TreeDrawer.cpp

/*=========================================================================
 
	Program: VascuSynth
	Module: $RCSfile: TreeDrawer.cpp,v $
	Language: C++
	Date: $Date: 2011/02/08 10:43:00 $
	Version: $Revision: 1.0 $

Copyright (c) 2011 Medical Imaging Analysis Lab, Simon Fraser University, 
British Columbia, Canada.
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ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHORS OR CONTRIBUTORS BE LIABLE FOR
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=========================================================================*/

#include "TreeDrawer.h"
#include "VascularTree.h"
#include "MersenneTwister.h"

#include <vector>
#include <cmath>

using namespace std;

// A parametric macro to allow the use of dynamic multi-dimensional arrays
#define arr(arr,x,y,z,dim) *(arr + (z + dim[2]*(y + dim[1]*(x))))

/**
 * Constructor
 */
TreeDrawer::TreeDrawer(VascularTree * _vt, double width, double * corner1, double * corner2){
	vt = _vt;

	imageVoxelWidth = width;
	mapVoxelWidth = vt->mapVoxelWidth;
	
    c1 = new double[3];
	c1[0] = corner1[0]; c1[1] = corner1[1]; c1[2]= corner1[2];
	
    c2 = new double[3];
	c2[0] = corner2[0]; c2[1] = corner2[1]; c2[2]= corner2[2];
	
	dim[2] = (int) ((fabs(corner2[2] - corner1[2]) * mapVoxelWidth / width) + 1);
	dim[1] = (int) ((fabs(corner2[1] - corner1[1]) * mapVoxelWidth / width) + 1);
	dim[0] = (int) ((fabs(corner2[0] - corner1[0]) * mapVoxelWidth / width) + 1);
	
	image = new unsigned char[dim[2]*dim[1]*dim[0]];
	
}

/**
 * maps a voxel to a point
 * 8 subsections in a voxel
 * if a voxel has corners (0,0,0) and (1,1,1)
 * 	section 0 has corners (0.0, 0.0, 0.0) and (0.5, 0.5, 0.5) => center = voxel center + (-0.25, -0.25, -0.25)
 * 	section 1 has corners (0.5, 0.0, 0.0) and (1.0, 0.5, 0.5) => center = voxel center + (+0.25, -0.25, -0.25)
 * 	section 2 has corners (0.0, 0.5, 0.0) and (0.5, 1.0, 0.5) => center = voxel center + (-0.25, +0.25, -0.25)
 * 	section 3 has corners (0.5, 0.5, 0.0) and (1.0, 1.0, 0.5) => center = voxel center + (+0.25, +0.25, -0.25)
 * 	section 4 has corners (0.0, 0.0, 0.5) and (0.5, 0.5, 1.0) => center = voxel center + (-0.25, -0.25, +0.25)
 * 	section 5 has corners (0.5, 0.0, 0.5) and (1.0, 0.5, 1.0) => center = voxel center + (+0.25, -0.25, +0.25)
 * 	section 6 has corners (0.0, 0.5, 0.5) and (0.5, 1.0, 1.0) => center = voxel center + (-0.25, +0.25, +0.25)
 * 	section 7 has corners (0.5, 0.5, 0.5) and (1.0, 1.0, 1.0) => center = voxel center + (+0.25, +0.25, +0.25)
 */
void TreeDrawer::voxelToPoint(int* voxel, int subSection, double *ret){
	ret[0] = ((double)voxel[0])*imageVoxelWidth / mapVoxelWidth;
	ret[1] = ((double)voxel[1])*imageVoxelWidth / mapVoxelWidth;
	ret[2] = ((double)voxel[2])*imageVoxelWidth / mapVoxelWidth;
	
	if(subSection == 0 || subSection == 2 || subSection == 4 || subSection == 6)
		ret[0] -= 0.25*imageVoxelWidth/mapVoxelWidth;
	if(subSection == 1 || subSection == 3 || subSection == 5 || subSection == 7)
		ret[0] += 0.25*imageVoxelWidth/mapVoxelWidth;
	if(subSection == 0 || subSection == 1 || subSection == 4 || subSection == 5)
		ret[1] -= 0.25*imageVoxelWidth/mapVoxelWidth;
	if(subSection == 2 || subSection == 3 || subSection == 6 || subSection == 7)
		ret[1] += 0.25*imageVoxelWidth/mapVoxelWidth;
	if(subSection == 0 || subSection == 1 || subSection == 2 || subSection == 3)
		ret[2] -= 0.25*imageVoxelWidth/mapVoxelWidth;
	if(subSection == 4 || subSection == 5 || subSection == 6 || subSection == 7)
		ret[2] += 0.25*imageVoxelWidth/mapVoxelWidth;
}

