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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 2661, Wed Apr 6 06:55:54 2011 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 150  Line 161 
161      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));
162  }  }
163    
164    // FIXME: do not go via CHM (should not be too hard, to just *drop* the x-slot, right?
165  SEXP Csparse_to_nz_pattern(SEXP x, SEXP tri)  SEXP Csparse_to_nz_pattern(SEXP x, SEXP tri)
166  {  {
167      CHM_SP chxs = AS_CHM_SP__(x);      CHM_SP chxs = AS_CHM_SP__(x);
# Line 163  Line 175 
175                                GET_SLOT(x, Matrix_DimNamesSym));                                GET_SLOT(x, Matrix_DimNamesSym));
176  }  }
177    
178    // n.CMatrix --> [dli].CMatrix  (not going through CHM!)
179    SEXP nz_pattern_to_Csparse(SEXP x, SEXP res_kind)
180    {
181        return nz2Csparse(x, asInteger(res_kind));
182    }
183    // n.CMatrix --> [dli].CMatrix  (not going through CHM!)
184    SEXP nz2Csparse(SEXP x, enum x_slot_kind r_kind)
185    {
186        const char *cl_x = class_P(x);
187        if(cl_x[0] != 'n') error(_("not a 'n.CMatrix'"));
188        if(cl_x[2] != 'C') error(_("not a CsparseMatrix"));
189        int nnz = LENGTH(GET_SLOT(x, Matrix_iSym));
190        SEXP ans;
191        char *ncl = strdup(cl_x);
192        double *dx_x; int *ix_x;
193        ncl[0] = (r_kind == x_double ? 'd' :
194                  (r_kind == x_logical ? 'l' :
195                   /* else (for now):  r_kind == x_integer : */ 'i'));
196        PROTECT(ans = NEW_OBJECT(MAKE_CLASS(ncl)));
197        // create a correct 'x' slot:
198        switch(r_kind) {
199            int i;
200        case x_double: // 'd'
201            dx_x = REAL(ALLOC_SLOT(ans, Matrix_xSym, REALSXP, nnz));
202            for (i=0; i < nnz; i++) dx_x[i] = 1.;
203            break;
204        case x_logical: // 'l'
205            ix_x = LOGICAL(ALLOC_SLOT(ans, Matrix_xSym, LGLSXP, nnz));
206            for (i=0; i < nnz; i++) ix_x[i] = TRUE;
207            break;
208        case x_integer: // 'i'
209            ix_x = INTEGER(ALLOC_SLOT(ans, Matrix_xSym, INTSXP, nnz));
210            for (i=0; i < nnz; i++) ix_x[i] = 1;
211            break;
212    
213        default:
214            error(_("nz2Csparse(): invalid/non-implemented r_kind = %d"),
215                  r_kind);
216        }
217    
218        // now copy all other slots :
219        slot_dup(ans, x, Matrix_iSym);
220        slot_dup(ans, x, Matrix_pSym);
221        slot_dup(ans, x, Matrix_DimSym);
222        slot_dup(ans, x, Matrix_DimNamesSym);
223        if(ncl[1] != 'g') { // symmetric or triangular ...
224            slot_dup_if_has(ans, x, Matrix_uploSym);
225            slot_dup_if_has(ans, x, Matrix_diagSym);
226        }
227        UNPROTECT(1);
228        return ans;
229    }
230    
231  SEXP Csparse_to_matrix(SEXP x)  SEXP Csparse_to_matrix(SEXP x)
232  {  {
233      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),
# Line 237  Line 302 
302          cha = AS_CHM_SP(a),          cha = AS_CHM_SP(a),
303          chb = AS_CHM_SP(b),          chb = AS_CHM_SP(b),
304          chc = cholmod_ssmult(cha, chb, /*out_stype:*/ 0,          chc = cholmod_ssmult(cha, chb, /*out_stype:*/ 0,
305                               cha->xtype, /*out sorted:*/ 1, &c);                                 /* values:= is_numeric (T/F) */ cha->xtype > 0,
306                                   /*out sorted:*/ 1, &c);
307      const char *cl_a = class_P(a), *cl_b = class_P(b);      const char *cl_a = class_P(a), *cl_b = class_P(b);
308      char diag[] = {'\0', '\0'};      char diag[] = {'\0', '\0'};
309      int uploT = 0;      int uploT = 0;
310      SEXP dn = allocVector(VECSXP, 2);      SEXP dn = PROTECT(allocVector(VECSXP, 2));
311      R_CheckStack();      R_CheckStack();
312    
313    #ifdef DEBUG_Matrix_verbose
314        Rprintf("DBG Csparse_C*_prod(%s, %s)\n", cl_a, cl_b);
315    #endif
316    
317      /* Preserve triangularity and even unit-triangularity if appropriate.      /* Preserve triangularity and even unit-triangularity if appropriate.
