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

# Diff of /pkg/src/Csparse.c

revision 1921, Sat Jun 23 18:08:17 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          cholmod_sparse *chx = as_cholmod_sparse(x);          CHM_SP chx = (CHM_SP) alloca(sizeof(cholmod_sparse));
44          cholmod_sort(chx, &c);          R_CheckStack();
45          Free(chx);          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
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 56  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      cholmod_sparse *chxs = as_cholmod_sparse(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 : */
117      cholmod_dense *chxd = cholmod_sparse_to_dense(chxs, &c);      CHM_DN chxd = cholmod_sparse_to_dense(chxs, &c);
118      int Rkind = (chxs->xtype == CHOLMOD_PATTERN)? -1 : Real_kind(x);      int Rkind = (chxs->xtype == CHOLMOD_PATTERN)? -1 : Real_kind(x);
119        R_CheckStack();
120
Free(chxs);
121      return chm_dense_to_SEXP(chxd, 1, Rkind, GET_SLOT(x, Matrix_DimNamesSym));      return chm_dense_to_SEXP(chxd, 1, Rkind, GET_SLOT(x, Matrix_DimNamesSym));
122  }  }
123
124  SEXP Csparse_to_nz_pattern(SEXP x, SEXP tri)  SEXP Csparse_to_nz_pattern(SEXP x, SEXP tri)
125  {  {
126      cholmod_sparse *chxs = as_cholmod_sparse(x);      CHM_SP chxs = AS_CHM_SP__(x);
127      cholmod_sparse      CHM_SP chxcp = cholmod_copy(chxs, chxs->stype, CHOLMOD_PATTERN, &c);
*chxcp = cholmod_copy(chxs, chxs->stype, CHOLMOD_PATTERN, &c);
128      int tr = asLogical(tri);      int tr = asLogical(tri);
129        R_CheckStack();
130
131      Free(chxs);      return chm_sparse_to_SEXP(chxcp, 1/*do_free*/,
return chm_sparse_to_SEXP(chxcp, 1,
132                                tr ? ((*uplo_P(x) == 'U') ? 1 : -1) : 0,                                tr ? ((*uplo_P(x) == 'U') ? 1 : -1) : 0,
133                                0, tr ? diag_P(x) : "",                                0, tr ? diag_P(x) : "",
134                                GET_SLOT(x, Matrix_DimNamesSym));                                GET_SLOT(x, Matrix_DimNamesSym));
# Line 88  Line 136
136
137  SEXP Csparse_to_matrix(SEXP x)  SEXP Csparse_to_matrix(SEXP x)
138  {  {
139      cholmod_sparse *chxs = as_cholmod_sparse(x);      return chm_dense_to_matrix(cholmod_sparse_to_dense(AS_CHM_SP__(x), &c),
140      cholmod_dense *chxd = cholmod_sparse_to_dense(chxs, &c);                                 1 /*do_free*/, GET_SLOT(x, Matrix_DimNamesSym));

Free(chxs);
return chm_dense_to_matrix(chxd, 1,
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      cholmod_sparse *chxs = as_cholmod_sparse(x);      CHM_SP chxs = AS_CHM_SP__(x);
146      cholmod_triplet *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;
149        R_CheckStack();
150
Free(chxs);
151      return chm_triplet_to_SEXP(chxt, 1,      return chm_triplet_to_SEXP(chxt, 1,
152                                 tr ? ((*uplo_P(x) == 'U') ? 1 : -1) : 0,                                 tr ? ((*uplo_P(x) == 'U') ? 1 : -1) : 0,
153                                 Rkind, tr ? diag_P(x) : "",                                 Rkind, tr ? diag_P(x) : "",
# Line 113  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      cholmod_sparse *chx = as_cholmod_sparse(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();
163
164      if (!(chx->stype))      if (!(chx->stype))
165          error(_("Nonsymmetric matrix in Csparse_symmetric_to_general"));          error(_("Nonsymmetric matrix in Csparse_symmetric_to_general"));
166      chgx = cholmod_copy(chx, /* stype: */ 0, chx->xtype, &c);      chgx = cholmod_copy(chx, /* stype: */ 0, chx->xtype, &c);
167      /* xtype: pattern, "real", complex or .. */      /* xtype: pattern, "real", complex or .. */
Free(chx);
168      return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",      return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",
