Menu
▾
▴
matplotlib-users
|
From: Michael R. <raw...@ya...> - 2012-09-19 17:30:13
|
Ubuntu 12.04 hdf5-tools installed from package manager netcdf-bin and python-netcdf installed from package manager I downloaded netCDF4-1.0fix1.tar.gz from http://code.google.com/p/netcdf4-python/downloads/list > python setup.py build /usr/bin/ld: cannot find -lhdf5_hl /usr/bin/ld: cannot find -lhdf5 collect2: ld returned 1 exit status /usr/bin/ld: cannot find -lhdf5_hl /usr/bin/ld: cannot find -lhdf5 collect2: ld returned 1 exit status error: Command "gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro build/temp.linux-i686-2.7/netCDF4.o -L/usr/local/lib -L/usr/local/lib -Wl,-R/usr/local/lib -Wl,-R/usr/local/lib -lnetcdf -lhdf5_hl -lhdf5 -lz -o build/lib.linux-i686-2.7/netCDF4.so" failed with exit status 1 |
|
From: Jeff W. <jef...@no...> - 2012-09-19 18:35:54
|
On 9/19/12 11:30 AM, Michael Rawlins wrote: > > Ubuntu 12.04 > > hdf5-tools installed from package manager > > netcdf-bin and python-netcdf installed from package manager > > I downloaded netCDF4-1.0fix1.tar.gz > <http://code.google.com/p/netcdf4-python/downloads/detail?name=netCDF4-1.0fix1.tar.gz&can=2&q=> > from http://code.google.com/p/netcdf4-python/downloads/list > > > python setup.py build > > > /usr/bin/ld: cannot find -lhdf5_hl > /usr/bin/ld: cannot find -lhdf5 > collect2: ld returned 1 exit status > /usr/bin/ld: cannot find -lhdf5_hl > /usr/bin/ld: cannot find -lhdf5 > collect2: ld returned 1 exit status > error: Command "gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions > -Wl,-Bsymbolic-functions -Wl,-z,relro > build/temp.linux-i686-2.7/netCDF4.o -L/usr/local/lib -L/usr/local/lib > -Wl,-R/usr/local/lib -Wl,-R/usr/local/lib -lnetcdf -lhdf5_hl -lhdf5 > -lz -o build/lib.linux-i686-2.7/netCDF4.so" failed with exit status 1 > > Michael: You're missing the hdf5 library. You should be able to install that (along with the netcdf version 4 library) using the Ubuntu package manager. I don't know what the relevant package names are. See the docs at netcdf4-python.googlecode.com for installation instructions (including how to install the dependencies). You can also file a help request there and I'll see it (since this is not really a basemap issue). -Jeff -- Jeffrey S. Whitaker Phone : (303)497-6313 Meteorologist FAX : (303)497-6449 NOAA/OAR/PSD R/PSD1 Email : Jef...@no... 325 Broadway Office : Skaggs Research Cntr 1D-113 Boulder, CO, USA 80303-3328 Web : http://tinyurl.com/5telg |
|
From: Michael R. <raw...@ya...> - 2012-09-19 19:15:08
|
________________________________ From: Jeff Whitaker <jef...@no...> To: Michael Rawlins <raw...@ya...>; Matplotlib Users <mat...@li...> Sent: Wednesday, September 19, 2012 2:35 PM Subject: Re: [Matplotlib-users] netcdf4-python build On 9/19/12 11:30 AM, Michael Rawlins wrote: > >Ubuntu 12.04 > > >hdf5-tools installed from package manager > > >netcdf-bin and python-netcdf installed from package manager > > >I downloaded netCDF4-1.0fix1.tar.gz from http://code.google.com/p/netcdf4-python/downloads/list > > >> python setup.py build > > > > >/usr/bin/ld: cannot find -lhdf5_hl >/usr/bin/ld: cannot find -lhdf5 >collect2: ld returned 1 exit status >/usr/bin/ld: cannot find -lhdf5_hl >/usr/bin/ld: cannot find -lhdf5 >collect2: ld returned 1 exit status >error: Command "gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro build/temp.linux-i686-2.7/netCDF4.o -L/usr/local/lib -L/usr/local/lib -Wl,-R/usr/local/lib -Wl,-R/usr/local/lib -lnetcdf -lhdf5_hl -lhdf5 -lz -o build/lib.linux-i686-2.7/netCDF4.so" failed with exit status 1 > > > Michael: You're missing the hdf5 library. You should be able to install that (along with the netcdf version 4 library) using the Ubuntu package manager. I don't know what the relevant package names are. See the docs at netcdf4-python.googlecode.com for installation instructions (including how to install the dependencies). You can also file a help request there and I'll see it (since this is not really a basemap issue). -Jeff Just installed h5utils from package manager. Getting same errors. In package manager I'm searching on hdf5. If there's a package there I'm missing, then it certainly is not obvious. Mike -- Jeffrey S. Whitaker Phone : (303)497-6313 Meteorologist FAX : (303)497-6449 NOAA/OAR/PSD R/PSD1 Email : Jef...@no... 325 Broadway Office : Skaggs Research Cntr 1D-113 Boulder, CO, USA 80303-3328 Web : http://tinyurl.com/5telg |
|