318       * Note that in that case, the multiplication itself should happen       * Note that in that case, the multiplication itself should happen
319       * faster.  But there's no support for that in CHOLMOD */       * faster.  But there's no support for that in CHOLMOD */
# Line 265  Line 335 
335                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));
336      SET_VECTOR_ELT(dn, 1,      SET_VECTOR_ELT(dn, 1,
337                     duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), 1)));                     duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), 1)));
338        UNPROTECT(1);
339      return chm_sparse_to_SEXP(chc, 1, uploT, /*Rkind*/0, diag, dn);      return chm_sparse_to_SEXP(chc, 1, uploT, /*Rkind*/0, diag, dn);
340  }  }
341    
# Line 278  Line 349 
349      const char *cl_a = class_P(a), *cl_b = class_P(b);      const char *cl_a = class_P(a), *cl_b = class_P(b);
350      char diag[] = {'\0', '\0'};      char diag[] = {'\0', '\0'};
351      int uploT = 0;      int uploT = 0;
352      SEXP dn = allocVector(VECSXP, 2);      SEXP dn = PROTECT(allocVector(VECSXP, 2));
353      R_CheckStack();      R_CheckStack();
354    
355      chTr = cholmod_transpose((tr) ? chb : cha, chb->xtype, &c);      chTr = cholmod_transpose((tr) ? chb : cha, chb->xtype, &c);
# Line 297  Line 368 
368              }              }
369              else diag[0]= 'N';              else diag[0]= 'N';
370          }          }
   
371      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
372                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), (tr) ? 0 : 1)));                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), (tr) ? 0 : 1)));
373      SET_VECTOR_ELT(dn, 1,      SET_VECTOR_ELT(dn, 1,
374                     duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), (tr) ? 0 : 1)));                     duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), (tr) ? 0 : 1)));
375        UNPROTECT(1);
376      return chm_sparse_to_SEXP(chc, 1, uploT, /*Rkind*/0, diag, dn);      return chm_sparse_to_SEXP(chc, 1, uploT, /*Rkind*/0, diag, dn);
377  }  }
378    
# Line 314  Line 385 
385                                          chb->xtype, &c);                                          chb->xtype, &c);
386      SEXP dn = PROTECT(allocVector(VECSXP, 2));      SEXP dn = PROTECT(allocVector(VECSXP, 2));
387      double one[] = {1,0}, zero[] = {0,0};      double one[] = {1,0}, zero[] = {0,0};
388        int nprot = 2;
389      R_CheckStack();      R_CheckStack();
390        /* Tim Davis, please FIXME:  currently (2010-11) *fails* when  a  is a pattern matrix:*/
391        if(cha->xtype == CHOLMOD_PATTERN) {
392            /* warning(_("Csparse_dense_prod(): cholmod_sdmult() not yet implemented for pattern./ ngCMatrix" */
393            /*        " --> slightly inefficient coercion")); */
394    
395            // This *fails* to produce a CHOLMOD_REAL ..
