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[matrix] Diff of /pkg/src/Csparse.c
 [matrix] / pkg / src / Csparse.c

# Diff of /pkg/src/Csparse.c

revision 1960, Fri Jul 6 16:54:43 2007 UTC revision 2235, Wed Jul 23 10:24:17 2008 UTC
# Line 1  Line 1
1                          /* Sparse matrices in compressed column-oriented form */                          /* Sparse matrices in compressed column-oriented form */
2  #include "Csparse.h"  #include "Csparse.h"
3    #include "Tsparse.h"
4  #include "chm_common.h"  #include "chm_common.h"
5
6  SEXP Csparse_validate(SEXP x)  SEXP Csparse_validate(SEXP x)
# Line 39  Line 40
40              }              }
41      }      }
42      if (!sorted) {      if (!sorted) {
43          CHM_SP chx = AS_CHM_SP(x);          CHM_SP chx = (CHM_SP) alloca(sizeof(cholmod_sparse));
44          R_CheckStack();          R_CheckStack();
45            as_cholmod_sparse(chx, x, FALSE, TRUE); /* includes cholmod_sort() ! */
46            /* as chx = AS_CHM_SP__(x)  but  ^^^^  sorting x in_place (no copying)*/
47
cholmod_sort(chx, &c);
48          /* Now re-check that row indices are *strictly* increasing          /* Now re-check that row indices are *strictly* increasing
49           * (and not just increasing) within each column : */           * (and not just increasing) within each column : */
50          for (j = 0; j < ncol; j++) {          for (j = 0; j < ncol; j++) {
# Line 57  Line 59
59      return ScalarLogical(1);      return ScalarLogical(1);
60  }  }
61
62    SEXP Rsparse_validate(SEXP x)
63    {
64        /* NB: we do *NOT* check a potential 'x' slot here, at all */
65        SEXP pslot = GET_SLOT(x, Matrix_pSym),
66            jslot = GET_SLOT(x, Matrix_jSym);
67        Rboolean sorted, strictly;
68        int i, k,
69            *dims = INTEGER(GET_SLOT(x, Matrix_DimSym)),
70            nrow = dims[0],
71            ncol = dims[1],
72            *xp = INTEGER(pslot),
73            *xj = INTEGER(jslot);
74
75        if (length(pslot) != dims[0] + 1)
76            return mkString(_("slot p must have length = nrow(.) + 1"));
77        if (xp[0] != 0)
78            return mkString(_("first element of slot p must be zero"));
79        if (length(jslot) < xp[nrow]) /* allow larger slots from over-allocation!*/
80            return
81                mkString(_("last element of slot p must match length of slots j and x"));
82        for (i = 0; i < length(jslot); i++) {
83            if (xj[i] < 0 || xj[i] >= ncol)
84                return mkString(_("all column indices must be between 0 and ncol-1"));
85        }
86        sorted = TRUE; strictly = TRUE;
87        for (i = 0; i < nrow; i++) {
88            if (xp[i] > xp[i+1])
89                return mkString(_("slot p must be non-decreasing"));
90            if(sorted)
91                for (k = xp[i] + 1; k < xp[i + 1]; k++) {
92                    if (xj[k] < xj[k - 1])
93                        sorted = FALSE;
94                    else if (xj[k] == xj[k - 1])
95                        strictly = FALSE;
96                }
97        }
98        if (!sorted)
99            /* cannot easily use cholmod_sort(.) ... -> "error out" :*/
100            return mkString(_("slot j is not increasing inside a column"));
