dsc
/
mxe
4
0
Fork 0
Code Issues Pull Requests Releases Wiki Activity

pkg stimfit: upgrade to use c++17, and remove the need for boost

Browse Source
pull/2264/head
Alois Schlögl 5 years ago
parent 42f2f271d9
commit 634de32667
5 changed files with 3326 additions and 74 deletions
Show Stats Download Patch File Download Diff File

47
src/stimfit-0001-configure.patch
Unescape View File

@ -1,47 +0,0 @@
diff --git a/configure.ac b/configure.ac
index 3786346..49312cd 100644
--- a/configure.ac
+++ b/configure.ac
@@ -147,7 +147,7 @@ AM_CONDITIONAL(WITH_BIOSIGLITE, test "$with_biosiglite" = "yes")
if test "$with_biosig2" = "yes" ; then
CPPFLAGS="${CPPFLAGS} -DWITH_BIOSIG2"
- LIBBIOSIG_LDFLAGS="-lbiosig2 -lcholmod"
+ LIBBIOSIG_LDFLAGS="-lbiosig -lcholmod"
elif test "$with_biosig" = "yes" ; then
CPPFLAGS="${CPPFLAGS} -DWITH_BIOSIG"
LIBBIOSIG_LDFLAGS="-lbiosig -lcholmod"
@@ -186,15 +186,11 @@ if test "$LAPACKLIB" = ""; then
AC_CHECK_LIB([lapack-3], [dgemm_], HAVE_LAPACK_3="yes")
if test "${HAVE_LAPACK_3}" != "yes" ; then
AC_CHECK_LIB([blas], [dgemm_], HAVE_ATLAS="yes")
- if test "${HAVE_ATLAS}" != "yes" ; then
- AC_MSG_ERROR([Couldn't find lapack.])
- else
- LIBLAPACK_LDFLAGS="-llapack -lblas"
- CPPFLAGS="${CPPFLAGS} -DHAVE_LAPACK "
- fi
+ LIBLAPACK_LDFLAGS="-llapack -lblas"
+ CPPFLAGS="${CPPFLAGS} -DHAVE_LAPACK "
else
LIBLAPACK_LDFLAGS="-llapack-3"
- CPPFLAGS="${CPPFLAGS} -DHAVE_LAPACK "
+ CPPFLAGS="${CPPFLAGS} -DHAVE_LAPACK "
fi
else
LIBLAPACK_LDFLAGS=-llapack3
@@ -326,14 +322,10 @@ fi
AC_CHECK_HEADER([hdf5.h], [], [AC_MSG_ERROR([Couldn't find hdf5 header])])
AC_CHECK_LIB([hdf5],[H5Fopen],HAVE_HDF5="yes")
-if test "${HAVE_HDF5}" != "yes" ; then
- AC_MSG_ERROR([Couldn't find hdf5 libraries.])
-else
if test "${HDF5_CFLAGS}" = ""; then
CPPFLAGS="${CPPFLAGS} -DH5_USE_16_API"
LIBHDF5_LDFLAGS="-lhdf5 -lhdf5_hl"
fi
-fi
AC_SUBST(LIBHDF5_LDFLAGS)
AC_ARG_ENABLE([debug],

25
src/stimfit-0003-lbiosig2.patch
Unescape View File

@ -1,25 +0,0 @@
diff --git a/Makefile.static b/Makefile.static
index 1e45833..7f3d997 100644
--- a/Makefile.static
+++ b/Makefile.static
@@ -217,11 +217,6 @@ LIBS += $(shell $(WXCONF) --libs net,adv,aui,core,base)
PREFIX ?= /usr
PKGCONF ?= $(CROSS)pkg-config
-ifeq (5,$(shell $(CXX) -v 2>&1 | awk '/gcc version / {print substr($$3,1,1)}' ))
- # g++-5 changes default ABI, if WX was compiled with an earlier compiler
- CXXFLAGS += -fabi-version=2
-endif
-
CPPFLAGS += -I$(WXDIR)
## HDF5 related stuff ##
@@ -258,7 +253,7 @@ endif
## BIOSIG related stuff ##
ifneq (,$(findstring WITH_BIOSIG2, $(DEFINES)))
- LIBS += -lbiosig2
+ LIBS += -lbiosig
else
ifneq (,$(findstring WITH_BIOSIG, $(DEFINES)))
LIBS += -lbiosig

2775
src/stimfit-0004-v0158diff.patch
View File

