nmatrix-atlas 0.2.0

data/ext/nmatrix/nm_memory.h

@@ -0,0 +1,60 @@
+/////////////////////////////////////////////////////////////////////
+// = NMatrix
+//
+// A linear algebra library for scientific computation in Ruby.
+// NMatrix is part of SciRuby.
+//
+// NMatrix was originally inspired by and derived from NArray, by
+// Masahiro Tanaka: http://narray.rubyforge.org
+//
+// == Copyright Information
+//
+// SciRuby is Copyright (c) 2010 - 2014, Ruby Science Foundation
+// NMatrix is Copyright (c) 2012 - 2014, John Woods and the Ruby Science Foundation
+//
+// Please see LICENSE.txt for additional copyright notices.
+//
+// == Contributing
+//
+// By contributing source code to SciRuby, you agree to be bound by
+// our Contributor Agreement:
+//
+// * https://github.com/SciRuby/sciruby/wiki/Contributor-Agreement
+//
+// == nm_memory.h
+//
+// Macros for memory allocation and freeing
+
+/**
+ * We define these macros, which just call the ruby ones, as this makes
+ * debugging memory issues (particularly those involving interaction with
+ * the ruby GC) easier, as it's posssible to add debugging code temporarily.
+ */
+#ifndef __NM_MEMORY_H__
+#define __NM_MEMORY_H__
+
+#include <ruby.h>
+
+#define NM_ALLOC(type) (ALLOC(type))
+
+#define NM_ALLOC_N(type, n) (ALLOC_N(type, n))
+
+#define NM_REALLOC_N(var, type, n) (REALLOC_N(var, type, n))
+
+#define NM_ALLOCA_N(type, n) (ALLOCA_N(type, n))
+
+#define NM_FREE(var) (xfree(var))
+
+#define NM_ALLOC_NONRUBY(type) ((type*) malloc(sizeof(type)))
+
+//Defines whether to do conservative gc registrations, i.e. those
+//registrations that we're not that sure are necessary.
+//#define NM_GC_CONSERVATIVE
+
+#ifdef NM_GC_CONSERVATIVE
+#define NM_CONSERVATIVE(statement) (statement)
+#else
+#define NM_CONSERVATIVE(statement)
+#endif //NM_GC_CONSERVATIVE
+
+#endif

data/ext/nmatrix/nmatrix.h

@@ -0,0 +1,408 @@
+/////////////////////////////////////////////////////////////////////
+// = NMatrix
+//
+// A linear algebra library for scientific computation in Ruby.
+// NMatrix is part of SciRuby.
+//
+// NMatrix was originally inspired by and derived from NArray, by
+// Masahiro Tanaka: http://narray.rubyforge.org
+//
+// == Copyright Information
+//
+// SciRuby is Copyright (c) 2010 - 2014, Ruby Science Foundation
+// NMatrix is Copyright (c) 2012 - 2014, John Woods and the Ruby Science Foundation
+//
+// Please see LICENSE.txt for additional copyright notices.
+//
+// == Contributing
+//
+// By contributing source code to SciRuby, you agree to be bound by
+// our Contributor Agreement:
+//
+// * https://github.com/SciRuby/sciruby/wiki/Contributor-Agreement
+//
+// == nmatrix.h
+//
+// C and C++ API for NMatrix, and main header file.
+
+#ifndef NMATRIX_H
+#define NMATRIX_H
+
+/*
+ * Standard Includes
+ */
+
+#include <ruby.h>
+
+#ifdef __cplusplus
+  #include <cmath>
+  #include <cstring>
+#else
+  #include <math.h>
+  #include <string.h>
+#endif
+
+#ifdef BENCHMARK
+  // SOURCE: http://stackoverflow.com/questions/2349776/how-can-i-benchmark-a-c-program-easily
+  #ifdef __cplusplus
+    #include <sys/ctime>
+    #include <sys/cresource>
+  #else
+    #include <sys/time.h>
+    #include <sys/resource.h>
+  #endif
+#endif
+
+#ifdef __cplusplus
+  #include "nm_memory.h"
+#endif
+
+/*
+ * Macros
+ */
+
+#define RUBY_ZERO INT2FIX(0)
+
+#ifndef SIZEOF_INT
+  #error SIZEOF_INT undefined
+#else
+  #if SIZEOF_INT == 8
+    #define DEFAULT_DTYPE  INT64
+    #define SIZE_T         INT64
+  #else
+    #if SIZEOF_INT == 4
+      #define DEFAULT_DTYPE INT32
+      #define SIZE_T        INT32
+    #else
+      #if SIZEOF_INT == 2
+        #define DEFAULT_DTYPE INT16
+        #define SIZE_T        INT16
+      #else
+        #error Unhandled SIZEOF_INT -- please #define SIZE_T and DEFAULT_DTYPE manually.
