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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 3023, Sat Dec 20 22:29:49 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"
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 */      /* NB: we do *NOT* check a potential 'x' slot here, at all */
11      SEXP pslot = GET_SLOT(x, Matrix_pSym),      SEXP pslot = GET_SLOT(x, Matrix_pSym),
12          islot = GET_SLOT(x, Matrix_iSym);          islot = GET_SLOT(x, Matrix_iSym);
13      Rboolean sorted, strictly;      int *dims = INTEGER(GET_SLOT(x, Matrix_DimSym)), j,
     int j, k,  
         *dims = INTEGER(GET_SLOT(x, Matrix_DimSym)),  
14          nrow = dims[0],          nrow = dims[0],
15          ncol = dims[1],          ncol = dims[1],
16          *xp = INTEGER(pslot),          *xp = INTEGER(pslot),
17          *xi = INTEGER(islot);          *xi = INTEGER(islot);
18    
19      if (length(pslot) != dims[1] + 1)      if (length(pslot) != dims[1] + 1)
20          return mkString(_("slot p must have length = ncol(.) + 1"));          return FALSE;
21      if (xp[0] != 0)      if (xp[0] != 0)
22          return mkString(_("first element of slot p must be zero"));          return FALSE;
23      if (length(islot) < xp[ncol]) /* allow larger slots from over-allocation!*/      if (length(islot) < xp[ncol]) /* allow larger slots from over-allocation!*/
24          return          return FALSE;
25              mkString(_("last element of slot p must match length of slots i and x"));      for (j = 0; j < xp[ncol]; j++) {
     for (j = 0; j < length(islot); j++) {  
26          if (xi[j] < 0 || xi[j] >= nrow)          if (xi[j] < 0 || xi[j] >= nrow)
27              return mkString(_("all row indices must be between 0 and nrow-1"));              return FALSE;
28      }      }
     sorted = TRUE; strictly = TRUE;  
29      for (j = 0; j < ncol; j++) {      for (j = 0; j < ncol; j++) {
30          if (xp[j] > xp[j+1])          if (xp[j] > xp[j+1])
31              return mkString(_("slot p must be non-decreasing"));              return FALSE;
         if(sorted)  
             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;  
32              }              }
33        return TRUE;
34      }      }
     if (!sorted) {  
         CHM_SP chx = AS_CHM_SP(x);  
         R_CheckStack();  
35    
36          cholmod_sort(chx, &c);  SEXP Csparse_validate(SEXP x) {
37          /* Now re-check that row indices are *strictly* increasing      return Csparse_validate_(x, FALSE);
          * (and not just increasing) within each column : */  
         for (j = 0; j < ncol; j++) {  
             for (k = xp[j] + 1; k < xp[j + 1]; k++)  
                 if (xi[k] == xi[k - 1])  
                     return mkString(_("slot i is not *strictly* increasing inside a column (even after cholmod_sort)"));  
38          }          }
39    
40      } else if(!strictly) {  /* sorted, but not strictly */  
41          return mkString(_("slot i is not *strictly* increasing inside a column"));  #define _t_Csparse_validate
42    #include "t_Csparse_validate.c"
43    
44    #define _t_Csparse_sort
45    #include "t_Csparse_validate.c"
46    
47    // R: .validateCsparse(x, sort.if.needed = FALSE) :
48    SEXP Csparse_validate2(SEXP x, SEXP maybe_modify) {
49        return Csparse_validate_(x, asLogical(maybe_modify));
50      }      }
51      return ScalarLogical(1);  
52    // R: Matrix:::.sortCsparse(x) :
53    SEXP Csparse_sort (SEXP x) {
54       int ok = Csparse_sort_2(x, TRUE); // modifying x directly
55       if(!ok) warning(_("Csparse_sort(x): x is not a valid (apart from sorting) CsparseMatrix"));
56       return x;
57  }  }
58    
59  SEXP Rsparse_validate(SEXP x)  SEXP Rsparse_validate(SEXP x)
# Line 109  Line 107 
107   * FIXME: replace by non-CHOLMOD code ! */   * FIXME: replace by non-CHOLMOD code ! */
108  SEXP Csparse_to_dense(SEXP x)  SEXP Csparse_to_dense(SEXP x)
109  {  {
110      CHM_SP chxs = AS_CHM_SP(x);      CHM_SP chxs = AS_CHM_SP__(x);
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 : */
# Line 120  Line 118 
118      return chm_dense_to_SEXP(chxd, 1, Rkind, GET_SLOT(x, Matrix_DimNamesSym));      return chm_dense_to_SEXP(chxd, 1, Rkind, GET_SLOT(x, Matrix_DimNamesSym));
119  }  }
120    
121    // FIXME: do not go via CHM (should not be too hard, to just *drop* the x-slot, right?
122  SEXP Csparse_to_nz_pattern(SEXP x, SEXP tri)  SEXP Csparse_to_nz_pattern(SEXP x, SEXP tri)
123  {  {
124      CHM_SP chxs = AS_CHM_SP(x);      CHM_SP chxs = AS_CHM_SP__(x);
125      CHM_SP chxcp = cholmod_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();
# Line 133  Line 132 
132                                GET_SLOT(x, Matrix_DimNamesSym));                                GET_SLOT(x, Matrix_DimNamesSym));
133  }  }
134    
135  SEXP Csparse_to_matrix(SEXP x)  // n.CMatrix --> [dli].CMatrix  (not going through CHM!)
136    SEXP nz_pattern_to_Csparse(SEXP x, SEXP res_kind)
137  {  {
138      return chm_dense_to_matrix(cholmod_sparse_to_dense(AS_CHM_SP(x), &c),      return nz2Csparse(x, asInteger(res_kind));
139    }
140    // n.CMatrix --> [dli].CMatrix  (not going through CHM!)
