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

Diff of /pkg/Matrix/src/Csparse.c

revision 1598, Fri Sep 29 09:39:34 2006 UTC revision 2299, Fri Oct 17 16:07:38 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    /** "Cheap" C version of  Csparse_validate() - *not* sorting : */
7    Rboolean isValid_Csparse(SEXP x)
8    {
9        /* NB: we do *NOT* check a potential 'x' slot here, at all */
10        SEXP pslot = GET_SLOT(x, Matrix_pSym),
11            islot = GET_SLOT(x, Matrix_iSym);
12        int *dims = INTEGER(GET_SLOT(x, Matrix_DimSym)), j,
13            nrow = dims[0],
14            ncol = dims[1],
15            *xp = INTEGER(pslot),
16            *xi = INTEGER(islot);
17
18        if (length(pslot) != dims[1] + 1)
19            return FALSE;
20        if (xp[0] != 0)
21            return FALSE;
22        if (length(islot) < xp[ncol]) /* allow larger slots from over-allocation!*/
23            return FALSE;
24        for (j = 0; j < xp[ncol]; j++) {
25            if (xi[j] < 0 || xi[j] >= nrow)
26                return FALSE;
27        }
28        for (j = 0; j < ncol; j++) {
29            if (xp[j] > xp[j + 1])
30                return FALSE;
31        }
32        return TRUE;
33    }
34
35  SEXP Csparse_validate(SEXP x)  SEXP Csparse_validate(SEXP x)
36  {  {
37      /* NB: we do *NOT* check a potential 'x' slot here, at all */      /* NB: we do *NOT* check a potential 'x' slot here, at all */
cholmod_sparse *chx = as_cholmod_sparse(x);
38      SEXP pslot = GET_SLOT(x, Matrix_pSym),      SEXP pslot = GET_SLOT(x, Matrix_pSym),
39          islot = GET_SLOT(x, Matrix_iSym);          islot = GET_SLOT(x, Matrix_iSym);
40      int j, k, ncol = length(pslot) - 1,      Rboolean sorted, strictly;
41        int j, k,
42          *dims = INTEGER(GET_SLOT(x, Matrix_DimSym)),          *dims = INTEGER(GET_SLOT(x, Matrix_DimSym)),
43          nrow, sorted, *xp = INTEGER(pslot),          nrow = dims[0],
44            ncol = dims[1],
45            *xp = INTEGER(pslot),
46          *xi = INTEGER(islot);          *xi = INTEGER(islot);
47
48      nrow = dims[0];      if (length(pslot) != dims[1] + 1)
49      if (length(pslot) <= 0)          return mkString(_("slot p must have length = ncol(.) + 1"));
return mkString(_("slot p must have length > 0"));
50      if (xp[0] != 0)      if (xp[0] != 0)
51          return mkString(_("first element of slot p must be zero"));          return mkString(_("first element of slot p must be zero"));
52      if (length(islot) != xp[ncol])      if (length(islot) < xp[ncol]) /* allow larger slots from over-allocation!*/
53          return          return
54              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"));
55      for (j = 0; j < length(islot); j++) {      for (j = 0; j < xp[ncol]; j++) {
56          if (xi[j] < 0 || xi[j] >= nrow)          if (xi[j] < 0 || xi[j] >= nrow)
57              return mkString(_("all row indices must be between 0 and nrow-1"));              return mkString(_("all row indices must be between 0 and nrow-1"));
58      }      }
59      sorted = TRUE;      sorted = TRUE; strictly = TRUE;
60      for (j = 0; j < ncol; j++) {      for (j = 0; j < ncol; j++) {
61          if (xp[j] > xp[j+1])          if (xp[j] > xp[j+1])
62              return mkString(_("slot p must be non-decreasing"));              return mkString(_("slot p must be non-decreasing"));
63            if(sorted) /* only act if >= 2 entries in column j : */
64                for (k = xp[j] + 1; k < xp[j + 1]; k++) {
65                    if (xi[k] < xi[k - 1])
66                        sorted = FALSE;
67                    else if (xi[k] == xi[k - 1])
68                        strictly = FALSE;
69                }
70        }
71        if (!sorted) {
72            CHM_SP chx = (CHM_SP) alloca(sizeof(cholmod_sparse));
73            R_CheckStack();
74            as_cholmod_sparse(chx, x, FALSE, TRUE); /* includes cholmod_l_sort() ! */
75            /* as chx = AS_CHM_SP__(x)  but  ^^^^  sorting x in_place (no copying)*/
76
77            /* Now re-check that row indices are *strictly* increasing
78             * (and not just increasing) within each column : */
79            for (j = 0; j < ncol; j++) {
