Ubuntu Manpage: h5import - Imports data into an existing or new HDF5 file.

Provided by: hdf5-tools_1.10.4+repack-11ubuntu1_amd64

NAME

       h5import - Imports data into an existing or new HDF5 file.

SYNOPSIS

       h5import infile -d dim_list [ -p pathname ] [ -t input_class ] [ -s input_size ] [infile ...]  -o outfile

       h5import infile -dims dim_list [ -path pathname ] [ -type input_class ] [ -size input_size ] [infile ...]
       -outfile outfile

       h5import infile -c config_file [infile ...]  -outfile outfile

       h5import -h

       h5import -help

DESCRIPTION

h5import converts data from one or more ASCII or binary files, infile, into the same number of HDF5
datasets in the existing or new HDF5 file, outfile. Data conversion is performed in accordance with the
user-specified type and storage properties specified in in_options.

The primary objective of h5import is to import floating point or integer data. The utility's design
allows for future versions that accept ASCII text files and store the contents as a compact array of one-
dimensional strings, but that capability is not implemented in HDF5 Release 1.6.

Input data and options

Input data can be provided in one of the follwing forms:

* As an ASCII, or plain-text, file containing either floating point or integer data

* As a binary file containing either 32-bit or 64-bit native floating point data

* As a binary file containing native integer data, signed or unsigned and 8-bit, 16-bit, 32-bit, or
64-bit.

* As an ASCII, or plain-text, file containing text data. (This feature is not implemented in HDF5
Release 1.6.)

Each input file, infile, contains a single n-dimensional array of values of one of the above types
expressed in the order of fastest-changing dimensions first.

Floating point data in an ASCII input file must be expressed in the fixed floating form (e.g., 323.56)
h5import is designed to accept scientific notation (e.g., 3.23E+02) in an ASCII, but that is not
implemented in HDF5 release 1.6.

Each input file can be associated with options specifying the datatype and storage properties. These
options can be specified either as command line arguments or in a configuration file. Note that exactly
one of these approaches must be used with a single input file.

Command line arguments, best used with simple input files, can be used to specify the class, size,
dimensions of the input data and a path identifying the output dataset.

The recommended means of specifying input data options is in a configuration file; this is also the only
means of specifying advanced storage features. See further discussion in "The configuration file" below.

The only required option for input data is dimension sizes; defaults are available for all others.

h5import will accept up to 30 input files in a single call. Other considerations, such as the maximum
length of a command line, may impose a more stringent limitation.

Output data and options:

The name of the output file is specified following the -o or -output option in outfile. The data from
each input file is stored as a separate dataset in this output file. outfile may be an existing file. If
it does not yet exist, h5import will create it.

Output dataset information and storage properties can be specified only by means of a configuration file.

Dataset path
If the groups in the path leading to the dataset do not exist, h5import will create them. If no
group is specified, the dataset will be created as a member of the root group. If no dataset name
is specified, the default name is dataset1 for the first input dataset, dataset2 for the second
input dataset, dataset3 for the third input dataset, etc. h5import does not overwrite a pre-
existing dataset of the specified or default name. When an existing dataset of a confilcting name
is encountered, h5import quits with an error; the current input file and any subsequent input
files are not processed.

Output type
Datatype parameters for output data

Output data class
Signed or unsigned integer or floating point

Output data size
8-, 16-, 32-, or 64-bit integer 32- or 64-bit floating point

Output architecture
IEEE, STD, NATIVE (Default), Other architectures are included in the h5import design but are not
implemented in this release.

Output byte order
Little- or big-endian. Relevant only if output architecture is IEEE, UNIX, or STD; fixed for
other architectures.

Dataset layout and storage properties
Denote how raw data is to be organized on the disk. If none of the following are specified, the
default configuration is contiguous layout and with no compression.

Layout Contiguous (Default), Chunked

External storage
Allows raw data to be stored in a non-HDF5 file or in an external HDF5 file. Requires contiguous
layout.

Compressed
Sets the type of compression and the level to which the dataset must be compressed. Requires
chunked layout.

Extendible
Allows the dimensions of the dataset increase over time and/or to be unlimited. Requires chunked
layout.

Compressed and extendible
Requires chunked layout.

FILES

A configuration file is specified with the -c config_file option:
h5import infile -c config_file [infile -

The configuration file is an ASCII file and must be organized as "Configuration_Keyword Value" pairs,
with one pair on each line. For example, the line indicating that the input data class (configuration
keyword INPUT-CLASS) is floating point in a text file (value TEXTFP) would appear as follows:
INPUT-CLASS TEXTFP

A configuration file may have the following keywords each followed by one of the following defined
values. One entry for each of the first two keywords, RANK and DIMENSION-SIZES, is required; all other
keywords are optional.

