def getCommonGrid(grid, res=None, lfilepath=False):
''' return definitions of commonly used grids (either from datasets or pickles) '''
# try pickle first
griddef = loadPickledGridDef(grid=grid, res=res, folder=grid_folder,
check=False, lfilepath=lfilepath)
# alternatively look in known datasets
if griddef is None:
try:
dataset = import_module(grid)
if res is None: griddef = dataset.default_grid
else: griddef = dataset.grid_def[res]
if lfilepath: griddef.filepath = None # monkey-patch...
except ImportError:
griddef = None
# assert (elon-slon) % dlon == 0
# lon = np.linspace(slon+dlon/2,elon-dlon/2,(elon-slon)/dlon)
# assert (elat-slat) % dlat == 0
# lat = np.linspace(slat+dlat/2,elat-dlat/2,(elat-slat)/dlat)
# # add new geographic coordinate axes for projected map
# xlon = Axis(coord=lon, atts=dict(grid='lon', long_name='longitude', units='deg E'))
# ylat = Axis(coord=lat, atts=dict(grid='lat', long_name='latitude', units='deg N'))
# gridstr = '{0:s}_{1:s}'.format(grid,res) if res is not None else grid
# return grid definition object (or None, if none found)
return griddef
def getCommonGrid(grid, res=None):
''' return definitions of commonly used grids (either from datasets or pickles) '''
# try pickle first
griddef = loadPickledGridDef(grid=grid, res=res, folder=grid_folder, check=False)
# alternatively look in known datasets
if griddef is None:
try:
dataset = import_module(grid)
if res is None:
griddef = dataset.default_grid
else:
griddef = dataset.grid_def[res]
except ImportError:
griddef = None
# assert (elon-slon) % dlon == 0
# lon = np.linspace(slon+dlon/2,elon-dlon/2,(elon-slon)/dlon)
# assert (elat-slat) % dlat == 0
# lat = np.linspace(slat+dlat/2,elat-dlat/2,(elat-slat)/dlat)
# # add new geographic coordinate axes for projected map
# xlon = Axis(coord=lon, atts=dict(grid='lon', long_name='longitude', units='deg E'))
# ylat = Axis(coord=lat, atts=dict(grid='lat', long_name='latitude', units='deg N'))
# gridstr = '{0:s}_{1:s}'.format(grid,res) if res is not None else grid
# return grid definition object (or None, if none found)
return griddef
def loadObservations(name=None, folder=None, period=None, grid=None, station=None, shape=None, lencl=False,
varlist=None, varatts=None, filepattern=None, filelist=None, resolution=None,
projection=None, geotransform=None, axes=None, lautoregrid=None, mode='climatology'):
''' A function to load standardized observational datasets. '''
# prepare input
if mode.lower() == 'climatology': # post-processed climatology files
# transform period
if period is None or period == '':
if name not in ('PCIC','PRISM','GPCC','NARR'):
raise ValueError("A period is required to load observational climatologies.")
elif isinstance(period,basestring):
period = tuple([int(prd) for prd in period.split('-')])
elif not isinstance(period,(int,np.integer)) and ( not isinstance(period,tuple) and len(period) == 2 ):
raise TypeError(period)
elif mode.lower() in ('time-series','timeseries'): # concatenated time-series files
period = None # to indicate time-series (but for safety, the input must be more explicit)
if lautoregrid is None: lautoregrid = False # this can take very long!
# cast/copy varlist
if isinstance(varlist,basestring): varlist = [varlist] # cast as list
elif varlist is not None: varlist = list(varlist) # make copy to avoid interference
# figure out station and shape options
if station and shape: raise ArgumentError()
elif station or shape:
if grid is not None: raise NotImplementedError('Currently observational station data can only be loaded from the native grid.')
if lautoregrid: raise GDALError('Station data can not be regridded, since it is not map data.')
lstation = bool(station); lshape = bool(shape)
grid = station if lstation else shape
# add station/shape parameters
if varlist:
params = stn_params if lstation else shp_params
for param in params:
if param not in varlist: varlist.append(param)
else:
lstation = False; lshape = False
# varlist (varlist = None means all variables)
if varatts is None: varatts = default_varatts.copy()
if varlist is not None: varlist = translateVarNames(varlist, varatts)
# filelist
if filelist is None:
filename = getFileName(name=name, resolution=resolution, period=period, grid=grid, filepattern=filepattern)
# check existance
filepath = '{:s}/{:s}'.format(folder,filename)
if not os.path.exists(filepath):
nativename = getFileName(name=name, resolution=resolution, period=period, grid=None, filepattern=filepattern)
nativepath = '{:s}/{:s}'.format(folder,nativename)
if os.path.exists(nativepath):
if lautoregrid:
from processing.regrid import performRegridding # causes circular reference if imported earlier
griddef = loadPickledGridDef(grid=grid, res=None, folder=grid_folder)
dataargs = dict(period=period, resolution=resolution)
performRegridding(name, 'climatology',griddef, dataargs) # default kwargs
else: raise IOError("The dataset '{:s}' for the selected grid ('{:s}') is not available - use the regrid module to generate it.".format(filename,grid) )
else: raise IOError("The dataset file '{:s}' does not exits!\n('{:s}')".format(filename,filepath))
# load dataset
dataset = DatasetNetCDF(name=name, folder=folder, filelist=[filename], varlist=varlist, varatts=varatts,
axes=axes, multifile=False, ncformat='NETCDF4')
# mask all shapes that are incomplete in dataset
if shape and lencl and 'shp_encl' in dataset:
dataset.load() # need to load data before masking; is cheap for shape averages, anyway
dataset.mask(mask='shp_encl', invert=True, skiplist=shp_params)
# correct ordinal number of shape (should start at 1, not 0)
if lshape:
if dataset.hasAxis('shapes'): raise AxisError("Axis 'shapes' should be renamed to 'shape'!")
