Re: [Hdf-forum] trying to build h4toh5 tools
Hi, Matt! You need to point the configure to both hdf4 and hdf5 libraries. Typing %configure --help will give --with-hdfeos2=DIR Specify path to external hdfeos2 library. option to specify the location of hdfeos2 library and the hdfeos2 library is built on top of the hdf4 library. Please refer to this document for building hdfeos2 library. http://hdfeos.org/software/hdfeos.php#ref_sec:hdf-eos2 Regards, -Original Message- From: hdf-forum-boun...@hdfgroup.org [mailto:hdf-forum-boun...@hdfgroup.org] On Behalf Of Matt Funk Sent: Thursday, May 13, 2010 3:35 PM To: HDF Users Discussion List Subject: Re: [Hdf-forum] trying to build h4toh5 tools Thanks for the reply. so wait though, do i need to point the configure to the hdf4 or hdf5 library? Currently i am pointing it to the hdf5 library (in fact i haven't even build the hdf4 library) thanks matt On 5/13/2010 2:20 PM, H. Joe Lee wrote: Hi, Matt! You may want to try '%make CC=/path/to/hdf4_install_dir/bin/h4cc' and see if it works. -- +1(217)265-7710 http://hdfeos.org -Original Message- From: hdf-forum-boun...@hdfgroup.org [mailto:hdf-forum-boun...@hdfgroup.org] On Behalf Of Matt Funk Sent: Thursday, May 13, 2010 3:12 PM To: HDF Users Discussion List Subject: [Hdf-forum] trying to build h4toh5 tools Hi, i am having problem building the h4toh5 tools on a machine. I tried the binaries first but that gave me a a core dump. Anyway, i build the hdf5-1.8.4-patch1 libs and then configured h4h5tools (and pointed the hdf5 build). The h4h5tools configures alright. However, when i issue: make i get the following: gcc -DPACKAGE_NAME=\H4H5Tools\ -DPACKAGE_TARNAME=\h4h5tools\ -DPACKAGE_VERSION=\2.1.1\ -DPACKAGE_STRING=\H4H5Tools\ 2.1.1\ -DPACKAGE_BUGREPORT=\h...@hdfgroup.org\ -DPACKAGE_URL=\\ -DPACKAGE=\h4h5tools\ -DVERSION=\2.1.1\ -DSTDC_HEADERS=1 -DHAVE_HDF5_H=1 -DHAVE_LIBHDF5=1 -I. -I/home/mafunk/CODE/RSET/externalPackages/src/hdf5-1.8.4-patch1/hdf5/include -m64 -MT h4toh5anno.o -MD -MP -MF .deps/h4toh5anno.Tpo -c -o h4toh5anno.o h4toh5anno.c In file included from h4toh5main.h:43, from h4toh5anno.c:77: h4toh5util.h:45:17: error: hdf.h: No such file or directory h4toh5util.h:46:19: error: mfhdf.h: No such file or directory In file included from h4toh5util.h:49, from h4toh5main.h:43, from h4toh5anno.c:77: h4toh5.h:25:19: error: hfile.h: No such file or directory In file included from h4toh5util.h:49, from h4toh5main.h:43, from h4toh5anno.c:77: what am i missing? thanks matt ___ Hdf-forum is for HDF software users discussion. Hdf-forum@hdfgroup.org http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org ___ Hdf-forum is for HDF software users discussion. Hdf-forum@hdfgroup.org http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org ___ Hdf-forum is for HDF software users discussion. Hdf-forum@hdfgroup.org http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org ___ Hdf-forum is for HDF software users discussion. Hdf-forum@hdfgroup.org http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
Re: [Hdf-forum] trying to build h4toh5 tools
