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

Diff of /pkg/Matrix/src/Csparse.c

revision 2279, Fri Oct 3 09:15:54 2008 UTC revision 2299, Fri Oct 17 16:07:38 2008 UTC
# Line 71  Line 71
71      if (!sorted) {      if (!sorted) {
72          CHM_SP chx = (CHM_SP) alloca(sizeof(cholmod_sparse));          CHM_SP chx = (CHM_SP) alloca(sizeof(cholmod_sparse));
73          R_CheckStack();          R_CheckStack();
74          as_cholmod_sparse(chx, x, FALSE, TRUE); /* includes cholmod_sort() ! */          as_cholmod_sparse(chx, x, FALSE, TRUE); /* includes cholmod_l_sort() ! */
75          /* as chx = AS_CHM_SP__(x)  but  ^^^^  sorting x in_place (no copying)*/          /* as chx = AS_CHM_SP__(x)  but  ^^^^  sorting x in_place (no copying)*/
76
77          /* Now re-check that row indices are *strictly* increasing          /* Now re-check that row indices are *strictly* increasing
# Line 79  Line 79
79          for (j = 0; j < ncol; j++) {          for (j = 0; j < ncol; j++) {
80              for (k = xp[j] + 1; k < xp[j + 1]; k++)              for (k = xp[j] + 1; k < xp[j + 1]; k++)
81                  if (xi[k] == xi[k - 1])                  if (xi[k] == xi[k - 1])
82                      return mkString(_("slot i is not *strictly* increasing inside a column (even after cholmod_sort)"));                      return mkString(_("slot i is not *strictly* increasing inside a column (even after cholmod_l_sort)"));
83          }          }
84
85      } else if(!strictly) {  /* sorted, but not strictly */      } else if(!strictly) {  /* sorted, but not strictly */
# Line 125  Line 125
125              }              }
126      }      }
127      if (!sorted)      if (!sorted)
128          /* cannot easily use cholmod_sort(.) ... -> "error out" :*/          /* cannot easily use cholmod_l_sort(.) ... -> "error out" :*/
129          return mkString(_("slot j is not increasing inside a column"));          return mkString(_("slot j is not increasing inside a column"));
130      else if(!strictly) /* sorted, but not strictly */      else if(!strictly) /* sorted, but not strictly */
131          return mkString(_("slot j is not *strictly* increasing inside a column"));          return mkString(_("slot j is not *strictly* increasing inside a column"));
# Line 143  Line 143
143      /* This loses the symmetry property, since cholmod_dense has none,      /* This loses the symmetry property, since cholmod_dense has none,
144       * BUT, much worse (FIXME!), it also transforms CHOLMOD_PATTERN ("n") matrices       * BUT, much worse (FIXME!), it also transforms CHOLMOD_PATTERN ("n") matrices
145       * to numeric (CHOLMOD_REAL) ones : */       * to numeric (CHOLMOD_REAL) ones : */
146      CHM_DN chxd = cholmod_sparse_to_dense(chxs, &c);      CHM_DN chxd = cholmod_l_sparse_to_dense(chxs, &c);
147      int Rkind = (chxs->xtype == CHOLMOD_PATTERN)? -1 : Real_kind(x);      int Rkind = (chxs->xtype == CHOLMOD_PATTERN)? -1 : Real_kind(x);
148      R_CheckStack();      R_CheckStack();
149
# Line 153  Line 153
153  SEXP Csparse_to_nz_pattern(SEXP x, SEXP tri)  SEXP Csparse_to_nz_pattern(SEXP x, SEXP tri)
154  {  {
155      CHM_SP chxs = AS_CHM_SP__(x);      CHM_SP chxs = AS_CHM_SP__(x);
156      CHM_SP chxcp = cholmod_copy(chxs, chxs->stype, CHOLMOD_PATTERN, &c);      CHM_SP chxcp = cholmod_l_copy(chxs, chxs->stype, CHOLMOD_PATTERN, &c);
157      int tr = asLogical(tri);      int tr = asLogical(tri);
158      R_CheckStack();      R_CheckStack();
159
# Line 165  Line 165
165
