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

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revision 1657, Wed Nov 1 16:29:53 2006 UTC revision 2049, Tue Aug 14 22:22:24 2007 UTC
# Line 7  Line 7 
7      /* NB: we do *NOT* check a potential 'x' slot here, at all */      /* NB: we do *NOT* check a potential 'x' slot here, at all */
8      SEXP pslot = GET_SLOT(x, Matrix_pSym),      SEXP pslot = GET_SLOT(x, Matrix_pSym),
9          islot = GET_SLOT(x, Matrix_iSym);          islot = GET_SLOT(x, Matrix_iSym);
10      int j, k, ncol, nrow, sorted,      Rboolean sorted, strictly;
11        int j, k,
12          *dims = INTEGER(GET_SLOT(x, Matrix_DimSym)),          *dims = INTEGER(GET_SLOT(x, Matrix_DimSym)),
13            nrow = dims[0],
14            ncol = dims[1],
15          *xp = INTEGER(pslot),          *xp = INTEGER(pslot),
16          *xi = INTEGER(islot);          *xi = INTEGER(islot);
17    
     nrow = dims[0];  
     ncol = dims[1];  
18      if (length(pslot) != dims[1] + 1)      if (length(pslot) != dims[1] + 1)
19          return mkString(_("slot p must have length = ncol(.) + 1"));          return mkString(_("slot p must have length = ncol(.) + 1"));
20      if (xp[0] != 0)      if (xp[0] != 0)
21          return mkString(_("first element of slot p must be zero"));          return mkString(_("first element of slot p must be zero"));
22      if (length(islot) != xp[ncol])      if (length(islot) < xp[ncol]) /* allow larger slots from over-allocation!*/
23          return          return
24              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"));
25      for (j = 0; j < length(islot); 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 mkString(_("all row indices must be between 0 and nrow-1"));
28      }      }
29      sorted = TRUE;      sorted = TRUE; strictly = TRUE;
30      for (j = 0; j < ncol; j++) {      for (j = 0; j < ncol; j++) {
31          if (xp[j] > xp[j+1])          if (xp[j] > xp[j+1])
32              return mkString(_("slot p must be non-decreasing"));              return mkString(_("slot p must be non-decreasing"));
33          for (k = xp[j] + 1; k < xp[j + 1]; k++)          if(sorted)
34              if (xi[k] < xi[k - 1]) sorted = FALSE;              for (k = xp[j] + 1; k < xp[j + 1]; k++) {
35                    if (xi[k] < xi[k - 1])
36                        sorted = FALSE;
37                    else if (xi[k] == xi[k - 1])
38                        strictly = FALSE;
39                }
40      }      }
41      if (!sorted) {      if (!sorted) {
42          cholmod_sparse *chx = as_cholmod_sparse(x);          CHM_SP chx = AS_CHM_SP(x);
43            R_CheckStack();
44    
45          cholmod_sort(chx, &c);          cholmod_sort(chx, &c);
46          Free(chx);          /* Now re-check that row indices are *strictly* increasing
47             * (and not just increasing) within each column : */
48            for (j = 0; j < ncol; j++) {
49                for (k = xp[j] + 1; k < xp[j + 1]; k++)
50                    if (xi[k] == xi[k - 1])
51                        return mkString(_("slot i is not *strictly* increasing inside a column (even after cholmod_sort)"));
52            }
53    
54        } else if(!strictly) {  /* sorted, but not strictly */
55            return mkString(_("slot i is not *strictly* increasing inside a column"));
56        }
57        return ScalarLogical(1);
58    }
59    
60    SEXP Rsparse_validate(SEXP x)
61    {
62        /* NB: we do *NOT* check a potential 'x' slot here, at all */
63        SEXP pslot = GET_SLOT(x, Matrix_pSym),
64            jslot = GET_SLOT(x, Matrix_jSym);
