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

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revision 923, Sun Sep 18 23:41:45 2005 UTC revision 2235, Wed Jul 23 10:24:17 2008 UTC
# Line 1  Line 1 
1                                  /* Sparse matrices in compress column-oriented form */                          /* Sparse matrices in compressed column-oriented form */
2  #include "Csparse.h"  #include "Csparse.h"
3  #ifdef USE_CHOLMOD  #include "Tsparse.h"
4  #include "chm_common.h"  #include "chm_common.h"
 #endif  /* USE_CHOLMOD */  
5    
6  SEXP Csparse_validate(SEXP x)  SEXP Csparse_validate(SEXP x)
7  {  {
8        /* NB: we do *NOT* check a potential 'x' slot here, at all */
9      SEXP pslot = GET_SLOT(x, Matrix_pSym),      SEXP pslot = GET_SLOT(x, Matrix_pSym),
10          islot = GET_SLOT(x, Matrix_iSym);          islot = GET_SLOT(x, Matrix_iSym);
11      int j, ncol = length(pslot) - 1,      Rboolean sorted, strictly;
12        int j, k,
13          *dims = INTEGER(GET_SLOT(x, Matrix_DimSym)),          *dims = INTEGER(GET_SLOT(x, Matrix_DimSym)),
14          nrow, *xp = INTEGER(pslot),          nrow = dims[0],
15            ncol = dims[1],
16            *xp = INTEGER(pslot),
17          *xi = INTEGER(islot);          *xi = INTEGER(islot);
18    
19      nrow = dims[0];      if (length(pslot) != dims[1] + 1)
20      if (length(pslot) <= 0)          return mkString(_("slot p must have length = ncol(.) + 1"));
         return mkString(_("slot p must have length > 0"));  
21      if (xp[0] != 0)      if (xp[0] != 0)
22          return mkString(_("first element of slot p must be zero"));          return mkString(_("first element of slot p must be zero"));
23      if (length(islot) != xp[ncol])      if (length(islot) < xp[ncol]) /* allow larger slots from over-allocation!*/
24          return mkString(_("last element of slot p must match length of slots i and x"));          return
25                mkString(_("last element of slot p must match length of slots i and x"));
26        for (j = 0; j < length(islot); j++) {
27            if (xi[j] < 0 || xi[j] >= nrow)
28                return mkString(_("all row indices must be between 0 and nrow-1"));
29        }
30        sorted = TRUE; strictly = TRUE;
31      for (j = 0; j < ncol; j++) {      for (j = 0; j < ncol; j++) {
32          if (xp[j] > xp[j+1])          if (xp[j] > xp[j+1])
33              return mkString(_("slot p must be non-decreasing"));              return mkString(_("slot p must be non-decreasing"));
34            if(sorted)
35                for (k = xp[j] + 1; k < xp[j + 1]; k++) {
36                    if (xi[k] < xi[k - 1])
37                        sorted = FALSE;
38                    else if (xi[k] == xi[k - 1])
39                        strictly = FALSE;
40      }      }
41      for (j = 0; j < length(islot); j++) {      }
42          if (xi[j] < 0 || xi[j] >= nrow)      if (!sorted) {
43              return mkString(_("all row indices must be between 0 and nrow-1"));          CHM_SP chx = (CHM_SP) alloca(sizeof(cholmod_sparse));
44            R_CheckStack();
45            as_cholmod_sparse(chx, x, FALSE, TRUE); /* includes cholmod_sort() ! */
46            /* as chx = AS_CHM_SP__(x)  but  ^^^^  sorting x in_place (no copying)*/
47    
48            /* Now re-check that row indices are *strictly* increasing
49             * (and not just increasing) within each column : */
50            for (j = 0; j < ncol; j++) {
51                for (k = xp[j] + 1; k < xp[j + 1]; k++)
52                    if (xi[k] == xi[k - 1])
