def testwrap(lon,coord,index):
ci = (coord[0],coord[1])
if len(coord)==2:
indic = 'ccn'
else:
indic = coord[2]
inter = lon.mapIntervalExt(ci,indic)
if inter is not None:
if inter[2]==-1:
result = inter
else:
result = (inter[0],inter[1])
else:
result = inter
if result!=index:
markError("%s ==> %s, not %s"%(`coord`,`result`,`index`))
#!/usr/bin/env python
# Test dataset I/O
print 'Test 1: Dataset I/O ... ',
import cdms2,numpy,string,os,sys
cdms2.setNetcdfUseParallelFlag(0)
from cdms2.variable import WriteNotImplemented
from cdms2.avariable import NotImplemented
from markError import NTIME,NLAT,NLON,x,clearError,markError,reportError
clearError()
pth = os.path.dirname(os.path.abspath(__file__))
f = cdms2.open(os.path.join(pth,'test.xml'))
if f.id!='test': markError('File id',f.id)
u = f.variables['u']
try:
scalar = u[0,0,0]
except:
markError("Scalar slice")
try:
s = u.size()
except:
markError("Size")
else:
if s!=1536: markError("Size",s)
fullu = u[:]
uslice = u[:,4:12,8:24]
comp = x[0,:,4:12,8:24]
from markError import NTIME, NLAT, NLON, x, clearError, markError, reportError
clearError()
print 'Test 6: TransientVariables ...',
f = cdms2.open(os.path.join(sys.prefix, 'sample_data', 'test.xml'))
v = f.variables['v']
vp = x[1, 1:, 4:12, 8:25]
vp2 = vp[1, 1:-1, 1:]
tv = v.subRegion((366., 731., 'ccn'), (-42., 42., 'ccn'), (90., 270.))
tvv = v[0:2, 0:10, 30:40]
try:
xx = tv[1, 7, 15]
except ValueError:
markError("Scalar slice of transient variable")
# Variable get: axis, grid, latitude, level, longitude, missing, order, time, len, typecode
vaxis0 = v.getAxis(0)
axis0 = tv.getAxis(0)
if not numpy.ma.allequal(axis0[:], vaxis0[1:]):
markError('getAxis: ' + ` axis0[:] `)
taxis = tv.getTime()
taxisarray = taxis[:]
vaxisarray = vaxis0[1:]
if not numpy.ma.allequal(taxisarray, vaxisarray):
markError('getTime: ' + ` taxisarray `)
vaxis1 = v.getAxis(1)
print 'Test 8: Regridding ...',
## lat = cdms2.createGaussianAxis(32)
## lon = cdms2.createUniformLongitudeAxis(0.0,64,360.0/64.)
## outgrid = cdms2.createRectGrid(lat,lon,'yx','gaussian')
outgrid = cdms2.createGaussianGrid(32)
pth = os.path.dirname(os.path.abspath(__file__))
f = cdms2.open(os.path.join(pth,'readonly.nc'))
u = f.variables['u']
ingrid = u.getGrid()
try:
sh = ingrid.shape
except:
markError('Grid shape')
regridf = Regridder(ingrid, outgrid)
newu = regridf(u)
if (abs(newu[0,0,-1]-488.4763488) > 1.e-3): markError('regrid',newu[0,0,-1])
newu = u.regrid(outgrid,regridTool='regrid2')
if (abs(newu[0,0,-1]-488.4763488) > 1.e-3): markError('regrid',newu[0,0,-1])
# Regrid TV
tv = u.subSlice(0)
newtv = regridf(tv)
if (abs(newtv[0,0,-1]-488.4763488) > 1.e-3): markError('regrid tv',newtv[0,0,-1])
newtv = tv.regrid(outgrid,regridTool='regrid2')
if (abs(newtv[0,0,-1]-488.4763488) > 1.e-3): markError('regrid tv',newtv[0,0,-1])
print xmlpath, 'written'
#--------------------------------------------------------------------------------------------------------------------------
if __name__ == '__main__':
from cdms2 import CDMSError
print 'Test 7: Database import ...',
from markError import clearError, markError, reportError
clearError()
import os, sys
argv = string.split(
'cdtest07.py -q -d test -x junk.xml u_2000.nc u_2001.nc u_2002.nc v_2000.nc v_2001.nc v_2002.nc'
)
pth = os.path.dirname(os.path.abspath(__file__))
os.chdir(pth)
try:
main(argv)
except CDMSError, e:
markError(str(e))
except Exception, err:
markError("Importing dataset")
err = os.system("diff junk.xml test.xml")
if err != 0: markError("Comparison with benchmark test.xml")
