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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 2304, Sun Oct 26 15:27:45 2008 UTC pkg/Matrix/src/Csparse.c revision 2784, Fri Jun 8 17:01:25 2012 UTC
# Line 1  Line 1 
1                          /* Sparse matrices in compressed column-oriented form */                          /* Sparse matrices in compressed column-oriented form */
2    
3  #include "Csparse.h"  #include "Csparse.h"
4  #include "Tsparse.h"  #include "Tsparse.h"
5  #include "chm_common.h"  #include "chm_common.h"
# Line 32  Line 33 
33      return TRUE;      return TRUE;
34  }  }
35    
36  SEXP Csparse_validate(SEXP x)  SEXP Csparse_validate(SEXP x) {
37        return Csparse_validate_(x, FALSE);
38    }
39    
40    SEXP Csparse_validate2(SEXP x, SEXP maybe_modify) {
41        return Csparse_validate_(x, asLogical(maybe_modify));
42    }
43    
44    SEXP Csparse_validate_(SEXP x, Rboolean maybe_modify)
45  {  {
46      /* NB: we do *NOT* check a potential 'x' slot here, at all */      /* NB: we do *NOT* check a potential 'x' slot here, at all */
47      SEXP pslot = GET_SLOT(x, Matrix_pSym),      SEXP pslot = GET_SLOT(x, Matrix_pSym),
# Line 69  Line 78 
78              }              }
79      }      }
80      if (!sorted) {      if (!sorted) {
81            if(maybe_modify) {
82                CHM_SP chx = (CHM_SP) alloca(sizeof(cholmod_sparse));
83                R_CheckStack();
84                as_cholmod_sparse(chx, x, FALSE, TRUE);/*-> cholmod_l_sort() ! */
85                /* as chx = AS_CHM_SP__(x)  but  ^^^^ sorting x in_place !!! */
86    
87                /* Now re-check that row indices are *strictly* increasing
88                 * (and not just increasing) within each column : */
89                for (j = 0; j < ncol; j++) {
90                    for (k = xp[j] + 1; k < xp[j + 1]; k++)
91                        if (xi[k] == xi[k - 1])
92                            return mkString(_("slot i is not *strictly* increasing inside a column (even after cholmod_l_sort)"));
93                }
94            } else { /* no modifying sorting : */
95          return mkString(_("row indices are not sorted within columns"));          return mkString(_("row indices are not sorted within columns"));
96            }
97      } else if(!strictly) {  /* sorted, but not strictly */      } else if(!strictly) {  /* sorted, but not strictly */
98          return mkString(_("slot i is not *strictly* increasing inside a column"));          return mkString(_("slot i is not *strictly* increasing inside a column"));
99      }      }
# Line 113  Line 137 
137              }              }
138      }      }
139      if (!sorted)      if (!sorted)
140          /* cannot easily use cholmod_l_sort(.) ... -> "error out" :*/          /* cannot easily use cholmod_sort(.) ... -> "error out" :*/
141          return mkString(_("slot j is not increasing inside a column"));          return mkString(_("slot j is not increasing inside a column"));
142      else if(!strictly) /* sorted, but not strictly */      else if(!strictly) /* sorted, but not strictly */
143          return mkString(_("slot j is not *strictly* increasing inside a column"));          return mkString(_("slot j is not *strictly* increasing inside a column"));
# Line 131  Line 155 
155      /* This loses the symmetry property, since cholmod_dense has none,      /* This loses the symmetry property, since cholmod_dense has none,
156       * BUT, much worse (FIXME!), it also transforms CHOLMOD_PATTERN ("n") matrices       * BUT, much worse (FIXME!), it also transforms CHOLMOD_PATTERN ("n") matrices
157       * to numeric (CHOLMOD_REAL) ones : */       * to numeric (CHOLMOD_REAL) ones : */
158      CHM_DN chxd = cholmod_l_sparse_to_dense(chxs, &c);      CHM_DN chxd = cholmod_sparse_to_dense(chxs, &c);
159      int Rkind = (chxs->xtype == CHOLMOD_PATTERN)? -1 : Real_kind(x);      int Rkind = (chxs->xtype == CHOLMOD_PATTERN)? -1 : Real_kind(x);
160      R_CheckStack();      R_CheckStack();
161    
162      return chm_dense_to_SEXP(chxd, 1, Rkind, GET_SLOT(x, Matrix_DimNamesSym));      return chm_dense_to_SEXP(chxd, 1, Rkind, GET_SLOT(x, Matrix_DimNamesSym));
163  }  }
164    
165    // FIXME: do not go via CHM (should not be too hard, to just *drop* the x-slot, right?
166  SEXP Csparse_to_nz_pattern(SEXP x, SEXP tri)  SEXP Csparse_to_nz_pattern(SEXP x, SEXP tri)
167  {  {
168      CHM_SP chxs = AS_CHM_SP__(x);      CHM_SP chxs = AS_CHM_SP__(x);
169      CHM_SP chxcp = cholmod_l_copy(chxs, chxs->stype, CHOLMOD_PATTERN, &c);      CHM_SP chxcp = cholmod_copy(chxs, chxs->stype, CHOLMOD_PATTERN, &c);
170      int tr = asLogical(tri);      int tr = asLogical(tri);
171      R_CheckStack();      R_CheckStack();
172    
# Line 151  Line 176 
176                                GET_SLOT(x, Matrix_DimNamesSym));                                GET_SLOT(x, Matrix_DimNamesSym));
177  }  }
178    
179    // n.CMatrix --> [dli].CMatrix  (not going through CHM!)
