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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 2901, Tue Sep 10 10:45:25 2013 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);
     /* NB: we do *NOT* check a potential 'x' slot here, at all */  
     SEXP pslot = GET_SLOT(x, Matrix_pSym),  
         islot = GET_SLOT(x, Matrix_iSym);  
     Rboolean sorted, strictly;  
     int j, k,  
         *dims = INTEGER(GET_SLOT(x, Matrix_DimSym)),  
         nrow = dims[0],  
         ncol = dims[1],  
         *xp = INTEGER(pslot),  
         *xi = INTEGER(islot);  
   
     if (length(pslot) != dims[1] + 1)  
         return mkString(_("slot p must have length = ncol(.) + 1"));  
     if (xp[0] != 0)  
         return mkString(_("first element of slot p must be zero"));  
     if (length(islot) < xp[ncol]) /* allow larger slots from over-allocation!*/  
         return  
             mkString(_("last element of slot p must match length of slots i and x"));  
     for (j = 0; j < xp[ncol]; j++) {  
         if (xi[j] < 0 || xi[j] >= nrow)  
             return mkString(_("all row indices must be between 0 and nrow-1"));  
38      }      }
     sorted = TRUE; strictly = TRUE;  
     for (j = 0; j < ncol; j++) {  
         if (xp[j] > xp[j + 1])  
             return mkString(_("slot p must be non-decreasing"));  
         if(sorted) /* only act if >= 2 entries in column j : */  
             for (k = xp[j] + 1; k < xp[j + 1]; k++) {  
                 if (xi[k] < xi[k - 1])  
                     sorted = FALSE;  
                 else if (xi[k] == xi[k - 1])  
                     strictly = FALSE;  
             }  
     }  
     if (!sorted) {  
         CHM_SP chx = (CHM_SP) alloca(sizeof(cholmod_sparse));  
         R_CheckStack();  
         as_cholmod_sparse(chx, x, FALSE, TRUE); /* includes cholmod_sort() ! */  
         /* as chx = AS_CHM_SP__(x)  but  ^^^^  sorting x in_place (no copying)*/  
39    
         /* Now re-check that row indices are *strictly* increasing  
          * (and not just increasing) within each column : */  
         for (j = 0; j < ncol; j++) {  
             for (k = xp[j] + 1; k < xp[j + 1]; k++)  
                 if (xi[k] == xi[k - 1])  
                     return mkString(_("slot i is not *strictly* increasing inside a column (even after cholmod_sort)"));  
         }  
40    
41      } else if(!strictly) {  /* sorted, but not strictly */  #define _t_Csparse_validate
42          return mkString(_("slot i is not *strictly* increasing inside a column"));  #include "t_Csparse_validate.c"
43    
44    #define _t_Csparse_sort
45    #include "t_Csparse_validate.c"
46    
47    // R: .validateCsparse(x, sort.if.needed = FALSE) :
48    SEXP Csparse_validate2(SEXP x, SEXP maybe_modify) {
49        return Csparse_validate_(x, asLogical(maybe_modify));
50      }      }
51      return ScalarLogical(1);  
52    // R: Matrix:::.sortCsparse(x) :
53    SEXP Csparse_sort (SEXP x) {
54       int ok = Csparse_sort_2(x, TRUE); // modifying x directly
55       if(!ok) warning(_("Csparse_sort(x): x is not a valid (apart from sorting) CsparseMatrix"));
56       return x;
57  }  }
58    
59  SEXP Rsparse_validate(SEXP x)  SEXP Rsparse_validate(SEXP x)
# Line 150  Line 118 
118      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));
119  }  }
120    
121    // FIXME: do not go via CHM (should not be too hard, to just *drop* the x-slot, right?
122  SEXP Csparse_to_nz_pattern(SEXP x, SEXP tri)  SEXP Csparse_to_nz_pattern(SEXP x, SEXP tri)
123  {  {
124      CHM_SP chxs = AS_CHM_SP__(x);      CHM_SP chxs = AS_CHM_SP__(x);
# Line 163  Line 132 
132                                GET_SLOT(x, Matrix_DimNamesSym));                                GET_SLOT(x, Matrix_DimNamesSym));
133  }  }
134    
135    // n.CMatrix --> [dli].CMatrix  (not going through CHM!)
