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// crm_svm_matrix.h - Support Vector Machine
////////////////////////////////////////////////////////////////////////
// This code is originally copyright and owned by William
// S. Yerazunis as file crm_neural_net. In return for addition of
// significant derivative work, Jennifer Barry is hereby granted a full
// unlimited license to use this code, includng license to relicense under
// other licenses.
////////////////////////////////////////////////////////////////////////
//
// Copyright 2009 William S. Yerazunis.
// This file is under GPLv3, as described in COPYING.
#ifndef __CRM_SVM_MATRIX__H
#define __CRM_SVM_MATRIX__H
#include "crm_svm_matrix_util.h"
/*******************************************************************
*A matrix/vector library that deals with different data structures
*for representing vectors transparently.
*
*The functions in matrix.c are commented. See them for
*details on this library.
******************************************************************/
#define MATR_DEFAULT_VECTOR_SIZE 1200 //sparse arrays start at this size
//unless otherwise specified
#define MATR_COMPACT 1
#define MATR_PRECISE 0
#define QSORT_COUNTING_CUTOFF 7e7 //with this many non-zero elts or above
//we use counting sort, not q-sort
extern int MATR_DEBUG_MODE; //debug setting. see crm_svm_matrix_util.h
//for possible modes
//Possible vector types.
typedef enum {
NON_SPARSE,
SPARSE_ARRAY,
SPARSE_LIST
} VectorType;
typedef enum {
COUNTING,
MERGE,
QSORT
} SortingAlgorithms;
typedef union {
PreciseSparseNode *pcurr;
CompactSparseNode *ccurr;
long nscurr;
} VectorIterator;
//data for non-sparse
//can be either doubles or ints
typedef union {
int *compact;
double *precise;
} NSData;
//vectors can be either expanding arrays, lists,
//or arrays of NSData
typedef union {
ExpandingArray *sparray; //SPARSSE_ARRAY vector
SparseElementList *splist; //SPARSE_LIST vector
NSData nsarray; //NON_SPARSE vector
} VectorData;
//vector struct
typedef struct {
VectorData data; //data stored in the vector
unsigned int dim; //# columns (dimension) in the vector
int nz, //# non-zero elements (nz = dim if v is NON_SPARSE)
compact, //flag for compactness
size, //starting size for expanding arrays
was_mapped; //1 if the vector was mapped into memory
VectorType type; //flag for type
} Vector;
//matrix struct
typedef struct {
Vector **data; //list of pointers to rows
unsigned int rows, //# rows in the matrix
cols; //# columns in the matrix
int nz, //# non-zero elements (nz = rows*cols if M is NON_SPARSE)
compact, //flag for compactness
size, //starting size for expanding arrays
was_mapped; //1 if the matrix was mapped into memory
VectorType type; //flag for type
} Matrix;
//Matrix functions
Matrix *matr_make(unsigned int rows, unsigned int cols, VectorType type,
int compact);
Matrix *matr_make_size(unsigned int rows, unsigned int cols, VectorType type,
int compact, int init_size);
void matr_set_row(Matrix *A, unsigned int r, Vector *v);
void matr_shallow_row_copy(Matrix *M, unsigned int r, Vector *v);
void matr_set_col(Matrix *A, unsigned int c, Vector *v);
void matr_add_row(Matrix *M);
void matr_add_nrows(Matrix *M, unsigned int n);
void matr_add_col(Matrix *M);
void matr_add_ncols(Matrix *M, unsigned int n);
void matr_remove_row(Matrix *M, unsigned int r);
void matr_erase_row(Matrix *M, unsigned int r);
void matr_remove_col(Matrix *M, unsigned int c);
ExpandingArray *matr_remove_zero_rows(Matrix *M);
ExpandingArray *matr_remove_zero_cols(Matrix *M);
void matr_append_matr(Matrix **to_ptr, Matrix *from);
void matr_vector(Matrix *M, Vector *v, Vector *ret);
void matr_vector_seq(Matrix **A, int nmatrices, unsigned int maxrows,
Vector *w, Vector *z);
void matr_transpose(Matrix *A, Matrix *T);