80          for (k = xp[j] + 1; k < xp[j + 1]; k++)          for (k = xp[j] + 1; k < xp[j + 1]; k++)
81              if (xi[k] < xi[k - 1]) sorted = FALSE;                  if (xi[k] == xi[k - 1])
82                        return mkString(_("slot i is not *strictly* increasing inside a column (even after cholmod_l_sort)"));
83            }
84
85        } else if(!strictly) {  /* sorted, but not strictly */
86            return mkString(_("slot i is not *strictly* increasing inside a column"));
87        }
88        return ScalarLogical(1);
89    }
90
91    SEXP Rsparse_validate(SEXP x)
92    {
93        /* NB: we do *NOT* check a potential 'x' slot here, at all */
94        SEXP pslot = GET_SLOT(x, Matrix_pSym),
95            jslot = GET_SLOT(x, Matrix_jSym);
96        Rboolean sorted, strictly;
97        int i, k,
98            *dims = INTEGER(GET_SLOT(x, Matrix_DimSym)),
99            nrow = dims[0],
100            ncol = dims[1],
101            *xp = INTEGER(pslot),
102            *xj = INTEGER(jslot);
103
104        if (length(pslot) != dims[0] + 1)
105            return mkString(_("slot p must have length = nrow(.) + 1"));
106        if (xp[0] != 0)
107            return mkString(_("first element of slot p must be zero"));
108        if (length(jslot) < xp[nrow]) /* allow larger slots from over-allocation!*/
109            return
110                mkString(_("last element of slot p must match length of slots j and x"));
111        for (i = 0; i < length(jslot); i++) {
112            if (xj[i] < 0 || xj[i] >= ncol)
113                return mkString(_("all column indices must be between 0 and ncol-1"));
114        }
115        sorted = TRUE; strictly = TRUE;
116        for (i = 0; i < nrow; i++) {
117            if (xp[i] > xp[i+1])
118                return mkString(_("slot p must be non-decreasing"));
119            if(sorted)
120                for (k = xp[i] + 1; k < xp[i + 1]; k++) {
121                    if (xj[k] < xj[k - 1])
122                        sorted = FALSE;
123                    else if (xj[k] == xj[k - 1])
124                        strictly = FALSE;
125                }
126      }      }
127      if (!sorted) cholmod_sort(chx, &c);      if (!sorted)
128      Free(chx);          /* cannot easily use cholmod_l_sort(.) ... -> "error out" :*/
129            return mkString(_("slot j is not increasing inside a column"));
130        else if(!strictly) /* sorted, but not strictly */
131            return mkString(_("slot j is not *strictly* increasing inside a column"));
132
133      return ScalarLogical(1);      return ScalarLogical(1);
134  }  }
135
136
137    /* Called from ../R/Csparse.R : */
138    /* Can only return [dln]geMatrix (no symm/triang);
139     * FIXME: replace by non-CHOLMOD code ! */
140  SEXP Csparse_to_dense(SEXP x)  SEXP Csparse_to_dense(SEXP x)
141  {  {
142      cholmod_sparse *chxs = as_cholmod_sparse(x);      CHM_SP chxs = AS_CHM_SP__(x);
143      cholmod_dense *chxd = cholmod_sparse_to_dense(chxs, &c);      /* This loses the symmetry property, since cholmod_dense has none,
144         * BUT, much worse (FIXME!), it also transforms CHOLMOD_PATTERN ("n") matrices
145         * to numeric (CHOLMOD_REAL) ones : */
146        CHM_DN chxd = cholmod_l_sparse_to_dense(chxs, &c);
147        int Rkind = (chxs->xtype == CHOLMOD_PATTERN)? -1 : Real_kind(x);
148        R_CheckStack();
149
150      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));
151  }  }
152
153  SEXP Csparse_to_nz_pattern(SEXP x, SEXP tri)  SEXP Csparse_to_nz_pattern(SEXP x, SEXP tri)
154  {  {
155      cholmod_sparse *chxs = as_cholmod_sparse(x);      CHM_SP chxs = AS_CHM_SP__(x);
156      cholmod_sparse      CHM_SP chxcp = cholmod_l_copy(chxs, chxs->stype, CHOLMOD_PATTERN, &c);
157          *chxcp = cholmod_copy(chxs, chxs->stype, CHOLMOD_PATTERN, &c);      int tr = asLogical(tri);
158      int uploT = 0; char *diag = "";      R_CheckStack();
159
160      Free(chxs);      return chm_sparse_to_SEXP(chxcp, 1/*do_free*/,
161      if (asLogical(tri)) {       /* triangular sparse matrices */                                tr ? ((*uplo_P(x) == 'U') ? 1 : -1) : 0,
162          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,
