HDF Tools Tutorial
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This document outlines a tutorial on HDF tools presented at the HDF and HDF-EOS Workshop XIV, detailing the features of HDFView and command-line tools. It covers practical applications such as viewing and editing file content, creating datasets, and using quality flags, along with command-line functionalities like h5ls, h5dump, h5repack, h5diff, and h5copy. The tutorial aims to enhance the understanding and utilization of HDF features among users.
HDF Tools Tutorial
- 1. The HDF Group HDF Tools Tutorial Peter Cao, The HDF Group Jonathan Kim, The HDF Group September 28-30, 2010 HDF and HDF-EOS Workshop XIV 1 www.hdfgroup.org
- 2. Tools Tutorial • HDFView • HDF5 Command-line tools September 28-30, 2010 HDF and HDF-EOS Workshop XIV 2 www.hdfgroup.org
- 3. HDFView • View file content • Edit file content • Show NPOESS/JPSS related features September 28-30, 2010 HDF and HDF-EOS Workshop XIV 3 www.hdfgroup.org
- 4. HDFView • Download HDF-Java 2.7 beta from http://www.hdfgroup.org/ftp/HDF5/hdf-java-2.7 • Download example files from ftp://ftp.hdfgroup.uiuc.edu/pub/outgoing/WorkshopXIV/HDF5-Files/ September 28-30, 2010 HDF and HDF-EOS Workshop XIV 4 www.hdfgroup.org
- 5. HDFView • View file content • • • • • Open OMI-Aura_L3.he5 Open groups (try expand all) Stretch the metadata view for showing metadata Double click on “ColumnAmountO3” to show data in table Use “Open As” to show “ColumnAmountO3” in image • View a subset • Open weather.h5 • Select from preview image or selection fields September 28-30, 2010 HDF and HDF-EOS Workshop XIV 5 www.hdfgroup.org
- 6. HDFView • Copy/paste a dataset and a group • Create a new file: tmp.h5 • Copy/paste “ColumnAmountO3” and show the image from the new file • Copy the group “GRIDS” to show the whole group is copied September 28-30, 2010 HDF and HDF-EOS Workshop XIV 6 www.hdfgroup.org
- 7. HDFView • Create a dataset and add an attribute • • • • • Create /d1 (32-bit float, 720x1440) Copy “ColumnAmountO3” to /d1 Add attribute “IMAGE_MINMAXRANGE = 123.0,447.0” Export /d1 to text file Create /d2 and import d1.txt September 28-30, 2010 HDF and HDF-EOS Workshop XIV 7 www.hdfgroup.org
- 8. HDFView • NPOESS/JPSS related features • Object reference • Region references • Quality flags September 28-30, 2010 HDF and HDF-EOS Workshop XIV 8 www.hdfgroup.org
- 9. HDFView • Object reference 1) 2) 3) 4) 5) 6) Open file: SVI-NPP.h5 Open “VIIRS-I1-SDR_Aggr” Click on object ID and shows object name Right mouse to click to open data as image Open data in table Select two cells and open them at once September 28-30, 2010 HDF and HDF-EOS Workshop XIV 9 www.hdfgroup.org
- 10. HDFView • Region references 1) 2) 3) 4) Open “VIIRS-I1-SDR_Gran” Right mouse to click to open data as image Open data in table Select two cells and open at once September 28-30, 2010 HDF and HDF-EOS Workshop XIV 10 www.hdfgroup.org
- 11. HDFView • Quality flags 1) Quality flags • • • • Land/Water Background SST Skin Quality SST Bulk Quality Aerosol Correction -- 1-bit -- 2-bits -- 2-bits -- 3-bits 2) Open QF_VIIRSI1SDR_Array 3) Use "Open As" on QF_VIIRSI1SDR_Array 4) Select first bit September 28-30, 2010 HDF and HDF-EOS Workshop XIV 11 www.hdfgroup.org
