Actual source code: vmatlab.c

  2: #include <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;
 69: 
 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: }
 96: 
 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;
120: 
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: }

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

140:   vmatlab->btype = type;
141:   return(0);
142: }

145: /*
146:         Actually opens the file 
147: */
151: PetscErrorCode  PetscViewerFileSetName_Matlab(PetscViewer viewer,const char name[])
152: {
153:   PetscViewer_Matlab  *vmatlab = (PetscViewer_Matlab*)viewer->data;
154:   PetscFileMode       type = vmatlab->btype;

157:   if (type == (PetscFileMode) -1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ORDER,"Must call PetscViewerFileSetMode() before PetscViewerFileSetName()");

159:   /* only first processor opens file */
160:   if (!vmatlab->rank){
161:     if (type == FILE_MODE_READ){
162:       vmatlab->ep = matOpen(name,"r");
163:     } else if (type == FILE_MODE_WRITE || type == FILE_MODE_WRITE) {
164:       vmatlab->ep = matOpen(name,"w");
165:     } else {
166:       SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Unknown file type");
167:     }
168:   }
169:   return(0);
170: }

175: PetscErrorCode PetscViewerDestroy_Matlab(PetscViewer v)
176: {
177:   PetscErrorCode     ierr;
178:   PetscViewer_Matlab *vf = (PetscViewer_Matlab*)v->data;

181:   if (vf->ep) matClose(vf->ep);
182:   PetscFree(vf);
183:   return(0);
184: }

189: PetscErrorCode  PetscViewerCreate_Matlab(PetscViewer viewer)
190: {
191:   PetscErrorCode     ierr;
192:   PetscViewer_Matlab *e;

195:   PetscNewLog(viewer,PetscViewer_Matlab,&e);
196:   MPI_Comm_rank(((PetscObject)viewer)->comm,&e->rank);
197:   e->btype     = (PetscFileMode)-1;
198:   viewer->data = (void*) e;
199:   PetscObjectComposeFunctionDynamic((PetscObject)viewer,"PetscViewerFileSetName_C","PetscViewerFileSetName_Matlab",
200:                                      PetscViewerFileSetName_Matlab);
201:   PetscObjectComposeFunctionDynamic((PetscObject)viewer,"PetscViewerFileSetMode_C","PetscViewerFileSetMode_Matlab",
202:                                      PetscViewerFileSetMode_Matlab);
203:   viewer->ops->destroy = PetscViewerDestroy_Matlab;
204:   return(0);
205: }

210: /*@C
211:    PetscViewerMatlabOpen - Opens a Matlab .mat file for output

213:    Collective on MPI_Comm

215:    Input Parameters:
216: +  comm - MPI communicator
217: .  name - name of file 
218: -  type - type of file
219: $    FILE_MODE_WRITE - create new file for MATLAB output
220: $    FILE_MODE_READ - open existing file for MATLAB input
221: $    FILE_MODE_WRITE - open existing file for MATLAB output

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

226:    Level: beginner

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

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

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

235:    Concepts: MATLAB .mat files
236:    Concepts: PetscViewerMatlab^creating

238: .seealso: PetscViewerASCIIOpen(), PetscViewerSetFormat(), PetscViewerDestroy(), PETSCVIEWERBINARY, PetscViewerBinaryOpen()
239:           VecView(), MatView(), VecLoad(), MatLoad()
240: @*/
241: PetscErrorCode  PetscViewerMatlabOpen(MPI_Comm comm,const char name[],PetscFileMode type,PetscViewer *binv)
242: {
244: 
246:   PetscViewerCreate(comm,binv);
247:   PetscViewerSetType(*binv,PETSCVIEWERMATLAB);
248:   PetscViewerFileSetMode(*binv,type);
249:   PetscViewerFileSetName(*binv,name);
250:   return(0);
251: }

253: static PetscMPIInt Petsc_Viewer_Matlab_keyval = MPI_KEYVAL_INVALID;

257: /*@C
258:      PETSC_VIEWER_MATLAB_ - Creates a Matlab PetscViewer shared by all processors 
259:                      in a communicator.

