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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 2279, Fri Oct 3 09:15:54 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 */
# Line 22  Line 52 
52      if (length(islot) < xp[ncol]) /* allow larger slots from over-allocation!*/      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      }      }
# Line 30  Line 60 
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)          if(sorted) /* only act if >= 2 entries in column j : */
64              for (k = xp[j] + 1; k < xp[j + 1]; k++) {              for (k = xp[j] + 1; k < xp[j + 1]; k++) {
65                  if (xi[k] < xi[k - 1])                  if (xi[k] < xi[k - 1])
66                      sorted = FALSE;                      sorted = FALSE;
# Line 39  Line 69 
69              }              }
70      }      }
71      if (!sorted) {      if (!sorted) {
72          CHM_SP chx = AS_CHM_SP(x);          CHM_SP chx = (CHM_SP) alloca(sizeof(cholmod_sparse));
73          R_CheckStack();          R_CheckStack();
74            as_cholmod_sparse(chx, x, FALSE, TRUE); /* includes cholmod_sort() ! */
75            /* as chx = AS_CHM_SP__(x)  but  ^^^^  sorting x in_place (no copying)*/
76    
         cholmod_sort(chx, &c);  
77          /* Now re-check that row indices are *strictly* increasing          /* Now re-check that row indices are *strictly* increasing
78           * (and not just increasing) within each column : */           * (and not just increasing) within each column : */
79          for (j = 0; j < ncol; j++) {          for (j = 0; j < ncol; j++) {
# Line 57  Line 88 
88      return ScalarLogical(1);      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)
128            /* cannot easily use cholmod_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);
134    }
135    
136    
137  /* Called from ../R/Csparse.R : */  /* Called from ../R/Csparse.R : */
138  /* Can only return [dln]geMatrix (no symm/triang);  /* Can only return [dln]geMatrix (no symm/triang);
139   * FIXME: replace by non-CHOLMOD code ! */   * FIXME: replace by non-CHOLMOD code ! */
140  SEXP Csparse_to_dense(SEXP x)  SEXP Csparse_to_dense(SEXP x)
141  {  {
142      CHM_SP chxs = AS_CHM_SP(x);      CHM_SP chxs = AS_CHM_SP__(x);
143      /* This loses the symmetry property, since cholmod_dense has none,      /* This loses the symmetry property, since cholmod_dense has none,
144       * BUT, much worse (FIXME!), it also transforms CHOLMOD_PATTERN ("n") matrices       * BUT, much worse (FIXME!), it also transforms CHOLMOD_PATTERN ("n") matrices
145       * to numeric (CHOLMOD_REAL) ones : */       * to numeric (CHOLMOD_REAL) ones : */
# Line 75  Line 152 
152    
153  SEXP Csparse_to_nz_pattern(SEXP x, SEXP tri)  SEXP Csparse_to_nz_pattern(SEXP x, SEXP tri)
154  {  {
155      CHM_SP chxs = AS_CHM_SP(x);      CHM_SP chxs = AS_CHM_SP__(x);
156      CHM_SP chxcp = cholmod_copy(chxs, chxs->stype, CHOLMOD_PATTERN, &c);      CHM_SP chxcp = cholmod_copy(chxs, chxs->stype, CHOLMOD_PATTERN, &c);
157      int tr = asLogical(tri);      int tr = asLogical(tri);
158      R_CheckStack();      R_CheckStack();
# Line 88  Line 165 
165    
166  SEXP Csparse_to_matrix(SEXP x)  SEXP Csparse_to_matrix(SEXP x)
167  {  {
168      return chm_dense_to_matrix(cholmod_sparse_to_dense(AS_CHM_SP(x), &c),      return chm_dense_to_matrix(cholmod_sparse_to_dense(AS_CHM_SP__(x), &c),
169                                 1 /*do_free*/, GET_SLOT(x, Matrix_DimNamesSym));                                 1 /*do_free*/, 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      CHM_SP chxs = AS_CHM_SP(x);      CHM_SP chxs = AS_CHM_SP__(x);
175      CHM_TR chxt = cholmod_sparse_to_triplet(chxs, &c);      CHM_TR chxt = cholmod_sparse_to_triplet(chxs, &c);
176      int tr = asLogical(tri);      int tr = asLogical(tri);
177      int Rkind = (chxs->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chxs->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
