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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 2784, Fri Jun 8 17:01:25 2012 UTC revision 3213, Tue Apr 18 20:14:20 2017 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 37  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 145  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' :
# Line 229  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 249  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 261  Line 351 
351      chgx = cholmod_copy(chx, /* stype: */ 0, chx->xtype, &c);      chgx = cholmod_copy(chx, /* stype: */ 0, chx->xtype, &c);
352      /* xtype: pattern, "real", complex or .. */      /* xtype: pattern, "real", complex or .. */
353      return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",      return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",
354                                GET_SLOT(x, Matrix_DimNamesSym));                                symmetric_DimNames(GET_SLOT(x, Matrix_DimNamesSym)));
355  }  }
356    
357  SEXP Csparse_general_to_symmetric(SEXP x, SEXP uplo)  SEXP Csparse_general_to_symmetric(SEXP x, SEXP uplo, SEXP sym_dmns)
358  {  {
359        int *adims = INTEGER(GET_SLOT(x, Matrix_DimSym)), n = adims[0];
360        if(n != adims[1]) {
361            error(_("Csparse_general_to_symmetric(): matrix is not square!"));
362            return R_NilValue; /* -Wall */
363        }
364      CHM_SP chx = AS_CHM_SP__(x), chgx;      CHM_SP chx = AS_CHM_SP__(x), chgx;
365      int uploT = (*CHAR(STRING_ELT(uplo,0)) == 'U') ? 1 : -1;      int uploT = (*CHAR(asChar(uplo)) == 'U') ? 1 : -1;
366      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
367      R_CheckStack();      R_CheckStack();
   
368      chgx = cholmod_copy(chx, /* stype: */ uploT, chx->xtype, &c);      chgx = cholmod_copy(chx, /* stype: */ uploT, chx->xtype, &c);
369    
370        SEXP dns = GET_SLOT(x, Matrix_DimNamesSym);
371        if(asLogical(sym_dmns))
372            dns = symmetric_DimNames(dns);
373        else if((!isNull(VECTOR_ELT(dns, 0)) &&
374                 !isNull(VECTOR_ELT(dns, 1))) ||
375                !isNull(getAttrib(dns, R_NamesSymbol))) {
376            /* symmetrize them if both are not NULL
377             * or names(dimnames(.)) is asymmetric : */
378            dns = PROTECT(duplicate(dns));
379            if(!equal_string_vectors(VECTOR_ELT(dns, 0),
380                                     VECTOR_ELT(dns, 1))) {
381                if(uploT == 1)
382                    SET_VECTOR_ELT(dns, 0, VECTOR_ELT(dns,1));
383                else
384                    SET_VECTOR_ELT(dns, 1, VECTOR_ELT(dns,0));
385            }
386            SEXP nms_dns = getAttrib(dns, R_NamesSymbol);
387            if(!isNull(nms_dns) &&  // names(dimnames(.)) :
388               !R_compute_identical(STRING_ELT(nms_dns, 0),
389                                    STRING_ELT(nms_dns, 1), 16)) {
390                if(uploT == 1)
391                    SET_STRING_ELT(nms_dns, 0, STRING_ELT(nms_dns,1));
392                else
393                    SET_STRING_ELT(nms_dns, 1, STRING_ELT(nms_dns,0));
394                setAttrib(dns, R_NamesSymbol, nms_dns);
395            }
396            UNPROTECT(1);
397        }
398      /* xtype: pattern, "real", complex or .. */      /* xtype: pattern, "real", complex or .. */
399      return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",      return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "", dns);
                               GET_SLOT(x, Matrix_DimNamesSym));  
400  }  }
401    
402  SEXP Csparse_transpose(SEXP x, SEXP tri)  SEXP Csparse_transpose(SEXP x, SEXP tri)
# Line 291  Line 413 
413      tmp = VECTOR_ELT(dn, 0);    /* swap the dimnames */      tmp = VECTOR_ELT(dn, 0);    /* swap the dimnames */