File diff suppressed because it is too large Load Diff

545
src/stimfit-0008-replace-boost.patch
Unescape View File

@ -0,0 +1,545 @@
diff --git a/Makefile.static b/Makefile.static
index f7c480ec..3f4758c0 100644
--- a/Makefile.static
+++ b/Makefile.static
@@ -51,6 +51,8 @@ endif
endif
DEFINES += -DWITH_BIOSIG2
+#DEFINES += -DWITH_LIBLEVMAR
+#DEFINES += -DWITH_OPENBLAS
DEFINES += -DHAVE_LAPACK
#DEFINES += -DWITHOUT_ABF
#DEFINES += -DWITHOUT_AXG
@@ -75,19 +77,20 @@ PY_VERSION := 2.7
vpath %.cpp ./src/stimfit:./src/stimfit/gui:./src/stimfit/gui/dlgs:./src/stimfit/gui/usrdlg:./src/libstfnum:./src/libstfio/:./src/libstfio/cfs/:./src/libstfio/atf/:./src/libstfio/abf/:./src/libstfio/abf/axon2:./src/libstfio/abf/axon/Common:./src/libstfio/abf/axon/AxAbfFio32:./src/libstfio/abf/axon/AxAtfFio32/:./src/libstfio/biosig/:./src/libstfio/hdf5/:./src/libstfio/heka/:./src/libstfio/igor:./src/libstfio/ascii/:./src/libstfio/axg/
-vpath %.c ./src/libstfnum/levmar/:./src/libstfio/igor/:./src/libstfio/cfs/
-vpath %.cpp ./src/libstfnum/:./src/libstfnum/levmar/:./src/stimfit/gui/:./src/stimfit/gui/dlgs/:./src/libstfio/:./src/libstfio/biosig/:./src/libstfio/igor/:./src/libstfio/cfs/
+ifeq (,$(findstring WITH_LIBLEVMAR, $(DEFINES)))
+ vpath %.c ./src/libstfnum/levmar/:./src/libstfio/igor/:./src/libstfio/cfs/
+ vpath %.cpp ./src/libstfnum/:./src/libstfnum/levmar/:./src/stimfit/gui/:./src/stimfit/gui/dlgs/:./src/libstfio/:./src/libstfio/biosig/:./src/libstfio/igor/:./src/libstfio/cfs/
+else
+ vpath %.c ./src/libstfio/igor/:./src/libstfio/cfs/
+ vpath %.cpp ./src/libstfnum/:./src/stimfit/gui/:./src/stimfit/gui/dlgs/:./src/libstfio/:./src/libstfio/biosig/:./src/libstfio/igor/:./src/libstfio/cfs/
+endif
+
SOURCES = ./src/stimfit/stf.cpp \
./src/libstfnum/stfnum.cpp \
./src/libstfnum/funclib.cpp \
./src/libstfnum/measure.cpp \
./src/libstfnum/fit.cpp \
- ./src/libstfnum/levmar/lm.c \
- ./src/libstfnum/levmar/Axb.c \
- ./src/libstfnum/levmar/misc.c \
- ./src/libstfnum/levmar/lmbc.c \
- ./src/libstfnum/levmar/lmlec.c \
./src/stimfit/gui/doc.cpp \
./src/stimfit/gui/zoom.cpp \
./src/stimfit/gui/childframe.cpp \
@@ -120,6 +123,12 @@ SOURCES = ./src/stimfit/stf.cpp \
./src/libstfio/igor/CrossPlatformFileIO.c \
./src/libstfio/cfs/cfs.c
+SOURCES_LEVMAR = ./src/libstfnum/levmar/lm.c \
+ ./src/libstfnum/levmar/Axb.c \
+ ./src/libstfnum/levmar/misc.c \
+ ./src/libstfnum/levmar/lmbc.c \
+ ./src/libstfnum/levmar/lmlec.c \
+
SOURCES_OPTIONAL = \
./src/libstfio/heka/hekalib.cpp \
@@ -174,8 +183,20 @@ SOURCES_AXG = ./src/libstfio/axg/axglib.cpp \
./src/libstfio/axg/byteswap.cpp \
### DEPENDENCIES ###
-ifneq (,$(findstring HAVE_LAPACK, $(DEFINES)))
- LIBS += -llapack -lblas
+ifeq (,$(findstring WITH_LIBLEVMAR, $(DEFINES)))