From: Johann R. <jr...@su...> - 2012-09-19 19:23:12
|
On 19/09/2012 21:14, Michael Rawlins wrote: > Just installed h5utils from package manager. Getting same errors. In > package manager I'm searching on hdf5. If there's a package there I'm > missing, then it certainly is not obvious. Try libhdf5-serial libhdf5-serial-dev Johann |
|
From: Michael R. <raw...@ya...> - 2012-09-19 20:44:04
|
________________________________ From: Johann Rohwer <jr...@su...> To: mat...@li... Sent: Wednesday, September 19, 2012 3:22 PM Subject: Re: [Matplotlib-users] netcdf4-python build On 19/09/2012 21:14, Michael Rawlins wrote: > Just installed h5utils from package manager. Getting same errors. In > package manager I'm searching on hdf5. If there's a package there I'm > missing, then it certainly is not obvious. Try libhdf5-serial libhdf5-serial-dev Johann After installing those two packages I was able build with setup.py in netCDF4-1.0/ Last few lines of the build: creating build/scripts.linux-i686-2.7 copying and adjusting utils/nc3tonc4 -> build/scripts.linux-i686-2.7 copying and adjusting utils/nc4tonc3 -> build/scripts.linux-i686-2.7 changing mode of build/scripts.linux-i686-2.7/nc3tonc4 from 644 to 755 changing mode of build/scripts.linux-i686-2.7/nc4tonc3 from 644 to 755 Here is my initialization: from mpl_toolkits.basemap import Basemap, shiftgrid, cm from netCDF4 import Dataset as NetCDFFile Here is result of execution of script: Traceback (most recent call last): File "map_PrcpBias_Northeast.py", line 21, in <module> from netCDF4 import Dataset as NetCDFFile I understand using the python-netcdf package is an option. Installed that but am getting an eror saying missing libhdf5_hl.so.6 when trying: from Scientific.IO.NetCDF import NetCDFFile MR ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ Matplotlib-users mailing list Mat...@li... https://lists.sourceforge.net/lists/listinfo/matplotlib-users |
|
From: Michael R. <raw...@ya...> - 2012-09-19 21:29:21
|
>________________________________
> From: Jeff Whitaker <jef...@no...>
>To: Michael Rawlins <raw...@ya...>
>Sent: Wednesday, September 19, 2012 4:57 PM
>Subject: Re: [Matplotlib-users] netcdf4-python build
>
>
>On 9/19/12 2:43 PM, Michael Rawlins wrote:
>
>
>>
>>
>>
>>
>>________________________________
>> From: Johann Rohwer <jr...@su...>
>>To: mat...@li...
>>Sent: Wednesday, September 19, 2012 3:22 PM
>>Subject: Re: [Matplotlib-users] netcdf4-python build
>>
>>On 19/09/2012 21:14, Michael Rawlins wrote:
>>
>>> Just installed h5utils from package manager. Getting
same errors. In
>>> package manager I'm searching on hdf5. If there's a
package there I'm
>>> missing, then it certainly is not obvious.
>>
>>Try
>>
>>libhdf5-serial
>>libhdf5-serial-dev
>>Johann
>>
>>
>>
>>After installing those two packages I was able build with setup.py in netCDF4-1.0/
>>
>>Last few lines of the build:
>>
>>creating build/scripts.linux-i686-2.7
>>copying and adjusting utils/nc3tonc4 ->
build/scripts.linux-i686-2.7
>>copying and adjusting utils/nc4tonc3 ->
build/scripts.linux-i686-2.7
>>changing mode of build/scripts.linux-i686-2.7/nc3tonc4 from
644 to 755
>>changing mode of build/scripts.linux-i686-2.7/nc4tonc3 from
644 to 755
>>
>>
>>Here is my initialization:
>>
>>from mpl_toolkits.basemap import Basemap, shiftgrid, cm
>>from netCDF4 import Dataset as NetCDFFile
>>
>>Here is result of execution of script:
>>
>>Traceback (most recent call last):
>> File "map_PrcpBias_Northeast.py", line 21, in <module>
>> from netCDF4 import Dataset as NetCDFFile
>>
>Michael: Please include the full traceback - what you posted
doesn't really tell us anything.
>
>
>How is full traceback obtained?
>
>
>
>
>>I understand using the python-netcdf package is an option.
Installed that but am getting an eror saying missing
libhdf5_hl.so.6 when trying:
>>
Do you have libhdf5_hl.so anywhere on your system after installing the libhdf5-serial package? According to this
>
>http://packages.ubuntu.com/lucid/i386/libhdf5-serial-1.8.4/filelist
>
>it should be installed in /usr/lib.
