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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 2223, Fri Jul 18 23:04:48 2008 UTC revision 2304, Sun Oct 26 15:27:45 2008 UTC
# Line 3  Line 3 
3  #include "Tsparse.h"  #include "Tsparse.h"
4  #include "chm_common.h"  #include "chm_common.h"
5    
6    /** "Cheap" C version of  Csparse_validate() - *not* sorting : */
7    Rboolean isValid_Csparse(SEXP x)
8    {
9        /* NB: we do *NOT* check a potential 'x' slot here, at all */
10        SEXP pslot = GET_SLOT(x, Matrix_pSym),
11            islot = GET_SLOT(x, Matrix_iSym);
12        int *dims = INTEGER(GET_SLOT(x, Matrix_DimSym)), j,
13            nrow = dims[0],
14            ncol = dims[1],
15            *xp = INTEGER(pslot),
16            *xi = INTEGER(islot);
17    
18        if (length(pslot) != dims[1] + 1)
19            return FALSE;
20        if (xp[0] != 0)
21            return FALSE;
22        if (length(islot) < xp[ncol]) /* allow larger slots from over-allocation!*/
23            return FALSE;
24        for (j = 0; j < xp[ncol]; j++) {
25            if (xi[j] < 0 || xi[j] >= nrow)
26                return FALSE;
27        }
28        for (j = 0; j < ncol; j++) {
29            if (xp[j] > xp[j + 1])
30                return FALSE;
31        }
32        return TRUE;
33    }
34    
35  SEXP Csparse_validate(SEXP x)  SEXP Csparse_validate(SEXP x)
36  {  {
37      /* NB: we do *NOT* check a potential 'x' slot here, at all */      /* NB: we do *NOT* check a potential 'x' slot here, at all */
# Line 23  Line 52 
52      if (length(islot) < xp[ncol]) /* allow larger slots from over-allocation!*/      if (length(islot) < xp[ncol]) /* allow larger slots from over-allocation!*/
53          return          return
54              mkString(_("last element of slot p must match length of slots i and x"));              mkString(_("last element of slot p must match length of slots i and x"));
55      for (j = 0; j < length(islot); j++) {      for (j = 0; j < xp[ncol]; j++) {
56          if (xi[j] < 0 || xi[j] >= nrow)          if (xi[j] < 0 || xi[j] >= nrow)
57              return mkString(_("all row indices must be between 0 and nrow-1"));              return mkString(_("all row indices must be between 0 and nrow-1"));
58      }      }
# Line 31  Line 60 
60      for (j = 0; j < ncol; j++) {      for (j = 0; j < ncol; j++) {
61          if (xp[j] > xp[j+1])          if (xp[j] > xp[j+1])
62              return mkString(_("slot p must be non-decreasing"));              return mkString(_("slot p must be non-decreasing"));
63          if(sorted)          if(sorted) /* only act if >= 2 entries in column j : */
64              for (k = xp[j] + 1; k < xp[j + 1]; k++) {              for (k = xp[j] + 1; k < xp[j + 1]; k++) {
65                  if (xi[k] < xi[k - 1])                  if (xi[k] < xi[k - 1])
66                      sorted = FALSE;                      sorted = FALSE;
# Line 40  Line 69 
69              }              }
70      }      }
71      if (!sorted) {      if (!sorted) {
72          CHM_SP chx = AS_CHM_SP__(x);          return mkString(_("row indices are not sorted within columns"));
         R_CheckStack();  
   
         cholmod_sort(chx, &c);  
         /* Now re-check that row indices are *strictly* increasing  
          * (and not just increasing) within each column : */  
         for (j = 0; j < ncol; j++) {  
             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_sort)"));  
         }  
   
73      } else if(!strictly) {  /* sorted, but not strictly */      } else if(!strictly) {  /* sorted, but not strictly */
74          return mkString(_("slot i is not *strictly* increasing inside a column"));          return mkString(_("slot i is not *strictly* increasing inside a column"));
75      }      }
# Line 95  Line 113 
113              }              }
114      }      }
115      if (!sorted)      if (!sorted)
116          /* cannot easily use cholmod_sort(.) ... -> "error out" :*/          /* cannot easily use cholmod_l_sort(.) ... -> "error out" :*/
117          return mkString(_("slot j is not increasing inside a column"));          return mkString(_("slot j is not increasing inside a column"));
118      else if(!strictly) /* sorted, but not strictly */      else if(!strictly) /* sorted, but not strictly */
