#include <general.h>
#include <stdio.h>

Include dependency graph for SparseMatrix.h:

This graph shows which files directly or indirectly include this file:

Data Structures
struct	SparseMatrix_struct

Macros
#define	SYMMETRY_EPSILON 0.0000001

#define	SparseMatrix_set_undirected(A) set_flag((A)->property, MATRIX_UNDIRECTED)

#define	SparseMatrix_set_symmetric(A) set_flag((A)->property, MATRIX_SYMMETRIC)

#define	SparseMatrix_set_pattern_symmetric(A) set_flag((A)->property, MATRIX_PATTERN_SYMMETRIC)

#define	SparseMatrix_set_skew(A) set_flag((A)->property, MATRIX_SKEW)

#define	SparseMatrix_set_hemitian(A) set_flag((A)->property, MATRIX_HERMITIAN)

#define	SparseMatrix_clear_undirected(A) clear_flag((A)->property, MATRIX_UNDIRECTED)

#define	SparseMatrix_clear_symmetric(A) clear_flag((A)->property, MATRIX_SYMMETRIC)

#define	SparseMatrix_clear_pattern_symmetric(A) clear_flag((A)->property, MATRIX_PATTERN_SYMMETRIC)

#define	SparseMatrix_clear_skew(A) clear_flag((A)->property, MATRIX_SKEW)

#define	SparseMatrix_clear_hemitian(A) clear_flag((A)->property, MATRIX_HERMITIAN)

#define	SparseMatrix_known_undirected(A) test_flag((A)->property, MATRIX_UNDIRECTED)

#define	SparseMatrix_known_symmetric(A) test_flag((A)->property, MATRIX_SYMMETRIC)

#define	SparseMatrix_known_strucural_symmetric(A) test_flag((A)->property, MATRIX_PATTERN_SYMMETRIC)

#define	SparseMatrix_known_skew(A) test_flag((A)->property, MATRIX_SKEW)

#define	SparseMatrix_known_hemitian(A) test_flag((A)->property, MATRIX_HERMITIAN)

Typedefs
typedef struct SparseMatrix_struct *	SparseMatrix

Enumerations
enum	{ FORMAT_CSC, FORMAT_CSR, FORMAT_COORD }

enum	{ UNMASKED = -10, MASKED = 1 }

enum	{ MATRIX_PATTERN_SYMMETRIC = 1<<0, MATRIX_SYMMETRIC = 1<<1, MATRIX_SKEW = 1<<2, MATRIX_HERMITIAN = 1<<3, MATRIX_UNDIRECTED = 1<<4 }

enum	{ BIPARTITE_RECT = 0, BIPARTITE_PATTERN_UNSYM, BIPARTITE_UNSYM, BIPARTITE_ALWAYS }

enum	{ MATRIX_TYPE_REAL = 1<<0, MATRIX_TYPE_COMPLEX = 1<<1, MATRIX_TYPE_INTEGER = 1<<2, MATRIX_TYPE_PATTERN = 1<<3, MATRIX_TYPE_UNKNOWN = 1<<4 }

enum	{ SUM_REPEATED_NONE = 0, SUM_REPEATED_ALL, SUM_REPEATED_REAL_PART, SUM_REPEATED_IMAGINARY_PART, SUM_IMGINARY_KEEP_LAST_REAL }

Functions
SparseMatrix	SparseMatrix_new (int m, int n, int nz, int type, int format)

SparseMatrix	SparseMatrix_general_new (int m, int n, int nz, int type, size_t sz, int format)

SparseMatrix	SparseMatrix_from_coordinate_format (SparseMatrix A)

SparseMatrix	SparseMatrix_from_coordinate_format_not_compacted (SparseMatrix A, int what_to_sum)

SparseMatrix	SparseMatrix_from_coordinate_arrays (int nz, int m, int n, int irn, int jcn, void *val, int type, size_t sz)

SparseMatrix	SparseMatrix_from_coordinate_arrays_not_compacted (int nz, int m, int n, int irn, int jcn, void *val, int type, size_t sz, int what_to_sum)

void	SparseMatrix_print (char *, SparseMatrix A)

void	SparseMatrix_export (FILE *f, SparseMatrix A)

SparseMatrix	SparseMatrix_import_binary (char *name)

SparseMatrix	SparseMatrix_import_binary_fp (FILE *f)

void	SparseMatrix_export_binary (char name, SparseMatrix A, int flag)

void	SparseMatrix_export_binary_fp (FILE *f, SparseMatrix A)

void	SparseMatrix_delete (SparseMatrix A)

SparseMatrix	SparseMatrix_add (SparseMatrix A, SparseMatrix B)

SparseMatrix	SparseMatrix_multiply (SparseMatrix A, SparseMatrix B)

SparseMatrix	SparseMatrix_multiply3 (SparseMatrix A, SparseMatrix B, SparseMatrix C)

SparseMatrix	SparseMatrix_sum_repeat_entries (SparseMatrix A, int what_to_sum)

SparseMatrix	SparseMatrix_coordinate_form_add_entries (SparseMatrix A, int nentries, int irn, int jcn, void *val)

int	SparseMatrix_is_symmetric (SparseMatrix A, int test_pattern_symmetry_only)

SparseMatrix	SparseMatrix_transpose (SparseMatrix A)

SparseMatrix	SparseMatrix_symmetrize (SparseMatrix A, int pattern_symmetric_only)

SparseMatrix	SparseMatrix_symmetrize_nodiag (SparseMatrix A, int pattern_symmetric_only)

void	SparseMatrix_multiply_vector (SparseMatrix A, real v, real *res, int transposed)

SparseMatrix	SparseMatrix_remove_diagonal (SparseMatrix A)

SparseMatrix	SparseMatrix_remove_upper (SparseMatrix A)

SparseMatrix	SparseMatrix_divide_row_by_degree (SparseMatrix A)

SparseMatrix	SparseMatrix_get_real_adjacency_matrix_symmetrized (SparseMatrix A)

