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make_motif34lib.cpp
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make_motif34lib.cpp
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#include "bct.h"
/*
* Our implementation of the BCT motif library does not include Mn ("M as a
* single number") because a C++ long is generally not large enough to contain
* the 12-digit numbers required for the four-node motif library.
*/
BCT_NAMESPACE::motif_mode_enum BCT_NAMESPACE::motif_mode = MILO;
BCT_NAMESPACE::motif_mode_enum BCT_NAMESPACE::get_motif_mode() { return motif_mode; }
void BCT_NAMESPACE::set_motif_mode(motif_mode_enum motif_mode) { BCT_NAMESPACE::motif_mode = motif_mode; }
/*
* Constructs the three-node motif library.
*/
MATRIX_T* BCT_NAMESPACE::motif3generate(VECTOR_T** ID, VECTOR_T** N) {
static MATRIX_T* M = NULL;
static VECTOR_T* _ID = NULL;
static VECTOR_T* _N = NULL;
if (M == NULL) {
// n=0;
int n = -1;
// M=false(54,6);
M = MATRIX_ID(calloc)(54, 6);
// CL=zeros(54,6,'uint8');
MATRIX_T* CL = zeros(54, 6);
// cl=zeros(1,6,'uint8');
VECTOR_T* cl = zeros_vector(6);
FP_T i_nondiag[] = { 1, 2, 3, 5, 6, 7 };
VECTOR_ID(view) i_nondiag_vv = VECTOR_ID(view_array)(i_nondiag, 6);
// for i=0:2^6-1
for (int i = 0; i < 64; i++) {
// m=dec2bin(i);
// m=[num2str(zeros(1,6-length(m)), '%d') m];
std::string m = dec2bin(i, 6);
// G=str2num ([ ...
// '0' ' ' m(3) ' ' m(5) ;
// m(1) ' ' '0' ' ' m(6) ;
// m(2) ' ' m(4) ' ' '0' ]);
MATRIX_T* G = MATRIX_ID(calloc)(3, 3);
for (int i = 0; i < 6; i++) {
int index = (int)i_nondiag[i];
if (m[i] == '1') {
ordinal_index_assign(G, index, 1.0);
}
}
// Ko=sum(G,2);
VECTOR_T* Ko = sum(G, 2);
// Ki=sum(G,1).';
VECTOR_T* Ki = sum(G, 1);
// if Ko+Ki,
VECTOR_T* Ko_add_Ki = copy(Ko);
VECTOR_ID(add)(Ko_add_Ki, Ki);
bool Ko_add_Ki_bool = to_bool(Ko_add_Ki);
VECTOR_ID(free)(Ko_add_Ki);
if (Ko_add_Ki_bool) {
// n=n+1;
n++;
// cl(:)=sortrows([Ko Ki]).';
MATRIX_T* Ko_Ki = concatenate_rows(Ko, Ki);
MATRIX_T* Ko_Ki_sorted = sortrows(Ko_Ki);
MATRIX_ID(free)(Ko_Ki);
MATRIX_T* Ko_Ki_transpose = MATRIX_ID(alloc)(2, G->size1);
MATRIX_ID(transpose_memcpy)(Ko_Ki_transpose, Ko_Ki_sorted);
MATRIX_ID(free)(Ko_Ki_sorted);
VECTOR_ID(free)(cl);
cl = to_vector(Ko_Ki_transpose);
MATRIX_ID(free)(Ko_Ki_transpose);
// CL(n,:)=cl;
MATRIX_ID(set_row)(CL, n, cl);
// M(n,:)=G([2:4 6:8]);
VECTOR_T* G_nondiag = ordinal_index(G, &i_nondiag_vv.vector);
MATRIX_ID(set_row)(M, n, G_nondiag);