reportError()
else:
datasetnode.dump(xmlpath)
if verbose:
print xmlpath,'written'
#--------------------------------------------------------------------------------------------------------------------------
if __name__ == '__main__':
from cdms2 import CDMSError
print 'Test 7: Database import ...',
from markError import clearError,markError,reportError
clearError()
import os,sys
argv = string.split('cdtest07.py -q -d test -x junk.xml u_2000.nc u_2001.nc u_2002.nc v_2000.nc v_2001.nc v_2002.nc')
os.chdir(os.path.join(sys.prefix,'sample_data'))
try:
main(argv)
except CDMSError,e:
markError(str(e))
except Exception,err:
markError("Importing dataset")
err = os.system("diff junk.xml test.xml")
if err!=0: markError("Comparison with benchmark test.xml")
reportError()
# Can't write a _FillValue attribute to a Variable
# J-Y Peterschmitt - LSCE - 07/2015
import cdms2, numpy, cdtime, os, sys
import numpy as np
from markError import NTIME, NLAT, NLON, x, clearError, markError, reportError
clearError()
data = np.random.random((10, 10))
data = np.ma.array(data, fill_value=1234.0)
data = np.ma.masked_less(data, 0.5)
dummy_grid = cdms2.createUniformGrid(10, 10, 1, 0, 10, 1)
dummy_var = cdms2.createVariable(data, axes=[dummy_grid.getLatitude(), dummy_grid.getLongitude()], id="my_var")
if dummy_var.fill_value != 1234.0:
markError("createVariable fill_value failed")
# Test if all fillvalue related attributes are changed
dummy_var.fill_value = 2.0e20
if (dummy_var.fill_value != 2.0e20) or (dummy_var._FillValue != 2.0e20) or (dummy_var.missing_value != 2.0e20):
markError("fill_value property failed (value 2.e20)")
dummy_var._FillValue = 1.33
if (dummy_var.fill_value != 1.33) or (dummy_var._FillValue != 1.33) or (dummy_var.missing_value != 1.33):
markError("fill_value property failed (value 1.33)")
dummy_var.dummy_att = "Dummy att"
dummy_var._dummy_att = "Dummy att starting with _"
dummy_var.units = "10e3 dummy"
clearError()
print 'Test 8: Regridding ...',
## lat = cdms2.createGaussianAxis(32)
## lon = cdms2.createUniformLongitudeAxis(0.0,64,360.0/64.)
## outgrid = cdms2.createRectGrid(lat,lon,'yx','gaussian')
outgrid = cdms2.createGaussianGrid(32)
f = cdms2.openDataset(os.path.join(get_sample_data_dir(), 'readonly.nc'))
u = f.variables['u']
ingrid = u.getGrid()
try:
sh = ingrid.shape
except:
markError('Grid shape')
regridf = Regridder(ingrid, outgrid)
newu = regridf(u)
if (abs(newu[0, 0, -1] - 488.4763488) > 1.e-3):
markError('regrid', newu[0, 0, -1])
newu = u.regrid(outgrid)
if (abs(newu[0, 0, -1] - 488.4763488) > 1.e-3):
markError('regrid', newu[0, 0, -1])
# Regrid TV
tv = u.subSlice(0)
newtv = regridf(tv)
if (abs(newtv[0, 0, -1] - 488.4763488) > 1.e-3):
markError('regrid tv', newtv[0, 0, -1])
import MV2
from markError import clearError,markError,reportError
print 'Test 15: reshape and mask and average ...',
a=MV2.arange(100)
try:
failed = False
a.shape=(10,10)
except:
failed = True
a = MV2.reshape(a,(10,10))
if failed is True: markError('shape should not have worked (protected attribute)')
if len(a.getAxisList())!=2: markError('reshape did not produce 2 axes')
a=MV2.masked_greater(a,23)
b=MV2.average(a,axis=0)
c=a-b
f2.close()
f3.close()
os.system(cdat_info.get_prefix()+"/bin/cdscan -q --forecast -x 'test_fc.xml' test_fc?")
# Read in the data.
fcs = cdms2.forecast.forecasts( 'test_fc.xml', ("2010-08-25","2010-08-27") )
vin = fcs('var')
fcaxis = vin._TransientVariable__domain[0][0]
tinaxis = vin._TransientVariable__domain[1][0]
xinaxis = vin._TransientVariable__domain[2][0]