166  SEXP Csparse_to_matrix(SEXP x)  SEXP Csparse_to_matrix(SEXP x)
167  {  {
168      return chm_dense_to_matrix(cholmod_sparse_to_dense(AS_CHM_SP__(x), &c),      return chm_dense_to_matrix(cholmod_l_sparse_to_dense(AS_CHM_SP__(x), &c),
169                                 1 /*do_free*/, GET_SLOT(x, Matrix_DimNamesSym));                                 1 /*do_free*/, GET_SLOT(x, Matrix_DimNamesSym));
170  }  }
171
172  SEXP Csparse_to_Tsparse(SEXP x, SEXP tri)  SEXP Csparse_to_Tsparse(SEXP x, SEXP tri)
173  {  {
174      CHM_SP chxs = AS_CHM_SP__(x);      CHM_SP chxs = AS_CHM_SP__(x);
175      CHM_TR chxt = cholmod_sparse_to_triplet(chxs, &c);      CHM_TR chxt = cholmod_l_sparse_to_triplet(chxs, &c);
176      int tr = asLogical(tri);      int tr = asLogical(tri);
177      int Rkind = (chxs->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chxs->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
178      R_CheckStack();      R_CheckStack();
# Line 192  Line 192
192
193      if (!(chx->stype))      if (!(chx->stype))
194          error(_("Nonsymmetric matrix in Csparse_symmetric_to_general"));          error(_("Nonsymmetric matrix in Csparse_symmetric_to_general"));
195      chgx = cholmod_copy(chx, /* stype: */ 0, chx->xtype, &c);      chgx = cholmod_l_copy(chx, /* stype: */ 0, chx->xtype, &c);
196      /* xtype: pattern, "real", complex or .. */      /* xtype: pattern, "real", complex or .. */
197      return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",      return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",
198                                GET_SLOT(x, Matrix_DimNamesSym));                                GET_SLOT(x, Matrix_DimNamesSym));
# Line 205  Line 205
205      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
206      R_CheckStack();      R_CheckStack();
207
208      chgx = cholmod_copy(chx, /* stype: */ uploT, chx->xtype, &c);      chgx = cholmod_l_copy(chx, /* stype: */ uploT, chx->xtype, &c);
209      /* xtype: pattern, "real", complex or .. */      /* xtype: pattern, "real", complex or .. */
210      return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",      return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",
211                                GET_SLOT(x, Matrix_DimNamesSym));                                GET_SLOT(x, Matrix_DimNamesSym));
# Line 217  Line 217
217       *       since cholmod (& cs) lacks sparse 'int' matrices */       *       since cholmod (& cs) lacks sparse 'int' matrices */
218      CHM_SP chx = AS_CHM_SP__(x);      CHM_SP chx = AS_CHM_SP__(x);
219      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
220      CHM_SP chxt = cholmod_transpose(chx, chx->xtype, &c);      CHM_SP chxt = cholmod_l_transpose(chx, chx->xtype, &c);
221      SEXP dn = PROTECT(duplicate(GET_SLOT(x, Matrix_DimNamesSym))), tmp;      SEXP dn = PROTECT(duplicate(GET_SLOT(x, Matrix_DimNamesSym))), tmp;
222      int tr = asLogical(tri);      int tr = asLogical(tri);
223      R_CheckStack();      R_CheckStack();
# Line 236  Line 236
236      CHM_SP      CHM_SP
237          cha = AS_CHM_SP(a),          cha = AS_CHM_SP(a),
238          chb = AS_CHM_SP(b),          chb = AS_CHM_SP(b),
239          chc = cholmod_ssmult(cha, chb, /*out_stype:*/ 0,          chc = cholmod_l_ssmult(cha, chb, /*out_stype:*/ 0,
240                               cha->xtype, /*out sorted:*/ 1, &c);                               cha->xtype, /*out sorted:*/ 1, &c);
241      const char *cl_a = class_P(a), *cl_b = class_P(b);      const char *cl_a = class_P(a), *cl_b = class_P(b);
242      char diag[] = {'\0', '\0'};      char diag[] = {'\0', '\0'};
# Line 281  Line 281
281      SEXP dn = allocVector(VECSXP, 2);      SEXP dn = allocVector(VECSXP, 2);
282      R_CheckStack();      R_CheckStack();
283
284      chTr = cholmod_transpose((tr) ? chb : cha, chb->xtype, &c);      chTr = cholmod_l_transpose((tr) ? chb : cha, chb->xtype, &c);
285      chc = cholmod_ssmult((tr) ? cha : chTr, (tr) ? chTr : chb,      chc = cholmod_l_ssmult((tr) ? cha : chTr, (tr) ? chTr : chb,
286                           /*out_stype:*/ 0, cha->xtype, /*out sorted:*/ 1, &c);                           /*out_stype:*/ 0, cha->xtype, /*out sorted:*/ 1, &c);
287      cholmod_free_sparse(&chTr, &c);      cholmod_l_free_sparse(&chTr, &c);
288
289      /* Preserve triangularity and unit-triangularity if appropriate;      /* Preserve triangularity and unit-triangularity if appropriate;
290       * see Csparse_Csparse_prod() for comments */       * see Csparse_Csparse_prod() for comments */
# Line 310  Line 310
310      CHM_SP cha = AS_CHM_SP(a);      CHM_SP cha = AS_CHM_SP(a);
311      SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));      SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));
312      CHM_DN chb = AS_CHM_DN(b_M);      CHM_DN chb = AS_CHM_DN(b_M);
313      CHM_DN chc = cholmod_allocate_dense(cha->nrow, chb->ncol, cha->nrow,      CHM_DN chc = cholmod_l_allocate_dense(cha->nrow, chb->ncol, cha->nrow,
314                                          chb->xtype, &c);                                          chb->xtype, &c);
315      SEXP dn = PROTECT(allocVector(VECSXP, 2));      SEXP dn = PROTECT(allocVector(VECSXP, 2));
316      double one[] = {1,0}, zero[] = {0,0};      double one[] = {1,0}, zero[] = {0,0};
317      R_CheckStack();      R_CheckStack();
318
319      cholmod_sdmult(cha, 0, one, zero, chb, chc, &c);      cholmod_l_sdmult(cha, 0, one, zero, chb, chc, &c);
320      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
321                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));
322      SET_VECTOR_ELT(dn, 1,      SET_VECTOR_ELT(dn, 1,
# Line 330  Line 330
330      CHM_SP cha = AS_CHM_SP(a);      CHM_SP cha = AS_CHM_SP(a);
331      SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));      SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));
332      CHM_DN chb = AS_CHM_DN(b_M);      CHM_DN chb = AS_CHM_DN(b_M);
333      CHM_DN chc = cholmod_allocate_dense(cha->ncol, chb->ncol, cha->ncol,      CHM_DN chc = cholmod_l_allocate_dense(cha->ncol, chb->ncol, cha->ncol,
334                                          chb->xtype, &c);                                          chb->xtype, &c);
335      SEXP dn = PROTECT(allocVector(VECSXP, 2));      SEXP dn = PROTECT(allocVector(VECSXP, 2));
336      double one[] = {1,0}, zero[] = {0,0};      double one[] = {1,0}, zero[] = {0,0};
337      R_CheckStack();      R_CheckStack();
338
339      cholmod_sdmult(cha, 1, one, zero, chb, chc, &c);      cholmod_l_sdmult(cha, 1, one, zero, chb, chc, &c);
340      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
341                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 1)));                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 1)));
342      SET_VECTOR_ELT(dn, 1,      SET_VECTOR_ELT(dn, 1,
# Line 354  Line 354
354      CHM_TR cht = trip ? AS_CHM_TR(x) : (CHM_TR) NULL;      CHM_TR cht = trip ? AS_CHM_TR(x) : (CHM_TR) NULL;
355      CHM_SP chcp, chxt,      CHM_SP chcp, chxt,
356          chx = (trip ?          chx = (trip ?
357                 cholmod_triplet_to_sparse(cht, cht->nnz, &c) :                 cholmod_l_triplet_to_sparse(cht, cht->nnz, &c) :
358                 AS_CHM_SP(x));                 AS_CHM_SP(x));
359      SEXP dn = PROTECT(allocVector(VECSXP, 2));      SEXP dn = PROTECT(allocVector(VECSXP, 2));
360      R_CheckStack();      R_CheckStack();
361
362      if (!tr) chxt = cholmod_transpose(chx, chx->xtype, &c);      if (!tr) chxt = cholmod_l_transpose(chx, chx->xtype, &c);
363      chcp = cholmod_aat((!tr) ? chxt : chx, (int *) NULL, 0, chx->xtype, &c);      chcp = cholmod_l_aat((!tr) ? chxt : chx, (int *) NULL, 0, chx->xtype, &c);
364      if(!chcp) {      if(!chcp) {
365          UNPROTECT(1);          UNPROTECT(1);
366          error(_("Csparse_crossprod(): error return from cholmod_aat()"));          error(_("Csparse_crossprod(): error return from cholmod_l_aat()"));
367      }      }
368      cholmod_band_inplace(0, chcp->ncol, chcp->xtype, chcp, &c);      cholmod_l_band_inplace(0, chcp->ncol, chcp->xtype, chcp, &c);
369      chcp->stype = 1;      chcp->stype = 1;
370      if (trip) cholmod_free_sparse(&chx, &c);      if (trip) cholmod_l_free_sparse(&chx, &c);
371      if (!tr) cholmod_free_sparse(&chxt, &c);      if (!tr) cholmod_l_free_sparse(&chxt, &c);
372      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
373                     duplicate(VECTOR_ELT(GET_SLOT(x, Matrix_DimNamesSym),                     duplicate(VECTOR_ELT(GET_SLOT(x, Matrix_DimNamesSym),
374                                          (tr) ? 0 : 1)));                                          (tr) ? 0 : 1)));
# Line 383  Line 383
383      /* dtCMatrix, etc; [1] = the second character =?= 't' for triangular */      /* dtCMatrix, etc; [1] = the second character =?= 't' for triangular */
384      int tr = (cl[1] == 't');      int tr = (cl[1] == 't');
385      CHM_SP chx = AS_CHM_SP__(x);      CHM_SP chx = AS_CHM_SP__(x);
386      CHM_SP ans = cholmod_copy(chx, chx->stype, chx->xtype, &c);      CHM_SP ans = cholmod_l_copy(chx, chx->stype, chx->xtype, &c);
387      double dtol = asReal(tol);      double dtol = asReal(tol);
388      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
389      R_CheckStack();      R_CheckStack();
390
391      if(!cholmod_drop(dtol, ans, &c))      if(!cholmod_l_drop(dtol, ans, &c))
392          error(_("cholmod_drop() failed"));          error(_("cholmod_l_drop() failed"));
393      return chm_sparse_to_SEXP(ans, 1,      return chm_sparse_to_SEXP(ans, 1,
394                                tr ? ((*uplo_P(x) == 'U') ? 1 : -1) : 0,                                tr ? ((*uplo_P(x) == 'U') ? 1 : -1) : 0,
395                                Rkind, tr ? diag_P(x) : "",                                Rkind, tr ? diag_P(x) : "",
# Line 403  Line 403
403      R_CheckStack();      R_CheckStack();
404
405      /* FIXME: currently drops dimnames */      /* FIXME: currently drops dimnames */
406      return chm_sparse_to_SEXP(cholmod_horzcat(chx, chy, 1, &c),      return chm_sparse_to_SEXP(cholmod_l_horzcat(chx, chy, 1, &c),
407                                1, 0, Rkind, "", R_NilValue);                                1, 0, Rkind, "", R_NilValue);
408  }  }
409
# Line 414  Line 414
414      R_CheckStack();      R_CheckStack();
415
416      /* FIXME: currently drops dimnames */      /* FIXME: currently drops dimnames */
417      return chm_sparse_to_SEXP(cholmod_vertcat(chx, chy, 1, &c),      return chm_sparse_to_SEXP(cholmod_l_vertcat(chx, chy, 1, &c),
