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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 3011, Mon Oct 6 17:00:48 2014 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  SEXP Csparse_to_matrix(SEXP x)  // 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      return chm_dense_to_matrix(cholmod_sparse_to_dense(AS_CHM_SP__(x), &c),      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 chk)
190    {
191        return chm_dense_to_matrix(cholmod_sparse_to_dense(AS_CHM_SP2(x, asLogical(chk)), &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  {  {
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,  #define CHM_SUB(_M_, _i_, _j_)                                  \
573                                                  INTEGER(j), csize,      cholmod_submatrix(_M_,                                      \
574                                                  TRUE, TRUE, &c),                        (rsize < 0) ? NULL : INTEGER(_i_), rsize, \
575                                1, 0, Rkind, "",                        (csize < 0) ? NULL : INTEGER(_j_), csize, \
576                                /* FIXME: drops dimnames */ R_NilValue);                        TRUE, TRUE, &c)
577  }      CHM_SP ans;
578        if (!chx->stype) {/* non-symmetric Matrix */
579            ans = CHM_SUB(chx, i, j);
580        }
581        else {
582            /* for now, cholmod_submatrix() only accepts "generalMatrix" */
583            CHM_SP tmp = cholmod_copy(chx, /* stype: */ 0, chx->xtype, &c);
584            ans = CHM_SUB(tmp, i, j);
585            cholmod_free_sparse(&tmp, &c);
586        }
587        // "FIXME": currently dropping dimnames, and adding them afterwards in R :
588        return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "", /* dimnames: */ R_NilValue);
589    }
590
591    #define _d_Csp_
592    #include "t_Csparse_subassign.c"
593
594    #define _l_Csp_
595    #include "t_Csparse_subassign.c"
596
597    #define _i_Csp_
598    #include "t_Csparse_subassign.c"
599
600    #define _n_Csp_
601    #include "t_Csparse_subassign.c"
602
603    #define _z_Csp_
604    #include "t_Csparse_subassign.c"
605
606
607
608  SEXP Csparse_MatrixMarket(SEXP x, SEXP fname)  SEXP Csparse_MatrixMarket(SEXP x, SEXP fname)
609  {  {
# Line 524  Line 632
632   *   *
633   * @return  a SEXP, either a (double) number or a length n-vector of diagonal entries   * @return  a SEXP, either a (double) number or a length n-vector of diagonal entries
634   */   */
635  SEXP diag_tC_ptr(int n, int *x_p, double *x_x, int *perm, SEXP resultKind)  SEXP diag_tC_ptr(int n, int *x_p, double *x_x, Rboolean is_U, int *perm,
636  /*                                ^^^^^^ FIXME[Generalize] to int / ... */  /*                                ^^^^^^ FIXME[Generalize] to int / ... */
637                     SEXP resultKind)
638  {  {
639      const char* res_ch = CHAR(STRING_ELT(resultKind,0));      const char* res_ch = CHAR(STRING_ELT(resultKind,0));
640      enum diag_kind { diag, diag_backpermuted, trace, prod, sum_log      enum diag_kind { diag, diag_backpermuted, trace, prod, sum_log, min, max, range
641      } res_kind = ((!strcmp(res_ch, "trace")) ? trace :      } res_kind = ((!strcmp(res_ch, "trace")) ? trace :
642                    ((!strcmp(res_ch, "sumLog")) ? sum_log :                    ((!strcmp(res_ch, "sumLog")) ? sum_log :
643                     ((!strcmp(res_ch, "prod")) ? prod :                     ((!strcmp(res_ch, "prod")) ? prod :
644                        ((!strcmp(res_ch, "min")) ? min :
645                         ((!strcmp(res_ch, "max")) ? max :
646                          ((!strcmp(res_ch, "range")) ? range :
647                      ((!strcmp(res_ch, "diag")) ? diag :                      ((!strcmp(res_ch, "diag")) ? diag :
648                       ((!strcmp(res_ch, "diagBack")) ? diag_backpermuted :                       ((!strcmp(res_ch, "diagBack")) ? diag_backpermuted :
649                        -1)))));                           -1))))))));
650      int i, n_x, i_from = 0;      int i, n_x, i_from;
651      SEXP ans = PROTECT(allocVector(REALSXP,      SEXP ans = PROTECT(allocVector(REALSXP,
652  /*                                 ^^^^  FIXME[Generalize] */  /*                                 ^^^^  FIXME[Generalize] */
