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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 2495, Wed Nov 11 08:45:21 2009 UTC pkg/Matrix/src/Csparse.c revision 2685, Fri Aug 5 19:52:10 2011 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 136  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 154  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 174  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 203  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 216  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 228  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 247  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                                 /* values:= is_numeric (T/F) */ cha->xtype > 0,                                 /* values:= is_numeric (T/F) */ cha->xtype > 0,
307                                 /*out sorted:*/ 1, &c);                                 /*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);
# Line 298  Line 353 
353      SEXP dn = PROTECT(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 327  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 347  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 371  Line 441 
441  #ifdef AS_CHM_DIAGU2N_FIXED_FINALLY  #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:*/  #else /* workaround needed:*/
444      CHM_TR cht = trip ? AS_CHM_TR__(Tsparse_diagU2N(x)) : (CHM_TR) NULL;      SEXP xx = PROTECT(Tsparse_diagU2N(x));
445        CHM_TR cht = trip ? AS_CHM_TR__(xx) : (CHM_TR) NULL;
446  #endif  #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 420  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 443  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 461  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 498  Line 579 
579      }      }
580  }  }
581    
582    /**
583     * "Indexing" aka subsetting : Compute  x[i,j], also for vectors i and j
584     * Working via CHOLMOD_submatrix, see ./CHOLMOD/MatrixOps/cholmod_submatrix.c
585     * @param x CsparseMatrix
586     * @param i row     indices (0-origin), or NULL (R's)
587     * @param j columns indices (0-origin), or NULL
588     *
589     * @return x[i,j]  still CsparseMatrix --- currently, this loses dimnames
590     */
591  SEXP Csparse_submatrix(SEXP x, SEXP i, SEXP j)  SEXP Csparse_submatrix(SEXP x, SEXP i, SEXP j)
592  {  {
593      CHM_SP chx = AS_CHM_SP__(x);      CHM_SP chx = AS_CHM_SP(x); /* << does diagU2N() when needed */
594      int rsize = (isNull(i)) ? -1 : LENGTH(i),      int rsize = (isNull(i)) ? -1 : LENGTH(i),
595          csize = (isNull(j)) ? -1 : LENGTH(j);          csize = (isNull(j)) ? -1 : LENGTH(j);
596      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
# Line 511  Line 601 
601      if (csize >= 0 && !isInteger(j))      if (csize >= 0 && !isInteger(j))
602          error(_("Index j must be NULL or integer"));          error(_("Index j must be NULL or integer"));
603    
604      return chm_sparse_to_SEXP(cholmod_l_submatrix(chx, INTEGER(i), rsize,      if (chx->stype) /* symmetricMatrix */
605                                                  INTEGER(j), csize,          /* for now, cholmod_submatrix() only accepts "generalMatrix" */
606            chx = cholmod_copy(chx, /* stype: */ 0, chx->xtype, &c);
607    
608        return chm_sparse_to_SEXP(cholmod_submatrix(chx,
609                                    (rsize < 0) ? NULL : INTEGER(i), rsize,
610                                    (csize < 0) ? NULL : INTEGER(j), csize,
611                                                  TRUE, TRUE, &c),                                                  TRUE, TRUE, &c),
612                                1, 0, Rkind, "",                                1, 0, Rkind, "",
613                                /* FIXME: drops dimnames */ R_NilValue);                                /* FIXME: drops dimnames */ R_NilValue);
614  }  }
615    
616    #define _d_Csp_
617    #include "t_Csparse_subassign.c"
618    
619    #define _l_Csp_
620    #include "t_Csparse_subassign.c"
621    
622    #define _i_Csp_
623    #include "t_Csparse_subassign.c"
624    
625    #define _n_Csp_
626    #include "t_Csparse_subassign.c"
627    
628    #define _z_Csp_
629    #include "t_Csparse_subassign.c"
630    
631    
632    
633  SEXP Csparse_MatrixMarket(SEXP x, SEXP fname)  SEXP Csparse_MatrixMarket(SEXP x, SEXP fname)
634  {  {
635      FILE *f = fopen(CHAR(asChar(fname)), "w");      FILE *f = fopen(CHAR(asChar(fname)), "w");
# Line 525  Line 637 
637      if (!f)      if (!f)
638          error(_("failure to open file \"%s\" for writing"),          error(_("failure to open file \"%s\" for writing"),
639                CHAR(asChar(fname)));                CHAR(asChar(fname)));
640      if (!cholmod_l_write_sparse(f, AS_CHM_SP(x),      if (!cholmod_write_sparse(f, AS_CHM_SP(x),
641                                (CHM_SP)NULL, (char*) NULL, &c))                                (CHM_SP)NULL, (char*) NULL, &c))
642          error(_("cholmod_l_write_sparse returned error code"));          error(_("cholmod_write_sparse returned error code"));
643      fclose(f);      fclose(f);
644      return R_NilValue;      return R_NilValue;
645  }  }
# Line 741  Line 853 
853      if (cls[1] != 'g')      if (cls[1] != 'g')
854          error(_("Only 'g'eneral sparse matrix types allowed"));          error(_("Only 'g'eneral sparse matrix types allowed"));
855                                  /* allocate and populate the triplet */                                  /* allocate and populate the triplet */
856      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,
857                                      xtype, &c);                                      xtype, &c);
858      T->x = x;      T->x = x;
859      tri = (int*)T->i;      tri = (int*)T->i;
# Line 751  Line 863 
863          trj[ii] = j[ii] - ((!mj && index1) ? 1 : 0);          trj[ii] = j[ii] - ((!mj && index1) ? 1 : 0);
864      }      }
865                                  /* create the cholmod_sparse structure */                                  /* create the cholmod_sparse structure */
866      A = cholmod_l_triplet_to_sparse(T, nnz, &c);      A = cholmod_triplet_to_sparse(T, nnz, &c);
867      cholmod_l_free_triplet(&T, &c);      cholmod_free_triplet(&T, &c);
868                                  /* copy the information to the SEXP */                                  /* copy the information to the SEXP */
869      ans = PROTECT(NEW_OBJECT(MAKE_CLASS(cls)));      ans = PROTECT(NEW_OBJECT(MAKE_CLASS(cls)));
870  /* 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 */
871                                  /* allocate and copy common slots */                                  /* allocate and copy common slots */
872      nnz = cholmod_l_nnz(A, &c);      nnz = cholmod_nnz(A, &c);
873      dims = INTEGER(ALLOC_SLOT(ans, Matrix_DimSym, INTSXP, 2));      dims = INTEGER(ALLOC_SLOT(ans, Matrix_DimSym, INTSXP, 2));
874      dims[0] = A->nrow; dims[1] = A->ncol;      dims[0] = A->nrow; dims[1] = A->ncol;
875      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 769  Line 881 
881      case 'l':      case 'l':
882          error(_("code not yet written for cls = \"lgCMatrix\""));          error(_("code not yet written for cls = \"lgCMatrix\""));
883      }      }
884      cholmod_l_free_sparse(&A, &c);  /* FIXME: dimnames are *NOT* put there yet (if non-NULL) */
885        cholmod_free_sparse(&A, &c);
886      UNPROTECT(1);      UNPROTECT(1);
887      return ans;      return ans;
888  }  }

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