def create_group(self,name):
'''
Create a new group with given name in a writable file.
f.create_group(name)
name -- a string specifying the group name.
'''
#print 'in create group'
#import pdb; pdb.set_trace()
g = self._obj.create_group(name)
if not g is None:
gp = _proxy(g,'str')
#gp.file = weakref.proxy(g)
gp.file = g
if self.parent is None:
gp.parent = weakref.proxy(self.groups['/'])
else:
gp.parent = weakref.proxy(self)
gp.ma_mode = self.ma_mode
gp.groups = nd.nioDict()
gp.groups.path = g.path
gp.variables = nd.nioDict()
gp.variables.path = g.path
if self.groups.topdict is None:
self.groups[name] = gp
self.groups['/'].groups[name] = gp
gp.groups.topdict = self.groups
gp.variables.topdict = self.variables
elif self.name is '/':
self.groups.topdict[name] = gp
self.groups[name] = gp
gp.groups.topdict = self.groups.topdict
gp.variables.topdict = self.variables.topdict
else:
path = self.path + '/' + name
self.groups.topdict[path] = gp
self.groups[name] = gp
gp.groups.topdict = self.groups.topdict
gp.variables.topdict = self.variables.topdict
return gp
else:
return None
def create_group(self,name):
'''
Create a new group with given name in a writable file.
f.create_group(name)
name -- a string specifying the group name.
'''
#print 'in create group'
#import pdb; pdb.set_trace()
g = self._obj.create_group(name)
if not g is None:
gp = _proxy(g,'str')
#gp.file = weakref.proxy(g)
gp.file = g
if self.parent is None:
gp.parent = weakref.proxy(self.groups['/'])
else:
gp.parent = weakref.proxy(self)
gp.ma_mode = self.ma_mode
gp.groups = nd.nioDict()
gp.groups.path = g.path
gp.variables = nd.nioDict()
gp.variables.path = g.path
if self.groups.topdict is None:
self.groups[name] = gp
self.groups['/'].groups[name] = gp
gp.groups.topdict = self.groups
gp.variables.topdict = self.variables
elif self.name is '/':
self.groups.topdict[name] = gp
self.groups[name] = gp
gp.groups.topdict = self.groups.topdict
gp.variables.topdict = self.variables.topdict
else:
path = self.path + '/' + name
self.groups.topdict[path] = gp
self.groups[name] = gp
gp.groups.topdict = self.groups.topdict
gp.variables.topdict = self.variables.topdict
return gp
else:
return None
def _create_coordinates_attriibute(file,var):
coords = nd.nioDict()
#print "creating coordinates attribute for ", var.name
if len(var.dimensions) == 1 and var.dimensions[0] == var.name:
coords[var.name] = var
return coords
if var.parent is None:
parent = file
else:
parent = var.parent
cnames = None
cdict = {}
if var.attributes.has_key('coordinates'):
s = var.attributes['coordinates'].replace(',',' ')
cnames = s.split()
#print var.attributes['coordinates']
dlist = []
if not cnames is None:
for c in cnames:
if c in parent.variables.keys():
cdict[c] = parent.variables[c]
if dlist.count(cdict[c].dimensions) == 0:
dlist.append(cdict[c].dimensions)
#if len(cdict) > 0: print cdict, dlist
dims = []
if len(dlist) == 1: # means there is only one set of coordinates involved
cd = dlist[0] # cd is the dimension tuple
dims = list(var.dimensions)
for d in cd:
if d in dims:
dims.remove(d)
coords[cd] = tuple(cdict.values())
for d in dims:
while not parent is None:
if d in parent.dimensions.keys():
for v in parent.variables.values():
if d == v.name and v.rank == 1:
coords[d] = v
break
parent = parent.parent
#print coords
return coords
def _create_coordinates_attriibute(file,var):
coords = nd.nioDict()
#print "creating coordinates attribute for ", var.name
if len(var.dimensions) == 1 and var.dimensions[0] == var.name:
coords[var.name] = var
return coords
if var.parent is None:
parent = file
else:
parent = var.parent
cnames = None
cdict = {}
if var.attributes.has_key('coordinates'):
s = var.attributes['coordinates'].replace(',',' ')
cnames = s.split()
#print var.attributes['coordinates']
dlist = []
if not cnames is None:
for c in cnames:
if c in parent.variables.keys():
cdict[c] = parent.variables[c]
if dlist.count(cdict[c].dimensions) == 0:
dlist.append(cdict[c].dimensions)
#if len(cdict) > 0: print cdict, dlist
dims = []
if len(dlist) == 1: # means there is only one set of coordinates involved
cd = dlist[0] # cd is the dimension tuple
dims = list(var.dimensions)
for d in cd:
if d in dims:
dims.remove(d)
coords[cd] = tuple(cdict.values())
for d in dims:
while not parent is None:
if d in parent.dimensions.keys():
for v in parent.variables.values():
if d == v.name and v.rank == 1:
coords[d] = v
break
parent = parent.parent
#print coords
return coords
def open_file(filename, mode = 'r', options=None, history='', format=''):
'''
Open a file containing data in a supported format for reading and/or writing.
