Revision: 4470
http://matplotlib.svn.sourceforge.net/matplotlib/?rev=4470&view=rev
Author: jswhit
Date: 2007-11-27 10:05:25 -0800 (Tue, 27 Nov 2007)
Log Message:
-----------
make automatic masking and rescaling of variable data optional
in NetCDFFile.
Modified Paths:
--------------
trunk/toolkits/basemap/lib/matplotlib/toolkits/basemap/pupynere.py
Modified: trunk/toolkits/basemap/lib/matplotlib/toolkits/basemap/pupynere.py
===================================================================
--- trunk/toolkits/basemap/lib/matplotlib/toolkits/basemap/pupynere.py
2007-11-27 17:40:45 UTC (rev 4469)
+++ trunk/toolkits/basemap/lib/matplotlib/toolkits/basemap/pupynere.py
2007-11-27 18:05:25 UTC (rev 4470)
@@ -56,7 +56,7 @@
_typecodes = dict([[_v,_k] for _k,_v in typemap.items()])
-def NetCDFFile(file):
+def NetCDFFile(file, maskandscale=True):
"""NetCDF File reader. API is the same as Scientific.IO.NetCDF.
If 'file' is a URL that starts with 'http', it is assumed
to be a remote OPenDAP dataset, and the python dap client is used
@@ -66,9 +66,18 @@
with a pure python NetCDF reader, otherwise PyNIO
(http://www.pyngl.ucar.edu/Nio.shtml) will be used (if it is installed).
PyNIO supports NetCDF version 4, GRIB1, GRIB2, HDF4 and HDFEOS2 files.
+ Data read from OPenDAP and NetCDF version 3 datasets will
+ automatically be converted to masked arrays if the variable has either
+ a 'missing_value' or '_FillValue' attribute, and some data points
+ are equal to the value specified by that attribute. In addition,
+ variables stored as integers that have the 'scale_factor' and
+ 'add_offset' attribute will automatically be rescaled to floats when
+ read. If PyNIO is used, neither of the automatic conversions will
+ be performed. To suppress these automatic conversions, set the
+ maskandscale keyword to False.
"""
if file.startswith('http'):
- return _RemoteFile(file)
+ return _RemoteFile(file,maskandscale)
else:
# use pynio if it is installed and the file cannot
# be read with the pure python netCDF reader. This allows
@@ -76,13 +85,13 @@
# to be read.
if has_pynio:
try:
- f = _LocalFile(file)
+ f = _LocalFile(file,maskandscale)
except:
f = nio.open_file(file)
# otherwise, use the pupynere netCDF 3 pure python reader.
# (will fail if file is not a netCDF version 3 file).
else:
- f = _LocalFile(file)
+ f = _LocalFile(file,maskandscale)
return f
def _maskandscale(var,datout):
@@ -99,8 +108,9 @@
class _RemoteFile(object):
"""A NetCDF file reader. API is the same as Scientific.IO.NetCDF."""
- def __init__(self, file):
+ def __init__(self, file, maskandscale):
self._buffer = open_remote(file)
+ self._maskandscale = maskandscale
self._parse()
def read(self, size=-1):
@@ -136,7 +146,7 @@
for k,d in self._buffer.iteritems():
if isinstance(d, GridType) or isinstance(d, ArrayType):
name = k
- self.variables[name] = _RemoteVariable(d)
+ self.variables[name] = _RemoteVariable(d,self._maskandscale)
def close(self):
# this is a no-op provided for compatibility
@@ -144,8 +154,9 @@
class _RemoteVariable(object):
- def __init__(self, var):
+ def __init__(self, var, maskandscale):
self._var = var
+ self._maskandscale = maskandscale
self.dtype = var.type
self.shape = var.shape
self.dimensions = var.dimensions
@@ -157,7 +168,10 @@
# - remove singleton dimensions
# - create a masked array using missing_value or _FillValue attribute
# - apply scale_factor and add_offset to packed integer data
- return _maskandscale(self,datout)
+ if self._maskandscale:
+ return _maskandscale(self,datout)
+ else:
+ return datout
def typecode(self):
return _typecodes[self.dtype]
@@ -166,8 +180,9 @@
class _LocalFile(object):
"""A NetCDF file reader. API is the same as Scientific.IO.NetCDF."""
- def __init__(self, file):
+ def __init__(self, file, maskandscale):
self._buffer = open(file, 'rb')
+ self._maskandscale = maskandscale
self._parse()
def read(self, size=-1):
@@ -295,7 +310,7 @@
# Read offset.
begin = [self._unpack_int, self._unpack_int64][self.version_byte-1]()
- return _LocalVariable(self._buffer.fileno(), nc_type, vsize, begin,
shape, dimensions, attributes, isrec, self._recsize)
+ return _LocalVariable(self._buffer.fileno(), nc_type, vsize, begin,
shape, dimensions, attributes, isrec, self._recsize,
maskandscale=self._maskandscale)
def _read_values(self, n, nc_type):
bytes = [1, 1, 2, 4, 4, 8]
@@ -335,7 +350,7 @@
class _LocalVariable(object):
- def __init__(self, fileno, nc_type, vsize, begin, shape, dimensions,
attributes, isrec=False, recsize=0):
+ def __init__(self, fileno, nc_type, vsize, begin, shape, dimensions,
attributes, isrec=False, recsize=0, maskandscale=True):
self._nc_type = nc_type
self._vsize = vsize
self._begin = begin
@@ -344,6 +359,7 @@
self.attributes = attributes # for ``dap.plugins.netcdf``
self.__dict__.update(attributes)
self._is_record = isrec
+ self._maskandscale = maskandscale
# Number of bytes and type.
self._bytes = [1, 1, 2, 4, 4, 8][self._nc_type-1]
@@ -378,7 +394,10 @@
# - remove singleton dimensions
# - create a masked array using missing_value or _FillValue attribute
# - apply scale_factor and add_offset to packed integer data
- return _maskandscale(self,datout)
+ if self._maskandscale:
+ return _maskandscale(self,datout)
+ else:
+ return datout
def getValue(self):
"""For scalars."""
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