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HDF5 Tools

HDF5 Tools. Peter Cao The HDF Group. A short demo of HDFView HDF5 command line tools. Outline. What is HDFView?. HDFView. HDF Application. Browser/Editor. Written in Java. For more information and download, visit www.hdfgroup.org/hdf-java-html. HDFView Demo.

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HDF5 Tools

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  1. HDF5 Tools Peter Cao The HDF Group HDF and HDF-EOS Workshop XII

  2. A short demo of HDFView HDF5 command line tools Outline HDF and HDF-EOS Workshop XII

  3. What is HDFView? HDFView HDF Application Browser/Editor Written in Java For more information and download, visit www.hdfgroup.org/hdf-java-html HDF and HDF-EOS Workshop XII

  4. HDFView Demo • Browse objects in an HDF5 file • Show data content in table, image • Make a subset • View attributes and metadata • Create a new HDF5 file and edit data content HDF and HDF-EOS Workshop XII

  5. HDFView 2.5 • Release planned in December, 2008 • Build with HDF4 2r4 and HDF5 1.8.2 • Fix bugs and add new features • Plug memory leaks • Support iRODS (Windows and linux only) • Use jdk 1.6.0_06 or above (for performance) Drop mac PowerPC HDF and HDF-EOS Workshop XII

  6. HDF5 Command Line Tools • Readers • h5dump, h5diff, h5ls, h5check, h5stat • Writers • h5repack, h5repart, h5import, h5jam, h5unjam, h5copy, h5mkgrp • Converters • h4toh5, h5toh4, gif2h5, h52gif HDF and HDF-EOS Workshop XII

  7. Where to Start? • Tools located in bin/ directory • Use “-h” option for help • Consult online help http://www.hdfgroup.org/hdf5tools.html • Email help desk help@hdfgroup.org HDF and HDF-EOS Workshop XII

  8. h5dump • Dumps contents of HDF5 file to stdout • ASCII text • XML • Binary HDF and HDF-EOS Workshop XII

  9. h5dump: Object Headers > h5dump -HSDS.h5 HDF5 "SDS.h5" { GROUP "/" { GROUP "Floats" { DATASET "FloatArray" { DATATYPE H5T_IEEE_F32LE DATASPACE SIMPLE { ( 4, 3 ) / ( 4, 3 ) } } } DATASET "IntArray" { DATATYPE H5T_STD_I32LE DATASPACE SIMPLE { ( 5, 6 ) / ( 5, 6 ) } } } } HDF and HDF-EOS Workshop XII

  10. h5dump: Dataset > h5dump –d /Floats/FloatArray SDS.h5 • HDF5 "SDS.h5" { • DATASET "/Floats/FloatArray" { • DATATYPE H5T_IEEE_F32LE • DATASPACE SIMPLE { ( 4, 3 ) / ( 4, 3 ) } • DATA { • (0,0): 0.01, 0.02, 0.03, • (1,0): 0.1, 0.2, 0.3, • (2,0): 1, 2, 3, • (3,0): 10, 20, 30 • } • } • } HDF and HDF-EOS Workshop XII

  11. h5dump: Binary Output -b F, --binary=[MEMORY|FILE|LE|BE] > h5dump -d /IntArray -o out_le.bin -b LE SDS.h5 0000000 00000000 00000001 00000002 00000003 00000004 00000005 0000030 0000000a 0000000b 0000000c 0000000d 0000000e 0000000f 0000060 00000014 00000015 00000016 00000017 00000018 00000019 0000110 0000001e 0000001f 00000020 00000021 00000022 00000023 0000140 00000028 00000029 0000002a 0000002b 0000002c 0000002d HDF and HDF-EOS Workshop XII

  12. h5diff Show differences between… two objects or two files HDF and HDF-EOS Workshop XII

  13. h5diff > h5diff SDS.h5 SDS2.h5 Dataset: </IntArray> 5 differences found HDF and HDF-EOS Workshop XII

  14. h5diff: Report Differences > h5diff SDS.h5 SDS2.h5 -r/IntArray Dataset: </IntArray> and </IntArray> position IntArray IntArray difference ------------------------------------------------------ [ 0 0 ] 0 10 10 [ 1 0 ] 10 100 90 [ 2 0 ] 20 200 180 [ 3 0 ] 30 300 270 [ 4 0 ] 40 400 360 5 differences found HDF and HDF-EOS Workshop XII

  15. h5diff: Unsolved Issues How to compare two files with different • Structures • Storage layouts • Properties HDF and HDF-EOS Workshop XII

  16. h5repack • Copies a file to a new file with • Compression filter • Data layout • Other user options HDF and HDF-EOS Workshop XII

  17. h5repack: Compression Filter • -f {GZIP|SZIP|SHUF|FLET|NBIT|SOFF|NONE} • For example • > h5repack -i SDS.h5 -o out.h5 -f GZIP=6 HDF and HDF-EOS Workshop XII