180    SEXP nz_pattern_to_Csparse(SEXP x, SEXP res_kind)
181    {
182        return nz2Csparse(x, asInteger(res_kind));
183    }
184    // n.CMatrix --> [dli].CMatrix  (not going through CHM!)
185    SEXP nz2Csparse(SEXP x, enum x_slot_kind r_kind)
186    {
187        const char *cl_x = class_P(x);
188        if(cl_x[0] != 'n') error(_("not a 'n.CMatrix'"));
189        if(cl_x[2] != 'C') error(_("not a CsparseMatrix"));
190        int nnz = LENGTH(GET_SLOT(x, Matrix_iSym));
191        SEXP ans;
192        char *ncl = strdup(cl_x);
193        double *dx_x; int *ix_x;
194        ncl[0] = (r_kind == x_double ? 'd' :
195                  (r_kind == x_logical ? 'l' :
196                   /* else (for now):  r_kind == x_integer : */ 'i'));
197        PROTECT(ans = NEW_OBJECT(MAKE_CLASS(ncl)));
198        // create a correct 'x' slot:
199        switch(r_kind) {
200            int i;
201        case x_double: // 'd'
202            dx_x = REAL(ALLOC_SLOT(ans, Matrix_xSym, REALSXP, nnz));
203            for (i=0; i < nnz; i++) dx_x[i] = 1.;
204            break;
205        case x_logical: // 'l'
206            ix_x = LOGICAL(ALLOC_SLOT(ans, Matrix_xSym, LGLSXP, nnz));
207            for (i=0; i < nnz; i++) ix_x[i] = TRUE;
208            break;
209        case x_integer: // 'i'
210            ix_x = INTEGER(ALLOC_SLOT(ans, Matrix_xSym, INTSXP, nnz));
211            for (i=0; i < nnz; i++) ix_x[i] = 1;
212            break;
213    
214        default:
215            error(_("nz2Csparse(): invalid/non-implemented r_kind = %d"),
216                  r_kind);
217        }
218    
219        // now copy all other slots :
220        slot_dup(ans, x, Matrix_iSym);
221        slot_dup(ans, x, Matrix_pSym);
222        slot_dup(ans, x, Matrix_DimSym);
223        slot_dup(ans, x, Matrix_DimNamesSym);
224        if(ncl[1] != 'g') { // symmetric or triangular ...
225            slot_dup_if_has(ans, x, Matrix_uploSym);
226            slot_dup_if_has(ans, x, Matrix_diagSym);
227        }
228        UNPROTECT(1);
229        return ans;
230    }
231    
232  SEXP Csparse_to_matrix(SEXP x)  SEXP Csparse_to_matrix(SEXP x)
233  {  {
234      return chm_dense_to_matrix(cholmod_l_sparse_to_dense(AS_CHM_SP__(x), &c),      return chm_dense_to_matrix(cholmod_sparse_to_dense(AS_CHM_SP__(x), &c),
235                                 1 /*do_free*/, GET_SLOT(x, Matrix_DimNamesSym));                                 1 /*do_free*/, GET_SLOT(x, Matrix_DimNamesSym));
236  }  }
237    
238  SEXP Csparse_to_Tsparse(SEXP x, SEXP tri)  SEXP Csparse_to_Tsparse(SEXP x, SEXP tri)
239  {  {
240      CHM_SP chxs = AS_CHM_SP__(x);      CHM_SP chxs = AS_CHM_SP__(x);
241      CHM_TR chxt = cholmod_l_sparse_to_triplet(chxs, &c);      CHM_TR chxt = cholmod_sparse_to_triplet(chxs, &c);
242      int tr = asLogical(tri);      int tr = asLogical(tri);
243      int Rkind = (chxs->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chxs->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
244      R_CheckStack();      R_CheckStack();
# Line 180  Line 258 
258    
259      if (!(chx->stype))      if (!(chx->stype))
260          error(_("Nonsymmetric matrix in Csparse_symmetric_to_general"));          error(_("Nonsymmetric matrix in Csparse_symmetric_to_general"));
261      chgx = cholmod_l_copy(chx, /* stype: */ 0, chx->xtype, &c);      chgx = cholmod_copy(chx, /* stype: */ 0, chx->xtype, &c);
262      /* xtype: pattern, "real", complex or .. */      /* xtype: pattern, "real", complex or .. */
263      return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",      return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",
264                                GET_SLOT(x, Matrix_DimNamesSym));                                GET_SLOT(x, Matrix_DimNamesSym));
# Line 193  Line 271 
271      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
272      R_CheckStack();      R_CheckStack();
273    
274      chgx = cholmod_l_copy(chx, /* stype: */ uploT, chx->xtype, &c);      chgx = cholmod_copy(chx, /* stype: */ uploT, chx->xtype, &c);
275      /* xtype: pattern, "real", complex or .. */      /* xtype: pattern, "real", complex or .. */
276      return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",      return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",
277                                GET_SLOT(x, Matrix_DimNamesSym));                                GET_SLOT(x, Matrix_DimNamesSym));
# Line 205  Line 283 
283       *       since cholmod (& cs) lacks sparse 'int' matrices */       *       since cholmod (& cs) lacks sparse 'int' matrices */
284      CHM_SP chx = AS_CHM_SP__(x);      CHM_SP chx = AS_CHM_SP__(x);
285      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
286      CHM_SP chxt = cholmod_l_transpose(chx, chx->xtype, &c);      CHM_SP chxt = cholmod_transpose(chx, chx->xtype, &c);
287      SEXP dn = PROTECT(duplicate(GET_SLOT(x, Matrix_DimNamesSym))), tmp;      SEXP dn = PROTECT(duplicate(GET_SLOT(x, Matrix_DimNamesSym))), tmp;
288      int tr = asLogical(tri);      int tr = asLogical(tri);
289      R_CheckStack();      R_CheckStack();
# Line 224  Line 302 
302      CHM_SP      CHM_SP
