// This program is free software; you can redistribute it and/or modify
// it under the terms of the GNU General Public License as published by
// the Free Software Foundation; either version 2 of the License, or
// (at your option) any later version.
//
// This program is distributed in the hope that it will be useful,
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
// GNU General Public License for more details.
//
// You should have received a copy of the GNU General Public License
// along with this program; if not, write to the Free Software
// Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
// http://www.gnu.org/copyleft/gpl.html

/*
* DAVID
* 
* This file modified by David Foster to improve clarity.
*/

/**
* Automatic thresholding technique based on the entopy of the histogram.
* See: P.K. Sahoo, S. Soltani, K.C. Wong and, Y.C. Chen "A Survey of
* Thresholding Techniques", Computer Vision, Graphics, and Image
* Processing, Vol. 41, pp.233-260, 1988.
*
* @author Jarek Sacha
*/

/*
This plugin does automatic thresholding based on the entopy of the histogram.
The method is very similar to Otsu's method. Rather than maximising
the inter-class variance, it maximises the inter-class entropy.
Entropy is a measure of the uncertainity of an event taking place.
You can calculate it as: S = -(sum)p*log2(p) so it is very
straightforward to do using the histogram data.
(p is the probability of a pixel greyscale value in the image,
and (sum) is the greek capital sigma. It is customary to use log in base 2. 
*/

// This algorithm was taken from the ImageJ sourcecodes
// http://rsb.info.nih.gov/ij/plugins/entropy.html
// and adopted for the FreeImage library
//
// Copyright (C) 2007-2008:
// monday2000  monday2000@yandex.ru

#include "FreeImage.h"
#include "Utilities.h"

////////////////////////////////////////////////////////////////////////////////

inline void SetPixel(BYTE *bits, unsigned x, BYTE* value)
{   // this function is simplified from FreeImage_SetPixelIndex
	
	*value ? bits[x >> 3] |= (0x80 >> (x & 0x7)) : bits[x >> 3] &= (0xFF7F >> (x & 0x7));
}

////////////////////////////////////////////////////////////////////////////////

FIBITMAP* ProcessFilter(FIBITMAP* src_dib)
{
	// get source image size
	unsigned width = FreeImage_GetWidth(src_dib);
	
	unsigned height = FreeImage_GetHeight(src_dib);
	
	unsigned src_pitch = FreeImage_GetPitch(src_dib);
	
	unsigned bpp = FreeImage_GetBPP(src_dib);
	
	unsigned btpp = bpp/8;
	
	FIBITMAP* dst_dib = FreeImage_Allocate(width, height, 1);
	
	// Build a monochrome palette
	RGBQUAD *pal = FreeImage_GetPalette(dst_dib);
	pal[0].rgbRed = pal[0].rgbGreen = pal[0].rgbBlue = 0;
	pal[1].rgbRed = pal[1].rgbGreen = pal[1].rgbBlue = 255;
	
	unsigned dst_pitch = FreeImage_GetPitch(dst_dib);
	
	BYTE* src_bits = (BYTE*)FreeImage_GetBits(src_dib); // The image raster
	
	BYTE* dst_bits = (BYTE*)FreeImage_GetBits(dst_dib); // The image raster	
	
	BYTE* lines, *lined;
	
	int i, t;
	
	int hist[256] = {0};
	
	// build histogram first
	
	// for each line	
	for ( unsigned y = 0; y < height; y++ )
	{			
		lines = src_bits + y * src_pitch;
		
		// for each pixel
		for ( unsigned x = 0; x < width; x++)
		{
			hist[lines[x]]++;
		}		
	}
	/*
    * DAVID
    * 
    * For all i,
    *     normalizedHist[i] = (double) hist[i]/sum(hist)
    */
	// Normalize histogram, that is makes the sum of all bins equal to 1.
	double sum = 0;
	
	for (i = 0; i < 256; ++i)
		
		sum += hist[i];
	
	
	if (sum == 0)
	{
		// This should not normally happen, but...
		//throw new IllegalArgumentException("Empty histogram: sum of all bins is zero.");
		printf("Empty histogram: sum of all bins is zero.\n");
		
		return NULL;
	}
	
	double normalizedHist[256] = {0};
	
	for (i = 0; i < 256; i++)
		
		normalizedHist[i] = hist[i] / sum;
	
		/*
		* DAVID
		* 
		* pT = cumulative_sum(normalizedHist)
    */
	double pT[256] = {0};
	
	pT[0] = normalizedHist[0];
	
	for (i = 1; i < 256; i++)
		
		pT[i] = pT[i - 1] + normalizedHist[i];
	
	
	// Entropy for black and white parts of the histogram	
	double epsilon = 0;
	
	double hB[256] = {0};
	double hW[256] = {0};
	
	for (t = 0; t < 256; t++)
	{
		// Black entropy
		double pTB = pT[t];		// DAVID
		
		if (pTB > epsilon)
		{
			double hhB = 0;
			
			for (i = 0; i <= t; i++)
			{
				if (normalizedHist[i] > epsilon)
					
					hhB -= normalizedHist[i] / pTB * log(normalizedHist[i] / pTB);
				
			}
			hB[t] = hhB;
		}
		else
			
			hB[t] = 0;
		