# Test vin against original data, looking especially at the forecast axis.
# The following should be True, error otherwise:
if not vin.id == v1.id : markError("wrong variable ID")
if not numpy.alltrue( vin[0,:,:]==v1[:,:] ) : markError("wrong variable data for fc1")
if not numpy.alltrue( vin[1,:,:]==v2[:,:] ) : markError("wrong variable data for fc2")
if not vin.shape == (2,2,2) : markError("wrong variable shape")
if not numpy.allclose( tinaxis._data_ , taxis._data_ ) : markError( "wrong t axis data" )
if not numpy.allclose( xinaxis._data_ , xaxis._data_ ) : markError( "wrong x axis data" )
tinaxis=vin.getAxis(1)
print tinaxis
print tinaxis.isTime()
if not tinaxis.isTime()==True : markError( "time axis isn't time" )
if not xinaxis.isTime()==False : markError( "non-time axis is time" )
if not fcaxis.isTime()==False : markError( "forecast axis is time" )
if not fcaxis.isForecast()==True : markError( "forecast axis isn't forecast" )
if not fcaxis.shape == (3,) : markError( "forecast axis shape is wrong" )
#...Note that fcaxis is an Axis so its shape comes from len(fcaxis.node) which is the
# number of forecasts described in test_fc.xml; in contrast for TransientAxis the shape
import cdms2,os,sys
from cdms2.tvariable import TransientVariable as TV
import MV2
print 'Test 11: MV module (transient variable arithmetic) ... ',
from markError import NTIME,NLAT,NLON,x,clearError,markError,reportError
from markError import get_sample_data_dir
clearError()
d = cdms2.open(os.path.join(get_sample_data_dir(),'test.xml'))
ud = d['u']
vd = d['v']
udat = ud[:]
vdat = vd[:]
ulat = ud.getLatitude()
if not isinstance(udat, TV): markError('Slice does not return TV')
f = cdms2.open(os.path.join(get_sample_data_dir(),'u_2000.nc'))
uf = f['u']
vel = MV2.sqrt(ud*ud + vd*vd)
vel.id = 'velocity'
vel2 = MV2.sqrt(udat*udat + vdat*vdat)
vel2.id = 'velocity'
vel2.units = ud.units
if not MV2.allequal(vel,vel2): markError('Slice operators do not compare')
x1 = uf+1.0
x2 = 1.0-ud
x11 = -uf
x12 = MV2.absolute(ud)
x3 = uf+x2
## Automatically adapted for numpy.oldnumeric Aug 01, 2007 by
#!/usr/bin/env python
# Test dataset I/O
print 'Test 1: Dataset I/O ... ',
import cdms2,numpy,string,os,sys
from cdms2.variable import WriteNotImplemented
from cdms2.avariable import NotImplemented
from markError import NTIME,NLAT,NLON,x,clearError,markError,reportError
clearError()
f = cdms2.open(os.path.join(sys.prefix,'sample_data','test.xml'))
if f.id!='test': markError('File id',f.id)
u = f.variables['u']
try:
scalar = u[0,0,0]
except:
markError("Scalar slice")
try:
s = u.size()
except:
markError("Size")
else:
if s!=1536: markError("Size",s)
fullu = u[:]
uslice = u[:,4:12,8:24]
comp = x[0,:,4:12,8:24]
print "Test 11: MV module (transient variable arithmetic) ... ",
from markError import NTIME, NLAT, NLON, x, clearError, markError, reportError
clearError()
pth = os.path.dirname(os.path.abspath(__file__))
d = cdms2.open(os.path.join(pth, "test.xml"))
ud = d["u"]
vd = d["v"]
udat = ud[:]
vdat = vd[:]
ulat = ud.getLatitude()
if not isinstance(udat, TV):
markError("Slice does not return TV")
f = cdms2.open(os.path.join(pth, "u_2000.nc"))
uf = f["u"]
vel = MV2.sqrt(ud * ud + vd * vd)
vel.id = "velocity"
vel2 = MV2.sqrt(udat * udat + vdat * vdat)
vel2.id = "velocity"
vel2.units = ud.units
if not MV2.allequal(vel, vel2):
markError("Slice operators do not compare")
x1 = uf + 1.0
x2 = 1.0 - ud
x11 = -uf
x12 = MV2.absolute(ud)
g.write(tchunk)
g.close()
imo += 12
os.unlink('cdtest10_t_2001.nc')
os.unlink('cdtest10_t_2003.nc')
os.unlink('cdtest10_uv_2003.nc')
os.unlink('cdtest10_uv_2005.nc')
# Test filemap access ...
try:
shutil.copy2(os.path.join(pth,"cdtest10.xml"),"cdtest10.xml")
f = cdms2.open('cdtest10.xml')
except Exception,err:
print err
markError('Opening cdtest10.xml using filemap: Version 3.0 or greater required')
reportError()
sys.exit(1)
# Read u from 2001-7 to 2002-7 and compare
u = f.getVariable('u')
t = u.getTime()
t1 = cdtime.comptime(2001,7).torel(t.units).value
t2 = cdtime.comptime(2002,7).torel(t.units).value
uar2 = u.getRegion(time=(t1,t2,'con'))
uar2p = uar[18:30]
if not numpy.ma.allclose(uar2,uar2p): markError('u.getRegion() from 2001-7 to 2002-7 failed',uar2[0,0,0])
# Read u from 2003-7 to 2004-7 and compare
t1 = cdtime.comptime(2003,7).torel(t.units).value
t2 = cdtime.comptime(2004,7).torel(t.units).value
f2.close()
f3.close()
os.system(sys.prefix + "/bin/cdscan -q --forecast -x 'test_fc.xml' test_fc?")
# Read in the data.
fcs = cdms2.forecast.forecasts('test_fc.xml', ("2010-08-25", "2010-08-27"))
vin = fcs('var')
fcaxis = vin._TransientVariable__domain[0][0]
tinaxis = vin._TransientVariable__domain[1][0]
xinaxis = vin._TransientVariable__domain[2][0]
