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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 2223, Fri Jul 18 23:04:48 2008 UTC pkg/Matrix/src/Csparse.c revision 2685, Fri Aug 5 19:52:10 2011 UTC
# Line 1  Line 1 
1                          /* Sparse matrices in compressed column-oriented form */                          /* Sparse matrices in compressed column-oriented form */
2    
3  #include "Csparse.h"  #include "Csparse.h"
4  #include "Tsparse.h"  #include "Tsparse.h"
5  #include "chm_common.h"  #include "chm_common.h"
6    
7  SEXP Csparse_validate(SEXP x)  /** "Cheap" C version of  Csparse_validate() - *not* sorting : */
8    Rboolean isValid_Csparse(SEXP x)
9    {
10        /* NB: we do *NOT* check a potential 'x' slot here, at all */
11        SEXP pslot = GET_SLOT(x, Matrix_pSym),
12            islot = GET_SLOT(x, Matrix_iSym);
13        int *dims = INTEGER(GET_SLOT(x, Matrix_DimSym)), j,
14            nrow = dims[0],
15            ncol = dims[1],
16            *xp = INTEGER(pslot),
17            *xi = INTEGER(islot);
18    
19        if (length(pslot) != dims[1] + 1)
20            return FALSE;
21        if (xp[0] != 0)
22            return FALSE;
23        if (length(islot) < xp[ncol]) /* allow larger slots from over-allocation!*/
24            return FALSE;
25        for (j = 0; j < xp[ncol]; j++) {
26            if (xi[j] < 0 || xi[j] >= nrow)
27                return FALSE;
28        }
29        for (j = 0; j < ncol; j++) {
30            if (xp[j] > xp[j + 1])
31                return FALSE;
32        }
33        return TRUE;
34    }
35    
36    SEXP Csparse_validate(SEXP x) {
37        return Csparse_validate_(x, FALSE);
38    }
39    
40    SEXP Csparse_validate2(SEXP x, SEXP maybe_modify) {
41        return Csparse_validate_(x, asLogical(maybe_modify));
42    }
43    
44    SEXP Csparse_validate_(SEXP x, Rboolean maybe_modify)
45  {  {
46      /* NB: we do *NOT* check a potential 'x' slot here, at all */      /* NB: we do *NOT* check a potential 'x' slot here, at all */
47      SEXP pslot = GET_SLOT(x, Matrix_pSym),      SEXP pslot = GET_SLOT(x, Matrix_pSym),
# Line 23  Line 61 
61      if (length(islot) < xp[ncol]) /* allow larger slots from over-allocation!*/      if (length(islot) < xp[ncol]) /* allow larger slots from over-allocation!*/
62          return          return
63              mkString(_("last element of slot p must match length of slots i and x"));              mkString(_("last element of slot p must match length of slots i and x"));
64      for (j = 0; j < length(islot); j++) {      for (j = 0; j < xp[ncol]; j++) {
65          if (xi[j] < 0 || xi[j] >= nrow)          if (xi[j] < 0 || xi[j] >= nrow)
66              return mkString(_("all row indices must be between 0 and nrow-1"));              return mkString(_("all row indices must be between 0 and nrow-1"));
67      }      }
# Line 31  Line 69 
69      for (j = 0; j < ncol; j++) {      for (j = 0; j < ncol; j++) {
70          if (xp[j] > xp[j+1])          if (xp[j] > xp[j+1])
71              return mkString(_("slot p must be non-decreasing"));              return mkString(_("slot p must be non-decreasing"));
