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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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pkg/src/Csparse.c revision 1960, Fri Jul 6 16:54:43 2007 UTC pkg/Matrix/src/Csparse.c revision 2629, Sat Dec 11 18:50:49 2010 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    
161      return chm_dense_to_SEXP(chxd, 1, Rkind, GET_SLOT(x, Matrix_DimNamesSym));      return chm_dense_to_SEXP(chxd, 1, Rkind, GET_SLOT(x, Matrix_DimNamesSym));
162  }  }
163    
164    // FIXME: do not go via CHM (should not be too hard, to just *drop* the x-slot, right?
165  SEXP Csparse_to_nz_pattern(SEXP x, SEXP tri)  SEXP Csparse_to_nz_pattern(SEXP x, SEXP tri)
166  {  {
167      CHM_SP chxs = AS_CHM_SP(x);      CHM_SP chxs = AS_CHM_SP__(x);
168      CHM_SP chxcp = cholmod_copy(chxs, chxs->stype, CHOLMOD_PATTERN, &c);      CHM_SP chxcp = cholmod_l_copy(chxs, chxs->stype, CHOLMOD_PATTERN, &c);
169      int tr = asLogical(tri);      int tr = asLogical(tri);
170      R_CheckStack();      R_CheckStack();
171    
# Line 86  Line 175 
175                                GET_SLOT(x, Matrix_DimNamesSym));                                GET_SLOT(x, Matrix_DimNamesSym));
176  }  }
177    
178    // n.CMatrix --> [dli].CMatrix  (not going through CHM!)
179    SEXP nz_pattern_to_Csparse(SEXP x, SEXP res_kind)
180    {
181        return nz2Csparse(x, asInteger(res_kind));
182    }
183    // n.CMatrix --> [dli].CMatrix  (not going through CHM!)
184    SEXP nz2Csparse(SEXP x, enum x_slot_kind r_kind)
185    {
186        const char *cl_x = class_P(x);
187        if(cl_x[0] != 'n') error(_("not a 'n.CMatrix'"));
188        if(cl_x[2] != 'C') error(_("not a CsparseMatrix"));
189        int nnz = LENGTH(GET_SLOT(x, Matrix_iSym));
190        SEXP ans;
191        char *ncl = strdup(cl_x);
192        double *dx_x; int *ix_x;
193        ncl[0] = (r_kind == x_double ? 'd' :
194                  (r_kind == x_logical ? 'l' :
195                   /* else (for now):  r_kind == x_integer : */ 'i'));
196        PROTECT(ans = NEW_OBJECT(MAKE_CLASS(ncl)));
197        // create a correct 'x' slot:
198        switch(r_kind) {
199            int i;
200        case x_double: // 'd'
201            dx_x = REAL(ALLOC_SLOT(ans, Matrix_xSym, REALSXP, nnz));
202            for (i=0; i < nnz; i++) dx_x[i] = 1.;
203            break;
204        case x_logical: // 'l'
205            ix_x = LOGICAL(ALLOC_SLOT(ans, Matrix_xSym, LGLSXP, nnz));
206            for (i=0; i < nnz; i++) ix_x[i] = TRUE;
207            break;
208        case x_integer: // 'i'
209            ix_x = INTEGER(ALLOC_SLOT(ans, Matrix_xSym, INTSXP, nnz));
210            for (i=0; i < nnz; i++) ix_x[i] = 1;
211            break;
212    
213        default:
214            error(_("nz2Csparse(): invalid/non-implemented r_kind = %d"),
215                  r_kind);
216        }
217    
218        // now copy all other slots :
219        slot_dup(ans, x, Matrix_iSym);
220        slot_dup(ans, x, Matrix_pSym);
221        slot_dup(ans, x, Matrix_DimSym);
222        slot_dup(ans, x, Matrix_DimNamesSym);
223        if(ncl[1] != 'g') { // symmetric or triangular ...