+ SOURCES += $(SOURCES_LEVMAR)
+else
+ LIBS += -llevmar
+endif
+
+ifneq (,$(findstring WITH_OPENBLAS, $(DEFINES)))
+ LIBS += -lopenblas -lgomp -lpthread -lm
+ DEFINES += -I/usr/include/openblas
+ LDFLAGS += -L/usr/lib/openblas
+else
+ ifneq (,$(findstring HAVE_LAPACK, $(DEFINES)))
+ LIBS += -llapack -lblas
+ endif
endif
ifeq (,$(findstring WITHOUT_ABF, $(DEFINES)))
@@ -211,8 +232,8 @@ endif
CC ?= $(shell $(WXCONF) --cc)
CXX ?= $(shell $(WXCONF) --cxx)
CFLAGS = $(DEFINES) $(shell $(WXCONF) --cflags) -fstack-protector -O2
-CPPFLAGS = $(DEFINES) $(shell $(WXCONF) --cppflags) -std=gnu++11 -fstack-protector -O2
-CXXFLAGS = $(DEFINES) $(shell $(WXCONF) --cxxflags) -std=gnu++11 -fstack-protector -O2
+CPPFLAGS = $(DEFINES) $(shell $(WXCONF) --cppflags) -std=gnu++17 -fstack-protector -O2
+CXXFLAGS = $(DEFINES) $(shell $(WXCONF) --cxxflags) -std=gnu++17 -fstack-protector -O2
LIBS += $(shell $(WXCONF) --libs net,adv,aui,core,base)
@@ -227,11 +248,6 @@ mandir = ${datarootdir}/man
PKGCONF ?= $(CROSS)pkg-config
-ifeq (5,$(shell $(CXX) -v 2>&1 | awk '/gcc version / {print substr($$3,1,1)}' ))
- # g++-5 changes default ABI, if WX was compiled with an earlier compiler
- CXXFLAGS += -fabi-version=2
-endif
-
CPPFLAGS += -I$(WXDIR)
## HDF5 related stuff ##
@@ -261,7 +277,7 @@ else
LDFLAGS += -L/usr/lib/$(PLATFORM)
LIBS += -lhdf5_serial_hl -lhdf5_serial
else
- LIBS += -lhdf5_hl -lhdf5
+ LIBS += -lhdf5_hl -lhdf5 -lz
endif
endif
endif
@@ -283,9 +299,8 @@ LIBS += -lfftw3
ifeq (mingw,$(findstring mingw, $(WXCONF)))
LIBS += -lgfortran -lquadmath
- LIBS += -liberty -liconv
endif
-LIBS += -liconv -ltinyxml -lstdc++
+LIBS += -ltinyxml -lstdc++
##############################################################
diff --git a/configure.ac b/configure.ac
index 1f8c58f5..8f70fc5a 100644
--- a/configure.ac
+++ b/configure.ac
@@ -5,6 +5,7 @@ AM_SILENT_RULES([yes])
AC_CONFIG_MACRO_DIR([m4])
AC_PROG_CC
+AC_PROG_CC_STDC
AC_PROG_INSTALL
_LT_SET_OPTION([LT_INIT],[dlopen])
@@ -179,6 +180,8 @@ if test "$LAPACKLIB" = ""; then
LIBLAPACK_LDFLAGS="/usr/lib/liblapack.dylib -framework Accelerate"
CPPFLAGS="${CPPFLAGS} -DHAVE_LAPACK -DHAVE_LAPACK_SUFFIX"
else
+ AC_CHECK_LIB([openblas], [dgemm_], HAVE_OPENBLAS="yes",, [-lgomp -lpthread -lm])
+ if test "${HAVE_OPENBLAS}" != "yes" ; then
AC_CHECK_LIB([lapack], [dgemm_], HAVE_LAPACKX="yes")
if test "${HAVE_LAPACKX}" != "yes" ; then
AC_CHECK_LIB([lapack3], [dgemm_], HAVE_LAPACK3="yes")
@@ -186,15 +189,11 @@ if test "$LAPACKLIB" = ""; then
AC_CHECK_LIB([lapack-3], [dgemm_], HAVE_LAPACK_3="yes")
if test "${HAVE_LAPACK_3}" != "yes" ; then
AC_CHECK_LIB([blas], [dgemm_], HAVE_ATLAS="yes")
- if test "${HAVE_ATLAS}" != "yes" ; then
- AC_MSG_ERROR([Couldn't find lapack.])