# Test vin against original data, looking especially at the forecast axis.
# The following should be True, error otherwise:
if not vin.id == v1.id: markError("wrong variable ID")
if not numpy.alltrue(vin[0, :, :] == v1[:, :]):
markError("wrong variable data for fc1")
if not numpy.alltrue(vin[1, :, :] == v2[:, :]):
markError("wrong variable data for fc2")
if not vin.shape == (2, 2, 2): markError("wrong variable shape")
if not numpy.allclose(tinaxis._data_, taxis._data_):
markError("wrong t axis data")
if not numpy.allclose(xinaxis._data_, xaxis._data_):
markError("wrong x axis data")
tinaxis = vin.getAxis(1)
print tinaxis
print tinaxis.isTime()
if not tinaxis.isTime() == True: markError("time axis isn't time")
if not xinaxis.isTime() == False: markError("non-time axis is time")
if not fcaxis.isTime() == False: markError("forecast axis is time")
import MV2
from markError import clearError, markError, reportError
clearError()
print 'Test 15: reshape and mask and average ...',
a = MV2.arange(100)
try:
failed = False
a.shape = (10, 10)
except:
failed = True
a = MV2.reshape(a, (10, 10))
if failed is False:
markError('shape should not have worked (protected attribute)')
if len(a.getAxisList()) != 2: markError('reshape did not produce 2 axes')
a = MV2.masked_greater(a, 23)
b = MV2.average(a, axis=0)
c = a - b
reportError()
os.unlink('cdtest10_t_2001.nc')
os.unlink('cdtest10_t_2003.nc')
os.unlink('cdtest10_uv_2003.nc')
os.unlink('cdtest10_uv_2005.nc')
# Copy cdtest10.xml to working directory
shutil.copyfile(os.path.join(get_sample_data_dir(), 'cdtest10.xml'),
'cdtest10.xml')
# Test filemap access ...
try:
f = cdms2.open('cdtest10.xml')
except Exception, err:
print err
markError(
'Opening cdtest10.xml using filemap: Version 3.0 or greater required')
reportError()
sys.exit(1)
# Read u from 2001-7 to 2002-7 and compare
u = f.getVariable('u')
t = u.getTime()
t1 = cdtime.comptime(2001, 7).torel(t.units).value
t2 = cdtime.comptime(2002, 7).torel(t.units).value
uar2 = u.getRegion(time=(t1, t2, 'con'))
uar2p = uar[18:30]
if not numpy.ma.allclose(uar2, uar2p):
markError('u.getRegion() from 2001-7 to 2002-7 failed', uar2[0, 0, 0])
# Read u from 2003-7 to 2004-7 and compare
t1 = cdtime.comptime(2003, 7).torel(t.units).value
f = cdms2.createDataset("readwrite4.nc")
pth = os.path.dirname(os.path.abspath(__file__))
h = cdms2.open(os.path.join(pth, "readonly.nc"))
tobj = f.createAxis("time", numpy.ma.array([time[1]]))
tobj.units = "days since 2000-1-1"
latobj = f.createAxis("latitude", lat)
latobj.units = "degrees_north"
lonobj = f.createAxis("longitude", lon)
lonobj.units = "degrees_east"
var = f.createVariable("u", numpy.float, (tobj, latobj, lonobj))
var.units = "m/s"
try:
var[:] = u[0]
except:
markError("Setting a slice")
try:
var.assignValue(u[0])
except:
markError("Assigning an array")
try:
var[0, 4:12] = -u[0, 4:12]
except:
markError("Setting an item")
varattrs = var.attributes
var.long_name = "Test variable"
var.param = -99
if var.param != -99:
markError("R/W param: " + var.param)
if (not var.attributes.has_key("param")) or var.attributes["param"] != -99:
f2.close()
f3.close()
os.system("../Script/cdscan -q --forecast -x 'test_fc.xml' test_fc?")
# Read in the data.
fcs = cdms2.forecast.forecasts( 'test_fc.xml', ("2010-08-25","2010-08-27") )
vin = fcs('var')
fcaxis = vin._TransientVariable__domain[0][0]
tinaxis = vin._TransientVariable__domain[1][0]
xinaxis = vin._TransientVariable__domain[2][0]
# Test vin against original data, looking especially at the forecast axis.
# The following should be True, error otherwise:
if not vin.id == v1.id : markError("wrong variable ID")
if not numpy.alltrue( vin[0,:,:]==v1[:,:] ) : markError("wrong variable data for fc1")
if not numpy.alltrue( vin[1,:,:]==v2[:,:] ) : markError("wrong variable data for fc2")
if not vin.shape == (2,2,2) : markError("wrong variable shape")
if not numpy.alltrue( tinaxis._data_ == taxis._data_ ) : markError( "wrong t axis data" )
if not numpy.alltrue( xinaxis._data_ == xaxis._data_ ) : markError( "wrong x axis data" )
if not tinaxis.isTime()==True : markError( "time axis isn't time" )
if not xinaxis.isTime()==False : markError( "non-time axis is time" )
if not fcaxis.isTime()==False : markError( "forecast axis is time" )
if not fcaxis.isForecast()==True : markError( "forecast axis isn't forecast" )
if not fcaxis.shape == (3,) : markError( "forecast axis shape is wrong" )
#...Note that fcaxis is an Axis so its shape comes from len(fcaxis.node) which is the