224            slot_dup_if_has(ans, x, Matrix_uploSym);
225            slot_dup_if_has(ans, x, Matrix_diagSym);
226        }
227        UNPROTECT(1);
228        return ans;
229    }
230    
231  SEXP Csparse_to_matrix(SEXP x)  SEXP Csparse_to_matrix(SEXP x)
232  {  {
233      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),
234                                 1 /*do_free*/, GET_SLOT(x, Matrix_DimNamesSym));                                 1 /*do_free*/, GET_SLOT(x, Matrix_DimNamesSym));
235  }  }
236    
237  SEXP Csparse_to_Tsparse(SEXP x, SEXP tri)  SEXP Csparse_to_Tsparse(SEXP x, SEXP tri)
238  {  {
239      CHM_SP chxs = AS_CHM_SP(x);      CHM_SP chxs = AS_CHM_SP__(x);
240      CHM_TR chxt = cholmod_sparse_to_triplet(chxs, &c);      CHM_TR chxt = cholmod_l_sparse_to_triplet(chxs, &c);
241      int tr = asLogical(tri);      int tr = asLogical(tri);
242      int Rkind = (chxs->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chxs->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
243      R_CheckStack();      R_CheckStack();
# Line 109  Line 251 
251  /* this used to be called  sCMatrix_to_gCMatrix(..)   [in ./dsCMatrix.c ]: */  /* this used to be called  sCMatrix_to_gCMatrix(..)   [in ./dsCMatrix.c ]: */
252  SEXP Csparse_symmetric_to_general(SEXP x)  SEXP Csparse_symmetric_to_general(SEXP x)
253  {  {
254      CHM_SP chx = AS_CHM_SP(x), chgx;      CHM_SP chx = AS_CHM_SP__(x), chgx;
255      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
256      R_CheckStack();      R_CheckStack();
257    
258      if (!(chx->stype))      if (!(chx->stype))
259          error(_("Nonsymmetric matrix in Csparse_symmetric_to_general"));          error(_("Nonsymmetric matrix in Csparse_symmetric_to_general"));
260      chgx = cholmod_copy(chx, /* stype: */ 0, chx->xtype, &c);      chgx = cholmod_l_copy(chx, /* stype: */ 0, chx->xtype, &c);
261      /* xtype: pattern, "real", complex or .. */      /* xtype: pattern, "real", complex or .. */
262      return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",      return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",
263                                GET_SLOT(x, Matrix_DimNamesSym));                                GET_SLOT(x, Matrix_DimNamesSym));
# Line 123  Line 265 
265    
266  SEXP Csparse_general_to_symmetric(SEXP x, SEXP uplo)  SEXP Csparse_general_to_symmetric(SEXP x, SEXP uplo)
267  {  {
268      CHM_SP chx = AS_CHM_SP(x), chgx;      CHM_SP chx = AS_CHM_SP__(x), chgx;
269      int uploT = (*CHAR(asChar(uplo)) == 'U') ? 1 : -1;      int uploT = (*CHAR(STRING_ELT(uplo,0)) == 'U') ? 1 : -1;
270      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
271      R_CheckStack();      R_CheckStack();
272    
273      chgx = cholmod_copy(chx, /* stype: */ uploT, chx->xtype, &c);      chgx = cholmod_l_copy(chx, /* stype: */ uploT, chx->xtype, &c);
274      /* xtype: pattern, "real", complex or .. */      /* xtype: pattern, "real", complex or .. */
275      return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",      return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",
276                                GET_SLOT(x, Matrix_DimNamesSym));                                GET_SLOT(x, Matrix_DimNamesSym));
# Line 138  Line 280 
280  {  {
281      /* TODO: lgCMatrix & igC* currently go via double prec. cholmod -      /* TODO: lgCMatrix & igC* currently go via double prec. cholmod -
282       *       since cholmod (& cs) lacks sparse 'int' matrices */       *       since cholmod (& cs) lacks sparse 'int' matrices */
283      CHM_SP chx = AS_CHM_SP(x);      CHM_SP chx = AS_CHM_SP__(x);
284      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
285      CHM_SP chxt = cholmod_transpose(chx, chx->xtype, &c);      CHM_SP chxt = cholmod_l_transpose(chx, chx->xtype, &c);
286      SEXP dn = PROTECT(duplicate(GET_SLOT(x, Matrix_DimNamesSym))), tmp;      SEXP dn = PROTECT(duplicate(GET_SLOT(x, Matrix_DimNamesSym))), tmp;
287      int tr = asLogical(tri);      int tr = asLogical(tri);
288      R_CheckStack();      R_CheckStack();
# Line 156  Line 298 
298    
299  SEXP Csparse_Csparse_prod(SEXP a, SEXP b)  SEXP Csparse_Csparse_prod(SEXP a, SEXP b)
300  {  {
301      CHM_SP cha = AS_CHM_SP(a), chb = AS_CHM_SP(b);      CHM_SP
302      CHM_SP chc = cholmod_ssmult(cha, chb, 0, cha->xtype, 1, &c);          cha = AS_CHM_SP(a),
303      SEXP dn = allocVector(VECSXP, 2);          chb = AS_CHM_SP(b),
304            chc = cholmod_l_ssmult(cha, chb, /*out_stype:*/ 0,
305                                   /* values:= is_numeric (T/F) */ cha->xtype > 0,
306                                   /*out sorted:*/ 1, &c);
307        const char *cl_a = class_P(a), *cl_b = class_P(b);
308        char diag[] = {'\0', '\0'};
309        int uploT = 0;
310        SEXP dn = PROTECT(allocVector(VECSXP, 2));
311      R_CheckStack();      R_CheckStack();
312    
313    #ifdef DEBUG_Matrix_verbose
314        Rprintf("DBG Csparse_C*_prod(%s, %s)\n", cl_a, cl_b);
315    #endif
316    
317        /* Preserve triangularity and even unit-triangularity if appropriate.