65        Rboolean sorted, strictly;
66        int i, k,
67            *dims = INTEGER(GET_SLOT(x, Matrix_DimSym)),
68            nrow = dims[0],
69            ncol = dims[1],
70            *xp = INTEGER(pslot),
71            *xj = INTEGER(jslot);
72    
73        if (length(pslot) != dims[0] + 1)
74            return mkString(_("slot p must have length = nrow(.) + 1"));
75        if (xp[0] != 0)
76            return mkString(_("first element of slot p must be zero"));
77        if (length(jslot) < xp[nrow]) /* allow larger slots from over-allocation!*/
78            return
79                mkString(_("last element of slot p must match length of slots j and x"));
80        for (i = 0; i < length(jslot); i++) {
81            if (xj[i] < 0 || xj[i] >= ncol)
82                return mkString(_("all column indices must be between 0 and ncol-1"));
83        }
84        sorted = TRUE; strictly = TRUE;
85        for (i = 0; i < nrow; i++) {
86            if (xp[i] > xp[i+1])
87                return mkString(_("slot p must be non-decreasing"));
88            if(sorted)
89                for (k = xp[i] + 1; k < xp[i + 1]; k++) {
90                    if (xj[k] < xj[k - 1])
91                        sorted = FALSE;
92                    else if (xj[k] == xj[k - 1])
93                        strictly = FALSE;
94      }      }
95        }
96        if (!sorted)
97            /* cannot easily use cholmod_sort(.) ... -> "error out" :*/
98            return mkString(_("slot j is not increasing inside a column"));
99        else if(!strictly) /* sorted, but not strictly */
100            return mkString(_("slot j is not *strictly* increasing inside a column"));
101    
102      return ScalarLogical(1);      return ScalarLogical(1);
103  }  }
104    
105    
106    /* Called from ../R/Csparse.R : */
107    /* Can only return [dln]geMatrix (no symm/triang);
108     * FIXME: replace by non-CHOLMOD code ! */
109  SEXP Csparse_to_dense(SEXP x)  SEXP Csparse_to_dense(SEXP x)
110  {  {
111      cholmod_sparse *chxs = as_cholmod_sparse(x);      CHM_SP chxs = AS_CHM_SP(x);
112      cholmod_dense *chxd = cholmod_sparse_to_dense(chxs, &c);      /* This loses the symmetry property, since cholmod_dense has none,
113         * BUT, much worse (FIXME!), it also transforms CHOLMOD_PATTERN ("n") matrices
114         * to numeric (CHOLMOD_REAL) ones : */
115        CHM_DN chxd = cholmod_sparse_to_dense(chxs, &c);
116        int Rkind = (chxs->xtype == CHOLMOD_PATTERN)? -1 : Real_kind(x);
117        R_CheckStack();
118    
119      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));  
120  }  }
121    
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)  SEXP Csparse_to_matrix(SEXP x)
136  {  {
137      cholmod_sparse *chxs = as_cholmod_sparse(x);      return chm_dense_to_matrix(cholmod_sparse_to_dense(AS_CHM_SP(x), &c),
138      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));  
139  }  }
140    
141  SEXP Csparse_to_Tsparse(SEXP x, SEXP tri)  SEXP Csparse_to_Tsparse(SEXP x, SEXP tri)
142  {  {
143      cholmod_sparse *chxs = as_cholmod_sparse(x);      CHM_SP chxs = AS_CHM_SP(x);
144      cholmod_triplet *chxt = cholmod_sparse_to_triplet(chxs, &c);      CHM_TR chxt = cholmod_sparse_to_triplet(chxs, &c);
145      int uploT = 0;      int tr = asLogical(tri);
146      char *diag = "";      int Rkind = (chxs->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
147      int Rkind = (chxs->xtype == CHOLMOD_REAL) ? Real_kind(x) : 0;      R_CheckStack();
148    
149      Free(chxs);      return chm_triplet_to_SEXP(chxt, 1,
150      if (asLogical(tri)) {       /* triangular sparse matrices */                                 tr ? ((*uplo_P(x) == 'U') ? 1 : -1) : 0,
