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Www. The HDF Group 10/17/151 HDF5 Tools Tutorial ICALEPCS 2015

Jan 21, 2016

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10/17/151HDF5 Tools Tutorial ICALEPCS 2015www.hdfgroup.orgThe HDF Groupwww.hdfgroup.org1Copyright 2015 The HDF Group. All rights reserved. 10/17/152HDF5 ToolsSupported by The HDF Grouphttps://www.hdfgroup.org/tools/ GUI-based BrowsersHDF Compass (prototype)HDFViewHDF5 command-line toolsDistributed with the HDF5 libraryh5dump, h5ls, h5repack, h5diff, h5jam, h5copy, h5debugDistributed as stand-alone toolsh5check, converters between HDF4 and HDF5Supported on variety of platforms

ICALEPCS 2015www.hdfgroup.org2Copyright 2015 The HDF Group. All rights reserved. 10/17/153Aside: UNIX commands can be useful!headView superblockstringsView character data (attributes, datasets)View some HDF5 metadatahexdumpThe last resort to troubleshoot issues

ICALEPCS 2015www.hdfgroup.org3Copyright 2015 The HDF Group. All rights reserved. HDF Compass

10/17/154https://github.com/HDFGroup/hdf-compass/Please try it and let us know what do you think!ICALEPCS 2015www.hdfgroup.orgThis a prototype we have been playing with and considering supporting. It was acquired from Andrew Collette. We hope to get community involved in supporting and expanding it. The tools designed with plugin architecture in mind. There currently two plugins: HDF5 and OpeNDAP. It uses native graphic interfaces. Here is an example how it looks on Mac, like any other Apple App.Was released recently for Mac 10.10 and Windows. Tools can handle big files and many objects in the file, because it loads data on demand (the known issues with HDFView). Please try it and comment on github or send email to [email protected] 2015 The HDF Group. All rights reserved. 10/17/155HDFViewJava-based tool to access HDF4 and HDF5Used forViewing and modifying file contentCreating data in HDF files Exporting and importing dataGetting data to/from ExcelSupports features used in the JPSS filesUser blockSupports object and region references

ICALEPCS 2015www.hdfgroup.org5Copyright 2015 The HDF Group. All rights reserved. 10/17/156HDF5 command-line toolsICALEPCS 2015www.hdfgroup.orgThe HDF Groupwww.hdfgroup.org6Copyright 2015 The HDF Group. All rights reserved. 10/17/157HDF5 command-line tools infoSee HDF5 Reference Manualhttps://www.hdfgroup.org/HDF5/doc/RM/Tools.html

FlagUsed for-V (--version)Printing version of the HDF5 library-h (--help)Displaying online help--enable-error-stackTroubleshootingICALEPCS 2015www.hdfgroup.org7Copyright 2015 The HDF Group. All rights reserved. 10/17/158h5dumpDisplays HDF5 file according Data Description Language (DDL)Human readable and most comprehensive

FlagUsed for-H (--header)Suppressing data printing-p (--properties)Displaying properties of the objects, e.g., compression ratio-BPrinting superblock to find user block info-M (--packedbits)Displaying JPSS quality flags-R (--region)Displaying data pointed by region reference-N Searching for the object specified by nameICALEPCS 2015www.hdfgroup.org8Copyright 2015 The HDF Group. All rights reserved. 10/17/159h5lsProvides some internal information, such as objects offsets in the file to pass to h5debug

Flag(s)Used for-vVerbose output-gDisplaying information about the group-rListing objects recursively-dPrinting data for the datasetICALEPCS 2015www.hdfgroup.org9Copyright 2015 The HDF Group. All rights reserved. 10/17/1510h5jam/h5unjamAdds/removes user blockh5unjam -i -o -u

ICALEPCS 2015www.hdfgroup.org10Copyright 2015 The HDF Group. All rights reserved. 10/17/1511h5repackCreates new file with different properties

Flag(s)Used forNo flagsDeleting non-used space in the file-lChanging storage layout of the datasets in the file-fApplying (or removing) compressionICALEPCS 2015www.hdfgroup.org11Copyright 2015 The HDF Group. All rights reserved. 10/17/1512h5diffFinds differences in two filesNot good at comparing file structures

Flag(s)Used for-N (--nan)Disabling NaN detection---exclude-pathDisabling comparison of specified objectsICALEPCS 2015www.hdfgroup.org12We would like to create a tool based on more rigorously defined comparison.Copyright 2015 The HDF Group. All rights reserved. 10/17/1513h5diffFinds differences in two files

Flag(s)Used for-lChanging storage layout of the datasets in the file-fApplying (or removing) compressionICALEPCS 2015www.hdfgroup.org13Copyright 2015 The HDF Group. All rights reserved. 10/17/1514h5copyCopies a specified content within an HDF5 file or to a new HDF5 fileEasy to extract data to the new HDF5 fileLimitation cannot copy to / root group

Flag(s)Used for-fControlling copy options-f refCoping references and the objects they referenced ICALEPCS 2015www.hdfgroup.org14Copyright 2015 The HDF Group. All rights reserved. 10/17/1515h5checkUses file specification to checks file format consistencyUseful with corrupted files to see if any data can be salvaged

ICALEPCS 2015www.hdfgroup.org15Copyright 2015 The HDF Group. All rights reserved. Thank You!Questions?1610/17/15ICALEPCS 2015www.hdfgroup.orgThe HDF Groupwww.hdfgroup.org