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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 1657, Wed Nov 1 16:29:53 2006 UTC pkg/Matrix/src/Csparse.c revision 2889, Thu Aug 8 21:06:22 2013 UTC
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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, ncol, nrow, sorted,      int *dims = INTEGER(GET_SLOT(x, Matrix_DimSym)), j,
14          *dims = INTEGER(GET_SLOT(x, Matrix_DimSym)),          nrow = dims[0],
15            ncol = dims[1],
16          *xp = INTEGER(pslot),          *xp = INTEGER(pslot),
17          *xi = INTEGER(islot);          *xi = INTEGER(islot);
18    
     nrow = dims[0];  
     ncol = dims[1];  
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])      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;  
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 FALSE;
32        }
33        return TRUE;
34    }
35    
36    SEXP Csparse_validate(SEXP x) {
37        return Csparse_validate_(x, FALSE);
38    }
39    
40    
41    #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    
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)
60    {
61        /* NB: we do *NOT* check a potential 'x' slot here, at all */
62        SEXP pslot = GET_SLOT(x, Matrix_pSym),
63            jslot = GET_SLOT(x, Matrix_jSym);
64        Rboolean sorted, strictly;
65        int i, k,
66            *dims = INTEGER(GET_SLOT(x, Matrix_DimSym)),
67            nrow = dims[0],
68            ncol = dims[1],
69            *xp = INTEGER(pslot),
70            *xj = INTEGER(jslot);
71    
72        if (length(pslot) != dims[0] + 1)
73            return mkString(_("slot p must have length = nrow(.) + 1"));
74        if (xp[0] != 0)
75            return mkString(_("first element of slot p must be zero"));
76        if (length(jslot) < xp[nrow]) /* allow larger slots from over-allocation!*/
77            return
78                mkString(_("last element of slot p must match length of slots j and x"));
79        for (i = 0; i < length(jslot); i++) {
80            if (xj[i] < 0 || xj[i] >= ncol)
81                return mkString(_("all column indices must be between 0 and ncol-1"));
82        }
83        sorted = TRUE; strictly = TRUE;
84        for (i = 0; i < nrow; i++) {
85            if (xp[i] > xp[i+1])
86              return mkString(_("slot p must be non-decreasing"));              return mkString(_("slot p must be non-decreasing"));
87          for (k = xp[j] + 1; k < xp[j + 1]; k++)          if(sorted)
88              if (xi[k] < xi[k - 1]) sorted = FALSE;              for (k = xp[i] + 1; k < xp[i + 1]; k++) {
89                    if (xj[k] < xj[k - 1])
90                        sorted = FALSE;
91                    else if (xj[k] == xj[k - 1])
92                        strictly = FALSE;
93      }      }
     if (!sorted) {  
         cholmod_sparse *chx = as_cholmod_sparse(x);  
         cholmod_sort(chx, &c);  
         Free(chx);  
94      }      }
95        if (!sorted)
96            /* cannot easily use cholmod_sort(.) ... -> "error out" :*/
97            return mkString(_("slot j is not increasing inside a column"));
98        else if(!strictly) /* sorted, but not strictly */
99            return mkString(_("slot j is not *strictly* increasing inside a column"));
100    
101      return ScalarLogical(1);      return ScalarLogical(1);
102  }  }
103    
104    
105    /* Called from ../R/Csparse.R : */
106    /* Can only return [dln]geMatrix (no symm/triang);
107     * FIXME: replace by non-CHOLMOD code ! */
108  SEXP Csparse_to_dense(SEXP x)  SEXP Csparse_to_dense(SEXP x)
109  {  {
110      cholmod_sparse *chxs = as_cholmod_sparse(x);      CHM_SP chxs = AS_CHM_SP__(x);
111      cholmod_dense *chxd = cholmod_sparse_to_dense(chxs, &c);      /* This loses the symmetry property, since cholmod_dense has none,
112         * BUT, much worse (FIXME!), it also transforms CHOLMOD_PATTERN ("n") matrices
113         * to numeric (CHOLMOD_REAL) ones : */
114        CHM_DN chxd = cholmod_sparse_to_dense(chxs, &c);
115        int Rkind = (chxs->xtype == CHOLMOD_PATTERN)? -1 : Real_kind(x);
116        R_CheckStack();
117    
118      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));  
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      cholmod_sparse *chxs = as_cholmod_sparse(x);      CHM_SP chxs = AS_CHM_SP__(x);
125      cholmod_sparse      CHM_SP chxcp = cholmod_copy(chxs, chxs->stype, CHOLMOD_PATTERN, &c);
126          *chxcp = cholmod_copy(chxs, chxs->stype, CHOLMOD_PATTERN, &c);      int tr = asLogical(tri);
127      int uploT = 0; char *diag = "";      R_CheckStack();
128    
129      Free(chxs);      return chm_sparse_to_SEXP(chxcp, 1/*do_free*/,
130      if (asLogical(tri)) {       /* triangular sparse matrices */                                tr ? ((*uplo_P(x) == 'U') ? 1 : -1) : 0,
131          uploT = (strcmp(CHAR(asChar(GET_SLOT(x, Matrix_uploSym))), "U")) ?                                0, tr ? diag_P(x) : "",
             -1 : 1;  
         diag = CHAR(asChar(GET_SLOT(x, Matrix_diagSym)));  
     }  
     return chm_sparse_to_SEXP(chxcp, 1, uploT, 0, diag,  
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 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      cholmod_sparse *chxs = as_cholmod_sparse(x);      const char *cl_x = class_P(x);
144      cholmod_dense *chxd = cholmod_sparse_to_dense(chxs, &c);      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      Free(chxs);  SEXP Csparse_to_matrix(SEXP x)
190      return chm_dense_to_matrix(chxd, 1,  {
191                                 GET_SLOT(x, Matrix_DimNamesSym));      return chm_dense_to_matrix(cholmod_sparse_to_dense(AS_CHM_SP__(x), &c),
192                                   1 /*do_free*/, GET_SLOT(x, Matrix_DimNamesSym));
193  }  }
194    
195  SEXP Csparse_to_Tsparse(SEXP x, SEXP tri)  SEXP Csparse_to_Tsparse(SEXP x, SEXP tri)
196  {  {
197      cholmod_sparse *chxs = as_cholmod_sparse(x);      CHM_SP chxs = AS_CHM_SP__(x);