Hi, Matt! Building HDF-EOS2 is an option, not a requirement. However, having HDF4 library is a must. Here's the simplest way to configure and build h4toh5 tool if you want to skip building HDF-EOS2. %./configure --with-hdf5=/path/to/hdf5_library_install_prefix CC=/path/to/hdf4_library_install_prefix/bin/h4cc %make -Original Message- From: hdf-forum-boun...@hdfgroup.org [mailto:hdf-forum-boun...@hdfgroup.org] On Behalf Of Matt Funk Sent: Thursday, May 13, 2010 4:26 PM To: hdf-forum@hdfgroup.org Subject: Re: [Hdf-forum] trying to build h4toh5 tools Hi, how come it have to build the hdf-eos2 libraries. All i want to do is convert a regular hdf4 to hdf5 library matt On 5/13/2010 2:52 PM, H. Joe Lee wrote: Hi, Matt! You need to point the configure to both hdf4 and hdf5 libraries. Typing %configure --help will give --with-hdfeos2=DIR Specify path to external hdfeos2 library. option to specify the location of hdfeos2 library and the hdfeos2 library is built on top of the hdf4 library. Please refer to this document for building hdfeos2 library. http://hdfeos.org/software/hdfeos.php#ref_sec:hdf-eos2 Regards, -Original Message- From: hdf-forum-boun...@hdfgroup.org [mailto:hdf-forum-boun...@hdfgroup.org] On Behalf Of Matt Funk Sent: Thursday, May 13, 2010 3:35 PM To: HDF Users Discussion List Subject: Re: [Hdf-forum] trying to build h4toh5 tools Thanks for the reply. so wait though, do i need to point the configure to the hdf4 or hdf5 library? Currently i am pointing it to the hdf5 library (in fact i haven't even build the hdf4 library) thanks matt On 5/13/2010 2:20 PM, H. Joe Lee wrote: Hi, Matt! You may want to try '%make CC=/path/to/hdf4_install_dir/bin/h4cc' and see if it works. -- +1(217)265-7710 http://hdfeos.org -Original Message- From: hdf-forum-boun...@hdfgroup.org [mailto:hdf-forum-boun...@hdfgroup.org] On Behalf Of Matt Funk Sent: Thursday, May 13, 2010 3:12 PM To: HDF Users Discussion List Subject: [Hdf-forum] trying to build h4toh5 tools Hi, i am having problem building the h4toh5 tools on a machine. I tried the binaries first but that gave me a a core dump. Anyway, i build the hdf5-1.8.4-patch1 libs and then configured h4h5tools (and pointed the hdf5 build). The h4h5tools configures alright. However, when i issue: make i get the following: gcc -DPACKAGE_NAME=\H4H5Tools\ -DPACKAGE_TARNAME=\h4h5tools\ -DPACKAGE_VERSION=\2.1.1\ -DPACKAGE_STRING=\H4H5Tools\ 2.1.1\ -DPACKAGE_BUGREPORT=\h...@hdfgroup.org\ -DPACKAGE_URL=\\ -DPACKAGE=\h4h5tools\ -DVERSION=\2.1.1\ -DSTDC_HEADERS=1 -DHAVE_HDF5_H=1 -DHAVE_LIBHDF5=1 -I. -I/home/mafunk/CODE/RSET/externalPackages/src/hdf5-1.8.4-patch1/hdf5/include -m64 -MT h4toh5anno.o -MD -MP -MF .deps/h4toh5anno.Tpo -c -o h4toh5anno.o h4toh5anno.c In file included from h4toh5main.h:43, from h4toh5anno.c:77: h4toh5util.h:45:17: error: hdf.h: No such file or directory h4toh5util.h:46:19: error: mfhdf.h: No such file or directory In file included from h4toh5util.h:49, from h4toh5main.h:43, from h4toh5anno.c:77: h4toh5.h:25:19: error: hfile.h: No such file or directory In file included from h4toh5util.h:49, from h4toh5main.h:43, from h4toh5anno.c:77: what am i missing? thanks matt ___ Hdf-forum is for HDF software users discussion. Hdf-forum@hdfgroup.org http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org ___ Hdf-forum is for HDF software users discussion. Hdf-forum@hdfgroup.org http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org ___ Hdf-forum is for HDF software users discussion. Hdf-forum@hdfgroup.org http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org ___ Hdf-forum is for HDF software users discussion. Hdf-forum@hdfgroup.org http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org ___ Hdf-forum is for HDF software users discussion. Hdf-forum@hdfgroup.org http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org ___ Hdf-forum is for HDF software users discussion. Hdf-forum@hdfgroup.org http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
Re: [Hdf-forum] Map Projection and Visualizing Data
Hi, Bahar! If you're dealing with NASA HDF4 files, you can find MATLAB visualization examples here: http://hdfeos.org/zoo/ -- +1(217)265-7710 http://hdfeos.org On Tue, Jul 27, 2010 at 1:36 PM, Bahar Sadra baharsa...@gmail.com wrote: To whom I concern, I have questions about the HDF4 files, could you let me know how I can use projection for my data and how I can Visualize them. Both of the questions are in respect to MATLAB? Could you send my answer to my gmail please? Thank you so much for your attention and time. Best Regards, Bahar ___ Hdf-forum is for HDF software users discussion. Hdf-forum@hdfgroup.org http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org ___ Hdf-forum is for HDF software users discussion. Hdf-forum@hdfgroup.org http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
[Hdf-forum] Open Source Hadoop Project for both HDF4 and HDF5?
I'm wondering if there has been any open source software project for Hadoop that can work with *both* HDF4 and HDF5 directly as described in SciMATE[1] (i.e., HDF5 Adapter in Figure 2 from the paper) I think [2] is close but it seems to be only for NetCDF. p.s. I'm not looking for a solution that involves exporting data into XML from HDF. [1] http://www.cse.ohio-state.edu/~wayi/papers/SciMATE.pdf [2] https://github.com/four2five/SciHadoop -- HDF: Software that Powers Science ___ Hdf-forum is for HDF software users discussion. Hdf-forum@hdfgroup.org http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
Re: [Hdf-forum] Problems installing hdfview 2.9 on Mac Mountain Lion
One suggestion for a long-term solution. Would you please make the HDFView downloadable updatable from AppStore? -- HDF: Software that Powers Science On Tue, Feb 12, 2013 at 12:01 PM, Peter Cao x...@hdfgroup.org wrote: Hi all, When you run the HDFView installer on Mac Mountain Lion, you may get an error message saying the software is damaged and need to be moved to the trash. The error message is because of the OS X 10.8 GateKeeper that defaults to only running apps that are code-signed. Please use the workaround if you encounter such a problem: before you run the HDFView installer, run the this command on the installer xattr -d com.apple.quarantine ~/Downloads/hdfview_install_macosx_intel64.app We are working on a long-term solution for the problem. Thanks --pc ___ Hdf-forum is for HDF software users discussion. Hdf-forum@hdfgroup.org http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org ___ Hdf-forum is for HDF software users discussion. Hdf-forum@hdfgroup.org http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
Re: [Hdf-forum] recreating a file structure.