318         * Note that in that case, the multiplication itself should happen
319         * faster.  But there's no support for that in CHOLMOD */
320    
321        /* UGLY hack -- rather should have (fast!) C-level version of
322         *       is(a, "triangularMatrix") etc */
323        if (cl_a[1] == 't' && cl_b[1] == 't')
324            /* FIXME: fails for "Cholesky","BunchKaufmann"..*/
325            if(*uplo_P(a) == *uplo_P(b)) { /* both upper, or both lower tri. */
326                uploT = (*uplo_P(a) == 'U') ? 1 : -1;
327                if(*diag_P(a) == 'U' && *diag_P(b) == 'U') { /* return UNIT-triag. */
328                    /* "remove the diagonal entries": */
329                    chm_diagN2U(chc, uploT, /* do_realloc */ FALSE);
330                    diag[0]= 'U';
331                }
332                else diag[0]= 'N';
333            }
334      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
335                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));
336      SET_VECTOR_ELT(dn, 1,      SET_VECTOR_ELT(dn, 1,
337                     duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), 1)));                     duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), 1)));
338      return chm_sparse_to_SEXP(chc, 1, 0, 0, "", dn);      UNPROTECT(1);
339        return chm_sparse_to_SEXP(chc, 1, uploT, /*Rkind*/0, diag, dn);
340  }  }
341    
342  SEXP Csparse_Csparse_crossprod(SEXP a, SEXP b, SEXP trans)  SEXP Csparse_Csparse_crossprod(SEXP a, SEXP b, SEXP trans)
343  {  {
344      int tr = asLogical(trans);      int tr = asLogical(trans);
345      CHM_SP cha = AS_CHM_SP(a), chb = AS_CHM_SP(b), chTr, chc;      CHM_SP
346      SEXP dn = allocVector(VECSXP, 2);          cha = AS_CHM_SP(a),
347            chb = AS_CHM_SP(b),
348            chTr, chc;
349        const char *cl_a = class_P(a), *cl_b = class_P(b);
350        char diag[] = {'\0', '\0'};
351        int uploT = 0;
352        SEXP dn = PROTECT(allocVector(VECSXP, 2));
353      R_CheckStack();      R_CheckStack();
354    
355      chTr = cholmod_transpose((tr) ? chb : cha, chb->xtype, &c);      chTr = cholmod_l_transpose((tr) ? chb : cha, chb->xtype, &c);
356      chc = cholmod_ssmult((tr) ? cha : chTr, (tr) ? chTr : chb,      chc = cholmod_l_ssmult((tr) ? cha : chTr, (tr) ? chTr : chb,
357                           0, cha->xtype, 1, &c);                           /*out_stype:*/ 0, cha->xtype, /*out sorted:*/ 1, &c);
358      cholmod_free_sparse(&chTr, &c);      cholmod_l_free_sparse(&chTr, &c);
359    
360        /* Preserve triangularity and unit-triangularity if appropriate;
361         * see Csparse_Csparse_prod() for comments */
362        if (cl_a[1] == 't' && cl_b[1] == 't')
363            if(*uplo_P(a) != *uplo_P(b)) { /* one 'U', the other 'L' */
364                uploT = (*uplo_P(b) == 'U') ? 1 : -1;
365                if(*diag_P(a) == 'U' && *diag_P(b) == 'U') { /* return UNIT-triag. */
366                    chm_diagN2U(chc, uploT, /* do_realloc */ FALSE);
367                    diag[0]= 'U';
368                }
369                else diag[0]= 'N';
370            }
371      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
372                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), (tr) ? 0 : 1)));                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), (tr) ? 0 : 1)));
373      SET_VECTOR_ELT(dn, 1,      SET_VECTOR_ELT(dn, 1,
374                     duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), (tr) ? 0 : 1)));                     duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), (tr) ? 0 : 1)));
375      return chm_sparse_to_SEXP(chc, 1, 0, 0, "", dn);      UNPROTECT(1);
376        return chm_sparse_to_SEXP(chc, 1, uploT, /*Rkind*/0, diag, dn);
377  }  }
378    
379  SEXP Csparse_dense_prod(SEXP a, SEXP b)  SEXP Csparse_dense_prod(SEXP a, SEXP b)
# Line 192  Line 381 
381      CHM_SP cha = AS_CHM_SP(a);      CHM_SP cha = AS_CHM_SP(a);
382      SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));      SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));
383      CHM_DN chb = AS_CHM_DN(b_M);      CHM_DN chb = AS_CHM_DN(b_M);
384      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,
385                                          chb->xtype, &c);                                          chb->xtype, &c);
386      SEXP dn = PROTECT(allocVector(VECSXP, 2));      SEXP dn = PROTECT(allocVector(VECSXP, 2));
387      double one[] = {1,0}, zero[] = {0,0};      double one[] = {1,0}, zero[] = {0,0};
388        int nprot = 2;
389      R_CheckStack();      R_CheckStack();
390        /* Tim Davis, please FIXME:  currently (2010-11) *fails* when  a  is a pattern matrix:*/
391      cholmod_sdmult(cha, 0, one, zero, chb, chc, &c);      if(cha->xtype == CHOLMOD_PATTERN) {
392            /* warning(_("Csparse_dense_prod(): cholmod_sdmult() not yet implemented for pattern./ ngCMatrix" */
393            /*        " --> slightly inefficient coercion")); */
394    
395            // This *fails* to produce a CHOLMOD_REAL ..
