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[matrix] Diff of /pkg/Matrix/src/Csparse.c
 [matrix] / pkg / Matrix / src / Csparse.c

# Diff of /pkg/Matrix/src/Csparse.c

pkg/src/Csparse.c revision 2279, Fri Oct 3 09:15:54 2008 UTC pkg/Matrix/src/Csparse.c revision 2889, Thu Aug 8 21:06:22 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"));
}
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;
}
38      }      }
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),
# Line 200  Line 223
223
224  SEXP Csparse_general_to_symmetric(SEXP x, SEXP uplo)  SEXP Csparse_general_to_symmetric(SEXP x, SEXP uplo)
225  {  {
228            error(_("Csparse_general_to_symmetric(): matrix is not square!"));
229            return R_NilValue; /* -Wall */
230        }
231      CHM_SP chx = AS_CHM_SP__(x), chgx;      CHM_SP chx = AS_CHM_SP__(x), chgx;
232      int uploT = (*CHAR(STRING_ELT(uplo,0)) == 'U') ? 1 : -1;      int uploT = (*CHAR(STRING_ELT(uplo,0)) == 'U') ? 1 : -1;
233      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
234      R_CheckStack();      R_CheckStack();

235      chgx = cholmod_copy(chx, /* stype: */ uploT, chx->xtype, &c);      chgx = cholmod_copy(chx, /* stype: */ uploT, chx->xtype, &c);
236      /* xtype: pattern, "real", complex or .. */      /* xtype: pattern, "real", complex or .. */
237      return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",      return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",
# Line 237  Line 264
264          cha = AS_CHM_SP(a),          cha = AS_CHM_SP(a),
265          chb = AS_CHM_SP(b),          chb = AS_CHM_SP(b),
266          chc = cholmod_ssmult(cha, chb, /*out_stype:*/ 0,          chc = cholmod_ssmult(cha, chb, /*out_stype:*/ 0,
267                               cha->xtype, /*out sorted:*/ 1, &c);                                 /* values:= is_numeric (T/F) */ cha->xtype > 0,
268                                   /*out sorted:*/ 1, &c);
269      const char *cl_a = class_P(a), *cl_b = class_P(b);      const char *cl_a = class_P(a), *cl_b = class_P(b);
270      char diag[] = {'\0', '\0'};      char diag[] = {'\0', '\0'};
271      int uploT = 0;      int uploT = 0;
272      SEXP dn = allocVector(VECSXP, 2);      SEXP dn = PROTECT(allocVector(VECSXP, 2));
273      R_CheckStack();      R_CheckStack();
274
275    #ifdef DEBUG_Matrix_verbose
276        Rprintf("DBG Csparse_C*_prod(%s, %s)\n", cl_a, cl_b);
277    #endif
278
279      /* Preserve triangularity and even unit-triangularity if appropriate.      /* Preserve triangularity and even unit-triangularity if appropriate.
280       * Note that in that case, the multiplication itself should happen       * Note that in that case, the multiplication itself should happen
281       * faster.  But there's no support for that in CHOLMOD */       * faster.  But there's no support for that in CHOLMOD */
# Line 265  Line 297
297                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));
298      SET_VECTOR_ELT(dn, 1,      SET_VECTOR_ELT(dn, 1,
299                     duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), 1)));                     duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), 1)));
300        UNPROTECT(1);
301      return chm_sparse_to_SEXP(chc, 1, uploT, /*Rkind*/0, diag, dn);      return chm_sparse_to_SEXP(chc, 1, uploT, /*Rkind*/0, diag, dn);
302  }  }
303
# Line 278  Line 311
311      const char *cl_a = class_P(a), *cl_b = class_P(b);      const char *cl_a = class_P(a), *cl_b = class_P(b);
312      char diag[] = {'\0', '\0'};      char diag[] = {'\0', '\0'};
313      int uploT = 0;      int uploT = 0;
314      SEXP dn = allocVector(VECSXP, 2);      SEXP dn = PROTECT(allocVector(VECSXP, 2));
315      R_CheckStack();      R_CheckStack();
316
317      chTr = cholmod_transpose((tr) ? chb : cha, chb->xtype, &c);      chTr = cholmod_transpose((tr) ? chb : cha, chb->xtype, &c);
# Line 297  Line 330
330              }              }
331              else diag[0]= 'N';              else diag[0]= 'N';
332          }          }

333      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
334                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), (tr) ? 0 : 1)));                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), (tr) ? 0 : 1)));
