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

# Diff of /pkg/src/Csparse.c

revision 1708, Fri Dec 22 19:53:37 2006 UTC revision 2120, Tue Mar 4 21:44:41 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 7  Line 8
8      /* NB: we do *NOT* check a potential 'x' slot here, at all */      /* NB: we do *NOT* check a potential 'x' slot here, at all */
9      SEXP pslot = GET_SLOT(x, Matrix_pSym),      SEXP pslot = GET_SLOT(x, Matrix_pSym),
10          islot = GET_SLOT(x, Matrix_iSym);          islot = GET_SLOT(x, Matrix_iSym);
11      int j, k, sorted,      Rboolean sorted, strictly;
12        int j, k,
13          *dims = INTEGER(GET_SLOT(x, Matrix_DimSym)),          *dims = INTEGER(GET_SLOT(x, Matrix_DimSym)),
14          nrow = dims[0],          nrow = dims[0],
15          ncol = dims[1],          ncol = dims[1],
# Line 18  Line 20
20          return mkString(_("slot p must have length = ncol(.) + 1"));          return mkString(_("slot p must have length = ncol(.) + 1"));
21      if (xp[0] != 0)      if (xp[0] != 0)
22          return mkString(_("first element of slot p must be zero"));          return mkString(_("first element of slot p must be zero"));
23      if (length(islot) != xp[ncol])      if (length(islot) < xp[ncol]) /* allow larger slots from over-allocation!*/
24          return          return
25              mkString(_("last element of slot p must match length of slots i and x"));              mkString(_("last element of slot p must match length of slots i and x"));
26      for (j = 0; j < length(islot); j++) {      for (j = 0; j < length(islot); j++) {
27          if (xi[j] < 0 || xi[j] >= nrow)          if (xi[j] < 0 || xi[j] >= nrow)
28              return mkString(_("all row indices must be between 0 and nrow-1"));              return mkString(_("all row indices must be between 0 and nrow-1"));
29      }      }
30      sorted = TRUE;      sorted = TRUE; strictly = TRUE;
31      for (j = 0; j < ncol; j++) {      for (j = 0; j < ncol; j++) {
32          if (xp[j] > xp[j+1])          if (xp[j] > xp[j+1])
33              return mkString(_("slot p must be non-decreasing"));              return mkString(_("slot p must be non-decreasing"));
34          for (k = xp[j] + 1; k < xp[j + 1]; k++)          if(sorted)
35              if (xi[k] < xi[k - 1]) sorted = FALSE;              for (k = xp[j] + 1; k < xp[j + 1]; k++) {
36                    if (xi[k] < xi[k - 1])
37                        sorted = FALSE;
38                    else if (xi[k] == xi[k - 1])
39                        strictly = FALSE;
40                }
41      }      }
42      if (!sorted) {      if (!sorted) {
43          cholmod_sparse *chx = as_cholmod_sparse(x);          CHM_SP chx = AS_CHM_SP(x);
44            R_CheckStack();
45
46          cholmod_sort(chx, &c);          cholmod_sort(chx, &c);
47          Free(chx);          /* Now re-check that row indices are *strictly* increasing
48             * (and not just increasing) within each column : */
49            for (j = 0; j < ncol; j++) {
50                for (k = xp[j] + 1; k < xp[j + 1]; k++)
51                    if (xi[k] == xi[k - 1])
52                        return mkString(_("slot i is not *strictly* increasing inside a column (even after cholmod_sort)"));
53            }
54
55        } else if(!strictly) {  /* sorted, but not strictly */
56            return mkString(_("slot i is not *strictly* increasing inside a column"));
57      }      }
58      return ScalarLogical(1);      return ScalarLogical(1);
59  }  }
60
61    SEXP Rsparse_validate(SEXP x)
62    {
63        /* NB: we do *NOT* check a potential 'x' slot here, at all */