# number of forecasts described in test_fc.xml; in contrast for TransientAxis the shape
# would be len(fcaxis._data_) which is the number of forecasts that have been read.
if not fcaxis._data_ == [2010082500000L, 2010082600000L] : markError( "wrong forecast axis data" )
if not fcaxis.id == 'fctau0' : markError( "wrong forecast axis id" )
print 'Test 5: get/sub, time functions ...',
pth = os.path.dirname(os.path.abspath(__file__))
f = cdms2.open(os.path.join(pth, 'test.xml'))
v = f.variables['v']
vp = x[1, 1:, 4:12, 8:24]
wp = x[1, 2, 4:12]
xp = numpy.ma.concatenate((x[1, 1:, 4:12, 8:NLON], x[1, 1:, 4:12, 0:8]),
axis=2)
# getRegion - positional
s = v.getRegion((366., 731., 'ccn'), (-42., 42., 'ccn'), (90., 270., 'con'))
if not numpy.ma.allequal(vp, s): markError('getRegion/positional failed')
# getRegion - keyword
s = v.getRegion(latitude=(-42., 42., 'ccn'),
longitude=(90., 270., 'con'),
time=(366., 731., 'ccn'))
if not numpy.ma.allequal(vp, s): markError('getRegion/keyword failed')
# getRegion - wraparound
s4 = v.getRegion(time=(366., 731., 'ccn'),
latitude=(-42., 42., 'ccn'),
longitude=(90., 450., 'con'))
if not numpy.ma.allequal(xp, s4): markError('getRegion wraparound failed')
# getSlice - positional
s = v.getSlice(2, (4, 12), Ellipsis, squeeze=0)
print "Test 2: CdmsFile I/O ... ",
import cdms2, numpy, string, os, sys
from numpy.ma import masked
from markError import NTIME, NLAT, NLON, x, clearError, markError, reportError
clearError()
f = cdms2.open(os.path.join(sys.prefix, "sample_data", "readonly.nc"))
u = f.variables["u"]
umasked = f.variables["umasked"]
try:
s = u.size()
except:
markError("Size")
else:
if s != 512:
markError("Size", s)
uslice = u[:, 4:12, 8:24]
fullu = u[:]
uslicemask = umasked[:, 0:4, 8:24]
comp = x[0, 0, 4:12, 8:24]
compmask = x[0, 0, 0:4, 8:24]
compmask[1] = masked
lonaxis = f["longitude"]
if not numpy.ma.allequal(lonaxis.getValue(), lonaxis[:]):
markError("Axis getValue()")
print 'Test 2: CdmsFile I/O ... ',
import cdms2, numpy, string, os, sys
from numpy.ma import masked
from markError import NTIME, NLAT, NLON, x, clearError, markError, reportError
clearError()
f = cdms2.open(os.path.join(sys.prefix, 'sample_data', 'readonly.nc'))
u = f.variables['u']
umasked = f.variables['umasked']
try:
s = u.size()
except:
markError("Size")
else:
if s != 512: markError("Size", s)
uslice = u[:, 4:12, 8:24]
fullu = u[:]
uslicemask = umasked[:, 0:4, 8:24]
comp = x[0, 0, 4:12, 8:24]
compmask = x[0, 0, 0:4, 8:24]
compmask[1] = masked
lonaxis = f['longitude']
if not numpy.ma.allequal(lonaxis.getValue(), lonaxis[:]):
markError("Axis getValue()")
if not numpy.ma.allequal(uslice, comp): markError("Slice read")
print 'Test 2: CdmsFile I/O ... ',
import cdms2,numpy,string,os,sys
from numpy.ma import masked
from markError import NTIME,NLAT,NLON,x,clearError,markError,reportError
from markError import get_sample_data_dir
clearError()
f = cdms2.open(os.path.join(get_sample_data_dir(),'readonly.nc'))
u = f.variables['u']
umasked = f.variables['umasked']
try:
s = u.size()
except:
markError("Size")
else:
if s!=512: markError("Size",s)
uslice = u[:,4:12,8:24]
fullu = u[:]
uslicemask = umasked[:,0:4,8:24]
comp = x[0,0,4:12,8:24]
compmask = x[0,0,0:4,8:24]
compmask[1]=masked
lonaxis = f['longitude']
if not numpy.ma.allequal(lonaxis.getValue(), lonaxis[:]): markError("Axis getValue()")
if not numpy.ma.allequal(uslice,comp): markError("Slice read")
if not numpy.ma.allequal(uslicemask,compmask): markError("Slice read, masked")
latb = numpy.array([
-26.67690036,
-30.99890917,
])
lonb = numpy.array([
92.41822415,
94.4512163,
])
f = cdms2.open(os.path.join(sys.prefix, 'sample_data', 'sampleGenGrid3.nc'))