+      #endif
+    #endif
+  #endif
+#endif
+
+/*
+ * == Macros for Concurrent C and C++ Header Maintenance
+ *
+ * These macros look complicated, but they're really not so bad. They're also important: they ensure that whether our
+ * header file (nmatrix.h) is read by a C++ or a C compiler, all the same data structures and enumerators exist, albeit
+ * with slightly different names.
+ *
+ * "But wait," you say, "You use structs. Structs exist in C and C++. Why use a macro to set them up?"
+ *
+ * Well, in C, you have to be explicit about what a struct is. You can actually get around that requirement by using a
+ * typedef:
+ *
+ *   typedef struct STORAGE { ... } STORAGE;
+ *
+ * Also, we use C++ inheritance, which is obviously not allowed in C. So we have to ensure that the base class's members
+ * are exposed properly to our child classes.
+ *
+ * The macros also allow us to put all of our C++ types into namespaces. For C, we prefix everything with either nm_ or
+ * NM_ to distinguish our declarations from those in other libraries.
+ */
+
+
+#ifdef __cplusplus /* These are the C++ versions of the macros. */
+
+  /*
+   * If no block is given, return an enumerator. This copied straight out of ruby's include/ruby/intern.h.
+   *
+   * rb_enumeratorize is located in enumerator.c.
+   *
+   *    VALUE rb_enumeratorize(VALUE obj, VALUE meth, int argc, VALUE *argv) {
+   *      return enumerator_init(enumerator_allocate(rb_cEnumerator), obj, meth, argc, argv);
+   *    }
+   */
+
+//opening portion -- this allows unregistering any objects in use before returning
+  #define RETURN_SIZED_ENUMERATOR_PRE do { \
+    if (!rb_block_given_p()) {
+
+//remaining portion
+  #ifdef RUBY_2
+    #ifndef RETURN_SIZED_ENUMERATOR
+      #undef RETURN_SIZED_ENUMERATOR
+      // Ruby 2.0 and higher has rb_enumeratorize_with_size instead of rb_enumeratorize.
+      // We want to support both in the simplest way possible.
+      #define RETURN_SIZED_ENUMERATOR(obj, argc, argv, size_fn) \
+        return rb_enumeratorize_with_size((obj), ID2SYM(rb_frame_this_func()), (argc), (argv), (size_fn));  \
+      } \
+    } while (0)
+    #endif
+  #else
+    #undef RETURN_SIZED_ENUMERATOR
+    #define RETURN_SIZED_ENUMERATOR(obj, argc, argv, size_fn) \
+      return rb_enumeratorize((obj), ID2SYM(rb_frame_this_func()), (argc), (argv));   \
+      } \
+    } while (0)
+  #endif
+
+  #define NM_DECL_ENUM(enum_type, name)   nm::enum_type name
+  #define NM_DECL_STRUCT(type, name)      type          name;
+
+  #define NM_DEF_STORAGE_ELEMENTS    \
+    NM_DECL_ENUM(dtype_t, dtype);    \
+    size_t      dim;                 \
+    size_t*     shape;               \
+    size_t*     offset;              \
+    int         count;               \
+    STORAGE*    src;
+
+  #define NM_DEF_STORAGE_CHILD_STRUCT_PRE(name)    struct name : STORAGE {
+  #define NM_DEF_STORAGE_STRUCT_POST(name)         };
+
+  #define NM_DEF_STORAGE_STRUCT      \
+  struct STORAGE {                   \
+    NM_DEF_STORAGE_ELEMENTS;         \
+  };
+
+  #define NM_DEF_STRUCT_PRE(name)  struct name {
+  #define NM_DEF_STRUCT_POST(name) };
+
+  #define NM_DEF_ENUM(name, ...)          \
+    namespace nm {                        \
+      enum name {                         \
