From: Sachin B. <sk...@gm...> - 2011-04-08 14:38:29
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Chris.. Can you try to download the latest toolsUI jar file from Unidata site directly and try ? ftp://ftp.unidata.ucar.edu/pub/netcdf-java/v4.2/toolsUI-4.2.jar Remove the 'toolsui-4.0.49' from your matlab java path, add 'toolsUI-4.2.jar' ... then restart matlab. -skb 2011/4/8 Chris Wen <chr...@ho...> > Hi > > With the example file of bora_feb.nc in classcis format, some method like > varget and attget works fine. > The file that I use is of type NetCDF-4. As I use those methods with my > file, I get these exception: > att=nj_attget(uri,'enu'); > Java exception occurred: > java.lang.RuntimeException: java.lang.NoSuchMethodError: > ucar.unidata.util.SpecialMathFunction.log2(D)D > > at ucar.nc2.NetcdfFile.<init>(NetcdfFile.java:1315) > > at ucar.nc2.NetcdfFile.open(NetcdfFile.java:734) > > at ucar.nc2.NetcdfFile.open(NetcdfFile.java:389) > > at ucar.nc2.dataset.NetcdfDataset.openOrAcquireFile(NetcdfDataset.java:709) > > at ucar.nc2.dataset.NetcdfDataset.openDataset(NetcdfDataset.java:434) > > at ucar.nc2.dataset.NetcdfDataset.acquireDataset(NetcdfDataset.java:544) > > at ucar.nc2.dt.grid.GridDataset.open(GridDataset.java:88) > > at msstate.cstm.data.JDataset.<init>(Unknown Source) > > Caused by: java.lang.NoSuchMethodError: > ucar.unidata.util.SpecialMathFunction.log2(D)D > > at > ucar.nc2.iosp.hdf5.H5header$FractalHeap$IndirectBlock.<init>(H5header.java:4946) > > at ucar.nc2.iosp.hdf5.H5header$FractalHeap.<init>(H5header.java:4789) > > at ucar.nc2.iosp.hdf5.H5header.readGroupNew(H5header.java:3428) > > at ucar.nc2.iosp.hdf5.H5header.access$1100(H5header.java:64) > > at ucar.nc2.iosp.hdf5.H5header$H5Group.<init>(H5header.java:1769) > > at ucar.nc2.iosp.hdf5.H5header$H5Group.<init>(H5header.java:1734) > > at ucar.nc2.iosp.hdf5.H5header.readSuperBlock2(H5header.java:319) > > at ucar.nc2.iosp.hdf5.H5header.read(H5header.java:173) > > at ucar.nc2.iosp.hdf5.H5iosp.open(H5iosp.java:108) > > at ucar.nc2.NetcdfFile.<init>(NetcdfFile.java:1297) > > ... 7 more > . > MATLAB:nj_attget:Unable to create "mDataset" object > > It is supposed to also handle the Netcdf-4 file , isn't it? > > -Chris > ------------------------------ > To: chr...@ho... > CC: njt...@li... > Subject: Re: [njtbx-users] : Installation Problem....Anyone helps.. > From: emo...@us... > Date: Fri, 8 Apr 2011 09:41:42 -0400 > > > Chris- > > The toolsUI-4.0.49 I have is also ~18mb, but it's that size on a system > where the njTBX works fine. > > I notice you now also have this in your error msg: > (Ljava/lang/StringBuilder;IZ)V > > I'm wondering if the string parser is having lots of trouble and the 'L' is > really supposed to be a : or a /? > Ellyn > > Ellyn T. Montgomery, Oceanographer and Data Manager > U.S. Geological Survey > Woods Hole Coastal and Marine Science Center > 384 Woods Hole Road, Woods Hole, MA 02543-1598 > (508)457-2356 > > > From: Chris Wen <chr...@ho...> To: < > njt...@li...