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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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revision 2646, Mon Feb 21 10:57:49 2011 UTC revision 2984, Sat Apr 12 21:37:37 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 36  Line 37 
37      return Csparse_validate_(x, FALSE);      return Csparse_validate_(x, FALSE);
38  }  }
39    
 SEXP Csparse_validate2(SEXP x, SEXP maybe_modify) {  
     return Csparse_validate_(x, asLogical(maybe_modify));  
 }  
40    
41  SEXP Csparse_validate_(SEXP x, Rboolean maybe_modify)  #define _t_Csparse_validate
42  {  #include "t_Csparse_validate.c"
     /* 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);  
43    
44      if (length(pslot) != dims[1] + 1)  #define _t_Csparse_sort
45          return mkString(_("slot p must have length = ncol(.) + 1"));  #include "t_Csparse_validate.c"
     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;  
             }  
     }  
     if (!sorted) {  
         if(maybe_modify) {  
             CHM_SP chx = (CHM_SP) alloca(sizeof(cholmod_sparse));  
             R_CheckStack();  
             as_cholmod_sparse(chx, x, FALSE, TRUE);/*-> cholmod_l_sort() ! */  
             /* as chx = AS_CHM_SP__(x)  but  ^^^^ sorting x in_place !!! */  
46    
47              /* Now re-check that row indices are *strictly* increasing  // R: .validateCsparse(x, sort.if.needed = FALSE) :
48               * (and not just increasing) within each column : */  SEXP Csparse_validate2(SEXP x, SEXP maybe_modify) {
49              for (j = 0; j < ncol; j++) {      return Csparse_validate_(x, asLogical(maybe_modify));
                 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_l_sort)"));  
             }  
         } else { /* no modifying sorting : */  
             return mkString(_("row indices are not sorted within columns"));  
         }  
     } else if(!strictly) {  /* sorted, but not strictly */  
         return mkString(_("slot i is not *strictly* increasing inside a column"));  
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 136  Line 93 
93              }              }
94      }      }
95      if (!sorted)      if (!sorted)
96          /* cannot easily use cholmod_l_sort(.) ... -> "error out" :*/          /* cannot easily use cholmod_sort(.) ... -> "error out" :*/
97          return mkString(_("slot j is not increasing inside a column"));          return mkString(_("slot j is not increasing inside a column"));
98      else if(!strictly) /* sorted, but not strictly */      else if(!strictly) /* sorted, but not strictly */
99          return mkString(_("slot j is not *strictly* increasing inside a column"));          return mkString(_("slot j is not *strictly* increasing inside a column"));
# Line 154  Line 111 
111      /* This loses the symmetry property, since cholmod_dense has none,      /* This loses the symmetry property, since cholmod_dense has none,
112       * BUT, much worse (FIXME!), it also transforms CHOLMOD_PATTERN ("n") matrices       * BUT, much worse (FIXME!), it also transforms CHOLMOD_PATTERN ("n") matrices
113       * to numeric (CHOLMOD_REAL) ones : */       * to numeric (CHOLMOD_REAL) ones : */
114      CHM_DN chxd = cholmod_l_sparse_to_dense(chxs, &c);      CHM_DN chxd = cholmod_sparse_to_dense(chxs, &c);
115      int Rkind = (chxs->xtype == CHOLMOD_PATTERN)? -1 : Real_kind(x);      int Rkind = (chxs->xtype == CHOLMOD_PATTERN)? -1 : Real_kind(x);
116      R_CheckStack();      R_CheckStack();
117    
# Line 165  Line 122 
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);
