Newer
Older
Paul McCarthy
committed
/* MELODIC - Multivariate exploratory linear optimized decomposition into
independent components
Paul McCarthy
committed
melhlprfns.cc - misc functions
Christian F. Beckmann, FMRIB Analysis Group
Paul McCarthy
committed
Copyright (C) 1999-2013 University of Oxford */
/* CCOPYRIGHT */
#ifndef __MELODICHLPR_h
#define __MELODICHLPR_h
Paul McCarthy
committed
#include "armawrap/newmat.h"
#include "newimage/newimageall.h"
#ifdef __APPLE__
#include <mach/mach.h>
#define mmsg(msg) { \
struct task_basic_info t_info; \
mach_msg_type_number_t t_info_count = TASK_BASIC_INFO_COUNT; \
if (KERN_SUCCESS == task_info(mach_task_self(), TASK_BASIC_INFO, (task_info_t) &t_info, &t_info_count)) \
{ \
cout << " MEM: " << msg << " res: " << t_info.resident_size/1000000 << " virt: " << t_info.virtual_size/1000000 << "\n"; \
} \
}
#else
#define mmsg(msg) { \
cout << msg; \
}
#endif
namespace Melodic{
Paul McCarthy
committed
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
void update_mask(NEWIMAGE::volume<float>& mask, NEWMAT::Matrix& Data);
void del_vols(NEWIMAGE::volume4D<float>& in, int howmany);
NEWMAT::Matrix smoothColumns(const NEWMAT::Matrix& inp);
NEWMAT::Matrix calc_FFT(const NEWMAT::Matrix& Mat, const bool logpwr = 0);
NEWMAT::Matrix convert_to_pbsc(NEWMAT::Matrix& Mat);
NEWMAT::RowVector varnorm(NEWMAT::Matrix& in, int dim = 30, float level = 1.6, int econ = 20000);
void varnorm(NEWMAT::Matrix& in, const NEWMAT::RowVector& vars);
NEWMAT::RowVector varnorm(NEWMAT::Matrix& in, NEWMAT::SymmetricMatrix& Corr, int dim = 30, float level = 1.6, int econ = 20000);
NEWMAT::Matrix SP2(const NEWMAT::Matrix& in, const NEWMAT::Matrix& weights, int econ = 20000);
void SP3(NEWMAT::Matrix& in, const NEWMAT::Matrix& weights);
NEWMAT::RowVector Feta(int n1,int n2);
NEWMAT::RowVector cumsum(const NEWMAT::RowVector& Inp);
NEWMAT::Matrix corrcoef(const NEWMAT::Matrix& in1, const NEWMAT::Matrix& in2);
NEWMAT::Matrix corrcoef(const NEWMAT::Matrix& in1, const NEWMAT::Matrix& in2, const NEWMAT::Matrix& part);
float calc_white(const NEWMAT::Matrix& tmpE, const NEWMAT::RowVector& tmpD, const NEWMAT::RowVector& PercEV, int dim, NEWMAT::Matrix& param, NEWMAT::Matrix& paramS, NEWMAT::Matrix& white, NEWMAT::Matrix& dewhite);
float calc_white(const NEWMAT::Matrix& tmpE, const NEWMAT::RowVector& tmpD, const NEWMAT::RowVector& PercEV, int dim, NEWMAT::Matrix& white, NEWMAT::Matrix& dewhite);
void calc_white(const NEWMAT::Matrix& tmpE, const NEWMAT::RowVector& tmpD, int dim, NEWMAT::Matrix& param, NEWMAT::Matrix& paramS, NEWMAT::Matrix& white, NEWMAT::Matrix& dewhite);
void calc_white(const NEWMAT::Matrix& tmpE, const NEWMAT::RowVector& tmpD, int dim, NEWMAT::Matrix& white, NEWMAT::Matrix& dewhite);
void calc_white(const NEWMAT::SymmetricMatrix& Corr, int dim, NEWMAT::Matrix& white, NEWMAT::Matrix& dewhite);
void std_pca(const NEWMAT::Matrix& Mat, NEWMAT::SymmetricMatrix& Corr, NEWMAT::Matrix& evecs, NEWMAT::RowVector& evals, int econ = 20000);
void std_pca(const NEWMAT::Matrix& Mat, const NEWMAT::Matrix& weights, NEWMAT::SymmetricMatrix& Corr, NEWMAT::Matrix& evecs, NEWMAT::RowVector& evals, int econ = 20000);
void em_pca(const NEWMAT::Matrix& Mat, NEWMAT::Matrix& evecs, NEWMAT::RowVector& evals, int num_pc = 1, int iter = 20);