72          if(sorted)          if(sorted) /* only act if >= 2 entries in column j : */
73              for (k = xp[j] + 1; k < xp[j + 1]; k++) {              for (k = xp[j] + 1; k < xp[j + 1]; k++) {
74                  if (xi[k] < xi[k - 1])                  if (xi[k] < xi[k - 1])
75                      sorted = FALSE;                      sorted = FALSE;
# Line 40  Line 78 
78              }              }
79      }      }
80      if (!sorted) {      if (!sorted) {
81          CHM_SP chx = AS_CHM_SP__(x);          if(maybe_modify) {
82                CHM_SP chx = (CHM_SP) alloca(sizeof(cholmod_sparse));
83          R_CheckStack();          R_CheckStack();
84                as_cholmod_sparse(chx, x, FALSE, TRUE);/*-> cholmod_l_sort() ! */
85                /* as chx = AS_CHM_SP__(x)  but  ^^^^ sorting x in_place !!! */
86    
         cholmod_sort(chx, &c);  
87          /* Now re-check that row indices are *strictly* increasing          /* Now re-check that row indices are *strictly* increasing
88           * (and not just increasing) within each column : */           * (and not just increasing) within each column : */
89          for (j = 0; j < ncol; j++) {          for (j = 0; j < ncol; j++) {
90              for (k = xp[j] + 1; k < xp[j + 1]; k++)              for (k = xp[j] + 1; k < xp[j + 1]; k++)
91                  if (xi[k] == xi[k - 1])                  if (xi[k] == xi[k - 1])
92                      return mkString(_("slot i is not *strictly* increasing inside a column (even after cholmod_sort)"));                          return mkString(_("slot i is not *strictly* increasing inside a column (even after cholmod_l_sort)"));
93                }
94            } else { /* no modifying sorting : */
95                return mkString(_("row indices are not sorted within columns"));
96          }          }
   
97      } else if(!strictly) {  /* sorted, but not strictly */      } else if(!strictly) {  /* sorted, but not strictly */
98          return mkString(_("slot i is not *strictly* increasing inside a column"));          return mkString(_("slot i is not *strictly* increasing inside a column"));
99      }      }
# Line 120  Line 162 
162      return chm_dense_to_SEXP(chxd, 1, Rkind, GET_SLOT(x, Matrix_DimNamesSym));      return chm_dense_to_SEXP(chxd, 1, Rkind, GET_SLOT(x, Matrix_DimNamesSym));
163  }  }
164    
165    // FIXME: do not go via CHM (should not be too hard, to just *drop* the x-slot, right?
166  SEXP Csparse_to_nz_pattern(SEXP x, SEXP tri)  SEXP Csparse_to_nz_pattern(SEXP x, SEXP tri)
167  {  {
168      CHM_SP chxs = AS_CHM_SP__(x);      CHM_SP chxs = AS_CHM_SP__(x);
# Line 133  Line 176 
176                                GET_SLOT(x, Matrix_DimNamesSym));                                GET_SLOT(x, Matrix_DimNamesSym));
177  }  }
178    
179    // n.CMatrix --> [dli].CMatrix  (not going through CHM!)
180    SEXP nz_pattern_to_Csparse(SEXP x, SEXP res_kind)
181    {
182        return nz2Csparse(x, asInteger(res_kind));
183    }
184    // n.CMatrix --> [dli].CMatrix  (not going through CHM!)