303          cha = AS_CHM_SP(a),          cha = AS_CHM_SP(a),
304          chb = AS_CHM_SP(b),          chb = AS_CHM_SP(b),
305          chc = cholmod_l_ssmult(cha, chb, /*out_stype:*/ 0,          chc = cholmod_ssmult(cha, chb, /*out_stype:*/ 0,
306                               cha->xtype, /*out sorted:*/ 1, &c);                                 /* values:= is_numeric (T/F) */ cha->xtype > 0,
307                                   /*out sorted:*/ 1, &c);
308      const char *cl_a = class_P(a), *cl_b = class_P(b);      const char *cl_a = class_P(a), *cl_b = class_P(b);
309      char diag[] = {'\0', '\0'};      char diag[] = {'\0', '\0'};
310      int uploT = 0;      int uploT = 0;
311      SEXP dn = allocVector(VECSXP, 2);      SEXP dn = PROTECT(allocVector(VECSXP, 2));
312      R_CheckStack();      R_CheckStack();
313    
314    #ifdef DEBUG_Matrix_verbose
315        Rprintf("DBG Csparse_C*_prod(%s, %s)\n", cl_a, cl_b);
316    #endif
317    
318      /* Preserve triangularity and even unit-triangularity if appropriate.      /* Preserve triangularity and even unit-triangularity if appropriate.
319       * Note that in that case, the multiplication itself should happen       * Note that in that case, the multiplication itself should happen
320       * faster.  But there's no support for that in CHOLMOD */       * faster.  But there's no support for that in CHOLMOD */
# Line 253  Line 336 
336                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));
337      SET_VECTOR_ELT(dn, 1,      SET_VECTOR_ELT(dn, 1,
338                     duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), 1)));                     duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), 1)));
339        UNPROTECT(1);
340      return chm_sparse_to_SEXP(chc, 1, uploT, /*Rkind*/0, diag, dn);      return chm_sparse_to_SEXP(chc, 1, uploT, /*Rkind*/0, diag, dn);
341  }  }
342    
# Line 266  Line 350 
350      const char *cl_a = class_P(a), *cl_b = class_P(b);      const char *cl_a = class_P(a), *cl_b = class_P(b);
351      char diag[] = {'\0', '\0'};      char diag[] = {'\0', '\0'};
352      int uploT = 0;      int uploT = 0;
353      SEXP dn = allocVector(VECSXP, 2);      SEXP dn = PROTECT(allocVector(VECSXP, 2));
354      R_CheckStack();      R_CheckStack();
355    
356      chTr = cholmod_l_transpose((tr) ? chb : cha, chb->xtype, &c);      chTr = cholmod_transpose((tr) ? chb : cha, chb->xtype, &c);
357      chc = cholmod_l_ssmult((tr) ? cha : chTr, (tr) ? chTr : chb,      chc = cholmod_ssmult((tr) ? cha : chTr, (tr) ? chTr : chb,
358                           /*out_stype:*/ 0, cha->xtype, /*out sorted:*/ 1, &c);                           /*out_stype:*/ 0, cha->xtype, /*out sorted:*/ 1, &c);
359      cholmod_l_free_sparse(&chTr, &c);      cholmod_free_sparse(&chTr, &c);
360    
361      /* Preserve triangularity and unit-triangularity if appropriate;      /* Preserve triangularity and unit-triangularity if appropriate;
362       * see Csparse_Csparse_prod() for comments */       * see Csparse_Csparse_prod() for comments */
# Line 285  Line 369 
369              }              }
370              else diag[0]= 'N';              else diag[0]= 'N';
371          }          }
   
372      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
373                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), (tr) ? 0 : 1)));                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), (tr) ? 0 : 1)));
374      SET_VECTOR_ELT(dn, 1,      SET_VECTOR_ELT(dn, 1,
375                     duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), (tr) ? 0 : 1)));                     duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), (tr) ? 0 : 1)));
376        UNPROTECT(1);
377      return chm_sparse_to_SEXP(chc, 1, uploT, /*Rkind*/0, diag, dn);      return chm_sparse_to_SEXP(chc, 1, uploT, /*Rkind*/0, diag, dn);
378  }  }
379    
# Line 298  Line 382 
382      CHM_SP cha = AS_CHM_SP(a);      CHM_SP cha = AS_CHM_SP(a);
383      SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));      SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));
384      CHM_DN chb = AS_CHM_DN(b_M);      CHM_DN chb = AS_CHM_DN(b_M);
385      CHM_DN chc = cholmod_l_allocate_dense(cha->nrow, chb->ncol, cha->nrow,      CHM_DN chc = cholmod_allocate_dense(cha->nrow, chb->ncol, cha->nrow,
386                                          chb->xtype, &c);                                          chb->xtype, &c);
387      SEXP dn = PROTECT(allocVector(VECSXP, 2));      SEXP dn = PROTECT(allocVector(VECSXP, 2));
388      double one[] = {1,0}, zero[] = {0,0};      double one[] = {1,0}, zero[] = {0,0};
389        int nprot = 2;
390      R_CheckStack();      R_CheckStack();
391        /* Tim Davis, please FIXME:  currently (2010-11) *fails* when  a  is a pattern matrix:*/
392      cholmod_l_sdmult(cha, 0, one, zero, chb, chc, &c);      if(cha->xtype == CHOLMOD_PATTERN) {
393            /* warning(_("Csparse_dense_prod(): cholmod_sdmult() not yet implemented for pattern./ ngCMatrix" */
394            /*        " --> slightly inefficient coercion")); */
395    
396            // This *fails* to produce a CHOLMOD_REAL ..