53                        return mkString(_("slot i is not *strictly* increasing inside a column (even after cholmod_sort)"));
54            }
55    
56        } else if(!strictly) {  /* sorted, but not strictly */
57            return mkString(_("slot i is not *strictly* increasing inside a column"));
58      }      }
59      return ScalarLogical(1);      return ScalarLogical(1);
60  }  }
61    
62  SEXP Csparse_to_Tsparse(SEXP x)  SEXP Rsparse_validate(SEXP x)
63  {  {
64  #ifdef USE_CHOLMOD      /* NB: we do *NOT* check a potential 'x' slot here, at all */
65      cholmod_sparse *chxs = as_cholmod_sparse(x);      SEXP pslot = GET_SLOT(x, Matrix_pSym),
66      cholmod_triplet *chxt = cholmod_sparse_to_triplet(chxs, &c);          jslot = GET_SLOT(x, Matrix_jSym);
67        Rboolean sorted, strictly;
68      Free(chxs);      int i, k,
69      return chm_triplet_to_SEXP(chxt, 1);          *dims = INTEGER(GET_SLOT(x, Matrix_DimSym)),
70  #else          nrow = dims[0],
71      error("General conversion requires CHOLMOD");          ncol = dims[1],
72      return R_NilValue;          /* -Wall */          *xp = INTEGER(pslot),
73  #endif  /* USE_CHOLMOD */          *xj = INTEGER(jslot);
74  }  
75        if (length(pslot) != dims[0] + 1)
76  SEXP Csparse_transpose(SEXP x)          return mkString(_("slot p must have length = nrow(.) + 1"));
77  {      if (xp[0] != 0)
78  #ifdef USE_CHOLMOD          return mkString(_("first element of slot p must be zero"));
79      cholmod_sparse *chx = as_cholmod_sparse(x);      if (length(jslot) < xp[nrow]) /* allow larger slots from over-allocation!*/
80      cholmod_sparse *chxt = cholmod_transpose(chx, (int) chx->xtype, &c);          return
81                mkString(_("last element of slot p must match length of slots j and x"));
82      Free(chx);      for (i = 0; i < length(jslot); i++) {
83      return chm_sparse_to_SEXP(chxt, 1);          if (xj[i] < 0 || xj[i] >= ncol)
84  #else              return mkString(_("all column indices must be between 0 and ncol-1"));
85      error("General conversion requires CHOLMOD");      }
86      return R_NilValue;          /* -Wall */      sorted = TRUE; strictly = TRUE;
87  #endif  /* USE_CHOLMOD */      for (i = 0; i < nrow; i++) {
88            if (xp[i] > xp[i+1])
89                return mkString(_("slot p must be non-decreasing"));
90            if(sorted)
91                for (k = xp[i] + 1; k < xp[i + 1]; k++) {
92                    if (xj[k] < xj[k - 1])
93                        sorted = FALSE;
94                    else if (xj[k] == xj[k - 1])
95                        strictly = FALSE;
96                }
97        }
98        if (!sorted)
99            /* cannot easily use cholmod_sort(.) ... -> "error out" :*/
100            return mkString(_("slot j is not increasing inside a column"));
101        else if(!strictly) /* sorted, but not strictly */
102            return mkString(_("slot j is not *strictly* increasing inside a column"));
103    
104        return ScalarLogical(1);
105  }  }
106    
107    
108    /* Called from ../R/Csparse.R : */
109    /* Can only return [dln]geMatrix (no symm/triang);
110     * FIXME: replace by non-CHOLMOD code ! */
111    SEXP Csparse_to_dense(SEXP x)
112    {
113        CHM_SP chxs = AS_CHM_SP__(x);
114        /* This loses the symmetry property, since cholmod_dense has none,
115         * BUT, much worse (FIXME!), it also transforms CHOLMOD_PATTERN ("n") matrices
116         * to numeric (CHOLMOD_REAL) ones : */
117        CHM_DN chxd = cholmod_sparse_to_dense(chxs, &c);
118        int Rkind = (chxs->xtype == CHOLMOD_PATTERN)? -1 : Real_kind(x);
119        R_CheckStack();