void matr_multiply(Matrix *M1, Matrix *M2, Matrix *ret);
int matr_iszero(Matrix *M);
void matr_convert_nonsparse_to_sparray(Matrix *M, ExpandingArray *colMap);
void matr_print(Matrix *M);
void matr_write(Matrix *M, char *filename);
void matr_write_fp(Matrix *M, FILE *out);
size_t matr_write_bin(Matrix *M, char *filename);
size_t matr_write_bin_fp(Matrix *M, FILE *fp);
Matrix *matr_read_bin(char *filename);
Matrix *matr_read_bin_fp(FILE *fp);
Matrix *matr_map(void **addr, void *last_addr);
void matr_free(Matrix *M);
//inlined matrix functions defined in this file
//(inlining is compiler discretion)
static inline void matr_set(Matrix *M, unsigned int r, unsigned int c,
double d);
static inline double matr_get(Matrix *M, unsigned int r, unsigned int c);
static inline Vector *matr_get_row(Matrix *M, unsigned int r);
//Vector functions
Vector *vector_make(unsigned int dim, VectorType type, int compact);
Vector *vector_make_size(unsigned int dim, VectorType type, int compact,
int init_size);
void vector_copy(Vector *from, Vector *to);
void vector_set(Vector *v, unsigned int i, double d);
double vector_get(Vector *v, unsigned int i);
void vector_add_col(Vector *v);
void vector_add_ncols(Vector *v, unsigned int n);
void vector_remove_col(Vector *v, unsigned int c);
int vector_iszero(Vector *V);
int vector_equals(Vector *v1, Vector *v2);
void vector_zero(Vector *v);
void vector_add(Vector *v1, Vector *v2, Vector *ret);
void vector_multiply(Vector *v, double s, Vector *ret);
double dot(Vector *v1, Vector *v2);
void vector_add_multiple(Vector *base, Vector *toadd,
double factor, Vector *ret);
double vector_dist2(Vector *v1, Vector *v2);
void vector_convert_nonsparse_to_sparray(Vector *v, ExpandingArray *colMap);
void vector_print(Vector *v);
void vector_write(Vector *v, char *filename);
void vector_write_fp(Vector *v, FILE *out);
void vector_write_sp(Vector *v, char *filename);
void vector_write_sp_fp(Vector *v, FILE *out);
size_t vector_write_bin(Vector *v, char *filename);
size_t vector_write_bin_fp(Vector *v, FILE *fp);
Vector *vector_read_bin(char *filename);
Vector *vector_read_bin_fp(FILE *fp);
Vector *vector_map(void **addr, void *last_addr);
void *vector_memmove(void *to, Vector *from);
size_t vector_size(Vector *v);
void vector_free(Vector *v);
//inline'd functions defined in this file
//(inlining is compiler discretion)
static inline unsigned int vector_dim(Vector *v);
static inline int vector_num_elts(Vector *v);
static inline double norm2(Vector *v);
static inline double norm(Vector *v);
static inline double vector_dist(Vector *v1, Vector *v2) ;
//Vector iterator functions
void vectorit_zero_elt(VectorIterator *vit, Vector *v);
void vectorit_insert(VectorIterator *vit, unsigned int c, double d, Vector *v);
void vectorit_find(VectorIterator *vit, unsigned int c, Vector *v);
void vectorit_set_col(VectorIterator vit, unsigned int c, Vector *v);
//defined in this file - forced to be inline'd at high optimization
MY_INLINE void vectorit_set_at_beg(VectorIterator *vit, Vector *v);
MY_INLINE void vectorit_set_at_end(VectorIterator *vit, Vector *v);
MY_INLINE double vectorit_curr_val(VectorIterator vit, Vector *v);
MY_INLINE unsigned int vectorit_curr_col(VectorIterator vit, Vector *v);
MY_INLINE void vectorit_prev(VectorIterator *vit, Vector *v);
MY_INLINE void vectorit_next(VectorIterator *vit, Vector *v);
MY_INLINE int vectorit_past_end(VectorIterator vit, Vector *v);
MY_INLINE int vectorit_past_beg(VectorIterator vit, Vector *v);
MY_INLINE void vectorit_copy(VectorIterator from, VectorIterator *to);
/*************INLINE FUNCTION DEFINITIONS***********************************/
//Matrix
/*************************************************************************
*Gets a pointer to a row of a matrix.
