatenate 2 variables along axis.
<var1>,<var2>: Variables to be concatenated, in the order of \
<var1>, <var2>;
<axis>: int, index of axis to be concatenated along.
Return <result>
'''
import MV2 as MV
import numpy
try:
order=var1.getAxisListIndex()
except:
order=numpy.arange(var1.ndim) # if var1 is np.ndarray
var1=MV.array(var1)
var2=MV.array(var2)
try:
attdict=attribute_obj2dict(var1)
hasatt=True
except:
hasatt=False
if not hasattr(var1.getAxis(axis),'units'):
ax=var1.getAxis(axis)
ax.units=''
var1.setAxis(axis,ax)
if not hasattr(var2.getAxis(axis),'units'):
ax=var2.getAxis(axis)
ax.units=''
var2.setAxis(axis,ax)
if verbose:
print('# <cat>: Original order:',order)
if axis!=0:
#----Switch order------
order[axis]=0
order[0]=axis
if verbose:
print('# <cat>: New order:',order)
var1=var1(order=order)
var2=var2(order=order)
result=MV.concatenate((var1,var2))
#result=numpy.concatenate((var1,var2),axis=0)
#NOTE: There seems to be some problems with MV.concatenate() when axis
# is not 0, but can not remember what the problem is. That is why this function
# is written.
# And also some issues regards to the re-ordering and MV.concatenate()
# method defined here. When I concatenated something along the 2nd
# axis and do a MV.std(var,axis=2) (and numpy.std(), an attributeError was raised.
# But other times it works ok. Maybe because of some attributes of my
# variable is gone when putting into MV.std(). No idea why.
# That problem was solved by replacing MV.concatenate() with numpy.concatenate().
# But this will cause the output to be numpy.ndarray rather than MV.transientVariable.
# So be aware that this function may cause some errors if inputs <var1>,<var2>
# are numpy.ndarray.
#-------Switch back----------
result=result(order=order)
else:
result=MV.concatenate((var1,var2))
if hasatt:
result=attribute_dict2obj(attdict,result)
return result
def precip_variability_across_timescale(file, syr, eyr, dfrq, mip, dat, var,
fac, nperseg, noverlap, outdir, cmec):
"""
Regridding -> Anomaly -> Power spectra -> Domain&Frequency average -> Write
"""
psdmfm = {"RESULTS": {}}
f = cdms.open(file)
cal = f[var].getTime().calendar
if "360" in cal:
ldy = 30
else:
ldy = 31
print(dat, cal)
print("syr, eyr:", syr, eyr)
for iyr in range(syr, eyr + 1):
print(iyr)
do = (f(
var,
time=(
str(iyr) + "-1-1 0:0:0",
str(iyr) + "-12-" + str(ldy) + " 23:59:59",
),
) * float(fac))
# Regridding
rgtmp = Regrid2deg(do)
if iyr == syr:
drg = copy.deepcopy(rgtmp)
else:
drg = MV.concatenate((drg, rgtmp))
print(iyr, drg.shape)
f.close()
# Anomaly
if dfrq == "day":
ntd = 1
elif dfrq == "3hr":
ntd = 8
else:
sys.exit("ERROR: dfrq " + dfrq + " is not defined!")
