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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 2673, Fri May 20 16:19:18 2011 UTC revision 3270, Fri Mar 23 08:50:48 2018 UTC
# Line 1  Line 1 
1                          /* Sparse matrices in compressed column-oriented form */  /** @file Csparse.c
2     * The "CsparseMatrix" class from R package Matrix:
3     *
4     * Sparse matrices in compressed column-oriented form
5     */
6  #include "Csparse.h"  #include "Csparse.h"
7  #include "Tsparse.h"  #include "Tsparse.h"
8  #include "chm_common.h"  #include "chm_common.h"
# Line 36  Line 40 
40      return Csparse_validate_(x, FALSE);      return Csparse_validate_(x, FALSE);
41  }  }
42    
 SEXP Csparse_validate2(SEXP x, SEXP maybe_modify) {  
     return Csparse_validate_(x, asLogical(maybe_modify));  
 }  
43    
44  SEXP Csparse_validate_(SEXP x, Rboolean maybe_modify)  #define _t_Csparse_validate
45  {  #include "t_Csparse_validate.c"
     /* NB: we do *NOT* check a potential 'x' slot here, at all */  
     SEXP pslot = GET_SLOT(x, Matrix_pSym),  
         islot = GET_SLOT(x, Matrix_iSym);  
     Rboolean sorted, strictly;  
     int j, k,  
         *dims = INTEGER(GET_SLOT(x, Matrix_DimSym)),  
         nrow = dims[0],  
         ncol = dims[1],  
         *xp = INTEGER(pslot),  
         *xi = INTEGER(islot);  
46    
47      if (length(pslot) != dims[1] + 1)  #define _t_Csparse_sort
48          return mkString(_("slot p must have length = ncol(.) + 1"));  #include "t_Csparse_validate.c"
     if (xp[0] != 0)  
         return mkString(_("first element of slot p must be zero"));  
     if (length(islot) < xp[ncol]) /* allow larger slots from over-allocation!*/  
         return  
             mkString(_("last element of slot p must match length of slots i and x"));  
     for (j = 0; j < xp[ncol]; j++) {  
         if (xi[j] < 0 || xi[j] >= nrow)  
             return mkString(_("all row indices must be between 0 and nrow-1"));  
     }  
     sorted = TRUE; strictly = TRUE;  
     for (j = 0; j < ncol; j++) {  
         if (xp[j] > xp[j + 1])  
             return mkString(_("slot p must be non-decreasing"));  
         if(sorted) /* only act if >= 2 entries in column j : */  
             for (k = xp[j] + 1; k < xp[j + 1]; k++) {  
                 if (xi[k] < xi[k - 1])  
                     sorted = FALSE;  
                 else if (xi[k] == xi[k - 1])  
                     strictly = FALSE;  
             }  
     }  
     if (!sorted) {  
         if(maybe_modify) {  
             CHM_SP chx = (CHM_SP) alloca(sizeof(cholmod_sparse));  
             R_CheckStack();  
             as_cholmod_sparse(chx, x, FALSE, TRUE);/*-> cholmod_l_sort() ! */  
             /* as chx = AS_CHM_SP__(x)  but  ^^^^ sorting x in_place !!! */  
49    
50              /* Now re-check that row indices are *strictly* increasing  // R: .validateCsparse(x, sort.if.needed = FALSE) :
51               * (and not just increasing) within each column : */  SEXP Csparse_validate2(SEXP x, SEXP maybe_modify) {
52              for (j = 0; j < ncol; j++) {      return Csparse_validate_(x, asLogical(maybe_modify));
                 for (k = xp[j] + 1; k < xp[j + 1]; k++)  
                     if (xi[k] == xi[k - 1])  
                         return mkString(_("slot i is not *strictly* increasing inside a column (even after cholmod_l_sort)"));  
             }  
         } else { /* no modifying sorting : */  
             return mkString(_("row indices are not sorted within columns"));  
         }  
     } else if(!strictly) {  /* sorted, but not strictly */  
         return mkString(_("slot i is not *strictly* increasing inside a column"));  
53      }      }
54      return ScalarLogical(1);  
55    // R: Matrix:::.sortCsparse(x) :
56    SEXP Csparse_sort (SEXP x) {
57       int ok = Csparse_sort_2(x, TRUE); // modifying x directly
58       if(!ok) warning(_("Csparse_sort(x): x is not a valid (apart from sorting) CsparseMatrix"));
59       return x;
60  }  }
61    
62  SEXP Rsparse_validate(SEXP x)  SEXP Rsparse_validate(SEXP x)
# Line 144  Line 104 
104      return ScalarLogical(1);      return ScalarLogical(1);
105  }  }
106    
107    /** @brief From a CsparseMatrix, produce a dense one.
108  /* Called from ../R/Csparse.R : */   *
109  /* Can only return [dln]geMatrix (no symm/triang);   * Directly deals with symmetric, triangular and general.
110   * FIXME: replace by non-CHOLMOD code ! */   * Called from ../R/Csparse.R's  C2dense()
111  SEXP Csparse_to_dense(SEXP x)   *
112     * @param x a CsparseMatrix: currently all 9 of  "[dln][gst]CMatrix"
113     * @param symm_or_tri integer (NA, < 0, > 0, = 0) specifying the knowledge of the caller about x:
114     *      NA  : unknown => will be determined
115     *      = 0 : "generalMatrix" (not symm or tri);
116     *      < 0 : "triangularMatrix"
117     *      > 0 : "symmetricMatrix"
118     *
119     * @return a "denseMatrix"
120     */
121    SEXP Csparse_to_dense(SEXP x, SEXP symm_or_tri)
122  {  {
123      CHM_SP chxs = AS_CHM_SP__(x);      Rboolean is_sym, is_tri;
124      /* This loses the symmetry property, since cholmod_dense has none,      int is_sym_or_tri = asInteger(symm_or_tri),
125            ctype = 0; // <- default = "dgC"
126        static const char *valid[] = { MATRIX_VALID_Csparse, ""};
127        if(is_sym_or_tri == NA_INTEGER) { // find if  is(x, "symmetricMatrix") :
128            ctype = R_check_class_etc(x, valid);
129            is_sym = (ctype % 3 == 1);
130            is_tri = (ctype % 3 == 2);
131        } else {
132            is_sym = is_sym_or_tri > 0;
133            is_tri = is_sym_or_tri < 0;
134            // => both are FALSE  iff  is_.. == 0
135            if(is_sym || is_tri)
136                ctype = R_check_class_etc(x, valid);
137        }
138        CHM_SP chxs = AS_CHM_SP__(x);// -> chxs->stype = +- 1 <==> symmetric
139        R_CheckStack();
140        if(is_tri && *diag_P(x) == 'U') { // ==>  x := diagU2N(x), directly for chxs
141            CHM_SP eye = cholmod_speye(chxs->nrow, chxs->ncol, chxs->xtype, &c);
142            double one[] = {1, 0};
143            CHM_SP ans = cholmod_add(chxs, eye, one, one,
144                                     /* values: */ ((ctype / 3) != 2), // TRUE iff not "nMatrix"
145                                     TRUE, &c);
146            cholmod_free_sparse(&eye, &c);
147            chxs = cholmod_copy_sparse(ans, &c);
148            cholmod_free_sparse(&ans, &c);
149        }
150        /* The following loses the symmetry property, since cholmod_dense has none,
151       * BUT, much worse (FIXME!), it also transforms CHOLMOD_PATTERN ("n") matrices       * BUT, much worse (FIXME!), it also transforms CHOLMOD_PATTERN ("n") matrices
152       * to numeric (CHOLMOD_REAL) ones : */       * to numeric (CHOLMOD_REAL) ones {and we "revert" via chm_dense_to_SEXP()}: */
153      CHM_DN chxd = cholmod_sparse_to_dense(chxs, &c);      CHM_DN chxd = cholmod_sparse_to_dense(chxs, &c);
154        /* FIXME: The above FAILS for prod(dim(.)) > INT_MAX
155         * ----
156         * TODO: use cholmod_l_* but also the 'cl' global ==> many changes in chm_common.[ch]
157         * >>>>>>>>>>> TODO <<<<<<<<<<<<
158         * CHM_DN chxd = cholmod_l_sparse_to_dense(chxs, &cl); */
159        //                   ^^^ important when prod(dim(.)) > INT_MAX
160      int Rkind = (chxs->xtype == CHOLMOD_PATTERN)? -1 : Real_kind(x);      int Rkind = (chxs->xtype == CHOLMOD_PATTERN)? -1 : Real_kind(x);
     R_CheckStack();  
161    
162      return chm_dense_to_SEXP(chxd, 1, Rkind, GET_SLOT(x, Matrix_DimNamesSym));      SEXP ans = chm_dense_to_SEXP(chxd, 1, Rkind, GET_SLOT(x, Matrix_DimNamesSym),
163                                     /* transp: */ FALSE);
164        // -> a [dln]geMatrix
165        if(is_sym) { // ==> want  [dln]syMatrix
166            const char cl1 = class_P(ans)[0];
167            PROTECT(ans);
168            SEXP aa = PROTECT(NEW_OBJECT(MAKE_CLASS((cl1 == 'd') ? "dsyMatrix" :
169                                                    ((cl1 == 'l') ? "lsyMatrix" : "nsyMatrix"))));
170            // No need to duplicate() as slots of ans are freshly allocated and ans will not be used
171            SET_SLOT(aa, Matrix_xSym,       GET_SLOT(ans, Matrix_xSym));
172            SET_SLOT(aa, Matrix_DimSym,     GET_SLOT(ans, Matrix_DimSym));
173            SET_SLOT(aa, Matrix_DimNamesSym,GET_SLOT(ans, Matrix_DimNamesSym));
174            SET_SLOT(aa, Matrix_uploSym, mkString((chxs->stype > 0) ? "U" : "L"));
175            UNPROTECT(2);
176            return aa;
177        }
178        else if(is_tri) { // ==> want  [dln]trMatrix
179            const char cl1 = class_P(ans)[0];
180            PROTECT(ans);
181            SEXP aa = PROTECT(NEW_OBJECT(MAKE_CLASS((cl1 == 'd') ? "dtrMatrix" :
182                                                    ((cl1 == 'l') ? "ltrMatrix" : "ntrMatrix"))));
183            // No need to duplicate() as slots of ans are freshly allocated and ans will not be used
184            SET_SLOT(aa, Matrix_xSym,       GET_SLOT(ans, Matrix_xSym));
185            SET_SLOT(aa, Matrix_DimSym,     GET_SLOT(ans, Matrix_DimSym));
186            SET_SLOT(aa, Matrix_DimNamesSym,GET_SLOT(ans, Matrix_DimNamesSym));
187            slot_dup(aa, x, Matrix_uploSym);
188            /* already by NEW_OBJECT(..) above:
189               SET_SLOT(aa, Matrix_diagSym, mkString("N")); */
190            UNPROTECT(2);
191            return aa;
192        }
193        else
194            return ans;
195  }  }
196    
197  // FIXME: do not go via CHM (should not be too hard, to just *drop* the x-slot, right?  // FIXME: do not go via CHM (should not be too hard, to just *drop* the x-slot, right?