# Slice a file variable on a curvilinear grid: by coordinates ...
samp = f['sample']
x = samp(lat=(-32, -25), lon=(90, 95))
if not numpy.ma.allequal(x.data, datb):
markError('slicing a file variable by coordinates')
grid = x.getGrid()
if grid.shape != (2, ):
markError('grid shape is wrong')
lat = grid.getLatitude()
if not numpy.ma.allclose(lat.data, latb, atol=1.e-5):
markError('latitude array is wrong')
lon = grid.getLongitude()
if not numpy.ma.allclose(lon.data, lonb, atol=1.e-5):
markError('longitude array is wrong')
# ... and by index
y = samp[693:695]
if not numpy.ma.allequal(y, datb):
markError('slicing a file variable by index')
timestr = ['2000','2001','2002']
u = x[0]
f = cdms2.createDataset('readwrite3.nc')
tobj = f.createAxis('time',numpy.array([time[1]]))
tobj.units = 'days since 2000-1-1'
latobj = f.createAxis('latitude',lat)
latobj.units = 'degrees_north'
lonobj = f.createAxis('longitude',lon)
lonobj.units = 'degrees_east'
var = f.createVariable('u',cdms2.CdDouble,(tobj,latobj,lonobj))
var.units = 'm/s'
try:
var[:]=u[0]
except:
markError("Setting a slice")
try:
var.assignValue(u[0])
except:
markError("Assigning an array")
try:
var[0,4:12] = -u[0,4:12]
except:
markError("Setting an item")
var.long_name = 'Test variable'
var.param = -99
if var.param!=-99: markError("R/W param: "+var.param)
f.Conventions = 'CF1.0'
clearError()
print 'Test 6: TransientVariables ...',
pth = os.path.dirname(os.path.abspath(__file__))
f = cdms2.open(os.path.join(pth,'test.xml'))
v = f.variables['v']
vp = x[1,1:,4:12,8:25]
vp2 = vp[1,1:-1,1:]
tv = v.subRegion((366.,731.,'ccn'),(-42.,42.,'ccn'),(90.,270.))
tvv = v[0:2,0:10,30:40]
try:
xx = tv[1,7,15]
except ValueError:
markError("Scalar slice of transient variable")
# Variable get: axis, grid, latitude, level, longitude, missing, order, time, len, typecode
vaxis0 = v.getAxis(0)
axis0 = tv.getAxis(0)
if not numpy.ma.allequal(axis0[:],vaxis0[1:]): markError('getAxis: '+`axis0[:]`)
taxis = tv.getTime()
taxisarray = taxis[:]
vaxisarray = vaxis0[1:]
if not numpy.ma.allequal(taxisarray,vaxisarray): markError('getTime: '+`taxisarray`)
vaxis1 = v.getAxis(1)
lataxis = tv.getLatitude()
if not numpy.ma.allequal(lataxis[:],vaxis1[4:12]): markError('getLatitude: '+`lataxis[:]`)
import numpy as np
from markError import NTIME, NLAT, NLON, x, clearError, markError, reportError
clearError()
data = np.random.random((10, 10))
data = np.ma.array(data, fill_value=1234.0)
data = np.ma.masked_less(data, 0.5)
dummy_grid = cdms2.createUniformGrid(10, 10, 1, 0, 10, 1)
dummy_var = cdms2.createVariable(
data,
axes=[dummy_grid.getLatitude(),
dummy_grid.getLongitude()],
id='my_var')
if dummy_var.fill_value != 1234.0:
markError("createVariable fill_value failed")
# Test if all fillvalue related attributes are changed
dummy_var.fill_value = 2.e+20
if (dummy_var.fill_value != 2.e20) or \
(dummy_var._FillValue != 2.e20) or \
(dummy_var.missing_value != 2.e20) :
markError("fill_value property failed (value 2.e20)")
dummy_var._FillValue = 1.33
if (dummy_var.fill_value != 1.33) or \
(dummy_var._FillValue != 1.33) or \
(dummy_var.missing_value != 1.33) :
markError("fill_value property failed (value 1.33)")
dummy_var.dummy_att = 'Dummy att'
tchunk = t.subSlice((imo,imo+12))
g.write(tchunk)
g.close()
imo += 12
os.unlink('cdtest10_t_2001.nc')
os.unlink('cdtest10_t_2003.nc')
os.unlink('cdtest10_uv_2003.nc')
os.unlink('cdtest10_uv_2005.nc')
# Test filemap access ...
try:
f = cdms2.open('cdtest10.xml')
except Exception,err:
print err
markError('Opening cdtest10.xml using filemap: Version 3.0 or greater required')
reportError()
sys.exit(1)
# Read u from 2001-7 to 2002-7 and compare
u = f.getVariable('u')
t = u.getTime()
t1 = cdtime.comptime(2001,7).torel(t.units).value
t2 = cdtime.comptime(2002,7).torel(t.units).value
uar2 = u.getRegion(time=(t1,t2,'con'))
uar2p = uar[18:30]
if not numpy.ma.allclose(uar2,uar2p): markError('u.getRegion() from 2001-7 to 2002-7 failed',uar2[0,0,0])
# Read u from 2003-7 to 2004-7 and compare
t1 = cdtime.comptime(2003,7).torel(t.units).value
t2 = cdtime.comptime(2004,7).torel(t.units).value
[[0,0,0,0,0,0,],
[0,0,0,0,0,0,],
[0,0,0,0,0,0,],
[0,0,0,0,0,0,],
[1,1,1,1,1,0,]], 'b')
f = cdms2.open(os.path.join(pth,'sampleCurveGrid4.nc'))