		
		// White  entropy
		double pTW = 1 - pT[t];
		
		if (pTW > epsilon)
		{
			double hhW = 0;
			
			for (i = t + 1; i < 256; ++i)
			{
				if (normalizedHist[i] > epsilon)
					
					hhW -= normalizedHist[i] / pTW * log(normalizedHist[i] / pTW);
				
			}
			
			hW[t] = hhW;
		} 
		else
			
			hW[t] = 0;
	}
	
	// Find histogram index with maximum entropy
	// DAVID: ...where entropy[i] is defined to be (black_entropy[i] + white_entropy[i])
	double jMax = hB[0] + hW[0];
	
	int threshold = 0;
	
	for (t = 1; t < 256; ++t)
	{
		double j = hB[t] + hW[t];
		
		if (j > jMax)
		{
			jMax = j;
			threshold = t;
		}
	}	
	
	printf("threshold=%d\n", threshold);
	
	BYTE val;
	
	// for each line
	for ( y = 0; y < height; y++ )
	{
		lined = dst_bits + y * dst_pitch;
		
		lines = src_bits + y * src_pitch;
		
		// for all pixels
		for ( unsigned x = 0; x < width; x++)
		{
			val = (BYTE) ( ( lines[x] >= threshold ) ? 255 : 0 );			
			
			SetPixel(lined, x, &val);
		}		
	}
	
	// Copying the DPI...
	
	FreeImage_SetDotsPerMeterX(dst_dib, FreeImage_GetDotsPerMeterX(src_dib));
	
	FreeImage_SetDotsPerMeterY(dst_dib, FreeImage_GetDotsPerMeterY(src_dib));
	
	return dst_dib;
}

////////////////////////////////////////////////////////////////////////////////
/**
FreeImage error handler
@param fif Format / Plugin responsible for the error 
@param message Error message
*/
void FreeImageErrorHandler(FREE_IMAGE_FORMAT fif, const char *message) {
	printf("\n*** "); 
	printf("%s Format\n", FreeImage_GetFormatFromFIF(fif));
	printf(message);
	printf(" ***\n");
}

////////////////////////////////////////////////////////////////////////////////

/** Generic image loader

  @param lpszPathName Pointer to the full file name
  @param flag Optional load flag constant
  @return Returns the loaded dib if successful, returns NULL otherwise
*/

FIBITMAP* GenericLoader(const char* lpszPathName, int flag)
{	
	FREE_IMAGE_FORMAT fif = FIF_UNKNOWN;
	// check the file signature and deduce its format
	// (the second argument is currently not used by FreeImage)
	
	fif = FreeImage_GetFileType(lpszPathName, 0);
	
	FIBITMAP* dib;
	
	if(fif == FIF_UNKNOWN)
	{
		// no signature ?
		// try to guess the file format from the file extension
		fif = FreeImage_GetFIFFromFilename(lpszPathName);
	}
	
	// check that the plugin has reading capabilities ...
	if((fif != FIF_UNKNOWN) && FreeImage_FIFSupportsReading(fif))
	{
		// ok, let's load the file
		dib = FreeImage_Load(fif, lpszPathName, flag);
		
		// unless a bad file format, we are done !
		if (!dib)
		{
			printf("%s%s%s\n","File \"", lpszPathName, "\" not found.");
			return NULL;
		}
	}	
	
	return dib;
}

////////////////////////////////////////////////////////////////////////////////

int main(int argc, char *argv[]) {
	
	// call this ONLY when linking with FreeImage as a static library
#ifdef FREEIMAGE_LIB
	FreeImage_Initialise();
#endif // FREEIMAGE_LIB
	
	// initialize your own FreeImage error handler
	
	FreeImage_SetOutputMessage(FreeImageErrorHandler);
	
	if(argc != 2) {
		printf("Usage : ent_thres <input_file>\n");
		return 0;
	}
	
	FIBITMAP *dib = GenericLoader(argv[1], 0);
	
	if (dib)
	{		
		// bitmap is successfully loaded!
		
		if (FreeImage_GetImageType(dib) == FIT_BITMAP)
		{
			if (FreeImage_GetBPP(dib) == 8)
			{
				FIBITMAP* dst_dib = ProcessFilter(dib);
				
				if (dst_dib)
				{					
					// save the filtered bitmap
					const char *output_filename = "filtered.tif";
					
					// first, check the output format from the file name or file extension
					FREE_IMAGE_FORMAT out_fif = FreeImage_GetFIFFromFilename(output_filename);
					
					if(out_fif != FIF_UNKNOWN)
					{
						// then save the file
						FreeImage_Save(out_fif, dst_dib, output_filename, 0);
					}
					
					// free the loaded FIBITMAP
					FreeImage_Unload(dst_dib);					
				}
			}
			
			else
				
				printf("%s\n", "Unsupported color mode.");
		}
		
		else // non-FIT_BITMAP images are not supported.
			
			printf("%s\n", "Unsupported color mode.");
		
		FreeImage_Unload(dib);
	}	 
	
	// call this ONLY when linking with FreeImage as a static library
#ifdef FREEIMAGE_LIB
	FreeImage_DeInitialise();
#endif // FREEIMAGE_LIB
	
	return 0;