136    SEXP nz_pattern_to_Csparse(SEXP x, SEXP res_kind)
137    {
138        return nz2Csparse(x, asInteger(res_kind));
139    }
140    // n.CMatrix --> [dli].CMatrix  (not going through CHM!)
141    SEXP nz2Csparse(SEXP x, enum x_slot_kind r_kind)
142    {
143        const char *cl_x = class_P(x);
144        if(cl_x[0] != 'n') error(_("not a 'n.CMatrix'"));
145        if(cl_x[2] != 'C') error(_("not a CsparseMatrix"));
146        int nnz = LENGTH(GET_SLOT(x, Matrix_iSym));
147        SEXP ans;
148        char *ncl = alloca(strlen(cl_x) + 1); /* not much memory required */
149        strcpy(ncl, cl_x);
150        double *dx_x; int *ix_x;
151        ncl[0] = (r_kind == x_double ? 'd' :
152                  (r_kind == x_logical ? 'l' :
153                   /* else (for now):  r_kind == x_integer : */ 'i'));
154        PROTECT(ans = NEW_OBJECT(MAKE_CLASS(ncl)));
155        // create a correct 'x' slot:
156        switch(r_kind) {
157            int i;
158        case x_double: // 'd'
159            dx_x = REAL(ALLOC_SLOT(ans, Matrix_xSym, REALSXP, nnz));
160            for (i=0; i < nnz; i++) dx_x[i] = 1.;
161            break;
162        case x_logical: // 'l'
163            ix_x = LOGICAL(ALLOC_SLOT(ans, Matrix_xSym, LGLSXP, nnz));
164            for (i=0; i < nnz; i++) ix_x[i] = TRUE;
165            break;
166        case x_integer: // 'i'
167            ix_x = INTEGER(ALLOC_SLOT(ans, Matrix_xSym, INTSXP, nnz));
168            for (i=0; i < nnz; i++) ix_x[i] = 1;
169            break;
170    
171        default:
172            error(_("nz2Csparse(): invalid/non-implemented r_kind = %d"),
173                  r_kind);
174        }
175    
176        // now copy all other slots :
177        slot_dup(ans, x, Matrix_iSym);
178        slot_dup(ans, x, Matrix_pSym);
179        slot_dup(ans, x, Matrix_DimSym);
180        slot_dup(ans, x, Matrix_DimNamesSym);
181        if(ncl[1] != 'g') { // symmetric or triangular ...
182            slot_dup_if_has(ans, x, Matrix_uploSym);
183            slot_dup_if_has(ans, x, Matrix_diagSym);
184        }
185        UNPROTECT(1);
186        return ans;
187    }
188    
189  SEXP Csparse_to_matrix(SEXP x)  SEXP Csparse_to_matrix(SEXP x)
190  {  {
191      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),
192                                 1 /*do_free*/, GET_SLOT(x, Matrix_DimNamesSym));                                 1 /*do_free*/, GET_SLOT(x, Matrix_DimNamesSym));
193  }  }
194    SEXP Csparse_to_vector(SEXP x)
195    {
196        return chm_dense_to_vector(cholmod_sparse_to_dense(AS_CHM_SP__(x), &c), 1);
197    }
198    
199  SEXP Csparse_to_Tsparse(SEXP x, SEXP tri)  SEXP Csparse_to_Tsparse(SEXP x, SEXP tri)
200  {  {
# Line 200  Line 227 
227    
228  SEXP Csparse_general_to_symmetric(SEXP x, SEXP uplo)  SEXP Csparse_general_to_symmetric(SEXP x, SEXP uplo)
229  {  {
230        int *adims = INTEGER(GET_SLOT(x, Matrix_DimSym)), n = adims[0];
231        if(n != adims[1]) {
232            error(_("Csparse_general_to_symmetric(): matrix is not square!"));
233            return R_NilValue; /* -Wall */
234        }
235      CHM_SP chx = AS_CHM_SP__(x), chgx;      CHM_SP chx = AS_CHM_SP__(x), chgx;
236      int uploT = (*CHAR(STRING_ELT(uplo,0)) == 'U') ? 1 : -1;      int uploT = (*CHAR(STRING_ELT(uplo,0)) == 'U') ? 1 : -1;
237      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
238      R_CheckStack();      R_CheckStack();
   
239      chgx = cholmod_copy(chx, /* stype: */ uploT, chx->xtype, &c);      chgx = cholmod_copy(chx, /* stype: */ uploT, chx->xtype, &c);
240      /* xtype: pattern, "real", complex or .. */      /* xtype: pattern, "real", complex or .. */
241      return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",      return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",
# Line 237  Line 268 
268          cha = AS_CHM_SP(a),          cha = AS_CHM_SP(a),
269          chb = AS_CHM_SP(b),          chb = AS_CHM_SP(b),
