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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 2175, Wed Apr 23 11:23:50 2008 UTC pkg/Matrix/src/Csparse.c revision 2804, Thu Jun 28 13:45:01 2012 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 109  Line 151 
151   * FIXME: replace by non-CHOLMOD code ! */   * FIXME: replace by non-CHOLMOD code ! */
152  SEXP Csparse_to_dense(SEXP x)  SEXP Csparse_to_dense(SEXP x)
153  {  {
154      CHM_SP chxs = AS_CHM_SP(x);      CHM_SP chxs = AS_CHM_SP__(x);
155      /* This loses the symmetry property, since cholmod_dense has none,      /* This loses the symmetry property, since cholmod_dense has none,
156       * BUT, much worse (FIXME!), it also transforms CHOLMOD_PATTERN ("n") matrices       * BUT, much worse (FIXME!), it also transforms CHOLMOD_PATTERN ("n") matrices
157       * to numeric (CHOLMOD_REAL) ones : */       * to numeric (CHOLMOD_REAL) ones : */
# 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);
169      CHM_SP chxcp = cholmod_copy(chxs, chxs->stype, CHOLMOD_PATTERN, &c);      CHM_SP chxcp = cholmod_copy(chxs, chxs->stype, CHOLMOD_PATTERN, &c);
170      int tr = asLogical(tri);      int tr = asLogical(tri);
171      R_CheckStack();      R_CheckStack();
# 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 = alloca(strlen(cl_x) + 1); /* not much memory required */
193        strcpy(ncl, cl_x);
194        double *dx_x; int *ix_x;
195        ncl[0] = (r_kind == x_double ? 'd' :
196                  (r_kind == x_logical ? 'l' :
197                   /* else (for now):  r_kind == x_integer : */ 'i'));
198        PROTECT(ans = NEW_OBJECT(MAKE_CLASS(ncl)));
199        // create a correct 'x' slot:
200        switch(r_kind) {
201            int i;
202        case x_double: // 'd'
203            dx_x = REAL(ALLOC_SLOT(ans, Matrix_xSym, REALSXP, nnz));
204            for (i=0; i < nnz; i++) dx_x[i] = 1.;
205            break;
206        case x_logical: // 'l'
207            ix_x = LOGICAL(ALLOC_SLOT(ans, Matrix_xSym, LGLSXP, nnz));
208            for (i=0; i < nnz; i++) ix_x[i] = TRUE;
209            break;
210        case x_integer: // 'i'
211            ix_x = INTEGER(ALLOC_SLOT(ans, Matrix_xSym, INTSXP, nnz));
212            for (i=0; i < nnz; i++) ix_x[i] = 1;
213            break;
214    
215        default:
216            error(_("nz2Csparse(): invalid/non-implemented r_kind = %d"),
217                  r_kind);
218        }
219    
220        // now copy all other slots :
221        slot_dup(ans, x, Matrix_iSym);
222        slot_dup(ans, x, Matrix_pSym);
223        slot_dup(ans, x, Matrix_DimSym);
224        slot_dup(ans, x, Matrix_DimNamesSym);
225        if(ncl[1] != 'g') { // symmetric or triangular ...
