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We just wanted to have am__tar - # and am__untar set. - test -n "${am_cv_prog_tar_$1}" && break - - # tar/untar a dummy directory, and stop if the command works. - rm -rf conftest.dir - mkdir conftest.dir - echo GrepMe > conftest.dir/file - AM_RUN_LOG([tardir=conftest.dir && eval $am__tar_ >conftest.tar]) - rm -rf conftest.dir - if test -s conftest.tar; then - AM_RUN_LOG([$am__untar /dev/null 2>&1 && break - fi - done - rm -rf conftest.dir - - AC_CACHE_VAL([am_cv_prog_tar_$1], [am_cv_prog_tar_$1=$_am_tool]) - AC_MSG_RESULT([$am_cv_prog_tar_$1])]) - -AC_SUBST([am__tar]) -AC_SUBST([am__untar]) -]) # _AM_PROG_TAR - diff -Nru h5utils-1.13.1/arrayh4.c h5utils-1.13.2/arrayh4.c --- h5utils-1.13.1/arrayh4.c 2017-07-18 18:48:25.000000000 +0000 +++ h5utils-1.13.2/arrayh4.c 2023-01-15 20:12:37.000000000 +0000 @@ -1,4 +1,4 @@ -/* Copyright (c) 1999-2017 Massachusetts Institute of Technology +/* Copyright (c) 1999-2023 Massachusetts Institute of Technology * * Permission is hereby granted, free of charge, to any person obtaining * a copy of this software and associated documentation files (the diff -Nru h5utils-1.13.1/arrayh4.h h5utils-1.13.2/arrayh4.h --- h5utils-1.13.1/arrayh4.h 2017-07-18 18:48:25.000000000 +0000 +++ h5utils-1.13.2/arrayh4.h 2023-01-15 20:12:37.000000000 +0000 @@ -1,4 +1,4 @@ -/* Copyright (c) 1999-2017 Massachusetts Institute of Technology +/* Copyright (c) 1999-2023 Massachusetts Institute of Technology * * Permission is hereby granted, free of charge, to any person obtaining * a copy of this software and associated documentation files (the diff -Nru h5utils-1.13.1/arrayh5.h h5utils-1.13.2/arrayh5.h --- h5utils-1.13.1/arrayh5.h 2017-07-18 18:48:25.000000000 +0000 +++ h5utils-1.13.2/arrayh5.h 2023-01-15 20:12:37.000000000 +0000 @@ -1,4 +1,4 @@ -/* Copyright (c) 1999-2017 Massachusetts Institute of Technology +/* Copyright (c) 1999-2023 Massachusetts Institute of Technology * * Permission is hereby granted, free of charge, to any person obtaining * a copy of this software and associated documentation files (the diff -Nru h5utils-1.13.1/autogen.sh h5utils-1.13.2/autogen.sh --- h5utils-1.13.1/autogen.sh 1970-01-01 00:00:00.000000000 +0000 +++ h5utils-1.13.2/autogen.sh 2023-01-15 20:12:37.000000000 +0000 @@ -0,0 +1,8 @@ +#!/bin/sh + +# paranoia: sometimes autoconf doesn't get things right the first time +autoreconf --verbose --install --symlink --force +autoreconf --verbose --install --symlink --force +autoreconf --verbose --install --symlink --force + +./configure --with-hdf4 --enable-maintainer-mode "$@" diff -Nru h5utils-1.13.1/ChangeLog h5utils-1.13.2/ChangeLog --- h5utils-1.13.1/ChangeLog 2017-07-18 19:02:39.000000000 +0000 +++ h5utils-1.13.2/ChangeLog 2023-01-15 20:12:37.000000000 +0000 @@ -1,2 +1,2 @@ -See https://github.com/stevengj/h5utils for the complete git +See https://github.com/NanoComp/h5utils for the complete git history of h5utils. diff -Nru h5utils-1.13.1/compile h5utils-1.13.2/compile --- h5utils-1.13.1/compile 2015-01-05 22:11:43.000000000 +0000 +++ h5utils-1.13.2/compile 1970-01-01 00:00:00.000000000 +0000 @@ -1,347 +0,0 @@ -#! /bin/sh -# Wrapper for compilers which do not understand '-c -o'. - -scriptversion=2012-10-14.11; # UTC - -# Copyright (C) 1999-2014 Free Software Foundation, Inc. -# Written by Tom Tromey . -# -# This program is free software; you can redistribute it and/or modify -# it under the terms of the GNU General Public License as published by -# the Free Software Foundation; either version 2, or (at your option) -# any later version. -# -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. 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When coming back to configure, we -# need to make the FD available again. -if test "$no_create" != yes; then - ac_cs_success=: - ac_config_status_args= - test "$silent" = yes && - ac_config_status_args="$ac_config_status_args --quiet" - exec 5>/dev/null - $SHELL $CONFIG_STATUS $ac_config_status_args || ac_cs_success=false - exec 5>>config.log - # Use ||, not &&, to avoid exiting from the if with $? = 1, which - # would make configure fail if this is the last instruction. - $ac_cs_success || as_fn_exit 1 -fi -if test -n "$ac_unrecognized_opts" && test "$enable_option_checking" != no; then - { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: unrecognized options: $ac_unrecognized_opts" >&5 -$as_echo "$as_me: WARNING: unrecognized options: $ac_unrecognized_opts" >&2;} -fi - diff -Nru h5utils-1.13.1/configure.ac h5utils-1.13.2/configure.ac --- h5utils-1.13.1/configure.ac 2018-03-19 20:23:14.000000000 +0000 +++ h5utils-1.13.2/configure.ac 2023-01-15 20:12:37.000000000 +0000 @@ -1,5 +1,5 @@ # Process this file with autoconf to produce a configure script. -AC_INIT(h5utils, 1.13.1, stevenj@alum.mit.edu) +AC_INIT([h5utils],[1.13.2],[stevenj@alum.mit.edu]) AM_INIT_AUTOMAKE([foreign silent-rules 1.6]) AM_SILENT_RULES(yes) AC_CONFIG_SRCDIR([h5topng.c]) @@ -10,9 +10,6 @@ AC_PROG_CC AM_PROG_CC_C_O -# Checks for header files. -AC_HEADER_STDC - AC_CHECK_LIB(m, sin) AC_CHECK_FUNCS(snprintf) @@ -28,7 +25,7 @@ dnl add gcc warnings, in debug/maintainer mode only if test "$enable_debug" = yes || test "$USE_MAINTAINER_MODE" = yes; then - if test $ac_cv_prog_gcc = yes; then + if test $ac_cv_c_compiler_gnu = yes; then CFLAGS="$CFLAGS -Wall -W -Wcast-qual -Wpointer-arith -Wcast-align -pedantic -Wno-long-long -Wshadow -Wbad-function-cast -Wwrite-strings -Wstrict-prototypes -Wredundant-decls -Wnested-externs" # -Wundef -Wconversion -Wmissing-prototypes -Wmissing-declarations fi fi @@ -81,7 +78,7 @@ AC_CHECK_PROG(H5TOH4, h5toh4, h5toh4) AC_ARG_WITH(hdf4, - [AC_HELP_STRING([--with-hdf4], [build hdf4 utils even if h4toh5 and h5toh4 are present])], + [AS_HELP_STRING([--with-hdf4],[build hdf4 utils even if h4toh5 and h5toh4 are present])], ok=$withval, ok=maybe) if test "x$ok" = xyes; then H4TOH5="" @@ -121,7 +118,7 @@ ########################################################################### -AC_ARG_WITH(octave, [AC_HELP_STRING([--without-octave], [don't compile h5read Octave plugin])], ok=$withval, ok=yes) +AC_ARG_WITH(octave, [AS_HELP_STRING([--without-octave],[don't compile h5read Octave plugin])], ok=$withval, ok=yes) H5READ="" OCT_INSTALL_DIR="" @@ -160,7 +157,7 @@ ########################################################################### -AC_ARG_WITH(v5d, [AC_HELP_STRING([--with-v5d=], [use Vis5d in for h5tov5d])], ok=$withval, ok=yes) +AC_ARG_WITH(v5d, [AS_HELP_STRING([--with-v5d=],[use Vis5d in for h5tov5d])], ok=$withval, ok=yes) H5TOV5D=no V5D_FILES="" V5D_INCLUDES="" @@ -198,23 +195,23 @@ AC_CHECK_TYPES([uint16_t, uint32_t]) AC_MSG_CHECKING([for htons]) -AC_TRY_LINK([#if defined(HAVE_ARPA_INET_H) +AC_LINK_IFELSE([AC_LANG_PROGRAM([[#if defined(HAVE_ARPA_INET_H) #include #elif