125      CHM_SP chxcp = cholmod_l_copy(chxs, chxs->stype, CHOLMOD_PATTERN, &c);      CHM_SP chxcp = cholmod_copy(chxs, chxs->stype, CHOLMOD_PATTERN, &c);
126      int tr = asLogical(tri);      int tr = asLogical(tri);
127      R_CheckStack();      R_CheckStack();
128    
# Line 188  Line 145 
145      if(cl_x[2] != 'C') error(_("not a CsparseMatrix"));      if(cl_x[2] != 'C') error(_("not a CsparseMatrix"));
146      int nnz = LENGTH(GET_SLOT(x, Matrix_iSym));      int nnz = LENGTH(GET_SLOT(x, Matrix_iSym));
147      SEXP ans;      SEXP ans;
148      char *ncl = strdup(cl_x);      char *ncl = alloca(strlen(cl_x) + 1); /* not much memory required */
149        strcpy(ncl, cl_x);
150      double *dx_x; int *ix_x;      double *dx_x; int *ix_x;
151      ncl[0] = (r_kind == x_double ? 'd' :      ncl[0] = (r_kind == x_double ? 'd' :
152                (r_kind == x_logical ? 'l' :                (r_kind == x_logical ? 'l' :
# Line 228  Line 186 
186      return ans;      return ans;
187  }  }
188    
189  SEXP Csparse_to_matrix(SEXP x)  SEXP Csparse_to_matrix(SEXP x, SEXP chk)
190  {  {
191      return chm_dense_to_matrix(cholmod_l_sparse_to_dense(AS_CHM_SP__(x), &c),      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  {  {
201      CHM_SP chxs = AS_CHM_SP__(x);      CHM_SP chxs = AS_CHM_SP__(x);
202      CHM_TR chxt = cholmod_l_sparse_to_triplet(chxs, &c);      CHM_TR chxt = cholmod_sparse_to_triplet(chxs, &c);
203      int tr = asLogical(tri);      int tr = asLogical(tri);
204      int Rkind = (chxs->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chxs->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
205      R_CheckStack();      R_CheckStack();
# Line 257  Line 219 
219    
220      if (!(chx->stype))      if (!(chx->stype))
221          error(_("Nonsymmetric matrix in Csparse_symmetric_to_general"));          error(_("Nonsymmetric matrix in Csparse_symmetric_to_general"));
222      chgx = cholmod_l_copy(chx, /* stype: */ 0, chx->xtype, &c);      chgx = cholmod_copy(chx, /* stype: */ 0, chx->xtype, &c);
223      /* xtype: pattern, "real", complex or .. */      /* xtype: pattern, "real", complex or .. */
224      return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",      return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",
225                                GET_SLOT(x, Matrix_DimNamesSym));                                GET_SLOT(x, Matrix_DimNamesSym));
# Line 265  Line 227 
227    
228  SEXP Csparse_general_to_symmetric(SEXP x, SEXP uplo)  SEXP Csparse_general_to_symmetric(SEXP x, SEXP uplo)
229  {  {
230        int *adims = INTEGER(GET_SLOT(x, Matrix_DimSym)), n = adims[0];
231        if(n != adims[1]) {
232            error(_("Csparse_general_to_symmetric(): matrix is not square!"));
233            return R_NilValue; /* -Wall */
234        }
235      CHM_SP chx = AS_CHM_SP__(x), chgx;      CHM_SP chx = AS_CHM_SP__(x), chgx;
236      int uploT = (*CHAR(STRING_ELT(uplo,0)) == 'U') ? 1 : -1;      int uploT = (*CHAR(STRING_ELT(uplo,0)) == 'U') ? 1 : -1;
237      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
238      R_CheckStack();      R_CheckStack();
239        chgx = cholmod_copy(chx, /* stype: */ uploT, chx->xtype, &c);
     chgx = cholmod_l_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, "",
242                                GET_SLOT(x, Matrix_DimNamesSym));                                GET_SLOT(x, Matrix_DimNamesSym));
# Line 282  Line 248 
248       *       since cholmod (& cs) lacks sparse 'int' matrices */       *       since cholmod (& cs) lacks sparse 'int' matrices */
249      CHM_SP chx = AS_CHM_SP__(x);      CHM_SP chx = AS_CHM_SP__(x);