261:      Collective on MPI_Comm

263:      Input Parameter:
264: .    comm - the MPI communicator to share the Matlab PetscViewer
265:     
266:      Level: intermediate

268:    Options Database Keys:
269: $    -viewer_matlab_filename <name>

271:    Environmental variables:
272: -   PETSC_VIEWER_MATLAB_FILENAME

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

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

281: .seealso: PETSC_VIEWER_MATLAB_WORLD, PETSC_VIEWER_MATLAB_SELF, PetscViewerMatlabOpen(), PetscViewerCreate(),
282:           PetscViewerDestroy()
283: @*/
284: PetscViewer  PETSC_VIEWER_MATLAB_(MPI_Comm comm)
285: {
287:   PetscBool      flg;
288:   PetscViewer    viewer;
289:   char           fname[PETSC_MAX_PATH_LEN];
290:   MPI_Comm       ncomm;

293:   PetscCommDuplicate(comm,&ncomm,PETSC_NULL);if (ierr) {PetscError(PETSC_COMM_SELF,__LINE__,"PETSC_VIEWER_MATLAB_",__FILE__,__SDIR__,PETSC_ERR_PLIB,PETSC_ERROR_INITIAL," ");return(0);}
294:   if (Petsc_Viewer_Matlab_keyval == MPI_KEYVAL_INVALID) {
295:     MPI_Keyval_create(MPI_NULL_COPY_FN,MPI_NULL_DELETE_FN,&Petsc_Viewer_Matlab_keyval,0);
296:     if (ierr) {PetscError(PETSC_COMM_SELF,__LINE__,"PETSC_VIEWER_MATLAB_",__FILE__,__SDIR__,PETSC_ERR_PLIB,PETSC_ERROR_INITIAL," ");return(0);}
297:   }
298:   MPI_Attr_get(ncomm,Petsc_Viewer_Matlab_keyval,(void **)&viewer,(int*)&flg);
299:   if (ierr) {PetscError(PETSC_COMM_SELF,__LINE__,"PETSC_VIEWER_MATLAB_",__FILE__,__SDIR__,PETSC_ERR_PLIB,PETSC_ERROR_INITIAL," ");return(0);}
300:   if (!flg) { /* PetscViewer not yet created */
301:     PetscOptionsGetenv(ncomm,"PETSC_VIEWER_MATLAB_FILENAME",fname,PETSC_MAX_PATH_LEN,&flg);
302:     if (ierr) {PetscError(PETSC_COMM_SELF,__LINE__,"PETSC_VIEWER_MATLAB_",__FILE__,__SDIR__,PETSC_ERR_PLIB,PETSC_ERROR_INITIAL," ");return(0);}
303:     if (!flg) {
304:       PetscStrcpy(fname,"matlaboutput.mat");
305:       if (ierr) {PetscError(PETSC_COMM_SELF,__LINE__,"PETSC_VIEWER_MATLAB_",__FILE__,__SDIR__,PETSC_ERR_PLIB,PETSC_ERROR_INITIAL," ");return(0);}
306:     }
307:     PetscViewerMatlabOpen(ncomm,fname,FILE_MODE_WRITE,&viewer);
308:     if (ierr) {PetscError(PETSC_COMM_SELF,__LINE__,"PETSC_VIEWER_MATLAB_",__FILE__,__SDIR__,PETSC_ERR_PLIB,PETSC_ERROR_INITIAL," ");return(0);}
309:     PetscObjectRegisterDestroy((PetscObject)viewer);
310:     if (ierr) {PetscError(PETSC_COMM_SELF,__LINE__,"PETSC_VIEWER_MATLAB_",__FILE__,__SDIR__,PETSC_ERR_PLIB,PETSC_ERROR_INITIAL," ");return(0);}
311:     MPI_Attr_put(ncomm,Petsc_Viewer_Matlab_keyval,(void*)viewer);
312:     if (ierr) {PetscError(PETSC_COMM_SELF,__LINE__,"PETSC_VIEWER_MATLAB_",__FILE__,__SDIR__,PETSC_ERR_PLIB,PETSC_ERROR_INITIAL," ");return(0);}
313:   }
314:   PetscCommDestroy(&ncomm);
315:   if (ierr) {PetscError(PETSC_COMM_SELF,__LINE__,"PETSC_VIEWER_MATLAB_",__FILE__,__SDIR__,PETSC_ERR_PLIB,PETSC_ERROR_INITIAL," ");return(0);}
316:   PetscFunctionReturn(viewer);
317: }