gsl-nmatrix 1.15.3.0

data/gsl.gemspec

@@ -0,0 +1,36 @@
+lib = File.expand_path('../lib/', __FILE__)
+$:.unshift lib unless $:.include?(lib)
+
+Gem::Specification.new do |gem|
+  gem.name = "gsl-nmatrix"
+  gem.version = File.readlines('VERSION')[0].chomp
+  gem.summary = 'Ruby interface to GNU Scientific Library (NMatrix fork)'
+  gem.description = 'Ruby/GSL is a Ruby interface to the GNU Scientific Library, for numerical computing with Ruby'
+  gem.homepage = 'http://rb-gsl.rubyforge.org/'
+  gem.authors = ['Yoshiki Tsunesada', 'David MacMahon', 'John Woods', 'Masaomi Hakateyama']
+  gem.email = 'y-tsunesada@mm.em-net.ne.jp'
+
+  gem.files         = `git ls-files`.split("\n")
+  gem.test_files    = `git ls-files -- {test,spec,features}/*`.split("\n")
+  #gem.executables   = `git ls-files -- bin/*`.split("\n").map{ |f| File.basename(f) }
+  gem.extensions = %w[ ext/extconf.rb ]
+  gem.require_paths = ["lib", "lib/gsl", "lib/ool", "ext"]
+
+  gem.required_ruby_version = '>= 1.8.1'
+
+  gem.add_dependency 'nmatrix', "> 0.0.9"
+  # gem.add_dependency 'narray', '>= 0.5.9'
+
+  gem.has_rdoc = true
+  gem.rdoc_options = [
+      '--title', 'Ruby/GSL',
+      '--main', 'rdoc/index.rdoc',
+      '--exclude', 'ext/',
+      '--exclude', 'include/',
+      '--exclude', 'lib/',
+    ]
+  #gem.extra_rdoc_files = FileList['rdoc/*'].to_a
+
+
+end
+

data/include/rb_gsl.h

@@ -0,0 +1,162 @@
+/*
+  rb_gsl.h
+  Ruby/GSL: Ruby extension library for GSL (GNU Scientific Library)
+    (C) Copyright 2001-2004 by Yoshiki Tsunesada
+
+  Ruby/GSL is free software: you can redistribute it and/or modify it
+  under the terms of the GNU General Public License.
+  This library is distributed in the hope that it will be useful, but
+  WITHOUT ANY WARRANTY
+*/
+
+#ifndef ___RB_GSL_H___
+#define ___RB_GSL_H___
+
+#include <stdio.h>
+#include <string.h>
+#include <ctype.h>
+#include <stdlib.h>
+#include <gsl/gsl_mode.h>
+#include "rb_gsl_common.h"
+#include "rb_gsl_math.h"
+#include "rb_gsl_complex.h"
+#include "rb_gsl_array.h"
+#include "rb_gsl_function.h"
+#include "rb_gsl_poly.h"
+#include "rb_gsl_sf.h"
+#include "rb_gsl_linalg.h"
+#include "rb_gsl_eigen.h"
+#include "rb_gsl_fft.h"
+#include "rb_gsl_integration.h"
+#include "rb_gsl_rng.h"
+#include "rb_gsl_statistics.h"
+#include "rb_gsl_histogram.h"
+#include "rb_gsl_odeiv.h"
+#include "rb_gsl_interp.h"
+#include "rb_gsl_cheb.h"
+#include "rb_gsl_root.h"
+#include "rb_gsl_fit.h"
+#include "rb_gsl_const.h"
+#include "rb_gsl_config.h"
+
+
+#include "ruby.h"
+#ifdef RUBY_1_9_LATER
+#include "ruby/io.h"
+#else
+#include "rubyio.h"
+#endif
+
+void Init_gsl_error(VALUE module);
+void Init_gsl_math(VALUE module);
+void Init_gsl_complex(VALUE module);
+void Init_gsl_array(VALUE module);
+void Init_gsl_blas(VALUE module);
+void Init_gsl_sort(VALUE module);