SparseMatrix	SparseMatrix_normalize_to_rowsum1 (SparseMatrix A)

void	SparseMatrix_multiply_dense (SparseMatrix A, int ATranspose, real v, int vTransposed, real *res, int res_transpose, int dim)

SparseMatrix	SparseMatrix_apply_fun (SparseMatrix A, double(*fun)(double x))

SparseMatrix	SparseMatrix_apply_fun_general (SparseMatrix A, void(fun)(int i, int j, int n, double x))

SparseMatrix	SparseMatrix_copy (SparseMatrix A)

int	SparseMatrix_has_diagonal (SparseMatrix A)

SparseMatrix	SparseMatrix_normalize_by_row (SparseMatrix A)

SparseMatrix	SparseMatrix_crop (SparseMatrix A, real epsilon)

SparseMatrix	SparseMatrix_scaled_by_vector (SparseMatrix A, real *v, int apply_to_row)

SparseMatrix	SparseMatrix_multiply_by_scaler (SparseMatrix A, real s)

SparseMatrix	SparseMatrix_make_undirected (SparseMatrix A)

int	SparseMatrix_connectedQ (SparseMatrix A)

real	SparseMatrix_pseudo_diameter_only (SparseMatrix A)

real	SparseMatrix_pseudo_diameter_weighted (SparseMatrix A0, int root, int aggressive, int end1, int end2, int *connectedQ)

real	SparseMatrix_pseudo_diameter_unweighted (SparseMatrix A0, int root, int aggressive, int end1, int end2, int *connectedQ)

void	SparseMatrix_level_sets (SparseMatrix A, int root, int nlevel, int levelset_ptr, int levelset, int *mask, int reintialize_mask)

void	SparseMatrix_level_sets_khops (int khops, SparseMatrix A, int root, int nlevel, int levelset_ptr, int levelset, int *mask, int reintialize_mask)

void	SparseMatrix_weakly_connected_components (SparseMatrix A0, int ncomp, int comps, int *comps_ptr)

void	SparseMatrix_decompose_to_supervariables (SparseMatrix A, int ncluster, int cluster, int *clusterp)

SparseMatrix	SparseMatrix_get_submatrix (SparseMatrix A, int nrow, int ncol, int rindices, int cindices)

SparseMatrix	SparseMatrix_exclude_submatrix (SparseMatrix A, int nrow, int ncol, int rindices, int cindices)

SparseMatrix	SparseMatrix_get_augmented (SparseMatrix A)

SparseMatrix	SparseMatrix_to_square_matrix (SparseMatrix A, int bipartite_options)

SparseMatrix	SparseMatrix_largest_component (SparseMatrix A)

SparseMatrix	SparseMatrix_delete_empty_columns (SparseMatrix A, int *new2old, int nnew, int inplace)

SparseMatrix	SparseMatrix_delete_sparse_columns (SparseMatrix A, int threshold, int *new2old, int nnew, int inplace)

SparseMatrix	SparseMatrix_sort (SparseMatrix A)

SparseMatrix	SparseMatrix_set_entries_to_real_one (SparseMatrix A)

SparseMatrix	SparseMatrix_complement (SparseMatrix A, int undirected)

int	SparseMatrix_k_centers (SparseMatrix D, int weighted, int K, int root, int centers, int centering, real dist)

int	SparseMatrix_k_centers_user (SparseMatrix D, int weighted, int K, int centers_user, int centering, real *dist)

SparseMatrix	SparseMatrix_distance_matrix_k_centers (int K, SparseMatrix D, int weighted)

int	SparseMatrix_distance_matrix (SparseMatrix A, int weighted, real **dist_matrix)

SparseMatrix	SparseMatrix_distance_matrix_khops (int khops, SparseMatrix A, int weighted)

void	SparseMatrix_kcoreness (SparseMatrix A, int **coreness)

void	SparseMatrix_kcore_decomposition (SparseMatrix A, int coreness_max0, int coreness_ptr0, int *coreness_list0)

void	SparseMatrix_khairness (SparseMatrix A, int **hairness)

void	SparseMatrix_khair_decomposition (SparseMatrix A, int hairness_max0, int hairness_ptr0, int *hairness_list0)

SparseMatrix	SparseMatrix_from_dense (int m, int n, real *x)

void	SparseMatrix_page_rank (SparseMatrix A, real teleport_probablity, int weighted, real epsilon, real **page_rank)

Macro Definition Documentation

#define SparseMatrix_clear_hemitian ( A ) clear_flag((A)->property, MATRIX_HERMITIAN)

Definition at line 172 of file SparseMatrix.h.

#define SparseMatrix_clear_pattern_symmetric ( A ) clear_flag((A)->property, MATRIX_PATTERN_SYMMETRIC)

Definition at line 170 of file SparseMatrix.h.

#define SparseMatrix_clear_skew ( A ) clear_flag((A)->property, MATRIX_SKEW)

Definition at line 171 of file SparseMatrix.h.

#define SparseMatrix_clear_symmetric ( A ) clear_flag((A)->property, MATRIX_SYMMETRIC)

Definition at line 169 of file SparseMatrix.h.

#define SparseMatrix_clear_undirected ( A ) clear_flag((A)->property, MATRIX_UNDIRECTED)

Definition at line 168 of file SparseMatrix.h.

#define SparseMatrix_known_hemitian ( A ) test_flag((A)->property, MATRIX_HERMITIAN)

Definition at line 179 of file SparseMatrix.h.

#define SparseMatrix_known_skew ( A ) test_flag((A)->property, MATRIX_SKEW)

Definition at line 178 of file SparseMatrix.h.

#define SparseMatrix_known_strucural_symmetric ( A ) test_flag((A)->property, MATRIX_PATTERN_SYMMETRIC)

Definition at line 177 of file SparseMatrix.h.

Referenced by SparseMatrix_is_symmetric().

#define SparseMatrix_known_symmetric ( A ) test_flag((A)->property, MATRIX_SYMMETRIC)

Definition at line 176 of file SparseMatrix.h.

Referenced by SparseMatrix_is_symmetric().

#define SparseMatrix_known_undirected ( A ) test_flag((A)->property, MATRIX_UNDIRECTED)

Definition at line 175 of file SparseMatrix.h.