226            slot_dup_if_has(ans, x, Matrix_uploSym);
227            slot_dup_if_has(ans, x, Matrix_diagSym);
228        }
229        UNPROTECT(1);
230        return ans;
231    }
232    
233  SEXP Csparse_to_matrix(SEXP x)  SEXP Csparse_to_matrix(SEXP x)
234  {  {
235      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),
236                                 1 /*do_free*/, GET_SLOT(x, Matrix_DimNamesSym));                                 1 /*do_free*/, GET_SLOT(x, Matrix_DimNamesSym));
237  }  }
238    
239  SEXP Csparse_to_Tsparse(SEXP x, SEXP tri)  SEXP Csparse_to_Tsparse(SEXP x, SEXP tri)
240  {  {
241      CHM_SP chxs = AS_CHM_SP(x);      CHM_SP chxs = AS_CHM_SP__(x);
242      CHM_TR chxt = cholmod_sparse_to_triplet(chxs, &c);      CHM_TR chxt = cholmod_sparse_to_triplet(chxs, &c);
243      int tr = asLogical(tri);      int tr = asLogical(tri);
244      int Rkind = (chxs->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chxs->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
# Line 156  Line 253 
253  /* this used to be called  sCMatrix_to_gCMatrix(..)   [in ./dsCMatrix.c ]: */  /* this used to be called  sCMatrix_to_gCMatrix(..)   [in ./dsCMatrix.c ]: */
254  SEXP Csparse_symmetric_to_general(SEXP x)  SEXP Csparse_symmetric_to_general(SEXP x)
255  {  {
256      CHM_SP chx = AS_CHM_SP(x), chgx;      CHM_SP chx = AS_CHM_SP__(x), chgx;
257      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
258      R_CheckStack();      R_CheckStack();
259    
# Line 170  Line 267 
267    
268  SEXP Csparse_general_to_symmetric(SEXP x, SEXP uplo)  SEXP Csparse_general_to_symmetric(SEXP x, SEXP uplo)
269  {  {
270      CHM_SP chx = AS_CHM_SP(x), chgx;      CHM_SP chx = AS_CHM_SP__(x), chgx;
271      int uploT = (*CHAR(STRING_ELT(uplo,0)) == 'U') ? 1 : -1;      int uploT = (*CHAR(STRING_ELT(uplo,0)) == 'U') ? 1 : -1;
272      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
273      R_CheckStack();      R_CheckStack();
# Line 185  Line 282 
282  {  {
283      /* TODO: lgCMatrix & igC* currently go via double prec. cholmod -      /* TODO: lgCMatrix & igC* currently go via double prec. cholmod -
284       *       since cholmod (& cs) lacks sparse 'int' matrices */       *       since cholmod (& cs) lacks sparse 'int' matrices */
285      CHM_SP chx = AS_CHM_SP(x);      CHM_SP chx = AS_CHM_SP__(x);
286      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
287      CHM_SP chxt = cholmod_transpose(chx, chx->xtype, &c);      CHM_SP chxt = cholmod_transpose(chx, chx->xtype, &c);
288      SEXP dn = PROTECT(duplicate(GET_SLOT(x, Matrix_DimNamesSym))), tmp;      SEXP dn = PROTECT(duplicate(GET_SLOT(x, Matrix_DimNamesSym))), tmp;
# Line 204  Line 301 
301  SEXP Csparse_Csparse_prod(SEXP a, SEXP b)  SEXP Csparse_Csparse_prod(SEXP a, SEXP b)
302  {  {
303      CHM_SP      CHM_SP
304          cha = AS_CHM_SP(Csparse_diagU2N(a)),          cha = AS_CHM_SP(a),
305          chb = AS_CHM_SP(Csparse_diagU2N(b)),          chb = AS_CHM_SP(b),
306          chc = cholmod_ssmult(cha, chb, /*out_stype:*/ 0,          chc = cholmod_ssmult(cha, chb, /*out_stype:*/ 0,
307                               cha->xtype, /*out sorted:*/ 1, &c);                                 /* values:= is_numeric (T/F) */ cha->xtype > 0,
308                                   /*out sorted:*/ 1, &c);
309      const char *cl_a = class_P(a), *cl_b = class_P(b);      const char *cl_a = class_P(a), *cl_b = class_P(b);
310      char diag[] = {'\0', '\0'};      char diag[] = {'\0', '\0'};
311      int uploT = 0;      int uploT = 0;
312      SEXP dn = allocVector(VECSXP, 2);      SEXP dn = PROTECT(allocVector(VECSXP, 2));
313      R_CheckStack();      R_CheckStack();
314    
315    #ifdef DEBUG_Matrix_verbose
316        Rprintf("DBG Csparse_C*_prod(%s, %s)\n", cl_a, cl_b);
317    #endif
318    
319      /* Preserve triangularity and even unit-triangularity if appropriate.      /* Preserve triangularity and even unit-triangularity if appropriate.
