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

# Diff of /pkg/src/Csparse.c

revision 2175, Wed Apr 23 11:23:50 2008 UTC revision 2236, Wed Jul 23 16:48:14 2008 UTC
# Line 23  Line 23
23      if (length(islot) < xp[ncol]) /* allow larger slots from over-allocation!*/      if (length(islot) < xp[ncol]) /* allow larger slots from over-allocation!*/
24          return          return
25              mkString(_("last element of slot p must match length of slots i and x"));              mkString(_("last element of slot p must match length of slots i and x"));
26      for (j = 0; j < length(islot); j++) {      for (j = 0; j < xp[ncol]; j++) {
27          if (xi[j] < 0 || xi[j] >= nrow)          if (xi[j] < 0 || xi[j] >= nrow)
28              return mkString(_("all row indices must be between 0 and nrow-1"));              return mkString(_("all row indices must be between 0 and nrow-1"));
29      }      }
# Line 31  Line 31
31      for (j = 0; j < ncol; j++) {      for (j = 0; j < ncol; j++) {
32          if (xp[j] > xp[j+1])          if (xp[j] > xp[j+1])
33              return mkString(_("slot p must be non-decreasing"));              return mkString(_("slot p must be non-decreasing"));
34          if(sorted)          if(sorted) /* only act if >= 2 entries in column j : */
35              for (k = xp[j] + 1; k < xp[j + 1]; k++) {              for (k = xp[j] + 1; k < xp[j + 1]; k++) {
36                  if (xi[k] < xi[k - 1])                  if (xi[k] < xi[k - 1])
37                      sorted = FALSE;                      sorted = FALSE;
# Line 40  Line 40
40              }              }
41      }      }
42      if (!sorted) {      if (!sorted) {
43          CHM_SP chx = AS_CHM_SP(x);          CHM_SP chx = (CHM_SP) alloca(sizeof(cholmod_sparse));
44          R_CheckStack();          R_CheckStack();
45            as_cholmod_sparse(chx, x, FALSE, TRUE); /* includes cholmod_sort() ! */
46            /* as chx = AS_CHM_SP__(x)  but  ^^^^  sorting x in_place (no copying)*/
47
cholmod_sort(chx, &c);
48          /* Now re-check that row indices are *strictly* increasing          /* Now re-check that row indices are *strictly* increasing
49           * (and not just increasing) within each column : */           * (and not just increasing) within each column : */
50          for (j = 0; j < ncol; j++) {          for (j = 0; j < ncol; j++) {
# Line 109  Line 110
110   * FIXME: replace by non-CHOLMOD code ! */   * FIXME: replace by non-CHOLMOD code ! */
111  SEXP Csparse_to_dense(SEXP x)  SEXP Csparse_to_dense(SEXP x)
112  {  {
113      CHM_SP chxs = AS_CHM_SP(x);      CHM_SP chxs = AS_CHM_SP__(x);
114      /* This loses the symmetry property, since cholmod_dense has none,      /* This loses the symmetry property, since cholmod_dense has none,
115       * BUT, much worse (FIXME!), it also transforms CHOLMOD_PATTERN ("n") matrices       * BUT, much worse (FIXME!), it also transforms CHOLMOD_PATTERN ("n") matrices
116       * to numeric (CHOLMOD_REAL) ones : */       * to numeric (CHOLMOD_REAL) ones : */
# Line 122  Line 123
123
124  SEXP Csparse_to_nz_pattern(SEXP x, SEXP tri)  SEXP Csparse_to_nz_pattern(SEXP x, SEXP tri)
125  {  {
126      CHM_SP chxs = AS_CHM_SP(x);      CHM_SP chxs = AS_CHM_SP__(x);