396            // CHM_SP chd = cholmod_l_copy(cha, cha->stype, CHOLMOD_REAL, &c);
397            // --> use our Matrix-classes
398            SEXP da = PROTECT(nz2Csparse(a, x_double)); nprot++;
399            cha = AS_CHM_SP(da);
400        }
401      cholmod_sdmult(cha, 0, one, zero, chb, chc, &c);      cholmod_sdmult(cha, 0, one, zero, chb, chc, &c);
402      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
403                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));
404      SET_VECTOR_ELT(dn, 1,      SET_VECTOR_ELT(dn, 1,
405                     duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));                     duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));
406      UNPROTECT(2);      UNPROTECT(nprot);
407      return chm_dense_to_SEXP(chc, 1, 0, dn);      return chm_dense_to_SEXP(chc, 1, 0, dn);
408  }  }
409    
# Line 332  Line 414 
414      CHM_DN chb = AS_CHM_DN(b_M);      CHM_DN chb = AS_CHM_DN(b_M);
415      CHM_DN chc = cholmod_allocate_dense(cha->ncol, chb->ncol, cha->ncol,      CHM_DN chc = cholmod_allocate_dense(cha->ncol, chb->ncol, cha->ncol,
416                                          chb->xtype, &c);                                          chb->xtype, &c);
417      SEXP dn = PROTECT(allocVector(VECSXP, 2));      SEXP dn = PROTECT(allocVector(VECSXP, 2)); int nprot = 2;
418      double one[] = {1,0}, zero[] = {0,0};      double one[] = {1,0}, zero[] = {0,0};
419      R_CheckStack();      R_CheckStack();
420        // -- see Csparse_dense_prod() above :
421        if(cha->xtype == CHOLMOD_PATTERN) {
422            SEXP da = PROTECT(nz2Csparse(a, x_double)); nprot++;
423            cha = AS_CHM_SP(da);
424        }
425      cholmod_sdmult(cha, 1, one, zero, chb, chc, &c);      cholmod_sdmult(cha, 1, one, zero, chb, chc, &c);
426      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
427                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 1)));                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 1)));
428      SET_VECTOR_ELT(dn, 1,      SET_VECTOR_ELT(dn, 1,
429                     duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));                     duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));
430      UNPROTECT(2);      UNPROTECT(nprot);
431      return chm_dense_to_SEXP(chc, 1, 0, dn);      return chm_dense_to_SEXP(chc, 1, 0, dn);
432  }  }
433    
# Line 351  Line 437 
437  {  {
438      int trip = asLogical(triplet),      int trip = asLogical(triplet),
439          tr   = asLogical(trans); /* gets reversed because _aat is tcrossprod */          tr   = asLogical(trans); /* gets reversed because _aat is tcrossprod */
440    #ifdef AS_CHM_DIAGU2N_FIXED_FINALLY
441      CHM_TR cht = trip ? AS_CHM_TR(x) : (CHM_TR) NULL;      CHM_TR cht = trip ? AS_CHM_TR(x) : (CHM_TR) NULL;
442    #else /* workaround needed:*/
443        SEXP xx = PROTECT(Tsparse_diagU2N(x));
444        CHM_TR cht = trip ? AS_CHM_TR__(xx) : (CHM_TR) NULL;
445    #endif
446      CHM_SP chcp, chxt,      CHM_SP chcp, chxt,
447          chx = (trip ?          chx = (trip ?
448                 cholmod_triplet_to_sparse(cht, cht->nnz, &c) :                 cholmod_triplet_to_sparse(cht, cht->nnz, &c) :
# Line 373  Line 464 
464                     duplicate(VECTOR_ELT(GET_SLOT(x, Matrix_DimNamesSym),                     duplicate(VECTOR_ELT(GET_SLOT(x, Matrix_DimNamesSym),
465                                          (tr) ? 0 : 1)));                                          (tr) ? 0 : 1)));
466      SET_VECTOR_ELT(dn, 1, duplicate(VECTOR_ELT(dn, 0)));      SET_VECTOR_ELT(dn, 1, duplicate(VECTOR_ELT(dn, 0)));
467    #ifdef AS_CHM_DIAGU2N_FIXED_FINALLY
468      UNPROTECT(1);      UNPROTECT(1);
469    #else
470        UNPROTECT(2);
471    #endif
472      return chm_sparse_to_SEXP(chcp, 1, 0, 0, "", dn);      return chm_sparse_to_SEXP(chcp, 1, 0, 0, "", dn);
473  }  }
474    
475    /* Csparse_drop(x, tol):  drop entries with absolute value < tol, i.e,
476    *  at least all "explicit" zeros */
477  SEXP Csparse_drop(SEXP x, SEXP tol)  SEXP Csparse_drop(SEXP x, SEXP tol)
478  {  {
479      const char *cl = class_P(x);      const char *cl = class_P(x);
# Line 399  Line 496 
496  SEXP Csparse_horzcat(SEXP x, SEXP y)  SEXP Csparse_horzcat(SEXP x, SEXP y)
497  {  {
498      CHM_SP chx = AS_CHM_SP__(x), chy = AS_CHM_SP__(y);      CHM_SP chx = AS_CHM_SP__(x), chy = AS_CHM_SP__(y);
499      int Rkind = 0; /* only for "d" - FIXME */      int Rk_x = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0,
