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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 890, Thu Sep 1 17:18:08 2005 UTC revision 2298, Fri Oct 17 13:45:12 2008 UTC
# Line 5  Line 5 
5  extern "C" {  extern "C" {
6  #endif  #endif
7    
8  #include <Rdefines.h>  #include <ctype.h>
9  #include <Rconfig.h>  #include <R.h>  /* includes Rconfig.h */
10  #include <R.h>  /* to include Rconfig.h */  #include <Rversion.h>
11    #include <Rdefines.h> /* Rinternals.h + GET_SLOT etc */
12    
13  #ifdef ENABLE_NLS  #ifdef ENABLE_NLS
14  #include <libintl.h>  #include <libintl.h>
# Line 16  Line 17 
17  #define _(String) (String)  #define _(String) (String)
18  #endif  #endif
19    
20    #ifdef __GNUC__
21    # undef alloca
22    # define alloca(x) __builtin_alloca((x))
23    #elif defined(__sun) || defined(_AIX)
24    /* this is necessary (and sufficient) for Solaris 10 and AIX 6: */
25    # include <alloca.h>
26    #endif
27    
28    #define Alloca(n, t)   (t *) alloca( (size_t) ( (n) * sizeof(t) ) )
29    
30  SEXP triangularMatrix_validate(SEXP obj);  SEXP triangularMatrix_validate(SEXP obj);
31  SEXP symmetricMatrix_validate(SEXP obj);  SEXP symmetricMatrix_validate(SEXP obj);
32    SEXP dense_nonpacked_validate(SEXP obj);
33    
34  /* enum constants from cblas.h and some short forms */  /* enum constants from cblas.h and some short forms */
35  enum CBLAS_ORDER {CblasRowMajor=101, CblasColMajor=102};  enum CBLAS_ORDER {CblasRowMajor=101, CblasColMajor=102};
# Line 37  Line 49 
49  #define LFT CblasLeft  #define LFT CblasLeft
50  #define RGT CblasRight  #define RGT CblasRight
51    
52  char norm_type(char *typstr);  #if !defined(R_VERSION) || R_VERSION < R_Version(2, 7, 0)
53  char rcond_type(char *typstr);  char La_norm_type(const char *typstr);
54    char La_rcond_type(const char *typstr);
55    #endif
56    
57  double get_double_by_name(SEXP obj, char *nm);  double get_double_by_name(SEXP obj, char *nm);
58  SEXP set_double_by_name(SEXP obj, double val, char *nm);  SEXP set_double_by_name(SEXP obj, double val, char *nm);
59  SEXP as_det_obj(double val, int log, int sign);  SEXP as_det_obj(double val, int log, int sign);
60  SEXP get_factors(SEXP obj, char *nm);  SEXP get_factors(SEXP obj, char *nm);
61  SEXP set_factors(SEXP obj, SEXP val, char *nm);  SEXP set_factors(SEXP obj, SEXP val, char *nm);
62    
63    #if 0
64  SEXP dgCMatrix_set_Dim(SEXP x, int nrow);  SEXP dgCMatrix_set_Dim(SEXP x, int nrow);
65  int csc_unsorted_columns(int ncol, const int p[], const int i[]);  #endif  /* unused */
66  void csc_sort_columns(int ncol, const int p[], int i[], double x[]);  
67  SEXP triple_as_SEXP(int nrow, int ncol, int nz,  /* int csc_unsorted_columns(int ncol, const int p[], const int i[]); */
68                      const int Ti [], const int Tj [], const double Tx [],  /* void csc_sort_columns(int ncol, const int p[], int i[], double x[]); */
69                      char *Rclass);  /* SEXP csc_check_column_sorting(SEXP A); */
 SEXP csc_check_column_sorting(SEXP A);  
 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[]);  
70  SEXP Matrix_make_named(int TYP, char **names);  SEXP Matrix_make_named(int TYP, char **names);
71  SEXP check_scalar_string(SEXP sP, char *vals, char *nm);  SEXP check_scalar_string(SEXP sP, char *vals, char *nm);
72  double *packed_to_full(double *dest, const double *src, int n,  Rboolean equal_string_vectors(SEXP s1, SEXP s2);
73                         enum CBLAS_UPLO uplo);  
74  double *full_to_packed(double *dest, const double *src, int n,  void d_packed_getDiag(double *dest, SEXP x, int n);
75                         enum CBLAS_UPLO uplo, enum CBLAS_DIAG diag);  void l_packed_getDiag(   int *dest, SEXP x, int n);
76  double *packed_getDiag(double *dest, SEXP x);  void tr_d_packed_getDiag(double *dest, SEXP x);
77    void tr_l_packed_getDiag(   int *dest, SEXP x);
78    
79  SEXP Matrix_getElement(SEXP list, char *nm);  SEXP Matrix_getElement(SEXP list, char *nm);
80    
81    #define PACKED_TO_FULL(TYPE)                                            \
82    TYPE *packed_to_full_ ## TYPE(TYPE *dest, const TYPE *src,              \
83                                 int n, enum CBLAS_UPLO uplo)
84    PACKED_TO_FULL(double);
85    PACKED_TO_FULL(int);
86    #undef PACKED_TO_FULL
87    
88    #define FULL_TO_PACKED(TYPE)                                            \
89    TYPE *full_to_packed_ ## TYPE(TYPE *dest, const TYPE *src, int n,       \
90                                  enum CBLAS_UPLO uplo, enum CBLAS_DIAG diag)
91    FULL_TO_PACKED(double);
92    FULL_TO_PACKED(int);
93    #undef FULL_TO_PACKED
94    
95    
96  extern   /* stored pointers to symbols initialized in R_init_Matrix */  extern   /* stored pointers to symbols initialized in R_init_Matrix */
97  #include "Syms.h"  #include "Syms.h"
# Line 76  Line 103 
103  #define PACKED_LENGTH(n)   ((n) * ((n) + 1))/2  #define PACKED_LENGTH(n)   ((n) * ((n) + 1))/2
104    
105  /* duplicate the slot with name given by sym from src to dest */  /* duplicate the slot with name given by sym from src to dest */
106    
107  #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)))
108    
109    /* is not yet used: */
110    #define slot_nonNull_dup(dest, src, sym)                        \
111        if(GET_SLOT(src, sym) != R_NilValue)                        \
112            SET_SLOT(dest, sym, duplicate(GET_SLOT(src, sym)))
113    
114    /* TODO: Make this faster for the case where dimnames = list(NULL,NULL)
115     *       and hence don't have to be set ! */
116    #define SET_DimNames(dest, src) slot_dup(dest, src, Matrix_DimNamesSym)
117    
118    
119    #define uplo_P(_x_) CHAR(STRING_ELT(GET_SLOT(_x_, Matrix_uploSym), 0))
120    #define diag_P(_x_) CHAR(STRING_ELT(GET_SLOT(_x_, Matrix_diagSym), 0))
121    #define class_P(_x_) CHAR(asChar(getAttrib(_x_, R_ClassSymbol)))
122    
123    /* should also work for "matrix" matrices: */
124    #define Real_KIND(_x_)  (IS_S4_OBJECT(_x_) ? Real_kind(_x_) : \
125                             (isReal(_x_) ? 0 : (isLogical(_x_) ? 1 : -1)))
126    /* This one gives '0' also for integer "matrix" :*/
127    #define Real_KIND2(_x_) (IS_S4_OBJECT(_x_) ? Real_kind(_x_) : \
128                             (isLogical(_x_) ? 1 : 0))
129    
130    /* requires 'x' slot: */
131    #define Real_kind(_x_)  (isReal(GET_SLOT(_x_, Matrix_xSym)) ? 0 :       \
132                             (isLogical(GET_SLOT(_x_, Matrix_xSym)) ? 1 : -1))
133    
134    #define DECLARE_AND_GET_X_SLOT(__C_TYPE, __SEXP)        \
135        __C_TYPE *xx = __SEXP(GET_SLOT(x, Matrix_xSym))
136    
137    
138  /**  /**
139   * Check for valid length of a packed triangular array and return the   * Check for valid length of a packed triangular array and return the
140   * corresponding number of columns   * corresponding number of columns
# Line 104  Line 161 
161   * this behavior changes then ALLOC_SLOT must use SET_SLOT followed by   * this behavior changes then ALLOC_SLOT must use SET_SLOT followed by
162   * 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
163   * the slot.   * the slot.
164     * NOTE:  GET_SLOT(x, what)        :== R_do_slot       (x, what)
165     * ----   SET_SLOT(x, what, value) :== R_do_slot_assign(x, what, value)
166     * and the R_do_slot* are in src/main/attrib.c
167   *   *
168   * @param obj object in which to assign the slot   * @param obj object in which to assign the slot
169   * @param nm name of the slot, as an R name object   * @param nm name of the slot, as an R name object
# Line 142  Line 202 
202      return mj;      return mj;
203  }  }
204    
   
