Date: 2013-07-02T14:38:10+00:00

Actual source code: vmatlab.c
petsc-3.4.2 2013-07-02

      2: #include <petsc-private/viewerimpl.h>
      3: #include <mat.h>

      5: /*MC
      6:    PETSCVIEWERMATLAB - A viewer that saves the variables into a MATLAB .mat file that may be read into MATLAB
      7:        with load('filename').

      9:    Level: intermediate

     11:        Note: Currently can only save PETSc vectors to .mat files, not matrices (use the PETSCVIEWERBINARY and
     12:              ${PETSC_DIR}/bin/matlab/PetscBinaryRead.m to read matrices into matlab).

     14:              For parallel vectors obtained with DMCreateGlobalVector() or DMGetGlobalVector() the vectors are saved to
     15:              the .mat file in natural ordering. You can use DMView() to save the DMDA information to the .mat file
     16:              the fields in the MATLAB loaded da variable give the array dimensions so you can reshape the MATLAB
     17:              vector to the same multidimensional shape as it had in PETSc for plotting etc. For example,

     19: $             In your PETSc C/C++ code (assuming a two dimensional DMDA with one degree of freedom per node)
     20: $                PetscObjectSetName((PetscObject)x,"x");
     21: $                VecView(x,PETSC_VIEWER_MATLAB_WORLD);
     22: $                PetscObjectSetName((PetscObject)da,"da");
     23: $                DMView(x,PETSC_VIEWER_MATLAB_WORLD);
     24: $             Then from MATLAB
     25: $                load('matlaboutput.mat')   % matlaboutput.mat is the default filename
     26: $                xnew = zeros(da.n,da.m);
     27: $                xnew(:) = x;    % reshape one dimensional vector back to two dimensions

     29:               If you wish to put the same variable into the .mat file several times you need to give it a new
     30:               name before each call to view.

     32:               Use PetscViewerMatlabPutArray() to just put an array of doubles into the .mat file

     34: .seealso:  PETSC_VIEWER_MATLAB_(),PETSC_VIEWER_MATLAB_SELF(), PETSC_VIEWER_MATLAB_WORLD(),PetscViewerCreate(),
     35:            PetscViewerMatlabOpen(), VecView(), DMView(), PetscViewerMatlabPutArray(), PETSCVIEWERBINARY,
     36:            PETSC_ASCII_VIEWER, PetscViewerFileSetName(), PetscViewerFileSetMode()

     38: M*/

     40: typedef struct {
     41:   MATFile       *ep;
     42:   PetscMPIInt   rank;
     43:   PetscFileMode btype;
     44: } PetscViewer_Matlab;

     48: /*@C
     49:     PetscViewerMatlabPutArray - Puts an array into the MATLAB viewer.

     51:       Not collective: only processor zero saves the array

     53:     Input Parameters:
     54: +    mfile - the viewer
     55: .    m,n - the dimensions of the array
     56: .    array - the array (represented in one dimension)
     57: -    name - the name of the array

     59:    Level: advanced

     61:      Notes: Only writes array values on processor 0.

     63: @*/
     64: PetscErrorCode  PetscViewerMatlabPutArray(PetscViewer mfile,int m,int n,const PetscScalar *array,const char *name)
     65: {
     66:   PetscErrorCode     ierr;
     67:   PetscViewer_Matlab *ml = (PetscViewer_Matlab*)mfile->data;
     68:   mxArray            *mat;

     71:   if (!ml->rank) {
     72:     PetscInfo1(mfile,"Putting MATLAB array %s\n",name);
     73: #if !defined(PETSC_USE_COMPLEX)
     74:     mat  = mxCreateDoubleMatrix(m,n,mxREAL);
     75: #else
     76:     mat  = mxCreateDoubleMatrix(m,n,mxCOMPLEX);
     77: #endif
     78:     PetscMemcpy(mxGetPr(mat),array,m*n*sizeof(PetscScalar));
     79:     matPutVariable(ml->ep,name,mat);

     81:     PetscInfo1(mfile,"Put MATLAB array %s\n",name);
     82:   }
     83:   return(0);
     84: }

     88: PetscErrorCode  PetscViewerMatlabPutVariable(PetscViewer viewer,const char *name,void *mat)
     89: {
     90:   PetscViewer_Matlab *ml = (PetscViewer_Matlab*)viewer->data;

     93:   matPutVariable(ml->ep,name,(mxArray*)mat);
     94:   return(0);
     95: }

     99: /*@C
    100:     PetscViewerMatlabGetArray - Gets a variable from a MATLAB viewer into an array

    102:     Not Collective; only processor zero reads in the array

    104:     Input Parameters:
    105: +    mfile - the MATLAB file viewer
    106: .    m,n - the dimensions of the array
    107: .    array - the array (represented in one dimension)
    108: -    name - the name of the array

    110:    Level: advanced

    112:      Notes: Only reads in array values on processor 0.