if not dataset.hasAxis('shape'):
raise AxisError()
if dataset.shape.coord[0] == 0: dataset.shape.coord += 1
# figure out grid
if not lstation and not lshape:
if grid is None or grid == name:
dataset = addGDALtoDataset(dataset, projection=projection, geotransform=geotransform, gridfolder=grid_folder)
elif isinstance(grid,basestring): # load from pickle file
# griddef = loadPickledGridDef(grid=grid, res=None, filename=None, folder=grid_folder)
# add GDAL functionality to dataset
dataset = addGDALtoDataset(dataset, griddef=grid, gridfolder=grid_folder)
else: raise TypeError(dataset)
# N.B.: projection should be auto-detected, if geographic (lat/lon)
return dataset
if griddef is None:
print('GridDefinition object for {0:s} not found!'.format(gridstr))
else:
# save pickle
filename = '{0:s}/{1:s}'.format(grid_folder,griddef_pickle.format(gridstr))
filehandle = open(filename, 'w')
pickle.dump(griddef, filehandle)
filehandle.close()
print(' Saving Pickle to \'{0:s}\''.format(filename))
print('')
# load pickle to make sure it is right
del griddef
griddef = loadPickledGridDef(grid, res=res, folder=grid_folder)
print(griddef)
print('')
## create a new grid
elif mode == 'create_grid':
# parameters for UTM 17
name = 'grw1' # 1km resolution
geotransform = [500.e3,1.e3,0,4740.e3,0,1.e3]; size = (132,162)
# name = 'grw2' # 5km resolution
# geotransform = [500.e3,5.e3,0,4740.e3,0,5.e3]; size = (27,33)
projection = "+proj=utm +zone=17 +north +ellps=WGS84 +datum=WGS84 +units=m +no_defs"
# N.B.: [x_0, dx, 0, y_0, 0, dy]
# GT(0),GT(3) are the coordinates of the bottom left corner
# GT(1) & GT(5) are pixel width and height
sink = DatasetNetCDF(name='GPCC Climatology', folder=avgfolder, filelist=[filename], atts=source.atts, mode='w')
# sink = addGDALtoDataset(sink, griddef=source.griddef)
# initialize processing
CPU = CentralProcessingUnit(source, sink, tmp=True)
if period is not None:
# determine averaging interval
offset = source.time.getIndex(period[0]-1979)/12 # origin of monthly time-series is at January 1979
# start processing climatology
CPU.Climatology(period=period[1]-period[0], offset=offset, flush=False)
# CPU.sync(flush=True)
# get NARR coordinates
if grid is not 'GPCC':
griddef = loadPickledGridDef(grid=grid, res=None, folder=grid_folder)
#new_grid = import_module(grid[0:4]).__dict__[grid+'_grid']
# if grid == 'NARR':
# from datasets.NARR import NARR_grid
# reproject and resample (regrid) dataset
CPU.Regrid(griddef=griddef, flush=False)
# # shift longitude axis by 180 degrees left (i.e. -180 - 180 -> 0 - 360)
# print('')
# print(' +++ processing shift longitude +++ ')
# CPU.Shift(lon=-180, flush=True)
# print('\n')
#
# # shift longitude axis by 180 degrees left (i.e. -180 - 180 -> 0 - 360)
# print('')
# print(' +++ processing shift/roll +++ ')
## operational config for SON2
# project = 'SON'
# start_date = '2011-01-01'; end_date = None
# grid_name = 'son2'
## operational config for ASB2
# project = 'ASB'
# start_date = '2010-01-01'; end_date = None
# grid_name = 'asb2'
## define target grid/projection
# projection/UTM zone
tgt_size = None; tgt_geotrans = None # valid for native grid
if project == 'WRF':
# load pickled GridDef
from geodata.gdal import loadPickledGridDef
griddef = loadPickledGridDef(grid=grid_name, encoding='latin1')
print(griddef)
tgt_crs = genProj(griddef.projection.ExportToProj4(), name=grid_name)
tgt_geotrans = griddef.geotransform; tgt_size = griddef.size
elif project == 'SnoDAS':
tgt_crs = None # native grid
elif project.upper() in ('SON','GRW'):
# southern Ontario projection
tgt_crs = genProj("+proj=utm +zone=17 +north +ellps=WGS84 +datum=WGS84 +units=m +no_defs", name=grid_name)
elif project.upper() == 'CMB':
# southern Ontario projection
tgt_crs = genProj("+proj=utm +zone=11 +north +ellps=WGS84 +datum=WGS84 +units=m +no_defs", name=grid_name)