Hi, Bruce, You may also want to try h4mapwriter tool. Please take a look at sample XML outputs from the HDF4 files and see the map writer fits your purpose: http://www.hdfgroup.org/projects/h4map/h4map_examples.html -- HDF: Software that Powers Science On Sun, Feb 24, 2013 at 1:38 AM, bmrib...@hdfgroup.org wrote: Hi Bruce, The dumper hdp prints out sort of a file structure at the end of the output of dumpvg command. It starts at: Graphical representation of the file However, it also shows some internal vgroups and vdatas, so you'll have to look at the names/classes from the output above that, and match up with the indices to figure out which ones internal and can be ignored. You can look at the Reference Manual pages of Vgisinternal and VSisinternal for information about internal vgroups and vdatas. It is in the work to provide an option for hdp to suppress these internal objects. Please let us know if you have other questions. Thanks, Binh-Minh Quoting Bruce Bowler bbow...@bigelow.org: Mike, Thanks. Looks interesting, but I suppose I forgot to mention (blush), I'm dealing with HDF4. Poking around a bit, I see hdfls and friends, but they don't seem to provide as much detail as h5dump does. I suppose I could try and write it as hdf5 and then use h5toh4 and back convert it... I can probably figure it out, but I was hoping for something like a tree diagram of what's there etc. Oh well, I guess I know what I'll be doing this weekend :-( Bruce On Fri, 22 Feb 2013 13:19:14 -0500, Michael Jackson wrote: h5dump may be what you are looking for. It is part of the standard HDF5 distribution. ___ Mike JacksonPrincipal Software Engineer BlueQuartz SoftwareDayton, Ohio mike.jack...@bluequartz.net www.bluequartz.net On Feb 22, 2013, at 10:42 AM, Bruce Bowler wrote: Hi, I'm a newb at writing HDF files but have a small bit (really small) of experience reading HDF files in IDL and MATLAB. I have an HDF file that contains some data. I need to create a new file that has different data but has the same structure as the extant file. By structure, I mean vgroups, vdata, etc. Ideally I'd be creating this new file using MATLAB. It needs to be the same so a bit of 3rd party software that I don't have the source for can process the file properly. Is there a tool that will describe, in a fair bit of detail, the contents of the extant file such that I can figure out what calls I need to make to write the new one? Thanks. Bruce ___ Hdf-forum is for HDF software users discussion. Hdf-forum@hdfgroup.org http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org ___ Hdf-forum is for HDF software users discussion. Hdf-forum@hdfgroup.org http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org ___ Hdf-forum is for HDF software users discussion. Hdf-forum@hdfgroup.org http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org ___ Hdf-forum is for HDF software users discussion. Hdf-forum@hdfgroup.org http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
Re: [Hdf-forum] Assign projection HDF5
Hi, Would you please provide the URL of the sample HDF5 file that you have trouble with? Also, I'd appreciate if you could provide the URL of data user's guide if it's available. -- HDF: Software that Powers Science On Mon, Feb 25, 2013 at 12:01 PM, Geographer j_landm...@gmx.de wrote: Hi everyone, I am quite new to using HDF5 data and I think I've got a serious problem: I am using EUMETSAT's pre-operational NDVI product in HDF5 format. These data are projected with the geostationary satellite view (SR-ORG:81) but no spatial reference is given in the HDF5-file. What I could do already is write lat/lon for each pixel in a text file (from an envi geo-file) and produce hdf5-datasets of it. Is it possible to assign these x,y-values to the NDVI values contained in another dataset at least? Or is it - that would be wonderful - even possible to assign a projection mathematically? I have already tried out gdalwarp in fwtools, but it doesn't work. But for me analyses I need the data georeferenced urgently! Can anyone help? Thanks in advance, Johannes -- View this message in context: http://hdf-forum.184993.n3.nabble.com/Assign-projection-HDF5-tp4025928.html Sent from the hdf-forum mailing list archive at Nabble.com. ___ Hdf-forum is for HDF software users discussion. Hdf-forum@hdfgroup.org http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org ___ Hdf-forum is for HDF software users discussion. Hdf-forum@hdfgroup.org http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
Re: [Hdf-forum] H5 binary files differ
Hi, I think it's normal. Have you tried h5diff? It should tell nothing, which indicates that the files are same. -- HDF: Software that Powers Science On Wed, Mar 6, 2013 at 6:29 AM, Pradeep Jha prad...@ccs.engg.nagoya-u.ac.jp wrote: Hello, sometimes even when I use the same program to generate two h5 files from the same original binary data file, when I diff on the two h5 files, it tells me Binary files fileB.h5 and fileA.h5 differ. Is it normal? Pradeep ___ Hdf-forum is for HDF software users discussion. Hdf-forum@hdfgroup.org http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org ___ Hdf-forum is for HDF software users discussion. Hdf-forum@hdfgroup.org http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