#-------------------------------------------------------------
# Slice a file variable on a curvilinear grid: by coordinates ...
samp = f['sample']
x=samp()
x = samp(lat=(-10,30), lon=(90,150))
if not numpy.ma.allequal(x.data, datb):
markError('slicing a file variable by coordinates')
if not numpy.ma.allequal(x.mask, maskb):
markError('slicing a file variable by coordinates: invalid mask')
grid = x.getGrid()
if not (grid.shape==(5,6)):
markError('grid shape is wrong')
lat = grid.getLatitude()
if not numpy.ma.allclose(lat.data, latb, atol=1.e-5):
markError('latitude array is wrong')
lon = grid.getLongitude()
if not numpy.ma.allclose(lon.data, lonb, atol=1.e-5):
markError('longitude array is wrong')
# ... and by index
y = samp[14:19, 25:31]
clearError()
print 'Test 18: numpy types with NetCDF4 ...',
for t in [numpy.byte,numpy.short,numpy.int,numpy.int32,numpy.float,numpy.float32,numpy.double,numpy.ubyte,numpy.ushort,numpy.uint,numpy.int64,numpy.uint64]:
print 'Testing type:',t
data = numpy.array([0], dtype=t)
var = cdms2.createVariable(data)
f = cdms2.open('test_%s.nc'%data.dtype.char, 'w')
f.write(var, id='test')
f.close()
f=cdms2.open('test_%s.nc'%data.dtype.char)
s=f("test")
f.close()
os.unlink("test_%s.nc" % data.dtype.char)
print 'Done'
cdms2.setNetcdfShuffleFlag(0)
cdms2.setNetcdfDeflateFlag(0)
cdms2.setNetcdfDeflateLevelFlag(0)
var = cdms2.createVariable(numpy.array([0], dtype=numpy.int64))
f = cdms2.open('test.nc', 'w')
try:
f.write(var, id='test')
except Exception,err:
markError("Writing Netcdf4 type to NetCDF3 format")
os.unlink("test.nc")
f.close()
reportError()
)
maskb = numpy.array(
[[0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0], [1, 1, 1, 1, 1, 0]], "b"
)
f = cdms2.open(os.path.join(sys.prefix, "sample_data", "sampleCurveGrid4.nc"))
# -------------------------------------------------------------
# Slice a file variable on a curvilinear grid: by coordinates ...
samp = f["sample"]
x = samp()
x = samp(lat=(-10, 30), lon=(90, 150))
if not numpy.ma.allequal(x.data, datb):
markError("slicing a file variable by coordinates")
if not numpy.ma.allequal(x.mask, maskb):
markError("slicing a file variable by coordinates: invalid mask")
grid = x.getGrid()
if not (grid.shape == (5, 6)):
markError("grid shape is wrong")
lat = grid.getLatitude()
if not numpy.ma.allclose(lat.data, latb, atol=1.0e-5):
markError("latitude array is wrong")
lon = grid.getLongitude()
if not numpy.ma.allclose(lon.data, lonb, atol=1.0e-5):
markError("longitude array is wrong")
# ... and by index
y = samp[14:19, 25:31]
u = x[0]
f = cdms2.createDataset('readwrite.nc')
h = cdms2.open(os.path.join(get_sample_data_dir(),'readonly.nc'))
tobj = f.createAxis('time',numpy.ma.array([time[1]]))
tobj.units = 'days since 2000-1-1'
latobj = f.createAxis('latitude',lat)
latobj.units = 'degrees_north'
lonobj = f.createAxis('longitude',lon)
lonobj.units = 'degrees_east'
var = f.createVariable('u',numpy.float,(tobj,latobj,lonobj))
var.units = 'm/s'
try:
var[:]=u[0]
except:
markError("Setting a slice")
try:
var.assignValue(u[0])
except:
markError("Assigning an array")
try:
var[0,4:12] = -u[0,4:12]
except:
markError("Setting an item")
varattrs = var.attributes
var.long_name = 'Test variable'
var.param = -99
if var.param!=-99: markError("R/W param: "+var.param)
if (not var.attributes.has_key('param')) or var.attributes['param']!=-99: markError("Updating variable attributes")
import cdms2, numpy, os, sys
from markError import clearError,markError,reportError
from markError import get_sample_data_dir
clearError()
datb = numpy.array([ 693., 694.,])
latb = numpy.array([-26.67690036,-30.99890917,])
lonb = numpy.array([92.41822415, 94.4512163 ,])
f = cdms2.open(os.path.join(get_sample_data_dir(),'sampleGenGrid3.nc'))