397            // CHM_SP chd = cholmod_l_copy(cha, cha->stype, CHOLMOD_REAL, &c);
398            // --> use our Matrix-classes
399            SEXP da = PROTECT(nz2Csparse(a, x_double)); nprot++;
400            cha = AS_CHM_SP(da);
401        }
402        cholmod_sdmult(cha, 0, one, zero, chb, chc, &c);
403      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
404                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));
405      SET_VECTOR_ELT(dn, 1,      SET_VECTOR_ELT(dn, 1,
406                     duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));                     duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));
407      UNPROTECT(2);      UNPROTECT(nprot);
408      return chm_dense_to_SEXP(chc, 1, 0, dn);      return chm_dense_to_SEXP(chc, 1, 0, dn);
409  }  }
410    
# Line 318  Line 413 
413      CHM_SP cha = AS_CHM_SP(a);      CHM_SP cha = AS_CHM_SP(a);
414      SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));      SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));
415      CHM_DN chb = AS_CHM_DN(b_M);      CHM_DN chb = AS_CHM_DN(b_M);
416      CHM_DN chc = cholmod_l_allocate_dense(cha->ncol, chb->ncol, cha->ncol,      CHM_DN chc = cholmod_allocate_dense(cha->ncol, chb->ncol, cha->ncol,
417                                          chb->xtype, &c);                                          chb->xtype, &c);
418      SEXP dn = PROTECT(allocVector(VECSXP, 2));      SEXP dn = PROTECT(allocVector(VECSXP, 2)); int nprot = 2;
419      double one[] = {1,0}, zero[] = {0,0};      double one[] = {1,0}, zero[] = {0,0};
420      R_CheckStack();      R_CheckStack();
421        // -- see Csparse_dense_prod() above :
422      cholmod_l_sdmult(cha, 1, one, zero, chb, chc, &c);      if(cha->xtype == CHOLMOD_PATTERN) {
423            SEXP da = PROTECT(nz2Csparse(a, x_double)); nprot++;
424            cha = AS_CHM_SP(da);
425        }
426        cholmod_sdmult(cha, 1, one, zero, chb, chc, &c);
427      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
428                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 1)));                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 1)));
429      SET_VECTOR_ELT(dn, 1,      SET_VECTOR_ELT(dn, 1,
430                     duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));                     duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));
431      UNPROTECT(2);      UNPROTECT(nprot);
432      return chm_dense_to_SEXP(chc, 1, 0, dn);      return chm_dense_to_SEXP(chc, 1, 0, dn);
433  }  }
434    
# Line 339  Line 438 
438  {  {
439      int trip = asLogical(triplet),      int trip = asLogical(triplet),
440          tr   = asLogical(trans); /* gets reversed because _aat is tcrossprod */          tr   = asLogical(trans); /* gets reversed because _aat is tcrossprod */
441    #ifdef AS_CHM_DIAGU2N_FIXED_FINALLY
442      CHM_TR cht = trip ? AS_CHM_TR(x) : (CHM_TR) NULL;      CHM_TR cht = trip ? AS_CHM_TR(x) : (CHM_TR) NULL;
443    #else /* workaround needed:*/
444        SEXP xx = PROTECT(Tsparse_diagU2N(x));
445        CHM_TR cht = trip ? AS_CHM_TR__(xx) : (CHM_TR) NULL;
446    #endif
447      CHM_SP chcp, chxt,      CHM_SP chcp, chxt,
448          chx = (trip ?          chx = (trip ?
