Problem with reading int (H5T_STD_I32LE) data from hdf5 file
Mattias Linde
linde at acc.umu.se
Wed Mar 4 08:00:38 CST 2009
To: bug at octave.org
Cc: linde at acc.umu.se
Subject: Problem with reading int (H5T_STD_I32LE) data from hdf5 file
--------
Bug report for Octave 3.0.0 configured for x86_64-pc-linux-gnu
Description:
-----------
I have a hdf5 file with some data. The interesting stuff is one
sparse matrix and three int vectors.
The sparse matrix is read correctly.
The first int vector is read correctly.
The second and third int vector is read as float.
With the hdf5 utilities the data in the file looks correct.
I've used other utils (such as ViTables) to look at the data
and then see it as expected.
The octave version used right now is an ubuntu prebuilt one,
I did build 3.0.3 from source earlier today myself and had
the same problems with loading the h5-file.
Repeat-By:
---------
Use attached hdf5 file with testdata in octave:
1> load bug.h5;
2> Skeleton.Dimension
3> Skeleton.Permutation
4> Skeleton.InversePermutation
The first vector (Dimension) will be seen as ints (correctly).
Permutation and InversePermutation will be presented as floating point
numbers which is incorrect.
Also, the first numbers are 0 instead of the actual values they should have.
The data in the vector contains one 0 and after that number, the values
are correct.
Eg.
DATASET "value" {
DATATYPE H5T_STD_I32LE
DATASPACE SIMPLE { ( 42, 1 ) / ( 42, 1 ) }
DATA {
(0,0): 15,
(1,0): 16,
(2,0): 2,
(3,0): 17,
(4,0): 19,
(5,0): 0,
(6,0): 30,
(7,0): 3,
Will be seen as
Columns 1 through 21:
0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 30.00000 3.00000 18.00000
29.00000 1.00000 32.00000 20.00000 4.00000 36.00000 21.00000 5.00000 38.00000
22.00000 6.00000 34.00000
Fix:
---
Sorry, don't have one.
Configuration (please do not edit this section):
-----------------------------------------------
uname output: Linux a3 2.6.24-22-generic #1 SMP Mon Nov 24 19:35:06 UTC 2008 x86_64 GNU/Linux
configure opts: '--host=x86_64-linux-gnu' '--build=x86_64-linux-gnu' '--prefix=/usr' '--datadir=/usr/share' '--libdir=/usr/lib' '--libexecdir=/usr/lib' '--infodir=/usr/share/info' '--mandir=/usr/share/man' '--with-blas=-lblas-3gf' '--with-lapack=-llapackgf-3' '--with-hdf5' '--with-fftw' '--enable-shared' '--enable-rpath' '--disable-static' 'build_alias=x86_64-linux-gnu' 'host_alias=x86_64-linux-gnu' 'CC=gcc' 'CFLAGS=-g -O2' 'LDFLAGS=-Wl,-Bsymbolic-functions' 'CPPFLAGS=' 'CXX=g++' 'CXXFLAGS=-g -O2' 'F77=gfortran' 'FFLAGS=-g -O2'
Fortran compiler: gfortran
FFLAGS: -O2
F2C: @F2C@
F2CFLAGS: @F2CFLAGS@
FLIBS: -L/usr/lib/gcc/x86_64-linux-gnu/4.2.3 -L/usr/lib/gcc/x86_64-linux-gnu/4.2.3/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-linux-gnu/4.2.3/../../.. -lhdf5 -lz -lgfortranbegin -lgfortran -lm
CPPFLAGS:
INCFLAGS: -I. -I. -I./liboctave -I./src -I./libcruft/misc
C compiler: gcc, version 4.2.3 (Ubuntu 4.2.3-2ubuntu6)
CFLAGS: -O2
CPICFLAG: -fPIC
C++ compiler: g++, version 4.2.3
CXXFLAGS: -O2
CXXPICFLAG: -fPIC
LD_CXX: g++
LDFLAGS:
LIBFLAGS: -L.