+        __VA_ARGS__                       \
+      };                                  \
+    } // end of namespace nm
+
+#else   /* These are the C versions of the macros. */
+
+  #define NM_DECL_ENUM(enum_type, name)   nm_ ## enum_type name
+  #define NM_DECL_STRUCT(type, name)      struct NM_ ## type      name;
+
+  #define NM_DEF_STORAGE_ELEMENTS   \
+    NM_DECL_ENUM(dtype_t, dtype);   \
+    size_t      dim;                \
+    size_t*     shape;              \
+    size_t*     offset;             \
+    int         count;              \
+    NM_DECL_STRUCT(STORAGE*, src);
+  #define NM_DEF_STORAGE_CHILD_STRUCT_PRE(name)  typedef struct NM_ ## name { \
+                                                   NM_DEF_STORAGE_ELEMENTS;
+
+  #define NM_DEF_STORAGE_STRUCT_POST(name)       } NM_ ## name;
+
+  #define NM_DEF_STORAGE_STRUCT      \
+  typedef struct NM_STORAGE {        \
+    NM_DEF_STORAGE_ELEMENTS;         \
+  } NM_STORAGE;
+
+  #define NM_DEF_STRUCT_PRE(name)                typedef struct NM_ ## name {
+  #define NM_DEF_STRUCT_POST(name)               } NM_ ## name;
+
+  #define NM_DEF_ENUM(name, ...)     \
+    typedef enum nm_ ## name {       \
+      __VA_ARGS__                    \
+    } nm_ ## name;
+
+#endif      /* End of C/C++ Parallel Header Macro Definitions */
+
+
+/*
+ * Types
+ */
+
+#define NM_NUM_DTYPES 10  // data/data.h
+#define NM_NUM_STYPES 3   // storage/storage.h
+
+//#ifdef __cplusplus
+//namespace nm {
+//#endif
+
+/* Storage Type -- Dense or Sparse */
+NM_DEF_ENUM(stype_t,  DENSE_STORE = 0,
+                      LIST_STORE = 1,
+                      YALE_STORE = 2);
+
+/* Data Type */
+NM_DEF_ENUM(dtype_t,    BYTE                =  0,  // unsigned char
+                        INT8                =  1,  // char
+                        INT16               =  2,  // short
+                        INT32               =  3,  // int
+                        INT64               =  4,  // long
+                        FLOAT32         =  5,  // float
+                        FLOAT64         =  6,  // double
+                        COMPLEX64       =  7,  // Complex64 class
+                        COMPLEX128  =  8,  // Complex128 class
+                        RUBYOBJ         = 9);  // Ruby VALUE type
+
+NM_DEF_ENUM(symm_t,   NONSYMM   = 0,
+                      SYMM      = 1,
+                      SKEW      = 2,
+                      HERM      = 3,
+                      UPPER     = 4,
+                      LOWER     = 5);
+
+//#ifdef __cplusplus
+//}; // end of namespace nm
+//#endif
+
+/* struct STORAGE */
+NM_DEF_STORAGE_STRUCT;
+
+/* Dense Storage */
+NM_DEF_STORAGE_CHILD_STRUCT_PRE(DENSE_STORAGE); // struct DENSE_STORAGE : STORAGE {
+  void*     elements; // should go first to align with void* a in yale and NODE* first in list.
+  size_t*   stride;
+NM_DEF_STORAGE_STRUCT_POST(DENSE_STORAGE);     // };
+
+/* Yale Storage */
+NM_DEF_STORAGE_CHILD_STRUCT_PRE(YALE_STORAGE);
+  void*   a;      // should go first
+  size_t  ndnz; // Strictly non-diagonal non-zero count!
+  size_t  capacity;
+  size_t* ija;
+NM_DEF_STORAGE_STRUCT_POST(YALE_STORAGE);
+
+// FIXME: NODE and LIST should be put in some kind of namespace or something, at least in C++.
