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

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revision 1960, Fri Jul 6 16:54:43 2007 UTC revision 2319, Sun Jan 18 20:04:54 2009 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)  /** "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) {
36        return Csparse_validate_(x, FALSE);
37    }
38    
39    SEXP Csparse_validate2(SEXP x, SEXP maybe_modify) {
40        return Csparse_validate_(x, asLogical(maybe_modify));
41    }
42    
43    SEXP Csparse_validate_(SEXP x, Rboolean maybe_modify)
44  {  {
45      /* NB: we do *NOT* check a potential 'x' slot here, at all */      /* NB: we do *NOT* check a potential 'x' slot here, at all */
46      SEXP pslot = GET_SLOT(x, Matrix_pSym),      SEXP pslot = GET_SLOT(x, Matrix_pSym),
# Line 22  Line 60 
60      if (length(islot) < xp[ncol]) /* allow larger slots from over-allocation!*/      if (length(islot) < xp[ncol]) /* allow larger slots from over-allocation!*/
61          return          return
62              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"));
63      for (j = 0; j < length(islot); j++) {      for (j = 0; j < xp[ncol]; j++) {
64          if (xi[j] < 0 || xi[j] >= nrow)          if (xi[j] < 0 || xi[j] >= nrow)
65              return mkString(_("all row indices must be between 0 and nrow-1"));              return mkString(_("all row indices must be between 0 and nrow-1"));
66      }      }
# Line 30  Line 68 
68      for (j = 0; j < ncol; j++) {      for (j = 0; j < ncol; j++) {
69          if (xp[j] > xp[j+1])          if (xp[j] > xp[j+1])
70              return mkString(_("slot p must be non-decreasing"));              return mkString(_("slot p must be non-decreasing"));
71          if(sorted)          if(sorted) /* only act if >= 2 entries in column j : */
72              for (k = xp[j] + 1; k < xp[j + 1]; k++) {              for (k = xp[j] + 1; k < xp[j + 1]; k++) {
73                  if (xi[k] < xi[k - 1])                  if (xi[k] < xi[k - 1])
74                      sorted = FALSE;                      sorted = FALSE;
# Line 39  Line 77 
77              }              }
78      }      }
79      if (!sorted) {      if (!sorted) {
80          CHM_SP chx = AS_CHM_SP(x);          if(maybe_modify) {
81                CHM_SP chx = (CHM_SP) alloca(sizeof(cholmod_sparse));
82          R_CheckStack();          R_CheckStack();
83                as_cholmod_sparse(chx, x, FALSE, TRUE);/*-> cholmod_l_sort() ! */
84                /* as chx = AS_CHM_SP__(x)  but  ^^^^ sorting x in_place !!! */
85    
         cholmod_sort(chx, &c);  
86          /* Now re-check that row indices are *strictly* increasing          /* Now re-check that row indices are *strictly* increasing
87           * (and not just increasing) within each column : */           * (and not just increasing) within each column : */
88          for (j = 0; j < ncol; j++) {          for (j = 0; j < ncol; j++) {
89              for (k = xp[j] + 1; k < xp[j + 1]; k++)              for (k = xp[j] + 1; k < xp[j + 1]; k++)
90                  if (xi[k] == xi[k - 1])                  if (xi[k] == xi[k - 1])
91                      return mkString(_("slot i is not *strictly* increasing inside a column (even after cholmod_sort)"));                          return mkString(_("slot i is not *strictly* increasing inside a column (even after cholmod_l_sort)"));
92                }
93            } else { /* no modifying sorting : */
94                return mkString(_("row indices are not sorted within columns"));
95          }          }
   
96      } else if(!strictly) {  /* sorted, but not strictly */      } else if(!strictly) {  /* sorted, but not strictly */
97          return mkString(_("slot i is not *strictly* increasing inside a column"));          return mkString(_("slot i is not *strictly* increasing inside a column"));
98      }      }
99      return ScalarLogical(1);      return ScalarLogical(1);
100  }  }
101    
102    SEXP Rsparse_validate(SEXP x)
103    {
104        /* NB: we do *NOT* check a potential 'x' slot here, at all */
105        SEXP pslot = GET_SLOT(x, Matrix_pSym),
106            jslot = GET_SLOT(x, Matrix_jSym);
107        Rboolean sorted, strictly;
108        int i, k,
109            *dims = INTEGER(GET_SLOT(x, Matrix_DimSym)),
110            nrow = dims[0],
111            ncol = dims[1],
112            *xp = INTEGER(pslot),
113            *xj = INTEGER(jslot);
114    
115        if (length(pslot) != dims[0] + 1)
116            return mkString(_("slot p must have length = nrow(.) + 1"));
117        if (xp[0] != 0)
118            return mkString(_("first element of slot p must be zero"));
119        if (length(jslot) < xp[nrow]) /* allow larger slots from over-allocation!*/
120            return
121                mkString(_("last element of slot p must match length of slots j and x"));
