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first implementation of HDF5 format

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Antonin Portelli 2015-10-01 00:13:34 +01:00 committed by Antonin Portelli
parent c672c33189
commit 5e3247697d
17 changed files with 932 additions and 70 deletions
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307
acinclude.m4
View File

@ -232,4 +232,311 @@ AC_DEFUN([AX_CXX_COMPILE_STDCXX_11], [dnl
fi
])
# ===========================================================================
# http://www.gnu.org/software/autoconf-archive/ax_lib_hdf5.html
# ===========================================================================
#
# SYNOPSIS
#
# AX_LIB_HDF5([serial/parallel])
#
# DESCRIPTION
#
# This macro provides tests of the availability of HDF5 library.
#
# The optional macro argument should be either 'serial' or 'parallel'. The
# former only looks for serial HDF5 installations via h5cc. The latter
# only looks for parallel HDF5 installations via h5pcc. If the optional
# argument is omitted, serial installations will be preferred over
# parallel ones.
#
# The macro adds a --with-hdf5 option accepting one of three values:
#
# no - do not check for the HDF5 library.
# yes - do check for HDF5 library in standard locations.
# path - complete path to the HDF5 helper script h5cc or h5pcc.
#
# If HDF5 is successfully found, this macro calls
#
# AC_SUBST(HDF5_VERSION)
# AC_SUBST(HDF5_CC)
# AC_SUBST(HDF5_CFLAGS)
# AC_SUBST(HDF5_CPPFLAGS)
# AC_SUBST(HDF5_LDFLAGS)
# AC_SUBST(HDF5_LIBS)
# AC_SUBST(HDF5_FC)
# AC_SUBST(HDF5_FFLAGS)
# AC_SUBST(HDF5_FLIBS)
# AC_DEFINE(HAVE_HDF5)
#
# and sets with_hdf5="yes". Additionally, the macro sets
# with_hdf5_fortran="yes" if a matching Fortran wrapper script is found.
# Note that Autconf's Fortran support is not used to perform this check.
# H5CC and H5FC will contain the appropriate serial or parallel HDF5
# wrapper script locations.
#
# If HDF5 is disabled or not found, this macros sets with_hdf5="no" and
# with_hdf5_fortran="no".
#
# Your configuration script can test $with_hdf to take any further
# actions. HDF5_{C,CPP,LD}FLAGS may be used when building with C or C++.
# HDF5_F{FLAGS,LIBS} should be used when building Fortran applications.
#
# To use the macro, one would code one of the following in "configure.ac"
# before AC_OUTPUT:
#
# 1) dnl Check for HDF5 support
# AX_LIB_HDF5()
#
# 2) dnl Check for serial HDF5 support
# AX_LIB_HDF5([serial])
#
# 3) dnl Check for parallel HDF5 support
# AX_LIB_HDF5([parallel])
#
# One could test $with_hdf5 for the outcome or display it as follows
#
# echo "HDF5 support: $with_hdf5"
#
# You could also for example, override the default CC in "configure.ac" to
# enforce compilation with the compiler that HDF5 uses:
#
# AX_LIB_HDF5([parallel])
# if test "$with_hdf5" = "yes"; then
# CC="$HDF5_CC"
# else
# AC_MSG_ERROR([Unable to find HDF5, we need parallel HDF5.])
# fi
#
# LICENSE
#
# Copyright (c) 2009 Timothy Brown <tbrown@freeshell.org>
# Copyright (c) 2010 Rhys Ulerich <rhys.ulerich@gmail.com>
#
# Copying and distribution of this file, with or without modification, are
# permitted in any medium without royalty provided the copyright notice
# and this notice are preserved. This file is offered as-is, without any
# warranty.
AC_DEFUN([AX_LIB_HDF5], [
AC_REQUIRE([AC_PROG_SED])
AC_REQUIRE([AC_PROG_AWK])
AC_REQUIRE([AC_PROG_GREP])
dnl Check first argument is one of the recognized values.
dnl Fail eagerly if is incorrect as this simplifies case statements below.
if test "m4_normalize(m4_default([$1],[]))" = "" ; then
: # Recognized value
elif test "m4_normalize(m4_default([$1],[]))" = "serial" ; then
: # Recognized value
elif test "m4_normalize(m4_default([$1],[]))" = "parallel"; then
: # Recognized value
else
AC_MSG_ERROR([
Unrecognized value for AX[]_LIB_HDF5 within configure.ac.
If supplied, argument 1 must be either 'serial' or 'parallel'.
])
fi
dnl Add a default --with-hdf5 configuration option.
AC_ARG_WITH([hdf5],
AS_HELP_STRING(
[--with-hdf5=[yes/no/PATH]],
m4_case(m4_normalize([$1]),
[serial], [location of h5cc for serial HDF5 configuration],
[parallel], [location of h5pcc for parallel HDF5 configuration],
[location of h5cc or h5pcc for HDF5 configuration])
),
[if test "$withval" = "no"; then
with_hdf5="no"
elif test "$withval" = "yes"; then
with_hdf5="yes"
else
with_hdf5="yes"
H5CC="$withval"
fi],
[with_hdf5="yes"]
)
dnl Set defaults to blank
HDF5_CC=""
HDF5_VERSION=""
HDF5_CFLAGS=""
HDF5_CPPFLAGS=""
HDF5_LDFLAGS=""
HDF5_LIBS=""
HDF5_FC=""
HDF5_FFLAGS=""
HDF5_FLIBS=""
dnl Try and find hdf5 compiler tools and options.
if test "$with_hdf5" = "yes"; then
if test -z "$H5CC"; then
dnl Check to see if H5CC is in the path.
AC_PATH_PROGS(