+void Init_gsl_poly(VALUE module);
+void Init_gsl_poly_int(VALUE module);
+void Init_gsl_poly2(VALUE module);
+void Init_gsl_rational(VALUE module);
+void Init_gsl_sf(VALUE module);
+void Init_gsl_linalg(VALUE module);
+void Init_gsl_eigen(VALUE module);
+void Init_gsl_fft(VALUE module);
+void Init_gsl_signal(VALUE module);
+void Init_gsl_function(VALUE module);
+void Init_gsl_integration(VALUE module);
+
+void Init_gsl_rng(VALUE module);
+void Init_gsl_qrng(VALUE module);
+void Init_gsl_ran(VALUE module);
+void Init_gsl_cdf(VALUE module);
+void Init_gsl_stats(VALUE module);
+
+void Init_gsl_histogram(VALUE module);
+void Init_gsl_histogram2d(VALUE module);
+void Init_gsl_histogram3d(VALUE module);
+void Init_gsl_ntuple(VALUE module);
+void Init_gsl_monte(VALUE module);
+void Init_gsl_siman(VALUE module);
+
+void Init_gsl_odeiv(VALUE module);
+void Init_gsl_interp(VALUE module);
+void Init_gsl_spline(VALUE module);
+void Init_gsl_diff(VALUE module);
+#ifdef GSL_1_4_9_LATER
+void Init_gsl_deriv(VALUE module);
+#endif
+
+void Init_gsl_cheb(VALUE module);
+void Init_gsl_sum(VALUE module);
+void Init_gsl_dht(VALUE module);
+
+void Init_gsl_root(VALUE module);
+void Init_gsl_multiroot(VALUE module);
+void Init_gsl_min(VALUE module);
+void Init_gsl_multimin(VALUE module);
+void Init_gsl_fit(VALUE module);
+void Init_gsl_multifit(VALUE module);
+
+void Init_gsl_const(VALUE module);
+
+void Init_gsl_ieee(VALUE module);
+
+#ifdef HAVE_NMATRIX_H
+void Init_gsl_nmatrix(VALUE module);
+#else
+# ifdef HAVE_NARRAY_H
+void Init_gsl_narray(VALUE module);
+# endif
+#endif
+
+void Init_wavelet(VALUE module);
+
+void Init_gsl_graph(VALUE module);
+
+#ifdef HAVE_TENSOR_TENSOR_H
+void Init_tensor_init(VALUE module);
+void Init_tensor_int_init(VALUE module);
+#endif
+
+void Init_gsl_dirac(VALUE module);
+
+EXTERN VALUE cGSL_Object;
+
+void Init_tamu_anova(VALUE module);
+
+#ifdef HAVE_TAMU_ANOVA_TAMU_ANOVA_H
+#include "tamu_anova/tamu_anova.h"
+#endif
+
+#ifdef HAVE_OOL_OOL_VERSION_H
+void Init_ool(VALUE module);
+#endif
+
+#ifdef HAVE_JACOBI_H
+void Init_jacobi(VALUE module);
+#endif
+
+#ifdef HAVE_GSL_GSL_CQP_H
+void Init_cqp(VALUE module);
+#endif
+
+void Init_fresnel(VALUE module);
+
+#ifdef GSL_1_9_LATER
+void Init_bspline(VALUE module);
+#endif
+
+#ifdef HAVE_ALF_ALF_H
+#include "alf/alf.h"
+#endif
+void Init_alf(VALUE module);
+void Init_geometry(VALUE module);
+
+#ifdef GSL_1_14_LATER
+#include <gsl/gsl_multiset.h>
+extern VALUE cMultiset;
+void Init_multiset(VALUE module);
+
+#endif
+
+#endif

data/include/rb_gsl_array.h

@@ -0,0 +1,302 @@
+/*
+  rb_gsl_array.h
+  Ruby/GSL: Ruby extension library for GSL (GNU Scientific Library)
+    (C) Copyright 2001-2004 by Yoshiki Tsunesada
+
+  Ruby/GSL is free software: you can redistribute it and/or modify it
+  under the terms of the GNU General Public License.