653                                     (res_kind == diag ||                                     (res_kind == diag ||
654                                      res_kind == diag_backpermuted) ? n : 1));                                      res_kind == diag_backpermuted) ? n :
655                                       (res_kind == range ? 2 : 1)));
656      double *v = REAL(ans);      double *v = REAL(ans);
657  /*  ^^^^^^      ^^^^  FIXME[Generalize] */  /*  ^^^^^^      ^^^^  FIXME[Generalize] */
658
659        i_from = (is_U ? -1 : 0);
660
661  #define for_DIAG(v_ASSIGN)                                              \  #define for_DIAG(v_ASSIGN)                                              \
662      for(i = 0; i < n; i++, i_from += n_x) {                             \      for(i = 0; i < n; i++) {                                    \
663          /* looking at i-th column */                                    \          /* looking at i-th column */                                    \
664          n_x = x_p[i+1] - x_p[i];/* #{entries} in this column */ \          n_x = x_p[i+1] - x_p[i];/* #{entries} in this column */ \
665            if( is_U) i_from += n_x;                                \
666          v_ASSIGN;                                                       \          v_ASSIGN;                                                       \
667            if(!is_U) i_from += n_x;                                \
668      }      }
669
670      /* NOTA BENE: we assume  -- uplo = "L" i.e. lower triangular matrix      /* NOTA BENE: we assume  -- uplo = "L" i.e. lower triangular matrix
671       *            for uplo = "U" (makes sense with a "dtCMatrix" !),       *            for uplo = "U" (makes sense with a "dtCMatrix" !),
672       *            should use  x_x[i_from + (nx - 1)] instead of x_x[i_from],       *            should use  x_x[i_from + (n_x - 1)] instead of x_x[i_from],
673       *            where nx = (x_p[i+1] - x_p[i])       *            where n_x = (x_p[i+1] - x_p[i])
674       */       */
675
676      switch(res_kind) {      switch(res_kind) {
677      case trace:      case trace: // = sum
678          v[0] = 0.;          v[0] = 0.;
679          for_DIAG(v[0] += x_x[i_from]);          for_DIAG(v[0] += x_x[i_from]);
680          break;          break;
# Line 572  Line 689
689          for_DIAG(v[0] *= x_x[i_from]);          for_DIAG(v[0] *= x_x[i_from]);
690          break;          break;
691
692        case min:
693            v[0] = R_PosInf;
694            for_DIAG(if(v[0] > x_x[i_from]) v[0] = x_x[i_from]);
695            break;
696
697        case max:
698            v[0] = R_NegInf;
699            for_DIAG(if(v[0] < x_x[i_from]) v[0] = x_x[i_from]);
700            break;
701
702        case range:
703            v[0] = R_PosInf;
704            v[1] = R_NegInf;
705            for_DIAG(if(v[0] > x_x[i_from]) v[0] = x_x[i_from];
706                     if(v[1] < x_x[i_from]) v[1] = x_x[i_from]);
707            break;
708
709      case diag:      case diag:
710          for_DIAG(v[i] = x_x[i_from]);          for_DIAG(v[i] = x_x[i_from]);
711          break;          break;
# Line 579  Line 713
713      case diag_backpermuted:      case diag_backpermuted:
714          for_DIAG(v[i] = x_x[i_from]);          for_DIAG(v[i] = x_x[i_from]);
715
716          warning(_("resultKind = 'diagBack' (back-permuted) is experimental"));          warning(_("%s = '%s' (back-permuted) is experimental"),
717                    "resultKind", "diagBack");
718          /* now back_permute : */          /* now back_permute : */
719          for(i = 0; i < n; i++) {          for(i = 0; i < n; i++) {
720              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 723
723          break;          break;
724
725      default: /* -1 from above */      default: /* -1 from above */
726          error("diag_tC(): invalid 'resultKind'");          error(_("diag_tC(): invalid 'resultKind'"));
727          /* Wall: */ ans = R_NilValue; v = REAL(ans);          /* Wall: */ ans = R_NilValue; v = REAL(ans);
728      }      }
729
# Line 600  Line 735
735   * Extract the diagonal entries from *triangular* Csparse matrix  __or__ a   * Extract the diagonal entries from *triangular* Csparse matrix  __or__ a
736   * cholmod_sparse factor (LDL = TRUE).   * cholmod_sparse factor (LDL = TRUE).
