Changeset 12013


Ignore:
Timestamp:
04/16/12 18:37:27 (13 years ago)
Author:
Eric.Larour
Message:

Some debugging of compilation

Location:
issm/trunk-jpl
Files:
2 added
65 edited

Legend:

Unmodified
Added
Removed
  • issm/trunk-jpl/m4/issm_options.m4

    r12007 r12013  
    2323        dnl }}}
    2424        dnl Extensions{{{
     25        ISSMEXT=".exe"
    2526        AC_SUBST([ISSMEXT])
    2627        dnl }}}
  • issm/trunk-jpl/src/c/Makefile.am

    r12011 r12013  
    1515#sources
    1616#Core sources{{{1
    17 core_sources = ./include/macros.h\
     17core_sources = ./issm.h\
     18                                ./issm-binding.h\
     19                                ./include/macros.h\
    1820                                        ./include/typedefs.h\
    1921                                        ./include/types.h\
     
    749751                                        ./matlab/io/MatlabVectorToDoubleVector.cpp\
    750752                                    ./matlab/io/MatlabMatrixToDoubleMatrix.cpp\
    751                                         ./matlab/io/Container/Options.cpp\
     753                                        ./matlab/Container/Options.cpp\
    752754                                        ./matlab/objects/Bamg/BamgGeom.h\
    753755                                        ./matlab/objects/Bamg/BamgGeom.cpp\
  • issm/trunk-jpl/src/c/matlab/Container/Options.cpp

    r12011 r12013  
    1313#include <vector>
    1414#include <algorithm>
     15#include <mex.h>
    1516
    16 #include "./DataSet.h"
    17 #include "../shared/shared.h"
    18 #include "../io/io.h"
    19 #include "../include/include.h"
    20 #include "../shared/shared.h"
    21 #include "../EnumDefinitions/EnumDefinitions.h"
    22 #if _SERIAL_
    23 #include "../io/io.h"
    24 #endif
     17#include "../../Container/DataSet.h"
     18#include "../../shared/shared.h"
     19#include "../../io/io.h"
     20#include "../io/matlabio.h"
     21#include "../../include/include.h"
     22#include "../../shared/shared.h"
     23#include "../../EnumDefinitions/EnumDefinitions.h"
    2524/*}}}*/
    2625
  • issm/trunk-jpl/src/c/matlab/include/matlab_macros.h

    r12011 r12013  
    66#ifndef _MATLAB_MACROS_H_
    77#define _MATLAB_MACROS_H_
    8 
    9 #include "./typedefs.h"
    108
    119#ifdef HAVE_CONFIG_H
  • issm/trunk-jpl/src/c/matlab/io/CheckNumMatlabArguments.cpp

    r12011 r12013  
    99#endif
    1010
    11 
    12 #if defined(_HAVE_MATLAB_) && defined(_SERIAL_)
    1311
    1412#include "../../shared/Exceptions/exceptions.h"
     
    3230        return 1;
    3331}
    34 
    35 #endif
  • issm/trunk-jpl/src/c/matlab/io/FetchMatlabData.cpp

    r12011 r12013  
    99#endif
    1010
     11#include <mex.h>
    1112#include "../../shared/shared.h"
    1213#include "../../include/include.h"
    13 
    14 #if defined(_HAVE_MATLAB_) && defined(_SERIAL_)
    15 #include <mex.h>
    16 /*FUNCTION FetchData(DataSet** pdataset,const mxArray* dataref){{{1*/
    17 void FetchData(DataSet** pdataset,const mxArray* dataref){
    18 
    19         /*output*/
    20         DataSet* outdataset=NULL;
    21         char*    outdataset_buffer=NULL;
    22         int      outdataset_size;
    23 
    24         /*First, check that our reference is a double, otherwise, error out: */
    25         if (mxIsClass(dataref,"double")){
    26                        
    27                 /*We need to copy the data pointed by dataref, so that our dataset is not actually a pointer!:*/
    28                 if (!mxIsEmpty(dataref)){
    29                         outdataset_buffer=(char*)mxGetPr(dataref);
    30                         outdataset_size=mxGetM(dataref)*mxGetN(dataref);
    31                         if(outdataset_size)outdataset=DataSetDemarshall(outdataset_buffer);
    32                 }
    33         }
    34         else{
    35                 if (mxIsEmpty(dataref)){
    36                         /*Nothing to pick up. Just initialize pointer to NULL, and warn the server we are not uploading anything: */
    37                         outdataset_size=0;
    38                         outdataset=NULL;
    39                 }
    40                 else{
    41                         /*This is an error: we don't have the correct input!: */
    42                         _error_("Input parameter of class %s not supported yet",mxGetClassName(dataref));
    43                 }
    44         }
    45 
    46         /*Assign output pointers:*/
    47         *pdataset=outdataset;
    48 }
    49 /*}}}*/
     14#include "./matlabio.h"
     15
    5016/*FUNCTION FetchData(double** pmatrix,int* pM,int *pN,const mxArray* dataref){{{1*/
    5117void FetchData(double** pmatrix,int* pM,int *pN,const mxArray* dataref){
     