*
*INPUT: A: matrix from which to get a row.
* r: row to get.
*
*OUTPUT: A pointer to row r of matrix M.
*
*TIME:
* NON_SPARSE: O(1)
* SPARSE_ARRAY: O(1)
* SPARSE_LIST: O(1)
*************************************************************************/
static inline Vector *matr_get_row(Matrix *A, unsigned int r) {
//yay, easy :)
if (A && A->data && r >= 0 && r < A->rows) {
return A->data[r];
}
if (MATR_DEBUG_MODE) {
fprintf(stderr, "matr_get_row: bad arguments.\n");
}
return NULL;
}
/*************************************************************************
*Sets an entry of a matrix.
*
*INPUT: M: matrix in which to set an entry.
* r: row of the entry.
* c: column of the entry.
* d: value to set the entry to.
*
*TIME:
* NON_SPARSE: O(1)
* SPARSE_ARRAY: d is non-zero = ammortized O(lg(S/R)), d = 0 = O(S/R)
* SPARSE_LIST: O(S/R)
*************************************************************************/
static inline void matr_set(Matrix *M, unsigned int r, unsigned int c,
double d) {
int nz;
if (!M || !M->data || r < 0 || r >= M->rows || !M->data[r]) {
if (MATR_DEBUG_MODE) {
fprintf(stderr, "matr_set: bad arguments.\n");
}
return;
}
nz = M->data[r]->nz;
vector_set(M->data[r], c, d);
M->nz += M->data[r]->nz - nz;
}
/*************************************************************************
*Gets an entry of a matrix.
*
*INPUT: M: matrix from which to get an entry.
* r: row of the entry.
* c: column of the entry.
*
*OUTPUT: the value at r,c of matrix M
*
*TIME:
* NON_SPARSE: O(1)
* SPARSE_ARRAY: O(lg(S/R))
* SPARSE_LIST: O(S/R)
*************************************************************************/
static inline double matr_get(Matrix *M, unsigned int r, unsigned int c) {
if (!M || !M->data || r < 0 || r >= M->rows || !M->data[r]) {
if (MATR_DEBUG_MODE) {
fprintf(stderr, "matr_set: bad arguments.\n");
}
return 0;
}
return vector_get(M->data[r], c);
}
//Vector
/*************************************************************************
*Dimension of a vector.
*
*INPUT: v: vector
*
*OUTPUT: The dimension (ie number of rows/columns) of v
*
*TIME:
* NON_SPARSE: O(1)
* SPARSE_ARRAY: O(1)
* SPARSE_LIST: O(1)
*************************************************************************/
static inline unsigned int vector_dim(Vector *v) {
if (!v) {
return 0;
}
return v->dim;
}
/*************************************************************************
*Number of elements of a vector.
*
*INPUT: v: vector
*
*OUTPUT: The dimension (ie number of rows/columns) of v if v is NON_SPARSE
* or the number of non-zero elements of v if v is SPARSE
*
*TIME:
* NON_SPARSE: O(1)
* SPARSE_ARRAY: O(1)
* SPARSE_LIST: O(1)
*************************************************************************/
static inline int vector_num_elts(Vector *v) {
if (!v) {
return 0;
}
return v->nz;
}
/*************************************************************************
*Squared norm. Note that finding square roots can be time consuming so
*use this function to avoid that when possible.
*
*INPUT: v: vector to find the norm of
*
*OUTPUT: ||v||^2
*
*TIME:
* NON_SPARSE: O(c)
* SPARSE_ARRAY: O(s)
* SPARSE_LIST: O(s)
*************************************************************************/
static inline double norm2(Vector *v) {
return dot(v, v);
}
/*************************************************************************
*Norm of a vector.
*
*INPUT: v: vector to find the norm of
*
*OUTPUT: ||v||
*
*TIME:
* NON_SPARSE: O(c)
* SPARSE_ARRAY: O(s)
* SPARSE_LIST: O(s)
*************************************************************************/
static inline double norm(Vector *v) {
return (sqrt(dot(v,v)));
}
/*************************************************************************
*Distance between two vectors.
