Re: directory and FileInputStream issues.

Question

hello,
so i am having a problem with my code. the code will look though text files of images and perform some calculations. previously i copied the java code file to every directory where the calculations were to be performed. a long and tedious procedure. so, i altered the code such that the java file would remain in one place, and i would imput a pathway. i have done similarly with some other java files with success, but i am getting several errors, and no calculations. below is the code.
import java.util.*;
import java.io.*;
import javax.swing.*;
import java.text.*;
import java.lang.Object;
import java.text.DecimalFormat;
public class BPF
     public static void main(String args[]) throws Exception
////////////////////following data pertains to voxel values ////////////////////
          //String vHeight = JOptionPane.showInputDialog("Enter voxel height");
          Double voxelHeight = .4102; //Double.parseDouble(vHeight);
          double voxelWidth = voxelHeight;
          //String vDepth = JOptionPane.showInputDialog("Enter voxel depth");
          double voxelDepth = 6.5; //Double.parseDouble(vDepth);
          double voxelCube = voxelHeight * voxelWidth * voxelDepth;
          double volumeTotal = 0;
          double BPFratio = 0;
          double normalizedBPF = 0;
          int voxel;
          double lowCutOff = 250.00;
          double highCutOff = 900.00;
          double bgColor = -1;
          int nonParenchymaVoxels = 0;
          double voxelArea = voxelWidth * voxelHeight;
          int tissuePerimeterCount = 0;
//////////////////////////following code pertains to files//////////////////////
          //String fNumber = //JOptionPane.showInputDialog("Enter number of files");
          int numOfFiles = 19;//Integer.parseInt(fNumber);
          //String file =  //JOptionPane.showInputDialog("Enter name/number of first file");
          int fileName = 61;//Integer.parseInt(file);
          int count = 0;
          String fileNumber;
          String input;     // image.txt as string
          String deliminator = " \r\t\n.,:;?!/()[]{}|~\"*<>=+&^%$#@_";  // items i overlook when compiling input string 
          String filePath = JOptionPane.showInputDialog("Enter file execution path");
        String addendumOutPut;
         FileOutputStream outPut; // declare a file output object
        PrintStream p;
        try
                 outPut = new FileOutputStream(filePath + "Results.txt");// Creates a new file output stream connected to "BPF Results.txt"
                    p = new PrintStream(outPut);// Connect print stream to the output stream
        catch (Exception e)
                 System.err.println ("Error writing to file");
        for (int iterator = 1; iterator <= numOfFiles; iterator++)
                    System.out.println("\n" + "the count is " + iterator);     
                    fileNumber = String.valueOf(fileName);     // give String fileNumber the converted string value of fileName (the first file # in the list)
                    addendumOutPut = filePath + "addendumOutPut".concat(fileNumber); //add data to file each time loop runs
/*line 86*/          System.out.println("the starting value is: " + fileName);  
                    FileReader inputImage = new FileReader(fileNumber + ".txt");  //used to open the file
                    BufferedReader binputImage = new BufferedReader(inputImage);  //reads lines of text in file
                    Vector voxelValueVector = new Vector();     // complete input file as vector
//////////////////// placing text file numbers in vector ///////////////////////
                    while ((input = binputImage.readLine()) != null)
                              StringTokenizer numbers = new StringTokenizer(input, deliminator);
                              while (numbers.hasMoreTokens())
                                        count++;       //just to keep track of which film i am looking at
                                        String voxelValues = numbers.nextToken(); //reads #s 1by1, line by line
                                        voxel = Integer.valueOf(voxelValues).intValue();     //converts string to numerical (integer) value of pixel
                                        voxelValueVector.add(voxel);     // adds numerical value of pixel to vector
                    int voxelValueArray[] = new int[voxelValueVector.size()];     //creates array that is same size as vector
                    for (int i = 0; i < voxelValueVector.size(); i++)
                             Integer voxelValueList = (Integer)(voxelValueVector.get(i));     //make vector into integers
                             voxelValueArray[i] = voxelValueList.intValue();
                    for (int i = 0; i < voxelValueVector.size(); i++)
                              if (voxelValueArray[i] > bgColor)
                                   tissuePerimeterCount++; //number of voxels within perimeter
                                   if (voxelValueArray[i] <= lowCutOff || voxelValueArray[i] >= highCutOff)
                                             nonParenchymaVoxels++;     //non brain tissue