122        for (i = 0; i < length(jslot); i++) {
123            if (xj[i] < 0 || xj[i] >= ncol)
124                return mkString(_("all column indices must be between 0 and ncol-1"));
125        }
126        sorted = TRUE; strictly = TRUE;
127        for (i = 0; i < nrow; i++) {
128            if (xp[i] > xp[i+1])
129                return mkString(_("slot p must be non-decreasing"));
130            if(sorted)
131                for (k = xp[i] + 1; k < xp[i + 1]; k++) {
132                    if (xj[k] < xj[k - 1])
133                        sorted = FALSE;
134                    else if (xj[k] == xj[k - 1])
135                        strictly = FALSE;
136                }
137        }
138        if (!sorted)
139            /* cannot easily use cholmod_l_sort(.) ... -> "error out" :*/
140            return mkString(_("slot j is not increasing inside a column"));
141        else if(!strictly) /* sorted, but not strictly */
142            return mkString(_("slot j is not *strictly* increasing inside a column"));
143    
144        return ScalarLogical(1);
145    }
146    
147    
148  /* Called from ../R/Csparse.R : */  /* Called from ../R/Csparse.R : */
149  /* Can only return [dln]geMatrix (no symm/triang);  /* Can only return [dln]geMatrix (no symm/triang);
150   * FIXME: replace by non-CHOLMOD code ! */   * FIXME: replace by non-CHOLMOD code ! */
151  SEXP Csparse_to_dense(SEXP x)  SEXP Csparse_to_dense(SEXP x)
152  {  {
153      CHM_SP chxs = AS_CHM_SP(x);      CHM_SP chxs = AS_CHM_SP__(x);
154      /* This loses the symmetry property, since cholmod_dense has none,      /* This loses the symmetry property, since cholmod_dense has none,
155       * BUT, much worse (FIXME!), it also transforms CHOLMOD_PATTERN ("n") matrices       * BUT, much worse (FIXME!), it also transforms CHOLMOD_PATTERN ("n") matrices
156       * to numeric (CHOLMOD_REAL) ones : */       * to numeric (CHOLMOD_REAL) ones : */
157      CHM_DN chxd = cholmod_sparse_to_dense(chxs, &c);      CHM_DN chxd = cholmod_l_sparse_to_dense(chxs, &c);
158      int Rkind = (chxs->xtype == CHOLMOD_PATTERN)? -1 : Real_kind(x);      int Rkind = (chxs->xtype == CHOLMOD_PATTERN)? -1 : Real_kind(x);
159      R_CheckStack();      R_CheckStack();
160    
# Line 75  Line 163 
163    
164  SEXP Csparse_to_nz_pattern(SEXP x, SEXP tri)  SEXP Csparse_to_nz_pattern(SEXP x, SEXP tri)
165  {  {
166      CHM_SP chxs = AS_CHM_SP(x);      CHM_SP chxs = AS_CHM_SP__(x);
167      CHM_SP chxcp = cholmod_copy(chxs, chxs->stype, CHOLMOD_PATTERN, &c);      CHM_SP chxcp = cholmod_l_copy(chxs, chxs->stype, CHOLMOD_PATTERN, &c);
168      int tr = asLogical(tri);      int tr = asLogical(tri);
169      R_CheckStack();      R_CheckStack();
170    
# Line 88  Line 176 
176    
177  SEXP Csparse_to_matrix(SEXP x)  SEXP Csparse_to_matrix(SEXP x)
178  {  {
179      return chm_dense_to_matrix(cholmod_sparse_to_dense(AS_CHM_SP(x), &c),      return chm_dense_to_matrix(cholmod_l_sparse_to_dense(AS_CHM_SP__(x), &c),
180                                 1 /*do_free*/, GET_SLOT(x, Matrix_DimNamesSym));                                 1 /*do_free*/, GET_SLOT(x, Matrix_DimNamesSym));
181  }  }
182    
183  SEXP Csparse_to_Tsparse(SEXP x, SEXP tri)  SEXP Csparse_to_Tsparse(SEXP x, SEXP tri)
184  {  {
185      CHM_SP chxs = AS_CHM_SP(x);      CHM_SP chxs = AS_CHM_SP__(x);
186      CHM_TR chxt = cholmod_sparse_to_triplet(chxs, &c);      CHM_TR chxt = cholmod_l_sparse_to_triplet(chxs, &c);
187      int tr = asLogical(tri);      int tr = asLogical(tri);
188      int Rkind = (chxs->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chxs->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
189      R_CheckStack();      R_CheckStack();
# Line 109  Line 197 
197  /* this used to be called  sCMatrix_to_gCMatrix(..)   [in ./dsCMatrix.c ]: */  /* this used to be called  sCMatrix_to_gCMatrix(..)   [in ./dsCMatrix.c ]: */
198  SEXP Csparse_symmetric_to_general(SEXP x)  SEXP Csparse_symmetric_to_general(SEXP x)
199  {  {
200      CHM_SP chx = AS_CHM_SP(x), chgx;      CHM_SP chx = AS_CHM_SP__(x), chgx;
201      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
202      R_CheckStack();      R_CheckStack();
203    
204      if (!(chx->stype))      if (!(chx->stype))
205          error(_("Nonsymmetric matrix in Csparse_symmetric_to_general"));          error(_("Nonsymmetric matrix in Csparse_symmetric_to_general"));
206      chgx = cholmod_copy(chx, /* stype: */ 0, chx->xtype, &c);      chgx = cholmod_l_copy(chx, /* stype: */ 0, chx->xtype, &c);
207      /* xtype: pattern, "real", complex or .. */      /* xtype: pattern, "real", complex or .. */
208      return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",      return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",
209                                GET_SLOT(x, Matrix_DimNamesSym));                                GET_SLOT(x, Matrix_DimNamesSym));