320       * Note that in that case, the multiplication itself should happen       * Note that in that case, the multiplication itself should happen
321       * faster.  But there's no support for that in CHOLMOD */       * faster.  But there's no support for that in CHOLMOD */
# Line 235  Line 337 
337                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));
338      SET_VECTOR_ELT(dn, 1,      SET_VECTOR_ELT(dn, 1,
339                     duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), 1)));                     duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), 1)));
340        UNPROTECT(1);
341      return chm_sparse_to_SEXP(chc, 1, uploT, /*Rkind*/0, diag, dn);      return chm_sparse_to_SEXP(chc, 1, uploT, /*Rkind*/0, diag, dn);
342  }  }
343    
# Line 242  Line 345 
345  {  {
346      int tr = asLogical(trans);      int tr = asLogical(trans);
347      CHM_SP      CHM_SP
348          cha = AS_CHM_SP(Csparse_diagU2N(a)),          cha = AS_CHM_SP(a),
349          chb = AS_CHM_SP(Csparse_diagU2N(b)),          chb = AS_CHM_SP(b),
350          chTr, chc;          chTr, chc;
351      const char *cl_a = class_P(a), *cl_b = class_P(b);      const char *cl_a = class_P(a), *cl_b = class_P(b);
352      char diag[] = {'\0', '\0'};      char diag[] = {'\0', '\0'};
353      int uploT = 0;      int uploT = 0;
354      SEXP dn = allocVector(VECSXP, 2);      SEXP dn = PROTECT(allocVector(VECSXP, 2));
355      R_CheckStack();      R_CheckStack();
356    
357      chTr = cholmod_transpose((tr) ? chb : cha, chb->xtype, &c);      chTr = cholmod_transpose((tr) ? chb : cha, chb->xtype, &c);
# Line 267  Line 370 
370              }              }
371              else diag[0]= 'N';              else diag[0]= 'N';
372          }          }
   
373      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
374                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), (tr) ? 0 : 1)));                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), (tr) ? 0 : 1)));
375      SET_VECTOR_ELT(dn, 1,      SET_VECTOR_ELT(dn, 1,
376                     duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), (tr) ? 0 : 1)));                     duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), (tr) ? 0 : 1)));
377        UNPROTECT(1);
378      return chm_sparse_to_SEXP(chc, 1, uploT, /*Rkind*/0, diag, dn);      return chm_sparse_to_SEXP(chc, 1, uploT, /*Rkind*/0, diag, dn);
379  }  }
380    
381  SEXP Csparse_dense_prod(SEXP a, SEXP b)  SEXP Csparse_dense_prod(SEXP a, SEXP b)
382  {  {
383      CHM_SP cha = AS_CHM_SP(Csparse_diagU2N(a));      CHM_SP cha = AS_CHM_SP(a);
384      SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));      SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));
385      CHM_DN chb = AS_CHM_DN(b_M);      CHM_DN chb = AS_CHM_DN(b_M);
386      CHM_DN chc = cholmod_allocate_dense(cha->nrow, chb->ncol, cha->nrow,      CHM_DN chc = cholmod_allocate_dense(cha->nrow, chb->ncol, cha->nrow,
387                                          chb->xtype, &c);                                          chb->xtype, &c);
388      SEXP dn = PROTECT(allocVector(VECSXP, 2));      SEXP dn = PROTECT(allocVector(VECSXP, 2));
389      double one[] = {1,0}, zero[] = {0,0};      double one[] = {1,0}, zero[] = {0,0};
390        int nprot = 2;
391      R_CheckStack();      R_CheckStack();
392        /* Tim Davis, please FIXME:  currently (2010-11) *fails* when  a  is a pattern matrix:*/
393        if(cha->xtype == CHOLMOD_PATTERN) {
394            /* warning(_("Csparse_dense_prod(): cholmod_sdmult() not yet implemented for pattern./ ngCMatrix" */
395            /*        " --> slightly inefficient coercion")); */
396    
397            // This *fails* to produce a CHOLMOD_REAL ..
