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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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revision 2586, Sun Jul 25 02:32:06 2010 UTC revision 2661, Wed Apr 6 06:55:54 2011 UTC
# Line 136  Line 136 
136              }              }
137      }      }
138      if (!sorted)      if (!sorted)
139          /* cannot easily use cholmod_l_sort(.) ... -> "error out" :*/          /* cannot easily use cholmod_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 154  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_l_sparse_to_dense(chxs, &c);      CHM_DN chxd = cholmod_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    
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);
168      CHM_SP chxcp = cholmod_l_copy(chxs, chxs->stype, CHOLMOD_PATTERN, &c);      CHM_SP chxcp = cholmod_copy(chxs, chxs->stype, CHOLMOD_PATTERN, &c);
169      int tr = asLogical(tri);      int tr = asLogical(tri);
170      R_CheckStack();      R_CheckStack();
171    
# 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_sparse_to_dense(AS_CHM_SP__(x), &c),
234                                 1 /*do_free*/, GET_SLOT(x, Matrix_DimNamesSym));                                 1 /*do_free*/, GET_SLOT(x, Matrix_DimNamesSym));
235  }  }
236    
237  SEXP Csparse_to_Tsparse(SEXP x, SEXP tri)  SEXP Csparse_to_Tsparse(SEXP x, SEXP tri)
238  {  {
239      CHM_SP chxs = AS_CHM_SP__(x);      CHM_SP chxs = AS_CHM_SP__(x);
240      CHM_TR chxt = cholmod_l_sparse_to_triplet(chxs, &c);      CHM_TR chxt = cholmod_sparse_to_triplet(chxs, &c);
241      int tr = asLogical(tri);      int tr = asLogical(tri);
242      int Rkind = (chxs->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chxs->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
243      R_CheckStack();      R_CheckStack();
# Line 203  Line 257 
257    
258      if (!(chx->stype))      if (!(chx->stype))
259          error(_("Nonsymmetric matrix in Csparse_symmetric_to_general"));          error(_("Nonsymmetric matrix in Csparse_symmetric_to_general"));
260      chgx = cholmod_l_copy(chx, /* stype: */ 0, chx->xtype, &c);      chgx = cholmod_copy(chx, /* stype: */ 0, chx->xtype, &c);
261      /* xtype: pattern, "real", complex or .. */      /* xtype: pattern, "real", complex or .. */
262      return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",      return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",
263                                GET_SLOT(x, Matrix_DimNamesSym));                                GET_SLOT(x, Matrix_DimNamesSym));
# Line 216  Line 270 
270      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
271      R_CheckStack();      R_CheckStack();
272    
273      chgx = cholmod_l_copy(chx, /* stype: */ uploT, chx->xtype, &c);      chgx = cholmod_copy(chx, /* stype: */ uploT, chx->xtype, &c);
274      /* xtype: pattern, "real", complex or .. */      /* xtype: pattern, "real", complex or .. */
275      return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",      return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",
276                                GET_SLOT(x, Matrix_DimNamesSym));                                GET_SLOT(x, Matrix_DimNamesSym));
# Line 228  Line 282 
282       *       since cholmod (& cs) lacks sparse 'int' matrices */       *       since cholmod (& cs) lacks sparse 'int' matrices */
283      CHM_SP chx = AS_CHM_SP__(x);      CHM_SP chx = AS_CHM_SP__(x);
284      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
285      CHM_SP chxt = cholmod_l_transpose(chx, chx->xtype, &c);      CHM_SP chxt = cholmod_transpose(chx, chx->xtype, &c);
286      SEXP dn = PROTECT(duplicate(GET_SLOT(x, Matrix_DimNamesSym))), tmp;      SEXP dn = PROTECT(duplicate(GET_SLOT(x, Matrix_DimNamesSym))), tmp;
287      int tr = asLogical(tri);      int tr = asLogical(tri);
288      R_CheckStack();      R_CheckStack();
# Line 247  Line 301 
301      CHM_SP      CHM_SP