# Line 123  Line 211 
211    
212  SEXP Csparse_general_to_symmetric(SEXP x, SEXP uplo)  SEXP Csparse_general_to_symmetric(SEXP x, SEXP uplo)
213  {  {
214      CHM_SP chx = AS_CHM_SP(x), chgx;      CHM_SP chx = AS_CHM_SP__(x), chgx;
215      int uploT = (*CHAR(asChar(uplo)) == 'U') ? 1 : -1;      int uploT = (*CHAR(STRING_ELT(uplo,0)) == 'U') ? 1 : -1;
216      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
217      R_CheckStack();      R_CheckStack();
218    
219      chgx = cholmod_copy(chx, /* stype: */ uploT, chx->xtype, &c);      chgx = cholmod_l_copy(chx, /* stype: */ uploT, chx->xtype, &c);
220      /* xtype: pattern, "real", complex or .. */      /* xtype: pattern, "real", complex or .. */
221      return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",      return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",
222                                GET_SLOT(x, Matrix_DimNamesSym));                                GET_SLOT(x, Matrix_DimNamesSym));
# Line 138  Line 226 
226  {  {
227      /* TODO: lgCMatrix & igC* currently go via double prec. cholmod -      /* TODO: lgCMatrix & igC* currently go via double prec. cholmod -
228       *       since cholmod (& cs) lacks sparse 'int' matrices */       *       since cholmod (& cs) lacks sparse 'int' matrices */
229      CHM_SP chx = AS_CHM_SP(x);      CHM_SP chx = AS_CHM_SP__(x);
230      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
231      CHM_SP chxt = cholmod_transpose(chx, chx->xtype, &c);      CHM_SP chxt = cholmod_l_transpose(chx, chx->xtype, &c);
232      SEXP dn = PROTECT(duplicate(GET_SLOT(x, Matrix_DimNamesSym))), tmp;      SEXP dn = PROTECT(duplicate(GET_SLOT(x, Matrix_DimNamesSym))), tmp;
233      int tr = asLogical(tri);      int tr = asLogical(tri);
234      R_CheckStack();      R_CheckStack();
# Line 156  Line 244 
244    
245  SEXP Csparse_Csparse_prod(SEXP a, SEXP b)  SEXP Csparse_Csparse_prod(SEXP a, SEXP b)
246  {  {
247      CHM_SP cha = AS_CHM_SP(a), chb = AS_CHM_SP(b);      CHM_SP
248      CHM_SP chc = cholmod_ssmult(cha, chb, 0, cha->xtype, 1, &c);          cha = AS_CHM_SP(a),
249            chb = AS_CHM_SP(b),
250            chc = cholmod_l_ssmult(cha, chb, /*out_stype:*/ 0,
251                                 cha->xtype, /*out sorted:*/ 1, &c);
252        const char *cl_a = class_P(a), *cl_b = class_P(b);
253        char diag[] = {'\0', '\0'};
254        int uploT = 0;
255      SEXP dn = allocVector(VECSXP, 2);      SEXP dn = allocVector(VECSXP, 2);
256      R_CheckStack();      R_CheckStack();
257    
258        /* Preserve triangularity and even unit-triangularity if appropriate.
259         * Note that in that case, the multiplication itself should happen
260         * faster.  But there's no support for that in CHOLMOD */
261    
262        /* UGLY hack -- rather should have (fast!) C-level version of
263         *       is(a, "triangularMatrix") etc */
264        if (cl_a[1] == 't' && cl_b[1] == 't')
265            /* FIXME: fails for "Cholesky","BunchKaufmann"..*/
266            if(*uplo_P(a) == *uplo_P(b)) { /* both upper, or both lower tri. */
267                uploT = (*uplo_P(a) == 'U') ? 1 : -1;
268                if(*diag_P(a) == 'U' && *diag_P(b) == 'U') { /* return UNIT-triag. */
269                    /* "remove the diagonal entries": */
270                    chm_diagN2U(chc, uploT, /* do_realloc */ FALSE);
271                    diag[0]= 'U';
272                }
273                else diag[0]= 'N';
274            }
275      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
276                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));
277      SET_VECTOR_ELT(dn, 1,      SET_VECTOR_ELT(dn, 1,
278                     duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), 1)));                     duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), 1)));
279      return chm_sparse_to_SEXP(chc, 1, 0, 0, "", dn);      return chm_sparse_to_SEXP(chc, 1, uploT, /*Rkind*/0, diag, dn);
280  }  }
281    
282  SEXP Csparse_Csparse_crossprod(SEXP a, SEXP b, SEXP trans)  SEXP Csparse_Csparse_crossprod(SEXP a, SEXP b, SEXP trans)
283  {  {
284      int tr = asLogical(trans);      int tr = asLogical(trans);
285      CHM_SP cha = AS_CHM_SP(a), chb = AS_CHM_SP(b), chTr, chc;      CHM_SP
286            cha = AS_CHM_SP(a),
287            chb = AS_CHM_SP(b),
288            chTr, chc;
289        const char *cl_a = class_P(a), *cl_b = class_P(b);
290        char diag[] = {'\0', '\0'};
291        int uploT = 0;
292      SEXP dn = allocVector(VECSXP, 2);      SEXP dn = allocVector(VECSXP, 2);
293      R_CheckStack();      R_CheckStack();
294    
295      chTr = cholmod_transpose((tr) ? chb : cha, chb->xtype, &c);      chTr = cholmod_l_transpose((tr) ? chb : cha, chb->xtype, &c);
296      chc = cholmod_ssmult((tr) ? cha : chTr, (tr) ? chTr : chb,      chc = cholmod_l_ssmult((tr) ? cha : chTr, (tr) ? chTr : chb,