198      cholmod_triplet *chxt = cholmod_sparse_to_triplet(chxs, &c);      CHM_TR chxt = cholmod_sparse_to_triplet(chxs, &c);
199      int uploT = 0;      int tr = asLogical(tri);
200      char *diag = "";      int Rkind = (chxs->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
201      int Rkind = (chxs->xtype == CHOLMOD_REAL) ? Real_kind(x) : 0;      R_CheckStack();
202    
203      Free(chxs);      return chm_triplet_to_SEXP(chxt, 1,
204      if (asLogical(tri)) {       /* triangular sparse matrices */                                 tr ? ((*uplo_P(x) == 'U') ? 1 : -1) : 0,
205          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,  
206                                 GET_SLOT(x, Matrix_DimNamesSym));                                 GET_SLOT(x, Matrix_DimNamesSym));
207  }  }
208    
209  /* this used to be called  sCMatrix_to_gCMatrix(..)   [in ./dsCMatrix.c ]: */  /* this used to be called  sCMatrix_to_gCMatrix(..)   [in ./dsCMatrix.c ]: */
210  SEXP Csparse_symmetric_to_general(SEXP x)  SEXP Csparse_symmetric_to_general(SEXP x)
211  {  {
212      cholmod_sparse *chx = as_cholmod_sparse(x), *chgx;      CHM_SP chx = AS_CHM_SP__(x), chgx;
213      int Rkind = (chx->xtype == CHOLMOD_REAL) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
214        R_CheckStack();
215    
216      if (!(chx->stype))      if (!(chx->stype))
217          error(_("Nonsymmetric matrix in Csparse_symmetric_to_general"));          error(_("Nonsymmetric matrix in Csparse_symmetric_to_general"));
218      chgx = cholmod_copy(chx, /* stype: */ 0, chx->xtype, &c);      chgx = cholmod_copy(chx, /* stype: */ 0, chx->xtype, &c);
219      /* xtype: pattern, "real", complex or .. */      /* xtype: pattern, "real", complex or .. */
     Free(chx);  
220      return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",      return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",
221                                GET_SLOT(x, Matrix_DimNamesSym));                                GET_SLOT(x, Matrix_DimNamesSym));
222  }  }
223    
224  SEXP Csparse_general_to_symmetric(SEXP x, SEXP uplo)  SEXP Csparse_general_to_symmetric(SEXP x, SEXP uplo)
225  {  {
226      cholmod_sparse *chx = as_cholmod_sparse(x), *chgx;      int *adims = INTEGER(GET_SLOT(x, Matrix_DimSym)), n = adims[0];
227      int uploT = (*CHAR(asChar(uplo)) == 'U') ? -1 : 1;      if(n != adims[1]) {
228      int Rkind = (chx->xtype == CHOLMOD_REAL) ? Real_kind(x) : 0;          error(_("Csparse_general_to_symmetric(): matrix is not square!"));
229            return R_NilValue; /* -Wall */
230        }
231        CHM_SP chx = AS_CHM_SP__(x), chgx;
232        int uploT = (*CHAR(STRING_ELT(uplo,0)) == 'U') ? 1 : -1;
233        int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
234        R_CheckStack();
235      chgx = cholmod_copy(chx, /* stype: */ uploT, chx->xtype, &c);      chgx = cholmod_copy(chx, /* stype: */ uploT, chx->xtype, &c);
236      /* xtype: pattern, "real", complex or .. */      /* xtype: pattern, "real", complex or .. */
     Free(chx);  
237      return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",      return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",
238                                GET_SLOT(x, Matrix_DimNamesSym));                                GET_SLOT(x, Matrix_DimNamesSym));
239  }  }
240    
241  SEXP Csparse_transpose(SEXP x, SEXP tri)  SEXP Csparse_transpose(SEXP x, SEXP tri)
242  {  {
243      cholmod_sparse *chx = as_cholmod_sparse(x);      /* TODO: lgCMatrix & igC* currently go via double prec. cholmod -
244      int Rkind = (chx->xtype == CHOLMOD_REAL) ? Real_kind(x) : 0;       *       since cholmod (& cs) lacks sparse 'int' matrices */
245      cholmod_sparse *chxt = cholmod_transpose(chx, (int) chx->xtype, &c);      CHM_SP chx = AS_CHM_SP__(x);
246        int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
247        CHM_SP chxt = cholmod_transpose(chx, chx->xtype, &c);
248      SEXP dn = PROTECT(duplicate(GET_SLOT(x, Matrix_DimNamesSym))), tmp;      SEXP dn = PROTECT(duplicate(GET_SLOT(x, Matrix_DimNamesSym))), tmp;
249      int uploT = 0; char *diag = "";      int tr = asLogical(tri);
250        R_CheckStack();
251    
     Free(chx);  
252      tmp = VECTOR_ELT(dn, 0);    /* swap the dimnames */      tmp = VECTOR_ELT(dn, 0);    /* swap the dimnames */
253      SET_VECTOR_ELT(dn, 0, VECTOR_ELT(dn, 1));      SET_VECTOR_ELT(dn, 0, VECTOR_ELT(dn, 1));
254      SET_VECTOR_ELT(dn, 1, tmp);      SET_VECTOR_ELT(dn, 1, tmp);
255      UNPROTECT(1);      UNPROTECT(1);
256      if (asLogical(tri)) {       /* triangular sparse matrices */      return chm_sparse_to_SEXP(chxt, 1, /* SWAP 'uplo' for triangular */
257          uploT = (*uplo_P(x) == 'U') ? -1 : 1;                                tr ? ((*uplo_P(x) == 'U') ? -1 : 1) : 0,
258          diag = diag_P(x);                                Rkind, tr ? diag_P(x) : "", dn);
     }  
     return chm_sparse_to_SEXP(chxt, 1, uploT, Rkind, diag, dn);  
259  }  }
260    
261  SEXP Csparse_Csparse_prod(SEXP a, SEXP b)  SEXP Csparse_Csparse_prod(SEXP a, SEXP b)
262  {  {
263      cholmod_sparse *cha = as_cholmod_sparse(a),      CHM_SP
264          *chb = as_cholmod_sparse(b);          cha = AS_CHM_SP(a),
265      cholmod_sparse *chc = cholmod_ssmult(cha, chb, 0, cha->xtype, 1, &c);          chb = AS_CHM_SP(b),
266      SEXP dn = allocVector(VECSXP, 2);          chc = cholmod_ssmult(cha, chb, /*out_stype:*/ 0,
267                                   /* values:= is_numeric (T/F) */ cha->xtype > 0,
268                                   /*out sorted:*/ 1, &c);
269        const char *cl_a = class_P(a), *cl_b = class_P(b);
270        char diag[] = {'\0', '\0'};
271        int uploT = 0;
272        SEXP dn = PROTECT(allocVector(VECSXP, 2));
273        R_CheckStack();
274    
275      Free(cha); Free(chb);  #ifdef DEBUG_Matrix_verbose
276        Rprintf("DBG Csparse_C*_prod(%s, %s)\n", cl_a, cl_b);
277    #endif
278    
279        /* Preserve triangularity and even unit-triangularity if appropriate.