151          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,  
152                                 GET_SLOT(x, Matrix_DimNamesSym));                                 GET_SLOT(x, Matrix_DimNamesSym));
153  }  }
154    
155  /* this used to be called  sCMatrix_to_gCMatrix(..)   [in ./dsCMatrix.c ]: */  /* this used to be called  sCMatrix_to_gCMatrix(..)   [in ./dsCMatrix.c ]: */
156  SEXP Csparse_symmetric_to_general(SEXP x)  SEXP Csparse_symmetric_to_general(SEXP x)
157  {  {
158      cholmod_sparse *chx = as_cholmod_sparse(x), *chgx;      CHM_SP chx = AS_CHM_SP(x), chgx;
159      int Rkind = (chx->xtype == CHOLMOD_REAL) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
160        R_CheckStack();
161    
162      if (!(chx->stype))      if (!(chx->stype))
163          error(_("Nonsymmetric matrix in Csparse_symmetric_to_general"));          error(_("Nonsymmetric matrix in Csparse_symmetric_to_general"));
164      chgx = cholmod_copy(chx, /* stype: */ 0, chx->xtype, &c);      chgx = cholmod_copy(chx, /* stype: */ 0, chx->xtype, &c);
165      /* xtype: pattern, "real", complex or .. */      /* xtype: pattern, "real", complex or .. */
     Free(chx);  
166      return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",      return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",
167                                GET_SLOT(x, Matrix_DimNamesSym));                                GET_SLOT(x, Matrix_DimNamesSym));
168  }  }
169    
170  SEXP Csparse_general_to_symmetric(SEXP x, SEXP uplo)  SEXP Csparse_general_to_symmetric(SEXP x, SEXP uplo)
171  {  {
172      cholmod_sparse *chx = as_cholmod_sparse(x), *chgx;      CHM_SP chx = AS_CHM_SP(x), chgx;
173      int uploT = (*CHAR(asChar(uplo)) == 'U') ? -1 : 1;      int uploT = (*CHAR(asChar(uplo)) == 'U') ? 1 : -1;
174      int Rkind = (chx->xtype == CHOLMOD_REAL) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
175        R_CheckStack();
176    
177      chgx = cholmod_copy(chx, /* stype: */ uploT, chx->xtype, &c);      chgx = cholmod_copy(chx, /* stype: */ uploT, chx->xtype, &c);
178      /* xtype: pattern, "real", complex or .. */      /* xtype: pattern, "real", complex or .. */
     Free(chx);  
179      return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",      return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",
180                                GET_SLOT(x, Matrix_DimNamesSym));                                GET_SLOT(x, Matrix_DimNamesSym));
181  }  }
182    
183  SEXP Csparse_transpose(SEXP x, SEXP tri)  SEXP Csparse_transpose(SEXP x, SEXP tri)
184  {  {
185      cholmod_sparse *chx = as_cholmod_sparse(x);      /* TODO: lgCMatrix & igC* currently go via double prec. cholmod -
186      int Rkind = (chx->xtype == CHOLMOD_REAL) ? Real_kind(x) : 0;       *       since cholmod (& cs) lacks sparse 'int' matrices */
187      cholmod_sparse *chxt = cholmod_transpose(chx, (int) chx->xtype, &c);      CHM_SP chx = AS_CHM_SP(x);
188        int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
189        CHM_SP chxt = cholmod_transpose(chx, chx->xtype, &c);
190      SEXP dn = PROTECT(duplicate(GET_SLOT(x, Matrix_DimNamesSym))), tmp;      SEXP dn = PROTECT(duplicate(GET_SLOT(x, Matrix_DimNamesSym))), tmp;
191      int uploT = 0; char *diag = "";      int tr = asLogical(tri);
192        R_CheckStack();
193    
     Free(chx);  
194      tmp = VECTOR_ELT(dn, 0);    /* swap the dimnames */      tmp = VECTOR_ELT(dn, 0);    /* swap the dimnames */
195      SET_VECTOR_ELT(dn, 0, VECTOR_ELT(dn, 1));      SET_VECTOR_ELT(dn, 0, VECTOR_ELT(dn, 1));