500            Rk_y = (chy->xtype != CHOLMOD_PATTERN) ? Real_kind(y) : 0,
501            Rkind = /* logical if both x and y are */ (Rk_x == 1 && Rk_y == 1) ? 1 : 0;
502      R_CheckStack();      R_CheckStack();
503    
504      /* FIXME: currently drops dimnames */      /* TODO: currently drops dimnames - and we fix at R level */
505      return chm_sparse_to_SEXP(cholmod_horzcat(chx, chy, 1, &c),      return chm_sparse_to_SEXP(cholmod_horzcat(chx, chy, 1, &c),
506                                1, 0, Rkind, "", R_NilValue);                                1, 0, Rkind, "", R_NilValue);
507  }  }
# Line 410  Line 509 
509  SEXP Csparse_vertcat(SEXP x, SEXP y)  SEXP Csparse_vertcat(SEXP x, SEXP y)
510  {  {
511      CHM_SP chx = AS_CHM_SP__(x), chy = AS_CHM_SP__(y);      CHM_SP chx = AS_CHM_SP__(x), chy = AS_CHM_SP__(y);
512      int Rkind = 0; /* only for "d" - FIXME */      int Rk_x = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0,
513            Rk_y = (chy->xtype != CHOLMOD_PATTERN) ? Real_kind(y) : 0,
514            Rkind = /* logical if both x and y are */ (Rk_x == 1 && Rk_y == 1) ? 1 : 0;
515      R_CheckStack();      R_CheckStack();
516    
517      /* FIXME: currently drops dimnames */      /* TODO: currently drops dimnames - and we fix at R level */
518      return chm_sparse_to_SEXP(cholmod_vertcat(chx, chy, 1, &c),      return chm_sparse_to_SEXP(cholmod_vertcat(chx, chy, 1, &c),
519                                1, 0, Rkind, "", R_NilValue);                                1, 0, Rkind, "", R_NilValue);
520  }  }
# Line 477  Line 578 
578      }      }
579  }  }
580    
581    /**
582     * "Indexing" aka subsetting : Compute  x[i,j], also for vectors i and j
583     * Working via CHOLMOD_submatrix, see ./CHOLMOD/MatrixOps/cholmod_submatrix.c
584     * @param x CsparseMatrix
585     * @param i row     indices (0-origin), or NULL (R's)
586     * @param j columns indices (0-origin), or NULL
587     *
588     * @return x[i,j]  still CsparseMatrix --- currently, this loses dimnames
589     */
590  SEXP Csparse_submatrix(SEXP x, SEXP i, SEXP j)  SEXP Csparse_submatrix(SEXP x, SEXP i, SEXP j)
591  {  {
592      CHM_SP chx = AS_CHM_SP__(x);      CHM_SP chx = AS_CHM_SP(x); /* << does diagU2N() when needed */
593      int rsize = (isNull(i)) ? -1 : LENGTH(i),      int rsize = (isNull(i)) ? -1 : LENGTH(i),
594          csize = (isNull(j)) ? -1 : LENGTH(j);          csize = (isNull(j)) ? -1 : LENGTH(j);
595      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
# Line 490  Line 600 
600      if (csize >= 0 && !isInteger(j))      if (csize >= 0 && !isInteger(j))
601          error(_("Index j must be NULL or integer"));          error(_("Index j must be NULL or integer"));
602    
603      return chm_sparse_to_SEXP(cholmod_submatrix(chx, INTEGER(i), rsize,      if (chx->stype) /* symmetricMatrix */
604                                                  INTEGER(j), csize,          /* for now, cholmod_submatrix() only accepts "generalMatrix" */
605            chx = cholmod_copy(chx, /* stype: */ 0, chx->xtype, &c);
606    
607        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    
615    /**
616     * Subassignment:  x[i,j]  <- value
617     *
618     * @param x
619     * @param i_ integer row    index 0-origin vector (as returned from R .ind.prep2())
620     * @param j_ integer column index 0-origin vector
621     * @param value currently must be a dsparseVector {which is recycled if needed}
622     *
623     * @return a Csparse matrix like x, but with the values replaced
624     */
625    SEXP Csparse_subassign(SEXP x, SEXP i_, SEXP j_, SEXP value)
626    {
627        static const char
628            *valid_cM [] = {"dgCMatrix",// the only one, for "the moment", more later
629                            ""},
630            *valid_spv[] = {"dsparseVector",
631                            ""};
632    
633        int ctype = Matrix_check_class_etc(x, valid_cM);
634        if (ctype < 0)
635            error(_("invalid class of 'x' in Csparse_subassign()"));
636        // value: assume a  "dsparseVector" for now -- slots: (i, length, x)
637        ctype = Matrix_check_class_etc(value, valid_spv);
638        if (ctype < 0)
639            error(_("invalid class of 'value' in Csparse_subassign()"));
640    
641        SEXP ans,
642            pslot = GET_SLOT(x, Matrix_pSym),
643            islot = GET_SLOT(x, Matrix_iSym),
644            i_cp = PROTECT((TYPEOF(i_) == INTSXP) ?