297                           0, cha->xtype, 1, &c);                           /*out_stype:*/ 0, cha->xtype, /*out sorted:*/ 1, &c);
298      cholmod_free_sparse(&chTr, &c);      cholmod_l_free_sparse(&chTr, &c);
299    
300        /* Preserve triangularity and unit-triangularity if appropriate;
301         * see Csparse_Csparse_prod() for comments */
302        if (cl_a[1] == 't' && cl_b[1] == 't')
303            if(*uplo_P(a) != *uplo_P(b)) { /* one 'U', the other 'L' */
304                uploT = (*uplo_P(b) == 'U') ? 1 : -1;
305                if(*diag_P(a) == 'U' && *diag_P(b) == 'U') { /* return UNIT-triag. */
306                    chm_diagN2U(chc, uploT, /* do_realloc */ FALSE);
307                    diag[0]= 'U';
308                }
309                else diag[0]= 'N';
310            }
311    
312      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
313                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), (tr) ? 0 : 1)));                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), (tr) ? 0 : 1)));
314      SET_VECTOR_ELT(dn, 1,      SET_VECTOR_ELT(dn, 1,
315                     duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), (tr) ? 0 : 1)));                     duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), (tr) ? 0 : 1)));
316      return chm_sparse_to_SEXP(chc, 1, 0, 0, "", dn);      return chm_sparse_to_SEXP(chc, 1, uploT, /*Rkind*/0, diag, dn);
317  }  }
318    
319  SEXP Csparse_dense_prod(SEXP a, SEXP b)  SEXP Csparse_dense_prod(SEXP a, SEXP b)
# Line 192  Line 321 
321      CHM_SP cha = AS_CHM_SP(a);      CHM_SP cha = AS_CHM_SP(a);
322      SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));      SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));
323      CHM_DN chb = AS_CHM_DN(b_M);      CHM_DN chb = AS_CHM_DN(b_M);
324      CHM_DN chc = cholmod_allocate_dense(cha->nrow, chb->ncol, cha->nrow,      CHM_DN chc = cholmod_l_allocate_dense(cha->nrow, chb->ncol, cha->nrow,
325                                          chb->xtype, &c);                                          chb->xtype, &c);
326      SEXP dn = PROTECT(allocVector(VECSXP, 2));      SEXP dn = PROTECT(allocVector(VECSXP, 2));
327      double one[] = {1,0}, zero[] = {0,0};      double one[] = {1,0}, zero[] = {0,0};
328      R_CheckStack();      R_CheckStack();
329    
330      cholmod_sdmult(cha, 0, one, zero, chb, chc, &c);      cholmod_l_sdmult(cha, 0, one, zero, chb, chc, &c);
331      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
332                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));
333      SET_VECTOR_ELT(dn, 1,      SET_VECTOR_ELT(dn, 1,
# Line 212  Line 341 
341      CHM_SP cha = AS_CHM_SP(a);      CHM_SP cha = AS_CHM_SP(a);
342      SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));      SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));
343      CHM_DN chb = AS_CHM_DN(b_M);      CHM_DN chb = AS_CHM_DN(b_M);
344      CHM_DN chc = cholmod_allocate_dense(cha->ncol, chb->ncol, cha->ncol,      CHM_DN chc = cholmod_l_allocate_dense(cha->ncol, chb->ncol, cha->ncol,
345                                          chb->xtype, &c);                                          chb->xtype, &c);
346      SEXP dn = PROTECT(allocVector(VECSXP, 2));      SEXP dn = PROTECT(allocVector(VECSXP, 2));
347      double one[] = {1,0}, zero[] = {0,0};      double one[] = {1,0}, zero[] = {0,0};
348      R_CheckStack();      R_CheckStack();
349    
350      cholmod_sdmult(cha, 1, one, zero, chb, chc, &c);      cholmod_l_sdmult(cha, 1, one, zero, chb, chc, &c);
351      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
352                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 1)));                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 1)));
353      SET_VECTOR_ELT(dn, 1,      SET_VECTOR_ELT(dn, 1,
# Line 227  Line 356 
356      return chm_dense_to_SEXP(chc, 1, 0, dn);      return chm_dense_to_SEXP(chc, 1, 0, dn);
357  }  }
358    
359  /* Computes   x'x  or  x x'  -- see Csparse_Csparse_crossprod above for  x'y and x y' */  /* Computes   x'x  or  x x' -- *also* for Tsparse (triplet = TRUE)
360       see Csparse_Csparse_crossprod above for  x'y and x y' */
361  SEXP Csparse_crossprod(SEXP x, SEXP trans, SEXP triplet)  SEXP Csparse_crossprod(SEXP x, SEXP trans, SEXP triplet)
362  {  {
363      int trip = asLogical(triplet),      int trip = asLogical(triplet),
364          tr   = asLogical(trans); /* gets reversed because _aat is tcrossprod */          tr   = asLogical(trans); /* gets reversed because _aat is tcrossprod */
365      CHM_TR cht = trip ? AS_CHM_TR(x) : (CHM_TR) NULL;      CHM_TR cht = trip ? AS_CHM_TR(x) : (CHM_TR) NULL;
366      CHM_SP chcp, chxt,      CHM_SP chcp, chxt,
367          chx = trip ? cholmod_triplet_to_sparse(cht, cht->nnz, &c) : AS_CHM_SP(x);          chx = (trip ?