196      SET_VECTOR_ELT(dn, 1, tmp);      SET_VECTOR_ELT(dn, 1, tmp);
197      UNPROTECT(1);      UNPROTECT(1);
198      if (asLogical(tri)) {       /* triangular sparse matrices */      return chm_sparse_to_SEXP(chxt, 1, /* SWAP 'uplo' for triangular */
199          uploT = (*uplo_P(x) == 'U') ? -1 : 1;                                tr ? ((*uplo_P(x) == 'U') ? -1 : 1) : 0,
200          diag = diag_P(x);                                Rkind, tr ? diag_P(x) : "", dn);
     }  
     return chm_sparse_to_SEXP(chxt, 1, uploT, Rkind, diag, dn);  
201  }  }
202    
203  SEXP Csparse_Csparse_prod(SEXP a, SEXP b)  SEXP Csparse_Csparse_prod(SEXP a, SEXP b)
204  {  {
205      cholmod_sparse *cha = as_cholmod_sparse(a),      CHM_SP cha = AS_CHM_SP(a), chb = AS_CHM_SP(b);
206          *chb = as_cholmod_sparse(b);      CHM_SP chc = cholmod_ssmult(cha, chb, 0, cha->xtype, 1, &c);
     cholmod_sparse *chc = cholmod_ssmult(cha, chb, 0, cha->xtype, 1, &c);  
207      SEXP dn = allocVector(VECSXP, 2);      SEXP dn = allocVector(VECSXP, 2);
208        R_CheckStack();
209    
     Free(cha); Free(chb);  
210      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
211                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));
212      SET_VECTOR_ELT(dn, 1,      SET_VECTOR_ELT(dn, 1,
# Line 156  Line 214 
214      return chm_sparse_to_SEXP(chc, 1, 0, 0, "", dn);      return chm_sparse_to_SEXP(chc, 1, 0, 0, "", dn);
215  }  }
216    
217  SEXP Csparse_Csparse_crossprod(SEXP a, SEXP b)  SEXP Csparse_Csparse_crossprod(SEXP a, SEXP b, SEXP trans)
218  {  {
219      cholmod_sparse *cha = as_cholmod_sparse(a),      int tr = asLogical(trans);
220          *chb = as_cholmod_sparse(b);      CHM_SP cha = AS_CHM_SP(a), chb = AS_CHM_SP(b), chTr, chc;
     cholmod_sparse *chta = cholmod_transpose(cha, 1, &c);  
     cholmod_sparse *chc = cholmod_ssmult(chta, chb, 0, cha->xtype, 1, &c);  
221      SEXP dn = allocVector(VECSXP, 2);      SEXP dn = allocVector(VECSXP, 2);
222        R_CheckStack();
223    
224        chTr = cholmod_transpose((tr) ? chb : cha, chb->xtype, &c);
225        chc = cholmod_ssmult((tr) ? cha : chTr, (tr) ? chTr : chb,
226                             0, cha->xtype, 1, &c);
227        cholmod_free_sparse(&chTr, &c);
228    
     Free(cha); Free(chb); cholmod_free_sparse(&chta, &c);  
229      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
230                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 1)));                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), (tr) ? 0 : 1)));
231      SET_VECTOR_ELT(dn, 1,      SET_VECTOR_ELT(dn, 1,
232                     duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), 1)));                     duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), (tr) ? 0 : 1)));
233      return chm_sparse_to_SEXP(chc, 1, 0, 0, "", dn);      return chm_sparse_to_SEXP(chc, 1, 0, 0, "", dn);
234  }  }
235    
236  SEXP Csparse_dense_prod(SEXP a, SEXP b)  SEXP Csparse_dense_prod(SEXP a, SEXP b)
237  {  {
238      cholmod_sparse *cha = as_cholmod_sparse(a);      CHM_SP cha = AS_CHM_SP(a);
239      cholmod_dense *chb = as_cholmod_dense(PROTECT(mMatrix_as_dgeMatrix(b)));      SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));
240      cholmod_dense *chc =      CHM_DN chb = AS_CHM_DN(b_M);
241          cholmod_allocate_dense(cha->nrow, chb->ncol, cha->nrow, chb->xtype, &c);      CHM_DN chc = cholmod_allocate_dense(cha->nrow, chb->ncol, cha->nrow,
242      double alpha[] = {1,0}, beta[] = {0,0};                                          chb->xtype, &c);
243        SEXP dn = PROTECT(allocVector(VECSXP, 2));
