MATLAB's HDF5 Updates
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The document provides an overview of MATLAB's HDF5 low-level interface, introducing various packages and member functions, particularly highlighting the functionalities of 'h5l' for link handling. It discusses updates in R2009b, including enhanced speed, new library supports, and over 300 functions aligned with the HDF5 C API, particularly focusing on the 'h5copy' function for copying objects between files. Additionally, it mentions native support for NetCDF-3 and the potential for using NetCDF-Java in MATLAB.
MATLAB's HDF5 Updates
- 1. MATLAB's HDF5 Updates John Evans Image and Scientific Data Formats
- 2. Quick Overview The MATLAB HDF5 low-level interface is divided into “packages” that correspond to the HDF5 interfaces. One such class is “H5F”, which has “open” as a member function. H5, H5A, H5D, H5DS, H5E, H5F, H5G, H5I, H5L, H5ML(??), H5O, H5P, H5R, H5S, H5T, H5Z. H5ML is a special MATLAB “helper” package.
- 3. R2009b What's New In R2009b HDF5 offerings based on library version 1.8.1 Support for H5L, H5O, H5DS interfaces A little bit more speed! Over 300 functions in corresponding to HDF5 C API 3
- 4. R2009b Link Interface >> help H5L Contents for H5L: Link interface H5L.create_hard H5L.create_soft H5L.delete H5L.exists H5L.get_info H5L.get_val H5L.iterate H5L.iterate_by_name H5L.move H5L.visit H5L.visit_by_name - Creates a hard link - Creates a soft link - Deletes a link - Checks for the existence of a link - Returns information about a link - Returns the value of a symbolic link - Iterates through links in a group - Iterates through links in a group - Moves a link from one location to another - Iterate through all links in and below a group - Iterate through all links in and below a group 4
- 5. R2009b H5COPY >> help h5copy H5COPY copies an object from one HDF5 file to another file. h5copy(INPUTFILE,OUTPUTFILE,SRCOBJ,DSTOBJ) copies the source object name SRCOBJ in the input HDF5 file INPUTFILE to the destination identified by DSTOBJ in OUTPUTFILE. The behavior of the copy is to recursively copy all objects below the group, keep soft links as they are, keep external links as they are, update only the values of object references, and to copy attributes along with the object. This program was translated from the source code of "h5copy.c" written by Pedro Vicente Nunes and Quincey Koziol, THG. 5
- 6. R2009b H5COPY % open input file ifid = H5F.open(ifile,'H5F_ACC_RDONLY','H5P_DEFAULT'); % open output file if exist(ofile,'file') ofid = H5F.open(ofile,'H5F_ACC_RDWR','H5P_DEFAULT'); else fcpl = H5P.create('H5P_FILE_CREATE'); ofid = H5F.create(ofile,'H5F_ACC_TRUNC',fcpl,'H5P_DEFAULT'); H5P.close(fcpl); end % create property lists for copy ocpl = H5P.create('H5P_OBJECT_COPY'); 6
- 7. R2009b H5COPY % create link creation property list lcpl = H5P.create('H5P_LINK_CREATE'); % Set the intermediate creation property H5P.set_create_intermediate_group(lcpl,true); % do the copy H5O.copy(ifid,srcObjName,ofid,dstObjName,ocpl,lcpl); H5P.close(lcpl); H5P.close(ocpl); H5F.close(ifid); H5F.close(ofid); 7
- 8. NetCDF-4? Well, sort of... Native support for netCDF-3 since R2008b, not just yet for netCDF-4… … but NetCDF-4 is HDF5 under the hood, so you can read with low-level HDF5 interface now. Java? Yep, it's possible to use netcdf-java right now in MATLAB. 3rd party mex-file mexcdf recompiled statically with HDF5 and NetCDF-4.