>
>
>Yes it is in /usr/lib.
>
>
>Also, if I read this
>
>http://packages.ubuntu.com/natty/libnetcdf6
>
>correctly, just installing the libnetcdf6 and libnetcdf-dev packages
should be all you need to do - they depend on libhdf5-serial.
>
>-Jeff
>
>
>Both packages are installed.
>
>MR
>
>
>
>>from Scientific.IO.NetCDF import NetCDFFile
>>
>>MR
>>
>>
>>
>>------------------------------------------------------------------------------
>>Live Security Virtual Conference
>>Exclusive live event will cover all the ways today's
security and
>>threat landscape has changed and how IT managers can
respond. Discussions
>>will include endpoint security, mobile security and the
latest in malware
>>threats.
http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>>_______________________________________________
>>Matplotlib-users mailing list
>>Mat...@li...
>>https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>>
>>
>>
>>
>>
>>------------------------------------------------------------------------------
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>>
>>
>>_______________________________________________
Matplotlib-users mailing list Mat...@li... https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>
>
>--
Jeffrey S. Whitaker Phone : (303)497-6313
Meteorologist FAX : (303)497-6449
NOAA/OAR/PSD R/PSD1 Email : Jef...@no... 325 Broadway Office : Skaggs Research Cntr 1D-113
Boulder, CO, USA 80303-3328 Web : http://tinyurl.com/5telg
>
> |
|
From: Jeff W. <jef...@no...> - 2012-09-19 21:57:53
|
On 9/19/12 3:29 PM, Michael Rawlins wrote: > > > ------------------------------------------------------------------------ > *From:* Jeff Whitaker <jef...@no...> > *To:* Michael Rawlins <raw...@ya...> > *Sent:* Wednesday, September 19, 2012 4:57 PM > *Subject:* Re: [Matplotlib-users] netcdf4-python build > > On 9/19/12 2:43 PM, Michael Rawlins wrote: >> >> >> ------------------------------------------------------------------------ >> *From:* Johann Rohwer <jr...@su...> <mailto:jr...@su...> >> *To:* mat...@li... >> <mailto:mat...@li...> >> *Sent:* Wednesday, September 19, 2012 3:22 PM >> *Subject:* Re: [Matplotlib-users] netcdf4-python build >> >> On 19/09/2012 21:14, Michael Rawlins wrote: >> >> > Just installed h5utils from package manager. Getting same >> errors. In >> > package manager I'm searching on hdf5. If there's a package >> there I'm >> > missing, then it certainly is not obvious. >> >> Try >> >> libhdf5-serial >> libhdf5-serial-dev >> Johann >> >> >> >> After installing those two packages I was able build with >> setup.py <http://setup.py/> in netCDF4-1.0/ >> >> Last few lines of the build: >> >> creating build/scripts.linux-i686-2.7 >> copying and adjusting utils/nc3tonc4 -> build/scripts.linux-i686-2.7 >> copying and adjusting utils/nc4tonc3 -> build/scripts.linux-i686-2.7 >> changing mode of build/scripts.linux-i686-2.7/nc3tonc4 from 644 >> to 755 >> changing mode of build/scripts.linux-i686-2.7/nc4tonc3 from 644 >> to 755 >> >> >> Here is my initialization: >> >> from mpl_toolkits.basemap import Basemap, shiftgrid, cm >> from netCDF4 import Dataset as NetCDFFile >> >> Here is result of execution of script: >> >> Traceback (most recent call last): >> File "map_PrcpBias_Northeast.py >> <http://map_prcpbias_northeast.py/>", line 21, in <module> >> from netCDF4 import Dataset as NetCDFFile > > Michael: Please include the full traceback - what you posted > doesn't really tell us anything. > > > How is full traceback obtained? > Michael: I just meant for you to paste the full output, not just the first three lines. Since you apparently have all the libs installed, I don't understand what's going on. Please try deleting the netcdf4-python build directory, and then run 'python setup.py build' again, capturing the output in a file. Send me that file off-list and I'll see if I can suggest something. -Jeff > > > >> >> I understand using the python-netcdf package is an option. >> Installed that but am getting an eror saying missing >> libhdf5_hl.so.6 when trying: > Do you have libhdf5_hl.so anywhere on your system after installing > the libhdf5-serial package? According to this > > http://packages.ubuntu.com/lucid/i386/libhdf5-serial-1.8.4/filelist > > it should be installed in /usr/lib. > > > Yes it is in /usr/lib. > > > Also, if I read this > > http://packages.ubuntu.com/natty/libnetcdf6 > > correctly, just installing the libnetcdf6 and libnetcdf-dev > packages should be all you need to do - they depend on libhdf5-serial. > > -Jeff > > > Both packages are installed. > > MR > >> >> from Scientific.IO <http://scientific.io.net/>.NetCDF import >> NetCDFFile >> >> MR >> >> >> >> ------------------------------------------------------------------------------ >> Live Security Virtual Conference >> Exclusive live event will cover all the ways today's security and >> threat landscape has changed and how IT managers can respond. >> Discussions >> will include endpoint security, mobile security and the latest in >> malware >> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ >> _______________________________________________ >> Matplotlib-users mailing list >> Mat...@li... >> <mailto:Mat...@li...> >> https://lists.sourceforge.net/lists/listinfo/matplotlib-users >> >> >> >> >> ------------------------------------------------------------------------------ >> Live Security Virtual Conference >> Exclusive live event will cover all the ways today's security and >> threat landscape has changed and how IT managers can respond. Discussions >> will include endpoint security, mobile security and the latest in malware >> threats.http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ >> >> >> _______________________________________________ >> Matplotlib-users mailing list >> Mat...@li... <mailto:Mat...@li...> >> https://lists.sourceforge.net/lists/listinfo/matplotlib-users > > > -- > Jeffrey S. Whitaker Phone : (303)497-6313 > Meteorologist FAX : (303)497-6449 > NOAA/OAR/PSD R/PSD1 Email :Jef...@no... <mailto:Jef...@no...> > 325 Broadway Office : Skaggs Research Cntr 1D-113 > Boulder, CO, USA 80303-3328 Web : http://tinyurl.com/5telg > > > |
|
From: Michael R. <raw...@ya...> - 2012-09-19 22:20:45
|
>________________________________
> From: Jeff Whitaker <jef...@no...>
>To: Michael Rawlins <raw...@ya...>
>Cc: "mat...@li..." <mat...@li...>
>Sent: Wednesday, September 19, 2012 5:57 PM
>Subject: Re: [Matplotlib-users] netcdf4-python build
>
>
>On 9/19/12 3:29 PM, Michael Rawlins wrote:
>
>
>>
>>How is full traceback obtained?
>>>
>Michael: I just meant for you to paste the full output, not just
the first three lines.
>
>
>That's all that appears at standard output and I do not know how to generate/find anything else.
>
>
>Since you apparently have all the libs installed, I don't understand
what's going on. Please try deleting the netcdf4-python build
directory, and then run 'python setup.py build' again, capturing the
output in a file. Send me that file off-list and I'll see if I can
suggest something.
>
>-Jeff
>
>
>Out of build, after removing build/ directory:
>
>HDF5_DIR environment variable not set, checking some standard locations ..
>checking /home/rawlins ...
>checking /usr/local ...
>HDF5 found in /usr/local
>
>NETCDF4_DIR environment variable not set, checking standard locations..
>checking /home/rawlins ...
>checking /usr/local ...
>netCDF4 found in /usr/local
>running build
>running config_cc
>unifing config_cc, config, build_clib, build_ext, build commands --compiler opti
>ons
>running config_fc
>unifing config_fc, config, build_clib, build_ext, build commands --fcompiler opt
>ions
>running build_src
>build_src
>building py_modules sources
>building extension "netCDF4" sources
>build_src: building npy-pkg config files
>running build_py
>creating build
>creating build/lib.linux-i686-2.7
>copying netcdftime.py -> build/lib.linux-i686-2.7
>copying netCDF4_utils.py -> build/lib.linux-i686-2.7
>copying ordereddict.py -> build/lib.linux-i686-2.7
>running build_ext
>customize UnixCCompiler
>customize UnixCCompiler using build_ext
>building 'netCDF4' extension
>compiling C sources
>C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wst
>rict-prototypes -fPIC
>
>creating build/temp.linux-i686-2.7
>compile options: '-I/usr/local/include -I/usr/local/include -I/usr/lib/python2.7
>/dist-packages/numpy/core/include -I/usr/include/python2.7 -c'
>gcc: netCDF4.c
>netCDF4.c: In function '__pyx_f_7netCDF4__find_cmptype':
>netCDF4.c:46724:13: warning: '__pyx_v_xtype' may be used uninitialized in this f
>unction [-Wuninitialized]
>netCDF4.c:37881:11: note: '__pyx_v_xtype' was declared here
>gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -
>Wl,-z,relro build/temp.linux-i686-2.7/netCDF4.o -L/usr/local/lib -L/usr/local/li
>b -Wl,-R/usr/local/lib -Wl,-R/usr/local/lib -lnetcdf -lhdf5_hl -lhdf5 -lz -o bui