280         * Note that in that case, the multiplication itself should happen
281         * faster.  But there's no support for that in CHOLMOD */
282    
283        /* UGLY hack -- rather should have (fast!) C-level version of
284         *       is(a, "triangularMatrix") etc */
285        if (cl_a[1] == 't' && cl_b[1] == 't')
286            /* FIXME: fails for "Cholesky","BunchKaufmann"..*/
287            if(*uplo_P(a) == *uplo_P(b)) { /* both upper, or both lower tri. */
288                uploT = (*uplo_P(a) == 'U') ? 1 : -1;
289                if(*diag_P(a) == 'U' && *diag_P(b) == 'U') { /* return UNIT-triag. */
290                    /* "remove the diagonal entries": */
291                    chm_diagN2U(chc, uploT, /* do_realloc */ FALSE);
292                    diag[0]= 'U';
293                }
294                else diag[0]= 'N';
295            }
296      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
297                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));
298      SET_VECTOR_ELT(dn, 1,      SET_VECTOR_ELT(dn, 1,
299                     duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), 1)));                     duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), 1)));
300      return chm_sparse_to_SEXP(chc, 1, 0, 0, "", dn);      UNPROTECT(1);
301        return chm_sparse_to_SEXP(chc, 1, uploT, /*Rkind*/0, diag, dn);
302  }  }
303    
304  SEXP Csparse_Csparse_crossprod(SEXP a, SEXP b)  SEXP Csparse_Csparse_crossprod(SEXP a, SEXP b, SEXP trans)
305  {  {
306      cholmod_sparse *cha = as_cholmod_sparse(a),      int tr = asLogical(trans);
307          *chb = as_cholmod_sparse(b);      CHM_SP
308      cholmod_sparse *chta = cholmod_transpose(cha, 1, &c);          cha = AS_CHM_SP(a),
309      cholmod_sparse *chc = cholmod_ssmult(chta, chb, 0, cha->xtype, 1, &c);          chb = AS_CHM_SP(b),
310      SEXP dn = allocVector(VECSXP, 2);          chTr, chc;
311        const char *cl_a = class_P(a), *cl_b = class_P(b);
312        char diag[] = {'\0', '\0'};
313        int uploT = 0;
314        SEXP dn = PROTECT(allocVector(VECSXP, 2));
315        R_CheckStack();
316    
317      Free(cha); Free(chb); cholmod_free_sparse(&chta, &c);      chTr = cholmod_transpose((tr) ? chb : cha, chb->xtype, &c);
318        chc = cholmod_ssmult((tr) ? cha : chTr, (tr) ? chTr : chb,
319                             /*out_stype:*/ 0, cha->xtype, /*out sorted:*/ 1, &c);
320        cholmod_free_sparse(&chTr, &c);
321    
322        /* Preserve triangularity and unit-triangularity if appropriate;
323         * see Csparse_Csparse_prod() for comments */
324        if (cl_a[1] == 't' && cl_b[1] == 't')
325            if(*uplo_P(a) != *uplo_P(b)) { /* one 'U', the other 'L' */
326                uploT = (*uplo_P(b) == 'U') ? 1 : -1;
327                if(*diag_P(a) == 'U' && *diag_P(b) == 'U') { /* return UNIT-triag. */
328                    chm_diagN2U(chc, uploT, /* do_realloc */ FALSE);
329                    diag[0]= 'U';
330                }
331                else diag[0]= 'N';
332            }
333      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
334                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 1)));                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), (tr) ? 0 : 1)));
335      SET_VECTOR_ELT(dn, 1,      SET_VECTOR_ELT(dn, 1,
336                     duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), 1)));                     duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), (tr) ? 0 : 1)));
337      return chm_sparse_to_SEXP(chc, 1, 0, 0, "", dn);      UNPROTECT(1);
338        return chm_sparse_to_SEXP(chc, 1, uploT, /*Rkind*/0, diag, dn);
339  }  }
340    
341  SEXP Csparse_dense_prod(SEXP a, SEXP b)  SEXP Csparse_dense_prod(SEXP a, SEXP b)
342  {  {
343      cholmod_sparse *cha = as_cholmod_sparse(a);      CHM_SP cha = AS_CHM_SP(a);
344      cholmod_dense *chb = as_cholmod_dense(PROTECT(mMatrix_as_dgeMatrix(b)));      SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));
345      cholmod_dense *chc =      CHM_DN chb = AS_CHM_DN(b_M);
346          cholmod_allocate_dense(cha->nrow, chb->ncol, cha->nrow, chb->xtype, &c);      CHM_DN chc = cholmod_allocate_dense(cha->nrow, chb->ncol, cha->nrow,
347      double alpha[] = {1,0}, beta[] = {0,0};                                          chb->xtype, &c);
348        SEXP dn = PROTECT(allocVector(VECSXP, 2));
349      cholmod_sdmult(cha, 0, alpha, beta, chb, chc, &c);      double one[] = {1,0}, zero[] = {0,0};
350      Free(cha); Free(chb);      int nprot = 2;
351      UNPROTECT(1);      R_CheckStack();
352      return chm_dense_to_SEXP(chc, 1, 0);      /* Tim Davis, please FIXME:  currently (2010-11) *fails* when  a  is a pattern matrix:*/
353        if(cha->xtype == CHOLMOD_PATTERN) {
354            /* warning(_("Csparse_dense_prod(): cholmod_sdmult() not yet implemented for pattern./ ngCMatrix" */
355            /*        " --> slightly inefficient coercion")); */
356    
357            // This *fails* to produce a CHOLMOD_REAL ..