119          return mkString(_("slot j is not *strictly* increasing inside a column"));          return mkString(_("slot j is not *strictly* increasing inside a column"));
# Line 113  Line 131 
131      /* This loses the symmetry property, since cholmod_dense has none,      /* This loses the symmetry property, since cholmod_dense has none,
132       * BUT, much worse (FIXME!), it also transforms CHOLMOD_PATTERN ("n") matrices       * BUT, much worse (FIXME!), it also transforms CHOLMOD_PATTERN ("n") matrices
133       * to numeric (CHOLMOD_REAL) ones : */       * to numeric (CHOLMOD_REAL) ones : */
134      CHM_DN chxd = cholmod_sparse_to_dense(chxs, &c);      CHM_DN chxd = cholmod_l_sparse_to_dense(chxs, &c);
135      int Rkind = (chxs->xtype == CHOLMOD_PATTERN)? -1 : Real_kind(x);      int Rkind = (chxs->xtype == CHOLMOD_PATTERN)? -1 : Real_kind(x);
136      R_CheckStack();      R_CheckStack();
137    
# Line 123  Line 141 
141  SEXP Csparse_to_nz_pattern(SEXP x, SEXP tri)  SEXP Csparse_to_nz_pattern(SEXP x, SEXP tri)
142  {  {
143      CHM_SP chxs = AS_CHM_SP__(x);      CHM_SP chxs = AS_CHM_SP__(x);
144      CHM_SP chxcp = cholmod_copy(chxs, chxs->stype, CHOLMOD_PATTERN, &c);      CHM_SP chxcp = cholmod_l_copy(chxs, chxs->stype, CHOLMOD_PATTERN, &c);
145      int tr = asLogical(tri);      int tr = asLogical(tri);
146      R_CheckStack();      R_CheckStack();
147    
# Line 135  Line 153 
153    
154  SEXP Csparse_to_matrix(SEXP x)  SEXP Csparse_to_matrix(SEXP x)
155  {  {
156      return chm_dense_to_matrix(cholmod_sparse_to_dense(AS_CHM_SP__(x), &c),      return chm_dense_to_matrix(cholmod_l_sparse_to_dense(AS_CHM_SP__(x), &c),
157                                 1 /*do_free*/, GET_SLOT(x, Matrix_DimNamesSym));                                 1 /*do_free*/, GET_SLOT(x, Matrix_DimNamesSym));
158  }  }
159    
160  SEXP Csparse_to_Tsparse(SEXP x, SEXP tri)  SEXP Csparse_to_Tsparse(SEXP x, SEXP tri)
161  {  {
162      CHM_SP chxs = AS_CHM_SP__(x);      CHM_SP chxs = AS_CHM_SP__(x);
163      CHM_TR chxt = cholmod_sparse_to_triplet(chxs, &c);      CHM_TR chxt = cholmod_l_sparse_to_triplet(chxs, &c);
164      int tr = asLogical(tri);      int tr = asLogical(tri);
165      int Rkind = (chxs->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chxs->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
166      R_CheckStack();      R_CheckStack();
# Line 162  Line 180 
180    
181      if (!(chx->stype))      if (!(chx->stype))
182          error(_("Nonsymmetric matrix in Csparse_symmetric_to_general"));          error(_("Nonsymmetric matrix in Csparse_symmetric_to_general"));
183      chgx = cholmod_copy(chx, /* stype: */ 0, chx->xtype, &c);      chgx = cholmod_l_copy(chx, /* stype: */ 0, chx->xtype, &c);
184      /* xtype: pattern, "real", complex or .. */      /* xtype: pattern, "real", complex or .. */
185      return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",      return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",
186                                GET_SLOT(x, Matrix_DimNamesSym));                                GET_SLOT(x, Matrix_DimNamesSym));
# Line 175  Line 193 
193      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
194      R_CheckStack();      R_CheckStack();
195    
196      chgx = cholmod_copy(chx, /* stype: */ uploT, chx->xtype, &c);      chgx = cholmod_l_copy(chx, /* stype: */ uploT, chx->xtype, &c);
197      /* xtype: pattern, "real", complex or .. */      /* xtype: pattern, "real", complex or .. */
198      return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",      return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",
199                                GET_SLOT(x, Matrix_DimNamesSym));                                GET_SLOT(x, Matrix_DimNamesSym));
# Line 187  Line 205 
205       *       since cholmod (& cs) lacks sparse 'int' matrices */       *       since cholmod (& cs) lacks sparse 'int' matrices */
206      CHM_SP chx = AS_CHM_SP__(x);      CHM_SP chx = AS_CHM_SP__(x);
207      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
208      CHM_SP chxt = cholmod_transpose(chx, chx->xtype, &c);      CHM_SP chxt = cholmod_l_transpose(chx, chx->xtype, &c);
