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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 2834, Mon Sep 3 10:30:03 2012 UTC
# Line 1  Line 1 
1                          /* Sparse matrices in compressed column-oriented form */                          /* Sparse matrices in compressed column-oriented form */
2    
3  #include "Csparse.h"  #include "Csparse.h"
4  #include "Tsparse.h"  #include "Tsparse.h"
5  #include "chm_common.h"  #include "chm_common.h"
# Line 32  Line 33 
33      return TRUE;      return TRUE;
34  }  }
35    
36  SEXP Csparse_validate(SEXP x)  SEXP Csparse_validate(SEXP x) {
37        return Csparse_validate_(x, FALSE);
38    }
39    
40    SEXP Csparse_validate2(SEXP x, SEXP maybe_modify) {
41        return Csparse_validate_(x, asLogical(maybe_modify));
42    }
43    
44    SEXP Csparse_validate_(SEXP x, Rboolean maybe_modify)
45  {  {
46      /* NB: we do *NOT* check a potential 'x' slot here, at all */      /* NB: we do *NOT* check a potential 'x' slot here, at all */
47      SEXP pslot = GET_SLOT(x, Matrix_pSym),      SEXP pslot = GET_SLOT(x, Matrix_pSym),
# Line 69  Line 78 
78              }              }
79      }      }
80      if (!sorted) {      if (!sorted) {
81            if(maybe_modify) {
82          CHM_SP chx = (CHM_SP) alloca(sizeof(cholmod_sparse));          CHM_SP chx = (CHM_SP) alloca(sizeof(cholmod_sparse));
83          R_CheckStack();          R_CheckStack();
84          as_cholmod_sparse(chx, x, FALSE, TRUE); /* includes cholmod_sort() ! */              as_cholmod_sparse(chx, x, FALSE, TRUE);/*-> cholmod_l_sort() ! */
85          /* as chx = AS_CHM_SP__(x)  but  ^^^^  sorting x in_place (no copying)*/              /* as chx = AS_CHM_SP__(x)  but  ^^^^ sorting x in_place !!! */
86    
87          /* Now re-check that row indices are *strictly* increasing          /* Now re-check that row indices are *strictly* increasing
88           * (and not just increasing) within each column : */           * (and not just increasing) within each column : */
89          for (j = 0; j < ncol; j++) {          for (j = 0; j < ncol; j++) {
90              for (k = xp[j] + 1; k < xp[j + 1]; k++)              for (k = xp[j] + 1; k < xp[j + 1]; k++)
91                  if (xi[k] == xi[k - 1])                  if (xi[k] == xi[k - 1])
92                      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)"));
93                }
94            } else { /* no modifying sorting : */
95                return mkString(_("row indices are not sorted within columns"));
96          }          }
   
97      } else if(!strictly) {  /* sorted, but not strictly */      } else if(!strictly) {  /* sorted, but not strictly */
98          return mkString(_("slot i is not *strictly* increasing inside a column"));          return mkString(_("slot i is not *strictly* increasing inside a column"));
99      }      }
# Line 150  Line 162 
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);
# Line 163  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 = alloca(strlen(cl_x) + 1); /* not much memory required */
193        strcpy(ncl, cl_x);
194        double *dx_x; int *ix_x;
195        ncl[0] = (r_kind == x_double ? 'd' :
196                  (r_kind == x_logical ? 'l' :
197                   /* else (for now):  r_kind == x_integer : */ 'i'));
198        PROTECT(ans = NEW_OBJECT(MAKE_CLASS(ncl)));
199        // create a correct 'x' slot:
200        switch(r_kind) {
201            int i;
202        case x_double: // 'd'
203            dx_x = REAL(ALLOC_SLOT(ans, Matrix_xSym, REALSXP, nnz));
204            for (i=0; i < nnz; i++) dx_x[i] = 1.;
205            break;
206        case x_logical: // 'l'
207            ix_x = LOGICAL(ALLOC_SLOT(ans, Matrix_xSym, LGLSXP, nnz));
208            for (i=0; i < nnz; i++) ix_x[i] = TRUE;
209            break;
210        case x_integer: // 'i'
211            ix_x = INTEGER(ALLOC_SLOT(ans, Matrix_xSym, INTSXP, nnz));
212            for (i=0; i < nnz; i++) ix_x[i] = 1;
213            break;
214    
215        default:
216            error(_("nz2Csparse(): invalid/non-implemented r_kind = %d"),
217                  r_kind);
218        }
219    
220        // now copy all other slots :
221        slot_dup(ans, x, Matrix_iSym);
222        slot_dup(ans, x, Matrix_pSym);
223        slot_dup(ans, x, Matrix_DimSym);
224        slot_dup(ans, x, Matrix_DimNamesSym);
225        if(ncl[1] != 'g') { // symmetric or triangular ...