101        else if(!strictly) /* sorted, but not strictly */
102            return mkString(_("slot j is not *strictly* increasing inside a column"));
103
104        return ScalarLogical(1);
105    }
106
107
108  /* Called from ../R/Csparse.R : */  /* Called from ../R/Csparse.R : */
109  /* Can only return [dln]geMatrix (no symm/triang);  /* Can only return [dln]geMatrix (no symm/triang);
110   * FIXME: replace by non-CHOLMOD code ! */   * FIXME: replace by non-CHOLMOD code ! */
111  SEXP Csparse_to_dense(SEXP x)  SEXP Csparse_to_dense(SEXP x)
112  {  {
113      CHM_SP chxs = AS_CHM_SP(x);      CHM_SP chxs = AS_CHM_SP__(x);
114      /* This loses the symmetry property, since cholmod_dense has none,      /* This loses the symmetry property, since cholmod_dense has none,
115       * BUT, much worse (FIXME!), it also transforms CHOLMOD_PATTERN ("n") matrices       * BUT, much worse (FIXME!), it also transforms CHOLMOD_PATTERN ("n") matrices
116       * to numeric (CHOLMOD_REAL) ones : */       * to numeric (CHOLMOD_REAL) ones : */
# Line 75  Line 123
123
124  SEXP Csparse_to_nz_pattern(SEXP x, SEXP tri)  SEXP Csparse_to_nz_pattern(SEXP x, SEXP tri)
125  {  {
126      CHM_SP chxs = AS_CHM_SP(x);      CHM_SP chxs = AS_CHM_SP__(x);
127      CHM_SP chxcp = cholmod_copy(chxs, chxs->stype, CHOLMOD_PATTERN, &c);      CHM_SP chxcp = cholmod_copy(chxs, chxs->stype, CHOLMOD_PATTERN, &c);
128      int tr = asLogical(tri);      int tr = asLogical(tri);
129      R_CheckStack();      R_CheckStack();
# Line 88  Line 136
136
137  SEXP Csparse_to_matrix(SEXP x)  SEXP Csparse_to_matrix(SEXP x)
138  {  {
139      return chm_dense_to_matrix(cholmod_sparse_to_dense(AS_CHM_SP(x), &c),      return chm_dense_to_matrix(cholmod_sparse_to_dense(AS_CHM_SP__(x), &c),
140                                 1 /*do_free*/, GET_SLOT(x, Matrix_DimNamesSym));                                 1 /*do_free*/, GET_SLOT(x, Matrix_DimNamesSym));
141  }  }
142
143  SEXP Csparse_to_Tsparse(SEXP x, SEXP tri)  SEXP Csparse_to_Tsparse(SEXP x, SEXP tri)
144  {  {
145      CHM_SP chxs = AS_CHM_SP(x);      CHM_SP chxs = AS_CHM_SP__(x);
146      CHM_TR chxt = cholmod_sparse_to_triplet(chxs, &c);      CHM_TR chxt = cholmod_sparse_to_triplet(chxs, &c);
147      int tr = asLogical(tri);      int tr = asLogical(tri);
148      int Rkind = (chxs->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chxs->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
# Line 109  Line 157
157  /* this used to be called  sCMatrix_to_gCMatrix(..)   [in ./dsCMatrix.c ]: */  /* this used to be called  sCMatrix_to_gCMatrix(..)   [in ./dsCMatrix.c ]: */
158  SEXP Csparse_symmetric_to_general(SEXP x)  SEXP Csparse_symmetric_to_general(SEXP x)
159  {  {
160      CHM_SP chx = AS_CHM_SP(x), chgx;      CHM_SP chx = AS_CHM_SP__(x), chgx;
161      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
162      R_CheckStack();      R_CheckStack();
163
# Line 123  Line 171
171
172  SEXP Csparse_general_to_symmetric(SEXP x, SEXP uplo)  SEXP Csparse_general_to_symmetric(SEXP x, SEXP uplo)
173  {  {
174      CHM_SP chx = AS_CHM_SP(x), chgx;      CHM_SP chx = AS_CHM_SP__(x), chgx;
