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HDF5 Tools Update
Peter Cao
The HDF Group
xcao@hdfgroup.org
November 28, 2006
This report is based upon work supported in part by a Cooperative Agreement with NASA under NASA
NNG05GC60A. 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.
12/5/2011 HDF and HDF-EOS Workshop X, Landover, MD 1
Outline
• Overview of current tools
• New tools with HDF5 1.8 release
• A future tool: h5ub
12/5/2011 HDF and HDF-EOS Workshop X, Landover, MD 2
HDF5 Command Line Tools
• Readers
• h5dump, h5diff, h5ls
• new tools: h5check, h5stat
• Writers
• h5repack, h5repart, h5import, h5jam/h5unjam
• new tool: h5copy
• Converters
• h4toh5, h5toh4, gif2h5, h52gif
12/5/2011 HDF and HDF-EOS Workshop X, Landover, MD 3
Help Information
• Located at bin/ with binary release
• Use “-h” option for help
• Online help at
http://www.hdfgroup.org/hdf5tools.html
• For further help, bug report and feature request, send to
hdfhelp@hdfgroup.org
12/5/2011 HDF and HDF-EOS Workshop X, Landover, MD 4
h5dump
Dumps the content of an HDF5 file to stdout and
optionally to following types of files
• ASCII text file
• XML file
• Binary file (new feature)
12/5/2011 HDF and HDF-EOS Workshop X, Landover, MD 5
h5dump -H SDS.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 ) }
}
}
}
12/5/2011 HDF and HDF-EOS Workshop X, Landover, MD 6
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
}
}
}
12/5/2011 HDF and HDF-EOS Workshop X, Landover, MD 7
h5dump -x SDS.h5
12/5/2011 HDF and HDF-EOS Workshop X, Landover, MD 8
h5dump Binary Output
-b F, --binary=F
The form of the binary output (F):
• MEMORY -- for memory type
• FILE -- for the disk file type
• LE -- for pre-defined little endian type
• BE -- for pre-defined big endian type
12/5/2011 HDF and HDF-EOS Workshop X, Landover, MD 9
h5dump -d /IntArray -o out_le.bin -b LE SDS.h5
Dumps a 32-bit integer dataset, IntArray,
from SDS.h5 to a little endian binary file
out_le.bin
od --width=24 -t x4 out_le.bin
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
12/5/2011 HDF and HDF-EOS Workshop X, Landover, MD 10
h5diff
Using h5diff, you can
• compares two objects in the same file
• compares two objects between two files
• compares all objects between two files
12/5/2011 HDF and HDF-EOS Workshop X, Landover, MD 11
h5diff SDS.h5 SDS2.h5
• Dataset: </IntArray> and </IntArray>
• 5 differences found
12/5/2011 HDF and HDF-EOS Workshop X, Landover, MD 12
h5diff SDS.h5 SDS2.h5 -r /IntArray
• Dataset: </IntArray> and </IntArray>
• position IntArray IntArray difference
• ------------------------------------------------------------
• [00] 0 10 10
• [10] 10 100 90
• [20] 20 200 180
• [30] 30 300 270
• [40] 40 400 360
• 5 differences found
12/5/2011 HDF and HDF-EOS Workshop X, Landover, MD 13
h5repack
Copies an HDF5 file to a new file with/without
compression/chunking
• Remove un-used space
• Apply compression filter
• Apply layout
12/5/2011 HDF and HDF-EOS Workshop X, Landover, MD 14
h5repack: new filters
-f FILTER
• GZIP, to apply GZIP compression
• SZIP, to apply SZIP compression
• SHUF, to apply the HDF5 shuffle filter
• FLET, to apply the HDF5 checksum filter
• NBIT, to apply NBIT compression
• SOFF, to apply the HDF5 Scale/Offset filter
• NONE, to remove all filters
For example