358            // CHM_SP chd = cholmod_l_copy(cha, cha->stype, CHOLMOD_REAL, &c);
359            // --> use our Matrix-classes
360            SEXP da = PROTECT(nz2Csparse(a, x_double)); nprot++;
361            cha = AS_CHM_SP(da);
362        }
363        cholmod_sdmult(cha, 0, one, zero, chb, chc, &c);
364        SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
365                       duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));
366        SET_VECTOR_ELT(dn, 1,
367                       duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));
368        UNPROTECT(nprot);
369        return chm_dense_to_SEXP(chc, 1, 0, dn);
370  }  }
371    
372  SEXP Csparse_dense_crossprod(SEXP a, SEXP b)  SEXP Csparse_dense_crossprod(SEXP a, SEXP b)
373  {  {
374      cholmod_sparse *cha = as_cholmod_sparse(a);      CHM_SP cha = AS_CHM_SP(a);
375      cholmod_dense *chb = as_cholmod_dense(PROTECT(mMatrix_as_dgeMatrix(b)));      SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));
376      cholmod_dense *chc =      CHM_DN chb = AS_CHM_DN(b_M);
377          cholmod_allocate_dense(cha->ncol, chb->ncol, cha->ncol, chb->xtype, &c);      CHM_DN chc = cholmod_allocate_dense(cha->ncol, chb->ncol, cha->ncol,
378      double alpha[] = {1,0}, beta[] = {0,0};                                          chb->xtype, &c);
379        SEXP dn = PROTECT(allocVector(VECSXP, 2)); int nprot = 2;
380      cholmod_sdmult(cha, 1, alpha, beta, chb, chc, &c);      double one[] = {1,0}, zero[] = {0,0};
381      Free(cha); Free(chb);      R_CheckStack();
382      UNPROTECT(1);      // -- see Csparse_dense_prod() above :
383      return chm_dense_to_SEXP(chc, 1, 0);      if(cha->xtype == CHOLMOD_PATTERN) {
384            SEXP da = PROTECT(nz2Csparse(a, x_double)); nprot++;
385            cha = AS_CHM_SP(da);
386        }
387        cholmod_sdmult(cha, 1, one, zero, chb, chc, &c);
388        SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
389                       duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 1)));
390        SET_VECTOR_ELT(dn, 1,
391                       duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));
392        UNPROTECT(nprot);
393        return chm_dense_to_SEXP(chc, 1, 0, dn);
394  }  }
395    
396    /* Computes   x'x  or  x x' -- *also* for Tsparse (triplet = TRUE)
397       see Csparse_Csparse_crossprod above for  x'y and x y' */
398  SEXP Csparse_crossprod(SEXP x, SEXP trans, SEXP triplet)  SEXP Csparse_crossprod(SEXP x, SEXP trans, SEXP triplet)
399  {  {
400      int trip = asLogical(triplet),      int trip = asLogical(triplet),
401          tr   = asLogical(trans); /* gets reversed because _aat is tcrossprod */          tr   = asLogical(trans); /* gets reversed because _aat is tcrossprod */
402      cholmod_triplet  #ifdef AS_CHM_DIAGU2N_FIXED_FINALLY
403          *cht = trip ? as_cholmod_triplet(x) : (cholmod_triplet*) NULL;      CHM_TR cht = trip ? AS_CHM_TR(x) : (CHM_TR) NULL;
404      cholmod_sparse *chcp, *chxt,  #else /* workaround needed:*/
405          *chx = trip ? cholmod_triplet_to_sparse(cht, cht->nnz, &c)      SEXP xx = PROTECT(Tsparse_diagU2N(x));
406          : as_cholmod_sparse(x);      CHM_TR cht = trip ? AS_CHM_TR__(xx) : (CHM_TR) NULL;
407    #endif
408        CHM_SP chcp, chxt,
409            chx = (trip ?