  18. h5repack: Data Layout -l {CHUNK| COMPA| CONTI} For example> h5repack -i SDS.h5 -o out.h5 -l CHUNK=1000x1000 HDF and HDF-EOS Workshop XII

  19. h5repack: File Format Version The test file was created with HDF5 1.6.5. The root group of the file contains 100 groups. Each group at the root contains 9 sub groups. Each sub group contains one compound dataset. The compound dataset has 40 members of type 32 bit integer HDF and HDF-EOS Workshop XII

  20. h5import Imports binary/ASCII data into an HDF5 file h5import infile -c config_file [infile -c config_file2 ...] -outfile outfile For example > h5import float5x4x2.txt -c First_set.conf -o First_set.h5 PATH work/First-set INPUT-CLASS TEXTFP RANK 3 DIMENSION-SIZES 5 2 4 OUTPUT-CLASS FP OUTPUT-SIZE 64 OUTPUT-ARCHITECTURE IEEE OUTPUT-BYTE-ORDER LE CHUNKED-DIMENSION-SIZES 2 2 2 MAXIMUM-DIMENSIONS 8 8 -1 GROUP "/" { GROUP "work" { DATASET "First-set" { DATATYPE H5T_IEEE_F64LE DATASPACE SIMPLE { ( 5, 2, 4 ) / ( 8, 8, H5S_UNLIMITED ) } DATA { (0,0,0): 1.01, 1.02, 1.03, 1.04, (0,1,0): 1.11, 1.12, 1.13, 1.14, (1,0,0): 1.21, 1.22, 1.23, 1.24, (1,1,0): 1.31, 1.32, 1.33, 1.34, (2,0,0): 1.41, 1.42, 1.43, 1.44, … } } } }} HDF and HDF-EOS Workshop XII

  21. h5import: Requested Features • Make it interchangeable with • h5dump • Excel spreadsheet HDF and HDF-EOS Workshop XII

  22. New for 1.6.6+ and 1.8.0+ h5copy h5mkgrp h5stat h5check HDF and HDF-EOS Workshop XII

  23. h5copy • Copies an object within a file or across files / / Floats IntArray FloatArray FloatArray HDF and HDF-EOS Workshop XII

  24. h5copy –f shallow DST1 floats -f shallow SRC f32 64-bit floats integers DST2 i1 i2 f32 64-bit floats f1 f2 f32 64-bit f1 f2 HDF and HDF-EOS Workshop XII

  25. h5mkgrp • Creates a group or group structure > h5mkgrp test.h5 /info /data /data/test1 /data/test2 / info data test1 test2 HDF and HDF-EOS Workshop XII

  26. h5stat • Prints statistics about HDF5 file • Header size • Raw data size • Attributes, datatypes, etc. • Helps • Troubleshoot overhead in HDF5 files • Choose specific object’s properties and storage strategies HDF and HDF-EOS Workshop XII

  27. h5stat: Example >h5stat hdf5_test.h5 Filename: hdf5_test.h5 File information # of unique groups: 4 # of unique datasets: 13 … Object header size: (total/unused) Groups: 288/32 Datasets: 6824/864 … Dataset storage information: Total raw data size: 1769009 … HDF and HDF-EOS Workshop XII

  28. h5check • Verifies whether an HDF5 file is compliant with a specific HDF5 File Format. • By default, the file is checked against 1.8.x. • Use -f16 option to check against 1.6.x. HDF and HDF-EOS Workshop XII

  29. h5check > h5check --verbose=2 example.h5 VALIDATING example.h5 according to library version 1.8.0 FOUND super block signature VALIDATING the super block at physical address 0... Validating version 2 superblock... VALIDATING the object header at logical address 48... VALIDATING version 2 object header ... FOUND Version 2 object header signature VALIDATING version 2 btree at logical address 1864... VALIDATING version 2 btree header at logical address 1864… : No non-compliance errors found HDF and HDF-EOS Workshop XII

  30. h5check > h5check --verbose=2 –f16 example.h5 VALIDATING example.h5 according to library version 1.6.6 VALIDATING the super block at physical address 0... Validating version 0/1 superblock... ***Error*** Errors found when checking superblock. Validation stopped. Disk Format Level 0-File Metadata-->0A-File Signature and Super Block Superblock v.0/1:Unable to read root symbol table entry ***End of Error messages*** Non-compliance errors found HDF and HDF-EOS Workshop XII

  31. Thank You! This presentation is based upon work supported in part by a Cooperative Agreement with NASA under NASA NNX06AC83A. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Aeronautics and Space Administration HDF and HDF-EOS Workshop XII

  32. Questions/comments? HDF and HDF-EOS Workshop XII

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