270          chc = cholmod_ssmult(cha, chb, /*out_stype:*/ 0,          chc = cholmod_ssmult(cha, chb, /*out_stype:*/ 0,
271                               cha->xtype, /*out sorted:*/ 1, &c);                                 /* values:= is_numeric (T/F) */ cha->xtype > 0,
272                                   /*out sorted:*/ 1, &c);
273      const char *cl_a = class_P(a), *cl_b = class_P(b);      const char *cl_a = class_P(a), *cl_b = class_P(b);
274      char diag[] = {'\0', '\0'};      char diag[] = {'\0', '\0'};
275      int uploT = 0;      int uploT = 0;
276      SEXP dn = allocVector(VECSXP, 2);      SEXP dn = PROTECT(allocVector(VECSXP, 2));
277      R_CheckStack();      R_CheckStack();
278    
279    #ifdef DEBUG_Matrix_verbose
280        Rprintf("DBG Csparse_C*_prod(%s, %s)\n", cl_a, cl_b);
281    #endif
282    
283      /* Preserve triangularity and even unit-triangularity if appropriate.      /* Preserve triangularity and even unit-triangularity if appropriate.
284       * Note that in that case, the multiplication itself should happen       * Note that in that case, the multiplication itself should happen
285       * faster.  But there's no support for that in CHOLMOD */       * faster.  But there's no support for that in CHOLMOD */
# Line 265  Line 301 
301                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));
302      SET_VECTOR_ELT(dn, 1,      SET_VECTOR_ELT(dn, 1,
303                     duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), 1)));                     duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), 1)));
304        UNPROTECT(1);
305      return chm_sparse_to_SEXP(chc, 1, uploT, /*Rkind*/0, diag, dn);      return chm_sparse_to_SEXP(chc, 1, uploT, /*Rkind*/0, diag, dn);
306  }  }
307    
# Line 278  Line 315 
315      const char *cl_a = class_P(a), *cl_b = class_P(b);      const char *cl_a = class_P(a), *cl_b = class_P(b);
316      char diag[] = {'\0', '\0'};      char diag[] = {'\0', '\0'};
317      int uploT = 0;      int uploT = 0;
318      SEXP dn = allocVector(VECSXP, 2);      SEXP dn = PROTECT(allocVector(VECSXP, 2));
319      R_CheckStack();      R_CheckStack();
320    
321      chTr = cholmod_transpose((tr) ? chb : cha, chb->xtype, &c);      chTr = cholmod_transpose((tr) ? chb : cha, chb->xtype, &c);
# Line 297  Line 334 
334              }              }
335              else diag[0]= 'N';              else diag[0]= 'N';
336          }          }
   
337      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
338                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), (tr) ? 0 : 1)));                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), (tr) ? 0 : 1)));
339      SET_VECTOR_ELT(dn, 1,      SET_VECTOR_ELT(dn, 1,
340                     duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), (tr) ? 0 : 1)));                     duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), (tr) ? 0 : 1)));
341        UNPROTECT(1);
342      return chm_sparse_to_SEXP(chc, 1, uploT, /*Rkind*/0, diag, dn);      return chm_sparse_to_SEXP(chc, 1, uploT, /*Rkind*/0, diag, dn);
343  }  }
344    
# Line 314  Line 351 
351                                          chb->xtype, &c);                                          chb->xtype, &c);
352      SEXP dn = PROTECT(allocVector(VECSXP, 2));      SEXP dn = PROTECT(allocVector(VECSXP, 2));
353      double one[] = {1,0}, zero[] = {0,0};      double one[] = {1,0}, zero[] = {0,0};
354        int nprot = 2;
355      R_CheckStack();      R_CheckStack();
356        /* Tim Davis, please FIXME:  currently (2010-11) *fails* when  a  is a pattern matrix:*/
357        if(cha->xtype == CHOLMOD_PATTERN) {
358            /* warning(_("Csparse_dense_prod(): cholmod_sdmult() not yet implemented for pattern./ ngCMatrix" */
359            /*        " --> slightly inefficient coercion")); */
360    
361            // This *fails* to produce a CHOLMOD_REAL ..