645                           duplicate(i_) : coerceVector(i_, INTSXP)),
646            j_cp = PROTECT((TYPEOF(j_) == INTSXP) ?
647                           duplicate(j_) : coerceVector(j_, INTSXP)),
648            // for d.CMatrix and l.CMatrix  but not n.CMatrix
649            xslot = GET_SLOT(x, Matrix_xSym);
650    
651        int *dims = INTEGER(GET_SLOT(x, Matrix_DimSym)),
652            nrow = dims[0],
653            ncol = dims[1],
654            *xp = INTEGER(pslot),
655            *xi = INTEGER(islot),
656            *ii = INTEGER(i_cp), len_i = LENGTH(i_cp),
657            *jj = INTEGER(j_cp), len_j = LENGTH(j_cp),
658            i, j, k;
659        int    *val_i = INTEGER(GET_SLOT(value, Matrix_iSym));
660        double *val_x =   REAL (GET_SLOT(value, Matrix_xSym));
661        int len_val = asInteger(GET_SLOT(value, Matrix_lengthSym));
662        int p_last = xp[0];
663    
664        // for d.CMatrix only:
665        double *xx = REAL(xslot);
666        double ind; // the index that goes all the way from 1:(len_i * len_j)
667    
668        PROTECT(ans = duplicate(x));
669        for(j = 0; j < ncol; j++) {
670        }
671        UNPROTECT(3);
672        return ans;
673    }
674    
675  SEXP Csparse_MatrixMarket(SEXP x, SEXP fname)  SEXP Csparse_MatrixMarket(SEXP x, SEXP fname)
676  {  {
677      FILE *f = fopen(CHAR(asChar(fname)), "w");      FILE *f = fopen(CHAR(asChar(fname)), "w");
# Line 588  Line 763 
763          break;          break;
764    
765      default: /* -1 from above */      default: /* -1 from above */
766          error("diag_tC(): invalid 'resultKind'");          error(_("diag_tC(): invalid 'resultKind'"));
767          /* Wall: */ ans = R_NilValue; v = REAL(ans);          /* Wall: */ ans = R_NilValue; v = REAL(ans);
768      }      }
769    
# Line 618  Line 793 
793    
794      return diag_tC_ptr(n, x_p, x_x, perm, resultKind);      return diag_tC_ptr(n, x_p, x_x, perm, resultKind);
795  }  }
796    
797    /**
798     * Create a Csparse matrix object from indices and/or pointers.
799     *
800     * @param cls name of actual class of object to create
801     * @param i optional integer vector of length nnz of row indices
802     * @param j optional integer vector of length nnz of column indices
803     * @param p optional integer vector of length np of row or column pointers
804     * @param np length of integer vector p.  Must be zero if p == (int*)NULL
805     * @param x optional vector of values
806     * @param nnz length of vectors i, j and/or x, whichever is to be used
807     * @param dims optional integer vector of length 2 to be used as
808     *     dimensions.  If dims == (int*)NULL then the maximum row and column
809     *     index are used as the dimensions.
810     * @param dimnames optional list of length 2 to be used as dimnames
811     * @param index1 indicator of 1-based indices
812     *
813     * @return an SEXP of class cls inheriting from CsparseMatrix.
