hdf5 tools

HDF5 Tools

Peter Cao

The HDF Group

October 15-18, 2008 1HDF and HDF-EOS Workshop XII

Outline

2

• A short demo of HDFView

• HDF5 command line tools

October 15-18, 2008 HDF and HDF-EOS Workshop XII

What is HDFView?

3

For more information and download, visit

www.hdfgroup.org/hdf-java-html

HDFView

HDF Application Browser/Editor Written in Java

October 15-18, 2008 HDF and HDF-EOS Workshop XII

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


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

HDF5 Command Line Tools

October 15-18, 2008 6

h5dump, h5diff, h5ls, h5check, h5stat

h5repack, h5repart, h5import, h5jam, h5unjam, h5copy, h5mkgrp

h4toh5, h5toh4, gif2h5, h52gif

Readers

Writers

Converters

HDF and HDF-EOS Workshop XII

Where to Start?

October 15-18, 2008 7

Tools located in bin/ directory

1. Use “-h” option for help

2. Consult online help http://www.hdfgroup.org/hdf5tools.html

3. Email help desk [email protected]


h5dump

October 15-18, 2008 8

Dumps contents of HDF5 file to stdout

• ASCII text• XML • Binary


h5dump: Object Headers

October 15-18, 2008 9

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 ) } } }}

> h5dump -H SDS.h5


h5dump: Dataset

October 15-18, 2008 10

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

}

}

}

> h5dump –d /Floats/FloatArray SDS.h5


h5dump: Binary Output

October 15-18, 2008 11

-b F, --binary=[MEMORY|FILE|LE|BE]

0000000 00000000 00000001 00000002 00000003 00000004 000000050000030 0000000a 0000000b 0000000c 0000000d 0000000e 0000000f0000060 00000014 00000015 00000016 00000017 00000018 000000190000110 0000001e 0000001f 00000020 00000021 00000022 000000230000140 00000028 00000029 0000002a 0000002b 0000002c 0000002d

> h5dump -d /IntArray -o out_le.bin -b LE SDS.h5


h5diff

October 15-18, 2008 12

Showdifferencesbetween…

two objects or

two files


h5diff

October 15-18, 2008 13

Dataset: </IntArray>5 differences found

> h5diff SDS.h5 SDS2.h5


h5diff: Report Differences

October 15-18, 2008 14

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

> h5diff SDS.h5 SDS2.h5 -r /IntArray


h5diff: Unsolved Issues

How to compare two files with different Structures Storage layouts Properties


h5repack

October 15-18, 2008 16

Copies a file to a new file with • Compression filter• Data layout• Other user options


h5repack: Compression Filter

October 15-18, 2008 17

-f {GZIP|SZIP|SHUF|FLET|NBIT|SOFF|NONE}

For example

> h5repack -i SDS.h5 -o out.h5 -f GZIP=6


h5repack: Data Layout

October 15-18, 2008 18

-l {CHUNK| COMPA| CONTI}

For example> h5repack -i SDS.h5 -o out.h5 -l CHUNK=1000x1000


h5repack: File Format Version

October 15-18, 2008 19

h5repack options File size in bytes

Original file 3,167,264

--latest 2,267,346

--latest –compact=9 2,162,254

--latest –compact=9 –ssize=50:dtype 299,882

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


h5import

October 15-18, 2008 20

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, … } } }}}

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


h5import: Requested Features

October 15-18, 2008 21

• Make it interchangeable with h5dump Excel spreadsheet


New for 1.6.6+ and 1.8.0+

October 15-18, 2008 22

h5stath5mkgrp

h5copy

h5check


h5copy

• Copies an object within a file or across files

October 15-18, 2008 23

/

FloatArray

FloatsIntArray

/

FloatArray


h5copy –f shallow

October 15-18, 2008 24

SRC

i1

floatsintegers

64-biti2 f32

f2f1

DST2

floats

64-bitf32

f2f1

DST1

floats

64-bitf32-f shallow


h5mkgrp

• Creates a group or group structure

October 15-18, 2008 25

/

info data

test1 test2

> h5mkgrp test.h5 /info /data /data/test1 /data/test2


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

26October 15-18, 2008 HDF and HDF-EOS Workshop XII

h5stat: Example

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

…


>h5stat hdf5_test.h5

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.


h5check

October 15-18, 2008 29

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

> h5check --verbose=2 example.h5


> 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

h5check


October 15-18, 2008 31

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

Thank You!


Questions/comments?


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