- else
- LIBLAPACK_LDFLAGS="-llapack -lblas"
- CPPFLAGS="${CPPFLAGS} -DHAVE_LAPACK "
- fi
+ LIBLAPACK_LDFLAGS="-llapack -lblas"
+ CPPFLAGS="${CPPFLAGS} -DHAVE_LAPACK "
else
LIBLAPACK_LDFLAGS="-llapack-3"
- CPPFLAGS="${CPPFLAGS} -DHAVE_LAPACK "
+ CPPFLAGS="${CPPFLAGS} -DHAVE_LAPACK "
fi
else
LIBLAPACK_LDFLAGS=-llapack3
@@ -204,6 +203,10 @@ if test "$LAPACKLIB" = ""; then
LIBLAPACK_LDFLAGS="-llapack -lblas"
CPPFLAGS="${CPPFLAGS} -DHAVE_LAPACK "
fi
+ else
+ LIBLAPACK_LDFLAGS="-lopenblas"
+ CPPFLAGS="${CPPFLAGS} -DWITH_OPENBLAS -DHAVE_LAPACK"
+ fi
fi
fi
AC_SUBST(LIBLAPACK_LDFLAGS)
@@ -326,14 +329,10 @@ fi
AC_CHECK_HEADER([hdf5.h], [], [AC_MSG_ERROR([Couldn't find hdf5 header])])
AC_CHECK_LIB([hdf5],[H5Fopen],HAVE_HDF5="yes")
-if test "${HAVE_HDF5}" != "yes" ; then
- AC_MSG_ERROR([Couldn't find hdf5 libraries.])
-else
if test "${HDF5_CFLAGS}" = ""; then
CPPFLAGS="${CPPFLAGS} -DH5_USE_16_API"
LIBHDF5_LDFLAGS="-lhdf5 -lhdf5_hl"
fi
-fi
AC_SUBST(LIBHDF5_LDFLAGS)
AC_ARG_ENABLE([debug],
diff --git a/src/libstfio/abf/axon/Common/ArrayPtr.hpp b/src/libstfio/abf/axon/Common/ArrayPtr.hpp
index 8584824a..65fecd9b 100755
--- a/src/libstfio/abf/axon/Common/ArrayPtr.hpp
+++ b/src/libstfio/abf/axon/Common/ArrayPtr.hpp
@@ -14,7 +14,11 @@
#pragma once
#include <stdlib.h>
-#include <boost/shared_array.hpp>
+#if (__cplusplus < 201402L)
+# include <boost/shared_array.hpp>
+#else
+# include <memory>
+#endif
#if defined(__UNIX__) || defined(__STF__)
#define max(a,b) (((a) > (b)) ? (a) : (b))
@@ -29,7 +33,11 @@ template<class ITEM>
class CArrayPtr
{
private: // Private data.
+#if (__cplusplus < 201402L)
boost::shared_array<ITEM> m_pArray;
+#else
+ std::shared_ptr<ITEM> m_pArray;
+#endif
private: // Prevent copy constructors and operator=().