410                   cholmod_triplet_to_sparse(cht, cht->nnz, &c) :
411                   AS_CHM_SP(x));
412      SEXP dn = PROTECT(allocVector(VECSXP, 2));      SEXP dn = PROTECT(allocVector(VECSXP, 2));
413        R_CheckStack();
414    
415      if (!tr)      if (!tr) chxt = cholmod_transpose(chx, chx->xtype, &c);
         chxt = cholmod_transpose(chx, chx->xtype, &c);  
416      chcp = cholmod_aat((!tr) ? chxt : chx, (int *) NULL, 0, chx->xtype, &c);      chcp = cholmod_aat((!tr) ? chxt : chx, (int *) NULL, 0, chx->xtype, &c);
417      if(!chcp)      if(!chcp) {
418            UNPROTECT(1);
419          error(_("Csparse_crossprod(): error return from cholmod_aat()"));          error(_("Csparse_crossprod(): error return from cholmod_aat()"));
420        }
421      cholmod_band_inplace(0, chcp->ncol, chcp->xtype, chcp, &c);      cholmod_band_inplace(0, chcp->ncol, chcp->xtype, chcp, &c);
422      chcp->stype = 1;      chcp->stype = 1;
423      if (trip) {      if (trip) cholmod_free_sparse(&chx, &c);
         cholmod_free_sparse(&chx, &c);  
         Free(cht);  
     } else {  
         Free(chx);  
     }  
424      if (!tr) cholmod_free_sparse(&chxt, &c);      if (!tr) cholmod_free_sparse(&chxt, &c);
425                                  /* create dimnames */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
     SET_VECTOR_ELT(dn, 0,  
426                     duplicate(VECTOR_ELT(GET_SLOT(x, Matrix_DimNamesSym),                     duplicate(VECTOR_ELT(GET_SLOT(x, Matrix_DimNamesSym),
427                                          (tr) ? 1 : 0)));                                          (tr) ? 0 : 1)));
428      SET_VECTOR_ELT(dn, 1, duplicate(VECTOR_ELT(dn, 0)));      SET_VECTOR_ELT(dn, 1, duplicate(VECTOR_ELT(dn, 0)));
429    #ifdef AS_CHM_DIAGU2N_FIXED_FINALLY
430      UNPROTECT(1);      UNPROTECT(1);
431    #else
432        UNPROTECT(2);
433    #endif
434      return chm_sparse_to_SEXP(chcp, 1, 0, 0, "", dn);      return chm_sparse_to_SEXP(chcp, 1, 0, 0, "", dn);
435  }  }
436    
437    /* Csparse_drop(x, tol):  drop entries with absolute value < tol, i.e,
438    *  at least all "explicit" zeros */
439  SEXP Csparse_drop(SEXP x, SEXP tol)  SEXP Csparse_drop(SEXP x, SEXP tol)
440  {  {
441      cholmod_sparse *chx = as_cholmod_sparse(x),      const char *cl = class_P(x);
442          *ans = cholmod_copy(chx, chx->stype, chx->xtype, &c);      /* dtCMatrix, etc; [1] = the second character =?= 't' for triangular */
443        int tr = (cl[1] == 't');
444        CHM_SP chx = AS_CHM_SP__(x);
445        CHM_SP ans = cholmod_copy(chx, chx->stype, chx->xtype, &c);
446      double dtol = asReal(tol);      double dtol = asReal(tol);
447      int Rkind = (chx->xtype == CHOLMOD_REAL) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
448        R_CheckStack();
449    
450      if(!cholmod_drop(dtol, ans, &c))      if(!cholmod_drop(dtol, ans, &c))
451          error(_("cholmod_drop() failed"));          error(_("cholmod_drop() failed"));
452      Free(chx);     return chm_sparse_to_SEXP(ans, 1,
453      /* FIXME: currently drops dimnames */                                tr ? ((*uplo_P(x) == 'U') ? 1 : -1) : 0,
454      return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "", R_NilValue);                                Rkind, tr ? diag_P(x) : "",
455                                  GET_SLOT(x, Matrix_DimNamesSym));
456  }  }
457    
   
458  SEXP Csparse_horzcat(SEXP x, SEXP y)  SEXP Csparse_horzcat(SEXP x, SEXP y)
459  {  {
460      cholmod_sparse *chx = as_cholmod_sparse(x),      CHM_SP chx = AS_CHM_SP__(x), chy = AS_CHM_SP__(y);
461          *chy = as_cholmod_sparse(y), *ans;      int Rk_x = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0,
462      int Rkind = 0; /* only for "d" - FIXME */          Rk_y = (chy->xtype != CHOLMOD_PATTERN) ? Real_kind(y) : 0,
463            Rkind = /* logical if both x and y are */ (Rk_x == 1 && Rk_y == 1) ? 1 : 0;
464      ans = cholmod_horzcat(chx, chy, 1, &c);      R_CheckStack();
465      Free(chx); Free(chy);  
466      /* FIXME: currently drops dimnames */      /* TODO: currently drops dimnames - and we fix at R level */
467      return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "", R_NilValue);      return chm_sparse_to_SEXP(cholmod_horzcat(chx, chy, 1, &c),
468                                  1, 0, Rkind, "", R_NilValue);
469  }  }
470    
471  SEXP Csparse_vertcat(SEXP x, SEXP y)  SEXP Csparse_vertcat(SEXP x, SEXP y)
472  {  {
473      cholmod_sparse *chx = as_cholmod_sparse(x),      CHM_SP chx = AS_CHM_SP__(x), chy = AS_CHM_SP__(y);
474          *chy = as_cholmod_sparse(y), *ans;      int Rk_x = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0,
475      int Rkind = 0; /* only for "d" - FIXME */          Rk_y = (chy->xtype != CHOLMOD_PATTERN) ? Real_kind(y) : 0,
476            Rkind = /* logical if both x and y are */ (Rk_x == 1 && Rk_y == 1) ? 1 : 0;
477      ans = cholmod_vertcat(chx, chy, 1, &c);      R_CheckStack();
478      Free(chx); Free(chy);  
479      /* FIXME: currently drops dimnames */      /* TODO: currently drops dimnames - and we fix at R level */
480      return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "", R_NilValue);      return chm_sparse_to_SEXP(cholmod_vertcat(chx, chy, 1, &c),
481                                  1, 0, Rkind, "", R_NilValue);
482  }  }
483    
484  SEXP Csparse_band(SEXP x, SEXP k1, SEXP k2)  SEXP Csparse_band(SEXP x, SEXP k1, SEXP k2)
485  {  {
486      cholmod_sparse *chx = as_cholmod_sparse(x), *ans;      CHM_SP chx = AS_CHM_SP__(x);
487      int Rkind = (chx->xtype == CHOLMOD_REAL) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
488        CHM_SP ans = cholmod_band(chx, asInteger(k1), asInteger(k2), chx->xtype, &c);
489        R_CheckStack();
490    
491      ans = cholmod_band(chx, asInteger(k1), asInteger(k2), chx->xtype, &c);      return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "",
492      Free(chx);                                GET_SLOT(x, Matrix_DimNamesSym));
     return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "", R_NilValue);  
493  }  }
494    
495  SEXP Csparse_diagU2N(SEXP x)  SEXP Csparse_diagU2N(SEXP x)
496  {  {
497      cholmod_sparse *chx = as_cholmod_sparse(x);      const char *cl = class_P(x);
498      cholmod_sparse *eye = cholmod_speye(chx->nrow, chx->ncol, chx->xtype, &c);      /* dtCMatrix, etc; [1] = the second character =?= 't' for triangular */