244        double one[] = {1,0}, zero[] = {0,0};
245        R_CheckStack();
246    
247      cholmod_sdmult(cha, 0, alpha, beta, chb, chc, &c);      cholmod_sdmult(cha, 0, one, zero, chb, chc, &c);
248      Free(cha); Free(chb);      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
249      UNPROTECT(1);                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));
250      return chm_dense_to_SEXP(chc, 1, 0);      SET_VECTOR_ELT(dn, 1,
251                       duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));
252        UNPROTECT(2);
253        return chm_dense_to_SEXP(chc, 1, 0, dn);
254  }  }
255    
256  SEXP Csparse_dense_crossprod(SEXP a, SEXP b)  SEXP Csparse_dense_crossprod(SEXP a, SEXP b)
257  {  {
258      cholmod_sparse *cha = as_cholmod_sparse(a);      CHM_SP cha = AS_CHM_SP(a);
259      cholmod_dense *chb = as_cholmod_dense(PROTECT(mMatrix_as_dgeMatrix(b)));      SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));
260      cholmod_dense *chc =      CHM_DN chb = AS_CHM_DN(b_M);
261          cholmod_allocate_dense(cha->ncol, chb->ncol, cha->ncol, chb->xtype, &c);      CHM_DN chc = cholmod_allocate_dense(cha->ncol, chb->ncol, cha->ncol,
262      double alpha[] = {1,0}, beta[] = {0,0};                                          chb->xtype, &c);
263        SEXP dn = PROTECT(allocVector(VECSXP, 2));
264        double one[] = {1,0}, zero[] = {0,0};
265        R_CheckStack();
266    
267      cholmod_sdmult(cha, 1, alpha, beta, chb, chc, &c);      cholmod_sdmult(cha, 1, one, zero, chb, chc, &c);
268      Free(cha); Free(chb);      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
269      UNPROTECT(1);                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 1)));
270      return chm_dense_to_SEXP(chc, 1, 0);      SET_VECTOR_ELT(dn, 1,
271                       duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));
272        UNPROTECT(2);
273        return chm_dense_to_SEXP(chc, 1, 0, dn);
274  }  }
275    
276    /* Computes   x'x  or  x x'  -- see Csparse_Csparse_crossprod above for  x'y and x y' */
277  SEXP Csparse_crossprod(SEXP x, SEXP trans, SEXP triplet)  SEXP Csparse_crossprod(SEXP x, SEXP trans, SEXP triplet)
278  {  {
279      int trip = asLogical(triplet),      int trip = asLogical(triplet),
280          tr   = asLogical(trans); /* gets reversed because _aat is tcrossprod */          tr   = asLogical(trans); /* gets reversed because _aat is tcrossprod */
281      cholmod_triplet      CHM_TR cht = trip ? AS_CHM_TR(x) : (CHM_TR) NULL;
282          *cht = trip ? as_cholmod_triplet(x) : (cholmod_triplet*) NULL;      CHM_SP chcp, chxt,
283      cholmod_sparse *chcp, *chxt,          chx = trip ? cholmod_triplet_to_sparse(cht, cht->nnz, &c) : AS_CHM_SP(x);
         *chx = trip ? cholmod_triplet_to_sparse(cht, cht->nnz, &c)  
         : as_cholmod_sparse(x);  
284      SEXP dn = PROTECT(allocVector(VECSXP, 2));      SEXP dn = PROTECT(allocVector(VECSXP, 2));
285        R_CheckStack();
286    
287      if (!tr)      if (!tr) chxt = cholmod_transpose(chx, chx->xtype, &c);
         chxt = cholmod_transpose(chx, chx->xtype, &c);  
288      chcp = cholmod_aat((!tr) ? chxt : chx, (int *) NULL, 0, chx->xtype, &c);      chcp = cholmod_aat((!tr) ? chxt : chx, (int *) NULL, 0, chx->xtype, &c);
289      if(!chcp)      if(!chcp) error(_("Csparse_crossprod(): error return from cholmod_aat()"));
         error(_("Csparse_crossprod(): error return from cholmod_aat()"));  
290      cholmod_band_inplace(0, chcp->ncol, chcp->xtype, chcp, &c);      cholmod_band_inplace(0, chcp->ncol, chcp->xtype, chcp, &c);