198  SEXP Csparse_to_nz_pattern(SEXP x, SEXP tri)  SEXP Csparse2nz(SEXP x, Rboolean tri)
199  {  {
200      CHM_SP chxs = AS_CHM_SP__(x);      CHM_SP chxs = AS_CHM_SP__(x);
201      CHM_SP chxcp = cholmod_copy(chxs, chxs->stype, CHOLMOD_PATTERN, &c);      CHM_SP chxcp = cholmod_copy(chxs, chxs->stype, CHOLMOD_PATTERN, &c);
     int tr = asLogical(tri);  
202      R_CheckStack();      R_CheckStack();
203    
204      return chm_sparse_to_SEXP(chxcp, 1/*do_free*/,      return chm_sparse_to_SEXP(chxcp, 1/*do_free*/,
205                                tr ? ((*uplo_P(x) == 'U') ? 1 : -1) : 0,                                tri ? ((*uplo_P(x) == 'U') ? 1 : -1) : 0,
206                                0, tr ? diag_P(x) : "",                                /* Rkind: pattern */ 0,
207                                  /* diag = */ tri ? diag_P(x) : "",
208                                GET_SLOT(x, Matrix_DimNamesSym));                                GET_SLOT(x, Matrix_DimNamesSym));
209  }  }
210    SEXP Csparse_to_nz_pattern(SEXP x, SEXP tri)
211    {
212        int tr_ = asLogical(tri);
213        if(tr_ == NA_LOGICAL) {
214            warning(_("Csparse_to_nz_pattern(x, tri = NA): 'tri' is taken as TRUE"));
215            tr_ = TRUE;
216        }
217        return Csparse2nz(x, (Rboolean) tr_);
218    }
219    
220  // n.CMatrix --> [dli].CMatrix  (not going through CHM!)  // n.CMatrix --> [dli].CMatrix  (not going through CHM!)
221  SEXP nz_pattern_to_Csparse(SEXP x, SEXP res_kind)  SEXP nz_pattern_to_Csparse(SEXP x, SEXP res_kind)
222  {  {
223      return nz2Csparse(x, asInteger(res_kind));      return nz2Csparse(x, asInteger(res_kind));
224  }  }
225    
226  // n.CMatrix --> [dli].CMatrix  (not going through CHM!)  // n.CMatrix --> [dli].CMatrix  (not going through CHM!)
227    // NOTE: use chm_MOD_xtype(() to change type of  'cholmod_sparse' matrix
228  SEXP nz2Csparse(SEXP x, enum x_slot_kind r_kind)  SEXP nz2Csparse(SEXP x, enum x_slot_kind r_kind)
229  {  {
230      const char *cl_x = class_P(x);      const char *cl_x = class_P(x);
231      if(cl_x[0] != 'n') error(_("not a 'n.CMatrix'"));      // quick check - if ok, fast
232      if(cl_x[2] != 'C') error(_("not a CsparseMatrix"));      if(cl_x[0] != 'n' || cl_x[2] != 'C') {
233            // e.g. class = "A", from  setClass("A", contains = "ngCMatrix")
234            static const char *valid[] = { MATRIX_VALID_nCsparse, ""};
235            int ctype = R_check_class_etc(x, valid);
236            if(ctype < 0)
237                error(_("not a 'n.CMatrix'"));
238            else // fine : get a valid  cl_x  class_P()-like string :
239                cl_x = valid[ctype];
240        }
241      int nnz = LENGTH(GET_SLOT(x, Matrix_iSym));      int nnz = LENGTH(GET_SLOT(x, Matrix_iSym));
242      SEXP ans;      SEXP ans;
243      char *ncl = strdup(cl_x);      char *ncl = alloca(strlen(cl_x) + 1); /* not much memory required */
244        strcpy(ncl, cl_x);
245      double *dx_x; int *ix_x;      double *dx_x; int *ix_x;
246      ncl[0] = (r_kind == x_double ? 'd' :      ncl[0] = (r_kind == x_double ? 'd' :
247                (r_kind == x_logical ? 'l' :                (r_kind == x_logical ? 'l' :
248                 /* else (for now):  r_kind == x_integer : */ 'i'));                 /* else (for now):  r_kind == x_integer : */ 'i'));
249      PROTECT(ans = NEW_OBJECT(MAKE_CLASS(ncl)));      PROTECT(ans = NEW_OBJECT_OF_CLASS(ncl));
250      // create a correct 'x' slot:      // create a correct 'x' slot:
251      switch(r_kind) {      switch(r_kind) {
252          int i;          int i;
# Line 228  Line 281 
281      return ans;      return ans;
282  }  }
283    
284  SEXP Csparse_to_matrix(SEXP x)  SEXP Csparse_to_matrix(SEXP x, SEXP chk, SEXP symm)
285  {  {
286      return chm_dense_to_matrix(cholmod_sparse_to_dense(AS_CHM_SP__(x), &c),      int is_sym = asLogical(symm);
287                                 1 /*do_free*/, GET_SLOT(x, Matrix_DimNamesSym));      if(is_sym == NA_LOGICAL) { // find if  is(x, "symmetricMatrix") :
288            static const char *valid[] = { MATRIX_VALID_Csparse, ""};
289            int ctype = R_check_class_etc(x, valid);
290            is_sym = (ctype % 3 == 1);
291        }
292        return chm_dense_to_matrix(
293            cholmod_sparse_to_dense(AS_CHM_SP2(x, asLogical(chk)), &c),
294            1 /*do_free*/,
295            (is_sym
296             ? symmetric_DimNames(GET_SLOT(x, Matrix_DimNamesSym))
297             :                    GET_SLOT(x, Matrix_DimNamesSym)));
298    }
299    
300    SEXP Csparse_to_vector(SEXP x)
301    {
302        return chm_dense_to_vector(cholmod_sparse_to_dense(AS_CHM_SP__(x), &c), 1);
303  }  }
304    
305  SEXP Csparse_to_Tsparse(SEXP x, SEXP tri)  SEXP Csparse_to_Tsparse(SEXP x, SEXP tri)
# Line 248  Line 316 
316                                 GET_SLOT(x, Matrix_DimNamesSym));                                 GET_SLOT(x, Matrix_DimNamesSym));
317  }  }
318    
319  /* this used to be called  sCMatrix_to_gCMatrix(..)   [in ./dsCMatrix.c ]: */  SEXP Csparse_to_tCsparse(SEXP x, SEXP uplo, SEXP diag)
320    {
321        CHM_SP chxs = AS_CHM_SP__(x);
322        int Rkind = (chxs->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
323        R_CheckStack();
324        return chm_sparse_to_SEXP(chxs, /* dofree = */ 0,
325                                  /* uploT = */ (*CHAR(asChar(uplo)) == 'U')? 1: -1,
326                                   Rkind, /* diag = */ CHAR(STRING_ELT(diag, 0)),
327                                   GET_SLOT(x, Matrix_DimNamesSym));
328    }
329    
330    SEXP Csparse_to_tTsparse(SEXP x, SEXP uplo, SEXP diag)
331    {
332        CHM_SP chxs = AS_CHM_SP__(x);
333        CHM_TR chxt = cholmod_sparse_to_triplet(chxs, &c);
334        int Rkind = (chxs->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
335        R_CheckStack();
336        return chm_triplet_to_SEXP(chxt, 1,
337                                  /* uploT = */ (*CHAR(asChar(uplo)) == 'U')? 1: -1,
338                                   Rkind, /* diag = */ CHAR(STRING_ELT(diag, 0)),
339                                   GET_SLOT(x, Matrix_DimNamesSym));
340    }
341    
342    
343  SEXP Csparse_symmetric_to_general(SEXP x)  SEXP Csparse_symmetric_to_general(SEXP x)
344  {  {
345      CHM_SP chx = AS_CHM_SP__(x), chgx;      CHM_SP chx = AS_CHM_SP__(x), chgx;
# Line 258  Line 349 
349      if (!(chx->stype))      if (!(chx->stype))
350          error(_("Nonsymmetric matrix in Csparse_symmetric_to_general"));          error(_("Nonsymmetric matrix in Csparse_symmetric_to_general"));
351      chgx = cholmod_copy(chx, /* stype: */ 0, chx->xtype, &c);      chgx = cholmod_copy(chx, /* stype: */ 0, chx->xtype, &c);
     /* xtype: pattern, "real", complex or .. */  
352      return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",      return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",
353                                GET_SLOT(x, Matrix_DimNamesSym));                                symmetric_DimNames(GET_SLOT(x, Matrix_DimNamesSym)));
354  }  }
355    
356  SEXP Csparse_general_to_symmetric(SEXP x, SEXP uplo)  SEXP Csparse_general_to_symmetric(SEXP x, SEXP uplo, SEXP sym_dmns)
357  {  {
358        int *adims = INTEGER(GET_SLOT(x, Matrix_DimSym)), n = adims[0];
359        if(n != adims[1]) {
360            error(_("Csparse_general_to_symmetric(): matrix is not square!"));
361            return R_NilValue; /* -Wall */
362        }
363      CHM_SP chx = AS_CHM_SP__(x), chgx;      CHM_SP chx = AS_CHM_SP__(x), chgx;
364      int uploT = (*CHAR(STRING_ELT(uplo,0)) == 'U') ? 1 : -1;      int uploT = (*CHAR(asChar(uplo)) == 'U') ? 1 : -1;
365      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
366      R_CheckStack();      R_CheckStack();
   
367      chgx = cholmod_copy(chx, /* stype: */ uploT, chx->xtype, &c);      chgx = cholmod_copy(chx, /* stype: */ uploT, chx->xtype, &c);
368      /* xtype: pattern, "real", complex or .. */  
369      return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",      SEXP dns = GET_SLOT(x, Matrix_DimNamesSym);
370                                GET_SLOT(x, Matrix_DimNamesSym));      if(asLogical(sym_dmns))