449                 cholmod_l_triplet_to_sparse(cht, cht->nnz, &c) :                 cholmod_triplet_to_sparse(cht, cht->nnz, &c) :
450                 AS_CHM_SP(x));                 AS_CHM_SP(x));
451      SEXP dn = PROTECT(allocVector(VECSXP, 2));      SEXP dn = PROTECT(allocVector(VECSXP, 2));
452      R_CheckStack();      R_CheckStack();
453    
454      if (!tr) chxt = cholmod_l_transpose(chx, chx->xtype, &c);      if (!tr) chxt = cholmod_transpose(chx, chx->xtype, &c);
455      chcp = cholmod_l_aat((!tr) ? chxt : chx, (int *) NULL, 0, chx->xtype, &c);      chcp = cholmod_aat((!tr) ? chxt : chx, (int *) NULL, 0, chx->xtype, &c);
456      if(!chcp) {      if(!chcp) {
457          UNPROTECT(1);          UNPROTECT(1);
458          error(_("Csparse_crossprod(): error return from cholmod_l_aat()"));          error(_("Csparse_crossprod(): error return from cholmod_aat()"));
459      }      }
460      cholmod_l_band_inplace(0, chcp->ncol, chcp->xtype, chcp, &c);      cholmod_band_inplace(0, chcp->ncol, chcp->xtype, chcp, &c);
461      chcp->stype = 1;      chcp->stype = 1;
462      if (trip) cholmod_l_free_sparse(&chx, &c);      if (trip) cholmod_free_sparse(&chx, &c);
463      if (!tr) cholmod_l_free_sparse(&chxt, &c);      if (!tr) cholmod_free_sparse(&chxt, &c);
464      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
465                     duplicate(VECTOR_ELT(GET_SLOT(x, Matrix_DimNamesSym),                     duplicate(VECTOR_ELT(GET_SLOT(x, Matrix_DimNamesSym),
466                                          (tr) ? 0 : 1)));                                          (tr) ? 0 : 1)));
467      SET_VECTOR_ELT(dn, 1, duplicate(VECTOR_ELT(dn, 0)));      SET_VECTOR_ELT(dn, 1, duplicate(VECTOR_ELT(dn, 0)));
468    #ifdef AS_CHM_DIAGU2N_FIXED_FINALLY
469      UNPROTECT(1);      UNPROTECT(1);
470    #else
471        UNPROTECT(2);
472    #endif
473      return chm_sparse_to_SEXP(chcp, 1, 0, 0, "", dn);      return chm_sparse_to_SEXP(chcp, 1, 0, 0, "", dn);
474  }  }
475    
476    /* Csparse_drop(x, tol):  drop entries with absolute value < tol, i.e,
477    *  at least all "explicit" zeros */
478  SEXP Csparse_drop(SEXP x, SEXP tol)  SEXP Csparse_drop(SEXP x, SEXP tol)
479  {  {
480      const char *cl = class_P(x);      const char *cl = class_P(x);
481      /* dtCMatrix, etc; [1] = the second character =?= 't' for triangular */      /* dtCMatrix, etc; [1] = the second character =?= 't' for triangular */
482      int tr = (cl[1] == 't');      int tr = (cl[1] == 't');
483      CHM_SP chx = AS_CHM_SP__(x);      CHM_SP chx = AS_CHM_SP__(x);
484      CHM_SP ans = cholmod_l_copy(chx, chx->stype, chx->xtype, &c);      CHM_SP ans = cholmod_copy(chx, chx->stype, chx->xtype, &c);
485      double dtol = asReal(tol);      double dtol = asReal(tol);
486      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
487      R_CheckStack();      R_CheckStack();
488    
489      if(!cholmod_l_drop(dtol, ans, &c))      if(!cholmod_drop(dtol, ans, &c))
490          error(_("cholmod_l_drop() failed"));          error(_("cholmod_drop() failed"));
491      return chm_sparse_to_SEXP(ans, 1,      return chm_sparse_to_SEXP(ans, 1,
492                                tr ? ((*uplo_P(x) == 'U') ? 1 : -1) : 0,                                tr ? ((*uplo_P(x) == 'U') ? 1 : -1) : 0,
493                                Rkind, tr ? diag_P(x) : "",                                Rkind, tr ? diag_P(x) : "",
# Line 387  Line 497 
497  SEXP Csparse_horzcat(SEXP x, SEXP y)  SEXP Csparse_horzcat(SEXP x, SEXP y)
498  {  {
499      CHM_SP chx = AS_CHM_SP__(x), chy = AS_CHM_SP__(y);      CHM_SP chx = AS_CHM_SP__(x), chy = AS_CHM_SP__(y);
500      int Rkind = 0; /* only for "d" - FIXME */      int Rk_x = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0,
501            Rk_y = (chy->xtype != CHOLMOD_PATTERN) ? Real_kind(y) : 0,
502            Rkind = /* logical if both x and y are */ (Rk_x == 1 && Rk_y == 1) ? 1 : 0;
503      R_CheckStack();      R_CheckStack();
504    
505      /* FIXME: currently drops dimnames */      /* TODO: currently drops dimnames - and we fix at R level */
506      return chm_sparse_to_SEXP(cholmod_l_horzcat(chx, chy, 1, &c),      return chm_sparse_to_SEXP(cholmod_horzcat(chx, chy, 1, &c),
507                                1, 0, Rkind, "", R_NilValue);                                1, 0, Rkind, "", R_NilValue);
508  }  }
509    
510  SEXP Csparse_vertcat(SEXP x, SEXP y)  SEXP Csparse_vertcat(SEXP x, SEXP y)
511  {  {
512      CHM_SP chx = AS_CHM_SP__(x), chy = AS_CHM_SP__(y);      CHM_SP chx = AS_CHM_SP__(x), chy = AS_CHM_SP__(y);
513      int Rkind = 0; /* only for "d" - FIXME */      int Rk_x = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0,
514            Rk_y = (chy->xtype != CHOLMOD_PATTERN) ? Real_kind(y) : 0,