396            // CHM_SP chd = cholmod_l_copy(cha, cha->stype, CHOLMOD_REAL, &c);
397            // --> use our Matrix-classes
398            SEXP da = PROTECT(nz2Csparse(a, x_double)); nprot++;
399            cha = AS_CHM_SP(da);
400        }
401        cholmod_l_sdmult(cha, 0, one, zero, chb, chc, &c);
402      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
403                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));
404      SET_VECTOR_ELT(dn, 1,      SET_VECTOR_ELT(dn, 1,
405                     duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));                     duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));
406      UNPROTECT(2);      UNPROTECT(nprot);
407      return chm_dense_to_SEXP(chc, 1, 0, dn);      return chm_dense_to_SEXP(chc, 1, 0, dn);
408  }  }
409    
# Line 212  Line 412 
412      CHM_SP cha = AS_CHM_SP(a);      CHM_SP cha = AS_CHM_SP(a);
413      SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));      SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));
414      CHM_DN chb = AS_CHM_DN(b_M);      CHM_DN chb = AS_CHM_DN(b_M);
415      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,
416                                          chb->xtype, &c);                                          chb->xtype, &c);
417      SEXP dn = PROTECT(allocVector(VECSXP, 2));      SEXP dn = PROTECT(allocVector(VECSXP, 2)); int nprot = 2;
418      double one[] = {1,0}, zero[] = {0,0};      double one[] = {1,0}, zero[] = {0,0};
419      R_CheckStack();      R_CheckStack();
420        // -- see Csparse_dense_prod() above :
421      cholmod_sdmult(cha, 1, one, zero, chb, chc, &c);      if(cha->xtype == CHOLMOD_PATTERN) {
422            SEXP da = PROTECT(nz2Csparse(a, x_double)); nprot++;
423            cha = AS_CHM_SP(da);
424        }
425        cholmod_l_sdmult(cha, 1, one, zero, chb, chc, &c);
426      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
427                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 1)));                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 1)));
428      SET_VECTOR_ELT(dn, 1,      SET_VECTOR_ELT(dn, 1,
429                     duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));                     duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));
430      UNPROTECT(2);      UNPROTECT(nprot);
431      return chm_dense_to_SEXP(chc, 1, 0, dn);      return chm_dense_to_SEXP(chc, 1, 0, dn);
432  }  }
433    
434  /* 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)
435       see Csparse_Csparse_crossprod above for  x'y and x y' */
436  SEXP Csparse_crossprod(SEXP x, SEXP trans, SEXP triplet)  SEXP Csparse_crossprod(SEXP x, SEXP trans, SEXP triplet)
437  {  {
438      int trip = asLogical(triplet),      int trip = asLogical(triplet),
439          tr   = asLogical(trans); /* gets reversed because _aat is tcrossprod */          tr   = asLogical(trans); /* gets reversed because _aat is tcrossprod */
440    #ifdef AS_CHM_DIAGU2N_FIXED_FINALLY
441      CHM_TR cht = trip ? AS_CHM_TR(x) : (CHM_TR) NULL;      CHM_TR cht = trip ? AS_CHM_TR(x) : (CHM_TR) NULL;
442    #else /* workaround needed:*/
443        SEXP xx = PROTECT(Tsparse_diagU2N(x));
444        CHM_TR cht = trip ? AS_CHM_TR__(xx) : (CHM_TR) NULL;
445    #endif
446      CHM_SP chcp, chxt,      CHM_SP chcp, chxt,
447          chx = trip ? cholmod_triplet_to_sparse(cht, cht->nnz, &c) : AS_CHM_SP(x);          chx = (trip ?
448                   cholmod_l_triplet_to_sparse(cht, cht->nnz, &c) :
449                   AS_CHM_SP(x));
450      SEXP dn = PROTECT(allocVector(VECSXP, 2));      SEXP dn = PROTECT(allocVector(VECSXP, 2));
451      R_CheckStack();      R_CheckStack();
452    
453      if (!tr) chxt = cholmod_transpose(chx, chx->xtype, &c);      if (!tr) chxt = cholmod_l_transpose(chx, chx->xtype, &c);
454      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);
455      if(!chcp) error(_("Csparse_crossprod(): error return from cholmod_aat()"));      if(!chcp) {
456      cholmod_band_inplace(0, chcp->ncol, chcp->xtype, chcp, &c);          UNPROTECT(1);
457            error(_("Csparse_crossprod(): error return from cholmod_l_aat()"));
458        }
459        cholmod_l_band_inplace(0, chcp->ncol, chcp->xtype, chcp, &c);
460      chcp->stype = 1;      chcp->stype = 1;
461      if (trip) cholmod_free_sparse(&chx, &c);      if (trip) cholmod_l_free_sparse(&chx, &c);
462      if (!tr) cholmod_free_sparse(&chxt, &c);      if (!tr) cholmod_l_free_sparse(&chxt, &c);
463      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
464                     duplicate(VECTOR_ELT(GET_SLOT(x, Matrix_DimNamesSym),                     duplicate(VECTOR_ELT(GET_SLOT(x, Matrix_DimNamesSym),
465                                          (tr) ? 0 : 1)));                                          (tr) ? 0 : 1)));