141    SEXP nz2Csparse(SEXP x, enum x_slot_kind r_kind)
142    {
143        const char *cl_x = class_P(x);
144        if(cl_x[0] != 'n') error(_("not a 'n.CMatrix'"));
145        if(cl_x[2] != 'C') error(_("not a CsparseMatrix"));
146        int nnz = LENGTH(GET_SLOT(x, Matrix_iSym));
147        SEXP ans;
148        char *ncl = alloca(strlen(cl_x) + 1); /* not much memory required */
149        strcpy(ncl, cl_x);
150        double *dx_x; int *ix_x;
151        ncl[0] = (r_kind == x_double ? 'd' :
152                  (r_kind == x_logical ? 'l' :
153                   /* else (for now):  r_kind == x_integer : */ 'i'));
154        PROTECT(ans = NEW_OBJECT(MAKE_CLASS(ncl)));
155        // create a correct 'x' slot:
156        switch(r_kind) {
157            int i;
158        case x_double: // 'd'
159            dx_x = REAL(ALLOC_SLOT(ans, Matrix_xSym, REALSXP, nnz));
160            for (i=0; i < nnz; i++) dx_x[i] = 1.;
161            break;
162        case x_logical: // 'l'
163            ix_x = LOGICAL(ALLOC_SLOT(ans, Matrix_xSym, LGLSXP, nnz));
164            for (i=0; i < nnz; i++) ix_x[i] = TRUE;
165            break;
166        case x_integer: // 'i'
167            ix_x = INTEGER(ALLOC_SLOT(ans, Matrix_xSym, INTSXP, nnz));
168            for (i=0; i < nnz; i++) ix_x[i] = 1;
169            break;
170    
171        default:
172            error(_("nz2Csparse(): invalid/non-implemented r_kind = %d"),
173                  r_kind);
174        }
175    
176        // now copy all other slots :
177        slot_dup(ans, x, Matrix_iSym);
178        slot_dup(ans, x, Matrix_pSym);
179        slot_dup(ans, x, Matrix_DimSym);
180        slot_dup(ans, x, Matrix_DimNamesSym);
181        if(ncl[1] != 'g') { // symmetric or triangular ...
182            slot_dup_if_has(ans, x, Matrix_uploSym);
183            slot_dup_if_has(ans, x, Matrix_diagSym);
184        }
185        UNPROTECT(1);
186        return ans;
187    }
188    
189    SEXP Csparse_to_matrix(SEXP x, SEXP chk)
190    {
191        return chm_dense_to_matrix(cholmod_sparse_to_dense(AS_CHM_SP2(x, asLogical(chk)), &c),
192                                 1 /*do_free*/, GET_SLOT(x, Matrix_DimNamesSym));                                 1 /*do_free*/, GET_SLOT(x, Matrix_DimNamesSym));
193  }  }
194    SEXP Csparse_to_vector(SEXP x)
195    {
196        return chm_dense_to_vector(cholmod_sparse_to_dense(AS_CHM_SP__(x), &c), 1);
197    }
198    
199  SEXP Csparse_to_Tsparse(SEXP x, SEXP tri)  SEXP Csparse_to_Tsparse(SEXP x, SEXP tri)
200  {  {
201      CHM_SP chxs = AS_CHM_SP(x);      CHM_SP chxs = AS_CHM_SP__(x);
202      CHM_TR chxt = cholmod_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;
# Line 153  Line 210 
210                                 GET_SLOT(x, Matrix_DimNamesSym));                                 GET_SLOT(x, Matrix_DimNamesSym));
211  }  }
212    
213    SEXP Csparse_to_tCsparse(SEXP x, SEXP uplo, SEXP diag)
214    {
215        CHM_SP chxs = AS_CHM_SP__(x);
216        int Rkind = (chxs->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
217        R_CheckStack();
218        return chm_sparse_to_SEXP(chxs, /* dofree = */ 0,
219                                  /* uploT = */ (*CHAR(asChar(uplo)) == 'U')? 1: -1,
220                                   Rkind, /* diag = */ CHAR(STRING_ELT(diag, 0)),
221                                   GET_SLOT(x, Matrix_DimNamesSym));
222    }
223    
224    SEXP Csparse_to_tTsparse(SEXP x, SEXP uplo, SEXP diag)
225    {
226        CHM_SP chxs = AS_CHM_SP__(x);
227        CHM_TR chxt = cholmod_sparse_to_triplet(chxs, &c);
228        int Rkind = (chxs->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
229        R_CheckStack();
230        return chm_triplet_to_SEXP(chxt, 1,
231                                  /* uploT = */ (*CHAR(asChar(uplo)) == 'U')? 1: -1,
232                                   Rkind, /* diag = */ CHAR(STRING_ELT(diag, 0)),
233                                   GET_SLOT(x, Matrix_DimNamesSym));
234    }
235    
236    
237  /* this used to be called  sCMatrix_to_gCMatrix(..)   [in ./dsCMatrix.c ]: */  /* this used to be called  sCMatrix_to_gCMatrix(..)   [in ./dsCMatrix.c ]: */
238  SEXP Csparse_symmetric_to_general(SEXP x)  SEXP Csparse_symmetric_to_general(SEXP x)
239  {  {
240      CHM_SP chx = AS_CHM_SP(x), chgx;      CHM_SP chx = AS_CHM_SP__(x), chgx;
241      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
242      R_CheckStack();      R_CheckStack();
243    
# Line 170  Line 251 
251    
252  SEXP Csparse_general_to_symmetric(SEXP x, SEXP uplo)  SEXP Csparse_general_to_symmetric(SEXP x, SEXP uplo)
253  {  {
254      CHM_SP chx = AS_CHM_SP(x), chgx;      int *adims = INTEGER(GET_SLOT(x, Matrix_DimSym)), n = adims[0];
255      int uploT = (*CHAR(STRING_ELT(uplo,0)) == 'U') ? 1 : -1;      if(n != adims[1]) {