[H5CC],
m4_case(m4_normalize([$1]),
[serial], [h5cc],
[parallel], [h5pcc],
[h5cc h5pcc]),
[])
else
AC_MSG_CHECKING([Using provided HDF5 C wrapper])
AC_MSG_RESULT([$H5CC])
fi
AC_MSG_CHECKING([for HDF5 libraries])
if test ! -f "$H5CC" || test ! -x "$H5CC"; then
AC_MSG_RESULT([no])
AC_MSG_WARN(m4_case(m4_normalize([$1]),
[serial], [
Unable to locate serial HDF5 compilation helper script 'h5cc'.
Please specify --with-hdf5=<LOCATION> as the full path to h5cc.
HDF5 support is being disabled (equivalent to --with-hdf5=no).
], [parallel],[
Unable to locate parallel HDF5 compilation helper script 'h5pcc'.
Please specify --with-hdf5=<LOCATION> as the full path to h5pcc.
HDF5 support is being disabled (equivalent to --with-hdf5=no).
], [
Unable to locate HDF5 compilation helper scripts 'h5cc' or 'h5pcc'.
Please specify --with-hdf5=<LOCATION> as the full path to h5cc or h5pcc.
HDF5 support is being disabled (equivalent to --with-hdf5=no).
]))
with_hdf5="no"
with_hdf5_fortran="no"
else
dnl Get the h5cc output
HDF5_SHOW=$(eval $H5CC -show)
dnl Get the actual compiler used
HDF5_CC=$(eval $H5CC -show | $AWK '{print $[]1}')
if test "$HDF5_CC" = "ccache"; then
HDF5_CC=$(eval $H5CC -show | $AWK '{print $[]2}')
fi
dnl h5cc provides both AM_ and non-AM_ options
dnl depending on how it was compiled either one of
dnl these are empty. Lets roll them both into one.
dnl Look for "HDF5 Version: X.Y.Z"
HDF5_VERSION=$(eval $H5CC -showconfig | $GREP 'HDF5 Version:' \
| $AWK '{print $[]3}')
dnl A ideal situation would be where everything we needed was
dnl in the AM_* variables. However most systems are not like this
dnl and seem to have the values in the non-AM variables.
dnl
dnl We try the following to find the flags:
dnl (1) Look for "NAME:" tags
dnl (2) Look for "H5_NAME:" tags
dnl (3) Look for "AM_NAME:" tags
dnl
HDF5_tmp_flags=$(eval $H5CC -showconfig \
| $GREP 'FLAGS\|Extra libraries:' \
| $AWK -F: '{printf("%s "), $[]2}' )
dnl Find the installation directory and append include/
HDF5_tmp_inst=$(eval $H5CC -showconfig \
| $GREP 'Installation point:' \
| $AWK '{print $[]NF}' )
dnl Add this to the CPPFLAGS
HDF5_CPPFLAGS="-I${HDF5_tmp_inst}/include"
dnl Now sort the flags out based upon their prefixes
for arg in $HDF5_SHOW $HDF5_tmp_flags ; do
case "$arg" in
-I*) echo $HDF5_CPPFLAGS | $GREP -e "$arg" 2>&1 >/dev/null \
|| HDF5_CPPFLAGS="$arg $HDF5_CPPFLAGS"
;;
-L*) echo $HDF5_LDFLAGS | $GREP -e "$arg" 2>&1 >/dev/null \
|| HDF5_LDFLAGS="$arg $HDF5_LDFLAGS"
;;
-l*) echo $HDF5_LIBS | $GREP -e "$arg" 2>&1 >/dev/null \
|| HDF5_LIBS="$arg $HDF5_LIBS"
;;
esac
done
HDF5_LIBS="$HDF5_LIBS -lhdf5"
AC_MSG_RESULT([yes (version $[HDF5_VERSION])])
dnl See if we can compile
ax_lib_hdf5_save_CC=$CC
ax_lib_hdf5_save_CPPFLAGS=$CPPFLAGS
ax_lib_hdf5_save_LIBS=$LIBS
ax_lib_hdf5_save_LDFLAGS=$LDFLAGS
CC=$HDF5_CC
CPPFLAGS=$HDF5_CPPFLAGS
LIBS=$HDF5_LIBS
LDFLAGS=$HDF5_LDFLAGS
AC_CHECK_HEADER([hdf5.h], [ac_cv_hadf5_h=yes], [ac_cv_hadf5_h=no])
AC_CHECK_LIB([hdf5], [H5Fcreate], [ac_cv_libhdf5=yes],
[ac_cv_libhdf5=no])
if test "$ac_cv_hadf5_h" = "no" && test "$ac_cv_libhdf5" = "no" ; then
AC_MSG_WARN([Unable to compile HDF5 test program])
fi
dnl Look for HDF5's high level library
AC_HAVE_LIBRARY([hdf5_hl], [HDF5_LIBS="$HDF5_LIBS -lhdf5_hl"], [], [])
CC=$ax_lib_hdf5_save_CC
CPPFLAGS=$ax_lib_hdf5_save_CPPFLAGS
LIBS=$ax_lib_hdf5_save_LIBS
LDFLAGS=$ax_lib_hdf5_save_LDFLAGS
AC_MSG_CHECKING([for matching HDF5 Fortran wrapper])
dnl Presume HDF5 Fortran wrapper is just a name variant from H5CC
H5FC=$(eval echo -n $H5CC | $SED -n 's/cc$/fc/p')
if test -x "$H5FC"; then
AC_MSG_RESULT([$H5FC])
with_hdf5_fortran="yes"
AC_SUBST([H5FC])
dnl Again, pry any remaining -Idir/-Ldir from compiler wrapper
for arg in `$H5FC -show`
do
case "$arg" in #(
-I*) echo $HDF5_FFLAGS | $GREP -e "$arg" >/dev/null \
|| HDF5_FFLAGS="$arg $HDF5_FFLAGS"
;;#(
-L*) echo $HDF5_FFLAGS | $GREP -e "$arg" >/dev/null \
|| HDF5_FFLAGS="$arg $HDF5_FFLAGS"
dnl HDF5 installs .mod files in with libraries,
dnl but some compilers need to find them with -I
echo $HDF5_FFLAGS | $GREP -e "-I${arg#-L}" >/dev/null \
|| HDF5_FFLAGS="-I${arg#-L} $HDF5_FFLAGS"
;;
esac
done
dnl Make Fortran link line by inserting Fortran libraries
for arg in $HDF5_LIBS
do
case "$arg" in #(
-lhdf5_hl) HDF5_FLIBS="$HDF5_FLIBS -lhdf5hl_fortran $arg"
;; #(
-lhdf5) HDF5_FLIBS="$HDF5_FLIBS -lhdf5_fortran $arg"
;; #(
*) HDF5_FLIBS="$HDF5_FLIBS $arg"
;;
esac
done
else
AC_MSG_RESULT([no])
with_hdf5_fortran="no"
fi
AC_SUBST([HDF5_VERSION])
AC_SUBST([HDF5_CC])
AC_SUBST([HDF5_CFLAGS])
AC_SUBST([HDF5_CPPFLAGS])
AC_SUBST([HDF5_LDFLAGS])
AC_SUBST([HDF5_LIBS])
AC_SUBST([HDF5_FC])
AC_SUBST([HDF5_FFLAGS])
AC_SUBST([HDF5_FLIBS])
AC_DEFINE([HAVE_HDF5], [1], [Defined if you have HDF5 support])
fi
fi
])