clim, anom = ClimAnom(drg, ntd, syr, eyr)
# Power spectum of total
freqs, ps, rn, sig95 = Powerspectrum(drg, nperseg, noverlap)
# Domain & Frequency average
psdmfm_forced = Avg_PS_DomFrq(ps, freqs, ntd, dat, mip, "forced")
# Write data (nc file)
outfilename = "PS_pr." + str(dfrq) + "_regrid.180x90_" + dat + ".nc"
with cdms.open(
os.path.join(outdir(output_type="diagnostic_results"),
outfilename), "w") as out:
out.write(freqs, id="freqs")
out.write(ps, id="power")
out.write(rn, id="rednoise")
out.write(sig95, id="sig95")
# Power spectum of anomaly
freqs, ps, rn, sig95 = Powerspectrum(anom, nperseg, noverlap)
# Domain & Frequency average
psdmfm_unforced = Avg_PS_DomFrq(ps, freqs, ntd, dat, mip, "unforced")
# Write data (nc file)
outfilename = "PS_pr." + str(
dfrq) + "_regrid.180x90_" + dat + "_unforced.nc"
with cdms.open(
os.path.join(outdir(output_type="diagnostic_results"),
outfilename), "w") as out:
out.write(freqs, id="freqs")
out.write(ps, id="power")
out.write(rn, id="rednoise")
out.write(sig95, id="sig95")
# Write data (json file)
psdmfm["RESULTS"][dat] = {}
psdmfm["RESULTS"][dat]["forced"] = psdmfm_forced
psdmfm["RESULTS"][dat]["unforced"] = psdmfm_unforced
outfilename = ("PS_pr." + str(dfrq) + "_regrid.180x90_area.freq.mean_" +
dat + ".json")
JSON = pcmdi_metrics.io.base.Base(outdir(output_type="metrics_results"),
outfilename)
JSON.write(
psdmfm,
json_structure=[
"model+realization", "variability type", "domain", "frequency"
],
sort_keys=True,
indent=4,
separators=(",", ": "),
)
if cmec:
JSON.write_cmec(indent=4, separators=(",", ": "))
ct1 = MV2.TransientVariable([1, 1, 2, 0, 1])
ctr = MV2.choose(ct1, [numpy.ma.masked, 10, 20, 30, 40])
if not MV2.allclose(ctr, [10, 10, 20, 100, 10]): markError('choose error 1')
ctx = MV2.TransientVariable([1, 2, 3, 150, 4])
cty = -MV2.TransientVariable([1, 2, 3, 150, 4])
ctr = MV2.choose(MV2.greater(ctx, 100), (ctx, 100))
if not MV2.allclose(ctr, [1, 2, 3, 100, 4]): markError('choose error 2')
ctr = MV2.choose(MV2.greater(ctx, 100), (ctx, cty))
if not MV2.allclose(ctr, [1, 2, 3, -150, 4]): markError('choose error 3')
## concatenate(arrays, axis=0, axisid=None, axisattributes=None)
## Concatenate the arrays along the given axis. Give the extended axis the id and
## attributes provided - by default, those of the first array.
try:
xcon = MV2.concatenate((ud, vd))
except:
markError('Concatenate error')
## isMaskedVariable(x)
## Is x a masked variable, that is, an instance of AbstractVariable?
im1 = MV2.isMaskedVariable(xones)
im2 = MV2.isMaskedVariable(xmasked)
## outerproduct(a, b)
## outerproduct(a,b) = {a[i]*b[j]}, has shape (len(a),len(b))
xouter = MV2.outerproduct(MV2.arange(16.), MV2.arange(32.))
lat = uf.getLatitude()
lon = uf.getLongitude()
xouter.setAxis(0, lat)
xouter.setAxis(1, lon)
pth + 'u_2002.nc',
]
for file in files:
f = cdms.open(file)
u = f('u')
if file == files[0]: # First file
sh = list(u.shape) # Create a list with the shape of the data
sh.insert(0, 1) # Insert value 1 in front of the list
accumulation = u
newdim = MV.reshape(u, sh) # Create a new 1D dimension
else:
# add u at the end of accumaltion on dimension 0
accumulation = MV.concatenate((accumulation, u))
tmp = MV.reshape(u, sh) # Create a new 1D dimension
newdim = MV.concatenate(
(newdim, tmp)) # Add u to the newdim over the new dimension
f.close()
print accumulation.shape # All time added over the same dimension
print newdim.shape # Has a new dimension for years
avg = MV.average(accumulation)
std = genutil.statistics.std(newdim)
print avg.shape
print std.shape
def read(self):
""" Lecture des fichiers NetCDF de NAR SST """
import cdms2, sys, os, glob
import numpy, MV2
import cdtime
from vacumm.misc.axes import create_lon
from vacumm.misc.grid import create_grid, set_grid
from vacumm.misc.atime import create_time
from vacumm.misc.phys.units import kel2degc
# -- Dans le cas d'un NAR SST on lit la grille lon lat dans le fichier grid
# -- Lecture de la grille
znar = self.ZONE_NAR
gridfile = "grid_%(znar)s.nc" % vars()
f = cdms2.open(gridfile)
la = f('latitude')
lo = f('longitude')
f.close()
# -- Creation des axes longitude et latitude
lat_axis = create_lon(la, id='latitude')
lon_axis = create_lon(lo, id='longitude')
# -- Creation de la grille
grid = create_grid(lon_axis, lat_axis)