371            dns = symmetric_DimNames(dns);
372        else if((!isNull(VECTOR_ELT(dns, 0)) &&
373                 !isNull(VECTOR_ELT(dns, 1))) ||
374                !isNull(getAttrib(dns, R_NamesSymbol))) {
375            /* symmetrize them if both are not NULL
376             * or names(dimnames(.)) is asymmetric : */
377            dns = PROTECT(duplicate(dns));
378            if(!equal_string_vectors(VECTOR_ELT(dns, 0),
379                                     VECTOR_ELT(dns, 1))) {
380                if(uploT == 1)
381                    SET_VECTOR_ELT(dns, 0, VECTOR_ELT(dns,1));
382                else
383                    SET_VECTOR_ELT(dns, 1, VECTOR_ELT(dns,0));
384            }
385            SEXP nms_dns = getAttrib(dns, R_NamesSymbol);
386            if(!isNull(nms_dns) &&  // names(dimnames(.)) :
387               !R_compute_identical(STRING_ELT(nms_dns, 0),
388                                    STRING_ELT(nms_dns, 1), 16)) {
389                if(uploT == 1)
390                    SET_STRING_ELT(nms_dns, 0, STRING_ELT(nms_dns,1));
391                else
392                    SET_STRING_ELT(nms_dns, 1, STRING_ELT(nms_dns,0));
393                setAttrib(dns, R_NamesSymbol, nms_dns);
394            }
395            UNPROTECT(1);
396        }
397        /* Rkind: pattern, "real", complex or .. */
398        return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "", dns);
399  }  }
400    
401  SEXP Csparse_transpose(SEXP x, SEXP tri)  SEXP Csparse_transpose(SEXP x, SEXP tri)
# Line 290  Line 412 
412      tmp = VECTOR_ELT(dn, 0);    /* swap the dimnames */      tmp = VECTOR_ELT(dn, 0);    /* swap the dimnames */
413      SET_VECTOR_ELT(dn, 0, VECTOR_ELT(dn, 1));      SET_VECTOR_ELT(dn, 0, VECTOR_ELT(dn, 1));
414      SET_VECTOR_ELT(dn, 1, tmp);      SET_VECTOR_ELT(dn, 1, tmp);
415        tmp = PROTECT(getAttrib(dn, R_NamesSymbol));
416        if(!isNull(tmp)) { // swap names(dimnames(.)):
417            SEXP nms_dns = PROTECT(allocVector(VECSXP, 2));
418            SET_VECTOR_ELT(nms_dns, 1, STRING_ELT(tmp, 0));
419            SET_VECTOR_ELT(nms_dns, 0, STRING_ELT(tmp, 1));
420            setAttrib(dn, R_NamesSymbol, nms_dns);
421      UNPROTECT(1);      UNPROTECT(1);
422      return chm_sparse_to_SEXP(chxt, 1, /* SWAP 'uplo' for triangular */      }
423    
424        SEXP ans = chm_sparse_to_SEXP(chxt, 1, /* SWAP 'uplo' for triangular */
425                                tr ? ((*uplo_P(x) == 'U') ? -1 : 1) : 0,                                tr ? ((*uplo_P(x) == 'U') ? -1 : 1) : 0,
426                                Rkind, tr ? diag_P(x) : "", dn);                                Rkind, tr ? diag_P(x) : "", dn);
427        UNPROTECT(2);
428        return ans;
429  }  }
430    
431  SEXP Csparse_Csparse_prod(SEXP a, SEXP b)  /** @brief  A %*% B  - for matrices of class CsparseMatrix (R package "Matrix")
432     *
433     * @param a
434     * @param b
435     * @param bool_arith
436     *
437     * @return
438     *
439     * NOTA BENE:  cholmod_ssmult(A,B, ...) ->  ./CHOLMOD/MatrixOps/cholmod_ssmult.c
440     * ---------  computes a patter*n* matrix __always_ when
441     * *one* of A or B is pattern*n*, because of this (line 73-74):
442       ---------------------------------------------------------------------------
443        values = values &&
444            (A->xtype != CHOLMOD_PATTERN) && (B->xtype != CHOLMOD_PATTERN) ;
445       ---------------------------------------------------------------------------
446     * ==> Often need to copy the patter*n* to a *l*ogical matrix first !!!
447     */
448    SEXP Csparse_Csparse_prod(SEXP a, SEXP b, SEXP bool_arith)
449  {  {
450      CHM_SP      CHM_SP
451          cha = AS_CHM_SP(a),          cha = AS_CHM_SP(a),
452          chb = AS_CHM_SP(b),          chb = AS_CHM_SP(b), chc;
         chc = cholmod_ssmult(cha, chb, /*out_stype:*/ 0,  
                                /* values:= is_numeric (T/F) */ cha->xtype > 0,  
                                /*out sorted:*/ 1, &c);  
     const char *cl_a = class_P(a), *cl_b = class_P(b);  
     char diag[] = {'\0', '\0'};  
     int uploT = 0;  
     SEXP dn = PROTECT(allocVector(VECSXP, 2));  
453      R_CheckStack();      R_CheckStack();
454        static const char *valid_tri[] = { MATRIX_VALID_tri_Csparse, "" };
455        char diag[] = {'\0', '\0'};
456        int uploT = 0, nprot = 1,
457            do_bool = asLogical(bool_arith); // TRUE / NA / FALSE
458        Rboolean
459            a_is_n = (cha->xtype == CHOLMOD_PATTERN),
460            b_is_n = (chb->xtype == CHOLMOD_PATTERN),
461            force_num = (do_bool == FALSE),
462            maybe_bool= (do_bool == NA_LOGICAL);
463    
464  #ifdef DEBUG_Matrix_verbose  #ifdef DEBUG_Matrix_verbose
465      Rprintf("DBG Csparse_C*_prod(%s, %s)\n", cl_a, cl_b);      Rprintf("DBG Csparse_C*_prod(%s, %s)\n", class_P(a), class_P(b));
466  #endif  #endif
467    
468        if(a_is_n && (force_num || (maybe_bool && !b_is_n))) {
469            /* coerce 'a' to  double;
470             * have no CHOLMOD function (pattern -> logical) --> use "our" code */
471            SEXP da = PROTECT(nz2Csparse(a, x_double)); nprot++;
472            cha = AS_CHM_SP(da);
473            R_CheckStack();
474            a_is_n = FALSE;
475        }
476        else if(b_is_n && (force_num || (maybe_bool && !a_is_n))) {
477            // coerce 'b' to  double
478            SEXP db = PROTECT(nz2Csparse(b, x_double)); nprot++;
479            chb = AS_CHM_SP(db);
480            R_CheckStack();
481            b_is_n = FALSE;
482        }
483        chc = cholmod_ssmult(cha, chb, /*out_stype:*/ 0,
484                             /* values : */ do_bool != TRUE,
485                             /* sorted = TRUE: */ 1, &c);
486    
487      /* Preserve triangularity and even unit-triangularity if appropriate.      /* Preserve triangularity and even unit-triangularity if appropriate.
488       * Note that in that case, the multiplication itself should happen       * Note that in that case, the multiplication itself should happen
489       * faster.  But there's no support for that in CHOLMOD */       * faster.  But there's no support for that in CHOLMOD */
490    
491      /* UGLY hack -- rather should have (fast!) C-level version of      if(R_check_class_etc(a, valid_tri) >= 0 &&
492       *       is(a, "triangularMatrix") etc */         R_check_class_etc(b, valid_tri) >= 0)
     if (cl_a[1] == 't' && cl_b[1] == 't')  
         /* FIXME: fails for "Cholesky","BunchKaufmann"..*/  
493          if(*uplo_P(a) == *uplo_P(b)) { /* both upper, or both lower tri. */          if(*uplo_P(a) == *uplo_P(b)) { /* both upper, or both lower tri. */
494              uploT = (*uplo_P(a) == 'U') ? 1 : -1;              uploT = (*uplo_P(a) == 'U') ? 1 : -1;
495              if(*diag_P(a) == 'U' && *diag_P(b) == 'U') { /* return UNIT-triag. */              if(*diag_P(a) == 'U' && *diag_P(b) == 'U') { /* return UNIT-triag. */
# Line 331  Line 499 
499              }              }
500              else diag[0]= 'N';              else diag[0]= 'N';
501          }          }
502    
503        SEXP dn = PROTECT(allocVector(VECSXP, 2));
504      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
505                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));
506      SET_VECTOR_ELT(dn, 1,      SET_VECTOR_ELT(dn, 1,
507                     duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), 1)));                     duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), 1)));
508      UNPROTECT(1);      UNPROTECT(nprot);
509      return chm_sparse_to_SEXP(chc, 1, uploT, /*Rkind*/0, diag, dn);      return chm_sparse_to_SEXP(chc, 1, uploT, /*Rkind*/0, diag, dn);
510  }  }
511    
512  SEXP Csparse_Csparse_crossprod(SEXP a, SEXP b, SEXP trans)  /** @brief [t]crossprod (<Csparse>, <Csparse>)
513     *
514     * @param a a "CsparseMatrix" object
515     * @param b a "CsparseMatrix" object
516     * @param trans trans = FALSE:  crossprod(a,b)
517     *              trans = TRUE : tcrossprod(a,b)
518     * @param bool_arith logical (TRUE / NA / FALSE): Should boolean arithmetic be used.
519     *
520     * @return a CsparseMatrix, the (t)cross product of a and b.