205  /**  /**
206   * Return the linear index of the (row, col) entry in a csc structure.   * Check if slot(obj, "x") contains any NA (or NaN).
  * If the entry is not found and missing is 0 an error is signaled;  
  * otherwise the missing value is returned.  
207   *   *
208   * @param p vector of column pointers   * @param obj   a 'Matrix' object with an 'x' slot.
  * @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.  
209   *   *
210   * @return index of element at (row, col) if it exists, otherwise missing   * @return Rboolean :== any(is.na(slot(obj, "x") )
211   */   */
212  static R_INLINE int  static R_INLINE
213  check_csc_index(const int p[], const int i[], int row, int col, int missing)  Rboolean any_NA(SEXP obj)
214  {  {
215      int k, k2 = p[col + 1];      double *x = REAL(GET_SLOT(obj, Matrix_xSym));
216                                  /* linear search - perhaps replace by bsearch */      int i, n = LENGTH(GET_SLOT(obj, Matrix_xSym));
217      for (k = p[col]; k < k2; k++) if (i[k] == row) return k;      for(i=0; i < n; i++)
218      if (!missing)          if(ISNAN(x[i])) return TRUE;
219          error("row %d and column %d not defined in rowind and colptr",      /* else */
220                row, col);      return FALSE;
     return missing;  
221  }  }
222    
 SEXP alloc3Darray(SEXPTYPE mode, int nrow, int ncol, int nface);  
223    
224  /**  void make_d_matrix_triangular(double *x, SEXP from);
225   * Calculate the zero-based index in a row-wise packed lower triangular matrix.  void make_i_matrix_triangular(   int *x, SEXP from);
  * This is used for the arrays of blocked sparse matrices.  
  *  
  * @param i column number (zero-based)  
  * @param k row number (zero-based)  
  *  
  * @return The index of the (k,i) element of a packed lower triangular matrix  
  */  
 static R_INLINE  
 int Lind(int k, int i)  
 {  
     if (k < i) error("Lind(k = %d, i = %d) must have k >= i", k, i);  
     return (k * (k + 1))/2 + i;  
 }  
226    
227  /**  void make_d_matrix_symmetric(double *to, SEXP from);
228   * Check for a complete match on matrix dimensions  void make_i_matrix_symmetric(   int *to, SEXP from);
  *  
  * @param xd dimensions of first matrix  
  * @param yd dimensions of second matrix  
  *  
  * @return 1 if dimensions match, otherwise 0  
  */  
 static R_INLINE  
 int match_mat_dims(const int xd[], const int yd[])  
 {  
     return xd[0] == yd[0] && xd[1] == yd[1];  
 }  
229    
230  double *expand_csc_column(double *dest, int m, int j,  SEXP Matrix_expand_pointers(SEXP pP);
                           const int Ap[], const int Ai[], const double Ax[]);  
231    
232  /**  SEXP dup_mMatrix_as_dgeMatrix(SEXP A);
233   * Apply a permutation to an integer vector  SEXP dup_mMatrix_as_geMatrix (SEXP A);
234   *  
235   * @param i vector of 0-based indices  SEXP new_dgeMatrix(int nrow, int ncol);
236   * @param n length of vector i  SEXP m_encodeInd (SEXP ij, SEXP di);
237   * @param perm 0-based permutation vector of length max(i) + 1  SEXP m_encodeInd2(SEXP i, SEXP j, SEXP di);
238   */  
239  static R_INLINE void  
240  int_permute(int i[], int n, const int perm[])  static R_INLINE SEXP
241    mMatrix_as_dgeMatrix(SEXP A)
242  {  {
243      int j;      return strcmp(class_P(A), "dgeMatrix") ? dup_mMatrix_as_dgeMatrix(A) : A;
     for (j = 0; j < n; j++) i[j] = perm[i[j]];  
244  }  }
245    
246  /**  static R_INLINE SEXP
247   * Force index pairs to be in the upper triangle of a matrix  mMatrix_as_geMatrix(SEXP A)
  *  
  * @param i vector of 0-based row indices  
  * @param j vector of 0-based column indices  
  * @param nnz length of index vectors  
  */  
 static R_INLINE void  
 make_upper_triangular(int i[], int j[], int nnz)  
248  {  {
249      int k;      return strcmp(class_P(A) + 1, "geMatrix") ? dup_mMatrix_as_geMatrix(A) : A;
     for (k = 0; k < nnz; k++) {  
         if (i[k] > j[k]) {  
             int tmp = i[k];  
             i[k] = j[k];  
             j[k] = tmp;  
         }  
     }  
250  }  }
251    
 void make_array_triangular(double *x, SEXP from);  
   