    560526}
    561527/*}}}*/
    562 /*FUNCTION FetchData(Parameters** pparameters, DataHandle dataref){{{1*/
    563 void FetchData(Parameters** pparameters, DataHandle dataref){
    564 
    565         int i,j;
    566         int count;
    567 
    568         /*output: */
    569         Param* param=NULL;
    570         Parameters* parameters=NULL;
    571 
    572         /*intermediary: */
    573         int M,N;
    574         double* tmatrix=NULL;
    575         double* matrix=NULL;
    576         char**  stringarray=NULL;
    577         double** array=NULL;
    578         int*     mdims_array=NULL;
    579         int*     ndims_array=NULL;
    580         int nfields;
    581         char* name=NULL;
    582         mxArray* pfield=NULL;
    583         mxArray* pfield2=NULL;
    584         int enum_type;
    585 
    586 
    587         /*First, create parameters : */
    588         parameters=new Parameters();
    589 
    590         /*go through matlab params structure, and create Param object for each field: */
    591 
    592         nfields=mxGetNumberOfFields(dataref);
    593 
    594         for(count=0;count<nfields;count++){
    595 
    596                 /*Get i'th field: */
    597                 name=(char*)mxGetFieldNameByNumber(dataref,count);
    598                 enum_type=StringToEnumx(name);
    599                 pfield=mxGetFieldByNumber(dataref,0,count);
    600                 _assert_(pfield);
    601                
    602                 /*Check type of field: */
    603                 if (mxIsClass(pfield,"double")){
    604                        
    605                         M=mxGetM(pfield);
    606                         N=mxGetN(pfield);
    607 
    608                         if (M==0 | N==0){
    609                                 _error_("array in parameters structure field %s is of size 0",name);
    610                         }
    611                         if (M==1 && N==1){
    612                                 /*we have a simple scalar: */
    613                                 param= new DoubleParam(enum_type,*mxGetPr(pfield));
    614                                 parameters->AddObject(param);
    615 
    616                         }
    617                         else{
    618                                 if (N==1){
    619                                        
    620                                         /*vector: */
    621                                         param= new DoubleVecParam(enum_type,mxGetPr(pfield),M);
    622                                         parameters->AddObject(param);
    623 
    624                                 }
    625                                 else{
    626                                         /*matrix: first, transpose, then plug into Param */
    627                                         matrix=mxGetPr(pfield);
    628                                         tmatrix=(double*)xmalloc(M*N*sizeof(double));
    629                                         for (i=0;i<M;i++){
    630                                                 for(j=0;j<N;j++){
    631                                                         *(tmatrix+N*i+j)=*(matrix+M*j+i);
    632                                                 }
    633                                         }
    634 
    635                                         param= new DoubleMatParam(enum_type,tmatrix,M,N);
    636                                         parameters->AddObject(param);
    637        
    638                                         /*Free ressources:*/
    639                                         xfree((void**)&tmatrix);
    640                                 }
    641                         }
    642 
    643                 }
    644                 else if (mxIsClass(pfield,"logical")){
    645 
    646                         M=mxGetM(pfield);
    647                         N=mxGetN(pfield);
    648 
    649                         if (M==0 | N==0){
    650                                 _error_("array in parameters structure field %s is of size 0",name);
    651                         }
    652                         if (M==1 && N==1){
    653                                 /*we have a simple bool: */
    654                                 param= new BoolParam(enum_type,*mxGetLogicals(pfield));
    655                                 parameters->AddObject(param);
    656 
    657                         }
    658                         else{
    659                                 _error_("Matrices of Booleans not supported yet in parameters");
    660                         }
    661                 }
    662                 else if (mxIsClass(pfield,"char")){
    663                         /* we have a string parameter:*/
    664                        
    665                         int stringlen;
    666                         char* string=NULL;
    667                        
    668                         stringlen = mxGetM(pfield)*mxGetN(pfield)+1;
    669                         string = (char*)xmalloc(sizeof(mxChar)*stringlen);
    670                         mxGetString(pfield,string,stringlen);
    671 
    672                         param= new StringParam(enum_type,string);
    673                         parameters->AddObject(param);
    674 
    675                         xfree((void**)&string);
    676                 }
    677                 else if (mxIsClass(pfield,"cell")){
    678 
    679                         /*This can be a string array, or a matrix array. Check the first
    680                          *element type to decide: */
    681                         pfield2=mxGetCell(pfield,0);
    682                         if (mxIsClass(pfield2,"char")){
    683                                
    684                                 /*string array: */
    685                                 M=mxGetM(pfield);
    686                                 stringarray=(char**)xmalloc(M*sizeof(char*));
    687 
    688                                 for(i=0;i<M;i++){
    689                                         char* descriptor=NULL;
    690                                         pfield2=mxGetCell(pfield,i);
    691                                         FetchData(&descriptor,pfield2);
    692                                         stringarray[i]=descriptor;
    693                                 }
    694 
    695                                 param= new StringArrayParam(enum_type,stringarray,M);
    696                                 parameters->AddObject(param);
    697 
    698                                 /*Free ressources:*/
    699                                 for(i=0;i<M;i++){
    700                                         char* descriptor=stringarray[i];
    701                                         xfree((void**)&descriptor);
    702                                 }
    703                                 xfree((void**)&stringarray);
    704 
    705                         }
    706                         else{
    707                                
    708                                 /*matrix array: */
    709                                 M=mxGetM(pfield);
    710                                 array=(double**)xmalloc(M*sizeof(double*));
    711                                 mdims_array=(int*)xmalloc(M*sizeof(int));
    712                                 ndims_array=(int*)xmalloc(M*sizeof(int));
    713 
    714                                 for(i=0;i<M;i++){
    715                                         double* matrix=NULL;
    716                                         int     m,n;
    717                                         pfield2=mxGetCell(pfield,i);
    718                                         FetchData(&matrix,&m,&n,pfield2);
    719                                         array[i]=matrix;
    720                                         mdims_array[i]=m;
    721                                         ndims_array[i]=n;
    722                                 }
    723 
    724                                 param= new DoubleMatArrayParam(enum_type,array,M,mdims_array,ndims_array);
    725                                 parameters->AddObject(param);
    726 
    727                                 /*Free ressources:*/
    728                                 for(i=0;i<M;i++){
    729                                         double* matrix=array[i];
    730                                         xfree((void**)&matrix);
    731                                 }
    732                                 xfree((void**)&array);
    733                                 xfree((void**)&mdims_array);
    734                                 xfree((void**)&ndims_array);
    735                         }
    736                 }
    737                 else _error_("Parameters structure field %s has a format that is not supported: %s",name,mxGetClassName(pfield));
    738         }
    739 
    740         /*Assign output pointers:*/
    741         *pparameters=parameters;
    742 }
    743 /*}}}*/
    744 #endif
  • issm/trunk-jpl/src/c/matlab/io/MatlabMatrixToMatrix.cpp