521     */
522    SEXP Csparse_Csparse_crossprod(SEXP a, SEXP b, SEXP trans, SEXP bool_arith)
523  {  {
524      int tr = asLogical(trans);      int tr = asLogical(trans), nprot = 1,
525            do_bool = asLogical(bool_arith); // TRUE / NA / FALSE
526      CHM_SP      CHM_SP
527          cha = AS_CHM_SP(a),          cha = AS_CHM_SP(a),
528          chb = AS_CHM_SP(b),          chb = AS_CHM_SP(b),
529          chTr, chc;          chTr, chc;
530      const char *cl_a = class_P(a), *cl_b = class_P(b);      R_CheckStack();
531        static const char *valid_tri[] = { MATRIX_VALID_tri_Csparse, "" };
532      char diag[] = {'\0', '\0'};      char diag[] = {'\0', '\0'};
533      int uploT = 0;      int uploT = 0;
534      SEXP dn = PROTECT(allocVector(VECSXP, 2));      Rboolean
535      R_CheckStack();          a_is_n = (cha->xtype == CHOLMOD_PATTERN),
536            b_is_n = (chb->xtype == CHOLMOD_PATTERN),
537            force_num = (do_bool == FALSE),
538            maybe_bool= (do_bool == NA_LOGICAL);
539    
540        if(a_is_n && (force_num || (maybe_bool && !b_is_n))) {
541            // coerce 'a' to  double
542            SEXP da = PROTECT(nz2Csparse(a, x_double)); nprot++;
543            cha = AS_CHM_SP(da);
544            R_CheckStack();
545            // a_is_n = FALSE;
546        }
547        else if(b_is_n && (force_num || (maybe_bool && !a_is_n))) {
548            // coerce 'b' to  double
549            SEXP db = PROTECT(nz2Csparse(b, x_double)); nprot++;
550            chb = AS_CHM_SP(db);
551            R_CheckStack();
552            // b_is_n = FALSE;
553        }
554        else if(do_bool == TRUE) { // Want boolean arithmetic: sufficient if *one* is pattern:
555            if(!a_is_n && !b_is_n) {
556                // coerce 'a' to pattern
557                SEXP da = PROTECT(Csparse2nz(a, /* tri = */
558                                             R_check_class_etc(a, valid_tri) >= 0)); nprot++;
559                cha = AS_CHM_SP(da);
560                R_CheckStack();
561                // a_is_n = TRUE;
562            }
563        }
564      chTr = cholmod_transpose((tr) ? chb : cha, chb->xtype, &c);      chTr = cholmod_transpose((tr) ? chb : cha, chb->xtype, &c);
565      chc = cholmod_ssmult((tr) ? cha : chTr, (tr) ? chTr : chb,      chc = cholmod_ssmult((tr) ? cha : chTr, (tr) ? chTr : chb,
566                           /*out_stype:*/ 0, cha->xtype, /*out sorted:*/ 1, &c);                           /*out_stype:*/ 0, /* values : */ do_bool != TRUE,
567                             /* sorted = TRUE: */ 1, &c);
568      cholmod_free_sparse(&chTr, &c);      cholmod_free_sparse(&chTr, &c);
569    
570      /* Preserve triangularity and unit-triangularity if appropriate;      /* Preserve triangularity and unit-triangularity if appropriate;
571       * see Csparse_Csparse_prod() for comments */       * see Csparse_Csparse_prod() for comments */
572      if (cl_a[1] == 't' && cl_b[1] == 't')      if(R_check_class_etc(a, valid_tri) >= 0 &&
573           R_check_class_etc(b, valid_tri) >= 0)
574          if(*uplo_P(a) != *uplo_P(b)) { /* one 'U', the other 'L' */          if(*uplo_P(a) != *uplo_P(b)) { /* one 'U', the other 'L' */
575              uploT = (*uplo_P(b) == 'U') ? 1 : -1;              uploT = (*uplo_P(b) == 'U') ? 1 : -1;
576              if(*diag_P(a) == 'U' && *diag_P(b) == 'U') { /* return UNIT-triag. */              if(*diag_P(a) == 'U' && *diag_P(b) == 'U') { /* return UNIT-triag. */
# Line 368  Line 579 
579              }              }
580              else diag[0]= 'N';              else diag[0]= 'N';
581          }          }
582    
583        SEXP dn = PROTECT(allocVector(VECSXP, 2));
584      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
585                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), (tr) ? 0 : 1)));                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym),
586                                            (tr) ? 0 : 1)));
587      SET_VECTOR_ELT(dn, 1,      SET_VECTOR_ELT(dn, 1,
588                     duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), (tr) ? 0 : 1)));                     duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym),
589      UNPROTECT(1);                                          (tr) ? 0 : 1)));
590        UNPROTECT(nprot);
591      return chm_sparse_to_SEXP(chc, 1, uploT, /*Rkind*/0, diag, dn);      return chm_sparse_to_SEXP(chc, 1, uploT, /*Rkind*/0, diag, dn);
592  }  }
593    
594  SEXP Csparse_dense_prod(SEXP a, SEXP b)  /**
595     * All (dense * sparse)  Matrix products and cross products
596     *
597     *   f( f(<Csparse>)  %*%  f(<dense>) )   where  f ()  is either t () [tranpose] or the identity.
598     *
599     * @param a CsparseMatrix  (n x m)
600     * @param b numeric vector, matrix, or denseMatrix (m x k) or (k x m)  if `transp` is '2' or 'B'
601     * @param transp character.
602     *        = " " : nothing transposed {apart from a}
603     *        = "2" : "transpose 2nd arg": use  t(b) instead of b (= 2nd argument)
604     *        = "c" : "transpose c":       Return  t(c) instead of c
605     *        = "B" : "transpose both":    use t(b) and return t(c) instead of c
606     * NB: For "2", "c", "B", need to transpose a *dense* matrix, B or C --> chm_transpose_dense()
607     *
608     * @return a dense matrix, the matrix product c = g(a,b) :
609     *
610     *                                                Condition (R)   Condition (C)
611     *   R notation            Math notation          cross  transp   t.a t.b t.ans
612     *   ~~~~~~~~~~~~~~~~~     ~~~~~~~~~~~~~~~~~~     ~~~~~~~~~~~~~   ~~~~~~~~~~~~~
613     *   c <-   a %*%   b      C :=      A B            .       " "    .   .   .
614     *   c <-   a %*% t(b)     C :=      A B'           .       "2"    .   |   .
615     *   c <- t(a %*%   b)     C := (A B)'  = B'A'      .       "c"    .   .   |
616     *   c <- t(a %*% t(b))    C := (A B')' = B A'      .       "B"    .   |   |
617     *
618     *   c <-   t(a) %*%   b   C :=      A'B           TRUE     " "    |   .   .
619     *   c <-   t(a) %*% t(b)  C :=      A'B'          TRUE     "2"    |   |   .
620     *   c <- t(t(a) %*%   b)  C := (A'B)'  = B'A      TRUE     "c"    |   .   |
621     *   c <- t(t(a) %*% t(b)) C := (A'B')' = B A      TRUE     "B"    |   |   |
622     */
623    SEXP Csp_dense_products(SEXP a, SEXP b,
624                            Rboolean transp_a, Rboolean transp_b, Rboolean transp_ans)
625  {  {
626      CHM_SP cha = AS_CHM_SP(a);      CHM_SP cha = AS_CHM_SP(a);
627      SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));      int a_nc = transp_a ? cha->nrow : cha->ncol,
628      CHM_DN chb = AS_CHM_DN(b_M);          a_nr = transp_a ? cha->ncol : cha->nrow;
629      CHM_DN chc = cholmod_allocate_dense(cha->nrow, chb->ncol, cha->nrow,      Rboolean
630                                          chb->xtype, &c);          maybe_transp_b = (a_nc == 1),
631      SEXP dn = PROTECT(allocVector(VECSXP, 2));          b_is_vector = FALSE;
632        /* NOTE: trans_b {<--> "use t(b) instead of b" }
633           ----  "interferes" with the  case automatic treatment of *vector* b.
634           In that case,  t(b) or b is used "whatever make more sense",
635           according to the general R philosophy of treating vectors in matrix products.
636        */
637    
638        /* repeating a "cheap part" of  mMatrix_as_dgeMatrix2(b, .)  to see if
639         * we have a vector that we might 'transpose_if_vector' : */
640        static const char *valid[] = {"_NOT_A_CLASS_", MATRIX_VALID_ddense, ""};
641        /* int ctype = R_check_class_etc(b, valid);
642         * if (ctype > 0)   /.* a ddenseMatrix object */
643        if (R_check_class_etc(b, valid) < 0) {
644            // not a ddenseM*:  is.matrix() or vector:
645            b_is_vector = !isMatrix(b);
646        }
647    
648        if(b_is_vector) {
649            /* determine *if* we want/need to transpose at all:
650             * if (length(b) == ncol(A)) have match: use dim = c(n, 1) (<=> do *not* transp);
651             *  otherwise, try to transpose: ok  if (ncol(A) == 1) [see also above]:  */
652            maybe_transp_b = (LENGTH(b) != a_nc);
653            // Here, we transpose already in mMatrix_as_dge*()  ==> don't do it later:
654            transp_b = FALSE;
655        }
656        SEXP b_M = PROTECT(mMatrix_as_dgeMatrix2(b, maybe_transp_b));
657    
658        CHM_DN chb = AS_CHM_DN(b_M), b_t;
659        R_CheckStack();
660        int ncol_b;
661        if(transp_b) { // transpose b:
662            b_t = cholmod_allocate_dense(chb->ncol, chb->nrow, chb->ncol, chb->xtype, &c);
663            chm_transpose_dense(b_t, chb);
664            ncol_b = b_t->ncol;
665        } else
666            ncol_b = chb->ncol;
667        // Result C {with dim() before it may be transposed}:
668        CHM_DN chc = cholmod_allocate_dense(a_nr, ncol_b, a_nr, chb->xtype, &c);
669      double one[] = {1,0}, zero[] = {0,0};      double one[] = {1,0}, zero[] = {0,0};
670      int nprot = 2;      int nprot = 2;
671      R_CheckStack();  
672      /* Tim Davis, please FIXME:  currently (2010-11) *fails* when  a  is a pattern matrix:*/      /* Tim Davis, please FIXME:  currently (2010-11) *fails* when  a  is a pattern matrix:*/
673      if(cha->xtype == CHOLMOD_PATTERN) {      if(cha->xtype == CHOLMOD_PATTERN) {
674          /* warning(_("Csparse_dense_prod(): cholmod_sdmult() not yet implemented for pattern./ ngCMatrix" */          /* warning(_("Csparse_dense_prod(): cholmod_sdmult() not yet implemented for pattern./ ngCMatrix" */
675          /*        " --> slightly inefficient coercion")); */          /*        " --> slightly inefficient coercion")); */
   
676          // This *fails* to produce a CHOLMOD_REAL ..          // This *fails* to produce a CHOLMOD_REAL ..
