tira/biomodels/flow_dep.h

/*
Copyright <2017> <David Mayerich>
Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
#pragma once
#include <fstream>									// Required for ofstream, etc.
#include <iomanip>									// Required for setw
#include <iostream>									// Required for cout, cin, etc.
#include <tuple>									// Required for returning multiple values from a function
using namespace std;
class flow
{
public:
	void backupToTxt(unsigned int nL, double **D, char filename[]);
	tuple<int, int> copySrcDesRadLen(char filename[]);
	void copyToArray(int *src, int *dest, double *radii, double *len);
	int getDangleNodes(int datarow, int numNodes, int *row, int *column, int *dangleNodes);
	void inversion(double **a, int n, double **b);
protected:
	float determinant(double **a, int n);
	int minor(double **src, double **dest, int row, int col, int order);
};
/* Function to find the dangle nodes in a network */
// Created by Cherub P. Harder (8/10/2015), U of Houston
// Modified by Cherub P. Harder on 8/12/2015
int flow::getDangleNodes(int datarow, int numNodes, int *column1, int *column2, int *dangleNodes)
{
	int count = datarow, diff1 = 0, diff2 = 0, numPress = 0, st = 0;
	// Find matching nodes within column2
	for( int i = 0; i < count; i++ )
	{
		for( int y = i+1; y < datarow; y++ )
		{
			if( column2[i] == column2[y] )			// Is there a match?
			{
				st = column2[i];					// Save the matching node
//				cout << endl << column2[i] << " = " << column2[y] << endl; // Display the matching nodes
				memmove(column2+i, column2+i+1, (datarow-(i+1)) * sizeof(column2[0])); // Move up the rows
													// taking the places of the rows before them starting
													// with where the matching node is located
				column2[datarow-1] = st;			// Place the matching node at the very end of the array--
													// this is for comparison purpose so that the other match-
													// ing node will be moved as well and then omitted later.
				diff1++;							// Count the matching node
				// Display the updated array (with the matching node moved to the bottommost row)
/*				cout << "Updated array:" << endl;
				for( int k = 0; k < datarow; k++ )
					cout << column2[k] << endl;
*/
				// Decrement the counters
				// NOTE: The counters need to be decremented because the rows had been moved up, so the same
				// locations need to be read again because they contain different values now after the move.
				i--;								// Decrement i to read the node that took over the place
													// of the matching node. Otherwise, it will be skipped.
				y--;								// Decrement y to read the following node for comparison
				count--;							// The maximum count need to be decremented so that the
													// matching nodes that had been moved will not be read again.
													// However, the maximum count (datarow) for finding a match
													// will not be decremented because the remaining matching
													// node that has not been moved yet needs to be moved and
													// the only way to do that is to match it with its duplicate.
			}
		}
	}
	
	// Store the nodes that have no duplicates
	// NOTE: This will only save the nodes that have not been moved to the bottom.
//	cout << "\ndangleNodes array:" << endl;
	for( int j = 0; j < datarow-diff1; j++ )
	{
		dangleNodes[numPress] = column2[j];
//		cout << dangleNodes[j] << endl;				// DELETE!!!
		numPress++;									// Count the non-duplicated node
	}
	// Find if the non-duplicated nodes have a match from column1
	count = datarow-diff1;							// Reinitialize the counter
	for( int i = 0; i < count; i++ )
	{
		for( int j = 0; j < datarow; j++ )
		{
			if( dangleNodes[i] == column1[j] )		// Is there a match?
			{
				st = column1[j];					// Save the matching node
//				cout << endl << dangleNodes[i] << " = " << column1[j] << endl; // Display the matching nodes
				memmove(dangleNodes+i, dangleNodes+i+1, (datarow-diff1-(i+1)) * sizeof(dangleNodes[0]));
				dangleNodes[count-1] = st;			// Move the matching node to the bottom of the array
				diff2++;							// Count the matching node
				// Display the updated array
/*				cout << "Updated dangleNodes array:" << endl;
				for( int k = 0; k < count-1; k++ )
				{
					cout << dangleNodes[k] << endl;
				}
*/
				// Decrement the counters
				i--;
				j--;
				count--;
				numPress--;							// Decrement to the exact number of dangle nodes
			}
		}
	}
	return numPress;								// Number of dangle nodes
}
// Function to make a backup copy of the contents of a matrix to a .txt file
// Created by Cherub P. Harder (8/10/2015), U of Houston
void flow::backupToTxt(unsigned int nL, double **D, char filename[])
{
	ofstream output_file(filename);
	