Referenced by makeDotGraph().

#define SparseMatrix_set_hemitian ( A ) set_flag((A)->property, MATRIX_HERMITIAN)

Definition at line 165 of file SparseMatrix.h.

#define SparseMatrix_set_pattern_symmetric ( A ) set_flag((A)->property, MATRIX_PATTERN_SYMMETRIC)

Definition at line 163 of file SparseMatrix.h.

Referenced by DistanceMatrix_restrict_cluster(), SparseMatrix_get_augmented(), SparseMatrix_is_symmetric(), SparseMatrix_symmetrize(), and SparseMatrix_symmetrize_nodiag().

#define SparseMatrix_set_skew ( A ) set_flag((A)->property, MATRIX_SKEW)

Definition at line 164 of file SparseMatrix.h.

#define SparseMatrix_set_symmetric ( A ) set_flag((A)->property, MATRIX_SYMMETRIC)

Definition at line 162 of file SparseMatrix.h.

Referenced by DistanceMatrix_restrict_cluster(), SparseMatrix_get_augmented(), SparseMatrix_is_symmetric(), SparseMatrix_symmetrize(), and SparseMatrix_symmetrize_nodiag().

#define SparseMatrix_set_undirected ( A ) set_flag((A)->property, MATRIX_UNDIRECTED)

Definition at line 161 of file SparseMatrix.h.

Referenced by SparseMatrix_make_undirected().

#define SYMMETRY_EPSILON 0.0000001

Definition at line 19 of file SparseMatrix.h.

Referenced by SparseMatrix_is_symmetric().

Typedef Documentation

typedef struct SparseMatrix_struct* SparseMatrix

Definition at line 40 of file SparseMatrix.h.

Enumeration Type Documentation

anonymous enum

Enumerator
FORMAT_CSC
FORMAT_CSR
FORMAT_COORD

Definition at line 20 of file SparseMatrix.h.

anonymous enum

Enumerator
UNMASKED
MASKED

Definition at line 21 of file SparseMatrix.h.

anonymous enum

Enumerator
MATRIX_PATTERN_SYMMETRIC
MATRIX_SYMMETRIC
MATRIX_SKEW
MATRIX_HERMITIAN
MATRIX_UNDIRECTED

Definition at line 22 of file SparseMatrix.h.

anonymous enum

Enumerator
BIPARTITE_RECT
BIPARTITE_PATTERN_UNSYM
BIPARTITE_UNSYM
BIPARTITE_ALWAYS

Definition at line 23 of file SparseMatrix.h.

anonymous enum

Enumerator
MATRIX_TYPE_REAL
MATRIX_TYPE_COMPLEX
MATRIX_TYPE_INTEGER
MATRIX_TYPE_PATTERN
MATRIX_TYPE_UNKNOWN

Definition at line 42 of file SparseMatrix.h.

anonymous enum

Enumerator
SUM_REPEATED_NONE
SUM_REPEATED_ALL
SUM_REPEATED_REAL_PART
SUM_REPEATED_IMAGINARY_PART
SUM_IMGINARY_KEEP_LAST_REAL

Definition at line 82 of file SparseMatrix.h.

Function Documentation

SparseMatrix SparseMatrix_add	(	SparseMatrix	A,
		SparseMatrix	B
	)

SparseMatrix SparseMatrix_apply_fun	(	SparseMatrix	A,
		double(*)(double x)	fun
	)

Definition at line 2355 of file SparseMatrix.c.

References SparseMatrix_struct::a, for(), SparseMatrix_struct::format, FORMAT_CSR, SparseMatrix_struct::ia, SparseMatrix_struct::m, MATRIX_TYPE_REAL, real, and SparseMatrix_struct::type.

SparseMatrix SparseMatrix_apply_fun_general	(	SparseMatrix	A,
		void()(int i, int j, int n, double x)	fun
	)

Definition at line 2378 of file SparseMatrix.c.

References SparseMatrix_struct::a, for(), SparseMatrix_struct::format, FORMAT_CSR, SparseMatrix_struct::ia, SparseMatrix_struct::ja, SparseMatrix_struct::m, MATRIX_TYPE_COMPLEX, MATRIX_TYPE_REAL, real, and SparseMatrix_struct::type.

SparseMatrix SparseMatrix_complement	(	SparseMatrix	A,
		int	undirected
	)

Definition at line 3332 of file SparseMatrix.c.

References assert, FREE, SparseMatrix_struct::ia, SparseMatrix_struct::ja, SparseMatrix_struct::m, MALLOC, MATRIX_TYPE_PATTERN, SparseMatrix_struct::n, NULL, SparseMatrix_struct::nz, SparseMatrix_delete(), SparseMatrix_from_coordinate_arrays(), SparseMatrix_symmetrize(), and TRUE.

int SparseMatrix_connectedQ ( SparseMatrix A )

Definition at line 2854 of file SparseMatrix.c.

References FALSE, FREE, SparseMatrix_struct::m, SparseMatrix_struct::n, NULL, SparseMatrix_delete(), SparseMatrix_is_symmetric(), SparseMatrix_level_sets(), SparseMatrix_symmetrize(), and TRUE.

SparseMatrix SparseMatrix_coordinate_form_add_entries	(	SparseMatrix	A,
		int	nentries,
		int *	irn,
		int *	jcn,
		void *	val
	)

Definition at line 1968 of file SparseMatrix.c.

References SparseMatrix_struct::a, assert, SparseMatrix_struct::format, FORMAT_COORD, SparseMatrix_struct::ia, SparseMatrix_struct::ja, SparseMatrix_struct::m, MAX, MEMCPY, SparseMatrix_struct::n, SparseMatrix_struct::nz, SparseMatrix_struct::nzmax, and SparseMatrix_struct::size.

Referenced by call_tri(), call_tri2(), Multilevel_MQ_Clustering_establish(), SparseMatrix_distance_matrix_k_centers(), and SparseMatrix_distance_matrix_khops().

SparseMatrix SparseMatrix_crop	(	SparseMatrix	A,
		real	epsilon
	)

Definition at line 2402 of file SparseMatrix.c.