515            Rkind = /* logical if both x and y are */ (Rk_x == 1 && Rk_y == 1) ? 1 : 0;
516      R_CheckStack();      R_CheckStack();
517    
518      /* FIXME: currently drops dimnames */      /* TODO: currently drops dimnames - and we fix at R level */
519      return chm_sparse_to_SEXP(cholmod_l_vertcat(chx, chy, 1, &c),      return chm_sparse_to_SEXP(cholmod_vertcat(chx, chy, 1, &c),
520                                1, 0, Rkind, "", R_NilValue);                                1, 0, Rkind, "", R_NilValue);
521  }  }
522    
# Line 410  Line 524 
524  {  {
525      CHM_SP chx = AS_CHM_SP__(x);      CHM_SP chx = AS_CHM_SP__(x);
526      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
527      CHM_SP ans = cholmod_l_band(chx, asInteger(k1), asInteger(k2), chx->xtype, &c);      CHM_SP ans = cholmod_band(chx, asInteger(k1), asInteger(k2), chx->xtype, &c);
528      R_CheckStack();      R_CheckStack();
529    
530      return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "",      return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "",
# Line 428  Line 542 
542      }      }
543      else { /* unit triangular (diag='U'): "fill the diagonal" & diag:= "N" */      else { /* unit triangular (diag='U'): "fill the diagonal" & diag:= "N" */
544          CHM_SP chx = AS_CHM_SP__(x);          CHM_SP chx = AS_CHM_SP__(x);
545          CHM_SP eye = cholmod_l_speye(chx->nrow, chx->ncol, chx->xtype, &c);          CHM_SP eye = cholmod_speye(chx->nrow, chx->ncol, chx->xtype, &c);
546          double one[] = {1, 0};          double one[] = {1, 0};
547          CHM_SP ans = cholmod_l_add(chx, eye, one, one, TRUE, TRUE, &c);          CHM_SP ans = cholmod_add(chx, eye, one, one, TRUE, TRUE, &c);
548          int uploT = (*uplo_P(x) == 'U') ? 1 : -1;          int uploT = (*uplo_P(x) == 'U') ? 1 : -1;
549          int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;          int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
550    
551          R_CheckStack();          R_CheckStack();
552          cholmod_l_free_sparse(&eye, &c);          cholmod_free_sparse(&eye, &c);
553          return chm_sparse_to_SEXP(ans, 1, uploT, Rkind, "N",          return chm_sparse_to_SEXP(ans, 1, uploT, Rkind, "N",
554                                    GET_SLOT(x, Matrix_DimNamesSym));                                    GET_SLOT(x, Matrix_DimNamesSym));
555      }      }
# Line 452  Line 566 
566      }      }
567      else { /* triangular with diag='N'): now drop the diagonal */      else { /* triangular with diag='N'): now drop the diagonal */
568          /* duplicate, since chx will be modified: */          /* duplicate, since chx will be modified: */
569          CHM_SP chx = AS_CHM_SP__(duplicate(x));          SEXP xx = PROTECT(duplicate(x));
570            CHM_SP chx = AS_CHM_SP__(xx);
571          int uploT = (*uplo_P(x) == 'U') ? 1 : -1,          int uploT = (*uplo_P(x) == 'U') ? 1 : -1,
572              Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;              Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
573          R_CheckStack();          R_CheckStack();
574    
575          chm_diagN2U(chx, uploT, /* do_realloc */ FALSE);          chm_diagN2U(chx, uploT, /* do_realloc */ FALSE);
576    
577            UNPROTECT(1);
578          return chm_sparse_to_SEXP(chx, /*dofree*/ 0/* or 1 ?? */,          return chm_sparse_to_SEXP(chx, /*dofree*/ 0/* or 1 ?? */,
579                                    uploT, Rkind, "U",                                    uploT, Rkind, "U",
580                                    GET_SLOT(x, Matrix_DimNamesSym));                                    GET_SLOT(x, Matrix_DimNamesSym));
581      }      }
582  }  }
583    
584    /**
585     * "Indexing" aka subsetting : Compute  x[i,j], also for vectors i and j
586     * Working via CHOLMOD_submatrix, see ./CHOLMOD/MatrixOps/cholmod_submatrix.c
587     * @param x CsparseMatrix
588     * @param i row     indices (0-origin), or NULL (R's)
589     * @param j columns indices (0-origin), or NULL
590     *
591     * @return x[i,j]  still CsparseMatrix --- currently, this loses dimnames
592     */
593  SEXP Csparse_submatrix(SEXP x, SEXP i, SEXP j)  SEXP Csparse_submatrix(SEXP x, SEXP i, SEXP j)
594  {  {
595      CHM_SP chx = AS_CHM_SP__(x);      CHM_SP chx = AS_CHM_SP(x); /* << does diagU2N() when needed */
596      int rsize = (isNull(i)) ? -1 : LENGTH(i),      int rsize = (isNull(i)) ? -1 : LENGTH(i),
597          csize = (isNull(j)) ? -1 : LENGTH(j);          csize = (isNull(j)) ? -1 : LENGTH(j);
598      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
# Line 478  Line 603 
603      if (csize >= 0 && !isInteger(j))      if (csize >= 0 && !isInteger(j))
604          error(_("Index j must be NULL or integer"));          error(_("Index j must be NULL or integer"));
605    