12
configure.ac
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@ -58,10 +58,14 @@ AC_ARG_WITH([LatCore],
[AM_LDFLAGS="$AM_LDFLAGS -L$with_LatCore/lib"],
[]
)
CFLAGS="$AM_CFLAGS $CFLAGS"
CXXFLAGS="$AM_CXXFLAGS $CXXFLAGS"
LDFLAGS="$AM_LDFLAGS $LDFLAGS"
AX_LIB_HDF5()
if test x$with_hdf5 = xno; then
AC_MSG_ERROR([HDF5 library not found])
fi
CFLAGS="$AM_CFLAGS $HDF5_CFLAGS $CFLAGS"
CXXFLAGS="$AM_CXXFLAGS $HDF5_CPPFLAGS $CXXFLAGS"
LDFLAGS="$AM_LDFLAGS $HDF5_LDFLAGS $LDFLAGS"
LIBS="$LIBS $HDF5_LIBS -lhdf5_cpp"
# Get compilers informations
AX_COMPILER_VENDOR

15
examples/exMat.cpp
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@ -1,5 +1,5 @@
#include <iostream>
#include <LatAnalyze/AsciiFile.hpp>
#include <LatAnalyze/Io.hpp>
#include <LatAnalyze/Mat.hpp>
#include <LatAnalyze/Math.hpp>
@ -8,9 +8,8 @@ using namespace Latan;
int main(void)
{
AsciiFile F;
DMat A(2, 3), B(3, 2);
const string fileName = "exMat.dat";
const string fileName = "exMat.h5";
A << 1, 2, 3,
4, 5, 6;
@ -26,9 +25,11 @@ int main(void)
cout << "cos(A)=\n" << A.unaryExpr(StdMath::cos) << '\n' << endl;
// write
cout << "-- saving A*B..." << endl;
F.open(fileName, File::Mode::append);
F.save(A*B, "AB");
cout << "-- saving and loading A*B using '" + fileName + "'..." << endl;
Io::save(A*B, fileName, File::Mode::write, "AB");
DMat C = Io::load<DMat>(fileName);
cout << C << endl;
return EXIT_SUCCESS;
}

2
examples/exRand.cpp
View File

@ -1,5 +1,5 @@
#include <iostream>
#include <LatAnalyze/AsciiFile.hpp>
#include <LatAnalyze/Io.hpp>
#include <LatAnalyze/CompiledFunction.hpp>
#include <LatAnalyze/Plot.hpp>
#include <LatAnalyze/RandGen.hpp>

12
lib/AsciiFile.cpp
View File

@ -89,6 +89,12 @@ void AsciiFile::save(const RandGenState &state, const std::string &name)
fileStream_ << "#L latan_end rg_state " << endl;
}
// read first name ////////////////////////////////////////////////////////////
string AsciiFile::getFirstName(void)
{
return load();
}
// tests ///////////////////////////////////////////////////////////////////////
bool AsciiFile::isOpen() const
{
@ -118,7 +124,9 @@ void AsciiFile::open(const string &name, const unsigned int mode)
else
{
ios_base::openmode stdMode = static_cast<ios_base::openmode>(0);
name_ = name;
mode_ = mode;
if (mode & Mode::write)
{
stdMode |= ios::out|ios::trunc;
@ -131,8 +139,6 @@ void AsciiFile::open(const string &name, const unsigned int mode)
{
stdMode |= ios::out|ios::app;
}
name_ = name;
mode_ = mode;
isParsed_ = false;
fileStream_.open(name_.c_str(), stdMode);
if (mode_ & Mode::read)

3
lib/AsciiFile.hpp
View File

@ -24,6 +24,7 @@
#include <LatAnalyze/File.hpp>
#include <LatAnalyze/Mat.hpp>
#include <LatAnalyze/MatSample.hpp>
#include <LatAnalyze/ParserState.hpp>
#include <LatAnalyze/RandGen.hpp>
#include <fstream>
@ -67,6 +68,8 @@ public:
virtual void save(const DMat &m, const std::string &name);
virtual void save(const DMatSample &s, const std::string &name);
virtual void save(const RandGenState &state, const std::string &name);
// read first name
virtual std::string getFirstName(void);
// tests
virtual bool isOpen(void) const;
// IO

40
lib/File.hpp
View File

@ -17,12 +17,11 @@
* along with LatAnalyze 3. If not, see <http://www.gnu.org/licenses/>.
*/
#ifndef Latan_Io_hpp_
#define Latan_Io_hpp_
#ifndef Latan_File_hpp_
#define Latan_File_hpp_
#include <LatAnalyze/Global.hpp>
#include <LatAnalyze/IoObject.hpp>
#include <LatAnalyze/ParserState.hpp>
#include <LatAnalyze/Mat.hpp>
#include <LatAnalyze/MatSample.hpp>
#include <LatAnalyze/RandGen.hpp>
@ -64,6 +63,8 @@ public:
virtual void save(const DMat &m, const std::string &name) = 0;
virtual void save(const DMatSample &state, const std::string &name) = 0;
virtual void save(const RandGenState &state, const std::string &name) = 0;
// read first name
virtual std::string getFirstName(void) = 0;
// tests
virtual bool isOpen(void) const = 0;
// IO
@ -114,39 +115,6 @@ const IoT& File::getData(const std::string &name) const
}
}
/******************************************************************************
* Static IO functions *
******************************************************************************/
class Io
{
public:
template <typename IoT, typename FileType>
static IoT load(const std::string &fileName, const std::string &name = "");
template <typename IoT, typename FileType>
static void save(const IoT &data, const std::string &fileName,
const unsigned int mode = File::Mode::write,
const std::string &name = "");
};
// template implementation /////////////////////////////////////////////////////
template <typename IoT, typename FileType>
IoT Io::load(const std::string &fileName, const std::string &name)
{
FileType file(fileName, File::Mode::read);
return file.template read<IoT>(name);
}
template <typename IoT, typename FileType>
void Io::save(const IoT &data, const std::string &fileName,
const unsigned int mode, const std::string &name)
{
FileType file(fileName, mode);
std::string realName = (name.empty()) ? fileName : name;
file.save(data, realName);
}
END_LATAN_NAMESPACE
#endif

