main.cpp

#include <i3d/image3d.h>

#include "params.h"
#include "graphics.h"
#include "../cmath3d/TriangleMesh.h"

//create some shared objects...
ParamsClass params;
void ParamsSetup(void);
//
ActiveMesh mesh;

int LoadNewMesh(int fileNo);
int RenderMesh(int fileNo);

int main(void)
{
	ParamsSetup();

/*
	//SURFACE FITTING:

	//char filename[]="../sample_input/samplecell.stl";
	//char filename[]="../sample_input/torus_100_30.stl";
	char filename[]="../sample_input/sphere.stl";

	int retval=mesh.ImportSTL(filename);
	if (retval) 
	{
		std::cout << "some error reading file: " << retval << "\n";
		return(1);
	}

	std::cout << "mesh: " << filename << "\n";
	std::cout << "vertices  #: " << mesh.Pos.size() << "\n";
	std::cout << "triangles #: " << mesh.ID.size()/3 << "\n";
	std::cout << "normals   #: " << mesh.norm.size() << "\n";

	mesh.CenterMesh(params.sceneCentre);

	//work with mesh
	float surf_coeff[10];
	mesh.CalcQuadricSurface_Taubin(10,surf_coeff);
*/


	//ISBI:
	//for (int i=0; i < 50; ++i)
	for (int i=10; i < 11; ++i)
	{
		LoadNewMesh(i);
		RenderMesh(i);
	}

/*
	initializeGL();
	loopGL();
	closeGL();
*/

	return(0);
}


void ParamsSetup(void)
{
	//set up the environment
   params.sceneOffset=Vector3d<float>(0.f);
   params.sceneSize=Vector3d<float>(15.f,15.f,15.f); //for torus
   //params.sceneSize=Vector3d<float>(150.f,150.f,150.f); //for sample cell

	params.sceneCentre=params.sceneSize;
	params.sceneCentre/=2.0f;
	params.sceneCentre+=params.sceneOffset;

	params.sceneOuterBorder=Vector3d<float>(2.f);
	params.sceneBorderColour.r=0.7f;
	params.sceneBorderColour.g=0.7f;
	params.sceneBorderColour.b=0.0f;

	params.inputCellsFilename="cells/cell%d.txt";
	params.numberOfAgents=2;

	params.friendshipDuration=10.f;
	params.maxCellSpeed=0.20f;

	//adapted for cell cycle length of 24 hours
	params.cellCycleLength=14.5*60; //[min]

	params.currTime=0.0f; //all three are in units of minutes
	params.incrTime=1.0f;
	params.stopTime=50.0f;

	params.imgSizeX=500; //pixels
	params.imgSizeY=500;
	params.imgResX=1.0f; //pixels per micrometer
	params.imgResY=1.0f;

	params.imgOutlineFilename="Outline%05d.tif";
	params.imgPhantomFilename="Phantom%05d.tif";
	params.imgMaskFilename="Mask%05d.tif";
	params.imgFluoFilename="FluoImg%05d.tif";
	params.imgPhCFilename="PhCImg%05d.tif";
	params.tracksFilename="tracks.txt";
}


int LoadNewMesh(int fileNo)
{
	char VTK_nucleusSurf[1024];
	char VTK_nucleus[1024];
	char VTK_fTreeA[1024];
	char VTK_fTreeB[1024];

	sprintf(VTK_nucleusSurf,"../sample_sequence/ID05_t%03d_nucleusSurf.vtk",fileNo);
	sprintf(VTK_nucleus,    "../sample_sequence/ID05_t%03d_nucleus.vtk",fileNo);
	sprintf(VTK_fTreeA,     "../sample_sequence/ID05_t%03d_fTree01.vtk",fileNo);
	sprintf(VTK_fTreeB,     "../sample_sequence/ID05_t%03d_fTree02.vtk",fileNo);

	int retval=mesh.ImportVTK(VTK_nucleusSurf);
	//int retval=mesh.ImportVTK_Volumetric(VTK_nucleus);
	if (retval) 
	{
		std::cout << "some error reading nucleus: " << retval << "\n";
		return(1);
	}

	retval=mesh.ImportVTK_Ftree(VTK_fTreeA);
	if (retval) 
	{
		std::cout << "some error reading f-tree: " << retval << "\n";
		return(2);
	}

	retval=mesh.ImportVTK_Ftree(VTK_fTreeB);
	if (retval) 
	{
		std::cout << "some error reading f-tree: " << retval << "\n";
		return(2);
	}

	mesh.CenterMesh(params.sceneCentre);
	std::cout << "loaded mesh #" << fileNo << "\n";

	return(0);
}


int RenderMesh(int fileNo)
{
	i3d::Image3d<i3d::GRAY16> mask;
	mask.SetOffset(i3d::Offset(0.0,0.0,0.0));
	mask.SetResolution(i3d::Resolution(20.0,20.0,20.0));    //for sample cell
	mask.MakeRoom(300,300,300);
	mask.GetVoxelData()=0;
	mesh.RenderMask(mask);

	char fileName[1024];
	sprintf(fileName,"mesh_t%03d.tif",fileNo);
	mask.SaveImage(fileName);
	std::cout << "rendered mesh #" << fileNo << "\n";

	i3d::Image3d<i3d::GRAY16> texture;
	mesh.RenderOneTimeTexture(mask,texture);
	sprintf(fileName,"text_t%03d.tif",fileNo);
	texture.SaveImage(fileName);
	std::cout << "textured mesh #" << fileNo << "\n";

	return(0);
}