398            // CHM_SP chd = cholmod_l_copy(cha, cha->stype, CHOLMOD_REAL, &c);
399            // --> use our Matrix-classes
400            SEXP da = PROTECT(nz2Csparse(a, x_double)); nprot++;
401            cha = AS_CHM_SP(da);
402        }
403      cholmod_sdmult(cha, 0, one, zero, chb, chc, &c);      cholmod_sdmult(cha, 0, one, zero, chb, chc, &c);
404      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
405                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));
406      SET_VECTOR_ELT(dn, 1,      SET_VECTOR_ELT(dn, 1,
407                     duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));                     duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));
408      UNPROTECT(2);      UNPROTECT(nprot);
409      return chm_dense_to_SEXP(chc, 1, 0, dn);      return chm_dense_to_SEXP(chc, 1, 0, dn);
410  }  }
411    
412  SEXP Csparse_dense_crossprod(SEXP a, SEXP b)  SEXP Csparse_dense_crossprod(SEXP a, SEXP b)
413  {  {
414      CHM_SP cha = AS_CHM_SP(Csparse_diagU2N(a));      CHM_SP cha = AS_CHM_SP(a);
415      SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));      SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));
416      CHM_DN chb = AS_CHM_DN(b_M);      CHM_DN chb = AS_CHM_DN(b_M);
417      CHM_DN chc = cholmod_allocate_dense(cha->ncol, chb->ncol, cha->ncol,      CHM_DN chc = cholmod_allocate_dense(cha->ncol, chb->ncol, cha->ncol,
418                                          chb->xtype, &c);                                          chb->xtype, &c);
419      SEXP dn = PROTECT(allocVector(VECSXP, 2));      SEXP dn = PROTECT(allocVector(VECSXP, 2)); int nprot = 2;
420      double one[] = {1,0}, zero[] = {0,0};      double one[] = {1,0}, zero[] = {0,0};
421      R_CheckStack();      R_CheckStack();
422        // -- see Csparse_dense_prod() above :
423        if(cha->xtype == CHOLMOD_PATTERN) {
424            SEXP da = PROTECT(nz2Csparse(a, x_double)); nprot++;
425            cha = AS_CHM_SP(da);
426        }
427      cholmod_sdmult(cha, 1, one, zero, chb, chc, &c);      cholmod_sdmult(cha, 1, one, zero, chb, chc, &c);
428      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
429                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 1)));                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 1)));
430      SET_VECTOR_ELT(dn, 1,      SET_VECTOR_ELT(dn, 1,
431                     duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));                     duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));
432      UNPROTECT(2);      UNPROTECT(nprot);
433      return chm_dense_to_SEXP(chc, 1, 0, dn);      return chm_dense_to_SEXP(chc, 1, 0, dn);
434  }  }
435    
# Line 321  Line 439 
439  {  {
440      int trip = asLogical(triplet),      int trip = asLogical(triplet),
441          tr   = asLogical(trans); /* gets reversed because _aat is tcrossprod */          tr   = asLogical(trans); /* gets reversed because _aat is tcrossprod */
442      CHM_TR cht = trip ? AS_CHM_TR(Tsparse_diagU2N(x)) : (CHM_TR) NULL;  #ifdef AS_CHM_DIAGU2N_FIXED_FINALLY
443        CHM_TR cht = trip ? AS_CHM_TR(x) : (CHM_TR) NULL;
444    #else /* workaround needed:*/
445        SEXP xx = PROTECT(Tsparse_diagU2N(x));
446        CHM_TR cht = trip ? AS_CHM_TR__(xx) : (CHM_TR) NULL;
447    #endif
448      CHM_SP chcp, chxt,      CHM_SP chcp, chxt,
449          chx = (trip ?          chx = (trip ?
450                 cholmod_triplet_to_sparse(cht, cht->nnz, &c) :                 cholmod_triplet_to_sparse(cht, cht->nnz, &c) :
451                 AS_CHM_SP(Csparse_diagU2N(x)));                 AS_CHM_SP(x));
452      SEXP dn = PROTECT(allocVector(VECSXP, 2));      SEXP dn = PROTECT(allocVector(VECSXP, 2));
