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ThreeB 1.1
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Draw samples from the spot states given the spots positions and some data. More...
#include <sampled_multispot.h>
Public Member Functions | |
| GibbsSampler (const vector< vector< double > > &pixel_intensities_, const vector< vector< double > > &spot_intensities_, const vector< Vector< 4 > > &spots_, const Matrix< 3 > A_, const Vector< 3 > pi_, double variance_, int sample_iterations_) | |
| void | set_variance (double v) |
| void | reset () |
| template<class T > | |
| void | next (T &rng) |
| const vector< vector< State > > & | sample () const |
| const vector< vector< double > > & | sample_intensities () const |
Private Attributes | |
| const vector< vector< double > > & | pixel_intensities |
| const vector< vector< double > > & | spot_intensities |
| const vector< Vector< 4 > > | spots |
| const Matrix< 3 > | A |
| const Vector< 3 > | pi |
| const double | base_variance |
| double | variance |
| const int | sample_iterations |
| const int | num_frames |
| const int | num_pixels |
| const vector< int > | O |
| vector< vector< State > > | current_sample |
| vector< vector< double > > | current_sample_intensities |
Draw samples from the spot states given the spots positions and some data.
Variable naming matches that in FitSpots.
Definition at line 188 of file sampled_multispot.h.
| SampledMultispot::GibbsSampler::GibbsSampler | ( | const vector< vector< double > > & | pixel_intensities_, |
| const vector< vector< double > > & | spot_intensities_, | ||
| const vector< Vector< 4 > > & | spots_, | ||
| const Matrix< 3 > | A_, | ||
| const Vector< 3 > | pi_, | ||
| double | variance_, | ||
| int | sample_iterations_ | ||
| ) | [inline] |
Definition at line 207 of file sampled_multispot.h.
References assert_same_size(), and spot_intensities.
:pixel_intensities(pixel_intensities_), //pixel_intensities: [frame][pixels] spot_intensities(spot_intensities_), //spot_intensities: [spot][pixel] spots(spots_), A(A_), pi(pi_), base_variance(variance_), variance(variance_), sample_iterations(sample_iterations_), num_frames(pixel_intensities.size()), num_pixels(pixel_intensities[0].size()), //Observations vector. As usual for this application, the observations are just //numbered integers which refer to data held elsewhere. O(sequence(num_frames)), //Start all spots OFF, so the intensity is 0. OFF is 1 or 2, not 0!!! //sample_list: [sample][spot][frame]: list of samples drawn using Gibbs sampling current_sample(spots.size(), vector<State>(num_frames, 2)), //current sample [spot][frame] //pixel intensities assosciated with the current sample [frame][pixel] current_sample_intensities(num_frames, vector<double>(num_pixels)) { //Check a bunch of stuff assert_same_size(pixel_intensities); assert_same_size(spot_intensities); }
| void SampledMultispot::GibbsSampler::set_variance | ( | double | v | ) | [inline] |
Update the noide variance.
Used for adding thermal noise.
| v | noise variance. |
Definition at line 241 of file sampled_multispot.h.
Referenced by NegativeFreeEnergy::operator()().
{
variance = v;
}
| void SampledMultispot::GibbsSampler::reset | ( | ) | [inline] |
Reset the gibbs sampler oro the initial state (all spots off)
Definition at line 248 of file sampled_multispot.h.
{
vector<State> off(num_frames, 2);
fill(current_sample.begin(), current_sample.end(), off);
vector<double> black(num_pixels);
fill(current_sample_intensities.begin(), current_sample_intensities.end(), black);
variance = base_variance;
}
| void SampledMultispot::GibbsSampler::next | ( | T & | rng | ) | [inline] |
Get the next sample.
| rng | Random number generator |
Definition at line 260 of file sampled_multispot.h.
References SampledMultispot::add_spot(), forward_algorithm_delta(), SampledMultispot::remove_spot(), and spot_intensities.
Referenced by FreeEnergyHessian::hessian(), NegativeFreeEnergy::operator()(), and FitSpots::try_modifying_model().
{
for(int j=0; j < sample_iterations; j++)
for(int k=0; k < (int) spots.size(); k++)
{
//Subtract off the spot we're interested in.
remove_spot(current_sample_intensities, spot_intensities[k], current_sample[k]);
//Now current_sample_intensities is the image value for every spot in every frame,
//except the current spot, which is always set to off. This allows us to add it in
//easily.
SpotWithBackground B(current_sample_intensities, spot_intensities[k], pixel_intensities, variance);
vector<array<double, 3> > delta = forward_algorithm_delta(A, pi, B, O);
current_sample[k] = backward_sampling<3,State, T>(A, delta, rng);
//Put the newly sampled spot in
add_spot(current_sample_intensities, spot_intensities[k], current_sample[k]);
}
}
| const vector<vector<State> >& SampledMultispot::GibbsSampler::sample | ( | ) | const [inline] |
Retrieve the current sample.
Definition at line 286 of file sampled_multispot.h.
Referenced by FreeEnergyHessian::hessian(), and FitSpots::try_modifying_model().
{
return current_sample;
}
| const vector<vector<double> >& SampledMultispot::GibbsSampler::sample_intensities | ( | ) | const [inline] |
Retrieve the intensities for the current sample.
Definition at line 291 of file sampled_multispot.h.
Referenced by FreeEnergyHessian::hessian(), NegativeFreeEnergy::operator()(), and FitSpots::try_modifying_model().
{
return current_sample_intensities;
}
const vector<vector<double> >& SampledMultispot::GibbsSampler::pixel_intensities [private] |
Definition at line 190 of file sampled_multispot.h.
const vector<vector<double> >& SampledMultispot::GibbsSampler::spot_intensities [private] |
Definition at line 191 of file sampled_multispot.h.
const vector<Vector<4> > SampledMultispot::GibbsSampler::spots [private] |
Definition at line 192 of file sampled_multispot.h.
const Matrix<3> SampledMultispot::GibbsSampler::A [private] |
Definition at line 193 of file sampled_multispot.h.
const Vector<3> SampledMultispot::GibbsSampler::pi [private] |
Definition at line 194 of file sampled_multispot.h.
const double SampledMultispot::GibbsSampler::base_variance [private] |
Definition at line 195 of file sampled_multispot.h.
double SampledMultispot::GibbsSampler::variance [private] |
Definition at line 196 of file sampled_multispot.h.
const int SampledMultispot::GibbsSampler::sample_iterations [private] |
Definition at line 198 of file sampled_multispot.h.
const int SampledMultispot::GibbsSampler::num_frames [private] |
Definition at line 199 of file sampled_multispot.h.
const int SampledMultispot::GibbsSampler::num_pixels [private] |
Definition at line 199 of file sampled_multispot.h.
const vector<int> SampledMultispot::GibbsSampler::O [private] |
Definition at line 200 of file sampled_multispot.h.
vector<vector<State> > SampledMultispot::GibbsSampler::current_sample [private] |
Definition at line 202 of file sampled_multispot.h.
vector<vector<double> > SampledMultispot::GibbsSampler::current_sample_intensities [private] |
Definition at line 203 of file sampled_multispot.h.
1.7.4