//////////////////////////////////////////////////////////////////////////
//
//
//                              cell.cpp   
//
//
//                           Michael Boland
//                          2 September 1995
//
//
// Revisions:
//    13Oct95:  Added normalization of intensity feature to cell_moments
//                M. Boland
//    21Dec95:  Added cell_obj_moments(). -M. Boland
//    02Jan96:  Added capabiliity for multi-color images -M. Boland
//    07Jan96:  Changed normalization of pixels to total cell intensity 
//               instead of avg. intensity. -M. Boland
//    13Jan96:  Added test code for use in determining z=1 for Zernike
//               calculations. -M. Boland
//    19Jan96:  Moved cell_moments(), cell_object_moments(), and 
//               cell_zernike() to separate files. -M.Boland
//
//////////////////////////////////////////////////////////////////////////


#include 
#include 
#include 
#include 

#include "cell.h"


Cell::Cell()
{
	for(int i = 1; i <= MAX_COLORS; i++)
	{
		cell_intensity[i] = 0.0 ;
	}
	cell_num_objects = 0 ;
	cell_num_pixels = 0 ;
	cell_num_colors = 0 ;
}


Cell::Cell(ifstream& infile) 
{

	for(int i = 1; i <= MAX_COLORS; i++)
	{
		cell_intensity[i] = 0.0 ;
	}
	cell_num_objects = 0 ;
	cell_num_pixels = 0 ;
	cell_num_colors = 0 ;

	if (!infile)
	{
		cerr << "cell.cpp: invalid infile. \n" ;
		return ;
	}

	Object* new_object ;	
	int size = 0 ;
	int label = 0 ;
	int x, y, z, intensity[MAX_COLORS] ;
	char ch ;

	while(!infile.eof())
	{

		if (!(infile >> size) || !(infile >> label))
		{
			cerr << "cell.cpp: 1:Invalid input file. \n" ;
			return ;
		}
		
		new_object = new Object ;

		for (int index = 0; index < size ; index++)
		{
			cell_num_colors = 1 ;

			if (!(infile >> x) || !(infile >> y) || !(infile >> z) 
					|| !(infile >> intensity[1])) 
			{
				cerr << "cell.cpp: 2:Invalid input file. \n" ;
				return ; 
			}
	
			do 
			{
				ch = infile.get() ;
				if (!(isspace(ch)))
				{
					infile.putback(ch) ;
					cell_num_colors++ ;
					if (!(infile >> intensity[cell_num_colors]))
					{
						cerr << "cell.cpp: 3:Invalid input file. \n" ;
						return ;
					}
				}
			} while (ch != '\n') ;		

			if (!(new_object->object_set_num_colors(cell_num_colors)))
			{
				cerr << "cell.cpp: Unable to set number of colors.\n" ;
				return ;
			}

			if (!(new_object->object_add_pixel(x, y, z, intensity)))
			{
				cerr << "cell.cpp: Unable to add pixel to object.\n" ;
				return ;
			}
			
			cell_num_pixels++ ;

		} // endfor

		if (!cell_add_object(new_object))
		{
			cerr << "cell.cpp: Unable to add new object. \n" ;
			return ;
		}

		//
		// Needed to check for CR in last line of file
		//

		do
		{
			ch = infile.get() ;
		} while(isspace(ch)) ;
		infile.putback(ch) ;

	} // endwhile
	
	infile.close() ;

}


Cell::~Cell() { } ;


int Cell::cell_add_object(Object* new_object)
{
	if (!objects.list_add(new_object))
	{
		cerr << "cell.cpp: Unable to create new Object \n" ;
		return(0) ;
	}
	
	cell_num_objects++ ;
	for(int color = 1; color <= cell_num_colors ; color++)
	{
		cell_intensity[color] += new_object->object_color_intensity(color) ;
	}

	return(1) ;
}


double Cell::cell_color_intensity(int color)
{
	if (color <= cell_num_colors)
		return(cell_intensity[color]) ;
	else return(0.0) ;
}


Pixel* Cell::cell_pixel_array()
{
	Object* obj_ptr ;
	Pixel* pixel_ptr ;
	//
	// allocate space for pixels
	//
	Pixel* pixel_array = new Pixel[cell_num_pixels] ; 

	long pixel_index = 0 ;
	int color_index ;

	if (!(obj_ptr=objects.list_top()))
	{
		cerr << "cell_pixel_array(): No objects.\n" ;
		return(0) ;
	}

	do
	{
		if (pixel_ptr = obj_ptr->pixels.list_top())
		do
		{
			pixel_array[pixel_index].x = pixel_ptr->x ;
			pixel_array[pixel_index].y = pixel_ptr->y ;
			pixel_array[pixel_index].z = pixel_ptr->z ;

			for (color_index=1; color_index <= MAX_COLORS; color_index++)
				pixel_array[pixel_index].intensity[color_index] =
					pixel_ptr->intensity[color_index] ;

			pixel_index++ ;

		} while (pixel_ptr = obj_ptr->pixels.list_next()) ;
	} while (obj_ptr = objects.list_next()) ;

	return(pixel_array) ;
}