226            slot_dup_if_has(ans, x, Matrix_uploSym);
227            slot_dup_if_has(ans, x, Matrix_diagSym);
228        }
229        UNPROTECT(1);
230        return ans;
231    }
232    
233  SEXP Csparse_to_matrix(SEXP x)  SEXP Csparse_to_matrix(SEXP x)
234  {  {
235      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 200  Line 267 
267    
268  SEXP Csparse_general_to_symmetric(SEXP x, SEXP uplo)  SEXP Csparse_general_to_symmetric(SEXP x, SEXP uplo)
269  {  {
270        int *adims = INTEGER(GET_SLOT(x, Matrix_DimSym)), n = adims[0];
271        if(n != adims[1]) {
272            error(_("Csparse_general_to_symmetric(): matrix is not square!"));
273            return R_NilValue; /* -Wall */
274        }
275      CHM_SP chx = AS_CHM_SP__(x), chgx;      CHM_SP chx = AS_CHM_SP__(x), chgx;
276      int uploT = (*CHAR(STRING_ELT(uplo,0)) == 'U') ? 1 : -1;      int uploT = (*CHAR(STRING_ELT(uplo,0)) == 'U') ? 1 : -1;
277      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
278      R_CheckStack();      R_CheckStack();
   
279      chgx = cholmod_copy(chx, /* stype: */ uploT, chx->xtype, &c);      chgx = cholmod_copy(chx, /* stype: */ uploT, chx->xtype, &c);
280      /* xtype: pattern, "real", complex or .. */      /* xtype: pattern, "real", complex or .. */
281      return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",      return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",
# Line 237  Line 308 
308          cha = AS_CHM_SP(a),          cha = AS_CHM_SP(a),
309          chb = AS_CHM_SP(b),          chb = AS_CHM_SP(b),
310          chc = cholmod_ssmult(cha, chb, /*out_stype:*/ 0,          chc = cholmod_ssmult(cha, chb, /*out_stype:*/ 0,
311                               cha->xtype, /*out sorted:*/ 1, &c);                                 /* values:= is_numeric (T/F) */ cha->xtype > 0,
312                                   /*out sorted:*/ 1, &c);
313      const char *cl_a = class_P(a), *cl_b = class_P(b);      const char *cl_a = class_P(a), *cl_b = class_P(b);
314      char diag[] = {'\0', '\0'};      char diag[] = {'\0', '\0'};
315      int uploT = 0;      int uploT = 0;
316      SEXP dn = allocVector(VECSXP, 2);      SEXP dn = PROTECT(allocVector(VECSXP, 2));
317      R_CheckStack();      R_CheckStack();
318    
319    #ifdef DEBUG_Matrix_verbose
320        Rprintf("DBG Csparse_C*_prod(%s, %s)\n", cl_a, cl_b);
321    #endif
322    
323      /* Preserve triangularity and even unit-triangularity if appropriate.      /* Preserve triangularity and even unit-triangularity if appropriate.