> Date: 04/08/2011 09:22 AM Subject: Re: > [njtbx-users] : Installation Problem....Anyone helps.. > ------------------------------ > > > > Skb > > I tried those methods you told me, it still does not work: > 1. I found the size of toolUI is not the same as the size described in the > installation page, in which it is toolsUI-4.0.49.jar<http://sourceforge.net/projects/njtbx/files/njTBX-downloads/toolsUI-4.0.49.jar/download>(~15mb), > while the size of toolsUI I got is 18mb. The toolsUI that I downloaded is > from the path the installation page gives. > > 2. > clear classes > clear cache > import ucar.nc2.dt.grid.GridDataset > > uri='C:\NetCDFLab\Tools\matlab-njTbx-2.0.05\matlab-njTbx-2.0.05\examples\data\ > bora_feb.nc'; > nc=GridDataset.open(uri); > nc.getDetailInfo; > ??? Java exception occurred: > java.lang.NoSuchMethodError: > ucar.unidata.util.Format.tab(Ljava/lang/StringBuilder;IZ)V > > at ucar.nc2.dt.grid.GeoGrid.getInfo(GeoGrid.java:854) > > at ucar.nc2.dt.grid.GridDataset.getInfo(GridDataset.java:315) > > at ucar.nc2.dt.grid.GridDataset.getDetailInfo(GridDataset.java:338) > > The above exception is what I got. > > -Chris > > ------------------------------ > From: sk...@gm... > Date: Thu, 7 Apr 2011 11:12:26 -0400 > Subject: Re: [njtbx-users] FW: Installation Problem....Anyone helps.. > To: chr...@ho... > CC: njt...@li... > > Chris, > > Not sure of the source of the problem, but I would try these simple steps. > > 1. Make sure that both jar files you have downloaded from sourceforge are > of correct size. > I mean there may be a slight chance that they didn't download > completely/correctly. > If you do find discrepancy in files, then please download them again and > restart matlab. > > 2. Ruling out which jar is giving problem. Please run this sequence in > matlab. > Use local data file that came with njtbx. You would find that in > 'examples/data/*bora_feb.nc* <http://bora_feb.nc/>'. > > >>clear classes > >>clear cache > >> import ucar.nc2.dt.grid.GridDataset > > >> uri=' examples/data/*bora_feb.nc* <http://bora_feb.nc/>'; > >> nc=GridDataset.open(uri); > > >> nc.getDetailInfo > > > Let me know if there is any success. We will go from here. > > > thanks.. > > -skb > > 2011/4/7 Chris Wen <*chr...@ho...* <chr...@ho...>> > > Hi > > 1.I found this: > *Prinstallation Requirements*<http://sourceforge.net/apps/trac/njtbx/wiki/DownloadNjtbx-current#Pre-installationRequirements> > Before you proceed to download, make sure that you meet the following > minimum requirements. > > - Java Runtime 1.5 or higher (1.6 recommended). Type "version -java" in > Matlab if you are unsure. > - Matlab version 2006b or higher > > > Matlab version 2006b is released with MATLAB 7.2, while my Matlab is 7.0.4. > However on the Start page, it is said that it should work on any version > of Matlab that supports Java (Matlab 6.5 and later). I feel a little bit > confused.. > > > 2.No, it throw this exception: > url='*http://geoport.whoi.edu/thredds/dodsC/bathy/crm_vol1.nc*<http://geoport.whoi.edu/thredds/dodsC/bathy/crm_vol1.nc> > '; > nc=mDataset(url); > Java exception occurred: > java.lang.IllegalAccessError: tried to access method > ucar.unidata.util.StringUtil.replace(Ljava/lang/String;[C[Ljava/lang/String;)Ljava/lang/String; > from class ucar.nc2.NCdumpW > > at ucar.nc2.NCdumpW.encodeString(NCdumpW.java:894) > > at ucar.nc2.Attribute.toString(Attribute.java:280) > > at ucar.nc2.Variable.writeCDL(Variable.java:1122) > > at ucar.nc2.Variable.writeCDL(Variable.java:1098) > > at