120    
121        return chm_dense_to_SEXP(chxd, 1, Rkind, GET_SLOT(x, Matrix_DimNamesSym));
122    }
123    
124    SEXP Csparse_to_nz_pattern(SEXP x, SEXP tri)
125    {
126        CHM_SP chxs = AS_CHM_SP__(x);
127        CHM_SP chxcp = cholmod_copy(chxs, chxs->stype, CHOLMOD_PATTERN, &c);
128        int tr = asLogical(tri);
129        R_CheckStack();
130    
131        return chm_sparse_to_SEXP(chxcp, 1/*do_free*/,
132                                  tr ? ((*uplo_P(x) == 'U') ? 1 : -1) : 0,
133                                  0, tr ? diag_P(x) : "",
134                                  GET_SLOT(x, Matrix_DimNamesSym));
135    }
136    
137    SEXP Csparse_to_matrix(SEXP x)
138    {
139        return chm_dense_to_matrix(cholmod_sparse_to_dense(AS_CHM_SP__(x), &c),
140                                   1 /*do_free*/, GET_SLOT(x, Matrix_DimNamesSym));
141    }
142    
143    SEXP Csparse_to_Tsparse(SEXP x, SEXP tri)
144    {
145        CHM_SP chxs = AS_CHM_SP__(x);
146        CHM_TR chxt = cholmod_sparse_to_triplet(chxs, &c);
147        int tr = asLogical(tri);
148        int Rkind = (chxs->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
149        R_CheckStack();
150    
151        return chm_triplet_to_SEXP(chxt, 1,
152                                   tr ? ((*uplo_P(x) == 'U') ? 1 : -1) : 0,
153                                   Rkind, tr ? diag_P(x) : "",
154                                   GET_SLOT(x, Matrix_DimNamesSym));
155    }
156    
157    /* this used to be called  sCMatrix_to_gCMatrix(..)   [in ./dsCMatrix.c ]: */
158    SEXP Csparse_symmetric_to_general(SEXP x)
159    {
160        CHM_SP chx = AS_CHM_SP__(x), chgx;
161        int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
162        R_CheckStack();
163    
164        if (!(chx->stype))
165            error(_("Nonsymmetric matrix in Csparse_symmetric_to_general"));
166        chgx = cholmod_copy(chx, /* stype: */ 0, chx->xtype, &c);
167        /* xtype: pattern, "real", complex or .. */
168        return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",
169                                  GET_SLOT(x, Matrix_DimNamesSym));
170    }
171    
172    SEXP Csparse_general_to_symmetric(SEXP x, SEXP uplo)
173    {
174        CHM_SP chx = AS_CHM_SP__(x), chgx;
175        int uploT = (*CHAR(STRING_ELT(uplo,0)) == 'U') ? 1 : -1;
176        int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
177        R_CheckStack();
178    
179        chgx = cholmod_copy(chx, /* stype: */ uploT, chx->xtype, &c);
180        /* xtype: pattern, "real", complex or .. */
181        return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",
182                                  GET_SLOT(x, Matrix_DimNamesSym));
183    }
184    
185    SEXP Csparse_transpose(SEXP x, SEXP tri)
186    {
187        /* TODO: lgCMatrix & igC* currently go via double prec. cholmod -
188         *       since cholmod (& cs) lacks sparse 'int' matrices */
189        CHM_SP chx = AS_CHM_SP__(x);
190        int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
191        CHM_SP chxt = cholmod_transpose(chx, chx->xtype, &c);
192        SEXP dn = PROTECT(duplicate(GET_SLOT(x, Matrix_DimNamesSym))), tmp;
193        int tr = asLogical(tri);
194        R_CheckStack();
195    
196        tmp = VECTOR_ELT(dn, 0);    /* swap the dimnames */
197        SET_VECTOR_ELT(dn, 0, VECTOR_ELT(dn, 1));
198        SET_VECTOR_ELT(dn, 1, tmp);
199        UNPROTECT(1);
200        return chm_sparse_to_SEXP(chxt, 1, /* SWAP 'uplo' for triangular */
201                                  tr ? ((*uplo_P(x) == 'U') ? -1 : 1) : 0,