>ld/lib.linux-i686-2.7/netCDF4.so
>running scons
>running build_scripts
>creating build/scripts.linux-i686-2.7
>copying and adjusting utils/nc3tonc4 -> build/scripts.linux-i686-2.7
>copying and adjusting utils/nc4tonc3 -> build/scripts.linux-i686-2.7
>changing mode of build/scripts.linux-i686-2.7/nc3tonc4 from 644 to 755
>changing mode of build/scripts.linux-i686-2.7/nc4tonc3 from 644 to 755
>
> |
|
From: Michael R. <raw...@ya...> - 2012-09-21 14:31:07
|
After the build, I determined that 'install' was also needed. > python setup.py install completed with no errors. OK, finally built and installed. But now my matplotlib script gives this error: Traceback (most recent call last): File "map_PrcpBias_Northeast.py", line 21, in <module> from netCDF4 import Dataset as NetCDFFile ImportError: /usr/local/lib/python2.7/dist-packages/netCDF4.so: undefined symbol: nc_inq_var_endian So, checking shared library dependencies: > ldd /usr/local/lib/python2.7/dist-packages/netCDF4.so linux-gate.so.1 => (0xb776a000) libnetcdf.so.7 => /usr/local/lib/libnetcdf.so.7 (0xb7604000) libpthread.so.0 => /lib/i386-linux-gnu/libpthread.so.0 (0xb75d3000) libc.so.6 => /lib/i386-linux-gnu/libc.so.6 (0xb742d000) libm.so.6 => /lib/i386-linux-gnu/libm.so.6 (0xb7401000) /lib/ld-linux.so.2 (0xb776b000) and > ldd /usr/local/lib/libnetcdf.so.7 linux-gate.so.1 => (0xb7765000) libm.so.6 => /lib/i386-linux-gnu/libm.so.6 (0xb7663000) libc.so.6 => /lib/i386-linux-gnu/libc.so.6 (0xb74be000) /lib/ld-linux.so.2 (0xb7766000) no libhdf5 there. Can this be fixed? MR |
|
From: Damon M. <dam...@gm...> - 2012-09-21 18:50:47
|
On Friday, September 21, 2012, Michael Rawlins wrote: > > After the build, I determined that 'install' was also needed. > > > python setup.py install > > completed with no errors. OK, finally built and installed. But now my > matplotlib script gives this error: > > Traceback (most recent call last): > File "map_PrcpBias_Northeast.py", line 21, in <module> > from netCDF4 import Dataset as NetCDFFile > ImportError: /usr/local/lib/python2.7/dist-packages/netCDF4.so: undefined > symbol: nc_inq_var_endian > > > So, checking shared library dependencies: > > > ldd /usr/local/lib/python2.7/dist-packages/netCDF4.so > > linux-gate.so.1 => (0xb776a000) > libnetcdf.so.7 => /usr/local/lib/libnetcdf.so.7 (0xb7604000) > libpthread.so.0 => /lib/i386-linux-gnu/libpthread.so.0 (0xb75d3000) > libc.so.6 => /lib/i386-linux-gnu/libc.so.6 (0xb742d000) > libm.so.6 => /lib/i386-linux-gnu/libm.so.6 (0xb7401000) > /lib/ld-linux.so.2 (0xb776b000) > > and > > > ldd /usr/local/lib/libnetcdf.so.7 > > linux-gate.so.1 => (0xb7765000) > libm.so.6 => /lib/i386-linux-gnu/libm.so.6 (0xb7663000) > libc.so.6 => /lib/i386-linux-gnu/libc.so.6 (0xb74be000) > /lib/ld-linux.so.2 (0xb7766000) > > no libhdf5 there. Can this be fixed? > > MR > > > > >From what I remember dealing with the netcdf c library, you have to explicitly set a compile flag to enable hdf5 support. That was a while ago, though. I'm not sure if things have changed. Hope this helps. -- Damon McDougall http://www.damon-is-a-geek.com B2.39 Mathematics Institute University of Warwick Coventry West Midlands CV4 7AL United Kingdom |
|
From: Michael R. <raw...@ya...> - 2012-09-22 00:59:37
|
>________________________________ > From: Damon McDougall <dam...@gm...> >To: Michael Rawlins <raw...@ya...> >Cc: "mat...@li..." <mat...@li...> >Sent: Friday, September 21, 2012 2:50 PM >Subject: Re: [Matplotlib-users] netcdf4-python build > > > > >From what I remember dealing with the netcdf c library, you have to explicitly set a compile flag to enable hdf5 support. That was a while ago, though. I'm not sure if things have changed. > > >Hope this helps. > > > > >I did not do a source compile. > >I've reinstalled libhdf5-serial-1.8.4 package and now have the right HDF5 library files. Successfully built and installed netCDF4-1.0. My script loads in module but a read/write issue is present. This is code that worked on previous system. Error: > > File "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. > >data.missing_value=-9.99 . > >MR > |
|
From: Michael R. <raw...@ya...> - 2012-09-26 14:27:11
|
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", 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 |
|
From: Benjamin R. <ben...@ou...> - 2012-09-26 14:33:36
|