368                   cholmod_l_triplet_to_sparse(cht, cht->nnz, &c) :
369                   AS_CHM_SP(x));
370      SEXP dn = PROTECT(allocVector(VECSXP, 2));      SEXP dn = PROTECT(allocVector(VECSXP, 2));
371      R_CheckStack();      R_CheckStack();
372    
373      if (!tr) chxt = cholmod_transpose(chx, chx->xtype, &c);      if (!tr) chxt = cholmod_l_transpose(chx, chx->xtype, &c);
374      chcp = cholmod_aat((!tr) ? chxt : chx, (int *) NULL, 0, chx->xtype, &c);      chcp = cholmod_l_aat((!tr) ? chxt : chx, (int *) NULL, 0, chx->xtype, &c);
375      if(!chcp) error(_("Csparse_crossprod(): error return from cholmod_aat()"));      if(!chcp) {
376      cholmod_band_inplace(0, chcp->ncol, chcp->xtype, chcp, &c);          UNPROTECT(1);
377            error(_("Csparse_crossprod(): error return from cholmod_l_aat()"));
378        }
379        cholmod_l_band_inplace(0, chcp->ncol, chcp->xtype, chcp, &c);
380      chcp->stype = 1;      chcp->stype = 1;
381      if (trip) cholmod_free_sparse(&chx, &c);      if (trip) cholmod_l_free_sparse(&chx, &c);
382      if (!tr) cholmod_free_sparse(&chxt, &c);      if (!tr) cholmod_l_free_sparse(&chxt, &c);
383      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
384                     duplicate(VECTOR_ELT(GET_SLOT(x, Matrix_DimNamesSym),                     duplicate(VECTOR_ELT(GET_SLOT(x, Matrix_DimNamesSym),
385                                          (tr) ? 0 : 1)));                                          (tr) ? 0 : 1)));
# Line 255  Line 390 
390    
391  SEXP Csparse_drop(SEXP x, SEXP tol)  SEXP Csparse_drop(SEXP x, SEXP tol)
392  {  {
393      CHM_SP chx = AS_CHM_SP(x);      const char *cl = class_P(x);
394      CHM_SP ans = cholmod_copy(chx, chx->stype, chx->xtype, &c);      /* dtCMatrix, etc; [1] = the second character =?= 't' for triangular */
395        int tr = (cl[1] == 't');
396        CHM_SP chx = AS_CHM_SP__(x);
397        CHM_SP ans = cholmod_l_copy(chx, chx->stype, chx->xtype, &c);
398      double dtol = asReal(tol);      double dtol = asReal(tol);
399      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
400      R_CheckStack();      R_CheckStack();
401    
402      if(!cholmod_drop(dtol, ans, &c))      if(!cholmod_l_drop(dtol, ans, &c))
403          error(_("cholmod_drop() failed"));          error(_("cholmod_l_drop() failed"));
404      return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "",      return chm_sparse_to_SEXP(ans, 1,
405                                  tr ? ((*uplo_P(x) == 'U') ? 1 : -1) : 0,
406                                  Rkind, tr ? diag_P(x) : "",
407                                GET_SLOT(x, Matrix_DimNamesSym));                                GET_SLOT(x, Matrix_DimNamesSym));
408  }  }
409    
410  SEXP Csparse_horzcat(SEXP x, SEXP y)  SEXP Csparse_horzcat(SEXP x, SEXP y)
411  {  {
412      CHM_SP chx = AS_CHM_SP(x), chy = AS_CHM_SP(y);      CHM_SP chx = AS_CHM_SP__(x), chy = AS_CHM_SP__(y);
413      int Rkind = 0; /* only for "d" - FIXME */      int Rkind = 0; /* only for "d" - FIXME */
414      R_CheckStack();      R_CheckStack();
415    
416      /* FIXME: currently drops dimnames */      /* FIXME: currently drops dimnames */
417      return chm_sparse_to_SEXP(cholmod_horzcat(chx, chy, 1, &c),      return chm_sparse_to_SEXP(cholmod_l_horzcat(chx, chy, 1, &c),
418                                1, 0, Rkind, "", R_NilValue);                                1, 0, Rkind, "", R_NilValue);
419  }  }
420    
421  SEXP Csparse_vertcat(SEXP x, SEXP y)  SEXP Csparse_vertcat(SEXP x, SEXP y)
422  {  {
423      CHM_SP chx = AS_CHM_SP(x), chy = AS_CHM_SP(y);      CHM_SP chx = AS_CHM_SP__(x), chy = AS_CHM_SP__(y);
424      int Rkind = 0; /* only for "d" - FIXME */      int Rkind = 0; /* only for "d" - FIXME */
425      R_CheckStack();      R_CheckStack();
426    
427      /* FIXME: currently drops dimnames */      /* FIXME: currently drops dimnames */
428      return chm_sparse_to_SEXP(cholmod_vertcat(chx, chy, 1, &c),      return chm_sparse_to_SEXP(cholmod_l_vertcat(chx, chy, 1, &c),
429                                1, 0, Rkind, "", R_NilValue);                                1, 0, Rkind, "", R_NilValue);
430  }  }
431    
432  SEXP Csparse_band(SEXP x, SEXP k1, SEXP k2)  SEXP Csparse_band(SEXP x, SEXP k1, SEXP k2)
433  {  {
434      CHM_SP chx = AS_CHM_SP(x);      CHM_SP chx = AS_CHM_SP__(x);
435      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
436      CHM_SP ans = cholmod_band(chx, asInteger(k1), asInteger(k2), chx->xtype, &c);      CHM_SP ans = cholmod_l_band(chx, asInteger(k1), asInteger(k2), chx->xtype, &c);
437      R_CheckStack();      R_CheckStack();
438    
439      return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "",      return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "",
# Line 302  Line 442 
442    
443  SEXP Csparse_diagU2N(SEXP x)  SEXP Csparse_diagU2N(SEXP x)