362            // CHM_SP chd = cholmod_l_copy(cha, cha->stype, CHOLMOD_REAL, &c);
363            // --> use our Matrix-classes
364            SEXP da = PROTECT(nz2Csparse(a, x_double)); nprot++;
365            cha = AS_CHM_SP(da);
366        }
367      cholmod_sdmult(cha, 0, one, zero, chb, chc, &c);      cholmod_sdmult(cha, 0, one, zero, chb, chc, &c);
368      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
369                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));
370      SET_VECTOR_ELT(dn, 1,      SET_VECTOR_ELT(dn, 1,
371                     duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));                     duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));
372      UNPROTECT(2);      UNPROTECT(nprot);
373      return chm_dense_to_SEXP(chc, 1, 0, dn);      return chm_dense_to_SEXP(chc, 1, 0, dn);
374  }  }
375    
# Line 332  Line 380 
380      CHM_DN chb = AS_CHM_DN(b_M);      CHM_DN chb = AS_CHM_DN(b_M);
381      CHM_DN chc = cholmod_allocate_dense(cha->ncol, chb->ncol, cha->ncol,      CHM_DN chc = cholmod_allocate_dense(cha->ncol, chb->ncol, cha->ncol,
382                                          chb->xtype, &c);                                          chb->xtype, &c);
383      SEXP dn = PROTECT(allocVector(VECSXP, 2));      SEXP dn = PROTECT(allocVector(VECSXP, 2)); int nprot = 2;
384      double one[] = {1,0}, zero[] = {0,0};      double one[] = {1,0}, zero[] = {0,0};
385      R_CheckStack();      R_CheckStack();
386        // -- see Csparse_dense_prod() above :
387        if(cha->xtype == CHOLMOD_PATTERN) {
388            SEXP da = PROTECT(nz2Csparse(a, x_double)); nprot++;
389            cha = AS_CHM_SP(da);
390        }
391      cholmod_sdmult(cha, 1, one, zero, chb, chc, &c);      cholmod_sdmult(cha, 1, one, zero, chb, chc, &c);
392      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
393                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 1)));                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 1)));
394      SET_VECTOR_ELT(dn, 1,      SET_VECTOR_ELT(dn, 1,
395                     duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));                     duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));
396      UNPROTECT(2);      UNPROTECT(nprot);
397      return chm_dense_to_SEXP(chc, 1, 0, dn);      return chm_dense_to_SEXP(chc, 1, 0, dn);
398  }  }
399    
# Line 351  Line 403 
403  {  {
404      int trip = asLogical(triplet),      int trip = asLogical(triplet),
405          tr   = asLogical(trans); /* gets reversed because _aat is tcrossprod */          tr   = asLogical(trans); /* gets reversed because _aat is tcrossprod */
406    #ifdef AS_CHM_DIAGU2N_FIXED_FINALLY
407      CHM_TR cht = trip ? AS_CHM_TR(x) : (CHM_TR) NULL;      CHM_TR cht = trip ? AS_CHM_TR(x) : (CHM_TR) NULL;
408    #else /* workaround needed:*/
409        SEXP xx = PROTECT(Tsparse_diagU2N(x));
410        CHM_TR cht = trip ? AS_CHM_TR__(xx) : (CHM_TR) NULL;
411    #endif
412      CHM_SP chcp, chxt,      CHM_SP chcp, chxt,
413          chx = (trip ?          chx = (trip ?