250      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
251      CHM_SP chxt = cholmod_l_transpose(chx, chx->xtype, &c);      CHM_SP chxt = cholmod_transpose(chx, chx->xtype, &c);
252      SEXP dn = PROTECT(duplicate(GET_SLOT(x, Matrix_DimNamesSym))), tmp;      SEXP dn = PROTECT(duplicate(GET_SLOT(x, Matrix_DimNamesSym))), tmp;
253      int tr = asLogical(tri);      int tr = asLogical(tri);
254      R_CheckStack();      R_CheckStack();
# Line 301  Line 267 
267      CHM_SP      CHM_SP
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_l_ssmult(cha, chb, /*out_stype:*/ 0,          chc = cholmod_ssmult(cha, chb, /*out_stype:*/ 0,
271                                 /* values:= is_numeric (T/F) */ cha->xtype > 0,                                 /* values:= is_numeric (T/F) */ cha->xtype > 0,
272                                 /*out sorted:*/ 1, &c);                                 /*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);
# Line 352  Line 318 
318      SEXP dn = PROTECT(allocVector(VECSXP, 2));      SEXP dn = PROTECT(allocVector(VECSXP, 2));
319      R_CheckStack();      R_CheckStack();
320    
321      chTr = cholmod_l_transpose((tr) ? chb : cha, chb->xtype, &c);      chTr = cholmod_transpose((tr) ? chb : cha, chb->xtype, &c);
322      chc = cholmod_l_ssmult((tr) ? cha : chTr, (tr) ? chTr : chb,      chc = cholmod_ssmult((tr) ? cha : chTr, (tr) ? chTr : chb,
323                           /*out_stype:*/ 0, cha->xtype, /*out sorted:*/ 1, &c);                           /*out_stype:*/ 0, cha->xtype, /*out sorted:*/ 1, &c);
324      cholmod_l_free_sparse(&chTr, &c);      cholmod_free_sparse(&chTr, &c);
325    
326      /* Preserve triangularity and unit-triangularity if appropriate;      /* Preserve triangularity and unit-triangularity if appropriate;
327       * see Csparse_Csparse_prod() for comments */       * see Csparse_Csparse_prod() for comments */
# Line 381  Line 347 
347      CHM_SP cha = AS_CHM_SP(a);      CHM_SP cha = AS_CHM_SP(a);
348      SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));      SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));
349      CHM_DN chb = AS_CHM_DN(b_M);      CHM_DN chb = AS_CHM_DN(b_M);
350      CHM_DN chc = cholmod_l_allocate_dense(cha->nrow, chb->ncol, cha->nrow,      CHM_DN chc = cholmod_allocate_dense(cha->nrow, chb->ncol, cha->nrow,
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};
# Line 398  Line 364 
364          SEXP da = PROTECT(nz2Csparse(a, x_double)); nprot++;          SEXP da = PROTECT(nz2Csparse(a, x_double)); nprot++;
365          cha = AS_CHM_SP(da);          cha = AS_CHM_SP(da);
366      }      }
367      cholmod_l_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,
# Line 412  Line 378 
378      CHM_SP cha = AS_CHM_SP(a);      CHM_SP cha = AS_CHM_SP(a);
379      SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));      SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));
380      CHM_DN chb = AS_CHM_DN(b_M);      CHM_DN chb = AS_CHM_DN(b_M);
381      CHM_DN chc = cholmod_l_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)); int nprot = 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};
# Line 422  Line 388 
388          SEXP da = PROTECT(nz2Csparse(a, x_double)); nprot++;          SEXP da = PROTECT(nz2Csparse(a, x_double)); nprot++;
389          cha = AS_CHM_SP(da);          cha = AS_CHM_SP(da);
390      }      }
391      cholmod_l_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,
# Line 445  Line 411 
411  #endif  #endif
412      CHM_SP chcp, chxt,      CHM_SP chcp, chxt,
413          chx = (trip ?          chx = (trip ?