    114: @*/
    115: PetscErrorCode  PetscViewerMatlabGetArray(PetscViewer mfile,int m,int n,PetscScalar *array,const char *name)
    116: {
    117:   PetscErrorCode     ierr;
    118:   PetscViewer_Matlab *ml = (PetscViewer_Matlab*)mfile->data;
    119:   mxArray            *mat;

    122:   if (!ml->rank) {
    123:     PetscInfo1(mfile,"Getting MATLAB array %s\n",name);
    124:     mat  = matGetVariable(ml->ep,name);
    125:     if (!mat) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_LIB,"Unable to get array %s from matlab",name);
    126:     PetscMemcpy(array,mxGetPr(mat),m*n*sizeof(PetscScalar));
    127:     PetscInfo1(mfile,"Got MATLAB array %s\n",name);
    128:   }
    129:   return(0);
    130: }

    134: PetscErrorCode  PetscViewerFileSetMode_Matlab(PetscViewer viewer,PetscFileMode type)
    135: {
    136:   PetscViewer_Matlab *vmatlab = (PetscViewer_Matlab*)viewer->data;

    139:   vmatlab->btype = type;
    140:   return(0);
    141: }

    143: /*
    144:         Actually opens the file
    145: */
    148: PetscErrorCode  PetscViewerFileSetName_Matlab(PetscViewer viewer,const char name[])
    149: {
    150:   PetscViewer_Matlab *vmatlab = (PetscViewer_Matlab*)viewer->data;
    151:   PetscFileMode      type     = vmatlab->btype;

    154:   if (type == (PetscFileMode) -1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ORDER,"Must call PetscViewerFileSetMode() before PetscViewerFileSetName()");
    155:   if (vmatlab->ep) matClose(vmatlab->ep);

    157:   /* only first processor opens file */
    158:   if (!vmatlab->rank) {
    159:     if (type == FILE_MODE_READ) vmatlab->ep = matOpen(name,"r");
    160:     else if (type == FILE_MODE_WRITE || type == FILE_MODE_WRITE) vmatlab->ep = matOpen(name,"w");
    161:     else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Unknown file type");
    162:   }
    163:   return(0);
    164: }

    168: PetscErrorCode PetscViewerDestroy_Matlab(PetscViewer v)
    169: {
    170:   PetscErrorCode     ierr;
    171:   PetscViewer_Matlab *vf = (PetscViewer_Matlab*)v->data;

    174:   if (vf->ep) matClose(vf->ep);
    175:   PetscFree(vf);
    176:   return(0);
    177: }

    181: PETSC_EXTERN PetscErrorCode PetscViewerCreate_Matlab(PetscViewer viewer)
    182: {
    183:   PetscErrorCode     ierr;
    184:   PetscViewer_Matlab *e;

    187:   PetscNewLog(viewer,PetscViewer_Matlab,&e);
    188:   MPI_Comm_rank(PetscObjectComm((PetscObject)viewer),&e->rank);
    189:   e->btype     = (PetscFileMode)-1;
    190:   viewer->data = (void*) e;

    192:   PetscObjectComposeFunction((PetscObject)viewer,"PetscViewerFileSetName_C",PetscViewerFileSetName_Matlab);
    193:   PetscObjectComposeFunction((PetscObject)viewer,"PetscViewerFileSetMode_C",PetscViewerFileSetMode_Matlab);

    195:   viewer->ops->destroy = PetscViewerDestroy_Matlab;
    196:   return(0);
    197: }

    201: /*@C
    202:    PetscViewerMatlabOpen - Opens a Matlab .mat file for output

    204:    Collective on MPI_Comm

    206:    Input Parameters:
    207: +  comm - MPI communicator
    208: .  name - name of file
    209: -  type - type of file
    210: $    FILE_MODE_WRITE - create new file for MATLAB output
    211: $    FILE_MODE_READ - open existing file for MATLAB input
    212: $    FILE_MODE_WRITE - open existing file for MATLAB output

    214:    Output Parameter:
    215: .  binv - PetscViewer for MATLAB output to use with the specified file

    217:    Level: beginner

    219:    Note: This PetscViewer should be destroyed with PetscViewerDestroy().

    221:     For writing files it only opens the file on processor 0 in the communicator.

    223:      This only saves Vecs it cannot be used to save Mats. We recommend using the PETSCVIEWERBINARY to save objects to be loaded into MATLAB
    224:      instead of this routine.

    226:    Concepts: MATLAB .mat files
    227:    Concepts: PetscViewerMatlab^creating

    229: .seealso: PetscViewerASCIIOpen(), PetscViewerSetFormat(), PetscViewerDestroy(), PETSCVIEWERBINARY, PetscViewerBinaryOpen()
    230:           VecView(), MatView(), VecLoad(), MatLoad()
    231: @*/
    232: PetscErrorCode  PetscViewerMatlabOpen(MPI_Comm comm,const char name[],PetscFileMode type,PetscViewer *binv)
    233: {

    237:   PetscViewerCreate(comm,binv);
    238:   PetscViewerSetType(*binv,PETSCVIEWERMATLAB);
    239:   PetscViewerFileSetMode(*binv,type);
    240:   PetscViewerFileSetName(*binv,name);
    241:   return(0);
    242: }

    244: static PetscMPIInt Petsc_Viewer_Matlab_keyval = MPI_KEYVAL_INVALID;

    248: /*@C
    249:      PETSC_VIEWER_MATLAB_ - Creates a Matlab PetscViewer shared by all processors
    250:                      in a communicator.