606      return chm_sparse_to_SEXP(cholmod_l_submatrix(chx, INTEGER(i), rsize,      if (!chx->stype) {/* non-symmetric Matrix */
607                                                  INTEGER(j), csize,          return chm_sparse_to_SEXP(cholmod_submatrix(chx,
608                                                        (rsize < 0) ? NULL : INTEGER(i), rsize,
609                                                        (csize < 0) ? NULL : INTEGER(j), csize,
610                                                  TRUE, TRUE, &c),                                                  TRUE, TRUE, &c),
611                                1, 0, Rkind, "",                                1, 0, Rkind, "",
612                                /* FIXME: drops dimnames */ R_NilValue);                                /* FIXME: drops dimnames */ R_NilValue);
613  }  }
614                                    /* for now, cholmod_submatrix() only accepts "generalMatrix" */
615        CHM_SP tmp = cholmod_copy(chx, /* stype: */ 0, chx->xtype, &c);
616        CHM_SP ans = cholmod_submatrix(tmp,
617                                       (rsize < 0) ? NULL : INTEGER(i), rsize,
618                                       (csize < 0) ? NULL : INTEGER(j), csize,
619                                       TRUE, TRUE, &c);
620        cholmod_free_sparse(&tmp, &c);
621        return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "", R_NilValue);
622    }
623    
624    #define _d_Csp_
625    #include "t_Csparse_subassign.c"
626    
627    #define _l_Csp_
628    #include "t_Csparse_subassign.c"
629    
630    #define _i_Csp_
631    #include "t_Csparse_subassign.c"
632    
633    #define _n_Csp_
634    #include "t_Csparse_subassign.c"
635    
636    #define _z_Csp_
637    #include "t_Csparse_subassign.c"
638    
639    
640    
641  SEXP Csparse_MatrixMarket(SEXP x, SEXP fname)  SEXP Csparse_MatrixMarket(SEXP x, SEXP fname)
642  {  {
# Line 492  Line 645 
645      if (!f)      if (!f)
646          error(_("failure to open file \"%s\" for writing"),          error(_("failure to open file \"%s\" for writing"),
647                CHAR(asChar(fname)));                CHAR(asChar(fname)));
648      if (!cholmod_l_write_sparse(f, AS_CHM_SP(x),      if (!cholmod_write_sparse(f, AS_CHM_SP(x),
649                                (CHM_SP)NULL, (char*) NULL, &c))                                (CHM_SP)NULL, (char*) NULL, &c))
650          error(_("cholmod_l_write_sparse returned error code"));          error(_("cholmod_write_sparse returned error code"));
651      fclose(f);      fclose(f);
652      return R_NilValue;      return R_NilValue;
653  }  }
# Line 567  Line 720 
720      case diag_backpermuted:      case diag_backpermuted:
721          for_DIAG(v[i] = x_x[i_from]);          for_DIAG(v[i] = x_x[i_from]);
722    
723          warning(_("resultKind = 'diagBack' (back-permuted) is experimental"));          warning(_("%s = '%s' (back-permuted) is experimental"),
724                    "resultKind", "diagBack");
725          /* now back_permute : */          /* now back_permute : */
726          for(i = 0; i < n; i++) {          for(i = 0; i < n; i++) {
727              double tmp = v[i]; v[i] = v[perm[i]]; v[perm[i]] = tmp;              double tmp = v[i]; v[i] = v[perm[i]]; v[perm[i]] = tmp;
# Line 576  Line 730 
730          break;          break;
731    
732      default: /* -1 from above */      default: /* -1 from above */
733          error("diag_tC(): invalid 'resultKind'");          error(_("diag_tC(): invalid 'resultKind'"));
734          /* Wall: */ ans = R_NilValue; v = REAL(ans);          /* Wall: */ ans = R_NilValue; v = REAL(ans);
735      }      }
736    
# Line 606  Line 760 
760    
761      return diag_tC_ptr(n, x_p, x_x, perm, resultKind);      return diag_tC_ptr(n, x_p, x_x, perm, resultKind);
762  }  }
763    
764    /**
765     * Create a Csparse matrix object from indices and/or pointers.
766     *
767     * @param cls name of actual class of object to create
768     * @param i optional integer vector of length nnz of row indices
769     * @param j optional integer vector of length nnz of column indices
770     * @param p optional integer vector of length np of row or column pointers
771     * @param np length of integer vector p.  Must be zero if p == (int*)NULL
772     * @param x optional vector of values
773     * @param nnz length of vectors i, j and/or x, whichever is to be used
774     * @param dims optional integer vector of length 2 to be used as
775     *     dimensions.  If dims == (int*)NULL then the maximum row and column
776     *     index are used as the dimensions.
777     * @param dimnames optional list of length 2 to be used as dimnames
778     * @param index1 indicator of 1-based indices
779     *
780     * @return an SEXP of class cls inheriting from CsparseMatrix.