414      SET_VECTOR_ELT(dn, 0, VECTOR_ELT(dn, 1));      SET_VECTOR_ELT(dn, 0, VECTOR_ELT(dn, 1));
415      SET_VECTOR_ELT(dn, 1, tmp);      SET_VECTOR_ELT(dn, 1, tmp);
416        tmp = PROTECT(getAttrib(dn, R_NamesSymbol));
417        if(!isNull(tmp)) { // swap names(dimnames(.)):
418            SEXP nms_dns = PROTECT(allocVector(VECSXP, 2));
419            SET_VECTOR_ELT(nms_dns, 1, STRING_ELT(tmp, 0));
420            SET_VECTOR_ELT(nms_dns, 0, STRING_ELT(tmp, 1));
421            setAttrib(dn, R_NamesSymbol, nms_dns);
422      UNPROTECT(1);      UNPROTECT(1);
423      return chm_sparse_to_SEXP(chxt, 1, /* SWAP 'uplo' for triangular */      }
424    
425        SEXP ans = chm_sparse_to_SEXP(chxt, 1, /* SWAP 'uplo' for triangular */
426                                tr ? ((*uplo_P(x) == 'U') ? -1 : 1) : 0,                                tr ? ((*uplo_P(x) == 'U') ? -1 : 1) : 0,
427                                Rkind, tr ? diag_P(x) : "", dn);                                Rkind, tr ? diag_P(x) : "", dn);
428        UNPROTECT(2);
429        return ans;
430  }  }
431    
432  SEXP Csparse_Csparse_prod(SEXP a, SEXP b)  /** @brief  A %*% B  - for matrices of class CsparseMatrix (R package "Matrix")
433     *
434     * @param a
435     * @param b
436     * @param bool_arith
437     *
438     * @return
439     *
440     * NOTA BENE:  cholmod_ssmult(A,B, ...) ->  ./CHOLMOD/MatrixOps/cholmod_ssmult.c
441     * ---------  computes a patter*n* matrix __always_ when
442     * *one* of A or B is pattern*n*, because of this (line 73-74):
443       ---------------------------------------------------------------------------
444        values = values &&
445            (A->xtype != CHOLMOD_PATTERN) && (B->xtype != CHOLMOD_PATTERN) ;
446       ---------------------------------------------------------------------------
447     * ==> Often need to copy the patter*n* to a *l*ogical matrix first !!!
448     */
449    SEXP Csparse_Csparse_prod(SEXP a, SEXP b, SEXP bool_arith)
450  {  {
451      CHM_SP      CHM_SP
452          cha = AS_CHM_SP(a),          cha = AS_CHM_SP(a),
453          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));  
454      R_CheckStack();      R_CheckStack();
455        static const char *valid_tri[] = { MATRIX_VALID_tri_Csparse, "" };
456        char diag[] = {'\0', '\0'};
457        int uploT = 0, nprot = 1,
458            do_bool = asLogical(bool_arith); // TRUE / NA / FALSE
459        Rboolean
460            a_is_n = (cha->xtype == CHOLMOD_PATTERN),
461            b_is_n = (chb->xtype == CHOLMOD_PATTERN),
462            force_num = (do_bool == FALSE),
463            maybe_bool= (do_bool == NA_LOGICAL);
464    
465  #ifdef DEBUG_Matrix_verbose  #ifdef DEBUG_Matrix_verbose
466      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));
467  #endif  #endif
468    
469        if(a_is_n && (force_num || (maybe_bool && !b_is_n))) {
470            /* coerce 'a' to  double;
471             * have no CHOLMOD function (pattern -> logical) --> use "our" code */
472            SEXP da = PROTECT(nz2Csparse(a, x_double)); nprot++;
473            cha = AS_CHM_SP(da);
474            R_CheckStack();
475            a_is_n = FALSE;
476        }
477        else if(b_is_n && (force_num || (maybe_bool && !a_is_n))) {
478            // coerce 'b' to  double
479            SEXP db = PROTECT(nz2Csparse(b, x_double)); nprot++;
480            chb = AS_CHM_SP(db);
481            R_CheckStack();
482            b_is_n = FALSE;
483        }
484        chc = cholmod_ssmult(cha, chb, /*out_stype:*/ 0,
485                             /* values : */ do_bool != TRUE,
486                             /* sorted = TRUE: */ 1, &c);
487    
488      /* Preserve triangularity and even unit-triangularity if appropriate.      /* Preserve triangularity and even unit-triangularity if appropriate.
