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[matrix] Diff of /pkg/src/Mutils.h
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Diff of /pkg/src/Mutils.h

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revision 766, Tue Jun 7 23:03:34 2005 UTC revision 2354, Mon Mar 30 15:31:23 2009 UTC
# Line 1  Line 1 
1  #ifndef MATRIX_MUTILS_H  #ifndef MATRIX_MUTILS_H
2  #define MATRIX_MUTILS_H  #define MATRIX_MUTILS_H
3    
4    #define Matrix_with_SPQR
5    
6  #ifdef __cplusplus  #ifdef __cplusplus
7  extern "C" {  extern "C" {
8  #endif  #endif
9    
10  #include <Rdefines.h>  #include <ctype.h>
11  #include <Rconfig.h>  #include <R.h>  /* includes Rconfig.h */
12  #include <R.h>  /* to include Rconfig.h */  #include <Rversion.h>
13    #include <Rdefines.h> /* Rinternals.h + GET_SLOT etc */
14    
15  #ifdef ENABLE_NLS  #ifdef ENABLE_NLS
16  #include <libintl.h>  #include <libintl.h>
# Line 16  Line 19 
19  #define _(String) (String)  #define _(String) (String)
20  #endif  #endif
21    
22    #ifdef __GNUC__
23    # undef alloca
24    # define alloca(x) __builtin_alloca((x))
25    #elif defined(__sun) || defined(_AIX)
26    /* this is necessary (and sufficient) for Solaris 10 and AIX 6: */
27    # include <alloca.h>
28    #endif
29    
30    #define Alloca(n, t)   (t *) alloca( (size_t) ( (n) * sizeof(t) ) )
31    
32    SEXP triangularMatrix_validate(SEXP obj);
33    SEXP symmetricMatrix_validate(SEXP obj);
34    SEXP dense_nonpacked_validate(SEXP obj);
35    
36  /* enum constants from cblas.h and some short forms */  /* enum constants from cblas.h and some short forms */
37  enum CBLAS_ORDER {CblasRowMajor=101, CblasColMajor=102};  enum CBLAS_ORDER {CblasRowMajor=101, CblasColMajor=102};
38  enum CBLAS_TRANSPOSE {CblasNoTrans=111, CblasTrans=112, CblasConjTrans=113};  enum CBLAS_TRANSPOSE {CblasNoTrans=111, CblasTrans=112, CblasConjTrans=113};
# Line 34  Line 51 
51  #define LFT CblasLeft  #define LFT CblasLeft
52  #define RGT CblasRight  #define RGT CblasRight
53    
54  char norm_type(char *typstr);  #if !defined(R_VERSION) || R_VERSION < R_Version(2, 7, 0)
55  char rcond_type(char *typstr);  char La_norm_type(const char *typstr);
56    char La_rcond_type(const char *typstr);
57    #endif
58    
59  double get_double_by_name(SEXP obj, char *nm);  double get_double_by_name(SEXP obj, char *nm);
60  SEXP set_double_by_name(SEXP obj, double val, char *nm);  SEXP set_double_by_name(SEXP obj, double val, char *nm);
61  SEXP as_det_obj(double val, int log, int sign);  SEXP as_det_obj(double val, int log, int sign);
62  SEXP get_factors(SEXP obj, char *nm);  SEXP get_factors(SEXP obj, char *nm);
63  SEXP set_factors(SEXP obj, SEXP val, char *nm);  SEXP set_factors(SEXP obj, SEXP val, char *nm);
64    
65    #if 0
66  SEXP dgCMatrix_set_Dim(SEXP x, int nrow);  SEXP dgCMatrix_set_Dim(SEXP x, int nrow);
67  int csc_unsorted_columns(int ncol, const int p[], const int i[]);  #endif  /* unused */
68  void csc_sort_columns(int ncol, const int p[], int i[], double x[]);  
69  SEXP triple_as_SEXP(int nrow, int ncol, int nz,  /* int csc_unsorted_columns(int ncol, const int p[], const int i[]); */
70                      const int Ti [], const int Tj [], const double Tx [],  /* void csc_sort_columns(int ncol, const int p[], int i[], double x[]); */
71                      char *Rclass);  /* SEXP csc_check_column_sorting(SEXP A); */
72  SEXP csc_check_column_sorting(SEXP A);  SEXP Matrix_make_named(int TYP, const char **names);
 void csc_compTr(int m, int n, int nnz,  
                 const int xp[], const int xi[], const double xx[],  
                 int ap[], int ai[], double ax[]);  
 void ssc_symbolic_permute(int n, int upper, const int perm[],  
                           int Ap[], int Ai[]);  
 SEXP Matrix_make_named(int TYP, char **names);  
73  SEXP check_scalar_string(SEXP sP, char *vals, char *nm);  SEXP check_scalar_string(SEXP sP, char *vals, char *nm);