Re: [Hdf-forum] Problems copy data from HDF view into Excel
Hi Maarten, In the TableView window [1], you'll see Copy menu under Table menubar. Please try to use the Copy menu item after selecting a few data sets. For some reason, Mac's Meta-C short cut key didn't work with HDFView but clicking the menu item explicitly worked for me. I think this should be fixed for user's convenience in the future. [1] http://www.hdfgroup.org/hdf-java-html/hdfview/UsersGuide/ug05spreadsheet.html#ug05save -- HDF: Software that Powers Science On Wed, Mar 27, 2013 at 4:05 PM, Grootendorst, Maarten maarten.grootendo...@kcl.ac.uk wrote: Dear all, I have installed the Mac intel 64-bit version of HDFview on my macbook. I opened a .h5 file and I wanted to copy a column with data and subsequently paste it in Excel. However, HDFview does not allows me to copy data. Did anyone experience this problem before? If so, how can you copy data from an .h5 file in Excel? Looking forward hearing from you. Kind regards, Maarten ___ Hdf-forum is for HDF software users discussion. Hdf-forum@hdfgroup.org http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org ___ Hdf-forum is for HDF software users discussion. Hdf-forum@hdfgroup.org http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
Re: [Hdf-forum] Problems copy data from HDF view into Excel
BTW, Windows style Ctrl+C and Ctrl+V works, too. -- HDF: Software that Powers Science On Wed, Mar 27, 2013 at 4:30 PM, H. Joe Lee hyok...@hdfgroup.org wrote: Hi Maarten, In the TableView window [1], you'll see Copy menu under Table menubar. Please try to use the Copy menu item after selecting a few data sets. For some reason, Mac's Meta-C short cut key didn't work with HDFView but clicking the menu item explicitly worked for me. I think this should be fixed for user's convenience in the future. [1] http://www.hdfgroup.org/hdf-java-html/hdfview/UsersGuide/ug05spreadsheet.html#ug05save -- HDF: Software that Powers Science On Wed, Mar 27, 2013 at 4:05 PM, Grootendorst, Maarten maarten.grootendo...@kcl.ac.uk wrote: Dear all, I have installed the Mac intel 64-bit version of HDFview on my macbook. I opened a .h5 file and I wanted to copy a column with data and subsequently paste it in Excel. However, HDFview does not allows me to copy data. Did anyone experience this problem before? If so, how can you copy data from an .h5 file in Excel? Looking forward hearing from you. Kind regards, Maarten ___ Hdf-forum is for HDF software users discussion. Hdf-forum@hdfgroup.org http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org ___ Hdf-forum is for HDF software users discussion. Hdf-forum@hdfgroup.org http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
Re: [Hdf-forum] h5gen or any h5dump-generated-XML to HDF5
Here's one hack you guys can try without asking a new tool. Create NcML file (a variant of XML) and use NetCDF-Java to generate an NetCDF-3 file [1]. Then convert the NetCDF-3 to NetCDF-4 using NCO [2]. The converted NetCDF-4 file is HDF5 file. You got the HDF5 from XML (NcML). Q.E.D. [1] http://www.unidata.ucar.edu/software/netcdf/ncml/ [2] http://hdfeos.net/software/nco.php -- HDF: Software that Powers Science On Thu, Apr 11, 2013 at 11:59 AM, Peter Cao x...@hdfgroup.org wrote: Hi Andy, Our HDF5/XML development is in halt because there is little demand for it. Could you give us more details on what exact you need for HDF5/XML? Assume what you have now: 1) XML files based on your XML standard or schema 2) Raw data in binary Assume below is what you need 1) convert XML structure to HDF5 file structure 2) import the data to HDF5 datasets Here is what you need: 1) an XSLT to transform your XML file to HDF5 XML files 2) generate HDF5 files from your HDF5 XML files. #1) should be straightforward. #2) can be hard. we currently do not have a tool to convert XML to HDF5. FYI: we are moving to support HDF5/JSON. The work is still in RD stage. When HDF5/JSON is available, you can write an XSLT to convert your XML files to HDF5 JSON. Thanks --pc On 4/11/2013 10:07 AM, mdehsadn wrote: Could I ask if there has been progress on HDF5/XML? I am part of a initiative developing data format standards for biochemical data. We already have an established XML based standard, where data arrays are stored as Base-64 encoded binary. These files are averaging about 2Gb or more each now. We want to establish a sister binary format, quite possibly based on HDF5. It seems that with HDF5/XML, we could simply create an XSLT transform and that would be it. Otherwise, we would have to describe the mapping and implement convertors in C or Java. Kind regards, Andy -- View this message in context: http://hdf-forum.184993.n3.nabble.com/h5gen-or-any-h5dump-generated-XML-to-HDF5-tp3719793p4026080.html Sent from the hdf-forum mailing list archive at Nabble.com. ___ Hdf-forum is for HDF software users discussion. Hdf-forum@hdfgroup.org http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org ___ Hdf-forum is for HDF software users discussion. Hdf-forum@hdfgroup.org http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org ___ Hdf-forum is for HDF software users discussion. Hdf-forum@hdfgroup.org http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
Re: [Hdf-forum] Tools to edit hdf5 files?