256            error(_("Csparse_general_to_symmetric(): matrix is not square!"));
257            return R_NilValue; /* -Wall */
258        }
259        CHM_SP chx = AS_CHM_SP__(x), chgx;
260        int uploT = (*CHAR(asChar(uplo)) == 'U') ? 1 : -1;
261      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
262      R_CheckStack();      R_CheckStack();
   
263      chgx = cholmod_copy(chx, /* stype: */ uploT, chx->xtype, &c);      chgx = cholmod_copy(chx, /* stype: */ uploT, chx->xtype, &c);
264    
265        /* need _symmetric_ dimnames */
266        SEXP dns = PROTECT(duplicate(GET_SLOT(x, Matrix_DimNamesSym))),
267            nms_dns = getAttrib(dns, R_NamesSymbol);
268        if(!equal_string_vectors(VECTOR_ELT(dns, 0),
269                                 VECTOR_ELT(dns, 1))) {
270            if(uploT == 1)
271                SET_VECTOR_ELT(dns, 0, VECTOR_ELT(dns,1));
272            else
273                SET_VECTOR_ELT(dns, 1, VECTOR_ELT(dns,0));
274        }
275        if(!isNull(nms_dns) &&  // names(dimnames(.)) :
276           !R_compute_identical(STRING_ELT(nms_dns, 0),
277                                STRING_ELT(nms_dns, 1), 15)) {
278            if(uploT == 1)
279                SET_STRING_ELT(nms_dns, 0, STRING_ELT(nms_dns,1));
280            else
281                SET_STRING_ELT(nms_dns, 1, STRING_ELT(nms_dns,0));
282            setAttrib(dns, R_NamesSymbol, nms_dns);
283        }
284    
285        UNPROTECT(1);
286      /* xtype: pattern, "real", complex or .. */      /* xtype: pattern, "real", complex or .. */
287      return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",      return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "", dns);
                               GET_SLOT(x, Matrix_DimNamesSym));  
288  }  }
289    
290  SEXP Csparse_transpose(SEXP x, SEXP tri)  SEXP Csparse_transpose(SEXP x, SEXP tri)
291  {  {
292      /* TODO: lgCMatrix & igC* currently go via double prec. cholmod -      /* TODO: lgCMatrix & igC* currently go via double prec. cholmod -
293       *       since cholmod (& cs) lacks sparse 'int' matrices */       *       since cholmod (& cs) lacks sparse 'int' matrices */
294      CHM_SP chx = AS_CHM_SP(x);      CHM_SP chx = AS_CHM_SP__(x);
295      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
296      CHM_SP chxt = cholmod_transpose(chx, chx->xtype, &c);      CHM_SP chxt = cholmod_transpose(chx, chx->xtype, &c);
297      SEXP dn = PROTECT(duplicate(GET_SLOT(x, Matrix_DimNamesSym))), tmp;      SEXP dn = PROTECT(duplicate(GET_SLOT(x, Matrix_DimNamesSym))), tmp;
# Line 195  Line 301 
301      tmp = VECTOR_ELT(dn, 0);    /* swap the dimnames */      tmp = VECTOR_ELT(dn, 0);    /* swap the dimnames */
302      SET_VECTOR_ELT(dn, 0, VECTOR_ELT(dn, 1));      SET_VECTOR_ELT(dn, 0, VECTOR_ELT(dn, 1));
303      SET_VECTOR_ELT(dn, 1, tmp);      SET_VECTOR_ELT(dn, 1, tmp);
304        if(!isNull(tmp = getAttrib(dn, R_NamesSymbol))) { // swap names(dimnames(.)):
305            SEXP nms_dns = PROTECT(allocVector(VECSXP, 2));
306            SET_VECTOR_ELT(nms_dns, 1, STRING_ELT(tmp, 0));
307            SET_VECTOR_ELT(nms_dns, 0, STRING_ELT(tmp, 1));
308            setAttrib(dn, R_NamesSymbol, nms_dns);
309            UNPROTECT(1);
310        }
311      UNPROTECT(1);      UNPROTECT(1);
312      return chm_sparse_to_SEXP(chxt, 1, /* SWAP 'uplo' for triangular */      return chm_sparse_to_SEXP(chxt, 1, /* SWAP 'uplo' for triangular */
313                                tr ? ((*uplo_P(x) == 'U') ? -1 : 1) : 0,                                tr ? ((*uplo_P(x) == 'U') ? -1 : 1) : 0,
# Line 204  Line 317 
317  SEXP Csparse_Csparse_prod(SEXP a, SEXP b)  SEXP Csparse_Csparse_prod(SEXP a, SEXP b)
318  {  {
319      CHM_SP      CHM_SP
320          cha = AS_CHM_SP(Csparse_diagU2N(a)),          cha = AS_CHM_SP(a),
321          chb = AS_CHM_SP(Csparse_diagU2N(b)),          chb = AS_CHM_SP(b),
322          chc = cholmod_ssmult(cha, chb, /*out_stype:*/ 0,          chc = cholmod_ssmult(cha, chb, /*out_stype:*/ 0,
323                               cha->xtype, /*out sorted:*/ 1, &c);                                 /* values:= is_numeric (T/F) */ cha->xtype > 0,
324                                   /*out sorted:*/ 1, &c);
325      const char *cl_a = class_P(a), *cl_b = class_P(b);      const char *cl_a = class_P(a), *cl_b = class_P(b);
326      char diag[] = {'\0', '\0'};      char diag[] = {'\0', '\0'};
327      int uploT = 0;      int uploT = 0;
328      SEXP dn = allocVector(VECSXP, 2);      SEXP dn = PROTECT(allocVector(VECSXP, 2));
329      R_CheckStack();      R_CheckStack();
330    
331    #ifdef DEBUG_Matrix_verbose
332        Rprintf("DBG Csparse_C*_prod(%s, %s)\n", cl_a, cl_b);
333    #endif
334    
335      /* Preserve triangularity and even unit-triangularity if appropriate.      /* Preserve triangularity and even unit-triangularity if appropriate.