74  double *packed_to_full(double *dest, const double *src, int n,  Rboolean equal_string_vectors(SEXP s1, SEXP s2);
75                         enum CBLAS_UPLO uplo);  
76  double *full_to_packed(double *dest, const double *src, int n,  void d_packed_getDiag(double *dest, SEXP x, int n);
77                         enum CBLAS_UPLO uplo, enum CBLAS_DIAG diag);  void l_packed_getDiag(   int *dest, SEXP x, int n);
78  double *packed_getDiag(double *dest, SEXP x);  void tr_d_packed_getDiag(double *dest, SEXP x);
79    void tr_l_packed_getDiag(   int *dest, SEXP x);
80    
81    SEXP Matrix_getElement(SEXP list, char *nm);
82    
83    #define PACKED_TO_FULL(TYPE)                                            \
84    TYPE *packed_to_full_ ## TYPE(TYPE *dest, const TYPE *src,              \
85                                 int n, enum CBLAS_UPLO uplo)
86    PACKED_TO_FULL(double);
87    PACKED_TO_FULL(int);
88    #undef PACKED_TO_FULL
89    
90    #define FULL_TO_PACKED(TYPE)                                            \
91    TYPE *full_to_packed_ ## TYPE(TYPE *dest, const TYPE *src, int n,       \
92                                  enum CBLAS_UPLO uplo, enum CBLAS_DIAG diag)
93    FULL_TO_PACKED(double);
94    FULL_TO_PACKED(int);
95    #undef FULL_TO_PACKED
96    
97    
98  extern   /* stored pointers to symbols initialized in R_init_Matrix */  extern   /* stored pointers to symbols initialized in R_init_Matrix */
# Line 72  Line 105 
105  #define PACKED_LENGTH(n)   ((n) * ((n) + 1))/2  #define PACKED_LENGTH(n)   ((n) * ((n) + 1))/2
106    
107  /* duplicate the slot with name given by sym from src to dest */  /* duplicate the slot with name given by sym from src to dest */
108    
109  #define slot_dup(dest, src, sym)  SET_SLOT(dest, sym, duplicate(GET_SLOT(src, sym)))  #define slot_dup(dest, src, sym)  SET_SLOT(dest, sym, duplicate(GET_SLOT(src, sym)))
110    
111    /* is not yet used: */
112    #define slot_nonNull_dup(dest, src, sym)                        \
113        if(GET_SLOT(src, sym) != R_NilValue)                        \
114            SET_SLOT(dest, sym, duplicate(GET_SLOT(src, sym)))
115    
116    /* TODO: Make this faster for the case where dimnames = list(NULL,NULL)
117     *       and hence don't have to be set ! */
118    #define SET_DimNames(dest, src) slot_dup(dest, src, Matrix_DimNamesSym)
119    
120    
121    #define uplo_P(_x_) CHAR(STRING_ELT(GET_SLOT(_x_, Matrix_uploSym), 0))
122    #define diag_P(_x_) CHAR(STRING_ELT(GET_SLOT(_x_, Matrix_diagSym), 0))
123    #define class_P(_x_) CHAR(asChar(getAttrib(_x_, R_ClassSymbol)))
124    
125    /* should also work for "matrix" matrices: */
126    #define Real_KIND(_x_)  (IS_S4_OBJECT(_x_) ? Real_kind(_x_) : \
127                             (isReal(_x_) ? 0 : (isLogical(_x_) ? 1 : -1)))
128    /* This one gives '0' also for integer "matrix" :*/
129    #define Real_KIND2(_x_) (IS_S4_OBJECT(_x_) ? Real_kind(_x_) : \
130                             (isLogical(_x_) ? 1 : 0))
131    
132    /* requires 'x' slot: */
133    #define Real_kind(_x_)  (isReal(GET_SLOT(_x_, Matrix_xSym)) ? 0 :       \
134                             (isLogical(GET_SLOT(_x_, Matrix_xSym)) ? 1 : -1))
135    
136    #define DECLARE_AND_GET_X_SLOT(__C_TYPE, __SEXP)        \
137        __C_TYPE *xx = __SEXP(GET_SLOT(x, Matrix_xSym))
138    
139    
140  /**  /**
141   * Check for valid length of a packed triangular array and return the   * Check for valid length of a packed triangular array and return the
142   * corresponding number of columns   * corresponding number of columns
# Line 100  Line 163 
163   * this behavior changes then ALLOC_SLOT must use SET_SLOT followed by   * this behavior changes then ALLOC_SLOT must use SET_SLOT followed by
164   * GET_SLOT to ensure that the value returned is indeed the SEXP in   * GET_SLOT to ensure that the value returned is indeed the SEXP in
165   * the slot.   * the slot.