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_l_ssmult(cha, chb, /*out_stype:*/ 0,          chc = cholmod_ssmult(cha, chb, /*out_stype:*/ 0,
305                                 /* values:= is_numeric (T/F) */ cha->xtype > 0,                                 /* values:= is_numeric (T/F) */ cha->xtype > 0,
306                                 /*out sorted:*/ 1, &c);                                 /*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);
# Line 298  Line 352 
352      SEXP dn = PROTECT(allocVector(VECSXP, 2));      SEXP dn = PROTECT(allocVector(VECSXP, 2));
353      R_CheckStack();      R_CheckStack();
354    
355      chTr = cholmod_l_transpose((tr) ? chb : cha, chb->xtype, &c);      chTr = cholmod_transpose((tr) ? chb : cha, chb->xtype, &c);
356      chc = cholmod_l_ssmult((tr) ? cha : chTr, (tr) ? chTr : chb,      chc = cholmod_ssmult((tr) ? cha : chTr, (tr) ? chTr : chb,
357                           /*out_stype:*/ 0, cha->xtype, /*out sorted:*/ 1, &c);                           /*out_stype:*/ 0, cha->xtype, /*out sorted:*/ 1, &c);
358      cholmod_l_free_sparse(&chTr, &c);      cholmod_free_sparse(&chTr, &c);
359    
360      /* Preserve triangularity and unit-triangularity if appropriate;      /* Preserve triangularity and unit-triangularity if appropriate;
361       * see Csparse_Csparse_prod() for comments */       * see Csparse_Csparse_prod() for comments */
# Line 327  Line 381 
381      CHM_SP cha = AS_CHM_SP(a);      CHM_SP cha = AS_CHM_SP(a);
382      SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));      SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));
383      CHM_DN chb = AS_CHM_DN(b_M);      CHM_DN chb = AS_CHM_DN(b_M);
384      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,
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      cholmod_l_sdmult(cha, 0, one, zero, chb, chc, &c);      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);
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 347  Line 412 
412      CHM_SP cha = AS_CHM_SP(a);      CHM_SP cha = AS_CHM_SP(a);
413      SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));      SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));
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_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      cholmod_l_sdmult(cha, 1, one, zero, chb, chc, &c);      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);
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 376  Line 445 
445  #endif  #endif
446      CHM_SP chcp, chxt,      CHM_SP chcp, chxt,
447          chx = (trip ?          chx = (trip ?
448                 cholmod_l_triplet_to_sparse(cht, cht->nnz, &c) :                 cholmod_triplet_to_sparse(cht, cht->nnz, &c) :
449                 AS_CHM_SP(x));                 AS_CHM_SP(x));
450      SEXP dn = PROTECT(allocVector(VECSXP, 2));      SEXP dn = PROTECT(allocVector(VECSXP, 2));
451      R_CheckStack();      R_CheckStack();
452    
453      if (!tr) chxt = cholmod_l_transpose(chx, chx->xtype, &c);      if (!tr) chxt = cholmod_transpose(chx, chx->xtype, &c);
454      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);
455      if(!chcp) {      if(!chcp) {
456          UNPROTECT(1);          UNPROTECT(1);
457          error(_("Csparse_crossprod(): error return from cholmod_l_aat()"));          error(_("Csparse_crossprod(): error return from cholmod_aat()"));
458      }      }
459      cholmod_l_band_inplace(0, chcp->ncol, chcp->xtype, chcp, &c);      cholmod_band_inplace(0, chcp->ncol, chcp->xtype, chcp, &c);
460      chcp->stype = 1;      chcp->stype = 1;
461      if (trip) cholmod_l_free_sparse(&chx, &c);      if (trip) cholmod_free_sparse(&chx, &c);
462      if (!tr) cholmod_l_free_sparse(&chxt, &c);      if (!tr) cholmod_free_sparse(&chxt, &c);
463      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
464                     duplicate(VECTOR_ELT(GET_SLOT(x, Matrix_DimNamesSym),                     duplicate(VECTOR_ELT(GET_SLOT(x, Matrix_DimNamesSym),