453      R_CheckStack();      R_CheckStack();
454    
# Line 343  Line 466 
466                     duplicate(VECTOR_ELT(GET_SLOT(x, Matrix_DimNamesSym),                     duplicate(VECTOR_ELT(GET_SLOT(x, Matrix_DimNamesSym),
467                                          (tr) ? 0 : 1)));                                          (tr) ? 0 : 1)));
468      SET_VECTOR_ELT(dn, 1, duplicate(VECTOR_ELT(dn, 0)));      SET_VECTOR_ELT(dn, 1, duplicate(VECTOR_ELT(dn, 0)));
469    #ifdef AS_CHM_DIAGU2N_FIXED_FINALLY
470      UNPROTECT(1);      UNPROTECT(1);
471    #else
472        UNPROTECT(2);
473    #endif
474      return chm_sparse_to_SEXP(chcp, 1, 0, 0, "", dn);      return chm_sparse_to_SEXP(chcp, 1, 0, 0, "", dn);
475  }  }
476    
477    /* Csparse_drop(x, tol):  drop entries with absolute value < tol, i.e,
478    *  at least all "explicit" zeros */
479  SEXP Csparse_drop(SEXP x, SEXP tol)  SEXP Csparse_drop(SEXP x, SEXP tol)
480  {  {
481      const char *cl = class_P(x);      const char *cl = class_P(x);
482      /* dtCMatrix, etc; [1] = the second character =?= 't' for triangular */      /* dtCMatrix, etc; [1] = the second character =?= 't' for triangular */
483      int tr = (cl[1] == 't');      int tr = (cl[1] == 't');
484      CHM_SP chx = AS_CHM_SP(x);      CHM_SP chx = AS_CHM_SP__(x);
485      CHM_SP ans = cholmod_copy(chx, chx->stype, chx->xtype, &c);      CHM_SP ans = cholmod_copy(chx, chx->stype, chx->xtype, &c);
486      double dtol = asReal(tol);      double dtol = asReal(tol);
487      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
# Line 368  Line 497 
497    
498  SEXP Csparse_horzcat(SEXP x, SEXP y)  SEXP Csparse_horzcat(SEXP x, SEXP y)
499  {  {
500      CHM_SP chx = AS_CHM_SP(x), chy = AS_CHM_SP(y);      CHM_SP chx = AS_CHM_SP__(x), chy = AS_CHM_SP__(y);
501      int Rkind = 0; /* only for "d" - FIXME */      int Rk_x = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0,
502            Rk_y = (chy->xtype != CHOLMOD_PATTERN) ? Real_kind(y) : 0,
503            Rkind = /* logical if both x and y are */ (Rk_x == 1 && Rk_y == 1) ? 1 : 0;
504      R_CheckStack();      R_CheckStack();
505    
506      /* FIXME: currently drops dimnames */      /* TODO: currently drops dimnames - and we fix at R level */
507      return chm_sparse_to_SEXP(cholmod_horzcat(chx, chy, 1, &c),      return chm_sparse_to_SEXP(cholmod_horzcat(chx, chy, 1, &c),
508                                1, 0, Rkind, "", R_NilValue);                                1, 0, Rkind, "", R_NilValue);
509  }  }
510    
511  SEXP Csparse_vertcat(SEXP x, SEXP y)  SEXP Csparse_vertcat(SEXP x, SEXP y)
512  {  {
513      CHM_SP chx = AS_CHM_SP(x), chy = AS_CHM_SP(y);      CHM_SP chx = AS_CHM_SP__(x), chy = AS_CHM_SP__(y);
514      int Rkind = 0; /* only for "d" - FIXME */      int Rk_x = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0,
515            Rk_y = (chy->xtype != CHOLMOD_PATTERN) ? Real_kind(y) : 0,
516            Rkind = /* logical if both x and y are */ (Rk_x == 1 && Rk_y == 1) ? 1 : 0;
517      R_CheckStack();      R_CheckStack();
518    
519      /* FIXME: currently drops dimnames */      /* TODO: currently drops dimnames - and we fix at R level */
520      return chm_sparse_to_SEXP(cholmod_vertcat(chx, chy, 1, &c),      return chm_sparse_to_SEXP(cholmod_vertcat(chx, chy, 1, &c),
521                                1, 0, Rkind, "", R_NilValue);                                1, 0, Rkind, "", R_NilValue);
522  }  }
523    
524  SEXP Csparse_band(SEXP x, SEXP k1, SEXP k2)  SEXP Csparse_band(SEXP x, SEXP k1, SEXP k2)
525  {  {
526      CHM_SP chx = AS_CHM_SP(x);      CHM_SP chx = AS_CHM_SP__(x);
527      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