+  This library is distributed in the hope that it will be useful, but
+  WITHOUT ANY WARRANTY
+*/
+
+#ifndef ___RB_GSL_ARRAY_H___
+#define ___RB_GSL_ARRAY_H___
+
+#include <math.h>
+#include <gsl/gsl_errno.h>
+#include <gsl/gsl_complex.h>
+#include <gsl/gsl_block.h>
+#include <gsl/gsl_vector.h>
+#include <gsl/gsl_vector_complex.h>
+#include <gsl/gsl_vector_complex_double.h>
+#include <gsl/gsl_matrix.h>
+#include <gsl/gsl_matrix_complex_double.h>
+#include <gsl/gsl_permutation.h>
+#include <gsl/gsl_combination.h>
+#include <gsl/gsl_sort.h>
+#include <gsl/gsl_sort_vector.h>
+#include <gsl/gsl_linalg.h>
+#include <gsl/gsl_eigen.h>
+#include <gsl/gsl_odeiv.h>
+#include <gsl/gsl_blas.h>
+#include "rb_gsl_config.h"
+
+#include "ruby.h"
+#ifdef RUBY_1_9_LATER
+#include "ruby/io.h"
+#else
+#include "rubyio.h"
+#endif
+
+#include "rb_gsl_common.h"
+
+typedef gsl_permutation gsl_index;
+
+#ifdef HAVE_NARRAY_H
+EXTERN VALUE cNArray;
+#endif
+
+#ifdef HAVE_NMATRIX_H
+EXTERN VALUE cNMatrix;
+#endif
+
+EXTERN VALUE cgsl_block, cgsl_block_int;
+EXTERN VALUE cgsl_block_uchar;
+EXTERN VALUE cgsl_block_complex;
+EXTERN VALUE cgsl_vector, cgsl_vector_complex;
+EXTERN VALUE cgsl_vector_col;
+EXTERN VALUE cgsl_vector_col_view;
+EXTERN VALUE cgsl_vector_complex_col;
+EXTERN VALUE cgsl_vector_complex_col_view;
+EXTERN VALUE cgsl_vector_view, cgsl_vector_complex_view;
+EXTERN VALUE cgsl_vector_view_ro, cgsl_vector_col_view_ro;
+EXTERN VALUE cgsl_vector_complex_view_ro;
+
+EXTERN VALUE cgsl_vector_int, cgsl_vector_int_col;
+EXTERN VALUE cgsl_vector_int_view, cgsl_vector_int_col_view;
+EXTERN VALUE cgsl_vector_int_view_ro, cgsl_vector_int_col_view_ro;
+
+EXTERN VALUE cgsl_matrix, cgsl_matrix_complex;
+EXTERN VALUE cgsl_matrix_view_ro;
+EXTERN VALUE cgsl_matrix_complex_view_ro;
+EXTERN VALUE cgsl_matrix_view, cgsl_matrix_complex_view;
+EXTERN VALUE cgsl_matrix_int, cgsl_matrix_int_view;
+EXTERN VALUE cgsl_matrix_int_view_ro;
+EXTERN VALUE cgsl_permutation;
+EXTERN VALUE cgsl_index;
+EXTERN VALUE cgsl_function;
+EXTERN VALUE mgsl_narray;
+
+EXTERN VALUE mDirac;
+
+gsl_matrix_view* gsl_matrix_view_alloc();
+void gsl_matrix_view_free(gsl_matrix_view * mv);
+gsl_vector_view* gsl_vector_view_alloc();
+void gsl_vector_view_free(gsl_vector_view * v);
+gsl_vector_complex_view* gsl_vector_complex_view_alloc();
+void gsl_vector_complex_view_free(gsl_vector_view * vv);
+gsl_matrix_complex_view* gsl_matrix_complex_view_alloc();
+void gsl_matrix_complex_view_free(gsl_matrix_view * vv);
+
+VALUE rb_gsl_vector_new(int argc, VALUE *argv, VALUE klass);
+
+gsl_vector* get_cvector(VALUE v);
+VALUE make_rarray_from_cvector(const gsl_vector *v);
+VALUE make_rarray_from_cpermutation(const gsl_permutation *v);
+gsl_vector* make_cvector_from_rarrays(VALUE a);