On Wed, Sep 26, 2012 at 10:27 AM, Michael Rawlins <raw...@ya...>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", 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 |
|
From: Michael R. <raw...@ya...> - 2012-09-26 18:07:15
|
>________________________________
> From: Benjamin Root <ben...@ou...>
>To: Michael Rawlins <raw...@ya...>
>Cc: "mat...@li..." <mat...@li...>
>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 <raw...@ya...> 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", 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
>
>
>
>
>
> |
|
From: Benjamin R. <ben...@ou...> - 2012-09-26 19:41:54
|
On Wed, Sep 26, 2012 at 2:07 PM, Michael Rawlins <raw...@ya...>wrote:
>
>
> ------------------------------
> *From:* Benjamin Root <ben...@ou...>
> *To:* Michael Rawlins <raw...@ya...>
> *Cc:* "mat...@li..." <
> mat...@li...>
> *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 <raw...@ya...>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", 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
|
|
From: Jeff W. <jef...@no...> - 2012-09-26 21:10:24
|
On 9/26/12 1:41 PM, Benjamin Root wrote: > > > On Wed, Sep 26, 2012 at 2:07 PM, Michael Rawlins <raw...@ya... > <mailto:raw...@ya...>> wrote: > > > > ------------------------------------------------------------------------ > *From:* Benjamin Root <ben...@ou... <mailto:ben...@ou...>> > *To:* Michael Rawlins <raw...@ya... > <mailto:raw...@ya...>> > *Cc:* "mat...@li... > <mailto:mat...@li...>" > <mat...@li... > <mailto:mat...@li...>> > *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 > <raw...@ya... <mailto:raw...@ya...>> 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 : Jef...@no... 325 Broadway Office : Skaggs Research Cntr 1D-113 Boulder, CO, USA 80303-3328 Web : http://tinyurl.com/5telg |
|
From: Michael R. <raw...@ya...> - 2012-09-26 22:23:12
|
>________________________________ > From: Jeff Whitaker <jef...@no...> >To: Benjamin Root <ben...@ou...>; Michael Rawlins <ra...@ge...>; Matplotlib Users <mat...@li...> >Sent: Wednesday, September 26, 2012 5:10 PM >Subject: Re: [Matplotlib-users] error reading netcdf file > > >Michael: You can't change an attribute in a read-only dataset. It should never have worked. > >-Jeff > > Thanks Jeff and Ben. Below is a complete version of one such program I use. I was give the program by a colleague and I do not know who wrote that code. My previous post showed only as far as the missing data statement. I'm relatively new to this software. It looks like the missing value goes into the maskdat array and maskdat is an input to pcolor function. Perhaps the best way is to get it working (shading a map) with just the array from the netCDF file read. Essentailly the missing value is to shade some grids outside the region white. Mike #!/usr/bin/env python # v0.5 19 June 2010 # General purpose plotter of 2-D gridded data from NetCDF files, # plotted with map boundaries. # NetCDF file should have data in either 2-D, 3-D or 4-D arrays. # 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 netCDF3 import Dataset as NetCDFFile from mpl_toolkits.basemap import NetCDFFile from pylab import * alloptions, otherargs= getopt.getopt(sys.argv[1:],'ro:p:X:Y:v:t:l:u:n:') # note the : after o and p proj='lam' #plotfile=None #plotfile='testmap2.png' usejetrev=False colorbounds=[None,None] extratext="" xvar=None yvar=None thevar=None thetitle='Bias - Winter Air Temperature' #thetitle='Bias - Spring Air Temperature' #thetitle='Bias - Summer Air Temperature' #thetitle='Bias - Autumn Air Temperature' therec=None thelev=None cbot=None ctop=None startlon=-180 #default assumption for starting longitude for theopt,thearg in alloptions: print theopt,thearg if theopt=='-o': # -o needs filename after it, which is now thearg plotfile=thearg elif theopt=='-p': proj=thearg elif theopt=='-X': xvar=thearg elif theopt=='-Y': yvar=thearg elif theopt=='-v': thevar=thearg elif theopt=='-t': thetitle=thearg elif theopt=='-l': cbot=thearg elif theopt=='-u': ctop=thearg elif theopt=='-n': therec=thearg elif theopt=='-m': thelev=thearg elif theopt=='-r': usejetrev=True else: #something went wrong print "hmm, what are these??? ", theopt, thearg sys.exit() print otherargs try: ncname=otherargs[0] ncfile = NetCDFFile(ncname, 'r') except: # ncname = raw_input("\nenter NetCDF file name =>") # ncfile = NetCDFFile(ncname, 'r') ncfile = NetCDFFile('simple_xy.nc', 'r') # Here's filename if verbose>0: #examine the NetCDF file print "GLOBAL