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

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pkg/src/Mutils.h revision 565, Tue Feb 22 01:15:45 2005 UTC pkg/Matrix/src/Mutils.h revision 2850, Mon Oct 22 13:00:35 2012 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  #include <Rdefines.h>  #undef Matrix_with_SPQR
 #include <Rconfig.h>  
 #include "cblas.h"  
5    
6  /* short forms of some enum constants from cblas.h */  #ifdef __cplusplus
7    extern "C" {
8    #endif
9    
10    #include <stdint.h> // C99 for int64_t
11    #include <ctype.h>
12    #include <R.h>  /* includes Rconfig.h */
13    #include <Rversion.h>
14    #include <Rdefines.h> /* Rinternals.h + GET_SLOT etc */
15    
16    #ifdef ENABLE_NLS
17    #include <libintl.h>
18    #define _(String) dgettext ("Matrix", String)
19    #else
20    #define _(String) (String)
21    /* Note that this is not yet supported (for Windows, e.g.) in R 2.9.0 : */
22    #define dngettext(pkg, String, StringP, N) (N > 1 ? StringP : String)
23    #endif
24    
25    #ifdef __GNUC__
26    # undef alloca
27    # define alloca(x) __builtin_alloca((x))
28    #elif defined(__sun) || defined(_AIX)
29    /* this is necessary (and sufficient) for Solaris 10 and AIX 6: */
30    # include <alloca.h>
31    #endif
32    
33    #ifndef LONG_VECTOR_SUPPORT
34    // notably for  R <= 2.15.x :
35    # define XLENGTH(x) LENGTH(x)
36    # if R_VERSION < R_Version(2,16,0)
37      typedef int R_xlen_t;
38    # endif
39    #endif
40    
41    #define Alloca(n, t)   (t *) alloca( (size_t) ( (n) * sizeof(t) ) )
42    
43    SEXP triangularMatrix_validate(SEXP obj);
44    SEXP symmetricMatrix_validate(SEXP obj);
45    SEXP dense_nonpacked_validate(SEXP obj);
46    
47    // La_norm_type() & La_rcond_type()  have been in R_ext/Lapack.h
48    //  but have still not been available to package writers ...
49    char La_norm_type (const char *typstr);
50    char La_rcond_type(const char *typstr);
51    
52    /* enum constants from cblas.h and some short forms */
53    enum CBLAS_ORDER {CblasRowMajor=101, CblasColMajor=102};
54    enum CBLAS_TRANSPOSE {CblasNoTrans=111, CblasTrans=112, CblasConjTrans=113};
55    enum CBLAS_UPLO {CblasUpper=121, CblasLower=122};
56    enum CBLAS_DIAG {CblasNonUnit=131, CblasUnit=132};
57    enum CBLAS_SIDE {CblasLeft=141, CblasRight=142};
58  #define RMJ CblasRowMajor  #define RMJ CblasRowMajor
59  #define CMJ CblasColMajor  #define CMJ CblasColMajor
60  #define NTR CblasNoTrans  #define NTR CblasNoTrans
# Line 18  Line 67 
67  #define LFT CblasLeft  #define LFT CblasLeft
68  #define RGT CblasRight  #define RGT CblasRight
69    
 char norm_type(char *typstr);  
 char rcond_type(char *typstr);  
70  double get_double_by_name(SEXP obj, char *nm);  double get_double_by_name(SEXP obj, char *nm);
71  SEXP set_double_by_name(SEXP obj, double val, char *nm);  SEXP set_double_by_name(SEXP obj, double val, char *nm);
72  SEXP as_det_obj(double val, int log, int sign);  SEXP as_det_obj(double val, int log, int sign);
73  SEXP get_factors(SEXP obj, char *nm);  SEXP get_factors(SEXP obj, char *nm);
74  SEXP set_factors(SEXP obj, SEXP val, char *nm);  SEXP set_factors(SEXP obj, SEXP val, char *nm);
75    
76    #if 0
77  SEXP dgCMatrix_set_Dim(SEXP x, int nrow);  SEXP dgCMatrix_set_Dim(SEXP x, int nrow);
78  int csc_unsorted_columns(int ncol, const int p[], const int i[]);  #endif  /* unused */
79  void csc_sort_columns(int ncol, const int p[], int i[], double x[]);  
80  SEXP triple_as_SEXP(int nrow, int ncol, int nz,  /* int csc_unsorted_columns(int ncol, const int p[], const int i[]); */