315
lib/Hdf5File.cpp Normal file
View File

@ -0,0 +1,315 @@
/*
* Hdf5File.cpp, part of LatAnalyze 3
*
* Copyright (C) 2013 - 2015 Antonin Portelli
*
* LatAnalyze 3 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 3 of the License, or
* (at your option) any later version.
*
* LatAnalyze 3 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 LatAnalyze 3. If not, see <http://www.gnu.org/licenses/>.
*/
#include <LatAnalyze/Hdf5File.hpp>
#include <LatAnalyze/IoObject.hpp>
#include <LatAnalyze/includes.hpp>
using namespace std;
using namespace Latan;
#ifndef H5_NO_NAMESPACE
using namespace H5NS;
#endif
constexpr unsigned int maxGroupNameSize = 1024u;
const short dMatType = static_cast<short>(IoObject::IoType::dMat);
const short dMatSampleType = static_cast<short>(IoObject::IoType::dMatSample);
const short rgStateType = static_cast<short>(IoObject::IoType::rgState);
/******************************************************************************
* Hdf5File implementation *
******************************************************************************/
// constructors ////////////////////////////////////////////////////////////////
Hdf5File::Hdf5File(void)
{}
Hdf5File::Hdf5File(const std::string &name, const unsigned int mode)
{
open(name, mode);
}
// destructor //////////////////////////////////////////////////////////////////
Hdf5File::~Hdf5File(void)
{
close();
}
// access //////////////////////////////////////////////////////////////////////
void Hdf5File::save(const DMat &m, const string &name)
{
Group group;
Attribute attr;
DataSet dataset;
hsize_t dim[2] = {static_cast<hsize_t>(m.rows()),
static_cast<hsize_t>(m.cols())};
hsize_t attrDim = 1;
DataSpace dataSpace(2, dim), attrSpace(1, &attrDim);
group = h5File_->createGroup(name.c_str());
attr = group.createAttribute("type", PredType::NATIVE_SHORT, attrSpace);
attr.write(PredType::NATIVE_SHORT, &dMatType);
dataset = group.createDataSet("data", PredType::NATIVE_DOUBLE, dataSpace);
dataset.write(m.data(), PredType::NATIVE_DOUBLE);
}
void Hdf5File::save(const DMatSample &sample, const string &name)
{
Group group;
Attribute attr;
DataSet dataset;
hsize_t dim[2] = {static_cast<hsize_t>(sample[central].rows()),
static_cast<hsize_t>(sample[central].cols())};
hsize_t attrDim = 1;
DataSpace dataSpace(2, dim), attrSpace(1, &attrDim);
const long int nSample = sample.size();
string datasetName;
group = h5File_->createGroup(name.c_str());
attr = group.createAttribute("type", PredType::NATIVE_SHORT, attrSpace);
attr.write(PredType::NATIVE_SHORT, &dMatSampleType);
attr = group.createAttribute("nSample", PredType::NATIVE_LONG, attrSpace);
attr.write(PredType::NATIVE_LONG, &nSample);
FOR_STAT_ARRAY(sample, s)
{
datasetName = (s == central) ? "data_C" : ("data_S_" + strFrom(s));
dataset = group.createDataSet(datasetName, PredType::NATIVE_DOUBLE,
dataSpace);
dataset.write(sample[s].data(), PredType::NATIVE_DOUBLE);
}
}
void Hdf5File::save(const RandGenState &state, const string &name)
{
Group group;
Attribute attr;
DataSet dataset;
hsize_t dim = RLXG_STATE_SIZE;
hsize_t attrDim = 1;
DataSpace dataSpace(1, &dim), attrSpace(1, &attrDim);
group = h5File_->createGroup(name.c_str());
attr = group.createAttribute("type", PredType::NATIVE_SHORT, attrSpace);
attr.write(PredType::NATIVE_SHORT, &rgStateType);
dataset = group.createDataSet("data", PredType::NATIVE_DOUBLE, dataSpace);
dataset.write(state.data(), PredType::NATIVE_DOUBLE);
}
// read first name ////////////////////////////////////////////////////////////
