mpi/fruitfly/general/fileParsing.java

   1 package mpi.fruitfly.general;
   2
   3 /**
   4  * <p>Title: file parsing</p>
   5  *
   6  * <p>Description: Class for parsing different file types needed</p>
   7  *
   8  * <p>Copyright: Copyright (c) 2006</p>
   9  *
  10  * <p>Company: mpi-cbg</p>
  11  *
  12  * @author Stephan Preibisch
  13  * @version 1.0
  14  */
  15
  16 import java.io.BufferedReader;
  17 import java.io.IOException;
  18 import java.io.FileReader;
  19 import java.util.ArrayList;
  20 import java.util.Iterator;
  21
  22 import static mpi.fruitfly.general.fileAccess.*;
  23 import ij.IJ;
  24
  25
  26 public class fileParsing
  27 {
  28     public static float[][] parseFilter(String fileName)
  29     {
  30         // open file
  31         BufferedReader in = openFileRead(fileName);
  32         if (in == null)
  33             return null;
  34
  35         // read file
  36         ArrayList file = new ArrayList();
  37         try
  38         {
  39             while (in.ready()) file.add(in.readLine());
  40         }
  41         catch (Exception e)
  42         {
  43             System.err.println("mpi.fruitfly.general.readFilter("+fileName+"): " + e);
  44             return null;
  45         }
  46
  47         // parse data
  48         if (file.size() == 0)
  49         {
  50             System.err.println("mpi.fruitfly.general.readFilter("+fileName+"): " + "Filter-file is empty.");
  51             return null;
  52         }
  53
  54         String line[];
  55         Iterator<String> i = file.iterator();
  56         ArrayList data = new ArrayList();
  57
  58         int maxX  = 0;
  59
  60         while (i.hasNext())
  61         {
  62             try
  63             {
  64                 line = i.next().trim().split(" ");
  65                 if (line.length > maxX)
  66                     maxX = line.length;
  67                 data.add(line);
  68             }
  69             catch (Exception e)
  70             {
  71                 System.err.println("mpi.fruitfly.general.readFilter("+fileName+"): " + e);
  72                 return null;
  73             }
  74         }
  75
  76         if (maxX == 0)
  77         {
  78             System.err.println("mpi.fruitfly.general.readFilter(" + fileName + "): " + "Filter-file has no entries.");
  79             return null;
  80         }
  81
  82         float[][] filter = new float[maxX][file.size()];
  83         Iterator<String[]> j = data.iterator();
  84         int y = 0;
  85
  86         while (j.hasNext())
  87         {
  88             try
  89             {
  90                 line = j.next();
  91                 for  (int x = 0; x < line.length; x++)
  92                     filter[x][y] = Float.parseFloat(line[x]);
  93                 y++;
  94             }
  95             catch (Exception e)
  96             {
  97                 System.err.println("mpi.fruitfly.general.readFilter("+fileName+"), line "+(y+1)+": " + e);
  98                 return null;
  99             }
 100         }
 101
 102         if (IJ.debugMode)
 103         {
 104             for (y = 0; y < filter[0].length; y++)
 105             {
 106                 String numbers = "";
 107                 for (int x = 0; x < filter.length; x++)
 108                     numbers += filter[x][y] + " ";
 109                 IJ.log(numbers);
 110             }
 111
 112         }
 113
 114         return filter;
 115     }
 116 }