+gsl_vector* make_cvector_from_rarray(VALUE a);
+void cvector_set_from_carray(gsl_vector *v, const double *a);
+void cvector_set_from_rarrays(gsl_vector *v, VALUE ary);
+void cvector_set_from_rarray(gsl_vector *v, VALUE ary);
+void carray_set_from_cvector(double *a, const gsl_vector *v);
+void carray_set_from_rarrays(double *a, VALUE ary);
+void carray_set_from_rarray(double *a, VALUE ary);
+int is_vector_p(VALUE obj);
+void check_vector(VALUE obj);
+int is_vector_complex_p(VALUE obj);
+void check_vector_complex(VALUE obj);
+int is_matrix_p(VALUE obj);
+void check_matrix(VALUE obj);
+int is_matrix_complex_p(VALUE obj);
+void check_matrix_complex(VALUE obj);
+gsl_complex* make_complex(double re, double im);
+int is_permutation_p(VALUE obj);
+void check_permutation(VALUE obj);
+int is_combination_p(VALUE obj);
+void check_combination(VALUE obj);
+gsl_vector* get_vector(VALUE ary);
+gsl_matrix* make_matrix_clone(const gsl_matrix *m);
+gsl_matrix_int* make_matrix_int_clone(const gsl_matrix_int *m);
+VALUE make_matrix_clone2(VALUE vm);
+gsl_matrix_complex* make_matrix_complex_clone(const gsl_matrix_complex *m);
+int is_matrix_complex_p(VALUE obj);
+void check_matrix_complex(VALUE obj);
+
+double* get_vector_ptr(VALUE ary, size_t *stride, size_t *n);
+
+
+gsl_matrix_complex* matrix_to_complex(const gsl_matrix *m);
+
+void gsl_matrix_complex_mul(gsl_matrix_complex *mnew, const gsl_matrix_complex *m, 
+			    const gsl_matrix_complex *mb);
+void gsl_matrix_mul(gsl_matrix *mnew, gsl_matrix *m, gsl_matrix *b);
+void gsl_matrix_complex_mul_vector(gsl_vector_complex *vnew, 
+				   const gsl_matrix_complex *m, 
+				   const gsl_vector_complex *v);
+void gsl_matrix_mul_vector(gsl_vector *vnew, 
+			   const gsl_matrix *m, const gsl_vector *v);
+gsl_vector_complex* vector_to_complex(const gsl_vector *v);
+
+gsl_vector* make_vector_clone(const gsl_vector *v);
+gsl_vector_complex* make_vector_complex_clone(const gsl_vector_complex *v);
+int gsl_vector_complex_add(gsl_vector_complex *cv, const gsl_vector_complex *cv2);
+int gsl_vector_complex_sub(gsl_vector_complex *cv, const gsl_vector_complex *cv2);
+int gsl_vector_complex_mul(gsl_vector_complex *cv, const gsl_vector_complex *cv2);
+int gsl_vector_complex_div(gsl_vector_complex *cv, const gsl_vector_complex *cv2);
+int gsl_vector_complex_add_constant(gsl_vector_complex *cv, gsl_complex b);
+int gsl_vector_complex_scale(gsl_vector_complex *cv, gsl_complex b);
+gsl_vector_view* rb_gsl_make_vector_view(double *data, size_t size, size_t stride);
+gsl_vector_int_view* rb_gsl_make_vector_int_view(int *data, size_t size, size_t stride);
+
+void Init_gsl_array_complex(VALUE module);
+void Init_gsl_vector(VALUE module);
+void Init_gsl_vector_complex(VALUE module);
+void Init_gsl_matrix(VALUE module);