# -- Creation d'un objet cdms nomme self.data et d'un tableau cumt pour les dates extraites des noms de fichiers
self.data = () #Initialise un tuple
# =============== ATTENTION ====================
# Initialiser self.data pour ne pas dupliquer en memoire !!!!!!!!!
# ============================================
#cumt = [] # Initialise un array
# -- Boucle sur les fichiers presents dans le WORKDIR
#url_file_def="%(YYYY)s%(MM)s%(DD)s%(HH)s%(ext)s"%vars()
#self.ctdeb
# -- Ancienne methode
#files = glob.glob(os.path.join(self.WORKDIR, '2*.nc'))
#files.sort()
# --
# -- Methode amelioree
# Cree une liste
files = []
# Cree la liste des fichiers correspondants a la periode consideree
ctest = self.ctdeb
while ctest <= self.ctfin:
flnme_only = '%(#)04d%(##)02d%(###)02d*.nc' % {
'#': ctest.year,
'##': ctest.month,
'###': ctest.day
}
files.extend(glob.glob(os.path.join(self.WORKDIR, flnme_only)))
ctest = ctest.add(1, cdtime.Days)
# --
for filename in files:
# -- Lecture du fichier filename
f = cdms2.open(filename)
temp = f('sea_surface_temperature')
# =============== ATTENTION ==================================
# Verifier que temp utilise tout le temps le meme espace memoire ... voir du cote de cdms
# ==========================================================
f.close()
# -- Extraction de la date et heure du nom du fichier
#ty = numpy.int(filename[-15:-11])
#tm = numpy.int(filename[-11:-9])
#tj = numpy.int(filename[-9:-7])
#th = numpy.int(filename[-7:-5])
#tt = cdtime.comptime(ty,tm,tj,th)
#cumt.append(tt)
# -- Transfert de temp dans l'objet cdat self.data (concatenation)
# =============== ATTENTION ====================
# Faire une variable intermediaire qui sera au prealable allouee en memoire pour eviter
# trop de copies en memoire !!!!!!!!!!!!!!!!
# ============================================
self.data += temp,
# -- Creation de l'axe temporel
#taxis = create_time(cumt)
# -- MV2.concatenate pour concatener les informations dans self.data (entre autre construit l'axe temporel)
self.data = MV2.concatenate(self.data)
# -- Attribution de la grille a l'objet self.data
set_grid(self.data, grid, axes=True)
# -- Informations sur le dataset
self.data.name = "NAR_SST"
self.data.units = "degree_Celsius"
self.data.standard_name = "satellite_sea_surface_temperature"
self.data.long_name = "Satellite Sea Surface Temperature - NAR"
# -- Change unit
self.data = kel2degc(self.data)
f = cdms2.open(
os.path.join(cdms2.__path__[0], '..', '..', '..', '..', 'sample_data',
'clt.nc'))
s = f("clt")
cdutil.setTimeBoundsMonthly(s)
print 'Getting JJA, which should be inexistant in data'
if cdutil.JJA(s[:5]) is not None:
raise RuntimeError, "data w/o season did not return None"
## Create a year worth of data w/o JJA
s1 = s[:5]
s2 = s[8:12]
s3 = MV2.concatenate((s1, s2))
t = MV2.concatenate((s1.getTime()[:], s2.getTime()[:]))
t = cdms2.createAxis(t, id='time')
t.units = s.getTime().units
t.designateTime()
s3.setAxis(0, t)
cdutil.setTimeBoundsMonthly(s3)
if cdutil.JJA(s3) is not None:
raise RuntimeError, "data w/o season did not return None"
if cdutil.JJA.departures(s3) is not None:
raise RuntimeError, "data w/o season did not return None for dep"
if cdutil.JJA.climatology(s3) is not None:
raise RuntimeError, "data w/o season did not return None for clim"
# Now gets seasonal cycle, should have JJA all missing
def regrid_models(variable, experiment):
#get the shape from CESM2
model = "CESM2"
rip = "r1i1p1f1"
allfiles = sorted(
glob.glob("/home/kdm2144/DROUGHT/DOWNLOADED_RAW/" + "/" + variable +
"/" + model + "/*." + experiment + ".*." + rip + ".*"))