175      int uploT = (*CHAR(asChar(uplo)) == 'U') ? 1 : -1;      int uploT = (*CHAR(STRING_ELT(uplo,0)) == 'U') ? 1 : -1;
176      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
177      R_CheckStack();      R_CheckStack();
178
# Line 138  Line 186
186  {  {
187      /* TODO: lgCMatrix & igC* currently go via double prec. cholmod -      /* TODO: lgCMatrix & igC* currently go via double prec. cholmod -
188       *       since cholmod (& cs) lacks sparse 'int' matrices */       *       since cholmod (& cs) lacks sparse 'int' matrices */
189      CHM_SP chx = AS_CHM_SP(x);      CHM_SP chx = AS_CHM_SP__(x);
190      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
191      CHM_SP chxt = cholmod_transpose(chx, chx->xtype, &c);      CHM_SP chxt = cholmod_transpose(chx, chx->xtype, &c);
192      SEXP dn = PROTECT(duplicate(GET_SLOT(x, Matrix_DimNamesSym))), tmp;      SEXP dn = PROTECT(duplicate(GET_SLOT(x, Matrix_DimNamesSym))), tmp;
# Line 156  Line 204
204
205  SEXP Csparse_Csparse_prod(SEXP a, SEXP b)  SEXP Csparse_Csparse_prod(SEXP a, SEXP b)
206  {  {
207      CHM_SP cha = AS_CHM_SP(a), chb = AS_CHM_SP(b);      CHM_SP
208      CHM_SP chc = cholmod_ssmult(cha, chb, 0, cha->xtype, 1, &c);          cha = AS_CHM_SP(a),
209            chb = AS_CHM_SP(b),
210            chc = cholmod_ssmult(cha, chb, /*out_stype:*/ 0,
211                                 cha->xtype, /*out sorted:*/ 1, &c);
212        const char *cl_a = class_P(a), *cl_b = class_P(b);
213        char diag[] = {'\0', '\0'};
214        int uploT = 0;
215      SEXP dn = allocVector(VECSXP, 2);      SEXP dn = allocVector(VECSXP, 2);
216      R_CheckStack();      R_CheckStack();
217
218        /* Preserve triangularity and even unit-triangularity if appropriate.
219         * Note that in that case, the multiplication itself should happen
220         * faster.  But there's no support for that in CHOLMOD */
221
222        /* UGLY hack -- rather should have (fast!) C-level version of
223         *       is(a, "triangularMatrix") etc */
224        if (cl_a[1] == 't' && cl_b[1] == 't')
225            /* FIXME: fails for "Cholesky","BunchKaufmann"..*/
226            if(*uplo_P(a) == *uplo_P(b)) { /* both upper, or both lower tri. */
227                uploT = (*uplo_P(a) == 'U') ? 1 : -1;
228                if(*diag_P(a) == 'U' && *diag_P(b) == 'U') { /* return UNIT-triag. */
229                    /* "remove the diagonal entries": */
230                    chm_diagN2U(chc, uploT, /* do_realloc */ FALSE);
231                    diag[0]= 'U';
232                }
233                else diag[0]= 'N';
234            }
235      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
236                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));
237      SET_VECTOR_ELT(dn, 1,      SET_VECTOR_ELT(dn, 1,
238                     duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), 1)));                     duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), 1)));
239      return chm_sparse_to_SEXP(chc, 1, 0, 0, "", dn);      return chm_sparse_to_SEXP(chc, 1, uploT, /*Rkind*/0, diag, dn);
240  }  }
241
242  SEXP Csparse_Csparse_crossprod(SEXP a, SEXP b, SEXP trans)  SEXP Csparse_Csparse_crossprod(SEXP a, SEXP b, SEXP trans)