    r12011 r12013  
     1/*!\file MatlabMatrixToMatrix.cpp
     2 */
     3
     4/*Headers:*/
     5/*{{{1*/
     6#ifdef HAVE_CONFIG_H
     7        #include <config.h>
     8#else
     9#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
     10#endif
     11
     12#include <mex.h>
     13#include <stdio.h>
     14#include <string.h>
     15#include "./matlabio.h"
     16#include "../../objects/objects.h"
     17#include "../../shared/shared.h"
     18#include "../../Container/Container.h"
     19#include "../../include/include.h"
     20#include "../../toolkits/toolkits.h"
     21       
     22/*}}}*/
     23
    124Matrix* MatlabMatrixToMatrix(const mxArray* mxmatrix){
    225
  • issm/trunk-jpl/src/c/matlab/io/MatlabMatrixToPetscMatrix.cpp

    r12011 r12013  
    1111
    1212
    13 #if defined(_HAVE_MATLAB_) && defined(_SERIAL_)
    14 
    1513/*Petsc includes: */
    1614#include "petscmat.h"
     
    2119#include "mex.h"
    2220
    23 #include "../../../shared/shared.h"
     21#include "../../shared/shared.h"
    2422
    2523int MatlabMatrixToPetscMatrix(Mat* pmatrix,int* pmatrix_rows,int* pmatrix_cols,const mxArray* mxmatrix){
     
    121119        return 1;
    122120}
    123 #endif
  • issm/trunk-jpl/src/c/matlab/io/MatlabMatrixToSeqMat.cpp

    r12011 r12013  
     1/*!\file MatlabMatrixToSeqMat.cpp
     2 */
     3
     4/*Headers:*/
     5/*{{{1*/
     6#ifdef HAVE_CONFIG_H
     7        #include <config.h>
     8#else
     9#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
     10#endif
     11
     12#include <mex.h>
     13#include <stdio.h>
     14#include <string.h>
     15#include "../../toolkits/toolkits.h"
     16#include "../../shared/shared.h"
     17#include "./matlabio.h"
     18
     19/*}}}*/
     20
    121SeqMat* MatlabMatrixToSeqMat(const mxArray* dataref){
    222
  • issm/trunk-jpl/src/c/matlab/io/MatlabNArrayToNArray.cpp

    r12011 r12013  
    1313#include "../../include/include.h"
    1414
    15 #if defined(_HAVE_MATLAB_) && defined(_SERIAL_)
    1615#include <mex.h>
    1716
     
    272271}
    273272/*}}}*/
    274 #endif
  • issm/trunk-jpl/src/c/matlab/io/MatlabVectorToPetscVector.cpp

    r12011 r12013  
    1010#endif
    1111
    12 
    13 #if defined(_HAVE_MATLAB_) && defined(_SERIAL_)
    14 
    1512/*Petsc includes: */
    1613#include "petscmat.h"
     
    2118#include "mex.h"
    2219
    23 #include "../../../shared/shared.h"
     20#include "../../shared/shared.h"
    2421
    2522int MatlabVectorToPetscVector(Vec* pvector,int* pvector_rows,const mxArray* mxvector){
     