737   *   *
738     * @param obj -- now a cholmod_sparse factor or a dtCMatrix
739   * @param pslot  'p' (column pointer)   slot of Csparse matrix/factor   * @param pslot  'p' (column pointer)   slot of Csparse matrix/factor
740   * @param xslot  'x' (non-zero entries) slot of Csparse matrix/factor   * @param xslot  'x' (non-zero entries) slot of Csparse matrix/factor
741   * @param perm_slot  'perm' (= permutation vector) slot of corresponding CHMfactor;   * @param perm_slot  'perm' (= permutation vector) slot of corresponding CHMfactor;
# Line 608  Line 744
744   *   *
745   * @return  a SEXP, either a (double) number or a length n-vector of diagonal entries   * @return  a SEXP, either a (double) number or a length n-vector of diagonal entries
746   */   */
747  SEXP diag_tC(SEXP pslot, SEXP xslot, SEXP perm_slot, SEXP resultKind)  SEXP diag_tC(SEXP obj, SEXP resultKind)
748  {  {
749
750        SEXP
751            pslot = GET_SLOT(obj, Matrix_pSym),
752            xslot = GET_SLOT(obj, Matrix_xSym);
753        Rboolean is_U = (R_has_slot(obj, Matrix_uploSym) &&
754                         *CHAR(asChar(GET_SLOT(obj, Matrix_uploSym))) == 'U');
755      int n = length(pslot) - 1, /* n = ncol(.) = nrow(.) */      int n = length(pslot) - 1, /* n = ncol(.) = nrow(.) */
756          *x_p  = INTEGER(pslot),          *x_p  = INTEGER(pslot), pp = -1, *perm;
*perm = INTEGER(perm_slot);
757      double *x_x = REAL(xslot);      double *x_x = REAL(xslot);
758  /*  ^^^^^^        ^^^^ FIXME[Generalize] to INTEGER(.) / LOGICAL(.) / ... xslot !*/  /*  ^^^^^^        ^^^^ FIXME[Generalize] to INTEGER(.) / LOGICAL(.) / ... xslot !*/
759
760      return diag_tC_ptr(n, x_p, x_x, perm, resultKind);      if(R_has_slot(obj, Matrix_permSym))
761            perm = INTEGER(GET_SLOT(obj, Matrix_permSym));
762        else perm = &pp;
763
764        return diag_tC_ptr(n, x_p, x_x, is_U, perm, resultKind);
765    }
766
767
768    /**
769     * Create a Csparse matrix object from indices and/or pointers.
770     *
771     * @param cls name of actual class of object to create
772     * @param i optional integer vector of length nnz of row indices
773     * @param j optional integer vector of length nnz of column indices
774     * @param p optional integer vector of length np of row or column pointers
775     * @param np length of integer vector p.  Must be zero if p == (int*)NULL
776     * @param x optional vector of values
777     * @param nnz length of vectors i, j and/or x, whichever is to be used
778     * @param dims optional integer vector of length 2 to be used as
779     *     dimensions.  If dims == (int*)NULL then the maximum row and column
780     *     index are used as the dimensions.
781     * @param dimnames optional list of length 2 to be used as dimnames
782     * @param index1 indicator of 1-based indices
783     *
784     * @return an SEXP of class cls inheriting from CsparseMatrix.