	for( unsigned int i = 0; i < nL; i++ )
	{
		for( int j = 0; j < 4; j++ )
		{
			if( j < 3 )
				output_file << D[i][j] << "\t";
			else
				output_file << D[i][j];
		}
		output_file << "\n";
	}
	output_file.close( );
}
// Function to make separate copies of the source nodes, destination nodes, radii, and lengths
// Created by Cherub P. Harder (8/10/2015), U of Houston
tuple<int, int> flow::copySrcDesRadLen(char filename[])
{
	int cnt = 0, numElements = 0, numNodes = 0;
	float number = 0.0;
	ofstream srcData("srcCol.txt");					// A .txt file to store the source nodes
	ofstream desData("destCol.txt");				// A .txt file to store the destination nodes
	ofstream radiiData("radii.txt");				// A .txt file to store the radii
	ofstream lenData("lengths.txt");				// A .txt file to store the lengths
	FILE *fp = fopen(filename, "r");				// Create a variable of type FILE* and open the file using
													// the fopen function and assign the file to the variable
	// Check if the file exists
	if(fp == NULL)									// Alternative: if(!fp)
	{
		printf("Error! File does not exist.\n");
		getchar( );									// Pause
		exit(-1);									// NOTE: Must include stdlib.h.
	}
	// Store data to their respective .txt files
	while(fscanf(fp, "%f", &number) == 1)
	{
		cnt++;										// Increment counter
		// Store to srcCol.txt
		if(cnt == 1)
			srcData << number << endl;
		// Store to destCol.txt
		if(cnt == 2)
			desData << number << endl;
		// Save the current number of nodes
		if(cnt < 3)
		{
			if(number > numNodes)
				numNodes = (int)number;
		}
		// Store to radii.txt
		if(cnt == 3)
			radiiData << number << endl;
		// Store to lengths.txt
		if(cnt == 4)
		{
			lenData << number << endl;
			numElements++;							// Count the elements
			cnt = 0;								// Reset counter
		}
	}
	srcData.close( );
	desData.close( );
	radiiData.close( );
	lenData.close( );
	return make_tuple(numNodes, numElements);		// Return two values
}
// Function to copy data for .txt files to their respective arrays
// Created by Cherub P. Harder (8/11/2015), U of Houston
void flow::copyToArray(int *src, int *dest, double *radii, double *len)
{
	int v = 0;
	double tmp = 0, R = 0, L = 0;
	
	// Store source node values to the array src
	ifstream readSrc("srcCol.txt");
	while( readSrc >> tmp )
	{
		src[v] = (int)tmp;
		v++;
	}
	readSrc.close( );
	// Store destination node values to the array dest
	v = 0;											// Reset counter
	ifstream readDest("destCol.txt");
	while( readDest >> tmp )
	{
		dest[v] = (int)tmp;
		v++;
	}
	readDest.close( );
	// Store radius values to the array radii
	v = 0;											// Reset counter
	ifstream readRad("radii.txt");
	while( readRad >> tmp )
	{
		radii[v] = tmp;
		v++;
	}
	readRad.close( );
	// Store length values to the array len
	v = 0;											// Reset counter
	ifstream readLen("lengths.txt");
	while( readLen >> tmp )
	{
		len[v] = tmp;
		v++;
	}
	readLen.close( );
}
// Function to find the inverse of a square matrix
void flow::inversion(double **a, int n, double **b)
{
	// Get 1 over the determinant of A
	double det = (double)(1.0/determinant(a, n));
//	cerr << "\n1/det(C) = " << det << endl;				// DELETE!!!
    // Memory allocation
    double *tmp = new double[(n-1) * (n-1)];
    double **m = new double * [n-1];
    for( int i = 0; i < n-1; i++ )
		m[i] = tmp + ( i * (n-1) );
 
    for( int j = 0; j < n; j++)
    {
		for( int i = 0; i < n; i++ )
        {
			// Get the cofactor (matrix) of a(j,i)
            minor(a, m, j, i, n);
            b[i][j] = det * determinant( m, n-1 );
            if( (i+j)%2 == 1 )
                b[i][j] = -b[i][j];
        }
    }
 