202                                  Rkind, tr ? diag_P(x) : "", dn);
203    }
204    
205  SEXP Csparse_Csparse_prod(SEXP a, SEXP b)  SEXP Csparse_Csparse_prod(SEXP a, SEXP b)
206  {  {
207  #ifdef USE_CHOLMOD      CHM_SP
208      cholmod_sparse *cha = as_cholmod_sparse(a), *chb = as_cholmod_sparse(b);          cha = AS_CHM_SP(a),
209      cholmod_sparse *chc = cholmod_ssmult(cha, chb, 0, (int) cha->xtype, 1, &c);          chb = AS_CHM_SP(b),
210            chc = cholmod_ssmult(cha, chb, /*out_stype:*/ 0,
211      Free(cha); Free(chb);                               cha->xtype, /*out sorted:*/ 1, &c);
212      return chm_sparse_to_SEXP(chc, 1);      const char *cl_a = class_P(a), *cl_b = class_P(b);
213  #else      char diag[] = {'\0', '\0'};
214      error("General multiplication requires CHOLMOD");      int uploT = 0;
215      return R_NilValue;          /* -Wall */      SEXP dn = allocVector(VECSXP, 2);
216  #endif  /* USE_CHOLMOD */      R_CheckStack();
217    
218        /* Preserve triangularity and even unit-triangularity if appropriate.
219         * Note that in that case, the multiplication itself should happen
220         * faster.  But there's no support for that in CHOLMOD */
221    
222        /* UGLY hack -- rather should have (fast!) C-level version of
223         *       is(a, "triangularMatrix") etc */
224        if (cl_a[1] == 't' && cl_b[1] == 't')
225            /* FIXME: fails for "Cholesky","BunchKaufmann"..*/
226            if(*uplo_P(a) == *uplo_P(b)) { /* both upper, or both lower tri. */
227                uploT = (*uplo_P(a) == 'U') ? 1 : -1;
228                if(*diag_P(a) == 'U' && *diag_P(b) == 'U') { /* return UNIT-triag. */
229                    /* "remove the diagonal entries": */
230                    chm_diagN2U(chc, uploT, /* do_realloc */ FALSE);
231                    diag[0]= 'U';
232                }
233                else diag[0]= 'N';
234            }
235        SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
236                       duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));
237        SET_VECTOR_ELT(dn, 1,
238                       duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), 1)));
239        return chm_sparse_to_SEXP(chc, 1, uploT, /*Rkind*/0, diag, dn);
240    }
241    
242    SEXP Csparse_Csparse_crossprod(SEXP a, SEXP b, SEXP trans)
243    {
244        int tr = asLogical(trans);
245        CHM_SP
246            cha = AS_CHM_SP(a),
247            chb = AS_CHM_SP(b),
248            chTr, chc;
249        const char *cl_a = class_P(a), *cl_b = class_P(b);
250        char diag[] = {'\0', '\0'};
251        int uploT = 0;
252        SEXP dn = allocVector(VECSXP, 2);
253        R_CheckStack();
254    
255        chTr = cholmod_transpose((tr) ? chb : cha, chb->xtype, &c);
256        chc = cholmod_ssmult((tr) ? cha : chTr, (tr) ? chTr : chb,
257                             /*out_stype:*/ 0, cha->xtype, /*out sorted:*/ 1, &c);
258        cholmod_free_sparse(&chTr, &c);
259    
260        /* Preserve triangularity and unit-triangularity if appropriate;
261         * see Csparse_Csparse_prod() for comments */
262        if (cl_a[1] == 't' && cl_b[1] == 't')
263            if(*uplo_P(a) != *uplo_P(b)) { /* one 'U', the other 'L' */
264                uploT = (*uplo_P(b) == 'U') ? 1 : -1;
265                if(*diag_P(a) == 'U' && *diag_P(b) == 'U') { /* return UNIT-triag. */
266                    chm_diagN2U(chc, uploT, /* do_realloc */ FALSE);
267                    diag[0]= 'U';
268                }
269                else diag[0]= 'N';
270            }
271    