+NM_DEF_STRUCT_PRE(NODE); // struct NODE {
+  size_t key;
+  void*  val;
+  NM_DECL_STRUCT(NODE*, next);  // NODE* next;
+NM_DEF_STRUCT_POST(NODE); // };
+
+NM_DEF_STRUCT_PRE(LIST); // struct LIST {
+  NM_DECL_STRUCT(NODE*, first); // NODE* first;
+NM_DEF_STRUCT_POST(LIST); // };
+
+/* List-of-Lists Storage */
+NM_DEF_STORAGE_CHILD_STRUCT_PRE(LIST_STORAGE); // struct LIST_STORAGE : STORAGE {
+  // List storage specific elements.
+  void* default_val;
+  NM_DECL_STRUCT(LIST*, rows); // LIST* rows;
+NM_DEF_STORAGE_STRUCT_POST(LIST_STORAGE);      // };
+
+
+
+/* NMATRIX Object */
+NM_DEF_STRUCT_PRE(NMATRIX);   // struct NMATRIX {
+  NM_DECL_ENUM(stype_t, stype);       // stype_t stype;     // Method of storage (csc, dense, etc).
+  NM_DECL_STRUCT(STORAGE*, storage);  // STORAGE* storage;  // Pointer to storage struct.
+NM_DEF_STRUCT_POST(NMATRIX);  // };
+
+/* Structs for dealing with VALUEs in use so that they don't get GC'd */
+
+NM_DEF_STRUCT_PRE(NM_GC_LL_NODE);       // struct NM_GC_LL_NODE {
+  VALUE* val;                           //   VALUE* val;
+  size_t n;                             //   size_t n;
+  NM_DECL_STRUCT(NM_GC_LL_NODE*, next); //   NM_GC_LL_NODE* next;
+NM_DEF_STRUCT_POST(NM_GC_LL_NODE);      // };
+
+NM_DEF_STRUCT_PRE(NM_GC_HOLDER);        // struct NM_GC_HOLDER {
+  NM_DECL_STRUCT(NM_GC_LL_NODE*, start); //  NM_GC_LL_NODE* start;
+NM_DEF_STRUCT_POST(NM_GC_HOLDER);       // };
+
+#define NM_MAX_RANK 15
+
+#define UnwrapNMatrix(obj,var)  Data_Get_Struct(obj, NMATRIX, var)
+
+#define NM_STORAGE(val)         (NM_STRUCT(val)->storage)
+#ifdef __cplusplus
+  #define NM_STRUCT(val)              ((NMATRIX*)(DATA_PTR(val)))
+  #define NM_STORAGE_LIST(val)        ((LIST_STORAGE*)(NM_STORAGE(val)))
+  #define NM_STORAGE_YALE(val)        ((YALE_STORAGE*)(NM_STORAGE(val)))
+  #define NM_STORAGE_DENSE(val)       ((DENSE_STORAGE*)(NM_STORAGE(val)))
+#else
+  #define NM_STRUCT(val)              ((struct NM_NMATRIX*)(DATA_PTR(val)))
+  #define NM_STORAGE_LIST(val)        ((struct NM_LIST_STORAGE*)(NM_STORAGE(val)))
+  #define NM_STORAGE_YALE(val)        ((struct NM_YALE_STORAGE*)(NM_STORAGE(val)))
+  #define NM_STORAGE_DENSE(val)       ((struct NM_DENSE_STORAGE*)(NM_STORAGE(val)))
+#endif
+
+#define NM_SRC(val)             (NM_STORAGE(val)->src)
+#define NM_DIM(val)             (NM_STORAGE(val)->dim)
+#define NM_DTYPE(val)           (NM_STORAGE(val)->dtype)
+#define NM_STYPE(val)           (NM_STRUCT(val)->stype)
+#define NM_SHAPE(val,i)         (NM_STORAGE(val)->shape[(i)])
+#define NM_SHAPE0(val)          (NM_STORAGE(val)->shape[0])
+#define NM_SHAPE1(val)          (NM_STORAGE(val)->shape[1])
+#define NM_DEFAULT_VAL(val)     (NM_STORAGE_LIST(val)->default_val)
+
+#define NM_DENSE_COUNT(val)     (nm_storage_count_max_elements(NM_STORAGE_DENSE(val)))
+#define NM_DENSE_ELEMENTS(val)  (NM_STORAGE_DENSE(val)->elements)
+#define NM_SIZEOF_DTYPE(val)    (DTYPE_SIZES[NM_DTYPE(val)])