string Hdf5File::getFirstName(void)
{
return getFirstGroupName();
}
// tests ///////////////////////////////////////////////////////////////////////
bool Hdf5File::isOpen(void) const
{
return (h5File_ != nullptr);
}
// IO //////////////////////////////////////////////////////////////////////////
void Hdf5File::close(void)
{
if (isOpen())
{
h5File_->close();
}
h5File_.reset(nullptr);
name_ = "";
mode_ = Mode::null;
deleteData();
}
void Hdf5File::open(const string &name, const unsigned int mode)
{
if (isOpen())
{
LATAN_ERROR(Io, "file already opened with name '" + name_ + "'");
}
else
{
unsigned int h5Mode = 0;
name_ = name;
mode_ = mode;
if (mode & Mode::write)
{
h5Mode |= H5F_ACC_TRUNC;
}
if (mode & Mode::read)
{
h5Mode |= H5F_ACC_RDONLY;
}
if (mode & Mode::append)
{
h5Mode |= H5F_ACC_RDWR|H5F_ACC_CREAT;
}
h5File_.reset(new H5File(name_.c_str(), h5Mode));
}
}
string Hdf5File::getFirstGroupName(void)
{
string res;
if ((mode_ & Mode::read)&&(isOpen()))
{
auto firstGroupName = [](hid_t loc_id, const char *name, void *fname)
{
H5G_stat_t statbuf;
H5Gget_objinfo(loc_id, name, 0, &statbuf);
if ((statbuf.type == H5G_GROUP) && (strlen((char *)fname) == 0))
{
strncpy((char *)fname, name, maxGroupNameSize);
}
return 0;
};
char groupName[maxGroupNameSize];
h5File_->iterateElems("/", nullptr, firstGroupName, groupName);
res = groupName;
}
else
{
if (isOpen())
{
LATAN_ERROR(Io, "file '" + name_ + "' is not opened in read mode");
}
else
{
LATAN_ERROR(Io, "file '" + name_ + "' is not opened");
}
return "";
}
return res;
}
void Hdf5File::load(DMat &m, const DataSet &d)
{
DataSpace dataspace;
hsize_t dim[2];
dataspace = d.getSpace();
dataspace.getSimpleExtentDims(dim);
m.resize(dim[0], dim[1]);
d.read(m.data(), PredType::NATIVE_DOUBLE);
}
void Hdf5File::load(RandGenState &state, const DataSet &d)
{
DataSpace dataspace;
hsize_t dim[1];
dataspace = d.getSpace();
dataspace.getSimpleExtentDims(dim);
if (dim[0] != RLXG_STATE_SIZE)
{
// error here
}
d.read(state.data(), PredType::NATIVE_INT);
}
string Hdf5File::load(const string &name)
{
if ((mode_ & Mode::read)&&(isOpen()))
{
string groupName;
Group group;
Attribute attribute;
DataSet dataset;
IoObject::IoType type;
groupName = (name.empty()) ? getFirstGroupName() : name;
group = h5File_->openGroup(groupName.c_str());
attribute = group.openAttribute("type");
attribute.read(PredType::NATIVE_SHORT, &type);
switch (type)
{
case IoObject::IoType::dMat:
{
DMat *pt = new DMat;
data_[groupName].reset(pt);
dataset = group.openDataSet("data");
load(*pt, dataset);
break;
}
case IoObject::IoType::dMatSample:
{
DMatSample *pt = new DMatSample;
long int nSample;
data_[groupName].reset(pt);
attribute = group.openAttribute("nSample");
attribute.read(PredType::NATIVE_LONG, &nSample);
pt->resize(nSample);
FOR_STAT_ARRAY(*pt, s)
{
if (s == central)
{
dataset = group.openDataSet("data_C");
}
else
{
dataset = group.openDataSet("data_S_" + strFrom(s));
}
load((*pt)[s], dataset);
}
break;
}
case IoObject::IoType::rgState:
{
RandGenState *pt = new RandGenState;
data_[groupName].reset(pt);
dataset = group.openDataSet("data");
load(*pt, dataset);
break;
}
default:
{
LATAN_ERROR(Io, "unknown data type ("
+ strFrom(static_cast<int>(type)) + ") "
" (" + name_ + ":" + groupName + ")");
break;
}
}
return groupName;
}
else
{
if (isOpen())
{
LATAN_ERROR(Io, "file '" + name_ + "' is not opened in read mode");
}
else
{
LATAN_ERROR(Io, "file '" + name_ + "' is not opened");
}
return "";
}
}