    10097        return 1;
    10198}
    102 #endif
  • issm/trunk-jpl/src/c/matlab/io/MatlabVectorToSeqVec.cpp

    r12011 r12013  
     1/*!\file MatlabVectorToSeqVec.cpp
     2 */
     3
     4/*Headers:*/
     5/*{{{1*/
     6#ifdef HAVE_CONFIG_H
     7        #include <config.h>
     8#else
     9#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
     10#endif
     11
     12#include <mex.h>
     13#include <stdio.h>
     14#include <string.h>
     15#include "../../toolkits/toolkits.h"
     16#include "../../shared/shared.h"
     17#include "./matlabio.h"
     18
     19/*}}}*/
     20
    121SeqVec* MatlabVectorToSeqVec(const mxArray* dataref){
    222
  • issm/trunk-jpl/src/c/matlab/io/MatlabVectorToVector.cpp

    r12011 r12013  
     1/*!\file MatlabVectorToVector.cpp
     2 */
     3
     4/*Headers:*/
     5/*{{{1*/
     6#ifdef HAVE_CONFIG_H
     7        #include <config.h>
     8#else
     9#error "Cannot compile with HAVE_CONFIG_H symbol! run configure first!"
     10#endif
     11
     12#include <mex.h>
     13#include <stdio.h>
     14#include <string.h>
     15#include "./matlabio.h"
     16#include "../../objects/objects.h"
     17#include "../../shared/shared.h"
     18#include "../../Container/Container.h"
     19#include "../../include/include.h"
     20#include "../../toolkits/toolkits.h"
     21       
     22/*}}}*/
    123
    224Vector* MatlabVectorToVector(const mxArray* mxvector){
  • issm/trunk-jpl/src/c/matlab/io/OptionParse.cpp

    r12011 r12013  
    1313#include "./matlabio.h"
    1414
    15 #if defined(_HAVE_MATLAB_) && defined(_SERIAL_)
    1615#include <mex.h>
    1716
     
    191190        return(option);
    192191}/*}}}*/
    193 
    194 #endif
  • issm/trunk-jpl/src/c/matlab/io/PetscMatrixToDoubleMatrix.cpp

    r12011 r12013  
    1919#include "mex.h"
    2020
    21 #include "../../../shared/shared.h"
     21#include "../../shared/shared.h"
    2222#include <string>
    2323
  • issm/trunk-jpl/src/c/matlab/io/PetscVectorToDoubleVector.cpp

    r12011 r12013  
    1818#include "mex.h"
    1919
    20 #include "../../../shared/shared.h"
     20#include "../../shared/shared.h"
    2121#include <string>
    2222
     
    3434        /*Get size of vector: */
    3535        if(vector){
    36                 VecGetSize(vector,&rows);
     36                VecGetSize(petsc_vector,&rows);
    3737                if(rows){
    3838                        idxm=(int*)xmalloc(rows*sizeof(int));
     
    4040                        for(i=0;i<rows;i++)idxm[i]=i;
    4141
    42                         VecGetValues(vector,rows,idxm,vector);
     42                        VecGetValues(petsc_vector,rows,idxm,vector);
    4343                }
    4444        }
  • issm/trunk-jpl/src/c/matlab/io/PrintfFunction.cpp

    r12011 r12013  
    99#include "../../include/include.h"
    1010
    11 #if defined(_HAVE_MATLAB_) && defined(_SERIAL_)
    1211#include "mex.h"
    13 #endif
    1412
    1513int PrintfFunction(char* format,...){
  • issm/trunk-jpl/src/c/matlab/io/WriteMatlabData.cpp

    r12011 r12013  
    1111#include "../../include/include.h"
    1212#include "../../shared/shared.h"
     13#include "./matlabio.h"
    1314
    14 #if defined(_HAVE_MATLAB_) && defined(_SERIAL_)
    1515#include <mex.h>
    1616
    17 /*FUNCTION WriteData(mxArray** pdataref,DataSet* dataset){{{1*/
    18 void WriteData(mxArray** pdataref,DataSet* dataset){
    19 
    20         mxArray* dataref=NULL;
    21         char* marshalled_dataset=NULL;
    22         int   marshalled_dataset_size;
    23 
    24         /*Write a dataset: */
    25         if(dataset){
    26                         /* marshall the dataset: */
    27                         marshalled_dataset=dataset->Marshall();
    28                         marshalled_dataset_size=dataset->MarshallSize();
    29                        
    30                         dataref = mxCreateDoubleMatrix(0,0,mxREAL);
    31                         mxSetM(dataref,(mwSize)(marshalled_dataset_size/sizeof(double)));
    32                         mxSetN(dataref,(mwSize)1);
    33                         mxSetPr(dataref,(double*)marshalled_dataset);   
    34         }
    35         else{
    36                 /* return empty matrix: */
    37                 dataref=mxCreateDoubleMatrix(0,0,mxREAL);
    38         }
    39         *pdataref=dataref;
    40        
    41 }
    42 /*}}}*/
    4317/*FUNCTION WriteData(mxArray** pdataref,Matrix* matrix){{{1*/
    4418void WriteData(mxArray** pdataref,Matrix* matrix){
    4519               
     20        int i,j;
    4621        mxArray* dataref=NULL;
    4722        double*  matrix_ptr=NULL;
     