64        SEXP pslot = GET_SLOT(x, Matrix_pSym),
65            jslot = GET_SLOT(x, Matrix_jSym);
66        Rboolean sorted, strictly;
67        int i, k,
68            *dims = INTEGER(GET_SLOT(x, Matrix_DimSym)),
69            nrow = dims[0],
70            ncol = dims[1],
71            *xp = INTEGER(pslot),
72            *xj = INTEGER(jslot);
73
74        if (length(pslot) != dims[0] + 1)
75            return mkString(_("slot p must have length = nrow(.) + 1"));
76        if (xp[0] != 0)
77            return mkString(_("first element of slot p must be zero"));
78        if (length(jslot) < xp[nrow]) /* allow larger slots from over-allocation!*/
79            return
80                mkString(_("last element of slot p must match length of slots j and x"));
81        for (i = 0; i < length(jslot); i++) {
82            if (xj[i] < 0 || xj[i] >= ncol)
83                return mkString(_("all column indices must be between 0 and ncol-1"));
84        }
85        sorted = TRUE; strictly = TRUE;
86        for (i = 0; i < nrow; i++) {
87            if (xp[i] > xp[i+1])
88                return mkString(_("slot p must be non-decreasing"));
89            if(sorted)
90                for (k = xp[i] + 1; k < xp[i + 1]; k++) {
91                    if (xj[k] < xj[k - 1])
92                        sorted = FALSE;
93                    else if (xj[k] == xj[k - 1])
94                        strictly = FALSE;
95                }
96        }
97        if (!sorted)
98            /* cannot easily use cholmod_sort(.) ... -> "error out" :*/
99            return mkString(_("slot j is not increasing inside a column"));
100        else if(!strictly) /* sorted, but not strictly */
101            return mkString(_("slot j is not *strictly* increasing inside a column"));
102
103        return ScalarLogical(1);
104    }
105
106
107    /* Called from ../R/Csparse.R : */
108    /* Can only return [dln]geMatrix (no symm/triang);
109     * FIXME: replace by non-CHOLMOD code ! */
110  SEXP Csparse_to_dense(SEXP x)  SEXP Csparse_to_dense(SEXP x)
111  {  {
112      cholmod_sparse *chxs = as_cholmod_sparse(x);      CHM_SP chxs = AS_CHM_SP(x);
113      cholmod_dense *chxd = cholmod_sparse_to_dense(chxs, &c);      /* This loses the symmetry property, since cholmod_dense has none,
114         * BUT, much worse (FIXME!), it also transforms CHOLMOD_PATTERN ("n") matrices
115         * to numeric (CHOLMOD_REAL) ones : */
116        CHM_DN chxd = cholmod_sparse_to_dense(chxs, &c);
117        int Rkind = (chxs->xtype == CHOLMOD_PATTERN)? -1 : Real_kind(x);
118        R_CheckStack();
119
120      Free(chxs);      return chm_dense_to_SEXP(chxd, 1, Rkind, GET_SLOT(x, Matrix_DimNamesSym));
return chm_dense_to_SEXP(chxd, 1, Real_kind(x),
GET_SLOT(x, Matrix_DimNamesSym));
121  }  }
122
123  SEXP Csparse_to_nz_pattern(SEXP x, SEXP tri)  SEXP Csparse_to_nz_pattern(SEXP x, SEXP tri)
124  {  {
125      cholmod_sparse *chxs = as_cholmod_sparse(x);      CHM_SP chxs = AS_CHM_SP(x);
126      cholmod_sparse      CHM_SP chxcp = cholmod_copy(chxs, chxs->stype, CHOLMOD_PATTERN, &c);
127          *chxcp = cholmod_copy(chxs, chxs->stype, CHOLMOD_PATTERN, &c);      int tr = asLogical(tri);
128      int uploT = 0; char *diag = "";      R_CheckStack();
129
130      Free(chxs);      return chm_sparse_to_SEXP(chxcp, 1/*do_free*/,
131      if (asLogical(tri)) {       /* triangular sparse matrices */                                tr ? ((*uplo_P(x) == 'U') ? 1 : -1) : 0,
132          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,