f = cdms.open(allfiles[0])
data = f(variable)
#for model in get_ok_models("SW"):
grid = data.getGrid()
nyears = 86 #historical runs begin in 2015-2100
model_shape = (12 * nyears, ) + grid.shape
f.close()
models = dh.get_ok_models("SW")
nmodels = len(models)
bigshape = (nmodels, ) + model_shape
allmodels = MV.zeros(bigshape)
for modeli in range(nmodels):
model = models[modeli]
print(model)
#Get landmask
landthresh = 1
fixedvardirec = external_drive + "DROUGHT/fixedvar/"
#Get the land fraction
landfiles = glob.glob(fixedvardirec + "sftlf*" + model + ".*")
if len(landfiles) == 1:
fland = cdms.open(landfiles[0])
landfrac = fland("sftlf")
fland.close()
else:
print("can't find land fraction file for", model)
print(landfiles)
continue
allfiles_rips = sorted(
glob.glob("/home/kdm2144/DROUGHT/DOWNLOADED_RAW/" + "/" +
variable + "/" + model + "/*." + experiment + ".*"))
rips = sorted(np.unique([x.split(".")[3] for x in allfiles_rips]))
if len(rips) > 0:
rip = rips[0]
else:
continue
allfiles = sorted(
glob.glob("/home/kdm2144/DROUGHT/DOWNLOADED_RAW/" + "/" +
variable + "/" + model + "/*." + experiment + ".*." +
rip + ".*"))
if len(allfiles) >= nyears:
for i in range(nyears):
f = cdms.open(allfiles[i])
data = f(variable)
landdata = cmip5.cdms_clone(
np.repeat(.01 * landfrac.asma()[np.newaxis], 12, axis=0) *
data, data)
data_regrid = landdata.regrid(grid, regridTool='regrid2')
if i == 0:
bigdata = data_regrid
else:
bigdata = MV.concatenate((bigdata, data_regrid))
f.close()
allmodels[modeli] = bigdata
else:
allmodels[modeli] = 1.e20
allmodels = MV.masked_where(np.abs(allmodels) > 1.e10, allmodels)
modax = cmip5.make_model_axis(models)
tax = cdms.createAxis(np.arange(12 * 86))
tax.units = "months since 2015-1-1"
tax.designateTime()
tax.id = 'time'
allmodels.setAxis(0, modax)
allmodels.setAxis(1, tax)
cdutil.setTimeBoundsMonthly(allmodels)
allmodels.setAxis(2, data_regrid.getLatitude())
allmodels.setAxis(3, data_regrid.getLongitude())
allmodels.name = variable
allmodels.id = variable
return allmodels
# Verifier que temp utilise tout le temps le meme espace memoire ... voir du cote de cdms
# ==========================================================
f.close()
# -- Transfert de temp dans l'objet cdat self.data (concatenation)
# =============== ATTENTION ====================
# Faire une variable intermediaire qui sera au prealable allouee en memoire pour eviter
# trop de copies en memoire !!!!!!!!!!!!!!!!
# ============================================
self.data += (temp,)
# -- Creation de l'axe temporel
# taxis = create_time(cumt)
# -- MV2.concatenate pour concatener les informations dans self.data (entre autre construit l'axe temporel)
self.data = MV2.concatenate(self.data)
# -- Informations sur le dataset
# self.data.name = "SEVIRI_SST"
self.data.units = "degree_Celsius"
self.data.standard_name = "satellite_sea_surface_temperature"
self.data.long_name = "Satellite Sea Surface Temperature - SEVIRI"
# -- Change unit
self.data = kel2degc(self.data)
# -- Fin de lecture des donnees
# ----------------------------------------------------
def read_assim(self, cfg=None):
""" Lecture des fichiers NetCDF de SST SEVIRI formatte pour l'assimilation """
def read(self, verbose=False, cfg=None):
""" Lecture des fichiers NetCDF de NAR SST """
import cdms2,sys,os, glob
import numpy,MV2
import cdtime
from vacumm.misc.axes import create_lon, set_order
from vacumm.misc.grid import create_grid, set_grid
from vacumm.misc.atime import create_time
from vacumm.misc.phys.units import kel2degc
import gc
# Get the configuration file information
#cfg = self.get_config()