72
lib/Hdf5File.hpp Normal file
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@ -0,0 +1,72 @@
/*
* Hdf5File.hpp, part of LatAnalyze 3
*
* Copyright (C) 2013 - 2015 Antonin Portelli
*
* LatAnalyze 3 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 3 of the License, or
* (at your option) any later version.
*
* LatAnalyze 3 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 LatAnalyze 3. If not, see <http://www.gnu.org/licenses/>.
*/
#ifndef Latan_Hdf5File_hpp_
#define Latan_Hdf5File_hpp_
#include <LatAnalyze/Global.hpp>
#include <LatAnalyze/File.hpp>
#include <LatAnalyze/Mat.hpp>
#include <LatAnalyze/MatSample.hpp>
#include <LatAnalyze/RandGen.hpp>
#include <H5Cpp.h>
BEGIN_LATAN_NAMESPACE
#ifndef H5_NO_NAMESPACE
#define H5NS H5
#endif
/******************************************************************************
* HDF5 datafile class *
******************************************************************************/
class Hdf5File: public File
{
public:
// constructors
Hdf5File(void);
Hdf5File(const std::string &name, const unsigned int mode);
// destructor
virtual ~Hdf5File(void);
// access
virtual void save(const DMat &m, const std::string &name);
virtual void save(const DMatSample &s, const std::string &name);
virtual void save(const RandGenState &state, const std::string &name);
// read first name
virtual std::string getFirstName(void);
// tests
virtual bool isOpen(void) const;
// IO
virtual void close(void);
virtual void open(const std::string &name, const unsigned int mode);
private:
// IO
std::string getFirstGroupName(void);
virtual std::string load(const std::string &name = "");
void load(DMat &m, const H5NS::DataSet &d);
void load(DMatSample &s, const H5NS::DataSet &d);
void load(RandGenState &state, const H5NS::DataSet &d);
private:
// file name
std::unique_ptr<H5NS::H5File> h5File_{nullptr};
};
END_LATAN_NAMESPACE
#endif // Latan_Hdf5File_hpp_