81                      const int Ti [], const int Tj [], const double Tx [],  /* void csc_sort_columns(int ncol, const int p[], int i[], double x[]); */
82                      char *Rclass);  /* SEXP csc_check_column_sorting(SEXP A); */
83  SEXP csc_check_column_sorting(SEXP A);  
84  void csc_components_transpose(int m, int n, int nnz,  SEXP check_scalar_string(SEXP sP, char *vals, char *nm);
85                                const int xp[], const int xi[],  Rboolean equal_string_vectors(SEXP s1, SEXP s2);
86                                const double xx[],  
87                                int ap[], int ai[], double ax[]);  void d_packed_getDiag(double *dest, SEXP x, int n);
88  void ssc_symbolic_permute(int n, int upper, const int perm[],  void l_packed_getDiag(   int *dest, SEXP x, int n);
89                            int Ap[], int Ai[]);  SEXP d_packed_setDiag(double *diag, int l_d, SEXP x, int n);
90  double *nlme_symmetrize(double *a, const int nc);  SEXP l_packed_setDiag(   int *diag, int l_d, SEXP x, int n);
91  void nlme_check_Lapack_error(int info, const char *laName);  SEXP d_packed_addDiag(double *diag, int l_d, SEXP x, int n);
92  SEXP nlme_replaceSlot(SEXP obj, SEXP names, SEXP value);  
93  SEXP nlme_weight_matrix_list(SEXP MLin, SEXP wts, SEXP adjst, SEXP MLout);  void tr_d_packed_getDiag(double *dest, SEXP x, int n);
94  SEXP Matrix_make_named(int TYP, char **names);  void tr_l_packed_getDiag(   int *dest, SEXP x, int n);
95                                  /* stored pointers to symbols */  
96                                  /* initialized in R_init_Matrix */  SEXP tr_d_packed_setDiag(double *diag, int l_d, SEXP x, int n);
97  extern  SEXP tr_l_packed_setDiag(   int *diag, int l_d, SEXP x, int n);
98    SEXP tr_d_packed_addDiag(double *diag, int l_d, SEXP x, int n);
99    
100    SEXP Matrix_getElement(SEXP list, char *nm);
101    
102    #define PACKED_TO_FULL(TYPE)                                            \
103    TYPE *packed_to_full_ ## TYPE(TYPE *dest, const TYPE *src,              \
104                                 int n, enum CBLAS_UPLO uplo)
105    PACKED_TO_FULL(double);
106    PACKED_TO_FULL(int);
107    #undef PACKED_TO_FULL
108    
109    #define FULL_TO_PACKED(TYPE)                                            \
110    TYPE *full_to_packed_ ## TYPE(TYPE *dest, const TYPE *src, int n,       \
111                                  enum CBLAS_UPLO uplo, enum CBLAS_DIAG diag)
112    FULL_TO_PACKED(double);
113    FULL_TO_PACKED(int);
114    #undef FULL_TO_PACKED
115    
116    
117    extern   /* stored pointers to symbols initialized in R_init_Matrix */
118  #include "Syms.h"  #include "Syms.h"
119    
120  /* zero an array */  /* zero an array */
121  #define AZERO(x, n) {int _I_, _SZ_ = (n); for(_I_ = 0; _I_ < _SZ_; _I_++) (x)[_I_] = 0;}  #define AZERO(x, n) {int _I_, _SZ_ = (n); for(_I_ = 0; _I_ < _SZ_; _I_++) (x)[_I_] = 0;}
122    
123    /* number of elements in one triangle of a square matrix of order n */
124    #define PACKED_LENGTH(n)   ((n) * ((n) + 1))/2
125    
126    /* duplicate the slot with name given by sym from src to dest */
127    
128    #define slot_dup(dest, src, sym)  SET_SLOT(dest, sym, duplicate(GET_SLOT(src, sym)))
129    
130    /* is not yet used: */
131    #define slot_nonNull_dup(dest, src, sym)                        \
132        if(GET_SLOT(src, sym) != R_NilValue)                        \
133            SET_SLOT(dest, sym, duplicate(GET_SLOT(src, sym)))
134    
135    #define slot_dup_if_has(dest, src, sym)                         \