elif project.upper() == 'ASB':
# Assiniboin projection
tgt_crs = genProj("+proj=utm +zone=14 +ellps=GRS80 +towgs84=0,0,0,0,0,0,0 +units=m +no_defs", name=grid_name)
# grid definition (mostly UTM grids for HGS)
def loadObservations(name=None, folder=None, period=None, grid=None, station=None, shape=None, lencl=False,
varlist=None, varatts=None, filepattern=None, filelist=None, resolution=None,
projection=None, geotransform=None, axes=None, lautoregrid=None, mode='climatology'):
''' A function to load standardized observational datasets. '''
# prepare input
if mode.lower() == 'climatology': # post-processed climatology files
# transform period
if period is None or period == '':
if name not in ('PCIC','PRISM','GPCC','NARR'):
raise ValueError, "A period is required to load observational climatologies."
elif isinstance(period,basestring):
period = tuple([int(prd) for prd in period.split('-')])
elif not isinstance(period,(int,np.integer)) and ( not isinstance(period,tuple) and len(period) == 2 ):
raise TypeError
elif mode.lower() in ('time-series','timeseries'): # concatenated time-series files
period = None # to indicate time-series (but for safety, the input must be more explicit)
if lautoregrid is None: lautoregrid = False # this can take very long!
# cast/copy varlist
if isinstance(varlist,basestring): varlist = [varlist] # cast as list
elif varlist is not None: varlist = list(varlist) # make copy to avoid interference
# figure out station and shape options
if station and shape: raise ArgumentError
elif station or shape:
if grid is not None: raise NotImplementedError, 'Currently observational station data can only be loaded from the native grid.'
if lautoregrid: raise GDALError, 'Station data can not be regridded, since it is not map data.'
lstation = bool(station); lshape = bool(shape)
grid = station if lstation else shape
# add station/shape parameters
if varlist:
params = stn_params if lstation else shp_params
for param in params:
if param not in varlist: varlist.append(param)
else:
lstation = False; lshape = False
# varlist (varlist = None means all variables)
if varatts is None: varatts = default_varatts.copy()
if varlist is not None: varlist = translateVarNames(varlist, varatts)
# filelist
if filelist is None:
filename = getFileName(name=name, resolution=resolution, period=period, grid=grid, filepattern=filepattern)
# check existance
filepath = '{:s}/{:s}'.format(folder,filename)
if not os.path.exists(filepath):
nativename = getFileName(name=name, resolution=resolution, period=period, grid=None, filepattern=filepattern)
nativepath = '{:s}/{:s}'.format(folder,nativename)
if os.path.exists(nativepath):
if lautoregrid:
from processing.regrid import performRegridding # causes circular reference if imported earlier
griddef = loadPickledGridDef(grid=grid, res=None, folder=grid_folder)
dataargs = dict(period=period, resolution=resolution)
performRegridding(name, 'climatology',griddef, dataargs) # default kwargs
else: raise IOError, "The dataset '{:s}' for the selected grid ('{:s}') is not available - use the regrid module to generate it.".format(filename,grid)
else: raise IOError, "The dataset file '{:s}' does not exits!\n('{:s}')".format(filename,filepath)
# load dataset
dataset = DatasetNetCDF(name=name, folder=folder, filelist=[filename], varlist=varlist, varatts=varatts,
axes=axes, multifile=False, ncformat='NETCDF4')
# mask all shapes that are incomplete in dataset
if shape and lencl and 'shp_encl' in dataset:
dataset.load() # need to load data before masking; is cheap for shape averages, anyway
dataset.mask(mask='shp_encl', invert=True, skiplist=shp_params)
# correct ordinal number of shape (should start at 1, not 0)
if lshape:
if dataset.hasAxis('shapes'): raise AxisError, "Axis 'shapes' should be renamed to 'shape'!"