# Line 109  Line 186 
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      CHM_SP chx = AS_CHM_SP(x), chgx;      CHM_SP chx = AS_CHM_SP__(x), chgx;
190      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
191      R_CheckStack();      R_CheckStack();
192    
# Line 123  Line 200 
200    
201  SEXP Csparse_general_to_symmetric(SEXP x, SEXP uplo)  SEXP Csparse_general_to_symmetric(SEXP x, SEXP uplo)
202  {  {
203      CHM_SP chx = AS_CHM_SP(x), chgx;      CHM_SP chx = AS_CHM_SP__(x), chgx;
204      int uploT = (*CHAR(asChar(uplo)) == 'U') ? 1 : -1;      int uploT = (*CHAR(STRING_ELT(uplo,0)) == 'U') ? 1 : -1;
205      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
206      R_CheckStack();      R_CheckStack();
207    
# Line 138  Line 215 
215  {  {
216      /* TODO: lgCMatrix & igC* currently go via double prec. cholmod -      /* TODO: lgCMatrix & igC* currently go via double prec. cholmod -
217       *       since cholmod (& cs) lacks sparse 'int' matrices */       *       since cholmod (& cs) lacks sparse 'int' matrices */
218      CHM_SP chx = AS_CHM_SP(x);      CHM_SP chx = AS_CHM_SP__(x);
219      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
220      CHM_SP chxt = cholmod_transpose(chx, chx->xtype, &c);      CHM_SP chxt = cholmod_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;
# Line 156  Line 233 
233    
234  SEXP Csparse_Csparse_prod(SEXP a, SEXP b)  SEXP Csparse_Csparse_prod(SEXP a, SEXP b)
235  {  {
236      CHM_SP cha = AS_CHM_SP(a), chb = AS_CHM_SP(b);      CHM_SP
237      CHM_SP chc = cholmod_ssmult(cha, chb, 0, cha->xtype, 1, &c);          cha = AS_CHM_SP(a),
238            chb = AS_CHM_SP(b),
239            chc = cholmod_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();      R_CheckStack();
246    
247        /* 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)  SEXP Csparse_Csparse_crossprod(SEXP a, SEXP b, SEXP trans)
272  {  {
273      int tr = asLogical(trans);      int tr = asLogical(trans);
274      CHM_SP cha = AS_CHM_SP(a), chb = AS_CHM_SP(b), chTr, chc;      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);      SEXP dn = allocVector(VECSXP, 2);
282      R_CheckStack();      R_CheckStack();
283    
284      chTr = cholmod_transpose((tr) ? chb : cha, chb->xtype, &c);      chTr = cholmod_transpose((tr) ? chb : cha, chb->xtype, &c);
285      chc = cholmod_ssmult((tr) ? cha : chTr, (tr) ? chTr : chb,      chc = cholmod_ssmult((tr) ? cha : chTr, (tr) ? chTr : chb,
286                           0, cha->xtype, 1, &c);                           /*out_stype:*/ 0, cha->xtype, /*out sorted:*/ 1, &c);
287      cholmod_free_sparse(&chTr, &c);      cholmod_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 */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
302                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), (tr) ? 0 : 1)));                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), (tr) ? 0 : 1)));
303      SET_VECTOR_ELT(dn, 1,      SET_VECTOR_ELT(dn, 1,
304                     duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), (tr) ? 0 : 1)));                     duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), (tr) ? 0 : 1)));
305      return chm_sparse_to_SEXP(chc, 1, 0, 0, "", dn);      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)
# Line 227  Line 345 
345      return chm_dense_to_SEXP(chc, 1, 0, dn);      return chm_dense_to_SEXP(chc, 1, 0, dn);
346  }  }
347    
348  /* 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)
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      CHM_TR cht = trip ? AS_CHM_TR(x) : (CHM_TR) NULL;      CHM_TR cht = trip ? AS_CHM_TR(x) : (CHM_TR) NULL;
355      CHM_SP chcp, chxt,      CHM_SP chcp, chxt,
356          chx = trip ? cholmod_triplet_to_sparse(cht, cht->nnz, &c) : AS_CHM_SP(x);          chx = (trip ?