    5227               
    5328                #ifdef _HAVE_PETSC_
    54                 PetscMatrixToDoubleMatrix(&tmatrix_ptr,&rows,&cols);
     29                PetscMatrixToDoubleMatrix(&tmatrix_ptr,&rows,&cols,matrix->matrix);
    5530                #else
    5631                matrix_ptr=matrix->matrix->ToSerial();
     
    208183}
    209184/*}}}*/
    210 /*FUNCTION WriteData(mxArray** pdataref,Parameters* parameters){{{1*/
    211 void WriteData(mxArray** pdataref,Parameters* parameters){
    212 
    213         int i;
    214 
    215         /*output: */
    216         mxArray  *dataref     = NULL;
    217         mwSize    nfields;
    218         char    **fnames      = NULL;
    219         mwSize    onebyone[2] = {1,1};
    220         mwSize    ndim        = 2;
    221 
    222         /*intermediary: */
    223         Param*      param=NULL;
    224 
    225         /*Recover data from the parameters dataset: */
    226         nfields=(mwSize)parameters->Size();
    227         fnames=(char**)mxMalloc(nfields*sizeof(char*));
    228        
    229         /*Build structure in matlab workspace with all the parameter fields: */
    230         for(i=0;i<nfields;i++){
    231                 param=(Param*)parameters->GetObjectByOffset(i);
    232                 param->GetParameterName(&fnames[i]);
    233         }
    234         /*Initialize structure: */
    235         dataref=mxCreateStructArray( ndim,onebyone,nfields,(const char**)fnames);
    236 
    237         /*Fill each field: */
    238         for(i=0;i<nfields;i++){
    239 
    240                 param=(Param*)parameters->GetObjectByOffset(i);
    241                 param->SetMatlabField(dataref);
    242         }
    243                
    244         /*Assign output pointers:*/
    245         *pdataref=dataref;
    246 
    247 }
    248 /*}}}*/
    249 #endif
  • issm/trunk-jpl/src/c/matlab/io/matlabio.h

    r12011 r12013  
    1616#include "../../include/include.h"
    1717
    18 class DataSet;
    19 class Parameters;
    20 
    2118#include <mex.h>
    2219
    23 void WriteData(mxArray** pdataref,DataSet* dataset);
    2420void WriteData(mxArray** pdataref,Matrix* matrix);
    2521void WriteData(mxArray** pdataref,double* matrix, int M,int N);
     
    3127void WriteData(mxArray** pdataref,double scalar);
    3228void WriteData(mxArray** pdataref,char* string);
    33 void WriteData(DataHandle* pdataref,Parameters* parameters);
    3429
    35 void FetchData(DataSet** pdataset,const mxArray* dataref);
    3630void FetchData(double** pmatrix,int* pM,int *pN,const mxArray* dataref);
    3731void FetchData(double** pmatrix,int* pnumel,int* pndims,int** psize,const mxArray* dataref);
     
    5044void FetchData(int* pinteger,const mxArray* dataref);
    5145void FetchData(bool* pbool,const mxArray* dataref);
    52 void FetchData(Parameters** pparameters, DataHandle dataref);
    5346
    5447Option* OptionParse(char* name, const mxArray* prhs[]);
  • issm/trunk-jpl/src/c/matlab/io/mxGetAssignedField.cpp

    r12011 r12013  
    1414#endif
    1515
    16 #if defined(_HAVE_MATLAB_) && defined(_SERIAL_)
    1716#include "mex.h"
    1817
     
    4544        return mxfield;
    4645}
    47 #endif
  • issm/trunk-jpl/src/c/matlab/objects/Bamg/BamgGeom.cpp

    r12011 r12013  
     1/*!\file BamgGeom.cpp
     2 */
     3
    14#include <stdio.h>
    2 #include "../objects.h"
    3 #include "../../io/io.h"
    4 #include "../../shared/shared.h"
     5#include "../../../objects/objects.h"
     6#include "../../../io/io.h"
     7#include "../../../shared/shared.h"
     8#include "../../io/matlabio.h"
     9#include <mex.h>
    510
    611/*Constructors/Destructors*/
  • issm/trunk-jpl/src/c/matlab/objects/Bamg/BamgMesh.cpp

    r12011 r12013  
     1/*!\file BamgMesh.cpp
     2 */
     3
    14#include <stdio.h>
    2 #include "../objects.h"
    3 #include "../../io/io.h"
    4 #include "../../shared/shared.h"
     5#include "../../../objects/objects.h"
     6#include "../../../io/io.h"
     7#include "../../../shared/shared.h"
     8#include "../../io/matlabio.h"
    59
    610/*Constructors/Destructors*/
  • issm/trunk-jpl/src/c/matlab/objects/Bamg/BamgOpts.cpp

