Merge branch 'CMV-SIM+' into master_main

.*swp

.DS_store

findMaxDilation

geomCentres

erodeFixedRadius

histogram

Fluo-N2DH-SIM+

*.log

*.zip

*.dat

01

02

CMV

fakeRes*

g++ -o findMaxDilation findMaxDilation.cpp  -li3dcore -li3dalgo -Xlinker -defsym -Xlinker MAIN__=main

g++ -o erodeFixedRadius erodeFixedRadius.cpp  -li3dcore -li3dalgo -Xlinker -defsym -Xlinker MAIN__=main

g++ -o geomCentres geomCentres.cpp  -li3dcore -li3dalgo -Xlinker -defsym -Xlinker MAIN__=main

#include <i3d/image3d.h>

#include <i3d/regions.h>

#include <i3d/morphology.h>

#include <set>

template <class VT>

bool reduceMarkers(const i3d::Image3d<VT>& traIn, i3d::Image3d<VT>& traOut, const int erosionSize)

{

	//find set of labels

	std::set<int> setOfMarkers;

	std::map<int,int> sizesOfMarkers;

	const VT* inP = traIn.GetFirstVoxelAddr();

	const VT* const inPL = inP + traIn.GetImageSize();

	while (inP != inPL)

	{

		if (*inP > 0)

		{

			setOfMarkers.insert(*inP);

			++sizesOfMarkers[*inP];

		}

		++inP;

	}

	//erode the whole image

	i3d::ErosionO(traIn,traOut,erosionSize);

	//image for individual labels/markers

	i3d::Image3d<VT> tmpImg;

	tmpImg.CopyMetaData(traOut);

	//

	//for the CCA around it

	i3d::LabeledImage3d<size_t,i3d::GRAY16> lblImg;

	//running pointers...

	VT* tmpP, * outP;

	VT* const outPL = traOut.GetFirstVoxelAddr() + traOut.GetImageSize();

	//process label by label and keep only its largest connected component

	for (int label : setOfMarkers)

	{

		//copy out the label from traOut, CCA on it, remove non-largest CC in the traOut image

		//std::cout << "found label: " << label << " (volume=" << sizesOfMarkers[label] << ")\n";

		if (sizesOfMarkers[label] < 1000)

		{

			std::cout << "label " << label << ": too small (" << sizesOfMarkers[label] << ") to be reduced\n";

			//have to restore it again (because the out image is already eroded)

			inP  = traIn.GetFirstVoxelAddr();

			outP = traOut.GetFirstVoxelAddr();

			while (inP != inPL)

			{

				*outP = *inP == label ? label : *outP;

				++inP; ++outP;

			}

			continue;

		}

		int originalLabelAfterErosionSize = 0;

		//copy out the single label from traOut to tmpImg

		tmpP = tmpImg.GetFirstVoxelAddr();

		outP = traOut.GetFirstVoxelAddr();

		while (outP != outPL)

		{

			if (*outP == label)

			{

				*tmpP = 1;

				++originalLabelAfterErosionSize;

			}

			else *tmpP = 0;

			++outP; ++tmpP;

		}

		//CCA on it

		lblImg.CreateForegroundRegionsFF(tmpImg);

		//find largest CC

		int largestSize = 0;

		size_t largestLabel = 0;

		for (const auto& c : lblImg.components)

		{

			//std::cout << "considering comp: " << c.first << " of volume " << c.second.volume << "\n";

			if (c.second.volume > largestSize)

			{

				largestSize = c.second.volume;

				largestLabel = c.first;

			}

		}

		//DEBUG

		std::cout << "label " << label << ": "

		          << largestSize << " px is the largest component (of label "

		          << largestLabel << " from " << lblImg.components.size() << " components), ";

		//remove non-largest CC in the traOut image

		int howMuchWasRemoved = 0;

		size_t* lblP = lblImg.GetFirstVoxelAddr();

		outP = traOut.GetFirstVoxelAddr();

		while (outP != outPL)

		{

			//in the territory of the original marker but not in its largest component?

			if (*outP == label && *lblP != largestLabel)

			{

				*outP = 0;

				++howMuchWasRemoved;

			}

			++lblP; ++outP;

		}

		//break the whole thing if we experience a label that got diminished by this erosion

		int howMuchIsLeft = originalLabelAfterErosionSize - howMuchWasRemoved;

		if (howMuchIsLeft != lblImg.components[largestLabel].volume) std::cout << "ERROR! ";

		std::cout << howMuchWasRemoved << " px was removed, and " << howMuchIsLeft << " px is left\n";

		if (howMuchIsLeft < 9) return false;

	}

	return true;

}

int main(int argc, char** argv)

{

	if (argc != 3)

	{

		std::cout << "params: TRAmarkers_G16.tif  participantRes_G16.tif\n";

		return -1;

	}

	i3d::Image3d<i3d::GRAY16> resImg(argv[2]);

	i3d::Image3d<i3d::GRAY16> traImg(argv[1]);

	i3d::Image3d<i3d::GRAY16> reducedTraImg;

	char fn[128];

	if ( !reduceMarkers(traImg,reducedTraImg,6) )

		std::cout << "PROBLEM WITH EROSION!\n";

	//find last '/'

	int FSpos = 0;

	int i = 0;

	while (argv[1][i] != 0)

	{

		if (argv[1][i] == '/') FSpos = i;

		++i;

	}

	sprintf(fn,"/temp/");

	int j = 6;

	while (FSpos < i) fn[j++] = argv[1][FSpos++];

	fn[j] = 0;

	std::cout << "managed and saving: " << fn << "\n";

	reducedTraImg.SaveImage(fn);

	return 0;

}

for i in  02/silverGT_ulman/gtReference/Fluo-N2DH-SIM+/02_GT/TRA/man_track*tif; do ./erodeFixedRadius $i  fakeRes.tif ; done

//then move from /temp/man_track* to somewhere...