136        if(R_has_slot(src, sym))                                    \
137            SET_SLOT(dest, sym, duplicate(GET_SLOT(src, sym)))
138    
139    /* TODO: Make this faster for the case where dimnames = list(NULL,NULL)
140     *       and hence don't have to be set ! */
141    #define SET_DimNames(dest, src) slot_dup(dest, src, Matrix_DimNamesSym)
142    
143    
144    #define uplo_P(_x_) CHAR(STRING_ELT(GET_SLOT(_x_, Matrix_uploSym), 0))
145    #define diag_P(_x_) CHAR(STRING_ELT(GET_SLOT(_x_, Matrix_diagSym), 0))
146    #define Diag_P(_x_) (R_has_slot(x, Matrix_diagSym) ?                    \
147                         CHAR(STRING_ELT(GET_SLOT(_x_, Matrix_diagSym), 0)) : " ")
148    #define class_P(_x_) CHAR(asChar(getAttrib(_x_, R_ClassSymbol)))
149    
150    
151    // Define this "Cholmod compatible" to some degree
152    enum x_slot_kind {x_pattern=-1, x_double=0, x_logical=1, x_integer=2, x_complex=3};
153    //                  n             d           l            i            z
154    
155    /* should also work for "matrix" matrices: */
156    #define Real_KIND(_x_)  (IS_S4_OBJECT(_x_) ? Real_kind(_x_) : \
157                             (isReal(_x_) ? x_double : (isLogical(_x_) ? x_logical : -1)))
158    /* This one gives '0' also for integer "matrix" :*/
159    #define Real_KIND2(_x_) (IS_S4_OBJECT(_x_) ? Real_kind(_x_) : \
160                             (isLogical(_x_) ? x_logical : 0))
161    
162    /* requires 'x' slot: */
163    #define Real_kind(_x_)  (isReal(GET_SLOT(_x_, Matrix_xSym)) ? 0 :       \
164                             (isLogical(GET_SLOT(_x_, Matrix_xSym)) ? 1 : -1))
165    
166    #define DECLARE_AND_GET_X_SLOT(__C_TYPE, __SEXP)        \
167        __C_TYPE *xx = __SEXP(GET_SLOT(x, Matrix_xSym))
168    
169    
170    /**
171     * Check for valid length of a packed triangular array and return the
172     * corresponding number of columns
173     *
174     * @param len length of a packed triangular array
175     *
176     * @return number of columns
177     */
178    static R_INLINE
179    int packed_ncol(int len)
180    {
181        int disc = 8 * len + 1;     /* discriminant */
182        int sqrtd = (int) sqrt((double) disc);
183    
184        if (len < 0 || disc != sqrtd * sqrtd)
185            error(_("invalid 'len' = %d in packed_ncol"));
186        return (sqrtd - 1)/2;
187    }
188    
189  /**  /**
190   * Allocate an SEXP of given type and length, assign it as slot nm in   * Allocate an SEXP of given type and length, assign it as slot nm in
191   * the object, and return the SEXP.  The validity of this function   * the object, and return the SEXP.  The validity of this function
# Line 58  Line 193 
193   * this behavior changes then ALLOC_SLOT must use SET_SLOT followed by   * this behavior changes then ALLOC_SLOT must use SET_SLOT followed by
194   * 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
195   * the slot.   * the slot.
196     * NOTE:  GET_SLOT(x, what)        :== R_do_slot       (x, what)
197     * ----   SET_SLOT(x, what, value) :== R_do_slot_assign(x, what, value)
198     * and the R_do_slot* are in src/main/attrib.c
199   *   *
200   * @param obj object in which to assign the slot   * @param obj object in which to assign the slot
201   * @param nm name of the slot, as an R name object   * @param nm name of the slot, as an R name object
# Line 76  Line 214 
214  }  }
215    
216  /**  /**
217   * Expand the column pointers in the array mp into a full set of column indices   * Expand compressed pointers in the array mp into a full set of indices
218   * in the array mj.   * in the array mj.