335      SET_VECTOR_ELT(dn, 1,      SET_VECTOR_ELT(dn, 1,
336                     duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), (tr) ? 0 : 1)));                     duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), (tr) ? 0 : 1)));
337        UNPROTECT(1);
338      return chm_sparse_to_SEXP(chc, 1, uploT, /*Rkind*/0, diag, dn);      return chm_sparse_to_SEXP(chc, 1, uploT, /*Rkind*/0, diag, dn);
339  }  }
340
# Line 314  Line 347
347                                          chb->xtype, &c);                                          chb->xtype, &c);
348      SEXP dn = PROTECT(allocVector(VECSXP, 2));      SEXP dn = PROTECT(allocVector(VECSXP, 2));
349      double one[] = {1,0}, zero[] = {0,0};      double one[] = {1,0}, zero[] = {0,0};
350        int nprot = 2;
351      R_CheckStack();      R_CheckStack();
352        /* Tim Davis, please FIXME:  currently (2010-11) *fails* when  a  is a pattern matrix:*/
353        if(cha->xtype == CHOLMOD_PATTERN) {
354            /* warning(_("Csparse_dense_prod(): cholmod_sdmult() not yet implemented for pattern./ ngCMatrix" */
355            /*        " --> slightly inefficient coercion")); */
356
357            // This *fails* to produce a CHOLMOD_REAL ..
358            // CHM_SP chd = cholmod_l_copy(cha, cha->stype, CHOLMOD_REAL, &c);
359            // --> use our Matrix-classes
360            SEXP da = PROTECT(nz2Csparse(a, x_double)); nprot++;
361            cha = AS_CHM_SP(da);
362        }
363      cholmod_sdmult(cha, 0, one, zero, chb, chc, &c);      cholmod_sdmult(cha, 0, one, zero, chb, chc, &c);
364      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
365                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));
366      SET_VECTOR_ELT(dn, 1,      SET_VECTOR_ELT(dn, 1,
367                     duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));                     duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));
368      UNPROTECT(2);      UNPROTECT(nprot);
369      return chm_dense_to_SEXP(chc, 1, 0, dn);      return chm_dense_to_SEXP(chc, 1, 0, dn);
370  }  }
371
# Line 332  Line 376
376      CHM_DN chb = AS_CHM_DN(b_M);      CHM_DN chb = AS_CHM_DN(b_M);
377      CHM_DN chc = cholmod_allocate_dense(cha->ncol, chb->ncol, cha->ncol,      CHM_DN chc = cholmod_allocate_dense(cha->ncol, chb->ncol, cha->ncol,
378                                          chb->xtype, &c);                                          chb->xtype, &c);
379      SEXP dn = PROTECT(allocVector(VECSXP, 2));      SEXP dn = PROTECT(allocVector(VECSXP, 2)); int nprot = 2;
380      double one[] = {1,0}, zero[] = {0,0};      double one[] = {1,0}, zero[] = {0,0};
381      R_CheckStack();      R_CheckStack();
382        // -- see Csparse_dense_prod() above :
383        if(cha->xtype == CHOLMOD_PATTERN) {
384            SEXP da = PROTECT(nz2Csparse(a, x_double)); nprot++;
385            cha = AS_CHM_SP(da);
386        }
387      cholmod_sdmult(cha, 1, one, zero, chb, chc, &c);      cholmod_sdmult(cha, 1, one, zero, chb, chc, &c);
388      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
389                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 1)));                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 1)));
390      SET_VECTOR_ELT(dn, 1,      SET_VECTOR_ELT(dn, 1,
391                     duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));                     duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));
392      UNPROTECT(2);      UNPROTECT(nprot);
393      return chm_dense_to_SEXP(chc, 1, 0, dn);      return chm_dense_to_SEXP(chc, 1, 0, dn);
394  }  }
395
# Line 351  Line 399
399  {  {
400      int trip = asLogical(triplet),      int trip = asLogical(triplet),
401          tr   = asLogical(trans); /* gets reversed because _aat is tcrossprod */          tr   = asLogical(trans); /* gets reversed because _aat is tcrossprod */
402    #ifdef AS_CHM_DIAGU2N_FIXED_FINALLY
403      CHM_TR cht = trip ? AS_CHM_TR(x) : (CHM_TR) NULL;      CHM_TR cht = trip ? AS_CHM_TR(x) : (CHM_TR) NULL;
404    #else /* workaround needed:*/
405        SEXP xx = PROTECT(Tsparse_diagU2N(x));
406        CHM_TR cht = trip ? AS_CHM_TR__(xx) : (CHM_TR) NULL;
407    #endif
408      CHM_SP chcp, chxt,      CHM_SP chcp, chxt,
409          chx = (trip ?          chx = (trip ?