42
lib/Io.cpp Normal file
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@ -0,0 +1,42 @@
/*
* Io.cpp, part of LatAnalyze 3
*
* Copyright (C) 2013 - 2015 Antonin Portelli
*
* LatAnalyze 3 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 3 of the License, or
* (at your option) any later version.
*
* LatAnalyze 3 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 LatAnalyze 3. If not, see <http://www.gnu.org/licenses/>.
*/
#include <LatAnalyze/Io.hpp>
#include <LatAnalyze/includes.hpp>
using namespace std;
using namespace Latan;
string Io::getFirstName(const string &fileName)
{
string ext = extension(fileName);
if (ext == "h5")
{
return getFirstName<Hdf5File>(fileName);
}
else if ((ext == "dat")||(ext == "sample")||(ext == "seed"))
{
return getFirstName<AsciiFile>(fileName);
}
else
{
LATAN_ERROR(Io, "unknown file extension '" + ext + "'");
}
}

120
lib/Io.hpp Normal file
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@ -0,0 +1,120 @@
/*
* Io.hpp, part of LatAnalyze 3
*
* Copyright (C) 2013 - 2015 Antonin Portelli
*
* LatAnalyze 3 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 3 of the License, or
* (at your option) any later version.
*
* LatAnalyze 3 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 LatAnalyze 3. If not, see <http://www.gnu.org/licenses/>.
*/
#ifndef Latan_Io_hpp_
#define Latan_Io_hpp_
#include <LatAnalyze/Global.hpp>
#include <LatAnalyze/AsciiFile.hpp>
#include <LatAnalyze/Hdf5File.hpp>
BEGIN_LATAN_NAMESPACE
/******************************************************************************
* Static IO functions *
******************************************************************************/
class Io
{
public:
template <typename IoT, typename FileType>
static IoT load(const std::string &fileName, const std::string &name = "");
template <typename IoT>
static IoT load(const std::string &fileName, const std::string &name = "");
template <typename IoT, typename FileType>
static void save(const IoT &data, const std::string &fileName,
const unsigned int mode = File::Mode::write,
const std::string &name = "");
template <typename IoT>
static void save(const IoT &data, const std::string &fileName,
const unsigned int mode = File::Mode::write,
const std::string &name = "");
template <typename FileType>
static std::string getFirstName(const std::string &fileName);
static std::string getFirstName(const std::string &fileName);
};
// template implementation /////////////////////////////////////////////////////
template <typename IoT, typename FileType>
IoT Io::load(const std::string &fileName, const std::string &name)
{
FileType file(fileName, File::Mode::read);
return file.template read<IoT>(name);
}
template <typename IoT>
IoT Io::load(const std::string &fileName, const std::string &name)
{
std::string ext = extension(fileName);
if (ext == "h5")
{
return load<IoT, Hdf5File>(fileName, name);
}
else if ((ext == "dat")||(ext == "sample")||(ext == "seed"))
{
return load<IoT, AsciiFile>(fileName, name);
}
else
{
LATAN_ERROR(Io, "unknown file extension '" + ext + "'");
}
}
template <typename IoT, typename FileType>
void Io::save(const IoT &data, const std::string &fileName,
const unsigned int mode, const std::string &name)
{
FileType file(fileName, mode);
std::string realName = (name.empty()) ? fileName : name;
file.save(data, realName);
}
template <typename IoT>
void Io::save(const IoT &data, const std::string &fileName,
const unsigned int mode, const std::string &name)
{
std::string ext = extension(fileName);
if (ext == "h5")
{
save<IoT, Hdf5File>(data, fileName, mode, name);
}
else if ((ext == "dat")||(ext == "sample")||(ext == "seed"))
{
save<IoT, AsciiFile>(data, fileName, mode, name);
}
else
{
LATAN_ERROR(Io, "unknown file extension '" + ext + "'");
}
}
template <typename FileType>
std::string Io::getFirstName(const std::string &fileName)
{
FileType file(fileName, File::Mode::read);
return file.getFirstName();
}
END_LATAN_NAMESPACE
#endif // Latan_Io_hpp_

2
lib/IoObject.hpp
View File

@ -30,7 +30,7 @@ BEGIN_LATAN_NAMESPACE
class IoObject
{
public:
enum class IoType
enum class IoType: short int
{
noType = 0,
dMat = 1,

