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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 1710, Tue Dec 26 15:57:06 2006 UTC pkg/Matrix/src/Csparse.c revision 2725, Sat Oct 8 19:48:44 2011 UTC
# Line 1  Line 1 
1                          /* Sparse matrices in compressed column-oriented form */                          /* Sparse matrices in compressed column-oriented form */
2    
3  #include "Csparse.h"  #include "Csparse.h"
4    #include "Tsparse.h"
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      int j, k, sorted,      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 */
47        SEXP pslot = GET_SLOT(x, Matrix_pSym),
48            islot = GET_SLOT(x, Matrix_iSym);
49        Rboolean sorted, strictly;
50        int j, k,
51          *dims = INTEGER(GET_SLOT(x, Matrix_DimSym)),          *dims = INTEGER(GET_SLOT(x, Matrix_DimSym)),
52          nrow = dims[0],          nrow = dims[0],
53          ncol = dims[1],          ncol = dims[1],
# Line 18  Line 58 
58          return mkString(_("slot p must have length = ncol(.) + 1"));          return mkString(_("slot p must have length = ncol(.) + 1"));
59      if (xp[0] != 0)      if (xp[0] != 0)
60          return mkString(_("first element of slot p must be zero"));          return mkString(_("first element of slot p must be zero"));
61      if (length(islot) != xp[ncol])      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      }      }
68      sorted = TRUE;      sorted = TRUE; strictly = TRUE;
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          for (k = xp[j] + 1; k < xp[j + 1]; k++)          if(sorted) /* only act if >= 2 entries in column j : */
73              if (xi[k] < xi[k - 1]) sorted = FALSE;              for (k = xp[j] + 1; k < xp[j + 1]; k++) {
74                    if (xi[k] < xi[k - 1])
75                        sorted = FALSE;
76                    else if (xi[k] == xi[k - 1])
77                        strictly = FALSE;
78                }
79      }      }
80      if (!sorted) {      if (!sorted) {
81          cholmod_sparse *chx = as_cholmod_sparse(x);          if(maybe_modify) {
82          cholmod_sort(chx, &c);              CHM_SP chx = (CHM_SP) alloca(sizeof(cholmod_sparse));
83          Free(chx);              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    
87                /* Now re-check that row indices are *strictly* increasing
88                 * (and not just increasing) within each column : */
89                for (j = 0; j < ncol; j++) {
90                    for (k = xp[j] + 1; k < xp[j + 1]; k++)
91                        if (xi[k] == xi[k - 1])
92                            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 */
98            return mkString(_("slot i is not *strictly* increasing inside a column"));
99      }      }
100      return ScalarLogical(1);      return ScalarLogical(1);
101  }  }
102    
103    SEXP Rsparse_validate(SEXP x)
104    {
105        /* NB: we do *NOT* check a potential 'x' slot here, at all */
106        SEXP pslot = GET_SLOT(x, Matrix_pSym),
107            jslot = GET_SLOT(x, Matrix_jSym);
108        Rboolean sorted, strictly;
109        int i, k,
110            *dims = INTEGER(GET_SLOT(x, Matrix_DimSym)),
111            nrow = dims[0],
112            ncol = dims[1],
113            *xp = INTEGER(pslot),
114            *xj = INTEGER(jslot);
115    
116        if (length(pslot) != dims[0] + 1)
117            return mkString(_("slot p must have length = nrow(.) + 1"));
118        if (xp[0] != 0)
119            return mkString(_("first element of slot p must be zero"));
120        if (length(jslot) < xp[nrow]) /* allow larger slots from over-allocation!*/
121            return
122                mkString(_("last element of slot p must match length of slots j and x"));
123        for (i = 0; i < length(jslot); i++) {
124            if (xj[i] < 0 || xj[i] >= ncol)
125                return mkString(_("all column indices must be between 0 and ncol-1"));
126        }
127        sorted = TRUE; strictly = TRUE;
128        for (i = 0; i < nrow; i++) {
129            if (xp[i] > xp[i+1])
130                return mkString(_("slot p must be non-decreasing"));
131            if(sorted)
132                for (k = xp[i] + 1; k < xp[i + 1]; k++) {
133                    if (xj[k] < xj[k - 1])
134                        sorted = FALSE;
135                    else if (xj[k] == xj[k - 1])
136                        strictly = FALSE;
137                }
138        }
139        if (!sorted)
140            /* cannot easily use cholmod_sort(.) ... -> "error out" :*/
141            return mkString(_("slot j is not increasing inside a column"));
142        else if(!strictly) /* sorted, but not strictly */
143            return mkString(_("slot j is not *strictly* increasing inside a column"));
144    
145        return ScalarLogical(1);
146    }
147    
148    
149    /* Called from ../R/Csparse.R : */
150    /* Can only return [dln]geMatrix (no symm/triang);
151     * FIXME: replace by non-CHOLMOD code ! */
152  SEXP Csparse_to_dense(SEXP x)  SEXP Csparse_to_dense(SEXP x)
153  {  {
154      cholmod_sparse *chxs = as_cholmod_sparse(x);      CHM_SP chxs = AS_CHM_SP__(x);
155      cholmod_dense *chxd = cholmod_sparse_to_dense(chxs, &c);      /* This loses the symmetry property, since cholmod_dense has none,
156         * BUT, much worse (FIXME!), it also transforms CHOLMOD_PATTERN ("n") matrices
157         * to numeric (CHOLMOD_REAL) ones : */
158        CHM_DN chxd = cholmod_sparse_to_dense(chxs, &c);
159        int Rkind = (chxs->xtype == CHOLMOD_PATTERN)? -1 : Real_kind(x);
160        R_CheckStack();
161    
162      Free(chxs);      return chm_dense_to_SEXP(chxd, 1, Rkind, GET_SLOT(x, Matrix_DimNamesSym));
     return chm_dense_to_SEXP(chxd, 1, Real_kind(x),  
                              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      cholmod_sparse *chxs = as_cholmod_sparse(x);      CHM_SP chxs = AS_CHM_SP__(x);
169      cholmod_sparse      CHM_SP chxcp = cholmod_copy(chxs, chxs->stype, CHOLMOD_PATTERN, &c);
170          *chxcp = cholmod_copy(chxs, chxs->stype, CHOLMOD_PATTERN, &c);      int tr = asLogical(tri);