489       * Note that in that case, the multiplication itself should happen       * Note that in that case, the multiplication itself should happen
490       * faster.  But there's no support for that in CHOLMOD */       * faster.  But there's no support for that in CHOLMOD */
491    
492      /* UGLY hack -- rather should have (fast!) C-level version of      if(R_check_class_etc(a, valid_tri) >= 0 &&
493       *       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"..*/  
494          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. */
495              uploT = (*uplo_P(a) == 'U') ? 1 : -1;              uploT = (*uplo_P(a) == 'U') ? 1 : -1;
496              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 332  Line 500 
500              }              }
501              else diag[0]= 'N';              else diag[0]= 'N';
502          }          }
503    
504        SEXP dn = PROTECT(allocVector(VECSXP, 2));
505      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
506                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));
507      SET_VECTOR_ELT(dn, 1,      SET_VECTOR_ELT(dn, 1,
508                     duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), 1)));                     duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), 1)));
509      UNPROTECT(1);      UNPROTECT(nprot);
510      return chm_sparse_to_SEXP(chc, 1, uploT, /*Rkind*/0, diag, dn);      return chm_sparse_to_SEXP(chc, 1, uploT, /*Rkind*/0, diag, dn);
511  }  }
512    
513  SEXP Csparse_Csparse_crossprod(SEXP a, SEXP b, SEXP trans)  /** @brief [t]crossprod (<Csparse>, <Csparse>)
514     *
515     * @param a a "CsparseMatrix" object
516     * @param b a "CsparseMatrix" object
517     * @param trans trans = FALSE:  crossprod(a,b)
518     *              trans = TRUE : tcrossprod(a,b)
519     * @param bool_arith logical (TRUE / NA / FALSE): Should boolean arithmetic be used.
520     *
521     * @return a CsparseMatrix, the (t)cross product of a and b.
522     */
523    SEXP Csparse_Csparse_crossprod(SEXP a, SEXP b, SEXP trans, SEXP bool_arith)
524  {  {
525      int tr = asLogical(trans);      int tr = asLogical(trans), nprot = 1,
526            do_bool = asLogical(bool_arith); // TRUE / NA / FALSE
527      CHM_SP      CHM_SP
528          cha = AS_CHM_SP(a),          cha = AS_CHM_SP(a),
529          chb = AS_CHM_SP(b),          chb = AS_CHM_SP(b),
530          chTr, chc;          chTr, chc;
531      const char *cl_a = class_P(a), *cl_b = class_P(b);      R_CheckStack();
532        static const char *valid_tri[] = { MATRIX_VALID_tri_Csparse, "" };
533      char diag[] = {'\0', '\0'};      char diag[] = {'\0', '\0'};
534      int uploT = 0;      int uploT = 0;
535      SEXP dn = PROTECT(allocVector(VECSXP, 2));      Rboolean
536      R_CheckStack();          a_is_n = (cha->xtype == CHOLMOD_PATTERN),
537            b_is_n = (chb->xtype == CHOLMOD_PATTERN),
538            force_num = (do_bool == FALSE),
539            maybe_bool= (do_bool == NA_LOGICAL);
540    
541        if(a_is_n && (force_num || (maybe_bool && !b_is_n))) {
542            // coerce 'a' to  double
543            SEXP da = PROTECT(nz2Csparse(a, x_double)); nprot++;
544            cha = AS_CHM_SP(da);
545            R_CheckStack();
546            // a_is_n = FALSE;
547        }
548        else if(b_is_n && (force_num || (maybe_bool && !a_is_n))) {
549            // coerce 'b' to  double
550            SEXP db = PROTECT(nz2Csparse(b, x_double)); nprot++;
551            chb = AS_CHM_SP(db);
552            R_CheckStack();
553            // b_is_n = FALSE;
554        }
555        else if(do_bool == TRUE) { // Want boolean arithmetic: sufficient if *one* is pattern:
556            if(!a_is_n && !b_is_n) {
557                // coerce 'a' to pattern
558                SEXP da = PROTECT(Csparse2nz(a, /* tri = */
559                                             R_check_class_etc(a, valid_tri) >= 0)); nprot++;
560                cha = AS_CHM_SP(da);
561                R_CheckStack();