466      SET_VECTOR_ELT(dn, 1, duplicate(VECTOR_ELT(dn, 0)));      SET_VECTOR_ELT(dn, 1, duplicate(VECTOR_ELT(dn, 0)));
467    #ifdef AS_CHM_DIAGU2N_FIXED_FINALLY
468      UNPROTECT(1);      UNPROTECT(1);
469    #else
470        UNPROTECT(2);
471    #endif
472      return chm_sparse_to_SEXP(chcp, 1, 0, 0, "", dn);      return chm_sparse_to_SEXP(chcp, 1, 0, 0, "", dn);
473  }  }
474    
475  SEXP Csparse_drop(SEXP x, SEXP tol)  SEXP Csparse_drop(SEXP x, SEXP tol)
476  {  {
477      CHM_SP chx = AS_CHM_SP(x);      const char *cl = class_P(x);
478      CHM_SP ans = cholmod_copy(chx, chx->stype, chx->xtype, &c);      /* dtCMatrix, etc; [1] = the second character =?= 't' for triangular */
479        int tr = (cl[1] == 't');
480        CHM_SP chx = AS_CHM_SP__(x);
481        CHM_SP ans = cholmod_l_copy(chx, chx->stype, chx->xtype, &c);
482      double dtol = asReal(tol);      double dtol = asReal(tol);
483      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
484      R_CheckStack();      R_CheckStack();
485    
486      if(!cholmod_drop(dtol, ans, &c))      if(!cholmod_l_drop(dtol, ans, &c))
487          error(_("cholmod_drop() failed"));          error(_("cholmod_l_drop() failed"));
488      return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "",      return chm_sparse_to_SEXP(ans, 1,
489                                  tr ? ((*uplo_P(x) == 'U') ? 1 : -1) : 0,
490                                  Rkind, tr ? diag_P(x) : "",
491                                GET_SLOT(x, Matrix_DimNamesSym));                                GET_SLOT(x, Matrix_DimNamesSym));
492  }  }
493    
494  SEXP Csparse_horzcat(SEXP x, SEXP y)  SEXP Csparse_horzcat(SEXP x, SEXP y)
495  {  {
496      CHM_SP chx = AS_CHM_SP(x), chy = AS_CHM_SP(y);      CHM_SP chx = AS_CHM_SP__(x), chy = AS_CHM_SP__(y);
497      int Rkind = 0; /* only for "d" - FIXME */      int Rk_x = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0,
498            Rk_y = (chy->xtype != CHOLMOD_PATTERN) ? Real_kind(y) : 0,
499            Rkind = /* logical if both x and y are */ (Rk_x == 1 && Rk_y == 1) ? 1 : 0;
500      R_CheckStack();      R_CheckStack();
501    
502      /* FIXME: currently drops dimnames */      /* TODO: currently drops dimnames - and we fix at R level */
503      return chm_sparse_to_SEXP(cholmod_horzcat(chx, chy, 1, &c),      return chm_sparse_to_SEXP(cholmod_l_horzcat(chx, chy, 1, &c),
504                                1, 0, Rkind, "", R_NilValue);                                1, 0, Rkind, "", R_NilValue);
505  }  }
506    
507  SEXP Csparse_vertcat(SEXP x, SEXP y)  SEXP Csparse_vertcat(SEXP x, SEXP y)
508  {  {
509      CHM_SP chx = AS_CHM_SP(x), chy = AS_CHM_SP(y);      CHM_SP chx = AS_CHM_SP__(x), chy = AS_CHM_SP__(y);
510      int Rkind = 0; /* only for "d" - FIXME */      int Rk_x = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0,
511            Rk_y = (chy->xtype != CHOLMOD_PATTERN) ? Real_kind(y) : 0,
512            Rkind = /* logical if both x and y are */ (Rk_x == 1 && Rk_y == 1) ? 1 : 0;
513      R_CheckStack();      R_CheckStack();
514    
515      /* FIXME: currently drops dimnames */      /* TODO: currently drops dimnames - and we fix at R level */
516      return chm_sparse_to_SEXP(cholmod_vertcat(chx, chy, 1, &c),      return chm_sparse_to_SEXP(cholmod_l_vertcat(chx, chy, 1, &c),
517                                1, 0, Rkind, "", R_NilValue);                                1, 0, Rkind, "", R_NilValue);
518  }  }
519    
520  SEXP Csparse_band(SEXP x, SEXP k1, SEXP k2)  SEXP Csparse_band(SEXP x, SEXP k1, SEXP k2)
521  {  {
522      CHM_SP chx = AS_CHM_SP(x);      CHM_SP chx = AS_CHM_SP__(x);
523      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
524      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);
525      R_CheckStack();      R_CheckStack();
526    
527      return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "",      return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "",
# Line 302  Line 530 
530    
531  SEXP Csparse_diagU2N(SEXP x)  SEXP Csparse_diagU2N(SEXP x)
532  {  {
533      if (*diag_P(x) != 'U') {/* "trivially fast" when there's no 'diag' slot at all */      const char *cl = class_P(x);
534        /* dtCMatrix, etc; [1] = the second character =?= 't' for triangular */
535        if (cl[1] != 't' || *diag_P(x) != 'U') {
536            /* "trivially fast" when not triangular (<==> no 'diag' slot),
537               or not *unit* triangular */
538          return (x);          return (x);
539      }      }
540      else {      else { /* unit triangular (diag='U'): "fill the diagonal" & diag:= "N" */
541          CHM_SP chx = AS_CHM_SP(x);          CHM_SP chx = AS_CHM_SP__(x);
542          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);
543          double one[] = {1, 0};          double one[] = {1, 0};
544          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);