171      int uploT = 0; char *diag = "";      R_CheckStack();
172    
173      Free(chxs);      return chm_sparse_to_SEXP(chxcp, 1/*do_free*/,
174      if (asLogical(tri)) {       /* triangular sparse matrices */                                tr ? ((*uplo_P(x) == 'U') ? 1 : -1) : 0,
175          uploT = (*uplo_P(x) == 'U') ? 1 : -1;                                0, tr ? diag_P(x) : "",
         diag = CHAR(asChar(GET_SLOT(x, Matrix_diagSym)));  
     }  
     return chm_sparse_to_SEXP(chxcp, 1, uploT, 0, diag,  
176                                GET_SLOT(x, Matrix_DimNamesSym));                                GET_SLOT(x, Matrix_DimNamesSym));
177  }  }
178    
179  SEXP Csparse_to_matrix(SEXP x)  // 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      cholmod_sparse *chxs = as_cholmod_sparse(x);      const char *cl_x = class_P(x);
188      cholmod_dense *chxd = cholmod_sparse_to_dense(chxs, &c);      if(cl_x[0] != 'n') error(_("not a 'n.CMatrix'"));
189        if(cl_x[2] != 'C') error(_("not a CsparseMatrix"));
190        int nnz = LENGTH(GET_SLOT(x, Matrix_iSym));
191        SEXP ans;
192        char *ncl = strdup(cl_x);
193        double *dx_x; int *ix_x;
194        ncl[0] = (r_kind == x_double ? 'd' :
195                  (r_kind == x_logical ? 'l' :
196                   /* else (for now):  r_kind == x_integer : */ 'i'));
197        PROTECT(ans = NEW_OBJECT(MAKE_CLASS(ncl)));
198        // create a correct 'x' slot:
199        switch(r_kind) {
200            int i;
201        case x_double: // 'd'
202            dx_x = REAL(ALLOC_SLOT(ans, Matrix_xSym, REALSXP, nnz));
203            for (i=0; i < nnz; i++) dx_x[i] = 1.;
204            break;
205        case x_logical: // 'l'
206            ix_x = LOGICAL(ALLOC_SLOT(ans, Matrix_xSym, LGLSXP, nnz));
207            for (i=0; i < nnz; i++) ix_x[i] = TRUE;
208            break;
209        case x_integer: // 'i'
210            ix_x = INTEGER(ALLOC_SLOT(ans, Matrix_xSym, INTSXP, nnz));
211            for (i=0; i < nnz; i++) ix_x[i] = 1;
212            break;
213    
214        default:
215            error(_("nz2Csparse(): invalid/non-implemented r_kind = %d"),
216                  r_kind);
217        }
218    
219        // now copy all other slots :
220        slot_dup(ans, x, Matrix_iSym);
221        slot_dup(ans, x, Matrix_pSym);
222        slot_dup(ans, x, Matrix_DimSym);
223        slot_dup(ans, x, Matrix_DimNamesSym);
224        if(ncl[1] != 'g') { // symmetric or triangular ...
225            slot_dup_if_has(ans, x, Matrix_uploSym);
226            slot_dup_if_has(ans, x, Matrix_diagSym);
227        }
228        UNPROTECT(1);
229        return ans;
230    }
231    
232      Free(chxs);  SEXP Csparse_to_matrix(SEXP x)
233      return chm_dense_to_matrix(chxd, 1,  {
234                                 GET_SLOT(x, Matrix_DimNamesSym));      return chm_dense_to_matrix(cholmod_sparse_to_dense(AS_CHM_SP__(x), &c),
235                                   1 /*do_free*/, GET_SLOT(x, Matrix_DimNamesSym));
236  }  }
237    
238  SEXP Csparse_to_Tsparse(SEXP x, SEXP tri)  SEXP Csparse_to_Tsparse(SEXP x, SEXP tri)
239  {  {
240      cholmod_sparse *chxs = as_cholmod_sparse(x);      CHM_SP chxs = AS_CHM_SP__(x);
241      cholmod_triplet *chxt = cholmod_sparse_to_triplet(chxs, &c);      CHM_TR chxt = cholmod_sparse_to_triplet(chxs, &c);
242      int uploT = 0;      int tr = asLogical(tri);
243      char *diag = "";      int Rkind = (chxs->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
244      int Rkind = (chxs->xtype == CHOLMOD_REAL) ? Real_kind(x) : 0;      R_CheckStack();
245    
246      Free(chxs);      return chm_triplet_to_SEXP(chxt, 1,
247      if (asLogical(tri)) {       /* triangular sparse matrices */                                 tr ? ((*uplo_P(x) == 'U') ? 1 : -1) : 0,
248          uploT = (*uplo_P(x) == 'U') ? 1 : -1;                                 Rkind, tr ? diag_P(x) : "",
         diag = diag_P(x);  
     }  
     return chm_triplet_to_SEXP(chxt, 1, uploT, Rkind, diag,  
249                                 GET_SLOT(x, Matrix_DimNamesSym));                                 GET_SLOT(x, Matrix_DimNamesSym));
250  }  }
251    
252  /* this used to be called  sCMatrix_to_gCMatrix(..)   [in ./dsCMatrix.c ]: */  /* this used to be called  sCMatrix_to_gCMatrix(..)   [in ./dsCMatrix.c ]: */
253  SEXP Csparse_symmetric_to_general(SEXP x)  SEXP Csparse_symmetric_to_general(SEXP x)
254  {  {
255      cholmod_sparse *chx = as_cholmod_sparse(x), *chgx;      CHM_SP chx = AS_CHM_SP__(x), chgx;
256      int Rkind = (chx->xtype == CHOLMOD_REAL) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
257        R_CheckStack();
258    
259      if (!(chx->stype))      if (!(chx->stype))
260          error(_("Nonsymmetric matrix in Csparse_symmetric_to_general"));          error(_("Nonsymmetric matrix in Csparse_symmetric_to_general"));
261      chgx = cholmod_copy(chx, /* stype: */ 0, chx->xtype, &c);      chgx = cholmod_copy(chx, /* stype: */ 0, chx->xtype, &c);
262      /* xtype: pattern, "real", complex or .. */      /* xtype: pattern, "real", complex or .. */
     Free(chx);  
263      return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",      return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",
264                                GET_SLOT(x, Matrix_DimNamesSym));                                GET_SLOT(x, Matrix_DimNamesSym));
265  }  }
266    
267  SEXP Csparse_general_to_symmetric(SEXP x, SEXP uplo)  SEXP Csparse_general_to_symmetric(SEXP x, SEXP uplo)
268  {  {
269      cholmod_sparse *chx = as_cholmod_sparse(x), *chgx;      CHM_SP chx = AS_CHM_SP__(x), chgx;
270      int uploT = (*CHAR(asChar(uplo)) == 'U') ? 1 : -1;      int uploT = (*CHAR(STRING_ELT(uplo,0)) == 'U') ? 1 : -1;
271      int Rkind = (chx->xtype == CHOLMOD_REAL) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
272        R_CheckStack();
273    
274      chgx = cholmod_copy(chx, /* stype: */ uploT, chx->xtype, &c);      chgx = cholmod_copy(chx, /* stype: */ uploT, chx->xtype, &c);
275      /* xtype: pattern, "real", complex or .. */      /* xtype: pattern, "real", complex or .. */