defined(HAVE_NETINET_IN_H) #include -#endif], [unsigned short i; htons(i);], [htons=yes - AC_DEFINE([HAVE_HTONS],1,[Define if you have htons.])], htons=no) +#endif]], [[unsigned short i; htons(i);]])],[htons=yes + AC_DEFINE([HAVE_HTONS],1,[Define if you have htons.])],[htons=no]) AC_MSG_RESULT($htons) AC_CHECK_SIZEOF(float) AC_MSG_CHECKING([for htonl]) -AC_TRY_LINK([#if defined(HAVE_ARPA_INET_H) +AC_LINK_IFELSE([AC_LANG_PROGRAM([[#if defined(HAVE_ARPA_INET_H) #include #elif defined(HAVE_NETINET_IN_H) #include -#endif], [unsigned long i; htonl(i);], [htonl=yes - AC_DEFINE([HAVE_HTONL],1,[Define if you have htonl.])], htonl=no) +#endif]], [[unsigned long i; htonl(i);]])],[htonl=yes + AC_DEFINE([HAVE_HTONL],1,[Define if you have htonl.])],[htonl=no]) AC_MSG_RESULT($htonl) if test "x$htons" != xyes -o "x$htonl" != xyes; then @@ -235,6 +232,10 @@ AC_DEFINE_UNQUOTED(DATADIR, "$datadir_val", [datadir installation prefix]) AC_SUBST(datadir_val) +# check for POSIX wordexp function if we need expand ~ etcetera +AC_CHECK_HEADERS([wordexp.h]) +AC_CHECK_FUNCS(wordexp) + ########################################################################### AC_SUBST(MORE_H5UTILS) AC_SUBST(MORE_H5UTILS_MANS) diff -Nru h5utils-1.13.1/COPYING h5utils-1.13.2/COPYING --- h5utils-1.13.1/COPYING 2018-03-19 20:24:22.000000000 +0000 +++ h5utils-1.13.2/COPYING 2023-01-15 20:12:37.000000000 +0000 @@ -1,7 +1,7 @@ ############################################################################# The h5utils package is - Copyright (c) 1999-2018 by the Massachusetts Institute of Technology + Copyright (c) 1999-2023 by the Massachusetts Institute of Technology ############################################################################# The following license applies to all files in the diff -Nru h5utils-1.13.1/copyright.h h5utils-1.13.2/copyright.h --- h5utils-1.13.1/copyright.h 2017-07-18 18:48:25.000000000 +0000 +++ h5utils-1.13.2/copyright.h 2023-01-15 20:12:37.000000000 +0000 @@ -4,7 +4,7 @@ /* License and copyright string for inclusion in program output: */ #define COPYRIGHT \ -"Copyright (c) 1999-2017 Massachusetts Institute of Technology\n"\ +"Copyright (c) 1999-2023 Massachusetts Institute of Technology\n"\ "\n"\ "Permission is hereby granted, free of charge, to any person obtaining\n"\ "a copy of this software and associated documentation files (the\n"\ diff -Nru h5utils-1.13.1/debian/changelog h5utils-1.13.2/debian/changelog --- h5utils-1.13.1/debian/changelog 2022-12-01 09:29:50.000000000 +0000 +++ h5utils-1.13.2/debian/changelog 2023-01-16 04:48:32.000000000 +0000 @@ -1,3 +1,13 @@ +h5utils (1.13.2-1) unstable; urgency=medium + + * Team upload. + * New upstream release. + * Update watch file to fix filenamemangle. + * Update GitHub repo URL. + * Update copyright file. + + -- Bas Couwenberg Mon, 16 Jan 2023 05:48:32 +0100 + h5utils (1.13.1-5) unstable; urgency=medium * Team upload. diff -Nru h5utils-1.13.1/debian/control h5utils-1.13.2/debian/control --- h5utils-1.13.1/debian/control 2022-11-27 18:43:23.000000000 +0000 +++ h5utils-1.13.2/debian/control 2023-01-16 04:48:32.000000000 +0000 @@ -12,7 +12,7 @@ Standards-Version: 4.6.1 Vcs-Browser: https://salsa.debian.org/debian-gis-team/h5utils Vcs-Git: https://salsa.debian.org/debian-gis-team/h5utils.git -Homepage: https://github.com/stevengj/h5utils +Homepage: https://github.com/NanoComp/h5utils Rules-Requires-Root: no Package: h5utils diff -Nru h5utils-1.13.1/debian/copyright h5utils-1.13.2/debian/copyright --- h5utils-1.13.1/debian/copyright 2018-03-20 07:11:23.000000000 +0000 +++ h5utils-1.13.2/debian/copyright 2023-01-16 04:48:32.000000000 +0000 @@ -1,14 +1,14 @@ Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: h5utils Upstream-Contact: Steven G. Johnson -Source: https://github.com/stevengj/h5utils +Source: https://github.com/NanoComp/h5utils Files: * -Copyright: 1999-2018, Massachusetts Institute of Technology +Copyright: 1999-2023, Massachusetts Institute of Technology License: Expat Files: h5tov5d.c -Copyright: 1999-2017, Massachusetts Institute of Technology +Copyright: 1999-2023, Massachusetts Institute of Technology License: GPL-2+ Files: debian/* diff -Nru h5utils-1.13.1/debian/patches/acute-accent-in-manual-page.patch h5utils-1.13.2/debian/patches/acute-accent-in-manual-page.patch --- h5utils-1.13.1/debian/patches/acute-accent-in-manual-page.patch 2021-09-12 12:31:14.000000000 +0000 +++ h5utils-1.13.2/debian/patches/acute-accent-in-manual-page.patch 2023-01-16 04:48:32.000000000 +0000 @@ -1,5 +1,6 @@ Description: Don't use \' groff sequence for apostrophe. Author: Bas Couwenberg +Forwarded: https://github.com/NanoComp/h5utils/pull/17 --- a/doc/man/h5fromh4.1 +++ b/doc/man/h5fromh4.1 diff -Nru h5utils-1.13.1/debian/upstream/metadata h5utils-1.13.2/debian/upstream/metadata --- h5utils-1.13.1/debian/upstream/metadata 2019-12-09 08:10:19.000000000 +0000 +++ h5utils-1.13.2/debian/upstream/metadata 2023-01-16 04:48:32.000000000 +0000 @@ -1,5 +1,5 @@ --- -Bug-Database: https://github.com/stevengj/h5utils/issues -Bug-Submit: https://github.com/stevengj/h5utils/issues/new -Repository: https://github.com/stevengj/h5utils.git -Repository-Browse: https://github.com/stevengj/h5utils +Bug-Database: https://github.com/NanoComp/h5utils/issues +Bug-Submit: https://github.com/NanoComp/h5utils/issues/new +Repository: https://github.com/NanoComp/h5utils.git +Repository-Browse: https://github.com/NanoComp/h5utils diff -Nru h5utils-1.13.1/debian/watch h5utils-1.13.2/debian/watch --- h5utils-1.13.1/debian/watch 2021-10-23 17:04:41.000000000 +0000 +++ h5utils-1.13.2/debian/watch 2023-01-16 04:48:32.000000000 +0000 @@ -2,6 +2,6 @@ opts=\ dversionmangle=s/\+(debian|dfsg|ds|deb)\d*$//,\ uversionmangle=s/(\d)[_\.\-\+]?((RC|rc|pre|dev|beta|alpha)\d*)$/$1~$2/;s/RC/rc/,\ -filenamemangle=s/(?:.*?)?(?:rel|v|h5utils)?[\-\_]?(\d\S+)\.(tgz|tbz|txz|(?:tar\.(?:gz|bz2|xz)))/h5utils-$1.$2/ \ -https://github.com/stevengj/h5utils/tags \ -(?:.*?archive/(?:.*?/)?)?(?:rel|v|h5utils)?[\-\_]?(\d[\d\-\.]+)\.(?:tgz|tbz|txz|(?:tar\.(?:gz|bz2|xz))) +filenamemangle=s/(?:.*\/)?(?:rel|v|h5utils)?[\-\_]?(\d\S+)\.(tgz|tbz|txz|(?:tar\.(?:gz|bz2|xz)))/h5utils-$1.$2/ \ +https://github.com/NanoComp/h5utils/tags \ +(?:.*?/archive/(?:.*?/)?)?(?:rel|v|h5utils)?[\-\_]?(\d\S+)\.(?:tgz|tbz|txz|(?:tar\.