562                // a_is_n = TRUE;
563            }
564        }
565      chTr = cholmod_transpose((tr) ? chb : cha, chb->xtype, &c);      chTr = cholmod_transpose((tr) ? chb : cha, chb->xtype, &c);
566      chc = cholmod_ssmult((tr) ? cha : chTr, (tr) ? chTr : chb,      chc = cholmod_ssmult((tr) ? cha : chTr, (tr) ? chTr : chb,
567                           /*out_stype:*/ 0, cha->xtype, /*out sorted:*/ 1, &c);                           /*out_stype:*/ 0, /* values : */ do_bool != TRUE,
568                             /* sorted = TRUE: */ 1, &c);
569      cholmod_free_sparse(&chTr, &c);      cholmod_free_sparse(&chTr, &c);
570    
571      /* Preserve triangularity and unit-triangularity if appropriate;      /* Preserve triangularity and unit-triangularity if appropriate;
572       * see Csparse_Csparse_prod() for comments */       * see Csparse_Csparse_prod() for comments */
573      if (cl_a[1] == 't' && cl_b[1] == 't')      if(R_check_class_etc(a, valid_tri) >= 0 &&
574           R_check_class_etc(b, valid_tri) >= 0)
575          if(*uplo_P(a) != *uplo_P(b)) { /* one 'U', the other 'L' */          if(*uplo_P(a) != *uplo_P(b)) { /* one 'U', the other 'L' */
576              uploT = (*uplo_P(b) == 'U') ? 1 : -1;              uploT = (*uplo_P(b) == 'U') ? 1 : -1;
577              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 369  Line 580 
580              }              }
581              else diag[0]= 'N';              else diag[0]= 'N';
582          }          }
583    
584        SEXP dn = PROTECT(allocVector(VECSXP, 2));
585      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
586                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), (tr) ? 0 : 1)));                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym),
587                                            (tr) ? 0 : 1)));
588      SET_VECTOR_ELT(dn, 1,      SET_VECTOR_ELT(dn, 1,
589                     duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), (tr) ? 0 : 1)));                     duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym),
590      UNPROTECT(1);                                          (tr) ? 0 : 1)));
591        UNPROTECT(nprot);
592      return chm_sparse_to_SEXP(chc, 1, uploT, /*Rkind*/0, diag, dn);      return chm_sparse_to_SEXP(chc, 1, uploT, /*Rkind*/0, diag, dn);
593  }  }
594    
595  SEXP Csparse_dense_prod(SEXP a, SEXP b)  /**
596     * All (dense * sparse)  Matrix products and cross products
597     *
598     *   f( f(<Csparse>)  %*%  f(<dense>) )   where  f ()  is either t () [tranpose] or the identity.
599     *
600     * @param a CsparseMatrix  (n x m)
601     * @param b numeric vector, matrix, or denseMatrix (m x k) or (k x m)  if `transp` is '2' or 'B'
602     * @param transp character.
603     *        = " " : nothing transposed {apart from a}
604     *        = "2" : "transpose 2nd arg": use  t(b) instead of b (= 2nd argument)
605     *        = "c" : "transpose c":       Return  t(c) instead of c
606     *        = "B" : "transpose both":    use t(b) and return t(c) instead of c
607     * NB: For "2", "c", "B", need to transpose a *dense* matrix, B or C --> chm_transpose_dense()
608     *
609     * @return a dense matrix, the matrix product c = g(a,b) :
610     *
611     *                                                Condition (R)   Condition (C)
612     *   R notation            Math notation          cross  transp   t.a t.b t.ans
613     *   ~~~~~~~~~~~~~~~~~     ~~~~~~~~~~~~~~~~~~     ~~~~~~~~~~~~~   ~~~~~~~~~~~~~
614     *   c <-   a %*%   b      C :=      A B            .       " "    .   .   .
615     *   c <-   a %*% t(b)     C :=      A B'           .       "2"    .   |   .
616     *   c <- t(a %*%   b)     C := (A B)'  = B'A'      .       "c"    .   .   |
617     *   c <- t(a %*% t(b))    C := (A B')' = B A'      .       "B"    .   |   |
618     *
619     *   c <-   t(a) %*%   b   C :=      A'B           TRUE     " "    |   .   .
620     *   c <-   t(a) %*% t(b)  C :=      A'B'          TRUE     "2"    |   |   .