545          int uploT = (*uplo_P(x) == 'U') ? 1 : -1;          int uploT = (*uplo_P(x) == 'U') ? 1 : -1;
546          int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;          int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
547    
548          R_CheckStack();          R_CheckStack();
549          cholmod_free_sparse(&eye, &c);          cholmod_l_free_sparse(&eye, &c);
550          return chm_sparse_to_SEXP(ans, 1, uploT, Rkind, "N",          return chm_sparse_to_SEXP(ans, 1, uploT, Rkind, "N",
551                                    GET_SLOT(x, Matrix_DimNamesSym));                                    GET_SLOT(x, Matrix_DimNamesSym));
552      }      }
553  }  }
554    
555    SEXP Csparse_diagN2U(SEXP x)
556    {
557        const char *cl = class_P(x);
558        /* dtCMatrix, etc; [1] = the second character =?= 't' for triangular */
559        if (cl[1] != 't' || *diag_P(x) != 'N') {
560            /* "trivially fast" when not triangular (<==> no 'diag' slot),
561               or already *unit* triangular */
562            return (x);
563        }
564        else { /* triangular with diag='N'): now drop the diagonal */
565            /* duplicate, since chx will be modified: */
566            CHM_SP chx = AS_CHM_SP__(duplicate(x));
567            int uploT = (*uplo_P(x) == 'U') ? 1 : -1,
568                Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
569            R_CheckStack();
570    
571            chm_diagN2U(chx, uploT, /* do_realloc */ FALSE);
572    
573            return chm_sparse_to_SEXP(chx, /*dofree*/ 0/* or 1 ?? */,
574                                      uploT, Rkind, "U",
575                                      GET_SLOT(x, Matrix_DimNamesSym));
576        }
577    }
578    
579    /**
580     * "Indexing" aka subsetting : Compute  x[i,j], also for vectors i and j
581     * Working via CHOLMOD_submatrix, see ./CHOLMOD/MatrixOps/cholmod_submatrix.c
582     * @param x CsparseMatrix
583     * @param i row     indices (0-origin), or NULL (R's)
584     * @param j columns indices (0-origin), or NULL
585     *
586     * @return x[i,j]  still CsparseMatrix --- currently, this loses dimnames
587     */
588  SEXP Csparse_submatrix(SEXP x, SEXP i, SEXP j)  SEXP Csparse_submatrix(SEXP x, SEXP i, SEXP j)
589  {  {
590      CHM_SP chx = AS_CHM_SP(x);      CHM_SP chx = AS_CHM_SP(x); /* << does diagU2N() when needed */
591      int rsize = (isNull(i)) ? -1 : LENGTH(i),      int rsize = (isNull(i)) ? -1 : LENGTH(i),
592          csize = (isNull(j)) ? -1 : LENGTH(j);          csize = (isNull(j)) ? -1 : LENGTH(j);
593      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
# Line 333  Line 598 
598      if (csize >= 0 && !isInteger(j))      if (csize >= 0 && !isInteger(j))
599          error(_("Index j must be NULL or integer"));          error(_("Index j must be NULL or integer"));
600    
601      return chm_sparse_to_SEXP(cholmod_submatrix(chx, INTEGER(i), rsize,      if (chx->stype) /* symmetricMatrix */
602                                                  INTEGER(j), csize,          /* for now, cholmod_submatrix() only accepts "generalMatrix" */
603            chx = cholmod_l_copy(chx, /* stype: */ 0, chx->xtype, &c);
604    
605        return chm_sparse_to_SEXP(cholmod_l_submatrix(chx,
606                                    (rsize < 0) ? NULL : INTEGER(i), rsize,
607                                    (csize < 0) ? NULL : INTEGER(j), csize,
608                                                  TRUE, TRUE, &c),                                                  TRUE, TRUE, &c),
609                                1, 0, Rkind, "",                                1, 0, Rkind, "",
610                                /* FIXME: drops dimnames */ R_NilValue);                                /* FIXME: drops dimnames */ R_NilValue);
611  }  }
612    
613    SEXP Csparse_MatrixMarket(SEXP x, SEXP fname)
614    {
615        FILE *f = fopen(CHAR(asChar(fname)), "w");
616    
617        if (!f)
618            error(_("failure to open file \"%s\" for writing"),
619                  CHAR(asChar(fname)));
620        if (!cholmod_l_write_sparse(f, AS_CHM_SP(x),
621                                  (CHM_SP)NULL, (char*) NULL, &c))
622            error(_("cholmod_l_write_sparse returned error code"));
623        fclose(f);
624        return R_NilValue;
625    }
626    
627    
628    /**
629     * Extract the diagonal entries from *triangular* Csparse matrix  __or__ a
630     * cholmod_sparse factor (LDL = TRUE).
631     *
632     * @param n  dimension of the matrix.
633     * @param x_p  'p' (column pointer) slot contents
634     * @param x_x  'x' (non-zero entries) slot contents
635     * @param perm 'perm' (= permutation vector) slot contents; only used for "diagBack"
636     * @param resultKind a (SEXP) string indicating which kind of result is desired.