219   *   *
220   * @param ncol number of columns   * @param ncol number of columns (or rows)
221   * @param mp column pointer vector of length ncol + 1   * @param mp column pointer vector of length ncol + 1
222   * @param mj vector of length mp[ncol] - 1 to hold the result   * @param mj vector of length mp[ncol] to hold the result
223   *   *
224   * @return mj   * @return mj
225   */   */
226  static R_INLINE  static R_INLINE
227  int* expand_column_pointers(int ncol, const int mp[], int mj[])  int* expand_cmprPt(int ncol, const int mp[], int mj[])
228  {  {
229      int j;      int j;
230      for (j = 0; j < ncol; j++) {      for (j = 0; j < ncol; j++) {
# Line 96  Line 234 
234      return mj;      return mj;
235  }  }
236    
   
237  /**  /**
238   * 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.  
  *  
  * @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.  
239   *   *
240   * @return index of element at (row, col) if it exists, otherwise missing   * @param obj   a 'Matrix' object with a (double precision) 'x' slot.
241     *
242     * @return Rboolean :== any(is.na(slot(obj, "x") )
243   */   */
244  static R_INLINE int  static R_INLINE
245  check_csc_index(const int p[], const int i[], int row, int col, int missing)  Rboolean any_NA_in_x(SEXP obj)
246  {  {
247      int k, k2 = p[col + 1];      double *x = REAL(GET_SLOT(obj, Matrix_xSym));
248                                  /* linear search - perhaps replace by bsearch */      int i, n = LENGTH(GET_SLOT(obj, Matrix_xSym));
249      for (k = p[col]; k < k2; k++) if (i[k] == row) return k;      for(i=0; i < n; i++)
250      if (!missing)          if(ISNAN(x[i])) return TRUE;
251          error("row %d and column %d not defined in rowind and colptr",      /* else */
252                row, col);      return FALSE;
     return missing;  
253  }  }
254    
255  SEXP alloc3Darray(SEXPTYPE mode, int nrow, int ncol, int nface);  SEXP Mmatrix(SEXP args);
256    
257  /**  void make_d_matrix_triangular(double *x, SEXP from);
258   * Calculate the zero-based index in a row-wise packed lower triangular matrix.  void make_i_matrix_triangular(   int *x, SEXP from);
259   * This is used for the arrays of blocked sparse matrices.  
260   *  void make_d_matrix_symmetric(double *to, SEXP from);
261   * @param i column number (zero-based)  void make_i_matrix_symmetric(   int *to, SEXP from);
262   * @param k row number (zero-based)  
263   *  SEXP Matrix_expand_pointers(SEXP pP);
264   * @return The index of the (k,i) element of a packed lower triangular matrix  
265   */  SEXP dup_mMatrix_as_dgeMatrix(SEXP A);
266  static R_INLINE  SEXP dup_mMatrix_as_geMatrix (SEXP A);
267  int Lind(int k, int i)  
268    SEXP new_dgeMatrix(int nrow, int ncol);
269    SEXP m_encodeInd (SEXP ij, SEXP di, SEXP chk_bnds);
270    SEXP m_encodeInd2(SEXP i, SEXP j, SEXP di, SEXP chk_bnds);
271    
272    
273    static R_INLINE SEXP
274    mMatrix_as_dgeMatrix(SEXP A)
275  {  {
276      if (k < i) error("Lind(k = %d, i = %d) must have k >= i", k, i);      return strcmp(class_P(A), "dgeMatrix") ? dup_mMatrix_as_dgeMatrix(A) : A;
     return (k * (k + 1))/2 + i;  
277  }  }
278    
279  /**  static R_INLINE SEXP
280   * Check for a complete match on matrix dimensions  mMatrix_as_geMatrix(SEXP A)
  *  
  * @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[])  
281  {  {
282      return xd[0] == yd[0] && xd[1] == yd[1];      return strcmp(class_P(A) + 1, "geMatrix") ? dup_mMatrix_as_geMatrix(A) : A;
283  }  }
284    
285  double *expand_csc_column(double *dest, int m, int j,  // Keep centralized --- *and* in sync with ../inst/include/Matrix.h :
286                            const int Ap[], const int Ai[], const double Ax[]);  #define MATRIX_VALID_dense                      \