*
*INPUT: v1: first vector
* v2: second vector
*
*OUTPUT: ||v1 - v2||
*
*TIME:
* Both NON_SPARSE: O(c)
* One NON_SPARSE, one SPARSE: O(s) + O(c)
* Both SPARSE: O(s_1) + O(s_2)
*************************************************************************/
static inline double vector_dist(Vector *v1, Vector *v2) {
double d = vector_dist2(v1, v2);
if (d > 0) {
return sqrt(d);
}
return -1;
}
//Vector Iterator functions
/*************************************************************************
*Set the iterator to the beginning of a vector.
*
*INPUT: v: vector to traverse from the beginning
*
*OUTPUT: vit is set to the beginning of vector v
*
*TIME:
* NON_SPARSE: O(1)
* SPARSE_ARRAY: O(1)
* SPARSE_LIST: O(1)
*************************************************************************/
MY_INLINE void vectorit_set_at_beg(VectorIterator *vit, Vector *v) {
if (!v || !vit) {
if (MATR_DEBUG_MODE) {
fprintf(stderr, "vectorit_set_at_beg: null arguments.\n");
}
if (vit) {
vit->nscurr = -1;
}
return;
}
switch (v->type) {
case NON_SPARSE:
{
vit->nscurr = 0;
return;
}
case SPARSE_ARRAY:
{
//nscurr needs to be the actual index
//in order that zero-ing an element in vector_add etc
//doesn't mess things up
if (!v->data.sparray) {
vit->nscurr = 0;
} else {
vit->nscurr = v->data.sparray->first_elt;
}
return;
}
case SPARSE_LIST:
{
if (v->compact) {
if (v->data.splist) {
vit->ccurr = (v->data.splist->head.compact);
} else {
vit->ccurr = NULL;
}
} else {
if (v->data.splist) {
vit->pcurr = (v->data.splist->head.precise);
} else {
vit->pcurr = NULL;
}
}
return;
}
default:
{
vit->nscurr = -1;
return;
}
}
}
/*************************************************************************
*Set the iterator to the end of a vector.
*
*INPUT: v: vector to traverse from the end
*
*OUTPUT: vit is set to the end of vector v
*
*TIME:
* NON_SPARSE: O(1)
* SPARSE_ARRAY: O(1)
* SPARSE_LIST: O(1)
*************************************************************************/
MY_INLINE void vectorit_set_at_end(VectorIterator *vit, Vector *v) {
if (!v || !vit) {
if (MATR_DEBUG_MODE) {
fprintf(stderr, "vectorit_set_at_end: null arguments.\n");
}
if (vit) {
vit->nscurr = -1;
}
return;
}
switch (v->type) {
case NON_SPARSE:
{
vit->nscurr = v->dim-1;
break;
}
case SPARSE_ARRAY:
{
if (!v->data.sparray) {
vit->nscurr = 0;
} else {
vit->nscurr = v->data.sparray->last_elt;
}
break;
}
case SPARSE_LIST:
{
if (v->compact) {
if (!v->data.splist) {
vit->ccurr = NULL;
} else {
vit->ccurr = v->data.splist->tail.compact;
}
} else {
if (!v->data.splist) {
vit->pcurr = NULL;
} else {
vit->pcurr = v->data.splist->tail.precise;
}
}
break;
}
default:
{
vit->nscurr = -1;
if (MATR_DEBUG_MODE) {
fprintf(stderr, "vectorit_set_at_end: unrecognized type.\n");
}
return;
}
}
}
/*************************************************************************
*Get the value (data) of the element that the iterator is pointing to.
*
*INPUT: vit: the vector iterator, pointing to some element in v
* v: the vector vit is traversing
*
*OUTPUT: The data associated with the element vit is pointing to or
* -RAND_MAX if vit is not traversing v.