243  {  {
244      int tr = asLogical(trans);      int tr = asLogical(trans);
245      CHM_SP cha = AS_CHM_SP(a), chb = AS_CHM_SP(b), chTr, chc;      CHM_SP
246            cha = AS_CHM_SP(a),
247            chb = AS_CHM_SP(b),
248            chTr, chc;
249        const char *cl_a = class_P(a), *cl_b = class_P(b);
250        char diag[] = {'\0', '\0'};
251        int uploT = 0;
252      SEXP dn = allocVector(VECSXP, 2);      SEXP dn = allocVector(VECSXP, 2);
253      R_CheckStack();      R_CheckStack();
254
255      chTr = cholmod_transpose((tr) ? chb : cha, chb->xtype, &c);      chTr = cholmod_transpose((tr) ? chb : cha, chb->xtype, &c);
256      chc = cholmod_ssmult((tr) ? cha : chTr, (tr) ? chTr : chb,      chc = cholmod_ssmult((tr) ? cha : chTr, (tr) ? chTr : chb,
257                           0, cha->xtype, 1, &c);                           /*out_stype:*/ 0, cha->xtype, /*out sorted:*/ 1, &c);
258      cholmod_free_sparse(&chTr, &c);      cholmod_free_sparse(&chTr, &c);
259
260        /* Preserve triangularity and unit-triangularity if appropriate;
261         * see Csparse_Csparse_prod() for comments */
262        if (cl_a[1] == 't' && cl_b[1] == 't')
263            if(*uplo_P(a) != *uplo_P(b)) { /* one 'U', the other 'L' */
264                uploT = (*uplo_P(b) == 'U') ? 1 : -1;
265                if(*diag_P(a) == 'U' && *diag_P(b) == 'U') { /* return UNIT-triag. */
266                    chm_diagN2U(chc, uploT, /* do_realloc */ FALSE);
267                    diag[0]= 'U';
268                }
269                else diag[0]= 'N';
270            }
271
272      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
273                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), (tr) ? 0 : 1)));                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), (tr) ? 0 : 1)));
274      SET_VECTOR_ELT(dn, 1,      SET_VECTOR_ELT(dn, 1,
275                     duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), (tr) ? 0 : 1)));                     duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), (tr) ? 0 : 1)));
276      return chm_sparse_to_SEXP(chc, 1, 0, 0, "", dn);      return chm_sparse_to_SEXP(chc, 1, uploT, /*Rkind*/0, diag, dn);
277  }  }
278
279  SEXP Csparse_dense_prod(SEXP a, SEXP b)  SEXP Csparse_dense_prod(SEXP a, SEXP b)
# Line 227  Line 316
316      return chm_dense_to_SEXP(chc, 1, 0, dn);      return chm_dense_to_SEXP(chc, 1, 0, dn);
317  }  }
318
319  /* 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)
320       see Csparse_Csparse_crossprod above for  x'y and x y' */
321  SEXP Csparse_crossprod(SEXP x, SEXP trans, SEXP triplet)  SEXP Csparse_crossprod(SEXP x, SEXP trans, SEXP triplet)
322  {  {
323      int trip = asLogical(triplet),      int trip = asLogical(triplet),
324          tr   = asLogical(trans); /* gets reversed because _aat is tcrossprod */          tr   = asLogical(trans); /* gets reversed because _aat is tcrossprod */
325      CHM_TR cht = trip ? AS_CHM_TR(x) : (CHM_TR) NULL;      CHM_TR cht = trip ? AS_CHM_TR(x) : (CHM_TR) NULL;
326      CHM_SP chcp, chxt,      CHM_SP chcp, chxt,
327          chx = trip ? cholmod_triplet_to_sparse(cht, cht->nnz, &c) : AS_CHM_SP(x);          chx = (trip ?