185    SEXP nz2Csparse(SEXP x, enum x_slot_kind r_kind)
186    {
187        const char *cl_x = class_P(x);
188        if(cl_x[0] != 'n') error(_("not a 'n.CMatrix'"));
189        if(cl_x[2] != 'C') error(_("not a CsparseMatrix"));
190        int nnz = LENGTH(GET_SLOT(x, Matrix_iSym));
191        SEXP ans;
192        char *ncl = strdup(cl_x);
193        double *dx_x; int *ix_x;
194        ncl[0] = (r_kind == x_double ? 'd' :
195                  (r_kind == x_logical ? 'l' :
196                   /* else (for now):  r_kind == x_integer : */ 'i'));
197        PROTECT(ans = NEW_OBJECT(MAKE_CLASS(ncl)));
198        // create a correct 'x' slot:
199        switch(r_kind) {
200            int i;
201        case x_double: // 'd'
202            dx_x = REAL(ALLOC_SLOT(ans, Matrix_xSym, REALSXP, nnz));
203            for (i=0; i < nnz; i++) dx_x[i] = 1.;
204            break;
205        case x_logical: // 'l'
206            ix_x = LOGICAL(ALLOC_SLOT(ans, Matrix_xSym, LGLSXP, nnz));
207            for (i=0; i < nnz; i++) ix_x[i] = TRUE;
208            break;
209        case x_integer: // 'i'
210            ix_x = INTEGER(ALLOC_SLOT(ans, Matrix_xSym, INTSXP, nnz));
211            for (i=0; i < nnz; i++) ix_x[i] = 1;
212            break;
213    
214        default:
215            error(_("nz2Csparse(): invalid/non-implemented r_kind = %d"),
216                  r_kind);
217        }
218    
219        // now copy all other slots :
220        slot_dup(ans, x, Matrix_iSym);
221        slot_dup(ans, x, Matrix_pSym);
222        slot_dup(ans, x, Matrix_DimSym);
223        slot_dup(ans, x, Matrix_DimNamesSym);
224        if(ncl[1] != 'g') { // symmetric or triangular ...
225            slot_dup_if_has(ans, x, Matrix_uploSym);
226            slot_dup_if_has(ans, x, Matrix_diagSym);
227        }
228        UNPROTECT(1);
229        return ans;
230    }
231    
232  SEXP Csparse_to_matrix(SEXP x)  SEXP Csparse_to_matrix(SEXP x)
233  {  {
234      return chm_dense_to_matrix(cholmod_sparse_to_dense(AS_CHM_SP__(x), &c),      return chm_dense_to_matrix(cholmod_sparse_to_dense(AS_CHM_SP__(x), &c),
# Line 207  Line 303 
303          cha = AS_CHM_SP(a),          cha = AS_CHM_SP(a),
304          chb = AS_CHM_SP(b),          chb = AS_CHM_SP(b),
305          chc = cholmod_ssmult(cha, chb, /*out_stype:*/ 0,          chc = cholmod_ssmult(cha, chb, /*out_stype:*/ 0,
306                               cha->xtype, /*out sorted:*/ 1, &c);                                 /* values:= is_numeric (T/F) */ cha->xtype > 0,
307                                   /*out sorted:*/ 1, &c);
308      const char *cl_a = class_P(a), *cl_b = class_P(b);      const char *cl_a = class_P(a), *cl_b = class_P(b);
309      char diag[] = {'\0', '\0'};      char diag[] = {'\0', '\0'};
310      int uploT = 0;      int uploT = 0;
311      SEXP dn = allocVector(VECSXP, 2);      SEXP dn = PROTECT(allocVector(VECSXP, 2));
312      R_CheckStack();      R_CheckStack();
313    
314    #ifdef DEBUG_Matrix_verbose
315        Rprintf("DBG Csparse_C*_prod(%s, %s)\n", cl_a, cl_b);
316    #endif
317    
318      /* Preserve triangularity and even unit-triangularity if appropriate.      /* Preserve triangularity and even unit-triangularity if appropriate.