814     */
815    SEXP create_Csparse(char* cls, int* i, int* j, int* p, int np,
816                        void* x, int nnz, int* dims, SEXP dimnames,
817                        int index1)
818    {
819        SEXP ans;
820        int *ij = (int*)NULL, *tri, *trj,
821            mi, mj, mp, nrow = -1, ncol = -1;
822        int xtype = -1;             /* -Wall */
823        CHM_TR T;
824        CHM_SP A;
825    
826        if (np < 0 || nnz < 0)
827            error(_("negative vector lengths not allowed: np = %d, nnz = %d"),
828                  np, nnz);
829        if (1 != ((mi = (i == (int*)NULL)) +
830                  (mj = (j == (int*)NULL)) +
831                  (mp = (p == (int*)NULL))))
832            error(_("exactly 1 of 'i', 'j' or 'p' must be NULL"));
833        if (mp) {
834            if (np) error(_("np = %d, must be zero when p is NULL"), np);
835        } else {
836            if (np) {               /* Expand p to form i or j */
837                if (!(p[0])) error(_("p[0] = %d, should be zero"), p[0]);
838                for (int ii = 0; ii < np; ii++)
839                    if (p[ii] > p[ii + 1])
840                        error(_("p must be non-decreasing"));
841                if (p[np] != nnz)
842                    error("p[np] = %d != nnz = %d", p[np], nnz);
843                ij = Calloc(nnz, int);
844                if (mi) {
845                    i = ij;
846                    nrow = np;
847                } else {
848                    j = ij;
849                    ncol = np;
850                }
851                /* Expand p to 0-based indices */
852                for (int ii = 0; ii < np; ii++)
853                    for (int jj = p[ii]; jj < p[ii + 1]; jj++) ij[jj] = ii;
854            } else {
855                if (nnz)
856                    error(_("Inconsistent dimensions: np = 0 and nnz = %d"),
857                          nnz);
858            }
859        }
860        /* calculate nrow and ncol */
861        if (nrow < 0) {
862            for (int ii = 0; ii < nnz; ii++) {
863                int i1 = i[ii] + (index1 ? 0 : 1); /* 1-based index */
864                if (i1 < 1) error(_("invalid row index at position %d"), ii);
865                if (i1 > nrow) nrow = i1;
866            }
867        }
868        if (ncol < 0) {
869            for (int jj = 0; jj < nnz; jj++) {
870                int j1 = j[jj] + (index1 ? 0 : 1);
871                if (j1 < 1) error(_("invalid column index at position %d"), jj);
872                if (j1 > ncol) ncol = j1;
873            }
874        }
875        if (dims != (int*)NULL) {
876            if (dims[0] > nrow) nrow = dims[0];
877            if (dims[1] > ncol) ncol = dims[1];
878        }
879        /* check the class name */
880        if (strlen(cls) != 8)
881            error(_("strlen of cls argument = %d, should be 8"), strlen(cls));
882        if (!strcmp(cls + 2, "CMatrix"))
883            error(_("cls = \"%s\" does not end in \"CMatrix\""), cls);
884        switch(cls[0]) {
885        case 'd':
886        case 'l':
887            xtype = CHOLMOD_REAL;
888        break;
889        case 'n':
890            xtype = CHOLMOD_PATTERN;
891            break;
892        default:
893            error(_("cls = \"%s\" must begin with 'd', 'l' or 'n'"), cls);
894        }
895        if (cls[1] != 'g')
896            error(_("Only 'g'eneral sparse matrix types allowed"));
897        /* allocate and populate the triplet */
898        T = cholmod_allocate_triplet((size_t)nrow, (size_t)ncol, (size_t)nnz, 0,
899                                     xtype, &c);
900        T->x = x;
901        tri = (int*)T->i;
902        trj = (int*)T->j;
903        for (int ii = 0; ii < nnz; ii++) {
904            tri[ii] = i[ii] - ((!mi && index1) ? 1 : 0);
905            trj[ii] = j[ii] - ((!mj && index1) ? 1 : 0);
906        }
907        /* create the cholmod_sparse structure */
908        A = cholmod_triplet_to_sparse(T, nnz, &c);
909        cholmod_free_triplet(&T, &c);
910        /* copy the information to the SEXP */
911        ans = PROTECT(NEW_OBJECT(MAKE_CLASS(cls)));
912    /* FIXME: This has been copied from chm_sparse_to_SEXP in chm_common.c */
913        /* allocate and copy common slots */
914        nnz = cholmod_nnz(A, &c);
915        dims = INTEGER(ALLOC_SLOT(ans, Matrix_DimSym, INTSXP, 2));
916        dims[0] = A->nrow; dims[1] = A->ncol;
917        Memcpy(INTEGER(ALLOC_SLOT(ans, Matrix_pSym, INTSXP, A->ncol + 1)), (int*)A->p, A->ncol + 1);
918        Memcpy(INTEGER(ALLOC_SLOT(ans, Matrix_iSym, INTSXP, nnz)), (int*)A->i, nnz);
919        switch(cls[1]) {
920        case 'd':
921            Memcpy(REAL(ALLOC_SLOT(ans, Matrix_xSym, REALSXP, nnz)), (double*)A->x, nnz);
922            break;
923        case 'l':
924            error(_("code not yet written for cls = \"lgCMatrix\""));
925        }
926    /* FIXME: dimnames are *NOT* put there yet (if non-NULL) */
927        cholmod_free_sparse(&A, &c);
928        UNPROTECT(1);
929        return ans;
930    }

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