324       * Note that in that case, the multiplication itself should happen       * Note that in that case, the multiplication itself should happen
325       * faster.  But there's no support for that in CHOLMOD */       * faster.  But there's no support for that in CHOLMOD */
# Line 265  Line 341 
341                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));
342      SET_VECTOR_ELT(dn, 1,      SET_VECTOR_ELT(dn, 1,
343                     duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), 1)));                     duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), 1)));
344        UNPROTECT(1);
345      return chm_sparse_to_SEXP(chc, 1, uploT, /*Rkind*/0, diag, dn);      return chm_sparse_to_SEXP(chc, 1, uploT, /*Rkind*/0, diag, dn);
346  }  }
347    
# Line 278  Line 355 
355      const char *cl_a = class_P(a), *cl_b = class_P(b);      const char *cl_a = class_P(a), *cl_b = class_P(b);
356      char diag[] = {'\0', '\0'};      char diag[] = {'\0', '\0'};
357      int uploT = 0;      int uploT = 0;
358      SEXP dn = allocVector(VECSXP, 2);      SEXP dn = PROTECT(allocVector(VECSXP, 2));
359      R_CheckStack();      R_CheckStack();
360    
361      chTr = cholmod_transpose((tr) ? chb : cha, chb->xtype, &c);      chTr = cholmod_transpose((tr) ? chb : cha, chb->xtype, &c);
# Line 297  Line 374 
374              }              }
375              else diag[0]= 'N';              else diag[0]= 'N';
376          }          }
   
377      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
378                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), (tr) ? 0 : 1)));                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), (tr) ? 0 : 1)));
379      SET_VECTOR_ELT(dn, 1,      SET_VECTOR_ELT(dn, 1,
380                     duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), (tr) ? 0 : 1)));                     duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), (tr) ? 0 : 1)));
381        UNPROTECT(1);
382      return chm_sparse_to_SEXP(chc, 1, uploT, /*Rkind*/0, diag, dn);      return chm_sparse_to_SEXP(chc, 1, uploT, /*Rkind*/0, diag, dn);
383  }  }
384    
# Line 314  Line 391 
391                                          chb->xtype, &c);                                          chb->xtype, &c);
392      SEXP dn = PROTECT(allocVector(VECSXP, 2));      SEXP dn = PROTECT(allocVector(VECSXP, 2));
393      double one[] = {1,0}, zero[] = {0,0};      double one[] = {1,0}, zero[] = {0,0};
394        int nprot = 2;
395      R_CheckStack();      R_CheckStack();
396        /* Tim Davis, please FIXME:  currently (2010-11) *fails* when  a  is a pattern matrix:*/
397        if(cha->xtype == CHOLMOD_PATTERN) {
398            /* warning(_("Csparse_dense_prod(): cholmod_sdmult() not yet implemented for pattern./ ngCMatrix" */
399            /*        " --> slightly inefficient coercion")); */
400    
401            // This *fails* to produce a CHOLMOD_REAL ..
402            // CHM_SP chd = cholmod_l_copy(cha, cha->stype, CHOLMOD_REAL, &c);
403            // --> use our Matrix-classes
404            SEXP da = PROTECT(nz2Csparse(a, x_double)); nprot++;
405            cha = AS_CHM_SP(da);
406        }
407      cholmod_sdmult(cha, 0, one, zero, chb, chc, &c);      cholmod_sdmult(cha, 0, one, zero, chb, chc, &c);
408      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
409                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));
410      SET_VECTOR_ELT(dn, 1,      SET_VECTOR_ELT(dn, 1,
411                     duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));                     duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));
412      UNPROTECT(2);      UNPROTECT(nprot);
413      return chm_dense_to_SEXP(chc, 1, 0, dn);      return chm_dense_to_SEXP(chc, 1, 0, dn);
414  }  }
415    
# Line 332  Line 420 
420      CHM_DN chb = AS_CHM_DN(b_M);      CHM_DN chb = AS_CHM_DN(b_M);
421      CHM_DN chc = cholmod_allocate_dense(cha->ncol, chb->ncol, cha->ncol,      CHM_DN chc = cholmod_allocate_dense(cha->ncol, chb->ncol, cha->ncol,
422                                          chb->xtype, &c);                                          chb->xtype, &c);
423      SEXP dn = PROTECT(allocVector(VECSXP, 2));      SEXP dn = PROTECT(allocVector(VECSXP, 2)); int nprot = 2;
424      double one[] = {1,0}, zero[] = {0,0};      double one[] = {1,0}, zero[] = {0,0};
425      R_CheckStack();      R_CheckStack();
426        // -- see Csparse_dense_prod() above :
427        if(cha->xtype == CHOLMOD_PATTERN) {
428            SEXP da = PROTECT(nz2Csparse(a, x_double)); nprot++;
429            cha = AS_CHM_SP(da);
430        }
431      cholmod_sdmult(cha, 1, one, zero, chb, chc, &c);      cholmod_sdmult(cha, 1, one, zero, chb, chc, &c);
432      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
433                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 1)));                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 1)));
434      SET_VECTOR_ELT(dn, 1,      SET_VECTOR_ELT(dn, 1,
435                     duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));                     duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));
436      UNPROTECT(2);      UNPROTECT(nprot);
437      return chm_dense_to_SEXP(chc, 1, 0, dn);      return chm_dense_to_SEXP(chc, 1, 0, dn);
438  }  }
439    
# Line 351  Line 443 
443  {  {
444      int trip = asLogical(triplet),      int trip = asLogical(triplet),
445          tr   = asLogical(trans); /* gets reversed because _aat is tcrossprod */          tr   = asLogical(trans); /* gets reversed because _aat is tcrossprod */
446    #ifdef AS_CHM_DIAGU2N_FIXED_FINALLY
447      CHM_TR cht = trip ? AS_CHM_TR(x) : (CHM_TR) NULL;      CHM_TR cht = trip ? AS_CHM_TR(x) : (CHM_TR) NULL;
448    #else /* workaround needed:*/
449        SEXP xx = PROTECT(Tsparse_diagU2N(x));
450        CHM_TR cht = trip ? AS_CHM_TR__(xx) : (CHM_TR) NULL;
451    #endif
452      CHM_SP chcp, chxt,      CHM_SP chcp, chxt,
453          chx = (trip ?          chx = (trip ?