127      CHM_SP chxcp = cholmod_copy(chxs, chxs->stype, CHOLMOD_PATTERN, &c);      CHM_SP chxcp = cholmod_copy(chxs, chxs->stype, CHOLMOD_PATTERN, &c);
128      int tr = asLogical(tri);      int tr = asLogical(tri);
129      R_CheckStack();      R_CheckStack();
# Line 135  Line 136
136
137  SEXP Csparse_to_matrix(SEXP x)  SEXP Csparse_to_matrix(SEXP x)
138  {  {
139      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),
140                                 1 /*do_free*/, GET_SLOT(x, Matrix_DimNamesSym));                                 1 /*do_free*/, GET_SLOT(x, Matrix_DimNamesSym));
141  }  }
142
143  SEXP Csparse_to_Tsparse(SEXP x, SEXP tri)  SEXP Csparse_to_Tsparse(SEXP x, SEXP tri)
144  {  {
145      CHM_SP chxs = AS_CHM_SP(x);      CHM_SP chxs = AS_CHM_SP__(x);
146      CHM_TR chxt = cholmod_sparse_to_triplet(chxs, &c);      CHM_TR chxt = cholmod_sparse_to_triplet(chxs, &c);
147      int tr = asLogical(tri);      int tr = asLogical(tri);
148      int Rkind = (chxs->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chxs->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
# Line 156  Line 157
157  /* this used to be called  sCMatrix_to_gCMatrix(..)   [in ./dsCMatrix.c ]: */  /* this used to be called  sCMatrix_to_gCMatrix(..)   [in ./dsCMatrix.c ]: */
158  SEXP Csparse_symmetric_to_general(SEXP x)  SEXP Csparse_symmetric_to_general(SEXP x)
159  {  {
160      CHM_SP chx = AS_CHM_SP(x), chgx;      CHM_SP chx = AS_CHM_SP__(x), chgx;
161      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
162      R_CheckStack();      R_CheckStack();
163
# Line 170  Line 171
171
172  SEXP Csparse_general_to_symmetric(SEXP x, SEXP uplo)  SEXP Csparse_general_to_symmetric(SEXP x, SEXP uplo)
173  {  {
174      CHM_SP chx = AS_CHM_SP(x), chgx;      CHM_SP chx = AS_CHM_SP__(x), chgx;
175      int uploT = (*CHAR(STRING_ELT(uplo,0)) == 'U') ? 1 : -1;      int uploT = (*CHAR(STRING_ELT(uplo,0)) == 'U') ? 1 : -1;
176      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
177      R_CheckStack();      R_CheckStack();
# Line 185  Line 186
186  {  {
187      /* TODO: lgCMatrix & igC* currently go via double prec. cholmod -      /* TODO: lgCMatrix & igC* currently go via double prec. cholmod -
188       *       since cholmod (& cs) lacks sparse 'int' matrices */       *       since cholmod (& cs) lacks sparse 'int' matrices */
189      CHM_SP chx = AS_CHM_SP(x);      CHM_SP chx = AS_CHM_SP__(x);
190      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
191      CHM_SP chxt = cholmod_transpose(chx, chx->xtype, &c);      CHM_SP chxt = cholmod_transpose(chx, chx->xtype, &c);
192      SEXP dn = PROTECT(duplicate(GET_SLOT(x, Matrix_DimNamesSym))), tmp;      SEXP dn = PROTECT(duplicate(GET_SLOT(x, Matrix_DimNamesSym))), tmp;
# Line 204  Line 205
205  SEXP Csparse_Csparse_prod(SEXP a, SEXP b)  SEXP Csparse_Csparse_prod(SEXP a, SEXP b)
206  {  {
207      CHM_SP      CHM_SP
208          cha = AS_CHM_SP(Csparse_diagU2N(a)),          cha = AS_CHM_SP(a),
209          chb = AS_CHM_SP(Csparse_diagU2N(b)),          chb = AS_CHM_SP(b),
210          chc = cholmod_ssmult(cha, chb, /*out_stype:*/ 0,          chc = cholmod_ssmult(cha, chb, /*out_stype:*/ 0,
211                               cha->xtype, /*out sorted:*/ 1, &c);                               cha->xtype, /*out sorted:*/ 1, &c);