133                                GET_SLOT(x, Matrix_DimNamesSym));                                GET_SLOT(x, Matrix_DimNamesSym));
134  }  }
135
136  SEXP Csparse_to_matrix(SEXP x)  SEXP Csparse_to_matrix(SEXP x)
137  {  {
138      cholmod_sparse *chxs = as_cholmod_sparse(x);      return chm_dense_to_matrix(cholmod_sparse_to_dense(AS_CHM_SP(x), &c),
139      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));
140  }  }
141
142  SEXP Csparse_to_Tsparse(SEXP x, SEXP tri)  SEXP Csparse_to_Tsparse(SEXP x, SEXP tri)
143  {  {
144      cholmod_sparse *chxs = as_cholmod_sparse(x);      CHM_SP chxs = AS_CHM_SP(x);
145      cholmod_triplet *chxt = cholmod_sparse_to_triplet(chxs, &c);      CHM_TR chxt = cholmod_sparse_to_triplet(chxs, &c);
146      int uploT = 0;      int tr = asLogical(tri);
147      char *diag = "";      int Rkind = (chxs->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
148      int Rkind = (chxs->xtype == CHOLMOD_REAL) ? Real_kind(x) : 0;      R_CheckStack();
149
150      Free(chxs);      return chm_triplet_to_SEXP(chxt, 1,
151      if (asLogical(tri)) {       /* triangular sparse matrices */                                 tr ? ((*uplo_P(x) == 'U') ? 1 : -1) : 0,
152          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,
153                                 GET_SLOT(x, Matrix_DimNamesSym));                                 GET_SLOT(x, Matrix_DimNamesSym));
154  }  }
155
156  /* this used to be called  sCMatrix_to_gCMatrix(..)   [in ./dsCMatrix.c ]: */  /* this used to be called  sCMatrix_to_gCMatrix(..)   [in ./dsCMatrix.c ]: */
157  SEXP Csparse_symmetric_to_general(SEXP x)  SEXP Csparse_symmetric_to_general(SEXP x)
158  {  {
159      cholmod_sparse *chx = as_cholmod_sparse(x), *chgx;      CHM_SP chx = AS_CHM_SP(x), chgx;
160      int Rkind = (chx->xtype == CHOLMOD_REAL) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
161        R_CheckStack();
162
163      if (!(chx->stype))      if (!(chx->stype))
164          error(_("Nonsymmetric matrix in Csparse_symmetric_to_general"));          error(_("Nonsymmetric matrix in Csparse_symmetric_to_general"));
165      chgx = cholmod_copy(chx, /* stype: */ 0, chx->xtype, &c);      chgx = cholmod_copy(chx, /* stype: */ 0, chx->xtype, &c);
166      /* xtype: pattern, "real", complex or .. */      /* xtype: pattern, "real", complex or .. */
Free(chx);
167      return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",      return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",
168                                GET_SLOT(x, Matrix_DimNamesSym));                                GET_SLOT(x, Matrix_DimNamesSym));
169  }  }
170
171  SEXP Csparse_general_to_symmetric(SEXP x, SEXP uplo)  SEXP Csparse_general_to_symmetric(SEXP x, SEXP uplo)
172  {  {
173      cholmod_sparse *chx = as_cholmod_sparse(x), *chgx;      CHM_SP chx = AS_CHM_SP(x), chgx;
174      int uploT = (*CHAR(asChar(uplo)) == 'U') ? -1 : 1;      int uploT = (*CHAR(STRING_ELT(uplo,0)) == 'U') ? 1 : -1;
175      int Rkind = (chx->xtype == CHOLMOD_REAL) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
176        R_CheckStack();
177
178      chgx = cholmod_copy(chx, /* stype: */ uploT, chx->xtype, &c);      chgx = cholmod_copy(chx, /* stype: */ uploT, chx->xtype, &c);
179      /* xtype: pattern, "real", complex or .. */      /* xtype: pattern, "real", complex or .. */
Free(chx);
180      return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",      return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",
181                                GET_SLOT(x, Matrix_DimNamesSym));                                GET_SLOT(x, Matrix_DimNamesSym));
182  }  }
183