 SEXP Matrix_expand_pointers(SEXP pP);  
   
   
252  /**  /**
253   * Elementwise increment dest by src   * Return the 0-based index of a string match in a vector of strings
254     * terminated by an empty string.  Returns -1 for no match.
255   *   *
256   * @param dest vector to be incremented   * @param class string to match
257   * @param src vector to be added to dest   * @param valid vector of possible matches terminated by an empty string
  * @param n length of vectors  
258   *   *
259   * @return dest   * @return index of match or -1 for no match
260   */   */
261  static R_INLINE double*  static R_INLINE int
262  vecIncrement(double dest[], const double src[], int n) {  Matrix_check_class(const char *class, char **valid)
263      int i;  {
264      for (i = 0; i < n; i++) dest[i] += src[i];      int ans;
265      return dest;      for (ans = 0; ; ans++) {
266            if (!strlen(valid[ans])) return -1;
267            if (!strcmp(class, valid[ans])) return ans;
268  }  }
   
 /**  
  * Elementwise sum of src1 and src2 into dest  
  *  
  * @param dest vector to be incremented  
  * @param src1 vector to be added  
  * @param src1 second vector to be added  
  * @param n length of vectors  
  *  
  * @return dest  
  */  
 static R_INLINE double*  
 vecSum(double dest[], const double src1[], const double src2[],  
        int n) {  
     int i;  
     for (i = 0; i < n; i++) dest[i] = src1[i] + src2[i];  
     return dest;  
269  }  }
270    
271    
272  #ifdef __cplusplus  #ifdef __cplusplus
273  }  }
274  #endif  #endif

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