    r12011 r12013  
     1/*!\file BamgOpts.cpp
     2 */
     3
    14#include <stdio.h>
    2 #include "../../shared/shared.h"
    3 #include "../../include/include.h"
    4 #include "../objects.h"
    5 #include "../../io/io.h"
     5#include "../../../objects/objects.h"
     6#include "../../../io/io.h"
     7#include "../../../shared/shared.h"
     8#include "../../io/matlabio.h"
     9#include "../../../include/include.h"
    610
    711/*Constructors/Destructors*/
  • issm/trunk-jpl/src/c/modules/modules.h

    r11952 r12013  
    111111#include "./TimeAdaptx/TimeAdaptx.h"
    112112#include "./TriaSearchx/TriaSearchx.h"
    113 #ifdef _SERIAL_
    114113#include "./TriMeshx/TriMeshx.h"
    115 #endif
    116114#include "./ThicknessAbsMisfitx/ThicknessAbsMisfitx.h"
    117115#include "./ThicknessAbsGradientx/ThicknessAbsGradientx.h"
  • issm/trunk-jpl/src/c/objects/Numerics/Matrix.h

    r12011 r12013  
    2121#endif
    2222
    23 #if defined(_HAVE_MATLAB_) && defined(_SERIAL_)
    24 #include "mex.h"
    25 #endif
    2623class Vector;
    2724
  • issm/trunk-jpl/src/c/shared/Wrapper/wrappershared.h

    r11935 r12013  
    88#include "../../objects/objects.h"
    99
    10 #ifdef _SERIAL_
    1110int ModuleBoot(void);
    1211int ModuleEnd(void);
    13 #endif
    1412
    1513#endif
  • issm/trunk-jpl/src/mex/AverageFilter/AverageFilter.h

    r11933 r12013  
    1515#include "../../c/Container/Container.h"
    1616#include "../../c/shared/shared.h"
     17#include "../../c/issm-binding.h"
    1718
    1819#undef __FUNCT__
  • issm/trunk-jpl/src/mex/BamgConvertMesh/BamgConvertMesh.cpp

    r11933 r12013  
    6464
    6565        /*Generate output Matlab Structures*/
    66         bamggeom->SetMatlabStructureFields(BAMGGEOMOUT);
    67         bamgmesh->SetMatlabStructureFields(BAMGMESHOUT);
     66        bamggeom->SetStructureFields((void*)BAMGGEOMOUT);
     67        bamgmesh->SetStructureFields((void*)BAMGMESHOUT);
    6868
    6969        /*Clean up*/
  • issm/trunk-jpl/src/mex/BamgConvertMesh/BamgConvertMesh.h

    r11933 r12013  
    1313#include "../../c/Container/Container.h"
    1414#include "../../c/shared/shared.h"
     15#include "../../c/issm-binding.h"
    1516
    1617#undef __FUNCT__
  • issm/trunk-jpl/src/mex/BamgMesher/BamgMesher.cpp

    r6412 r12013  
    3636
    3737        /*Generate output Matlab Structures*/
    38         bamggeom_out->SetMatlabStructureFields(BAMGGEOMOUT);
    39         bamgmesh_out->SetMatlabStructureFields(BAMGMESHOUT);
     38        bamggeom_out->SetStructureFields((void*)BAMGGEOMOUT);
     39        bamgmesh_out->SetStructureFields((void*)BAMGMESHOUT);
    4040
    4141        /*Free ressources: */
  • issm/trunk-jpl/src/mex/BamgMesher/BamgMesher.h

    r11933 r12013  
    1313#include "../../c/Container/Container.h"
    1414#include "../../c/shared/shared.h"
     15#include "../../c/issm-binding.h"
    1516
    1617#undef __FUNCT__
  • issm/trunk-jpl/src/mex/BamgTriangulate/BamgTriangulate.h

    r11933 r12013  
    1313#include "../../c/Container/Container.h"
    1414#include "../../c/shared/shared.h"
     15#include "../../c/issm-binding.h"
    1516
    1617#undef __FUNCT__
  • issm/trunk-jpl/src/mex/Chaco/Chaco.h

    r11933 r12013  
    1717#include "../../c/Container/Container.h"
    1818#include "../../c/shared/shared.h"
     19#include "../../c/issm-binding.h"
    1920   
    2021/* serial input macros: */
  • issm/trunk-jpl/src/mex/ContourToMesh/ContourToMesh.h

    r11933 r12013  
    1515#include "../../c/Container/Container.h"
    1616#include "../../c/shared/shared.h"
     17#include "../../c/issm-binding.h"
    1718
    1819#undef __FUNCT__
  • issm/trunk-jpl/src/mex/ContourToNodes/ContourToNodes.h

    r11933 r12013  
    1515#include "../../c/Container/Container.h"
    1616#include "../../c/shared/shared.h"
     17#include "../../c/issm-binding.h"
    1718
    1819#undef __FUNCT__
  • issm/trunk-jpl/src/mex/ElementConnectivity/ElementConnectivity.h