454                 cholmod_triplet_to_sparse(cht, cht->nnz, &c) :                 cholmod_triplet_to_sparse(cht, cht->nnz, &c) :
# Line 373  Line 470 
470                     duplicate(VECTOR_ELT(GET_SLOT(x, Matrix_DimNamesSym),                     duplicate(VECTOR_ELT(GET_SLOT(x, Matrix_DimNamesSym),
471                                          (tr) ? 0 : 1)));                                          (tr) ? 0 : 1)));
472      SET_VECTOR_ELT(dn, 1, duplicate(VECTOR_ELT(dn, 0)));      SET_VECTOR_ELT(dn, 1, duplicate(VECTOR_ELT(dn, 0)));
473    #ifdef AS_CHM_DIAGU2N_FIXED_FINALLY
474      UNPROTECT(1);      UNPROTECT(1);
475    #else
476        UNPROTECT(2);
477    #endif
478      return chm_sparse_to_SEXP(chcp, 1, 0, 0, "", dn);      return chm_sparse_to_SEXP(chcp, 1, 0, 0, "", dn);
479  }  }
480    
481    /* Csparse_drop(x, tol):  drop entries with absolute value < tol, i.e,
482    *  at least all "explicit" zeros */
483  SEXP Csparse_drop(SEXP x, SEXP tol)  SEXP Csparse_drop(SEXP x, SEXP tol)
484  {  {
485      const char *cl = class_P(x);      const char *cl = class_P(x);
# Line 399  Line 502 
502  SEXP Csparse_horzcat(SEXP x, SEXP y)  SEXP Csparse_horzcat(SEXP x, SEXP y)
503  {  {
504      CHM_SP chx = AS_CHM_SP__(x), chy = AS_CHM_SP__(y);      CHM_SP chx = AS_CHM_SP__(x), chy = AS_CHM_SP__(y);
505      int Rkind = 0; /* only for "d" - FIXME */      int Rk_x = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0,
506            Rk_y = (chy->xtype != CHOLMOD_PATTERN) ? Real_kind(y) : 0,
507            Rkind = /* logical if both x and y are */ (Rk_x == 1 && Rk_y == 1) ? 1 : 0;
508      R_CheckStack();      R_CheckStack();
509    
510      /* FIXME: currently drops dimnames */      /* TODO: currently drops dimnames - and we fix at R level */
511      return chm_sparse_to_SEXP(cholmod_horzcat(chx, chy, 1, &c),      return chm_sparse_to_SEXP(cholmod_horzcat(chx, chy, 1, &c),
512                                1, 0, Rkind, "", R_NilValue);                                1, 0, Rkind, "", R_NilValue);
513  }  }
# Line 410  Line 515 
515  SEXP Csparse_vertcat(SEXP x, SEXP y)  SEXP Csparse_vertcat(SEXP x, SEXP y)
516  {  {
517      CHM_SP chx = AS_CHM_SP__(x), chy = AS_CHM_SP__(y);      CHM_SP chx = AS_CHM_SP__(x), chy = AS_CHM_SP__(y);
518      int Rkind = 0; /* only for "d" - FIXME */      int Rk_x = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0,
519            Rk_y = (chy->xtype != CHOLMOD_PATTERN) ? Real_kind(y) : 0,
520            Rkind = /* logical if both x and y are */ (Rk_x == 1 && Rk_y == 1) ? 1 : 0;
521      R_CheckStack();      R_CheckStack();
522    
523      /* FIXME: currently drops dimnames */      /* TODO: currently drops dimnames - and we fix at R level */
524      return chm_sparse_to_SEXP(cholmod_vertcat(chx, chy, 1, &c),      return chm_sparse_to_SEXP(cholmod_vertcat(chx, chy, 1, &c),
525                                1, 0, Rkind, "", R_NilValue);                                1, 0, Rkind, "", R_NilValue);
526  }  }
# Line 464  Line 571 
571      }      }
572      else { /* triangular with diag='N'): now drop the diagonal */      else { /* triangular with diag='N'): now drop the diagonal */