528      CHM_SP ans = cholmod_band(chx, asInteger(k1), asInteger(k2), chx->xtype, &c);      CHM_SP ans = cholmod_band(chx, asInteger(k1), asInteger(k2), chx->xtype, &c);
529      R_CheckStack();      R_CheckStack();
# Line 409  Line 542 
542          return (x);          return (x);
543      }      }
544      else { /* unit triangular (diag='U'): "fill the diagonal" & diag:= "N" */      else { /* unit triangular (diag='U'): "fill the diagonal" & diag:= "N" */
545          CHM_SP chx = AS_CHM_SP(x);          CHM_SP chx = AS_CHM_SP__(x);
546          CHM_SP eye = cholmod_speye(chx->nrow, chx->ncol, chx->xtype, &c);          CHM_SP eye = cholmod_speye(chx->nrow, chx->ncol, chx->xtype, &c);
547          double one[] = {1, 0};          double one[] = {1, 0};
548          CHM_SP ans = cholmod_add(chx, eye, one, one, TRUE, TRUE, &c);          CHM_SP ans = cholmod_add(chx, eye, one, one, TRUE, TRUE, &c);
# Line 434  Line 567 
567      }      }
568      else { /* triangular with diag='N'): now drop the diagonal */      else { /* triangular with diag='N'): now drop the diagonal */
569          /* duplicate, since chx will be modified: */          /* duplicate, since chx will be modified: */
570          CHM_SP chx = AS_CHM_SP(duplicate(x));          SEXP xx = PROTECT(duplicate(x));
571            CHM_SP chx = AS_CHM_SP__(xx);
572          int uploT = (*uplo_P(x) == 'U') ? 1 : -1,          int uploT = (*uplo_P(x) == 'U') ? 1 : -1,
573              Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;              Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
574          R_CheckStack();          R_CheckStack();
575    
576          chm_diagN2U(chx, uploT, /* do_realloc */ FALSE);          chm_diagN2U(chx, uploT, /* do_realloc */ FALSE);
577    
578            UNPROTECT(1);
579          return chm_sparse_to_SEXP(chx, /*dofree*/ 0/* or 1 ?? */,          return chm_sparse_to_SEXP(chx, /*dofree*/ 0/* or 1 ?? */,
580                                    uploT, Rkind, "U",                                    uploT, Rkind, "U",
581                                    GET_SLOT(x, Matrix_DimNamesSym));                                    GET_SLOT(x, Matrix_DimNamesSym));
582      }      }
583  }  }
584    
585    /**
586     * "Indexing" aka subsetting : Compute  x[i,j], also for vectors i and j
587     * Working via CHOLMOD_submatrix, see ./CHOLMOD/MatrixOps/cholmod_submatrix.c
588     * @param x CsparseMatrix
589     * @param i row     indices (0-origin), or NULL (R's)
590     * @param j columns indices (0-origin), or NULL
591     *
592     * @return x[i,j]  still CsparseMatrix --- currently, this loses dimnames
593     */
594  SEXP Csparse_submatrix(SEXP x, SEXP i, SEXP j)  SEXP Csparse_submatrix(SEXP x, SEXP i, SEXP j)
595  {  {
596      CHM_SP chx = AS_CHM_SP(x);      CHM_SP chx = AS_CHM_SP(x); /* << does diagU2N() when needed */
597      int rsize = (isNull(i)) ? -1 : LENGTH(i),      int rsize = (isNull(i)) ? -1 : LENGTH(i),
598          csize = (isNull(j)) ? -1 : LENGTH(j);          csize = (isNull(j)) ? -1 : LENGTH(j);
599      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
# Line 460  Line 604 
604      if (csize >= 0 && !isInteger(j))      if (csize >= 0 && !isInteger(j))
605          error(_("Index j must be NULL or integer"));          error(_("Index j must be NULL or integer"));
606    
607      return chm_sparse_to_SEXP(cholmod_submatrix(chx, INTEGER(i), rsize,      if (!chx->stype) {/* non-symmetric Matrix */
608                                                  INTEGER(j), csize,          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                                    /* for now, cholmod_submatrix() only accepts "generalMatrix" */