     Free(chx);  
276      return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",      return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",
277                                GET_SLOT(x, Matrix_DimNamesSym));                                GET_SLOT(x, Matrix_DimNamesSym));
278  }  }
279    
280  SEXP Csparse_transpose(SEXP x, SEXP tri)  SEXP Csparse_transpose(SEXP x, SEXP tri)
281  {  {
282      cholmod_sparse *chx = as_cholmod_sparse(x);      /* TODO: lgCMatrix & igC* currently go via double prec. cholmod -
283      int Rkind = (chx->xtype == CHOLMOD_REAL) ? Real_kind(x) : 0;       *       since cholmod (& cs) lacks sparse 'int' matrices */
284      cholmod_sparse *chxt = cholmod_transpose(chx, (int) chx->xtype, &c);      CHM_SP chx = AS_CHM_SP__(x);
285        int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
286        CHM_SP chxt = cholmod_transpose(chx, chx->xtype, &c);
287      SEXP dn = PROTECT(duplicate(GET_SLOT(x, Matrix_DimNamesSym))), tmp;      SEXP dn = PROTECT(duplicate(GET_SLOT(x, Matrix_DimNamesSym))), tmp;
288      int uploT = 0; char *diag = "";      int tr = asLogical(tri);
289        R_CheckStack();
290    
     Free(chx);  
291      tmp = VECTOR_ELT(dn, 0);    /* swap the dimnames */      tmp = VECTOR_ELT(dn, 0);    /* swap the dimnames */
292      SET_VECTOR_ELT(dn, 0, VECTOR_ELT(dn, 1));      SET_VECTOR_ELT(dn, 0, VECTOR_ELT(dn, 1));
293      SET_VECTOR_ELT(dn, 1, tmp);      SET_VECTOR_ELT(dn, 1, tmp);
294      UNPROTECT(1);      UNPROTECT(1);
295      if (asLogical(tri)) { /* triangular sparse matrices : SWAP 'uplo' */      return chm_sparse_to_SEXP(chxt, 1, /* SWAP 'uplo' for triangular */
296          uploT = (*uplo_P(x) == 'U') ? -1 : 1;                                tr ? ((*uplo_P(x) == 'U') ? -1 : 1) : 0,
297          diag = diag_P(x);                                Rkind, tr ? diag_P(x) : "", dn);
     }  
     return chm_sparse_to_SEXP(chxt, 1, uploT, Rkind, diag, dn);  
298  }  }
299    
300  SEXP Csparse_Csparse_prod(SEXP a, SEXP b)  SEXP Csparse_Csparse_prod(SEXP a, SEXP b)
301  {  {
302      cholmod_sparse      CHM_SP
303          *cha = as_cholmod_sparse(a),          cha = AS_CHM_SP(a),
304          *chb = as_cholmod_sparse(b);          chb = AS_CHM_SP(b),
305      cholmod_sparse *chc = cholmod_ssmult(cha, chb, 0, cha->xtype, 1, &c);          chc = cholmod_ssmult(cha, chb, /*out_stype:*/ 0,
306      SEXP dn = allocVector(VECSXP, 2);                                 /* values:= is_numeric (T/F) */ cha->xtype > 0,
307                                   /*out sorted:*/ 1, &c);
308        const char *cl_a = class_P(a), *cl_b = class_P(b);
309        char diag[] = {'\0', '\0'};
310        int uploT = 0;
311        SEXP dn = PROTECT(allocVector(VECSXP, 2));
312        R_CheckStack();
313    
314      Free(cha); Free(chb);  #ifdef DEBUG_Matrix_verbose
315        Rprintf("DBG Csparse_C*_prod(%s, %s)\n", cl_a, cl_b);
316    #endif
317    
318        /* Preserve triangularity and even unit-triangularity if appropriate.
319         * Note that in that case, the multiplication itself should happen
320         * faster.  But there's no support for that in CHOLMOD */
321    
322        /* UGLY hack -- rather should have (fast!) C-level version of
323         *       is(a, "triangularMatrix") etc */
324        if (cl_a[1] == 't' && cl_b[1] == 't')
325            /* FIXME: fails for "Cholesky","BunchKaufmann"..*/
326            if(*uplo_P(a) == *uplo_P(b)) { /* both upper, or both lower tri. */
327                uploT = (*uplo_P(a) == 'U') ? 1 : -1;
328                if(*diag_P(a) == 'U' && *diag_P(b) == 'U') { /* return UNIT-triag. */
329                    /* "remove the diagonal entries": */
330                    chm_diagN2U(chc, uploT, /* do_realloc */ FALSE);
331                    diag[0]= 'U';
332                }
333                else diag[0]= 'N';
334            }
335      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
336                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));
337      SET_VECTOR_ELT(dn, 1,      SET_VECTOR_ELT(dn, 1,
338                     duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), 1)));                     duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), 1)));
339      return chm_sparse_to_SEXP(chc, 1, 0, 0, "", dn);      UNPROTECT(1);
340        return chm_sparse_to_SEXP(chc, 1, uploT, /*Rkind*/0, diag, dn);
341  }  }
342    
343  SEXP Csparse_Csparse_crossprod(SEXP a, SEXP b, SEXP trans)  SEXP Csparse_Csparse_crossprod(SEXP a, SEXP b, SEXP trans)
344  {  {
345      int tr = asLogical(trans);      int tr = asLogical(trans);
346      cholmod_sparse      CHM_SP
347          *cha = as_cholmod_sparse(a),          cha = AS_CHM_SP(a),
348          *chb = as_cholmod_sparse(b);          chb = AS_CHM_SP(b),
349      cholmod_sparse *chTr, *chc;          chTr, chc;
350      SEXP dn = allocVector(VECSXP, 2);      const char *cl_a = class_P(a), *cl_b = class_P(b);
351        char diag[] = {'\0', '\0'};
352  /*     cholmod_sparse *chTr = cholmod_transpose(cha, 1, &c); */      int uploT = 0;
353  /*     cholmod_sparse *chc = cholmod_ssmult(chTr, chb, 0, cha->xtype, 1, &c); */      SEXP dn = PROTECT(allocVector(VECSXP, 2));
354        R_CheckStack();
     if (tr)  
         chTr = cholmod_transpose(chb, chb->xtype, &c);  
     else  
         chTr = cholmod_transpose(cha, cha->xtype, &c);  
     chc = cholmod_ssmult((tr) ? cha : chTr, (tr) ? chTr : chb,  
                          0, cha->xtype, 1, &c);  
355    
356      Free(cha); Free(chb); cholmod_free_sparse(&chTr, &c);      chTr = cholmod_transpose((tr) ? chb : cha, chb->xtype, &c);
357        chc = cholmod_ssmult((tr) ? cha : chTr, (tr) ? chTr : chb,
358                             /*out_stype:*/ 0, cha->xtype, /*out sorted:*/ 1, &c);
359        cholmod_free_sparse(&chTr, &c);
360    
361        /* Preserve triangularity and unit-triangularity if appropriate;
362         * see Csparse_Csparse_prod() for comments */
363        if (cl_a[1] == 't' && cl_b[1] == 't')
364            if(*uplo_P(a) != *uplo_P(b)) { /* one 'U', the other 'L' */