336       * Note that in that case, the multiplication itself should happen       * Note that in that case, the multiplication itself should happen
337       * faster.  But there's no support for that in CHOLMOD */       * faster.  But there's no support for that in CHOLMOD */
# Line 235  Line 353 
353                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));
354      SET_VECTOR_ELT(dn, 1,      SET_VECTOR_ELT(dn, 1,
355                     duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), 1)));                     duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), 1)));
356        UNPROTECT(1);
357      return chm_sparse_to_SEXP(chc, 1, uploT, /*Rkind*/0, diag, dn);      return chm_sparse_to_SEXP(chc, 1, uploT, /*Rkind*/0, diag, dn);
358  }  }
359    
# Line 242  Line 361 
361  {  {
362      int tr = asLogical(trans);      int tr = asLogical(trans);
363      CHM_SP      CHM_SP
364          cha = AS_CHM_SP(Csparse_diagU2N(a)),          cha = AS_CHM_SP(a),
365          chb = AS_CHM_SP(Csparse_diagU2N(b)),          chb = AS_CHM_SP(b),
366          chTr, chc;          chTr, chc;
367      const char *cl_a = class_P(a), *cl_b = class_P(b);      const char *cl_a = class_P(a), *cl_b = class_P(b);
368      char diag[] = {'\0', '\0'};      char diag[] = {'\0', '\0'};
369      int uploT = 0;      int uploT = 0;
370      SEXP dn = allocVector(VECSXP, 2);      SEXP dn = PROTECT(allocVector(VECSXP, 2));
371      R_CheckStack();      R_CheckStack();
372    
373      chTr = cholmod_transpose((tr) ? chb : cha, chb->xtype, &c);      chTr = cholmod_transpose((tr) ? chb : cha, chb->xtype, &c);
# Line 267  Line 386 
386              }              }
387              else diag[0]= 'N';              else diag[0]= 'N';
388          }          }
   
389      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
390                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), (tr) ? 0 : 1)));                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), (tr) ? 0 : 1)));
391      SET_VECTOR_ELT(dn, 1,      SET_VECTOR_ELT(dn, 1,
392                     duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), (tr) ? 0 : 1)));                     duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), (tr) ? 0 : 1)));
393        UNPROTECT(1);
394      return chm_sparse_to_SEXP(chc, 1, uploT, /*Rkind*/0, diag, dn);      return chm_sparse_to_SEXP(chc, 1, uploT, /*Rkind*/0, diag, dn);
395  }  }
396    
397  SEXP Csparse_dense_prod(SEXP a, SEXP b)  SEXP Csparse_dense_prod(SEXP a, SEXP b)
398  {  {
399      CHM_SP cha = AS_CHM_SP(Csparse_diagU2N(a));      CHM_SP cha = AS_CHM_SP(a);
400      SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));      SEXP b_M = PROTECT(mMatrix_as_dgeMatrix2(b, // transpose_if_vector =
401                                                 cha->ncol == 1));
402      CHM_DN chb = AS_CHM_DN(b_M);      CHM_DN chb = AS_CHM_DN(b_M);
403      CHM_DN chc = cholmod_allocate_dense(cha->nrow, chb->ncol, cha->nrow,      CHM_DN chc = cholmod_allocate_dense(cha->nrow, chb->ncol, cha->nrow,
404                                          chb->xtype, &c);                                          chb->xtype, &c);
405      SEXP dn = PROTECT(allocVector(VECSXP, 2));      SEXP dn = PROTECT(allocVector(VECSXP, 2));
406      double one[] = {1,0}, zero[] = {0,0};      double one[] = {1,0}, zero[] = {0,0};
407        int nprot = 2;
408      R_CheckStack();      R_CheckStack();
409        /* Tim Davis, please FIXME:  currently (2010-11) *fails* when  a  is a pattern matrix:*/
410        if(cha->xtype == CHOLMOD_PATTERN) {
411            /* warning(_("Csparse_dense_prod(): cholmod_sdmult() not yet implemented for pattern./ ngCMatrix" */
412            /*        " --> slightly inefficient coercion")); */
413    
414            // This *fails* to produce a CHOLMOD_REAL ..
415            // CHM_SP chd = cholmod_l_copy(cha, cha->stype, CHOLMOD_REAL, &c);
416            // --> use our Matrix-classes
417            SEXP da = PROTECT(nz2Csparse(a, x_double)); nprot++;
418            cha = AS_CHM_SP(da);
419        }
420      cholmod_sdmult(cha, 0, one, zero, chb, chc, &c);      cholmod_sdmult(cha, 0, one, zero, chb, chc, &c);
421      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
422                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));
423      SET_VECTOR_ELT(dn, 1,      SET_VECTOR_ELT(dn, 1,
424                     duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));                     duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));
425      UNPROTECT(2);      UNPROTECT(nprot);
426      return chm_dense_to_SEXP(chc, 1, 0, dn);      return chm_dense_to_SEXP(chc, 1, 0, dn);
427  }  }
428    
429  SEXP Csparse_dense_crossprod(SEXP a, SEXP b)  SEXP Csparse_dense_crossprod(SEXP a, SEXP b)
430  {  {
431      CHM_SP cha = AS_CHM_SP(Csparse_diagU2N(a));      CHM_SP cha = AS_CHM_SP(a);
432      SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));      SEXP b_M = PROTECT(mMatrix_as_dgeMatrix2(b, // transpose_if_vector =
433                                                 cha->nrow == 1));
434      CHM_DN chb = AS_CHM_DN(b_M);      CHM_DN chb = AS_CHM_DN(b_M);
435      CHM_DN chc = cholmod_allocate_dense(cha->ncol, chb->ncol, cha->ncol,      CHM_DN chc = cholmod_allocate_dense(cha->ncol, chb->ncol, cha->ncol,
436                                          chb->xtype, &c);                                          chb->xtype, &c);
437      SEXP dn = PROTECT(allocVector(VECSXP, 2));      SEXP dn = PROTECT(allocVector(VECSXP, 2)); int nprot = 2;
438      double one[] = {1,0}, zero[] = {0,0};      double one[] = {1,0}, zero[] = {0,0};
439      R_CheckStack();      R_CheckStack();
440        // -- see Csparse_dense_prod() above :
441        if(cha->xtype == CHOLMOD_PATTERN) {
442            SEXP da = PROTECT(nz2Csparse(a, x_double)); nprot++;
443            cha = AS_CHM_SP(da);
444        }
445      cholmod_sdmult(cha, 1, one, zero, chb, chc, &c);      cholmod_sdmult(cha, 1, one, zero, chb, chc, &c);
446      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
447                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 1)));                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 1)));
448      SET_VECTOR_ELT(dn, 1,      SET_VECTOR_ELT(dn, 1,
449                     duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));                     duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));
450      UNPROTECT(2);      UNPROTECT(nprot);
451      return chm_dense_to_SEXP(chc, 1, 0, dn);      return chm_dense_to_SEXP(chc, 1, 0, dn);
452  }  }
453    
# Line 321  Line 457 
457  {  {
458      int trip = asLogical(triplet),      int trip = asLogical(triplet),
459          tr   = asLogical(trans); /* gets reversed because _aat is tcrossprod */          tr   = asLogical(trans); /* gets reversed because _aat is tcrossprod */
460      CHM_TR cht = trip ? AS_CHM_TR(Tsparse_diagU2N(x)) : (CHM_TR) NULL;  #ifdef AS_CHM_DIAGU2N_FIXED_FINALLY
461        CHM_TR cht = trip ? AS_CHM_TR(x) : (CHM_TR) NULL;
462    #else /* workaround needed:*/
463        SEXP xx = PROTECT(Tsparse_diagU2N(x));
464        CHM_TR cht = trip ? AS_CHM_TR__(xx) : (CHM_TR) NULL;
465    #endif
466      CHM_SP chcp, chxt,      CHM_SP chcp, chxt,
467          chx = (trip ?          chx = (trip ?