465                                          (tr) ? 0 : 1)));                                          (tr) ? 0 : 1)));
# 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);
480      /* dtCMatrix, etc; [1] = the second character =?= 't' for triangular */      /* dtCMatrix, etc; [1] = the second character =?= 't' for triangular */
481      int tr = (cl[1] == 't');      int tr = (cl[1] == 't');
482      CHM_SP chx = AS_CHM_SP__(x);      CHM_SP chx = AS_CHM_SP__(x);
483      CHM_SP ans = cholmod_l_copy(chx, chx->stype, chx->xtype, &c);      CHM_SP ans = cholmod_copy(chx, chx->stype, chx->xtype, &c);
484      double dtol = asReal(tol);      double dtol = asReal(tol);
485      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
486      R_CheckStack();      R_CheckStack();
487    
488      if(!cholmod_l_drop(dtol, ans, &c))      if(!cholmod_drop(dtol, ans, &c))
489          error(_("cholmod_l_drop() failed"));          error(_("cholmod_drop() failed"));
490      return chm_sparse_to_SEXP(ans, 1,      return chm_sparse_to_SEXP(ans, 1,
491                                tr ? ((*uplo_P(x) == 'U') ? 1 : -1) : 0,                                tr ? ((*uplo_P(x) == 'U') ? 1 : -1) : 0,
492                                Rkind, tr ? diag_P(x) : "",                                Rkind, tr ? diag_P(x) : "",
# Line 431  Line 502 
502      R_CheckStack();      R_CheckStack();
503    
504      /* TODO: currently drops dimnames - and we fix at R level */      /* 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_horzcat(chx, chy, 1, &c),
506                                1, 0, Rkind, "", R_NilValue);                                1, 0, Rkind, "", R_NilValue);
507  }  }
508    
# Line 444  Line 515 
515      R_CheckStack();      R_CheckStack();
516    
517      /* TODO: currently drops dimnames - and we fix at R level */      /* 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_vertcat(chx, chy, 1, &c),
519                                1, 0, Rkind, "", R_NilValue);                                1, 0, Rkind, "", R_NilValue);
520  }  }
521    
# Line 452  Line 523 
523  {  {
524      CHM_SP chx = AS_CHM_SP__(x);      CHM_SP chx = AS_CHM_SP__(x);
525      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
526      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);
527      R_CheckStack();      R_CheckStack();
528    
529      return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "",      return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "",
# Line 470  Line 541 
541      }      }
542      else { /* unit triangular (diag='U'): "fill the diagonal" & diag:= "N" */      else { /* unit triangular (diag='U'): "fill the diagonal" & diag:= "N" */
543          CHM_SP chx = AS_CHM_SP__(x);          CHM_SP chx = AS_CHM_SP__(x);
544          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);
545          double one[] = {1, 0};          double one[] = {1, 0};
546          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);
547          int uploT = (*uplo_P(x) == 'U') ? 1 : -1;          int uploT = (*uplo_P(x) == 'U') ? 1 : -1;
548          int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;          int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
549    
550          R_CheckStack();          R_CheckStack();
551          cholmod_l_free_sparse(&eye, &c);          cholmod_free_sparse(&eye, &c);
552          return chm_sparse_to_SEXP(ans, 1, uploT, Rkind, "N",          return chm_sparse_to_SEXP(ans, 1, uploT, Rkind, "N",
553                                    GET_SLOT(x, Matrix_DimNamesSym));                                    GET_SLOT(x, Matrix_DimNamesSym));
554      }      }
# Line 531  Line 602 
602    
603      if (chx->stype) /* symmetricMatrix */      if (chx->stype) /* symmetricMatrix */
604          /* for now, cholmod_submatrix() only accepts "generalMatrix" */          /* for now, cholmod_submatrix() only accepts "generalMatrix" */
605          chx = cholmod_l_copy(chx, /* stype: */ 0, chx->xtype, &c);          chx = cholmod_copy(chx, /* stype: */ 0, chx->xtype, &c);