621     *   c <- t(t(a) %*%   b)  C := (A'B)'  = B'A      TRUE     "c"    |   .   |
622     *   c <- t(t(a) %*% t(b)) C := (A'B')' = B A      TRUE     "B"    |   |   |
623     */
624    SEXP Csp_dense_products(SEXP a, SEXP b,
625                            Rboolean transp_a, Rboolean transp_b, Rboolean transp_ans)
626  {  {
627      CHM_SP cha = AS_CHM_SP(a);      CHM_SP cha = AS_CHM_SP(a);
628      SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));      int a_nc = transp_a ? cha->nrow : cha->ncol,
629      CHM_DN chb = AS_CHM_DN(b_M);          a_nr = transp_a ? cha->ncol : cha->nrow;
630      CHM_DN chc = cholmod_allocate_dense(cha->nrow, chb->ncol, cha->nrow,      Rboolean
631                                          chb->xtype, &c);          maybe_transp_b = (a_nc == 1),
632      SEXP dn = PROTECT(allocVector(VECSXP, 2));          b_is_vector = FALSE;
633        /* NOTE: trans_b {<--> "use t(b) instead of b" }
634           ----  "interferes" with the  case automatic treatment of *vector* b.
635           In that case,  t(b) or b is used "whatever make more sense",
636           according to the general R philosophy of treating vectors in matrix products.
637        */
638    
639        /* repeating a "cheap part" of  mMatrix_as_dgeMatrix2(b, .)  to see if
640         * we have a vector that we might 'transpose_if_vector' : */
641        static const char *valid[] = {"_NOT_A_CLASS_", MATRIX_VALID_ddense, ""};
642        /* int ctype = R_check_class_etc(b, valid);
643         * if (ctype > 0)   /.* a ddenseMatrix object */
644        if (R_check_class_etc(b, valid) < 0) {
645            // not a ddenseM*:  is.matrix() or vector:
646            b_is_vector = !isMatrix(b);
647        }
648    
649        if(b_is_vector) {
650            /* determine *if* we want/need to transpose at all:
651             * if (length(b) == ncol(A)) have match: use dim = c(n, 1) (<=> do *not* transp);
652             *  otherwise, try to transpose: ok  if (ncol(A) == 1) [see also above]:  */
653            maybe_transp_b = (LENGTH(b) != a_nc);
654            // Here, we transpose already in mMatrix_as_dge*()  ==> don't do it later:
655            transp_b = FALSE;
656        }
657        SEXP b_M = PROTECT(mMatrix_as_dgeMatrix2(b, maybe_transp_b));
658    
659        CHM_DN chb = AS_CHM_DN(b_M), b_t;
660        R_CheckStack();
661        int ncol_b;
662        if(transp_b) { // transpose b:
663            b_t = cholmod_allocate_dense(chb->ncol, chb->nrow, chb->ncol, chb->xtype, &c);
664            chm_transpose_dense(b_t, chb);
665            ncol_b = b_t->ncol;
666        } else
667            ncol_b = chb->ncol;
668        // Result C {with dim() before it may be transposed}:
669        CHM_DN chc = cholmod_allocate_dense(a_nr, ncol_b, a_nr, chb->xtype, &c);
670      double one[] = {1,0}, zero[] = {0,0};      double one[] = {1,0}, zero[] = {0,0};
671      int nprot = 2;      int nprot = 2;
672      R_CheckStack();  
673      /* 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:*/
674      if(cha->xtype == CHOLMOD_PATTERN) {      if(cha->xtype == CHOLMOD_PATTERN) {
675          /* warning(_("Csparse_dense_prod(): cholmod_sdmult() not yet implemented for pattern./ ngCMatrix" */          /* warning(_("Csparse_dense_prod(): cholmod_sdmult() not yet implemented for pattern./ ngCMatrix" */
# Line 399  Line 681 
681          SEXP da = PROTECT(nz2Csparse(a, x_double)); nprot++;          SEXP da = PROTECT(nz2Csparse(a, x_double)); nprot++;
682          cha = AS_CHM_SP(da);          cha = AS_CHM_SP(da);
683      }      }
684      cholmod_sdmult(cha, 0, one, zero, chb, chc, &c);  
685      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */      /* cholmod_sdmult(A, transp, alpha, beta, X,  Y,  &c): depending on transp == 0 / != 0:
686                     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:
687      SET_VECTOR_ELT(dn, 1,       *  Y := A*X  or  A'*X
688                     duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));       *                       NB: always  <sparse> %*% <dense> !