328                   cholmod_triplet_to_sparse(cht, cht->nnz, &c) :
329                   AS_CHM_SP(x));
330      SEXP dn = PROTECT(allocVector(VECSXP, 2));      SEXP dn = PROTECT(allocVector(VECSXP, 2));
331      R_CheckStack();      R_CheckStack();
332
333      if (!tr) chxt = cholmod_transpose(chx, chx->xtype, &c);      if (!tr) chxt = cholmod_transpose(chx, chx->xtype, &c);
334      chcp = cholmod_aat((!tr) ? chxt : chx, (int *) NULL, 0, chx->xtype, &c);      chcp = cholmod_aat((!tr) ? chxt : chx, (int *) NULL, 0, chx->xtype, &c);
335      if(!chcp) error(_("Csparse_crossprod(): error return from cholmod_aat()"));      if(!chcp) {
336            UNPROTECT(1);
337            error(_("Csparse_crossprod(): error return from cholmod_aat()"));
338        }
339      cholmod_band_inplace(0, chcp->ncol, chcp->xtype, chcp, &c);      cholmod_band_inplace(0, chcp->ncol, chcp->xtype, chcp, &c);
340      chcp->stype = 1;      chcp->stype = 1;
341      if (trip) cholmod_free_sparse(&chx, &c);      if (trip) cholmod_free_sparse(&chx, &c);
# Line 255  Line 350
350
351  SEXP Csparse_drop(SEXP x, SEXP tol)  SEXP Csparse_drop(SEXP x, SEXP tol)
352  {  {
353      CHM_SP chx = AS_CHM_SP(x);      const char *cl = class_P(x);
354        /* dtCMatrix, etc; [1] = the second character =?= 't' for triangular */
355        int tr = (cl[1] == 't');
356        CHM_SP chx = AS_CHM_SP__(x);
357      CHM_SP ans = cholmod_copy(chx, chx->stype, chx->xtype, &c);      CHM_SP ans = cholmod_copy(chx, chx->stype, chx->xtype, &c);
358      double dtol = asReal(tol);      double dtol = asReal(tol);
359      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
# Line 263  Line 361
361
362      if(!cholmod_drop(dtol, ans, &c))      if(!cholmod_drop(dtol, ans, &c))
363          error(_("cholmod_drop() failed"));          error(_("cholmod_drop() failed"));
364      return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "",      return chm_sparse_to_SEXP(ans, 1,
365                                  tr ? ((*uplo_P(x) == 'U') ? 1 : -1) : 0,
366                                  Rkind, tr ? diag_P(x) : "",
367                                GET_SLOT(x, Matrix_DimNamesSym));                                GET_SLOT(x, Matrix_DimNamesSym));
368  }  }
369
370  SEXP Csparse_horzcat(SEXP x, SEXP y)  SEXP Csparse_horzcat(SEXP x, SEXP y)
371  {  {
372      CHM_SP chx = AS_CHM_SP(x), chy = AS_CHM_SP(y);      CHM_SP chx = AS_CHM_SP__(x), chy = AS_CHM_SP__(y);
373      int Rkind = 0; /* only for "d" - FIXME */      int Rkind = 0; /* only for "d" - FIXME */
374      R_CheckStack();      R_CheckStack();
375
# Line 280  Line 380
380
381  SEXP Csparse_vertcat(SEXP x, SEXP y)  SEXP Csparse_vertcat(SEXP x, SEXP y)
382  {  {
383      CHM_SP chx = AS_CHM_SP(x), chy = AS_CHM_SP(y);      CHM_SP chx = AS_CHM_SP__(x), chy = AS_CHM_SP__(y);
384      int Rkind = 0; /* only for "d" - FIXME */      int Rkind = 0; /* only for "d" - FIXME */
385      R_CheckStack();      R_CheckStack();
386
# Line 291  Line 391
391
392  SEXP Csparse_band(SEXP x, SEXP k1, SEXP k2)  SEXP Csparse_band(SEXP x, SEXP k1, SEXP k2)
393  {  {
394      CHM_SP chx = AS_CHM_SP(x);      CHM_SP chx = AS_CHM_SP__(x);
395      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
396      CHM_SP ans = cholmod_band(chx, asInteger(k1), asInteger(k2), chx->xtype, &c);      CHM_SP ans = cholmod_band(chx, asInteger(k1), asInteger(k2), chx->xtype, &c);
397      R_CheckStack();      R_CheckStack();
# Line 302  Line 402
402
403  SEXP Csparse_diagU2N(SEXP x)  SEXP Csparse_diagU2N(SEXP x)
404  {  {
405      if (*diag_P(x) != 'U') {/* "trivially fast" when there's no 'diag' slot at all */      const char *cl = class_P(x);