499        if (cl[1] != 't' || *diag_P(x) != 'U') {
500            /* "trivially fast" when not triangular (<==> no 'diag' slot),
501               or not *unit* triangular */
502            return (x);
503        }
504        else { /* unit triangular (diag='U'): "fill the diagonal" & diag:= "N" */
505            CHM_SP chx = AS_CHM_SP__(x);
506            CHM_SP eye = cholmod_speye(chx->nrow, chx->ncol, chx->xtype, &c);
507      double one[] = {1, 0};      double one[] = {1, 0};
508      cholmod_sparse *ans = cholmod_add(chx, eye, one, one, TRUE, TRUE, &c);          CHM_SP ans = cholmod_add(chx, eye, one, one, TRUE, TRUE, &c);
509      int uploT = (strcmp(CHAR(asChar(GET_SLOT(x, Matrix_uploSym))), "U")) ?          int uploT = (*uplo_P(x) == 'U') ? 1 : -1;
510          -1 : 1;          int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
     int Rkind = (chx->xtype == CHOLMOD_REAL) ? Real_kind(x) : 0;  
511    
512      Free(chx); cholmod_free_sparse(&eye, &c);          R_CheckStack();
513            cholmod_free_sparse(&eye, &c);
514      return chm_sparse_to_SEXP(ans, 1, uploT, Rkind, "N",      return chm_sparse_to_SEXP(ans, 1, uploT, Rkind, "N",
515                                duplicate(GET_SLOT(x, Matrix_DimNamesSym)));                                    GET_SLOT(x, Matrix_DimNamesSym));
516        }
517    }
518    
519    SEXP Csparse_diagN2U(SEXP x)
520    {
521        const char *cl = class_P(x);
522        /* dtCMatrix, etc; [1] = the second character =?= 't' for triangular */
523        if (cl[1] != 't' || *diag_P(x) != 'N') {
524            /* "trivially fast" when not triangular (<==> no 'diag' slot),
525               or already *unit* triangular */
526            return (x);
527        }
528        else { /* triangular with diag='N'): now drop the diagonal */
529            /* duplicate, since chx will be modified: */
530            SEXP xx = PROTECT(duplicate(x));
531            CHM_SP chx = AS_CHM_SP__(xx);
532            int uploT = (*uplo_P(x) == 'U') ? 1 : -1,
533                Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
534            R_CheckStack();
535    
536            chm_diagN2U(chx, uploT, /* do_realloc */ FALSE);
537    
538            SEXP ans = chm_sparse_to_SEXP(chx, /*dofree*/ 0/* or 1 ?? */,
539                                          uploT, Rkind, "U",
540                                          GET_SLOT(x, Matrix_DimNamesSym));
541            UNPROTECT(1);// only now !
542            return ans;
543        }
544  }  }
545    
546    /**
547     * "Indexing" aka subsetting : Compute  x[i,j], also for vectors i and j
548     * Working via CHOLMOD_submatrix, see ./CHOLMOD/MatrixOps/cholmod_submatrix.c
549     * @param x CsparseMatrix
550     * @param i row     indices (0-origin), or NULL (R's)
551     * @param j columns indices (0-origin), or NULL
552     *
553     * @return x[i,j]  still CsparseMatrix --- currently, this loses dimnames
554     */
555  SEXP Csparse_submatrix(SEXP x, SEXP i, SEXP j)  SEXP Csparse_submatrix(SEXP x, SEXP i, SEXP j)
556  {  {
557      cholmod_sparse *chx = as_cholmod_sparse(x);      CHM_SP chx = AS_CHM_SP(x); /* << does diagU2N() when needed */
558      int rsize = (isNull(i)) ? -1 : LENGTH(i),      int rsize = (isNull(i)) ? -1 : LENGTH(i),
559          csize = (isNull(j)) ? -1 : LENGTH(j);          csize = (isNull(j)) ? -1 : LENGTH(j);
560      int Rkind = (chx->xtype == CHOLMOD_REAL) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
561        R_CheckStack();
562    
563      if (rsize >= 0 && !isInteger(i))      if (rsize >= 0 && !isInteger(i))
564          error(_("Index i must be NULL or integer"));          error(_("Index i must be NULL or integer"));
565      if (csize >= 0 && !isInteger(j))      if (csize >= 0 && !isInteger(j))
566          error(_("Index j must be NULL or integer"));          error(_("Index j must be NULL or integer"));
567      return chm_sparse_to_SEXP(cholmod_submatrix(chx, INTEGER(i), rsize,  
568                                                  INTEGER(j), csize,      if (!chx->stype) {/* non-symmetric Matrix */
569            return chm_sparse_to_SEXP(cholmod_submatrix(chx,
570                                                        (rsize < 0) ? NULL : INTEGER(i), rsize,
571                                                        (csize < 0) ? NULL : INTEGER(j), csize,
572                                                  TRUE, TRUE, &c),                                                  TRUE, TRUE, &c),
573                                1, 0, Rkind, "", R_NilValue);                                    1, 0, Rkind, "",
574                                      /* FIXME: drops dimnames */ R_NilValue);
575        }
576                                    /* for now, cholmod_submatrix() only accepts "generalMatrix" */
577        CHM_SP tmp = cholmod_copy(chx, /* stype: */ 0, chx->xtype, &c);
578        CHM_SP ans = cholmod_submatrix(tmp,
579                                       (rsize < 0) ? NULL : INTEGER(i), rsize,
580                                       (csize < 0) ? NULL : INTEGER(j), csize,
581                                       TRUE, TRUE, &c);
582        cholmod_free_sparse(&tmp, &c);
583        return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "", R_NilValue);
584    }
585    
586    #define _d_Csp_
587    #include "t_Csparse_subassign.c"
588    
589    #define _l_Csp_
590    #include "t_Csparse_subassign.c"
591    
592    #define _i_Csp_
593    #include "t_Csparse_subassign.c"
594    
595    #define _n_Csp_
596    #include "t_Csparse_subassign.c"
597    
598    #define _z_Csp_
599    #include "t_Csparse_subassign.c"
600    
601    
602    
603    SEXP Csparse_MatrixMarket(SEXP x, SEXP fname)
604    {
605        FILE *f = fopen(CHAR(asChar(fname)), "w");
606    
607        if (!f)
608            error(_("failure to open file \"%s\" for writing"),
609                  CHAR(asChar(fname)));
610        if (!cholmod_write_sparse(f, AS_CHM_SP(x),
611                                  (CHM_SP)NULL, (char*) NULL, &c))
612            error(_("cholmod_write_sparse returned error code"));
613        fclose(f);
614        return R_NilValue;
615    }
616    
617    
618    /**
619     * Extract the diagonal entries from *triangular* Csparse matrix  __or__ a
620     * cholmod_sparse factor (LDL = TRUE).