ucar.nc2.Variable.toString(Variable.java:1085) > > at java.util.Formatter$FormatSpecifier.printString(Unknown Source) > > at java.util.Formatter$FormatSpecifier.print(Unknown Source) > > at java.util.Formatter.format(Unknown Source) > > at java.util.Formatter.format(Unknown Source) > > at > ucar.nc2.dataset.CoordTransBuilder.makeCoordinateTransform(CoordTransBuilder.java:190) > > at > ucar.nc2.dataset.CoordSysBuilder.makeCoordinateTransforms(CoordSysBuilder.java:1019) > > at > ucar.nc2.dataset.CoordSysBuilder.buildCoordinateSystems(CoordSysBuilder.java:612) > > at ucar.nc2.dataset.NetcdfDataset.enhance(NetcdfDataset.java:503) > > at ucar.nc2.dataset.NetcdfDataset.<init>(NetcdfDataset.java:1174) > > at ucar.nc2.dataset.NetcdfDataset.openDataset(NetcdfDataset.java:440) > > at ucar.nc2.dataset.NetcdfDataset.acquireDataset(NetcdfDataset.java:544) > > at ucar.nc2.dt.grid.GridDataset.open(GridDataset.java:88) > > at msstate.cstm.data.JDataset.<init>(Unknown Source) > > -Chris > > > > > Date: Thu, 7 Apr 2011 07:58:34 -0400 > > > Subject: Re: [njtbx-users] Installation Problem....Anyone helps.. > > From: *rsi...@us...* <rsi...@us...> > > To: *chr...@ho...* <chr...@ho...> > > > > Chris, > > Does this work? > > > > url='*http://geoport.whoi.edu/thredds/dodsC/bathy/crm_vol1.nc*<http://geoport.whoi.edu/thredds/dodsC/bathy/crm_vol1.nc> > '; > > nc=mDataset(url); > > lon=nc{'lon'}(:); > > > > > 2011/4/7 Chris Wen <*chr...@ho...*<chr...@ho...> > >: > > > Hi > > > 1.I used the zip file.... > > > 2.I tried the new URL, but it still does not work... > > > version -java > > > ans = > > > Java 1.5.0 with Sun Microsystems Inc. Java HotSpot(TM) Client VM > > > (mixed mode) > > > ncRef='*http://geoport.whoi.edu/thredds/dodsC/bathy/crm_vol1.nc*<http://geoport.whoi.edu/thredds/dodsC/bathy/crm_vol1.nc> > '; > > > [data,geo]=nj_subsetGrid(ncRef,'topo',[-70.9 -70.1 41.15 41.65]); > > > ??? Error: File: nj_subsetGrid.m Line: 70 Column: 23 > > > Functions cannot be indexed using {} or . indexing. > > > Really appreciate your reply.... > > > -Chris > > > > > >> Date: Thu, 7 Apr 2011 07:09:34 -0400 > > >> Subject: Re: [njtbx-users] Installation Problem....Anyone helps.. > > >> From: *rsi...@us...* <rsi...@us...> > > >> To: *chr...@ho...* <chr...@ho...> > > >> CC: *njt...@li...*<njt...@li...> > > >> > > >> Chris, > > >> > > >> 1. Did you download the m-files from the SVN or did you use the zip > file? > > >> > > >> 2. I don't think this is the problem, but that bathy URL is down. Can > > >> you try this instead? > > >> > > >> ncRef='*http://geoport.whoi.edu/thredds/dodsC/bathy/crm_vol1.nc*<http://geoport.whoi.edu/thredds/dodsC/bathy/crm_vol1.nc> > ' > > >> [data,geo]=nj_subsetGrid(ncRef,'topo',[-70.9 -70.1 41.15 41.65]); > > >> > > >> -Rich > > >> > > >> 2011/4/7 Chris Wen <*chr...@ho...*<chr...@ho...