319       * Note that in that case, the multiplication itself should happen       * Note that in that case, the multiplication itself should happen
320       * faster.  But there's no support for that in CHOLMOD */       * faster.  But there's no support for that in CHOLMOD */
# Line 235  Line 336 
336                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));
337      SET_VECTOR_ELT(dn, 1,      SET_VECTOR_ELT(dn, 1,
338                     duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), 1)));                     duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), 1)));
339        UNPROTECT(1);
340      return chm_sparse_to_SEXP(chc, 1, uploT, /*Rkind*/0, diag, dn);      return chm_sparse_to_SEXP(chc, 1, uploT, /*Rkind*/0, diag, dn);
341  }  }
342    
# Line 248  Line 350 
350      const char *cl_a = class_P(a), *cl_b = class_P(b);      const char *cl_a = class_P(a), *cl_b = class_P(b);
351      char diag[] = {'\0', '\0'};      char diag[] = {'\0', '\0'};
352      int uploT = 0;      int uploT = 0;
353      SEXP dn = allocVector(VECSXP, 2);      SEXP dn = PROTECT(allocVector(VECSXP, 2));
354      R_CheckStack();      R_CheckStack();
355    
356      chTr = cholmod_transpose((tr) ? chb : cha, chb->xtype, &c);      chTr = cholmod_transpose((tr) ? chb : cha, chb->xtype, &c);
# Line 267  Line 369 
369              }              }
370              else diag[0]= 'N';              else diag[0]= 'N';
371          }          }
   
372      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
373                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), (tr) ? 0 : 1)));                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), (tr) ? 0 : 1)));
374      SET_VECTOR_ELT(dn, 1,      SET_VECTOR_ELT(dn, 1,
375                     duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), (tr) ? 0 : 1)));                     duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), (tr) ? 0 : 1)));
376        UNPROTECT(1);
377      return chm_sparse_to_SEXP(chc, 1, uploT, /*Rkind*/0, diag, dn);      return chm_sparse_to_SEXP(chc, 1, uploT, /*Rkind*/0, diag, dn);
378  }  }
379    
# Line 284  Line 386 
386                                          chb->xtype, &c);                                          chb->xtype, &c);
387      SEXP dn = PROTECT(allocVector(VECSXP, 2));      SEXP dn = PROTECT(allocVector(VECSXP, 2));
388      double one[] = {1,0}, zero[] = {0,0};      double one[] = {1,0}, zero[] = {0,0};
389        int nprot = 2;
390      R_CheckStack();      R_CheckStack();
391        /* Tim Davis, please FIXME:  currently (2010-11) *fails* when  a  is a pattern matrix:*/
392        if(cha->xtype == CHOLMOD_PATTERN) {
393            /* warning(_("Csparse_dense_prod(): cholmod_sdmult() not yet implemented for pattern./ ngCMatrix" */
394            /*        " --> slightly inefficient coercion")); */
395    
396            // This *fails* to produce a CHOLMOD_REAL ..
397            // CHM_SP chd = cholmod_l_copy(cha, cha->stype, CHOLMOD_REAL, &c);
398            // --> use our Matrix-classes
399            SEXP da = PROTECT(nz2Csparse(a, x_double)); nprot++;
400            cha = AS_CHM_SP(da);
401        }
402      cholmod_sdmult(cha, 0, one, zero, chb, chc, &c);      cholmod_sdmult(cha, 0, one, zero, chb, chc, &c);
403      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
404                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));
405      SET_VECTOR_ELT(dn, 1,      SET_VECTOR_ELT(dn, 1,
406                     duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));                     duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));