468                 cholmod_triplet_to_sparse(cht, cht->nnz, &c) :                 cholmod_triplet_to_sparse(cht, cht->nnz, &c) :
469                 AS_CHM_SP(Csparse_diagU2N(x)));                 AS_CHM_SP(x));
470      SEXP dn = PROTECT(allocVector(VECSXP, 2));      SEXP dn = PROTECT(allocVector(VECSXP, 2));
471      R_CheckStack();      R_CheckStack();
472    
# Line 343  Line 484 
484                     duplicate(VECTOR_ELT(GET_SLOT(x, Matrix_DimNamesSym),                     duplicate(VECTOR_ELT(GET_SLOT(x, Matrix_DimNamesSym),
485                                          (tr) ? 0 : 1)));                                          (tr) ? 0 : 1)));
486      SET_VECTOR_ELT(dn, 1, duplicate(VECTOR_ELT(dn, 0)));      SET_VECTOR_ELT(dn, 1, duplicate(VECTOR_ELT(dn, 0)));
487    #ifdef AS_CHM_DIAGU2N_FIXED_FINALLY
488      UNPROTECT(1);      UNPROTECT(1);
489    #else
490        UNPROTECT(2);
491    #endif
492      return chm_sparse_to_SEXP(chcp, 1, 0, 0, "", dn);      return chm_sparse_to_SEXP(chcp, 1, 0, 0, "", dn);
493  }  }
494    
495    /* Csparse_drop(x, tol):  drop entries with absolute value < tol, i.e,
496    *  at least all "explicit" zeros */
497  SEXP Csparse_drop(SEXP x, SEXP tol)  SEXP Csparse_drop(SEXP x, SEXP tol)
498  {  {
499      const char *cl = class_P(x);      const char *cl = class_P(x);
500      /* dtCMatrix, etc; [1] = the second character =?= 't' for triangular */      /* dtCMatrix, etc; [1] = the second character =?= 't' for triangular */
501      int tr = (cl[1] == 't');      int tr = (cl[1] == 't');
502      CHM_SP chx = AS_CHM_SP(x);      CHM_SP chx = AS_CHM_SP__(x);
503      CHM_SP ans = cholmod_copy(chx, chx->stype, chx->xtype, &c);      CHM_SP ans = cholmod_copy(chx, chx->stype, chx->xtype, &c);
504      double dtol = asReal(tol);      double dtol = asReal(tol);
505      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
# Line 368  Line 515 
515    
516  SEXP Csparse_horzcat(SEXP x, SEXP y)  SEXP Csparse_horzcat(SEXP x, SEXP y)
517  {  {
518      CHM_SP chx = AS_CHM_SP(x), chy = AS_CHM_SP(y);      CHM_SP chx = AS_CHM_SP__(x), chy = AS_CHM_SP__(y);
519      int Rkind = 0; /* only for "d" - FIXME */      int Rk_x = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0,
520            Rk_y = (chy->xtype != CHOLMOD_PATTERN) ? Real_kind(y) : 0,
521            Rkind = /* logical if both x and y are */ (Rk_x == 1 && Rk_y == 1) ? 1 : 0;
522      R_CheckStack();      R_CheckStack();
523    
524      /* FIXME: currently drops dimnames */      /* TODO: currently drops dimnames - and we fix at R level */
525      return chm_sparse_to_SEXP(cholmod_horzcat(chx, chy, 1, &c),      return chm_sparse_to_SEXP(cholmod_horzcat(chx, chy, 1, &c),
526                                1, 0, Rkind, "", R_NilValue);                                1, 0, Rkind, "", R_NilValue);
527  }  }
528    
529  SEXP Csparse_vertcat(SEXP x, SEXP y)  SEXP Csparse_vertcat(SEXP x, SEXP y)
530  {  {
531      CHM_SP chx = AS_CHM_SP(x), chy = AS_CHM_SP(y);      CHM_SP chx = AS_CHM_SP__(x), chy = AS_CHM_SP__(y);
532      int Rkind = 0; /* only for "d" - FIXME */      int Rk_x = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0,
533            Rk_y = (chy->xtype != CHOLMOD_PATTERN) ? Real_kind(y) : 0,
534            Rkind = /* logical if both x and y are */ (Rk_x == 1 && Rk_y == 1) ? 1 : 0;
535      R_CheckStack();      R_CheckStack();
536    
537      /* FIXME: currently drops dimnames */      /* TODO: currently drops dimnames - and we fix at R level */
538      return chm_sparse_to_SEXP(cholmod_vertcat(chx, chy, 1, &c),      return chm_sparse_to_SEXP(cholmod_vertcat(chx, chy, 1, &c),
539                                1, 0, Rkind, "", R_NilValue);                                1, 0, Rkind, "", R_NilValue);
540  }  }
541    
542  SEXP Csparse_band(SEXP x, SEXP k1, SEXP k2)  SEXP Csparse_band(SEXP x, SEXP k1, SEXP k2)
543  {  {
544      CHM_SP chx = AS_CHM_SP(x);      CHM_SP chx = AS_CHM_SP__(x);
545      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
546      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);
547      R_CheckStack();      R_CheckStack();
# Line 409  Line 560 
560          return (x);          return (x);
561      }      }
562      else { /* unit triangular (diag='U'): "fill the diagonal" & diag:= "N" */      else { /* unit triangular (diag='U'): "fill the diagonal" & diag:= "N" */
563          CHM_SP chx = AS_CHM_SP(x);          CHM_SP chx = AS_CHM_SP__(x);
564          CHM_SP eye = cholmod_speye(chx->nrow, chx->ncol, chx->xtype, &c);          CHM_SP eye = cholmod_speye(chx->nrow, chx->ncol, chx->xtype, &c);
565          double one[] = {1, 0};          double one[] = {1, 0};
566          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 585 
585      }      }
586      else { /* triangular with diag='N'): now drop the diagonal */      else { /* triangular with diag='N'): now drop the diagonal */
587          /* duplicate, since chx will be modified: */          /* duplicate, since chx will be modified: */
588          CHM_SP chx = AS_CHM_SP(duplicate(x));          SEXP xx = PROTECT(duplicate(x));
589            CHM_SP chx = AS_CHM_SP__(xx);
590          int uploT = (*uplo_P(x) == 'U') ? 1 : -1,          int uploT = (*uplo_P(x) == 'U') ? 1 : -1,
591              Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;              Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
592          R_CheckStack();          R_CheckStack();
593    
594          chm_diagN2U(chx, uploT, /* do_realloc */ FALSE);          chm_diagN2U(chx, uploT, /* do_realloc */ FALSE);
595    
596          return chm_sparse_to_SEXP(chx, /*dofree*/ 0/* or 1 ?? */,          SEXP ans = chm_sparse_to_SEXP(chx, /*dofree*/ 0/* or 1 ?? */,
597                                    uploT, Rkind, "U",                                    uploT, Rkind, "U",
598                                    GET_SLOT(x, Matrix_DimNamesSym));                                    GET_SLOT(x, Matrix_DimNamesSym));
