/*****************************************************************************
 -                                                                           -
 -                    POLONY SEQUENCER ACQUISITION SUITE                     -
 -                                Church Lab                                 -
 -                          Harvard Medical School                           -
 -                                                                           -
 -    Free software for running a Polony Sequencing automated microscope     -
 -                                                                           -
 - ========================================================================= -
 -                                                                           -
 -                                                                           -
 - autofocus.h                                                               -
 -                                                                           -
 -   Program to autofocus brightfield or fluorescence images of Polony beads -
 -                                                                           -
 -   Written by Greg Porreca, 02-15-2006                                     -
 -                                                                           -
 - Revised                                                                   -
 -                                                                           -
 -                                                                           -
 - This software may be used, modified, and distributed freely, but this     -
 - header may not be modified and must appear at the top of this file.       -
 -                                                                           -
 -                                                                           -
 *****************************************************************************/

#ifndef AUTOFOCUS_H
#define AUTOFOCUS_H


#include <stdio.h> //input and output functionality
#include <stdlib.h>
#include "chamcam.h"
#include "cfilter.h"
#include "cpifoc.h"
#include "reporter.h"
#include "cscope.h"
#include "acquisition.h"

class Autofocus{

public:

	Autofocus::Autofocus(Reporter*, CHamCam*, CFilter*, CScope*, CPifoc*, Acquisition*);
	Autofocus::~Autofocus();
	double Autofocus::autofocus_fl(int num_steps_coarse, double coarse_interval, double exposure, double sensitivity, int ex, int em);
	double Autofocus::compute_complexity(unsigned short int *curr_img);
	double Autofocus::autofocus_brightfield(int num_steps_coarse, double coarse_interval);
	double Autofocus::compute_complexity_autofocus(short unsigned int* curr_img);
	void Autofocus::setFocusAxis(int f_axis);



private:
	CHamCam* this_camera;
	CFilter* this_filter;
	Reporter* r;
	CScope* this_te2000;
	CPifoc* this_pifoc;
	Acquisition* acq;
	double exposure;
	double sensitivity;
	char log_string[500];
	int focus_axis;
};


#endif