#print cfg
# -- Creation d'un objet cdms nomme self.data et d'un tableau cumt pour les dates extraites des noms de fichiers
self.data = () #Initialise un tuple
# =============== ATTENTION ====================
# Initialiser self.data pour ne pas dupliquer en memoire !!!!!!!!!
# ============================================
# -- Methode amelioree
# Cree une liste
files = []
# Cree la liste des fichiers correspondants a la periode consideree
if cfg is None:
config = ConfigParser.RawConfigParser()
config.read(os.path.join(self.SCRIPT_DIR,'config.cfg'))
hr_satellites = config.get('Nar SST', 'hr_satellites')
else:
hr_satellites = cfg['Nar SST']['hr_satellites']
hr_satellites = hr_satellites.split(',')
#hr_satellites = cfg['hr_satellites']
#print hr_satellites
ctest = self.ctdeb
while ctest <= self.ctfin:
for isat, s_name in enumerate(hr_satellites):
flnme_only = '%04d%02d%02d*%s*.nc'%(ctest.year, ctest.month, ctest.day, s_name)
files.extend(glob.glob(os.path.join(flnme_only)))
ctest=ctest.add(1,cdtime.Days)
# --
if cfg is None:
lomin = float(config.get('Domain', 'lomin') )
lomax = float(config.get('Domain', 'lomax') )
lamin = float(config.get('Domain', 'lamin') )
lamax = float(config.get('Domain', 'lamax') )
else:
lomin = cfg['Domain']['lomin']
lomax = cfg['Domain']['lomax']
lamin = cfg['Domain']['lamin']
lamax = cfg['Domain']['lamax']
#print files
if files == []:
print 'No data file to read ...'
else:
# ---- Lecture et creation de la grille ----
#
# -- Lecture du fichier filename
f = cdms2.open(files[0])
lo = f.getVariable('lon')
la = f.getVariable('lat')
# -- Creation des axes longitude et latitude
# lat_axis = create_lon(la,id='latitude')
# lon_axis = create_lon(lo,id='longitude')
# -- Creation de la grille
grid = create_grid(lo, la)
del lo, la
for ifile, filename in enumerate(files):
# -- Lecture du fichier filename
f = cdms2.open(filename)
temp2 = f('sea_surface_temperature')
set_order(temp2, 'tyx') # pour que averager.py fontionne
# modif J.Gatti : utilisation de l'index de qualite (0:unprocessed 1:cloudy 2:bad 3:suspect 4:acceptable 5:excellent)
temp2.set_fill_value(temp2._FillValue)
conf=f('proximity_confidence')
MV2.putmask(temp2.data,conf.data<3,temp2._FillValue) # ne change que data
MV2.putmask(temp2.mask,conf.data<3,True) # ne change que mask
#autre methode
#--------------------
#temp2=MV2.masked_where(conf.data<3,temp2) # ne change que mask
#oldmask=temp2.mask
#temp2[:]=temp2.filled() # change data mais met mask a false partout
#temp2.mask=oldmask # remet le bon mask sans lien
del conf
# fin modif J.Gatti : utilisation de l'index de qualite
# -- Attribution de la grille a l'objet self.data
set_grid(temp2, grid, axes=True)
temp = temp2(lon=(lomin, lomax), lat=(lamin, lamax))
if verbose:
# == TEST OCCUPATION MEMOIRE ===
print ctest, 'Avant'
#print psutil.Process(os.getpid()).get_memory_percent()
#print psutil.Process(os.getpid()).get_memory_info()
#print 'CPU percent: ', psutil.cpu_percent(interval=0.1)
#print 'Used phymem: ', psutil.used_phymem()
#print 'Used virtmem: ', psutil.used_virtmem()
del temp2
if verbose:
# == TEST OCCUPATION MEMOIRE ===
print ctest, 'Apres del'
#print psutil.Process(os.getpid()).get_memory_percent()
#print psutil.Process(os.getpid()).get_memory_info()
#print 'CPU percent: ', psutil.cpu_percent(interval=0.1)
#print 'Used phymem: ', psutil.used_phymem()
#print 'Used virtmem: ', psutil.used_virtmem()
# =============== ATTENTION ==================================
# Verifier que temp utilise tout le temps le meme espace memoire ... voir du cote de cdms
# ==========================================================
f.close()