if not dataset.hasAxis('shape'):
raise AxisError
if dataset.shape.coord[0] == 0: dataset.shape.coord += 1
# figure out grid
if not lstation and not lshape:
if grid is None or grid == name:
dataset = addGDALtoDataset(dataset, projection=projection, geotransform=geotransform, gridfolder=grid_folder)
elif isinstance(grid,basestring): # load from pickle file
# griddef = loadPickledGridDef(grid=grid, res=None, filename=None, folder=grid_folder)
# add GDAL functionality to dataset
dataset = addGDALtoDataset(dataset, griddef=grid, gridfolder=grid_folder)
else: raise TypeError
# N.B.: projection should be auto-detected, if geographic (lat/lon)
return dataset
print('')
if res is None:
gridstr = grid
print(' *** Pickling Grid Definition for {0:s} *** '.format(grid))
else:
gridstr = '{0:s}_{1:s}'.format(grid,res)
print(' *** Pickling Grid Definition for {0:s} Resolution {1:s} *** '.format(grid,res))
print('')
# load GridDefinition
griddef = getCommonGrid(grid,res)
if griddef is None:
print('GridDefinition object for {0:s} not found!'.format(gridstr))
else:
# save pickle
filename = '{0:s}/{1:s}'.format(grid_folder,griddef_pickle.format(gridstr))
filehandle = open(filename, 'w')
pickle.dump(griddef, filehandle)
filehandle.close()
print(' Saving Pickle to \'{0:s}\''.format(filename))
print('')
# load pickle to make sure it is right
del griddef
griddef = loadPickledGridDef(grid, res=res, folder=grid_folder)
print(griddef)
print('')
'T2', 'Tmin', 'Tmax', 'Q2', 'pet',
'cldfrc', 'wetfrq', 'frzfrq'
],
lautoregrid=True)
cruclim = loadCRU(period=(1979, 2009),
grid=grid,
varlist=[
'T2', 'Tmin', 'Tmax', 'Q2', 'pet',
'cldfrc', 'wetfrq', 'frzfrq'
],
lautoregrid=True)
# grid definition
try:
griddef = loadPickledGridDef(grid=grid,
res=None,
folder=grid_folder)
grid_name = griddef.name
except IOError:
griddef = None
grid_name = grid
periodstr = '{0:4d}-{1:4d}'.format(*period)
print(
'\n *** Merging Climatology from {0:s} on {1:s} Grid *** \n'
.format(
periodstr,
grid,
))
## prepare target dataset
filename = getFileName(grid=grid_name,
def __init__(self):
self.name = 'const'
self.atts = dict(orog = dict(name='zs', units='m'), # surface altitude
# axes (don't have their own file)
class Axes(FileType):
''' A mock-filetype for axes. '''
def __init__(self):
self.atts = dict(time = dict(name='time', units='days', offset=-47116, atts=dict(long_name='Month since 1979')), # time coordinate (days since 1979-01-01)
# NOTE THAT THE CMIP5 DATASET HAVE DIFFERENT TIME OFFSETS BETWEEN MEMBERS !!!
# N.B.: the time coordinate is only used for the monthly time-series data, not the LTM
# the time offset is chose such that 1979 begins with the origin (time=0)
lon = dict(name='lon', units='deg E'), # west-east coordinate
lat = dict(name='lat', units='deg N'), # south-north coordinate
plev = dict(name='lev', units='')) # hybrid pressure coordinate
self.vars = self.atts.keys()
# Time-Series (monthly)
def loadCMIP5_TS(experiment=None, name=None, grid=None, filetypes=None, varlist=None, varatts=None,
translateVars=None, lautoregrid=None, load3D=False, ignore_list=None, lcheckExp=True,
lreplaceTime=True, lwrite=False, exps=None):
''' Get a properly formatted CESM dataset with a monthly time-series. (wrapper for loadCESM)'''
return loadCMIP5_All(experiment=experiment, name=name, grid=grid, period=None, station=None,
filetypes=filetypes, varlist=varlist, varatts=varatts, translateVars=translateVars,
lautoregrid=lautoregrid, load3D=load3D, ignore_list=ignore_list, mode='time-series',
lcheckExp=lcheckExp, lreplaceTime=lreplaceTime, lwrite=lwrite, exps=exps)
# load minimally pre-processed CESM climatology files
def loadCMIP5(experiment=None, name=None, grid=None, period=None, filetypes=None, varlist=None,
varatts=None, translateVars=None, lautoregrid=None, load3D=False, ignore_list=None,
lcheckExp=True, lreplaceTime=True, lencl=False, lwrite=False, exps=None):
''' Get a properly formatted monthly CESM climatology as NetCDFDataset. '''
return loadCMIP5_All(experiment=experiment, name=name, grid=grid, period=period, station=None,
filetypes=filetypes, varlist=varlist, varatts=varatts, translateVars=translateVars,
lautoregrid=lautoregrid, load3D=load3D, ignore_list=ignore_list, exps=exps,
mode='climatology', lcheckExp=lcheckExp, lreplaceTime=lreplaceTime, lwrite=lwrite)
# load any of the various pre-processed CESM climatology and time-series files
def loadCMIP5_All(experiment=None, name=None, grid=None, station=None, shape=None, period=None,
varlist=None, varatts=None, translateVars=None, lautoregrid=None, load3D=False,
ignore_list=None, mode='climatology', cvdp_mode=None, lcheckExp=True, exps=None,
lreplaceTime=True, filetypes=None, lencl=False, lwrite=False, check_vars=None):
''' Get any of the monthly CESM files as a properly formatted NetCDFDataset. '''
# period
if isinstance(period,(tuple,list)):
if not all(isNumber(period)): raise ValueError
elif isinstance(period,basestring): period = [int(prd) for prd in period.split('-')]
elif isinstance(period,(int,np.integer)) or period is None : pass # handled later
else: raise DateError, "Illegal period definition: {:s}".format(str(period))
# prepare input
lclim = False; lts = False; lcvdp = False; ldiag = False # mode switches
if mode.lower() == 'climatology': # post-processed climatology files
lclim = True
folder,experiment,name = getFolderName(name=name, experiment=experiment, folder=None, mode='avg', exps=exps)
if period is None: raise DateError, 'Currently CESM Climatologies have to be loaded with the period explicitly specified.'