(?:gz|bz2|xz))) diff -Nru h5utils-1.13.1/depcomp h5utils-1.13.2/depcomp --- h5utils-1.13.1/depcomp 2015-01-05 22:11:43.000000000 +0000 +++ h5utils-1.13.2/depcomp 1970-01-01 00:00:00.000000000 +0000 @@ -1,791 +0,0 @@ -#! /bin/sh -# depcomp - compile a program generating dependencies as side-effects - -scriptversion=2013-05-30.07; # UTC - -# Copyright (C) 1999-2014 Free Software Foundation, Inc. - -# This program is free software; you can redistribute it and/or modify -# it under the terms of the GNU General Public License as published by -# the Free Software Foundation; either version 2, or (at your option) -# any later version. - -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -# GNU General Public License for more details. - -# You should have received a copy of the GNU General Public License -# along with this program. If not, see . - -# As a special exception to the GNU General Public License, if you -# distribute this file as part of a program that contains a -# configuration script generated by Autoconf, you may include it under -# the same distribution terms that you use for the rest of that program. - -# Originally written by Alexandre Oliva . - -case $1 in - '') - echo "$0: No command. Try '$0 --help' for more information." 1>&2 - exit 1; - ;; - -h | --h*) - cat <<\EOF -Usage: depcomp [--help] [--version] PROGRAM [ARGS] - -Run PROGRAMS ARGS to compile a file, generating dependencies -as side-effects. - -Environment variables: - depmode Dependency tracking mode. - source Source file read by 'PROGRAMS ARGS'. - object Object file output by 'PROGRAMS ARGS'. - DEPDIR directory where to store dependencies. - depfile Dependency file to output. - tmpdepfile Temporary file to use when outputting dependencies. - libtool Whether libtool is used (yes/no). - -Report bugs to . -EOF - exit $? - ;; - -v | --v*) - echo "depcomp $scriptversion" - exit $? - ;; -esac - -# Get the directory component of the given path, and save it in the -# global variables '$dir'. Note that this directory component will -# be either empty or ending with a '/' character. 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We -# parameterize here, but still list the modes in the big case below, -# to make depend.m4 easier to write. Note that we *cannot* use a case -# here, because this file can only contain one case statement. -if test "$depmode" = hp; then - # HP compiler uses -M and no extra arg. - gccflag=-M - depmode=gcc -fi - -if test "$depmode" = dashXmstdout; then - # This is just like dashmstdout with a different argument. - dashmflag=-xM - depmode=dashmstdout -fi - -cygpath_u="cygpath -u -f -" -if test "$depmode" = msvcmsys; then - # This is just like msvisualcpp but w/o cygpath translation. - # Just convert the backslash-escaped backslashes to single forward - # slashes to satisfy depend.m4 - cygpath_u='sed s,\\\\,/,g' - depmode=msvisualcpp -fi - -if test "$depmode" = msvc7msys; then - # This is just like msvc7 but w/o cygpath translation. - # Just convert the backslash-escaped backslashes to single forward - # slashes to satisfy depend.m4 - cygpath_u='sed s,\\\\,/,g' - depmode=msvc7 -fi - -if test "$depmode" = xlc; then - # IBM C/C++ Compilers xlc/xlC can output gcc-like dependency information. - gccflag=-qmakedep=gcc,-MF - depmode=gcc -fi - -case "$depmode" in -gcc3) -## gcc 3 implements dependency tracking that does exactly what -## we want. 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It works by - # looking at the text of this script. This case will never be run, - # since it is checked for above. - exit 1 - ;; - -none) - exec "$@" - ;; - -*) - echo "Unknown depmode $depmode" 1>&2 - exit 1 - ;; -esac - -exit 0 - -# Local Variables: -# mode: shell-script -# sh-indentation: 2 -# eval: (add-hook 'write-file-hooks 'time-stamp) -# time-stamp-start: "scriptversion=" -# time-stamp-format: "%:y-%02m-%02d.%02H" -# time-stamp-time-zone: "UTC" -# time-stamp-end: "; # UTC" -# End: diff -Nru h5utils-1.13.1/doc/h4fromh5-man.md h5utils-1.13.2/doc/h4fromh5-man.md --- h5utils-1.13.1/doc/h4fromh5-man.md 1970-01-01 00:00:00.000000000 +0000 +++ h5utils-1.13.2/doc/h4fromh5-man.md 2023-01-15 20:12:37.000000000 +0000 @@ -0,0 +1,33 @@ +# h4fromh5: convert HDF5 scientific dataset to an HDF4 file + +## Synopsis + + h4fromh5[OPTION]... [HDF4FILE]... + +## Description + +`h4fromh5` takes one or more files in HDF5 format and outputs files in HDF4 format containing the datasets from the HDF5 files. (Currently, only a single dataset per HDF5 file is converted.) + +HDF4 and HDF5 are free, portable binary formats and supporting libraries developed by the National Center for Supercomputing Applications at the University of Illinois in Urbana-Champaign. + +A single +HDF5 (`.h5`) file can contain multiple data sets; by default, `h4fromh5` converts the first dataset, but this can be changed via the `-d` option, or by using the syntax `HDF5FILE:DATASET`. + +The most basic usage is something like `h4fromh5 foo.h5`, which will output a file `foo.hdf` containing the scientific dataset from `foo.h5`. + +## Options + +* `-h` — Display help on the command-line options and usage. +* `-V` — Print the version number and copyright info for `h4fromh5`. +* `-v` — Verbose output. +* `-T` — Transpose the output dataset (e.g. LxMxN becomes NxMxL). This is often useful because HDF5 programs typically follow C (row-major) conventions while HDF4 programs often follow Fortran (column-major, transposed) conventions for array ordering. +* `-o file` — Send HDF output to `file` rather than to the input filename with `.h5` replaced with `.hdf` (the default). +* `-d name` — Read from dataset `name` in the input; otherwise, the first dataset in the input file is used. Alternatively, use the syntax `HDF5FILE:DATASET` when the input file names are specified. + +## Bugs + +Report bugs by filing an issue at https://github.com/stevengj/h5utils + +## Authors + +Written by [Steven G. Johnson](http://math.mit.edu/~stevenj/). Copyright © 2017 by the Massachusetts Institute of Technology. diff -Nru h5utils-1.13.1/doc/h5fromh4-man.md h5utils-1.13.2/doc/h5fromh4-man.md --- h5utils-1.13.1/doc/h5fromh4-man.md 1970-01-01 00:00:00.000000000 +0000 +++ h5utils-1.13.2/doc/h5fromh4-man.md 2023-01-15 20:12:37.000000000 +0000 @@ -0,0 +1,37 @@ +# h5fromh4: convert HDF4 scientific datasets to an HDF5 file + +## Synopsis + + h5fromh4 [OPTION]... [HDF4FILE]... + +## Description + +`h5fromh4` takes one or more files in HDF4 format and outputs files in HDF5 format containing the datasets from the HDF4 files. (Currently, only a single dataset per HDF4 file is converted.) + +HDF4 and HDF5 are free, portable binary formats and supporting libraries 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, `h5fromh4` creates a dataset called `data`, but this can be changed via the `-d` option, or by using the syntax `HDF5FILE:DATASET` with the `-o` option. The `-a` option can be used to append new datasets to an existing HDF5 file. If the `-o` option is used and multiple HDF4 files are specified, all the HDF4 datasets are output into that HDF5 file with the input filenames (minus the `.hdf` suffix) used as the dataset names. + +The most basic usage is something like `h5fromh4 foo.hdf`, which will output a file `foo.h5` containing the scientific dataset from `foo.hdf`.