365                uploT = (*uplo_P(b) == 'U') ? 1 : -1;
366                if(*diag_P(a) == 'U' && *diag_P(b) == 'U') { /* return UNIT-triag. */
367                    chm_diagN2U(chc, uploT, /* do_realloc */ FALSE);
368                    diag[0]= 'U';
369                }
370                else diag[0]= 'N';
371            }
372      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
373                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), (tr) ? 0 : 1)));                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), (tr) ? 0 : 1)));
374      SET_VECTOR_ELT(dn, 1,      SET_VECTOR_ELT(dn, 1,
375                     duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), (tr) ? 0 : 1)));                     duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), (tr) ? 0 : 1)));
376      return chm_sparse_to_SEXP(chc, 1, 0, 0, "", dn);      UNPROTECT(1);
377        return chm_sparse_to_SEXP(chc, 1, uploT, /*Rkind*/0, diag, dn);
378  }  }
379    
380  SEXP Csparse_dense_prod(SEXP a, SEXP b)  SEXP Csparse_dense_prod(SEXP a, SEXP b)
381  {  {
382      cholmod_sparse *cha = as_cholmod_sparse(a);      CHM_SP cha = AS_CHM_SP(a);
383      SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));      SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));
384      cholmod_dense *chb = as_cholmod_dense(b_M);      CHM_DN chb = AS_CHM_DN(b_M);
385      cholmod_dense *chc =      CHM_DN chc = cholmod_allocate_dense(cha->nrow, chb->ncol, cha->nrow,
386          cholmod_allocate_dense(cha->nrow, chb->ncol, cha->nrow, chb->xtype, &c);                                          chb->xtype, &c);
387      SEXP dn = allocVector(VECSXP, 2);      SEXP dn = PROTECT(allocVector(VECSXP, 2));
388      double alpha[] = {1,0}, beta[] = {0,0};      double one[] = {1,0}, zero[] = {0,0};
389        int nprot = 2;
390      cholmod_sdmult(cha, 0, alpha, beta, chb, chc, &c);      R_CheckStack();
391      Free(cha); Free(chb);      /* Tim Davis, please FIXME:  currently (2010-11) *fails* when  a  is a pattern matrix:*/
392      UNPROTECT(1);      if(cha->xtype == CHOLMOD_PATTERN) {
393            /* warning(_("Csparse_dense_prod(): cholmod_sdmult() not yet implemented for pattern./ ngCMatrix" */
394            /*        " --> slightly inefficient coercion")); */
395    
396            // This *fails* to produce a CHOLMOD_REAL ..
397            // CHM_SP chd = cholmod_l_copy(cha, cha->stype, CHOLMOD_REAL, &c);
398            // --> use our Matrix-classes
399            SEXP da = PROTECT(nz2Csparse(a, x_double)); nprot++;
400            cha = AS_CHM_SP(da);
401        }
402        cholmod_sdmult(cha, 0, one, zero, chb, chc, &c);
403      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
404                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));
405      SET_VECTOR_ELT(dn, 1,      SET_VECTOR_ELT(dn, 1,
406                     duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));                     duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));
407        UNPROTECT(nprot);
408      return chm_dense_to_SEXP(chc, 1, 0, dn);      return chm_dense_to_SEXP(chc, 1, 0, dn);
409  }  }
410    
411  SEXP Csparse_dense_crossprod(SEXP a, SEXP b)  SEXP Csparse_dense_crossprod(SEXP a, SEXP b)
412  {  {
413      cholmod_sparse *cha = as_cholmod_sparse(a);      CHM_SP cha = AS_CHM_SP(a);
414      SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));      SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));
415      cholmod_dense *chb = as_cholmod_dense(b_M);      CHM_DN chb = AS_CHM_DN(b_M);
416      cholmod_dense *chc =      CHM_DN chc = cholmod_allocate_dense(cha->ncol, chb->ncol, cha->ncol,
417          cholmod_allocate_dense(cha->ncol, chb->ncol, cha->ncol, chb->xtype, &c);                                          chb->xtype, &c);
418      SEXP dn = allocVector(VECSXP, 2);      SEXP dn = PROTECT(allocVector(VECSXP, 2)); int nprot = 2;
419      double alpha[] = {1,0}, beta[] = {0,0};      double one[] = {1,0}, zero[] = {0,0};
420        R_CheckStack();
421      cholmod_sdmult(cha, 1, alpha, beta, chb, chc, &c);      // -- see Csparse_dense_prod() above :
422      Free(cha); Free(chb);      if(cha->xtype == CHOLMOD_PATTERN) {
423      UNPROTECT(1);          SEXP da = PROTECT(nz2Csparse(a, x_double)); nprot++;
424            cha = AS_CHM_SP(da);
425        }
426        cholmod_sdmult(cha, 1, one, zero, chb, chc, &c);
427      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
428                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 1)));                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 1)));
429      SET_VECTOR_ELT(dn, 1,      SET_VECTOR_ELT(dn, 1,
430                     duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));                     duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));
431        UNPROTECT(nprot);
432      return chm_dense_to_SEXP(chc, 1, 0, dn);      return chm_dense_to_SEXP(chc, 1, 0, dn);
433  }  }
434    
435  /* Computes   x'x  or  x x'  -- see Csparse_Csparse_crossprod above for  x'y and x y' */  /* Computes   x'x  or  x x' -- *also* for Tsparse (triplet = TRUE)
436       see Csparse_Csparse_crossprod above for  x'y and x y' */
437  SEXP Csparse_crossprod(SEXP x, SEXP trans, SEXP triplet)  SEXP Csparse_crossprod(SEXP x, SEXP trans, SEXP triplet)
438  {  {
439      int trip = asLogical(triplet),      int trip = asLogical(triplet),
440          tr   = asLogical(trans); /* gets reversed because _aat is tcrossprod */          tr   = asLogical(trans); /* gets reversed because _aat is tcrossprod */
441      cholmod_triplet  #ifdef AS_CHM_DIAGU2N_FIXED_FINALLY
442          *cht = trip ? as_cholmod_triplet(x) : (cholmod_triplet*) NULL;      CHM_TR cht = trip ? AS_CHM_TR(x) : (CHM_TR) NULL;
443      cholmod_sparse *chcp, *chxt,  #else /* workaround needed:*/
444          *chx = trip ? cholmod_triplet_to_sparse(cht, cht->nnz, &c)      SEXP xx = PROTECT(Tsparse_diagU2N(x));
445          : as_cholmod_sparse(x);      CHM_TR cht = trip ? AS_CHM_TR__(xx) : (CHM_TR) NULL;
446    #endif
447        CHM_SP chcp, chxt,
448            chx = (trip ?