f = Nio.open_file(filepath, mode='r',options=None, history='', format='')
filepath -- path of file with data in a supported format. Either the path must
end with an extension indicating the expected format of the file (it need not
be part of the actual file name), or it must be specified using the optional
'format' argument. Valid extensions include:
.nc, .cdf, .netcdf, .nc3, .nc4, -- NetCDF
.gr, .grb, .grib, .gr1, .grb1, .grib1, .gr2, .grb2, .grib2, -- GRIB
.hd, .hdf -- HDF
.h5, .hdf5 -- HDF5
.he2, .he4, .hdfeos -- HDFEOS
.he5, .hdfeos5 -- HDFEOS5
.shp, .mif, .gmt, .rt1 -- shapefiles, other formats supported by GDAL OGR
.ccm -- CCM history files
Extensions are handled case-insensitvely, i.e.: .grib, .GRIB, and .Grib all
indicate a GRIB file.
mode -- access mode (optional):
'r' -- open an existing file for reading
'w','r+','rw','a' -- open an existing file for modification
'c' -- create a new file open for writing
options -- instance of NioOptions class used to specify generic or
format-specific options.
history -- a string specifying text to be appended to the file's global
attribute. The attribute is created if it does not exist. Only valid
if the file is opened for writing.
format -- a string specifying the expected format. Valid strings are the
same as the extensions listed above without the initial period (.).
Returns an NioFile object.
'''
ma_mode = _get_masked_array_mode(options,_Nio.option_defaults)
use_axis_att = _get_axis_att(options,_Nio.option_defaults)
explicit_fill_values = _get_option_value(options,_Nio.option_defaults,'ExplicitFillValues')
mask_below_value = _get_option_value(options,_Nio.option_defaults,'MaskBelowValue')
mask_above_value = _get_option_value(options,_Nio.option_defaults,'MaskAboveValue')
file = _Nio.open_file(filename,mode,options,history,format)
file_proxy = _proxy(file, 'str', __del__=__del__,create_variable=create_variable,create_group=create_group,close=close)
setattr(file_proxy.__class__,'set_option',set_option)
file_proxy.file = file
file_proxy.parent = None
file_proxy.open = 1
if not (explicit_fill_values is None and mask_below_value is None and mask_above_value is None):
file_proxy.ma_mode = 'maskedexplicit'
else:
file_proxy.ma_mode = ma_mode
file_proxy.explicit_fill_values = explicit_fill_values
file_proxy.mask_below_value = mask_below_value
file_proxy.mask_above_value = mask_above_value
if use_axis_att:
cf_dims = _get_cf_dims(file_proxy)
newdims = {}
cf2dims = {}
dimensions = file_proxy.dimensions
for dim in dimensions:
try:
newdim = cf_dims[dim]
except KeyError:
newdim = dim
newdims[newdim] = dimensions[dim]
cf2dims[newdim] = dim
else:
cf2dims = None
newdims = file_proxy.dimensions
file_proxy.cf_dimensions = newdims
file_proxy.cf2dims = cf2dims
variable_proxies = nd.nioDict()
variable_proxies.path = '/'
variable_proxies.topdict = None
for var in file.variables.keys():
# print var, ": ", sys.getrefcount(file.variables[var])
vp = _proxy(file.variables[var],'str','len',
__setitem__=__setitem__,__getitem__=__getitem__,get_value=get_value,assign_value=assign_value)
vp.file = weakref.proxy(file_proxy)
# vp.file = file_proxy
vp.varname = var
vp.parent = None
variable_proxies[var] = vp
if use_axis_att:
newdims = []
dimensions = vp.dimensions
for dim in dimensions:
try:
newdim = cf_dims[dim]
except KeyError:
newdim = dim
newdims.append(newdim)
vp.cf_dimensions = tuple(newdims)
else:
vp.cf_dimensions = vp.dimensions
#print var, ": ", sys.getrefcount(file.variables[var])