272        SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
273                       duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), (tr) ? 0 : 1)));
274        SET_VECTOR_ELT(dn, 1,
275                       duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), (tr) ? 0 : 1)));
276        return chm_sparse_to_SEXP(chc, 1, uploT, /*Rkind*/0, diag, dn);
277  }  }
278    
279  SEXP Csparse_dense_prod(SEXP a, SEXP b)  SEXP Csparse_dense_prod(SEXP a, SEXP b)
280  {  {
281  #ifdef USE_CHOLMOD      CHM_SP cha = AS_CHM_SP(a);
282      cholmod_sparse *cha = as_cholmod_sparse(a);      SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));
283      cholmod_dense *chb = as_cholmod_dense(b);      CHM_DN chb = AS_CHM_DN(b_M);
284      cholmod_dense *chc = cholmod_allocate_dense(cha->nrow, chb->ncol,      CHM_DN chc = cholmod_allocate_dense(cha->nrow, chb->ncol, cha->nrow,
285                                                  cha->nrow, chb->xtype, &c);                                          chb->xtype, &c);
286      double alpha = 1, beta = 0;      SEXP dn = PROTECT(allocVector(VECSXP, 2));
287        double one[] = {1,0}, zero[] = {0,0};
288      cholmod_sdmult(cha, 0, &alpha, &beta, chb, chc, &c);      R_CheckStack();
289      Free(cha); Free(chb);  
290      return chm_dense_to_SEXP(chc, 1);      cholmod_sdmult(cha, 0, one, zero, chb, chc, &c);
291  #else      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
292      error("General multiplication requires CHOLMOD");                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));
293      return R_NilValue;          /* -Wall */      SET_VECTOR_ELT(dn, 1,
294  #endif  /* USE_CHOLMOD */                     duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));
295  }      UNPROTECT(2);
296        return chm_dense_to_SEXP(chc, 1, 0, dn);
297  SEXP Csparse_crossprod(SEXP x, SEXP trans)  }
 {  
 #ifdef USE_CHOLMOD  
     int tr = asLogical(trans);  /* gets reversed because _aat is trcrossprod */  
     cholmod_sparse *chx = as_cholmod_sparse(x), *chcp, *chxt;  
   
     if (!tr)  
         chxt = cholmod_transpose(chx, (int) chx->xtype, &c);  
     chcp = cholmod_aat((tr) ? chxt : chx, (int *) NULL, 0, chx->xtype, &c);  
298    
299      Free(chx);  SEXP Csparse_dense_crossprod(SEXP a, SEXP b)
300    {
301        CHM_SP cha = AS_CHM_SP(a);
302        SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));
303        CHM_DN chb = AS_CHM_DN(b_M);
304        CHM_DN chc = cholmod_allocate_dense(cha->ncol, chb->ncol, cha->ncol,
305                                            chb->xtype, &c);
306        SEXP dn = PROTECT(allocVector(VECSXP, 2));
307        double one[] = {1,0}, zero[] = {0,0};
308        R_CheckStack();
309    
310        cholmod_sdmult(cha, 1, one, zero, chb, chc, &c);
311        SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
312                       duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 1)));
313        SET_VECTOR_ELT(dn, 1,
314                       duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));
315        UNPROTECT(2);
316        return chm_dense_to_SEXP(chc, 1, 0, dn);
317    }
318    
319    /* Computes   x'x  or  x x' -- *also* for Tsparse (triplet = TRUE)
320       see Csparse_Csparse_crossprod above for  x'y and x y' */
321    SEXP Csparse_crossprod(SEXP x, SEXP trans, SEXP triplet)
322    {
323        int trip = asLogical(triplet),
324            tr   = asLogical(trans); /* gets reversed because _aat is tcrossprod */
325        CHM_TR cht = trip ? AS_CHM_TR(x) : (CHM_TR) NULL;
326        CHM_SP chcp, chxt,
327            chx = (trip ?