449                   cholmod_triplet_to_sparse(cht, cht->nnz, &c) :
450                   AS_CHM_SP(x));
451      SEXP dn = PROTECT(allocVector(VECSXP, 2));      SEXP dn = PROTECT(allocVector(VECSXP, 2));
452        R_CheckStack();
453    
454      if (!tr)      if (!tr) chxt = cholmod_transpose(chx, chx->xtype, &c);
         chxt = cholmod_transpose(chx, chx->xtype, &c);  
455      chcp = cholmod_aat((!tr) ? chxt : chx, (int *) NULL, 0, chx->xtype, &c);      chcp = cholmod_aat((!tr) ? chxt : chx, (int *) NULL, 0, chx->xtype, &c);
456      if(!chcp)      if(!chcp) {
457            UNPROTECT(1);
458          error(_("Csparse_crossprod(): error return from cholmod_aat()"));          error(_("Csparse_crossprod(): error return from cholmod_aat()"));
459        }
460      cholmod_band_inplace(0, chcp->ncol, chcp->xtype, chcp, &c);      cholmod_band_inplace(0, chcp->ncol, chcp->xtype, chcp, &c);
461      chcp->stype = 1;      chcp->stype = 1;
462      if (trip) {      if (trip) cholmod_free_sparse(&chx, &c);
         cholmod_free_sparse(&chx, &c);  
         Free(cht);  
     } else {  
         Free(chx);  
     }  
463      if (!tr) cholmod_free_sparse(&chxt, &c);      if (!tr) cholmod_free_sparse(&chxt, &c);
464                                  /* create dimnames */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
     SET_VECTOR_ELT(dn, 0,  
465                     duplicate(VECTOR_ELT(GET_SLOT(x, Matrix_DimNamesSym),                     duplicate(VECTOR_ELT(GET_SLOT(x, Matrix_DimNamesSym),
466                                          (tr) ? 0 : 1)));                                          (tr) ? 0 : 1)));
467      SET_VECTOR_ELT(dn, 1, duplicate(VECTOR_ELT(dn, 0)));      SET_VECTOR_ELT(dn, 1, duplicate(VECTOR_ELT(dn, 0)));
468    #ifdef AS_CHM_DIAGU2N_FIXED_FINALLY
469      UNPROTECT(1);      UNPROTECT(1);
470    #else
471        UNPROTECT(2);
472    #endif
473      return chm_sparse_to_SEXP(chcp, 1, 0, 0, "", dn);      return chm_sparse_to_SEXP(chcp, 1, 0, 0, "", dn);
474  }  }
475    
476    /* Csparse_drop(x, tol):  drop entries with absolute value < tol, i.e,
477    *  at least all "explicit" zeros */
478  SEXP Csparse_drop(SEXP x, SEXP tol)  SEXP Csparse_drop(SEXP x, SEXP tol)
479  {  {
480      cholmod_sparse *chx = as_cholmod_sparse(x),      const char *cl = class_P(x);
481          *ans = cholmod_copy(chx, chx->stype, chx->xtype, &c);      /* dtCMatrix, etc; [1] = the second character =?= 't' for triangular */
482        int tr = (cl[1] == 't');
483        CHM_SP chx = AS_CHM_SP__(x);
484        CHM_SP ans = cholmod_copy(chx, chx->stype, chx->xtype, &c);
485      double dtol = asReal(tol);      double dtol = asReal(tol);
486      int Rkind = (chx->xtype == CHOLMOD_REAL) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
487        R_CheckStack();
488    
489      if(!cholmod_drop(dtol, ans, &c))      if(!cholmod_drop(dtol, ans, &c))
490          error(_("cholmod_drop() failed"));          error(_("cholmod_drop() failed"));
491      Free(chx);     return chm_sparse_to_SEXP(ans, 1,
492      /* FIXME: currently drops dimnames */                                tr ? ((*uplo_P(x) == 'U') ? 1 : -1) : 0,
493      return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "", R_NilValue);                                Rkind, tr ? diag_P(x) : "",
494                                  GET_SLOT(x, Matrix_DimNamesSym));
495  }  }
496    
   
497  SEXP Csparse_horzcat(SEXP x, SEXP y)  SEXP Csparse_horzcat(SEXP x, SEXP y)
498  {  {
499      cholmod_sparse *chx = as_cholmod_sparse(x),      CHM_SP chx = AS_CHM_SP__(x), chy = AS_CHM_SP__(y);
500          *chy = as_cholmod_sparse(y), *ans;      int Rk_x = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0,
501      int Rkind = 0; /* only for "d" - FIXME */          Rk_y = (chy->xtype != CHOLMOD_PATTERN) ? Real_kind(y) : 0,
502            Rkind = /* logical if both x and y are */ (Rk_x == 1 && Rk_y == 1) ? 1 : 0;
503      ans = cholmod_horzcat(chx, chy, 1, &c);      R_CheckStack();
504      Free(chx); Free(chy);  
505      /* FIXME: currently drops dimnames */      /* TODO: currently drops dimnames - and we fix at R level */
506      return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "", R_NilValue);      return chm_sparse_to_SEXP(cholmod_horzcat(chx, chy, 1, &c),
507                                  1, 0, Rkind, "", R_NilValue);
508  }  }
509    
510  SEXP Csparse_vertcat(SEXP x, SEXP y)  SEXP Csparse_vertcat(SEXP x, SEXP y)
511  {  {
512      cholmod_sparse *chx = as_cholmod_sparse(x),      CHM_SP chx = AS_CHM_SP__(x), chy = AS_CHM_SP__(y);
513          *chy = as_cholmod_sparse(y), *ans;      int Rk_x = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0,
514      int Rkind = 0; /* only for "d" - FIXME */          Rk_y = (chy->xtype != CHOLMOD_PATTERN) ? Real_kind(y) : 0,
515            Rkind = /* logical if both x and y are */ (Rk_x == 1 && Rk_y == 1) ? 1 : 0;
516      ans = cholmod_vertcat(chx, chy, 1, &c);      R_CheckStack();
517      Free(chx); Free(chy);  
518      /* FIXME: currently drops dimnames */      /* TODO: currently drops dimnames - and we fix at R level */
519      return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "", R_NilValue);      return chm_sparse_to_SEXP(cholmod_vertcat(chx, chy, 1, &c),
520                                  1, 0, Rkind, "", R_NilValue);
521  }  }
522    
523  SEXP Csparse_band(SEXP x, SEXP k1, SEXP k2)  SEXP Csparse_band(SEXP x, SEXP k1, SEXP k2)
524  {  {
525      cholmod_sparse *chx = as_cholmod_sparse(x), *ans;      CHM_SP chx = AS_CHM_SP__(x);
526      int Rkind = (chx->xtype == CHOLMOD_REAL) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