414                 cholmod_l_triplet_to_sparse(cht, cht->nnz, &c) :                 cholmod_triplet_to_sparse(cht, cht->nnz, &c) :
415                 AS_CHM_SP(x));                 AS_CHM_SP(x));
416      SEXP dn = PROTECT(allocVector(VECSXP, 2));      SEXP dn = PROTECT(allocVector(VECSXP, 2));
417      R_CheckStack();      R_CheckStack();
418    
419      if (!tr) chxt = cholmod_l_transpose(chx, chx->xtype, &c);      if (!tr) chxt = cholmod_transpose(chx, chx->xtype, &c);
420      chcp = cholmod_l_aat((!tr) ? chxt : chx, (int *) NULL, 0, chx->xtype, &c);      chcp = cholmod_aat((!tr) ? chxt : chx, (int *) NULL, 0, chx->xtype, &c);
421      if(!chcp) {      if(!chcp) {
422          UNPROTECT(1);          UNPROTECT(1);
423          error(_("Csparse_crossprod(): error return from cholmod_l_aat()"));          error(_("Csparse_crossprod(): error return from cholmod_aat()"));
424      }      }
425      cholmod_l_band_inplace(0, chcp->ncol, chcp->xtype, chcp, &c);      cholmod_band_inplace(0, chcp->ncol, chcp->xtype, chcp, &c);
426      chcp->stype = 1;      chcp->stype = 1;
427      if (trip) cholmod_l_free_sparse(&chx, &c);      if (trip) cholmod_free_sparse(&chx, &c);
428      if (!tr) cholmod_l_free_sparse(&chxt, &c);      if (!tr) cholmod_free_sparse(&chxt, &c);
429      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
430                     duplicate(VECTOR_ELT(GET_SLOT(x, Matrix_DimNamesSym),                     duplicate(VECTOR_ELT(GET_SLOT(x, Matrix_DimNamesSym),
431                                          (tr) ? 0 : 1)));                                          (tr) ? 0 : 1)));
# Line 480  Line 446 
446      /* dtCMatrix, etc; [1] = the second character =?= 't' for triangular */      /* dtCMatrix, etc; [1] = the second character =?= 't' for triangular */
447      int tr = (cl[1] == 't');      int tr = (cl[1] == 't');
448      CHM_SP chx = AS_CHM_SP__(x);      CHM_SP chx = AS_CHM_SP__(x);
449      CHM_SP ans = cholmod_l_copy(chx, chx->stype, chx->xtype, &c);      CHM_SP ans = cholmod_copy(chx, chx->stype, chx->xtype, &c);
450      double dtol = asReal(tol);      double dtol = asReal(tol);
451      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
452      R_CheckStack();      R_CheckStack();
453    
454      if(!cholmod_l_drop(dtol, ans, &c))      if(!cholmod_drop(dtol, ans, &c))
455          error(_("cholmod_l_drop() failed"));          error(_("cholmod_drop() failed"));
456      return chm_sparse_to_SEXP(ans, 1,      return chm_sparse_to_SEXP(ans, 1,
457                                tr ? ((*uplo_P(x) == 'U') ? 1 : -1) : 0,                                tr ? ((*uplo_P(x) == 'U') ? 1 : -1) : 0,
458                                Rkind, tr ? diag_P(x) : "",                                Rkind, tr ? diag_P(x) : "",
# Line 502  Line 468 
468      R_CheckStack();      R_CheckStack();
469    
470      /* TODO: currently drops dimnames - and we fix at R level */      /* TODO: currently drops dimnames - and we fix at R level */
471      return chm_sparse_to_SEXP(cholmod_l_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  }  }
474    
# Line 515  Line 481 
481      R_CheckStack();      R_CheckStack();
482    
483      /* TODO: currently drops dimnames - and we fix at R level */      /* TODO: currently drops dimnames - and we fix at R level */
484      return chm_sparse_to_SEXP(cholmod_l_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  }  }
487    
# Line 523  Line 489 
489  {  {
490      CHM_SP chx = AS_CHM_SP__(x);      CHM_SP chx = AS_CHM_SP__(x);
491      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
492      CHM_SP ans = cholmod_l_band(chx, asInteger(k1), asInteger(k2), chx->xtype, &c);      CHM_SP ans = cholmod_band(chx, asInteger(k1), asInteger(k2), chx->xtype, &c);
493      R_CheckStack();      R_CheckStack();
494    
495      return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "",      return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "",
# Line 541  Line 507 
507      }      }