328                   cholmod_triplet_to_sparse(cht, cht->nnz, &c) :
329                   AS_CHM_SP(x));
330        SEXP dn = PROTECT(allocVector(VECSXP, 2));
331        R_CheckStack();
332    
333        if (!tr) chxt = cholmod_transpose(chx, chx->xtype, &c);
334        chcp = cholmod_aat((!tr) ? chxt : chx, (int *) NULL, 0, chx->xtype, &c);
335        if(!chcp) {
336            UNPROTECT(1);
337            error(_("Csparse_crossprod(): error return from cholmod_aat()"));
338        }
339        cholmod_band_inplace(0, chcp->ncol, chcp->xtype, chcp, &c);
340        chcp->stype = 1;
341        if (trip) cholmod_free_sparse(&chx, &c);
342      if (!tr) cholmod_free_sparse(&chxt, &c);      if (!tr) cholmod_free_sparse(&chxt, &c);
343      return chm_sparse_to_SEXP(chcp, 1);      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
344  #else                     duplicate(VECTOR_ELT(GET_SLOT(x, Matrix_DimNamesSym),
345      error("General transpose requires CHOLMOD");                                          (tr) ? 0 : 1)));
346      return R_NilValue;          /* -Wall */      SET_VECTOR_ELT(dn, 1, duplicate(VECTOR_ELT(dn, 0)));
347  #endif  /* USE_CHOLMOD */      UNPROTECT(1);
348        return chm_sparse_to_SEXP(chcp, 1, 0, 0, "", dn);
349    }
350    
351    SEXP Csparse_drop(SEXP x, SEXP tol)
352    {
353        const char *cl = class_P(x);
354        /* dtCMatrix, etc; [1] = the second character =?= 't' for triangular */
355        int tr = (cl[1] == 't');
356        CHM_SP chx = AS_CHM_SP__(x);
357        CHM_SP ans = cholmod_copy(chx, chx->stype, chx->xtype, &c);
358        double dtol = asReal(tol);
359        int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
360        R_CheckStack();
361    
362        if(!cholmod_drop(dtol, ans, &c))
363            error(_("cholmod_drop() failed"));
364        return chm_sparse_to_SEXP(ans, 1,
365                                  tr ? ((*uplo_P(x) == 'U') ? 1 : -1) : 0,
366                                  Rkind, tr ? diag_P(x) : "",
367                                  GET_SLOT(x, Matrix_DimNamesSym));
368    }
369    
370    SEXP Csparse_horzcat(SEXP x, SEXP y)
371    {
372        CHM_SP chx = AS_CHM_SP__(x), chy = AS_CHM_SP__(y);
373        int Rkind = 0; /* only for "d" - FIXME */
374        R_CheckStack();
375    
376        /* FIXME: currently drops dimnames */
377        return chm_sparse_to_SEXP(cholmod_horzcat(chx, chy, 1, &c),
378                                  1, 0, Rkind, "", R_NilValue);
379    }
380    
381    SEXP Csparse_vertcat(SEXP x, SEXP y)
382    {
383        CHM_SP chx = AS_CHM_SP__(x), chy = AS_CHM_SP__(y);
384        int Rkind = 0; /* only for "d" - FIXME */
385        R_CheckStack();
386    
387        /* FIXME: currently drops dimnames */
388        return chm_sparse_to_SEXP(cholmod_vertcat(chx, chy, 1, &c),
389                                  1, 0, Rkind, "", R_NilValue);
390    }
391    
392    SEXP Csparse_band(SEXP x, SEXP k1, SEXP k2)
393    {
394        CHM_SP chx = AS_CHM_SP__(x);
395        int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
396        CHM_SP ans = cholmod_band(chx, asInteger(k1), asInteger(k2), chx->xtype, &c);
397        R_CheckStack();
398    
399        return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "",
400                                  GET_SLOT(x, Matrix_DimNamesSym));
401    }
402    
403    SEXP Csparse_diagU2N(SEXP x)
404    {
405        const char *cl = class_P(x);
406        /* dtCMatrix, etc; [1] = the second character =?= 't' for triangular */
407        if (cl[1] != 't' || *diag_P(x) != 'U') {
408            /* "trivially fast" when not triangular (<==> no 'diag' slot),
409               or not *unit* triangular */