    252:      Collective on MPI_Comm

    254:      Input Parameter:
    255: .    comm - the MPI communicator to share the Matlab PetscViewer

    257:      Level: intermediate

    259:    Options Database Keys:
    260: $    -viewer_matlab_filename <name>

    262:    Environmental variables:
    263: -   PETSC_VIEWER_MATLAB_FILENAME

    265:      Notes:
    266:      Unlike almost all other PETSc routines, PETSC_VIEWER_MATLAB_ does not return
    267:      an error code.  The matlab PetscViewer is usually used in the form
    268: $       XXXView(XXX object,PETSC_VIEWER_MATLAB_(comm));

    270:      Use PETSC_VIEWER_SOCKET_() or PetscViewerSocketOpen() to communicator with an interactive MATLAB session.

    272: .seealso: PETSC_VIEWER_MATLAB_WORLD, PETSC_VIEWER_MATLAB_SELF, PetscViewerMatlabOpen(), PetscViewerCreate(),
    273:           PetscViewerDestroy()
    274: @*/
    275: PetscViewer  PETSC_VIEWER_MATLAB_(MPI_Comm comm)
    276: {
    278:   PetscBool      flg;
    279:   PetscViewer    viewer;
    280:   char           fname[PETSC_MAX_PATH_LEN];
    281:   MPI_Comm       ncomm;

    284:   PetscCommDuplicate(comm,&ncomm,NULL);if (ierr) {PetscError(PETSC_COMM_SELF,__LINE__,"PETSC_VIEWER_MATLAB_",__FILE__,__SDIR__,PETSC_ERR_PLIB,PETSC_ERROR_INITIAL," ");return(0);}
    285:   if (Petsc_Viewer_Matlab_keyval == MPI_KEYVAL_INVALID) {
    286:     MPI_Keyval_create(MPI_NULL_COPY_FN,MPI_NULL_DELETE_FN,&Petsc_Viewer_Matlab_keyval,0);
    287:     if (ierr) {PetscError(PETSC_COMM_SELF,__LINE__,"PETSC_VIEWER_MATLAB_",__FILE__,__SDIR__,PETSC_ERR_PLIB,PETSC_ERROR_INITIAL," ");return(0);}
    288:   }
    289:   MPI_Attr_get(ncomm,Petsc_Viewer_Matlab_keyval,(void**)&viewer,(int*)&flg);
    290:   if (ierr) {PetscError(PETSC_COMM_SELF,__LINE__,"PETSC_VIEWER_MATLAB_",__FILE__,__SDIR__,PETSC_ERR_PLIB,PETSC_ERROR_INITIAL," ");return(0);}
    291:   if (!flg) { /* PetscViewer not yet created */
    292:     PetscOptionsGetenv(ncomm,"PETSC_VIEWER_MATLAB_FILENAME",fname,PETSC_MAX_PATH_LEN,&flg);
    293:     if (ierr) {PetscError(PETSC_COMM_SELF,__LINE__,"PETSC_VIEWER_MATLAB_",__FILE__,__SDIR__,PETSC_ERR_PLIB,PETSC_ERROR_INITIAL," ");return(0);}
    294:     if (!flg) {
    295:       PetscStrcpy(fname,"matlaboutput.mat");
    296:       if (ierr) {PetscError(PETSC_COMM_SELF,__LINE__,"PETSC_VIEWER_MATLAB_",__FILE__,__SDIR__,PETSC_ERR_PLIB,PETSC_ERROR_INITIAL," ");return(0);}
    297:     }
    298:     PetscViewerMatlabOpen(ncomm,fname,FILE_MODE_WRITE,&viewer);
    299:     if (ierr) {PetscError(PETSC_COMM_SELF,__LINE__,"PETSC_VIEWER_MATLAB_",__FILE__,__SDIR__,PETSC_ERR_PLIB,PETSC_ERROR_INITIAL," ");return(0);}
    300:     PetscObjectRegisterDestroy((PetscObject)viewer);
    301:     if (ierr) {PetscError(PETSC_COMM_SELF,__LINE__,"PETSC_VIEWER_MATLAB_",__FILE__,__SDIR__,PETSC_ERR_PLIB,PETSC_ERROR_INITIAL," ");return(0);}
    302:     MPI_Attr_put(ncomm,Petsc_Viewer_Matlab_keyval,(void*)viewer);
    303:     if (ierr) {PetscError(PETSC_COMM_SELF,__LINE__,"PETSC_VIEWER_MATLAB_",__FILE__,__SDIR__,PETSC_ERR_PLIB,PETSC_ERROR_INITIAL," ");return(0);}
    304:   }
    305:   PetscCommDestroy(&ncomm);
    306:   if (ierr) {PetscError(PETSC_COMM_SELF,__LINE__,"PETSC_VIEWER_MATLAB_",__FILE__,__SDIR__,PETSC_ERR_PLIB,PETSC_ERROR_INITIAL," ");return(0);}
    307:   PetscFunctionReturn(viewer);
    308: }