References SparseMatrix_struct::a, ABS, for(), SparseMatrix_struct::ia, SparseMatrix_struct::ja, SparseMatrix_struct::m, MATRIX_TYPE_COMPLEX, MATRIX_TYPE_INTEGER, MATRIX_TYPE_PATTERN, MATRIX_TYPE_REAL, MATRIX_TYPE_UNKNOWN, NULL, SparseMatrix_struct::nz, real, and SparseMatrix_struct::type.

void SparseMatrix_decompose_to_supervariables	(	SparseMatrix	A,
		int *	ncluster,
		int **	cluster,
		int **	clusterp
	)

Definition at line 2875 of file SparseMatrix.c.

References FREE, SparseMatrix_struct::ia, SparseMatrix_struct::ja, SparseMatrix_struct::m, MALLOC, SparseMatrix_struct::n, and NULL.

void SparseMatrix_delete ( SparseMatrix A )

Definition at line 411 of file SparseMatrix.c.

References SparseMatrix_struct::a, FREE, SparseMatrix_struct::ia, and SparseMatrix_struct::ja.

Referenced by attached_clustering(), call_tri(), call_tri2(), DistanceMatrix_restrict_cluster(), main(), modularity_clustering(), mq_clustering(), Multilevel_coarsen(), Multilevel_delete(), Multilevel_MQ_Clustering_delete(), Multilevel_MQ_Clustering_establish(), SparseMatrix_complement(), SparseMatrix_connectedQ(), SparseMatrix_delete_sparse_columns(), SparseMatrix_distance_matrix(), SparseMatrix_distance_matrix_k_centers(), SparseMatrix_distance_matrix_khops(), SparseMatrix_get_real_adjacency_matrix_symmetrized(), SparseMatrix_is_symmetric(), SparseMatrix_k_centers(), SparseMatrix_k_centers_user(), SparseMatrix_multiply(), SparseMatrix_multiply3(), SparseMatrix_pseudo_diameter_unweighted(), SparseMatrix_pseudo_diameter_weighted(), SparseMatrix_sort(), SparseMatrix_symmetrize(), SparseMatrix_symmetrize_nodiag(), SparseMatrix_to_square_matrix(), SparseMatrix_transpose(), SparseMatrix_weakly_connected_components(), spring_electrical_embedding(), spring_electrical_embedding_fast(), spring_electrical_embedding_slow(), spring_electrical_spring_embedding(), spring_maxent_embedding(), SpringSmoother_delete(), SpringSmoother_new(), stress_model_core(), StressMajorizationSmoother2_new(), StressMajorizationSmoother_delete(), StressMajorizationSmoother_smooth(), TriangleSmoother_new(), and uniform_stress().

SparseMatrix SparseMatrix_delete_empty_columns	(	SparseMatrix	A,
		int **	new2old,
		int *	nnew,
		int	inplace
	)

Definition at line 3314 of file SparseMatrix.c.

References SparseMatrix_delete_sparse_columns().

SparseMatrix SparseMatrix_delete_sparse_columns	(	SparseMatrix	A,
		int	threshold,
		int **	new2old,
		int *	nnew,
		int	inplace
	)

Definition at line 3264 of file SparseMatrix.c.

References assert, FREE, SparseMatrix_struct::ia, SparseMatrix_struct::ja, SparseMatrix_struct::m, MALLOC, SparseMatrix_struct::n, SparseMatrix_copy(), SparseMatrix_delete(), and SparseMatrix_transpose().

Referenced by SparseMatrix_delete_empty_columns().

int SparseMatrix_distance_matrix	(	SparseMatrix	A,
		int	weighted,
		real **	dist_matrix
	)

Definition at line 3655 of file SparseMatrix.c.

References assert, FALSE, FREE, SparseMatrix_struct::m, MALLOC, SparseMatrix_struct::n, NULL, real, SparseMatrix_delete(), SparseMatrix_is_symmetric(), SparseMatrix_level_sets(), SparseMatrix_symmetrize(), and TRUE.

SparseMatrix SparseMatrix_distance_matrix_k_centers	(	int	K,
		SparseMatrix	D,
		int	weighted
	)

Definition at line 3709 of file SparseMatrix.c.

References assert, C, FALSE, FORMAT_COORD, FREE, SparseMatrix_struct::m, MATRIX_TYPE_REAL, SparseMatrix_struct::n, NULL, real, SparseMatrix_coordinate_form_add_entries(), SparseMatrix_delete(), SparseMatrix_from_coordinate_format(), SparseMatrix_k_centers(), and SparseMatrix_new().

SparseMatrix SparseMatrix_distance_matrix_khops	(	int	khops,
		SparseMatrix	A,
		int	weighted
	)

Definition at line 3747 of file SparseMatrix.c.

References assert, C, FALSE, FORMAT_COORD, FREE, SparseMatrix_struct::m, MALLOC, MATRIX_TYPE_REAL, SparseMatrix_struct::n, NULL, real, SparseMatrix_coordinate_form_add_entries(), SparseMatrix_delete(), SparseMatrix_from_coordinate_format(), SparseMatrix_is_symmetric(), SparseMatrix_level_sets_khops(), SparseMatrix_new(), SparseMatrix_symmetrize(), and TRUE.

SparseMatrix SparseMatrix_divide_row_by_degree ( SparseMatrix A )

Definition at line 2159 of file SparseMatrix.c.

References SparseMatrix_struct::a, assert, for(), SparseMatrix_struct::ia, SparseMatrix_struct::ja, SparseMatrix_struct::m, MATRIX_TYPE_COMPLEX, MATRIX_TYPE_INTEGER, MATRIX_TYPE_PATTERN, MATRIX_TYPE_REAL, MATRIX_TYPE_UNKNOWN, NULL, real, and SparseMatrix_struct::type.

SparseMatrix SparseMatrix_exclude_submatrix	(	SparseMatrix	A,
		int	nrow,
		int	ncol,
		int *	rindices,
		int *	cindices
	)

Definition at line 3195 of file SparseMatrix.c.

