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TestHHMM.cpp
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TestHHMM.cpp
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#ifndef TESTHHMM_CPP
#define TESTHHMM_CPP
#include "TestHHMM.h"
#include <iostream>
#include <utility>
#include <cmath>
#include <cfloat>
#include <dirent.h>
#include <fstream>
#include <memory>
#include "readSample.cpp"
namespace hhmm{
CPPUNIT_TEST_SUITE_REGISTRATION(TestHHMM);
const uint32_t _STATENUM = 3;
const uint32_t _DIM = 2;
bool isNear(long double x,long double y)
{
return fabs(x-y) < x * DBL_EPSILON;
}
void TestHHMM::setUp()
{
hhmm = new HHMM(2,2,3);
auto castn = [](baseHHMM* x){return dynamic_cast<nprodHHMM*>(x);};
auto castp = [](baseHHMM* x){return dynamic_cast<prodHHMM*>(x);};
vector<VectorXld> obs0 = read("sample0.txt");
vector<VectorXld> obs1 = read("sample1.txt");
// vector<uint32_t> obs1 = readSample("../sample1.txt");
// vector<long double> emit0 = {0.2,0.8};
// vector<long double> emit1 = {0.6,0.4};
//for(auto& a:obs0){cout << a << endl;}
VectorXld mean0(2);
mean0 << 3.0,2.0;
VectorXld mean1(2);
mean1 << 4.0,1.0;
MatrixXld variance0(2,2);
variance0 << 1.5,0.0,
0.0,2.5;
MatrixXld variance1(2,2);
variance1 << 2.3,0.0,
0.0,1.2;
MatrixXld trans(2,3);
trans << 0.5,0.4,0.1,
0.4,0.4,0.2;
MatrixXld trans2(2,3);
trans2 << 0.6,0.3,0.1,
0.2,0.6,0.2;
(hhmm->seq).push_back(up<Sequence>(new Sequence(obs0,2,3,2)));
(hhmm->seq).push_back(up<Sequence>(new Sequence(obs1,2,3,2)));
(hhmm->root).cpyTransMat(trans2);
castn(hhmm->root.children[0].get())->cpyTransMat(trans);
castn(hhmm->root.children[1].get())->cpyTransMat(trans);
castp(castn(hhmm->root.children[0].get())->children[0].get())->setMean() = mean0;
castp(castn(hhmm->root.children[0].get())->children[0].get())->setVariance().diagonal() = variance0.diagonal();
castp(castn(hhmm->root.children[0].get())->children[1].get())->setMean() = mean1;
castp(castn(hhmm->root.children[0].get())->children[1].get())->setVariance().diagonal() = variance1.diagonal();
castp(castn(hhmm->root.children[1].get())->children[0].get())->setMean() = mean0;
castp(castn(hhmm->root.children[1].get())->children[0].get())->setVariance().diagonal() = variance0.diagonal();
castp(castn(hhmm->root.children[1].get())->children[1].get())->setMean() = mean1;
castp(castn(hhmm->root.children[1].get())->children[1].get())->setVariance().diagonal() = variance1.diagonal();
castn(hhmm->root.children[0].get())->children[0]->setPi(0.3);
castn(hhmm->root.children[0].get())->children[1]->setPi(0.7);
castn(hhmm->root.children[1].get())->children[0]->setPi(0.3);
castn(hhmm->root.children[1].get())->children[1]->setPi(0.7);
hhmm->root.children[0]->setPi(0.4);
hhmm->root.children[1]->setPi(0.6);
}
void TestHHMM::tearDown()
{
delete hhmm;
}
void TestHHMM::TestEmitProb()
{
VectorXld test(3);
test << 3,4,3;
VectorXld mean(3);
mean << 1,3,3;
DM var(3);
for(uint32_t i=0;i<3;++i)
var.diagonal()[i] = 1;
auto a = prodHHMM(0,3,nullptr);
a.swpMean(mean);
a.swpVar(var);
long double estmt = pow(2*M_PI,-1.5)*exp(-2.5);
cout << a.emit(test) << " " << estmt << endl;
CPPUNIT_ASSERT(a.emit(test) == estmt);
}
void TestHHMM::TestForward()
{
cout << "in the Forward algorithm" << endl;
hhmm->forward(*(hhmm->seq[0]),&(hhmm->root),&(hhmm->seq[0]->param));
cout << hhmm->seq[0]->param.children[0]->alpha(0,0) << endl;
}
void TestHHMM::TestBackward()
{
cout << "in the Backward algorithm" << endl;
hhmm->forward(*(hhmm->seq[0]),&(hhmm->root),&(hhmm->seq[0]->param));
hhmm->backward(*(hhmm->seq[0]),&(hhmm->root),&(hhmm->seq[0]->param));
//debugAlphaAndBeta(*hhmm,*(hhmm->seq[0]),&(hhmm->root),&(hhmm->seq[0]->param));
}
void TestHHMM::debugAlphaAndBeta(HHMM& hhmm,Sequence& seq,baseHHMM* root,parameters* param)
{
//If it is the deepest level,it returns;
if(root->getLevel() == hhmm.depth-1){return;}
//Declear iterators.