    r11933 r12013  
    1515#include "../../c/Container/Container.h"
    1616#include "../../c/shared/shared.h"
     17#include "../../c/issm-binding.h"
    1718
    1819#undef __FUNCT__
  • issm/trunk-jpl/src/mex/EnumToString/EnumToString.h

    r11933 r12013  
    1313#include "../../c/Container/Container.h"
    1414#include "../../c/shared/shared.h"
     15#include "../../c/issm-binding.h"
    1516   
    1617/* serial input macros: */
  • issm/trunk-jpl/src/mex/Exp2Kml/Exp2Kml.h

    r11933 r12013  
    1313#include "../../c/Container/Container.h"
    1414#include "../../c/shared/shared.h"
     15#include "../../c/issm-binding.h"
    1516
    1617#undef __FUNCT__
  • issm/trunk-jpl/src/mex/HoleFiller/HoleFiller.h

    r11933 r12013  
    1515#include "../../c/Container/Container.h"
    1616#include "../../c/shared/shared.h"
     17#include "../../c/issm-binding.h"
    1718
    1819#undef __FUNCT__
  • issm/trunk-jpl/src/mex/InternalFront/InternalFront.h

    r11933 r12013  
    1313#include "../../c/include/globals.h"
    1414#include "../../c/shared/shared.h"
     15#include "../../c/issm-binding.h"
    1516#include "../../c/io/io.h"
    1617
  • issm/trunk-jpl/src/mex/InterpFromGridToMesh/InterpFromGridToMesh.h

    r11933 r12013  
    1313#include "../../c/Container/Container.h"
    1414#include "../../c/shared/shared.h"
     15#include "../../c/issm-binding.h"
    1516
    1617#undef __FUNCT__
  • issm/trunk-jpl/src/mex/InterpFromMesh2d/InterpFromMesh2d.h

    r11933 r12013  
    1313#include "../../c/Container/Container.h"
    1414#include "../../c/shared/shared.h"
     15#include "../../c/issm-binding.h"
    1516
    1617#undef __FUNCT__
  • issm/trunk-jpl/src/mex/InterpFromMeshToGrid/InterpFromMeshToGrid.h

    r11933 r12013  
    1515#include "../../c/Container/Container.h"
    1616#include "../../c/shared/shared.h"
     17#include "../../c/issm-binding.h"
    1718
    1819#undef __FUNCT__
  • issm/trunk-jpl/src/mex/InterpFromMeshToMesh2d/InterpFromMeshToMesh2d.h

    r11933 r12013  
    1313#include "../../c/Container/Container.h"
    1414#include "../../c/shared/shared.h"
     15#include "../../c/issm-binding.h"
    1516
    1617#undef __FUNCT__
  • issm/trunk-jpl/src/mex/InterpFromMeshToMesh3d/InterpFromMeshToMesh3d.h

    r11933 r12013  
    1313#include "../../c/Container/Container.h"
    1414#include "../../c/shared/shared.h"
     15#include "../../c/issm-binding.h"
    1516
    1617#undef __FUNCT__
  • issm/trunk-jpl/src/mex/KMLFileRead/KMLFileRead.h

    r11933 r12013  
    1313#include "../../c/Container/Container.h"
    1414#include "../../c/shared/shared.h"
     15#include "../../c/issm-binding.h"
    1516
    1617#undef __FUNCT__
  • issm/trunk-jpl/src/mex/KMLMeshWrite/KMLMeshWrite.h

    r11933 r12013  
    1313#include "../../c/Container/Container.h"
    1414#include "../../c/shared/shared.h"
     15#include "../../c/issm-binding.h"
    1516
    1617#undef __FUNCT__
  • issm/trunk-jpl/src/mex/KMLOverlay/KMLOverlay.h

    r11933 r12013  
    1313#include "../../c/Container/Container.h"
    1414#include "../../c/shared/shared.h"
     15#include "../../c/issm-binding.h"
    1516
    1617#undef __FUNCT__
  • issm/trunk-jpl/src/mex/Kml2Exp/Kml2Exp.h

    r11933 r12013  
    1313#include "../../c/Container/Container.h"
    1414#include "../../c/shared/shared.h"
     15#include "../../c/issm-binding.h"
    1516
    1617#undef __FUNCT__
  • issm/trunk-jpl/src/mex/Ll2xy/Ll2xy.h

    r11933 r12013  
    1313#include "../../c/Container/Container.h"
    1414#include "../../c/shared/shared.h"
     15#include "../../c/issm-binding.h"
    1516
    1617#undef __FUNCT__
  • issm/trunk-jpl/src/mex/Makefile.am

    r11997 r12013  
    5555if MATLAB
    5656AM_LDFLAGS  = $(MEXLINK)
    57 AM_CXXFLAGS +=  -DMATLAB -D_GNU_SOURCE -fPIC -fno-omit-frame-pointer -pthread
     57AM_CXXFLAGS +=  -D_HAVE_MATLAB_ -D_GNU_SOURCE -fPIC -fno-omit-frame-pointer -pthread
    5858LDADD       += $(MEXLIB) ../c/libISSMMatlab.a
    5959
     