163                                GET_SLOT(x, Matrix_DimNamesSym));                                GET_SLOT(x, Matrix_DimNamesSym));
164  }  }
165
166  SEXP Csparse_to_matrix(SEXP x)  SEXP Csparse_to_matrix(SEXP x)
167  {  {
168      cholmod_sparse *chxs = as_cholmod_sparse(x);      return chm_dense_to_matrix(cholmod_l_sparse_to_dense(AS_CHM_SP__(x), &c),
169      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));
170  }  }
171
172  SEXP Csparse_to_Tsparse(SEXP x, SEXP tri)  SEXP Csparse_to_Tsparse(SEXP x, SEXP tri)
173  {  {
174      cholmod_sparse *chxs = as_cholmod_sparse(x);      CHM_SP chxs = AS_CHM_SP__(x);
175      cholmod_triplet *chxt = cholmod_sparse_to_triplet(chxs, &c);      CHM_TR chxt = cholmod_l_sparse_to_triplet(chxs, &c);
176      int uploT = 0;      int tr = asLogical(tri);
177      char *diag = "";      int Rkind = (chxs->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
178      int Rkind = (chxs->xtype == CHOLMOD_REAL) ? Real_kind(x) : 0;      R_CheckStack();
179
180      Free(chxs);      return chm_triplet_to_SEXP(chxt, 1,
181      if (asLogical(tri)) {       /* triangular sparse matrices */                                 tr ? ((*uplo_P(x) == 'U') ? 1 : -1) : 0,
182          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,
183                                 GET_SLOT(x, Matrix_DimNamesSym));                                 GET_SLOT(x, Matrix_DimNamesSym));
184  }  }
185
186  /* this used to be called  sCMatrix_to_gCMatrix(..)   [in ./dsCMatrix.c ]: */  /* this used to be called  sCMatrix_to_gCMatrix(..)   [in ./dsCMatrix.c ]: */
187  SEXP Csparse_symmetric_to_general(SEXP x)  SEXP Csparse_symmetric_to_general(SEXP x)
188  {  {
189      cholmod_sparse *chx = as_cholmod_sparse(x), *chgx;      CHM_SP chx = AS_CHM_SP__(x), chgx;
190      int Rkind = (chx->xtype == CHOLMOD_REAL) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
191        R_CheckStack();
192
193      if (!(chx->stype))      if (!(chx->stype))
194          error(_("Nonsymmetric matrix in Csparse_symmetric_to_general"));          error(_("Nonsymmetric matrix in Csparse_symmetric_to_general"));
195      chgx = cholmod_copy(chx, /* stype: */ 0, chx->xtype, &c);      chgx = cholmod_l_copy(chx, /* stype: */ 0, chx->xtype, &c);
196      /* xtype: pattern, "real", complex or .. */      /* xtype: pattern, "real", complex or .. */
Free(chx);
197      return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",      return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",
198                                GET_SLOT(x, Matrix_DimNamesSym));                                GET_SLOT(x, Matrix_DimNamesSym));
199  }  }
200
201  #ifdef _not_yet_FIXME_  SEXP Csparse_general_to_symmetric(SEXP x, SEXP uplo)
/* MM: This would seem useful; e.g. lsC* can hardly be coerced to ! */
SEXP Csparse_general_to_symmetric(SEXP x,
int stype)/*-1 : "L", +1 : "U" */
202  {  {
203      cholmod_sparse *chx = as_cholmod_sparse(x), *chgx;      CHM_SP chx = AS_CHM_SP__(x), chgx;
204      int Rkind = (chx->xtype == CHOLMOD_REAL) ? Real_kind(x) : 0;      int uploT = (*CHAR(STRING_ELT(uplo,0)) == 'U') ? 1 : -1;
205        int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
206        R_CheckStack();
207
208      chgx = cholmod_copy(chx, /* stype: */ stype, chx->xtype, &c);      chgx = cholmod_l_copy(chx, /* stype: */ uploT, chx->xtype, &c);
209      /* xtype: pattern, "real", complex or .. */      /* xtype: pattern, "real", complex or .. */
Free(chx);
210      return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",      return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",
211                                GET_SLOT(x, Matrix_DimNamesSym));                                GET_SLOT(x, Matrix_DimNamesSym));
212  }  }
213
#endif

214  SEXP Csparse_transpose(SEXP x, SEXP tri)  SEXP Csparse_transpose(SEXP x, SEXP tri)
215  {  {
216      cholmod_sparse *chx = as_cholmod_sparse(x);      /* TODO: lgCMatrix & igC* currently go via double prec. cholmod -
217      int Rkind = (chx->xtype == CHOLMOD_REAL) ? Real_kind(x) : 0;       *       since cholmod (& cs) lacks sparse 'int' matrices */
218      cholmod_sparse *chxt = cholmod_transpose(chx, (int) chx->xtype, &c);      CHM_SP chx = AS_CHM_SP__(x);