508      else { /* unit triangular (diag='U'): "fill the diagonal" & diag:= "N" */      else { /* unit triangular (diag='U'): "fill the diagonal" & diag:= "N" */
509          CHM_SP chx = AS_CHM_SP__(x);          CHM_SP chx = AS_CHM_SP__(x);
510          CHM_SP eye = cholmod_l_speye(chx->nrow, chx->ncol, chx->xtype, &c);          CHM_SP eye = cholmod_speye(chx->nrow, chx->ncol, chx->xtype, &c);
511          double one[] = {1, 0};          double one[] = {1, 0};
512          CHM_SP ans = cholmod_l_add(chx, eye, one, one, TRUE, TRUE, &c);          CHM_SP ans = cholmod_add(chx, eye, one, one, TRUE, TRUE, &c);
513          int uploT = (*uplo_P(x) == 'U') ? 1 : -1;          int uploT = (*uplo_P(x) == 'U') ? 1 : -1;
514          int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;          int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
515    
516          R_CheckStack();          R_CheckStack();
517          cholmod_l_free_sparse(&eye, &c);          cholmod_free_sparse(&eye, &c);
518          return chm_sparse_to_SEXP(ans, 1, uploT, Rkind, "N",          return chm_sparse_to_SEXP(ans, 1, uploT, Rkind, "N",
519                                    GET_SLOT(x, Matrix_DimNamesSym));                                    GET_SLOT(x, Matrix_DimNamesSym));
520      }      }
# Line 565  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    
# Line 600  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      if (chx->stype) /* symmetricMatrix */      if (!chx->stype) {/* non-symmetric Matrix */
573          /* for now, cholmod_submatrix() only accepts "generalMatrix" */          return chm_sparse_to_SEXP(cholmod_submatrix(chx,
         chx = cholmod_l_copy(chx, /* stype: */ 0, chx->xtype, &c);  
   
     return chm_sparse_to_SEXP(cholmod_l_submatrix(chx,  
574                                  (rsize < 0) ? NULL : INTEGER(i), rsize,                                  (rsize < 0) ? NULL : INTEGER(i), rsize,
575                                  (csize < 0) ? NULL : INTEGER(j), csize,                                  (csize < 0) ? NULL : INTEGER(j), csize,
576                                                    TRUE, TRUE, &c),                                                    TRUE, TRUE, &c),
577                                1, 0, Rkind, "",                                1, 0, Rkind, "",
578                                /* FIXME: drops dimnames */ R_NilValue);                                /* FIXME: drops dimnames */ R_NilValue);
579  }  }
580                                    /* for now, cholmod_submatrix() only accepts "generalMatrix" */
581        CHM_SP tmp = cholmod_copy(chx, /* stype: */ 0, chx->xtype, &c);
582        CHM_SP ans = cholmod_submatrix(tmp,
583                                       (rsize < 0) ? NULL : INTEGER(i), rsize,
584                                       (csize < 0) ? NULL : INTEGER(j), csize,
585                                       TRUE, TRUE, &c);
586        cholmod_free_sparse(&tmp, &c);
587        return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "", R_NilValue);
588    }
589    
590    #define _d_Csp_
591    #include "t_Csparse_subassign.c"
592    
593    #define _l_Csp_
594    #include "t_Csparse_subassign.c"
595    
596    #define _i_Csp_
597    #include "t_Csparse_subassign.c"
598    
599    #define _n_Csp_
600    #include "t_Csparse_subassign.c"
601    
602    #define _z_Csp_
603    #include "t_Csparse_subassign.c"
604    
605    
606    
607  SEXP Csparse_MatrixMarket(SEXP x, SEXP fname)  SEXP Csparse_MatrixMarket(SEXP x, SEXP fname)
608  {  {
# Line 619  Line 611 
611      if (!f)      if (!f)
612          error(_("failure to open file \"%s\" for writing"),          error(_("failure to open file \"%s\" for writing"),
613                CHAR(asChar(fname)));                CHAR(asChar(fname)));
614      if (!cholmod_l_write_sparse(f, AS_CHM_SP(x),      if (!cholmod_write_sparse(f, AS_CHM_SP(x),
615                                (CHM_SP)NULL, (char*) NULL, &c))                                (CHM_SP)NULL, (char*) NULL, &c))