elif mode.lower() in ('time-series','timeseries'): # concatenated time-series files
lts = True
folder,experiment,name = getFolderName(name=name, experiment=experiment, folder=None, mode='avg', exps=exps)
lclim = False; period = None; periodstr = None # to indicate time-series (but for safety, the input must be more explicit)
if lautoregrid is None: lautoregrid = False # this can take very long!
elif mode.lower() == 'cvdp': # concatenated time-series files
lcvdp = True
folder,experiment,name = getFolderName(name=name, experiment=experiment, folder=None, mode='cvdp',
cvdp_mode=cvdp_mode, exps=exps)
if period is None:
if not isinstance(experiment,Exp): raise DatasetError, 'Periods can only be inferred for registered datasets.'
period = (experiment.beginyear, experiment.endyear)
elif mode.lower() == 'diag': # concatenated time-series files
ldiag = True
folder,experiment,name = getFolderName(name=name, experiment=experiment, folder=None, mode='diag', exps=exps)
raise NotImplementedError, "Loading AMWG diagnostic files is not supported yet."
else: raise NotImplementedError,"Unsupported mode: '{:s}'".format(mode)
# cast/copy varlist
if isinstance(varlist,basestring): varlist = [varlist] # cast as list
elif varlist is not None: varlist = list(varlist) # make copy to avoid interference
# handle stations and shapes
if station and shape: raise ArgumentError
elif station or shape:
if grid is not None: raise NotImplementedError, 'Currently CESM station data can only be loaded from the native grid.'
if lcvdp: raise NotImplementedError, 'CVDP data is not available as station data.'
if lautoregrid: raise GDALError, 'Station data can not be regridded, since it is not map data.'
lstation = bool(station); lshape = bool(shape)
# add station/shape parameters
if varlist:
params = stn_params if lstation else shp_params
for param in params:
if param not in varlist: varlist.append(param)
else:
lstation = False; lshape = False
# period
if isinstance(period,(int,np.integer)):
if not isinstance(experiment,Exp): raise DatasetError, 'Integer periods are only supported for registered datasets.'
period = (experiment.beginyear, experiment.beginyear+period)
if lclim: periodstr = '_{0:4d}-{1:4d}'.format(*period)
elif lcvdp: periodstr = '{0:4d}-{1:4d}'.format(period[0],period[1]-1)
else: periodstr = ''
# N.B.: the period convention in CVDP is that the end year is included
# generate filelist and attributes based on filetypes and domain
if filetypes is None: filetypes = ['atm','lnd']
elif isinstance(filetypes,(list,tuple,set,basestring)):
if isinstance(filetypes,basestring): filetypes = [filetypes]
else: filetypes = list(filetypes)
# interprete/replace WRF filetypes (for convenience)
tmp = []
for ft in filetypes:
if ft in ('const','drydyn3d','moist3d','rad','plev3d','srfc','xtrm','hydro'):
if 'atm' not in tmp: tmp.append('atm')
elif ft in ('lsm','snow'):
if 'lnd' not in tmp: tmp.append('lnd')
elif ft in ('aux'): pass # currently not supported
# elif ft in (,):
# if 'atm' not in tmp: tmp.append('atm')
# if 'lnd' not in tmp: tmp.append('lnd')
else: tmp.append(ft)
filetypes = tmp; del tmp
if 'axes' not in filetypes: filetypes.append('axes')
else: raise TypeError
atts = dict(); filelist = []; typelist = []
for filetype in filetypes:
fileclass = fileclasses[filetype]
if lclim and fileclass.climfile is not None: filelist.append(fileclass.climfile)
elif lts and fileclass.tsfile is not None: filelist.append(fileclass.tsfile)
elif lcvdp and fileclass.cvdpfile is not None: filelist.append(fileclass.cvdpfile)
elif ldiag and fileclass.diagfile is not None: filelist.append(fileclass.diagfile)
typelist.append(filetype)
atts.update(fileclass.atts)
# figure out ignore list
if ignore_list is None: ignore_list = set(ignore_list_2D)
elif isinstance(ignore_list,(list,tuple)): ignore_list = set(ignore_list)
elif not isinstance(ignore_list,set): raise TypeError
if not load3D: ignore_list.update(ignore_list_3D)
if lautoregrid is None: lautoregrid = not load3D # don't auto-regrid 3D variables - takes too long!