- 9. References MathWorks: http://www.mathworks.com HDF5TOOLS: go to http://www.mathworks.com/matlabcentral/fileexchange/ and search for HDF5TOOLS NetCDF Java Library: http://www.unidata.ucar.edu/software/netcdf-java/ SNCTOOLS: http://mexcdf.sourceforge.net/ HDF5 Group: go to http://www.hdfgroup.org/ftp/HDF5/examples/examples-by-api/ and look for the MATLAB examples
- 10. References MathWorks: http://www.mathworks.com HDF5TOOLS: go to http://www.mathworks.com/matlabcentral/fileexchange/ and search for HDF5TOOLS NetCDF Java Library: http://www.unidata.ucar.edu/software/netcdf-java/ SNCTOOLS: http://mexcdf.sourceforge.net/ HDF5 Group: go to http://www.hdfgroup.org/ftp/HDF5/examples/examples-by-api/ and look for the MATLAB examples
Editor's Notes
- #4: Must be suitable for customers as the slide will be made available for external use at the time of release. Motivation One or two sentences describing the problem in terms of how customers phrased or think of the issue. Consider both the feature and the workflow motivations. Solution (Added Details) More details as appropriate. How does it integrate with other features and products? Doc Reference In addition to release notes, which should be the source for most of the information on this slide. Add a doc reference if possible. Demo Shipping demo name Limitations, Known Problems, and Workarounds What are the current limitations? Are there problems end users are likely to run into? Are there Workarounds? Is anything likely to break, not just feature or product but interoperability with other products? Questions and Debugging Tips (for MathWorks Support team) What questions might end users ask? What should Support try out when end users run into problems? Are there any debugging tips or processes Support should follow? Release Number – Tech Marketing to add icon closer to release date.
- #5: Must be suitable for customers as the slide will be made available for external use at the time of release. Motivation One or two sentences describing the problem in terms of how customers phrased or think of the issue. Consider both the feature and the workflow motivations. Solution (Added Details) More details as appropriate. How does it integrate with other features and products? Doc Reference In addition to release notes, which should be the source for most of the information on this slide. Add a doc reference if possible. Demo Shipping demo name Limitations, Known Problems, and Workarounds What are the current limitations? Are there problems end users are likely to run into? Are there Workarounds? Is anything likely to break, not just feature or product but interoperability with other products? Questions and Debugging Tips (for MathWorks Support team) What questions might end users ask? What should Support try out when end users run into problems? Are there any debugging tips or processes Support should follow? Release Number – Tech Marketing to add icon closer to release date.
- #6: Must be suitable for customers as the slide will be made available for external use at the time of release. Motivation One or two sentences describing the problem in terms of how customers phrased or think of the issue. Consider both the feature and the workflow motivations. Solution (Added Details) More details as appropriate. How does it integrate with other features and products? Doc Reference In addition to release notes, which should be the source for most of the information on this slide. Add a doc reference if possible. Demo Shipping demo name Limitations, Known Problems, and Workarounds What are the current limitations? Are there problems end users are likely to run into? Are there Workarounds? Is anything likely to break, not just feature or product but interoperability with other products? Questions and Debugging Tips (for MathWorks Support team) What questions might end users ask? What should Support try out when end users run into problems? Are there any debugging tips or processes Support should follow? Release Number – Tech Marketing to add icon closer to release date.
- #7: Must be suitable for customers as the slide will be made available for external use at the time of release. Motivation One or two sentences describing the problem in terms of how customers phrased or think of the issue. Consider both the feature and the workflow motivations. Solution (Added Details) More details as appropriate. How does it integrate with other features and products? Doc Reference In addition to release notes, which should be the source for most of the information on this slide. Add a doc reference if possible. Demo Shipping demo name Limitations, Known Problems, and Workarounds What are the current limitations? Are there problems end users are likely to run into? Are there Workarounds? Is anything likely to break, not just feature or product but interoperability with other products? Questions and Debugging Tips (for MathWorks Support team) What questions might end users ask? What should Support try out when end users run into problems? Are there any debugging tips or processes Support should follow? Release Number – Tech Marketing to add icon closer to release date.
- #8: Must be suitable for customers as the slide will be made available for external use at the time of release. Motivation One or two sentences describing the problem in terms of how customers phrased or think of the issue. Consider both the feature and the workflow motivations. Solution (Added Details) More details as appropriate. How does it integrate with other features and products? Doc Reference In addition to release notes, which should be the source for most of the information on this slide. Add a doc reference if possible. Demo Shipping demo name Limitations, Known Problems, and Workarounds What are the current limitations? Are there problems end users are likely to run into? Are there Workarounds? Is anything likely to break, not just feature or product but interoperability with other products? Questions and Debugging Tips (for MathWorks Support team) What questions might end users ask? What should Support try out when end users run into problems? Are there any debugging tips or processes Support should follow? Release Number – Tech Marketing to add icon closer to release date.