444  {  {
445      if (*diag_P(x) != 'U') {/* "trivially fast" when there's no 'diag' slot at all */      const char *cl = class_P(x);
446        /* dtCMatrix, etc; [1] = the second character =?= 't' for triangular */
447        if (cl[1] != 't' || *diag_P(x) != 'U') {
448            /* "trivially fast" when not triangular (<==> no 'diag' slot),
449               or not *unit* triangular */
450          return (x);          return (x);
451      }      }
452      else {      else { /* unit triangular (diag='U'): "fill the diagonal" & diag:= "N" */
453          CHM_SP chx = AS_CHM_SP(x);          CHM_SP chx = AS_CHM_SP__(x);
454          CHM_SP eye = cholmod_speye(chx->nrow, chx->ncol, chx->xtype, &c);          CHM_SP eye = cholmod_l_speye(chx->nrow, chx->ncol, chx->xtype, &c);
455          double one[] = {1, 0};          double one[] = {1, 0};
456          CHM_SP ans = cholmod_add(chx, eye, one, one, TRUE, TRUE, &c);          CHM_SP ans = cholmod_l_add(chx, eye, one, one, TRUE, TRUE, &c);
457          int uploT = (*uplo_P(x) == 'U') ? 1 : -1;          int uploT = (*uplo_P(x) == 'U') ? 1 : -1;
458          int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;          int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
459    
460          R_CheckStack();          R_CheckStack();
461          cholmod_free_sparse(&eye, &c);          cholmod_l_free_sparse(&eye, &c);
462          return chm_sparse_to_SEXP(ans, 1, uploT, Rkind, "N",          return chm_sparse_to_SEXP(ans, 1, uploT, Rkind, "N",
463                                    GET_SLOT(x, Matrix_DimNamesSym));                                    GET_SLOT(x, Matrix_DimNamesSym));
464      }      }
465  }  }
466    
467    SEXP Csparse_diagN2U(SEXP x)
468    {
469        const char *cl = class_P(x);
470        /* dtCMatrix, etc; [1] = the second character =?= 't' for triangular */
471        if (cl[1] != 't' || *diag_P(x) != 'N') {
472            /* "trivially fast" when not triangular (<==> no 'diag' slot),
473               or already *unit* triangular */
474            return (x);
475        }
476        else { /* triangular with diag='N'): now drop the diagonal */
477            /* duplicate, since chx will be modified: */
478            CHM_SP chx = AS_CHM_SP__(duplicate(x));
479            int uploT = (*uplo_P(x) == 'U') ? 1 : -1,
480                Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
481            R_CheckStack();
482    
483            chm_diagN2U(chx, uploT, /* do_realloc */ FALSE);
484    
485            return chm_sparse_to_SEXP(chx, /*dofree*/ 0/* or 1 ?? */,
486                                      uploT, Rkind, "U",
487                                      GET_SLOT(x, Matrix_DimNamesSym));
488        }
489    }
490    
491  SEXP Csparse_submatrix(SEXP x, SEXP i, SEXP j)  SEXP Csparse_submatrix(SEXP x, SEXP i, SEXP j)
492  {  {
493      CHM_SP chx = AS_CHM_SP(x);      CHM_SP chx = AS_CHM_SP__(x);
494      int rsize = (isNull(i)) ? -1 : LENGTH(i),      int rsize = (isNull(i)) ? -1 : LENGTH(i),
495          csize = (isNull(j)) ? -1 : LENGTH(j);          csize = (isNull(j)) ? -1 : LENGTH(j);
496      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
# Line 333  Line 501 
501      if (csize >= 0 && !isInteger(j))      if (csize >= 0 && !isInteger(j))
502          error(_("Index j must be NULL or integer"));          error(_("Index j must be NULL or integer"));
503    
504      return chm_sparse_to_SEXP(cholmod_submatrix(chx, INTEGER(i), rsize,      return chm_sparse_to_SEXP(cholmod_l_submatrix(chx, INTEGER(i), rsize,
505                                                  INTEGER(j), csize,                                                  INTEGER(j), csize,
506                                                  TRUE, TRUE, &c),                                                  TRUE, TRUE, &c),
507                                1, 0, Rkind, "",                                1, 0, Rkind, "",
508                                /* FIXME: drops dimnames */ R_NilValue);                                /* FIXME: drops dimnames */ R_NilValue);
509  }  }
510    
511    SEXP Csparse_MatrixMarket(SEXP x, SEXP fname)
512    {
513        FILE *f = fopen(CHAR(asChar(fname)), "w");
514    
515        if (!f)
516            error(_("failure to open file \"%s\" for writing"),
517                  CHAR(asChar(fname)));
518        if (!cholmod_l_write_sparse(f, AS_CHM_SP(x),
519                                  (CHM_SP)NULL, (char*) NULL, &c))
520            error(_("cholmod_l_write_sparse returned error code"));
521        fclose(f);
522        return R_NilValue;
523    }
524    
525    
526    /**
527     * Extract the diagonal entries from *triangular* Csparse matrix  __or__ a
528     * cholmod_sparse factor (LDL = TRUE).
529     *
530     * @param n  dimension of the matrix.