file_proxy.variables = variable_proxies
group_proxies = nd.nioDict()
group_proxies.path = '/'
group_proxies.topdict = None
for group in file.groups.keys():
# print group, ": ", sys.getrefcount(file.groups[group])
gp = _proxy(file.groups[group], 'str')
gp.file = weakref.proxy(file.groups[group])
gp.ma_mode = file_proxy.ma_mode
#gp.file = file_proxy
group_proxies[group] = gp
v_proxy_refs = nd.nioDict()
v_proxy_refs.path = file.groups[group].path
v_proxy_refs.topdict = weakref.proxy(file_proxy.variables)
#v_proxy_refs.topdict = file_proxy.variables
for var in file.groups[group].variables.keys():
#print file.groups[group].variables[var].path
vp = file_proxy.variables[file.groups[group].variables[var].path]
#print vp is file_proxy.variables[file.groups[group].variables[var].path]
vp.parent = weakref.proxy(gp)
#vp.parent = gp
v_proxy_refs[var] = weakref.proxy(vp)
#v_proxy_refs[var] = vp
gp.variables = v_proxy_refs
#print group, ": ", sys.getrefcount(file.groups[group])
file_proxy.groups = group_proxies
# all the groups need proxies before we can do this
for group in file.groups.keys():
g = file.groups[group]
gp = file_proxy.groups[group]
sl = group.rfind('/')
if sl == -1:
gp.parent = weakref.proxy(file_proxy.groups['/'])
#gp.parent = file_proxy.groups['/']
elif sl == 0:
gp.parent = weakref.proxy(file_proxy)
else:
gp.parent = weakref.proxy(file_proxy.groups[group[0:sl]])
#gp.parent = file_proxy.groups[group[0:sl]]
g_proxy_refs = nd.nioDict()
g_proxy_refs.path = g.path
g_proxy_refs.topdict = weakref.proxy(file_proxy.groups)
#g_proxy_refs.topdict = file_proxy.groups
for grp in g.groups.keys():
grp_obj = g.groups[grp]
#print grp_obj.path
gproxy = file_proxy.groups[grp_obj.path]
g_proxy_refs[grp] = gproxy
gp.groups = g_proxy_refs
# for var in file.variables.keys():
# file_proxy.variables[var].coordinates = _create_coordinates_attriibute(file_proxy,file_proxy.variables[var])
#print file_proxy, file_proxy.variables
return file_proxy
def open_file(filename, mode = 'r', options=None, history='', format=''):
'''
Open a file containing data in a supported format for reading and/or writing.
f = Nio.open_file(filepath, mode='r',options=None, history='', format='')
filepath -- path of file with data in a supported format. Either the path must
end with an extension indicating the expected format of the file (it need not
be part of the actual file name), or it must be specified using the optional
'format' argument. Valid extensions include:
.nc, .cdf, .netcdf, .nc3, .nc4, -- NetCDF
.gr, .grb, .grib, .gr1, .grb1, .grib1, .gr2, .grb2, .grib2, -- GRIB
.hd, .hdf -- HDF
.h5, .hdf5 -- HDF5
.he2, .he4, .hdfeos -- HDFEOS
.he5, .hdfeos5 -- HDFEOS5
.shp, .mif, .gmt, .rt1 -- shapefiles, other formats supported by GDAL OGR
.ccm -- CCM history files
Extensions are handled case-insensitvely, i.e.: .grib, .GRIB, and .Grib all
indicate a GRIB file.
mode -- access mode (optional):
'r' -- open an existing file for reading
'w','r+','rw','a' -- open an existing file for modification
'c' -- create a new file open for writing
options -- instance of NioOptions class used to specify generic or
format-specific options.
history -- a string specifying text to be appended to the file's global
attribute. The attribute is created if it does not exist. Only valid
if the file is opened for writing.
format -- a string specifying the expected format. Valid strings are the
same as the extensions listed above without the initial period (.).
Returns an NioFile object.