RLD_FLAG: -Wl,-rpath -Wl,/usr/lib/octave-3.0.0
BLAS_LIBS: -llapackgf-3 -lblas-3gf
FFTW_LIBS: -lfftw3
LIBS: -lreadline -lncurses -ldl -lhdf5 -lz -lm
LEXLIB:
LIBGLOB:
SED: /bin/sed
DEFS:
-DPACKAGE_NAME="" -DPACKAGE_TARNAME="" -DPACKAGE_VERSION=""
-DPACKAGE_STRING="" -DPACKAGE_BUGREPORT="" -DOCTAVE_SOURCE=1
-D_GNU_SOURCE=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1
-DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1
-DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DSEPCHAR=':'
-DSEPCHAR_STR=":" -D__NO_MATH_INLINES=1 -DCXX_NEW_FRIEND_TEMPLATE_DECL=1
-DCXX_ISO_COMPLIANT_LIBRARY=1 -DCXX_ABI=unknown -DHAVE_LIBM=1
-DHAVE_QHULL=1 -DHAVE_PCRE=1 -DHAVE_REGEXEC=1 -DHAVE_REGEX=1
-DHAVE_ZLIB_H=1 -DHAVE_ZLIB=1 -DHAVE_HDF5_H=1 -DHAVE_HDF5=1
-DHAVE_H5GGET_NUM_OBJS=1 -DHAVE_FFTW3=1 -DHAVE_GLPK_H=1 -DHAVE_GLPK=1
-DHAVE_CURL_CURL_H=1 -DHAVE_CURL=1 -DHAVE_IEEE754_DATA_FORMAT=1
-DF77_FUNC(name,NAME)=name ## _ -DF77_FUNC_(name,NAME)=name ## _
-DHAVE_BLAS=1 -DHAVE_SUITESPARSE_UMFPACK_H=1 -DHAVE_UMFPACK=1
-DUMFPACK_SEPARATE_SPLIT=1 -DHAVE_SUITESPARSE_COLAMD_H=1
-DHAVE_COLAMD=1 -DHAVE_SUITESPARSE_CCOLAMD_H=1 -DHAVE_CCOLAMD=1
-DHAVE_SUITESPARSE_CHOLMOD_H=1 -DHAVE_CHOLMOD=1 -DHAVE_SUITESPARSE_CS_H=1
-DHAVE_CXSPARSE=1 -DHAVE_GETHOSTNAME=1 -DHAVE_GETPWNAM=1 -DHAVE_DEV_T=1
-DHAVE_INO_T=1 -DHAVE_NLINK_T=1 -DHAVE_NLINK_T=1 -DHAVE_LONG_LONG_INT=1
-DHAVE_UNSIGNED_LONG_LONG_INT=1 -DHAVE_SIGSET_T=1 -DHAVE_SIG_ATOMIC_T=1
-DSIZEOF_SHORT=2 -DSIZEOF_INT=4 -DSIZEOF_LONG=8 -DSIZEOF_LONG_LONG=8
-DHAVE_ALLOCA_H=1 -DHAVE_ALLOCA=1 -DNPOS=std::string::npos
-DHAVE_PLACEMENT_DELETE=1 -DHAVE_DYNAMIC_AUTO_ARRAYS=1 -DSTDC_HEADERS=1
-DHAVE_DIRENT_H=1 -DTIME_WITH_SYS_TIME=1 -DHAVE_SYS_WAIT_H=1
-DHAVE_ASSERT_H=1 -DHAVE_CURSES_H=1 -DHAVE_DLFCN_H=1 -DHAVE_FCNTL_H=1
-DHAVE_FLOAT_H=1 -DHAVE_GRP_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_LIMITS_H=1
-DHAVE_LOCALE_H=1 -DHAVE_MEMORY_H=1 -DHAVE_NCURSES_H=1 -DHAVE_POLL_H=1
-DHAVE_PWD_H=1 -DHAVE_STDINT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1
-DHAVE_SYS_IOCTL_H=1 -DHAVE_SYS_PARAM_H=1 -DHAVE_SYS_POLL_H=1
-DHAVE_SYS_RESOURCE_H=1 -DHAVE_SYS_SELECT_H=1 -DHAVE_SYS_STAT_H=1
-DHAVE_SYS_TIME_H=1 -DHAVE_SYS_TIMES_H=1 -DHAVE_SYS_TYPES_H=1
-DHAVE_SYS_UTSNAME_H=1 -DHAVE_TERMCAP_H=1 -DHAVE_UNISTD_H=1
-DHAVE_UTIME_H=1 -DHAVE_SSTREAM=1 -DHAVE_TERMIO_H=1 -DHAVE_SGTTY_H=1
-DHAVE_GLOB_H=1 -DHAVE_FNMATCH_H=1 -DHAVE_FNMATCH=1 -DHAVE_GLOB=1
-DHAVE_ATEXIT=1 -DHAVE_BASENAME=1 -DHAVE_BCOPY=1 -DHAVE_BZERO=1
-DHAVE_CANONICALIZE_FILE_NAME=1 -DHAVE_CHMOD=1 -DHAVE_DUP2=1
-DHAVE_ENDGRENT=1 -DHAVE_ENDPWENT=1 -DHAVE_EXECVP=1 -DHAVE_FCNTL=1
-DHAVE_FORK=1 -DHAVE_GETCWD=1 -DHAVE_GETEGID=1 -DHAVE_GETEUID=1
-DHAVE_GETGID=1 -DHAVE_GETGRENT=1 -DHAVE_GETGRGID=1 -DHAVE_GETGRNAM=1
-DHAVE_GETPGRP=1 -DHAVE_GETPID=1 -DHAVE_GETPPID=1 -DHAVE_GETPWENT=1
-DHAVE_GETPWUID=1 -DHAVE_GETTIMEOFDAY=1 -DHAVE_GETUID=1 -DHAVE_GETWD=1
-DHAVE_KILL=1 -DHAVE_LGAMMA=1 -DHAVE_LINK=1 -DHAVE_LOCALTIME_R=1