407      UNPROTECT(2);      UNPROTECT(nprot);
408      return chm_dense_to_SEXP(chc, 1, 0, dn);      return chm_dense_to_SEXP(chc, 1, 0, dn);
409  }  }
410    
# Line 302  Line 415 
415      CHM_DN chb = AS_CHM_DN(b_M);      CHM_DN chb = AS_CHM_DN(b_M);
416      CHM_DN chc = cholmod_allocate_dense(cha->ncol, chb->ncol, cha->ncol,      CHM_DN chc = cholmod_allocate_dense(cha->ncol, chb->ncol, cha->ncol,
417                                          chb->xtype, &c);                                          chb->xtype, &c);
418      SEXP dn = PROTECT(allocVector(VECSXP, 2));      SEXP dn = PROTECT(allocVector(VECSXP, 2)); int nprot = 2;
419      double one[] = {1,0}, zero[] = {0,0};      double one[] = {1,0}, zero[] = {0,0};
420      R_CheckStack();      R_CheckStack();
421        // -- see Csparse_dense_prod() above :
422        if(cha->xtype == CHOLMOD_PATTERN) {
423            SEXP da = PROTECT(nz2Csparse(a, x_double)); nprot++;
424            cha = AS_CHM_SP(da);
425        }
426      cholmod_sdmult(cha, 1, one, zero, chb, chc, &c);      cholmod_sdmult(cha, 1, one, zero, chb, chc, &c);
427      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
428                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 1)));                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 1)));
429      SET_VECTOR_ELT(dn, 1,      SET_VECTOR_ELT(dn, 1,
430                     duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));                     duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));
431      UNPROTECT(2);      UNPROTECT(nprot);
432      return chm_dense_to_SEXP(chc, 1, 0, dn);      return chm_dense_to_SEXP(chc, 1, 0, dn);
433  }  }
434    
# Line 321  Line 438 
438  {  {
439      int trip = asLogical(triplet),      int trip = asLogical(triplet),
440          tr   = asLogical(trans); /* gets reversed because _aat is tcrossprod */          tr   = asLogical(trans); /* gets reversed because _aat is tcrossprod */
441    #ifdef AS_CHM_DIAGU2N_FIXED_FINALLY
442      CHM_TR cht = trip ? AS_CHM_TR(x) : (CHM_TR) NULL;      CHM_TR cht = trip ? AS_CHM_TR(x) : (CHM_TR) NULL;
443    #else /* workaround needed:*/
444        SEXP xx = PROTECT(Tsparse_diagU2N(x));
445        CHM_TR cht = trip ? AS_CHM_TR__(xx) : (CHM_TR) NULL;
446    #endif
447      CHM_SP chcp, chxt,      CHM_SP chcp, chxt,
448          chx = (trip ?          chx = (trip ?
449                 cholmod_triplet_to_sparse(cht, cht->nnz, &c) :                 cholmod_triplet_to_sparse(cht, cht->nnz, &c) :
# Line 343  Line 465 
465                     duplicate(VECTOR_ELT(GET_SLOT(x, Matrix_DimNamesSym),                     duplicate(VECTOR_ELT(GET_SLOT(x, Matrix_DimNamesSym),
466                                          (tr) ? 0 : 1)));                                          (tr) ? 0 : 1)));
467      SET_VECTOR_ELT(dn, 1, duplicate(VECTOR_ELT(dn, 0)));      SET_VECTOR_ELT(dn, 1, duplicate(VECTOR_ELT(dn, 0)));
468    #ifdef AS_CHM_DIAGU2N_FIXED_FINALLY
469      UNPROTECT(1);      UNPROTECT(1);
470    #else
471        UNPROTECT(2);
472    #endif
473      return chm_sparse_to_SEXP(chcp, 1, 0, 0, "", dn);      return chm_sparse_to_SEXP(chcp, 1, 0, 0, "", dn);
474  }  }
475    
476    /* Csparse_drop(x, tol):  drop entries with absolute value < tol, i.e,
477    *  at least all "explicit" zeros */
478  SEXP Csparse_drop(SEXP x, SEXP tol)  SEXP Csparse_drop(SEXP x, SEXP tol)
479  {  {
480      const char *cl = class_P(x);      const char *cl = class_P(x);
# Line 369  Line 497 
497  SEXP Csparse_horzcat(SEXP x, SEXP y)  SEXP Csparse_horzcat(SEXP x, SEXP y)
498  {  {
499      CHM_SP chx = AS_CHM_SP__(x), chy = AS_CHM_SP__(y);      CHM_SP chx = AS_CHM_SP__(x), chy = AS_CHM_SP__(y);