166     * NOTE:  GET_SLOT(x, what)        :== R_do_slot       (x, what)
167     * ----   SET_SLOT(x, what, value) :== R_do_slot_assign(x, what, value)
168     * and the R_do_slot* are in src/main/attrib.c
169   *   *
170   * @param obj object in which to assign the slot   * @param obj object in which to assign the slot
171   * @param nm name of the slot, as an R name object   * @param nm name of the slot, as an R name object
# Line 138  Line 204 
204      return mj;      return mj;
205  }  }
206    
   
207  /**  /**
208   * Return the linear index of the (row, col) entry in a csc structure.   * Check if slot(obj, "x") contains any NA (or NaN).
209   * If the entry is not found and missing is 0 an error is signaled;   *
210   * otherwise the missing value is returned.   * @param obj   a 'Matrix' object with an 'x' slot.
  *  
  * @param p vector of column pointers  
  * @param i vector of row indices  
  * @param row row index  
  * @param col column index  
  * @param missing the value to return is the row, col entry does not  
  * exist.  If this is zero and the row, col entry does not exist an  
  * error is signaled.  
211   *   *
212   * @return index of element at (row, col) if it exists, otherwise missing   * @return Rboolean :== any(is.na(slot(obj, "x") )
213   */   */
214  static R_INLINE int  static R_INLINE
215  check_csc_index(const int p[], const int i[], int row, int col, int missing)  Rboolean any_NA(SEXP obj)
216  {  {
217      int k, k2 = p[col + 1];      double *x = REAL(GET_SLOT(obj, Matrix_xSym));
218                                  /* linear search - perhaps replace by bsearch */      int i, n = LENGTH(GET_SLOT(obj, Matrix_xSym));
219      for (k = p[col]; k < k2; k++) if (i[k] == row) return k;      for(i=0; i < n; i++)
220      if (!missing)          if(ISNAN(x[i])) return TRUE;
221          error("row %d and column %d not defined in rowind and colptr",      /* else */
222                row, col);      return FALSE;
     return missing;  
223  }  }
224    
 SEXP alloc3Darray(SEXPTYPE mode, int nrow, int ncol, int nface);  
225    
226  /**  void make_d_matrix_triangular(double *x, SEXP from);
227   * Calculate the zero-based index in a row-wise packed lower triangular matrix.  void make_i_matrix_triangular(   int *x, SEXP from);
228   * This is used for the arrays of blocked sparse matrices.  
229   *  void make_d_matrix_symmetric(double *to, SEXP from);
230   * @param i column number (zero-based)  void make_i_matrix_symmetric(   int *to, SEXP from);
231   * @param k row number (zero-based)  
232   *  SEXP Matrix_expand_pointers(SEXP pP);
233   * @return The index of the (k,i) element of a packed lower triangular matrix  
234   */  SEXP dup_mMatrix_as_dgeMatrix(SEXP A);
235  static R_INLINE  SEXP dup_mMatrix_as_geMatrix (SEXP A);
236  int Lind(int k, int i)  
237    SEXP new_dgeMatrix(int nrow, int ncol);
238    SEXP m_encodeInd (SEXP ij, SEXP di);
239    SEXP m_encodeInd2(SEXP i, SEXP j, SEXP di);
240    
241    
242    static R_INLINE SEXP
243    mMatrix_as_dgeMatrix(SEXP A)
244    {
245        return strcmp(class_P(A), "dgeMatrix") ? dup_mMatrix_as_dgeMatrix(A) : A;
246    }
247    
248    static R_INLINE SEXP
249    mMatrix_as_geMatrix(SEXP A)
250  {  {
251      if (k < i) error("Lind(k = %d, i = %d) must have k >= i", k, i);      return strcmp(class_P(A) + 1, "geMatrix") ? dup_mMatrix_as_geMatrix(A) : A;
     return (k * (k + 1))/2 + i;  
252  }  }
253    
254  /**  /**
255   * Check for a complete match on matrix dimensions   * Return the 0-based index of a string match in a vector of strings
256     * terminated by an empty string.  Returns -1 for no match.