h5repack -i SDS2.h5 -o SDS2_compressed.h5 /IntArray:GZIP=9
12/5/2011 HDF and HDF-EOS Workshop X, Landover, MD 15
h5repack: data layout
-l LAYOUT
• CHUNK, to apply chunking layout
• COMPA, to apply compact layout
• CONTI, to apply continuous layout
For example
h5repack -i SDS.h5 -o SDS_chunk.h5
-l /Floats/FloatArray,/IntArray:CHUNK=2x3
12/5/2011 HDF and HDF-EOS Workshop X, Landover, MD 16
new h5repack: using H5Ocopy()
90.00 80.97
80.00
70.00
60.00
48.39
50.00 41.62
40.00 32.06
30.18
30.00
17.30 18.83
20.00 13.52 15.34
8.32
10.00
0.27 0.03
0.00
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New h5repack Old h5repack
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12/5/2011 HDF and HDF-EOS Workshop X, Landover, MD 17
h5repart
Repartitions a file or family of files
For example
h5repart -m 200m int16kx16k.h5 part200m%d.h5
200 MB part200m0.h5
200 MB part200m1.h5
977 MB 200 MB part200m2.h5
200 MB part200m3.h5
177 MB part200m1.h5
12/5/2011 HDF and HDF-EOS Workshop X, Landover, MD 18
h5import
Imports binary/ASCII data into an HDF5 file
• h5import infile -c config_file [infile -c config_file2 ...] -outfile outfile
For eaxmple
h5import float5x4x2.txt -c First_set.conf -o First_set.h5
GROUP "/" {
GROUP "work" {
DATASET "First-set" {
PATH work/First-set DATATYPE H5T_IEEE_F64LE
INPUT-CLASS TEXTFP DATASPACE SIMPLE { ( 5, 2, 4 ) / ( 8, 8, H5S_UNLIMITED ) }
RANK 3 DATA {
DIMENSION-SIZES 5 2 4 (0,0,0): 1.01, 1.02, 1.03, 1.04,
OUTPUT-CLASS FP (0,1,0): 1.11, 1.12, 1.13, 1.14,
OUTPUT-SIZE 64 (1,0,0): 1.21, 1.22, 1.23, 1.24,
OUTPUT-ARCHITECTURE IEEE (1,1,0): 1.31, 1.32, 1.33, 1.34,
OUTPUT-BYTE-ORDER LE (2,0,0): 1.41, 1.42, 1.43, 1.44,
CHUNKED-DIMENSION-SIZES 2 2 2 (2,1,0): 1.51, 1.52, 1.53, 1.54,
MAXIMUM-DIMENSIONS 8 8 -1 (3,0,0): 2.01, 2.02, 2.03, 2.04,
(3,1,0): 2.11, 2.12, 2.13, 2.14,
(4,0,0): 2.21, 2.22, 2.23, 2.24,
(4,1,0): 2.31, 2.32, 2.33, 2.34
}
}
}
}}
12/5/2011 HDF and HDF-EOS Workshop X, Landover, MD 19
h5jam/h5unjam
• h5jam -- add text to User Block
h5jam -u test_ub.txt -i test_ub.h5
• h5unjam -- remove text from User Block
h5unjam -i test_ub.h5 -o out_ub.txt -o out_ub.h5
12/5/2011 HDF and HDF-EOS Workshop X, Landover, MD 20
h5ls
• Lists selected information about file objects in the
specified format
For Example,
h5ls -r SDS2.h5
/Floats Group
/Floats/DoubleArray Dataset {10, 5}
/Floats/FloatArray Dataset {4, 3}
/Floats/subs Group
/IntArray Dataset {5, 6}
12/5/2011 HDF and HDF-EOS Workshop X, Landover, MD 21
gif2h5 / h52gif
• gif2h5 – converts a GIF file into HDF5
gif2h5 apollo17_earth.gif apollo17_earth.h5
• h52gif – converts an HDF5 file into GIF
h52gif apollo17_earth.h5 apollo17_earth2.gif -i /apollo17_earth.gif/Image0 -p "/apollo17_earth.gif/Global Palette"
12/5/2011 HDF and HDF-EOS Workshop X, Landover, MD 22
h5toh4 / h4toh5
• h5toh4 -- Converts an HDF5 file to an HDF4 file
• h4toh5 -- Converts an HDF4 file to an HDF5 file
12/5/2011 HDF and HDF-EOS Workshop X, Landover, MD 23
New tools
• h5copy
• h5check
• h5stat
12/5/2011 HDF and HDF-EOS Workshop X, Landover, MD 24
h5copy
• Copies an object from one location to another
location within a file or across files
• http://hdfgroup.com/RFC/h5copy/h5copy.htm
/
/
Floats
IntArray
FloatArray
FloatArray
12/5/2011 HDF and HDF-EOS Workshop X, Landover, MD 25
h5copy
usage: h5copy [OPTIONS] [OBJECTS...]