616        CHM_SP tmp = cholmod_copy(chx, /* stype: */ 0, chx->xtype, &c);
617        CHM_SP ans = cholmod_submatrix(tmp,
618                                       (rsize < 0) ? NULL : INTEGER(i), rsize,
619                                       (csize < 0) ? NULL : INTEGER(j), csize,
620                                       TRUE, TRUE, &c);
621        cholmod_free_sparse(&tmp, &c);
622        return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "", R_NilValue);
623    }
624    
625    #define _d_Csp_
626    #include "t_Csparse_subassign.c"
627    
628    #define _l_Csp_
629    #include "t_Csparse_subassign.c"
630    
631    #define _i_Csp_
632    #include "t_Csparse_subassign.c"
633    
634    #define _n_Csp_
635    #include "t_Csparse_subassign.c"
636    
637    #define _z_Csp_
638    #include "t_Csparse_subassign.c"
639    
640    
641    
642  SEXP Csparse_MatrixMarket(SEXP x, SEXP fname)  SEXP Csparse_MatrixMarket(SEXP x, SEXP fname)
643  {  {
# Line 474  Line 646 
646      if (!f)      if (!f)
647          error(_("failure to open file \"%s\" for writing"),          error(_("failure to open file \"%s\" for writing"),
648                CHAR(asChar(fname)));                CHAR(asChar(fname)));
649      if (!cholmod_write_sparse(f, AS_CHM_SP(Csparse_diagU2N(x)),      if (!cholmod_write_sparse(f, AS_CHM_SP(x),
650                                (CHM_SP)NULL, (char*) NULL, &c))                                (CHM_SP)NULL, (char*) NULL, &c))
651          error(_("cholmod_write_sparse returned error code"));          error(_("cholmod_write_sparse returned error code"));
652      fclose(f);      fclose(f);
# Line 549  Line 721 
721      case diag_backpermuted:      case diag_backpermuted:
722          for_DIAG(v[i] = x_x[i_from]);          for_DIAG(v[i] = x_x[i_from]);
723    
724          warning(_("resultKind = 'diagBack' (back-permuted) is experimental"));          warning(_("%s = '%s' (back-permuted) is experimental"),
725                    "resultKind", "diagBack");
726          /* now back_permute : */          /* now back_permute : */
727          for(i = 0; i < n; i++) {          for(i = 0; i < n; i++) {
728              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 558  Line 731 
731          break;          break;
732    
733      default: /* -1 from above */      default: /* -1 from above */
734          error("diag_tC(): invalid 'resultKind'");          error(_("diag_tC(): invalid 'resultKind'"));
735          /* Wall: */ ans = R_NilValue; v = REAL(ans);          /* Wall: */ ans = R_NilValue; v = REAL(ans);
736      }      }
737    
# Line 588  Line 761 
761    
762      return diag_tC_ptr(n, x_p, x_x, perm, resultKind);      return diag_tC_ptr(n, x_p, x_x, perm, resultKind);
763  }  }
764    
765    /**
766     * Create a Csparse matrix object from indices and/or pointers.
767     *
768     * @param cls name of actual class of object to create
769     * @param i optional integer vector of length nnz of row indices
770     * @param j optional integer vector of length nnz of column indices
771     * @param p optional integer vector of length np of row or column pointers
772     * @param np length of integer vector p.  Must be zero if p == (int*)NULL
773     * @param x optional vector of values
774     * @param nnz length of vectors i, j and/or x, whichever is to be used
775     * @param dims optional integer vector of length 2 to be used as
776     *     dimensions.  If dims == (int*)NULL then the maximum row and column
777     *     index are used as the dimensions.
778     * @param dimnames optional list of length 2 to be used as dimnames
779     * @param index1 indicator of 1-based indices
780     *
781     * @return an SEXP of class cls inheriting from CsparseMatrix.