406        /* dtCMatrix, etc; [1] = the second character =?= 't' for triangular */
407        if (cl[1] != 't' || *diag_P(x) != 'U') {
408            /* "trivially fast" when not triangular (<==> no 'diag' slot),
409               or not *unit* triangular */
410          return (x);          return (x);
411      }      }
412      else {      else { /* unit triangular (diag='U'): "fill the diagonal" & diag:= "N" */
413          CHM_SP chx = AS_CHM_SP(x);          CHM_SP chx = AS_CHM_SP__(x);
414          CHM_SP eye = cholmod_speye(chx->nrow, chx->ncol, chx->xtype, &c);          CHM_SP eye = cholmod_speye(chx->nrow, chx->ncol, chx->xtype, &c);
415          double one[] = {1, 0};          double one[] = {1, 0};
416          CHM_SP ans = cholmod_add(chx, eye, one, one, TRUE, TRUE, &c);          CHM_SP ans = cholmod_add(chx, eye, one, one, TRUE, TRUE, &c);
# Line 320  Line 424
424      }      }
425  }  }
426
427    SEXP Csparse_diagN2U(SEXP x)
428    {
429        const char *cl = class_P(x);
430        /* dtCMatrix, etc; [1] = the second character =?= 't' for triangular */
431        if (cl[1] != 't' || *diag_P(x) != 'N') {
432            /* "trivially fast" when not triangular (<==> no 'diag' slot),
433               or already *unit* triangular */
434            return (x);
435        }
436        else { /* triangular with diag='N'): now drop the diagonal */
437            /* duplicate, since chx will be modified: */
438            CHM_SP chx = AS_CHM_SP__(duplicate(x));
439            int uploT = (*uplo_P(x) == 'U') ? 1 : -1,
440                Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
441            R_CheckStack();
442
443            chm_diagN2U(chx, uploT, /* do_realloc */ FALSE);
444
445            return chm_sparse_to_SEXP(chx, /*dofree*/ 0/* or 1 ?? */,
446                                      uploT, Rkind, "U",
447                                      GET_SLOT(x, Matrix_DimNamesSym));
448        }
449    }
450
451  SEXP Csparse_submatrix(SEXP x, SEXP i, SEXP j)  SEXP Csparse_submatrix(SEXP x, SEXP i, SEXP j)
452  {  {
453      CHM_SP chx = AS_CHM_SP(x);      CHM_SP chx = AS_CHM_SP__(x);
454      int rsize = (isNull(i)) ? -1 : LENGTH(i),      int rsize = (isNull(i)) ? -1 : LENGTH(i),
455          csize = (isNull(j)) ? -1 : LENGTH(j);          csize = (isNull(j)) ? -1 : LENGTH(j);
456      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
# Line 339  Line 467
467                                1, 0, Rkind, "",                                1, 0, Rkind, "",
468                                /* FIXME: drops dimnames */ R_NilValue);                                /* FIXME: drops dimnames */ R_NilValue);
469  }  }
470
471    SEXP Csparse_MatrixMarket(SEXP x, SEXP fname)
472    {
473        FILE *f = fopen(CHAR(asChar(fname)), "w");
474
475        if (!f)
476            error(_("failure to open file \"%s\" for writing"),
477                  CHAR(asChar(fname)));
478        if (!cholmod_write_sparse(f, AS_CHM_SP(x),
479                                  (CHM_SP)NULL, (char*) NULL, &c))
480            error(_("cholmod_write_sparse returned error code"));
481        fclose(f);
482        return R_NilValue;
483    }
484
485
486    /**
487     * Extract the diagonal entries from *triangular* Csparse matrix  __or__ a
488     * cholmod_sparse factor (LDL = TRUE).
489     *
490     * @param n  dimension of the matrix.
491     * @param x_p  'p' (column pointer) slot contents
492     * @param x_x  'x' (non-zero entries) slot contents
493     * @param perm 'perm' (= permutation vector) slot contents; only used for "diagBack"
494     * @param resultKind a (SEXP) string indicating which kind of result is desired.
