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[matrix] Diff of /pkg/src/Csparse.c
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Diff of /pkg/src/Csparse.c

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revision 2175, Wed Apr 23 11:23:50 2008 UTC revision 2223, Fri Jul 18 23:04:48 2008 UTC
# Line 40  Line 40 
40              }              }
41      }      }
42      if (!sorted) {      if (!sorted) {
43          CHM_SP chx = AS_CHM_SP(x);          CHM_SP chx = AS_CHM_SP__(x);
44          R_CheckStack();          R_CheckStack();
45    
46          cholmod_sort(chx, &c);          cholmod_sort(chx, &c);
# Line 109  Line 109 
109   * FIXME: replace by non-CHOLMOD code ! */   * FIXME: replace by non-CHOLMOD code ! */
110  SEXP Csparse_to_dense(SEXP x)  SEXP Csparse_to_dense(SEXP x)
111  {  {
112      CHM_SP chxs = AS_CHM_SP(x);      CHM_SP chxs = AS_CHM_SP__(x);
113      /* This loses the symmetry property, since cholmod_dense has none,      /* This loses the symmetry property, since cholmod_dense has none,
114       * BUT, much worse (FIXME!), it also transforms CHOLMOD_PATTERN ("n") matrices       * BUT, much worse (FIXME!), it also transforms CHOLMOD_PATTERN ("n") matrices
115       * to numeric (CHOLMOD_REAL) ones : */       * to numeric (CHOLMOD_REAL) ones : */
# Line 122  Line 122 
122    
123  SEXP Csparse_to_nz_pattern(SEXP x, SEXP tri)  SEXP Csparse_to_nz_pattern(SEXP x, SEXP tri)
124  {  {
125      CHM_SP chxs = AS_CHM_SP(x);      CHM_SP chxs = AS_CHM_SP__(x);
126      CHM_SP chxcp = cholmod_copy(chxs, chxs->stype, CHOLMOD_PATTERN, &c);      CHM_SP chxcp = cholmod_copy(chxs, chxs->stype, CHOLMOD_PATTERN, &c);
127      int tr = asLogical(tri);      int tr = asLogical(tri);
128      R_CheckStack();      R_CheckStack();
# Line 135  Line 135 
135    
136  SEXP Csparse_to_matrix(SEXP x)  SEXP Csparse_to_matrix(SEXP x)
137  {  {
138      return chm_dense_to_matrix(cholmod_sparse_to_dense(AS_CHM_SP(x), &c),      return chm_dense_to_matrix(cholmod_sparse_to_dense(AS_CHM_SP__(x), &c),
139                                 1 /*do_free*/, GET_SLOT(x, Matrix_DimNamesSym));                                 1 /*do_free*/, GET_SLOT(x, Matrix_DimNamesSym));
140  }  }
141    
142  SEXP Csparse_to_Tsparse(SEXP x, SEXP tri)  SEXP Csparse_to_Tsparse(SEXP x, SEXP tri)
143  {  {
144      CHM_SP chxs = AS_CHM_SP(x);      CHM_SP chxs = AS_CHM_SP__(x);
145      CHM_TR chxt = cholmod_sparse_to_triplet(chxs, &c);      CHM_TR chxt = cholmod_sparse_to_triplet(chxs, &c);
146      int tr = asLogical(tri);      int tr = asLogical(tri);
147      int Rkind = (chxs->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chxs->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
# Line 156  Line 156 
156  /* this used to be called  sCMatrix_to_gCMatrix(..)   [in ./dsCMatrix.c ]: */  /* this used to be called  sCMatrix_to_gCMatrix(..)   [in ./dsCMatrix.c ]: */
157  SEXP Csparse_symmetric_to_general(SEXP x)  SEXP Csparse_symmetric_to_general(SEXP x)
158  {  {
159      CHM_SP chx = AS_CHM_SP(x), chgx;      CHM_SP chx = AS_CHM_SP__(x), chgx;
160      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
161      R_CheckStack();      R_CheckStack();
162    
# Line 170  Line 170 
170    
171  SEXP Csparse_general_to_symmetric(SEXP x, SEXP uplo)  SEXP Csparse_general_to_symmetric(SEXP x, SEXP uplo)
172  {  {
173      CHM_SP chx = AS_CHM_SP(x), chgx;      CHM_SP chx = AS_CHM_SP__(x), chgx;
174      int uploT = (*CHAR(STRING_ELT(uplo,0)) == 'U') ? 1 : -1;      int uploT = (*CHAR(STRING_ELT(uplo,0)) == 'U') ? 1 : -1;
175      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