209      SEXP dn = PROTECT(duplicate(GET_SLOT(x, Matrix_DimNamesSym))), tmp;      SEXP dn = PROTECT(duplicate(GET_SLOT(x, Matrix_DimNamesSym))), tmp;
210      int tr = asLogical(tri);      int tr = asLogical(tri);
211      R_CheckStack();      R_CheckStack();
# Line 206  Line 224 
224      CHM_SP      CHM_SP
225          cha = AS_CHM_SP(a),          cha = AS_CHM_SP(a),
226          chb = AS_CHM_SP(b),          chb = AS_CHM_SP(b),
227          chc = cholmod_ssmult(cha, chb, /*out_stype:*/ 0,          chc = cholmod_l_ssmult(cha, chb, /*out_stype:*/ 0,
228                               cha->xtype, /*out sorted:*/ 1, &c);                               cha->xtype, /*out sorted:*/ 1, &c);
229      const char *cl_a = class_P(a), *cl_b = class_P(b);      const char *cl_a = class_P(a), *cl_b = class_P(b);
230      char diag[] = {'\0', '\0'};      char diag[] = {'\0', '\0'};
# Line 251  Line 269 
269      SEXP dn = allocVector(VECSXP, 2);      SEXP dn = allocVector(VECSXP, 2);
270      R_CheckStack();      R_CheckStack();
271    
272      chTr = cholmod_transpose((tr) ? chb : cha, chb->xtype, &c);      chTr = cholmod_l_transpose((tr) ? chb : cha, chb->xtype, &c);
273      chc = cholmod_ssmult((tr) ? cha : chTr, (tr) ? chTr : chb,      chc = cholmod_l_ssmult((tr) ? cha : chTr, (tr) ? chTr : chb,
274                           /*out_stype:*/ 0, cha->xtype, /*out sorted:*/ 1, &c);                           /*out_stype:*/ 0, cha->xtype, /*out sorted:*/ 1, &c);
275      cholmod_free_sparse(&chTr, &c);      cholmod_l_free_sparse(&chTr, &c);
276    
277      /* Preserve triangularity and unit-triangularity if appropriate;      /* Preserve triangularity and unit-triangularity if appropriate;
278       * see Csparse_Csparse_prod() for comments */       * see Csparse_Csparse_prod() for comments */
# Line 280  Line 298 
298      CHM_SP cha = AS_CHM_SP(a);      CHM_SP cha = AS_CHM_SP(a);
299      SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));      SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));
300      CHM_DN chb = AS_CHM_DN(b_M);      CHM_DN chb = AS_CHM_DN(b_M);
301      CHM_DN chc = cholmod_allocate_dense(cha->nrow, chb->ncol, cha->nrow,      CHM_DN chc = cholmod_l_allocate_dense(cha->nrow, chb->ncol, cha->nrow,
302                                          chb->xtype, &c);                                          chb->xtype, &c);
303      SEXP dn = PROTECT(allocVector(VECSXP, 2));      SEXP dn = PROTECT(allocVector(VECSXP, 2));
304      double one[] = {1,0}, zero[] = {0,0};      double one[] = {1,0}, zero[] = {0,0};
305      R_CheckStack();      R_CheckStack();
306    
307      cholmod_sdmult(cha, 0, one, zero, chb, chc, &c);      cholmod_l_sdmult(cha, 0, one, zero, chb, chc, &c);
308      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
309                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));
310      SET_VECTOR_ELT(dn, 1,      SET_VECTOR_ELT(dn, 1,
# Line 300  Line 318 
318      CHM_SP cha = AS_CHM_SP(a);      CHM_SP cha = AS_CHM_SP(a);
319      SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));      SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));
320      CHM_DN chb = AS_CHM_DN(b_M);      CHM_DN chb = AS_CHM_DN(b_M);
321      CHM_DN chc = cholmod_allocate_dense(cha->ncol, chb->ncol, cha->ncol,      CHM_DN chc = cholmod_l_allocate_dense(cha->ncol, chb->ncol, cha->ncol,
322                                          chb->xtype, &c);                                          chb->xtype, &c);
323      SEXP dn = PROTECT(allocVector(VECSXP, 2));      SEXP dn = PROTECT(allocVector(VECSXP, 2));
324      double one[] = {1,0}, zero[] = {0,0};      double one[] = {1,0}, zero[] = {0,0};
325      R_CheckStack();      R_CheckStack();
326    
327      cholmod_sdmult(cha, 1, one, zero, chb, chc, &c);      cholmod_l_sdmult(cha, 1, one, zero, chb, chc, &c);
328      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
329                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 1)));                     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 1)));
330      SET_VECTOR_ELT(dn, 1,      SET_VECTOR_ELT(dn, 1,
# Line 324  Line 342 
342      CHM_TR cht = trip ? AS_CHM_TR(x) : (CHM_TR) NULL;      CHM_TR cht = trip ? AS_CHM_TR(x) : (CHM_TR) NULL;
343      CHM_SP chcp, chxt,      CHM_SP chcp, chxt,
344          chx = (trip ?          chx = (trip ?