677          // CHM_SP chd = cholmod_l_copy(cha, cha->stype, CHOLMOD_REAL, &c);          // CHM_SP chd = cholmod_l_copy(cha, cha->stype, CHOLMOD_REAL, &cl);
678          // --> use our Matrix-classes  
679            // --> use our Matrix-classes: they work:
680          SEXP da = PROTECT(nz2Csparse(a, x_double)); nprot++;          SEXP da = PROTECT(nz2Csparse(a, x_double)); nprot++;
681          cha = AS_CHM_SP(da);          cha = AS_CHM_SP(da);
682      }      }
683      cholmod_sdmult(cha, 0, one, zero, chb, chc, &c);  
684      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */      /* cholmod_sdmult(A, transp, alpha, beta, X,  Y,  &c): depending on transp == 0 / != 0:
685                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));       *  Y := alpha*(A*X) + beta*Y or alpha*(A'*X) + beta*Y;  here, alpha = 1, beta = 0:
686      SET_VECTOR_ELT(dn, 1,       *  Y := A*X  or  A'*X
687                     duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));       *                       NB: always  <sparse> %*% <dense> !
688         */
689        cholmod_sdmult(cha, transp_a, one, zero, (transp_b ? b_t : chb), /* -> */ chc, &c);
690    
691        SEXP dn = PROTECT(allocVector(VECSXP, 2));  /* establish dimnames */
692        SET_VECTOR_ELT(dn, transp_ans ? 1 : 0,
693                       duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), transp_a ? 1 : 0)));
694        SET_VECTOR_ELT(dn, transp_ans ? 0 : 1,
695                       duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym),
696                                            transp_b ? 0 : 1)));
697        if(transp_b) cholmod_free_dense(&b_t, &c);
698      UNPROTECT(nprot);      UNPROTECT(nprot);
699      return chm_dense_to_SEXP(chc, 1, 0, dn);      return chm_dense_to_SEXP(chc, 1, 0, dn, transp_ans);
700  }  }
701    
702  SEXP Csparse_dense_crossprod(SEXP a, SEXP b)  
703    SEXP Csparse_dense_prod(SEXP a, SEXP b, SEXP transp)
704  {  {
705      CHM_SP cha = AS_CHM_SP(a);      return
706      SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));          Csp_dense_products(a, b,
707      CHM_DN chb = AS_CHM_DN(b_M);                  /* transp_a = */ FALSE,
708      CHM_DN chc = cholmod_allocate_dense(cha->ncol, chb->ncol, cha->ncol,                  /* transp_b   = */ (*CHAR(asChar(transp)) == '2' || *CHAR(asChar(transp)) == 'B'),
709                                          chb->xtype, &c);                  /* transp_ans = */ (*CHAR(asChar(transp)) == 'c' || *CHAR(asChar(transp)) == 'B'));
     SEXP dn = PROTECT(allocVector(VECSXP, 2)); int nprot = 2;  
     double one[] = {1,0}, zero[] = {0,0};  
     R_CheckStack();  
     // -- see Csparse_dense_prod() above :  
     if(cha->xtype == CHOLMOD_PATTERN) {  
         SEXP da = PROTECT(nz2Csparse(a, x_double)); nprot++;  
         cha = AS_CHM_SP(da);  
710      }      }
711      cholmod_sdmult(cha, 1, one, zero, chb, chc, &c);  
712      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */  SEXP Csparse_dense_crossprod(SEXP a, SEXP b, SEXP transp)
713                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 1)));  {
714      SET_VECTOR_ELT(dn, 1,      return
715                     duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));          Csp_dense_products(a, b,
716      UNPROTECT(nprot);                  /* transp_a = */ TRUE,
717      return chm_dense_to_SEXP(chc, 1, 0, dn);                  /* transp_b   = */ (*CHAR(asChar(transp)) == '2' || *CHAR(asChar(transp)) == 'B'),
718                    /* transp_ans = */ (*CHAR(asChar(transp)) == 'c' || *CHAR(asChar(transp)) == 'B'));
719  }  }
720    
721  /* Computes   x'x  or  x x' -- *also* for Tsparse (triplet = TRUE)  
722     see Csparse_Csparse_crossprod above for  x'y and x y' */  /** @brief Computes   x'x  or  x x' -- *also* for Tsparse (triplet = TRUE)
723  SEXP Csparse_crossprod(SEXP x, SEXP trans, SEXP triplet)      see Csparse_Csparse_crossprod above for  x'y and x y'
724    */
725    SEXP Csparse_crossprod(SEXP x, SEXP trans, SEXP triplet, SEXP bool_arith)
726  {  {
727      int trip = asLogical(triplet),      int tripl = asLogical(triplet),
728          tr   = asLogical(trans); /* gets reversed because _aat is tcrossprod */          tr   = asLogical(trans), /* gets reversed because _aat is tcrossprod */
729            do_bool = asLogical(bool_arith); // TRUE / NA / FALSE
730  #ifdef AS_CHM_DIAGU2N_FIXED_FINALLY  #ifdef AS_CHM_DIAGU2N_FIXED_FINALLY
731      CHM_TR cht = trip ? AS_CHM_TR(x) : (CHM_TR) NULL;      CHM_TR cht = tripl ? AS_CHM_TR(x) : (CHM_TR) NULL;  int nprot = 1;
732  #else /* workaround needed:*/  #else /* workaround needed:*/
733      SEXP xx = PROTECT(Tsparse_diagU2N(x));      SEXP xx = PROTECT(Tsparse_diagU2N(x));
734      CHM_TR cht = trip ? AS_CHM_TR__(xx) : (CHM_TR) NULL;      CHM_TR cht = tripl ? AS_CHM_TR__(xx) : (CHM_TR) NULL; int nprot = 2;
735  #endif  #endif
736      CHM_SP chcp, chxt,      CHM_SP chcp, chxt, chxc,
737          chx = (trip ?          chx = (tripl ?
738                 cholmod_triplet_to_sparse(cht, cht->nnz, &c) :                 cholmod_triplet_to_sparse(cht, cht->nnz, &c) :
739                 AS_CHM_SP(x));                 AS_CHM_SP(x));
740      SEXP dn = PROTECT(allocVector(VECSXP, 2));      SEXP dn = PROTECT(allocVector(VECSXP, 2));
741      R_CheckStack();      R_CheckStack();
742        Rboolean
743            x_is_n = (chx->xtype == CHOLMOD_PATTERN),
744            x_is_sym = chx->stype != 0,
745            force_num = (do_bool == FALSE);
746    
747        if(x_is_n && force_num) {
748            // coerce 'x' to  double
749            SEXP dx = PROTECT(nz2Csparse(x, x_double)); nprot++;
750            chx = AS_CHM_SP(dx);
751            R_CheckStack();
752        }
753        else if(do_bool == TRUE && !x_is_n) { // Want boolean arithmetic; need patter[n]
754            // coerce 'x' to pattern
755            static const char *valid_tri[] = { MATRIX_VALID_tri_Csparse, "" };
756            SEXP dx = PROTECT(Csparse2nz(x, /* tri = */
757                                         R_check_class_etc(x, valid_tri) >= 0)); nprot++;
758            chx = AS_CHM_SP(dx);
759            R_CheckStack();
760        }
761    
762      if (!tr) chxt = cholmod_transpose(chx, chx->xtype, &c);      if (!tr) chxt = cholmod_transpose(chx, chx->xtype, &c);
763      chcp = cholmod_aat((!tr) ? chxt : chx, (int *) NULL, 0, chx->xtype, &c);  
764        if (x_is_sym) // cholmod_aat() does not like symmetric
765            chxc = cholmod_copy(tr ? chx : chxt, /* stype: */ 0,
766                                chx->xtype, &c);
767        // CHOLMOD/Core/cholmod_aat.c :
768        chcp = cholmod_aat(x_is_sym ? chxc : (tr ? chx : chxt),
769                           (int *) NULL, 0, /* mode: */ chx->xtype, &c);
770      if(!chcp) {      if(!chcp) {
771          UNPROTECT(1);          UNPROTECT(1);
772          error(_("Csparse_crossprod(): error return from cholmod_aat()"));          error(_("Csparse_crossprod(): error return from cholmod_aat()"));
773      }      }
774      cholmod_band_inplace(0, chcp->ncol, chcp->xtype, chcp, &c);      cholmod_band_inplace(0, chcp->ncol, chcp->xtype, chcp, &c);
775      chcp->stype = 1;      chcp->stype = 1; // symmetric
776      if (trip) cholmod_free_sparse(&chx, &c);      if (tripl) cholmod_free_sparse(&chx, &c);
777      if (!tr) cholmod_free_sparse(&chxt, &c);      if (!tr) cholmod_free_sparse(&chxt, &c);
778      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
779                     duplicate(VECTOR_ELT(GET_SLOT(x, Matrix_DimNamesSym),                     duplicate(VECTOR_ELT(GET_SLOT(x, Matrix_DimNamesSym),
780                                          (tr) ? 0 : 1)));                                          (tr) ? 0 : 1)));
781      SET_VECTOR_ELT(dn, 1, duplicate(VECTOR_ELT(dn, 0)));      SET_VECTOR_ELT(dn, 1, duplicate(VECTOR_ELT(dn, 0)));
782  #ifdef AS_CHM_DIAGU2N_FIXED_FINALLY      UNPROTECT(nprot);
783      UNPROTECT(1);      // FIXME: uploT for symmetric ?
 #else  
     UNPROTECT(2);  
 #endif  
784      return chm_sparse_to_SEXP(chcp, 1, 0, 0, "", dn);      return chm_sparse_to_SEXP(chcp, 1, 0, 0, "", dn);
785  }  }
786    
787  /* Csparse_drop(x, tol):  drop entries with absolute value < tol, i.e,  /** @brief Csparse_drop(x, tol):  drop entries with absolute value < tol, i.e,
788  *  at least all "explicit" zeros */   *  at least all "explicit" zeros. */
789  SEXP Csparse_drop(SEXP x, SEXP tol)  SEXP Csparse_drop(SEXP x, SEXP tol)
790  {  {
791      const char *cl = class_P(x);      const char *cl = class_P(x);
792      /* dtCMatrix, etc; [1] = the second character =?= 't' for triangular */      /* dtCMatrix, etc; [1] = the second character =?= 't' for triangular */
793      int tr = (cl[1] == 't');      int tr = (cl[1] == 't'); // FIXME - rather  R_check_class_etc(..)
