SceneObject::SceneObject(const std::string name, const std::string modelPath,
const int numFrames,
const std::string boundingBoxSetPath) :
offset(0,0,0), rotation(0,0,0), boundingBoxSet(boundingBoxSetPath) {
initLogger();
this->name = name;
animating = false;
framesWaited = 0;
frameDelay = 1;
currentFrame = 0;
this->numFrames = numFrames;
if (numFrames > 1) {
LOGINFO("Loading " + name + " animated model (this may take a while):");
for (int idx = 0; idx < numFrames; ++idx) {
std::stringstream lss;
lss << "Frame " << idx + 1 << " of " << numFrames << "...";
LOGINFO(lss.str());
std::stringstream ss;
ss << std::setfill('0') << std::setw(6) << idx + 1;
std::string frameNum = ss.str();
Model model1(modelPath + "_" + frameNum + ".obj");
model.push_back(model1);
}
}
else {
Model model1(modelPath);
model.push_back(model1);
}
}
void abcAncError::print(funkyPars *pars){
if(doAncError==0)
return;
/// if(doAncError==2){
// model2(pars);
//} else if(doAncError==1) {
model1(pars);
if(currentChr==-1)
currentChr=pars->refId;
if(currentChr!=pars->refId){
fprintf(outfile2,"Chr: \t %s\n",header->target_name[currentChr]);
for(int i=0;i<nInd;i++){
for(int j=0;j<125;j++)
fprintf(outfile2,"%lu\t",alleleCountsChr[i][j]);
fprintf(outfile2,"\n");
}
for(int i=0;i<nInd;i++)
for(int j=0;j<256;j++)
alleleCountsChr[i][j]=0;
currentChr=pars->refId;
}
//}
}
int main()
{
tc_matrix efm, output, params;
copasi_model m1, m2;
m1 = model1();
//m1 = cReadSBMLFile("model1.sbml");
output = cSimulateDeterministic(m1, 0, 10, 100); //model, start, end, num. points
printf("rows = %i\n",output.rows);
tc_printMatrixToFile("output.tab", output);
tc_deleteMatrix(output);
//printf("%s\n",m1.errorMessage);
/*params = tc_createMatrix(3,3);
tc_setRowName(params,0,"k1");
tc_setRowName(params,1,"k2");
tc_setRowName(params,2,"k3");
tc_setMatrixValue(params, 0, 0, 1);
tc_setMatrixValue(params, 0, 1, 0.0);
tc_setMatrixValue(params, 0, 2, 5.0);
tc_setMatrixValue(params, 1, 0, 1);
tc_setMatrixValue(params, 1, 1, 0.0);
tc_setMatrixValue(params, 1, 2, 5.0);
tc_setMatrixValue(params, 2, 0, 1);
tc_setMatrixValue(params, 2, 1, 0.0);
tc_setMatrixValue(params, 2, 2, 5.0);
cSetValue(m1,"k1",2.0);
cSetValue(m1,"k2",1.0);
cSetValue(m1,"k3",1.0);*/
//cSetOptimizerIterations(10);
//output = cOptimize(m1, "output.tab", params);
//tc_printMatrixToFile("params.out", output);
//tc_deleteMatrix(output);
//cleanup
cRemoveModel(m1);
copasi_end();
return 0;
}
void MultiMinTest::testChol2D() {
valarray<double> data(0.5 , 2);
valarray<bool> mask(true, 2);
valarray<double> weights(1.0, 2);
valarray<double> model1(2);
valarray<double> model2(2);
model1[0] = 0.0;
model1[1] = 1.0;
model2[0] = 1.0;
model2[1] = 0.0;
valarray<double> c(2);
valarray<double> b(2);
valarray<valarray<double> > a(b, 2);
MultiMin::chol2D(c, b, a, data, 0, 2, mask, weights, model1, model2);
CPPUNIT_ASSERT(c[0] == 0.5);
CPPUNIT_ASSERT(c[1] == 0.5);
}
TEST(var1_test, same)
{
Eigen::VectorXd phi0(2), veps_one(2), veps_two(2);
Eigen::MatrixXd phi1(2,2);
phi0 << 2, 3;
phi1 << .90, 0, 0, .30;
veps_one << 1.0, 0.25;
veps_two << 2.0, 3.25;
alps::alea::util::var1_model<double> model1(phi0, phi1, veps_one);
alps::alea::util::var1_model<double> model2(phi0, phi1, veps_two);
std::cerr << "EXACT MEAN=" << model1.mean().transpose() << "\n";
alps::alea::autocorr_acc<double> acc1(2), acc2(2);
fill(model1, acc1, 400000);
fill(model2, acc2, 400000);
alps::alea::autocorr_result<double> res1 = acc1.finalize();
print_result(std::cerr, res1);
alps::alea::autocorr_result<double> res2 = acc2.finalize();
print_result(std::cerr, res2);
// perform T2 test manually
alps::alea::var_result<double> diff = alps::alea::internal::pool_var(res1, res2);
print_result(std::cerr, diff);
alps::alea::t2_result t2 = alps::alea::t2_test(diff.mean(), diff.var(),
diff.observations(), 1, 1e-10);
print_t2(std::cerr, t2);
ASSERT_GE(t2.pvalue(), 0.01);
// Perform T2 test automatically
t2 = alps::alea::test_mean(res1, res2);
ASSERT_GE(t2.pvalue(), 0.01);
}