345                 cholmod_triplet_to_sparse(cht, cht->nnz, &c) :                 cholmod_l_triplet_to_sparse(cht, cht->nnz, &c) :
346                 AS_CHM_SP(x));                 AS_CHM_SP(x));
347      SEXP dn = PROTECT(allocVector(VECSXP, 2));      SEXP dn = PROTECT(allocVector(VECSXP, 2));
348      R_CheckStack();      R_CheckStack();
349    
350      if (!tr) chxt = cholmod_transpose(chx, chx->xtype, &c);      if (!tr) chxt = cholmod_l_transpose(chx, chx->xtype, &c);
351      chcp = cholmod_aat((!tr) ? chxt : chx, (int *) NULL, 0, chx->xtype, &c);      chcp = cholmod_l_aat((!tr) ? chxt : chx, (int *) NULL, 0, chx->xtype, &c);
352      if(!chcp) {      if(!chcp) {
353          UNPROTECT(1);          UNPROTECT(1);
354          error(_("Csparse_crossprod(): error return from cholmod_aat()"));          error(_("Csparse_crossprod(): error return from cholmod_l_aat()"));
355      }      }
356      cholmod_band_inplace(0, chcp->ncol, chcp->xtype, chcp, &c);      cholmod_l_band_inplace(0, chcp->ncol, chcp->xtype, chcp, &c);
357      chcp->stype = 1;      chcp->stype = 1;
358      if (trip) cholmod_free_sparse(&chx, &c);      if (trip) cholmod_l_free_sparse(&chx, &c);
359      if (!tr) cholmod_free_sparse(&chxt, &c);      if (!tr) cholmod_l_free_sparse(&chxt, &c);
360      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */      SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
361                     duplicate(VECTOR_ELT(GET_SLOT(x, Matrix_DimNamesSym),                     duplicate(VECTOR_ELT(GET_SLOT(x, Matrix_DimNamesSym),
362                                          (tr) ? 0 : 1)));                                          (tr) ? 0 : 1)));
# Line 353  Line 371 
371      /* dtCMatrix, etc; [1] = the second character =?= 't' for triangular */      /* dtCMatrix, etc; [1] = the second character =?= 't' for triangular */
372      int tr = (cl[1] == 't');      int tr = (cl[1] == 't');
373      CHM_SP chx = AS_CHM_SP__(x);      CHM_SP chx = AS_CHM_SP__(x);
374      CHM_SP ans = cholmod_copy(chx, chx->stype, chx->xtype, &c);      CHM_SP ans = cholmod_l_copy(chx, chx->stype, chx->xtype, &c);
375      double dtol = asReal(tol);      double dtol = asReal(tol);
376      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
377      R_CheckStack();      R_CheckStack();
378    
379      if(!cholmod_drop(dtol, ans, &c))      if(!cholmod_l_drop(dtol, ans, &c))
380          error(_("cholmod_drop() failed"));          error(_("cholmod_l_drop() failed"));
381      return chm_sparse_to_SEXP(ans, 1,      return chm_sparse_to_SEXP(ans, 1,
382                                tr ? ((*uplo_P(x) == 'U') ? 1 : -1) : 0,                                tr ? ((*uplo_P(x) == 'U') ? 1 : -1) : 0,
383                                Rkind, tr ? diag_P(x) : "",                                Rkind, tr ? diag_P(x) : "",
# Line 373  Line 391 
391      R_CheckStack();      R_CheckStack();
392    
393      /* FIXME: currently drops dimnames */      /* FIXME: currently drops dimnames */
394      return chm_sparse_to_SEXP(cholmod_horzcat(chx, chy, 1, &c),      return chm_sparse_to_SEXP(cholmod_l_horzcat(chx, chy, 1, &c),
395                                1, 0, Rkind, "", R_NilValue);                                1, 0, Rkind, "", R_NilValue);
396  }  }
397    
# Line 384  Line 402 
402      R_CheckStack();      R_CheckStack();
403    
404      /* FIXME: currently drops dimnames */      /* FIXME: currently drops dimnames */
405      return chm_sparse_to_SEXP(cholmod_vertcat(chx, chy, 1, &c),      return chm_sparse_to_SEXP(cholmod_l_vertcat(chx, chy, 1, &c),