184  SEXP Csparse_transpose(SEXP x, SEXP tri)  SEXP Csparse_transpose(SEXP x, SEXP tri)
185  {  {
186      cholmod_sparse *chx = as_cholmod_sparse(x);      /* TODO: lgCMatrix & igC* currently go via double prec. cholmod -
187      int Rkind = (chx->xtype == CHOLMOD_REAL) ? Real_kind(x) : 0;       *       since cholmod (& cs) lacks sparse 'int' matrices */
188      cholmod_sparse *chxt = cholmod_transpose(chx, (int) chx->xtype, &c);      CHM_SP chx = AS_CHM_SP(x);
189        int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
190        CHM_SP chxt = cholmod_transpose(chx, chx->xtype, &c);
191      SEXP dn = PROTECT(duplicate(GET_SLOT(x, Matrix_DimNamesSym))), tmp;      SEXP dn = PROTECT(duplicate(GET_SLOT(x, Matrix_DimNamesSym))), tmp;
192      int uploT = 0; char *diag = "";      int tr = asLogical(tri);
193        R_CheckStack();
194
Free(chx);
195      tmp = VECTOR_ELT(dn, 0);    /* swap the dimnames */      tmp = VECTOR_ELT(dn, 0);    /* swap the dimnames */
196      SET_VECTOR_ELT(dn, 0, VECTOR_ELT(dn, 1));      SET_VECTOR_ELT(dn, 0, VECTOR_ELT(dn, 1));
197      SET_VECTOR_ELT(dn, 1, tmp);      SET_VECTOR_ELT(dn, 1, tmp);
198      UNPROTECT(1);      UNPROTECT(1);
199      if (asLogical(tri)) {       /* triangular sparse matrices */      return chm_sparse_to_SEXP(chxt, 1, /* SWAP 'uplo' for triangular */
200          uploT = (*uplo_P(x) == 'U') ? -1 : 1;                                tr ? ((*uplo_P(x) == 'U') ? -1 : 1) : 0,
201          diag = diag_P(x);                                Rkind, tr ? diag_P(x) : "", dn);
}
return chm_sparse_to_SEXP(chxt, 1, uploT, Rkind, diag, dn);
202  }  }
203
204  SEXP Csparse_Csparse_prod(SEXP a, SEXP b)  SEXP Csparse_Csparse_prod(SEXP a, SEXP b)
205  {  {
206      cholmod_sparse      CHM_SP
207          *cha = as_cholmod_sparse(a),          cha = AS_CHM_SP(Csparse_diagU2N(a)),
208          *chb = as_cholmod_sparse(b);          chb = AS_CHM_SP(Csparse_diagU2N(b)),
209      cholmod_sparse *chc = cholmod_ssmult(cha, chb, 0, cha->xtype, 1, &c);          chc = cholmod_ssmult(cha, chb, 0, cha->xtype, 1, &c);
210      SEXP dn = allocVector(VECSXP, 2);      SEXP dn = allocVector(VECSXP, 2);
211        R_CheckStack();
212
Free(cha); Free(chb);
213      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
214                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));
215      SET_VECTOR_ELT(dn, 1,      SET_VECTOR_ELT(dn, 1,
# Line 161  Line 220
220  SEXP Csparse_Csparse_crossprod(SEXP a, SEXP b, SEXP trans)  SEXP Csparse_Csparse_crossprod(SEXP a, SEXP b, SEXP trans)
221  {  {
222      int tr = asLogical(trans);      int tr = asLogical(trans);
223      cholmod_sparse      CHM_SP
224          *cha = as_cholmod_sparse(a),          cha = AS_CHM_SP(Csparse_diagU2N(a)),
225          *chb = as_cholmod_sparse(b);          chb = AS_CHM_SP(Csparse_diagU2N(b)),
226      cholmod_sparse *chTr, *chc;          chTr, chc;
227      SEXP dn = allocVector(VECSXP, 2);      SEXP dn = allocVector(VECSXP, 2);
228        R_CheckStack();
229
230  /*     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);
231      chc = cholmod_ssmult((tr) ? cha : chTr, (tr) ? chTr : chb,      chc = cholmod_ssmult((tr) ? cha : chTr, (tr) ? chTr : chb,
232                           0, cha->xtype, 1, &c);                           0, cha->xtype, 1, &c);
233        cholmod_free_sparse(&chTr, &c);
Free(cha); Free(chb); cholmod_free_sparse(&chTr, &c);
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), (tr) ? 0 : 1)));                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), (tr) ? 0 : 1)));
# Line 188  Line 241
241