-DHAVE_LSTAT=1 -DHAVE_MEMMOVE=1 -DHAVE_MKDIR=1 -DHAVE_MKFIFO=1
-DHAVE_MKSTEMP=1 -DHAVE_ON_EXIT=1 -DHAVE_PIPE=1 -DHAVE_POLL=1
-DHAVE_PUTENV=1 -DHAVE_RAISE=1 -DHAVE_READLINK=1 -DHAVE_REALPATH=1
-DHAVE_RENAME=1 -DHAVE_RINDEX=1 -DHAVE_RMDIR=1 -DHAVE_ROUND=1
-DHAVE_SELECT=1 -DHAVE_SETGRENT=1 -DHAVE_SETLOCALE=1
-DHAVE_SETPWENT=1 -DHAVE_SETVBUF=1 -DHAVE_SIGACTION=1
-DHAVE_SIGLONGJMP=1 -DHAVE_SIGPENDING=1 -DHAVE_SIGPROCMASK=1
-DHAVE_SIGSUSPEND=1 -DHAVE_SNPRINTF=1 -DHAVE_STAT=1 -DHAVE_STRCASECMP=1
-DHAVE_STRDUP=1 -DHAVE_STRERROR=1 -DHAVE_STRNCASECMP=1 -DHAVE_STRPTIME=1
-DHAVE_STRSIGNAL=1 -DHAVE_SYMLINK=1 -DHAVE_TEMPNAM=1 -DHAVE_TGAMMA=1
-DHAVE_UMASK=1 -DHAVE_UNAME=1 -DHAVE_UNLINK=1 -DHAVE_USLEEP=1
-DHAVE_UTIME=1 -DHAVE_VFPRINTF=1 -DHAVE_VSPRINTF=1 -DHAVE_VSNPRINTF=1
-DHAVE_WAITPID=1 -DHAVE_STRFTIME=1 -DHAVE_LIBDL=1 -DHAVE_DLOPEN=1
-DHAVE_DLSYM=1 -DHAVE_DLERROR=1 -DHAVE_DLCLOSE=1 -DHAVE_DLOPEN_API=1
-DENABLE_DYNAMIC_LINKING=1 -DHAVE_TIMEVAL=1 -DHAVE_FINITE=1
-DHAVE_ISNAN=1 -DHAVE_ISINF=1 -DHAVE_COPYSIGN=1 -DHAVE_DECL_SIGNBIT=1
-DHAVE_ACOSH=1 -DHAVE_ASINH=1 -DHAVE_ATANH=1 -DHAVE_ERF=1 -DHAVE_ERFC=1
-DHAVE_EXP2=1 -DHAVE_LOG2=1 -DHAVE_STRUCT_STAT_ST_BLKSIZE=1
-DHAVE_STRUCT_STAT_ST_BLOCKS=1 -DHAVE_STRUCT_STAT_ST_RDEV=1
-DHAVE_STRUCT_TM_TM_ZONE=1 -DHAVE_TM_ZONE=1 -DUSE_READLINE=1
-DEXCEPTION_IN_MATH=1 -DRETSIGTYPE=void -DHAVE_DECL_SYS_SIGLIST=1
-DHAVE_POSIX_SIGNALS=1 -DRETSIGTYPE_IS_VOID=1 -DHAVE_GETRUSAGE=1
-DHAVE_TIMES=1 -DYYTEXT_POINTER=1 -DGNUPLOT_BINARY="gnuplot"
User-preferences (please do not edit this section):
--------------------------------------------------
EDITOR = vim
EXEC_PATH = /usr/lib/octave/3.0.0/site/exec/x86_64-pc-linux-gnu:/usr/lib/octave/api-v32/site/exec/x86_64-pc-linux-gnu:/usr/lib/octave/site/exec/x86_64-pc-linux-gnu:/usr/lib/octave/3.0.0/exec/x86_64-pc-linux-gnu:/usr/bin:/home/linde/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:.:/home/linde/bin
IMAGE_PATH = .:/usr/share/octave/3.0.0/imagelib
PAGER = pager
PS1 = \s:\#>
PS2 = >
PS4 = +
beep_on_error = 0
completion_append_char =
crash_dumps_octave_core = 1
echo_executing_commands = 0
fixed_point_format = 0
gnuplot_binary = gnuplot
gnuplot_command_end =
gnuplot_command_plot = pl
gnuplot_command_replot = rep
gnuplot_command_splot = sp
gnuplot_command_title = t
gnuplot_command_using = u
gnuplot_command_with = w
history_file = /home/linde/.octave_hist
history_size = 1024
ignore_function_time_stamp = system
info_file = /usr/share/info/octave3.0.info
info_program = info
makeinfo_program = makeinfo
max_recursion_depth = 256
output_max_field_width = 5
output_precision = 5
page_output_immediately = 0
page_screen_output = 1
print_answer_id_name = 1
print_empty_dimensions = 1
save_precision = 16
saving_history = 1
sighup_dumps_octave_core = 1
sigterm_dumps_octave_core = 1
silent_functions = 0
split_long_rows = 1
string_fill_char =
struct_levels_to_print = 2
suppress_verbose_help_message = 0
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