RANK rank
An integer specifying the number of dimensions in the dataset. Example: RANK 4 for a
4-dimensional dataset.

DIMENSION-SIZES dim_sizes
Sizes of the dataset dimensions. (Required) A string of space-separated integers specifying the
sizes of the dimensions in the dataset. The number of sizes in this entry must match the value in
the RANK entry. The fastest-changing dimension must be listed first. Example: DIMENSION_SIZES 4
3 4 38 for a 38x4x3x4 dataset.

PATH path
Path of the output dataset. The full HDF5 pathname identifying the output dataset relative to the
root group within the output file. I.e., path is a string consisting of optional group names, each
followed by a slash, and ending with a dataset name. If the groups in the path do no exist, they
will be created. If PATH is not specified, the output dataset is stored as a member of the root
group and the default dataset name is dataset1 for the first input dataset, dataset2 for the
second input dataset, dataset3 for the third input dataset, etc. Note that h5import does not
overwrite a pre-existing dataset of the specified or default name. When an existing dataset of a
confilcting name is encountered, h5import quits with an error; the current input file and any
subsequent input files are not processed. Example: The configuration file entry "PATH
grp1/grp2/dataset1" indicates that the output dataset dataset1 will be written in the group grp2/
which is in the group grp1/, a member of the root group in the output file.

INPUT-CLASS {TEXTIN|TEXTUIN|TEXTFP|TEXTFPE|IN|UIN|FP|STR}
A string denoting the type of input data.
TEXTIN Input is signed integer data in an ASCII file.
TEXTUIN Input is unsigned integer data in an ASCII file.
TEXTFP Input is floating point data in fixed notation (e.g., 325.34) in an ASCII file.
TEXTFPE Input is floating point data in scientific notation (e.g., 3.2534E+02) in an ASCII file.
(Not implemented in this release.)
IN Input is signed integer data in a binary file.
UIN Input is unsigned integer data in a binary file.
FP Input is floating point data in a binary file. (Default)
STR Input is character data in an ASCII file. With this value, the configuration keywords RANK,
DIMENSION-SIZES, OUTPUT-CLASS, OUTPUT-SIZE, OUTPUT-ARCHITECTURE, and OUTPUT-BYTE-ORDER will be
ignored. (Not implemented in this release.)

INPUT-SIZE {8|16|32|64}
An integer denoting the size of the input data, in bits. For signed and unsigned integer data
(TEXTIN, TEXTUIN, IN, or UIN) any of 8, 16, 32, or 64 may be used. The default is 32. For
floating point data (TEXTFP, TEXTFPE, or FP), either 32 or 64 may be specified. The default is
32.

OUTPUT-CLASS {IN|UIN|FP|STR}
A string denoting the type of output data.
IN Output is signed integer data. (Default if INPUT-CLASS is IN or TEXTIN)
UIN Output is unsigned integer data. (Default if INPUT-CLASS is UIN or TEXTUIN)
FP Output is floating point data. (Default if INPUT-CLASS is not specified or is FP, TEXTFP, or
TEXTFPE)
STR Output is character data, to be written as a 1-dimensional array of strings. (Default if
INPUT-CLASS is STR) (Not implemented in this release.)

OUTPUT-SIZE {8|16|32|64}
An integer denoting the size of the output data, in bits. For signed and unsigned integer data
(IN or UIN), any of the four sizes are valid. The default is the same as INPUT-SIZE, else 32. For
floating point data (FP), either 32 or 64 may be specified. The default is the same as INPUT-
SIZE, else 32.

OUTPUT-ARCHITECTURE {NATIVE|STD|IEEE|INTEL|CRAY|MIPS|ALPHA|UNIX}
A string denoting the type of output architecture. See the "Predefined Atomic Types" section in
the "HDF5 Datatypes" chapter of the HDF5 User's Guide for a discussion of these architectures.
INTEL, CRAY, MIPS, ALPHA, and UNIX are not implemented in this release. (Default: NATIVE)

OUTPUT-BYTE-ORDER {BE|LE}
A string denoting the output byte order. This entry is ignored if the OUTPUT-ARCHITECTURE is not
specified or if it is not specified as IEEE, UNIX, or STD.
BE Big-endian. (Default)
LE Little-endian.

The following options are disabled by default, making the default storage properties no chunking, no
compression, no external storage, and no extensible dimensions.

CHUNKED-DIMENSION-SIZES chunk_dims
Dimension sizes of the chunk for chunked output data. A string of space-separated integers
specifying the dimension sizes of the chunk for chunked output data. The number of dimensions must
correspond to the value of RANK. The presence of this field indicates that the output dataset is
to be stored in chunked layout; if this configuration field is absent, the dataset will be stored
in contiguous layout.

COMPRESSION-TYPE {GZIP}
Type of compression to be used with chunked storage. Requires that CHUNKED-DIMENSION-SIZES be
specified. GZIP is gzip compression. Othe compression algorithms are not implemented in
this release of h5import.