527        CHM_SP ans = cholmod_band(chx, asInteger(k1), asInteger(k2), chx->xtype, &c);
528        R_CheckStack();
529    
530      ans = cholmod_band(chx, asInteger(k1), asInteger(k2), chx->xtype, &c);      return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "",
531      Free(chx);                                GET_SLOT(x, Matrix_DimNamesSym));
     return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "", R_NilValue);  
532  }  }
533    
534  SEXP Csparse_diagU2N(SEXP x)  SEXP Csparse_diagU2N(SEXP x)
535  {  {
536      if (*diag_P(x) != 'U') {/* "trivially fast" when there's no 'diag' slot at all */      const char *cl = class_P(x);
537        /* dtCMatrix, etc; [1] = the second character =?= 't' for triangular */
538        if (cl[1] != 't' || *diag_P(x) != 'U') {
539            /* "trivially fast" when not triangular (<==> no 'diag' slot),
540               or not *unit* triangular */
541          return (x);          return (x);
542      }      }
543      else {      else { /* unit triangular (diag='U'): "fill the diagonal" & diag:= "N" */
544          cholmod_sparse *chx = as_cholmod_sparse(x);          CHM_SP chx = AS_CHM_SP__(x);
545          cholmod_sparse *eye = cholmod_speye(chx->nrow, chx->ncol, chx->xtype, &c);          CHM_SP eye = cholmod_speye(chx->nrow, chx->ncol, chx->xtype, &c);
546          double one[] = {1, 0};          double one[] = {1, 0};
547          cholmod_sparse *ans = cholmod_add(chx, eye, one, one, TRUE, TRUE, &c);          CHM_SP ans = cholmod_add(chx, eye, one, one, TRUE, TRUE, &c);
548          int uploT = (*uplo_P(x) == 'U') ? 1 : -1;          int uploT = (*uplo_P(x) == 'U') ? 1 : -1;
549          int Rkind = (chx->xtype == CHOLMOD_REAL) ? Real_kind(x) : 0;          int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
550    
551          Free(chx); cholmod_free_sparse(&eye, &c);          R_CheckStack();
552            cholmod_free_sparse(&eye, &c);
553          return chm_sparse_to_SEXP(ans, 1, uploT, Rkind, "N",          return chm_sparse_to_SEXP(ans, 1, uploT, Rkind, "N",
554                                    duplicate(GET_SLOT(x, Matrix_DimNamesSym)));                                    GET_SLOT(x, Matrix_DimNamesSym));
555      }      }
556  }  }
557    
558    SEXP Csparse_diagN2U(SEXP x)
559    {
560        const char *cl = class_P(x);
561        /* dtCMatrix, etc; [1] = the second character =?= 't' for triangular */
562        if (cl[1] != 't' || *diag_P(x) != 'N') {
563            /* "trivially fast" when not triangular (<==> no 'diag' slot),
564               or already *unit* triangular */
565            return (x);
566        }
567        else { /* triangular with diag='N'): now drop the diagonal */
568            /* duplicate, since chx will be modified: */
569            CHM_SP chx = AS_CHM_SP__(duplicate(x));
570            int uploT = (*uplo_P(x) == 'U') ? 1 : -1,
571                Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
572            R_CheckStack();
573    
574            chm_diagN2U(chx, uploT, /* do_realloc */ FALSE);
575    
576            return chm_sparse_to_SEXP(chx, /*dofree*/ 0/* or 1 ?? */,
577                                      uploT, Rkind, "U",
578                                      GET_SLOT(x, Matrix_DimNamesSym));
579        }
580    }
581    
582    /**
583     * "Indexing" aka subsetting : Compute  x[i,j], also for vectors i and j
584     * Working via CHOLMOD_submatrix, see ./CHOLMOD/MatrixOps/cholmod_submatrix.c
585     * @param x CsparseMatrix
586     * @param i row     indices (0-origin), or NULL (R's)
587     * @param j columns indices (0-origin), or NULL
588     *
589     * @return x[i,j]  still CsparseMatrix --- currently, this loses dimnames
590     */
591  SEXP Csparse_submatrix(SEXP x, SEXP i, SEXP j)  SEXP Csparse_submatrix(SEXP x, SEXP i, SEXP j)
592  {  {
593      cholmod_sparse *chx = as_cholmod_sparse(x);      CHM_SP chx = AS_CHM_SP(x); /* << does diagU2N() when needed */
594      int rsize = (isNull(i)) ? -1 : LENGTH(i),      int rsize = (isNull(i)) ? -1 : LENGTH(i),
595          csize = (isNull(j)) ? -1 : LENGTH(j);          csize = (isNull(j)) ? -1 : LENGTH(j);
596      int Rkind = (chx->xtype == CHOLMOD_REAL) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
597        R_CheckStack();
598    
599      if (rsize >= 0 && !isInteger(i))      if (rsize >= 0 && !isInteger(i))
600          error(_("Index i must be NULL or integer"));          error(_("Index i must be NULL or integer"));
601      if (csize >= 0 && !isInteger(j))      if (csize >= 0 && !isInteger(j))
602          error(_("Index j must be NULL or integer"));          error(_("Index j must be NULL or integer"));
603      return chm_sparse_to_SEXP(cholmod_submatrix(chx, INTEGER(i), rsize,  
604                                                  INTEGER(j), csize,      if (chx->stype) /* symmetricMatrix */
605            /* for now, cholmod_submatrix() only accepts "generalMatrix" */
606            chx = cholmod_copy(chx, /* stype: */ 0, chx->xtype, &c);
607    
608        return chm_sparse_to_SEXP(cholmod_submatrix(chx,
609                                    (rsize < 0) ? NULL : INTEGER(i), rsize,
610                                    (csize < 0) ? NULL : INTEGER(j), csize,
611                                                  TRUE, TRUE, &c),                                                  TRUE, TRUE, &c),
612                                1, 0, Rkind, "", R_NilValue);                                1, 0, Rkind, "",
613                                  /* FIXME: drops dimnames */ R_NilValue);
614    }
615    
616    #define _d_Csp_