219        int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
220        CHM_SP chxt = cholmod_l_transpose(chx, chx->xtype, &c);
221      SEXP dn = PROTECT(duplicate(GET_SLOT(x, Matrix_DimNamesSym))), tmp;      SEXP dn = PROTECT(duplicate(GET_SLOT(x, Matrix_DimNamesSym))), tmp;
222      int uploT = 0; char *diag = "";      int tr = asLogical(tri);
223        R_CheckStack();
224
Free(chx);
225      tmp = VECTOR_ELT(dn, 0);    /* swap the dimnames */      tmp = VECTOR_ELT(dn, 0);    /* swap the dimnames */
226      SET_VECTOR_ELT(dn, 0, VECTOR_ELT(dn, 1));      SET_VECTOR_ELT(dn, 0, VECTOR_ELT(dn, 1));
227      SET_VECTOR_ELT(dn, 1, tmp);      SET_VECTOR_ELT(dn, 1, tmp);
228      UNPROTECT(1);      UNPROTECT(1);
229      if (asLogical(tri)) {       /* triangular sparse matrices */      return chm_sparse_to_SEXP(chxt, 1, /* SWAP 'uplo' for triangular */
230          uploT = (*uplo_P(x) == 'U') ? -1 : 1;                                tr ? ((*uplo_P(x) == 'U') ? -1 : 1) : 0,
231          diag = diag_P(x);                                Rkind, tr ? diag_P(x) : "", dn);
}
return chm_sparse_to_SEXP(chxt, 1, uploT, Rkind, diag, dn);
232  }  }
233
234  SEXP Csparse_Csparse_prod(SEXP a, SEXP b)  SEXP Csparse_Csparse_prod(SEXP a, SEXP b)
235  {  {
236      cholmod_sparse *cha = as_cholmod_sparse(a),      CHM_SP
237          *chb = as_cholmod_sparse(b);          cha = AS_CHM_SP(a),
238      cholmod_sparse *chc = cholmod_ssmult(cha, chb, 0, cha->xtype, 1, &c);          chb = AS_CHM_SP(b),
239            chc = cholmod_l_ssmult(cha, chb, /*out_stype:*/ 0,
240                                 cha->xtype, /*out sorted:*/ 1, &c);
241        const char *cl_a = class_P(a), *cl_b = class_P(b);
242        char diag[] = {'\0', '\0'};
243        int uploT = 0;
244      SEXP dn = allocVector(VECSXP, 2);      SEXP dn = allocVector(VECSXP, 2);
245        R_CheckStack();
246
247      Free(cha); Free(chb);      /* Preserve triangularity and even unit-triangularity if appropriate.
248         * Note that in that case, the multiplication itself should happen
249         * faster.  But there's no support for that in CHOLMOD */
250
251        /* UGLY hack -- rather should have (fast!) C-level version of
252         *       is(a, "triangularMatrix") etc */
253        if (cl_a[1] == 't' && cl_b[1] == 't')
254            /* FIXME: fails for "Cholesky","BunchKaufmann"..*/
255            if(*uplo_P(a) == *uplo_P(b)) { /* both upper, or both lower tri. */
256                uploT = (*uplo_P(a) == 'U') ? 1 : -1;
257                if(*diag_P(a) == 'U' && *diag_P(b) == 'U') { /* return UNIT-triag. */
258                    /* "remove the diagonal entries": */
259                    chm_diagN2U(chc, uploT, /* do_realloc */ FALSE);
260                    diag[0]= 'U';
261                }
262                else diag[0]= 'N';
263            }
264      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
265                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));
266      SET_VECTOR_ELT(dn, 1,      SET_VECTOR_ELT(dn, 1,
267                     duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), 1)));                     duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), 1)));
268      return chm_sparse_to_SEXP(chc, 1, 0, 0, "", dn);      return chm_sparse_to_SEXP(chc, 1, uploT, /*Rkind*/0, diag, dn);
269    }
270
271    SEXP Csparse_Csparse_crossprod(SEXP a, SEXP b, SEXP trans)
272    {
273        int tr = asLogical(trans);
274        CHM_SP
275            cha = AS_CHM_SP(a),
276            chb = AS_CHM_SP(b),
277            chTr, chc;
278        const char *cl_a = class_P(a), *cl_b = class_P(b);
279        char diag[] = {'\0', '\0'};
280        int uploT = 0;
281        SEXP dn = allocVector(VECSXP, 2);
282        R_CheckStack();
283
284        chTr = cholmod_l_transpose((tr) ? chb : cha, chb->xtype, &c);
285        chc = cholmod_l_ssmult((tr) ? cha : chTr, (tr) ? chTr : chb,
286                             /*out_stype:*/ 0, cha->xtype, /*out sorted:*/ 1, &c);
287        cholmod_l_free_sparse(&chTr, &c);
288
289        /* Preserve triangularity and unit-triangularity if appropriate;
290         * see Csparse_Csparse_prod() for comments */
291        if (cl_a[1] == 't' && cl_b[1] == 't')