+void Init_gsl_matrix_complex(VALUE module);
+void Init_gsl_matrix(VALUE module);
+void Init_gsl_permutation(VALUE module);
+void Init_gsl_combination(VALUE module);
+void Init_gsl_matrix_int(VALUE module);
+
+VALUE rb_gsl_range2ary(VALUE obj);
+
+void Init_gsl_vector_int();
+gsl_vector_int_view* rb_gsl_vector_int_view_alloc(size_t n);
+void rb_gsl_vector_int_view_free(gsl_vector_int_view *v);
+gsl_vector_int* make_vector_int_clone(const gsl_vector_int *v);
+gsl_matrix_int_view* rb_gsl_matrix_int_view_alloc();
+void rb_gsl_matrix_int_view_free(gsl_matrix_int_view *v);
+VALUE rb_gsl_matrix_to_i(VALUE obj);
+VALUE rb_gsl_matrix_int_to_f(VALUE obj);
+void gsl_matrix_int_mul_vector(gsl_vector_int *vnew, 
+			       const gsl_matrix_int *m, const gsl_vector_int *v);
+VALUE rb_gsl_vector_to_i(VALUE obj);
+VALUE make_rarray_from_cvector_int(const gsl_vector_int *v);
+VALUE rb_gsl_vector_int_to_f(VALUE obj);
+VALUE rb_gsl_vector_uminus(VALUE obj);
+VALUE rb_gsl_vector_print(VALUE obj);
+void gsl_vector_print(const gsl_vector *v, VALUE klass);
+int rbgsl_vector_equal(const gsl_vector *v1, const gsl_vector *v2, double eps);
+
+#ifndef GSL_1_2_LATER
+int gsl_matrix_complex_add(gsl_matrix_complex * a, const gsl_matrix_complex * b);
+int gsl_matrix_complex_sub(gsl_matrix_complex * a, const gsl_matrix_complex * b);
+int gsl_matrix_complex_mul_elements(gsl_matrix_complex * a, const gsl_matrix_complex * b);
+int gsl_matrix_complex_div_elements(gsl_matrix_complex * a, const gsl_matrix_complex * b);
+int gsl_matrix_complex_scale(gsl_matrix_complex * a, const gsl_complex x);
+int gsl_matrix_complex_add_constant(gsl_matrix_complex * a, const gsl_complex x);
+int gsl_matrix_complex_add_diagonal(gsl_matrix_complex * a, const gsl_complex x);
+#endif
+
+void Init_gsl_vector_init(VALUE module);
+void Init_gsl_vector_int_init(VALUE module);
+void Init_gsl_matrix_init(VALUE module);
+void Init_gsl_matrix_int_init(VALUE module);
+
+gsl_matrix* gsl_matrix_alloc_from_array_sizes(VALUE ary, 
+						     VALUE nn1, VALUE nn2);
+gsl_matrix* gsl_matrix_alloc_from_arrays(int argc, VALUE *argv);
+
+gsl_matrix* gsl_matrix_alloc_from_vector_sizes(VALUE ary,
+					      VALUE nn1, VALUE nn2);
+gsl_matrix* gsl_matrix_alloc_from_vectors(int argc, VALUE *argv);
+gsl_matrix_int* gsl_matrix_int_alloc_from_array_sizes(VALUE ary, 
+						     VALUE nn1, VALUE nn2);
+gsl_matrix_int* gsl_matrix_int_alloc_from_arrays(int argc, VALUE *argv);
+
+gsl_matrix_int* gsl_matrix_int_alloc_from_vector_sizes(VALUE ary,
+					      VALUE nn1, VALUE nn2);
+gsl_matrix_int* gsl_matrix_int_alloc_from_vectors(int argc, VALUE *argv);
+
+VALUE rb_gsl_matrix_do_something(VALUE obj, void (*f)(gsl_matrix *));
+VALUE rb_gsl_matrix_int_do_something(VALUE obj, void (*f)(gsl_matrix_int *));