` + +## Options + +* `-h` — Display help on the command-line options and usage. + +* `-V` — Print the version number and copyright info for `h5fromh4` + +* `-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. + +* `-o` `file` — Send HDF5 output to `file` rather than to the input filename with .hdf replaced with .h5 (the default). If multiple input files were specified, this causes all input datasets to be stored in `file` (rather than in separate files), with the input filenames (minus the .hdf suffix) as the dataset names. + +* `-d` `name` — Write to dataset `name` in the output; otherwise, the output dataset is called "data" by default. Alternatively, use the syntax `HDF5FILE:DATASET` with the `-o` option. + +## Bugs + +Report bugs by filing an issue at https://github.com/stevengj/h5utils + +## Authors + +Written by [Steven G. Johnson](http://math.mit.edu/~stevenj/). Copyright © 2017 by the Massachusetts Institute of Technology. diff -Nru h5utils-1.13.1/doc/h5fromtxt-man.md h5utils-1.13.2/doc/h5fromtxt-man.md --- h5utils-1.13.1/doc/h5fromtxt-man.md 1970-01-01 00:00:00.000000000 +0000 +++ h5utils-1.13.2/doc/h5fromtxt-man.md 2023-01-15 20:12:37.000000000 +0000 @@ -0,0 +1,50 @@ +# 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 University 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 < +#endif + +/* shell expansion on a path, used for CMAP_DIR */ +char *shell_expand(const char *path) +{ +#if defined(HAVE_WORDEXP) && defined(HAVE_WORDEXP_H) + wordexp_t p; + char *newpath; + wordexp(path, &p, 0); + newpath = my_strdup(p.we_wordc == 1 ? p.we_wordv[0] : path); + wordfree(&p); + return newpath; +#else + return my_strdup(path); +#endif +} + void usage(FILE *f) { fprintf(f, "Usage: h5topng [options] []\n" @@ -135,21 +154,22 @@ return c; } -colormap_t get_cmap(const char *colormap, int invert, double scale_alpha, - int verbose) +colormap_t get_cmap(const char *cmap_dir, + const char *colormap, int invert, double scale_alpha, + int verbose) { int i; colormap_t cmap = {0, NULL}; FILE *cmap_f = NULL; char *cmap_fname = (char *) malloc(sizeof(char) * - (strlen(CMAP_DIR) + (strlen(cmap_dir) + strlen(colormap) + 1)); CHECK(cmap_fname, "out of memory"); if (colormap[0] == '-') { invert = 1; colormap++; } - strcpy(cmap_fname, CMAP_DIR); strcat(cmap_fname, colormap); + strcpy(cmap_fname, cmap_dir); strcat(cmap_fname, colormap); if (colormap[0] == '.' || colormap[0] == '/' || !(cmap_f = fopen(cmap_fname, "r"))) { free(cmap_fname); @@ -241,7 +261,7 @@ int islice_min[4] = {0,0,0,0}, islice_max[4] = {0,0,0,0}, islice_step[4] = {1,1,1,1}; int err; int nx, ny; - char *colormap = NULL, *overlay_colormap = NULL; + char *colormap = NULL, *overlay_colormap = NULL, *cmap_dir = NULL; int overlay_invert = 0; colormap_t cmap = { 0, NULL }; colormap_t overlay_cmap = { 0, NULL }; @@ -259,6 +279,9 @@ colormap = my_strdup(CMAP_DEFAULT); overlay_colormap = my_strdup(OVERLAY_CMAP_DEFAULT); + /* do tilde and $foo expansion on CMAP_DIR */ + cmap_dir = shell_expand(CMAP_DIR); + while ((c = getopt(argc, argv, "ho:x:y:z:t:0c:m:M:RC:b:d:vX:Y:S:TrZs:Va:A:8")) != -1) switch (c) { case 'h': @@ -372,9 +395,9 @@ CHECK(!overlay_fname || !eight_bit, "-8 option is not currently supported with -A"); - cmap = get_cmap(colormap, invert, 1.0, verbose); + cmap = get_cmap(cmap_dir, colormap, invert, 1.0, verbose); if (overlay_fname) - overlay_cmap = get_cmap(overlay_colormap, overlay_invert, + overlay_cmap = get_cmap(cmap_dir, overlay_colormap, overlay_invert, overlay_opacity, verbose); if (optind == argc) { /* no parameters left */ @@ -592,6 +615,6 @@ if (cmap.rgba != gray_colors) free(cmap.rgba); free(colormap); - + free(cmap_dir); return EXIT_SUCCESS; } diff -Nru h5utils-1.13.1/h5totxt.c h5utils-1.13.2/h5totxt.c --- h5utils-1.13.1/h5totxt.c 2017-07-18 18:48:25.000000000 +0000 +++ h5utils-1.13.2/h5totxt.c 2023-01-15 20:12:37.000000000 +0000 @@ -1,4 +1,4 @@ -/* Copyright (c) 1999-2017 Massachusetts Institute of Technology +/* Copyright (c) 1999-2023 Massachusetts Institute of Technology * * Permission is hereby granted, free of charge, to any person obtaining * a copy of this software and associated documentation files (the diff -Nru h5utils-1.13.1/h5tov5d.c h5utils-1.13.2/h5tov5d.c --- h5utils-1.13.1/h5tov5d.c 2017-07-18 18:48:25.000000000 +0000 +++ h5utils-1.13.2/h5tov5d.c 2023-01-15 20:12:37.000000000 +0000 @@ -1,4 +1,4 @@ -/* Copyright (c) 1999-2017 Massachusetts Institute of Technology +/* Copyright (c) 1999-2023 Massachusetts Institute of Technology * * [ IMPORTANT: Note that the following is DIFFERENT from the license * for the rest of the h5utils package. ] @@ -306,7 +306,7 @@ return EXIT_SUCCESS; case 'V': printf("h5tov5d " PACKAGE_VERSION " by Steven G. Johnson\n" - "Copyright (c) 1999-2017 Massachusetts Institute of Technology\n" + "Copyright (c) 1999-2023 Massachusetts Institute of Technology\n" "\n" "This program is free software; you can redistribute it and/or modify\n" "it under the terms of the GNU General Public License as published by\n" diff -Nru h5utils-1.13.1/h5tovtk.c h5utils-1.13.2/h5tovtk.c --- h5utils-1.13.1/h5tovtk.c 2017-07-18 18:48:25.000000000 +0000 +++ h5utils-1.13.2/h5tovtk.c 2023-01-15 20:12:37.000000000 +0000 @@ -1,4 +1,4 @@ -/* Copyright (c) 1999-2017 Massachusetts Institute of Technology +/* Copyright (c) 1999-2023 Massachusetts Institute of Technology * * Permission is hereby granted, free of charge, to any person obtaining * a copy of this software and associated documentation files (the diff -Nru h5utils-1.13.1/h5utils.c h5utils-1.13.2/h5utils.c --- h5utils-1.13.1/h5utils.c 2017-07-18 18:48:25.000000000 +0000 +++ h5utils-1.13.2/h5utils.c 2023-01-15 20:12:37.000000000 +0000 @@ -1,4 +1,4 @@ -/* Copyright (c) 1999-2017 Massachusetts Institute of Technology +/* Copyright (c) 1999-2023 Massachusetts Institute of Technology * * Permission is hereby granted, free of charge, to any person obtaining * a copy of this software and associated documentation files (the @@ -31,10 +31,13 @@ char *my_strdup(const char *s) { - char *sd = (char *) malloc(sizeof(char) * (strlen(s) + 1)); - CHECK(sd, "out of memory"); - strcpy(sd, s); - return sd; + if (s) { + char *sd = (char *) malloc(sizeof(char) * (strlen(s) + 1)); + CHECK(sd, "out of memory"); + strcpy(sd, s); + return sd; + } + return NULL; } char *replace_suffix(const char *s, const char *old_suff, const char *new_suff) diff -Nru h5utils-1.13.1/h5utils.h h5utils-1.13.2/h5utils.h --- h5utils-1.13.1/h5utils.h 2017-07-18 18:48:25.000000000 +0000 +++ h5utils-1.13.2/h5utils.h 2023-01-15 20:12:37.000000000 +0000 @@ -1,4 +1,4 @@ -/* Copyright (c) 1999-2017 Massachusetts Institute of Technology +/* Copyright (c) 1999-2023 Massachusetts Institute of Technology * * Permission is hereby granted, free of charge, to any person obtaining * a copy of this software and associated documentation files (the diff -Nru h5utils-1.13.1/install-sh h5utils-1.13.2/install-sh --- h5utils-1.13.1/install-sh 2015-01-05 22:11:43.000000000 +0000 +++ h5utils-1.13.2/install-sh 1970-01-01 00:00:00.000000000 +0000 @@ -1,501 +0,0 @@ -#!