169                                GET_SLOT(x, Matrix_DimNamesSym));                                GET_SLOT(x, Matrix_DimNamesSym));
170  }  }
171
172  SEXP Csparse_general_to_symmetric(SEXP x, SEXP uplo)  SEXP Csparse_general_to_symmetric(SEXP x, SEXP uplo)
173  {  {
174      cholmod_sparse *chx = as_cholmod_sparse(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();
178
179      chgx = cholmod_copy(chx, /* stype: */ uploT, chx->xtype, &c);      chgx = cholmod_copy(chx, /* stype: */ uploT, chx->xtype, &c);
180      /* xtype: pattern, "real", complex or .. */      /* xtype: pattern, "real", complex or .. */
Free(chx);
181      return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",      return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",
182                                GET_SLOT(x, Matrix_DimNamesSym));                                GET_SLOT(x, Matrix_DimNamesSym));
183  }  }
# Line 142  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      cholmod_sparse *chx = as_cholmod_sparse(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      cholmod_sparse *chxt = cholmod_transpose(chx, (int) 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;
193      int tr = asLogical(tri);      int tr = asLogical(tri);
194        R_CheckStack();
195
Free(chx);
196      tmp = VECTOR_ELT(dn, 0);    /* swap the dimnames */      tmp = VECTOR_ELT(dn, 0);    /* swap the dimnames */
197      SET_VECTOR_ELT(dn, 0, VECTOR_ELT(dn, 1));      SET_VECTOR_ELT(dn, 0, VECTOR_ELT(dn, 1));
198      SET_VECTOR_ELT(dn, 1, tmp);      SET_VECTOR_ELT(dn, 1, tmp);
# Line 160  Line 204
204
205  SEXP Csparse_Csparse_prod(SEXP a, SEXP b)  SEXP Csparse_Csparse_prod(SEXP a, SEXP b)
206  {  {
207      cholmod_sparse      CHM_SP
208          *cha = as_cholmod_sparse(a),          cha = AS_CHM_SP(a),
209          *chb = as_cholmod_sparse(b);          chb = AS_CHM_SP(b),
210      cholmod_sparse *chc = cholmod_ssmult(cha, chb, 0, cha->xtype, 1, &c);          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();
217
218      Free(cha); Free(chb);      /* 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      cholmod_sparse      CHM_SP
246          *cha = as_cholmod_sparse(a),          cha = AS_CHM_SP(a),
247          *chb = as_cholmod_sparse(b);          chb = AS_CHM_SP(b),
248      cholmod_sparse *chTr, *chc;          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();
254
255  /*     cholmod_sparse *chTr = cholmod_transpose(cha, 1, &c); */      chTr = cholmod_transpose((tr) ? chb : cha, chb->xtype, &c);
/*     cholmod_sparse *chc = cholmod_ssmult(chTr, chb, 0, cha->xtype, 1, &c); */

if (tr)
chTr = cholmod_transpose(chb, chb->xtype, &c);
else
chTr = cholmod_transpose(cha, cha->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);
259
260      Free(cha); Free(chb); cholmod_free_sparse(&chTr, &c);      /* 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)
280  {  {
281      cholmod_sparse *cha = as_cholmod_sparse(a);      CHM_SP cha = AS_CHM_SP(a);
282      SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));      SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));
283      cholmod_dense *chb = as_cholmod_dense(b_M);      CHM_DN chb = AS_CHM_DN(b_M);
284      cholmod_dense *chc =      CHM_DN chc = cholmod_allocate_dense(cha->nrow, chb->ncol, cha->nrow,
285          cholmod_allocate_dense(cha->nrow, chb->ncol, cha->nrow, chb->xtype, &c);                                          chb->xtype, &c);
286      SEXP dn = allocVector(VECSXP, 2);      SEXP dn = PROTECT(allocVector(VECSXP, 2));
287      double alpha[] = {1,0}, beta[] = {0,0};      double one[] = {1,0}, zero[] = {0,0};
288        R_CheckStack();
289
290      cholmod_sdmult(cha, 0, alpha, beta, chb, chc, &c);      cholmod_sdmult(cha, 0, one, zero, chb, chc, &c);
Free(cha); Free(chb);
UNPROTECT(1);
291      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
292                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));