794      CHM_SP chx = AS_CHM_SP__(x);      CHM_SP chx = AS_CHM_SP__(x);
795      CHM_SP ans = cholmod_copy(chx, chx->stype, chx->xtype, &c);      CHM_SP ans = cholmod_copy(chx, chx->stype, chx->xtype, &c);
796      double dtol = asReal(tol);      double dtol = asReal(tol);
# Line 493  Line 805 
805                                GET_SLOT(x, Matrix_DimNamesSym));                                GET_SLOT(x, Matrix_DimNamesSym));
806  }  }
807    
808    /** @brief Horizontal Concatenation -  cbind( <Csparse>,  <Csparse>)
809     */
810  SEXP Csparse_horzcat(SEXP x, SEXP y)  SEXP Csparse_horzcat(SEXP x, SEXP y)
811  {  {
812      CHM_SP chx = AS_CHM_SP__(x), chy = AS_CHM_SP__(y);  #define CSPARSE_CAT(_KIND_)                                             \
813      int Rk_x = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0,      CHM_SP chx = AS_CHM_SP__(x), chy = AS_CHM_SP__(y);                  \
814          Rk_y = (chy->xtype != CHOLMOD_PATTERN) ? Real_kind(y) : 0,      R_CheckStack();                                                     \
815          Rkind = /* logical if both x and y are */ (Rk_x == 1 && Rk_y == 1) ? 1 : 0;      int Rk_x = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : x_pattern, \
816      R_CheckStack();          Rk_y = (chy->xtype != CHOLMOD_PATTERN) ? Real_kind(y) : x_pattern, Rkind; \
817        if(Rk_x == x_pattern || Rk_y == x_pattern) { /* at least one of them is patter"n" */ \
818            if(Rk_x == x_pattern && Rk_y == x_pattern) { /* fine */         \
819            } else { /* only one is a patter"n"                             \
820                      * "Bug" in cholmod_horzcat()/vertcat():               \
821                      * returns patter"n" matrix if one of them is */       \
822                Rboolean ok;                                                \
823                if(Rk_x == x_pattern) {                                     \
824                    ok = chm_MOD_xtype(CHOLMOD_REAL, chx, &c); Rk_x = 0;    \
825                } else if(Rk_y == x_pattern) {                              \
826                    ok = chm_MOD_xtype(CHOLMOD_REAL, chy, &c); Rk_y = 0;    \
827                } else                                                      \
828                    error(_("Impossible Rk_x/Rk_y in Csparse_%s(), please report"), _KIND_); \
829                if(!ok)                                                     \
830                    error(_("chm_MOD_xtype() was not successful in Csparse_%s(), please report"), \
831                          _KIND_);                                          \
832            }                                                               \
833        }                                                                   \
834        Rkind = /* logical if both x and y are */ (Rk_x == 1 && Rk_y == 1) ? 1 : 0
835    
836        CSPARSE_CAT("horzcat");
837        // TODO: currently drops dimnames - and we fix at R level;
838    
     /* TODO: currently drops dimnames - and we fix at R level */  
839      return chm_sparse_to_SEXP(cholmod_horzcat(chx, chy, 1, &c),      return chm_sparse_to_SEXP(cholmod_horzcat(chx, chy, 1, &c),
840                                1, 0, Rkind, "", R_NilValue);                                1, 0, Rkind, "", R_NilValue);
841  }  }
842    
843    /** @brief Vertical Concatenation -  rbind( <Csparse>,  <Csparse>)
844     */
845  SEXP Csparse_vertcat(SEXP x, SEXP y)  SEXP Csparse_vertcat(SEXP x, SEXP y)
846  {  {
847      CHM_SP chx = AS_CHM_SP__(x), chy = AS_CHM_SP__(y);      CSPARSE_CAT("vertcat");
848      int Rk_x = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0,      // TODO: currently drops dimnames - and we fix at R level;
         Rk_y = (chy->xtype != CHOLMOD_PATTERN) ? Real_kind(y) : 0,  
         Rkind = /* logical if both x and y are */ (Rk_x == 1 && Rk_y == 1) ? 1 : 0;  
     R_CheckStack();  
849    
     /* TODO: currently drops dimnames - and we fix at R level */  
850      return chm_sparse_to_SEXP(cholmod_vertcat(chx, chy, 1, &c),      return chm_sparse_to_SEXP(cholmod_vertcat(chx, chy, 1, &c),
851                                1, 0, Rkind, "", R_NilValue);                                1, 0, Rkind, "", R_NilValue);
852  }  }
# Line 565  Line 897 
897      }      }
898      else { /* triangular with diag='N'): now drop the diagonal */      else { /* triangular with diag='N'): now drop the diagonal */
899          /* duplicate, since chx will be modified: */          /* duplicate, since chx will be modified: */
900          CHM_SP chx = AS_CHM_SP__(duplicate(x));          SEXP xx = PROTECT(duplicate(x));
901            CHM_SP chx = AS_CHM_SP__(xx);
902          int uploT = (*uplo_P(x) == 'U') ? 1 : -1,          int uploT = (*uplo_P(x) == 'U') ? 1 : -1,
903              Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;              Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
904          R_CheckStack();          R_CheckStack();
905    
906          chm_diagN2U(chx, uploT, /* do_realloc */ FALSE);          chm_diagN2U(chx, uploT, /* do_realloc */ FALSE);
907    
908          return chm_sparse_to_SEXP(chx, /*dofree*/ 0/* or 1 ?? */,          SEXP ans = chm_sparse_to_SEXP(chx, /*dofree*/ 0/* or 1 ?? */,
909                                    uploT, Rkind, "U",                                    uploT, Rkind, "U",
910                                    GET_SLOT(x, Matrix_DimNamesSym));                                    GET_SLOT(x, Matrix_DimNamesSym));
911            UNPROTECT(1);// only now !
912            return ans;
913      }      }
914  }  }
915    
916  /**  /**
917   * "Indexing" aka subsetting : Compute  x[i,j], also for vectors i and j   * Indexing aka subsetting : Compute  x[i,j], also for vectors i and j
918   * Working via CHOLMOD_submatrix, see ./CHOLMOD/MatrixOps/cholmod_submatrix.c   * Working via CHOLMOD_submatrix, see ./CHOLMOD/MatrixOps/cholmod_submatrix.c
919   * @param x CsparseMatrix   * @param x CsparseMatrix
920   * @param i row     indices (0-origin), or NULL (R's)   * @param i row     indices (0-origin), or NULL (R, not C)
921   * @param j columns indices (0-origin), or NULL   * @param j columns indices (0-origin), or NULL
922   *   *
923   * @return x[i,j]  still CsparseMatrix --- currently, this loses dimnames   * @return x[i,j]  still CsparseMatrix --- currently, this loses dimnames
# Line 600  Line 935 
935      if (csize >= 0 && !isInteger(j))      if (csize >= 0 && !isInteger(j))
936          error(_("Index j must be NULL or integer"));          error(_("Index j must be NULL or integer"));
937    
938      if (chx->stype) /* symmetricMatrix */      /* Must treat 'NA's in i[] and j[] here -- they are *not* treated by Cholmod!
939          /* for now, cholmod_submatrix() only accepts "generalMatrix" */       * haveNA := ...
940          chx = cholmod_copy(chx, /* stype: */ 0, chx->xtype, &c);         if(haveNA) {
941             a. i = removeNA(i); j =removeNA(j), and remember where they were
942      return chm_sparse_to_SEXP(cholmod_submatrix(chx,           b. ans = CHM_SUB(.., i, j)
943                                  (rsize < 0) ? NULL : INTEGER(i), rsize,           c. add NA rows and/or columns to 'ans' according to
944                                  (csize < 0) ? NULL : INTEGER(j), csize,              place of NA's in i and/or j.
945                                                    TRUE, TRUE, &c),         } else {
946                                1, 0, Rkind, "",           ans = CHM_SUB(.....)  // == current code
                               /* FIXME: drops dimnames */ R_NilValue);  
947  }  }
   
 /**  
  * Subassignment:  x[i,j]  <- value  
  *  
  * @param x  
  * @param i_ integer row    index 0-origin vector (as returned from R .ind.prep2())  
  * @param j_ integer column index 0-origin vector  
  * @param value currently must be a dsparseVector {which is recycled if needed}  
  *  
  * @return a Csparse matrix like x, but with the values replaced  
948   */   */
949  SEXP Csparse_subassign(SEXP x, SEXP i_, SEXP j_, SEXP value)  #define CHM_SUB(_M_, _i_, _j_)                                  \
950  {      cholmod_submatrix(_M_,                                      \
951      static const char                        (rsize < 0) ? NULL : INTEGER(_i_), rsize, \
952          *valid_cM [] = {"dgCMatrix",// the only one, for "the moment", more later                        (csize < 0) ? NULL : INTEGER(_j_), csize, \
953                          ""},                        TRUE, TRUE, &c)
954          *valid_spv[] = {"dsparseVector",      CHM_SP ans;
955                          ""};      if (!chx->stype) {/* non-symmetric Matrix */
956            ans = CHM_SUB(chx, i, j);
957        }
958        else { /* symmetric : "dsCMatrix";
959                  currently, cholmod_submatrix() only accepts "generalMatrix" */
960            CHM_SP tmp = cholmod_copy(chx, /* stype: */ 0, chx->xtype, &c);
961            ans = CHM_SUB(tmp, i, j);
962            cholmod_free_sparse(&tmp, &c);
963        }
964    
965        // "FIXME": currently dropping dimnames, and adding them afterwards in R :
966        /* // dimnames: */
967        /* SEXP x_dns = GET_SLOT(x, Matrix_DimNamesSym), */
968        /*  dn = PROTECT(allocVector(VECSXP, 2)); */
969        return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "", /* dimnames: */ R_NilValue);
970    }
971    #undef CHM_SUB
972    
973    #define _d_Csp_
974    #include "t_Csparse_subassign.c"
975    
976    #define _l_Csp_
977    #include "t_Csparse_subassign.c"
978    
979      int ctype = Matrix_check_class_etc(x, valid_cM);  #define _i_Csp_
980      if (ctype < 0)  #include "t_Csparse_subassign.c"
         error(_("invalid class of 'x' in Csparse_subassign()"));  
     // value: assume a  "dsparseVector" for now -- slots: (i, length, x)  
     ctype = Matrix_check_class_etc(value, valid_spv);  
     if (ctype < 0)  
         error(_("invalid class of 'value' in Csparse_subassign()"));  
   
     SEXP ans,  
         pslot = GET_SLOT(x, Matrix_pSym),  
         islot = GET_SLOT(x, Matrix_iSym),  
         i_cp = PROTECT((TYPEOF(i_) == INTSXP) ?  