VECTOR_ID(free)(G_nondiag);
}
MATRIX_ID(free)(G);
VECTOR_ID(free)(Ko);
VECTOR_ID(free)(Ki);
}
VECTOR_ID(free)(cl);
// [u1 u2 ID]=unique(CL,'rows');
MATRIX_T* u1 = unique_rows(CL, "last", NULL, &_ID);
MATRIX_ID(free)(CL);
MATRIX_ID(free)(u1);
VECTOR_ID(add_constant)(_ID, 1.0);
// id_mika= [1 3 4 6 7 8 11];
int id_mika[] = { 1, 3, 4, 6, 7, 8, 11 };
// id_olaf= -[3 6 1 11 4 7 8];
int id_olaf[] = { 3, 6, 1, 11, 4, 7, 8};
// %convert IDs into Sporns & Kotter classification
if (motif_mode == SPORNS) {
for (int i = 0; i < (int)_ID->size; i++) {
for (int j = 0; j < 7; j++) {
if ((int)VECTOR_ID(get)(_ID, i) == id_mika[j]) {
VECTOR_ID(set)(_ID, i, id_olaf[j]);
break;
}
}
}
}
// [X ind]=sortrows(ID);
VECTOR_T* ind_v;
VECTOR_T* X = sortrows(_ID, &ind_v);
VECTOR_ID(free)(X);
gsl_permutation* ind = to_permutation(ind_v);
VECTOR_ID(free)(ind_v);
// ID=ID(ind,:);
VECTOR_T* _ID_permuted = permute(ind, _ID);
VECTOR_ID(free)(_ID);
_ID = _ID_permuted;
// M=M(ind,:);
MATRIX_T* M_permuted = permute_rows(ind, M);
MATRIX_ID(free)(M);
M = M_permuted;
gsl_permutation_free(ind);
// N=sum(M,2);
_N = sum(M, 2);
}
if (ID != NULL) {
*ID = copy(_ID);
}
if (N != NULL) {
*N = copy(_N);
}
return copy(M);
}
/*
* Constructs the four-node motif library.
*/
MATRIX_T* BCT_NAMESPACE::motif4generate(VECTOR_T** ID, VECTOR_T** N) {
static MATRIX_T* M = NULL;
static VECTOR_T* _ID = NULL;
static VECTOR_T* _N = NULL;
if (M == NULL) {
// n=0;
int n = -1;
// M=false(3834,12);
M = MATRIX_ID(calloc)(3834, 12);
// CL=zeros(3834,16,'uint8');
MATRIX_T* CL = zeros(3834, 16);
// cl=zeros(1,16,'uint8');
VECTOR_T* cl = zeros_vector(16);
FP_T i_nondiag[] = { 1, 2, 3, 4, 6, 7, 8, 9, 11, 12, 13, 14 };
VECTOR_ID(view) i_nondiag_vv = VECTOR_ID(view_array)(i_nondiag, 12);
// for i=0:2^12-1
for (int i = 0; i < 4096; i++) {
// m=dec2bin(i);
// m=[num2str(zeros(1,12-length(m)), '%d') m];
std::string m = dec2bin(i, 12);
// G=str2num ([ ...
// '0' ' ' m(4) ' ' m(7) ' ' m(10) ;
// m(1) ' ' '0' ' ' m(8) ' ' m(11) ;
// m(2) ' ' m(5) ' ' '0' ' ' m(12) ;
// m(3) ' ' m(6) ' ' m(9) ' ' '0' ]);
MATRIX_T* G = MATRIX_ID(calloc)(4, 4);
for (int i = 0; i < 12; i++) {
int index = (int)i_nondiag[i];
if (m[i] == '1') {
ordinal_index_assign(G, index, 1.0);
}
}
// Gs=G+G.';
MATRIX_T* Gs = MATRIX_ID(alloc)(4, 4);
MATRIX_ID(transpose_memcpy)(Gs, G);
MATRIX_ID(add)(Gs, G);
// v=Gs(1,:);
VECTOR_T* v = VECTOR_ID(alloc)(4);
MATRIX_ID(get_row)(v, Gs, 0);