410                 cholmod_triplet_to_sparse(cht, cht->nnz, &c) :                 cholmod_triplet_to_sparse(cht, cht->nnz, &c) :
# Line 373  Line 426
426                     duplicate(VECTOR_ELT(GET_SLOT(x, Matrix_DimNamesSym),                     duplicate(VECTOR_ELT(GET_SLOT(x, Matrix_DimNamesSym),
427                                          (tr) ? 0 : 1)));                                          (tr) ? 0 : 1)));
428      SET_VECTOR_ELT(dn, 1, duplicate(VECTOR_ELT(dn, 0)));      SET_VECTOR_ELT(dn, 1, duplicate(VECTOR_ELT(dn, 0)));
429    #ifdef AS_CHM_DIAGU2N_FIXED_FINALLY
430      UNPROTECT(1);      UNPROTECT(1);
431    #else
432        UNPROTECT(2);
433    #endif
434      return chm_sparse_to_SEXP(chcp, 1, 0, 0, "", dn);      return chm_sparse_to_SEXP(chcp, 1, 0, 0, "", dn);
435  }  }
436
437    /* Csparse_drop(x, tol):  drop entries with absolute value < tol, i.e,
438    *  at least all "explicit" zeros */
439  SEXP Csparse_drop(SEXP x, SEXP tol)  SEXP Csparse_drop(SEXP x, SEXP tol)
440  {  {
441      const char *cl = class_P(x);      const char *cl = class_P(x);
# Line 399  Line 458
458  SEXP Csparse_horzcat(SEXP x, SEXP y)  SEXP Csparse_horzcat(SEXP x, SEXP y)
459  {  {
460      CHM_SP chx = AS_CHM_SP__(x), chy = AS_CHM_SP__(y);      CHM_SP chx = AS_CHM_SP__(x), chy = AS_CHM_SP__(y);
461      int Rkind = 0; /* only for "d" - FIXME */      int Rk_x = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0,
462            Rk_y = (chy->xtype != CHOLMOD_PATTERN) ? Real_kind(y) : 0,
463            Rkind = /* logical if both x and y are */ (Rk_x == 1 && Rk_y == 1) ? 1 : 0;
464      R_CheckStack();      R_CheckStack();
465
466      /* FIXME: currently drops dimnames */      /* TODO: currently drops dimnames - and we fix at R level */
467      return chm_sparse_to_SEXP(cholmod_horzcat(chx, chy, 1, &c),      return chm_sparse_to_SEXP(cholmod_horzcat(chx, chy, 1, &c),
468                                1, 0, Rkind, "", R_NilValue);                                1, 0, Rkind, "", R_NilValue);
469  }  }
# Line 410  Line 471
471  SEXP Csparse_vertcat(SEXP x, SEXP y)  SEXP Csparse_vertcat(SEXP x, SEXP y)
472  {  {
473      CHM_SP chx = AS_CHM_SP__(x), chy = AS_CHM_SP__(y);      CHM_SP chx = AS_CHM_SP__(x), chy = AS_CHM_SP__(y);
474      int Rkind = 0; /* only for "d" - FIXME */      int Rk_x = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0,
475            Rk_y = (chy->xtype != CHOLMOD_PATTERN) ? Real_kind(y) : 0,
476            Rkind = /* logical if both x and y are */ (Rk_x == 1 && Rk_y == 1) ? 1 : 0;
477      R_CheckStack();      R_CheckStack();
478
479      /* FIXME: currently drops dimnames */      /* TODO: currently drops dimnames - and we fix at R level */
480      return chm_sparse_to_SEXP(cholmod_vertcat(chx, chy, 1, &c),      return chm_sparse_to_SEXP(cholmod_vertcat(chx, chy, 1, &c),
481                                1, 0, Rkind, "", R_NilValue);                                1, 0, Rkind, "", R_NilValue);
482  }  }
# Line 464  Line 527
527      }      }
528      else { /* triangular with diag='N'): now drop the diagonal */      else { /* triangular with diag='N'): now drop the diagonal */
529          /* duplicate, since chx will be modified: */          /* duplicate, since chx will be modified: */
530          CHM_SP chx = AS_CHM_SP__(duplicate(x));          SEXP xx = PROTECT(duplicate(x));
531            CHM_SP chx = AS_CHM_SP__(xx);
532          int uploT = (*uplo_P(x) == 'U') ? 1 : -1,          int uploT = (*uplo_P(x) == 'U') ? 1 : -1,
533              Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;              Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