293      SET_VECTOR_ELT(dn, 1,      SET_VECTOR_ELT(dn, 1,
294                     duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));                     duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));
295        UNPROTECT(2);
296      return chm_dense_to_SEXP(chc, 1, 0, dn);      return chm_dense_to_SEXP(chc, 1, 0, dn);
297  }  }
298
299  SEXP Csparse_dense_crossprod(SEXP a, SEXP b)  SEXP Csparse_dense_crossprod(SEXP a, SEXP b)
300  {  {
301      cholmod_sparse *cha = as_cholmod_sparse(a);      CHM_SP cha = AS_CHM_SP(a);
302      SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));      SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));
303      cholmod_dense *chb = as_cholmod_dense(b_M);      CHM_DN chb = AS_CHM_DN(b_M);
304      cholmod_dense *chc =      CHM_DN chc = cholmod_allocate_dense(cha->ncol, chb->ncol, cha->ncol,
305          cholmod_allocate_dense(cha->ncol, chb->ncol, cha->ncol, chb->xtype, &c);                                          chb->xtype, &c);
306      SEXP dn = allocVector(VECSXP, 2);      SEXP dn = PROTECT(allocVector(VECSXP, 2));
307      double alpha[] = {1,0}, beta[] = {0,0};      double one[] = {1,0}, zero[] = {0,0};
308        R_CheckStack();
309
310      cholmod_sdmult(cha, 1, alpha, beta, chb, chc, &c);      cholmod_sdmult(cha, 1, one, zero, chb, chc, &c);
Free(cha); Free(chb);
UNPROTECT(1);
311      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
312                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 1)));                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 1)));
313      SET_VECTOR_ELT(dn, 1,      SET_VECTOR_ELT(dn, 1,
314                     duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));                     duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));
315        UNPROTECT(2);
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      cholmod_triplet      CHM_TR cht = trip ? AS_CHM_TR(x) : (CHM_TR) NULL;
326          *cht = trip ? as_cholmod_triplet(x) : (cholmod_triplet*) NULL;      CHM_SP chcp, chxt,
327      cholmod_sparse *chcp, *chxt,          chx = (trip ?
328          *chx = trip ? cholmod_triplet_to_sparse(cht, cht->nnz, &c)                 cholmod_triplet_to_sparse(cht, cht->nnz, &c) :
329          : as_cholmod_sparse(x);                 AS_CHM_SP(x));
330      SEXP dn = PROTECT(allocVector(VECSXP, 2));      SEXP dn = PROTECT(allocVector(VECSXP, 2));
331        R_CheckStack();
332
333      if (!tr)      if (!tr) chxt = cholmod_transpose(chx, chx->xtype, &c);
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)      if(!chcp) {
336            UNPROTECT(1);
337          error(_("Csparse_crossprod(): error return from cholmod_aat()"));          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) {      if (trip) cholmod_free_sparse(&chx, &c);
cholmod_free_sparse(&chx, &c);
Free(cht);
} else {
Free(chx);
}
342      if (!tr) cholmod_free_sparse(&chxt, &c);      if (!tr) cholmod_free_sparse(&chxt, &c);
343                                  /* create dimnames */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
SET_VECTOR_ELT(dn, 0,
344                     duplicate(VECTOR_ELT(GET_SLOT(x, Matrix_DimNamesSym),                     duplicate(VECTOR_ELT(GET_SLOT(x, Matrix_DimNamesSym),
345                                          (tr) ? 0 : 1)));                                          (tr) ? 0 : 1)));
346      SET_VECTOR_ELT(dn, 1, duplicate(VECTOR_ELT(dn, 0)));      SET_VECTOR_ELT(dn, 1, duplicate(VECTOR_ELT(dn, 0)));
# Line 279  Line 350
350
351  SEXP Csparse_drop(SEXP x, SEXP tol)  SEXP Csparse_drop(SEXP x, SEXP tol)
352  {  {
353      cholmod_sparse *chx = as_cholmod_sparse(x),      const char *cl = class_P(x);
354          *ans = cholmod_copy(chx, chx->stype, chx->xtype, &c);      /* 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);
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;
360        R_CheckStack();
361