414                 cholmod_triplet_to_sparse(cht, cht->nnz, &c) :                 cholmod_triplet_to_sparse(cht, cht->nnz, &c) :
# Line 373  Line 430 
430                     duplicate(VECTOR_ELT(GET_SLOT(x, Matrix_DimNamesSym),                     duplicate(VECTOR_ELT(GET_SLOT(x, Matrix_DimNamesSym),
431                                          (tr) ? 0 : 1)));                                          (tr) ? 0 : 1)));
432      SET_VECTOR_ELT(dn, 1, duplicate(VECTOR_ELT(dn, 0)));      SET_VECTOR_ELT(dn, 1, duplicate(VECTOR_ELT(dn, 0)));
433    #ifdef AS_CHM_DIAGU2N_FIXED_FINALLY
434      UNPROTECT(1);      UNPROTECT(1);
435    #else
436        UNPROTECT(2);
437    #endif
438      return chm_sparse_to_SEXP(chcp, 1, 0, 0, "", dn);      return chm_sparse_to_SEXP(chcp, 1, 0, 0, "", dn);
439  }  }
440    
441    /* Csparse_drop(x, tol):  drop entries with absolute value < tol, i.e,
442    *  at least all "explicit" zeros */
443  SEXP Csparse_drop(SEXP x, SEXP tol)  SEXP Csparse_drop(SEXP x, SEXP tol)
444  {  {
445      const char *cl = class_P(x);      const char *cl = class_P(x);
# Line 399  Line 462 
462  SEXP Csparse_horzcat(SEXP x, SEXP y)  SEXP Csparse_horzcat(SEXP x, SEXP y)
463  {  {
464      CHM_SP chx = AS_CHM_SP__(x), chy = AS_CHM_SP__(y);      CHM_SP chx = AS_CHM_SP__(x), chy = AS_CHM_SP__(y);
465      int Rkind = 0; /* only for "d" - FIXME */      int Rk_x = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0,
466            Rk_y = (chy->xtype != CHOLMOD_PATTERN) ? Real_kind(y) : 0,
467            Rkind = /* logical if both x and y are */ (Rk_x == 1 && Rk_y == 1) ? 1 : 0;
468      R_CheckStack();      R_CheckStack();
469    
470      /* FIXME: currently drops dimnames */      /* TODO: currently drops dimnames - and we fix at R level */
471      return chm_sparse_to_SEXP(cholmod_horzcat(chx, chy, 1, &c),      return chm_sparse_to_SEXP(cholmod_horzcat(chx, chy, 1, &c),
472                                1, 0, Rkind, "", R_NilValue);                                1, 0, Rkind, "", R_NilValue);
473  }  }
# Line 410  Line 475 
475  SEXP Csparse_vertcat(SEXP x, SEXP y)  SEXP Csparse_vertcat(SEXP x, SEXP y)
476  {  {
477      CHM_SP chx = AS_CHM_SP__(x), chy = AS_CHM_SP__(y);      CHM_SP chx = AS_CHM_SP__(x), chy = AS_CHM_SP__(y);
478      int Rkind = 0; /* only for "d" - FIXME */      int Rk_x = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0,
479            Rk_y = (chy->xtype != CHOLMOD_PATTERN) ? Real_kind(y) : 0,
480            Rkind = /* logical if both x and y are */ (Rk_x == 1 && Rk_y == 1) ? 1 : 0;
481      R_CheckStack();      R_CheckStack();
482    
483      /* FIXME: currently drops dimnames */      /* TODO: currently drops dimnames - and we fix at R level */
484      return chm_sparse_to_SEXP(cholmod_vertcat(chx, chy, 1, &c),      return chm_sparse_to_SEXP(cholmod_vertcat(chx, chy, 1, &c),
485                                1, 0, Rkind, "", R_NilValue);                                1, 0, Rkind, "", R_NilValue);
486  }  }
# Line 464  Line 531 
531      }      }
532      else { /* triangular with diag='N'): now drop the diagonal */      else { /* triangular with diag='N'): now drop the diagonal */
533          /* duplicate, since chx will be modified: */          /* duplicate, since chx will be modified: */
534          CHM_SP chx = AS_CHM_SP__(duplicate(x));          SEXP xx = PROTECT(duplicate(x));
535            CHM_SP chx = AS_CHM_SP__(xx);
536          int uploT = (*uplo_P(x) == 'U') ? 1 : -1,          int uploT = (*uplo_P(x) == 'U') ? 1 : -1,
537              Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;              Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