257   *   *
258   * @param xd dimensions of first matrix   * @param class string to match
259   * @param yd dimensions of second matrix   * @param valid vector of possible matches terminated by an empty string
260   *   *
261   * @return 1 if dimensions match, otherwise 0   * @return index of match or -1 for no match
262   */   */
263  static R_INLINE  static R_INLINE int
264  int match_mat_dims(const int xd[], const int yd[])  Matrix_check_class(const char *class, char **valid)
265  {  {
266      return xd[0] == yd[0] && xd[1] == yd[1];      int ans;
267        for (ans = 0; ; ans++) {
268            if (!strlen(valid[ans])) return -1;
269            if (!strcmp(class, valid[ans])) return ans;
270        }
271  }  }
   
 double *expand_csc_column(double *dest, int m, int j,  
                           const int Ap[], const int Ai[], const double Ax[]);  
272    
273  /**  /**
274   * Apply a permutation to an integer vector   * Return the 0-based index of an is() match in a vector of class-name
275     * strings terminated by an empty string.  Returns -1 for no match.
276   *   *
277   * @param i vector of 0-based indices   * @param x  an R object, about which we want is(x, .) information.
278   * @param n length of vector i   * @param valid vector of possible matches terminated by an empty string.
279   * @param perm 0-based permutation vector of length max(i) + 1   * @param rho  the environment in which the class definitions exist.
280     *
281     * @return index of match or -1 for no match
282   */   */
283  static R_INLINE void  static R_INLINE int
284  int_permute(int i[], int n, const int perm[])  Matrix_check_class_and_super(SEXP x, char **valid, SEXP rho)
285  {  {
286      int j;      int ans;
287      for (j = 0; j < n; j++) i[j] = perm[i[j]];      SEXP cl = getAttrib(x, R_ClassSymbol);
288        char *class = strdup(CHAR(asChar(cl)));
289        for (ans = 0; ; ans++) {
290            if (!strlen(valid[ans]))
291                break;
292            if (!strcmp(class, valid[ans])) return ans;
293        }
294        /* if not found directly, now search the non-virtual super classes :*/
295        if(IS_S4_OBJECT(x)) {
296            /* now try the superclasses, i.e.,  try   is(x, "....") : */
297            SEXP classExts = GET_SLOT(eval(lang2(install("getClassDef"), cl), rho),
298                                      install("contains")),
299                superCl = eval(lang3(install(".selectSuperClasses"),
300                                     classExts,
301                                     /* dropVirtual = */ ScalarLogical(1)),
302                               rho);
303            int i;
304            const char *s_class;
305            for(i=0; i < length(superCl); i++) {
306                s_class = CHAR(STRING_ELT(superCl, i));
307                for (ans = 0; ; ans++) {
308                    if (!strlen(valid[ans]))
309                        break;
310                    if (!strcmp(s_class, valid[ans])) return ans;
311                }
312            }
313        }
314        return -1;
315  }  }
316    
317  /**  /**
318   * Force index pairs to be in the upper triangle of a matrix   * Return the 0-based index of an is() match in a vector of class-name
319     * strings terminated by an empty string.  Returns -1 for no match.
320   *   *
321   * @param i vector of 0-based row indices   * @param x  an R object, about which we want is(x, .) information.
322   * @param j vector of 0-based column indices   * @param valid vector of possible matches terminated by an empty string.
323   * @param nnz length of index vectors   *
324     * @return index of match or -1 for no match
325   */   */
326  static R_INLINE void  static R_INLINE int
327  make_upper_triangular(int i[], int j[], int nnz)  Matrix_check_class_etc(SEXP x, char **valid)
328  {  {
329      int k;      SEXP cl = getAttrib(x, R_ClassSymbol),
330      for (k = 0; k < nnz; k++) {          pkg = getAttrib(cl, install("package")), /* ==R== packageSlot(class(x)) */
331          if (i[k] > j[k]) {          rho = (isNull(pkg) ? R_GlobalEnv
332              int tmp = i[k];                 : eval(lang2(install(".M.classEnv"), cl), R_GlobalEnv));
333              i[k] = j[k];      return Matrix_check_class_and_super(x, valid, rho);
             j[k] = tmp;  
         }  
334      }      }
 }  
   
 void make_array_triangular(double *x, SEXP from);  
335    
 SEXP Matrix_expand_pointers(SEXP pP);  
336    
337  #ifdef __cplusplus  #ifdef __cplusplus
338  }  }

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