292            if(*uplo_P(a) != *uplo_P(b)) { /* one 'U', the other 'L' */
293                uploT = (*uplo_P(b) == 'U') ? 1 : -1;
294                if(*diag_P(a) == 'U' && *diag_P(b) == 'U') { /* return UNIT-triag. */
295                    chm_diagN2U(chc, uploT, /* do_realloc */ FALSE);
296                    diag[0]= 'U';
297                }
298                else diag[0]= 'N';
299            }
300
301        SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
302                       duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), (tr) ? 0 : 1)));
303        SET_VECTOR_ELT(dn, 1,
304                       duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), (tr) ? 0 : 1)));
305        return chm_sparse_to_SEXP(chc, 1, uploT, /*Rkind*/0, diag, dn);
306  }  }
307
308  SEXP Csparse_dense_prod(SEXP a, SEXP b)  SEXP Csparse_dense_prod(SEXP a, SEXP b)
309  {  {
310      cholmod_sparse *cha = as_cholmod_sparse(a);      CHM_SP cha = AS_CHM_SP(a);
311      cholmod_dense *chb = as_cholmod_dense(PROTECT(mMatrix_as_dgeMatrix(b)));      SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));
312      cholmod_dense *chc =      CHM_DN chb = AS_CHM_DN(b_M);
313          cholmod_allocate_dense(cha->nrow, chb->ncol, cha->nrow, chb->xtype, &c);      CHM_DN chc = cholmod_l_allocate_dense(cha->nrow, chb->ncol, cha->nrow,
314      double alpha[] = {1,0}, beta[] = {0,0};                                          chb->xtype, &c);
315        SEXP dn = PROTECT(allocVector(VECSXP, 2));
316        double one[] = {1,0}, zero[] = {0,0};
317        R_CheckStack();
318
319      cholmod_sdmult(cha, 0, alpha, beta, chb, chc, &c);      cholmod_l_sdmult(cha, 0, one, zero, chb, chc, &c);
320      Free(cha); Free(chb);      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
321      UNPROTECT(1);                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));
322      return chm_dense_to_SEXP(chc, 1, 0);      SET_VECTOR_ELT(dn, 1,
323                       duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));
324        UNPROTECT(2);
325        return chm_dense_to_SEXP(chc, 1, 0, dn);
326  }  }
327
328  SEXP Csparse_dense_crossprod(SEXP a, SEXP b)  SEXP Csparse_dense_crossprod(SEXP a, SEXP b)
329  {  {
330      cholmod_sparse *cha = as_cholmod_sparse(a);      CHM_SP cha = AS_CHM_SP(a);
331      cholmod_dense *chb = as_cholmod_dense(PROTECT(mMatrix_as_dgeMatrix(b)));      SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));
332      cholmod_dense *chc =      CHM_DN chb = AS_CHM_DN(b_M);
333          cholmod_allocate_dense(cha->ncol, chb->ncol, cha->ncol, chb->xtype, &c);      CHM_DN chc = cholmod_l_allocate_dense(cha->ncol, chb->ncol, cha->ncol,
334      double alpha[] = {1,0}, beta[] = {0,0};                                          chb->xtype, &c);
335        SEXP dn = PROTECT(allocVector(VECSXP, 2));
336        double one[] = {1,0}, zero[] = {0,0};
337        R_CheckStack();
338
339      cholmod_sdmult(cha, 1, alpha, beta, chb, chc, &c);      cholmod_l_sdmult(cha, 1, one, zero, chb, chc, &c);
340      Free(cha); Free(chb);      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
341      UNPROTECT(1);                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 1)));
342      return chm_dense_to_SEXP(chc, 1, 0);      SET_VECTOR_ELT(dn, 1,
343                       duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));
344        UNPROTECT(2);
345        return chm_dense_to_SEXP(chc, 1, 0, dn);
346  }  }
347
348    /* Computes   x'x  or  x x' -- *also* for Tsparse (triplet = TRUE)
349       see Csparse_Csparse_crossprod above for  x'y and x y' */
350  SEXP Csparse_crossprod(SEXP x, SEXP trans, SEXP triplet)  SEXP Csparse_crossprod(SEXP x, SEXP trans, SEXP triplet)
351  {  {
352      int trip = asLogical(triplet),      int trip = asLogical(triplet),
353          tr   = asLogical(trans); /* gets reversed because _aat is tcrossprod */          tr   = asLogical(trans); /* gets reversed because _aat is tcrossprod */
354      cholmod_triplet      CHM_TR cht = trip ? AS_CHM_TR(x) : (CHM_TR) NULL;
355          *cht = trip ? as_cholmod_triplet(x) : (cholmod_triplet*) NULL;      CHM_SP chcp, chxt,
356      cholmod_sparse *chcp, *chxt,          chx = (trip ?