# translate varlist
if varatts is not None: atts.update(varatts)
lSST = False
if varlist is not None:
varlist = list(varlist)
if 'SST' in varlist: # special handling of name SST variable, as it is part of Ts
varlist.remove('SST')
if not 'Ts' in varlist: varlist.append('Ts')
lSST = True # Ts is renamed to SST below
if translateVars is None: varlist = list(varlist) + translateVarNames(varlist, atts) # also aff translations, just in case
elif translateVars is True: varlist = translateVarNames(varlist, atts)
# N.B.: DatasetNetCDF does never apply translation!
# NetCDF file mode
ncmode = 'rw' if lwrite else 'r'
# get grid or station-set name
if lstation:
# the station name can be inserted as the grid name
gridstr = '_'+station.lower(); # only use lower case for filenames
griddef = None
elif lshape:
# the station name can be inserted as the grid name
gridstr = '_'+shape.lower(); # only use lower case for filenames
griddef = None
else:
if grid is None or grid == experiment.grid:
gridstr = ''; griddef = None
else:
gridstr = '_'+grid.lower() # only use lower case for filenames
griddef = loadPickledGridDef(grid=grid, res=None, filename=None, folder=grid_folder, check=True)
# insert grid name and period
filenames = []
for filetype,fileformat in zip(typelist,filelist):
if lclim: filename = fileformat.format(gridstr,periodstr) # put together specfic filename for climatology
elif lts: filename = fileformat.format(gridstr) # or for time-series
elif lcvdp: filename = fileformat.format(experiment.name if experiment else name,periodstr) # not implemented: gridstr
elif ldiag: raise NotImplementedError
else: raise DatasetError
filenames.append(filename) # append to list (passed to DatasetNetCDF later)
# check existance
filepath = '{:s}/{:s}'.format(folder,filename)
if not os.path.exists(filepath):
nativename = fileformat.format('',periodstr) # original filename (before regridding)
nativepath = '{:s}/{:s}'.format(folder,nativename)
if os.path.exists(nativepath):
if lautoregrid:
from processing.regrid import performRegridding # causes circular reference if imported earlier
griddef = loadPickledGridDef(grid=grid, res=None, folder=grid_folder)
dataargs = dict(experiment=experiment, filetypes=[filetype], period=period)
print("The '{:s}' (CESM) dataset for the grid ('{:s}') is not available:\n Attempting regridding on-the-fly.".format(name,filename,grid))
if performRegridding('CESM','climatology' if lclim else 'time-series', griddef, dataargs): # default kwargs
raise IOError, "Automatic regridding failed!"
print("Output: '{:s}'".format(name,filename,grid,filepath))
else: raise IOError, "The '{:s}' (CESM) dataset '{:s}' for the selected grid ('{:s}') is not available - use the regrid module to generate it.".format(name,filename,grid)
else: raise IOError, "The '{:s}' (CESM) dataset file '{:s}' does not exits!\n({:s})".format(name,filename,folder)
# load dataset
#print varlist, filenames
if experiment: title = experiment.title
else: title = name
dataset = DatasetNetCDF(name=name, folder=folder, filelist=filenames, varlist=varlist, axes=None,
varatts=atts, title=title, multifile=False, ignore_list=ignore_list,
ncformat='NETCDF4', squeeze=True, mode=ncmode, check_vars=check_vars)
# replace time axis
if lreplaceTime:
if lts or lcvdp:
# check time axis and center at 1979-01 (zero-based)
if experiment is None: ys = period[0]; ms = 1
else: ys,ms,ds = [int(t) for t in experiment.begindate.split('-')]; assert ds == 1
if dataset.hasAxis('time'):
ts = (ys-1979)*12 + (ms-1); te = ts+len(dataset.time) # month since 1979 (Jan 1979 = 0)
atts = dict(long_name='Month since 1979-01')
timeAxis = Axis(name='time', units='month', coord=np.arange(ts,te,1, dtype='int16'), atts=atts)
dataset.replaceAxis(dataset.time, timeAxis, asNC=False, deepcopy=False)
if dataset.hasAxis('year'):
ts = ys-1979; te = ts+len(dataset.year) # month since 1979 (Jan 1979 = 0)
atts = dict(long_name='Years since 1979-01')
yearAxis = Axis(name='year', units='year', coord=np.arange(ts,te,1, dtype='int16'), atts=atts)
dataset.replaceAxis(dataset.year, yearAxis, asNC=False, deepcopy=False)
elif lclim:
if dataset.hasAxis('time') and not dataset.time.units.lower() in monthlyUnitsList:
atts = dict(long_name='Month of the Year')
timeAxis = Axis(name='time', units='month', coord=np.arange(1,13, dtype='int16'), atts=atts)
assert len(dataset.time) == len(timeAxis), dataset.time
dataset.replaceAxis(dataset.time, timeAxis, asNC=False, deepcopy=False)
elif dataset.hasAxis('year'): raise NotImplementedError, dataset
# rename SST
if lSST: dataset['SST'] = dataset.Ts
# correct ordinal number of shape (should start at 1, not 0)
if lshape:
# mask all shapes that are incomplete in dataset
if lencl and 'shp_encl' in dataset: dataset.mask(mask='shp_encl', invert=True)
if dataset.hasAxis('shapes'): raise AxisError, "Axis 'shapes' should be renamed to 'shape'!"