538          R_CheckStack();          R_CheckStack();
539    
540          chm_diagN2U(chx, uploT, /* do_realloc */ FALSE);          chm_diagN2U(chx, uploT, /* do_realloc */ FALSE);
541    
542          return chm_sparse_to_SEXP(chx, /*dofree*/ 0/* or 1 ?? */,          SEXP ans = chm_sparse_to_SEXP(chx, /*dofree*/ 0/* or 1 ?? */,
543                                    uploT, Rkind, "U",                                    uploT, Rkind, "U",
544                                    GET_SLOT(x, Matrix_DimNamesSym));                                    GET_SLOT(x, Matrix_DimNamesSym));
545            UNPROTECT(1);// only now !
546            return ans;
547      }      }
548  }  }
549    
550    /**
551     * "Indexing" aka subsetting : Compute  x[i,j], also for vectors i and j
552     * Working via CHOLMOD_submatrix, see ./CHOLMOD/MatrixOps/cholmod_submatrix.c
553     * @param x CsparseMatrix
554     * @param i row     indices (0-origin), or NULL (R's)
555     * @param j columns indices (0-origin), or NULL
556     *
557     * @return x[i,j]  still CsparseMatrix --- currently, this loses dimnames
558     */
559  SEXP Csparse_submatrix(SEXP x, SEXP i, SEXP j)  SEXP Csparse_submatrix(SEXP x, SEXP i, SEXP j)
560  {  {
561      CHM_SP chx = AS_CHM_SP__(x);      CHM_SP chx = AS_CHM_SP(x); /* << does diagU2N() when needed */
562      int rsize = (isNull(i)) ? -1 : LENGTH(i),      int rsize = (isNull(i)) ? -1 : LENGTH(i),
563          csize = (isNull(j)) ? -1 : LENGTH(j);          csize = (isNull(j)) ? -1 : LENGTH(j);
564      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
# Line 490  Line 569 
569      if (csize >= 0 && !isInteger(j))      if (csize >= 0 && !isInteger(j))
570          error(_("Index j must be NULL or integer"));          error(_("Index j must be NULL or integer"));
571    
572      return chm_sparse_to_SEXP(cholmod_submatrix(chx, INTEGER(i), rsize,      if (!chx->stype) {/* non-symmetric Matrix */
573                                                  INTEGER(j), csize,          return chm_sparse_to_SEXP(cholmod_submatrix(chx,
574                                                        (rsize < 0) ? NULL : INTEGER(i), rsize,
575                                                        (csize < 0) ? NULL : INTEGER(j), csize,
576                                                  TRUE, TRUE, &c),                                                  TRUE, TRUE, &c),
577                                1, 0, Rkind, "",                                1, 0, Rkind, "",
578                                /* FIXME: drops dimnames */ R_NilValue);                                /* FIXME: drops dimnames */ R_NilValue);
579  }  }
580                                    /* for now, cholmod_submatrix() only accepts "generalMatrix" */
581        CHM_SP tmp = cholmod_copy(chx, /* stype: */ 0, chx->xtype, &c);
582        CHM_SP ans = cholmod_submatrix(tmp,
583                                       (rsize < 0) ? NULL : INTEGER(i), rsize,
584                                       (csize < 0) ? NULL : INTEGER(j), csize,
585                                       TRUE, TRUE, &c);
586        cholmod_free_sparse(&tmp, &c);
587        return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "", R_NilValue);
588    }
589    
590    #define _d_Csp_
591    #include "t_Csparse_subassign.c"
592    
593    #define _l_Csp_
594    #include "t_Csparse_subassign.c"
595    
596    #define _i_Csp_
597    #include "t_Csparse_subassign.c"
598    
599    #define _n_Csp_
600    #include "t_Csparse_subassign.c"
601    
602    #define _z_Csp_
603    #include "t_Csparse_subassign.c"
604    
605    
606    