357          *chx = trip ? cholmod_triplet_to_sparse(cht, cht->nnz, &c)                 cholmod_l_triplet_to_sparse(cht, cht->nnz, &c) :
358          : as_cholmod_sparse(x);                 AS_CHM_SP(x));
359      SEXP dn = PROTECT(allocVector(VECSXP, 2));      SEXP dn = PROTECT(allocVector(VECSXP, 2));
360        R_CheckStack();
361
362      if (!tr)      if (!tr) chxt = cholmod_l_transpose(chx, chx->xtype, &c);
363          chxt = cholmod_transpose(chx, chx->xtype, &c);      chcp = cholmod_l_aat((!tr) ? chxt : chx, (int *) NULL, 0, chx->xtype, &c);
364      chcp = cholmod_aat((!tr) ? chxt : chx, (int *) NULL, 0, chx->xtype, &c);      if(!chcp) {
365      if(!chcp)          UNPROTECT(1);
366          error("Csparse_crossprod(): error return from cholmod_aat()");          error(_("Csparse_crossprod(): error return from cholmod_l_aat()"));
367      cholmod_band_inplace(0, chcp->ncol, chcp->xtype, chcp, &c);      }
368        cholmod_l_band_inplace(0, chcp->ncol, chcp->xtype, chcp, &c);
369      chcp->stype = 1;      chcp->stype = 1;
370      if (trip) {      if (trip) cholmod_l_free_sparse(&chx, &c);
371          cholmod_free_sparse(&chx, &c);      if (!tr) cholmod_l_free_sparse(&chxt, &c);
372          Free(cht);      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
} else {
Free(chx);
}
if (!tr) cholmod_free_sparse(&chxt, &c);
/* create dimnames */
SET_VECTOR_ELT(dn, 0,
373                     duplicate(VECTOR_ELT(GET_SLOT(x, Matrix_DimNamesSym),                     duplicate(VECTOR_ELT(GET_SLOT(x, Matrix_DimNamesSym),
374                                          (tr) ? 1 : 0)));                                          (tr) ? 0 : 1)));
375      SET_VECTOR_ELT(dn, 1, duplicate(VECTOR_ELT(dn, 0)));      SET_VECTOR_ELT(dn, 1, duplicate(VECTOR_ELT(dn, 0)));
376      UNPROTECT(1);      UNPROTECT(1);
377      return chm_sparse_to_SEXP(chcp, 1, 0, 0, "", dn);      return chm_sparse_to_SEXP(chcp, 1, 0, 0, "", dn);
378  }  }
379
380    SEXP Csparse_drop(SEXP x, SEXP tol)
381    {
382        const char *cl = class_P(x);
383        /* dtCMatrix, etc; [1] = the second character =?= 't' for triangular */
384        int tr = (cl[1] == 't');
385        CHM_SP chx = AS_CHM_SP__(x);
386        CHM_SP ans = cholmod_l_copy(chx, chx->stype, chx->xtype, &c);
387        double dtol = asReal(tol);
388        int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
389        R_CheckStack();
390
391        if(!cholmod_l_drop(dtol, ans, &c))
392            error(_("cholmod_l_drop() failed"));
393        return chm_sparse_to_SEXP(ans, 1,
394                                  tr ? ((*uplo_P(x) == 'U') ? 1 : -1) : 0,
395                                  Rkind, tr ? diag_P(x) : "",
396                                  GET_SLOT(x, Matrix_DimNamesSym));
397    }
398
399  SEXP Csparse_horzcat(SEXP x, SEXP y)  SEXP Csparse_horzcat(SEXP x, SEXP y)
400  {  {
401      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;
402      int Rkind = 0; /* only for "d" - FIXME */      int Rkind = 0; /* only for "d" - FIXME */
403        R_CheckStack();
404
ans = cholmod_horzcat(chx, chy, 1, &c);
Free(chx); Free(chy);
405      /* FIXME: currently drops dimnames */      /* FIXME: currently drops dimnames */
406      return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "", R_NilValue);      return chm_sparse_to_SEXP(cholmod_l_horzcat(chx, chy, 1, &c),
407                                  1, 0, Rkind, "", R_NilValue);
408  }  }
409
410  SEXP Csparse_vertcat(SEXP x, SEXP y)  SEXP Csparse_vertcat(SEXP x, SEXP y)
411  {  {
412      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;
413      int Rkind = 0; /* only for "d" - FIXME */      int Rkind = 0; /* only for "d" - FIXME */
414        R_CheckStack();
415
ans = cholmod_vertcat(chx, chy, 1, &c);
Free(chx); Free(chy);
416      /* FIXME: currently drops dimnames */      /* FIXME: currently drops dimnames */
417      return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "", R_NilValue);      return chm_sparse_to_SEXP(cholmod_l_vertcat(chx, chy, 1, &c),
418                                  1, 0, Rkind, "", R_NilValue);
419  }  }
420
421  SEXP Csparse_band(SEXP x, SEXP k1, SEXP k2)  SEXP Csparse_band(SEXP x, SEXP k1, SEXP k2)
422  {  {
423      cholmod_sparse *chx = as_cholmod_sparse(x), *ans;      CHM_SP chx = AS_CHM_SP__(x);
424      int Rkind = (chx->xtype == CHOLMOD_REAL) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
425        CHM_SP ans = cholmod_l_band(chx, asInteger(k1), asInteger(k2), chx->xtype, &c);
426        R_CheckStack();
427
428      ans = cholmod_band(chx, asInteger(k1), asInteger(k2), chx->xtype, &c);      return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "",
429      Free(chx);                                GET_SLOT(x, Matrix_DimNamesSym));
return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "", R_NilValue);
430  }  }
431