212      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 243
243  {  {
244      int tr = asLogical(trans);      int tr = asLogical(trans);
245      CHM_SP      CHM_SP
246          cha = AS_CHM_SP(Csparse_diagU2N(a)),          cha = AS_CHM_SP(a),
247          chb = AS_CHM_SP(Csparse_diagU2N(b)),          chb = AS_CHM_SP(b),
248          chTr, chc;          chTr, chc;
249      const char *cl_a = class_P(a), *cl_b = class_P(b);      const char *cl_a = class_P(a), *cl_b = class_P(b);
250      char diag[] = {'\0', '\0'};      char diag[] = {'\0', '\0'};
# Line 277  Line 278
278
279  SEXP Csparse_dense_prod(SEXP a, SEXP b)  SEXP Csparse_dense_prod(SEXP a, SEXP b)
280  {  {
281      CHM_SP cha = AS_CHM_SP(Csparse_diagU2N(a));      CHM_SP cha = AS_CHM_SP(a);
282      SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));      SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));
283      CHM_DN chb = AS_CHM_DN(b_M);      CHM_DN chb = AS_CHM_DN(b_M);
284      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 298
298
299  SEXP Csparse_dense_crossprod(SEXP a, SEXP b)  SEXP Csparse_dense_crossprod(SEXP a, SEXP b)
300  {  {
301      CHM_SP cha = AS_CHM_SP(Csparse_diagU2N(a));      CHM_SP cha = AS_CHM_SP(a);
302      SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));      SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));
303      CHM_DN chb = AS_CHM_DN(b_M);      CHM_DN chb = AS_CHM_DN(b_M);
304      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 322
322  {  {
323      int trip = asLogical(triplet),      int trip = asLogical(triplet),
324          tr   = asLogical(trans); /* gets reversed because _aat is tcrossprod */          tr   = asLogical(trans); /* gets reversed because _aat is tcrossprod */
325      CHM_TR cht = trip ? AS_CHM_TR(Tsparse_diagU2N(x)) : (CHM_TR) NULL;      CHM_TR cht = trip ? AS_CHM_TR(x) : (CHM_TR) NULL;
326      CHM_SP chcp, chxt,      CHM_SP chcp, chxt,
327          chx = (trip ?          chx = (trip ?
328                 cholmod_triplet_to_sparse(cht, cht->nnz, &c) :                 cholmod_triplet_to_sparse(cht, cht->nnz, &c) :
329                 AS_CHM_SP(Csparse_diagU2N(x)));                 AS_CHM_SP(x));
330      SEXP dn = PROTECT(allocVector(VECSXP, 2));      SEXP dn = PROTECT(allocVector(VECSXP, 2));
331      R_CheckStack();      R_CheckStack();
332
# Line 352  Line 353
353      const char *cl = class_P(x);      const char *cl = class_P(x);
354      /* dtCMatrix, etc; [1] = the second character =?= 't' for triangular */      /* dtCMatrix, etc; [1] = the second character =?= 't' for triangular */
355      int tr = (cl[1] == 't');      int tr = (cl[1] == 't');
356      CHM_SP chx = AS_CHM_SP(x);      CHM_SP chx = AS_CHM_SP__(x);
357      CHM_SP ans = cholmod_copy(chx, chx->stype, chx->xtype, &c);      CHM_SP ans = cholmod_copy(chx, chx->stype, chx->xtype, &c);
358      double dtol = asReal(tol);      double dtol = asReal(tol);
359      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
# Line 368  Line 369
369
370  SEXP Csparse_horzcat(SEXP x, SEXP y)  SEXP Csparse_horzcat(SEXP x, SEXP y)
371  {  {
372      CHM_SP chx = AS_CHM_SP(x), chy = AS_CHM_SP(y);      CHM_SP chx = AS_CHM_SP__(x), chy = AS_CHM_SP__(y);
373      int Rkind = 0; /* only for "d" - FIXME */      int Rkind = 0; /* only for "d" - FIXME */