/bin/sh -# install - install a program, script, or datafile - -scriptversion=2013-12-25.23; # UTC - -# This originates from X11R5 (mit/util/scripts/install.sh), which was -# later released in X11R6 (xc/config/util/install.sh) with the -# following copyright and license. -# -# Copyright (C) 1994 X Consortium -# -# Permission is hereby granted, free of charge, to any person obtaining a copy -# of this software and associated documentation files (the "Software"), to -# deal in the Software without restriction, including without limitation the -# rights to use, copy, modify, merge, publish, distribute, sublicense, and/or -# sell copies of the Software, and to permit persons to whom the Software is -# furnished to do so, subject to the following conditions: -# -# The above copyright notice and this permission notice shall be included in -# all copies or substantial portions of the Software. -# -# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE -# X CONSORTIUM BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN -# AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNEC- -# TION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. -# -# Except as contained in this notice, the name of the X Consortium shall not -# be used in advertising or otherwise to promote the sale, use or other deal- -# ings in this Software without prior written authorization from the X Consor- -# tium. -# -# -# FSF changes to this file are in the public domain. -# -# Calling this script install-sh is preferred over install.sh, to prevent -# 'make' implicit rules from creating a file called install from it -# when there is no Makefile. -# -# This script is compatible with the BSD install script, but was written -# from scratch. - -tab=' ' -nl=' -' -IFS=" $tab$nl" - -# Set DOITPROG to "echo" to test this script. - -doit=${DOITPROG-} -doit_exec=${doit:-exec} - -# Put in absolute file names if you don't have them in your path; -# or use environment vars. - -chgrpprog=${CHGRPPROG-chgrp} -chmodprog=${CHMODPROG-chmod} -chownprog=${CHOWNPROG-chown} -cmpprog=${CMPPROG-cmp} -cpprog=${CPPROG-cp} -mkdirprog=${MKDIRPROG-mkdir} -mvprog=${MVPROG-mv} -rmprog=${RMPROG-rm} -stripprog=${STRIPPROG-strip} - -posix_mkdir= - -# Desired mode of installed file. -mode=0755 - -chgrpcmd= -chmodcmd=$chmodprog -chowncmd= -mvcmd=$mvprog -rmcmd="$rmprog -f" -stripcmd= - -src= -dst= -dir_arg= -dst_arg= - -copy_on_change=false -is_target_a_directory=possibly - -usage="\ -Usage: $0 [OPTION]... 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DIRECTORY - or: $0 [OPTION]... -t DIRECTORY SRCFILES... - or: $0 [OPTION]... -d DIRECTORIES... - -In the 1st form, copy SRCFILE to DSTFILE. -In the 2nd and 3rd, copy all SRCFILES to DIRECTORY. -In the 4th, create DIRECTORIES. - -Options: - --help display this help and exit. - --version display version info and exit. - - -c (ignored) - -C install only if different (preserve the last data modification time) - -d create directories instead of installing files. - -g GROUP $chgrpprog installed files to GROUP. - -m MODE $chmodprog installed files to MODE. - -o USER $chownprog installed files to USER. - -s $stripprog installed files. - -t DIRECTORY install into DIRECTORY. - -T report an error if DSTFILE is a directory. - -Environment variables override the default commands: - CHGRPPROG CHMODPROG CHOWNPROG CMPPROG CPPROG MKDIRPROG MVPROG - RMPROG STRIPPROG -" - -while test $# -ne 0; do - case $1 in - -c) ;; - - -C) copy_on_change=true;; - - -d) dir_arg=true;; - - -g) chgrpcmd="$chgrpprog $2" - shift;; - - --help) echo "$usage"; exit $?;; - - -m) mode=$2 - case $mode in - *' '* | *"$tab"* | *"$nl"* | *'*'* | *'?'* | *'['*) - echo "$0: invalid mode: $mode" >&2 - exit 1;; - esac - shift;; - - -o) chowncmd="$chownprog $2" - shift;; - - -s) stripcmd=$stripprog;; - - -t) - is_target_a_directory=always - dst_arg=$2 - # Protect names problematic for 'test' and other utilities. - case $dst_arg in - -* | [=\(\)!]) dst_arg=./$dst_arg;; - esac - shift;; - - -T) is_target_a_directory=never;; - - --version) echo "$0 $scriptversion"; exit $?;; - - --) shift - break;; - - -*) echo "$0: invalid option: $1" >&2 - exit 1;; - - *) break;; - esac - shift -done - -# We allow the use of options -d and -T together, by making -d -# take the precedence; this is for compatibility with GNU install. - -if test -n "$dir_arg"; then - if test -n "$dst_arg"; then - echo "$0: target directory not allowed when installing a directory." >&2 - exit 1 - fi -fi - -if test $# -ne 0 && test -z "$dir_arg$dst_arg"; then - # When -d is used, all remaining arguments are directories to create. - # When -t is used, the destination is already specified. - # Otherwise, the last argument is the destination. Remove it from $@. - for arg - do - if test -n "$dst_arg"; then - # $@ is not empty: it contains at least $arg. - set fnord "$@" "$dst_arg" - shift # fnord - fi - shift # arg - dst_arg=$arg - # Protect names problematic for 'test' and other utilities. - case $dst_arg in - -* | [=\(\)!]) dst_arg=./$dst_arg;; - esac - done -fi - -if test $# -eq 0; then - if test -z "$dir_arg"; then - echo "$0: no input file specified." >&2 - exit 1 - fi - # It's OK to call 'install-sh -d' without argument. - # This can happen when creating conditional directories. - exit 0 -fi - -if test -z "$dir_arg"; then - if test $# -gt 1 || test "$is_target_a_directory" = always; then - if test ! -d "$dst_arg"; then - echo "$0: $dst_arg: Is not a directory." >&2 - exit 1 - fi - fi -fi - -if test -z "$dir_arg"; then - do_exit='(exit $ret); exit $ret' - trap "ret=129; $do_exit" 1 - trap "ret=130; $do_exit" 2 - trap "ret=141; $do_exit" 13 - trap "ret=143; $do_exit" 15 - - # Set umask so as not to create temps with too-generous modes. - # However, 'strip' requires both read and write access to temps. - case $mode in - # Optimize common cases. - *644) cp_umask=133;; - *755) cp_umask=22;; - - *[0-7]) - if test -z "$stripcmd"; then - u_plus_rw= - else - u_plus_rw='% 200' - fi - cp_umask=`expr '(' 777 - $mode % 1000 ')' $u_plus_rw`;; - *) - if test -z "$stripcmd"; then - u_plus_rw= - else - u_plus_rw=,u+rw - fi - cp_umask=$mode$u_plus_rw;; - esac -fi - -for src -do - # Protect names problematic for 'test' and other utilities. - case $src in - -* | [=\(\)!]) src=./$src;; - esac - - if test -n "$dir_arg"; then - dst=$src - dstdir=$dst - test -d "$dstdir" - dstdir_status=$? - else - - # Waiting for this to be detected by the "$cpprog $src $dsttmp" command - # might cause directories to be created, which would be especially bad - # if $src (and thus $dsttmp) contains '*'. - if test ! -f "$src" && test ! -d "$src"; then - echo "$0: $src does not exist." >&2 - exit 1 - fi - - if test -z "$dst_arg"; then - echo "$0: no destination specified." >&2 - exit 1 - fi - dst=$dst_arg - - # If destination is a directory, append the input filename; won't work - # if double slashes aren't ignored. - if test -d "$dst"; then - if test "$is_target_a_directory" = never; then - echo "$0: $dst_arg: Is a directory" >&2 - exit 1 - fi - dstdir=$dst - dst=$dstdir/`basename "$src"` - dstdir_status=0 - else - dstdir=`dirname "$dst"` - test -d "$dstdir" - dstdir_status=$? - fi - fi - - obsolete_mkdir_used=false - - if test $dstdir_status != 0; then - case $posix_mkdir in - '') - # Create intermediate dirs using mode 755 as modified by the umask. - # This is like FreeBSD 'install' as of 1997-10-28. - umask=`umask` - case $stripcmd.