406                                1, 0, Rkind, "", R_NilValue);                                1, 0, Rkind, "", R_NilValue);
407  }  }
408    
# Line 392  Line 410 
410  {  {
411      CHM_SP chx = AS_CHM_SP__(x);      CHM_SP chx = AS_CHM_SP__(x);
412      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;      int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
413      CHM_SP ans = cholmod_band(chx, asInteger(k1), asInteger(k2), chx->xtype, &c);      CHM_SP ans = cholmod_l_band(chx, asInteger(k1), asInteger(k2), chx->xtype, &c);
414      R_CheckStack();      R_CheckStack();
415    
416      return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "",      return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "",
# Line 410  Line 428 
428      }      }
429      else { /* unit triangular (diag='U'): "fill the diagonal" & diag:= "N" */      else { /* unit triangular (diag='U'): "fill the diagonal" & diag:= "N" */
430          CHM_SP chx = AS_CHM_SP__(x);          CHM_SP chx = AS_CHM_SP__(x);
431          CHM_SP eye = cholmod_speye(chx->nrow, chx->ncol, chx->xtype, &c);          CHM_SP eye = cholmod_l_speye(chx->nrow, chx->ncol, chx->xtype, &c);
432          double one[] = {1, 0};          double one[] = {1, 0};
433          CHM_SP ans = cholmod_add(chx, eye, one, one, TRUE, TRUE, &c);          CHM_SP ans = cholmod_l_add(chx, eye, one, one, TRUE, TRUE, &c);
434          int uploT = (*uplo_P(x) == 'U') ? 1 : -1;          int uploT = (*uplo_P(x) == 'U') ? 1 : -1;
435          int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;          int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
436    
437          R_CheckStack();          R_CheckStack();
438          cholmod_free_sparse(&eye, &c);          cholmod_l_free_sparse(&eye, &c);
439          return chm_sparse_to_SEXP(ans, 1, uploT, Rkind, "N",          return chm_sparse_to_SEXP(ans, 1, uploT, Rkind, "N",
440                                    GET_SLOT(x, Matrix_DimNamesSym));                                    GET_SLOT(x, Matrix_DimNamesSym));
441      }      }
# Line 460  Line 478 
478      if (csize >= 0 && !isInteger(j))      if (csize >= 0 && !isInteger(j))
479          error(_("Index j must be NULL or integer"));          error(_("Index j must be NULL or integer"));
480    
481      return chm_sparse_to_SEXP(cholmod_submatrix(chx, INTEGER(i), rsize,      return chm_sparse_to_SEXP(cholmod_l_submatrix(chx, INTEGER(i), rsize,
482                                                  INTEGER(j), csize,                                                  INTEGER(j), csize,
483                                                  TRUE, TRUE, &c),                                                  TRUE, TRUE, &c),
484                                1, 0, Rkind, "",                                1, 0, Rkind, "",
# Line 474  Line 492 
492      if (!f)      if (!f)
493          error(_("failure to open file \"%s\" for writing"),          error(_("failure to open file \"%s\" for writing"),
494                CHAR(asChar(fname)));                CHAR(asChar(fname)));
495      if (!cholmod_write_sparse(f, AS_CHM_SP(x),      if (!cholmod_l_write_sparse(f, AS_CHM_SP(x),
496                                (CHM_SP)NULL, (char*) NULL, &c))                                (CHM_SP)NULL, (char*) NULL, &c))
497          error(_("cholmod_write_sparse returned error code"));          error(_("cholmod_l_write_sparse returned error code"));
498      fclose(f);      fclose(f);
499      return R_NilValue;      return R_NilValue;
500  }  }

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