+#define NM_REF(val,slice)       (RefFuncs[NM_STYPE(val)]( NM_STORAGE(val), slice, NM_SIZEOF_DTYPE(val) ))
+
+#define NM_MAX(a,b) (((a)>(b))?(a):(b))
+#define NM_MIN(a,b) (((a)>(b))?(b):(a))
+#define NM_SWAP(a,b,tmp) {(tmp)=(a);(a)=(b);(b)=(tmp);}
+
+#define NM_CHECK_ALLOC(x) if (!x) rb_raise(rb_eNoMemError, "insufficient memory");
+
+#define RB_FILE_EXISTS(fn)   (rb_funcall(rb_const_get(rb_cObject, rb_intern("File")), rb_intern("exists?"), 1, (fn)) == Qtrue)
+
+#define CheckNMatrixType(v)   if (TYPE(v) != T_DATA || (RDATA(v)->dfree != (RUBY_DATA_FUNC)nm_delete && RDATA(v)->dfree != (RUBY_DATA_FUNC)nm_delete_ref)) rb_raise(rb_eTypeError, "expected NMatrix on left-hand side of operation");
+
+#define NM_IsNMatrix(obj) \
+  (rb_obj_is_kind_of(obj, cNMatrix) == Qtrue)
+
+#define NM_IsNVector(obj) \
+  (rb_obj_is_kind_of(obj, cNVector) == Qtrue)
+
+#define RB_P(OBJ) \
+  rb_funcall(rb_stderr, rb_intern("print"), 1, rb_funcall(OBJ, rb_intern("object_id"), 0)); \
+  rb_funcall(rb_stderr, rb_intern("puts"), 1, rb_funcall(OBJ, rb_intern("inspect"), 0));
+
+
+#ifdef __cplusplus
+typedef VALUE (*METHOD)(...);
+
+//}; // end of namespace nm
+#endif
+
+// In the init code below, we need to use NMATRIX for c++ and NM_NMATRIX for c
+// this macro chooses the correct one:
+#ifdef __cplusplus
+  #define _NMATRIX NMATRIX
+  #define _STORAGE STORAGE
+#else
+  #define _NMATRIX NM_NMATRIX
+  #define _STORAGE NM_STORAGE
+#endif
+
+/*
+ * Functions
+ */
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+  void Init_nmatrix();
+  // External API
+  VALUE rb_nmatrix_dense_create(NM_DECL_ENUM(dtype_t, dtype), size_t* shape, size_t dim, void* elements, size_t length);
+  VALUE rb_nvector_dense_create(NM_DECL_ENUM(dtype_t, dtype), void* elements, size_t length);
+
+  NM_DECL_ENUM(dtype_t, nm_dtype_guess(VALUE));   // (This is a function)
+  NM_DECL_ENUM(dtype_t, nm_dtype_min(VALUE));
+
+  // Non-API functions needed by other cpp files.
+  _NMATRIX* nm_create(NM_DECL_ENUM(stype_t, stype), _STORAGE* storage);
+  _NMATRIX* nm_cast_with_ctype_args(_NMATRIX* self, NM_DECL_ENUM(stype_t, new_stype), NM_DECL_ENUM(dtype_t, new_dtype), void* init_ptr);
+  VALUE    nm_cast(VALUE self, VALUE new_stype_symbol, VALUE new_dtype_symbol, VALUE init);
+  void     nm_mark(_NMATRIX* mat);
+  void     nm_delete(_NMATRIX* mat);
+  void     nm_delete_ref(_NMATRIX* mat);
+  void     nm_register_values(VALUE* vals, size_t n);
+  void     nm_register_value(VALUE* val);
+  void     nm_unregister_value(VALUE* val);
+  void     nm_unregister_values(VALUE* vals, size_t n);
+  void     nm_register_storage(NM_DECL_ENUM(stype_t, stype), const _STORAGE* storage);
+  void     nm_unregister_storage(NM_DECL_ENUM(stype_t, stype), const _STORAGE* storage);
+  void     nm_register_nmatrix(_NMATRIX* nmatrix);
+  void     nm_unregister_nmatrix(_NMATRIX* nmatrix);
+  void     nm_completely_unregister_value(VALUE* val);
+
+#ifdef __cplusplus
+}
+#endif
+
+#undef _NMATRIX
+#undef _STORAGE
+
+#endif // NMATRIX_H