689         */
690        cholmod_sdmult(cha, transp_a, one, zero, (transp_b ? b_t : chb), /* -> */ chc, &c);
691    
692        SEXP dn = PROTECT(allocVector(VECSXP, 2));  /* establish dimnames */
693        SET_VECTOR_ELT(dn, transp_ans ? 1 : 0,
694                       duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), transp_a ? 1 : 0)));
695        SET_VECTOR_ELT(dn, transp_ans ? 0 : 1,
696                       duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym),
697                                            transp_b ? 0 : 1)));
698        if(transp_b) cholmod_free_dense(&b_t, &c);
699      UNPROTECT(nprot);      UNPROTECT(nprot);
700      return chm_dense_to_SEXP(chc, 1, 0, dn);      return chm_dense_to_SEXP(chc, 1, 0, dn, transp_ans);
701  }  }
702    
703  SEXP Csparse_dense_crossprod(SEXP a, SEXP b)  
704    SEXP Csparse_dense_prod(SEXP a, SEXP b, SEXP transp)
705  {  {
706      CHM_SP cha = AS_CHM_SP(a);      return
707      SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));          Csp_dense_products(a, b,
708      CHM_DN chb = AS_CHM_DN(b_M);                  /* transp_a = */ FALSE,
709      CHM_DN chc = cholmod_allocate_dense(cha->ncol, chb->ncol, cha->ncol,                  /* transp_b   = */ (*CHAR(asChar(transp)) == '2' || *CHAR(asChar(transp)) == 'B'),
710                                          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);  
711      }      }
712      cholmod_sdmult(cha, 1, one, zero, chb, chc, &c);  
713      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */  SEXP Csparse_dense_crossprod(SEXP a, SEXP b, SEXP transp)
714                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 1)));  {
715      SET_VECTOR_ELT(dn, 1,      return
716                     duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));          Csp_dense_products(a, b,
717      UNPROTECT(nprot);                  /* transp_a = */ TRUE,
718      return chm_dense_to_SEXP(chc, 1, 0, dn);                  /* transp_b   = */ (*CHAR(asChar(transp)) == '2' || *CHAR(asChar(transp)) == 'B'),
719                    /* transp_ans = */ (*CHAR(asChar(transp)) == 'c' || *CHAR(asChar(transp)) == 'B'));
720  }  }
721    
722  /* Computes   x'x  or  x x' -- *also* for Tsparse (triplet = TRUE)  
723     see Csparse_Csparse_crossprod above for  x'y and x y' */  /** @brief Computes   x'x  or  x x' -- *also* for Tsparse (triplet = TRUE)
724  SEXP Csparse_crossprod(SEXP x, SEXP trans, SEXP triplet)      see Csparse_Csparse_crossprod above for  x'y and x y'
725    */
726    SEXP Csparse_crossprod(SEXP x, SEXP trans, SEXP triplet, SEXP bool_arith)
727  {  {
728      int trip = asLogical(triplet),      int tripl = asLogical(triplet),
729          tr   = asLogical(trans); /* gets reversed because _aat is tcrossprod */          tr   = asLogical(trans), /* gets reversed because _aat is tcrossprod */
730            do_bool = asLogical(bool_arith); // TRUE / NA / FALSE
731  #ifdef AS_CHM_DIAGU2N_FIXED_FINALLY  #ifdef AS_CHM_DIAGU2N_FIXED_FINALLY
732      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;
733  #else /* workaround needed:*/  #else /* workaround needed:*/
734      SEXP xx = PROTECT(Tsparse_diagU2N(x));      SEXP xx = PROTECT(Tsparse_diagU2N(x));
735      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;
736  #endif  #endif
737      CHM_SP chcp, chxt,      CHM_SP chcp, chxt, chxc,
738          chx = (trip ?          chx = (tripl ?