*
*TIME:
* NON_SPARSE: O(1)
* SPARSE_ARRAY: O(1)
* SPARSE_LIST: O(1)
*************************************************************************/
MY_INLINE double vectorit_curr_val(VectorIterator vit, Vector *v) {
if (!v) {
//if (MATR_DEBUG_MODE) {
//fprintf(stderr, "vectorit_curr_col: null vector.\n");
//}
return -RAND_MAX;
}
switch (v->type) {
case SPARSE_ARRAY:
if (v->data.sparray &&
vit.nscurr >= v->data.sparray->first_elt &&
vit.nscurr <= v->data.sparray->last_elt) {
if (v->compact && v->data.sparray->data.compact) {
return (double)v->data.sparray->data.compact[vit.nscurr].s.data;
}
if (!(v->compact) && (v->data.sparray->data.precise)) {
return v->data.sparray->data.precise[vit.nscurr].s.data;
}
}
return -RAND_MAX;
case SPARSE_LIST:
{
if (v->compact && vit.ccurr) {
return (double)vit.ccurr->data.data;
}
if (!(v->compact) && vit.pcurr) {
return vit.pcurr->data.data;
}
return -RAND_MAX;
}
case NON_SPARSE:
{
if (vit.nscurr >= 0 && vit.nscurr < v->dim) {
if (v->compact && v->data.nsarray.compact) {
return (double)v->data.nsarray.compact[vit.nscurr];
}
if (!(v->compact) && v->data.nsarray.precise) {
return v->data.nsarray.precise[vit.nscurr];
}
}
return -RAND_MAX;
}
default:
{
return -RAND_MAX;
}
}
return -RAND_MAX;
}
/*************************************************************************
*Get the column of the element that the iterator is pointing to.
*
*INPUT: vit: the vector iterator, pointing to some element in v
* v: the vector vit is traversing
*
*OUTPUT: The column associated with the element vit is pointing to or v->dim
* if vit is past the beginning or end of v.
*
*TIME:
* NON_SPARSE: O(1)
* SPARSE_ARRAY: O(1)
* SPARSE_LIST: O(1)
*
*WARNINGS:
*1) This returns v->dim even if vit is past the BEGINNING of v. This is
* because column numbers need to be unsigned. Therefore, you need
* to explicitly check if an iterator is past the beginning of a vector
* - you can't count on this returning a negative value if the iterator
* is past the beginning.
*************************************************************************/
MY_INLINE unsigned int vectorit_curr_col(VectorIterator vit, Vector *v) {
if (!v) {
if (MATR_DEBUG_MODE) {
fprintf(stderr, "vectorit_curr_col: null vector.\n");
}
return MAX_INT_VAL;
}
switch (v->type) {
case SPARSE_ARRAY:
if (v->data.sparray && v->data.sparray->data.compact &&
vit.nscurr >= v->data.sparray->first_elt &&
vit.nscurr <= v->data.sparray->last_elt) {
if (v->compact && v->data.sparray->data.compact) {
return v->data.sparray->data.compact[vit.nscurr].s.col;
}
if (!(v->compact) && (v->data.sparray->data.precise)) {
return v->data.sparray->data.precise[vit.nscurr].s.col;
}
}
return v->dim;
case SPARSE_LIST:
{
if (v->compact && vit.ccurr) {
return vit.ccurr->data.col;
}
if (!(v->compact) && vit.pcurr) {
return vit.pcurr->data.col;
}
return v->dim;
}
case NON_SPARSE:
{
return vit.nscurr;
}
default:
{
return v->dim;
}
}
return v->dim;
}
/*************************************************************************
*Move to the previous element in the vector. Sets past_beg and unsets
*past_end if appropriate.
*
*INPUT: v: the vector vit is traversing
*
*OUTPUT: vit points to the previous element in the vector or is past_beg.
*
*TIME:
* NON_SPARSE: O(1)
* SPARSE_ARRAY: O(1)
* SPARSE_LIST: O(1)
*************************************************************************/
MY_INLINE void vectorit_prev(VectorIterator *vit, Vector *v) {
if (!v || !vit) {
if (MATR_DEBUG_MODE) {
fprintf(stderr, "vectorit_prev: null arguments.\n");
}
if (vit) {
vit->nscurr = -1;
}
return;
}
switch (v->type) {
case NON_SPARSE:
case SPARSE_ARRAY:
vit->nscurr--;
return;
case SPARSE_LIST:
if ((v->compact)) {
if (vit->ccurr) {
vit->ccurr = vit->ccurr->prev;
} else {
vit->ccurr = v->data.splist->tail.compact;
}
} else {
if (vit->pcurr) {
vit->pcurr = vit->pcurr->prev;
} else {
vit->pcurr = v->data.splist->tail.precise;
}
}
default:
return;
}
}
/*************************************************************************
*Move to the next element in the vector.