531     * @param x_p  'p' (column pointer) slot contents
532     * @param x_x  'x' (non-zero entries) slot contents
533     * @param perm 'perm' (= permutation vector) slot contents; only used for "diagBack"
534     * @param resultKind a (SEXP) string indicating which kind of result is desired.
535     *
536     * @return  a SEXP, either a (double) number or a length n-vector of diagonal entries
537     */
538    SEXP diag_tC_ptr(int n, int *x_p, double *x_x, int *perm, SEXP resultKind)
539    /*                                ^^^^^^ FIXME[Generalize] to int / ... */
540    {
541        const char* res_ch = CHAR(STRING_ELT(resultKind,0));
542        enum diag_kind { diag, diag_backpermuted, trace, prod, sum_log
543        } res_kind = ((!strcmp(res_ch, "trace")) ? trace :
544                      ((!strcmp(res_ch, "sumLog")) ? sum_log :
545                       ((!strcmp(res_ch, "prod")) ? prod :
546                        ((!strcmp(res_ch, "diag")) ? diag :
547                         ((!strcmp(res_ch, "diagBack")) ? diag_backpermuted :
548                          -1)))));
549        int i, n_x, i_from = 0;
550        SEXP ans = PROTECT(allocVector(REALSXP,
551    /*                                 ^^^^  FIXME[Generalize] */
552                                       (res_kind == diag ||
553                                        res_kind == diag_backpermuted) ? n : 1));
554        double *v = REAL(ans);
555    /*  ^^^^^^      ^^^^  FIXME[Generalize] */
556    
557    #define for_DIAG(v_ASSIGN)                                              \
558        for(i = 0; i < n; i++, i_from += n_x) {                             \
559            /* looking at i-th column */                                    \
560            n_x = x_p[i+1] - x_p[i];/* #{entries} in this column */ \
561            v_ASSIGN;                                                       \
562        }
563    
564        /* NOTA BENE: we assume  -- uplo = "L" i.e. lower triangular matrix
565         *            for uplo = "U" (makes sense with a "dtCMatrix" !),
566         *            should use  x_x[i_from + (nx - 1)] instead of x_x[i_from],
567         *            where nx = (x_p[i+1] - x_p[i])
568         */
569    
570        switch(res_kind) {
571        case trace:
572            v[0] = 0.;
573            for_DIAG(v[0] += x_x[i_from]);
574            break;
575    
576        case sum_log:
577            v[0] = 0.;
578            for_DIAG(v[0] += log(x_x[i_from]));
579            break;
580    
581        case prod:
582            v[0] = 1.;
583            for_DIAG(v[0] *= x_x[i_from]);
584            break;
585    
586        case diag:
587            for_DIAG(v[i] = x_x[i_from]);
588            break;
589    
590        case diag_backpermuted:
591            for_DIAG(v[i] = x_x[i_from]);
592    
593            warning(_("resultKind = 'diagBack' (back-permuted) is experimental"));
594            /* now back_permute : */
595            for(i = 0; i < n; i++) {
596                double tmp = v[i]; v[i] = v[perm[i]]; v[perm[i]] = tmp;
597                /*^^^^ FIXME[Generalize] */
598            }
599            break;
600    
601        default: /* -1 from above */
602            error("diag_tC(): invalid 'resultKind'");
603            /* Wall: */ ans = R_NilValue; v = REAL(ans);
604        }
605    
606        UNPROTECT(1);
607        return ans;
608    }
609    
610    /**
611     * Extract the diagonal entries from *triangular* Csparse matrix  __or__ a
612     * cholmod_sparse factor (LDL = TRUE).
613     *
614     * @param pslot  'p' (column pointer)   slot of Csparse matrix/factor
615     * @param xslot  'x' (non-zero entries) slot of Csparse matrix/factor
616     * @param perm_slot  'perm' (= permutation vector) slot of corresponding CHMfactor;
617     *                   only used for "diagBack"
618     * @param resultKind a (SEXP) string indicating which kind of result is desired.
619     *
620     * @return  a SEXP, either a (double) number or a length n-vector of diagonal entries
621     */
622    SEXP diag_tC(SEXP pslot, SEXP xslot, SEXP perm_slot, SEXP resultKind)
623    {
624        int n = length(pslot) - 1, /* n = ncol(.) = nrow(.) */
625            *x_p  = INTEGER(pslot),
626            *perm = INTEGER(perm_slot);
627        double *x_x = REAL(xslot);
628    /*  ^^^^^^        ^^^^ FIXME[Generalize] to INTEGER(.) / LOGICAL(.) / ... xslot !*/
629    
630        return diag_tC_ptr(n, x_p, x_x, perm, resultKind);
631    }
632    
633    /**
634     * Create a Csparse matrix object from indices and/or pointers.
635     *
636     * @param cls name of actual class of object to create
637     * @param i optional integer vector of length nnz of row indices
638     * @param j optional integer vector of length nnz of column indices
639     * @param p optional integer vector of length np of row or column pointers
640     * @param np length of integer vector p.  Must be zero if p == (int*)NULL
641     * @param x optional vector of values
642     * @param nnz length of vectors i, j and/or x, whichever is to be used
643     * @param dims optional integer vector of length 2 to be used as
644     *     dimensions.  If dims == (int*)NULL then the maximum row and column
645     *     index are used as the dimensions.
646     * @param dimnames optional list of length 2 to be used as dimnames
647     * @param index1 indicator of 1-based indices
648     *
649     * @return an SEXP of class cls inheriting from CsparseMatrix.