if not dataset.hasAxis('shape'): raise AxisError
if dataset.shape.coord[0] == 0: dataset.shape.coord += 1
# check
if len(dataset) == 0: raise DatasetError, 'Dataset is empty - check source file or variable list!'
# add projection, if applicable
if not ( lstation or lshape ):
dataset = addGDALtoDataset(dataset, griddef=griddef, gridfolder=grid_folder, lwrap360=True, geolocator=True)
# return formatted dataset
return dataset
## Dataset API
dataset_name = 'CMIP5' # dataset name
root_folder # root folder of the dataset
avgfolder # root folder for monthly averages
outfolder # root folder for direct WRF output
ts_file_pattern = 'cmip5{0:s}{1:s}_monthly.nc' # filename pattern: filetype, grid
clim_file_pattern = 'cmip5{0:s}{1:s}_clim{2:s}.nc' # filename pattern: filetype, grid, period
data_folder = root_folder # folder for user data
grid_def = {'':None} # there are too many...
grid_res = {'':1.} # approximate grid resolution at 45 degrees latitude
default_grid = None
# functions to access specific datasets
loadLongTermMean = None # WRF doesn't have that...
loadClimatology = loadCESM # pre-processed, standardized climatology
loadTimeSeries = loadCESM_TS # time-series data
#loadStationClimatology = loadCESM_Stn # pre-processed, standardized climatology at stations
#loadStationTimeSeries = loadCESM_StnTS # time-series data at stations
#loadShapeClimatology = loadCESM_Shp # climatologies without associated grid (e.g. provinces or basins)
#loadShapeTimeSeries = loadCESM_ShpTS # time-series without associated grid (e.g. provinces or basins)
## (ab)use main execution for quick test
if __name__ == '__main__':
# set mode/parameters
# mode = 'test_climatology'
# mode = 'test_timeseries'
# mode = 'test_ensemble'
# mode = 'test_point_climatology'
# mode = 'test_point_timeseries'
# mode = 'test_point_ensemble'
# mode = 'test_cvdp'
mode = 'pickle_grid'
# mode = 'shift_lon'
# experiments = ['Ctrl-1', 'Ctrl-A', 'Ctrl-B', 'Ctrl-C']
# experiments += ['Ctrl-2050', 'Ctrl-A-2050', 'Ctrl-B-2050', 'Ctrl-C-2050']
experiments = ('Ctrl-1',)
periods = (15,)
filetypes = ('atm',) # ['atm','lnd','ice']
grids = ('cesm1x1',)*len(experiments) # grb1_d01
# pntset = 'shpavg'
pntset = 'ecprecip'
from projects.CESM_experiments import Exp, CESM_exps, ensembles
# N.B.: importing Exp through CESM_experiments is necessary, otherwise some isinstance() calls fail
# pickle grid definition
if mode == 'pickle_grid':
for grid,experiment in zip(grids,experiments):
print('')
print(' *** Pickling Grid Definition for {0:s} *** '.format(grid))
print('')
# load GridDefinition
dataset = loadCESM(experiment=CESM_exps[experiment], grid=None, filetypes=['lnd'], period=(1979,1989))
griddef = dataset.griddef
#del griddef.xlon, griddef.ylat
print griddef
griddef.name = grid
print(' Loading Definition from \'{0:s}\''.format(dataset.name))
# save pickle
filename = '{0:s}/{1:s}'.format(grid_folder,griddef_pickle.format(grid))
if os.path.exists(filename): os.remove(filename) # overwrite
filehandle = open(filename, 'w')
pickle.dump(griddef, filehandle)
filehandle.close()
print(' Saving Pickle to \'{0:s}\''.format(filename))
print('')
# load pickle to make sure it is right
del griddef
griddef = loadPickledGridDef(grid, res=None, folder=grid_folder)
print(griddef)
print('')
print griddef.wrap360
grid_name = 'son2'
##
# project = 'SNW'
# grid_name = 'snw2'
## operational config for ASB2
# project = 'ASB'
# grid_name = 'asb2'
## define target grid/projection
# projection/UTM zone
tgt_size = None
tgt_geotrans = None # valid for native grid
if project == 'WRF':
# load pickled GridDef
from geodata.gdal import loadPickledGridDef
griddef = loadPickledGridDef(grid=grid_name, encoding='latin1')
print(griddef)
tgt_crs = genCRS(griddef.projection.ExportToProj4(), name=grid_name)
tgt_geotrans = griddef.geotransform
tgt_size = griddef.size
elif project == 'Geo':
# generic geographic lat/lon
tgt_crs = genCRS(name=grid_name)
elif project == 'ARB':
# Projection for ARB model
tgt_crs = genCRS(