607  SEXP Csparse_MatrixMarket(SEXP x, SEXP fname)  SEXP Csparse_MatrixMarket(SEXP x, SEXP fname)
608  {  {
# Line 579  Line 686 
686      case diag_backpermuted:      case diag_backpermuted:
687          for_DIAG(v[i] = x_x[i_from]);          for_DIAG(v[i] = x_x[i_from]);
688    
689          warning(_("resultKind = 'diagBack' (back-permuted) is experimental"));          warning(_("%s = '%s' (back-permuted) is experimental"),
690                    "resultKind", "diagBack");
691          /* now back_permute : */          /* now back_permute : */
692          for(i = 0; i < n; i++) {          for(i = 0; i < n; i++) {
693              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 696 
696          break;          break;
697    
698      default: /* -1 from above */      default: /* -1 from above */
699          error("diag_tC(): invalid 'resultKind'");          error(_("diag_tC(): invalid 'resultKind'"));
700          /* Wall: */ ans = R_NilValue; v = REAL(ans);          /* Wall: */ ans = R_NilValue; v = REAL(ans);
701      }      }
702    
# Line 618  Line 726 
726    
727      return diag_tC_ptr(n, x_p, x_x, perm, resultKind);      return diag_tC_ptr(n, x_p, x_x, perm, resultKind);
728  }  }
729    
730    /**
731     * Create a Csparse matrix object from indices and/or pointers.
732     *
733     * @param cls name of actual class of object to create
734     * @param i optional integer vector of length nnz of row indices
735     * @param j optional integer vector of length nnz of column indices
736     * @param p optional integer vector of length np of row or column pointers
737     * @param np length of integer vector p.  Must be zero if p == (int*)NULL
738     * @param x optional vector of values
739     * @param nnz length of vectors i, j and/or x, whichever is to be used
740     * @param dims optional integer vector of length 2 to be used as
741     *     dimensions.  If dims == (int*)NULL then the maximum row and column
742     *     index are used as the dimensions.
743     * @param dimnames optional list of length 2 to be used as dimnames
744     * @param index1 indicator of 1-based indices
745     *
746     * @return an SEXP of class cls inheriting from CsparseMatrix.
747     */
748    SEXP create_Csparse(char* cls, int* i, int* j, int* p, int np,
749                        void* x, int nnz, int* dims, SEXP dimnames,
750                        int index1)
751    {
752        SEXP ans;
753        int *ij = (int*)NULL, *tri, *trj,
754            mi, mj, mp, nrow = -1, ncol = -1;
755        int xtype = -1;             /* -Wall */
756        CHM_TR T;
757        CHM_SP A;
758    
759        if (np < 0 || nnz < 0)
760            error(_("negative vector lengths not allowed: np = %d, nnz = %d"),
761                  np, nnz);
762        if (1 != ((mi = (i == (int*)NULL)) +
763                  (mj = (j == (int*)NULL)) +
764                  (mp = (p == (int*)NULL))))
765            error(_("exactly 1 of 'i', 'j' or 'p' must be NULL"));
766        if (mp) {
767            if (np) error(_("np = %d, must be zero when p is NULL"), np);
768        } else {
769            if (np) {               /* Expand p to form i or j */
770                if (!(p[0])) error(_("p[0] = %d, should be zero"), p[0]);
771                for (int ii = 0; ii < np; ii++)
772                    if (p[ii] > p[ii + 1])
773                        error(_("p must be non-decreasing"));
774                if (p[np] != nnz)
775                    error("p[np] = %d != nnz = %d", p[np], nnz);
776                ij = Calloc(nnz, int);
777                if (mi) {
778                    i = ij;
779                    nrow = np;