374      R_CheckStack();      R_CheckStack();
375
# Line 379  Line 380
380
381  SEXP Csparse_vertcat(SEXP x, SEXP y)  SEXP Csparse_vertcat(SEXP x, SEXP y)
382  {  {
383      CHM_SP chx = AS_CHM_SP(x), chy = AS_CHM_SP(y);      CHM_SP chx = AS_CHM_SP__(x), chy = AS_CHM_SP__(y);
384      int Rkind = 0; /* only for "d" - FIXME */      int Rkind = 0; /* only for "d" - FIXME */
385      R_CheckStack();      R_CheckStack();
386
# Line 390  Line 391
391
392  SEXP Csparse_band(SEXP x, SEXP k1, SEXP k2)  SEXP Csparse_band(SEXP x, SEXP k1, SEXP k2)
393  {  {
394      CHM_SP chx = AS_CHM_SP(x);      CHM_SP chx = AS_CHM_SP__(x);
395      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
396      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);
397      R_CheckStack();      R_CheckStack();
# Line 409  Line 410
410          return (x);          return (x);
411      }      }
412      else { /* unit triangular (diag='U'): "fill the diagonal" & diag:= "N" */      else { /* unit triangular (diag='U'): "fill the diagonal" & diag:= "N" */
413          CHM_SP chx = AS_CHM_SP(x);          CHM_SP chx = AS_CHM_SP__(x);
414          CHM_SP eye = cholmod_speye(chx->nrow, chx->ncol, chx->xtype, &c);          CHM_SP eye = cholmod_speye(chx->nrow, chx->ncol, chx->xtype, &c);
415          double one[] = {1, 0};          double one[] = {1, 0};
416          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 435
435      }      }
436      else { /* triangular with diag='N'): now drop the diagonal */      else { /* triangular with diag='N'): now drop the diagonal */
437          /* duplicate, since chx will be modified: */          /* duplicate, since chx will be modified: */
438          CHM_SP chx = AS_CHM_SP(duplicate(x));          CHM_SP chx = AS_CHM_SP__(duplicate(x));
439          int uploT = (*uplo_P(x) == 'U') ? 1 : -1,          int uploT = (*uplo_P(x) == 'U') ? 1 : -1,
440              Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;              Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
441          R_CheckStack();          R_CheckStack();
# Line 449  Line 450
450
451  SEXP Csparse_submatrix(SEXP x, SEXP i, SEXP j)  SEXP Csparse_submatrix(SEXP x, SEXP i, SEXP j)
452  {  {
453      CHM_SP chx = AS_CHM_SP(x);      CHM_SP chx = AS_CHM_SP__(x);
454      int rsize = (isNull(i)) ? -1 : LENGTH(i),      int rsize = (isNull(i)) ? -1 : LENGTH(i),
455          csize = (isNull(j)) ? -1 : LENGTH(j);          csize = (isNull(j)) ? -1 : LENGTH(j);
456      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
# Line 474  Line 475
475      if (!f)      if (!f)
476          error(_("failure to open file \"%s\" for writing"),          error(_("failure to open file \"%s\" for writing"),
477                CHAR(asChar(fname)));                CHAR(asChar(fname)));
478      if (!cholmod_write_sparse(f, AS_CHM_SP(Csparse_diagU2N(x)),      if (!cholmod_write_sparse(f, AS_CHM_SP(x),
479                                (CHM_SP)NULL, (char*) NULL, &c))                                (CHM_SP)NULL, (char*) NULL, &c))
480          error(_("cholmod_write_sparse returned error code"));          error(_("cholmod_write_sparse returned error code"));
481      fclose(f);      fclose(f);

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 Removed from v.2175 changed lines Added in v.2236