242  SEXP Csparse_dense_prod(SEXP a, SEXP b)  SEXP Csparse_dense_prod(SEXP a, SEXP b)
243  {  {
244      cholmod_sparse *cha = as_cholmod_sparse(a);      CHM_SP cha = AS_CHM_SP(Csparse_diagU2N(a));
245      SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));      SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));
246      cholmod_dense *chb = as_cholmod_dense(b_M);      CHM_DN chb = AS_CHM_DN(b_M);
247      cholmod_dense *chc =      CHM_DN chc = cholmod_allocate_dense(cha->nrow, chb->ncol, cha->nrow,
248          cholmod_allocate_dense(cha->nrow, chb->ncol, cha->nrow, chb->xtype, &c);                                          chb->xtype, &c);
249      SEXP dn = allocVector(VECSXP, 2);      SEXP dn = PROTECT(allocVector(VECSXP, 2));
250      double alpha[] = {1,0}, beta[] = {0,0};      double one[] = {1,0}, zero[] = {0,0};
251        R_CheckStack();
252
253      cholmod_sdmult(cha, 0, alpha, beta, chb, chc, &c);      cholmod_sdmult(cha, 0, one, zero, chb, chc, &c);
Free(cha); Free(chb);
UNPROTECT(1);
254      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
255                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));
256      SET_VECTOR_ELT(dn, 1,      SET_VECTOR_ELT(dn, 1,
257                     duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));                     duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));
258        UNPROTECT(2);
259      return chm_dense_to_SEXP(chc, 1, 0, dn);      return chm_dense_to_SEXP(chc, 1, 0, dn);
260  }  }
261
262  SEXP Csparse_dense_crossprod(SEXP a, SEXP b)  SEXP Csparse_dense_crossprod(SEXP a, SEXP b)
263  {  {
264      cholmod_sparse *cha = as_cholmod_sparse(a);      CHM_SP cha = AS_CHM_SP(Csparse_diagU2N(a));
265      SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));      SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));
266      cholmod_dense *chb = as_cholmod_dense(b_M);      CHM_DN chb = AS_CHM_DN(b_M);
267      cholmod_dense *chc =      CHM_DN chc = cholmod_allocate_dense(cha->ncol, chb->ncol, cha->ncol,
268          cholmod_allocate_dense(cha->ncol, chb->ncol, cha->ncol, chb->xtype, &c);                                          chb->xtype, &c);
269      SEXP dn = allocVector(VECSXP, 2);      SEXP dn = PROTECT(allocVector(VECSXP, 2));
270      double alpha[] = {1,0}, beta[] = {0,0};      double one[] = {1,0}, zero[] = {0,0};
271        R_CheckStack();
272
273      cholmod_sdmult(cha, 1, alpha, beta, chb, chc, &c);      cholmod_sdmult(cha, 1, one, zero, chb, chc, &c);
Free(cha); Free(chb);
UNPROTECT(1);
274      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
275                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 1)));                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 1)));
276      SET_VECTOR_ELT(dn, 1,      SET_VECTOR_ELT(dn, 1,
277                     duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));                     duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));
278        UNPROTECT(2);
279      return chm_dense_to_SEXP(chc, 1, 0, dn);      return chm_dense_to_SEXP(chc, 1, 0, dn);
280  }  }
281
# Line 231  Line 284
284  {  {
285      int trip = asLogical(triplet),      int trip = asLogical(triplet),
286          tr   = asLogical(trans); /* gets reversed because _aat is tcrossprod */          tr   = asLogical(trans); /* gets reversed because _aat is tcrossprod */
287      cholmod_triplet      CHM_TR cht = trip ? AS_CHM_TR(Tsparse_diagU2N(x)) : (CHM_TR) NULL;
288          *cht = trip ? as_cholmod_triplet(x) : (cholmod_triplet*) NULL;      CHM_SP chcp, chxt,
289      cholmod_sparse *chcp, *chxt,          chx = (trip ?