500      int Rkind = 0; /* only for "d" - FIXME */      int Rk_x = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0,
501            Rk_y = (chy->xtype != CHOLMOD_PATTERN) ? Real_kind(y) : 0,
502            Rkind = /* logical if both x and y are */ (Rk_x == 1 && Rk_y == 1) ? 1 : 0;
503      R_CheckStack();      R_CheckStack();
504    
505      /* FIXME: currently drops dimnames */      /* TODO: currently drops dimnames - and we fix at R level */
506      return chm_sparse_to_SEXP(cholmod_horzcat(chx, chy, 1, &c),      return chm_sparse_to_SEXP(cholmod_horzcat(chx, chy, 1, &c),
507                                1, 0, Rkind, "", R_NilValue);                                1, 0, Rkind, "", R_NilValue);
508  }  }
# Line 380  Line 510 
510  SEXP Csparse_vertcat(SEXP x, SEXP y)  SEXP Csparse_vertcat(SEXP x, SEXP y)
511  {  {
512      CHM_SP chx = AS_CHM_SP__(x), chy = AS_CHM_SP__(y);      CHM_SP chx = AS_CHM_SP__(x), chy = AS_CHM_SP__(y);
513      int Rkind = 0; /* only for "d" - FIXME */      int Rk_x = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0,
514            Rk_y = (chy->xtype != CHOLMOD_PATTERN) ? Real_kind(y) : 0,
515            Rkind = /* logical if both x and y are */ (Rk_x == 1 && Rk_y == 1) ? 1 : 0;
516      R_CheckStack();      R_CheckStack();
517    
518      /* FIXME: currently drops dimnames */      /* TODO: currently drops dimnames - and we fix at R level */
519      return chm_sparse_to_SEXP(cholmod_vertcat(chx, chy, 1, &c),      return chm_sparse_to_SEXP(cholmod_vertcat(chx, chy, 1, &c),
520                                1, 0, Rkind, "", R_NilValue);                                1, 0, Rkind, "", R_NilValue);
521  }  }
# Line 447  Line 579 
579      }      }
580  }  }
581    
582    /**
583     * "Indexing" aka subsetting : Compute  x[i,j], also for vectors i and j
584     * Working via CHOLMOD_submatrix, see ./CHOLMOD/MatrixOps/cholmod_submatrix.c
585     * @param x CsparseMatrix
586     * @param i row     indices (0-origin), or NULL (R's)
587     * @param j columns indices (0-origin), or NULL
588     *
589     * @return x[i,j]  still CsparseMatrix --- currently, this loses dimnames
590     */
591  SEXP Csparse_submatrix(SEXP x, SEXP i, SEXP j)  SEXP Csparse_submatrix(SEXP x, SEXP i, SEXP j)
592  {  {
593      CHM_SP chx = AS_CHM_SP__(x);      CHM_SP chx = AS_CHM_SP(x); /* << does diagU2N() when needed */
594      int rsize = (isNull(i)) ? -1 : LENGTH(i),      int rsize = (isNull(i)) ? -1 : LENGTH(i),
595          csize = (isNull(j)) ? -1 : LENGTH(j);          csize = (isNull(j)) ? -1 : LENGTH(j);
596      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
# Line 460  Line 601 
601      if (csize >= 0 && !isInteger(j))      if (csize >= 0 && !isInteger(j))
602          error(_("Index j must be NULL or integer"));          error(_("Index j must be NULL or integer"));
603    
604      return chm_sparse_to_SEXP(cholmod_submatrix(chx, INTEGER(i), rsize,      if (chx->stype) /* symmetricMatrix */
605                                                  INTEGER(j), csize,          /* for now, cholmod_submatrix() only accepts "generalMatrix" */
606            chx = cholmod_copy(chx, /* stype: */ 0, chx->xtype, &c);
607    
608        return chm_sparse_to_SEXP(cholmod_submatrix(chx,
609                                    (rsize < 0) ? NULL : INTEGER(i), rsize,
610                                    (csize < 0) ? NULL : INTEGER(j), csize,
611                                                  TRUE, TRUE, &c),                                                  TRUE, TRUE, &c),
612                                1, 0, Rkind, "",                                1, 0, Rkind, "",