$umask in - # Optimize common cases. - *[2367][2367]) mkdir_umask=$umask;; - .*0[02][02] | .[02][02] | .[02]) mkdir_umask=22;; - - *[0-7]) - mkdir_umask=`expr $umask + 22 \ - - $umask % 100 % 40 + $umask % 20 \ - - $umask % 10 % 4 + $umask % 2 - `;; - *) mkdir_umask=$umask,go-w;; - esac - - # With -d, create the new directory with the user-specified mode. - # Otherwise, rely on $mkdir_umask. - if test -n "$dir_arg"; then - mkdir_mode=-m$mode - else - mkdir_mode= - fi - - posix_mkdir=false - case $umask in - *[123567][0-7][0-7]) - # POSIX mkdir -p sets u+wx bits regardless of umask, which - # is incompatible with FreeBSD 'install' when (umask & 300) != 0. - ;; - *) - tmpdir=${TMPDIR-/tmp}/ins$RANDOM-$$ - trap 'ret=$?; rmdir "$tmpdir/d" "$tmpdir" 2>/dev/null; exit $ret' 0 - - if (umask $mkdir_umask && - exec $mkdirprog $mkdir_mode -p -- "$tmpdir/d") >/dev/null 2>&1 - then - if test -z "$dir_arg" || { - # Check for POSIX incompatibilities with -m. - # HP-UX 11.23 and IRIX 6.5 mkdir -m -p sets group- or - # other-writable bit of parent directory when it shouldn't. - # FreeBSD 6.1 mkdir -m -p sets mode of existing directory. - ls_ld_tmpdir=`ls -ld "$tmpdir"` - case $ls_ld_tmpdir in - d????-?r-*) different_mode=700;; - d????-?--*) different_mode=755;; - *) false;; - esac && - $mkdirprog -m$different_mode -p -- "$tmpdir" && { - ls_ld_tmpdir_1=`ls -ld "$tmpdir"` - test "$ls_ld_tmpdir" = "$ls_ld_tmpdir_1" - } - } - then posix_mkdir=: - fi - rmdir "$tmpdir/d" "$tmpdir" - else - # Remove any dirs left behind by ancient mkdir implementations. - rmdir ./$mkdir_mode ./-p ./-- 2>/dev/null - fi - trap '' 0;; - esac;; - esac - - if - $posix_mkdir && ( - umask $mkdir_umask && - $doit_exec $mkdirprog $mkdir_mode -p -- "$dstdir" - ) - then : - else - - # The umask is ridiculous, or mkdir does not conform to POSIX, - # or it failed possibly due to a race condition. Create the - # directory the slow way, step by step, checking for races as we go. - - case $dstdir in - /*) prefix='/';; - [-=\(\)!]*) prefix='./';; - *) prefix='';; - esac - - oIFS=$IFS - IFS=/ - set -f - set fnord $dstdir - shift - set +f - IFS=$oIFS - - prefixes= - - for d - do - test X"$d" = X && continue - - prefix=$prefix$d - if test -d "$prefix"; then - prefixes= - else - if $posix_mkdir; then - (umask=$mkdir_umask && - $doit_exec $mkdirprog $mkdir_mode -p -- "$dstdir") && break - # Don't fail if two instances are running concurrently. - test -d "$prefix" || exit 1 - else - case $prefix in - *\'*) qprefix=`echo "$prefix" | sed "s/'/'\\\\\\\\''/g"`;; - *) qprefix=$prefix;; - esac - prefixes="$prefixes '$qprefix'" - fi - fi - prefix=$prefix/ - done - - if test -n "$prefixes"; then - # Don't fail if two instances are running concurrently. - (umask $mkdir_umask && - eval "\$doit_exec \$mkdirprog $prefixes") || - test -d "$dstdir" || exit 1 - obsolete_mkdir_used=true - fi - fi - fi - - if test -n "$dir_arg"; then - { test -z "$chowncmd" || $doit $chowncmd "$dst"; } && - { test -z "$chgrpcmd" || $doit $chgrpcmd "$dst"; } && - { test "$obsolete_mkdir_used$chowncmd$chgrpcmd" = false || - test -z "$chmodcmd" || $doit $chmodcmd $mode "$dst"; } || exit 1 - else - - # Make a couple of temp file names in the proper directory. - dsttmp=$dstdir/_inst.$$_ - rmtmp=$dstdir/_rm.$$_ - - # Trap to clean up those temp files at exit. - trap 'ret=$?; rm -f "$dsttmp" "$rmtmp" && exit $ret' 0 - - # Copy the file name to the temp name. - (umask $cp_umask && $doit_exec $cpprog "$src" "$dsttmp") && - - # and set any options; do chmod last to preserve setuid bits. - # - # If any of these fail, we abort the whole thing. If we want to - # ignore errors from any of these, just make sure not to ignore - # errors from the above "$doit $cpprog $src $dsttmp" command. - # - { test -z "$chowncmd" || $doit $chowncmd "$dsttmp"; } && - { test -z "$chgrpcmd" || $doit $chgrpcmd "$dsttmp"; } && - { test -z "$stripcmd" || $doit $stripcmd "$dsttmp"; } && - { test -z "$chmodcmd" || $doit $chmodcmd $mode "$dsttmp"; } && - - # If -C, don't bother to copy if it wouldn't change the file. - if $copy_on_change && - old=`LC_ALL=C ls -dlL "$dst" 2>/dev/null` && - new=`LC_ALL=C ls -dlL "$dsttmp" 2>/dev/null` && - set -f && - set X $old && old=:$2:$4:$5:$6 && - set X $new && new=:$2:$4:$5:$6 && - set +f && - test "$old" = "$new" && - $cmpprog "$dst" "$dsttmp" >/dev/null 2>&1 - then - rm -f "$dsttmp" - else - # Rename the file to the real destination. - $doit $mvcmd -f "$dsttmp" "$dst" 2>/dev/null || - - # The rename failed, perhaps because mv can't rename something else - # to itself, or perhaps because mv is so ancient that it does not - # support -f. - { - # Now remove or move aside any old file at destination location. - # We try this two ways since rm can't unlink itself on some - # systems and the destination file might be busy for other - # reasons. 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Thanks to + Daisuke Fujimura (@fd00 on github) for posting patches. + +* Moved hosting to Github and translated documentation to Markdown. + +## h5utils 1.12.1 ## + +*6/24/09* + +* Use `octave-config`, if available, to detect octave-plugin installation path (thanks to Debian bug report #516453 for suggestion). + +## h5utils 1.12 ## + +*6/12/09* + +* The vertical axis in `h5topng` is now reversed to correspond to what most people seem to expect: increasing coordinates correspond to "up" and "right" in the image, rather than "down" and "right" in the image as in previous versions. +* Fixed failure in `h5tovtk -2`; thanks to Karen Lee for the bug report. +* Fixed installation of `h5read.oct` for Octave 3.x. + +## h5utils 1.11.1 ## + +*4/28/08* + +* Fixed failure to find colormap files in h5topng 1.11 (due to changes in autoconf 2.60); thanks to bug report from Jiangjun Zheng. + +## h5utils 1.11 ## + +*4/24/08* + +* h5tovtk no longer reverses the dimensions; thanks to Andreas Wilde for the suggestion. +* Fix compilation failure with HDF5 1.8. + +## h5utils 1.10.1 ## + +*9/20/06* + +* Fixed build problem on Cygwin due to missing "`.exe`" extension. Thanks to Ken