287            "dmatrix", "dgeMatrix",                 \
288  #endif          "lmatrix", "lgeMatrix",                 \
289            "nmatrix", "ngeMatrix",                 \
290            "zmatrix", "zgeMatrix"
291    
292    #define MATRIX_VALID_Csparse                    \
293     "dgCMatrix", "dsCMatrix", "dtCMatrix",         \
294     "lgCMatrix", "lsCMatrix", "ltCMatrix",         \
295     "ngCMatrix", "nsCMatrix", "ntCMatrix",         \
296     "zgCMatrix", "zsCMatrix", "ztCMatrix"
297    
298    #define MATRIX_VALID_Tsparse                    \
299     "dgTMatrix", "dsTMatrix", "dtTMatrix",         \
300     "lgTMatrix", "lsTMatrix", "ltTMatrix",         \
301     "ngTMatrix", "nsTMatrix", "ntTMatrix",         \
302     "zgTMatrix", "zsTMatrix", "ztTMatrix"
303    
304    #define MATRIX_VALID_Rsparse                    \
305     "dgRMatrix", "dsRMatrix", "dtRMatrix",         \
306     "lgRMatrix", "lsRMatrix", "ltRMatrix",         \
307     "ngRMatrix", "nsRMatrix", "ntRMatrix",         \
308     "zgRMatrix", "zsRMatrix", "ztRMatrix"
309    
310    #define MATRIX_VALID_CHMfactor "dCHMsuper", "dCHMsimpl", "nCHMsuper", "nCHMsimpl"
311    
312  /**  /**
313   * Apply a permutation to an integer vector   * Return the 0-based index of a string match in a vector of strings
314     * terminated by an empty string.  Returns -1 for no match.
315     *
316     * @param class string to match
317     * @param valid vector of possible matches terminated by an empty string
318   *   *
319   * @param i vector of 0-based indices   * @return index of match or -1 for no match
  * @param n length of vector i  
  * @param perm 0-based permutation vector of length max(i) + 1  
320   */   */
321  static R_INLINE void  static R_INLINE int
322  int_permute(int i[], int n, const int perm[])  Matrix_check_class(char *class, const char **valid)
323  {  {
324      int j;      int ans;
325      for (j = 0; j < n; j++) i[j] = perm[i[j]];      for (ans = 0; ; ans++) {
326            if (!strlen(valid[ans])) return -1;
327            if (!strcmp(class, valid[ans])) return ans;
328        }
329  }  }
330    
331  /**  /**
332   * Force index pairs to be in the upper triangle of a matrix   * These are the ones "everyone" should use -- is() versions, also looking
333   *   * at super classes:
  * @param i vector of 0-based row indices  
  * @param j vector of 0-based column indices  
  * @param nnz length of index vectors  
334   */   */
335  static R_INLINE void  # define Matrix_check_class_etc R_check_class_etc
336  make_upper_triangular(int i[], int j[], int nnz)  # define Matrix_check_class_and_super R_check_class_and_super
337  {  
338      int k;  /** Accessing  *sparseVectors :  fast (and recycling)  v[i] for v = ?sparseVector:
339      for (k = 0; k < nnz; k++) {   * -> ./sparseVector.c  -> ./t_sparseVector.c :
340          if (i[k] > j[k]) {   */
341              int tmp = i[k];  // Type_ans sparseVector_sub(int64_t i, int nnz_v, int* v_i, Type_ans* v_x, int len_v):
342              i[k] = j[k];  
343              j[k] = tmp;  /* Define all of
344          }   *  dsparseVector_sub(....)
345      }   *  isparseVector_sub(....)
346     *  lsparseVector_sub(....)
347     *  nsparseVector_sub(....)
348     *  zsparseVector_sub(....)
349     */
350    #define _dspV_
351    #include "t_sparseVector.c"
352    
353    #define _ispV_
354    #include "t_sparseVector.c"
355    
356    #define _lspV_
357    #include "t_sparseVector.c"
358    
359    #define _nspV_
360    #include "t_sparseVector.c"
361    
362    #define _zspV_
363    #include "t_sparseVector.c"
364    
365    
366    #ifdef __cplusplus
367  }  }
368    #endif
369    
370    #endif /* MATRIX_MUTILS_H_ */

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