573          /* duplicate, since chx will be modified: */          /* duplicate, since chx will be modified: */
574          CHM_SP chx = AS_CHM_SP__(duplicate(x));          SEXP xx = PROTECT(duplicate(x));
575            CHM_SP chx = AS_CHM_SP__(xx);
576          int uploT = (*uplo_P(x) == 'U') ? 1 : -1,          int uploT = (*uplo_P(x) == 'U') ? 1 : -1,
577              Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;              Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
578          R_CheckStack();          R_CheckStack();
579    
580          chm_diagN2U(chx, uploT, /* do_realloc */ FALSE);          chm_diagN2U(chx, uploT, /* do_realloc */ FALSE);
581    
582          return chm_sparse_to_SEXP(chx, /*dofree*/ 0/* or 1 ?? */,          SEXP ans = chm_sparse_to_SEXP(chx, /*dofree*/ 0/* or 1 ?? */,
583                                    uploT, Rkind, "U",                                    uploT, Rkind, "U",
584                                    GET_SLOT(x, Matrix_DimNamesSym));                                    GET_SLOT(x, Matrix_DimNamesSym));
585            UNPROTECT(1);// only now !
586            return ans;
587      }      }
588  }  }
589    
590    /**
591     * "Indexing" aka subsetting : Compute  x[i,j], also for vectors i and j
592     * Working via CHOLMOD_submatrix, see ./CHOLMOD/MatrixOps/cholmod_submatrix.c
593     * @param x CsparseMatrix
594     * @param i row     indices (0-origin), or NULL (R's)
595     * @param j columns indices (0-origin), or NULL
596     *
597     * @return x[i,j]  still CsparseMatrix --- currently, this loses dimnames
598     */
599  SEXP Csparse_submatrix(SEXP x, SEXP i, SEXP j)  SEXP Csparse_submatrix(SEXP x, SEXP i, SEXP j)
600  {  {
601      CHM_SP chx = AS_CHM_SP__(x);      CHM_SP chx = AS_CHM_SP(x); /* << does diagU2N() when needed */
602      int rsize = (isNull(i)) ? -1 : LENGTH(i),      int rsize = (isNull(i)) ? -1 : LENGTH(i),
603          csize = (isNull(j)) ? -1 : LENGTH(j);          csize = (isNull(j)) ? -1 : LENGTH(j);
604      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
# Line 490  Line 609 
609      if (csize >= 0 && !isInteger(j))      if (csize >= 0 && !isInteger(j))
610          error(_("Index j must be NULL or integer"));          error(_("Index j must be NULL or integer"));
611    
612      return chm_sparse_to_SEXP(cholmod_submatrix(chx, INTEGER(i), rsize,      if (!chx->stype) {/* non-symmetric Matrix */
613                                                  INTEGER(j), csize,          return chm_sparse_to_SEXP(cholmod_submatrix(chx,
614                                                        (rsize < 0) ? NULL : INTEGER(i), rsize,
615                                                        (csize < 0) ? NULL : INTEGER(j), csize,
616                                                  TRUE, TRUE, &c),                                                  TRUE, TRUE, &c),
617                                1, 0, Rkind, "",                                1, 0, Rkind, "",
618                                /* FIXME: drops dimnames */ R_NilValue);                                /* FIXME: drops dimnames */ R_NilValue);
619  }  }
620                                    /* for now, cholmod_submatrix() only accepts "generalMatrix" */