785     */
786    SEXP create_Csparse(char* cls, int* i, int* j, int* p, int np,
787                        void* x, int nnz, int* dims, SEXP dimnames,
788                        int index1)
789    {
790        SEXP ans;
791        int *ij = (int*)NULL, *tri, *trj,
792            mi, mj, mp, nrow = -1, ncol = -1;
793        int xtype = -1;             /* -Wall */
794        CHM_TR T;
795        CHM_SP A;
796
797        if (np < 0 || nnz < 0)
798            error(_("negative vector lengths not allowed: np = %d, nnz = %d"),
799                  np, nnz);
800        if (1 != ((mi = (i == (int*)NULL)) +
801                  (mj = (j == (int*)NULL)) +
802                  (mp = (p == (int*)NULL))))
803            error(_("exactly 1 of 'i', 'j' or 'p' must be NULL"));
804        if (mp) {
805            if (np) error(_("np = %d, must be zero when p is NULL"), np);
806        } else {
807            if (np) {               /* Expand p to form i or j */
808                if (!(p[0])) error(_("p[0] = %d, should be zero"), p[0]);
809                for (int ii = 0; ii < np; ii++)
810                    if (p[ii] > p[ii + 1])
811                        error(_("p must be non-decreasing"));
812                if (p[np] != nnz)
813                    error("p[np] = %d != nnz = %d", p[np], nnz);
814                ij = Calloc(nnz, int);
815                if (mi) {
816                    i = ij;
817                    nrow = np;
818                } else {
819                    j = ij;
820                    ncol = np;
821                }
822                /* Expand p to 0-based indices */
823                for (int ii = 0; ii < np; ii++)
824                    for (int jj = p[ii]; jj < p[ii + 1]; jj++) ij[jj] = ii;
825            } else {
826                if (nnz)
827                    error(_("Inconsistent dimensions: np = 0 and nnz = %d"),
828                          nnz);
829            }
830        }
831        /* calculate nrow and ncol */
832        if (nrow < 0) {
833            for (int ii = 0; ii < nnz; ii++) {
834                int i1 = i[ii] + (index1 ? 0 : 1); /* 1-based index */
835                if (i1 < 1) error(_("invalid row index at position %d"), ii);
836                if (i1 > nrow) nrow = i1;
837            }
838        }
839        if (ncol < 0) {
840            for (int jj = 0; jj < nnz; jj++) {
841                int j1 = j[jj] + (index1 ? 0 : 1);
842                if (j1 < 1) error(_("invalid column index at position %d"), jj);
843                if (j1 > ncol) ncol = j1;
844            }
845        }
846        if (dims != (int*)NULL) {
847            if (dims[0] > nrow) nrow = dims[0];
848            if (dims[1] > ncol) ncol = dims[1];
849        }
850        /* check the class name */
851        if (strlen(cls) != 8)
852            error(_("strlen of cls argument = %d, should be 8"), strlen(cls));
853        if (!strcmp(cls + 2, "CMatrix"))
854            error(_("cls = \"%s\" does not end in \"CMatrix\""), cls);
855        switch(cls[0]) {
856        case 'd':
857        case 'l':
858            xtype = CHOLMOD_REAL;
859        break;
860        case 'n':
861            xtype = CHOLMOD_PATTERN;
862            break;
863        default:
864            error(_("cls = \"%s\" must begin with 'd', 'l' or 'n'"), cls);
865        }
866        if (cls[1] != 'g')
867            error(_("Only 'g'eneral sparse matrix types allowed"));
868        /* allocate and populate the triplet */
869        T = cholmod_allocate_triplet((size_t)nrow, (size_t)ncol, (size_t)nnz, 0,
870                                     xtype, &c);
871        T->x = x;
872        tri = (int*)T->i;
873        trj = (int*)T->j;
874        for (int ii = 0; ii < nnz; ii++) {
875            tri[ii] = i[ii] - ((!mi && index1) ? 1 : 0);
876            trj[ii] = j[ii] - ((!mj && index1) ? 1 : 0);
877        }
878        /* create the cholmod_sparse structure */
879        A = cholmod_triplet_to_sparse(T, nnz, &c);
880        cholmod_free_triplet(&T, &c);
881        /* copy the information to the SEXP */
882        ans = PROTECT(NEW_OBJECT(MAKE_CLASS(cls)));
883    /* FIXME: This has been copied from chm_sparse_to_SEXP in chm_common.c */
884        /* allocate and copy common slots */
885        nnz = cholmod_nnz(A, &c);
886        dims = INTEGER(ALLOC_SLOT(ans, Matrix_DimSym, INTSXP, 2));
887        dims[0] = A->nrow; dims[1] = A->ncol;
888        Memcpy(INTEGER(ALLOC_SLOT(ans, Matrix_pSym, INTSXP, A->ncol + 1)), (int*)A->p, A->ncol + 1);
889        Memcpy(INTEGER(ALLOC_SLOT(ans, Matrix_iSym, INTSXP, nnz)), (int*)A->i, nnz);
890        switch(cls[1]) {
891        case 'd':
892            Memcpy(REAL(ALLOC_SLOT(ans, Matrix_xSym, REALSXP, nnz)), (double*)A->x, nnz);
893            break;
894        case 'l':
895            error(_("code not yet written for cls = \"lgCMatrix\""));
896        }
897    /* FIXME: dimnames are *NOT* put there yet (if non-NULL) */
898        cholmod_free_sparse(&A, &c);
899        UNPROTECT(1);
900        return ans;
901  }  }

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