void em_pca(const NEWMAT::Matrix& Mat, NEWMAT::Matrix& guess, NEWMAT::Matrix& evecs, NEWMAT::RowVector& evals, int num_pc = 1, int iter = 20);
float rankapprox(const NEWMAT::Matrix& Mat, NEWMAT::Matrix& cols, NEWMAT::Matrix& rows, int dim = 1);
NEWMAT::RowVector krfact(const NEWMAT::Matrix& Mat, NEWMAT::Matrix& cols, NEWMAT::Matrix& rows);
NEWMAT::RowVector krfact(const NEWMAT::Matrix& Mat, int colnum, NEWMAT::Matrix& cols, NEWMAT::Matrix& rows);
NEWMAT::Matrix krprod(const NEWMAT::Matrix& cols, const NEWMAT::Matrix& rows);
NEWMAT::Matrix krapprox(const NEWMAT::Matrix& Mat, int size_col, int dim = 1);
void adj_eigspec(const NEWMAT::RowVector& in, NEWMAT::RowVector& out1, NEWMAT::RowVector& out2, NEWMAT::RowVector& out3, int& out4, int num_vox, float resels);
void adj_eigspec(const NEWMAT::RowVector& in, NEWMAT::RowVector& out1, NEWMAT::RowVector& out2);
int ppca_dim(const NEWMAT::Matrix& in, const NEWMAT::Matrix& weights, NEWMAT::Matrix& PPCA, NEWMAT::RowVector& AdjEV, NEWMAT::RowVector& PercEV, NEWMAT::SymmetricMatrix& Corr, NEWMAT::Matrix& tmpE, NEWMAT::RowVector &tmpD, float resels, std::string which);
int ppca_dim(const NEWMAT::Matrix& in, const NEWMAT::Matrix& weights, NEWMAT::Matrix& PPCA, NEWMAT::RowVector& AdjEV, NEWMAT::RowVector& PercEV, float resels, std::string which);
int ppca_dim(const NEWMAT::Matrix& in, const NEWMAT::Matrix& weights, float resels, std::string which);
NEWMAT::ColumnVector ppca_select(NEWMAT::Matrix& PPCAest, int& dim, int maxEV, std::string which);
NEWMAT::Matrix ppca_est(const NEWMAT::RowVector& eigenvalues, const int N1, const float N2);
NEWMAT::Matrix ppca_est(const NEWMAT::RowVector& eigenvalues, const int N);
NEWMAT::ColumnVector acf(const NEWMAT::ColumnVector& in, int order);
NEWMAT::ColumnVector pacf(const NEWMAT::ColumnVector& in, int maxorder = 1);
NEWMAT::Matrix est_ar(const NEWMAT::Matrix& Mat, int maxorder);
NEWMAT::ColumnVector gen_ar(const NEWMAT::ColumnVector& in, int maxorder = 1);
NEWMAT::Matrix gen_ar(const NEWMAT::Matrix& in, int maxorder);
NEWMAT::Matrix gen_arCorr(const NEWMAT::Matrix& in, int maxorder);
class basicGLM{
public:
Paul McCarthy
committed
//constructor
basicGLM(){}
Paul McCarthy
committed
//destructor
~basicGLM(){}
Paul McCarthy
committed
void olsfit(const NEWMAT::Matrix& data, const NEWMAT::Matrix& design,
const NEWMAT::Matrix& contrasts, int DOFadjust = -1);
inline NEWMAT::Matrix& get_t(){return t;}
inline NEWMAT::Matrix& get_z(){return z;}
inline NEWMAT::Matrix& get_p(){return p;}
inline NEWMAT::Matrix& get_f_fmf(){return f_fmf;}
inline NEWMAT::Matrix& get_pf_fmf(){return pf_fmf;}
inline NEWMAT::Matrix& get_cbeta(){return cbeta;}
inline NEWMAT::Matrix& get_beta(){return beta;}
inline NEWMAT::Matrix& get_varcb(){return varcb;}
inline NEWMAT::Matrix& get_sigsq(){return sigsq;}
inline NEWMAT::Matrix& get_residu(){return residu;}
inline int get_dof(){return dof;}
Paul McCarthy
committed
private:
Paul McCarthy
committed
NEWMAT::Matrix beta;
NEWMAT::Matrix residu;
NEWMAT::Matrix sigsq;
NEWMAT::Matrix varcb;
NEWMAT::Matrix cbeta;
NEWMAT::Matrix f_fmf, pf_fmf;
int dof;
Paul McCarthy
committed
NEWMAT::Matrix t;
NEWMAT::Matrix z;
NEWMAT::Matrix p;
};
// Matrix glm_ols(const Matrix& dat, const Matrix& design);
}
#endif