CArrayPtr(const CArrayPtr &);
diff --git a/src/libstfio/abf/axon/Common/FileReadCache.hpp b/src/libstfio/abf/axon/Common/FileReadCache.hpp
index 86b52ebc..8f3cdadc 100755
--- a/src/libstfio/abf/axon/Common/FileReadCache.hpp
+++ b/src/libstfio/abf/axon/Common/FileReadCache.hpp
@@ -13,7 +13,11 @@
#define INC_FILEREADCACHE_HPP
#include "./../Common/FileIO.hpp"
-#include <boost/shared_array.hpp>
+#if (__cplusplus < 201402L)
+# include <boost/shared_array.hpp>
+#else
+# include <memory>
+#endif
//-----------------------------------------------------------------------------------------------
// CFileReadCache class definition
@@ -27,7 +31,11 @@ private:
UINT m_uCacheSize;
UINT m_uCacheStart;
UINT m_uCacheCount;
+#if (__cplusplus < 201402L)
boost::shared_array<BYTE> m_pItemCache;
+#else
+ std::shared_ptr<BYTE> m_pItemCache;
+#endif
private: // Unimplemented default member functions.
// Declare but don't define copy constructors to prevent use of defaults.
diff --git a/src/libstfio/abf/axon2/ProtocolReaderABF2.hpp b/src/libstfio/abf/axon2/ProtocolReaderABF2.hpp
index 85205cb9..d44a22c8 100644
--- a/src/libstfio/abf/axon2/ProtocolReaderABF2.hpp
+++ b/src/libstfio/abf/axon2/ProtocolReaderABF2.hpp
@@ -16,6 +16,8 @@
#include "../axon/AxAbfFio32/filedesc.hpp"
#if (__cplusplus < 201103)
#include <boost/shared_ptr.hpp>
+#else
+ #include <memory>
#endif
//===============================================================================================
diff --git a/src/libstfio/stfio.h b/src/libstfio/stfio.h
index 4b5aaa70..64bd2cf0 100644
--- a/src/libstfio/stfio.h
+++ b/src/libstfio/stfio.h
@@ -25,7 +25,12 @@
#define _STFIO_H_
#include <iostream>
-#include <boost/function.hpp>
+#if (__cplusplus < 201103)
+# include <boost/function.hpp>
+#else
+# include <algorithm>
+# include <functional>
+#endif
#include <vector>
#include <deque>
#include <map>
diff --git a/src/libstfnum/fit.cpp b/src/libstfnum/fit.cpp
index a2d4e119..3d6cf0a3 100755
--- a/src/libstfnum/fit.cpp
+++ b/src/libstfnum/fit.cpp
@@ -13,7 +13,11 @@
// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
#include "./fit.h"
-#include "./levmar/levmar.h"
+#if defined(WITH_LIBLEVMAR)
+ #include <levmar.h>
+#else
+ #include "./levmar/levmar.h"
+#endif
#include <float.h>
#include <cmath>
@@ -154,7 +158,6 @@ Vector_double stfnum::get_scale(Vector_double& data, double oldx) {
xyscale[1] = 0;
xyscale[2] = 1.0/amp;
xyscale[3] = off;
-
return xyscale;
}
@@ -191,7 +194,8 @@ double stfnum::lmFit( const Vector_double& data, double dt,
constrains_lm_ub[n_p] = DBL_MAX;
}
if ( can_scale ) {
- if (fitFunc.pInfo[n_p].scale == stfnum::noscale) {
+ //if (fitFunc.pInfo[n_p].scale == stfnum::noscale) {
+ if (!fitFunc.pInfo[n_p].scale) {
can_scale = false;
}
}
diff --git a/src/libstfnum/funclib.cpp b/src/libstfnum/funclib.cpp
index 7757c2eb..8db0856e 100755
--- a/src/libstfnum/funclib.cpp
+++ b/src/libstfnum/funclib.cpp
@@ -44,11 +44,11 @@ std::vector< stfnum::storedFunc > stfnum::GetFuncLib() {
// Biexponential function, free fit:
std::vector<stfnum::parInfo> parInfoBExp=getParInfoExp(2);
funcList.push_back(stfnum::storedFunc(
- "Biexponential",parInfoBExp,fexp,fexp_init,fexp_jac,true,outputWTau));
+ "Biexponential A(1-exp(-t/Tau_0)exp(-t/Tau_1)",parInfoBExp,fexp,fexp_init,fexp_jac,true,outputWTau));
// Biexponential function, offset fixed to baseline:
parInfoBExp[4].toFit=false;
- funcList.push_back(stfnum::storedFunc("Biexponential, offset fixed to baseline",