*
*INPUT: v: the vector vit is traversing
*
*OUTPUT: vit points to the next element in the vector or is past_end.
*
*TIME:
* NON_SPARSE: O(1)
* SPARSE_ARRAY: O(1)
* SPARSE_LIST: O(1)
*************************************************************************/
MY_INLINE void vectorit_next(VectorIterator *vit, Vector *v) {
if (!v || !vit) {
//if (MATR_DEBUG_MODE) {
//fprintf(stderr, "vectorit_next: null arguments.\n");
//}
return;
}
switch (v->type) {
case NON_SPARSE:
case SPARSE_ARRAY:
vit->nscurr++;
return;
case SPARSE_LIST:
if ((v->compact)) {
if (vit->ccurr) {
vit->ccurr = vit->ccurr->next;
} else {
vit->ccurr = v->data.splist->head.compact;
}
} else {
if (vit->pcurr) {
vit->pcurr = vit->pcurr->next;
} else {
vit->pcurr = v->data.splist->head.precise;
}
}
default:
return;
}
}
/*************************************************************************
*Checks if an iterator is past the end of the vector.
*
*INPUT: vit: the iterator
* v: the vector vit is traversing
*
*OUTPUT: 1 if vit is past the end of v, 0 else
*
*TIME:
* NON_SPARSE: O(1)
* SPARSE_ARRAY: O(1)
* SPARSE_LIST: O(1)
*************************************************************************/
MY_INLINE int vectorit_past_end(VectorIterator vit, Vector *v) {
if (!v) {
if (MATR_DEBUG_MODE) {
fprintf(stderr, "vectorit_past_end: null arguments.\n");
}
return 1;
}
switch (v->type) {
case SPARSE_ARRAY:
if (!v->data.sparray || vit.nscurr > v->data.sparray->last_elt ||
v->data.sparray->first_elt > v->data.sparray->last_elt) {
return 1;
}
return 0;
case SPARSE_LIST:
if (v->compact && !vit.ccurr) {
return 1;
}
if (!(v->compact) && !vit.pcurr) {
return 1;
}
return 0;
case NON_SPARSE:
if (vit.nscurr >= v->dim) {
return 1;
}
return 0;
default:
return 1;
}
}
/*************************************************************************
*Checks if an iterator is past the beginning of the vector.
*
*INPUT: vit: the iterator
* v: the vector vit is traversing
*
*OUTPUT: 1 if vit is past the beginning of v, 0 else
*
*TIME:
* NON_SPARSE: O(1)
* SPARSE_ARRAY: O(1)
* SPARSE_LIST: O(1)
*************************************************************************/
MY_INLINE int vectorit_past_beg(VectorIterator vit, Vector *v) {
if (!v) {
if (MATR_DEBUG_MODE) {
fprintf(stderr, "vectorit_past_end: null arguments.\n");
}
return 1;
}
switch (v->type) {
case SPARSE_ARRAY:
if (!(v->data.sparray) || vit.nscurr < v->data.sparray->first_elt
|| v->data.sparray->first_elt > v->data.sparray->last_elt) {
return 1;
}
return 0;
case SPARSE_LIST:
if (v->compact && !vit.ccurr) {
return 1;
}
if (!(v->compact) && !vit.pcurr) {
return 1;
}
return 0;
case NON_SPARSE:
if (vit.nscurr < 0) {
return 1;
}
return 0;
default:
return 1;
}
}
/*************************************************************************
*Copy one vector iterator to another.
*
*INPUT: from: vector iterator to copy from
*
*OUTPUT: to = from.
*
*TIME:
* NON_SPARSE: O(1)
* SPARSE_ARRAY: O(1)
* SPARSE_LIST: O(1)
*************************************************************************/
MY_INLINE void vectorit_copy(VectorIterator from, VectorIterator *to) {
if (!to) {
if (MATR_DEBUG_MODE) {
fprintf(stderr, "vectorit_copy: null to vector.\n");
}
return;
}
to->nscurr = from.nscurr;
}
#endif //crm_svm_matrix.h
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