Man Linux: Main Page and Category List


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


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


       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
       University 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.


       -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 correspond 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

       -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

       -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.


       Send bug reports to S. G. Johnson,


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