+ funcList.push_back(stfnum::storedFunc("Biexponential, offset fixed to baseline A(1-exp(-t/Tau_0)exp(-t/Tau_1)+Baseline",
parInfoBExp,fexp,fexp_init,fexp_jac,true,outputWTau));
// Biexponential function, starting with a delay, start fixed to baseline:
@@ -62,7 +62,7 @@ std::vector< stfnum::storedFunc > stfnum::GetFuncLib() {
parInfoBExpDe[4].toFit=true; parInfoBExpDe[4].desc="tau2"; parInfoBExpDe[4].scale=stfnum::xscale; parInfoBExpDe[4].unscale=stfnum::xunscale;
// parInfoBExpDe[4].constrained = true; parInfoBExpDe[4].constr_lb = 1.0e-16; parInfoBExpDe[4].constr_ub = DBL_MAX;
funcList.push_back(stfnum::storedFunc(
- "Biexponential with delay, start fixed to baseline, delay constrained to > 0",
+ "Biexponential with delay, start fixed to baseline, delay constrained to > 0; A(1-exp(-(t-Delay)/Tau_0)exp(-(t-Delay)/Tau_1)+Baseline",
parInfoBExpDe,fexpbde,fexpbde_init,stfnum::nojac,false));
// Triexponential function, free fit:
@@ -153,8 +153,8 @@ Vector_double stfnum::fexp_jac(double x, const Vector_double& p) {
void stfnum::fexp_init(const Vector_double& data, double base, double peak, double RTLoHi, double HalfWidth, double dt, Vector_double& pInit ) {
// Find out direction:
bool increasing = data[0] < data[data.size()-1];
- Vector_double::const_iterator max_el = std::max_element(data.begin(), data.end());
- Vector_double::const_iterator min_el = std::min_element(data.begin(), data.end());
+ Vector_double::const_iterator max_el = std::max(data.begin(), data.end());
+ Vector_double::const_iterator min_el = std::min(data.begin(), data.end());
double floor = (increasing ? (*max_el+1.0e-9) : (*min_el-1.0e-9));
Vector_double peeled( stfio::vec_scal_minus(data, floor));
if (increasing) peeled = stfio::vec_scal_mul(peeled, -1.0);
diff --git a/src/libstfnum/stfnum.cpp b/src/libstfnum/stfnum.cpp
index 9809d20b..9743843c 100755
--- a/src/libstfnum/stfnum.cpp
+++ b/src/libstfnum/stfnum.cpp
@@ -709,10 +709,10 @@ stfnum::deconvolve(const Vector_double& dataIn, const Vector_double& templ,
int SR, double hipass, double lopass, stfio::ProgressInfo& progDlg)
{
// Normalize data
- double fmax = *std::max_element(dataIn.begin(), dataIn.end());
- double fmin = *std::min_element(dataIn.begin(), dataIn.end());
- Vector_double data = stfio::vec_scal_minus(dataIn, fmin);
- data = stfio::vec_scal_div(data, fmax-fmin);
+ double fmax = *std::max_element(dataIn.begin(), dataIn.end());
+ double fmin = *std::min_element(dataIn.begin(), dataIn.end());
+ Vector_double data = stfio::vec_scal_minus(dataIn, fmin);
+ data = stfio::vec_scal_div(data, fmax-fmin);
bool skipped = false;
progDlg.Update( 0, "Starting deconvolution...", &skipped );
diff --git a/src/libstfnum/stfnum.h b/src/libstfnum/stfnum.h
index 3ac112ba..9225cb65 100755
--- a/src/libstfnum/stfnum.h
+++ b/src/libstfnum/stfnum.h
@@ -33,7 +33,15 @@
#include <vector>
#include <complex>
#include <deque>
-#include <boost/function.hpp>
+
+#if (__cplusplus < 201103)
+# include <boost/function.hpp>
+#else
+# include <algorithm>
+# include <cassert>
+# include <functional>
+#endif
+
#ifdef _OPENMP
#include <omp.h>
#endif
@@ -42,8 +50,8 @@
#ifdef _MSC_VER
#define INFINITY (DBL_MAX+DBL_MAX)
#ifndef NAN
- static const unsigned long __nan[2] = {0xffffffff, 0x7fffffff};
- #define NAN (*(const float *) __nan)
+ static const unsigned long __nan[2] = {0xffffffff, 0x7fffffff};
+ #define NAN (*(const float *) __nan)
#endif
#endif
@@ -61,6 +69,8 @@ namespace stfnum {
* that takes a double (the x-value) and a vector of parameters and returns
* the function's result (the y-value).