290          *chx = trip ? cholmod_triplet_to_sparse(cht, cht->nnz, &c)                 cholmod_triplet_to_sparse(cht, cht->nnz, &c) :
291          : as_cholmod_sparse(x);                 AS_CHM_SP(Csparse_diagU2N(x)));
292      SEXP dn = PROTECT(allocVector(VECSXP, 2));      SEXP dn = PROTECT(allocVector(VECSXP, 2));
293        R_CheckStack();
294
295      if (!tr)      if (!tr) chxt = cholmod_transpose(chx, chx->xtype, &c);
chxt = cholmod_transpose(chx, chx->xtype, &c);
296      chcp = cholmod_aat((!tr) ? chxt : chx, (int *) NULL, 0, chx->xtype, &c);      chcp = cholmod_aat((!tr) ? chxt : chx, (int *) NULL, 0, chx->xtype, &c);
297      if(!chcp)      if(!chcp) {
298            UNPROTECT(1);
299          error(_("Csparse_crossprod(): error return from cholmod_aat()"));          error(_("Csparse_crossprod(): error return from cholmod_aat()"));
300        }
301      cholmod_band_inplace(0, chcp->ncol, chcp->xtype, chcp, &c);      cholmod_band_inplace(0, chcp->ncol, chcp->xtype, chcp, &c);
302      chcp->stype = 1;      chcp->stype = 1;
303      if (trip) {      if (trip) cholmod_free_sparse(&chx, &c);
cholmod_free_sparse(&chx, &c);
Free(cht);
} else {
Free(chx);
}
304      if (!tr) cholmod_free_sparse(&chxt, &c);      if (!tr) cholmod_free_sparse(&chxt, &c);
305                                  /* create dimnames */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
SET_VECTOR_ELT(dn, 0,
306                     duplicate(VECTOR_ELT(GET_SLOT(x, Matrix_DimNamesSym),                     duplicate(VECTOR_ELT(GET_SLOT(x, Matrix_DimNamesSym),
307                                          (tr) ? 0 : 1)));                                          (tr) ? 0 : 1)));
308      SET_VECTOR_ELT(dn, 1, duplicate(VECTOR_ELT(dn, 0)));      SET_VECTOR_ELT(dn, 1, duplicate(VECTOR_ELT(dn, 0)));
# Line 263  Line 312
312
313  SEXP Csparse_drop(SEXP x, SEXP tol)  SEXP Csparse_drop(SEXP x, SEXP tol)
314  {  {
315      cholmod_sparse *chx = as_cholmod_sparse(x),      CHM_SP chx = AS_CHM_SP(x);
316          *ans = cholmod_copy(chx, chx->stype, chx->xtype, &c);      CHM_SP ans = cholmod_copy(chx, chx->stype, chx->xtype, &c);
317      double dtol = asReal(tol);      double dtol = asReal(tol);
318      int Rkind = (chx->xtype == CHOLMOD_REAL) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
319        R_CheckStack();
320
321      if(!cholmod_drop(dtol, ans, &c))      if(!cholmod_drop(dtol, ans, &c))
322          error(_("cholmod_drop() failed"));          error(_("cholmod_drop() failed"));
323      Free(chx);      return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "",
324      /* FIXME: currently drops dimnames */                                GET_SLOT(x, Matrix_DimNamesSym));
return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "", R_NilValue);
325  }  }
326

327  SEXP Csparse_horzcat(SEXP x, SEXP y)  SEXP Csparse_horzcat(SEXP x, SEXP y)
328  {  {
329      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;
330      int Rkind = 0; /* only for "d" - FIXME */      int Rkind = 0; /* only for "d" - FIXME */
331        R_CheckStack();
332
ans = cholmod_horzcat(chx, chy, 1, &c);
Free(chx); Free(chy);
333      /* FIXME: currently drops dimnames */      /* FIXME: currently drops dimnames */
334      return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "", R_NilValue);      return chm_sparse_to_SEXP(cholmod_horzcat(chx, chy, 1, &c),
335                                  1, 0, Rkind, "", R_NilValue);
336  }  }
337
338  SEXP Csparse_vertcat(SEXP x, SEXP y)  SEXP Csparse_vertcat(SEXP x, SEXP y)
339  {  {
340      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;
341      int Rkind = 0; /* only for "d" - FIXME */      int Rkind = 0; /* only for "d" - FIXME */
342        R_CheckStack();
343
ans = cholmod_vertcat(chx, chy, 1, &c);
Free(chx); Free(chy);
344      /* FIXME: currently drops dimnames */      /* FIXME: currently drops dimnames */
345      return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "", R_NilValue);      return chm_sparse_to_SEXP(cholmod_vertcat(chx, chy, 1, &c),
346                                  1, 0, Rkind, "", R_NilValue);
347  }  }
348
349  SEXP Csparse_band(SEXP x, SEXP k1, SEXP k2)  SEXP Csparse_band(SEXP x, SEXP k1, SEXP k2)
350  {  {
351      cholmod_sparse *chx = as_cholmod_sparse(x), *ans;      CHM_SP chx = AS_CHM_SP(x);