ATTRIBUTES:" allattr=dir(ncfile) normalattr=dir(NetCDFFile('/tmp/throwaway.nc','w')) for item in allattr: if item not in normalattr: print item,': ',getattr(ncfile,item) # for name in ncfile.ncattrs(): # print name,'=', getattr(ncfile,name) # if name=='Conventions' and getattr(ncfile,name)=='COARDS ': # nmcrean=True # startlon=0. # print "guessing this is an NMC reananalysis file " # else: # nmcrean=False print "\n\nDIMENSIONS:" for name in ncfile.dimensions.keys(): print "\nDIMENSION:", try: print name, ncfile.variables[name][:] except: print name, ncfile.dimensions[name] try: print ' ',ncfile.variables[name].units except: pass try: print ' ',ncfile.variables[name].gridtype except: pass print "\n'*****************'\nVARIABLES:" for name in ncfile.variables.keys(): if name in ncfile.dimensions.keys(): continue print "\nVARIABLE:", print name, ncfile.variables[name].dimensions, try: print ' ',ncfile.variables[name].units except: pass try: print " missing value=",ncfile.variables[name].missing _value except: pass # print "********************\n" #if not xvar: xvar=raw_input("\nenter X variable=>") 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,: ,:] #WRF print "shape of lond2d:", lon2d.shape #print type(lon1d),lon1d,type(lon1d[1]),lon1d[1] # #if not yvar: yvar=raw_input("\nenter Y variable=>") 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,: ,:] #WRF print "shape of lat2d:", lat2d.shape # #if not thevar: thevar=raw_input("\nenter variable to plot=>") #thevar='nseasondays' thevar='diff' #thevar='mean' 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=0 #data.missing_value=-999 data.missing_value=-9.99 try: mval=data.missing_value print " using specified missing value =",mval except: mval=1.e30 print " faking missing value=",mval # make a masked array: using missing value(s) in mval maskdat=ma.masked_values(slice,mval) datamax=max(maskdat.compressed().flat) datamin=min(maskdat.compressed().flat) print "\n"+thevar+" has maximum ", datamax," and minimum:", datamin #colorbounds=[None,None] #if not cbot: cbot=raw_input("enter lower bound on color scale =>") #if cbot: colorbounds[0]=float(cbot) #if not ctop: ctop=raw_input("enter upper bound on color scale =>") #if ctop: colorbounds[1]=float(ctop) colorbounds=[-3,3] # for diff in C print "using clim=",colorbounds # shift lons and lats by 1/2 grid increment (so values represent the vertices # of the grid box surrounding the data value, as pcolor expects). if type(lon1d)!=type(False): #lon1d does exist delon = lon1d[1]-lon1d[0] delat = lat1d[1]-lat1d[0] lons = zeros(len(lon1d)+1,'d') lats = zeros(len(lat1d)+1,'d') lons[0:len(lon1d)] = lon1d-0.5*delon lons[-1] = lon1d[-1]+0.5*delon lats[0:len(lat1d)] = lat1d-0.5*delon lats[-1] = lat1d[-1]+0.5*delon lons, lats = meshgrid(lons, lats) else: xdim,ydim=lon2d.shape lons=zeros([xdim+1,ydim+1],'d') lats=zeros([xdim+1,ydim+1],'d') for i in range(1,xdim): for j in range(1,ydim): lats[i,j]=.5*lat2d[i,j]+.5*lat2d[i-1,j-1] lons[i,j]=.5*lon2d[i,j]+.5*lon2d[i-1,j-1] for i in range(1,xdim): lons[i,-1]=-lons[i,-3]+2*lons[i,-2] lats[i,-1]=-lats[i,-3]+2*lats[i,-2] lons[i,0]=-lons[i,2]+2*lons[i,1] lats[i,0]=-lats[i,2]+2*lats[i,1] for j in range(ydim+1): lons[-1,j]=-lons[-3,j]+2*lons[-2,j] lats[-1,j]=-lats[-3,j]+2*lats[-2,j] lons[0,j]=2*lons[1,j]-lons[2,j] lats[0,j]=2*lats[1,j]-lats[2,j] # # alter a matplotlib color table, # cm.jet is very useful scheme, but reversed colors are better for drought cmap = cm.get_cmap('jet', 10) # 10 discrete colors #cmap = cm.get_cmap('summer_r', 10) # 10 discrete colors print "\nPlotting, please wait...maybe more than 10 seconds" if proj=='lam': #Lambert Conformal # m = Basemap(llcrnrlon=-118.0,llcrnrlat=24.,urcrnrlon=-60.0,urcrnrlat=48. 0,\ # resolution='l',area_thresh=1000.,projection='lcc',\ # lat_1=70.,lon_0=-98.) 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.,-66.,2.) else: #cylindrical is default # m = Basemap(llcrnrlon=-180.,llcrnrlat=-90,urcrnrlon=180.,urcrnrlat=90.,\ # resolution='c',area_thresh=10000.,projection='cyl') m = Basemap(llcrnrlon=startlon,llcrnrlat=-90,urcrnrlon=startlon+360.,urc rnrlat=90.,\ resolution='c',area_thresh=10000.,projection='cyl') xtxt=1. ytxt=0. parallels = arange(-90.,90.,30.) if startlon==-180: meridians = arange(-180.,180.,60.) else: meridians = arange(0.,360.,60.) if verbose>1: print m.