myit<parameters> pit,pend;
myit<baseHHMM> rit,rend;
hhmm.setIterator<parameters>(pit,pend,rit,rend,param,root);
for(;pit != pend && rit != rend;++pit,++rit){
debugAlphaAndBeta(hhmm,seq,rit->get(),pit->get());
}
cout << "level is " << root->getLevel()+1 << endl;
for(uint32_t i=0;i<seq.size();++i){
for(uint32_t j=i;j<seq.size();++j){
long double BETA = 0.0,ALPHA = 0.0;
hhmm.setIterator<parameters>(pit,pend,rit,rend,param,root);
for(;pit != pend && rit != rend;++pit,++rit){
BETA += (*pit)->beta(i,j) * (*rit)->getPi();
ALPHA += (*pit)->alpha(i,j) * cast_nprod(root)->trans(rit->get());
}
cout << "index: " << i << " " << j << endl;
cout << BETA << " " << ALPHA << endl;
}
}
}
void TestHHMM::TestAuxIn()
{
cout << "in the AuxIn algorithm" << endl;
hhmm->forward(*(hhmm->seq[0]),&(hhmm->root),&(hhmm->seq[0]->param));
hhmm->backward(*(hhmm->seq[0]),&(hhmm->root),&(hhmm->seq[0]->param));
hhmm->auxIn(*(hhmm->seq[0]),&(hhmm->root),&(hhmm->seq[0]->param));
// auto& eI0 = hhmm->seq[0]->param.children[0]->etaIn;
// for(auto& a:eI0){cout << a << " ";}
// cout << endl;
// auto& eI1 = hhmm->seq[0]->param.children[1]->etaIn;
// for(auto& a:eI1){cout << a << " ";}
// cout << endl;
// auto& eI00 = hhmm->seq[0]->param.children[0]->children[0]->etaIn;
// for(auto& a:eI00){cout << a << " ";}
// cout << endl;
// auto& eI11 = hhmm->seq[0]->param.children[0]->children[1]->etaIn;
// for(auto& a:eI11){cout << a << " ";}
// cout << endl;
}
void TestHHMM::TestAuxOut()
{
cout << "in the AuxOut algorithm" << endl;
hhmm->forward(*(hhmm->seq[0]),&(hhmm->root),&(hhmm->seq[0]->param));
hhmm->backward(*(hhmm->seq[0]),&(hhmm->root),&(hhmm->seq[0]->param));
hhmm->auxIn(*(hhmm->seq[0]),&(hhmm->root),&(hhmm->seq[0]->param));
hhmm->auxOut(*(hhmm->seq[0]),&(hhmm->root),&(hhmm->seq[0]->param));
// auto& eO = hhmm->seq[0]->param.children[0]->etaOut;
// for(auto& a:eO){cout << a << " ";}
// cout << endl;
// auto& e1 = hhmm->seq[0]->param.children[1]->etaOut;
// for(auto& a:e1){cout << a << " ";}
// cout << endl;
// auto& e00 = hhmm->seq[0]->param.children[0]->children[0]->etaOut;
// for(auto& a:e00){cout << a << " ";}
// cout << endl;
// auto& e01 = hhmm->seq[0]->param.children[0]->children[1]->etaOut;
// for(auto& a:e01){cout << a << " ";}
// cout << endl;
}
void TestHHMM::TestHorizon()
{
cout << "in the Horizon algorithm" << endl;
hhmm->forward(*(hhmm->seq[0]),&(hhmm->root),&(hhmm->seq[0]->param));
hhmm->backward(*(hhmm->seq[0]),&(hhmm->root),&(hhmm->seq[0]->param));
hhmm->auxOut(*(hhmm->seq[0]),&(hhmm->root),&(hhmm->seq[0]->param));
hhmm->auxIn(*(hhmm->seq[0]),&(hhmm->root),&(hhmm->seq[0]->param));
hhmm->horizon(*(hhmm->seq[0]),&(hhmm->root),&(hhmm->seq[0]->param));
// for(uint32_t i=0;i<hhmm->seq[0]->size();++i){
// for(uint32_t j=0;j<=hhmm->stateNum;++j){
// cout << hhmm->seq[0]->param.children[0]->children[0]->xiContent(i,j) << " ";
// }