739                 cholmod_triplet_to_sparse(cht, cht->nnz, &c) :                 cholmod_triplet_to_sparse(cht, cht->nnz, &c) :
740                 AS_CHM_SP(x));                 AS_CHM_SP(x));
741      SEXP dn = PROTECT(allocVector(VECSXP, 2));      SEXP dn = PROTECT(allocVector(VECSXP, 2));
742      R_CheckStack();      R_CheckStack();
743        Rboolean
744            x_is_n = (chx->xtype == CHOLMOD_PATTERN),
745            x_is_sym = chx->stype != 0,
746            force_num = (do_bool == FALSE);
747    
748        if(x_is_n && force_num) {
749            // coerce 'x' to  double
750            SEXP dx = PROTECT(nz2Csparse(x, x_double)); nprot++;
751            chx = AS_CHM_SP(dx);
752            R_CheckStack();
753        }
754        else if(do_bool == TRUE && !x_is_n) { // Want boolean arithmetic; need patter[n]
755            // coerce 'x' to pattern
756            static const char *valid_tri[] = { MATRIX_VALID_tri_Csparse, "" };
757            SEXP dx = PROTECT(Csparse2nz(x, /* tri = */
758                                         R_check_class_etc(x, valid_tri) >= 0)); nprot++;
759            chx = AS_CHM_SP(dx);
760            R_CheckStack();
761        }
762    
763      if (!tr) chxt = cholmod_transpose(chx, chx->xtype, &c);      if (!tr) chxt = cholmod_transpose(chx, chx->xtype, &c);
764      chcp = cholmod_aat((!tr) ? chxt : chx, (int *) NULL, 0, chx->xtype, &c);  
765        if (x_is_sym) // cholmod_aat() does not like symmetric
766            chxc = cholmod_copy(tr ? chx : chxt, /* stype: */ 0,
767                                chx->xtype, &c);
768        // CHOLMOD/Core/cholmod_aat.c :
769        chcp = cholmod_aat(x_is_sym ? chxc : (tr ? chx : chxt),
770                           (int *) NULL, 0, /* mode: */ chx->xtype, &c);
771      if(!chcp) {      if(!chcp) {
772          UNPROTECT(1);          UNPROTECT(1);
773          error(_("Csparse_crossprod(): error return from cholmod_aat()"));          error(_("Csparse_crossprod(): error return from cholmod_aat()"));
774      }      }
775      cholmod_band_inplace(0, chcp->ncol, chcp->xtype, chcp, &c);      cholmod_band_inplace(0, chcp->ncol, chcp->xtype, chcp, &c);
776      chcp->stype = 1;      chcp->stype = 1; // symmetric
777      if (trip) cholmod_free_sparse(&chx, &c);      if (tripl) cholmod_free_sparse(&chx, &c);
778      if (!tr) cholmod_free_sparse(&chxt, &c);      if (!tr) cholmod_free_sparse(&chxt, &c);
779      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
780                     duplicate(VECTOR_ELT(GET_SLOT(x, Matrix_DimNamesSym),                     duplicate(VECTOR_ELT(GET_SLOT(x, Matrix_DimNamesSym),
781                                          (tr) ? 0 : 1)));                                          (tr) ? 0 : 1)));
782      SET_VECTOR_ELT(dn, 1, duplicate(VECTOR_ELT(dn, 0)));      SET_VECTOR_ELT(dn, 1, duplicate(VECTOR_ELT(dn, 0)));
783  #ifdef AS_CHM_DIAGU2N_FIXED_FINALLY      UNPROTECT(nprot);
784      UNPROTECT(1);      // FIXME: uploT for symmetric ?
 #else  
     UNPROTECT(2);  
 #endif  
785      return chm_sparse_to_SEXP(chcp, 1, 0, 0, "", dn);      return chm_sparse_to_SEXP(chcp, 1, 0, 0, "", dn);
786  }  }
787    
788  /* 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,
789  *  at least all "explicit" zeros */   *  at least all "explicit" zeros. */
790  SEXP Csparse_drop(SEXP x, SEXP tol)  SEXP Csparse_drop(SEXP x, SEXP tol)
791  {  {
792      const char *cl = class_P(x);      const char *cl = class_P(x);
793      /* dtCMatrix, etc; [1] = the second character =?= 't' for triangular */      /* dtCMatrix, etc; [1] = the second character =?= 't' for triangular */
794      int tr = (cl[1] == 't');      int tr = (cl[1] == 't'); // FIXME - rather  R_check_class_etc(..)