291      chcp->stype = 1;      chcp->stype = 1;
292      if (trip) {      if (trip) cholmod_free_sparse(&chx, &c);
         cholmod_free_sparse(&chx, &c);  
         Free(cht);  
     } else {  
         Free(chx);  
     }  
293      if (!tr) cholmod_free_sparse(&chxt, &c);      if (!tr) cholmod_free_sparse(&chxt, &c);
294                                  /* create dimnames */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
     SET_VECTOR_ELT(dn, 0,  
295                     duplicate(VECTOR_ELT(GET_SLOT(x, Matrix_DimNamesSym),                     duplicate(VECTOR_ELT(GET_SLOT(x, Matrix_DimNamesSym),
296                                          (tr) ? 1 : 0)));                                          (tr) ? 0 : 1)));
297      SET_VECTOR_ELT(dn, 1, duplicate(VECTOR_ELT(dn, 0)));      SET_VECTOR_ELT(dn, 1, duplicate(VECTOR_ELT(dn, 0)));
298      UNPROTECT(1);      UNPROTECT(1);
299      return chm_sparse_to_SEXP(chcp, 1, 0, 0, "", dn);      return chm_sparse_to_SEXP(chcp, 1, 0, 0, "", dn);
# Line 236  Line 301 
301    
302  SEXP Csparse_drop(SEXP x, SEXP tol)  SEXP Csparse_drop(SEXP x, SEXP tol)
303  {  {
304      cholmod_sparse *chx = as_cholmod_sparse(x),      CHM_SP chx = AS_CHM_SP(x);
305          *ans = cholmod_copy(chx, chx->stype, chx->xtype, &c);      CHM_SP ans = cholmod_copy(chx, chx->stype, chx->xtype, &c);
306      double dtol = asReal(tol);      double dtol = asReal(tol);
307      int Rkind = (chx->xtype == CHOLMOD_REAL) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
308        R_CheckStack();
309    
310      if(!cholmod_drop(dtol, ans, &c))      if(!cholmod_drop(dtol, ans, &c))
311          error(_("cholmod_drop() failed"));          error(_("cholmod_drop() failed"));
312      Free(chx);      return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "",
313      /* FIXME: currently drops dimnames */                                GET_SLOT(x, Matrix_DimNamesSym));
     return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "", R_NilValue);  
314  }  }
315    
   
316  SEXP Csparse_horzcat(SEXP x, SEXP y)  SEXP Csparse_horzcat(SEXP x, SEXP y)
317  {  {
318      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;  
319      int Rkind = 0; /* only for "d" - FIXME */      int Rkind = 0; /* only for "d" - FIXME */
320        R_CheckStack();
321    
     ans = cholmod_horzcat(chx, chy, 1, &c);  
     Free(chx); Free(chy);  
322      /* FIXME: currently drops dimnames */      /* FIXME: currently drops dimnames */
323      return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "", R_NilValue);      return chm_sparse_to_SEXP(cholmod_horzcat(chx, chy, 1, &c),
324                                  1, 0, Rkind, "", R_NilValue);
325  }  }
326    
327  SEXP Csparse_vertcat(SEXP x, SEXP y)  SEXP Csparse_vertcat(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_vertcat(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_vertcat(chx, chy, 1, &c),
335                                  1, 0, Rkind, "", R_NilValue);
336  }  }
337    
338  SEXP Csparse_band(SEXP x, SEXP k1, SEXP k2)  SEXP Csparse_band(SEXP x, SEXP k1, SEXP k2)
339  {  {
340      cholmod_sparse *chx = as_cholmod_sparse(x), *ans;      CHM_SP chx = AS_CHM_SP(x);
341      int Rkind = (chx->xtype == CHOLMOD_REAL) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
342        CHM_SP ans = cholmod_band(chx, asInteger(k1), asInteger(k2), chx->xtype, &c);
343        R_CheckStack();
344    
345      ans = cholmod_band(chx, asInteger(k1), asInteger(k2), chx->xtype, &c);      return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "",
346      Free(chx);                                GET_SLOT(x, Matrix_DimNamesSym));
