OxygenationMap.cpp

/*=========================================================================
 
	Program: VascuSynth
	Module: $RCSfile: OxygenationMap.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.
All rights reserved.

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* The name of the Insight Consortium, nor the names of any consortium members,
nor of any contributors, may be used to endorse or promote products derived
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* Modified source versions must be plainly marked as such, and must not be
misrepresented as being the original software.

* Free for non-commercial use only.  For commercial use, explicit approval 
must be requested by contacting the Authors.

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* Modifications of the source code must also be released as open source

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AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHORS OR CONTRIBUTORS BE LIABLE FOR
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=========================================================================*/

#include <iostream>
#include <vector>
#include <fstream>
#include <string>
#include <cstring>
#include <stdlib.h>
#include <cmath>

#include "MersenneTwister.h"
#include "OxygenationMap.h"
#include "SupplyMap.h"

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, takes the supply map and random seed
 */
OxygenationMap::OxygenationMap(SupplyMap *sMap, int randSeed):rand(){
	
    supply = sMap;
    
    //if the user specifies a random seed, then seed the mersenne twister
    //random number generator with the seed they have specified.  Otherwise
    //the seed will be somewhat random (the CPU time).
    if (randSeed > 0) {
        long unsigned int a = (long unsigned int) randSeed;
        rand.seed(a);
    }
    
    
}

/**
 * calculate the sum of the current effective map.  This is used to select
 * a candidate node that has high demand for oxygen.
 */
double OxygenationMap::sum(){
	double acc = 0;
	
	for(int i = 0; i < dim[0]; i++){
		for(int j = 0; j < dim[1]; j++){
			for(int k = 0; k < dim[2]; k++)
				acc += arr(effectiveMap_d, i, j, k, dim);
		}
	}
	
	return acc;
}

/**
 * select a candidate terminal node
 */
void OxygenationMap::candidate(double sum, int *cand){
	//MTRand rand;
	double r = rand.rand()*sum;
	
	double acc = 0;
	for(int i = 0; i < dim[0]; i++){
		for(int j = 0; j < dim[1]; j++){
			for(int k = 0; k < dim[2]; k++){
				acc += arr(effectiveMap_d, i, j, k, dim);
				if(acc >= r){
					cand[0] = i;
					cand[1] = j;
					cand[2] = k;
					return;
				}
			}
		}
	}
	
	return;
}

/**
 * update the effective map using cand (candidate as a new terminal node
 */
void OxygenationMap::applyCandidate(int cand[]){
	int temp[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++){
				temp[0] = i; temp[1] = j; temp[2] = k;
				arr(effectiveMap_d, i, j, k, dim) *= supply->reduction(cand, temp);
			}
		}
	}
}


/**
 * determine if source is visible from target with respect to 
 * the oxygenation map (uses original map - not effective map)
 */
bool OxygenationMap::visible(double source[], double target[]){
	
	
	double vect[3];
	vect[0] = target[0] - source[0];
	vect[1] = target[1] - source[1];
	vect[2] = target[2] - source[2];
	
	double pos[3];
	pos[0] = source[0]; pos[1] = source[1]; pos[2] =  source[2];
	
	int voxel[3];
	voxel[0] = (int)(source[0]+0.5); voxel[1] = (int)(source[1]+0.5); voxel[2] = (int)(source[2]+0.5);
	
	int targetVoxel[3];
	targetVoxel[0] =(int)(target[0]+0.5); targetVoxel[1] =(int)(target[1]+0.5); targetVoxel[2] =(int)(target[2]+0.5);

	int i;
		
	while( !(voxel[0] == targetVoxel[0] && voxel[1] == targetVoxel[1] && voxel[2] == targetVoxel[2]) &&
			!((fabs(pos[0] - target[0]) < 1e-10) && (fabs(pos[1] - target[1]) < 1e-10) && (fabs(pos[2] - target[2]) < 1e-10))){
					
		double mult = 1e50;
		double dir = 0.5;
		
		for(i = 0; i < 3; i++){
			
			if(vect[i] < 0) {
				dir = -0.5;
			} else {
				dir = 0.5;
			}
			
			double singleMult = fabs((voxel[i]-pos[i] + dir)/vect[i]);
			
			
			while (singleMult == 0) {
                
				// singleMult should always be > 0, this will only present itself as a problem 
				// when vect[i] < 0 - where pos[i] moves to x.5 - when it should move to x.5 - c 
				// where c is some small positive number
                
				dir *= 1.000000001;
				singleMult = fabs((voxel[i]-pos[i] + dir)/vect[i]);
                
			}
			
			if(singleMult < mult) {
				mult = singleMult;
			}
			
		}
		
		for(i = 0; i < 3; i++){
			pos[i] += mult*vect[i];
			voxel[i] = (int)(pos[i]+0.5);
		}
				
		if(arr(map_d, voxel[0], voxel[1], voxel[2], dim) == 0) {
			return false;
		}
			
	}
		
	return true;

}


/**
 * load a file containing the description of an oxygenation map
 */
void OxygenationMap::loadMap(string filename){
			
	char * tempFilename;
	
	tempFilename = new char[filename.size()+1];
	strcpy(tempFilename, filename.c_str());
	
	int lastIndex = strlen(tempFilename)-1;
	
	while ((tempFilename[lastIndex] == '\r') || (tempFilename[lastIndex] == '\n') || (tempFilename[lastIndex] == ' ')) {
		tempFilename[lastIndex] = '\0';
		lastIndex--;
	}
	
	ifstream mapFile;
	mapFile.open(tempFilename, ios::in);
	string line;
		
	
	if(mapFile.is_open()){
		
		// defining i,j,k,l outside of the for stament 
        // so this is compatable with both VC++ 6.0 and later versions
		int i;
        int j;
        int k; 

		getline(mapFile, line);
		char* tok = new char[line.size()];
		strcpy(tok, line.c_str());
		
		for(i = 0; i < 3; i++){
			char * temp = strtok((i == 0? tok : NULL), " ");
			if(temp == NULL) {
				break;
			}
			dim[i] = atoi(temp);
		}
		
		map_d = new double[dim[0]*dim[1]*dim[2]];
		effectiveMap_d = new double[dim[0]*dim[1]*dim[2]];

		for(i = 0; i < dim[0]; i++) {
			for(j = 0; j < dim[1]; j++) {
				for(k = 0; k < dim[2]; k++){
					arr(map_d, i, j, k, dim) = 0;
					arr(effectiveMap_d, i, j, k, dim) = 0;
				}
			}
		}

		while(!mapFile.eof()){
			getline(mapFile, line);
						
			tok = new char[line.size()];
			strcpy(tok, line.c_str());

			int region[6];
			for(i = 0; i < 6; i++){
				char * temp = strtok((i == 0? tok : NULL), " ");
				if(temp == NULL) {
					break;
				}
				region[i] = atoi(temp);
			}
				
			if(mapFile.eof()) {
				break;
			}

			getline(mapFile, line);
			tok = new char[line.size()];
			strcpy(tok, line.c_str());

			double value = atof(line.c_str());
			
			for(i = region[0]; i < region[3]; i++) {
				for(j = region[1]; j< region[4]; j++) {
					for(k = region[2]; k < region[5]; k++){
						arr(map_d, i, j,k, dim) = value;
						arr(effectiveMap_d, i, j, k, dim) = value;
					}
				}
			}
			
		}
		
		mapFile.close();
	
    } else {
    
        //error reading the mapfile
        throw "Could not read the OxygenationMap file";
        
        
    }

}