621        CHM_SP tmp = cholmod_copy(chx, /* stype: */ 0, chx->xtype, &c);
622        CHM_SP ans = cholmod_submatrix(tmp,
623                                       (rsize < 0) ? NULL : INTEGER(i), rsize,
624                                       (csize < 0) ? NULL : INTEGER(j), csize,
625                                       TRUE, TRUE, &c);
626        cholmod_free_sparse(&tmp, &c);
627        return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "", R_NilValue);
628    }
629    
630    #define _d_Csp_
631    #include "t_Csparse_subassign.c"
632    
633    #define _l_Csp_
634    #include "t_Csparse_subassign.c"
635    
636    #define _i_Csp_
637    #include "t_Csparse_subassign.c"
638    
639    #define _n_Csp_
640    #include "t_Csparse_subassign.c"
641    
642    #define _z_Csp_
643    #include "t_Csparse_subassign.c"
644    
645    
646    
647  SEXP Csparse_MatrixMarket(SEXP x, SEXP fname)  SEXP Csparse_MatrixMarket(SEXP x, SEXP fname)
648  {  {
# Line 579  Line 726 
726      case diag_backpermuted:      case diag_backpermuted:
727          for_DIAG(v[i] = x_x[i_from]);          for_DIAG(v[i] = x_x[i_from]);
728    
729          warning(_("resultKind = 'diagBack' (back-permuted) is experimental"));          warning(_("%s = '%s' (back-permuted) is experimental"),
730                    "resultKind", "diagBack");
731          /* now back_permute : */          /* now back_permute : */
732          for(i = 0; i < n; i++) {          for(i = 0; i < n; i++) {
733              double tmp = v[i]; v[i] = v[perm[i]]; v[perm[i]] = tmp;              double tmp = v[i]; v[i] = v[perm[i]]; v[perm[i]] = tmp;
# Line 588  Line 736 
736          break;          break;
737    
738      default: /* -1 from above */      default: /* -1 from above */
739          error("diag_tC(): invalid 'resultKind'");          error(_("diag_tC(): invalid 'resultKind'"));
740          /* Wall: */ ans = R_NilValue; v = REAL(ans);          /* Wall: */ ans = R_NilValue; v = REAL(ans);
741      }      }
742    
# Line 618  Line 766 
766    
767      return diag_tC_ptr(n, x_p, x_x, perm, resultKind);      return diag_tC_ptr(n, x_p, x_x, perm, resultKind);
768  }  }
769    
770    /**
771     * Create a Csparse matrix object from indices and/or pointers.
772     *
773     * @param cls name of actual class of object to create
774     * @param i optional integer vector of length nnz of row indices
775     * @param j optional integer vector of length nnz of column indices
776     * @param p optional integer vector of length np of row or column pointers
777     * @param np length of integer vector p.  Must be zero if p == (int*)NULL
778     * @param x optional vector of values
779     * @param nnz length of vectors i, j and/or x, whichever is to be used
780     * @param dims optional integer vector of length 2 to be used as
781     *     dimensions.  If dims == (int*)NULL then the maximum row and column
782     *     index are used as the dimensions.
783     * @param dimnames optional list of length 2 to be used as dimnames
784     * @param index1 indicator of 1-based indices
785     *
786     * @return an SEXP of class cls inheriting from CsparseMatrix.