    6262if PYTHON
    6363AM_LDFLAGS  = $(PYTHONLINK)
    64 AM_CXXFLAGS +=  -DNPY_NO_DEPRECATED_API
     64AM_CXXFLAGS +=  -D_HAVE_PYTHON_ -DNPY_NO_DEPRECATED_API
    6565LDADD       += $(BOOSTLIB) $(PYTHONLIB) ../c/libISSMPython.a
    6666endif
  • issm/trunk-jpl/src/mex/MeshPartition/MeshPartition.h

    r11933 r12013  
    1515#include "../../c/Container/Container.h"
    1616#include "../../c/shared/shared.h"
     17#include "../../c/issm-binding.h"
    1718
    1819#undef CLEANUP
  • issm/trunk-jpl/src/mex/MeshProfileIntersection/MeshProfileIntersection.h

    r11933 r12013  
    1515#include "../../c/Container/Container.h"
    1616#include "../../c/shared/shared.h"
     17#include "../../c/issm-binding.h"
    1718
    1819#undef __FUNCT__
  • issm/trunk-jpl/src/mex/PointCloudFindNeighbors/PointCloudFindNeighbors.h

    r11933 r12013  
    1515#include "../../c/Container/Container.h"
    1616#include "../../c/shared/shared.h"
     17#include "../../c/issm-binding.h"
    1718
    1819#undef __FUNCT__
  • issm/trunk-jpl/src/mex/PropagateFlagsFromConnectivity/PropagateFlagsFromConnectivity.h

    r11933 r12013  
    1515#include "../../c/Container/Container.h"
    1616#include "../../c/shared/shared.h"
     17#include "../../c/issm-binding.h"
    1718
    1819#undef __FUNCT__
  • issm/trunk-jpl/src/mex/Scotch/Scotch.h

    r11933 r12013  
    1717#include "../../c/Container/Container.h"
    1818#include "../../c/shared/shared.h"
     19#include "../../c/issm-binding.h"
    1920   
    2021#undef __FUNCT__
  • issm/trunk-jpl/src/mex/Shp2Kml/Shp2Kml.h

    r11933 r12013  
    1313#include "../../c/Container/Container.h"
    1414#include "../../c/shared/shared.h"
     15#include "../../c/issm-binding.h"
    1516
    1617#undef __FUNCT__
  • issm/trunk-jpl/src/mex/StringToEnum/StringToEnum.h

    r11933 r12013  
    1313#include "../../c/Container/Container.h"
    1414#include "../../c/shared/shared.h"
     15#include "../../c/issm-binding.h"
    1516   
    1617/* serial input macros: */
  • issm/trunk-jpl/src/mex/TriMesh/TriMesh.h

    r11997 r12013  
    2525#include "../../c/Container/Container.h"
    2626#include "../../c/shared/shared.h"
     27#include "../../c/issm-binding.h"
    2728#include "../../c/io/io.h"
    2829#include "../../c/EnumDefinitions/EnumDefinitions.h"
  • issm/trunk-jpl/src/mex/TriMeshNoDensity/TriMeshNoDensity.h

    r11933 r12013  
    1414#include "../../c/Container/Container.h"
    1515#include "../../c/shared/shared.h"
     16#include "../../c/issm-binding.h"
    1617
    1718void TriMeshNoDensityUsage(void);
  • issm/trunk-jpl/src/mex/TriMeshProcessRifts/TriMeshProcessRifts.h

    r11933 r12013  
    1414#include "../../c/Container/Container.h"
    1515#include "../../c/shared/shared.h"
     16#include "../../c/issm-binding.h"
    1617#include "../../c/EnumDefinitions/EnumDefinitions.h"
    1718
  • issm/trunk-jpl/src/mex/TriMeshRefine/TriMeshRefine.h

    r11933 r12013  
    1414#include "../../c/Container/Container.h"
    1515#include "../../c/shared/shared.h"
     16#include "../../c/issm-binding.h"
    1617
    1718void TriMeshRefineUsage(void);
  • issm/trunk-jpl/src/mex/TriMeshRifts/TriMeshRifts.h

    r11933 r12013  
    1414#include "../../c/Container/Container.h"
    1515#include "../../c/shared/shared.h"
     16#include "../../c/issm-binding.h"
    1617
    1718void TriMeshRiftsUsage(void);
  • issm/trunk-jpl/src/mex/TriaSearch/TriaSearch.h

    r11933 r12013  
    1212#include "../../c/Container/Container.h"
    1313#include "../../c/shared/shared.h"
     14#include "../../c/issm-binding.h"
    1415
    1516#undef __FUNCT__
  • issm/trunk-jpl/src/mex/Xy2ll/Xy2ll.h

    r11933 r12013  
    1313#include "../../c/Container/Container.h"
    1414#include "../../c/shared/shared.h"
     15#include "../../c/issm-binding.h"
    1516
    1617#undef __FUNCT__
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