534          R_CheckStack();          R_CheckStack();
535
536          chm_diagN2U(chx, uploT, /* do_realloc */ FALSE);          chm_diagN2U(chx, uploT, /* do_realloc */ FALSE);
537
538          return chm_sparse_to_SEXP(chx, /*dofree*/ 0/* or 1 ?? */,          SEXP ans = chm_sparse_to_SEXP(chx, /*dofree*/ 0/* or 1 ?? */,
539                                    uploT, Rkind, "U",                                    uploT, Rkind, "U",
540                                    GET_SLOT(x, Matrix_DimNamesSym));                                    GET_SLOT(x, Matrix_DimNamesSym));
541            UNPROTECT(1);// only now !
542            return ans;
543      }      }
544  }  }
545
546    /**
547     * "Indexing" aka subsetting : Compute  x[i,j], also for vectors i and j
548     * Working via CHOLMOD_submatrix, see ./CHOLMOD/MatrixOps/cholmod_submatrix.c
549     * @param x CsparseMatrix
550     * @param i row     indices (0-origin), or NULL (R's)
551     * @param j columns indices (0-origin), or NULL
552     *
553     * @return x[i,j]  still CsparseMatrix --- currently, this loses dimnames
554     */
555  SEXP Csparse_submatrix(SEXP x, SEXP i, SEXP j)  SEXP Csparse_submatrix(SEXP x, SEXP i, SEXP j)
556  {  {
557      CHM_SP chx = AS_CHM_SP__(x);      CHM_SP chx = AS_CHM_SP(x); /* << does diagU2N() when needed */
558      int rsize = (isNull(i)) ? -1 : LENGTH(i),      int rsize = (isNull(i)) ? -1 : LENGTH(i),
559          csize = (isNull(j)) ? -1 : LENGTH(j);          csize = (isNull(j)) ? -1 : LENGTH(j);
560      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
# Line 490  Line 565
565      if (csize >= 0 && !isInteger(j))      if (csize >= 0 && !isInteger(j))
566          error(_("Index j must be NULL or integer"));          error(_("Index j must be NULL or integer"));
567
568      return chm_sparse_to_SEXP(cholmod_submatrix(chx, INTEGER(i), rsize,      if (!chx->stype) {/* non-symmetric Matrix */
569                                                  INTEGER(j), csize,          return chm_sparse_to_SEXP(cholmod_submatrix(chx,
570                                                        (rsize < 0) ? NULL : INTEGER(i), rsize,
571                                                        (csize < 0) ? NULL : INTEGER(j), csize,
572                                                  TRUE, TRUE, &c),                                                  TRUE, TRUE, &c),
573                                1, 0, Rkind, "",                                1, 0, Rkind, "",
574                                /* FIXME: drops dimnames */ R_NilValue);                                /* FIXME: drops dimnames */ R_NilValue);
575  }  }
576                                    /* for now, cholmod_submatrix() only accepts "generalMatrix" */
577        CHM_SP tmp = cholmod_copy(chx, /* stype: */ 0, chx->xtype, &c);
578        CHM_SP ans = cholmod_submatrix(tmp,
579                                       (rsize < 0) ? NULL : INTEGER(i), rsize,
580                                       (csize < 0) ? NULL : INTEGER(j), csize,
581                                       TRUE, TRUE, &c);
582        cholmod_free_sparse(&tmp, &c);
583        return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "", R_NilValue);
584    }
585
586    #define _d_Csp_
587    #include "t_Csparse_subassign.c"
588
589    #define _l_Csp_
590    #include "t_Csparse_subassign.c"
591
592    #define _i_Csp_
593    #include "t_Csparse_subassign.c"
594
595    #define _n_Csp_
596    #include "t_Csparse_subassign.c"
597
598    #define _z_Csp_
599    #include "t_Csparse_subassign.c"
600
601
602