606    
607      return chm_sparse_to_SEXP(cholmod_l_submatrix(chx,      return chm_sparse_to_SEXP(cholmod_submatrix(chx,
608                                  (rsize < 0) ? NULL : INTEGER(i), rsize,                                  (rsize < 0) ? NULL : INTEGER(i), rsize,
609                                  (csize < 0) ? NULL : INTEGER(j), csize,                                  (csize < 0) ? NULL : INTEGER(j), csize,
610                                                    TRUE, TRUE, &c),                                                    TRUE, TRUE, &c),
# Line 541  Line 612 
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 548  Line 679 
679      if (!f)      if (!f)
680          error(_("failure to open file \"%s\" for writing"),          error(_("failure to open file \"%s\" for writing"),
681                CHAR(asChar(fname)));                CHAR(asChar(fname)));
682      if (!cholmod_l_write_sparse(f, AS_CHM_SP(x),      if (!cholmod_write_sparse(f, AS_CHM_SP(x),
683                                (CHM_SP)NULL, (char*) NULL, &c))                                (CHM_SP)NULL, (char*) NULL, &c))
684          error(_("cholmod_l_write_sparse returned error code"));          error(_("cholmod_write_sparse returned error code"));
685      fclose(f);      fclose(f);
686      return R_NilValue;      return R_NilValue;
687  }  }
# Line 764  Line 895 
895      if (cls[1] != 'g')      if (cls[1] != 'g')
896          error(_("Only 'g'eneral sparse matrix types allowed"));          error(_("Only 'g'eneral sparse matrix types allowed"));
897                                  /* allocate and populate the triplet */                                  /* allocate and populate the triplet */
898      T = cholmod_l_allocate_triplet((size_t)nrow, (size_t)ncol, (size_t)nnz, 0,      T = cholmod_allocate_triplet((size_t)nrow, (size_t)ncol, (size_t)nnz, 0,
899                                      xtype, &c);                                      xtype, &c);
900      T->x = x;      T->x = x;
901      tri = (int*)T->i;      tri = (int*)T->i;
# Line 774  Line 905 
905          trj[ii] = j[ii] - ((!mj && index1) ? 1 : 0);          trj[ii] = j[ii] - ((!mj && index1) ? 1 : 0);
906      }      }
907                                  /* create the cholmod_sparse structure */                                  /* create the cholmod_sparse structure */
908      A = cholmod_l_triplet_to_sparse(T, nnz, &c);      A = cholmod_triplet_to_sparse(T, nnz, &c);
909      cholmod_l_free_triplet(&T, &c);      cholmod_free_triplet(&T, &c);
910                                  /* copy the information to the SEXP */                                  /* copy the information to the SEXP */
911      ans = PROTECT(NEW_OBJECT(MAKE_CLASS(cls)));      ans = PROTECT(NEW_OBJECT(MAKE_CLASS(cls)));
912  /* FIXME: This has been copied from chm_sparse_to_SEXP in chm_common.c */  /* FIXME: This has been copied from chm_sparse_to_SEXP in chm_common.c */
913                                  /* allocate and copy common slots */                                  /* allocate and copy common slots */
914      nnz = cholmod_l_nnz(A, &c);      nnz = cholmod_nnz(A, &c);
915      dims = INTEGER(ALLOC_SLOT(ans, Matrix_DimSym, INTSXP, 2));      dims = INTEGER(ALLOC_SLOT(ans, Matrix_DimSym, INTSXP, 2));
916      dims[0] = A->nrow; dims[1] = A->ncol;      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);      Memcpy(INTEGER(ALLOC_SLOT(ans, Matrix_pSym, INTSXP, A->ncol + 1)), (int*)A->p, A->ncol + 1);
# Line 792  Line 923 
923      case 'l':      case 'l':
924          error(_("code not yet written for cls = \"lgCMatrix\""));          error(_("code not yet written for cls = \"lgCMatrix\""));
925      }      }
926      cholmod_l_free_sparse(&A, &c);  /* FIXME: dimnames are *NOT* put there yet (if non-NULL) */
927        cholmod_free_sparse(&A, &c);
928      UNPROTECT(1);      UNPROTECT(1);
929      return ans;      return ans;
930  }  }

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