# Slice a file variable on a curvilinear grid: by coordinates ...
samp = f['sample']
x = samp(lat=(-32,-25), lon=(90,95))
if not numpy.ma.allequal(x.data, datb):
markError('slicing a file variable by coordinates')
grid = x.getGrid()
if grid.shape!=(2,):
markError('grid shape is wrong')
lat = grid.getLatitude()
if not numpy.ma.allclose(lat.data, latb, atol=1.e-5):
markError('latitude array is wrong')
lon = grid.getLongitude()
if not numpy.ma.allclose(lon.data, lonb, atol=1.e-5):
markError('longitude array is wrong')
# ... and by index
y = samp[693:695]
if not numpy.ma.allequal(y, datb):
markError('slicing a file variable by index')
from markError import NTIME,NLAT,NLON,x,clearError,markError,reportError
from markError import get_sample_data_dir
clearError()
print 'Test 5: get/sub, time functions ...',
f = cdms2.open(os.path.join(get_sample_data_dir(),'test.xml'))
v = f.variables['v']
vp = x[1,1:,4:12,8:24]
wp = x[1,2,4:12]
xp = numpy.ma.concatenate((x[1,1:,4:12,8:NLON],x[1,1:,4:12,0:8]),axis=2)
# getRegion - positional
s = v.getRegion((366.,731.,'ccn'),(-42.,42.,'ccn'),(90.,270.,'con'))
if not numpy.ma.allequal(vp,s): markError('getRegion/positional failed')
# getRegion - keyword
s = v.getRegion(latitude=(-42.,42.,'ccn'),longitude=(90.,270.,'con'),time=(366.,731.,'ccn'))
if not numpy.ma.allequal(vp,s): markError('getRegion/keyword failed')
# getRegion - wraparound
s4 = v.getRegion(time=(366.,731.,'ccn'),latitude=(-42.,42.,'ccn'),longitude=(90.,450.,'con'))
if not numpy.ma.allequal(xp,s4): markError('getRegion wraparound failed')
# getSlice - positional
s = v.getSlice(2,(4,12),Ellipsis,squeeze=0)
if not numpy.ma.allequal(wp,s): markError('getSlice/positional failed')
# getSlice - keyword
s = v.getSlice(latitude=(4,12), time=2)
def testCal(a,b,c,d,e,f,g,cal=cdtime.MixedCalendar):
x = cdtime.comptime(d,e,f)
units = "days since %d-%d-%d"%(a,b,c)
r = x.torel(units,cal)
if not isEqual(r.value,g):
markError('component => relative failed: %s %s'%(`x`,`r`))
r2 = cdtime.reltime(g, units)
x2 = r2.tocomp(cal)
if not cmpYear(x,x2):
markError('relative => component failed: %s %s'%(`r2`,`x2`))
units2 = "days since %d-%d-%d"%(d,e,f)
r3 = cdtime.reltime(10.0,units2)
r4 = r3.torel(units)
if not isEqual(r4.value,(10.0+g)):
markError('relative => relative: %s %s'%(`r3`,`r4`))
bb = cdtime.comptime(a,b,c)
x2 = bb.add(g,cdtime.Day,cal)
if not cmpYear(x,x2):
markError('component add failed: %s %s'%(`bb`,`x2`))
x2 = x.sub(g,cdtime.Day,cal)
if not cmpYear(bb,x2):
markError('component sub failed: %s %s'%(`x`,`x2`))
r2 = cdtime.reltime(g, units)
r3 = r2.add(1000.0,cdtime.Day,cal)
if not isEqual(r3.value, g+1000.0):
markError('relative add failed: %s %s'%(`r2`,`r3`))
r3 = r2.sub(1000.0,cdtime.Day,cal)
if not isEqual(r3.value, g-1000.0):
markError('relative sub failed: %s %s'%(`r2`,`r3`))
from cdms2.tvariable import TransientVariable as TV
import MV2
print 'Test 11: MV module (transient variable arithmetic) ... ',
from markError import NTIME, NLAT, NLON, x, clearError, markError, reportError
clearError()
pth = os.path.dirname(os.path.abspath(__file__))
d = cdms2.open(os.path.join(pth, 'test.xml'))
ud = d['u']
vd = d['v']
udat = ud[:]
vdat = vd[:]
ulat = ud.getLatitude()
if not isinstance(udat, TV): markError('Slice does not return TV')
f = cdms2.open(os.path.join(pth, 'u_2000.nc'))
uf = f['u']
vel = MV2.sqrt(ud * ud + vd * vd)
vel.id = 'velocity'
vel2 = MV2.sqrt(udat * udat + vdat * vdat)
vel2.id = 'velocity'
vel2.units = ud.units
if not MV2.allequal(vel, vel2): markError('Slice operators do not compare')
x1 = uf + 1.0
x2 = 1.0 - ud
x11 = -uf
x12 = MV2.absolute(ud)
x3 = uf + x2
[[0,0,0,0,0,0,],
[0,0,0,0,0,0,],
[0,0,0,0,0,0,],
[0,0,0,0,0,0,],
[1,1,1,1,1,0,]], 'b')
f = cdms2.open(os.path.join(get_sample_data_dir(),'sampleCurveGrid4.nc'))
#-------------------------------------------------------------
# Slice a file variable on a curvilinear grid: by coordinates ...
samp = f['sample']
x=samp()
x = samp(lat=(-10,30), lon=(90,150))
if not numpy.ma.allequal(x.data, datb):
markError('slicing a file variable by coordinates')
if not numpy.ma.allequal(x.mask, maskb):
markError('slicing a file variable by coordinates: invalid mask')
grid = x.getGrid()
if not (grid.shape==(5,6)):
markError('grid shape is wrong')
lat = grid.getLatitude()
if not numpy.ma.allclose(lat.data, latb, atol=1.e-5):
markError('latitude array is wrong')
lon = grid.getLongitude()
if not numpy.ma.allclose(lon.data, lonb, atol=1.e-5):
markError('longitude array is wrong')
# ... and by index
y = samp[14:19, 25:31]