COMPRESSION-PARAM [1-9]
Compression level. Required if COMPRESSION-TYPE is specified. Gzip compression levels: 1 will
result in the fastest compression while 9 will result in the best compression ratio. (Default: 6.
The default gzip compression level is 6; not all compression methods will have a default level.)

EXTERNAL-STORAGE external_file
Name of an external file in which to create the output dataset. Cannot be used with CHUNKED-
DIMENSIONS-SIZES, COMPRESSION-TYPE, OR MAXIMUM-DIMENSIONS. A string specifying the name of an
external file.

MAXIMUM-DIMENSIONS max_dims
Maximum sizes of all dimensions. Requires that CHUNKED-DIMENSION-SIZES be specified. A string of
space-separated integers specifying the maximum size of each dimension of the output dataset. A
value of -1 for any dimension implies unlimited size for that particular dimension. The number of
dimensions must correspond to the value of RANK.

OPTIONS

-h[elp]
prints the h5import usage summary

infile(s)
Name of the Input file(s).

-d[ims] dim_list
Input data dimensions. dim_list is a string of comma-separated numbers with no spaces describing
the dimensions of the input data. For example, a 50 x 100 2-dimensional array would be specified
as -dims 50,100. Required argument: if no configuration file is used, this command-line argument
is mandatory.

-p[athname] pathname
pathname is a string consisting of one or more strings separated by slashes (/) specifying the
path of the dataset in the output file. If the groups in the path do no exist, they will be
created. Optional argument: if not specified, the default path is dataset1 for the first input
dataset, dataset2 for the second input dataset, dataset3 for the third input dataset, etc.
h5import does not overwrite a pre-existing dataset of the specified or default name. When an
existing dataset of a confilcting name is encountered, h5import quits with an error; the current
input file and any subsequent input files are not processed.

-t[ype] input_class
input_class specifies the class of the input data and determines the class of the output data.
Valid values are as defined in the Keyword/Values table in the section "The configuration file"
above. Optional argument: if not specified, the default value is FP.

-s[size] input_size
input_size specifies the size in bits of the input data and determines the size of the output
data. Valid values for signed or unsigned integers are 8, 16, 32, and 64. Valid values for
floating point data are 32 and 64. Optional argument: if not specified, the default value is 32.

-c config_file
config_file specifies a configuration file. This argument replaces all other arguments except
infile and -o outfile

outfile
Name of the HDF5 output file.

NOTES

       If the -c config_file option is used with an input file, no other argument can be used  with  that  input
       file.  If  the  -c  config_file  option is not used with an input data file, the -d dim_list argument (or
       -dims dim_list) must be used and any combination of the remaining options may be used. Any arguments used
       must appear in exactly the order used in the syntax declarations immediately above.

       Note  that  while only the -dims argument is required, arguments must used in the order in which they are
       listed below.

EXAMPLES

       Using command-line arguments:

       This command creates a file out1 containing a single 2x3x4 32-bit integer dataset. Since no  pathname  is
       specified, the dataset is stored in out1 as /dataset1.
              h5import infile -dims 2,3,4 -type TEXTIN -size 32 -o out1

       This  command  creates a file out2 containing a single a 20x50 64-bit floating point dataset. The dataset
       is stored in out2 as /bin1/dset1.
              h5import infile -dims 20,50 -path bin1/dset1 -type FP -size 64 -o out2

       Sample configuration files: The following configuration file specifies the following:

       o      The input data is a 5x2x4 floating point array in an ASCII file.

       o      The output dataset will be saved in chunked layout, with chunk dimension sizes of 2x2x2.

       o      The output datatype will be 64-bit floating point, little-endian, IEEE.

       o      The output dataset will be stored in outfile at /work/h5/pkamat/First-set.

       o      The maximum dimension sizes of the output dataset will be 8x8x(unlimited).

              PATH work/h5/pkamat/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

       The next configuration file specifies the following:

       o      The input data is a 6x3x5x2x4 integer array in a binary file.

       o      The output dataset will be saved in chunked layout, with chunk dimension sizes of 2x2x2x2x2.

       o      The output datatype will be 32-bit integer in NATIVE format (as  the  output  architecure  is  not
              specified).

       o      The output dataset will be compressed using Gzip compression with a compression level of 7.

       o      The output dataset will be stored in outfile at /Second-set.

              PATH Second-set
              INPUT-CLASS IN
              RANK 5
              DIMENSION-SIZES 6 3 5 2 4
              OUTPUT-CLASS IN
              OUTPUT-SIZE 32
              CHUNKED-DIMENSION-SIZES 2 2 2 2 2
              COMPRESSION-TYPE GZIP
              COMPRESSION-PARAM 7