mirror of
https://github.com/aportelli/LatAnalyze.git
synced 2025-04-07 10:05:55 +01:00
first implementation of HDF5 format
This commit is contained in:
parent
c672c33189
commit
5e3247697d
307
acinclude.m4
307
acinclude.m4
@ -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 $arg"
|
||||
;;
|
||||
esac
|
||||
done
|
||||
else
|
||||
AC_MSG_RESULT([no])
|
||||
with_hdf5_fortran="no"
|
||||
fi
|
||||
|
||||
AC_SUBST([HDF5_VERSION])
|
||||
AC_SUBST([HDF5_CC])
|
||||
AC_SUBST([HDF5_CFLAGS])
|
||||
AC_SUBST([HDF5_CPPFLAGS])
|
||||
AC_SUBST([HDF5_LDFLAGS])
|
||||
AC_SUBST([HDF5_LIBS])
|
||||
AC_SUBST([HDF5_FC])
|
||||
AC_SUBST([HDF5_FFLAGS])
|
||||
AC_SUBST([HDF5_FLIBS])
|
||||
AC_DEFINE([HAVE_HDF5], [1], [Defined if you have HDF5 support])
|
||||
fi
|
||||
fi
|
||||
])
|
||||
|
||||
|
12
configure.ac
12
configure.ac
@ -58,10 +58,14 @@ AC_ARG_WITH([LatCore],
|
||||
[AM_LDFLAGS="$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
|
||||
|
@ -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;
|
||||
}
|
||||
|
@ -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>
|
||||
|
@ -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)
|
||||
|
@ -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
40
lib/File.hpp
@ -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
315
lib/Hdf5File.cpp
Normal 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
72
lib/Hdf5File.hpp
Normal file
@ -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
42
lib/Io.cpp
Normal file
@ -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
120
lib/Io.hpp
Normal file
@ -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_
|
@ -30,7 +30,7 @@ BEGIN_LATAN_NAMESPACE
|
||||
class IoObject
|
||||
{
|
||||
public:
|
||||
enum class IoType
|
||||
enum class IoType: short int
|
||||
{
|
||||
noType = 0,
|
||||
dMat = 1,
|
||||
|
@ -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 \
|
||||
|
@ -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;
|
||||
}
|
||||
|
@ -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;
|
||||
|
||||
|
@ -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;
|
||||
|
@ -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;
|
||||
}
|
||||
|
Loading…
x
Reference in New Issue
Block a user