     return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "", R_NilValue);  
347  }  }
348    
349  SEXP Csparse_diagU2N(SEXP x)  SEXP Csparse_diagU2N(SEXP x)
350  {  {
351      cholmod_sparse *chx = as_cholmod_sparse(x);      if (*diag_P(x) != 'U') {/* "trivially fast" when there's no 'diag' slot at all */
352      cholmod_sparse *eye = cholmod_speye(chx->nrow, chx->ncol, chx->xtype, &c);          return (x);
353        }
354        else {
355            CHM_SP chx = AS_CHM_SP(x);
356            CHM_SP eye = cholmod_speye(chx->nrow, chx->ncol, chx->xtype, &c);
357      double one[] = {1, 0};      double one[] = {1, 0};
358      cholmod_sparse *ans = cholmod_add(chx, eye, one, one, TRUE, TRUE, &c);          CHM_SP ans = cholmod_add(chx, eye, one, one, TRUE, TRUE, &c);
359      int uploT = (strcmp(CHAR(asChar(GET_SLOT(x, Matrix_uploSym))), "U")) ?          int uploT = (*uplo_P(x) == 'U') ? 1 : -1;
360          -1 : 1;          int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
     int Rkind = (chx->xtype == CHOLMOD_REAL) ? Real_kind(x) : 0;  
361    
362      Free(chx); cholmod_free_sparse(&eye, &c);          R_CheckStack();
363            cholmod_free_sparse(&eye, &c);
364      return chm_sparse_to_SEXP(ans, 1, uploT, Rkind, "N",      return chm_sparse_to_SEXP(ans, 1, uploT, Rkind, "N",
365                                duplicate(GET_SLOT(x, Matrix_DimNamesSym)));                                    GET_SLOT(x, Matrix_DimNamesSym));
366        }
367  }  }
368    
369  SEXP Csparse_submatrix(SEXP x, SEXP i, SEXP j)  SEXP Csparse_submatrix(SEXP x, SEXP i, SEXP j)
370  {  {
371      cholmod_sparse *chx = as_cholmod_sparse(x);      CHM_SP chx = AS_CHM_SP(x);
372      int rsize = (isNull(i)) ? -1 : LENGTH(i),      int rsize = (isNull(i)) ? -1 : LENGTH(i),
373          csize = (isNull(j)) ? -1 : LENGTH(j);          csize = (isNull(j)) ? -1 : LENGTH(j);
374      int Rkind = (chx->xtype == CHOLMOD_REAL) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
375        R_CheckStack();
376    
377      if (rsize >= 0 && !isInteger(i))      if (rsize >= 0 && !isInteger(i))
378          error(_("Index i must be NULL or integer"));          error(_("Index i must be NULL or integer"));
379      if (csize >= 0 && !isInteger(j))      if (csize >= 0 && !isInteger(j))
380          error(_("Index j must be NULL or integer"));          error(_("Index j must be NULL or integer"));
381    
382      return chm_sparse_to_SEXP(cholmod_submatrix(chx, INTEGER(i), rsize,      return chm_sparse_to_SEXP(cholmod_submatrix(chx, INTEGER(i), rsize,
383                                                  INTEGER(j), csize,                                                  INTEGER(j), csize,
384                                                  TRUE, TRUE, &c),                                                  TRUE, TRUE, &c),
385                                1, 0, Rkind, "", R_NilValue);                                1, 0, Rkind, "",
386                                  /* FIXME: drops dimnames */ R_NilValue);
387    }
388    
389    SEXP Csparse_MatrixMarket(SEXP x, SEXP fname)
390    {
391        FILE *f = fopen(CHAR(asChar(fname)), "w");
392    
393        if (!f)
394            error(_("failure to open file \"%s\" for writing"),
395                  CHAR(asChar(fname)));
396        if (!cholmod_write_sparse(f, AS_CHM_SP(x), (CHM_SP)NULL,
397                                  (char*) NULL, &c))
398            error(_("cholmod_write_sparse returned error code"));
399        fclose(f);
400        return R_NilValue;
401  }  }
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