617    #include "t_Csparse_subassign.c"
618    
619    #define _l_Csp_
620    #include "t_Csparse_subassign.c"
621    
622    #define _i_Csp_
623    #include "t_Csparse_subassign.c"
624    
625    #define _n_Csp_
626    #include "t_Csparse_subassign.c"
627    
628    #define _z_Csp_
629    #include "t_Csparse_subassign.c"
630    
631    
632    
633    SEXP Csparse_MatrixMarket(SEXP x, SEXP fname)
634    {
635        FILE *f = fopen(CHAR(asChar(fname)), "w");
636    
637        if (!f)
638            error(_("failure to open file \"%s\" for writing"),
639                  CHAR(asChar(fname)));
640        if (!cholmod_write_sparse(f, AS_CHM_SP(x),
641                                  (CHM_SP)NULL, (char*) NULL, &c))
642            error(_("cholmod_write_sparse returned error code"));
643        fclose(f);
644        return R_NilValue;
645    }
646    
647    
648    /**
649     * Extract the diagonal entries from *triangular* Csparse matrix  __or__ a
650     * cholmod_sparse factor (LDL = TRUE).
651     *
652     * @param n  dimension of the matrix.
653     * @param x_p  'p' (column pointer) slot contents
654     * @param x_x  'x' (non-zero entries) slot contents
655     * @param perm 'perm' (= permutation vector) slot contents; only used for "diagBack"
656     * @param resultKind a (SEXP) string indicating which kind of result is desired.
657     *
658     * @return  a SEXP, either a (double) number or a length n-vector of diagonal entries
659     */
660    SEXP diag_tC_ptr(int n, int *x_p, double *x_x, int *perm, SEXP resultKind)
661    /*                                ^^^^^^ FIXME[Generalize] to int / ... */
662    {
663        const char* res_ch = CHAR(STRING_ELT(resultKind,0));
664        enum diag_kind { diag, diag_backpermuted, trace, prod, sum_log
665        } res_kind = ((!strcmp(res_ch, "trace")) ? trace :
666                      ((!strcmp(res_ch, "sumLog")) ? sum_log :
667                       ((!strcmp(res_ch, "prod")) ? prod :
668                        ((!strcmp(res_ch, "diag")) ? diag :
669                         ((!strcmp(res_ch, "diagBack")) ? diag_backpermuted :
670                          -1)))));
671        int i, n_x, i_from = 0;
672        SEXP ans = PROTECT(allocVector(REALSXP,
673    /*                                 ^^^^  FIXME[Generalize] */
674                                       (res_kind == diag ||
675                                        res_kind == diag_backpermuted) ? n : 1));
676        double *v = REAL(ans);
677    /*  ^^^^^^      ^^^^  FIXME[Generalize] */
678    
679    #define for_DIAG(v_ASSIGN)                                              \
680        for(i = 0; i < n; i++, i_from += n_x) {                             \
681            /* looking at i-th column */                                    \
682            n_x = x_p[i+1] - x_p[i];/* #{entries} in this column */ \
683            v_ASSIGN;                                                       \
684        }
685    
686        /* NOTA BENE: we assume  -- uplo = "L" i.e. lower triangular matrix
687         *            for uplo = "U" (makes sense with a "dtCMatrix" !),
688         *            should use  x_x[i_from + (nx - 1)] instead of x_x[i_from],
689         *            where nx = (x_p[i+1] - x_p[i])
690         */
691    
692        switch(res_kind) {
693        case trace:
694            v[0] = 0.;
695            for_DIAG(v[0] += x_x[i_from]);
696            break;
697    
698        case sum_log:
699            v[0] = 0.;
700            for_DIAG(v[0] += log(x_x[i_from]));
701            break;
702    
703        case prod:
704            v[0] = 1.;
705            for_DIAG(v[0] *= x_x[i_from]);
706            break;
707    
708        case diag:
709            for_DIAG(v[i] = x_x[i_from]);
710            break;
711    
712        case diag_backpermuted:
713            for_DIAG(v[i] = x_x[i_from]);
714    
715            warning(_("resultKind = 'diagBack' (back-permuted) is experimental"));
716            /* now back_permute : */
717            for(i = 0; i < n; i++) {
718                double tmp = v[i]; v[i] = v[perm[i]]; v[perm[i]] = tmp;
719                /*^^^^ FIXME[Generalize] */
720            }
721            break;
722    
723        default: /* -1 from above */
724            error(_("diag_tC(): invalid 'resultKind'"));
725            /* Wall: */ ans = R_NilValue; v = REAL(ans);
726        }
727    
728        UNPROTECT(1);
729        return ans;
730    }
731    
732    /**
733     * Extract the diagonal entries from *triangular* Csparse matrix  __or__ a
734     * cholmod_sparse factor (LDL = TRUE).
735     *
736     * @param pslot  'p' (column pointer)   slot of Csparse matrix/factor
737     * @param xslot  'x' (non-zero entries) slot of Csparse matrix/factor
738     * @param perm_slot  'perm' (= permutation vector) slot of corresponding CHMfactor;
739     *                   only used for "diagBack"
740     * @param resultKind a (SEXP) string indicating which kind of result is desired.
741     *
742     * @return  a SEXP, either a (double) number or a length n-vector of diagonal entries
743     */
744    SEXP diag_tC(SEXP pslot, SEXP xslot, SEXP perm_slot, SEXP resultKind)
745    {
746        int n = length(pslot) - 1, /* n = ncol(.) = nrow(.) */
747            *x_p  = INTEGER(pslot),
748            *perm = INTEGER(perm_slot);
749        double *x_x = REAL(xslot);
750    /*  ^^^^^^        ^^^^ FIXME[Generalize] to INTEGER(.) / LOGICAL(.) / ... xslot !*/
751    
752        return diag_tC_ptr(n, x_p, x_x, perm, resultKind);
753    }
754    
755    /**
756     * Create a Csparse matrix object from indices and/or pointers.