References FREE, SparseMatrix_struct::m, MALLOC, SparseMatrix_struct::n, and SparseMatrix_get_submatrix().

void SparseMatrix_export	(	FILE *	f,
		SparseMatrix	A
	)

Definition at line 778 of file SparseMatrix.c.

References assert, SparseMatrix_struct::format, FORMAT_COORD, FORMAT_CSC, and FORMAT_CSR.

void SparseMatrix_export_binary	(	char *	name,
		SparseMatrix	A,
		int *	flag
	)

Definition at line 646 of file SparseMatrix.c.

References SparseMatrix_export_binary_fp().

void SparseMatrix_export_binary_fp	(	FILE *	f,
		SparseMatrix	A
	)

Definition at line 626 of file SparseMatrix.c.

References SparseMatrix_struct::a, SparseMatrix_struct::format, FORMAT_COORD, SparseMatrix_struct::ia, SparseMatrix_struct::ja, SparseMatrix_struct::m, SparseMatrix_struct::n, SparseMatrix_struct::nz, SparseMatrix_struct::nzmax, SparseMatrix_struct::property, SparseMatrix_struct::size, and SparseMatrix_struct::type.

Referenced by SparseMatrix_export_binary().

SparseMatrix SparseMatrix_from_coordinate_arrays	(	int	nz,
		int	m,
		int	n,
		int *	irn,
		int *	jcn,
		void *	val,
		int	type,
		size_t	sz
	)

Definition at line 957 of file SparseMatrix.c.

References SUM_REPEATED_ALL.

Referenced by attached_clustering(), DistanceMatrix_restrict_cluster(), Import_coord_clusters_from_dot(), makeMatrix(), SparseMatrix_complement(), SparseMatrix_from_coordinate_format(), SparseMatrix_get_augmented(), SparseMatrix_get_submatrix(), and SparseMatrix_import_dot().

SparseMatrix SparseMatrix_from_coordinate_arrays_not_compacted	(	int	nz,
		int	m,
		int	n,
		int *	irn,
		int *	jcn,
		void *	val,
		int	type,
		size_t	sz,
		int	what_to_sum
	)

Definition at line 962 of file SparseMatrix.c.

Referenced by SparseMatrix_from_coordinate_format_not_compacted().

SparseMatrix SparseMatrix_from_coordinate_format ( SparseMatrix A )

SparseMatrix SparseMatrix_from_coordinate_format_not_compacted	(	SparseMatrix	A,
		int	what_to_sum
	)

Definition at line 812 of file SparseMatrix.c.

References SparseMatrix_struct::a, assert, SparseMatrix_struct::format, FORMAT_COORD, SparseMatrix_struct::ia, SparseMatrix_struct::ja, SparseMatrix_struct::m, SparseMatrix_struct::n, NULL, SparseMatrix_struct::nz, SparseMatrix_struct::size, SparseMatrix_from_coordinate_arrays_not_compacted(), and SparseMatrix_struct::type.

SparseMatrix SparseMatrix_from_dense	(	int	m,
		int	n,
		real *	x
	)

Definition at line 3631 of file SparseMatrix.c.

References SparseMatrix_struct::a, for(), FORMAT_CSR, SparseMatrix_struct::ia, SparseMatrix_struct::ja, MATRIX_TYPE_REAL, SparseMatrix_struct::nz, real, and SparseMatrix_new().

SparseMatrix SparseMatrix_general_new	(	int	m,
		int	n,
		int	nz,
		int	type,
		size_t	sz,
		int	format
	)

Definition at line 397 of file SparseMatrix.c.

Referenced by SparseMatrix_copy(), and SparseMatrix_import_binary_fp().

SparseMatrix SparseMatrix_get_augmented ( SparseMatrix A )

Definition at line 2974 of file SparseMatrix.c.

References SparseMatrix_struct::a, assert, FREE, SparseMatrix_struct::ia, SparseMatrix_struct::ja, SparseMatrix_struct::m, MALLOC, MEMCPY, SparseMatrix_struct::n, NULL, SparseMatrix_struct::nz, SparseMatrix_struct::size, SparseMatrix_from_coordinate_arrays(), SparseMatrix_set_pattern_symmetric, SparseMatrix_set_symmetric, and SparseMatrix_struct::type.

Referenced by SparseMatrix_to_square_matrix().

SparseMatrix SparseMatrix_get_real_adjacency_matrix_symmetrized ( SparseMatrix A )

SparseMatrix SparseMatrix_get_submatrix	(	SparseMatrix	A,
		int	nrow,
		int	ncol,
		int *	rindices,
		int *	cindices
	)

Definition at line 3040 of file SparseMatrix.c.

References SparseMatrix_struct::a, FREE, SparseMatrix_struct::ia, SparseMatrix_struct::ja, SparseMatrix_struct::m, MALLOC, MATRIX_TYPE_COMPLEX, MATRIX_TYPE_INTEGER, MATRIX_TYPE_PATTERN, MATRIX_TYPE_REAL, MATRIX_TYPE_UNKNOWN, SparseMatrix_struct::n, NULL, real, SparseMatrix_struct::size, SparseMatrix_from_coordinate_arrays(), and SparseMatrix_struct::type.

Referenced by SparseMatrix_exclude_submatrix(), and SparseMatrix_largest_component().

int SparseMatrix_has_diagonal ( SparseMatrix A )

Definition at line 2483 of file SparseMatrix.c.

References FALSE, SparseMatrix_struct::ia, SparseMatrix_struct::ja, SparseMatrix_struct::m, and TRUE.

SparseMatrix SparseMatrix_import_binary ( char * name )

Definition at line 707 of file SparseMatrix.c.

References NULL, and SparseMatrix_import_binary_fp().

SparseMatrix SparseMatrix_import_binary_fp ( FILE * f )

Definition at line 662 of file SparseMatrix.c.

References SparseMatrix_struct::a, FORMAT_COORD, SparseMatrix_struct::ia, SparseMatrix_struct::ja, SparseMatrix_struct::m, NULL, SparseMatrix_struct::nz, SparseMatrix_struct::property, SparseMatrix_struct::size, and SparseMatrix_general_new().