                        duplicate(i_) : coerceVector(i_, INTSXP)),  
         j_cp = PROTECT((TYPEOF(j_) == INTSXP) ?  
                        duplicate(j_) : coerceVector(j_, INTSXP)),  
         // for d.CMatrix and l.CMatrix  but not n.CMatrix:  
         xslot = GET_SLOT(x, Matrix_xSym);  
   
     int *dims = INTEGER(GET_SLOT(x, Matrix_DimSym)),  
         nrow = dims[0],  
         ncol = dims[1],  
         *xp = INTEGER(pslot),  
         *xi = INTEGER(islot),  
         *ii = INTEGER(i_cp), len_i = LENGTH(i_cp),  
         *jj = INTEGER(j_cp), len_j = LENGTH(j_cp),  
         i, j, k;  
     int    *val_i = INTEGER(GET_SLOT(value, Matrix_iSym));  
     // for dsparseVector only:  
     double *val_x =   REAL (GET_SLOT(value, Matrix_xSym));  
     int len_val = asInteger(GET_SLOT(value, Matrix_lengthSym));  
     int p_last = xp[0];  
   
     // for d.CMatrix only:  
     double *xx = REAL(xslot);  
     double ind; // the index that goes all the way from 1:(len_i * len_j)  
   
     PROTECT(ans = duplicate(x));  
     for(j = 0; j < ncol; j++) {  
 // FIXME  
 // ....  
 // ....  
 // ....  
 // ....  
981    
982    #define _n_Csp_
983    #include "t_Csparse_subassign.c"
984    
985    #define _z_Csp_
986    #include "t_Csparse_subassign.c"
987    
988    
989    
   
   
 // ....  
 // ....  
 // ....  
 // ....  
 // ....  
     }  
     UNPROTECT(3);  
     return ans;  
 }  
   
990  SEXP Csparse_MatrixMarket(SEXP x, SEXP fname)  SEXP Csparse_MatrixMarket(SEXP x, SEXP fname)
991  {  {
992      FILE *f = fopen(CHAR(asChar(fname)), "w");      FILE *f = fopen(CHAR(asChar(fname)), "w");
# Line 717  Line 1014 
1014   *   *
1015   * @return  a SEXP, either a (double) number or a length n-vector of diagonal entries   * @return  a SEXP, either a (double) number or a length n-vector of diagonal entries
1016   */   */
1017  SEXP diag_tC_ptr(int n, int *x_p, double *x_x, int *perm, SEXP resultKind)  SEXP diag_tC_ptr(int n, int *x_p, double *x_x, Rboolean is_U, int *perm,
1018  /*                                ^^^^^^ FIXME[Generalize] to int / ... */  /*                                ^^^^^^ FIXME[Generalize] to int / ... */
1019                     SEXP resultKind)
1020  {  {
1021      const char* res_ch = CHAR(STRING_ELT(resultKind,0));      const char* res_ch = CHAR(STRING_ELT(resultKind,0));
1022      enum diag_kind { diag, diag_backpermuted, trace, prod, sum_log      enum diag_kind { diag, diag_backpermuted, trace, prod, sum_log, min, max, range
1023      } res_kind = ((!strcmp(res_ch, "trace")) ? trace :      } res_kind = ((!strcmp(res_ch, "trace")) ? trace :
1024                    ((!strcmp(res_ch, "sumLog")) ? sum_log :                    ((!strcmp(res_ch, "sumLog")) ? sum_log :
1025                     ((!strcmp(res_ch, "prod")) ? prod :                     ((!strcmp(res_ch, "prod")) ? prod :
1026                        ((!strcmp(res_ch, "min")) ? min :
1027                         ((!strcmp(res_ch, "max")) ? max :
1028                          ((!strcmp(res_ch, "range")) ? range :
1029                      ((!strcmp(res_ch, "diag")) ? diag :                      ((!strcmp(res_ch, "diag")) ? diag :
1030                       ((!strcmp(res_ch, "diagBack")) ? diag_backpermuted :                       ((!strcmp(res_ch, "diagBack")) ? diag_backpermuted :
1031                        -1)))));                           -1))))))));
1032      int i, n_x, i_from = 0;      int i, n_x, i_from;
1033      SEXP ans = PROTECT(allocVector(REALSXP,      SEXP ans = PROTECT(allocVector(REALSXP,
1034  /*                                 ^^^^  FIXME[Generalize] */  /*                                 ^^^^  FIXME[Generalize] */
1035                                     (res_kind == diag ||                                     (res_kind == diag ||
1036                                      res_kind == diag_backpermuted) ? n : 1));                                      res_kind == diag_backpermuted) ? n :
1037                                       (res_kind == range ? 2 : 1)));
1038      double *v = REAL(ans);      double *v = REAL(ans);
1039  /*  ^^^^^^      ^^^^  FIXME[Generalize] */  /*  ^^^^^^      ^^^^  FIXME[Generalize] */
1040    
1041        i_from = (is_U ? -1 : 0);
1042    
1043  #define for_DIAG(v_ASSIGN)                                              \  #define for_DIAG(v_ASSIGN)                                              \
1044      for(i = 0; i < n; i++, i_from += n_x) {                             \      for(i = 0; i < n; i++) {                                    \
1045          /* looking at i-th column */                                    \          /* looking at i-th column */                                    \
1046          n_x = x_p[i+1] - x_p[i];/* #{entries} in this column */ \          n_x = x_p[i+1] - x_p[i];/* #{entries} in this column */ \
1047            if( is_U) i_from += n_x;                                \
1048          v_ASSIGN;                                                       \          v_ASSIGN;                                                       \
1049            if(!is_U) i_from += n_x;                                \
1050      }      }
1051    
1052      /* NOTA BENE: we assume  -- uplo = "L" i.e. lower triangular matrix      /* NOTA BENE: we assume  -- uplo = "L" i.e. lower triangular matrix
1053       *            for uplo = "U" (makes sense with a "dtCMatrix" !),       *            for uplo = "U" (makes sense with a "dtCMatrix" !),
1054       *            should use  x_x[i_from + (nx - 1)] instead of x_x[i_from],       *            should use  x_x[i_from + (n_x - 1)] instead of x_x[i_from],
1055       *            where nx = (x_p[i+1] - x_p[i])       *            where n_x = (x_p[i+1] - x_p[i])
1056       */       */
1057    
1058      switch(res_kind) {      switch(res_kind) {
1059      case trace:      case trace: // = sum
1060          v[0] = 0.;          v[0] = 0.;
1061          for_DIAG(v[0] += x_x[i_from]);          for_DIAG(v[0] += x_x[i_from]);
1062          break;          break;
# Line 765  Line 1071 
1071          for_DIAG(v[0] *= x_x[i_from]);          for_DIAG(v[0] *= x_x[i_from]);
1072          break;          break;
1073    
1074        case min:
1075            v[0] = R_PosInf;
1076            for_DIAG(if(v[0] > x_x[i_from]) v[0] = x_x[i_from]);
1077            break;
1078    
1079        case max:
1080            v[0] = R_NegInf;
1081            for_DIAG(if(v[0] < x_x[i_from]) v[0] = x_x[i_from]);
1082            break;
1083    
1084        case range:
1085            v[0] = R_PosInf;
1086            v[1] = R_NegInf;
1087            for_DIAG(if(v[0] > x_x[i_from]) v[0] = x_x[i_from];
1088                     if(v[1] < x_x[i_from]) v[1] = x_x[i_from]);
1089            break;
1090    
1091      case diag:      case diag:
1092          for_DIAG(v[i] = x_x[i_from]);          for_DIAG(v[i] = x_x[i_from]);
1093          break;          break;
# Line 772  Line 1095 
1095      case diag_backpermuted:      case diag_backpermuted:
1096          for_DIAG(v[i] = x_x[i_from]);          for_DIAG(v[i] = x_x[i_from]);
1097    
1098          warning(_("resultKind = 'diagBack' (back-permuted) is experimental"));          warning(_("%s = '%s' (back-permuted) is experimental"),
1099                    "resultKind", "diagBack");
1100          /* now back_permute : */          /* now back_permute : */
1101          for(i = 0; i < n; i++) {          for(i = 0; i < n; i++) {
1102              double tmp = v[i]; v[i] = v[perm[i]]; v[perm[i]] = tmp;              double tmp = v[i]; v[i] = v[perm[i]]; v[perm[i]] = tmp;
# Line 793  Line 1117 
1117   * Extract the diagonal entries from *triangular* Csparse matrix  __or__ a   * Extract the diagonal entries from *triangular* Csparse matrix  __or__ a
1118   * cholmod_sparse factor (LDL = TRUE).   * cholmod_sparse factor (LDL = TRUE).
1119   *   *
1120     * @param obj -- now a cholmod_sparse factor or a dtCMatrix
1121   * @param pslot  'p' (column pointer)   slot of Csparse matrix/factor   * @param pslot  'p' (column pointer)   slot of Csparse matrix/factor
1122   * @param xslot  'x' (non-zero entries) slot of Csparse matrix/factor   * @param xslot  'x' (non-zero entries) slot of Csparse matrix/factor
1123   * @param perm_slot  'perm' (= permutation vector) slot of corresponding CHMfactor;   * @param perm_slot  'perm' (= permutation vector) slot of corresponding CHMfactor;
# Line 801  Line 1126 
1126   *   *
1127   * @return  a SEXP, either a (double) number or a length n-vector of diagonal entries   * @return  a SEXP, either a (double) number or a length n-vector of diagonal entries
1128   */   */
1129  SEXP diag_tC(SEXP pslot, SEXP xslot, SEXP perm_slot, SEXP resultKind)  SEXP diag_tC(SEXP obj, SEXP resultKind)
1130  {  {
1131    
1132        SEXP
1133            pslot = GET_SLOT(obj, Matrix_pSym),
1134            xslot = GET_SLOT(obj, Matrix_xSym);
1135        Rboolean is_U = (R_has_slot(obj, Matrix_uploSym) &&
1136                         *CHAR(asChar(GET_SLOT(obj, Matrix_uploSym))) == 'U');
1137      int n = length(pslot) - 1, /* n = ncol(.) = nrow(.) */      int n = length(pslot) - 1, /* n = ncol(.) = nrow(.) */
1138          *x_p  = INTEGER(pslot),          *x_p  = INTEGER(pslot), pp = -1, *perm;
         *perm = INTEGER(perm_slot);  
1139      double *x_x = REAL(xslot);      double *x_x = REAL(xslot);
1140  /*  ^^^^^^        ^^^^ FIXME[Generalize] to INTEGER(.) / LOGICAL(.) / ... xslot !*/  /*  ^^^^^^        ^^^^ FIXME[Generalize] to INTEGER(.) / LOGICAL(.) / ... xslot !*/
1141    
1142      return diag_tC_ptr(n, x_p, x_x, perm, resultKind);      if(R_has_slot(obj, Matrix_permSym))
1143            perm = INTEGER(GET_SLOT(obj, Matrix_permSym));
1144        else perm = &pp;
1145    
1146        return diag_tC_ptr(n, x_p, x_x, is_U, perm, resultKind);
1147  }  }
1148    
1149    
1150  /**  /**
1151   * Create a Csparse matrix object from indices and/or pointers.   * Create a Csparse matrix object from indices and/or pointers.