613                                /* FIXME: drops dimnames */ R_NilValue);                                /* FIXME: drops dimnames */ R_NilValue);
614  }  }
615    
616    #define _d_Csp_
617    #include "t_Csparse_subassign.c"
618    
619    #define _l_Csp_
620    #include "t_Csparse_subassign.c"
621    
622    #define _i_Csp_
623    #include "t_Csparse_subassign.c"
624    
625    #define _n_Csp_
626    #include "t_Csparse_subassign.c"
627    
628    #define _z_Csp_
629    #include "t_Csparse_subassign.c"
630    
631    
632    
633  SEXP Csparse_MatrixMarket(SEXP x, SEXP fname)  SEXP Csparse_MatrixMarket(SEXP x, SEXP fname)
634  {  {
635      FILE *f = fopen(CHAR(asChar(fname)), "w");      FILE *f = fopen(CHAR(asChar(fname)), "w");
# Line 558  Line 721 
721          break;          break;
722    
723      default: /* -1 from above */      default: /* -1 from above */
724          error("diag_tC(): invalid 'resultKind'");          error(_("diag_tC(): invalid 'resultKind'"));
725          /* Wall: */ ans = R_NilValue; v = REAL(ans);          /* Wall: */ ans = R_NilValue; v = REAL(ans);
726      }      }
727    
# Line 588  Line 751 
751    
752      return diag_tC_ptr(n, x_p, x_x, perm, resultKind);      return diag_tC_ptr(n, x_p, x_x, perm, resultKind);
753  }  }
754    
755    /**
756     * Create a Csparse matrix object from indices and/or pointers.
757     *
758     * @param cls name of actual class of object to create
759     * @param i optional integer vector of length nnz of row indices
760     * @param j optional integer vector of length nnz of column indices
761     * @param p optional integer vector of length np of row or column pointers
762     * @param np length of integer vector p.  Must be zero if p == (int*)NULL
763     * @param x optional vector of values
764     * @param nnz length of vectors i, j and/or x, whichever is to be used
765     * @param dims optional integer vector of length 2 to be used as
766     *     dimensions.  If dims == (int*)NULL then the maximum row and column
767     *     index are used as the dimensions.
768     * @param dimnames optional list of length 2 to be used as dimnames
769     * @param index1 indicator of 1-based indices
770     *
771     * @return an SEXP of class cls inheriting from CsparseMatrix.
772     */
773    SEXP create_Csparse(char* cls, int* i, int* j, int* p, int np,
774                        void* x, int nnz, int* dims, SEXP dimnames,
775                        int index1)
776    {
777        SEXP ans;
778        int *ij = (int*)NULL, *tri, *trj,
779            mi, mj, mp, nrow = -1, ncol = -1;
780        int xtype = -1;             /* -Wall */
781        CHM_TR T;
782        CHM_SP A;
783    
784        if (np < 0 || nnz < 0)
785            error(_("negative vector lengths not allowed: np = %d, nnz = %d"),
786                  np, nnz);
787        if (1 != ((mi = (i == (int*)NULL)) +
788                  (mj = (j == (int*)NULL)) +
789                  (mp = (p == (int*)NULL))))
790            error(_("exactly 1 of 'i', 'j' or 'p' must be NULL"));
791        if (mp) {
792            if (np) error(_("np = %d, must be zero when p is NULL"), np);
793        } else {
794            if (np) {               /* Expand p to form i or j */
795                if (!(p[0])) error(_("p[0] = %d, should be zero"), p[0]);
796                for (int ii = 0; ii < np; ii++)
797                    if (p[ii] > p[ii + 1])
798                        error(_("p must be non-decreasing"));
799                if (p[np] != nnz)
800                    error("p[np] = %d != nnz = %d", p[np], nnz);
801                ij = Calloc(nnz, int);
802                if (mi) {
803                    i = ij;