'+proj=laea +lat_0=45 +lon_0=-100 +x_0=0 +y_0=0 +ellps=sphere +units=m +no_defs',
name=grid_name)
elif project == 'Hugo':
# Hugo's projection for Quebec
tgt_crs = genCRS(
def loadXArray(varname=None, varlist=None, folder=None, grid=None, bias_correction=None, resolution=None, varatts=None,
filename_pattern=None, default_varlist=None, resampling=None, mask_and_scale=True, varmap=None,
lgeoref=True, geoargs=None, chunks=None, lautoChunk=False, lskip=False, **kwargs):
''' function to open a dataset where variables are stored in separate files and non-native grids are stored in subfolders;
this mainly applies to high-resolution, high-frequency (daily) observations (e.g. SnoDAS); datasets are opened using xarray '''
if grid:
folder = '{}/{}'.format(folder,grid) # non-native grids are stored in sub-folders
# auto-detect resampling folders
if resampling is None:
old_folder = os.getcwd()
os.chdir(folder)
# inspect folder
nc_file = False; default_folder = False; folder_list = []
for item in os.listdir():
if os.path.isfile(item):
if item.endswith('.nc'): nc_file = True
elif os.path.isdir(item):
if item.lower() == 'default': default_folder = item
folder_list.append(item)
else:
raise IOError(item)
os.chdir(old_folder) # return
# evaluate findings
if nc_file: resampling = None
elif default_folder: resampling = default_folder
elif len(folder_list) == 1: resampling = folder_list[0]
if resampling:
folder = '{}/{}'.format(folder,resampling) # different resampling options are stored in subfolders
#
# load variables
if bias_correction is None and 'resolution' in kwargs: bias_correction = kwargs['resolution'] # allow backdoor
if varname and varlist: raise ValueError(varname,varlist)
elif varname:
varlist = [varname] # load a single variable
elif varlist is None:
varlist = default_varlist
# apply varmap in reverse to varlist
if varmap is None and varatts is not None:
varmap = {name:atts.get('name',name) for name,atts in varatts.items()}
if varmap is not None:
ravmap = {value:key for key,value in varmap.items()}
varlist = [ravmap.get(varname,varname) for varname in varlist]
# construct dataset
xds = None
for varname in varlist:
if grid: varname = '{}_{}'.format(varname,grid) # also append non-native grid name to varname
if bias_correction: varname = '{}_{}'.format(bias_correction,varname) # prepend bias correction method
filename = filename_pattern.format(VAR=varname, RES=resolution).lower()
filepath = '{}/{}'.format(folder,filename)
if os.path.exists(filepath):
# load dataset
ds = xr.open_dataset(filepath, chunks=chunks, mask_and_scale=mask_and_scale, **kwargs)
# N.B.: the use of open_mfdataset is problematic, because it does not play nicely with chunking -
# by default it loads everything as one chunk, and it only respects chunking, if chunks are
# specified explicitly at the initial load time (later chunking seems to have no effect!)
# merge into new dataset
if xds is None: xds = ds
else: xds.update(ds)
elif not lskip:
raise IOError("The dataset file '{}' was not found in folder:\n '{}'".format(filename,folder))
# rewrite chunking, if desired (this happens here, so we can infer chunking from dimension sizes)
if lautoChunk:
xds = autoChunkXArray(xds, chunks=chunks)
# rename and apply attributes
if varatts or varmap:
xds = updateVariableAttrs(xds, varatts=varatts, varmap=varmap)
# add projection info
if lgeoref:
if geoargs is not None:
# check
if 'proj4' in xds.attrs and 'proj4' in geoargs:
if xds.attrs['proj4'] != geoargs['proj4']:
raise ValueError(xds.attrs['proj4'])
# custom options
xds = addGeoReference(xds, **geoargs)
# default options
elif 'proj4' in xds.attrs:
# read projection string
xds = addGeoReference(xds, proj4_string=xds.attrs['proj4'])
elif grid:
# load griddef from pickle
from geodata.gdal import loadPickledGridDef
griddef = loadPickledGridDef(grid=grid)
xds = addGeoReference(xds, proj4_string=griddef.projection.ExportToProj4(),)
else:
# use default lat/lon, if it works...
xds = addGeoReference(xds,)
return xds