357                   cholmod_triplet_to_sparse(cht, cht->nnz, &c) :
358                   AS_CHM_SP(x));
359      SEXP dn = PROTECT(allocVector(VECSXP, 2));      SEXP dn = PROTECT(allocVector(VECSXP, 2));
360      R_CheckStack();      R_CheckStack();
361    
362      if (!tr) chxt = cholmod_transpose(chx, chx->xtype, &c);      if (!tr) chxt = cholmod_transpose(chx, chx->xtype, &c);
363      chcp = cholmod_aat((!tr) ? chxt : chx, (int *) NULL, 0, chx->xtype, &c);      chcp = cholmod_aat((!tr) ? chxt : chx, (int *) NULL, 0, chx->xtype, &c);
364      if(!chcp) error(_("Csparse_crossprod(): error return from cholmod_aat()"));      if(!chcp) {
365            UNPROTECT(1);
366            error(_("Csparse_crossprod(): error return from cholmod_aat()"));
367        }
368      cholmod_band_inplace(0, chcp->ncol, chcp->xtype, chcp, &c);      cholmod_band_inplace(0, chcp->ncol, chcp->xtype, chcp, &c);
369      chcp->stype = 1;      chcp->stype = 1;
370      if (trip) cholmod_free_sparse(&chx, &c);      if (trip) cholmod_free_sparse(&chx, &c);
# Line 255  Line 379 
379    
380  SEXP Csparse_drop(SEXP x, SEXP tol)  SEXP Csparse_drop(SEXP x, SEXP tol)
381  {  {
382      CHM_SP chx = AS_CHM_SP(x);      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_copy(chx, chx->stype, chx->xtype, &c);      CHM_SP ans = cholmod_copy(chx, chx->stype, chx->xtype, &c);
387      double dtol = asReal(tol);      double dtol = asReal(tol);
388      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
# Line 263  Line 390 
390    
391      if(!cholmod_drop(dtol, ans, &c))      if(!cholmod_drop(dtol, ans, &c))
392          error(_("cholmod_drop() failed"));          error(_("cholmod_drop() failed"));
393      return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "",      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));                                GET_SLOT(x, Matrix_DimNamesSym));
397  }  }
398    
399  SEXP Csparse_horzcat(SEXP x, SEXP y)  SEXP Csparse_horzcat(SEXP x, SEXP y)
400  {  {
401      CHM_SP chx = AS_CHM_SP(x), chy = AS_CHM_SP(y);      CHM_SP chx = AS_CHM_SP__(x), chy = AS_CHM_SP__(y);
402      int Rkind = 0; /* only for "d" - FIXME */      int Rkind = 0; /* only for "d" - FIXME */
403      R_CheckStack();      R_CheckStack();
404    
# Line 280  Line 409 
409    
410  SEXP Csparse_vertcat(SEXP x, SEXP y)  SEXP Csparse_vertcat(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    
# Line 291  Line 420 
420    
421  SEXP Csparse_band(SEXP x, SEXP k1, SEXP k2)  SEXP Csparse_band(SEXP x, SEXP k1, SEXP k2)
422  {  {
423      CHM_SP chx = AS_CHM_SP(x);      CHM_SP chx = AS_CHM_SP__(x);
424      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
425      CHM_SP ans = cholmod_band(chx, asInteger(k1), asInteger(k2), chx->xtype, &c);      CHM_SP ans = cholmod_band(chx, asInteger(k1), asInteger(k2), chx->xtype, &c);
426      R_CheckStack();      R_CheckStack();
# Line 302  Line 431 
431    
432  SEXP Csparse_diagU2N(SEXP x)  SEXP Csparse_diagU2N(SEXP x)
433  {  {
434      if (*diag_P(x) != 'U') {/* "trivially fast" when there's no 'diag' slot at all */      const char *cl = class_P(x);
435        /* 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);          return (x);
440      }      }
441      else {      else { /* unit triangular (diag='U'): "fill the diagonal" & diag:= "N" */
442          CHM_SP chx = AS_CHM_SP(x);          CHM_SP chx = AS_CHM_SP__(x);
443          CHM_SP eye = cholmod_speye(chx->nrow, chx->ncol, chx->xtype, &c);          CHM_SP eye = cholmod_speye(chx->nrow, chx->ncol, chx->xtype, &c);
444          double one[] = {1, 0};          double one[] = {1, 0};
445          CHM_SP ans = cholmod_add(chx, eye, one, one, TRUE, TRUE, &c);          CHM_SP ans = cholmod_add(chx, eye, one, one, TRUE, TRUE, &c);
# Line 320  Line 453 
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      CHM_SP chx = AS_CHM_SP(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_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
# Line 339  Line 496 
496                                1, 0, Rkind, "",                                1, 0, Rkind, "",
497                                /* FIXME: drops dimnames */ R_NilValue);                                /* 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_write_sparse(f, AS_CHM_SP(x),
508                                  (CHM_SP)NULL, (char*) NULL, &c))
509            error(_("cholmod_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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