804                    nrow = np;
805                } else {
806                    j = ij;
807                    ncol = np;
808                }
809                /* Expand p to 0-based indices */
810                for (int ii = 0; ii < np; ii++)
811                    for (int jj = p[ii]; jj < p[ii + 1]; jj++) ij[jj] = ii;
812            } else {
813                if (nnz)
814                    error(_("Inconsistent dimensions: np = 0 and nnz = %d"),
815                          nnz);
816            }
817        }
818        /* calculate nrow and ncol */
819        if (nrow < 0) {
820            for (int ii = 0; ii < nnz; ii++) {
821                int i1 = i[ii] + (index1 ? 0 : 1); /* 1-based index */
822                if (i1 < 1) error(_("invalid row index at position %d"), ii);
823                if (i1 > nrow) nrow = i1;
824            }
825        }
826        if (ncol < 0) {
827            for (int jj = 0; jj < nnz; jj++) {
828                int j1 = j[jj] + (index1 ? 0 : 1);
829                if (j1 < 1) error(_("invalid column index at position %d"), jj);
830                if (j1 > ncol) ncol = j1;
831            }
832        }
833        if (dims != (int*)NULL) {
834            if (dims[0] > nrow) nrow = dims[0];
835            if (dims[1] > ncol) ncol = dims[1];
836        }
837        /* check the class name */
838        if (strlen(cls) != 8)
839            error(_("strlen of cls argument = %d, should be 8"), strlen(cls));
840        if (!strcmp(cls + 2, "CMatrix"))
841            error(_("cls = \"%s\" does not end in \"CMatrix\""), cls);
842        switch(cls[0]) {
843        case 'd':
844        case 'l':
845            xtype = CHOLMOD_REAL;
846        break;
847        case 'n':
848            xtype = CHOLMOD_PATTERN;
849            break;
850        default:
851            error(_("cls = \"%s\" must begin with 'd', 'l' or 'n'"), cls);
852        }
853        if (cls[1] != 'g')
854            error(_("Only 'g'eneral sparse matrix types allowed"));
855        /* allocate and populate the triplet */
856        T = cholmod_allocate_triplet((size_t)nrow, (size_t)ncol, (size_t)nnz, 0,
857                                     xtype, &c);
858        T->x = x;
859        tri = (int*)T->i;
860        trj = (int*)T->j;
861        for (int ii = 0; ii < nnz; ii++) {
862            tri[ii] = i[ii] - ((!mi && index1) ? 1 : 0);
863            trj[ii] = j[ii] - ((!mj && index1) ? 1 : 0);
864        }
865        /* create the cholmod_sparse structure */
866        A = cholmod_triplet_to_sparse(T, nnz, &c);
867        cholmod_free_triplet(&T, &c);
868        /* copy the information to the SEXP */
869        ans = PROTECT(NEW_OBJECT(MAKE_CLASS(cls)));
870    /* FIXME: This has been copied from chm_sparse_to_SEXP in chm_common.c */
871        /* allocate and copy common slots */
872        nnz = cholmod_nnz(A, &c);
873        dims = INTEGER(ALLOC_SLOT(ans, Matrix_DimSym, INTSXP, 2));
874        dims[0] = A->nrow; dims[1] = A->ncol;
875        Memcpy(INTEGER(ALLOC_SLOT(ans, Matrix_pSym, INTSXP, A->ncol + 1)), (int*)A->p, A->ncol + 1);
876        Memcpy(INTEGER(ALLOC_SLOT(ans, Matrix_iSym, INTSXP, nnz)), (int*)A->i, nnz);
877        switch(cls[1]) {
878        case 'd':
879            Memcpy(REAL(ALLOC_SLOT(ans, Matrix_xSym, REALSXP, nnz)), (double*)A->x, nnz);
880            break;
881        case 'l':
882            error(_("code not yet written for cls = \"lgCMatrix\""));
883        }
884    /* FIXME: dimnames are *NOT* put there yet (if non-NULL) */
885        cholmod_free_sparse(&A, &c);
886        UNPROTECT(1);
887        return ans;
888    }

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