# -- Transfert de temp dans l'objet cdat self.data (concatenation)
# =============== ATTENTION ====================
# Faire une variable intermediaire qui sera au prealable allouee en memoire pour eviter
# trop de copies en memoire !!!!!!!!!!!!!!!!
# ============================================
#self.data += temp,
if ifile == 0:
self.data = temp
else:
self.data = MV2.concatenate((self.data, temp))
if verbose:
# == TEST OCCUPATION MEMOIRE ===
print ctest, 'Avant gccollect'
#print psutil.Process(os.getpid()).get_memory_percent()
#print psutil.Process(os.getpid()).get_memory_info()
#print 'CPU percent: ', psutil.cpu_percent(interval=0.1)
#print 'Used phymem: ', psutil.used_phymem()
#print 'Used virtmem: ', psutil.used_virtmem()
print gc.collect()
gc.collect()
if verbose:
# == TEST OCCUPATION MEMOIRE ===
print ctest, 'Apres gccollect'
#print psutil.Process(os.getpid()).get_memory_percent()
#print psutil.Process(os.getpid()).get_memory_info()
#print 'CPU percent: ', psutil.cpu_percent(interval=0.1)
#print 'Used phymem: ', psutil.used_phymem()
#print 'Used virtmem: ', psutil.used_virtmem()
# -- Creation de l'axe temporel
#taxis = create_time(cumt)
# -- MV2.concatenate pour concatener les informations dans self.data (entre autre construit l'axe temporel)
#self.data = MV2.concatenate(self.data)
# -- Informations sur le dataset
#self.data.name = "NAR_SST"
self.data.units = "degree_Celsius"
self.data.standard_name = "satellite_sea_surface_temperature"
self.data.long_name = "Satellite Sea Surface Temperature - NAR"
# -- Change unit
self.data = kel2degc(self.data)
iaxis = TransientVirtualAxis(idi, ni)
jaxis = TransientVirtualAxis(idj, nj)
lataxis = TransientAxis2D(lat,
axes=(iaxis, jaxis),
attributes={'units': lat_units},
id="latitude")
lonaxis = TransientAxis2D(lon,
axes=(iaxis, jaxis),
attributes={'units': lon_units},
id="longitude")
curvegrid = TransientGenericGrid(lataxis, lonaxis, tempmask=None)
attributs = None
vid = None
if hasattr(v, 'attributes'): attributs = v.attributes
if hasattr(v, 'id'): vid = v.id
axis0 = v.getAxis(0)
return cdms2.createVariable(v, axes=[axis0,iaxis,jaxis], grid=curvegrid, \
attributes=attributs, id=v.id)
lat = MV2.array([[-20, -10, 0, -15, -5]], 'f')
lon = MV2.array([[0, 10, 20, 50, 60]], 'f')
data1 = MV2.array([[[2, 3, 1, 6, 2]]], 'f')
data2 = MV2.array([[[2, 3, 1, 6, 2]]], 'f')
data1 = CurveGrid(data1, lat, lon)
data2 = CurveGrid(data2, lat, lon)
result = MV2.concatenate([data1, data2], axis=0)
def testConcatenate(self):
xcon = MV2.concatenate((self.u_file, self.v_file))
self.assertEqual(xcon.shape,
(self.u_file.shape[0] + self.v_file.shape[0],
self.u_file.shape[1], self.u_file.shape[2]))
pth+'u_2002.nc',
]
for file in files:
f=cdms.open(file)
u=f('u')
if file == files[0]: # First file
sh=list(u.shape) # Create a list with the shape of the data
sh.insert(0,1) # Insert value 1 in front of the list
accumulation = u
newdim = MV.reshape(u,sh) # Create a new 1D dimension
else:
# add u at the end of accumaltion on dimension 0
accumulation = MV.concatenate((accumulation,u))
tmp = MV.reshape(u,sh) # Create a new 1D dimension
newdim = MV.concatenate((newdim,tmp)) # Add u to the newdim over the new dimension
f.close()
print accumulation.shape # All time added over the same dimension
print newdim.shape # Has a new dimension for years
avg = MV.average(accumulation)
std = genutil.statistics.std(newdim)
print avg.shape
print std.shape
temporary[region] = d_sub_aave(
time=(start_t, end_t))
continue
else:
# n-1 year 7/1~12/31
part1 = copy.copy(temporary[region])
# n year 1/1~6/30
part2 = d_sub_aave(time=(cdtime.comptime(
year), cdtime.comptime(year, 6, 30, 23,
59, 59)))
start_t = cdtime.comptime(year, 7, 1)
end_t = cdtime.comptime(
year, 12, 31, 23, 59, 59)
temporary[region] = d_sub_aave(
time=(start_t, end_t))
d_sub_aave = MV2.concatenate(
[part1, part2], axis=0)
if debug:
print('debug: ', region, year,
d_sub_aave.getTime().asComponentTime())
# get pentad time series
list_d_sub_aave_chunks = list(
divide_chunks_advanced(d_sub_aave, n, debug=debug))
pentad_time_series = []
for d_sub_aave_chunk in list_d_sub_aave_chunks:
# ignore when chunk length is shorter than defined
if d_sub_aave_chunk.shape[0] >= n:
ave_chunk = MV2.average(
d_sub_aave_chunk, axis=0)
pentad_time_series.append(float(ave_chunk))
if debug:
