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

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pkg/src/Csparse.c revision 2279, Fri Oct 3 09:15:54 2008 UTC pkg/Matrix/src/Csparse.c revision 2586, Sun Jul 25 02:32:06 2010 UTC
# Line 32  Line 32 
32      return TRUE;      return TRUE;
33  }  }
34    
35  SEXP Csparse_validate(SEXP x)  SEXP Csparse_validate(SEXP x) {
36        return Csparse_validate_(x, FALSE);
37    }
38    
39    SEXP Csparse_validate2(SEXP x, SEXP maybe_modify) {
40        return Csparse_validate_(x, asLogical(maybe_modify));
41    }
42    
43    SEXP Csparse_validate_(SEXP x, Rboolean maybe_modify)
44  {  {
45      /* NB: we do *NOT* check a potential 'x' slot here, at all */      /* NB: we do *NOT* check a potential 'x' slot here, at all */
46      SEXP pslot = GET_SLOT(x, Matrix_pSym),      SEXP pslot = GET_SLOT(x, Matrix_pSym),
# Line 69  Line 77 
77              }              }
78      }      }
79      if (!sorted) {      if (!sorted) {
80            if(maybe_modify) {
81          CHM_SP chx = (CHM_SP) alloca(sizeof(cholmod_sparse));          CHM_SP chx = (CHM_SP) alloca(sizeof(cholmod_sparse));
82          R_CheckStack();          R_CheckStack();
83          as_cholmod_sparse(chx, x, FALSE, TRUE); /* includes cholmod_sort() ! */              as_cholmod_sparse(chx, x, FALSE, TRUE);/*-> cholmod_l_sort() ! */
84          /* as chx = AS_CHM_SP__(x)  but  ^^^^  sorting x in_place (no copying)*/              /* as chx = AS_CHM_SP__(x)  but  ^^^^ sorting x in_place !!! */
85    
86          /* Now re-check that row indices are *strictly* increasing          /* Now re-check that row indices are *strictly* increasing
87           * (and not just increasing) within each column : */           * (and not just increasing) within each column : */
88          for (j = 0; j < ncol; j++) {          for (j = 0; j < ncol; j++) {
89              for (k = xp[j] + 1; k < xp[j + 1]; k++)              for (k = xp[j] + 1; k < xp[j + 1]; k++)
90                  if (xi[k] == xi[k - 1])                  if (xi[k] == xi[k - 1])
91                      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)"));
92                }
93            } else { /* no modifying sorting : */
94                return mkString(_("row indices are not sorted within columns"));
95          }          }
   
96      } else if(!strictly) {  /* sorted, but not strictly */      } else if(!strictly) {  /* sorted, but not strictly */
97          return mkString(_("slot i is not *strictly* increasing inside a column"));          return mkString(_("slot i is not *strictly* increasing inside a column"));
98      }      }
# Line 125  Line 136 
136              }              }
137      }      }
138      if (!sorted)      if (!sorted)
139          /* cannot easily use cholmod_sort(.) ... -> "error out" :*/          /* cannot easily use cholmod_l_sort(.) ... -> "error out" :*/
140          return mkString(_("slot j is not increasing inside a column"));          return mkString(_("slot j is not increasing inside a column"));
141      else if(!strictly) /* sorted, but not strictly */      else if(!strictly) /* sorted, but not strictly */
142          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 154 
154      /* This loses the symmetry property, since cholmod_dense has none,      /* This loses the symmetry property, since cholmod_dense has none,
155       * BUT, much worse (FIXME!), it also transforms CHOLMOD_PATTERN ("n") matrices       * BUT, much worse (FIXME!), it also transforms CHOLMOD_PATTERN ("n") matrices
156       * to numeric (CHOLMOD_REAL) ones : */       * to numeric (CHOLMOD_REAL) ones : */
157      CHM_DN chxd = cholmod_sparse_to_dense(chxs, &c);      CHM_DN chxd = cholmod_l_sparse_to_dense(chxs, &c);
158      int Rkind = (chxs->xtype == CHOLMOD_PATTERN)? -1 : Real_kind(x);      int Rkind = (chxs->xtype == CHOLMOD_PATTERN)? -1 : Real_kind(x);
159      R_CheckStack();      R_CheckStack();
160    
# Line 153  Line 164 
164  SEXP Csparse_to_nz_pattern(SEXP x, SEXP tri)  SEXP Csparse_to_nz_pattern(SEXP x, SEXP tri)
165  {  {
166      CHM_SP chxs = AS_CHM_SP__(x);      CHM_SP chxs = AS_CHM_SP__(x);
167      CHM_SP chxcp = cholmod_copy(chxs, chxs->stype, CHOLMOD_PATTERN, &c);      CHM_SP chxcp = cholmod_l_copy(chxs, chxs->stype, CHOLMOD_PATTERN, &c);
168      int tr = asLogical(tri);      int tr = asLogical(tri);
169      R_CheckStack();      R_CheckStack();
170    
# Line 165  Line 176 
176    
177  SEXP Csparse_to_matrix(SEXP x)  SEXP Csparse_to_matrix(SEXP x)
178  {  {
179      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),
180                                 1 /*do_free*/, GET_SLOT(x, Matrix_DimNamesSym));                                 1 /*do_free*/, GET_SLOT(x, Matrix_DimNamesSym));
181  }  }
182    
183  SEXP Csparse_to_Tsparse(SEXP x, SEXP tri)  SEXP Csparse_to_Tsparse(SEXP x, SEXP tri)
184  {  {
185      CHM_SP chxs = AS_CHM_SP__(x);      CHM_SP chxs = AS_CHM_SP__(x);
186      CHM_TR chxt = cholmod_sparse_to_triplet(chxs, &c);      CHM_TR chxt = cholmod_l_sparse_to_triplet(chxs, &c);
187      int tr = asLogical(tri);      int tr = asLogical(tri);
188      int Rkind = (chxs->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chxs->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
189      R_CheckStack();      R_CheckStack();
# Line 192  Line 203 
203    
204      if (!(chx->stype))      if (!(chx->stype))
205          error(_("Nonsymmetric matrix in Csparse_symmetric_to_general"));          error(_("Nonsymmetric matrix in Csparse_symmetric_to_general"));
206      chgx = cholmod_copy(chx, /* stype: */ 0, chx->xtype, &c);      chgx = cholmod_l_copy(chx, /* stype: */ 0, chx->xtype, &c);
207      /* xtype: pattern, "real", complex or .. */      /* xtype: pattern, "real", complex or .. */
208      return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",      return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",
209                                GET_SLOT(x, Matrix_DimNamesSym));                                GET_SLOT(x, Matrix_DimNamesSym));
# Line 205  Line 216 
216      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
217      R_CheckStack();      R_CheckStack();
218    
219      chgx = cholmod_copy(chx, /* stype: */ uploT, chx->xtype, &c);      chgx = cholmod_l_copy(chx, /* stype: */ uploT, chx->xtype, &c);
220      /* xtype: pattern, "real", complex or .. */      /* xtype: pattern, "real", complex or .. */
221      return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",      return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",
222                                GET_SLOT(x, Matrix_DimNamesSym));                                GET_SLOT(x, Matrix_DimNamesSym));
# Line 217  Line 228 
228       *       since cholmod (& cs) lacks sparse 'int' matrices */       *       since cholmod (& cs) lacks sparse 'int' matrices */
229      CHM_SP chx = AS_CHM_SP__(x);      CHM_SP chx = AS_CHM_SP__(x);
230      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
231      CHM_SP chxt = cholmod_transpose(chx, chx->xtype, &c);      CHM_SP chxt = cholmod_l_transpose(chx, chx->xtype, &c);
232      SEXP dn = PROTECT(duplicate(GET_SLOT(x, Matrix_DimNamesSym))), tmp;      SEXP dn = PROTECT(duplicate(GET_SLOT(x, Matrix_DimNamesSym))), tmp;
233      int tr = asLogical(tri);      int tr = asLogical(tri);
234      R_CheckStack();      R_CheckStack();
# Line 236  Line 247 
247      CHM_SP      CHM_SP
248          cha = AS_CHM_SP(a),          cha = AS_CHM_SP(a),
249          chb = AS_CHM_SP(b),          chb = AS_CHM_SP(b),
250          chc = cholmod_ssmult(cha, chb, /*out_stype:*/ 0,          chc = cholmod_l_ssmult(cha, chb, /*out_stype:*/ 0,
251                               cha->xtype, /*out sorted:*/ 1, &c);                                 /* values:= is_numeric (T/F) */ cha->xtype > 0,
252                                   /*out sorted:*/ 1, &c);
253      const char *cl_a = class_P(a), *cl_b = class_P(b);      const char *cl_a = class_P(a), *cl_b = class_P(b);
254      char diag[] = {'\0', '\0'};      char diag[] = {'\0', '\0'};
255      int uploT = 0;      int uploT = 0;
256      SEXP dn = allocVector(VECSXP, 2);      SEXP dn = PROTECT(allocVector(VECSXP, 2));
257      R_CheckStack();      R_CheckStack();
258    
259    #ifdef DEBUG_Matrix_verbose
260        Rprintf("DBG Csparse_C*_prod(%s, %s)\n", cl_a, cl_b);
261    #endif
262    
263      /* Preserve triangularity and even unit-triangularity if appropriate.      /* Preserve triangularity and even unit-triangularity if appropriate.
264       * Note that in that case, the multiplication itself should happen       * Note that in that case, the multiplication itself should happen
265       * faster.  But there's no support for that in CHOLMOD */       * faster.  But there's no support for that in CHOLMOD */
# Line 265  Line 281 
281                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));
282      SET_VECTOR_ELT(dn, 1,      SET_VECTOR_ELT(dn, 1,
283                     duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), 1)));                     duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), 1)));
284        UNPROTECT(1);
285      return chm_sparse_to_SEXP(chc, 1, uploT, /*Rkind*/0, diag, dn);      return chm_sparse_to_SEXP(chc, 1, uploT, /*Rkind*/0, diag, dn);
286  }  }
287    
# Line 278  Line 295 
295      const char *cl_a = class_P(a), *cl_b = class_P(b);      const char *cl_a = class_P(a), *cl_b = class_P(b);
296      char diag[] = {'\0', '\0'};      char diag[] = {'\0', '\0'};
297      int uploT = 0;      int uploT = 0;
298      SEXP dn = allocVector(VECSXP, 2);      SEXP dn = PROTECT(allocVector(VECSXP, 2));
299      R_CheckStack();      R_CheckStack();
300    
301      chTr = cholmod_transpose((tr) ? chb : cha, chb->xtype, &c);      chTr = cholmod_l_transpose((tr) ? chb : cha, chb->xtype, &c);
302      chc = cholmod_ssmult((tr) ? cha : chTr, (tr) ? chTr : chb,      chc = cholmod_l_ssmult((tr) ? cha : chTr, (tr) ? chTr : chb,
303                           /*out_stype:*/ 0, cha->xtype, /*out sorted:*/ 1, &c);                           /*out_stype:*/ 0, cha->xtype, /*out sorted:*/ 1, &c);
304      cholmod_free_sparse(&chTr, &c);      cholmod_l_free_sparse(&chTr, &c);
305    
306      /* Preserve triangularity and unit-triangularity if appropriate;      /* Preserve triangularity and unit-triangularity if appropriate;
307       * see Csparse_Csparse_prod() for comments */       * see Csparse_Csparse_prod() for comments */
# Line 297  Line 314 
314              }              }
315              else diag[0]= 'N';              else diag[0]= 'N';
316          }          }
   
317      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
318                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), (tr) ? 0 : 1)));                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), (tr) ? 0 : 1)));
319      SET_VECTOR_ELT(dn, 1,      SET_VECTOR_ELT(dn, 1,
320                     duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), (tr) ? 0 : 1)));                     duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), (tr) ? 0 : 1)));
321        UNPROTECT(1);
322      return chm_sparse_to_SEXP(chc, 1, uploT, /*Rkind*/0, diag, dn);      return chm_sparse_to_SEXP(chc, 1, uploT, /*Rkind*/0, diag, dn);
323  }  }
324    
# Line 310  Line 327 
327      CHM_SP cha = AS_CHM_SP(a);      CHM_SP cha = AS_CHM_SP(a);
328      SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));      SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));
329      CHM_DN chb = AS_CHM_DN(b_M);      CHM_DN chb = AS_CHM_DN(b_M);
330      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,
331                                          chb->xtype, &c);                                          chb->xtype, &c);
332      SEXP dn = PROTECT(allocVector(VECSXP, 2));      SEXP dn = PROTECT(allocVector(VECSXP, 2));
333      double one[] = {1,0}, zero[] = {0,0};      double one[] = {1,0}, zero[] = {0,0};
334      R_CheckStack();      R_CheckStack();
335    
336      cholmod_sdmult(cha, 0, one, zero, chb, chc, &c);      cholmod_l_sdmult(cha, 0, one, zero, chb, chc, &c);
337      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
338                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));
339      SET_VECTOR_ELT(dn, 1,      SET_VECTOR_ELT(dn, 1,
# Line 330  Line 347 
347      CHM_SP cha = AS_CHM_SP(a);      CHM_SP cha = AS_CHM_SP(a);
348      SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));      SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));
349      CHM_DN chb = AS_CHM_DN(b_M);      CHM_DN chb = AS_CHM_DN(b_M);
350      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,
351                                          chb->xtype, &c);                                          chb->xtype, &c);
352      SEXP dn = PROTECT(allocVector(VECSXP, 2));      SEXP dn = PROTECT(allocVector(VECSXP, 2));
353      double one[] = {1,0}, zero[] = {0,0};      double one[] = {1,0}, zero[] = {0,0};
354      R_CheckStack();      R_CheckStack();
355    
356      cholmod_sdmult(cha, 1, one, zero, chb, chc, &c);      cholmod_l_sdmult(cha, 1, one, zero, chb, chc, &c);
357      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
358                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 1)));                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 1)));
359      SET_VECTOR_ELT(dn, 1,      SET_VECTOR_ELT(dn, 1,
# Line 351  Line 368 
368  {  {
369      int trip = asLogical(triplet),      int trip = asLogical(triplet),
370          tr   = asLogical(trans); /* gets reversed because _aat is tcrossprod */          tr   = asLogical(trans); /* gets reversed because _aat is tcrossprod */
371    #ifdef AS_CHM_DIAGU2N_FIXED_FINALLY
372      CHM_TR cht = trip ? AS_CHM_TR(x) : (CHM_TR) NULL;      CHM_TR cht = trip ? AS_CHM_TR(x) : (CHM_TR) NULL;
373    #else /* workaround needed:*/
374        SEXP xx = PROTECT(Tsparse_diagU2N(x));
375        CHM_TR cht = trip ? AS_CHM_TR__(xx) : (CHM_TR) NULL;
376    #endif
377      CHM_SP chcp, chxt,      CHM_SP chcp, chxt,
378          chx = (trip ?          chx = (trip ?
379                 cholmod_triplet_to_sparse(cht, cht->nnz, &c) :                 cholmod_l_triplet_to_sparse(cht, cht->nnz, &c) :
380                 AS_CHM_SP(x));                 AS_CHM_SP(x));
381      SEXP dn = PROTECT(allocVector(VECSXP, 2));      SEXP dn = PROTECT(allocVector(VECSXP, 2));
382      R_CheckStack();      R_CheckStack();
383    
384      if (!tr) chxt = cholmod_transpose(chx, chx->xtype, &c);      if (!tr) chxt = cholmod_l_transpose(chx, chx->xtype, &c);
385      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);
386      if(!chcp) {      if(!chcp) {
387          UNPROTECT(1);          UNPROTECT(1);
388          error(_("Csparse_crossprod(): error return from cholmod_aat()"));          error(_("Csparse_crossprod(): error return from cholmod_l_aat()"));
389      }      }
390      cholmod_band_inplace(0, chcp->ncol, chcp->xtype, chcp, &c);      cholmod_l_band_inplace(0, chcp->ncol, chcp->xtype, chcp, &c);
391      chcp->stype = 1;      chcp->stype = 1;
392      if (trip) cholmod_free_sparse(&chx, &c);      if (trip) cholmod_l_free_sparse(&chx, &c);
393      if (!tr) cholmod_free_sparse(&chxt, &c);      if (!tr) cholmod_l_free_sparse(&chxt, &c);
394      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
395                     duplicate(VECTOR_ELT(GET_SLOT(x, Matrix_DimNamesSym),                     duplicate(VECTOR_ELT(GET_SLOT(x, Matrix_DimNamesSym),
396                                          (tr) ? 0 : 1)));                                          (tr) ? 0 : 1)));
397      SET_VECTOR_ELT(dn, 1, duplicate(VECTOR_ELT(dn, 0)));      SET_VECTOR_ELT(dn, 1, duplicate(VECTOR_ELT(dn, 0)));
398    #ifdef AS_CHM_DIAGU2N_FIXED_FINALLY
399      UNPROTECT(1);      UNPROTECT(1);
400    #else
401        UNPROTECT(2);
402    #endif
403      return chm_sparse_to_SEXP(chcp, 1, 0, 0, "", dn);      return chm_sparse_to_SEXP(chcp, 1, 0, 0, "", dn);
404  }  }
405    
# Line 383  Line 409 
409      /* dtCMatrix, etc; [1] = the second character =?= 't' for triangular */      /* dtCMatrix, etc; [1] = the second character =?= 't' for triangular */
410      int tr = (cl[1] == 't');      int tr = (cl[1] == 't');
411      CHM_SP chx = AS_CHM_SP__(x);      CHM_SP chx = AS_CHM_SP__(x);
412      CHM_SP ans = cholmod_copy(chx, chx->stype, chx->xtype, &c);      CHM_SP ans = cholmod_l_copy(chx, chx->stype, chx->xtype, &c);
413      double dtol = asReal(tol);      double dtol = asReal(tol);
414      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
415      R_CheckStack();      R_CheckStack();
416    
417      if(!cholmod_drop(dtol, ans, &c))      if(!cholmod_l_drop(dtol, ans, &c))
418          error(_("cholmod_drop() failed"));          error(_("cholmod_l_drop() failed"));
419      return chm_sparse_to_SEXP(ans, 1,      return chm_sparse_to_SEXP(ans, 1,
420                                tr ? ((*uplo_P(x) == 'U') ? 1 : -1) : 0,                                tr ? ((*uplo_P(x) == 'U') ? 1 : -1) : 0,
421                                Rkind, tr ? diag_P(x) : "",                                Rkind, tr ? diag_P(x) : "",
# Line 399  Line 425 
425  SEXP Csparse_horzcat(SEXP x, SEXP y)  SEXP Csparse_horzcat(SEXP x, SEXP y)
426  {  {
427      CHM_SP chx = AS_CHM_SP__(x), chy = AS_CHM_SP__(y);      CHM_SP chx = AS_CHM_SP__(x), chy = AS_CHM_SP__(y);
428      int Rkind = 0; /* only for "d" - FIXME */      int Rk_x = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0,
429            Rk_y = (chy->xtype != CHOLMOD_PATTERN) ? Real_kind(y) : 0,
430            Rkind = /* logical if both x and y are */ (Rk_x == 1 && Rk_y == 1) ? 1 : 0;
431      R_CheckStack();      R_CheckStack();
432    
433      /* FIXME: currently drops dimnames */      /* TODO: currently drops dimnames - and we fix at R level */
434      return chm_sparse_to_SEXP(cholmod_horzcat(chx, chy, 1, &c),      return chm_sparse_to_SEXP(cholmod_l_horzcat(chx, chy, 1, &c),
435                                1, 0, Rkind, "", R_NilValue);                                1, 0, Rkind, "", R_NilValue);
436  }  }
437    
438  SEXP Csparse_vertcat(SEXP x, SEXP y)  SEXP Csparse_vertcat(SEXP x, SEXP y)
439  {  {
440      CHM_SP chx = AS_CHM_SP__(x), chy = AS_CHM_SP__(y);      CHM_SP chx = AS_CHM_SP__(x), chy = AS_CHM_SP__(y);
441      int Rkind = 0; /* only for "d" - FIXME */      int Rk_x = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0,
442            Rk_y = (chy->xtype != CHOLMOD_PATTERN) ? Real_kind(y) : 0,
443            Rkind = /* logical if both x and y are */ (Rk_x == 1 && Rk_y == 1) ? 1 : 0;
444      R_CheckStack();      R_CheckStack();
445    
446      /* FIXME: currently drops dimnames */      /* TODO: currently drops dimnames - and we fix at R level */
447      return chm_sparse_to_SEXP(cholmod_vertcat(chx, chy, 1, &c),      return chm_sparse_to_SEXP(cholmod_l_vertcat(chx, chy, 1, &c),
448                                1, 0, Rkind, "", R_NilValue);                                1, 0, Rkind, "", R_NilValue);
449  }  }
450    
# Line 422  Line 452 
452  {  {
453      CHM_SP chx = AS_CHM_SP__(x);      CHM_SP chx = AS_CHM_SP__(x);
454      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
455      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);
456      R_CheckStack();      R_CheckStack();
457    
458      return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "",      return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "",
# Line 440  Line 470 
470      }      }
471      else { /* unit triangular (diag='U'): "fill the diagonal" & diag:= "N" */      else { /* unit triangular (diag='U'): "fill the diagonal" & diag:= "N" */
472          CHM_SP chx = AS_CHM_SP__(x);          CHM_SP chx = AS_CHM_SP__(x);
473          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);
474          double one[] = {1, 0};          double one[] = {1, 0};
475          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);
476          int uploT = (*uplo_P(x) == 'U') ? 1 : -1;          int uploT = (*uplo_P(x) == 'U') ? 1 : -1;
477          int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;          int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
478    
479          R_CheckStack();          R_CheckStack();
480          cholmod_free_sparse(&eye, &c);          cholmod_l_free_sparse(&eye, &c);
481          return chm_sparse_to_SEXP(ans, 1, uploT, Rkind, "N",          return chm_sparse_to_SEXP(ans, 1, uploT, Rkind, "N",
482                                    GET_SLOT(x, Matrix_DimNamesSym));                                    GET_SLOT(x, Matrix_DimNamesSym));
483      }      }
# Line 477  Line 507 
507      }      }
508  }  }
509    
510    /**
511     * "Indexing" aka subsetting : Compute  x[i,j], also for vectors i and j
512     * Working via CHOLMOD_submatrix, see ./CHOLMOD/MatrixOps/cholmod_submatrix.c
513     * @param x CsparseMatrix
514     * @param i row     indices (0-origin), or NULL (R's)
515     * @param j columns indices (0-origin), or NULL
516     *
517     * @return x[i,j]  still CsparseMatrix --- currently, this loses dimnames
518     */
519  SEXP Csparse_submatrix(SEXP x, SEXP i, SEXP j)  SEXP Csparse_submatrix(SEXP x, SEXP i, SEXP j)
520  {  {
521      CHM_SP chx = AS_CHM_SP__(x);      CHM_SP chx = AS_CHM_SP(x); /* << does diagU2N() when needed */
522      int rsize = (isNull(i)) ? -1 : LENGTH(i),      int rsize = (isNull(i)) ? -1 : LENGTH(i),
523          csize = (isNull(j)) ? -1 : LENGTH(j);          csize = (isNull(j)) ? -1 : LENGTH(j);
524      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
# Line 490  Line 529 
529      if (csize >= 0 && !isInteger(j))      if (csize >= 0 && !isInteger(j))
530          error(_("Index j must be NULL or integer"));          error(_("Index j must be NULL or integer"));
531    
532      return chm_sparse_to_SEXP(cholmod_submatrix(chx, INTEGER(i), rsize,      if (chx->stype) /* symmetricMatrix */
533                                                  INTEGER(j), csize,          /* for now, cholmod_submatrix() only accepts "generalMatrix" */
534            chx = cholmod_l_copy(chx, /* stype: */ 0, chx->xtype, &c);
535    
536        return chm_sparse_to_SEXP(cholmod_l_submatrix(chx,
537                                    (rsize < 0) ? NULL : INTEGER(i), rsize,
538                                    (csize < 0) ? NULL : INTEGER(j), csize,
539                                                  TRUE, TRUE, &c),                                                  TRUE, TRUE, &c),
540                                1, 0, Rkind, "",                                1, 0, Rkind, "",
541                                /* FIXME: drops dimnames */ R_NilValue);                                /* FIXME: drops dimnames */ R_NilValue);
# Line 504  Line 548 
548      if (!f)      if (!f)
549          error(_("failure to open file \"%s\" for writing"),          error(_("failure to open file \"%s\" for writing"),
550                CHAR(asChar(fname)));                CHAR(asChar(fname)));
551      if (!cholmod_write_sparse(f, AS_CHM_SP(x),      if (!cholmod_l_write_sparse(f, AS_CHM_SP(x),
552                                (CHM_SP)NULL, (char*) NULL, &c))                                (CHM_SP)NULL, (char*) NULL, &c))
553          error(_("cholmod_write_sparse returned error code"));          error(_("cholmod_l_write_sparse returned error code"));
554      fclose(f);      fclose(f);
555      return R_NilValue;      return R_NilValue;
556  }  }
# Line 588  Line 632 
632          break;          break;
633    
634      default: /* -1 from above */      default: /* -1 from above */
635          error("diag_tC(): invalid 'resultKind'");          error(_("diag_tC(): invalid 'resultKind'"));
636          /* Wall: */ ans = R_NilValue; v = REAL(ans);          /* Wall: */ ans = R_NilValue; v = REAL(ans);
637      }      }
638    
# Line 618  Line 662 
662    
663      return diag_tC_ptr(n, x_p, x_x, perm, resultKind);      return diag_tC_ptr(n, x_p, x_x, perm, resultKind);
664  }  }
665    
666    /**
667     * Create a Csparse matrix object from indices and/or pointers.
668     *
669     * @param cls name of actual class of object to create
670     * @param i optional integer vector of length nnz of row indices
671     * @param j optional integer vector of length nnz of column indices
672     * @param p optional integer vector of length np of row or column pointers
673     * @param np length of integer vector p.  Must be zero if p == (int*)NULL
674     * @param x optional vector of values
675     * @param nnz length of vectors i, j and/or x, whichever is to be used
676     * @param dims optional integer vector of length 2 to be used as
677     *     dimensions.  If dims == (int*)NULL then the maximum row and column
678     *     index are used as the dimensions.
679     * @param dimnames optional list of length 2 to be used as dimnames
680     * @param index1 indicator of 1-based indices
681     *
682     * @return an SEXP of class cls inheriting from CsparseMatrix.
683     */
684    SEXP create_Csparse(char* cls, int* i, int* j, int* p, int np,
685                        void* x, int nnz, int* dims, SEXP dimnames,
686                        int index1)
687    {
688        SEXP ans;
689        int *ij = (int*)NULL, *tri, *trj,
690            mi, mj, mp, nrow = -1, ncol = -1;
691        int xtype = -1;             /* -Wall */
692        CHM_TR T;
693        CHM_SP A;
694    
695        if (np < 0 || nnz < 0)
696            error(_("negative vector lengths not allowed: np = %d, nnz = %d"),
697                  np, nnz);
698        if (1 != ((mi = (i == (int*)NULL)) +
699                  (mj = (j == (int*)NULL)) +
700                  (mp = (p == (int*)NULL))))
701            error(_("exactly 1 of 'i', 'j' or 'p' must be NULL"));
702        if (mp) {
703            if (np) error(_("np = %d, must be zero when p is NULL"), np);
704        } else {
705            if (np) {               /* Expand p to form i or j */
706                if (!(p[0])) error(_("p[0] = %d, should be zero"), p[0]);
707                for (int ii = 0; ii < np; ii++)
708                    if (p[ii] > p[ii + 1])
709                        error(_("p must be non-decreasing"));
710                if (p[np] != nnz)
711                    error("p[np] = %d != nnz = %d", p[np], nnz);
712                ij = Calloc(nnz, int);
713                if (mi) {
714                    i = ij;
715                    nrow = np;
716                } else {
717                    j = ij;
718                    ncol = np;
719                }
720                                    /* Expand p to 0-based indices */
721                for (int ii = 0; ii < np; ii++)
722                    for (int jj = p[ii]; jj < p[ii + 1]; jj++) ij[jj] = ii;
723            } else {
724                if (nnz)
725                    error(_("Inconsistent dimensions: np = 0 and nnz = %d"),
726                          nnz);
727            }
728        }
729                                    /* calculate nrow and ncol */
730        if (nrow < 0) {
731            for (int ii = 0; ii < nnz; ii++) {
732                int i1 = i[ii] + (index1 ? 0 : 1); /* 1-based index */
733                if (i1 < 1) error(_("invalid row index at position %d"), ii);
734                if (i1 > nrow) nrow = i1;
735            }
736        }
737        if (ncol < 0) {
738            for (int jj = 0; jj < nnz; jj++) {
739                int j1 = j[jj] + (index1 ? 0 : 1);
740                if (j1 < 1) error(_("invalid column index at position %d"), jj);
741                if (j1 > ncol) ncol = j1;
742            }
743        }
744        if (dims != (int*)NULL) {
745            if (dims[0] > nrow) nrow = dims[0];
746            if (dims[1] > ncol) ncol = dims[1];
747        }
748                                    /* check the class name */
749        if (strlen(cls) != 8)
750            error(_("strlen of cls argument = %d, should be 8"), strlen(cls));
751        if (!strcmp(cls + 2, "CMatrix"))
752            error(_("cls = \"%s\" does not end in \"CMatrix\""), cls);
753        switch(cls[0]) {
754        case 'd':
755        case 'l':
756               xtype = CHOLMOD_REAL;
757               break;
758        case 'n':
759               xtype = CHOLMOD_PATTERN;
760               break;
761        default:
762               error(_("cls = \"%s\" must begin with 'd', 'l' or 'n'"), cls);
763        }
764        if (cls[1] != 'g')
765            error(_("Only 'g'eneral sparse matrix types allowed"));
766                                    /* allocate and populate the triplet */
767        T = cholmod_l_allocate_triplet((size_t)nrow, (size_t)ncol, (size_t)nnz, 0,
768                                        xtype, &c);
769        T->x = x;
770        tri = (int*)T->i;
771        trj = (int*)T->j;
772        for (int ii = 0; ii < nnz; ii++) {
773            tri[ii] = i[ii] - ((!mi && index1) ? 1 : 0);
774            trj[ii] = j[ii] - ((!mj && index1) ? 1 : 0);
775        }
776                                    /* create the cholmod_sparse structure */
777        A = cholmod_l_triplet_to_sparse(T, nnz, &c);
778        cholmod_l_free_triplet(&T, &c);
779                                    /* copy the information to the SEXP */
780        ans = PROTECT(NEW_OBJECT(MAKE_CLASS(cls)));
781    /* FIXME: This has been copied from chm_sparse_to_SEXP in chm_common.c */
782                                    /* allocate and copy common slots */
783        nnz = cholmod_l_nnz(A, &c);
784        dims = INTEGER(ALLOC_SLOT(ans, Matrix_DimSym, INTSXP, 2));
785        dims[0] = A->nrow; dims[1] = A->ncol;
786        Memcpy(INTEGER(ALLOC_SLOT(ans, Matrix_pSym, INTSXP, A->ncol + 1)), (int*)A->p, A->ncol + 1);
787        Memcpy(INTEGER(ALLOC_SLOT(ans, Matrix_iSym, INTSXP, nnz)), (int*)A->i, nnz);
788        switch(cls[1]) {
789        case 'd':
790            Memcpy(REAL(ALLOC_SLOT(ans, Matrix_xSym, REALSXP, nnz)), (double*)A->x, nnz);
791            break;
792        case 'l':
793            error(_("code not yet written for cls = \"lgCMatrix\""));
794        }
795        cholmod_l_free_sparse(&A, &c);
796        UNPROTECT(1);
797        return ans;
798    }

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