418                                1, 0, Rkind, "", R_NilValue);                                1, 0, Rkind, "", R_NilValue);
419  }  }
420
# Line 422  Line 422
422  {  {
423      CHM_SP chx = AS_CHM_SP__(x);      CHM_SP chx = AS_CHM_SP__(x);
424      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
425      CHM_SP ans = cholmod_band(chx, asInteger(k1), asInteger(k2), chx->xtype, &c);      CHM_SP ans = cholmod_l_band(chx, asInteger(k1), asInteger(k2), chx->xtype, &c);
426      R_CheckStack();      R_CheckStack();
427
428      return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "",      return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "",
# Line 440  Line 440
440      }      }
441      else { /* unit triangular (diag='U'): "fill the diagonal" & diag:= "N" */      else { /* unit triangular (diag='U'): "fill the diagonal" & diag:= "N" */
442          CHM_SP chx = AS_CHM_SP__(x);          CHM_SP chx = AS_CHM_SP__(x);
443          CHM_SP eye = cholmod_speye(chx->nrow, chx->ncol, chx->xtype, &c);          CHM_SP eye = cholmod_l_speye(chx->nrow, chx->ncol, chx->xtype, &c);
444          double one[] = {1, 0};          double one[] = {1, 0};
445          CHM_SP ans = cholmod_add(chx, eye, one, one, TRUE, TRUE, &c);          CHM_SP ans = cholmod_l_add(chx, eye, one, one, TRUE, TRUE, &c);
446          int uploT = (*uplo_P(x) == 'U') ? 1 : -1;          int uploT = (*uplo_P(x) == 'U') ? 1 : -1;
447          int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;          int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
448
449          R_CheckStack();          R_CheckStack();
450          cholmod_free_sparse(&eye, &c);          cholmod_l_free_sparse(&eye, &c);
451          return chm_sparse_to_SEXP(ans, 1, uploT, Rkind, "N",          return chm_sparse_to_SEXP(ans, 1, uploT, Rkind, "N",
452                                    GET_SLOT(x, Matrix_DimNamesSym));                                    GET_SLOT(x, Matrix_DimNamesSym));
453      }      }
# Line 490  Line 490
490      if (csize >= 0 && !isInteger(j))      if (csize >= 0 && !isInteger(j))
491          error(_("Index j must be NULL or integer"));          error(_("Index j must be NULL or integer"));
492
493      return chm_sparse_to_SEXP(cholmod_submatrix(chx, INTEGER(i), rsize,      return chm_sparse_to_SEXP(cholmod_l_submatrix(chx, INTEGER(i), rsize,
494                                                  INTEGER(j), csize,                                                  INTEGER(j), csize,
495                                                  TRUE, TRUE, &c),                                                  TRUE, TRUE, &c),
496                                1, 0, Rkind, "",                                1, 0, Rkind, "",
# Line 504  Line 504
504      if (!f)      if (!f)
505          error(_("failure to open file \"%s\" for writing"),          error(_("failure to open file \"%s\" for writing"),
506                CHAR(asChar(fname)));                CHAR(asChar(fname)));
507      if (!cholmod_write_sparse(f, AS_CHM_SP(x),      if (!cholmod_l_write_sparse(f, AS_CHM_SP(x),
508                                (CHM_SP)NULL, (char*) NULL, &c))                                (CHM_SP)NULL, (char*) NULL, &c))
509          error(_("cholmod_write_sparse returned error code"));          error(_("cholmod_l_write_sparse returned error code"));
510      fclose(f);      fclose(f);
511      return R_NilValue;      return R_NilValue;
512  }  }

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 Removed from v.2279 changed lines Added in v.2299