782     */
783    SEXP create_Csparse(char* cls, int* i, int* j, int* p, int np,
784                        void* x, int nnz, int* dims, SEXP dimnames,
785                        int index1)
786    {
787        SEXP ans;
788        int *ij = (int*)NULL, *tri, *trj,
789            mi, mj, mp, nrow = -1, ncol = -1;
790        int xtype = -1;             /* -Wall */
791        CHM_TR T;
792        CHM_SP A;
793    
794        if (np < 0 || nnz < 0)
795            error(_("negative vector lengths not allowed: np = %d, nnz = %d"),
796                  np, nnz);
797        if (1 != ((mi = (i == (int*)NULL)) +
798                  (mj = (j == (int*)NULL)) +
799                  (mp = (p == (int*)NULL))))
800            error(_("exactly 1 of 'i', 'j' or 'p' must be NULL"));
801        if (mp) {
802            if (np) error(_("np = %d, must be zero when p is NULL"), np);
803        } else {
804            if (np) {               /* Expand p to form i or j */
805                if (!(p[0])) error(_("p[0] = %d, should be zero"), p[0]);
806                for (int ii = 0; ii < np; ii++)
807                    if (p[ii] > p[ii + 1])
808                        error(_("p must be non-decreasing"));
809                if (p[np] != nnz)
810                    error("p[np] = %d != nnz = %d", p[np], nnz);
811                ij = Calloc(nnz, int);
812                if (mi) {
813                    i = ij;
814                    nrow = np;
815                } else {
816                    j = ij;
817                    ncol = np;
818                }
819                /* Expand p to 0-based indices */
820                for (int ii = 0; ii < np; ii++)
821                    for (int jj = p[ii]; jj < p[ii + 1]; jj++) ij[jj] = ii;
822            } else {
823                if (nnz)
824                    error(_("Inconsistent dimensions: np = 0 and nnz = %d"),
825                          nnz);
826            }
827        }
828        /* calculate nrow and ncol */
829        if (nrow < 0) {
830            for (int ii = 0; ii < nnz; ii++) {
831                int i1 = i[ii] + (index1 ? 0 : 1); /* 1-based index */
832                if (i1 < 1) error(_("invalid row index at position %d"), ii);
833                if (i1 > nrow) nrow = i1;
834            }
835        }
836        if (ncol < 0) {
837            for (int jj = 0; jj < nnz; jj++) {
838                int j1 = j[jj] + (index1 ? 0 : 1);
839                if (j1 < 1) error(_("invalid column index at position %d"), jj);
840                if (j1 > ncol) ncol = j1;
841            }
842        }
843        if (dims != (int*)NULL) {
844            if (dims[0] > nrow) nrow = dims[0];
845            if (dims[1] > ncol) ncol = dims[1];
846        }
847        /* check the class name */
848        if (strlen(cls) != 8)
849            error(_("strlen of cls argument = %d, should be 8"), strlen(cls));
850        if (!strcmp(cls + 2, "CMatrix"))
851            error(_("cls = \"%s\" does not end in \"CMatrix\""), cls);
852        switch(cls[0]) {
853        case 'd':
854        case 'l':
855            xtype = CHOLMOD_REAL;
856        break;
857        case 'n':
858            xtype = CHOLMOD_PATTERN;
859            break;
860        default:
861            error(_("cls = \"%s\" must begin with 'd', 'l' or 'n'"), cls);
862        }
863        if (cls[1] != 'g')
864            error(_("Only 'g'eneral sparse matrix types allowed"));
865        /* allocate and populate the triplet */
866        T = cholmod_allocate_triplet((size_t)nrow, (size_t)ncol, (size_t)nnz, 0,
867                                     xtype, &c);
868        T->x = x;
869        tri = (int*)T->i;
870        trj = (int*)T->j;
871        for (int ii = 0; ii < nnz; ii++) {
872            tri[ii] = i[ii] - ((!mi && index1) ? 1 : 0);
873            trj[ii] = j[ii] - ((!mj && index1) ? 1 : 0);
874        }
875        /* create the cholmod_sparse structure */
876        A = cholmod_triplet_to_sparse(T, nnz, &c);
877        cholmod_free_triplet(&T, &c);
878        /* copy the information to the SEXP */
879        ans = PROTECT(NEW_OBJECT(MAKE_CLASS(cls)));
880    /* FIXME: This has been copied from chm_sparse_to_SEXP in chm_common.c */
881        /* allocate and copy common slots */
882        nnz = cholmod_nnz(A, &c);
883        dims = INTEGER(ALLOC_SLOT(ans, Matrix_DimSym, INTSXP, 2));
884        dims[0] = A->nrow; dims[1] = A->ncol;
885        Memcpy(INTEGER(ALLOC_SLOT(ans, Matrix_pSym, INTSXP, A->ncol + 1)), (int*)A->p, A->ncol + 1);
886        Memcpy(INTEGER(ALLOC_SLOT(ans, Matrix_iSym, INTSXP, nnz)), (int*)A->i, nnz);
887        switch(cls[1]) {
888        case 'd':
889            Memcpy(REAL(ALLOC_SLOT(ans, Matrix_xSym, REALSXP, nnz)), (double*)A->x, nnz);
890            break;
891        case 'l':
892            error(_("code not yet written for cls = \"lgCMatrix\""));
893        }
894    /* FIXME: dimnames are *NOT* put there yet (if non-NULL) */
895        cholmod_free_sparse(&A, &c);
896        UNPROTECT(1);
897        return ans;
898    }

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