637     *
638     * @return  a SEXP, either a (double) number or a length n-vector of diagonal entries
639     */
640    SEXP diag_tC_ptr(int n, int *x_p, double *x_x, int *perm, SEXP resultKind)
641    /*                                ^^^^^^ FIXME[Generalize] to int / ... */
642    {
643        const char* res_ch = CHAR(STRING_ELT(resultKind,0));
644        enum diag_kind { diag, diag_backpermuted, trace, prod, sum_log
645        } res_kind = ((!strcmp(res_ch, "trace")) ? trace :
646                      ((!strcmp(res_ch, "sumLog")) ? sum_log :
647                       ((!strcmp(res_ch, "prod")) ? prod :
648                        ((!strcmp(res_ch, "diag")) ? diag :
649                         ((!strcmp(res_ch, "diagBack")) ? diag_backpermuted :
650                          -1)))));
651        int i, n_x, i_from = 0;
652        SEXP ans = PROTECT(allocVector(REALSXP,
653    /*                                 ^^^^  FIXME[Generalize] */
654                                       (res_kind == diag ||
655                                        res_kind == diag_backpermuted) ? n : 1));
656        double *v = REAL(ans);
657    /*  ^^^^^^      ^^^^  FIXME[Generalize] */
658    
659    #define for_DIAG(v_ASSIGN)                                              \
660        for(i = 0; i < n; i++, i_from += n_x) {                             \
661            /* looking at i-th column */                                    \
662            n_x = x_p[i+1] - x_p[i];/* #{entries} in this column */ \
663            v_ASSIGN;                                                       \
664        }
665    
666        /* NOTA BENE: we assume  -- uplo = "L" i.e. lower triangular matrix
667         *            for uplo = "U" (makes sense with a "dtCMatrix" !),
668         *            should use  x_x[i_from + (nx - 1)] instead of x_x[i_from],
669         *            where nx = (x_p[i+1] - x_p[i])
670         */
671    
672        switch(res_kind) {
673        case trace:
674            v[0] = 0.;
675            for_DIAG(v[0] += x_x[i_from]);
676            break;
677    
678        case sum_log:
679            v[0] = 0.;
680            for_DIAG(v[0] += log(x_x[i_from]));
681            break;
682    
683        case prod:
684            v[0] = 1.;
685            for_DIAG(v[0] *= x_x[i_from]);
686            break;
687    
688        case diag:
689            for_DIAG(v[i] = x_x[i_from]);
690            break;
691    
692        case diag_backpermuted:
693            for_DIAG(v[i] = x_x[i_from]);
694    
695            warning(_("resultKind = 'diagBack' (back-permuted) is experimental"));
696            /* now back_permute : */
697            for(i = 0; i < n; i++) {
698                double tmp = v[i]; v[i] = v[perm[i]]; v[perm[i]] = tmp;
699                /*^^^^ FIXME[Generalize] */
700            }
701            break;
702    
703        default: /* -1 from above */
704            error(_("diag_tC(): invalid 'resultKind'"));
705            /* Wall: */ ans = R_NilValue; v = REAL(ans);
706        }
707    
708        UNPROTECT(1);
709        return ans;
710    }
711    
712    /**
713     * Extract the diagonal entries from *triangular* Csparse matrix  __or__ a
714     * cholmod_sparse factor (LDL = TRUE).
715     *
716     * @param pslot  'p' (column pointer)   slot of Csparse matrix/factor
717     * @param xslot  'x' (non-zero entries) slot of Csparse matrix/factor
718     * @param perm_slot  'perm' (= permutation vector) slot of corresponding CHMfactor;
719     *                   only used for "diagBack"
720     * @param resultKind a (SEXP) string indicating which kind of result is desired.
721     *
722     * @return  a SEXP, either a (double) number or a length n-vector of diagonal entries
723     */
724    SEXP diag_tC(SEXP pslot, SEXP xslot, SEXP perm_slot, SEXP resultKind)
725    {
726        int n = length(pslot) - 1, /* n = ncol(.) = nrow(.) */
727            *x_p  = INTEGER(pslot),
728            *perm = INTEGER(perm_slot);
729        double *x_x = REAL(xslot);
730    /*  ^^^^^^        ^^^^ FIXME[Generalize] to INTEGER(.) / LOGICAL(.) / ... xslot !*/
731    
732        return diag_tC_ptr(n, x_p, x_x, perm, resultKind);
733    }
734    
735    /**
736     * Create a Csparse matrix object from indices and/or pointers.
737     *
738     * @param cls name of actual class of object to create
739     * @param i optional integer vector of length nnz of row indices
740     * @param j optional integer vector of length nnz of column indices
741     * @param p optional integer vector of length np of row or column pointers
742     * @param np length of integer vector p.  Must be zero if p == (int*)NULL
743     * @param x optional vector of values
744     * @param nnz length of vectors i, j and/or x, whichever is to be used
745     * @param dims optional integer vector of length 2 to be used as
746     *     dimensions.  If dims == (int*)NULL then the maximum row and column
747     *     index are used as the dimensions.
748     * @param dimnames optional list of length 2 to be used as dimnames
749     * @param index1 indicator of 1-based indices
750     *
751     * @return an SEXP of class cls inheriting from CsparseMatrix.