1152   *   *
# Line 835  Line 1170 
1170                      int index1)                      int index1)
1171  {  {
1172      SEXP ans;      SEXP ans;
1173      int *ij = (int*)NULL, *tri, *trj,      int *ij = (int*)NULL, *tri, *trj, nrow = -1, ncol = -1;
         mi, mj, mp, nrow = -1, ncol = -1;  
1174      int xtype = -1;             /* -Wall */      int xtype = -1;             /* -Wall */
1175      CHM_TR T;      CHM_TR T;
1176      CHM_SP A;      CHM_SP A;
# Line 844  Line 1178 
1178      if (np < 0 || nnz < 0)      if (np < 0 || nnz < 0)
1179          error(_("negative vector lengths not allowed: np = %d, nnz = %d"),          error(_("negative vector lengths not allowed: np = %d, nnz = %d"),
1180                np, nnz);                np, nnz);
1181      if (1 != ((mi = (i == (int*)NULL)) +      int mi = (i == (int*)NULL), // := missing 'i'
1182                (mj = (j == (int*)NULL)) +          mj = (j == (int*)NULL), // := missing 'j'
1183                (mp = (p == (int*)NULL))))          mp = (p == (int*)NULL); // := missing 'p'
1184        if ((mi + mj + mp) != 1)
1185          error(_("exactly 1 of 'i', 'j' or 'p' must be NULL"));          error(_("exactly 1 of 'i', 'j' or 'p' must be NULL"));
1186      if (mp) {      if (mp) {
1187          if (np) error(_("np = %d, must be zero when p is NULL"), np);          if (np) error(_("np = %d, must be zero when p is NULL"), np);
# Line 897  Line 1232 
1232      /* check the class name */      /* check the class name */
1233      if (strlen(cls) != 8)      if (strlen(cls) != 8)
1234          error(_("strlen of cls argument = %d, should be 8"), strlen(cls));          error(_("strlen of cls argument = %d, should be 8"), strlen(cls));
1235      if (!strcmp(cls + 2, "CMatrix"))      if (strcmp(cls + 2, "CMatrix"))
1236          error(_("cls = \"%s\" does not end in \"CMatrix\""), cls);          error(_("cls = \"%s\" does not end in \"CMatrix\""), cls);
1237      switch(cls[0]) {      switch(cls[0]) {
1238      case 'd':      case 'd':
# Line 926  Line 1261 
1261      A = cholmod_triplet_to_sparse(T, nnz, &c);      A = cholmod_triplet_to_sparse(T, nnz, &c);
1262      cholmod_free_triplet(&T, &c);      cholmod_free_triplet(&T, &c);
1263      /* copy the information to the SEXP */      /* copy the information to the SEXP */
1264      ans = PROTECT(NEW_OBJECT(MAKE_CLASS(cls)));      ans = PROTECT(NEW_OBJECT_OF_CLASS(cls));
1265  /* FIXME: This has been copied from chm_sparse_to_SEXP in chm_common.c */  // FIXME: This has been copied from chm_sparse_to_SEXP in  chm_common.c
1266      /* allocate and copy common slots */      /* allocate and copy common slots */
1267      nnz = cholmod_nnz(A, &c);      nnz = cholmod_nnz(A, &c);
1268      dims = INTEGER(ALLOC_SLOT(ans, Matrix_DimSym, INTSXP, 2));      dims = INTEGER(ALLOC_SLOT(ans, Matrix_DimSym, INTSXP, 2));
1269      dims[0] = A->nrow; dims[1] = A->ncol;      dims[0] = A->nrow; dims[1] = A->ncol;
1270      Memcpy(INTEGER(ALLOC_SLOT(ans, Matrix_pSym, INTSXP, A->ncol + 1)), (int*)A->p, A->ncol + 1);      Memcpy(INTEGER(ALLOC_SLOT(ans, Matrix_pSym, INTSXP, A->ncol + 1)), (int*)A->p, A->ncol + 1);
1271      Memcpy(INTEGER(ALLOC_SLOT(ans, Matrix_iSym, INTSXP, nnz)), (int*)A->i, nnz);      Memcpy(INTEGER(ALLOC_SLOT(ans, Matrix_iSym, INTSXP, nnz)), (int*)A->i, nnz);
1272      switch(cls[1]) {      switch(cls[0]) {
1273      case 'd':      case 'd':
1274          Memcpy(REAL(ALLOC_SLOT(ans, Matrix_xSym, REALSXP, nnz)), (double*)A->x, nnz);          Memcpy(REAL(ALLOC_SLOT(ans, Matrix_xSym, REALSXP, nnz)), (double*)A->x, nnz);
1275          break;          break;
# Line 946  Line 1281 
1281      UNPROTECT(1);      UNPROTECT(1);
1282      return ans;      return ans;
1283  }  }
1284    
1285    /**
1286     * Create a Csparse matrix object from a traditional R matrix
1287     *
1288     * @param x   traditional R matrix (numeric, logical, ...)
1289     * @param cls class (a string)
1290     *
1291     * @return an SEXP of a class inheriting from CsparseMatrix.
1292     */
1293    SEXP matrix_to_Csparse(SEXP x, SEXP cls)
1294    {
1295        if (!isMatrix(x))
1296            error(_("%s must be (traditional R) matrix"), "'x'");
1297        SEXP d_x  = getAttrib(x, R_DimSymbol),
1298            dn_x  = getAttrib(x, R_DimNamesSymbol);
1299        int nr = INTEGER(d_x)[0],
1300            nc = INTEGER(d_x)[1];
1301    
1302        if (!(isString(cls) && LENGTH(cls) == 1))
1303            error(_("%s must be character string"), "'cls'");
1304        R_xlen_t ii, n = XLENGTH(x);
1305        int xtype = -1;
1306        if (n != ((R_xlen_t) nr) * nc)
1307            error(_("nrow * ncol = %d * %d must equal length(x) = %ld"), nr, nc, n);
1308    
1309        const char *ccls = CHAR(STRING_ELT(cls, 0));
1310        if (strlen(ccls) != 9)
1311            error(_("strlen of cls argument = %d, should be 9"), strlen(ccls));
1312        if (strcmp(ccls + 2, "CMatrix"))
1313            error(_("cls = \"%s\" does not end in \"CMatrix\""), ccls);
1314        switch(ccls[0]) {
1315        case 'd':
1316        case 'l':
1317            xtype = CHOLMOD_REAL;
1318        break;
1319        case 'n':
1320            xtype = CHOLMOD_PATTERN;
1321            break;
1322        default:
1323            error(_("cls = \"%s\" must begin with 'd', 'l' or 'n' for now"), ccls);
1324        }
1325        /* if (ccls[1] != 'g') */
1326        /*  error(_("Only 'g'eneral sparse matrix types allowed")); */
1327    
1328        SEXP ans = PROTECT(NEW_OBJECT_OF_CLASS(ccls));
1329        SET_SLOT(ans, Matrix_DimSym, d_x);
1330        SET_SLOT(ans, Matrix_DimNamesSym, (!isNull(dn_x) && LENGTH(dn_x) == 2)
1331                 ? duplicate(dn_x)
1332                 : allocVector(VECSXP, 2));
1333    
1334        int nz = 0, // current number of nonzero entries
1335            nnz = imax2(256, imax2(nr,nc));/* nnz := final number of nonzero entries, yet unknown;
1336                                               -- must start with guess and then grow */
1337        int *rp = INTEGER(ALLOC_SLOT(ans, Matrix_pSym, INTSXP, nc + 1)),
1338            *ri = Calloc(nnz, int); // to become i slot -- of not-yet-known length nnz
1339    
1340        rp[0] = 0; // always
1341    
1342        switch(TYPEOF(x)) {
1343        case LGLSXP: {
1344            if(xtype == CHOLMOD_PATTERN) {
1345    #         define _PATTERN_x
1346    #         include "t_matrix_to_Csp.c"
1347            } else {
1348    #         define _LOGICAL_x
1349    #         include "t_matrix_to_Csp.c"
1350            }
1351            break;
1352        }
1353        case REALSXP: {
1354    #       define _DOUBLE_x
1355    #       include "t_matrix_to_Csp.c"
1356            break;
1357        }
1358    /* case INTSXP: we would have to use
1359            x = coerceVector(x, REALSXP));
1360       and then fall through to REALSXP case, but we must *not* modify 'x' here
1361       FIXME: use a macro or (inline?) function with argument (y), where
1362       -----  SEXP y = PROTECT(coerceVector(x, REALSXP))
1363    
1364       ==> give error in INTSXP case, so caller (in R) must set  storage.mode(x) <- "double"
1365    */
1366    #ifdef _USING_INTEGER_NOT_READY__
1367        case INTSXP: {
1368    #       define _INTEGER_x
1369    #       include "t_matrix_to_Csp.c"
1370            break;
1371        }
1372    #endif
1373    #ifdef _USING_COMPLEX_NOT_READY__
1374        case CPLXSXP: {
1375    #       define _COMPLEX_x
1376    #       include "t_matrix_to_Csp.c"
1377            break;
1378        }
1379    #endif
1380        default:
1381            error(_("%s must be a logical or double vector"), "'x'");
1382            break;
1383        }
1384    
1385        Memcpy(INTEGER(ALLOC_SLOT(ans, Matrix_iSym,  INTSXP, nnz)), ri, nnz);
1386        Free(ri);
1387    
1388        UNPROTECT(1);
1389        return ans;
1390    }
1391    
1392    
1393    
1394    

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