495     *
496     * @return  a SEXP, either a (double) number or a length n-vector of diagonal entries
497     */
498    SEXP diag_tC_ptr(int n, int *x_p, double *x_x, int *perm, SEXP resultKind)
499    /*                                ^^^^^^ FIXME[Generalize] to int / ... */
500    {
501        const char* res_ch = CHAR(STRING_ELT(resultKind,0));
502        enum diag_kind { diag, diag_backpermuted, trace, prod, sum_log
503        } res_kind = ((!strcmp(res_ch, "trace")) ? trace :
504                      ((!strcmp(res_ch, "sumLog")) ? sum_log :
505                       ((!strcmp(res_ch, "prod")) ? prod :
506                        ((!strcmp(res_ch, "diag")) ? diag :
507                         ((!strcmp(res_ch, "diagBack")) ? diag_backpermuted :
508                          -1)))));
509        int i, n_x, i_from = 0;
510        SEXP ans = PROTECT(allocVector(REALSXP,
511    /*                                 ^^^^  FIXME[Generalize] */
512                                       (res_kind == diag ||
513                                        res_kind == diag_backpermuted) ? n : 1));
514        double *v = REAL(ans);
515    /*  ^^^^^^      ^^^^  FIXME[Generalize] */
516
517    #define for_DIAG(v_ASSIGN)                                              \
518        for(i = 0; i < n; i++, i_from += n_x) {                             \
519            /* looking at i-th column */                                    \
520            n_x = x_p[i+1] - x_p[i];/* #{entries} in this column */ \
521            v_ASSIGN;                                                       \
522        }
523
524        /* NOTA BENE: we assume  -- uplo = "L" i.e. lower triangular matrix
525         *            for uplo = "U" (makes sense with a "dtCMatrix" !),
526         *            should use  x_x[i_from + (nx - 1)] instead of x_x[i_from],
527         *            where nx = (x_p[i+1] - x_p[i])
528         */
529
530        switch(res_kind) {
531        case trace:
532            v[0] = 0.;
533            for_DIAG(v[0] += x_x[i_from]);
534            break;
535
536        case sum_log:
537            v[0] = 0.;
538            for_DIAG(v[0] += log(x_x[i_from]));
539            break;
540
541        case prod:
542            v[0] = 1.;
543            for_DIAG(v[0] *= x_x[i_from]);
544            break;
545
546        case diag:
547            for_DIAG(v[i] = x_x[i_from]);
548            break;
549
550        case diag_backpermuted:
551            for_DIAG(v[i] = x_x[i_from]);
552
553            warning(_("resultKind = 'diagBack' (back-permuted) is experimental"));
554            /* now back_permute : */
555            for(i = 0; i < n; i++) {
556                double tmp = v[i]; v[i] = v[perm[i]]; v[perm[i]] = tmp;
557                /*^^^^ FIXME[Generalize] */
558            }
559            break;
560
561        default: /* -1 from above */
562            error("diag_tC(): invalid 'resultKind'");
563            /* Wall: */ ans = R_NilValue; v = REAL(ans);
564        }
565
566        UNPROTECT(1);
567        return ans;
568    }
569
570    /**
571     * Extract the diagonal entries from *triangular* Csparse matrix  __or__ a
572     * cholmod_sparse factor (LDL = TRUE).
573     *
574     * @param pslot  'p' (column pointer)   slot of Csparse matrix/factor
575     * @param xslot  'x' (non-zero entries) slot of Csparse matrix/factor
576     * @param perm_slot  'perm' (= permutation vector) slot of corresponding CHMfactor;
577     *                   only used for "diagBack"
578     * @param resultKind a (SEXP) string indicating which kind of result is desired.
579     *
580     * @return  a SEXP, either a (double) number or a length n-vector of diagonal entries
581     */
582    SEXP diag_tC(SEXP pslot, SEXP xslot, SEXP perm_slot, SEXP resultKind)
583    {
584        int n = length(pslot) - 1, /* n = ncol(.) = nrow(.) */
585            *x_p  = INTEGER(pslot),
586            *perm = INTEGER(perm_slot);
587        double *x_x = REAL(xslot);
588    /*  ^^^^^^        ^^^^ FIXME[Generalize] to INTEGER(.) / LOGICAL(.) / ... xslot !*/
589
590        return diag_tC_ptr(n, x_p, x_x, perm, resultKind);
591    }

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