603  SEXP Csparse_MatrixMarket(SEXP x, SEXP fname)  SEXP Csparse_MatrixMarket(SEXP x, SEXP fname)
604  {  {
# Line 579  Line 682
682      case diag_backpermuted:      case diag_backpermuted:
683          for_DIAG(v[i] = x_x[i_from]);          for_DIAG(v[i] = x_x[i_from]);
684
685          warning(_("resultKind = 'diagBack' (back-permuted) is experimental"));          warning(_("%s = '%s' (back-permuted) is experimental"),
686                    "resultKind", "diagBack");
687          /* now back_permute : */          /* now back_permute : */
688          for(i = 0; i < n; i++) {          for(i = 0; i < n; i++) {
689              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 692
692          break;          break;
693
694      default: /* -1 from above */      default: /* -1 from above */
695          error("diag_tC(): invalid 'resultKind'");          error(_("diag_tC(): invalid 'resultKind'"));
696          /* Wall: */ ans = R_NilValue; v = REAL(ans);          /* Wall: */ ans = R_NilValue; v = REAL(ans);
697      }      }
698
# Line 618  Line 722
722
723      return diag_tC_ptr(n, x_p, x_x, perm, resultKind);      return diag_tC_ptr(n, x_p, x_x, perm, resultKind);
724  }  }
725
726    /**
727     * Create a Csparse matrix object from indices and/or pointers.
728     *
729     * @param cls name of actual class of object to create
730     * @param i optional integer vector of length nnz of row indices
731     * @param j optional integer vector of length nnz of column indices
732     * @param p optional integer vector of length np of row or column pointers
733     * @param np length of integer vector p.  Must be zero if p == (int*)NULL
734     * @param x optional vector of values
735     * @param nnz length of vectors i, j and/or x, whichever is to be used
736     * @param dims optional integer vector of length 2 to be used as
737     *     dimensions.  If dims == (int*)NULL then the maximum row and column
738     *     index are used as the dimensions.
739     * @param dimnames optional list of length 2 to be used as dimnames
740     * @param index1 indicator of 1-based indices
741     *
742     * @return an SEXP of class cls inheriting from CsparseMatrix.
743     */
744    SEXP create_Csparse(char* cls, int* i, int* j, int* p, int np,
745                        void* x, int nnz, int* dims, SEXP dimnames,
746                        int index1)
747    {
748        SEXP ans;
749        int *ij = (int*)NULL, *tri, *trj,
750            mi, mj, mp, nrow = -1, ncol = -1;
751        int xtype = -1;             /* -Wall */
752        CHM_TR T;
753        CHM_SP A;
754
755        if (np < 0 || nnz < 0)
756            error(_("negative vector lengths not allowed: np = %d, nnz = %d"),
757                  np, nnz);
758        if (1 != ((mi = (i == (int*)NULL)) +
759                  (mj = (j == (int*)NULL)) +
760                  (mp = (p == (int*)NULL))))
761            error(_("exactly 1 of 'i', 'j' or 'p' must be NULL"));
762        if (mp) {
763            if (np) error(_("np = %d, must be zero when p is NULL"), np);
764        } else {
765            if (np) {               /* Expand p to form i or j */
766                if (!(p[0])) error(_("p[0] = %d, should be zero"), p[0]);
767                for (int ii = 0; ii < np; ii++)
768                    if (p[ii] > p[ii + 1])
769                        error(_("p must be non-decreasing"));
770                if (p[np] != nnz)
771                    error("p[np] = %d != nnz = %d", p[np], nnz);
772                ij = Calloc(nnz, int);
773                if (mi) {
774                    i = ij;
775                    nrow = np;