    // Release memory
    // Delete [] minor[0];
    delete [] tmp;
    delete [] m;
}
// Function to find the determinant of a matrix using recursion
// Contribution by Edward Popko
// Modified by Cherub P. Harder (7/15/2015), U of Houston
// Arguments: a(double **) - pointer to a pointer of an arbitrary square matrix
//			  n(int) - dimension of the square matrix
float flow::determinant(double **a, int n)
{
	int i, j, j1, j2;								// General loop and matrix subscripts
    double det = 0;									// Initialize determinant
    double **m = NULL;								// Pointer to pointer to implement 2D square array
	// Display contents of matrix C (DELETE!!!)
/*	std::cout << "\nThe updated matrix C:\n";
	for( int j = 0; j < n; ++j )
	{
		std::cerr << "\t";
		for( int k = 0; k < n; ++k )
			std::cerr << left << setw(15) << a[j][k];
		std::cerr << endl;
	}
	getchar();					// DELETE!!!*/
	if(n < 1) { }									// Error condition - should never get here
    else if (n == 1)								// Should never get here
	{
		det = a[0][0];
	}
    else if(n == 2)									// Basic 2x2 sub-matrix determinate definition
	{												// When n == 2, this ends the recursion series
		det = a[0][0] * a[1][1] - a[1][0] * a[0][1];
	}
													// Recursion continues, solve next sub-matrix
    else											// Solve the next minor by building a sub-matrix
	{
		det = 0;									// Initialize determinant of sub-matrix
        for (j1 = 0; j1 < n; j1++)					// For each column in sub-matrix get space for the
		{											// pointer list
			m = (double **) malloc((n-1) * sizeof(double *));
            for (i = 0; i < n-1; i++)
				m[i] = (double *) malloc((n-1)* sizeof(double));
                       //     i[0][1][2][3]  first malloc
                       //  m -> +  +  +  +   space for 4 pointers
                       //       |  |  |  |          j  second malloc
                       //       |  |  |  +-> _ _ _ [0] pointers to
                       //       |  |  +----> _ _ _ [1] and memory for
                       //       |  +-------> _ a _ [2] 4 doubles
                       //       +----------> _ _ _ [3]
                       //
                       //                   a[1][2]
                       // Build sub-matrix with minor elements excluded
            
			for (i = 1; i < n; i++)
			{
				j2 = 0 ;							// Start at first sum-matrix column position
													// Loop to copy source matrix less one column
                for (j = 0; j < n; j++)
				{
					if (j == j1) continue;			// Do not copy the minor column element
					
					m[i-1][j2] = a[i][j];			// Copy source element into new sub-matrix
													// i-1 because new sub-matrix is one row
													// (and column) smaller with excluded minors
                    j2++;							// Move to next sub-matrix column position
				}
			}
			
			det += (double)pow(-1.0, 1.0 + j1 + 1.0) * a[0][j1] * determinant(m, n-1);
													// Sum x raised to y power
													// recursively get determinant of next
													// sub-matrix which is now one
													// row & column smaller
            for (i = 0; i < n-1; i++) free(m[i]);	// Free the storage allocated to
													// this minor's set of pointers
            free(m);								// Free the storage for the original
													// pointer to pointer
		}
	}
	
	return(det);
}
// Function to calculate the cofactor of element (row, col)
int flow::minor(double **src, double **dest, int row, int col, int order)
{
	// Indicate which col and row is being copied to dest
    int colCount=0,rowCount=0;
 
    for(int i = 0; i < order; i++)
    {
        if(i != row)
        {
            colCount = 0;
            for(int j = 0; j < order; j++)
            {
                // When j is not the element
                if( j != col )
                {
                    dest[rowCount][colCount] = src[i][j];
                    colCount++;
                }
            }
            rowCount++;
		}
    }
 
    return 1;
}