781     */
782    SEXP create_Csparse(char* cls, int* i, int* j, int* p, int np,
783                        void* x, int nnz, int* dims, SEXP dimnames,
784                        int index1)
785    {
786        SEXP ans;
787        int *ij = (int*)NULL, *tri, *trj,
788            mi, mj, mp, nrow = -1, ncol = -1;
789        int xtype = -1;             /* -Wall */
790        CHM_TR T;
791        CHM_SP A;
792    
793        if (np < 0 || nnz < 0)
794            error(_("negative vector lengths not allowed: np = %d, nnz = %d"),
795                  np, nnz);
796        if (1 != ((mi = (i == (int*)NULL)) +
797                  (mj = (j == (int*)NULL)) +
798                  (mp = (p == (int*)NULL))))
799            error(_("exactly 1 of 'i', 'j' or 'p' must be NULL"));
800        if (mp) {
801            if (np) error(_("np = %d, must be zero when p is NULL"), np);
802        } else {
803            if (np) {               /* Expand p to form i or j */
804                if (!(p[0])) error(_("p[0] = %d, should be zero"), p[0]);
805                for (int ii = 0; ii < np; ii++)
806                    if (p[ii] > p[ii + 1])
807                        error(_("p must be non-decreasing"));
808                if (p[np] != nnz)
809                    error("p[np] = %d != nnz = %d", p[np], nnz);
810                ij = Calloc(nnz, int);
811                if (mi) {
812                    i = ij;
813                    nrow = np;
814                } else {
815                    j = ij;
816                    ncol = np;
817                }
818                /* Expand p to 0-based indices */
819                for (int ii = 0; ii < np; ii++)
820                    for (int jj = p[ii]; jj < p[ii + 1]; jj++) ij[jj] = ii;
821            } else {
822                if (nnz)
823                    error(_("Inconsistent dimensions: np = 0 and nnz = %d"),
824                          nnz);
825            }
826        }
827        /* calculate nrow and ncol */
828        if (nrow < 0) {
829            for (int ii = 0; ii < nnz; ii++) {
830                int i1 = i[ii] + (index1 ? 0 : 1); /* 1-based index */
831                if (i1 < 1) error(_("invalid row index at position %d"), ii);
832                if (i1 > nrow) nrow = i1;
833            }
834        }
835        if (ncol < 0) {
836            for (int jj = 0; jj < nnz; jj++) {
837                int j1 = j[jj] + (index1 ? 0 : 1);
838                if (j1 < 1) error(_("invalid column index at position %d"), jj);
839                if (j1 > ncol) ncol = j1;
840            }
841        }
842        if (dims != (int*)NULL) {
843            if (dims[0] > nrow) nrow = dims[0];
844            if (dims[1] > ncol) ncol = dims[1];
845        }
846        /* check the class name */
847        if (strlen(cls) != 8)
848            error(_("strlen of cls argument = %d, should be 8"), strlen(cls));
849        if (!strcmp(cls + 2, "CMatrix"))
850            error(_("cls = \"%s\" does not end in \"CMatrix\""), cls);
851        switch(cls[0]) {
852        case 'd':
853        case 'l':
854            xtype = CHOLMOD_REAL;
855        break;
856        case 'n':
857            xtype = CHOLMOD_PATTERN;
858            break;
859        default:
860            error(_("cls = \"%s\" must begin with 'd', 'l' or 'n'"), cls);
861        }
862        if (cls[1] != 'g')
863            error(_("Only 'g'eneral sparse matrix types allowed"));
864        /* allocate and populate the triplet */
865        T = cholmod_allocate_triplet((size_t)nrow, (size_t)ncol, (size_t)nnz, 0,
866                                     xtype, &c);
867        T->x = x;
868        tri = (int*)T->i;
869        trj = (int*)T->j;
870        for (int ii = 0; ii < nnz; ii++) {
871            tri[ii] = i[ii] - ((!mi && index1) ? 1 : 0);
872            trj[ii] = j[ii] - ((!mj && index1) ? 1 : 0);
873        }
874        /* create the cholmod_sparse structure */
875        A = cholmod_triplet_to_sparse(T, nnz, &c);
876        cholmod_free_triplet(&T, &c);
877        /* copy the information to the SEXP */
878        ans = PROTECT(NEW_OBJECT(MAKE_CLASS(cls)));
879    /* FIXME: This has been copied from chm_sparse_to_SEXP in chm_common.c */
880        /* allocate and copy common slots */
881        nnz = cholmod_nnz(A, &c);
882        dims = INTEGER(ALLOC_SLOT(ans, Matrix_DimSym, INTSXP, 2));
883        dims[0] = A->nrow; dims[1] = A->ncol;
884        Memcpy(INTEGER(ALLOC_SLOT(ans, Matrix_pSym, INTSXP, A->ncol + 1)), (int*)A->p, A->ncol + 1);
885        Memcpy(INTEGER(ALLOC_SLOT(ans, Matrix_iSym, INTSXP, nnz)), (int*)A->i, nnz);
886        switch(cls[1]) {
887        case 'd':
888            Memcpy(REAL(ALLOC_SLOT(ans, Matrix_xSym, REALSXP, nnz)), (double*)A->x, nnz);
889            break;
890        case 'l':
891            error(_("code not yet written for cls = \"lgCMatrix\""));
892        }
893    /* FIXME: dimnames are *NOT* put there yet (if non-NULL) */
894        cholmod_free_sparse(&A, &c);
895        UNPROTECT(1);
896        return ans;
897    }

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