780                } else {
781                    j = ij;
782                    ncol = np;
783                }
784                /* Expand p to 0-based indices */
785                for (int ii = 0; ii < np; ii++)
786                    for (int jj = p[ii]; jj < p[ii + 1]; jj++) ij[jj] = ii;
787            } else {
788                if (nnz)
789                    error(_("Inconsistent dimensions: np = 0 and nnz = %d"),
790                          nnz);
791            }
792        }
793        /* calculate nrow and ncol */
794        if (nrow < 0) {
795            for (int ii = 0; ii < nnz; ii++) {
796                int i1 = i[ii] + (index1 ? 0 : 1); /* 1-based index */
797                if (i1 < 1) error(_("invalid row index at position %d"), ii);
798                if (i1 > nrow) nrow = i1;
799            }
800        }
801        if (ncol < 0) {
802            for (int jj = 0; jj < nnz; jj++) {
803                int j1 = j[jj] + (index1 ? 0 : 1);
804                if (j1 < 1) error(_("invalid column index at position %d"), jj);
805                if (j1 > ncol) ncol = j1;
806            }
807        }
808        if (dims != (int*)NULL) {
809            if (dims[0] > nrow) nrow = dims[0];
810            if (dims[1] > ncol) ncol = dims[1];
811        }
812        /* check the class name */
813        if (strlen(cls) != 8)
814            error(_("strlen of cls argument = %d, should be 8"), strlen(cls));
815        if (!strcmp(cls + 2, "CMatrix"))
816            error(_("cls = \"%s\" does not end in \"CMatrix\""), cls);
817        switch(cls[0]) {
818        case 'd':
819        case 'l':
820            xtype = CHOLMOD_REAL;
821        break;
822        case 'n':
823            xtype = CHOLMOD_PATTERN;
824            break;
825        default:
826            error(_("cls = \"%s\" must begin with 'd', 'l' or 'n'"), cls);
827        }
828        if (cls[1] != 'g')
829            error(_("Only 'g'eneral sparse matrix types allowed"));
830        /* allocate and populate the triplet */
831        T = cholmod_allocate_triplet((size_t)nrow, (size_t)ncol, (size_t)nnz, 0,
832                                     xtype, &c);
833        T->x = x;
834        tri = (int*)T->i;
835        trj = (int*)T->j;
836        for (int ii = 0; ii < nnz; ii++) {
837            tri[ii] = i[ii] - ((!mi && index1) ? 1 : 0);
838            trj[ii] = j[ii] - ((!mj && index1) ? 1 : 0);
839        }
840        /* create the cholmod_sparse structure */
841        A = cholmod_triplet_to_sparse(T, nnz, &c);
842        cholmod_free_triplet(&T, &c);
843        /* copy the information to the SEXP */
844        ans = PROTECT(NEW_OBJECT(MAKE_CLASS(cls)));
845    /* FIXME: This has been copied from chm_sparse_to_SEXP in chm_common.c */
846        /* allocate and copy common slots */
847        nnz = cholmod_nnz(A, &c);
848        dims = INTEGER(ALLOC_SLOT(ans, Matrix_DimSym, INTSXP, 2));
849        dims[0] = A->nrow; dims[1] = A->ncol;
850        Memcpy(INTEGER(ALLOC_SLOT(ans, Matrix_pSym, INTSXP, A->ncol + 1)), (int*)A->p, A->ncol + 1);
851        Memcpy(INTEGER(ALLOC_SLOT(ans, Matrix_iSym, INTSXP, nnz)), (int*)A->i, nnz);
852        switch(cls[1]) {
853        case 'd':
854            Memcpy(REAL(ALLOC_SLOT(ans, Matrix_xSym, REALSXP, nnz)), (double*)A->x, nnz);
855            break;
856        case 'l':
857            error(_("code not yet written for cls = \"lgCMatrix\""));
858        }
859    /* FIXME: dimnames are *NOT* put there yet (if non-NULL) */
860        cholmod_free_sparse(&A, &c);
861        UNPROTECT(1);
862        return ans;
863    }

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