// for j=1:2,
for (int j = 1; j <= 2; j++) {
// v=any(Gs(v~=0,:),1)+v;
VECTOR_T* v_neq_0 = compare_elements(v, fp_not_equal, 0.0);
VECTOR_T* Gs_cols = sequence(0, Gs->size2 - 1);
MATRIX_T* Gs_idx = log_ord_index(Gs, v_neq_0, Gs_cols);
VECTOR_ID(free)(v_neq_0);
VECTOR_ID(free)(Gs_cols);
if (Gs_idx != NULL) {
VECTOR_T* any_Gs_idx = any(Gs_idx, 1);
VECTOR_ID(add)(v, any_Gs_idx);
MATRIX_ID(free)(Gs_idx);
VECTOR_ID(free)(any_Gs_idx);
}
}
MATRIX_ID(free)(Gs);
// if v
bool v_bool = to_bool(v);
VECTOR_ID(free)(v);
if (v_bool) {
// n=n+1;
n++;
// G2=(G*G)~=0;
MATRIX_T* G_mul_G = mul(G, G);
MATRIX_T* G2 = compare_elements(G_mul_G, fp_not_equal, 0.0);
MATRIX_ID(free)(G_mul_G);
// Ko=sum(G,2);
VECTOR_T* Ko = sum(G, 2);
// Ki=sum(G,1).';
VECTOR_T* Ki = sum(G, 1);
// Ko2=sum(G2,2);
VECTOR_T* Ko2 = sum(G2, 2);
// Ki2=sum(G2,1).';
VECTOR_T* Ki2 = sum(G2, 1);
// cl(:)=sortrows([Ki Ko Ki2 Ko2]).';
MATRIX_T* Ki_Ko = concatenate_rows(Ki, Ko);
VECTOR_ID(free)(Ki);
VECTOR_ID(free)(Ko);
MATRIX_T* Ki_Ko_Ki2 = concatenate_rows(Ki_Ko, Ki2);
VECTOR_ID(free)(Ki2);
MATRIX_ID(free)(Ki_Ko);
MATRIX_T* Ki_Ko_Ki2_Ko2 = concatenate_rows(Ki_Ko_Ki2, Ko2);
VECTOR_ID(free)(Ko2);
MATRIX_ID(free)(Ki_Ko_Ki2);
MATRIX_T* Ks_sorted = sortrows(Ki_Ko_Ki2_Ko2);
MATRIX_ID(free)(Ki_Ko_Ki2_Ko2);
MATRIX_T* Ks_transpose = MATRIX_ID(alloc)(4, G->size1);
MATRIX_ID(transpose_memcpy)(Ks_transpose, Ks_sorted);
MATRIX_ID(free)(Ks_sorted);
VECTOR_ID(free)(cl);
cl = to_vector(Ks_transpose);
MATRIX_ID(free)(Ks_transpose);
// CL(n,:)=cl;
MATRIX_ID(set_row)(CL, n, cl);
// M(n,:)=G([2:5 7:10 12:15]);
VECTOR_T* G_nondiag = ordinal_index(G, &i_nondiag_vv.vector);
MATRIX_ID(set_row)(M, n, G_nondiag);
VECTOR_ID(free)(G_nondiag);
}
MATRIX_ID(free)(G);
}
VECTOR_ID(free)(cl);
// [u1 u2 ID]=unique(CL,'rows');
MATRIX_T* u1 = unique_rows(CL, "last", NULL, &_ID);
MATRIX_ID(free)(CL);
MATRIX_ID(free)(u1);
VECTOR_ID(add_constant)(_ID, 1.0);
// [X ind]=sortrows(ID);
VECTOR_T* ind_v;
VECTOR_T* X = sortrows(_ID, &ind_v);
VECTOR_ID(free)(X);
gsl_permutation* ind = to_permutation(ind_v);
VECTOR_ID(free)(ind_v);
// ID=ID(ind,:);
VECTOR_T* _ID_permuted = permute(ind, _ID);
VECTOR_ID(free)(_ID);
_ID = _ID_permuted;
// M=M(ind,:);
MATRIX_T* M_permuted = permute_rows(ind, M);
MATRIX_ID(free)(M);
M = M_permuted;
gsl_permutation_free(ind);
// N=sum(M,2);
_N = sum(M, 2);
}
if (ID != NULL) {
*ID = copy(_ID);
}
if (N != NULL) {
*N = copy(_N);
}
return copy(M);
}