__doc__ plt.rcParams['font.size'] = 20 xsize = rcParams['figure.figsize'][0] fig=figure(figsize=(xsize,m.aspect*xsize)) #ax = fig.add_axes([0.08,0.1,0.7,0.7],axisbg='white') ax = fig.add_axes([0.07,0.00,0.8,1.0],axisbg='white') # make a pcolor plot. x, y = m(lons, lats) p = m.pcolor(x,y,maskdat,shading='flat',cmap=cmap) clim(*colorbounds) # axes units units are left, bottom, width, height #cax = axes([0.85, 0.1, 0.05, 0.7]) # colorbar axes for map w/ no graticule cax = axes([0.88, 0.1, 0.06, 0.81]) # colorbar axes for map w/ graticule #if datamax>1000.: # colorbar(format='%7.1e', cax=cax) # draw colorbar #elif datamax>5.: # colorbar(format='%d', cax=cax) # draw colorbar #else: # colorbar(format='%5.2f', cax=cax) # draw colorbar colorbar(format='%3.1f', cax=cax) #text(0.7,1.02,'mm') text(0.3,1.02,'$^{o}$C',fontsize=20) axes(ax) # make the original axes current again # plot blue dot on Norman OK and label it as such. #if startlon==-180: # xpt,ypt = m(-97.4836,35.2556) #else: # xpt,ypt = m(-97.4836+360.,35.2556) #m.plot([xpt],[ypt],'bo') #text(xpt+xtxt,ypt+ytxt,'Norman') xpt,ypt = m(-70.7500,41.7500) text(xpt,ypt,'N') # draw coastlines and political boundaries. m.drawcoastlines(linewidth=2.0) m.drawcountries(linewidth=2.0) m.drawstates(linewidth=2.0) # draw parallels and meridians. # label on left, right and bottom of map. #m.drawparallels(parallels,labels=[1,0,0,0]) #m.drawmeridians(meridians,labels=[1,1,0,1]) if not thetitle: title(thevar+extratext,fontsize=20) else: title(thetitle,fontsize=20) #if plotfile: # savefig(plotfile, dpi=72, facecolor='w', bbox_inches='tight', edgecolor= 'w', orientation='portrait') #else: # show() plt.savefig('map.png') plt.savefig('map.eps') show() |
|
From: Michael R. <raw...@ya...> - 2012-09-27 14:47:01
|
----- Original Message ----- > From: Michael Rawlins <raw...@ya...> > To: Jeff Whitaker <jef...@no...>; Benjamin Root <ben...@ou...>; Matplotlib Users <mat...@li...> > Cc: > Sent: Wednesday, September 26, 2012 6:23 PM > Subject: Re: [Matplotlib-users] error reading netcdf file > > > >> ________________________________ >> From: Jeff Whitaker <jef...@no...> >> To: Benjamin Root <ben...@ou...>; Michael Rawlins > <ra...@ge...>; Matplotlib Users > <mat...@li...> >> Sent: Wednesday, September 26, 2012 5:10 PM >> Subject: Re: [Matplotlib-users] error reading netcdf file >> >> >> Michael: You can't change an attribute in a read-only dataset. It > should never have worked. >> >> -Jeff >> >> > > > Thanks Jeff and Ben. > > Below is a complete version of one such program I use. I was give the program by > a colleague and I do not know who wrote that code. My previous post showed only > as far as the missing data statement. > <snip> I've gotten my script to work by setting the missing value another way. I'm showing lines commented out as well. #data.missing_value=-9.99 #try: # mval=data.missing_value # print " using specified missing value =",mval #except: mval=-9.99 # print " faking missing value=",mval # make a masked array: using missing value(s) in mval maskdat=ma.masked_values(slice,mval) If I understand correctly, in previous versions the value of -9.99 was passed through the data.missing_value into mval. A mistake in coding that did not result in an error. I will implement the change. Tomorrow I'll check that this solution is backward compatible. Mike |
|
From: Benjamin R. <ben...@ou...> - 2012-09-27 18:29:36
|
Michael, The .missing_value attribute is not used anymore (It is ._FillValue now). Anyway, if your data had any value that matched ._FillValue, then, by default, netCDF4 will give you a masked array anyway. You will only need to set the mask if the fill value doesn't exist or if it is different from what you were expecting. Ben Root |
|
From: Michael R. <raw...@ya...> - 2012-09-27 23:57:35
|
>________________________________ > From: Benjamin Root <ben...@ou...> >To: Michael Rawlins <raw...@ya...> >Cc: Matplotlib Users <mat...@li...> >Sent: Thursday, September 27, 2012 2:29 PM >Subject: Re: [Matplotlib-users] error reading netcdf file > > >Michael, > >The .missing_value attribute is not used anymore (It is ._FillValue now). Anyway, if your data had any value that matched ._FillValue, then, by default, netCDF4 will give you a masked array anyway. You will only need to set the mask if the fill value doesn't exist or if it is different from what you were expecting. > >Ben Root > > > Thanks Ben. I'll play around with ._FillValue and masked arrays. Glad to have everything working again with this new OS. Mike |