176      R_CheckStack();      R_CheckStack();
# Line 185  Line 185 
185  {  {
186      /* TODO: lgCMatrix & igC* currently go via double prec. cholmod -      /* TODO: lgCMatrix & igC* currently go via double prec. cholmod -
187       *       since cholmod (& cs) lacks sparse 'int' matrices */       *       since cholmod (& cs) lacks sparse 'int' matrices */
188      CHM_SP chx = AS_CHM_SP(x);      CHM_SP chx = AS_CHM_SP__(x);
189      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
190      CHM_SP chxt = cholmod_transpose(chx, chx->xtype, &c);      CHM_SP chxt = cholmod_transpose(chx, chx->xtype, &c);
191      SEXP dn = PROTECT(duplicate(GET_SLOT(x, Matrix_DimNamesSym))), tmp;      SEXP dn = PROTECT(duplicate(GET_SLOT(x, Matrix_DimNamesSym))), tmp;
# Line 204  Line 204 
204  SEXP Csparse_Csparse_prod(SEXP a, SEXP b)  SEXP Csparse_Csparse_prod(SEXP a, SEXP b)
205  {  {
206      CHM_SP      CHM_SP
207          cha = AS_CHM_SP(Csparse_diagU2N(a)),          cha = AS_CHM_SP(a),
208          chb = AS_CHM_SP(Csparse_diagU2N(b)),          chb = AS_CHM_SP(b),
209          chc = cholmod_ssmult(cha, chb, /*out_stype:*/ 0,          chc = cholmod_ssmult(cha, chb, /*out_stype:*/ 0,
210                               cha->xtype, /*out sorted:*/ 1, &c);                               cha->xtype, /*out sorted:*/ 1, &c);
211      const char *cl_a = class_P(a), *cl_b = class_P(b);      const char *cl_a = class_P(a), *cl_b = class_P(b);
# Line 242  Line 242 
242  {  {
243      int tr = asLogical(trans);      int tr = asLogical(trans);
244      CHM_SP      CHM_SP
245          cha = AS_CHM_SP(Csparse_diagU2N(a)),          cha = AS_CHM_SP(a),
246          chb = AS_CHM_SP(Csparse_diagU2N(b)),          chb = AS_CHM_SP(b),
247          chTr, chc;          chTr, chc;
248      const char *cl_a = class_P(a), *cl_b = class_P(b);      const char *cl_a = class_P(a), *cl_b = class_P(b);
249      char diag[] = {'\0', '\0'};      char diag[] = {'\0', '\0'};
# Line 277  Line 277 
277    
278  SEXP Csparse_dense_prod(SEXP a, SEXP b)  SEXP Csparse_dense_prod(SEXP a, SEXP b)
279  {  {
280      CHM_SP cha = AS_CHM_SP(Csparse_diagU2N(a));      CHM_SP cha = AS_CHM_SP(a);
281      SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));      SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));
282      CHM_DN chb = AS_CHM_DN(b_M);      CHM_DN chb = AS_CHM_DN(b_M);
283      CHM_DN chc = cholmod_allocate_dense(cha->nrow, chb->ncol, cha->nrow,      CHM_DN chc = cholmod_allocate_dense(cha->nrow, chb->ncol, cha->nrow,
# Line 297  Line 297 
297    
298  SEXP Csparse_dense_crossprod(SEXP a, SEXP b)  SEXP Csparse_dense_crossprod(SEXP a, SEXP b)
299  {  {
300      CHM_SP cha = AS_CHM_SP(Csparse_diagU2N(a));      CHM_SP cha = AS_CHM_SP(a);
301      SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));      SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));
302      CHM_DN chb = AS_CHM_DN(b_M);      CHM_DN chb = AS_CHM_DN(b_M);
303      CHM_DN chc = cholmod_allocate_dense(cha->ncol, chb->ncol, cha->ncol,      CHM_DN chc = cholmod_allocate_dense(cha->ncol, chb->ncol, cha->ncol,
# Line 321  Line 321 
321  {  {
322      int trip = asLogical(triplet),      int trip = asLogical(triplet),
323          tr   = asLogical(trans); /* gets reversed because _aat is tcrossprod */          tr   = asLogical(trans); /* gets reversed because _aat is tcrossprod */
324      CHM_TR cht = trip ? AS_CHM_TR(Tsparse_diagU2N(x)) : (CHM_TR) NULL;      CHM_TR cht = trip ? AS_CHM_TR(x) : (CHM_TR) NULL;
325      CHM_SP chcp, chxt,      CHM_SP chcp, chxt,
326          chx = (trip ?          chx = (trip ?