621     *
622     * @param n  dimension of the matrix.
623     * @param x_p  'p' (column pointer) slot contents
624     * @param x_x  'x' (non-zero entries) slot contents
625     * @param perm 'perm' (= permutation vector) slot contents; only used for "diagBack"
626     * @param resultKind a (SEXP) string indicating which kind of result is desired.
627     *
628     * @return  a SEXP, either a (double) number or a length n-vector of diagonal entries
629     */
630    SEXP diag_tC_ptr(int n, int *x_p, double *x_x, int *perm, SEXP resultKind)
631    /*                                ^^^^^^ FIXME[Generalize] to int / ... */
632    {
633        const char* res_ch = CHAR(STRING_ELT(resultKind,0));
634        enum diag_kind { diag, diag_backpermuted, trace, prod, sum_log
635        } res_kind = ((!strcmp(res_ch, "trace")) ? trace :
636                      ((!strcmp(res_ch, "sumLog")) ? sum_log :
637                       ((!strcmp(res_ch, "prod")) ? prod :
638                        ((!strcmp(res_ch, "diag")) ? diag :
639                         ((!strcmp(res_ch, "diagBack")) ? diag_backpermuted :
640                          -1)))));
641        int i, n_x, i_from = 0;
642        SEXP ans = PROTECT(allocVector(REALSXP,
643    /*                                 ^^^^  FIXME[Generalize] */
644                                       (res_kind == diag ||
645                                        res_kind == diag_backpermuted) ? n : 1));
646        double *v = REAL(ans);
647    /*  ^^^^^^      ^^^^  FIXME[Generalize] */
648    
649    #define for_DIAG(v_ASSIGN)                                      \
650        for(i = 0; i < n; i++, i_from += n_x) {                     \
651            /* looking at i-th column */                            \
652            n_x = x_p[i+1] - x_p[i];/* #{entries} in this column */ \
653            v_ASSIGN;                                               \
654        }
655    
656        /* NOTA BENE: we assume  -- uplo = "L" i.e. lower triangular matrix
657         *            for uplo = "U" (makes sense with a "dtCMatrix" !),
658         *            should use  x_x[i_from + (nx - 1)] instead of x_x[i_from],
659         *            where nx = (x_p[i+1] - x_p[i])
660         */
661    
662        switch(res_kind) {
663        case trace:
664            v[0] = 0.;
665            for_DIAG(v[0] += x_x[i_from]);
666            break;
667    
668        case sum_log:
669            v[0] = 0.;
670            for_DIAG(v[0] += log(x_x[i_from]));
671            break;
672    
673        case prod:
674            v[0] = 1.;
675            for_DIAG(v[0] *= x_x[i_from]);
676            break;
677    
678        case diag:
679            for_DIAG(v[i] = x_x[i_from]);
680            break;
681    
682        case diag_backpermuted:
683            for_DIAG(v[i] = x_x[i_from]);
684    
685            warning(_("%s = '%s' (back-permuted) is experimental"),
686                    "resultKind", "diagBack");
687            /* now back_permute : */
688            for(i = 0; i < n; i++) {
689                double tmp = v[i]; v[i] = v[perm[i]]; v[perm[i]] = tmp;
690                /*^^^^ FIXME[Generalize] */
691            }
692            break;
693    
694        default: /* -1 from above */
695            error(_("diag_tC(): invalid 'resultKind'"));
696            /* Wall: */ ans = R_NilValue; v = REAL(ans);
697        }
698    
699        UNPROTECT(1);
700        return ans;
701    }
702    
703    /**
704     * Extract the diagonal entries from *triangular* Csparse matrix  __or__ a
705     * cholmod_sparse factor (LDL = TRUE).
706     *
707     * @param pslot  'p' (column pointer)   slot of Csparse matrix/factor
708     * @param xslot  'x' (non-zero entries) slot of Csparse matrix/factor
709     * @param perm_slot  'perm' (= permutation vector) slot of corresponding CHMfactor;
710     *                   only used for "diagBack"
711     * @param resultKind a (SEXP) string indicating which kind of result is desired.
712     *
713     * @return  a SEXP, either a (double) number or a length n-vector of diagonal entries
714     */
715    SEXP diag_tC(SEXP pslot, SEXP xslot, SEXP perm_slot, SEXP resultKind)
716    {
717        int n = length(pslot) - 1, /* n = ncol(.) = nrow(.) */
718            *x_p  = INTEGER(pslot),
719            *perm = INTEGER(perm_slot);
720        double *x_x = REAL(xslot);
721    /*  ^^^^^^        ^^^^ FIXME[Generalize] to INTEGER(.) / LOGICAL(.) / ... xslot !*/
722    
723        return diag_tC_ptr(n, x_p, x_x, perm, resultKind);
724    }
725    
726    /**
727     * Create a Csparse matrix object from indices and/or pointers.