795      CHM_SP chx = AS_CHM_SP__(x);      CHM_SP chx = AS_CHM_SP__(x);
796      CHM_SP ans = cholmod_copy(chx, chx->stype, chx->xtype, &c);      CHM_SP ans = cholmod_copy(chx, chx->stype, chx->xtype, &c);
797      double dtol = asReal(tol);      double dtol = asReal(tol);
# Line 494  Line 806 
806                                GET_SLOT(x, Matrix_DimNamesSym));                                GET_SLOT(x, Matrix_DimNamesSym));
807  }  }
808    
809    /** @brief Horizontal Concatenation -  cbind( <Csparse>,  <Csparse>)
810     */
811  SEXP Csparse_horzcat(SEXP x, SEXP y)  SEXP Csparse_horzcat(SEXP x, SEXP y)
812  {  {
813      CHM_SP chx = AS_CHM_SP__(x), chy = AS_CHM_SP__(y);  #define CSPARSE_CAT(_KIND_)                                             \
814      int Rk_x = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0,      CHM_SP chx = AS_CHM_SP__(x), chy = AS_CHM_SP__(y);                  \
815          Rk_y = (chy->xtype != CHOLMOD_PATTERN) ? Real_kind(y) : 0,      R_CheckStack();                                                     \
816          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) : -3,     \
817      R_CheckStack();          Rk_y = (chy->xtype != CHOLMOD_PATTERN) ? Real_kind(y) : -3, Rkind; \
818        if(Rk_x == -3 || Rk_y == -3) { /* at least one of them is patter"n" */ \
819            if(Rk_x == -3 && Rk_y == -3) { /* fine */                       \
820            } else { /* only one is a patter"n"                             \
821                      * "Bug" in cholmod_horzcat()/vertcat(): returns patter"n" matrix if one of them is */ \
822                Rboolean ok;                                                \
823                if(Rk_x == -3) {                                            \
824                    ok = chm_MOD_xtype(CHOLMOD_REAL, chx, &c); Rk_x = 0;    \
825                } else if(Rk_y == -3) {                                     \
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 574  Line 905 
905    
906          chm_diagN2U(chx, uploT, /* do_realloc */ FALSE);          chm_diagN2U(chx, uploT, /* do_realloc */ FALSE);
907    
908          UNPROTECT(1);          SEXP ans = chm_sparse_to_SEXP(chx, /*dofree*/ 0/* or 1 ?? */,
         return 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 603  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        /* Must treat 'NA's in i[] and j[] here -- they are *not* treated by Cholmod!
939         * haveNA := ...
940           if(haveNA) {
941             a. i = removeNA(i); j =removeNA(j), and remember where they were
942             b. ans = CHM_SUB(.., i, j)
943             c. add NA rows and/or columns to 'ans' according to
944                place of NA's in i and/or j.
945           } else {
946             ans = CHM_SUB(.....)  // == current code
947           }
948         */
949    #define CHM_SUB(_M_, _i_, _j_)                                  \
950        cholmod_submatrix(_M_,                                      \
951                          (rsize < 0) ? NULL : INTEGER(_i_), rsize, \
952                          (csize < 0) ? NULL : INTEGER(_j_), csize, \
953                          TRUE, TRUE, &c)
954        CHM_SP ans;
955      if (!chx->stype) {/* non-symmetric Matrix */      if (!chx->stype) {/* non-symmetric Matrix */
956          return chm_sparse_to_SEXP(cholmod_submatrix(chx,          ans = CHM_SUB(chx, i, j);
                                                     (rsize < 0) ? NULL : INTEGER(i), rsize,  
                                                     (csize < 0) ? NULL : INTEGER(j), csize,  
                                                     TRUE, TRUE, &c),  
                                   1, 0, Rkind, "",  
                                   /* FIXME: drops dimnames */ R_NilValue);  
957      }      }
958                                  /* for now, cholmod_submatrix() only accepts "generalMatrix" */      else { /* symmetric : "dsCMatrix";
959                  currently, cholmod_submatrix() only accepts "generalMatrix" */
960      CHM_SP tmp = cholmod_copy(chx, /* stype: */ 0, chx->xtype, &c);      CHM_SP tmp = cholmod_copy(chx, /* stype: */ 0, chx->xtype, &c);
961      CHM_SP ans = cholmod_submatrix(tmp,          ans = CHM_SUB(tmp, i, j);
                                    (rsize < 0) ? NULL : INTEGER(i), rsize,  
                                    (csize < 0) ? NULL : INTEGER(j), csize,  
                                    TRUE, TRUE, &c);  
962      cholmod_free_sparse(&tmp, &c);      cholmod_free_sparse(&tmp, &c);
     return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "", R_NilValue);  
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_  #define _d_Csp_
974  #include "t_Csparse_subassign.c"  #include "t_Csparse_subassign.c"
975    
# Line 665  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 713  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 742  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 750  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 876  Line 1262 
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(MAKE_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));

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