327                 cholmod_triplet_to_sparse(cht, cht->nnz, &c) :                 cholmod_triplet_to_sparse(cht, cht->nnz, &c) :
328                 AS_CHM_SP(Csparse_diagU2N(x)));                 AS_CHM_SP(x));
329      SEXP dn = PROTECT(allocVector(VECSXP, 2));      SEXP dn = PROTECT(allocVector(VECSXP, 2));
330      R_CheckStack();      R_CheckStack();
331    
# Line 352  Line 352 
352      const char *cl = class_P(x);      const char *cl = class_P(x);
353      /* dtCMatrix, etc; [1] = the second character =?= 't' for triangular */      /* dtCMatrix, etc; [1] = the second character =?= 't' for triangular */
354      int tr = (cl[1] == 't');      int tr = (cl[1] == 't');
355      CHM_SP chx = AS_CHM_SP(x);      CHM_SP chx = AS_CHM_SP__(x);
356      CHM_SP ans = cholmod_copy(chx, chx->stype, chx->xtype, &c);      CHM_SP ans = cholmod_copy(chx, chx->stype, chx->xtype, &c);
357      double dtol = asReal(tol);      double dtol = asReal(tol);
358      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
# Line 368  Line 368 
368    
369  SEXP Csparse_horzcat(SEXP x, SEXP y)  SEXP Csparse_horzcat(SEXP x, SEXP y)
370  {  {
371      CHM_SP chx = AS_CHM_SP(x), chy = AS_CHM_SP(y);      CHM_SP chx = AS_CHM_SP__(x), chy = AS_CHM_SP__(y);
372      int Rkind = 0; /* only for "d" - FIXME */      int Rkind = 0; /* only for "d" - FIXME */
373      R_CheckStack();      R_CheckStack();
374    
# Line 379  Line 379 
379    
380  SEXP Csparse_vertcat(SEXP x, SEXP y)  SEXP Csparse_vertcat(SEXP x, SEXP y)
381  {  {
382      CHM_SP chx = AS_CHM_SP(x), chy = AS_CHM_SP(y);      CHM_SP chx = AS_CHM_SP__(x), chy = AS_CHM_SP__(y);
383      int Rkind = 0; /* only for "d" - FIXME */      int Rkind = 0; /* only for "d" - FIXME */
384      R_CheckStack();      R_CheckStack();
385    
# Line 390  Line 390 
390    
391  SEXP Csparse_band(SEXP x, SEXP k1, SEXP k2)  SEXP Csparse_band(SEXP x, SEXP k1, SEXP k2)
392  {  {
393      CHM_SP chx = AS_CHM_SP(x);      CHM_SP chx = AS_CHM_SP__(x);
394      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
395      CHM_SP ans = cholmod_band(chx, asInteger(k1), asInteger(k2), chx->xtype, &c);      CHM_SP ans = cholmod_band(chx, asInteger(k1), asInteger(k2), chx->xtype, &c);
396      R_CheckStack();      R_CheckStack();
# Line 409  Line 409 
409          return (x);          return (x);
410      }      }
411      else { /* unit triangular (diag='U'): "fill the diagonal" & diag:= "N" */      else { /* unit triangular (diag='U'): "fill the diagonal" & diag:= "N" */
412          CHM_SP chx = AS_CHM_SP(x);          CHM_SP chx = AS_CHM_SP__(x);
413          CHM_SP eye = cholmod_speye(chx->nrow, chx->ncol, chx->xtype, &c);          CHM_SP eye = cholmod_speye(chx->nrow, chx->ncol, chx->xtype, &c);
414          double one[] = {1, 0};          double one[] = {1, 0};
415          CHM_SP ans = cholmod_add(chx, eye, one, one, TRUE, TRUE, &c);          CHM_SP ans = cholmod_add(chx, eye, one, one, TRUE, TRUE, &c);
# Line 434  Line 434 
434      }      }
435      else { /* triangular with diag='N'): now drop the diagonal */      else { /* triangular with diag='N'): now drop the diagonal */
436          /* duplicate, since chx will be modified: */          /* duplicate, since chx will be modified: */
437          CHM_SP chx = AS_CHM_SP(duplicate(x));          CHM_SP chx = AS_CHM_SP__(duplicate(x));
438          int uploT = (*uplo_P(x) == 'U') ? 1 : -1,          int uploT = (*uplo_P(x) == 'U') ? 1 : -1,
439              Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;              Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
440          R_CheckStack();          R_CheckStack();
# Line 449  Line 449 
449    
450  SEXP Csparse_submatrix(SEXP x, SEXP i, SEXP j)  SEXP Csparse_submatrix(SEXP x, SEXP i, SEXP j)
451  {  {
452      CHM_SP chx = AS_CHM_SP(x);      CHM_SP chx = AS_CHM_SP__(x);
453      int rsize = (isNull(i)) ? -1 : LENGTH(i),      int rsize = (isNull(i)) ? -1 : LENGTH(i),
454          csize = (isNull(j)) ? -1 : LENGTH(j);          csize = (isNull(j)) ? -1 : LENGTH(j);
455      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
# Line 474  Line 474 
474      if (!f)      if (!f)
475          error(_("failure to open file \"%s\" for writing"),          error(_("failure to open file \"%s\" for writing"),
476                CHAR(asChar(fname)));                CHAR(asChar(fname)));
477      if (!cholmod_write_sparse(f, AS_CHM_SP(Csparse_diagU2N(x)),      if (!cholmod_write_sparse(f, AS_CHM_SP(x),
478                                (CHM_SP)NULL, (char*) NULL, &c))                                (CHM_SP)NULL, (char*) NULL, &c))
479          error(_("cholmod_write_sparse returned error code"));          error(_("cholmod_write_sparse returned error code"));
480      fclose(f);      fclose(f);

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