Referenced by SparseMatrix_import_binary().

int SparseMatrix_is_symmetric	(	SparseMatrix	A,
		int	test_pattern_symmetry_only
	)

Definition at line 178 of file SparseMatrix.c.

References SparseMatrix_struct::a, ABS, assert, FALSE, SparseMatrix_struct::format, FORMAT_CSR, FREE, SparseMatrix_struct::ia, SparseMatrix_struct::ja, SparseMatrix_struct::m, MALLOC, MATRIX_TYPE_COMPLEX, MATRIX_TYPE_INTEGER, MATRIX_TYPE_PATTERN, MATRIX_TYPE_REAL, MATRIX_TYPE_UNKNOWN, SparseMatrix_struct::n, real, SparseMatrix_delete(), SparseMatrix_known_strucural_symmetric, SparseMatrix_known_symmetric, SparseMatrix_set_pattern_symmetric, SparseMatrix_set_symmetric, SparseMatrix_transpose(), SYMMETRY_EPSILON, TRUE, and SparseMatrix_struct::type.

Referenced by average_edge_length(), ideal_distance_matrix(), Multilevel_MQ_Clustering_init(), Multilevel_MQ_Clustering_new(), Multilevel_new(), SparseMatrix_connectedQ(), SparseMatrix_distance_matrix(), SparseMatrix_distance_matrix_khops(), SparseMatrix_k_centers(), SparseMatrix_k_centers_user(), SparseMatrix_pseudo_diameter_unweighted(), SparseMatrix_pseudo_diameter_weighted(), SparseMatrix_symmetrize(), SparseMatrix_symmetrize_nodiag(), SparseMatrix_to_square_matrix(), SparseMatrix_weakly_connected_components(), SparseStressMajorizationSmoother_new(), SpringSmoother_new(), stress_model_core(), StressMajorizationSmoother2_new(), TriangleSmoother_new(), uniform_stress(), and UniformStressSmoother_new().

int SparseMatrix_k_centers	(	SparseMatrix	D,
		int	weighted,
		int	K,
		int	root,
		int **	centers,
		int	centering,
		real **	dist
	)

Definition at line 3372 of file SparseMatrix.c.

References assert, FALSE, FREE, SparseMatrix_struct::m, MALLOC, MIN, SparseMatrix_struct::n, NULL, real, SparseMatrix_delete(), SparseMatrix_is_symmetric(), SparseMatrix_level_sets(), SparseMatrix_pseudo_diameter_unweighted(), SparseMatrix_pseudo_diameter_weighted(), SparseMatrix_symmetrize(), and TRUE.

Referenced by SparseMatrix_distance_matrix_k_centers().

int SparseMatrix_k_centers_user	(	SparseMatrix	D,
		int	weighted,
		int	K,
		int *	centers_user,
		int	centering,
		real **	dist
	)

Definition at line 3515 of file SparseMatrix.c.

References assert, FALSE, FREE, SparseMatrix_struct::m, MALLOC, MIN, SparseMatrix_struct::n, NULL, real, SparseMatrix_delete(), SparseMatrix_is_symmetric(), SparseMatrix_level_sets(), SparseMatrix_pseudo_diameter_unweighted(), SparseMatrix_pseudo_diameter_weighted(), SparseMatrix_symmetrize(), and TRUE.

void SparseMatrix_kcore_decomposition	(	SparseMatrix	A,
		int *	coreness_max0,
		int **	coreness_ptr0,
		int **	coreness_list0
	)

void SparseMatrix_kcoreness	(	SparseMatrix	A,
		int **	coreness
	)

void SparseMatrix_khair_decomposition	(	SparseMatrix	A,
		int *	hairness_max0,
		int **	hairness_ptr0,
		int **	hairness_list0
	)

void SparseMatrix_khairness	(	SparseMatrix	A,
		int **	hairness
	)

SparseMatrix SparseMatrix_largest_component ( SparseMatrix A )

Definition at line 3234 of file SparseMatrix.c.

References BIPARTITE_RECT, FREE, NULL, SparseMatrix_get_submatrix(), SparseMatrix_to_square_matrix(), and SparseMatrix_weakly_connected_components().

void SparseMatrix_level_sets	(	SparseMatrix	A,
		int	root,
		int *	nlevel,
		int **	levelset_ptr,
		int **	levelset,
		int **	mask,
		int	reintialize_mask
	)

Definition at line 2545 of file SparseMatrix.c.

References SparseMatrix_level_sets_internal().

Referenced by SparseMatrix_connectedQ(), SparseMatrix_distance_matrix(), SparseMatrix_k_centers(), SparseMatrix_k_centers_user(), SparseMatrix_pseudo_diameter_unweighted(), and SparseMatrix_weakly_connected_components().

void SparseMatrix_level_sets_khops	(	int	khops,
		SparseMatrix	A,
		int	root,
		int *	nlevel,
		int **	levelset_ptr,
		int **	levelset,
		int **	mask,
		int	reintialize_mask
	)

Definition at line 2552 of file SparseMatrix.c.

References SparseMatrix_level_sets_internal().

Referenced by SparseMatrix_distance_matrix_khops().

SparseMatrix SparseMatrix_make_undirected ( SparseMatrix A )

Definition at line 62 of file SparseMatrix.c.

References FALSE, SparseMatrix_remove_upper(), SparseMatrix_set_undirected, and SparseMatrix_symmetrize().

SparseMatrix SparseMatrix_multiply	(	SparseMatrix	A,
		SparseMatrix	B
	)

Definition at line 1401 of file SparseMatrix.c.

References SparseMatrix_struct::a, assert, C, for(), SparseMatrix_struct::format, FORMAT_CSR, FREE, SparseMatrix_struct::ia, SparseMatrix_struct::ja, SparseMatrix_struct::m, MALLOC, MATRIX_TYPE_COMPLEX, MATRIX_TYPE_INTEGER, MATRIX_TYPE_PATTERN, MATRIX_TYPE_REAL, MATRIX_TYPE_UNKNOWN, SparseMatrix_struct::n, NULL, SparseMatrix_struct::nz, real, SparseMatrix_delete(), SparseMatrix_new(), and SparseMatrix_struct::type.

