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h5totxt(1) [debian man page]

H5TOTXT(1)							      h5utils								H5TOTXT(1)

NAME

       h5totxt - generate comma-delimited text from 2d slices of HDF5 files

SYNOPSIS

       h5totxt [OPTION]... [HDF5FILE]...

DESCRIPTION

       h5totxt is a utility to generate comma-delimited text (and similar formats) from one-, two-, or more-dimensional slices of numeric datasets
       in HDF5 files.  This way, the data can easily be imported into spreadsheets and similar programs for analysis and visualization.

       HDF5 is a free, portable binary format and supporting library developed by the National Center for Supercomputing Applications at the  Uni-
       versity of Illinois in Urbana-Champaign.  A single h5 file can contain multiple data sets; by default, h5totxt takes the first dataset, but
       this can be changed via the -d option, or by using the syntax HDF5FILE:DATASET.

       By default, the entire dataset is dumped to the output.	in row-major order.  For 3d datasets, this corresponds to a sequence of yz slices,
       in order of increasing x, separated by blank lines.  If -T is specified, outputs in the transposed (column-major) order instead

       Often,  however,  you  want  only a one- or two-dimensional slice of multi-dimensional data.  To do this, you specify coordinates in one or
       more slice dimensions, via the -xyzt options.

       The most basic usage is something like 'h5totxt foo.h5', which will output comma-delimited text to stdout from the data in foo.h5.

OPTIONS

       -h     Display help on the command-line options and usage.

       -V     Print the version number and copyright info for h5totxt.

       -v     Verbose output.

       -o file
	      Send text output to file rather than to stdout (the default).

       -s sep Use the string sep to separate columns of the output rather than a comma (the default).

       -x ix, -y iy, -z iz, -t it
	      This tells h5totxt to use a particular slice of a multi-dimensional dataset.  e.g.  -x causes a yz plane (of a  3d  dataset)  to	be
	      used,  at an x index of ix (where the indices run from zero to one less than the maximum index in that direction).  Here, x/y/z cor-
	      respond to the first/second/third dimensions of the HDF5 dataset. The -t option specifies a slice in the last  dimension,  whichever
	      that might be.  See also the -0 option to shift the origin of the x/y/z slice coordinates to the dataset center.

       -0     Shift  the  origin  of  the x/y/z slice coordinates to the dataset center, so that e.g. -0 -x 0 (or more compactly -0x0) returns the
	      central x plane of the dataset instead of the edge x plane.  (-t coordinates are not affected.)

       -T     Transpose the data (interchange the dimension ordering).	By default, no transposition is done.

       -. numdigits
	      Output numdigits digits after the decimal point (defaults to 16).

       -d name
	      Use dataset name from the input files; otherwise, the first  dataset  from  each	file  is  used.   Alternatively,  use  the  syntax
	      HDF5FILE:DATASET,  which allows you to specify a different dataset for each file.  You can use the h5ls command (included with hdf5)
	      to find the names of datasets within a file.

BUGS

       Send bug reports to S. G. Johnson, stevenj@alum.mit.edu.

AUTHORS

       Written by Steven G. Johnson.  Copyright (c) 2005 by the Massachusetts Institute of Technology.

h5utils 							   March 9, 2002							H5TOTXT(1)

Check Out this Related Man Page

H5FROMTXT(1)							      h5utils							      H5FROMTXT(1)

NAME

       h5fromtxt - convert text input to an HDF5 file

SYNOPSIS

       h5fromtxt [OPTION]... [HDF5FILE]

DESCRIPTION

       h5fromtxt takes a series of numbers from standard input and outputs a multi-dimensional numeric dataset in an HDF5 file.

       HDF5  is a free, portable binary format and supporting library developed by the National Center for Supercomputing Applications at the Uni-
       versity of Illinois in Urbana-Champaign.  A single h5 file can contain multiple data sets; by default, h5fromtxt creates a  dataset  called
       "data",	but  this  can	be  changed  via  the -d option, or by using the syntax HDF5FILE:DATASET.  The -a option can be used to append new
       datasets to an existing HDF5 file.

       All characters besides the numbers (and associated decimal points, etcetera) in the input are ignored.  By default, the data is assumed	to
       be a two-dimensional MxN dataset where M is the number of rows (delimited by newlines) and N is the number of columns.  In this case, it is
       an error for the number of columns to vary between rows.  If M or N is 1 then the data is written as a one-dimensional dataset.

       Alternatively, you can specify the dimensions of the data explicitly via the -n size option, where size is e.g.	"2x2x2".   In  this  case,
       newlines  are ignored and the data is taken as an array of the given size stored in row-major ("C") order (where the last index varies most
       quickly as you step through the data).  e.g. a 2x2x2 array would be have the elements listed  in  the  order:  (0,0,0),	(0,0,1),  (0,1,0),
       (0,1,1), (1,0,0), (1,0,1), (1,1,0), (1,1,1).

       A simple example is:

	   h5fromtxt foo.h5 <<EOF
	   1 2 3 4
	   5 6 7 8
	   EOF

       which reads in a 2x4 space-delimited array from standard input.

OPTIONS

       -h     Display help on the command-line options and usage.

       -V     Print the version number and copyright info for h5fromtxt.

       -v     Verbose output.

       -a     If  the  HDF5  output file already exists, append the data as a new dataset rather than overwriting the file (the default behavior).
	      An existing dataset of the same name within the file is overwritten, however.

       -n size
	      Instead of trying to infer the dimensions of the array from the rows and columns of the input, treat the data as a sequence of  num-
	      bers  in row-major order forming an array of dimensions size.  size is of the form MxNxLx... (with M, N, L being numbers) and may be
	      of any dimensionality.

       -T     Transpose the input when it is written, reversing the dimensions.

       -d name
	      Write to dataset name in the output; otherwise, the output dataset is called "data"  by  default.   Alternatively,  use  the  syntax
	      HDF5FILE:DATASET.

BUGS

       Send bug reports to S. G. Johnson, stevenj@alum.mit.edu.

AUTHORS

       Written by Steven G. Johnson.  Copyright (c) 2005 by the Massachusetts Institute of Technology.

h5utils 							   March 9, 2002						      H5FROMTXT(1)
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