599            UNPROTECT(1);// only now !
600            return ans;
601      }      }
602  }  }
603    
604    /**
605     * "Indexing" aka subsetting : Compute  x[i,j], also for vectors i and j
606     * Working via CHOLMOD_submatrix, see ./CHOLMOD/MatrixOps/cholmod_submatrix.c
607     * @param x CsparseMatrix
608     * @param i row     indices (0-origin), or NULL (R's)
609     * @param j columns indices (0-origin), or NULL
610     *
611     * @return x[i,j]  still CsparseMatrix --- currently, this loses dimnames
612     */
613  SEXP Csparse_submatrix(SEXP x, SEXP i, SEXP j)  SEXP Csparse_submatrix(SEXP x, SEXP i, SEXP j)
614  {  {
615      CHM_SP chx = AS_CHM_SP(x);      CHM_SP chx = AS_CHM_SP(x); /* << does diagU2N() when needed */
616      int rsize = (isNull(i)) ? -1 : LENGTH(i),      int rsize = (isNull(i)) ? -1 : LENGTH(i),
617          csize = (isNull(j)) ? -1 : LENGTH(j);          csize = (isNull(j)) ? -1 : LENGTH(j);
618      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
# Line 460  Line 623 
623      if (csize >= 0 && !isInteger(j))      if (csize >= 0 && !isInteger(j))
624          error(_("Index j must be NULL or integer"));          error(_("Index j must be NULL or integer"));
625    
626      return chm_sparse_to_SEXP(cholmod_submatrix(chx, INTEGER(i), rsize,  #define CHM_SUB(_M_, _i_, _j_)                                  \
627                                                  INTEGER(j), csize,      cholmod_submatrix(_M_,                                      \
628                                                  TRUE, TRUE, &c),                        (rsize < 0) ? NULL : INTEGER(_i_), rsize, \
629                                1, 0, Rkind, "",                        (csize < 0) ? NULL : INTEGER(_j_), csize, \
630                                /* FIXME: drops dimnames */ R_NilValue);                        TRUE, TRUE, &c)
631  }      CHM_SP ans;
632        if (!chx->stype) {/* non-symmetric Matrix */
633            ans = CHM_SUB(chx, i, j);
634        }
635        else {
636            /* for now, cholmod_submatrix() only accepts "generalMatrix" */
637            CHM_SP tmp = cholmod_copy(chx, /* stype: */ 0, chx->xtype, &c);
638            ans = CHM_SUB(tmp, i, j);
639            cholmod_free_sparse(&tmp, &c);
640        }
641    
642        // "FIXME": currently dropping dimnames, and adding them afterwards in R :
643        /* // dimnames: */
644        /* SEXP x_dns = GET_SLOT(x, Matrix_DimNamesSym), */
645        /*  dn = PROTECT(allocVector(VECSXP, 2)); */
646        return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "", /* dimnames: */ R_NilValue);
647    }
648    
649    #define _d_Csp_
650    #include "t_Csparse_subassign.c"
651    
652    #define _l_Csp_
653    #include "t_Csparse_subassign.c"
654    
655    #define _i_Csp_
656    #include "t_Csparse_subassign.c"
657    
658    #define _n_Csp_
659    #include "t_Csparse_subassign.c"
660    
661    #define _z_Csp_
662    #include "t_Csparse_subassign.c"
663    
664    
665    
666  SEXP Csparse_MatrixMarket(SEXP x, SEXP fname)  SEXP Csparse_MatrixMarket(SEXP x, SEXP fname)
667  {  {
# Line 474  Line 670 
670      if (!f)      if (!f)
671          error(_("failure to open file \"%s\" for writing"),          error(_("failure to open file \"%s\" for writing"),
672                CHAR(asChar(fname)));                CHAR(asChar(fname)));
673      if (!cholmod_write_sparse(f, AS_CHM_SP(Csparse_diagU2N(x)),      if (!cholmod_write_sparse(f, AS_CHM_SP(x),
674                                (CHM_SP)NULL, (char*) NULL, &c))                                (CHM_SP)NULL, (char*) NULL, &c))
675          error(_("cholmod_write_sparse returned error code"));          error(_("cholmod_write_sparse returned error code"));
676      fclose(f);      fclose(f);
# Line 494  Line 690 
690   *   *
691   * @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
692   */   */
693  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,
694  /*                                ^^^^^^ FIXME[Generalize] to int / ... */  /*                                ^^^^^^ FIXME[Generalize] to int / ... */
695                     SEXP resultKind)
696  {  {
697      const char* res_ch = CHAR(STRING_ELT(resultKind,0));      const char* res_ch = CHAR(STRING_ELT(resultKind,0));
698      enum diag_kind { diag, diag_backpermuted, trace, prod, sum_log      enum diag_kind { diag, diag_backpermuted, trace, prod, sum_log, min, max, range
699      } res_kind = ((!strcmp(res_ch, "trace")) ? trace :      } res_kind = ((!strcmp(res_ch, "trace")) ? trace :
700                    ((!strcmp(res_ch, "sumLog")) ? sum_log :                    ((!strcmp(res_ch, "sumLog")) ? sum_log :
701                     ((!strcmp(res_ch, "prod")) ? prod :                     ((!strcmp(res_ch, "prod")) ? prod :
702                        ((!strcmp(res_ch, "min")) ? min :
703                         ((!strcmp(res_ch, "max")) ? max :
704                          ((!strcmp(res_ch, "range")) ? range :
705                      ((!strcmp(res_ch, "diag")) ? diag :                      ((!strcmp(res_ch, "diag")) ? diag :
706                       ((!strcmp(res_ch, "diagBack")) ? diag_backpermuted :                       ((!strcmp(res_ch, "diagBack")) ? diag_backpermuted :
707                        -1)))));                           -1))))))));
708      int i, n_x, i_from = 0;      int i, n_x, i_from;
709      SEXP ans = PROTECT(allocVector(REALSXP,      SEXP ans = PROTECT(allocVector(REALSXP,
710  /*                                 ^^^^  FIXME[Generalize] */  /*                                 ^^^^  FIXME[Generalize] */
711                                     (res_kind == diag ||                                     (res_kind == diag ||
712                                      res_kind == diag_backpermuted) ? n : 1));                                      res_kind == diag_backpermuted) ? n :