/**
 * checks if a point is inside a given tube
 */
bool TreeDrawer::inTube(double * point, double * p1, double * p2, double radius){
	if(inEnd(point, p1, radius))
		return true;
	
	double t = -((p2[0] - p1[0])*(p1[0] - point[0]) + 
				 (p2[1] - p1[1])*(p1[1] - point[1]) + 
				 (p2[2] - p1[2])*(p1[2] - point[2])) / 
				((p2[0] - p1[0])*(p2[0] - p1[0]) + 
				 (p2[1] - p1[1])*(p2[1] - p1[1]) +
				 (p2[2] - p1[2])*(p2[2] - p1[2]));
	
	if (t < 0 || t > 1) {
		return false;
	} else {
		double distance = pow(pow((((p2[0] - p1[0])*t + p1[0]) - point[0]), 2) + 
						    	pow((((p2[1] - p1[1])*t + p1[1]) - point[1]), 2) + 
								pow((((p2[2] - p1[2])*t + p1[2]) - point[2]), 2), 0.5);
		distance *= mapVoxelWidth;
		
        // this should be return (distance <= radius);
        if (distance <= radius) {
			return true;
		} else { 
			return false;
        }
	}
}

/**
 * checks if a point is in the end of a tube
 */
bool TreeDrawer::inEnd(double * point, double * p1, double radius){
    
    //same as above, no need for if, just return
	if(pow(pow(p1[0] - point[0], 2) +
			pow(p1[1] - point[1], 2) +
			pow(p1[2] - point[2], 2), 0.5)*mapVoxelWidth < radius)
		return true;

	return false;
}

/**
 * checks if a point is in the same region as a tube (used to improve performance)
 */
bool TreeDrawer::checkTube(double *point, double *to, double *from, double radius){
	double c1[3];
	c1[0] = (to[0] < from[0]? to[0] : from[0]) - radius/mapVoxelWidth;
	c1[1] = (to[1] < from[1]? to[1] : from[1]) - radius/mapVoxelWidth;
	c1[2] = (to[2] < from[2]? to[2] : from[2]) - radius/mapVoxelWidth;
	
	double c2[3];
	c2[0] = (to[0] > from[0]? to[0] : from[0]) + radius/mapVoxelWidth;
	c2[1] = (to[1] > from[1]? to[1] : from[1]) + radius/mapVoxelWidth;
	c2[2] = (to[2] > from[2]? to[2] : from[2]) + radius/mapVoxelWidth;
	
    //can do the same thing, return blah
	if(point[0]  >= c1[0] && point[0] <= c2[0] &&
			point[1]  >= c1[1] && point[1] <= c2[1] &&
			point[2]  >= c1[2] && point[2] <= c2[2])
		return true;
	return false;
	
}

/**
 * determines the intensity value at a specific voxel
 * in the range of 255 to 0
 */
unsigned char TreeDrawer::valueAtVoxel(int* voxel){
	
    int value = 0;
	int segments[] = {0,1,2,3,4,5,6,7};
	double *point = new double[3];
    int size = (int) vt->nt.nodes.size();
    
	for(int j = 1; j < size; j++){
		double * p1 = vt->nt.getPos(j);
		int parent = vt->nt.getParent(j);
		double * p2 = vt->nt.getPos(parent);
		double radius = vt->nt.getRadius(j);
		
		voxelToPoint(voxel, -1, point);
		if(checkTube(point, p1, p2, radius)){
			//for each of the 8 offsets of a point - check if the point is in a tube
			for(int i = 0; i < 7; i++){
				if(segments[i] == -1)
					continue;
				
				voxelToPoint(voxel, segments[i], point);
				if(inTube(point, p1, p2, radius)){
					value += 32;
					segments[i] = -1;
				}
			}
		}
		if(value == 256)
			break;
	}
	
	value--;
	
	if (value >= 256) {
		value = 255;
    }
    
	if (value < 0) {
		value = 0;
    }
    
	delete point;
	return (unsigned char)value;
}

/**
 * add some uniform noise to a voxel
 */
unsigned char TreeDrawer::addNoise_Uniform(unsigned char c, double lb, double ub){
        
	MTRand rand;
	int x = c + (int) (rand.rand()*(ub-lb) + lb);
	if (x > 255) {
		return (unsigned char)255;
	} else if (x < 0) {
		return (unsigned char)0;
	} else {
		return (unsigned char) x;
    }
}

/**
 * add some salt&pepper noise to a voxel
 */
unsigned char TreeDrawer::addNoise_saltPepper(unsigned char c, unsigned char valSalt, double probSalt, unsigned char valPepper, double probPepper){
	
