/*****************************************************************************
 -                                                                           -
 -                    POLONY SEQUENCER ACQUISITION SUITE                     -
 -                                Church Lab                                 -
 -                          Harvard Medical School                           -
 -                                                                           -
 -    Free software for running a Polony Sequencing automated microscope     -
 -                                                                           -
 - ========================================================================= -
 -                                                                           -
 -                                                                           -
 - autoexpose.h                                                              -
 -                                                                           -
 -   Program to perform automated exposure and sensitivity setting.  Adjusts -
 -   exposure and sensitivity to bring the background value for each channel -
 -   independently to a pre-determined value.  These pre-determined values   -
 -   have been manually selected to minimize interference between channels.  -
 -   In computing the intensity distribution for each channel, only pixels   -
 -   corresponding to beads are used.                                        -
 -                                                                           -
 -   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 AUTOEXPOSE_H
#define AUTOEXPOSE_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 Autoexpose{

public:
	Autoexpose::Autoexpose(Reporter*, CHamCam*, CFilter*, CScope*, CPifoc*, Acquisition*, short unsigned int*);
	Autoexpose::~Autoexpose();
	void Autoexpose::autoexpose(double *exposure, double *sensitivity, short unsigned int*, int fluorophore, char *cyclename); 
	int Autoexpose::getPeak(int *hist, int num_bins);
	void Autoexpose::calchist(short unsigned int *image, int *hist);
	void Autoexpose::dumptofile(int *histogram, double curr_exp, double curr_sens, char *cyclename);
	bool Autoexpose::save_image(short unsigned int *curr_img, char *filename, char *cyclename);


private:
	CHamCam* this_camera;
	CFilter* this_filter;
	Reporter* r;
	CScope* this_te2000;
	CPifoc* this_pifoc;
	Acquisition* acq;
	short unsigned int *brightfield_img;
	double exp;
	double sens;
	char log_string[500];
	
	double ae_sens;
	double min_exp;
	int min_exp;
	double step;
	
};


#endif