On 9/26/12 1:41 PM, Benjamin Root wrote:
On Wed, Sep 26, 2012 at 2:07 PM, Michael Rawlins <rawlin...@yahoo.com
<mailto:rawlin...@yahoo.com>> wrote:
------------------------------------------------------------------------
*From:* Benjamin Root <ben.r...@ou.edu <mailto:ben.r...@ou.edu>>
*To:* Michael Rawlins <rawlin...@yahoo.com
<mailto:rawlin...@yahoo.com>>
*Cc:* "matplotlib-users@lists.sourceforge.net
<mailto:matplotlib-users@lists.sourceforge.net>"
<matplotlib-users@lists.sourceforge.net
<mailto:matplotlib-users@lists.sourceforge.net>>
*Sent:* Wednesday, September 26, 2012 10:33 AM
*Subject:* Re: [Matplotlib-users] error reading netcdf file
On Wed, Sep 26, 2012 at 10:27 AM, Michael Rawlins
<rawlin...@yahoo.com <mailto:rawlin...@yahoo.com>> wrote:
Recently built and installed netCDF4-1.0. I'm running a
script that has worked on two other linux OS systems. Error:
File "test.py <http://test.py/>", line 96, in <module>
data.missing_value=-9.99
File "netCDF4.pyx", line 2570, in
netCDF4.Variable.__setattr__ (netCDF4.c:28242)
File "netCDF4.pyx", line 2392, in
netCDF4.Variable.setncattr (netCDF4.c:26309)
File "netCDF4.pyx", line 1013, in netCDF4._set_att
(netCDF4.c:12699)
AttributeError: NetCDF: Write to read only
The statement in the code triggers the error is:
data.missing_value=-9.99 .
MR
This typically happens when one opens a netCDF4 Dataset object
in 'r' mode, and/or if the file permissions for the file was
set to read-only. When modifying an attribute, it is
technically trying to write to the file.
Ben Root
Here is the file open statement:
ncfile = NetCDFFile('statsPrcp_Uncertainty2_winter.nc', 'r')
This worked fine in earlier versions. No where in the code do
I try to write to a netCDF file. So I'm confused as to why
specifying the read of the netCDF file would result in an
error when designating the missing data value.
Here's the code:
# Works with the netCDF files in the tutorial, and also the
# files available for download at:
# http://www.cdc.noaa.gov/cdc/data.ncep.reanalysis.html
# Adapted from the basemap example plotmap_pcolor.py,
# Some of the variable names from that example are retained.
#
# Uses basemap's pcolor function. Pcolor accepts arrays
# of the longitude and latitude points of the vertices on the
pixels,
# as well as an array with the numerical value in the pixel.
verbose=0 #verbose=2 says a bit more
import sys,getopt
from mpl_toolkits.basemap import Basemap, shiftgrid, cm
from netCDF4 import Dataset as NetCDFFile
#from mpl_toolkits.basemap import NetCDFFile
from pylab import *
import matplotlib.pyplot as plt
alloptions, otherargs=
getopt.getopt(sys.argv[1:],'ro:p:X:Y:v:t:l:u:n:') # note the :
after o and p
proj='lam'
cmap = cm.get_cmap('jet_r', 10) # 10 discrete colors
print "\nPlotting, please wait...maybe more than 10 seconds"
if proj=='lam': #Lambert Conformal
m =
Basemap(llcrnrlon=-80.6,llcrnrlat=38.4,urcrnrlon=-66.0,urcrnrlat=47.7,\
resolution='l',area_thresh=1000.,projection='lcc',\
lat_1=65.,lon_0=-73.3)
xtxt=200000. #offset for text
ytxt=200000.
parallels = arange(38.,48.,2.)
meridians = arange(-80.,-64.,2.)
xsize = rcParams['figure.figsize'][0]
fig=figure(figsize=(xsize,m.aspect*xsize))
#cax = axes([0.88, 0.1, 0.06, 0.81]) # colorbar axes for map
w/ graticule
############################################################################################
subplots_adjust(left=None, bottom=None, right=0.9, top=None,
wspace=0.05, hspace=0.03)
# Make the first map at upper left
plt.subplot(2,2,1)
ncfile = NetCDFFile('statsPrcp_Uncertainty2_winter.nc', 'r')
xvar='rlon'
print "shape of "+xvar+': ',ncfile.variables[xvar].shape
if ncfile.variables[xvar][:].ndim ==1:
print "X is independent of Y"
lon1d=ncfile.variables[xvar][:]
else:
lon1d=False
if ncfile.variables[xvar][:].ndim ==2:
lon2d=ncfile.variables[xvar][:]
if ncfile.variables[xvar][:].ndim ==3:
lon2d=ncfile.variables[xvar][0,:,:]
print "shape of lond2d:", lon2d.shape
yvar='rlat'
print "shape of "+yvar+': ',ncfile.variables[yvar].shape
if ncfile.variables[yvar][:].ndim ==1:
print "Y is independent of X"
lat1d=ncfile.variables[yvar][:]
else:
lat1d=False
if ncfile.variables[yvar][:].ndim ==2:
lat2d=ncfile.variables[yvar][:]
if ncfile.variables[yvar][:].ndim ==3:
lat2d=ncfile.variables[yvar][0,:,:]
print "shape of lat2d:", lat2d.shape
thevar='diff'
data=ncfile.variables[thevar]
dataa=data[:]
theshape=dataa.shape
try:
add_offset=ncfile.variables[thevar].add_offset
print "will use add_offset=",add_offset
except:
add_offset=0.
print "shape of "+thevar+': ',theshape
if len(theshape)>2:
print "there are apparently",theshape[0],"records"
if not therec: therec=raw_input("enter record number to
plot=>")
therec=int(therec)
extratext=" rec=%d" %therec
if len(theshape)>3:
print "there are apparently",theshape[1],"levels"
if not thelev: thelev=raw_input("enter level number to
plot=>")
thelev=int(thelev)
extratext=extratext+" lev=%d" %thelev
if len(theshape)>3:
slice=dataa[therec,thelev,:,:]+add_offset
elif len(theshape)>2:
slice=dataa[therec,:,:]+add_offset
else:
slice=dataa+add_offset
data.missing_value=-9.99
I think I know why this used to work in the past. I think netCDF4
used to recognize the "missing_value" attribute as a special value.
It is now ._FillValue. But I am still not sure you can save a value
to that attribute in a read-only Dataset. You might have to perform
the mask after extracting the data.
Note, setting the _FillValue *after* extracting the data to the
"dataa" variable won't change "dataa". I don't see how setting
data.missing_value is supposed to actually help you.
Ben Root
Michael: You can't change an attribute in a read-only dataset. It
should never have worked.
-Jeff
--
Jeffrey S. Whitaker Phone : (303)497-6313
Meteorologist FAX : (303)497-6449
NOAA/OAR/PSD R/PSD1 Email : jeffrey.s.whita...@noaa.gov
325 Broadway Office : Skaggs Research Cntr 1D-113
Boulder, CO, USA 80303-3328 Web : http://tinyurl.com/5telg
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