*/
+#if (__cplusplus < 201103)
+
typedef boost::function<double(double, const Vector_double&)> Func;
//! The jacobian of a stfnum::Func.
@@ -69,6 +79,17 @@ typedef boost::function<Vector_double(double, const Vector_double&)> Jac;
//! Scaling function for fit parameters
typedef boost::function<double(double, double, double, double, double)> Scale;
+#else
+
+typedef std::function<double(double, const Vector_double&)> Func;
+
+//! The jacobian of a stfnum::Func.
+typedef std::function<Vector_double(double, const Vector_double&)> Jac;
+
+//! Scaling function for fit parameters
+typedef std::function<double(double, double, double, double, double)> Scale;
+
+#endif
//! Dummy function, serves as a placeholder to initialize functions without a Jacobian.
Vector_double nojac( double x, const Vector_double& p);
@@ -203,16 +224,29 @@ private:
std::vector< std::string > colLabels;
};
+#if (__cplusplus < 201103)
//! Print the output of a fit into a stfnum::Table.
typedef boost::function<Table(const Vector_double&,const std::vector<stfnum::parInfo>,double)> Output;
//! Default fit output function, constructing a stfnum::Table from the parameters, their description and chisqr.
-Table defaultOutput(const Vector_double& pars,
+Table defaultOutput(const Vector_double& pars,
const std::vector<parInfo>& parsInfo,
double chisqr);
//! Initialising function for the parameters in stfnum::Func to start a fit.
typedef boost::function<void(const Vector_double&, double, double, double, double, double, Vector_double&)> Init;
+#else
+//! Print the output of a fit into a stfnum::Table.
+typedef std::function<Table(const Vector_double&,const std::vector<stfnum::parInfo>,double)> Output;
+
+//! Default fit output function, constructing a stfnum::Table from the parameters, their description and chisqr.
+Table defaultOutput(const Vector_double& pars,
+ const std::vector<parInfo>& parsInfo,
+ double chisqr);
+
+//! Initialising function for the parameters in stfnum::Func to start a fit.
+typedef std::function<void(const Vector_double&, double, double, double, double, double, Vector_double&)> Init;
+#endif
//! Function used for least-squares fitting.