432  SEXP Csparse_diagU2N(SEXP x)  SEXP Csparse_diagU2N(SEXP x)
433  {  {
434      cholmod_sparse *chx = as_cholmod_sparse(x);      const char *cl = class_P(x);
435      cholmod_sparse *eye = cholmod_speye(chx->nrow, chx->ncol, chx->xtype, &c);      /* dtCMatrix, etc; [1] = the second character =?= 't' for triangular */
436        if (cl[1] != 't' || *diag_P(x) != 'U') {
437            /* "trivially fast" when not triangular (<==> no 'diag' slot),
438               or not *unit* triangular */
439            return (x);
440        }
441        else { /* unit triangular (diag='U'): "fill the diagonal" & diag:= "N" */
442            CHM_SP chx = AS_CHM_SP__(x);
443            CHM_SP eye = cholmod_l_speye(chx->nrow, chx->ncol, chx->xtype, &c);
444      double one[] = {1, 0};      double one[] = {1, 0};
445      cholmod_sparse *ans = cholmod_add(chx, eye, one, one, TRUE, TRUE, &c);          CHM_SP ans = cholmod_l_add(chx, eye, one, one, TRUE, TRUE, &c);
446      int uploT = (strcmp(CHAR(asChar(GET_SLOT(x, Matrix_uploSym))), "U")) ?          int uploT = (*uplo_P(x) == 'U') ? 1 : -1;
447          -1 : 1;          int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
int Rkind = (chx->xtype == CHOLMOD_REAL) ? Real_kind(x) : 0;
448
449      Free(chx); cholmod_free_sparse(&eye, &c);          R_CheckStack();
450            cholmod_l_free_sparse(&eye, &c);
451      return chm_sparse_to_SEXP(ans, 1, uploT, Rkind, "N",      return chm_sparse_to_SEXP(ans, 1, uploT, Rkind, "N",
452                                duplicate(GET_SLOT(x, Matrix_DimNamesSym)));                                    GET_SLOT(x, Matrix_DimNamesSym));
453        }
454    }
455
456    SEXP Csparse_diagN2U(SEXP x)
457    {
458        const char *cl = class_P(x);
459        /* dtCMatrix, etc; [1] = the second character =?= 't' for triangular */
460        if (cl[1] != 't' || *diag_P(x) != 'N') {
461            /* "trivially fast" when not triangular (<==> no 'diag' slot),
462               or already *unit* triangular */
463            return (x);
464        }
465        else { /* triangular with diag='N'): now drop the diagonal */
466            /* duplicate, since chx will be modified: */
467            CHM_SP chx = AS_CHM_SP__(duplicate(x));
468            int uploT = (*uplo_P(x) == 'U') ? 1 : -1,
469                Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
470            R_CheckStack();
471
472            chm_diagN2U(chx, uploT, /* do_realloc */ FALSE);
473
474            return chm_sparse_to_SEXP(chx, /*dofree*/ 0/* or 1 ?? */,
475                                      uploT, Rkind, "U",
476                                      GET_SLOT(x, Matrix_DimNamesSym));
477        }
478  }  }
479
480  SEXP Csparse_submatrix(SEXP x, SEXP i, SEXP j)  SEXP Csparse_submatrix(SEXP x, SEXP i, SEXP j)
481  {  {
482      cholmod_sparse *chx = as_cholmod_sparse(x);      CHM_SP chx = AS_CHM_SP__(x);
483      int rsize = (isNull(i)) ? -1 : LENGTH(i),      int rsize = (isNull(i)) ? -1 : LENGTH(i),
484          csize = (isNull(j)) ? -1 : LENGTH(j);          csize = (isNull(j)) ? -1 : LENGTH(j);
485      int Rkind = (chx->xtype == CHOLMOD_REAL) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
486        R_CheckStack();
487
488      if (rsize >= 0 && !isInteger(i))      if (rsize >= 0 && !isInteger(i))
489          error(_("Index i must be NULL or integer"));          error(_("Index i must be NULL or integer"));
490      if (csize >= 0 && !isInteger(j))      if (csize >= 0 && !isInteger(j))
491          error(_("Index j must be NULL or integer"));          error(_("Index j must be NULL or integer"));
492      return chm_sparse_to_SEXP(cholmod_submatrix(chx, INTEGER(i), rsize,
493        return chm_sparse_to_SEXP(cholmod_l_submatrix(chx, INTEGER(i), rsize,
494                                                  INTEGER(j), csize,                                                  INTEGER(j), csize,
495                                                  TRUE, TRUE, &c),                                                  TRUE, TRUE, &c),
496                                1, 0, Rkind, "", R_NilValue);                                1, 0, Rkind, "",
497                                  /* FIXME: drops dimnames */ R_NilValue);
498    }
499
500    SEXP Csparse_MatrixMarket(SEXP x, SEXP fname)
501    {
502        FILE *f = fopen(CHAR(asChar(fname)), "w");
503
504        if (!f)
505            error(_("failure to open file \"%s\" for writing"),
506                  CHAR(asChar(fname)));
507        if (!cholmod_l_write_sparse(f, AS_CHM_SP(x),
508                                  (CHM_SP)NULL, (char*) NULL, &c))
509            error(_("cholmod_l_write_sparse returned error code"));
510        fclose(f);
511        return R_NilValue;
512    }
513
514
515    /**
516     * Extract the diagonal entries from *triangular* Csparse matrix  __or__ a
517     * cholmod_sparse factor (LDL = TRUE).