410            return (x);
411        }
412        else { /* unit triangular (diag='U'): "fill the diagonal" & diag:= "N" */
413            CHM_SP chx = AS_CHM_SP__(x);
414            CHM_SP eye = cholmod_speye(chx->nrow, chx->ncol, chx->xtype, &c);
415            double one[] = {1, 0};
416            CHM_SP ans = cholmod_add(chx, eye, one, one, TRUE, TRUE, &c);
417            int uploT = (*uplo_P(x) == 'U') ? 1 : -1;
418            int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
419    
420            R_CheckStack();
421            cholmod_free_sparse(&eye, &c);
422            return chm_sparse_to_SEXP(ans, 1, uploT, Rkind, "N",
423                                      GET_SLOT(x, Matrix_DimNamesSym));
424        }
425  }  }
426    
427    SEXP Csparse_diagN2U(SEXP x)
428    {
429        const char *cl = class_P(x);
430        /* dtCMatrix, etc; [1] = the second character =?= 't' for triangular */
431        if (cl[1] != 't' || *diag_P(x) != 'N') {
432            /* "trivially fast" when not triangular (<==> no 'diag' slot),
433               or already *unit* triangular */
434            return (x);
435        }
436        else { /* triangular with diag='N'): now drop the diagonal */
437            /* duplicate, since chx will be modified: */
438            CHM_SP chx = AS_CHM_SP__(duplicate(x));
439            int uploT = (*uplo_P(x) == 'U') ? 1 : -1,
440                Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
441            R_CheckStack();
442    
443            chm_diagN2U(chx, uploT, /* do_realloc */ FALSE);
444    
445            return chm_sparse_to_SEXP(chx, /*dofree*/ 0/* or 1 ?? */,
446                                      uploT, Rkind, "U",
447                                      GET_SLOT(x, Matrix_DimNamesSym));
448        }
449    }
450    
451    SEXP Csparse_submatrix(SEXP x, SEXP i, SEXP j)
452    {
453        CHM_SP chx = AS_CHM_SP__(x);
454        int rsize = (isNull(i)) ? -1 : LENGTH(i),
455            csize = (isNull(j)) ? -1 : LENGTH(j);
456        int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
457        R_CheckStack();
458    
459        if (rsize >= 0 && !isInteger(i))
460            error(_("Index i must be NULL or integer"));
461        if (csize >= 0 && !isInteger(j))
462            error(_("Index j must be NULL or integer"));
463    
464        return chm_sparse_to_SEXP(cholmod_submatrix(chx, INTEGER(i), rsize,
465                                                    INTEGER(j), csize,
466                                                    TRUE, TRUE, &c),
467                                  1, 0, Rkind, "",
468                                  /* FIXME: drops dimnames */ R_NilValue);
469    }
470    
471    SEXP Csparse_MatrixMarket(SEXP x, SEXP fname)
472    {
473        FILE *f = fopen(CHAR(asChar(fname)), "w");
474    
475        if (!f)
476            error(_("failure to open file \"%s\" for writing"),
477                  CHAR(asChar(fname)));
478        if (!cholmod_write_sparse(f, AS_CHM_SP(x),
479                                  (CHM_SP)NULL, (char*) NULL, &c))
480            error(_("cholmod_write_sparse returned error code"));
481        fclose(f);
482        return R_NilValue;
483    }
484    
485    
486    /**
487     * Extract the diagonal entries from *triangular* Csparse matrix  __or__ a
488     * cholmod_sparse factor (LDL = TRUE).
489     *
490     * @param n  dimension of the matrix.
491     * @param x_p  'p' (column pointer) slot contents
492     * @param x_x  'x' (non-zero entries) slot contents
493     * @param perm 'perm' (= permutation vector) slot contents; only used for "diagBack"
494     * @param resultKind a (SEXP) string indicating which kind of result is desired.