// cout << endl;
// }
}
void TestHHMM::TestVertical()
{
cout << "in the Vertical algorithm" << endl;
hhmm->forward(*(hhmm->seq[0]),&(hhmm->root),&(hhmm->seq[0]->param));
hhmm->backward(*(hhmm->seq[0]),&(hhmm->root),&(hhmm->seq[0]->param));
hhmm->auxOut(*(hhmm->seq[0]),&(hhmm->root),&(hhmm->seq[0]->param));
hhmm->auxIn(*(hhmm->seq[0]),&(hhmm->root),&(hhmm->seq[0]->param));
hhmm->vertical(*(hhmm->seq[0]),&(hhmm->root),&(hhmm->seq[0]->param));
for(uint32_t i=0;i<hhmm->seq[0]->size();++i){
cout << hhmm->seq[0]->param.children[0]->chi[i] << " ";
}
cout << endl;
for(uint32_t i=0;i<hhmm->seq[0]->size();++i){
cout << hhmm->seq[0]->param.children[1]->chi[i] << " ";
}
cout << endl;
}
void TestHHMM::TestCalcGamma()
{
cout << "in the calcGamma algorithm" << endl;
hhmm->forward(*(hhmm->seq[0]),&(hhmm->root),&(hhmm->seq[0]->param));
hhmm->backward(*(hhmm->seq[0]),&(hhmm->root),&(hhmm->seq[0]->param));
hhmm->auxOut(*(hhmm->seq[0]),&(hhmm->root),&(hhmm->seq[0]->param));
hhmm->auxIn(*(hhmm->seq[0]),&(hhmm->root),&(hhmm->seq[0]->param));
hhmm->vertical(*(hhmm->seq[0]),&(hhmm->root),&(hhmm->seq[0]->param));
for(uint32_t i=0;i<hhmm->seq[0]->size();++i){
cout << hhmm->seq[0]->param.children[0]->gammaIn[i] << " ";
}
cout << endl;
}
void TestHHMM::TestCalcTmpPi()
{
cout << "in the calcTmpPi algorithm" << endl;
hhmm->forward(*(hhmm->seq[0]),&(hhmm->root),&(hhmm->seq[0]->param));
hhmm->backward(*(hhmm->seq[0]),&(hhmm->root),&(hhmm->seq[0]->param));
hhmm->auxOut(*(hhmm->seq[0]),&(hhmm->root),&(hhmm->seq[0]->param));
hhmm->auxIn(*(hhmm->seq[0]),&(hhmm->root),&(hhmm->seq[0]->param));
hhmm->vertical(*(hhmm->seq[0]),&(hhmm->root),&(hhmm->seq[0]->param));
hhmm->calcTmpPi(*(hhmm->seq[0]),&(hhmm->root),&(hhmm->seq[0]->param));
}
void TestHHMM::TestCalcTmpTrans()
{
cout << "in the calcTmpTrans algorithm" << endl;
hhmm->forward(*(hhmm->seq[0]),&(hhmm->root),&(hhmm->seq[0]->param));
hhmm->backward(*(hhmm->seq[0]),&(hhmm->root),&(hhmm->seq[0]->param));
hhmm->auxOut(*(hhmm->seq[0]),&(hhmm->root),&(hhmm->seq[0]->param));
hhmm->auxIn(*(hhmm->seq[0]),&(hhmm->root),&(hhmm->seq[0]->param));
hhmm->vertical(*(hhmm->seq[0]),&(hhmm->root),&(hhmm->seq[0]->param));
hhmm->calcTmpTrans(*(hhmm->seq[0]),&(hhmm->root),&(hhmm->seq[0]->param));
}
// void TestHHMM::TestCalcTmpEmit()
// {
// cout << "in the calcTmpEmit algorithm" << endl;
// hhmm->forward(*(hhmm->seq[0]),&(hhmm->root),&(hhmm->seq[0]->param));
// hhmm->backward(*(hhmm->seq[0]),&(hhmm->root),&(hhmm->seq[0]->param));
// hhmm->auxOut(*(hhmm->seq[0]),&(hhmm->root),&(hhmm->seq[0]->param));
// hhmm->auxIn(*(hhmm->seq[0]),&(hhmm->root),&(hhmm->seq[0]->param));
// hhmm->vertical(*(hhmm->seq[0]),&(hhmm->root),&(hhmm->seq[0]->param));
// hhmm->calcTmpEmit(*(hhmm->seq[0]),&(hhmm->root),&(hhmm->seq[0]->param));
// }
void TestHHMM::TestEM()
{
cout << "in the EM algorithm" << endl;
hhmm->EM();
}
}
#endif