// Author: Jonathan Brandvein
// Copyright: disclaimed; derived from examples and not of substantial length

#include <iostream>
#include "itkImage.h"
#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"
#include "itkConnectedThresholdImageFilter.h"

using namespace std;
using namespace itk;

int main (int argc, char* argv[])
{
	// Picture typedefs
	typedef unsigned short PixelType;
	const unsigned int Dimension = 3;
	typedef Image< PixelType, Dimension > ImageType;

	// IO
	typedef ImageFileReader< ImageType > ReaderType;
	typedef ImageFileWriter< ImageType > WriterType;

	ReaderType::Pointer reader = ReaderType::New();
	WriterType::Pointer writer = WriterType::New();

	reader->SetFileName("Normal100-T2.mha");
	writer->SetFileName("Output.mhd");

	// Threshold filter	
	typedef ConnectedThresholdImageFilter< ImageType, ImageType > ConnectedFilterType;
	ConnectedFilterType::Pointer connectedThreshold = ConnectedFilterType::New();

	// 250 seems to be a good lower boundary, at least for the upper part of the segmentation.
	// If I wanted to, I could've raised the lower threshold and added more seeds to try to get
	// a more precise segmentation, but I wasn't sure what the lower part of the ventricles were
	// supposed to look like.
	// The upper bound is supposed to be higher than the max intensity observed in the image.
	const int lower_threshold = 250;
	const int upper_threshold = 600;
	const Index<3> seed = {{205, 236, 86}};

	connectedThreshold->AddSeed(seed);
	connectedThreshold->SetReplaceValue(100);
	connectedThreshold->SetLower(lower_threshold);
	connectedThreshold->SetUpper(upper_threshold);

	// Pipeline and execution
	connectedThreshold->SetInput(reader->GetOutput());
	writer->SetInput(connectedThreshold->GetOutput());

	try {
		writer->Update();
	} catch (ExceptionObject& err) {
		cerr << "Exception:\n" << err << endl;
		return 1;
	}

	return 0;
}