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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 2519, Fri Feb 5 17:20:14 2010 UTC pkg/Matrix/src/Csparse.c revision 2646, Mon Feb 21 10:57:49 2011 UTC
# Line 161  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 174  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_l_sparse_to_dense(AS_CHM_SP__(x), &c),      return chm_dense_to_matrix(cholmod_l_sparse_to_dense(AS_CHM_SP__(x), &c),
# Line 331  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_l_sdmult(cha, 0, one, zero, chb, chc, &c);      cholmod_l_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 349  Line 414 
414      CHM_DN chb = AS_CHM_DN(b_M);      CHM_DN chb = AS_CHM_DN(b_M);
415      CHM_DN chc = cholmod_l_allocate_dense(cha->ncol, chb->ncol, cha->ncol,      CHM_DN chc = cholmod_l_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_l_sdmult(cha, 1, one, zero, chb, chc, &c);      cholmod_l_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 403  Line 472 
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 425  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_l_horzcat(chx, chy, 1, &c),      return chm_sparse_to_SEXP(cholmod_l_horzcat(chx, chy, 1, &c),
506                                1, 0, Rkind, "", R_NilValue);                                1, 0, Rkind, "", R_NilValue);
507  }  }
# Line 436  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_l_vertcat(chx, chy, 1, &c),      return chm_sparse_to_SEXP(cholmod_l_vertcat(chx, chy, 1, &c),
519                                1, 0, Rkind, "", R_NilValue);                                1, 0, Rkind, "", R_NilValue);
520  }  }
# Line 788  Line 863 
863      case 'l':      case 'l':
864          error(_("code not yet written for cls = \"lgCMatrix\""));          error(_("code not yet written for cls = \"lgCMatrix\""));
865      }      }
866    /* FIXME: dimnames are *NOT* put there yet (if non-NULL) */
867      cholmod_l_free_sparse(&A, &c);      cholmod_l_free_sparse(&A, &c);
868      UNPROTECT(1);      UNPROTECT(1);
869      return ans;      return ans;

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