495     *
496     * @return  a SEXP, either a (double) number or a length n-vector of diagonal entries
497     */
498    SEXP diag_tC_ptr(int n, int *x_p, double *x_x, int *perm, SEXP resultKind)
499    /*                                ^^^^^^ FIXME[Generalize] to int / ... */
500    {
501        const char* res_ch = CHAR(STRING_ELT(resultKind,0));
502        enum diag_kind { diag, diag_backpermuted, trace, prod, sum_log
503        } res_kind = ((!strcmp(res_ch, "trace")) ? trace :
504                      ((!strcmp(res_ch, "sumLog")) ? sum_log :
505                       ((!strcmp(res_ch, "prod")) ? prod :
506                        ((!strcmp(res_ch, "diag")) ? diag :
507                         ((!strcmp(res_ch, "diagBack")) ? diag_backpermuted :
508                          -1)))));
509        int i, n_x, i_from = 0;
510        SEXP ans = PROTECT(allocVector(REALSXP,
511    /*                                 ^^^^  FIXME[Generalize] */
512                                       (res_kind == diag ||
513                                        res_kind == diag_backpermuted) ? n : 1));
514        double *v = REAL(ans);
515    /*  ^^^^^^      ^^^^  FIXME[Generalize] */
516    
517    #define for_DIAG(v_ASSIGN)                                              \
518        for(i = 0; i < n; i++, i_from += n_x) {                             \
519            /* looking at i-th column */                                    \
520            n_x = x_p[i+1] - x_p[i];/* #{entries} in this column */ \
521            v_ASSIGN;                                                       \
522        }
523    
524        /* NOTA BENE: we assume  -- uplo = "L" i.e. lower triangular matrix
525         *            for uplo = "U" (makes sense with a "dtCMatrix" !),
526         *            should use  x_x[i_from + (nx - 1)] instead of x_x[i_from],
527         *            where nx = (x_p[i+1] - x_p[i])
528         */
529    
530        switch(res_kind) {
531        case trace:
532            v[0] = 0.;
533            for_DIAG(v[0] += x_x[i_from]);
534            break;
535    
536        case sum_log:
537            v[0] = 0.;
538            for_DIAG(v[0] += log(x_x[i_from]));
539            break;
540    
541        case prod:
542            v[0] = 1.;
543            for_DIAG(v[0] *= x_x[i_from]);
544            break;
545    
546        case diag:
547            for_DIAG(v[i] = x_x[i_from]);
548            break;
549    
550        case diag_backpermuted:
551            for_DIAG(v[i] = x_x[i_from]);
552    
553            warning(_("resultKind = 'diagBack' (back-permuted) is experimental"));
554            /* now back_permute : */
555            for(i = 0; i < n; i++) {
556                double tmp = v[i]; v[i] = v[perm[i]]; v[perm[i]] = tmp;
557                /*^^^^ FIXME[Generalize] */
558            }
559            break;
560    
561        default: /* -1 from above */
562            error("diag_tC(): invalid 'resultKind'");
563            /* Wall: */ ans = R_NilValue; v = REAL(ans);
564        }
565    
566        UNPROTECT(1);
567        return ans;
568    }
569    
570    /**
571     * Extract the diagonal entries from *triangular* Csparse matrix  __or__ a
572     * cholmod_sparse factor (LDL = TRUE).
573     *
574     * @param pslot  'p' (column pointer)   slot of Csparse matrix/factor
575     * @param xslot  'x' (non-zero entries) slot of Csparse matrix/factor
576     * @param perm_slot  'perm' (= permutation vector) slot of corresponding CHMfactor;
577     *                   only used for "diagBack"
578     * @param resultKind a (SEXP) string indicating which kind of result is desired.
579     *
580     * @return  a SEXP, either a (double) number or a length n-vector of diagonal entries
581     */
582    SEXP diag_tC(SEXP pslot, SEXP xslot, SEXP perm_slot, SEXP resultKind)
583    {
584        int n = length(pslot) - 1, /* n = ncol(.) = nrow(.) */
585            *x_p  = INTEGER(pslot),
586            *perm = INTEGER(perm_slot);
587        double *x_x = REAL(xslot);
588    /*  ^^^^^^        ^^^^ FIXME[Generalize] to INTEGER(.) / LOGICAL(.) / ... xslot !*/
589    
590        return diag_tC_ptr(n, x_p, x_x, perm, resultKind);
591    }

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