713                                       (res_kind == range ? 2 : 1)));
714      double *v = REAL(ans);      double *v = REAL(ans);
715  /*  ^^^^^^      ^^^^  FIXME[Generalize] */  /*  ^^^^^^      ^^^^  FIXME[Generalize] */
716    
717        i_from = (is_U ? -1 : 0);
718    
719  #define for_DIAG(v_ASSIGN)                                              \  #define for_DIAG(v_ASSIGN)                                              \
720      for(i = 0; i < n; i++, i_from += n_x) {                             \      for(i = 0; i < n; i++) {                                    \
721          /* looking at i-th column */                                    \          /* looking at i-th column */                                    \
722          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 */ \
723            if( is_U) i_from += n_x;                                \
724          v_ASSIGN;                                                       \          v_ASSIGN;                                                       \
725            if(!is_U) i_from += n_x;                                \
726      }      }
727    
728      /* NOTA BENE: we assume  -- uplo = "L" i.e. lower triangular matrix      /* NOTA BENE: we assume  -- uplo = "L" i.e. lower triangular matrix
729       *            for uplo = "U" (makes sense with a "dtCMatrix" !),       *            for uplo = "U" (makes sense with a "dtCMatrix" !),
730       *            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],
731       *            where nx = (x_p[i+1] - x_p[i])       *            where n_x = (x_p[i+1] - x_p[i])
732       */       */
733    
734      switch(res_kind) {      switch(res_kind) {
735      case trace:      case trace: // = sum
736          v[0] = 0.;          v[0] = 0.;
737          for_DIAG(v[0] += x_x[i_from]);          for_DIAG(v[0] += x_x[i_from]);
738          break;          break;
# Line 542  Line 747 
747          for_DIAG(v[0] *= x_x[i_from]);          for_DIAG(v[0] *= x_x[i_from]);
748          break;          break;
749    
750        case min:
751            v[0] = R_PosInf;
752            for_DIAG(if(v[0] > x_x[i_from]) v[0] = x_x[i_from]);
753            break;
754    
755        case max:
756            v[0] = R_NegInf;
757            for_DIAG(if(v[0] < x_x[i_from]) v[0] = x_x[i_from]);
758            break;
759    
760        case range:
761            v[0] = R_PosInf;
762            v[1] = R_NegInf;
763            for_DIAG(if(v[0] > x_x[i_from]) v[0] = x_x[i_from];
764                     if(v[1] < x_x[i_from]) v[1] = x_x[i_from]);
765            break;
766    
767      case diag:      case diag:
768          for_DIAG(v[i] = x_x[i_from]);          for_DIAG(v[i] = x_x[i_from]);
769          break;          break;
# Line 549  Line 771 
771      case diag_backpermuted:      case diag_backpermuted:
772          for_DIAG(v[i] = x_x[i_from]);          for_DIAG(v[i] = x_x[i_from]);
773    
774          warning(_("resultKind = 'diagBack' (back-permuted) is experimental"));          warning(_("%s = '%s' (back-permuted) is experimental"),
775                    "resultKind", "diagBack");
776          /* now back_permute : */          /* now back_permute : */
777          for(i = 0; i < n; i++) {          for(i = 0; i < n; i++) {
778              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 781 
781          break;          break;
782    
783      default: /* -1 from above */      default: /* -1 from above */
784          error("diag_tC(): invalid 'resultKind'");          error(_("diag_tC(): invalid 'resultKind'"));
785          /* Wall: */ ans = R_NilValue; v = REAL(ans);          /* Wall: */ ans = R_NilValue; v = REAL(ans);
786      }      }
787    
# Line 570  Line 793 
793   * Extract the diagonal entries from *triangular* Csparse matrix  __or__ a   * Extract the diagonal entries from *triangular* Csparse matrix  __or__ a
794   * cholmod_sparse factor (LDL = TRUE).   * cholmod_sparse factor (LDL = TRUE).
795   *   *
796     * @param obj -- now a cholmod_sparse factor or a dtCMatrix
797   * @param pslot  'p' (column pointer)   slot of Csparse matrix/factor   * @param pslot  'p' (column pointer)   slot of Csparse matrix/factor
798   * @param xslot  'x' (non-zero entries) slot of Csparse matrix/factor   * @param xslot  'x' (non-zero entries) slot of Csparse matrix/factor
799   * @param perm_slot  'perm' (= permutation vector) slot of corresponding CHMfactor;   * @param perm_slot  'perm' (= permutation vector) slot of corresponding CHMfactor;
# Line 578  Line 802 
802   *   *
803   * @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
804   */   */
805  SEXP diag_tC(SEXP pslot, SEXP xslot, SEXP perm_slot, SEXP resultKind)  SEXP diag_tC(SEXP obj, SEXP resultKind)
806  {  {
807    
808        SEXP
809            pslot = GET_SLOT(obj, Matrix_pSym),
810            xslot = GET_SLOT(obj, Matrix_xSym);
811        Rboolean is_U = (R_has_slot(obj, Matrix_uploSym) &&
812                         *CHAR(asChar(GET_SLOT(obj, Matrix_uploSym))) == 'U');
813      int n = length(pslot) - 1, /* n = ncol(.) = nrow(.) */      int n = length(pslot) - 1, /* n = ncol(.) = nrow(.) */
814          *x_p  = INTEGER(pslot),          *x_p  = INTEGER(pslot), pp = -1, *perm;
         *perm = INTEGER(perm_slot);  
815      double *x_x = REAL(xslot);      double *x_x = REAL(xslot);
816  /*  ^^^^^^        ^^^^ FIXME[Generalize] to INTEGER(.) / LOGICAL(.) / ... xslot !*/  /*  ^^^^^^        ^^^^ FIXME[Generalize] to INTEGER(.) / LOGICAL(.) / ... xslot !*/
817    
818      return diag_tC_ptr(n, x_p, x_x, perm, resultKind);      if(R_has_slot(obj, Matrix_permSym))
819            perm = INTEGER(GET_SLOT(obj, Matrix_permSym));
820        else perm = &pp;
821    
822        return diag_tC_ptr(n, x_p, x_x, is_U, perm, resultKind);
823    }
824    
825    
826    /**
827     * Create a Csparse matrix object from indices and/or pointers.