752     */
753    SEXP create_Csparse(char* cls, int* i, int* j, int* p, int np,
754                        void* x, int nnz, int* dims, SEXP dimnames,
755                        int index1)
756    {
757        SEXP ans;
758        int *ij = (int*)NULL, *tri, *trj,
759            mi, mj, mp, nrow = -1, ncol = -1;
760        int xtype = -1;             /* -Wall */
761        CHM_TR T;
762        CHM_SP A;
763    
764        if (np < 0 || nnz < 0)
765            error(_("negative vector lengths not allowed: np = %d, nnz = %d"),
766                  np, nnz);
767        if (1 != ((mi = (i == (int*)NULL)) +
768                  (mj = (j == (int*)NULL)) +
769                  (mp = (p == (int*)NULL))))
770            error(_("exactly 1 of 'i', 'j' or 'p' must be NULL"));
771        if (mp) {
772            if (np) error(_("np = %d, must be zero when p is NULL"), np);
773        } else {
774            if (np) {               /* Expand p to form i or j */
775                if (!(p[0])) error(_("p[0] = %d, should be zero"), p[0]);
776                for (int ii = 0; ii < np; ii++)
777                    if (p[ii] > p[ii + 1])
778                        error(_("p must be non-decreasing"));
779                if (p[np] != nnz)
780                    error("p[np] = %d != nnz = %d", p[np], nnz);
781                ij = Calloc(nnz, int);
782                if (mi) {
783                    i = ij;
784                    nrow = np;
785                } else {
786                    j = ij;
787                    ncol = np;
788                }
789                                    /* Expand p to 0-based indices */
790                for (int ii = 0; ii < np; ii++)
791                    for (int jj = p[ii]; jj < p[ii + 1]; jj++) ij[jj] = ii;
792            } else {
793                if (nnz)
794                    error(_("Inconsistent dimensions: np = 0 and nnz = %d"),
795                          nnz);
796            }
797        }
798                                    /* calculate nrow and ncol */
799        if (nrow < 0) {
800            for (int ii = 0; ii < nnz; ii++) {
801                int i1 = i[ii] + (index1 ? 0 : 1); /* 1-based index */
802                if (i1 < 1) error(_("invalid row index at position %d"), ii);
803                if (i1 > nrow) nrow = i1;
804            }
805        }
806        if (ncol < 0) {
807            for (int jj = 0; jj < nnz; jj++) {
808                int j1 = j[jj] + (index1 ? 0 : 1);
809                if (j1 < 1) error(_("invalid column index at position %d"), jj);
810                if (j1 > ncol) ncol = j1;
811            }
812        }
813        if (dims != (int*)NULL) {
814            if (dims[0] > nrow) nrow = dims[0];
815            if (dims[1] > ncol) ncol = dims[1];
816        }
817                                    /* check the class name */
818        if (strlen(cls) != 8)
819            error(_("strlen of cls argument = %d, should be 8"), strlen(cls));
820        if (!strcmp(cls + 2, "CMatrix"))
821            error(_("cls = \"%s\" does not end in \"CMatrix\""), cls);
822        switch(cls[0]) {
823        case 'd':
824        case 'l':
825               xtype = CHOLMOD_REAL;
826               break;
827        case 'n':
828               xtype = CHOLMOD_PATTERN;
829               break;
830        default:
831               error(_("cls = \"%s\" must begin with 'd', 'l' or 'n'"), cls);
832        }
833        if (cls[1] != 'g')
834            error(_("Only 'g'eneral sparse matrix types allowed"));
835                                    /* allocate and populate the triplet */
836        T = cholmod_l_allocate_triplet((size_t)nrow, (size_t)ncol, (size_t)nnz, 0,
837                                        xtype, &c);
838        T->x = x;
839        tri = (int*)T->i;
840        trj = (int*)T->j;
841        for (int ii = 0; ii < nnz; ii++) {
842            tri[ii] = i[ii] - ((!mi && index1) ? 1 : 0);
843            trj[ii] = j[ii] - ((!mj && index1) ? 1 : 0);
844        }
845                                    /* create the cholmod_sparse structure */
846        A = cholmod_l_triplet_to_sparse(T, nnz, &c);
847        cholmod_l_free_triplet(&T, &c);
848                                    /* copy the information to the SEXP */
849        ans = PROTECT(NEW_OBJECT(MAKE_CLASS(cls)));
850    /* FIXME: This has been copied from chm_sparse_to_SEXP in chm_common.c */
851                                    /* allocate and copy common slots */
852        nnz = cholmod_l_nnz(A, &c);
853        dims = INTEGER(ALLOC_SLOT(ans, Matrix_DimSym, INTSXP, 2));
854        dims[0] = A->nrow; dims[1] = A->ncol;
855        Memcpy(INTEGER(ALLOC_SLOT(ans, Matrix_pSym, INTSXP, A->ncol + 1)), (int*)A->p, A->ncol + 1);
856        Memcpy(INTEGER(ALLOC_SLOT(ans, Matrix_iSym, INTSXP, nnz)), (int*)A->i, nnz);
857        switch(cls[1]) {
858        case 'd':
859            Memcpy(REAL(ALLOC_SLOT(ans, Matrix_xSym, REALSXP, nnz)), (double*)A->x, nnz);
860            break;
861        case 'l':
862            error(_("code not yet written for cls = \"lgCMatrix\""));
863        }
864        cholmod_l_free_sparse(&A, &c);
865        UNPROTECT(1);
866        return ans;
867    }

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