757     *
758     * @param cls name of actual class of object to create
759     * @param i optional integer vector of length nnz of row indices
760     * @param j optional integer vector of length nnz of column indices
761     * @param p optional integer vector of length np of row or column pointers
762     * @param np length of integer vector p.  Must be zero if p == (int*)NULL
763     * @param x optional vector of values
764     * @param nnz length of vectors i, j and/or x, whichever is to be used
765     * @param dims optional integer vector of length 2 to be used as
766     *     dimensions.  If dims == (int*)NULL then the maximum row and column
767     *     index are used as the dimensions.
768     * @param dimnames optional list of length 2 to be used as dimnames
769     * @param index1 indicator of 1-based indices
770     *
771     * @return an SEXP of class cls inheriting from CsparseMatrix.
772     */
773    SEXP create_Csparse(char* cls, int* i, int* j, int* p, int np,
774                        void* x, int nnz, int* dims, SEXP dimnames,
775                        int index1)
776    {
777        SEXP ans;
778        int *ij = (int*)NULL, *tri, *trj,
779            mi, mj, mp, nrow = -1, ncol = -1;
780        int xtype = -1;             /* -Wall */
781        CHM_TR T;
782        CHM_SP A;
783    
784        if (np < 0 || nnz < 0)
785            error(_("negative vector lengths not allowed: np = %d, nnz = %d"),
786                  np, nnz);
787        if (1 != ((mi = (i == (int*)NULL)) +
788                  (mj = (j == (int*)NULL)) +
789                  (mp = (p == (int*)NULL))))
790            error(_("exactly 1 of 'i', 'j' or 'p' must be NULL"));
791        if (mp) {
792            if (np) error(_("np = %d, must be zero when p is NULL"), np);
793        } else {
794            if (np) {               /* Expand p to form i or j */
795                if (!(p[0])) error(_("p[0] = %d, should be zero"), p[0]);
796                for (int ii = 0; ii < np; ii++)
797                    if (p[ii] > p[ii + 1])
798                        error(_("p must be non-decreasing"));
799                if (p[np] != nnz)
800                    error("p[np] = %d != nnz = %d", p[np], nnz);
801                ij = Calloc(nnz, int);
802                if (mi) {
803                    i = ij;
804                    nrow = np;
805                } else {
806                    j = ij;
807                    ncol = np;
808                }
809                /* Expand p to 0-based indices */
810                for (int ii = 0; ii < np; ii++)
811                    for (int jj = p[ii]; jj < p[ii + 1]; jj++) ij[jj] = ii;
812            } else {
813                if (nnz)
814                    error(_("Inconsistent dimensions: np = 0 and nnz = %d"),
815                          nnz);
816            }
817        }
818        /* calculate nrow and ncol */
819        if (nrow < 0) {
820            for (int ii = 0; ii < nnz; ii++) {
821                int i1 = i[ii] + (index1 ? 0 : 1); /* 1-based index */
822                if (i1 < 1) error(_("invalid row index at position %d"), ii);
823                if (i1 > nrow) nrow = i1;
824            }
825        }
826        if (ncol < 0) {
827            for (int jj = 0; jj < nnz; jj++) {
828                int j1 = j[jj] + (index1 ? 0 : 1);
829                if (j1 < 1) error(_("invalid column index at position %d"), jj);
830                if (j1 > ncol) ncol = j1;
831            }
832        }
833        if (dims != (int*)NULL) {
834            if (dims[0] > nrow) nrow = dims[0];
835            if (dims[1] > ncol) ncol = dims[1];
836        }
837        /* check the class name */
838        if (strlen(cls) != 8)
839            error(_("strlen of cls argument = %d, should be 8"), strlen(cls));
840        if (!strcmp(cls + 2, "CMatrix"))
841            error(_("cls = \"%s\" does not end in \"CMatrix\""), cls);
842        switch(cls[0]) {
843        case 'd':
844        case 'l':
845            xtype = CHOLMOD_REAL;
846        break;
847        case 'n':
848            xtype = CHOLMOD_PATTERN;
849            break;
850        default:
851            error(_("cls = \"%s\" must begin with 'd', 'l' or 'n'"), cls);
852        }
853        if (cls[1] != 'g')
854            error(_("Only 'g'eneral sparse matrix types allowed"));
855        /* allocate and populate the triplet */
856        T = cholmod_allocate_triplet((size_t)nrow, (size_t)ncol, (size_t)nnz, 0,
857                                     xtype, &c);
858        T->x = x;
859        tri = (int*)T->i;
860        trj = (int*)T->j;
861        for (int ii = 0; ii < nnz; ii++) {
862            tri[ii] = i[ii] - ((!mi && index1) ? 1 : 0);
863            trj[ii] = j[ii] - ((!mj && index1) ? 1 : 0);
864        }
865        /* create the cholmod_sparse structure */
866        A = cholmod_triplet_to_sparse(T, nnz, &c);
867        cholmod_free_triplet(&T, &c);
868        /* copy the information to the SEXP */
869        ans = PROTECT(NEW_OBJECT(MAKE_CLASS(cls)));
870    /* FIXME: This has been copied from chm_sparse_to_SEXP in chm_common.c */
871        /* allocate and copy common slots */
872        nnz = cholmod_nnz(A, &c);
873        dims = INTEGER(ALLOC_SLOT(ans, Matrix_DimSym, INTSXP, 2));
874        dims[0] = A->nrow; dims[1] = A->ncol;
875        Memcpy(INTEGER(ALLOC_SLOT(ans, Matrix_pSym, INTSXP, A->ncol + 1)), (int*)A->p, A->ncol + 1);
876        Memcpy(INTEGER(ALLOC_SLOT(ans, Matrix_iSym, INTSXP, nnz)), (int*)A->i, nnz);
877        switch(cls[1]) {
878        case 'd':
879            Memcpy(REAL(ALLOC_SLOT(ans, Matrix_xSym, REALSXP, nnz)), (double*)A->x, nnz);
880            break;
881        case 'l':
882            error(_("code not yet written for cls = \"lgCMatrix\""));
883        }
884    /* FIXME: dimnames are *NOT* put there yet (if non-NULL) */
885        cholmod_free_sparse(&A, &c);
886        UNPROTECT(1);
887        return ans;
888  }  }

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