Hi, I'm also interested in hearing how HDF users deal with this kind of data with existing tools. By the way, what's your domain that needs resizing data with varying dimensions (e.g., Earth science / Finance / Machine Learning / Life science)? I'm asking this because what kind sensor or software that you have generates such arrays with variable size data and how your existing solution manages them. I'd appreciate if you can give a specific example problem with some sample data. -- HDF: Software that Powers Science On Wed, May 8, 2013 at 4:00 AM, Roel Vanhout rvanh...@riks.nl wrote: Hello, Apologies if this is a question with an obvious answer, I've searched the web and archives long and hard and couldn't find an answer. I'm looking to replace some of the data files of our software with hdf5 to make it easier to edit them with external tools. Specifically, I need a way to edit multi-dimensional arrays of numeric data, for which I figures hdf5 would be a natural fit. However what I need are arrays with variable sizes. It seems to be complicated to do that through the API, none of the popular tools (HDFView, HDF Explorer) seem to support resizing data, and ViTables I haven't been able to get to run on Windows. So my question is - is hdf5 suitable as a data format for data with varying dimensions? What tools will let me work with that? Thanks. regards, Roel ___ Hdf-forum is for HDF software users discussion. Hdf-forum@hdfgroup.org http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org ___ Hdf-forum is for HDF software users discussion. Hdf-forum@hdfgroup.org http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
Re: [Hdf-forum] Tools to edit hdf5 files?
Hi Roel! +1 for However the whole point of me switching to hdf5 would be that other users (internally and externally) would have easy-to-use, GUI tools for working with this data. Some users struggle with the concept of an array with more than 2 dimensions - suggesting they work with command line tools, especially ones with large amounts of options and manuals of dozens of pages, would be a regression in terms of support burden for me. In my opinion, all HDF data manipulation should be done easily with your fingertips on tablets with 0 programming involved. -- HDF: Software that Powers Science On Thu, May 16, 2013 at 7:21 AM, Roel Vanhout rvanh...@riks.nl wrote: Hi, For me personally it wouldn't be much of a problem - I would write my own command line tools that drive the baseline tools anyway, or amend my existing C++ tools to resize arrays. However the whole point of me switching to hdf5 would be that other users (internally and externally) would have easy-to-use, GUI tools for working with this data. Some users struggle with the concept of an array with more than 2 dimensions - suggesting they work with command line tools, especially ones with large amounts of options and manuals of dozens of pages, would be a regression in terms of support burden for me. While HDF Explorer seems very capable in most respects and is very reasonably priced, it doesn't let you resize data sets, which is a showstopper for me. Thanks for taking the time to think about my issues! regards, Roel -Original Message- From: Hdf-forum [mailto:hdf-forum-boun...