                    double volumeBrainSurfaceCountour = tissuePerimeterCount * voxelCube; //volume of brain within perimeter including csf etc...
                    double parenchymaTissue = tissuePerimeterCount - nonParenchymaVoxels;     //voxel count of parenchyma tissue
                    double volumeParenchyma = parenchymaTissue * voxelCube;      //volume of parenchyma tissue
                    double volumeNonBrain = nonParenchymaVoxels * voxelCube;      //volume of non-brain elements
                    double ratio = parenchymaTissue / tissuePerimeterCount;          //BPF ratio
                    volumeTotal = volumeParenchyma + volumeTotal; //summation of parenchyma tissue
                    BPFratio = BPFratio + (volumeParenchyma * ratio); //running summation of ratio * parenchyma tissue - used for normalized BPF
                    addendumOutPut = filePath + "BPF Results.txt";
                    try
                             outPut  = new FileOutputStream(filePath + " Results.txt");// Create a new file output stream connected to "BPF Results.txt"
                              p = new PrintStream(outPut);// Connect print stream to the output stream
                              BufferedWriter addendumData = new BufferedWriter (new FileWriter(addendumOutPut, true));
                              System.out.println("The total number of voxels for " + fileName + " is: " + voxelValueVector.size());
                              System.out.println("The total number of voxels within tissue perimeter: " + tissuePerimeterCount);
                              System.out.println("The total volume of the brain (including csf) is: " + volumeBrainSurfaceCountour);
                              System.out.println("Volume of non-brain elements: " + volumeNonBrain);
                              System.out.println("Volume of brain elements: " + volumeParenchyma);
                              System.out.println("The BPF is: " + ratio);
                              System.out.println("BPF running count " + BPFratio);
                              addendumData.write("Stack " + fileName + "\n");
                              addendumData.write("Total volume " + " \t" + volumeBrainSurfaceCountour + "\n");
                              addendumData.write("Non-brain volume " + " \t" + volumeNonBrain + "\n");
                              addendumData.write("Parenchyma volume " + " \t" + volumeParenchyma + "\n");
                              addendumData.write("BPF " + " \t" + ratio + " \n" + "\n");
                              if (iterator == numOfFiles)
                                        addendumData.write("boo");
                                        normalizedBPF =  BPFratio / volumeTotal;
                                        System.out.println("normalized BPF is " + normalizedBPF);
                                        addendumData.write("Running Paryenchyma volume" + "\t" + volumeTotal + "\n");
                                        addendumData.write("total BPF" + "\t" + BPFratio + "\n");
                                        addendumData.write("Normalized BPF" + " \t" + normalizedBPF + "\n");
                               addendumData.close();
                               //System.out.println("The running volume tally is " + volumeTotal);
                              //System.out.println();
                              //System.out.println(count);
                    catch (IOException e)
                             System.out.println("IOException:");
                           e.printStackTrace();
                    fileName++;
                    tissuePerimeterCount = 0;
                    parenchymaTissue = 0;
                    volumeBrainSurfaceCountour = 0; //area of brain within perimeter including csf etc...
                    volumeParenchyma = 0;
                    ratio = 0;
                    nonParenchymaVoxels = 0;
}it is quite a bit to read through. i can say that the results.txt file is created, but it contains no data. the line
                    System.out.println("the starting value is: " + fileName);   is there for me to find at what point where i think the code stops functioning properly. (line 86).
the error messages are saying that
1. the text file (61.txt) cannot be found.
2. the remaining 4 errors pertain to FileInputStream
any help is greatly appreciated.

Answer 1

it has been a few days, and i completely forgot to post that i figured out the problem. when we last checked in, i was having problems with a code that would function when i copied the java file to a folder where it would be executed. as i needed to do this hundreds of times, it made more sense to input a pathway so i could have just one file. the problem...adding in the pathway produced a text file that contained no data. i posted my quagmire in the java forum and waited. it was met with a flurry of enthusiam that tended more towards sarcasm. i did eventually conquer the problem, so, here it is...
outPut  = new FileOutputStream(filePath + " Results.txt");was changed to:
outPut  = new FileOutputStream("Results.txt");...problem solved, and the program works like a swiss watch.