828     *
829     * @param cls name of actual class of object to create
830     * @param i optional integer vector of length nnz of row indices
831     * @param j optional integer vector of length nnz of column indices
832     * @param p optional integer vector of length np of row or column pointers
833     * @param np length of integer vector p.  Must be zero if p == (int*)NULL
834     * @param x optional vector of values
835     * @param nnz length of vectors i, j and/or x, whichever is to be used
836     * @param dims optional integer vector of length 2 to be used as
837     *     dimensions.  If dims == (int*)NULL then the maximum row and column
838     *     index are used as the dimensions.
839     * @param dimnames optional list of length 2 to be used as dimnames
840     * @param index1 indicator of 1-based indices
841     *
842     * @return an SEXP of class cls inheriting from CsparseMatrix.
843     */
844    SEXP create_Csparse(char* cls, int* i, int* j, int* p, int np,
845                        void* x, int nnz, int* dims, SEXP dimnames,
846                        int index1)
847    {
848        SEXP ans;
849        int *ij = (int*)NULL, *tri, *trj,
850            mi, mj, mp, nrow = -1, ncol = -1;
851        int xtype = -1;             /* -Wall */
852        CHM_TR T;
853        CHM_SP A;
854    
855        if (np < 0 || nnz < 0)
856            error(_("negative vector lengths not allowed: np = %d, nnz = %d"),
857                  np, nnz);
858        if (1 != ((mi = (i == (int*)NULL)) +
859                  (mj = (j == (int*)NULL)) +
860                  (mp = (p == (int*)NULL))))
861            error(_("exactly 1 of 'i', 'j' or 'p' must be NULL"));
862        if (mp) {
863            if (np) error(_("np = %d, must be zero when p is NULL"), np);
864        } else {
865            if (np) {               /* Expand p to form i or j */
866                if (!(p[0])) error(_("p[0] = %d, should be zero"), p[0]);
867                for (int ii = 0; ii < np; ii++)
868                    if (p[ii] > p[ii + 1])
869                        error(_("p must be non-decreasing"));
870                if (p[np] != nnz)
871                    error("p[np] = %d != nnz = %d", p[np], nnz);
872                ij = Calloc(nnz, int);
873                if (mi) {
874                    i = ij;
875                    nrow = np;
876                } else {
877                    j = ij;
878                    ncol = np;
879                }
880                /* Expand p to 0-based indices */
881                for (int ii = 0; ii < np; ii++)
882                    for (int jj = p[ii]; jj < p[ii + 1]; jj++) ij[jj] = ii;
883            } else {
884                if (nnz)
885                    error(_("Inconsistent dimensions: np = 0 and nnz = %d"),
886                          nnz);
887            }
888        }
889        /* calculate nrow and ncol */
890        if (nrow < 0) {
891            for (int ii = 0; ii < nnz; ii++) {
892                int i1 = i[ii] + (index1 ? 0 : 1); /* 1-based index */
893                if (i1 < 1) error(_("invalid row index at position %d"), ii);
894                if (i1 > nrow) nrow = i1;
895            }
896        }
897        if (ncol < 0) {
898            for (int jj = 0; jj < nnz; jj++) {
899                int j1 = j[jj] + (index1 ? 0 : 1);
900                if (j1 < 1) error(_("invalid column index at position %d"), jj);
901                if (j1 > ncol) ncol = j1;
902            }
903        }
904        if (dims != (int*)NULL) {
905            if (dims[0] > nrow) nrow = dims[0];
906            if (dims[1] > ncol) ncol = dims[1];
907        }
908        /* check the class name */
909        if (strlen(cls) != 8)
910            error(_("strlen of cls argument = %d, should be 8"), strlen(cls));
911        if (!strcmp(cls + 2, "CMatrix"))
912            error(_("cls = \"%s\" does not end in \"CMatrix\""), cls);
913        switch(cls[0]) {
914        case 'd':
915        case 'l':
916            xtype = CHOLMOD_REAL;
917        break;
918        case 'n':
919            xtype = CHOLMOD_PATTERN;
920            break;
921        default:
922            error(_("cls = \"%s\" must begin with 'd', 'l' or 'n'"), cls);
923        }
924        if (cls[1] != 'g')
925            error(_("Only 'g'eneral sparse matrix types allowed"));
926        /* allocate and populate the triplet */
927        T = cholmod_allocate_triplet((size_t)nrow, (size_t)ncol, (size_t)nnz, 0,
928                                     xtype, &c);
929        T->x = x;
930        tri = (int*)T->i;
931        trj = (int*)T->j;
932        for (int ii = 0; ii < nnz; ii++) {
933            tri[ii] = i[ii] - ((!mi && index1) ? 1 : 0);
934            trj[ii] = j[ii] - ((!mj && index1) ? 1 : 0);
935        }
936        /* create the cholmod_sparse structure */
937        A = cholmod_triplet_to_sparse(T, nnz, &c);
938        cholmod_free_triplet(&T, &c);
939        /* copy the information to the SEXP */
940        ans = PROTECT(NEW_OBJECT(MAKE_CLASS(cls)));
941    /* FIXME: This has been copied from chm_sparse_to_SEXP in chm_common.c */
942        /* allocate and copy common slots */
943        nnz = cholmod_nnz(A, &c);
944        dims = INTEGER(ALLOC_SLOT(ans, Matrix_DimSym, INTSXP, 2));
945        dims[0] = A->nrow; dims[1] = A->ncol;
946        Memcpy(INTEGER(ALLOC_SLOT(ans, Matrix_pSym, INTSXP, A->ncol + 1)), (int*)A->p, A->ncol + 1);
947        Memcpy(INTEGER(ALLOC_SLOT(ans, Matrix_iSym, INTSXP, nnz)), (int*)A->i, nnz);
948        switch(cls[1]) {
949        case 'd':
950            Memcpy(REAL(ALLOC_SLOT(ans, Matrix_xSym, REALSXP, nnz)), (double*)A->x, nnz);
951            break;
952        case 'l':
953            error(_("code not yet written for cls = \"lgCMatrix\""));
954        }
955    /* FIXME: dimnames are *NOT* put there yet (if non-NULL) */
956        cholmod_free_sparse(&A, &c);
957        UNPROTECT(1);
958        return ans;
959  }  }

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