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/*
* autopicker.h
*
* Created on: Sep 18, 2013
* Author: "Sjors H.W. Scheres"
*/
#ifndef AUTOPICKER_H_
#define AUTOPICKER_H_
#include "src/image.h"
#include "src/multidim_array.h"
#include "src/metadata_table.h"
#include "src/projector.h"
#include "src/ctf.h"
#include "src/fftw.h"
#include "src/time.h"
#include "src/mask.h"
struct Peak
{
int x;
int y;
int ref;
DOUBLE psi;
DOUBLE fom;
DOUBLE relative_fom;
};
class AutoPicker
{
public:
// I/O Parser
IOParser parser;
// Verbosity
int verb;
// Input & Output rootname
FileName fn_in, fn_ref, fns_autopick, fn_out;
// Pixel size (for low-pass filter and particle diameter)
DOUBLE angpix;
// Metadata of the micrographs
MetaDataTable MDmic;
// Particle diameter (in Angstroms)
DOUBLE particle_diameter;
int particle_radius2, decrease_radius;
// Low pass filetr cutoff (in Angstroms)
DOUBLE lowpass;
// Original size of the reference images
int particle_size;
// Dimension of the filtered image
int current_size;
// Vector with all original reference images
std::vector<MultidimArray<DOUBLE> > Mrefs;
// FTs of the reference images (either for autopicking or for feature calculation)
std::vector<Projector > PPref;
///// Autopicking stuff
// Re-read precalculated best_localCCF and SPI arrays from disc
bool do_read_fom_maps;
// Write precalculated best_localCCF and SPI arrays to disc
bool do_write_fom_maps;
// All micrographs to autopick from
std::vector<FileName> fn_micrographs;
// Original size of the micrographs
int micrograph_size, micrograph_xsize, micrograph_ysize;
// Is density in micrograph inverted wrt templates?
bool do_invert;
// Correct the references for CTF effects?
bool do_ctf;
// Keep the CTFs unchanged until the first peak?
bool intact_ctf_first_peak;
// Apart from keeping particle_size/2 away from the sides, should we exclude more? E.g. to get rid of Polara bar code?
int autopick_skip_side;
// In-plane rotational sampling (in degrees)
DOUBLE psi_sampling;
// Fraction of expected probability ratio to consider as peaks
DOUBLE min_fraction_expected_Pratio;
// Number of Angstroms any 2 particle peaks need to be apart
DOUBLE min_particle_distance;
// Maximum standard deviation of the noise prior to normalization to pick peaks from
DOUBLE max_stddev_noise;
// Removal of outlier pixel values
DOUBLE outlier_removal_zscore;
// Size of the downsize micrographs for autopicking
int downsize_mic;
// Number of non-zero pixels in the circular mask, and of its inverse (for background normalisation in do_diff2)
int nr_pixels_circular_mask, nr_pixels_circular_invmask;
// Array with Fourier-transform of the (circular) mask, and of its inverse
MultidimArray<Complex > Fmsk, Finvmsk;
public:
// Read command line arguments
void read(int argc, char **argv);
// Print usage instructions
void usage();
// Initialise some general stuff after reading
void initialise();
// General function to decide what to do
void run();
void autoPickOneMicrograph(FileName &fn_mic);
private:
// Uses Roseman2003 formulae to calculate stddev under the mask through FFTs
// The FFTs of the micrograph (Fmic), micrograph-squared (Fmic2) and the mask (Fmsk) need to be provided at downsize_mic
// The putput (Mstddev) will be at (binned) micrograph_size
void calculateStddevAndMeanUnderMask(const MultidimArray<Complex > &Fmic, const MultidimArray<Complex > &Fmic2,
MultidimArray<Complex > &Fmsk, int nr_nonzero_pixels_mask, MultidimArray<DOUBLE> &Mstddev, MultidimArray<DOUBLE> &Mmean);
// Peak search for all pixels above a given threshold in the map
void peakSearch(const MultidimArray<DOUBLE> &Mccf, const MultidimArray<DOUBLE> &Mpsi, const MultidimArray<DOUBLE> &Mstddev, int iref, int skip_side, std::vector<Peak> &peaks);
// Now prune the coordinates: within min_particle_distance: all peaks are the same cluster
// From each cluster, take the single peaks with the highest ccf
// If then, there is another peaks at a distance of at least min_particle_distance: take that one as well, and so forth...
void prunePeakClusters(std::vector<Peak> &peaks, int min_distance);
// Only keep those peaks that are at the given distance apart from each other
void removeTooCloselyNeighbouringPeaks(std::vector<Peak> &peaks, int min_distance);
};
#endif /* AUTOPICKER_H_ */
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