> > >: > > >> > Hi > > >> > > > >> > > > >> > > > >> > As it is said ‘njTBX uses only Java and M-files, thus should work > on > > >> > any > > >> > version of Matlab that supports Java (Matlab 6.5 and later) and on > any > > >> > platform. The library is freely available and the source code is > > >> > released > > >> > under the (MIT-style) ‘, thus my matlab, which is version 7(R14) > > >> > released at > > >> > Jan.29.2005, can also use njTBX? > > >> > > > >> > > > >> > > > >> > Following the installation instructions, I met a error: > > >> > > > >> > > > >> > > > >> >>> ncRef > > >> >>> ='* > http://coast-enviro.er.usgs.gov/thredds/dodsC/bathy/crm_vol1.nc*<http://coast-enviro.er.usgs.gov/thredds/dodsC/bathy/crm_vol1.nc> > '; > > >> > > > >> >>> [data,geo]=nj_subsetGrid(ncRef,'topo',[-70.9 -70.1 41.15 41.65]); > > >> > > > >> > ??? Error: File: nj_subsetGrid.m Line: 70 Column: 23 > > >> > > > >> > Functions cannot be indexed using {} or . indexing. > > >> > > > >> > > > >> > > > >> > Anybody can tell me the reason? > > >> > > > >> > > > >> > > > >> > My configuration seems correct: > > >> > > > >> > > > >> > > > >> >>> path > > >> > > > >> > > > >> > > > >> > MATLABPATH > > >> > > > >> > > > >> > > > >> > > > >> > C:\NetCDFLab\Tools\matlab-njTbx-2.0.05\matlab-njTbx-2.0.05\examples > > >> > > > >> > > > >> > > > >> > > C:\NetCDFLab\Tools\matlab-njTbx-2.0.05\matlab-njTbx-2.0.05\njTBX-2.0\Utilities > > >> > > > >> > > > >> > C:\NetCDFLab\Tools\matlab-njTbx-2.0.05\matlab-njTbx-2.0.05\seawater > > >> > > > >> > > > >> > C:\NetCDFLab\Tools\matlab-njTbx-2.0.05\matlab-njTbx-2.0.05\RPSstuff > > >> > > > >> > > > >> > C:\NetCDFLab\Tools\matlab-njTbx-2.0.05\matlab-njTbx-2.0.05\njTBX-2.0 > > >> > > > >> > > > >> > C:\NetCDFLab\Tools\matlab-njTbx-2.0.05\matlab-njTbx-2.0.05\njFunc > > >> > > > >> > > > >> > C:\NetCDFLab\Tools\matlab-njTbx-2.0.05\matlab-njTbx-2.0.05 > > >> > > > >> > C:\Program Files\MATLAB704\toolbox\matlab\general > > >> > > > >> > C:\Program Files\MATLAB704\toolbox\matlab\ops > > >> > > > >> > C:\Program Files\MATLAB704\toolbox\matlab\lang > > >> > > > >> > C:\Program Files\MATLAB704\toolbox\matlab\elmat > > >> > > > >> > C:\Program Files\MATLAB704\toolbox\matlab\elfun > > >> > > > >> > C:\Program Files\MATLAB704\toolbox\matlab\specfun > > >> > > > >> > C:\Program Files\MATLAB704\toolbox\matlab\matfun > > >> > > > >> > C:\Program Files\MATLAB704\toolbox\matlab\datafun > > >> > > > >> > C:\Program Files\MATLAB704\toolbox\matlab\polyfun > > >> > > > >> > C:\Program Files\MATLAB704\toolbox\matlab\funfun > > >> > > > >> > C:\Program Files\MATLAB704\toolbox\matlab\sparfun > > >> > > > >> > C:\Program Files\MATLAB704\toolbox\matlab\scribe > > >> > > > >> > C:\Program Files\MATLAB704\toolbox\matlab\graph2d > > >> > > > >> > …….. > > >> > > > >> > > > >> > > > >> >>> javaclasspath > > >> > > > >> > > > >> > > > >> > STATIC JAVA PATH > > >> > > > >> > > > >> > > > >> > > > >> > C:\NetCDFLab\Tools\njTools-2.0.12_jre1.5.jar > > >> > > > >> > > > >> > C:\NetCDFLab\Tools\toolsUI-4.0.49.jar > > >> > > > >> > C:\Program > > >> > Files\MATLAB704\java\patch > > >> > > > >> > C:\Program > > >> > Files\MATLAB704\java\jar\util.jar > > >> > > > >> > C:\Program > > >> > Files\MATLAB704\java\jar\widgets.jar > > >> > > > >> > C:\Program > > >> > Files\MATLAB704\java\jar\agent.jar > > >> > > > >> > C:\Program > > >> > Files\MATLAB704\java\jar\beans.jar > > >> > > > >> > C:\Program > > >> > Files\MATLAB704\java\jar\download.jar > > >> > > > >> > C:\Program > > >> > Files\MATLAB704\java\jar\hg.jar > > >> > > > >> > C:\Program > > >> > Files\MATLAB704\java\jar\ice.jar > > >> > > > >> > C:\Program > > >> > Files\MATLAB704\java\jar\ide.jar > > >> > > > >> > C:\Program > > >> > Files\MATLAB704\java\jar\jmi.jar > > >> > > > >> > C:\Program > > >> > Files\MATLAB704\java\jar\mde.jar > > >> > > > >> > > > >> > > > >> > …. > > >> > > > >> > The thing worth noticing is that the java path of njTools and > toolsUI is > > >> > located at STATIC JAVA PATH, which I think is OK. > > >> > > > >> > > > >> > > ------------------------------------------------------------------------------ > > >> > Xperia(TM) PLAY > > >> > It's a major breakthrough. An authentic gaming > > >> > smartphone on the nation's most reliable network. > > >> > And it wants your games. > > >> > *http://p.sf.net/sfu/verizon-sfdev*<http://p.sf.net/sfu/verizon-sfdev> > > >> > _______________________________________________ > > >> > njtbx-users mailing list > > >> > *njt...@li...*<njt...@li...> > > >> > *https://lists.sourceforge.net/lists/listinfo/njtbx-users*<https://lists.sourceforge.net/lists/listinfo/njtbx-users> > > >> > > > >> > > > >> > > >> > > >> > > >> -- > > >> Dr. Richard P. Signell (508) 457-2229 > > >> USGS, 384 Woods Hole Rd. > > >> Woods Hole, MA 02543-1598 > > > > > > > ------------------------------------------------------------------------------ > > > Xperia(TM) PLAY > > > It's a major breakthrough. An authentic gaming > > > smartphone on the nation's most reliable network. > > > And it wants your games. > > > *http://p.sf.net/sfu/verizon-sfdev*<http://p.sf.net/sfu/verizon-sfdev> > > > _______________________________________________ > > > njtbx-users mailing list > > > *njt...@li...*<njt...@li...> > > > *https://lists.sourceforge.net/lists/listinfo/njtbx-users*<https://lists.sourceforge.net/lists/listinfo/njtbx-users> > > > > > > > > > > > > > > -- > > Dr. Richard P. Signell (508) 457-2229 > > USGS, 384 Woods Hole Rd. > > Woods Hole, MA 02543-1598 > > > ------------------------------------------------------------------------------ > Xperia(TM) PLAY > It's a major breakthrough. An authentic gaming > smartphone on the nation's most reliable network. > And it wants your games.* > **http://p.sf.net/sfu/verizon-sfdev* <http://p.sf.net/sfu/verizon-sfdev> > _______________________________________________ > njtbx-users mailing list* > **njt...@li...* <njt...@li...>* > **https://lists.sourceforge.net/lists/listinfo/njtbx-users*<https://lists.sourceforge.net/lists/listinfo/njtbx-users> > > > > > -- > Sachin Bhate* > **http://njtbx.sourceforge.net/* <http://njtbx.sourceforge.net/> > ------------------------------------------------------------------------------ > Xperia(TM) PLAY > It's a major breakthrough. An authentic gaming > smartphone on the nation's most reliable network. > And it wants your games. > http://p.sf.net/sfu/verizon-sfdev > _______________________________________________ > njtbx-users mailing list > njt...@li... > https://lists.sourceforge.net/lists/listinfo/njtbx-users > > > > > ------------------------------------------------------------------------------ > Xperia(TM) PLAY > It's a major breakthrough. An authentic gaming > smartphone on the nation's most reliable network. > And it wants your games. > http://p.sf.net/sfu/verizon-sfdev > _______________________________________________ > njtbx-users mailing list > njt...@li... > https://lists.sourceforge.net/lists/listinfo/njtbx-users > > -- Sachin Bhate http://njtbx.sourceforge.net/ |