352      int Rkind = (chx->xtype == CHOLMOD_REAL) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
353        CHM_SP ans = cholmod_band(chx, asInteger(k1), asInteger(k2), chx->xtype, &c);
354        R_CheckStack();
355
356      ans = cholmod_band(chx, asInteger(k1), asInteger(k2), chx->xtype, &c);      return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "",
357      Free(chx);                                GET_SLOT(x, Matrix_DimNamesSym));
return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "", R_NilValue);
358  }  }
359
360  SEXP Csparse_diagU2N(SEXP x)  SEXP Csparse_diagU2N(SEXP x)
361  {  {
362      if (*diag_P(x) != 'U') {/* "trivially fast" when there's no 'diag' slot at all */      const char *cl = class_P(x);
363        /* dtCMatrix, etc; [1] = the second character =?= 't' for triangular */
364        if (cl[1] != 't' || *diag_P(x) != 'U') {
365            /* "trivially fast" when not triangular (<==> no 'diag' slot), or not *unit* triangular */
366          return (x);          return (x);
367      }      }
368      else {      else {
369          cholmod_sparse *chx = as_cholmod_sparse(x);          CHM_SP chx = AS_CHM_SP(x);
370          cholmod_sparse *eye = cholmod_speye(chx->nrow, chx->ncol, chx->xtype, &c);          CHM_SP eye = cholmod_speye(chx->nrow, chx->ncol, chx->xtype, &c);
371          double one[] = {1, 0};          double one[] = {1, 0};
372          cholmod_sparse *ans = cholmod_add(chx, eye, one, one, TRUE, TRUE, &c);          CHM_SP ans = cholmod_add(chx, eye, one, one, TRUE, TRUE, &c);
373          int uploT = (strcmp(CHAR(asChar(GET_SLOT(x, Matrix_uploSym))), "U")) ?          int uploT = (*uplo_P(x) == 'U') ? 1 : -1;
374              -1 : 1;          int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
int Rkind = (chx->xtype == CHOLMOD_REAL) ? Real_kind(x) : 0;
375
376          Free(chx); cholmod_free_sparse(&eye, &c);          R_CheckStack();
377            cholmod_free_sparse(&eye, &c);
378          return chm_sparse_to_SEXP(ans, 1, uploT, Rkind, "N",          return chm_sparse_to_SEXP(ans, 1, uploT, Rkind, "N",
379                                    duplicate(GET_SLOT(x, Matrix_DimNamesSym)));                                    GET_SLOT(x, Matrix_DimNamesSym));
380      }      }
381  }  }
382
383  SEXP Csparse_submatrix(SEXP x, SEXP i, SEXP j)  SEXP Csparse_submatrix(SEXP x, SEXP i, SEXP j)
384  {  {
385      cholmod_sparse *chx = as_cholmod_sparse(x);      CHM_SP chx = AS_CHM_SP(x);
386      int rsize = (isNull(i)) ? -1 : LENGTH(i),      int rsize = (isNull(i)) ? -1 : LENGTH(i),
387          csize = (isNull(j)) ? -1 : LENGTH(j);          csize = (isNull(j)) ? -1 : LENGTH(j);
388      int Rkind = (chx->xtype == CHOLMOD_REAL) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
389        R_CheckStack();
390
391      if (rsize >= 0 && !isInteger(i))      if (rsize >= 0 && !isInteger(i))
392          error(_("Index i must be NULL or integer"));          error(_("Index i must be NULL or integer"));
393      if (csize >= 0 && !isInteger(j))      if (csize >= 0 && !isInteger(j))
394          error(_("Index j must be NULL or integer"));          error(_("Index j must be NULL or integer"));
395
396      return chm_sparse_to_SEXP(cholmod_submatrix(chx, INTEGER(i), rsize,      return chm_sparse_to_SEXP(cholmod_submatrix(chx, INTEGER(i), rsize,
397                                                  INTEGER(j), csize,                                                  INTEGER(j), csize,
398                                                  TRUE, TRUE, &c),                                                  TRUE, TRUE, &c),
399                                1, 0, Rkind, "", R_NilValue);                                1, 0, Rkind, "",
400                                  /* FIXME: drops dimnames */ R_NilValue);
401    }
402
403    SEXP Csparse_MatrixMarket(SEXP x, SEXP fname)
404    {
405        FILE *f = fopen(CHAR(asChar(fname)), "w");
406
407        if (!f)
408            error(_("failure to open file \"%s\" for writing"),
409                  CHAR(asChar(fname)));
410        if (!cholmod_write_sparse(f, AS_CHM_SP(Csparse_diagU2N(x)),
411                                  (CHM_SP)NULL, (char*) NULL, &c))
412            error(_("cholmod_write_sparse returned error code"));
413        fclose(f);
414        return R_NilValue;
415  }  }

Legend:
 Removed from v.1708 changed lines Added in v.2120