728     *
729     * @param cls name of actual class of object to create
730     * @param i optional integer vector of length nnz of row indices
731     * @param j optional integer vector of length nnz of column indices
732     * @param p optional integer vector of length np of row or column pointers
733     * @param np length of integer vector p.  Must be zero if p == (int*)NULL
734     * @param x optional vector of values
735     * @param nnz length of vectors i, j and/or x, whichever is to be used
736     * @param dims optional integer vector of length 2 to be used as
737     *     dimensions.  If dims == (int*)NULL then the maximum row and column
738     *     index are used as the dimensions.
739     * @param dimnames optional list of length 2 to be used as dimnames
740     * @param index1 indicator of 1-based indices
741     *
742     * @return an SEXP of class cls inheriting from CsparseMatrix.
743     */
744    SEXP create_Csparse(char* cls, int* i, int* j, int* p, int np,
745                        void* x, int nnz, int* dims, SEXP dimnames,
746                        int index1)
747    {
748        SEXP ans;
749        int *ij = (int*)NULL, *tri, *trj,
750            mi, mj, mp, nrow = -1, ncol = -1;
751        int xtype = -1;             /* -Wall */
752        CHM_TR T;
753        CHM_SP A;
754    
755        if (np < 0 || nnz < 0)
756            error(_("negative vector lengths not allowed: np = %d, nnz = %d"),
757                  np, nnz);
758        if (1 != ((mi = (i == (int*)NULL)) +
759                  (mj = (j == (int*)NULL)) +
760                  (mp = (p == (int*)NULL))))
761            error(_("exactly 1 of 'i', 'j' or 'p' must be NULL"));
762        if (mp) {
763            if (np) error(_("np = %d, must be zero when p is NULL"), np);
764        } else {
765            if (np) {               /* Expand p to form i or j */
766                if (!(p[0])) error(_("p[0] = %d, should be zero"), p[0]);
767                for (int ii = 0; ii < np; ii++)
768                    if (p[ii] > p[ii + 1])
769                        error(_("p must be non-decreasing"));
770                if (p[np] != nnz)
771                    error("p[np] = %d != nnz = %d", p[np], nnz);
772                ij = Calloc(nnz, int);
773                if (mi) {
774                    i = ij;
775                    nrow = np;
776                } else {
777                    j = ij;
778                    ncol = np;
779                }
780                /* Expand p to 0-based indices */
781                for (int ii = 0; ii < np; ii++)
782                    for (int jj = p[ii]; jj < p[ii + 1]; jj++) ij[jj] = ii;
783            } else {
784                if (nnz)
785                    error(_("Inconsistent dimensions: np = 0 and nnz = %d"),
786                          nnz);
787            }
788        }
789        /* calculate nrow and ncol */
790        if (nrow < 0) {
791            for (int ii = 0; ii < nnz; ii++) {
792                int i1 = i[ii] + (index1 ? 0 : 1); /* 1-based index */
793                if (i1 < 1) error(_("invalid row index at position %d"), ii);
794                if (i1 > nrow) nrow = i1;
795            }
796        }
797        if (ncol < 0) {
798            for (int jj = 0; jj < nnz; jj++) {
799                int j1 = j[jj] + (index1 ? 0 : 1);
800                if (j1 < 1) error(_("invalid column index at position %d"), jj);
801                if (j1 > ncol) ncol = j1;
802            }
803        }
804        if (dims != (int*)NULL) {
805            if (dims[0] > nrow) nrow = dims[0];
806            if (dims[1] > ncol) ncol = dims[1];
807        }
808        /* check the class name */
809        if (strlen(cls) != 8)
810            error(_("strlen of cls argument = %d, should be 8"), strlen(cls));
811        if (!strcmp(cls + 2, "CMatrix"))
812            error(_("cls = \"%s\" does not end in \"CMatrix\""), cls);
813        switch(cls[0]) {
814        case 'd':
815        case 'l':
816            xtype = CHOLMOD_REAL;
817        break;
818        case 'n':
819            xtype = CHOLMOD_PATTERN;
820            break;
821        default:
822            error(_("cls = \"%s\" must begin with 'd', 'l' or 'n'"), cls);
823        }
824        if (cls[1] != 'g')
825            error(_("Only 'g'eneral sparse matrix types allowed"));
826        /* allocate and populate the triplet */
827        T = cholmod_allocate_triplet((size_t)nrow, (size_t)ncol, (size_t)nnz, 0,
828                                     xtype, &c);
829        T->x = x;
830        tri = (int*)T->i;
831        trj = (int*)T->j;
832        for (int ii = 0; ii < nnz; ii++) {
833            tri[ii] = i[ii] - ((!mi && index1) ? 1 : 0);
834            trj[ii] = j[ii] - ((!mj && index1) ? 1 : 0);
835        }
836        /* create the cholmod_sparse structure */
837        A = cholmod_triplet_to_sparse(T, nnz, &c);
838        cholmod_free_triplet(&T, &c);
839        /* copy the information to the SEXP */
840        ans = PROTECT(NEW_OBJECT(MAKE_CLASS(cls)));
841    /* FIXME: This has been copied from chm_sparse_to_SEXP in chm_common.c */
842        /* allocate and copy common slots */
843        nnz = cholmod_nnz(A, &c);
844        dims = INTEGER(ALLOC_SLOT(ans, Matrix_DimSym, INTSXP, 2));
845        dims[0] = A->nrow; dims[1] = A->ncol;
846        Memcpy(INTEGER(ALLOC_SLOT(ans, Matrix_pSym, INTSXP, A->ncol + 1)), (int*)A->p, A->ncol + 1);
847        Memcpy(INTEGER(ALLOC_SLOT(ans, Matrix_iSym, INTSXP, nnz)), (int*)A->i, nnz);
848        switch(cls[1]) {
849        case 'd':
850            Memcpy(REAL(ALLOC_SLOT(ans, Matrix_xSym, REALSXP, nnz)), (double*)A->x, nnz);
851            break;
852        case 'l':
853            error(_("code not yet written for cls = \"lgCMatrix\""));
854        }
855    /* FIXME: dimnames are *NOT* put there yet (if non-NULL) */
856        cholmod_free_sparse(&A, &c);
857        UNPROTECT(1);
858        return ans;
859  }  }

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