-i, --input input file name
-o, --output output file name
-s, --source source object name
-d, --destination destination object name
-f, --flag
shallow Copy only immediate members for groups
soft Expand soft links into new objects
ext Expand external links into new objects
ref Copy objects that are pointed by references
noattr Copy object without copying attributes
12/5/2011 HDF and HDF-EOS Workshop X, Landover, MD 26
h5copy
For example
h5copy -i SDS.h5 -o SDS_cp.h5 -s /Floats/FloatArray -d /FloatArray
/
/
Floats
IntArray
FloatArray
FloatArray SDS_cp.h5
SDS.h5
12/5/2011 HDF and HDF-EOS Workshop X, Landover, MD 27
h5copy -f shallow
/
floats
/ 64-bit
f32
integers floats
/
64-bit
i1 i2
floats
f32 f1 f2
64-bit
f32
f1 f2
12/5/2011 HDF and HDF-EOS Workshop X, Landover, MD 28
h5copy -f soft
/
/
dset_SL f1
/f1
f1 dset_SL
/
/f1
dset_SL
/f1
12/5/2011 HDF and HDF-EOS Workshop X, Landover, MD 29
h5copy -f ref
/
d1 d2
/
dset_ref
679
1287
d2
d1
/
dset_ref
1895
763 dset_ref
0
0
12/5/2011 HDF and HDF-EOS Workshop X, Landover, MD 30
h5copy todo
• Fix references embedded in compound datatype
• Follow external links
• Test functionalities
• Test performance
12/5/2011 HDF and HDF-EOS Workshop X, Landover, MD 31
h5stat
• Prints different statistics about HDF5 file
• Helps
• To troubleshoot size overhead in HDF5 files
• To choose specific object’s properties and storage
strategies
12/5/2011 HDF and HDF-EOS Workshop X, Landover, MD 32
h5check
A validation tool that verifies if an HDF5 file is
encoded according to the HDF5 File Format
Specification
12/5/2011 HDF and HDF-EOS Workshop X, Landover, MD 33
Why is it needed?
• Verify if the file is compliant with the File Format to ensure
the data model integrity and long term compatibility between
evolving versions of the HDF5 library
• As a verification tool required by the application of HDF5
File Format to be an ANSI standard
• Serves as a watch dog that the HDF5 library implementation
is compliant with the File Format
12/5/2011 HDF and HDF-EOS Workshop X, Landover, MD 34
What does it do?
Given a file, it scans through the encoded content
against the defined File Format
• If it finds any non-compliance, it prints out the error
and reason of non-compliance.
• After finding any non-compliance, it tries to continue
scanning the file if possible.
• Eventually, it exits with non-zero.
• If it does not find any non-compliance, it prints out an
approval statement at the end and exits with zero.
12/5/2011 HDF and HDF-EOS Workshop X, Landover, MD 35
How is it implemented? (1/2)
• The tool is coded from scratch and does not use the
formal HDF5 library API calls
• It does not link with the HDF5 library at all
• It may borrow coding, including algorithms or data
structure from the HDF5 library source code but
after close verification that they are in compliance
with the File Format.
12/5/2011 HDF and HDF-EOS Workshop X, Landover, MD 36
How is it implement? (2/2)
• It links external libraries that HDF5 library uses. E.g.,
• Zlib
• szlib
12/5/2011 HDF and HDF-EOS Workshop X, Landover, MD 37
How to use it?
• H5check [-vn] <filename>
-vn verboseness mode
n=0 Terse—only prints if the file is compliant or not
n=1 Default—prints its progress and all errors found
n=2 Verbose—prints everything it knows, usually for
debugging
12/5/2011 HDF and HDF-EOS Workshop X, Landover, MD 38
Example: a compliant file
• % h5check example1.h5
• VALIDATING example1.h5
• FOUND super block signature
• VALIDATING the super block at 0...
• VALIDATING the object header at 928...
• VALIDATING the btree at 384...
• FOUND btree signature.
• VALIDATING the local heap at 96...
• FOUND local heap signature.
• …
• Result: File is in compliance.
12/5/2011 HDF and HDF-EOS Workshop X, Landover, MD 39
Example: a non-compliant file
h5check invalid2.h5
• FOUND super block signature
• VALIDATING the super block at 0...
• VALIDATING the object header at 928...
• VALIDATING the btree at 384...
• FOUND btree signature.
• VALIDATING the SNOD at 1248...
• FOUND SNOD signature.
• VALIDATING the object header at 976...
• check_sym(at 1248): Errors from check_obj_header()
• decode_validate_messages(): Failure in type->decode().
• H5O_sdspace_decode(): Bad version number in simple dataspace message.
• VALIDATING the local heap at 96...
• FOUND local heap signature.
• Main(): Errors from check_obj_header().
• decode_validate_messages(): Failure in type->decode().
• H5O_attr_decode(): Can't decode attribute dataspace.
• H5O_sdspace_decode(): Bad version number in simple dataspace message.
• …
• Result: File is not in compliance.
12/5/2011 HDF and HDF-EOS Workshop X, Landover, MD 40
Implementation Status
• All basic File Format components are implemented
• Coding recognition of HDF5 files created by non-
default Virtual File Driver such as the Multi-File
format
• Alpha release planned in December 2006
12/5/2011 HDF and HDF-EOS Workshop X, Landover, MD 41
h5ub
• Combine nub, h5jam and h5unjam
• nub -- NPOESS user block tool for HDF5 files
(Richard)
• Plan for h5ub development
Design Implementation Testing Release
12/5/2011 HDF and HDF-EOS Workshop X, Landover, MD 42
