main.cpp

#include <i3d/image3d.h>
#include <i3d/transform.h>

#include <stdlib.h> //for rnd generator seeding
#include <time.h>
#include <unistd.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();

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

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

		RenderMesh(i);
		//RenderMesh(i+1);
		//RenderMesh(i+2);
	}

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

	return(0);
}


void ParamsSetup(void)
{
	//set up the environment
   params.sceneOffset=Vector3d<float>(0.f);
   params.sceneSize=Vector3d<float>(27.5f,27.5f,22.0f); //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";


	//re-seed the standard rnd generator
	//(which is used for Perlin texture)
	unsigned int seed=-1 * (int)time(NULL) * (int)getpid();
	srand(seed);
}


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);
	}

	std::cout << "loaded mesh #" << fileNo << "\n";

	//position the mesh somewhat inside the scene
	mesh.ScaleMesh(Vector3F(1.6f,1.6f,2.0f));
	//mesh.TranslateMesh(Vector3F(-8.0f,-8.0f,-4.f));
	mesh.TranslateMesh(params.sceneCentre);

	return(0);
}


int RenderMesh(int fileNo)
{
	//setup isotropic(!) image for sample cell
	i3d::Image3d<i3d::GRAY16> mask;
	mask.SetOffset(i3d::Offset(0.0,0.0,0.0));
	mask.SetResolution(i3d::Resolution(8.0,8.0,8.0));
	mask.MakeRoom(220,220,176);
	mask.GetVoxelData()=0;

	//renders the isotropic mask
	std::cout << "rendering mask #" << fileNo << "\n";
	mesh.RenderMask(mask);

	//renders and resamples the texture
	i3d::Image3d<i3d::GRAY16> texture;
	mesh.RenderOneTimeTexture(mask,texture);
	/*
	if (mesh.DotsFirstRun())
	{
		std::cout << "rendering texture first run\n";
		mesh.InitDots(mask);
	}
	else
	{
		std::cout << "rendering texture iteration\n";
		//mesh.BrownDots(mask);
	}
	std::cout << "rendering texture #" << fileNo << "\n";
	mesh.RenderDots(mask,texture);
	*/

	std::cout << "exporting texture #" << fileNo << "\n";
	char fileName[1024];
	sprintf(fileName,"text_t%03d.tif",fileNo);
	texture.SaveImage(fileName);

	//resample also the mask before exporting
	std::cout << "exporting mask #" << fileNo << "\n";
	i3d::Resample(mask,texture,
	              mask.GetSizeX(),mask.GetSizeY(),mask.GetSizeZ()/8);
	sprintf(fileName,"mask_t%03d.tif",fileNo);
	texture.SaveImage(fileName);

	return(0);
}