/*! Objects of this class are used for fitting functions
diff --git a/src/stimfit/gui/parentframe.cpp b/src/stimfit/gui/parentframe.cpp
index 3d54c153..94246c96 100755
--- a/src/stimfit/gui/parentframe.cpp
+++ b/src/stimfit/gui/parentframe.cpp
@@ -69,7 +69,11 @@
#include "./childframe.h"
#include "./parentframe.h"
-#include "./../../libstfnum/levmar/levmar.h"
+#if defined(WITH_LIBLEVMAR)
+ #include <levmar.h>
+#else
+ #include "./../../libstfnum/levmar/levmar.h"
+#endif
#include "./../res/16-em-down.xpm"
#include "./../res/16-em-open.xpm"
diff --git a/src/stimfit/stf.h b/src/stimfit/stf.h
index f44aeb8b..adb4156d 100644
--- a/src/stimfit/stf.h
+++ b/src/stimfit/stf.h
@@ -27,6 +27,9 @@
#ifndef _WINDOWS
#if (__cplusplus < 201103)
#include <boost/function.hpp>
+#else
+ #include <algorithm>
+ #include <memory>
#endif
#endif
diff --git a/stfconf.h b/stfconf.h
index 47eb76dc..7989b512 100644
--- a/stfconf.h
+++ b/stfconf.h
@@ -1,6 +1,45 @@
+/* stfconf.h. Generated from stfconf.h.in by configure. */
+/* stfconf.h.in. Generated from configure.ac by autoheader. */
+
+/* Define to 1 if you have the <dlfcn.h> header file. */
+#define HAVE_DLFCN_H 1
+
+/* Define to 1 if you have the <inttypes.h> header file. */
+#define HAVE_INTTYPES_H 1
+
+/* Define to 1 if you have the <memory.h> header file. */
+#define HAVE_MEMORY_H 1
+
+/* Define to 1 if you have the <stdint.h> header file. */
+#define HAVE_STDINT_H 1
+
+/* Define to 1 if you have the <stdlib.h> header file. */
+#define HAVE_STDLIB_H 1
+
+/* Define to 1 if you have the <strings.h> header file. */
+#define HAVE_STRINGS_H 1
+
+/* Define to 1 if you have the <string.h> header file. */
+#define HAVE_STRING_H 1
+
+/* Define to 1 if you have the <sys/stat.h> header file. */
+#define HAVE_SYS_STAT_H 1
+
+/* Define to 1 if you have the <sys/types.h> header file. */
+#define HAVE_SYS_TYPES_H 1
+
+/* Define to 1 if you have the <unistd.h> header file. */
+#define HAVE_UNISTD_H 1
+
+/* Define to the sub-directory where libtool stores uninstalled libraries. */
+#define LT_OBJDIR ".libs/"
+
/* Name of package */
#define PACKAGE "stimfit"
+/* Define to the address where bug reports for this package should be sent. */
+#define PACKAGE_BUGREPORT ""
+
/* Define to the full name of this package. */
#define PACKAGE_NAME "stimfit"
@@ -18,3 +57,6 @@
/* Define to 1 if you have the ANSI C header files. */
#define STDC_HEADERS 1
+
+/* Version number of package */
+#define VERSION "0.15.8"

8
src/stimfit.mk
Unescape View File

@ -8,7 +8,7 @@ $(PKG)_CHECKSUM := 8a5330612245d3f442ed640b0df91028aa4798301bb6844eaf1cf9b463dfc
$(PKG)_SUBDIR := stimfit-$($(PKG)_VERSION)windows
$(PKG)_FILE := stimfit-$($(PKG)_VERSION)windows.tar.gz
$(PKG)_URL := https://github.com/neurodroid/$(PKG)/archive/v$($(PKG)_VERSION)windows.tar.gz
$(PKG)_DEPS := cc libbiosig wxwidgets hdf5 boost fftw levmar openblas
$(PKG)_DEPS := cc libbiosig wxwidgets hdf5 tinyxml fftw levmar openblas
define $(PKG)_UPDATE
$(WGET) -q -O- 'https://github.com/neurodroid/stimfit/releases' | \
@ -18,7 +18,11 @@ endef
define $(PKG)_BUILD
cd '$(1)' && ./autogen.sh && CPPFLAGS="-std=gnu++11" \
#rm -rf '$(1)'
#rsync -avL ~/src/stimfit/* '$(1)/'
#git clone ~/src/stimfit '$(1)'
cd '$(1)' && ./autogen.sh && CPPFLAGS="-std=gnu++17" \
./configure --disable-python --with-biosig2 --with-pslope \
--with-hdf5-prefix=$(PREFIX)/$(TARGET) \
--with-wx-config=$(PREFIX)/$(TARGET)/bin/wx-config \

Write Preview
Loading…
Cancel
Save