Referenced by Multilevel_coarsen(), and Multilevel_MQ_Clustering_establish().

SparseMatrix SparseMatrix_multiply3	(	SparseMatrix	A,
		SparseMatrix	B,
		SparseMatrix	C
	)

Definition at line 1567 of file SparseMatrix.c.

References SparseMatrix_struct::a, assert, SparseMatrix_struct::format, FORMAT_CSR, FREE, SparseMatrix_struct::ia, SparseMatrix_struct::ja, SparseMatrix_struct::m, MALLOC, MATRIX_TYPE_COMPLEX, MATRIX_TYPE_INTEGER, MATRIX_TYPE_PATTERN, MATRIX_TYPE_REAL, MATRIX_TYPE_UNKNOWN, SparseMatrix_struct::n, NULL, SparseMatrix_struct::nz, real, SparseMatrix_delete(), SparseMatrix_new(), and SparseMatrix_struct::type.

Referenced by DistanceMatrix_restrict_cluster().

SparseMatrix SparseMatrix_multiply_by_scaler	(	SparseMatrix	A,
		real	s
	)

Definition at line 1355 of file SparseMatrix.c.

References SparseMatrix_struct::a, assert, for(), SparseMatrix_struct::format, FORMAT_CSR, FREE, SparseMatrix_struct::ia, SparseMatrix_struct::m, MALLOC, MATRIX_TYPE_COMPLEX, MATRIX_TYPE_INTEGER, MATRIX_TYPE_REAL, NULL, SparseMatrix_struct::nz, real, and SparseMatrix_struct::type.

void SparseMatrix_multiply_dense	(	SparseMatrix	A,
		int	ATranspose,
		real *	v,
		int	vTransposed,
		real **	res,
		int	res_transpose,
		int	dim
	)

Definition at line 1192 of file SparseMatrix.c.

Referenced by StressMajorizationSmoother_smooth().

void SparseMatrix_multiply_vector	(	SparseMatrix	A,
		real *	v,
		real **	res,
		int	transposed
	)

Definition at line 1217 of file SparseMatrix.c.

References SparseMatrix_struct::a, assert, SparseMatrix_struct::format, FORMAT_CSR, SparseMatrix_struct::ia, if(), SparseMatrix_struct::ja, SparseMatrix_struct::m, MALLOC, MATRIX_TYPE_INTEGER, MATRIX_TYPE_REAL, SparseMatrix_struct::n, NULL, real, and SparseMatrix_struct::type.

Referenced by Operator_matmul_apply(), and Operator_uniform_stress_matmul_apply().

SparseMatrix SparseMatrix_new	(	int	m,
		int	n,
		int	nz,
		int	type,
		int	format
	)

Definition at line 384 of file SparseMatrix.c.

Referenced by call_tri(), call_tri2(), Multilevel_MQ_Clustering_establish(), SparseMatrix_add(), SparseMatrix_distance_matrix_k_centers(), SparseMatrix_distance_matrix_khops(), SparseMatrix_from_dense(), SparseMatrix_get_real_adjacency_matrix_symmetrized(), SparseMatrix_import_dot(), SparseMatrix_multiply(), SparseMatrix_multiply3(), SparseMatrix_transpose(), SparseStressMajorizationSmoother_new(), SpringSmoother_new(), StressMajorizationSmoother2_new(), and UniformStressSmoother_new().

SparseMatrix SparseMatrix_normalize_by_row ( SparseMatrix A )

Definition at line 2272 of file SparseMatrix.c.

References SparseMatrix_struct::a, ABS, for(), SparseMatrix_struct::format, FORMAT_CSR, SparseMatrix_struct::ia, SparseMatrix_struct::m, MATRIX_TYPE_REAL, MAX, max, real, and SparseMatrix_struct::type.

SparseMatrix SparseMatrix_normalize_to_rowsum1 ( SparseMatrix A )

Definition at line 2243 of file SparseMatrix.c.

References SparseMatrix_struct::a, for(), SparseMatrix_struct::format, FORMAT_CSR, SparseMatrix_struct::ia, SparseMatrix_struct::m, MATRIX_TYPE_REAL, real, and SparseMatrix_struct::type.

void SparseMatrix_page_rank	(	SparseMatrix	A,
		real	teleport_probablity,
		int	weighted,
		real	epsilon,
		real **	page_rank
	)

Definition at line 4081 of file SparseMatrix.c.

References SparseMatrix_struct::a, ABS, assert, FALSE, FREE, SparseMatrix_struct::ia, SparseMatrix_struct::ja, SparseMatrix_struct::m, MACHINEACC, MALLOC, MATRIX_TYPE_COMPLEX, MATRIX_TYPE_INTEGER, MATRIX_TYPE_PATTERN, MATRIX_TYPE_REAL, MATRIX_TYPE_UNKNOWN, MAX, MEMCPY, SparseMatrix_struct::n, NULL, real, SparseMatrix_struct::type, and Verbose.

void SparseMatrix_print	(	char *	,
		SparseMatrix	A
	)

Definition at line 536 of file SparseMatrix.c.

References assert, SparseMatrix_struct::format, FORMAT_COORD, FORMAT_CSC, FORMAT_CSR, SparseMatrix_print_coord(), and SparseMatrix_print_csr().

real SparseMatrix_pseudo_diameter_only ( SparseMatrix A )

Definition at line 2849 of file SparseMatrix.c.

References FALSE, and SparseMatrix_pseudo_diameter_unweighted().

real SparseMatrix_pseudo_diameter_unweighted	(	SparseMatrix	A0,
		int	root,
		int	aggressive,
		int *	end1,
		int *	end2,
		int *	connectedQ
	)

Definition at line 2796 of file SparseMatrix.c.

References assert, FALSE, FREE, int, SparseMatrix_struct::m, MIN, NULL, real, SparseMatrix_delete(), SparseMatrix_is_symmetric(), SparseMatrix_level_sets(), SparseMatrix_pseudo_diameter_unweighted(), SparseMatrix_symmetrize(), and TRUE.