Hill for the bug report. + +## h5utils 1.10 ## + +*9/2/05* + +* Added `h4fromh5` utility. (NCSA seems to be no longer shipping the HDF5/HDF4 conversion tools with the latest HDF5 release.) +* Added `dkbluered` color map, which is similar to `bluered` but uses a somewhat wider range of colors. + +## h5utils 1.9.1 ## + +*8/5/04* + +* Fix `h5topng` compilation failure with some non-C99 compilers; thanks to Maarten van Reeuwijk for the bug report. + +## h5utils 1.9 ## + +*7/12/04* + +* Added new `h5math` utility, which creates and combines HDF5 datasets using a user-specified mathematical expression. (Requires [GNU libmatheval](http://www.gnu.org/software/libmatheval/) to be installed.) +* `h5topng`: Matlab-like `start:end` or `start:step:end` notation for slice indices, to allow a whole sequence of slices to be output as a sequence of PNG images. +* `h5topng`: if contour/overlay dataset does not have same dimensions as output data, it is periodically "tiled" over the output. + +## h5utils 1.8 ## + +*5/22/04* + +* New `-A` and `-a` options for `h5topng` to allow translucent overlays from one file onto another (an alternative or complement to the `-C` contour-overlay option). +* `h5topng` uses 24-bit direct color by default (use `-8` option for old 8-bit behavior). +* `h5topng` uses columns/rows for x/y by default (use `-T` to swap), the opposite of the old behavior. +* There is no default `-z 0` slice dimension in `h5topng`/`h5totxt` any more. You must specify a slice for 3+ dimensional data in `h5topng`. `h5totxt` dumps the whole data file by default unless one or more slices are specified. +* Support specifying multiple slice dimensions for 4+ dimensional datasets, with new `-t` option to indicate final dimension. +* Slices are also supported now in `h5tovtk` and `h5tov5d`. +* New `-.` option in `h5totxt` to specify number of significant digits; output 16 digits by default instead of 6, previously. + +## h5utils 1.7.2 ## + +*7/15/02* + +* Fixed C++ compilation problem for `g++` 3.x in `h5read` Octave plugin; thanks to Josselin Mouette for the patch. + +## h5utils 1.7.1 ## + +*3/16/02* + +* Fixed array overrun in `h5topng` that caused a floating-point exception on Alphas; thanks to Marin Soljacic for the bug report. + +## h5utils 1.7 ## + +*3/9/02* + +* `h5topng` now supports multiple, user-definable color tables, a number of which are provided. '''Incompatible change''': the `-c` option now has the syntax: `-c ''colortable''`. The old behavior corresponds to the included "`bluered`" colortable, invoked via: `-c bluered`. +* New `-R` option for `h5topng` to use a consistent color scale for all specified files. +* New `-0` option for `h5topng` and `h5totxt` that shifts the origin of the slice coordinates to the dataset center. +* Added `h5tovtk` program to output VTK (Visualization ToolKit) data files. +* Support `-T` (transpose dimensions) option in `h5tov5d`. +* Fixed bug in `h5topng` that caused extra rows/columns of garbage pixels to be written at the edges of images when scaling was used. +* When compiling the h5read Octave plugin, respect the `CPPFLAGS` and `LDFLAGS` environment variables. Thanks to Max Colice for the bug report. +* Fixed problem when `--without-h5tov5d` and `--without-h5fromh4` are used. Thanks to Nikola Ivanov Nikolov for the fix. + +## h5utils 1.6 ## + +*1/17/01* + +* Don't build `h5fromh4` if the superior `h4toh5` tool (from HDF5 1.4) is present. Also added `--{with,without}-h5fromh4` option to configure to force whether `h5fromh4` is built. + +## h5utils 1.5.1 ## + +*12/9/00* + +* Support manually disabling Octave plugin support (`configure --without-octave`) in case of C++ problems. +* Support Vis5d+ and Debian HDF header file locations. + +## h5utils 1.5 ## + +*7/9/00* + +* Added `h5fromh4` program to convert HDF4 datasets to HDF5 format. +* Added `-S ''s''` option to `h5topng` as a shortcut for `-X ''s'' -Y ''s''`. + +## h5utils 1.4 ## + +*5/28/00* + +* Added `h5fromtxt` program to convert text input to an HDF5 dataset. + +## h5utils 1.3.4 ## + +*1/31/00* + +* Improved -C contour plotting in h5topng. +* Fix in `h5topng` man page (thanks to Christoph Becher). + +## h5utils 1.3.3 ## + +*1/30/00* + +* Bug fix in `h5topng` (would sometimes output solid black images). Thanks to Karl Koch for the bug report. + +## h5utils 1.3.2 ## + +*1/28/00* + +* Added `h5topng -Z` option to center color scale on zero. +* Now support `h5topng -C ''filename:dataset''`. + +## h5utils 1.3.1 ## + +*1/27/00* + +* Bug fixes in dataset name-handling, especially when using `h5tov5d` to join multiple datasets into one output file. + +## h5utils 1.3 ## + +*1/21/00* + +* You can now specify individual datasets within a file by using ''filename'':''dataset'' instead of just ''filename'' with `h5topng`, `h5totxt`, and `h5tov5d`. + +## h5utils 1.2.3 ## + +*1/20/00* + +* Fixed minor bug in '`h5totxt -h`'. + +## h5utils 1.2.2 ## + +*1/12/00* + +* `Makefile` now includes `CPPFLAGS` in the compiler flags, making it easier to use header files in non-standard locations. (`CPPFLAGS` is the proper place to put `-I` flags for the configure script.) + +## h5utils 1.2.1 ## + +*1/1/00* + +* Modified `-o` option of `h5tov5d` to join datasets into a single Vis5d file. + +## h5utils 1.2 ## + +*12/31/99* + +* Added h5tov5d program for converting to Vis5d format. +* Improved installation; `h5read.oct` now goes into the sitewide Octave plugins directory, and things work correctly when only some of the utilities are compiled. + +## h5utils 1.1 ## + +*12/6/99* + +* Added `h5totxt` program for exporting 2d slices of HDF5 files to text suitable for importing into a spreadsheet. + +## h5utils 1.0 ## + +*11/22/99* + +* Initial release. diff -Nru h5utils-1.13.1/README.md h5utils-1.13.2/README.md --- h5utils-1.13.1/README.md 1970-01-01 00:00:00.000000000 +0000 +++ h5utils-1.13.2/README.md 2023-01-15 20:12:37.000000000 +0000 @@ -0,0 +1,76 @@ +![logo](doc/images/H5utils-logo.png) + +# H5utils + +**h5utils** is a set of utilities for visualization and conversion of scientific data in the free, portable [HDF5 format](http://www.hdfgroup.org/HDF5/). + +Besides providing a simple tool for batch visualization as [PNG](https://en.wikipedia.org/wiki/Portable_Network_Graphics) images, h5utils also includes programs to convert HDF5 datasets into the formats required by other free visualization software (e.g. plain text, [Vis5d](http://www.ssec.wisc.edu/~billh/vis5d.html), and [VTK](http://public.kitware.com/VTK/)). + +This package is developed by [Steven G. Johnson](http://math.mit.edu/~stevenj/), and is [free software](http://www.gnu.org/philosophy/free-sw.html) that should easily install under any Unix-like operating system (*e.g.