362      if(!cholmod_drop(dtol, ans, &c))      if(!cholmod_drop(dtol, ans, &c))
363          error(_("cholmod_drop() failed"));          error(_("cholmod_drop() failed"));
364      Free(chx);      return chm_sparse_to_SEXP(ans, 1,
365      return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "",                                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      cholmod_sparse *chx = as_cholmod_sparse(x),      CHM_SP chx = AS_CHM_SP__(x), chy = AS_CHM_SP__(y);
*chy = as_cholmod_sparse(y), *ans;
373      int Rkind = 0; /* only for "d" - FIXME */      int Rkind = 0; /* only for "d" - FIXME */
374        R_CheckStack();
375
ans = cholmod_horzcat(chx, chy, 1, &c);
Free(chx); Free(chy);
376      /* FIXME: currently drops dimnames */      /* FIXME: currently drops dimnames */
377      return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "", R_NilValue);      return chm_sparse_to_SEXP(cholmod_horzcat(chx, chy, 1, &c),
378                                  1, 0, Rkind, "", R_NilValue);
379  }  }
380
381  SEXP Csparse_vertcat(SEXP x, SEXP y)  SEXP Csparse_vertcat(SEXP x, SEXP y)
382  {  {
383      cholmod_sparse *chx = as_cholmod_sparse(x),      CHM_SP chx = AS_CHM_SP__(x), chy = AS_CHM_SP__(y);
*chy = as_cholmod_sparse(y), *ans;
384      int Rkind = 0; /* only for "d" - FIXME */      int Rkind = 0; /* only for "d" - FIXME */
385        R_CheckStack();
386
ans = cholmod_vertcat(chx, chy, 1, &c);
Free(chx); Free(chy);
387      /* FIXME: currently drops dimnames */      /* FIXME: currently drops dimnames */
388      return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "", R_NilValue);      return chm_sparse_to_SEXP(cholmod_vertcat(chx, chy, 1, &c),
389                                  1, 0, Rkind, "", R_NilValue);
390  }  }
391
392  SEXP Csparse_band(SEXP x, SEXP k1, SEXP k2)  SEXP Csparse_band(SEXP x, SEXP k1, SEXP k2)
393  {  {
394      cholmod_sparse *chx = as_cholmod_sparse(x), *ans;      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);
397        R_CheckStack();
398
ans = cholmod_band(chx, asInteger(k1), asInteger(k2), chx->xtype, &c);
Free(chx);
399      return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "",      return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "",
400                                GET_SLOT(x, Matrix_DimNamesSym));                                GET_SLOT(x, Matrix_DimNamesSym));
401  }  }
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          cholmod_sparse *chx = as_cholmod_sparse(x);          CHM_SP chx = AS_CHM_SP__(x);
414          cholmod_sparse *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          cholmod_sparse *ans = cholmod_add(chx, eye, one, one, TRUE, TRUE, &c);          CHM_SP ans = cholmod_add(chx, eye, one, one, TRUE, TRUE, &c);
417          int uploT = (*uplo_P(x) == 'U') ? 1 : -1;          int uploT = (*uplo_P(x) == 'U') ? 1 : -1;
418          int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;          int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
419
420          Free(chx); cholmod_free_sparse(&eye, &c);          R_CheckStack();
421            cholmod_free_sparse(&eye, &c);
422          return chm_sparse_to_SEXP(ans, 1, uploT, Rkind, "N",          return chm_sparse_to_SEXP(ans, 1, uploT, Rkind, "N",
423                                    GET_SLOT(x, Matrix_DimNamesSym));                                    GET_SLOT(x, Matrix_DimNamesSym));
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      cholmod_sparse *chx = as_cholmod_sparse(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;
457        R_CheckStack();
458
459      if (rsize >= 0 && !isInteger(i))      if (rsize >= 0 && !isInteger(i))
460          error(_("Index i must be NULL or integer"));          error(_("Index i must be NULL or integer"));
# Line 364  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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 Removed from v.1921 changed lines Added in v.2235