@hdfgroup.org] On Behalf Of H. Joe Lee Sent: Wednesday, May 15, 2013 20:33 To: HDF Users Discussion List Subject: Re: [Hdf-forum] Tools to edit hdf5 files? Hi, Roel! Thanks for your reply. I hope someone can write an easy-to-use GUI tool like MS Excel for HDF data array manipulation you described in near future. If you're not limited to GUI tool, I think script-language tool like NCL (free) IDL/MATLAB (commercial) can do the array manipulation you described. For example, you can easily read subset HDF5 array [1], reshape the array [2], and save it [3] in NetCDF-4 (which is HDF5 under the hood) in NCL. The only drawback of NCL compared to IDL/MATLAB is that it doesn't run on Windows but it supports Cygwin so you may want to try it. [1] http://hdfeos.org/zoo/NSIDC/GLAH13_633_2103_001_1317_0_01_0001.h5.ncl [2] http://hdfeos.org/zoo/LaRC/MISR_AM1_GRP_ELLIPSOID_GM_P117_O058421_BA_F03_0024_Blue_Radiance_RDQI.ncl [3] http://www.ncl.ucar.edu/Applications/netcdf4.shtml -- HDF: Software that Powers Science On Wed, May 15, 2013 at 5:10 AM, Roel Vanhout rvanh...@riks.nl wrote: Hello, Thanks for the replies. In response to H. Joe Lee, my application is in earth sciences, more specifically in land use modeling, and my data is configuration data for the model. It is in that sense that I may be using hdf5 in an untypical way, it is not data that is acquired by sensors or such, but the data in my hdf5 files represents calibration parameters for the model. Hence the need to be able to easily edit them, and to resize arrays - for example when you want to change the number of land use classes in a specific simulation, you need to be able to resize a 10x500x600 array to 8x500x600 (for example). We now use a multitude of solutions - xml files, 2d matrices in single files where the number of files is the 3rd dimension, etc. As for the question below, it is mostly (2), and sometimes (1). Example of (2) I gave earlier, an example of (1) is time series of 2d data - in some cases you enter values for e.g. 2000 and 2030, and the software interpolates the values for the years between that, but a user may enter data for 2000, 2010, 2020 and 2030. In that case, the length of that dimension of the array would be 4, whereas in the first case it would be 2. regards Roel From: Hdf-forum [mailto:hdf-forum-boun...@hdfgroup.org] On Behalf Of Peter Cao Sent: Friday, May 10, 2013 17:17 To: hdf-forum@hdfgroup.org Subject: Re: [Hdf-forum] Tools to edit hdf5 files? Could you be more specific on resizing data? Is it any of the following? 1) you defined your data as variable size and add/delete data from it, 2) you define fixed length of dimensions and extend/shrink the dimensions, or 3) you define as 2D and change it to 1D, 3D, etc. Thanks --pc On 5/8/2013 4:00 AM, Roel Vanhout wrote: Hello, Apologies if this is a question with an obvious answer, I've searched the web and archives long and hard and couldn't find an answer. I'm looking to replace some of the data files of our software with hdf5 to make it easier to edit them with external tools. Specifically, I need a way to edit multi-dimensional arrays of numeric data, for which I figures hdf5 would be a natural fit. However what I need are arrays with variable sizes. It seems
[Hdf-forum] HDF to GeoTIFF conversion project
Hi, HDF users! The HDF Group is going to start a pilot project of creating a tool that converts HDF to GeoTIFF through Apache Incubator project. Conversion to GeoTIFF will allow you to visualize NASA HDF/HDF-EOS through popular GIS tools such as ArcGIS and Google Earth Pro. We're writing a new proposal for the tool and we're looking for a few core developers who can contribute for the project: http://wiki.apache.org/incubator/HotdoGProposal If you're interested in joining the project, would you please let us know at eosh...@hdfgroup.org so that we can include your name in the project proposal? Regards, -- HDF: Software that Powers Science ___ Hdf-forum is for HDF software users discussion. Hdf-forum@hdfgroup.org http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