- 12. HDFView • Advanced features 1) Import/export images 2) Use HDF-EOS plugin September 28-30, 2010 HDF and HDF-EOS Workshop XIV 12 www.hdfgroup.org
- 13. HDF5 Command-line tools • • • • • September 28-30, 2010 h5ls h5dump h5repack h5diff h5copy HDF and HDF-EOS Workshop XIV 13 www.hdfgroup.org
- 14. h5ls • Show file content list • h5ls ami.h5 • h5ls –r ami.h5 September 28-30, 2010 HDF and HDF-EOS Workshop XIV 14 www.hdfgroup.org
- 15. h5dump • • • • • September 28-30, 2010 Structure Dataset Binary XML Region references HDF and HDF-EOS Workshop XIV 15 www.hdfgroup.org
- 16. h5dump • Structure • h5dump -H tools_diff1.h5 • h5dump -H ami.h5 September 28-30, 2010 HDF and HDF-EOS Workshop XIV 16 www.hdfgroup.org
- 17. h5dump • Dataset • Content • h5dump -d /EnSight_model/geometry/parts/part_2/quad4 ami.h5 • Information • h5dump –p –H -d /EnSight_model/geometry/parts/part_2/quad4 ami.h5 • Subset • H5dump -d /EnSight_model/geometry/parts/part_2/quad4 -s 10,0 -c 20,2 ami.h5 • <-s and –c must be used after –d> September 28-30, 2010 HDF and HDF-EOS Workshop XIV 17 www.hdfgroup.org
- 18. h5dump • Binary • h5dump -d /EnSight_model/geometry/parts/part_2/quad4 -b LE –o out.bin ami.h5 • XML • h5dump –x ami.h5 • Region • • h5dump -d /Data_Products/VIIRS-I1-SDR/VIIRS-I1-SDR_Gran_0 -s 3 -c 1 SVI-NPP.h5 h5dump –R -d /Data_Products/VIIRS-I1-SDR/VIIRS-I1-SDR_Gran_0 -s 3 -c 1 SVI-NPP.h5 • Packed fields <only 1.8.5+> September 28-30, 2010 HDF and HDF-EOS Workshop XIV 18 www.hdfgroup.org
- 19. h5repack • Remove inaccessible objects / junk spaces • Change storage layout • Apply compression filter Copies a file to a new file with different storage layouts and compression filters September 28-30, 2010 HDF and HDF-EOS Workshop XIV 19 www.hdfgroup.org
- 20. h5repack • Remove inaccessible objects • h5dump tools_junk.h5 • h5repack tools_junk.h5 tmp.h5 • Change layout • h5dump -H tools_bad_layout.h5 • h5repack tools_bad_layout.h5 tmp.h5 • h5repack -l CHUNK=16x16 tools_bad_layout.h5 tmp.h5 • Change compression • h5repack -f GZIP=6 tmp.h5 tmp2.h5 • More: use latest version, link storage, shared message, and etc September 28-30, 2010 HDF and HDF-EOS Workshop XIV 20 www.hdfgroup.org
- 21. h5diff Show differences between two files or two objects • Dataset • Whole file September 28-30, 2010 HDF and HDF-EOS Workshop XIV 21 www.hdfgroup.org
- 22. h5diff • Dataset • h5diff -r tools_diff1.h5 tools_diff2.h5 /g1/uint8 /x • Whole file • Run “h5ls –r tools_diff1.h5” and “h5ls -r tools_diff2.h5” • h5diff tools_diff1.h5 tools_diff2.h5 • h5diff –v tools_diff1.h5 tools_diff2.h5 • Follow symlinks • h5diff -r --follow-symlinks tools_diff1.h5 tools_diff2.h5 /sl1 September 28-30, 2010 HDF and HDF-EOS Workshop XIV 22 www.hdfgroup.org
- 23. h5copy • Dataset • Group Copies objects to files… September 28-30, 2010 HDF and HDF-EOS Workshop XIV 23 www.hdfgroup.org
- 24. h5copy • Dataset • h5copy -i tools_input.h5 -o tmp.h5 -s /g1/g2/f -d /float • Group • Default: h5copy -i tools_input.h5 -o tmp.h5 -s /g1 -d /g1 • Parent groups: h5copy -p -i tools_input.h5 -o tmp.h5 -s /g1/g2/f -d /g1/g2/f September 28-30, 2010 HDF and HDF-EOS Workshop XIV 24 www.hdfgroup.org
- 25. Thank You! Questions/comments? September 28-30, 2010 HDF and HDF-EOS Workshop XIV 25 www.hdfgroup.org