Referenced by SparseMatrix_k_centers(), SparseMatrix_k_centers_user(), SparseMatrix_pseudo_diameter_only(), and SparseMatrix_pseudo_diameter_unweighted().

real SparseMatrix_pseudo_diameter_weighted	(	SparseMatrix	A0,
		int	root,
		int	aggressive,
		int *	end1,
		int *	end2,
		int *	connectedQ
	)

Definition at line 2732 of file SparseMatrix.c.

References ABS, assert, FALSE, FREE, SparseMatrix_struct::m, MALLOC, MAX, SparseMatrix_struct::n, NULL, real, SparseMatrix_delete(), SparseMatrix_is_symmetric(), SparseMatrix_pseudo_diameter_weighted(), SparseMatrix_symmetrize(), and TRUE.

Referenced by SparseMatrix_k_centers(), SparseMatrix_k_centers_user(), and SparseMatrix_pseudo_diameter_weighted().

SparseMatrix SparseMatrix_remove_diagonal ( SparseMatrix A )

SparseMatrix SparseMatrix_remove_upper ( SparseMatrix A )

Definition at line 2073 of file SparseMatrix.c.

References SparseMatrix_struct::a, clear_flag, for(), SparseMatrix_struct::ia, SparseMatrix_struct::ja, SparseMatrix_struct::m, MATRIX_HERMITIAN, MATRIX_PATTERN_SYMMETRIC, MATRIX_SKEW, MATRIX_SYMMETRIC, MATRIX_TYPE_COMPLEX, MATRIX_TYPE_INTEGER, MATRIX_TYPE_PATTERN, MATRIX_TYPE_REAL, MATRIX_TYPE_UNKNOWN, NULL, SparseMatrix_struct::nz, SparseMatrix_struct::property, real, and SparseMatrix_struct::type.

Referenced by SparseMatrix_make_undirected().

SparseMatrix SparseMatrix_scaled_by_vector	(	SparseMatrix	A,
		real *	v,
		int	apply_to_row
	)

Definition at line 1324 of file SparseMatrix.c.

References SparseMatrix_struct::a, assert, SparseMatrix_struct::format, FORMAT_CSR, SparseMatrix_struct::ia, if(), SparseMatrix_struct::ja, SparseMatrix_struct::m, MATRIX_TYPE_REAL, real, and SparseMatrix_struct::type.

SparseMatrix SparseMatrix_set_entries_to_real_one ( SparseMatrix A )

Definition at line 3318 of file SparseMatrix.c.

References SparseMatrix_struct::a, FREE, MALLOC, MATRIX_TYPE_REAL, SparseMatrix_struct::nz, real, SparseMatrix_struct::size, and SparseMatrix_struct::type.

Referenced by modularity_clustering(), and mq_clustering().

SparseMatrix SparseMatrix_sort ( SparseMatrix A )

Definition at line 54 of file SparseMatrix.c.

References SparseMatrix_delete(), and SparseMatrix_transpose().

SparseMatrix SparseMatrix_sum_repeat_entries	(	SparseMatrix	A,
		int	what_to_sum
	)

SparseMatrix SparseMatrix_symmetrize	(	SparseMatrix	A,
		int	pattern_symmetric_only
	)

Definition at line 151 of file SparseMatrix.c.

References NULL, SparseMatrix_add(), SparseMatrix_copy(), SparseMatrix_delete(), SparseMatrix_is_symmetric(), SparseMatrix_set_pattern_symmetric, SparseMatrix_set_symmetric, and SparseMatrix_transpose().

Referenced by call_tri(), call_tri2(), get_distance_matrix(), modularity_clustering(), mq_clustering(), SparseMatrix_complement(), SparseMatrix_connectedQ(), SparseMatrix_distance_matrix(), SparseMatrix_distance_matrix_khops(), SparseMatrix_get_real_adjacency_matrix_symmetrized(), SparseMatrix_k_centers(), SparseMatrix_k_centers_user(), SparseMatrix_make_undirected(), SparseMatrix_pseudo_diameter_unweighted(), SparseMatrix_pseudo_diameter_weighted(), SparseMatrix_weakly_connected_components(), spring_electrical_embedding(), spring_electrical_embedding_fast(), spring_electrical_embedding_slow(), spring_electrical_spring_embedding(), spring_maxent_embedding(), and stress_model_core().

SparseMatrix SparseMatrix_symmetrize_nodiag	(	SparseMatrix	A,
		int	pattern_symmetric_only
	)

Definition at line 163 of file SparseMatrix.c.

References NULL, SparseMatrix_add(), SparseMatrix_copy(), SparseMatrix_delete(), SparseMatrix_is_symmetric(), SparseMatrix_remove_diagonal(), SparseMatrix_set_pattern_symmetric, SparseMatrix_set_symmetric, and SparseMatrix_transpose().

Referenced by Multilevel_new().

SparseMatrix SparseMatrix_to_square_matrix	(	SparseMatrix	A,
		int	bipartite_options
	)

Definition at line 3018 of file SparseMatrix.c.

References assert, BIPARTITE_ALWAYS, BIPARTITE_PATTERN_UNSYM, BIPARTITE_RECT, BIPARTITE_UNSYM, FALSE, SparseMatrix_struct::m, SparseMatrix_struct::n, SparseMatrix_delete(), SparseMatrix_get_augmented(), SparseMatrix_is_symmetric(), and TRUE.

Referenced by SparseMatrix_largest_component().

SparseMatrix SparseMatrix_transpose ( SparseMatrix A )

void SparseMatrix_weakly_connected_components	(	SparseMatrix	A0,
		int *	ncomp,
		int **	comps,
		int **	comps_ptr
	)

Definition at line 2558 of file SparseMatrix.c.

References FALSE, FREE, SparseMatrix_struct::m, MALLOC, NULL, SparseMatrix_delete(), SparseMatrix_is_symmetric(), SparseMatrix_level_sets(), SparseMatrix_symmetrize(), and TRUE.

Referenced by SparseMatrix_largest_component().

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