+
+VALUE rb_gsl_matrix_power(VALUE a, VALUE b);
+VALUE rb_gsl_matrix_int_power(VALUE a, VALUE b);
+
+void mygsl_vector_shift(gsl_vector *p, size_t n);
+void mygsl_vector_int_shift(gsl_vector_int *p, size_t n);
+void mygsl_vector_shift_scale2(gsl_vector *p, size_t n);
+void mygsl_vector_int_shift_scale2(gsl_vector_int *p, size_t n);
+
+VALUE rb_gsl_vector_to_s(VALUE obj);
+VALUE rb_gsl_vector_int_to_s(VALUE obj);
+
+VALUE rb_gsl_vector_add_constant(VALUE obj, VALUE x);
+VALUE rb_gsl_vector_int_add_constant(VALUE obj, VALUE x);
+VALUE rb_gsl_vector_scale(VALUE obj, VALUE x);
+VALUE rb_gsl_vector_scale_bang(VALUE obj, VALUE x);
+VALUE rb_gsl_vector_int_scale(VALUE obj, VALUE x);
+VALUE rb_gsl_vector_int_scale_bang(VALUE obj, VALUE x);
+gsl_vector_int* make_cvector_int_from_rarray(VALUE ary);
+void cvector_int_set_from_rarray(gsl_vector_int *v, VALUE ary);
+VALUE rb_gsl_range2vector(VALUE obj);
+VALUE rb_gsl_range2vector_int(VALUE obj);
+
+void Init_gsl_block_init(VALUE module);
+void Init_gsl_block_int_init(VALUE module);
+void Init_gsl_block_uchar_init(VALUE module);
+
+void Init_gsl_matrix_nmf(void);
+
+typedef enum {
+    NM_BYTE               =  0, // unsigned char
+    NM_INT8               =  1, // char
+    NM_INT16                =  2, // short
+    NM_INT32                =  3, // int
+    NM_INT64                =  4, // long
+    NM_FLOAT32          =  5, // float
+    NM_FLOAT64          =  6, // double
+    NM_COMPLEX64        =  7, // Complex64 class
+    NM_COMPLEX128     =  8, // Complex128 class
+    NM_RATIONAL32     =  9, // Rational32 class
+    NM_RATIONAL64     = 10, // Rational64 class
+    NM_RATIONAL128  = 11, // Rational128 class
+    NM_RUBYOBJ          = 12  // Ruby VALUE type
+} nm_dtype_old_t;
+
+extern VALUE nm_eDataTypeError;
+
+
+typedef struct nm_dense_storage {
+    nm_dtype_old_t  dtype;
+    size_t  rank;
+    size_t* shape;
+    size_t* offset;
+
+    size_t* stride;
+    int         count;
+    void*       src;
+    void*       elements;
+} DENSE_STORAGE;
+
+typedef enum {
+  NM_DENSE_STORE,
+  NM_LIST_STORE,
+  NM_YALE_STORE
+} nm_stype_t_old;
+
+
+typedef struct nm_storage {
+    // Common elements found in all storage types. Should not be re-arranged.
+    nm_dtype_old_t  dtype;
+    size_t  rank;
+    size_t* shape;
+    size_t* offset;
+
+    //virtual void empty(void) = 0;
+} STORAGE;
+
+typedef struct nmatrix {
+    // Method of storage (csc, dense, etc).
+    nm_stype_t_old      stype;
+    // Pointer to storage struct.
+    STORAGE*    storage;
+} NMATRIX;
+
+#define NM_STRUCT(val)          ((NMATRIX*)(DATA_PTR(val)))
+#define NM_STORAGE(val)         (NM_STRUCT(val)->storage)
+#define NM_DENSE_STORAGE(val)   ((DENSE_STORAGE*)(NM_STORAGE(val)))
+
+
+#endif