* GNU/Linux). + +# Download and Install + +The latest version is h5utils 1.13.1, which can be downloaded in source-code form at: + +* https://github.com/NanoComp/h5utils/releases/download/1.13.1/h5utils-1.13.1.tar.gz + +(Download this `.tar.gz` file rather than cloning the [git repo](https://github.com/NanoComp/h5utils) +unless you are a developer, since the git repo requires additional tools to build as described below.) + +What's new in each version is described in the [release notes](NEWS.md) file. + +h5utils is free software (a.k.a. [open source](http://www.opensource.org/)); see below for the license and copyright. + +## Installation + +h5utils is designed for Unix-like operating systems (*e.g.* GNU/Linux). We do not support Windows directly, although you may be able to install there too using free packages like [Cygwin](http://cygwin.com/). + +You must first download and install [HDF5](http://www.hdfgroup.org/HDF5/), if it is not already on your system. Also, the programs to convert (see below) to/from [PNG](http://www.libpng.org/pub/png/), [Vis5d](http://www.ssec.wisc.edu/~billh/vis5d.html), [GNU Octave](http://www.octave.org/), and [HDF(4)](http://www.hdfgroup.org/products/hdf4/) will only be built if the corresponding libraries/programs are installed. `h5math` will only be built if [GNU libmatheval](http://www.gnu.org/software/libmatheval/) is installed. + +To compile and install the package, you then just type the usual GNU build commands: +``` +./configure +make +make install +``` +See `./configure --help` for more options. You can use `make uninstall` to get rid of all the installed files. + +**Github**: If you are using the source [on github](https://github.com/NanoComp/h5utils) (via `git clone https://github.com/NanoComp/h5utils`), then you will also need to have [GNU autoconf, automake, and libtool](https://en.wikipedia.org/wiki/GNU_Build_System) installed, and run `sh autogen.sh` (in a Unix shell) to set up things before running `make` above (`autogen.sh` runs `./configure` for you). + +**Note:** if you get a message like `cannot compute sizeof (unsigned long)` when running `./configure`, it probably means you didn't install the HDF5 library properly: you need to tell the runtime linker where to find it. On GNU/Linux, make sure there is a line `/usr/local/lib` in `/etc/ld.so.conf` and run `/sbin/ldconfig` (assuming you installed HDF5 in the default location). + +*Note:* if you installed the [MPI](https://en.wikipedia.org/wiki/Message_Passing_Interface) (parallel) version of HDF5, you may get an error like `/usr/include/H5public.h:53:20: error: mpi.h: No such file or directory`. This can be fixed by telling the compiler where to find the MPI header files, e.g. via: `./configure CC=mpicc`. + +# h5utils Programs + +The included utilities are: + +* **h5totxt** and **h5fromtxt**: convert HDF5 datasets to/from ASCII text (e.g. comma- or tab-delimited). See the manual pages of [h5totxt](doc/h5totxt-man.md) and [h5fromtxt](doc/h5fromtxt-man.md) for more information. +* **h5topng**: convert 2d slices of HDF5 datasets to PNG images, with a variety of color tables and other options. See the [h5topng manual page](doc/h5topng-man.md) for more information. See [Color tables in h5topng](doc/h5topng-colors.md) for information on the color tables. +* **h5tov5d**: convert HDF5 datasets to the format used by the free 3d+ visualization tool [Vis5d](http://www.ssec.wisc.edu/~billh/vis5d.html). See the [manual page](doc/h5tov5d-man.md) for more information. **Note**: to install h5tov5d you must have first compiled Vis5d, and you must specify `--with-v5d=dir` to the h5utils `configure` script to specify the location `dir` of the Vis5d source directory. +* **h5tovtk**: convert HDF5 datasets to VTK format for use by the free [Visualization ToolKit](http://public.kitware.com/VTK/) (along with supporting programs like [MayaVi](http://mayavi.sourceforge.net/)). See the [manual page](doc/h5tovtk-man.md) for more information. +* **h5math**: create and combine HDF5 datasets with simple (pointwise) mathematical expressions. (Requires [GNU libmatheval](http://www.gnu.org/software/libmatheval/) to be installed.) See the [manual page](doc/h5math-man.md) for more information. +* **h5read.oct**: a plug-in for [GNU Octave](http://www.octave.org/) (a Matlab-like program) to read 2d slices of HDF5 datasets. (Recent versions of Octave also include native support for HDF5, although it can't read slices like the `h5read` plug-in.) +* **h5fromh4** and **h4fromh5**: convert HDF (version 4) datasets to and from HDF5. These utilities are nowadays somewhat redundant with the [h4toh5](http://hdfgroup.com/h4toh5/) and `h5toh4` programs provided by NCSA and the HDF Group (which are no longer bundled with HDF5, however). See the [h5fromh4](doc/h5fromh4-man.md) and [h4fromh5](doc/h4fromh5-man.md) manual pages for more information. + +To convert HDF5 to [CDF](http://nssdc.gsfc.nasa.gov/cdf/cdf_home.html) format, see the [hdf5-to-cdf](http://nssdc.gsfc.nasa.gov/cdf/html/FAQ.html#hdf5tocdf) program. + +# License and Copyright + +h5utils is Copyright © 1999–2023 Massachusetts Institute of Technology. + +*The following [MIT/expat license](https://opensource.org/licenses/MIT) governs the entire contents of h5utils except for the `h5tov5d.c` file. See below.* + +> Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: +> +>The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. +> +>THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. + +*The file `h5tov5d.c` and the resulting `h5tov5d` binary are under the following different license, the [GNU GPL](http://www.gnu.org/copyleft/gpl.html) since they link with files from the GPL-covered Vis5d:* + +>This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. +> +>This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. +> +>You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA. You can also find it on the GNU web site: http://www.gnu.org/copyleft/gpl.html diff -Nru h5utils-1.13.1/writepng.c h5utils-1.13.2/writepng.c --- h5utils-1.13.1/writepng.c 2017-07-18 18:48:25.000000000 +0000 +++ h5utils-1.13.2/writepng.c 2023-01-15 20:12:37.000000000 +0000 @@ -1,4 +1,4 @@ -/* Copyright (c) 1999-2017 Massachusetts Institute of Technology +/* Copyright (c) 1999-2023 Massachusetts Institute of Technology * * Permission is hereby granted, free of charge, to any person obtaining * a copy of this software and associated documentation files (the diff -Nru h5utils-1.13.1/writepng.h h5utils-1.13.2/writepng.h --- h5utils-1.13.1/writepng.h 2017-07-18 18:48:25.000000000 +0000 +++ h5utils-1.13.2/writepng.h 2023-01-15 20:12:37.000000000 +0000 @@ -1,4 +1,4 @@ -/* Copyright (c) 1999-2017 Massachusetts Institute of Technology +/* Copyright (c) 1999-2023 Massachusetts Institute of Technology * * Permission is hereby granted, free of charge, to any person obtaining * a copy of this software and associated documentation files (the