650     */
651    SEXP create_Csparse(char* cls, int* i, int* j, int* p, int np,
652                        void* x, int nnz, int* dims, SEXP dimnames,
653                        int index1)
654    {
655        SEXP ans;
656        int *ij = (int*)NULL, *tri, *trj,
657            mi, mj, mp, nrow = -1, ncol = -1;
658        int xtype = -1;             /* -Wall */
659        CHM_TR T;
660        CHM_SP A;
661    
662        if (np < 0 || nnz < 0)
663            error(_("negative vector lengths not allowed: np = %d, nnz = %d"),
664                  np, nnz);
665        if (1 != ((mi = (i == (int*)NULL)) +
666                  (mj = (j == (int*)NULL)) +
667                  (mp = (p == (int*)NULL))))
668            error(_("exactly 1 of 'i', 'j' or 'p' must be NULL"));
669        if (mp) {
670            if (np) error(_("np = %d, must be zero when p is NULL"), np);
671        } else {
672            if (np) {               /* Expand p to form i or j */
673                if (!(p[0])) error(_("p[0] = %d, should be zero"), p[0]);
674                for (int ii = 0; ii < np; ii++)
675                    if (p[ii] > p[ii + 1])
676                        error(_("p must be non-decreasing"));
677                if (p[np] != nnz)
678                    error(_("p[np] = %d != nnz = %d"), p[np], nnz);
679                ij = Calloc(nnz, int);
680                if (mi) {
681                    i = ij;
682                    nrow = np;
683                } else {
684                    j = ij;
685                    ncol = np;
686                }
687                                    /* Expand p to 0-based indices */
688                for (int ii = 0; ii < np; ii++)
689                    for (int jj = p[ii]; jj < p[ii + 1]; jj++) ij[jj] = ii;
690            } else {
691                if (nnz)
692                    error(_("Inconsistent dimensions: np = 0 and nnz = %d"),
693                          nnz);
694            }
695        }
696                                    /* calculate nrow and ncol */
697        if (nrow < 0) {
698            for (int ii = 0; ii < nnz; ii++) {
699                int i1 = i[ii] + (index1 ? 0 : 1); /* 1-based index */
700                if (i1 < 1) error(_("invalid row index at position %d"), ii);
701                if (i1 > nrow) nrow = i1;
702            }
703        }
704        if (ncol < 0) {
705            for (int jj = 0; jj < nnz; jj++) {
706                int j1 = j[jj] + (index1 ? 0 : 1);
707                if (j1 < 1) error(_("invalid column index at position %d"), jj);
708                if (j1 > ncol) ncol = j1;
709            }
710        }
711        if (dims != (int*)NULL) {
712            if (dims[0] > nrow) nrow = dims[0];
713            if (dims[1] > ncol) ncol = dims[1];
714        }
715                                    /* check the class name */
716        if (strlen(cls) != 8)
717            error(_("strlen of cls argument = %d, should be 8"), strlen(cls));
718        if (!strcmp(cls + 2, "CMatrix"))
719            error(_("cls = \"%s\" does not end in \"CMatrix\""), cls);
720        switch(cls[0]) {
721        case 'd':
722        case 'l':
723               xtype = CHOLMOD_REAL;
724               break;
725        case 'n':
726               xtype = CHOLMOD_PATTERN;
727               break;
728        default:
729               error(_("cls = \"%s\" must begin with 'd', 'l' or 'n'"), cls);
730        }
731        if (cls[1] != 'g')
732            error(_("Only 'g'eneral sparse matrix types allowed"));
733                                    /* allocate and populate the triplet */
734        T = cholmod_l_allocate_triplet((size_t)nrow, (size_t)ncol, (size_t)nnz, 0,
735                                        xtype, &c);
736        T->x = x;
737        tri = (int*)T->i;
738        trj = (int*)T->j;
739        for (int ii = 0; ii < nnz; ii++) {
740            tri[ii] = i[ii] - ((!mi && index1) ? 1 : 0);
741            trj[ii] = j[ii] - ((!mj && index1) ? 1 : 0);
742        }
743                                    /* create the cholmod_sparse structure */
744        A = cholmod_l_triplet_to_sparse(T, nnz, &c);
745        cholmod_l_free_triplet(&T, &c);
746                                    /* copy the information to the SEXP */
747        ans = PROTECT(NEW_OBJECT(MAKE_CLASS(cls)));
748    /* FIXME: This has been copied from chm_sparse_to_SEXP in chm_common.c */
749                                    /* allocate and copy common slots */
750        nnz = cholmod_l_nnz(A, &c);
751        dims = INTEGER(ALLOC_SLOT(ans, Matrix_DimSym, INTSXP, 2));
752        dims[0] = A->nrow; dims[1] = A->ncol;
753        Memcpy(INTEGER(ALLOC_SLOT(ans, Matrix_pSym, INTSXP, A->ncol + 1)), (int*)A->p, A->ncol + 1);
754        Memcpy(INTEGER(ALLOC_SLOT(ans, Matrix_iSym, INTSXP, nnz)), (int*)A->i, nnz);
755        switch(cls[1]) {
756        case 'd':
757            Memcpy(REAL(ALLOC_SLOT(ans, Matrix_xSym, REALSXP, nnz)), (double*)A->x, nnz);
758            break;
759        case 'l':
760            error(_("code not yet written for cls = \"lgCMatrix\""));
761        }
762        cholmod_l_free_sparse(&A, &c);
763        UNPROTECT(1);
764        return ans;
765    }

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