616          error(_("cholmod_l_write_sparse returned error code"));          error(_("cholmod_write_sparse returned error code"));
617      fclose(f);      fclose(f);
618      return R_NilValue;      return R_NilValue;
619  }  }
# Line 639  Line 631 
631   *   *
632   * @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
633   */   */
634  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,
635  /*                                ^^^^^^ FIXME[Generalize] to int / ... */  /*                                ^^^^^^ FIXME[Generalize] to int / ... */
636                     SEXP resultKind)
637  {  {
638      const char* res_ch = CHAR(STRING_ELT(resultKind,0));      const char* res_ch = CHAR(STRING_ELT(resultKind,0));
639      enum diag_kind { diag, diag_backpermuted, trace, prod, sum_log      enum diag_kind { diag, diag_backpermuted, trace, prod, sum_log, min, max, range
640      } res_kind = ((!strcmp(res_ch, "trace")) ? trace :      } res_kind = ((!strcmp(res_ch, "trace")) ? trace :
641                    ((!strcmp(res_ch, "sumLog")) ? sum_log :                    ((!strcmp(res_ch, "sumLog")) ? sum_log :
642                     ((!strcmp(res_ch, "prod")) ? prod :                     ((!strcmp(res_ch, "prod")) ? prod :
643                        ((!strcmp(res_ch, "min")) ? min :
644                         ((!strcmp(res_ch, "max")) ? max :
645                          ((!strcmp(res_ch, "range")) ? range :
646                      ((!strcmp(res_ch, "diag")) ? diag :                      ((!strcmp(res_ch, "diag")) ? diag :
647                       ((!strcmp(res_ch, "diagBack")) ? diag_backpermuted :                       ((!strcmp(res_ch, "diagBack")) ? diag_backpermuted :
648                        -1)))));                           -1))))))));
649      int i, n_x, i_from = 0;      int i, n_x, i_from;
650      SEXP ans = PROTECT(allocVector(REALSXP,      SEXP ans = PROTECT(allocVector(REALSXP,
651  /*                                 ^^^^  FIXME[Generalize] */  /*                                 ^^^^  FIXME[Generalize] */
652                                     (res_kind == diag ||                                     (res_kind == diag ||
653                                      res_kind == diag_backpermuted) ? n : 1));                                      res_kind == diag_backpermuted) ? n :
654                                       (res_kind == range ? 2 : 1)));
655      double *v = REAL(ans);      double *v = REAL(ans);
656  /*  ^^^^^^      ^^^^  FIXME[Generalize] */  /*  ^^^^^^      ^^^^  FIXME[Generalize] */
657    
658        i_from = (is_U ? -1 : 0);
659    
660  #define for_DIAG(v_ASSIGN)                                              \  #define for_DIAG(v_ASSIGN)                                              \
661      for(i = 0; i < n; i++, i_from += n_x) {                             \      for(i = 0; i < n; i++) {                                    \
662          /* looking at i-th column */                                    \          /* looking at i-th column */                                    \
663          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 */ \
664            if( is_U) i_from += n_x;                                \
665          v_ASSIGN;                                                       \          v_ASSIGN;                                                       \
666            if(!is_U) i_from += n_x;                                \
667      }      }
668    
669      /* NOTA BENE: we assume  -- uplo = "L" i.e. lower triangular matrix      /* NOTA BENE: we assume  -- uplo = "L" i.e. lower triangular matrix
670       *            for uplo = "U" (makes sense with a "dtCMatrix" !),       *            for uplo = "U" (makes sense with a "dtCMatrix" !),
671       *            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],
672       *            where nx = (x_p[i+1] - x_p[i])       *            where n_x = (x_p[i+1] - x_p[i])
