/*****************************************************************************
 -                                                                           -
 -                    POLONY SEQUENCER ACQUISITION SUITE                     -
 -                                Church Lab                                 -
 -                          Harvard Medical School                           -
 -                                                                           -
 -    Free software for running a Polony Sequencing automated microscope     -
 -                                                                           -
 - ========================================================================= -
 -                                                                           -
 -                                                                           -
 - autoexpose.cpp                                                            -
 -                                                                           -
 -   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.       -
 -                                                                           -
 -                                                                           -
 *****************************************************************************/

#include "Autoexpose.h"
#include<cmath>


Autoexpose::Autoexpose(Reporter* rep, CHamCam* cHamCam, CFilter* cFilter, CScope* cScope, CPifoc* cPifoc, Acquisition* acquis, short unsigned int *bf_img){
	r = rep;
	this_camera = cHamCam;
	this_filter = cFilter;
	this_te2000 = cScope;
	this_pifoc = cPifoc;
	acq = acquis;

	bf_thresh = 7500;

	ae_sens = 95;
	min_exp = 30;
	num_exp = 9;
	step_exp = 20;
}


Autoexpose::~Autoexpose(){;}


void Autoexpose::autoexpose(double *exposure, double *sensitivity, short unsigned int *bf_img, int fluorophores, char *cyclename){
	char debugimgfilename[500];
	int num_colors = 4;

	// Deal with image memory
	short unsigned int **image_ptr_stack;
	if(image_ptr_stack = (short unsigned int**)malloc(num_exp*4)==NULL){
		r->error("allocate memory for autoexpose pointer stack failed", 1);
	}

	brightfield_img = (short unsigned int*)malloc(1000000*sizeof(short unsigned int));
	for(int i=0; i<100000; i++){
		*(brightfield_img+i) = *(bf_img + i);
	}
	
	//UNCOMMENT THE NEXT LINE IF YOU WANT TO SAVE DEBUGGING IMAGES
	strcpy(debugimgfilename, "");
	sprintf(debugimgfilename, "%d_000000", 0);
	save_image(brightfield_img, debugimgfilename, cyclename);
	//
	
	//SET UP CAMERA FOR THE CORRECT NUMBER OF EXPOSURES
	if(!this_camera->SetupMultiple(num_exp*num_colors)){
		r->error("autoexpose: could not setup camera for acquisition", 1);
	}
	if(!this_camera->QueueCapture()){
		r->error("autoexpose: queue capture of multiple frames failed", 0);
	}

	//Iterate over all exposure/fluorophore combinations
	for(j=0; j<num_colors; j++){
		for(int i=0; i<num_exp; i++){
			if(!acq->acquire_expose_shutter(min_exp + (i*step_exp), ae_sens)){
				sprintf(log_string, "Error acquiring image %d, fluorophore %d in fluorescence autofocus stack", i, j);
				r->error(log_string, 0);
			}
			else{
				image_ptr_stack[(j*num_exp) + i] = acq->acquire_getdata((j*num_exp) + i);  
				}
		}
	}

	strcpy(debugimgfilename, "");
	sprintf(debugimgfilename, "%d_%03d%03d", fluorophore, (int)expose_num, (int)sens_num);
	save_image(image_ptr_stack[(i*num_sens)+j], debugimgfilename, cyclename);
	
	
	if(!this_camera->EndMultiple()){
		r->error("autoexpose: could not end multiple acquisition", 1);
	}
	r->log("autoexposure: assigning exposure variable in autoexpose",5);
	*exposure = max_exp;
	r->log("autoexposure: assigning sensitivity variable in autoexpose",5);
	*sensitivity = max_sens;
}


int Autoexpose::getPeak(int *hist, int num_bins){
	int curr_binval = 0;
	int curr_bin = 0;
	for(int i=0; i<num_bins; i++){
		if( (*(hist + i) > curr_binval) && (i < 16000)){
			curr_bin = i;
			curr_binval = *(hist + i);
		}
	}
	if(curr_bin == 0){
		r->error("ERROR: getPeak in autoexpose is finding peak at pixel intensity 0",0);
	}
	return curr_bin;
}



void Autoexpose::calchist(short unsigned int *image, int *hist){

	for(int i=0; i<16384; i++){
		*(hist + i) = 0;
	}

	num_nonzero_bf_pixels = 0;

	for(int j=0; j<1000000; j++){
		if(*(brightfield_img+j) > bf_thresh){
			(*(hist + (*(image + j))))++;
			num_nonzero_bf_pixels++;
		}
	}
	sprintf(log_string, "Current brightfield image has %d above thresh pixels.", num_nonzero_bf_pixels);
	r->log(log_string, 4);
}


  
void Autoexpose::dumptofile(int *histogram, double curr_exp, double curr_sens, char *cyclename){
	FILE *debugfile;
	int i;
	char debugfilename[500];

	//OPEN TEMP DEBUGFILE
	strcpy(debugfilename, "autoe_");
	strcat(debugfilename, cyclename);
	strcat(debugfilename, ".dat");
	if((debugfile = fopen(debugfilename, "a")) == NULL){
		fprintf(stderr, "Problem opening exposure info file %s. \n", debugfilename);
	}

	fprintf(debugfile, "%d\t%d", (int)(curr_exp * 1000), (int)(curr_sens));


	for(i=0; i<16384; i++){
		fprintf(debugfile, "\t%d", *(histogram + i));
	}
	fprintf(debugfile, "\n");

	fclose(debugfile);
}


bool Autoexpose::save_image(short unsigned int *curr_img, char *filename, char *cyclename){
	char img_output_fullname[500];
	FILE *img_outfile;

	strcpy(img_output_fullname, "");
	strcat(img_output_fullname, cyclename);
	strcat(img_output_fullname, "_");
	strcat(img_output_fullname, filename);
	strcat(img_output_fullname, ".raw");

	if((img_outfile = fopen(img_output_fullname, "w+b"))==NULL){
		sprintf(log_string, "ERROR opening raw output file %s", img_output_fullname);
		r->error(log_string, 0);
		return false;
	}
			
	fwrite(curr_img, 2, 1000000, img_outfile);
	fclose(img_outfile);
	return true;
}