    MTRand rand;
	double r = rand.rand();
	if(r <= probSalt) {
		return valSalt;
	} else if(r <= probPepper+ probSalt) {
		return valPepper;
	} else {
		return c;
    }
}

/**
 * add some gaussian noise to a voxel
 */
unsigned char TreeDrawer::addNoise_gaussian(unsigned char c, double median, double sigma){
    
	MTRand rand;
	int x = c + (int)(rand.randNorm(median, sigma));
	if(x > 255) {
		return (unsigned char)255;
	} else if(x < 0) {
		return (unsigned char)0;
	} else {
		return (unsigned char) x;
    }
}

/** 
 * draw the tree to a matrix
 */
void TreeDrawer::drawImage(){
	int voxel[3];
	for(int i = 0; i < dim[0]; i++){
		for(int j = 0; j < dim[1]; j++) {
			for(int k = 0; k < dim[2]; k++){
				voxel[0] = i; voxel[1] = j; voxel[2] = k;
				arr(image, i, j, k, dim) = valueAtVoxel(voxel);
			}
        }
	}
}

/**
 * add uniform noise to the matrix
 */
void TreeDrawer::addNoise_Uniform(double lb, double ub){
    
	for(int i = 0; i < dim[0]; i++) {
		for(int j = 0; j < dim[1]; j++) {
			for(int k = 0; k < dim[2]; k++) {
				arr(image, i, j, k, dim) = this->addNoise_Uniform(arr(image, i, j, k, dim), lb, ub);
            }
        }
    }
}

/**
 * add salt&pepper noise to the matrix
 */
void TreeDrawer::addNoise_saltPepper(unsigned char valSalt, double probSalt, unsigned char valPepper, double probPepper){
    
	for(int i = 0; i < dim[0]; i++) {
		for(int j = 0; j < dim[1]; j++) {
			for(int k = 0; k < dim[2]; k++) {
				arr(image, i, j, k, dim) = this->addNoise_saltPepper(arr(image, i, j, k, dim), valSalt, probSalt, valPepper, probPepper);
            }
        }
    }
			
}

/**
 * add gaussian noise to the matrix
 */
void TreeDrawer::addNoise_gaussian(double median, double sigma){
    
	for(int i = 0; i < dim[0]; i++) {
		for(int j = 0; j < dim[1]; j++) {
			for(int k = 0; k < dim[2]; k++) {
				arr(image, i, j, k, dim) = this->addNoise_gaussian(arr(image, i, j, k, dim), median, sigma);
            }
        }
    }
    
}


/**
 * add a single shadow @ (x,y,z)
 */
void TreeDrawer::addShadow(double x, double y, double z, double centerRatio, double r){
    
	for(int i = 0; i < dim[0]; i++) {
		for(int j = 0; j < dim[1]; j++) {
			for(int k = 0; k < dim[2]; k++){
				
                int voxel[3]; voxel[0] = i; voxel[1] = j; voxel[2] = k;
				double point[3]; voxelToPoint(voxel, -1, point);
				double dist = sqrt(pow((point[0]-x), 2) + pow((point[1]-y), 2) + pow((point[2]-z), 2));
				
				if(dist > r) {
					dist = r;
                }

				arr(image, i, j, k, dim) *= (dist/r) + (1- dist/r)*centerRatio;
                
			}
        }
    }
    
}

/**
 * add 'numShadows' shadows to the matrix
 */
void TreeDrawer::addShadows(int numShadows){
    
	MTRand rand;
	for(int i = 0; i < numShadows; i++){
	
        int segment = (int)(rand.rand()*(vt->nt.nodes.size()-1))+1;
		double * endPoint = vt->nt.getPos(segment);
		double * startPoint = vt->nt.getPos(vt->nt.getParent(segment));
		double length = sqrt(pow((startPoint[0]-endPoint[0]), 2) + pow((startPoint[1]-endPoint[1]), 2) + pow((startPoint[2]-endPoint[2]), 2));

		double strength = rand.rand();
		this->addShadow((startPoint[0]+endPoint[0])/2, (startPoint[1]+endPoint[1])/2, (startPoint[2]+endPoint[2])/2, strength, length);
	}
    
}

/**
 * get the value of the matrix at (x,y,z)
 */
unsigned char TreeDrawer::imageAt(int x, int y, int z){
	return arr(image, x, y, z, dim);
}

/**
 * copy the matrix
 */
TreeDrawer* TreeDrawer::copy(){
	TreeDrawer * copy = new TreeDrawer(vt, imageVoxelWidth, c1, c2);

	for(int i = 0; i < dim[0]*dim[1]*dim[2]; i++) {
		copy->image[i] = image[i];
    }

	return copy;
}