776                } else {
777                    j = ij;
778                    ncol = np;
779                }
780                /* Expand p to 0-based indices */
781                for (int ii = 0; ii < np; ii++)
782                    for (int jj = p[ii]; jj < p[ii + 1]; jj++) ij[jj] = ii;
783            } else {
784                if (nnz)
785                    error(_("Inconsistent dimensions: np = 0 and nnz = %d"),
786                          nnz);
787            }
788        }
789        /* calculate nrow and ncol */
790        if (nrow < 0) {
791            for (int ii = 0; ii < nnz; ii++) {
792                int i1 = i[ii] + (index1 ? 0 : 1); /* 1-based index */
793                if (i1 < 1) error(_("invalid row index at position %d"), ii);
794                if (i1 > nrow) nrow = i1;
795            }
796        }
797        if (ncol < 0) {
798            for (int jj = 0; jj < nnz; jj++) {
799                int j1 = j[jj] + (index1 ? 0 : 1);
800                if (j1 < 1) error(_("invalid column index at position %d"), jj);
801                if (j1 > ncol) ncol = j1;
802            }
803        }
804        if (dims != (int*)NULL) {
805            if (dims[0] > nrow) nrow = dims[0];
806            if (dims[1] > ncol) ncol = dims[1];
807        }
808        /* check the class name */
809        if (strlen(cls) != 8)
810            error(_("strlen of cls argument = %d, should be 8"), strlen(cls));
811        if (!strcmp(cls + 2, "CMatrix"))
812            error(_("cls = \"%s\" does not end in \"CMatrix\""), cls);
813        switch(cls[0]) {
814        case 'd':
815        case 'l':
816            xtype = CHOLMOD_REAL;
817        break;
818        case 'n':
819            xtype = CHOLMOD_PATTERN;
820            break;
821        default:
822            error(_("cls = \"%s\" must begin with 'd', 'l' or 'n'"), cls);
823        }
824        if (cls[1] != 'g')
825            error(_("Only 'g'eneral sparse matrix types allowed"));
826        /* allocate and populate the triplet */
827        T = cholmod_allocate_triplet((size_t)nrow, (size_t)ncol, (size_t)nnz, 0,
828                                     xtype, &c);
829        T->x = x;
830        tri = (int*)T->i;
831        trj = (int*)T->j;
832        for (int ii = 0; ii < nnz; ii++) {
833            tri[ii] = i[ii] - ((!mi && index1) ? 1 : 0);
834            trj[ii] = j[ii] - ((!mj && index1) ? 1 : 0);
835        }
836        /* create the cholmod_sparse structure */
837        A = cholmod_triplet_to_sparse(T, nnz, &c);
838        cholmod_free_triplet(&T, &c);
839        /* copy the information to the SEXP */
840        ans = PROTECT(NEW_OBJECT(MAKE_CLASS(cls)));
841    /* FIXME: This has been copied from chm_sparse_to_SEXP in chm_common.c */
842        /* allocate and copy common slots */
843        nnz = cholmod_nnz(A, &c);
844        dims = INTEGER(ALLOC_SLOT(ans, Matrix_DimSym, INTSXP, 2));
845        dims[0] = A->nrow; dims[1] = A->ncol;
846        Memcpy(INTEGER(ALLOC_SLOT(ans, Matrix_pSym, INTSXP, A->ncol + 1)), (int*)A->p, A->ncol + 1);
847        Memcpy(INTEGER(ALLOC_SLOT(ans, Matrix_iSym, INTSXP, nnz)), (int*)A->i, nnz);
848        switch(cls[1]) {
849        case 'd':
850            Memcpy(REAL(ALLOC_SLOT(ans, Matrix_xSym, REALSXP, nnz)), (double*)A->x, nnz);
851            break;
852        case 'l':
853            error(_("code not yet written for cls = \"lgCMatrix\""));
854        }
855    /* FIXME: dimnames are *NOT* put there yet (if non-NULL) */
856        cholmod_free_sparse(&A, &c);
857        UNPROTECT(1);
858        return ans;
859    }

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