518     *
519     * @param n  dimension of the matrix.
520     * @param x_p  'p' (column pointer) slot contents
521     * @param x_x  'x' (non-zero entries) slot contents
522     * @param perm 'perm' (= permutation vector) slot contents; only used for "diagBack"
523     * @param resultKind a (SEXP) string indicating which kind of result is desired.
524     *
525     * @return  a SEXP, either a (double) number or a length n-vector of diagonal entries
526     */
527    SEXP diag_tC_ptr(int n, int *x_p, double *x_x, int *perm, SEXP resultKind)
528    /*                                ^^^^^^ FIXME[Generalize] to int / ... */
529    {
530        const char* res_ch = CHAR(STRING_ELT(resultKind,0));
531        enum diag_kind { diag, diag_backpermuted, trace, prod, sum_log
532        } res_kind = ((!strcmp(res_ch, "trace")) ? trace :
533                      ((!strcmp(res_ch, "sumLog")) ? sum_log :
534                       ((!strcmp(res_ch, "prod")) ? prod :
535                        ((!strcmp(res_ch, "diag")) ? diag :
536                         ((!strcmp(res_ch, "diagBack")) ? diag_backpermuted :
537                          -1)))));
538        int i, n_x, i_from = 0;
539        SEXP ans = PROTECT(allocVector(REALSXP,
540    /*                                 ^^^^  FIXME[Generalize] */
541                                       (res_kind == diag ||
542                                        res_kind == diag_backpermuted) ? n : 1));
543        double *v = REAL(ans);
544    /*  ^^^^^^      ^^^^  FIXME[Generalize] */
545
546    #define for_DIAG(v_ASSIGN)                                              \
547        for(i = 0; i < n; i++, i_from += n_x) {                             \
548            /* looking at i-th column */                                    \
549            n_x = x_p[i+1] - x_p[i];/* #{entries} in this column */ \
550            v_ASSIGN;                                                       \
551        }
552
553        /* NOTA BENE: we assume  -- uplo = "L" i.e. lower triangular matrix
554         *            for uplo = "U" (makes sense with a "dtCMatrix" !),
555         *            should use  x_x[i_from + (nx - 1)] instead of x_x[i_from],
556         *            where nx = (x_p[i+1] - x_p[i])
557         */
558
559        switch(res_kind) {
560        case trace:
561            v[0] = 0.;
562            for_DIAG(v[0] += x_x[i_from]);
563            break;
564
565        case sum_log:
566            v[0] = 0.;
567            for_DIAG(v[0] += log(x_x[i_from]));
568            break;
569
570        case prod:
571            v[0] = 1.;
572            for_DIAG(v[0] *= x_x[i_from]);
573            break;
574
575        case diag:
576            for_DIAG(v[i] = x_x[i_from]);
577            break;
578
579        case diag_backpermuted:
580            for_DIAG(v[i] = x_x[i_from]);
581
582            warning(_("resultKind = 'diagBack' (back-permuted) is experimental"));
583            /* now back_permute : */
584            for(i = 0; i < n; i++) {
585                double tmp = v[i]; v[i] = v[perm[i]]; v[perm[i]] = tmp;
586                /*^^^^ FIXME[Generalize] */
587            }
588            break;
589
590        default: /* -1 from above */
591            error("diag_tC(): invalid 'resultKind'");
592            /* Wall: */ ans = R_NilValue; v = REAL(ans);
593        }
594
595        UNPROTECT(1);
596        return ans;
597    }
598
599    /**
600     * Extract the diagonal entries from *triangular* Csparse matrix  __or__ a
601     * cholmod_sparse factor (LDL = TRUE).
602     *
603     * @param pslot  'p' (column pointer)   slot of Csparse matrix/factor
604     * @param xslot  'x' (non-zero entries) slot of Csparse matrix/factor
605     * @param perm_slot  'perm' (= permutation vector) slot of corresponding CHMfactor;
606     *                   only used for "diagBack"
607     * @param resultKind a (SEXP) string indicating which kind of result is desired.
608     *
609     * @return  a SEXP, either a (double) number or a length n-vector of diagonal entries
610     */
611    SEXP diag_tC(SEXP pslot, SEXP xslot, SEXP perm_slot, SEXP resultKind)
612    {
613        int n = length(pslot) - 1, /* n = ncol(.) = nrow(.) */
614            *x_p  = INTEGER(pslot),
615            *perm = INTEGER(perm_slot);
616        double *x_x = REAL(xslot);
617    /*  ^^^^^^        ^^^^ FIXME[Generalize] to INTEGER(.) / LOGICAL(.) / ... xslot !*/
618
619        return diag_tC_ptr(n, x_p, x_x, perm, resultKind);
620  }  }

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