'''
ma_mode = _get_masked_array_mode(options,_Nio.option_defaults)
use_axis_att = _get_axis_att(options,_Nio.option_defaults)
explicit_fill_values = _get_option_value(options,_Nio.option_defaults,'ExplicitFillValues')
mask_below_value = _get_option_value(options,_Nio.option_defaults,'MaskBelowValue')
mask_above_value = _get_option_value(options,_Nio.option_defaults,'MaskAboveValue')
file = _Nio.open_file(filename,mode,options,history,format)
file_proxy = _proxy(file, 'str', __del__=__del__,create_variable=create_variable,create_group=create_group,close=close)
setattr(file_proxy.__class__,'set_option',set_option)
file_proxy.file = file
file_proxy.parent = None
file_proxy.open = 1
if not (explicit_fill_values is None and mask_below_value is None and mask_above_value is None):
file_proxy.ma_mode = 'maskedexplicit'
else:
file_proxy.ma_mode = ma_mode
file_proxy.explicit_fill_values = explicit_fill_values
file_proxy.mask_below_value = mask_below_value
file_proxy.mask_above_value = mask_above_value
if use_axis_att:
cf_dims = _get_cf_dims(file_proxy)
newdims = {}
cf2dims = {}
dimensions = file_proxy.dimensions
for dim in dimensions:
try:
newdim = cf_dims[dim]
except KeyError:
newdim = dim
newdims[newdim] = dimensions[dim]
cf2dims[newdim] = dim
else:
cf2dims = None
newdims = file_proxy.dimensions
file_proxy.cf_dimensions = newdims
file_proxy.cf2dims = cf2dims
variable_proxies = nd.nioDict()
variable_proxies.path = '/'
variable_proxies.topdict = None
for var in file.variables.keys():
# print var, ": ", sys.getrefcount(file.variables[var])
vp = _proxy(file.variables[var],'str','len',
__setitem__=__setitem__,__getitem__=__getitem__,get_value=get_value,assign_value=assign_value)
vp.file = weakref.proxy(file_proxy)
# vp.file = file_proxy
vp.varname = var
vp.parent = None
variable_proxies[var] = vp
if use_axis_att:
newdims = []
dimensions = vp.dimensions
for dim in dimensions:
try:
newdim = cf_dims[dim]
except KeyError:
newdim = dim
newdims.append(newdim)
vp.cf_dimensions = tuple(newdims)
else:
vp.cf_dimensions = vp.dimensions
#print var, ": ", sys.getrefcount(file.variables[var])
file_proxy.variables = variable_proxies
group_proxies = nd.nioDict()
group_proxies.path = '/'
group_proxies.topdict = None
for group in file.groups.keys():
# print group, ": ", sys.getrefcount(file.groups[group])
gp = _proxy(file.groups[group], 'str')
gp.file = weakref.proxy(file.groups[group])
gp.ma_mode = file_proxy.ma_mode
#gp.file = file_proxy
group_proxies[group] = gp
v_proxy_refs = nd.nioDict()
v_proxy_refs.path = file.groups[group].path
v_proxy_refs.topdict = weakref.proxy(file_proxy.variables)
#v_proxy_refs.topdict = file_proxy.variables
for var in file.groups[group].variables.keys():
#print file.groups[group].variables[var].path
vp = file_proxy.variables[file.groups[group].variables[var].path]
#print vp is file_proxy.variables[file.groups[group].variables[var].path]
vp.parent = weakref.proxy(gp)
#vp.parent = gp
v_proxy_refs[var] = weakref.proxy(vp)
#v_proxy_refs[var] = vp
gp.variables = v_proxy_refs
#print group, ": ", sys.getrefcount(file.groups[group])
file_proxy.groups = group_proxies
# all the groups need proxies before we can do this
for group in file.groups.keys():
g = file.groups[group]
gp = file_proxy.groups[group]
sl = group.rfind('/')
if sl == -1:
gp.parent = weakref.proxy(file_proxy.groups['/'])
#gp.parent = file_proxy.groups['/']
elif sl == 0:
gp.parent = weakref.proxy(file_proxy)
else:
gp.parent = weakref.proxy(file_proxy.groups[group[0:sl]])
#gp.parent = file_proxy.groups[group[0:sl]]
g_proxy_refs = nd.nioDict()
g_proxy_refs.path = g.path
g_proxy_refs.topdict = weakref.proxy(file_proxy.groups)
#g_proxy_refs.topdict = file_proxy.groups
for grp in g.groups.keys():
grp_obj = g.groups[grp]
#print grp_obj.path
gproxy = file_proxy.groups[grp_obj.path]
g_proxy_refs[grp] = gproxy
gp.groups = g_proxy_refs
# for var in file.variables.keys():
# file_proxy.variables[var].coordinates = _create_coordinates_attriibute(file_proxy,file_proxy.variables[var])
#print file_proxy, file_proxy.variables
return file_proxy