673       */       */
674    
675      switch(res_kind) {      switch(res_kind) {
676      case trace:      case trace: // = sum
677          v[0] = 0.;          v[0] = 0.;
678          for_DIAG(v[0] += x_x[i_from]);          for_DIAG(v[0] += x_x[i_from]);
679          break;          break;
# Line 687  Line 688 
688          for_DIAG(v[0] *= x_x[i_from]);          for_DIAG(v[0] *= x_x[i_from]);
689          break;          break;
690    
691        case min:
692            v[0] = R_PosInf;
693            for_DIAG(if(v[0] > x_x[i_from]) v[0] = x_x[i_from]);
694            break;
695    
696        case max:
697            v[0] = R_NegInf;
698            for_DIAG(if(v[0] < x_x[i_from]) v[0] = x_x[i_from]);
699            break;
700    
701        case range:
702            v[0] = R_PosInf;
703            v[1] = R_NegInf;
704            for_DIAG(if(v[0] > x_x[i_from]) v[0] = x_x[i_from];
705                     if(v[1] < x_x[i_from]) v[1] = x_x[i_from]);
706            break;
707    
708      case diag:      case diag:
709          for_DIAG(v[i] = x_x[i_from]);          for_DIAG(v[i] = x_x[i_from]);
710          break;          break;
# Line 694  Line 712 
712      case diag_backpermuted:      case diag_backpermuted:
713          for_DIAG(v[i] = x_x[i_from]);          for_DIAG(v[i] = x_x[i_from]);
714    
715          warning(_("resultKind = 'diagBack' (back-permuted) is experimental"));          warning(_("%s = '%s' (back-permuted) is experimental"),
716                    "resultKind", "diagBack");
717          /* now back_permute : */          /* now back_permute : */
718          for(i = 0; i < n; i++) {          for(i = 0; i < n; i++) {
719              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 715  Line 734 
734   * Extract the diagonal entries from *triangular* Csparse matrix  __or__ a   * Extract the diagonal entries from *triangular* Csparse matrix  __or__ a
735   * cholmod_sparse factor (LDL = TRUE).   * cholmod_sparse factor (LDL = TRUE).
736   *   *
737     * @param obj -- now a cholmod_sparse factor or a dtCMatrix
738   * @param pslot  'p' (column pointer)   slot of Csparse matrix/factor   * @param pslot  'p' (column pointer)   slot of Csparse matrix/factor
739   * @param xslot  'x' (non-zero entries) slot of Csparse matrix/factor   * @param xslot  'x' (non-zero entries) slot of Csparse matrix/factor
740   * @param perm_slot  'perm' (= permutation vector) slot of corresponding CHMfactor;   * @param perm_slot  'perm' (= permutation vector) slot of corresponding CHMfactor;
# Line 723  Line 743 
743   *   *
744   * @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
745   */   */
746  SEXP diag_tC(SEXP pslot, SEXP xslot, SEXP perm_slot, SEXP resultKind)  SEXP diag_tC(SEXP obj, SEXP resultKind)
747  {  {
748    
749        SEXP
750            pslot = GET_SLOT(obj, Matrix_pSym),
751            xslot = GET_SLOT(obj, Matrix_xSym);
752        Rboolean is_U = (R_has_slot(obj, Matrix_uploSym) &&
753                         *CHAR(asChar(GET_SLOT(obj, Matrix_uploSym))) == 'U');
754      int n = length(pslot) - 1, /* n = ncol(.) = nrow(.) */      int n = length(pslot) - 1, /* n = ncol(.) = nrow(.) */
755          *x_p  = INTEGER(pslot),          *x_p  = INTEGER(pslot), pp = -1, *perm;
         *perm = INTEGER(perm_slot);  
756      double *x_x = REAL(xslot);      double *x_x = REAL(xslot);
757  /*  ^^^^^^        ^^^^ FIXME[Generalize] to INTEGER(.) / LOGICAL(.) / ... xslot !*/  /*  ^^^^^^        ^^^^ FIXME[Generalize] to INTEGER(.) / LOGICAL(.) / ... xslot !*/
758    
759      return diag_tC_ptr(n, x_p, x_x, perm, resultKind);      if(R_has_slot(obj, Matrix_permSym))
760            perm = INTEGER(GET_SLOT(obj, Matrix_permSym));
761        else perm = &pp;
762    
763        return diag_tC_ptr(n, x_p, x_x, is_U, perm, resultKind);
764  }  }
765    
766    
767  /**  /**
768   * Create a Csparse matrix object from indices and/or pointers.   * Create a Csparse matrix object from indices and/or pointers.