787     */
788    SEXP create_Csparse(char* cls, int* i, int* j, int* p, int np,
789                        void* x, int nnz, int* dims, SEXP dimnames,
790                        int index1)
791    {
792        SEXP ans;
793        int *ij = (int*)NULL, *tri, *trj,
794            mi, mj, mp, nrow = -1, ncol = -1;
795        int xtype = -1;             /* -Wall */
796        CHM_TR T;
797        CHM_SP A;
798    
799        if (np < 0 || nnz < 0)
800            error(_("negative vector lengths not allowed: np = %d, nnz = %d"),
801                  np, nnz);
802        if (1 != ((mi = (i == (int*)NULL)) +
803                  (mj = (j == (int*)NULL)) +
804                  (mp = (p == (int*)NULL))))
805            error(_("exactly 1 of 'i', 'j' or 'p' must be NULL"));
806        if (mp) {
807            if (np) error(_("np = %d, must be zero when p is NULL"), np);
808        } else {
809            if (np) {               /* Expand p to form i or j */
810                if (!(p[0])) error(_("p[0] = %d, should be zero"), p[0]);
811                for (int ii = 0; ii < np; ii++)
812                    if (p[ii] > p[ii + 1])
813                        error(_("p must be non-decreasing"));
814                if (p[np] != nnz)
815                    error("p[np] = %d != nnz = %d", p[np], nnz);
816                ij = Calloc(nnz, int);
817                if (mi) {
818                    i = ij;
819                    nrow = np;
820                } else {
821                    j = ij;
822                    ncol = np;
823                }
824                /* Expand p to 0-based indices */
825                for (int ii = 0; ii < np; ii++)
826                    for (int jj = p[ii]; jj < p[ii + 1]; jj++) ij[jj] = ii;
827            } else {
828                if (nnz)
829                    error(_("Inconsistent dimensions: np = 0 and nnz = %d"),
830                          nnz);
831            }
832        }
833        /* calculate nrow and ncol */
834        if (nrow < 0) {
835            for (int ii = 0; ii < nnz; ii++) {
836                int i1 = i[ii] + (index1 ? 0 : 1); /* 1-based index */
837                if (i1 < 1) error(_("invalid row index at position %d"), ii);
838                if (i1 > nrow) nrow = i1;
839            }
840        }
841        if (ncol < 0) {
842            for (int jj = 0; jj < nnz; jj++) {
843                int j1 = j[jj] + (index1 ? 0 : 1);
844                if (j1 < 1) error(_("invalid column index at position %d"), jj);
845                if (j1 > ncol) ncol = j1;
846            }
847        }
848        if (dims != (int*)NULL) {
849            if (dims[0] > nrow) nrow = dims[0];
850            if (dims[1] > ncol) ncol = dims[1];
851        }
852        /* check the class name */
853        if (strlen(cls) != 8)
854            error(_("strlen of cls argument = %d, should be 8"), strlen(cls));
855        if (!strcmp(cls + 2, "CMatrix"))
856            error(_("cls = \"%s\" does not end in \"CMatrix\""), cls);
857        switch(cls[0]) {
858        case 'd':
859        case 'l':
860            xtype = CHOLMOD_REAL;
861        break;
862        case 'n':
863            xtype = CHOLMOD_PATTERN;
864            break;
865        default:
866            error(_("cls = \"%s\" must begin with 'd', 'l' or 'n'"), cls);
867        }
868        if (cls[1] != 'g')
869            error(_("Only 'g'eneral sparse matrix types allowed"));
870        /* allocate and populate the triplet */
871        T = cholmod_allocate_triplet((size_t)nrow, (size_t)ncol, (size_t)nnz, 0,
872                                     xtype, &c);
873        T->x = x;
874        tri = (int*)T->i;
875        trj = (int*)T->j;
876        for (int ii = 0; ii < nnz; ii++) {
877            tri[ii] = i[ii] - ((!mi && index1) ? 1 : 0);
878            trj[ii] = j[ii] - ((!mj && index1) ? 1 : 0);
879        }
880        /* create the cholmod_sparse structure */
881        A = cholmod_triplet_to_sparse(T, nnz, &c);
882        cholmod_free_triplet(&T, &c);
883        /* copy the information to the SEXP */
884        ans = PROTECT(NEW_OBJECT(MAKE_CLASS(cls)));
885    /* FIXME: This has been copied from chm_sparse_to_SEXP in chm_common.c */
886        /* allocate and copy common slots */
887        nnz = cholmod_nnz(A, &c);
888        dims = INTEGER(ALLOC_SLOT(ans, Matrix_DimSym, INTSXP, 2));
889        dims[0] = A->nrow; dims[1] = A->ncol;
890        Memcpy(INTEGER(ALLOC_SLOT(ans, Matrix_pSym, INTSXP, A->ncol + 1)), (int*)A->p, A->ncol + 1);
891        Memcpy(INTEGER(ALLOC_SLOT(ans, Matrix_iSym, INTSXP, nnz)), (int*)A->i, nnz);
892        switch(cls[1]) {
893        case 'd':
894            Memcpy(REAL(ALLOC_SLOT(ans, Matrix_xSym, REALSXP, nnz)), (double*)A->x, nnz);
895            break;
896        case 'l':
897            error(_("code not yet written for cls = \"lgCMatrix\""));
898        }
899    /* FIXME: dimnames are *NOT* put there yet (if non-NULL) */
900        cholmod_free_sparse(&A, &c);
901        UNPROTECT(1);
902        return ans;
903    }

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