4
lib/Makefile.am
View File

@ -29,8 +29,10 @@ libLatAnalyze_la_SOURCES = \
Global.cpp \
GslHybridRootFinder.cpp\
GslQagsIntegrator.cpp \
Hdf5File.cpp \
Histogram.cpp \
includes.hpp \
Io.cpp \
Mat.cpp \
Math.cpp \
MathInterpreter.cpp \
@ -62,8 +64,10 @@ libLatAnalyze_la_HEADERS = \
Global.hpp \
GslHybridRootFinder.hpp\
GslQagsIntegrator.hpp \
Hdf5File.hpp \
Histogram.hpp \
Integrator.hpp \
Io.hpp \
IoObject.hpp \
Mat.hpp \
Math.hpp \

4
utils/make_fake_sample.cpp
View File

@ -18,7 +18,7 @@
*/
#include <iostream>
#include <LatAnalyze/AsciiFile.hpp>
#include <LatAnalyze/Io.hpp>
#include <LatAnalyze/RandGen.hpp>
using namespace std;
@ -56,7 +56,7 @@ int main(int argc, char *argv[])
res[s](0, 0) = gen.gaussian(val, err);
}
}
Io::save<DMatSample, AsciiFile>(res, outFileName);
Io::save<DMatSample>(res, outFileName);
return EXIT_SUCCESS;
}

33
utils/resample.cpp
View File

@ -21,8 +21,8 @@
#include <map>
#include <libgen.h>
#include <unistd.h>
#include <LatAnalyze/AsciiFile.hpp>
#include <LatAnalyze/Dataset.hpp>
#include <LatAnalyze/Io.hpp>
#ifndef DEF_NSAMPLE
#define DEF_NSAMPLE 100
@ -109,15 +109,30 @@ int main(int argc, char *argv[])
}
for (unsigned int i = 0; i < dataFileName.size(); ++i)
{
AsciiFile dataFile;
std::unique_ptr<File> dataFile;
if (extension(dataFileName[i]) == "dat")
{
dataFile.reset(new AsciiFile);
}
else if (extension(dataFileName[i]) == "h5")
{
dataFile.reset(new Hdf5File);
}
else
{
cerr << "error: '" << dataFileName[i];
cerr << "' has an unknown extension" << endl;
return EXIT_FAILURE;
}
cout << '\r' << ProgressBar(i + 1, dataFileName.size());
dataFile.open(dataFileName[i], AsciiFile::Mode::read);
dataFile->open(dataFileName[i], AsciiFile::Mode::read);
for (const string &n: name)
{
data[n][i] = dataFile.read<DMat>(n);
data[n][i] = dataFile->read<DMat>(n);
}
dataFile.close();
dataFile->close();
}
cout << endl;
@ -129,7 +144,7 @@ int main(int argc, char *argv[])
cout << "-- resampling data..." << endl;
if (!stateFileName.empty())
{
state = Io::load<RandGenState, AsciiFile>(stateFileName);
state = Io::load<RandGenState>(stateFileName);
}
for (unsigned int i = 0; i < name.size(); ++i)
{
@ -142,8 +157,8 @@ int main(int argc, char *argv[])
g.setState(state);
}
s = data[name[i]].bootstrapMean(nSample, g);
Io::save<DMatSample, AsciiFile>(s, outDirName + "/" + outFileName,
File::Mode::write, outFileName);
Io::save<DMatSample>(s, outDirName + "/" + outFileName,
File::Mode::write, outFileName);
}
cout << endl;

2
utils/sample_combine.cpp
View File

@ -20,7 +20,7 @@
#include <iostream>
#include <libgen.h>
#include <unistd.h>
#include <LatAnalyze/AsciiFile.hpp>
#include <LatAnalyze/Io.hpp>
#include <LatAnalyze/CompiledFunction.hpp>
using namespace std;

17
utils/sample_read.cpp
View File

@ -18,27 +18,32 @@
*/
#include <iostream>
#include <LatAnalyze/AsciiFile.hpp>
#include <LatAnalyze/Io.hpp>
using namespace std;
using namespace Latan;
int main(int argc, char *argv[])
{
if (argc != 2)
if ((argc < 2) || (argc > 3))
{
cerr << "usage: " << argv[0] << " <file>" << endl;
cerr << "usage: " << argv[0] << " <file> [<copy>]" << endl;
return EXIT_FAILURE;
}
string fileName = argv[1];
string fileName = argv[1], copy = (argc >= 3) ? argv[2] : "";
cout << "-- loading sample from '" << fileName << "'..." << endl;
DMatSample s = Io::load<DMatSample, AsciiFile>(fileName);
DMatSample s = Io::load<DMatSample>(fileName);
string name = Io::getFirstName(fileName);
cout << scientific;
cout << "central value:\n" << s[central] << endl;
cout << "standard deviation:\n" << s.variance().cwiseSqrt() << endl;
if (!copy.empty())
{
Io::save(s, copy, File::Mode::write, name);
}
return EXIT_SUCCESS;
}