769   *   *
# Line 835  Line 865 
865      if (cls[1] != 'g')      if (cls[1] != 'g')
866          error(_("Only 'g'eneral sparse matrix types allowed"));          error(_("Only 'g'eneral sparse matrix types allowed"));
867                                  /* allocate and populate the triplet */                                  /* allocate and populate the triplet */
868      T = cholmod_l_allocate_triplet((size_t)nrow, (size_t)ncol, (size_t)nnz, 0,      T = cholmod_allocate_triplet((size_t)nrow, (size_t)ncol, (size_t)nnz, 0,
869                                      xtype, &c);                                      xtype, &c);
870      T->x = x;      T->x = x;
871      tri = (int*)T->i;      tri = (int*)T->i;
# Line 845  Line 875 
875          trj[ii] = j[ii] - ((!mj && index1) ? 1 : 0);          trj[ii] = j[ii] - ((!mj && index1) ? 1 : 0);
876      }      }
877                                  /* create the cholmod_sparse structure */                                  /* create the cholmod_sparse structure */
878      A = cholmod_l_triplet_to_sparse(T, nnz, &c);      A = cholmod_triplet_to_sparse(T, nnz, &c);
879      cholmod_l_free_triplet(&T, &c);      cholmod_free_triplet(&T, &c);
880                                  /* copy the information to the SEXP */                                  /* copy the information to the SEXP */
881      ans = PROTECT(NEW_OBJECT(MAKE_CLASS(cls)));      ans = PROTECT(NEW_OBJECT(MAKE_CLASS(cls)));
882  /* FIXME: This has been copied from chm_sparse_to_SEXP in chm_common.c */  /* FIXME: This has been copied from chm_sparse_to_SEXP in chm_common.c */
883                                  /* allocate and copy common slots */                                  /* allocate and copy common slots */
884      nnz = cholmod_l_nnz(A, &c);      nnz = cholmod_nnz(A, &c);
885      dims = INTEGER(ALLOC_SLOT(ans, Matrix_DimSym, INTSXP, 2));      dims = INTEGER(ALLOC_SLOT(ans, Matrix_DimSym, INTSXP, 2));
886      dims[0] = A->nrow; dims[1] = A->ncol;      dims[0] = A->nrow; dims[1] = A->ncol;
887      Memcpy(INTEGER(ALLOC_SLOT(ans, Matrix_pSym, INTSXP, A->ncol + 1)), (int*)A->p, A->ncol + 1);      Memcpy(INTEGER(ALLOC_SLOT(ans, Matrix_pSym, INTSXP, A->ncol + 1)), (int*)A->p, A->ncol + 1);
# Line 864  Line 894 
894          error(_("code not yet written for cls = \"lgCMatrix\""));          error(_("code not yet written for cls = \"lgCMatrix\""));
895      }      }
896  /* FIXME: dimnames are *NOT* put there yet (if non-NULL) */  /* FIXME: dimnames are *NOT* put there yet (if non-NULL) */
897      cholmod_l_free_sparse(&A, &c);      cholmod_free_sparse(&A, &c);
898      UNPROTECT(1);      UNPROTECT(1);
899      return ans;      return ans;
900  }  }

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