mpi/fruitfly/general/fileAccess.java

   1 package mpi.fruitfly.general;
   2
   3 import java.io.BufferedReader;
   4 import java.io.IOException;
   5 import java.io.PrintWriter;
   6 import java.io.FileWriter;
   7 import java.io.FileReader;
   8
   9 /**
  10  * <p>Title: file access</p>
  11  *
  12  * <p>Description: Class that manages general file access open, read, write</p>
  13  *
  14  * <p>Copyright: Copyright (c) 2006</p>
  15  *
  16  * <p>Company: mpi-cbg</p>
  17  *
  18  * @author Stephan Preibisch
  19  * @version 1.0
  20  */
  21
  22 import ij.*;
  23 import ij.process.ImageProcessor;
  24 import ij.io.Opener;
  25 import java.io.File;
  26 import ij.io.FileSaver;
  27
  28 public class fileAccess
  29 {
  30     public static void saveStack(ImageStack stack, String fileName, int numberLength)
  31     {
  32         for (int i = 1; i <= stack.getSize(); i++)
  33             new FileSaver(new ImagePlus("Image "+i,stack.getProcessor(i))).saveAsTiff(fileName + genNumberString(i, numberLength) + ".tif");
  34     }
  35
  36     public static ImagePlus openCompleteStack(String imageStackDir, String imageStackName, String imageStackExt, int numberLength, int startingNumber)
  37     {
  38         Opener open = new Opener();
  39
  40         ImagePlus impTmp = open.openImage(imageStackDir + imageStackName + genNumberString(startingNumber, numberLength) + imageStackExt);
  41         ImageStack stack = new ImageStack(impTmp.getWidth(), impTmp.getHeight());
  42
  43         File f = new File(imageStackDir);
  44         int countFiles = startingNumber;
  45         String fileName = "";
  46
  47         for (File entry : f.listFiles())
  48             if (entry.toString().startsWith(imageStackDir + imageStackName) && entry.toString().endsWith(imageStackExt))
  49             {
  50                 fileName = imageStackDir + imageStackName + genNumberString(countFiles++, numberLength) + imageStackExt;
  51
  52                 try
  53                 {
  54                     stack.addSlice(fileName, open.openImage(fileName).getProcessor());
  55                 }
  56                 catch (Exception e)
  57                 {
  58                     countFiles--;
  59                 };
  60
  61             }
  62
  63         System.out.println(countFiles + " files read.");
  64
  65         return new ImagePlus(imageStackName, stack);
  66     }
  67
  68     public static ImagePlus openStack(String imageStackDir, String imageStackName, String imageStackExt, int numberLength, int startingNumber, int endingNumber)
  69     {
  70         Opener open = new Opener();
  71
  72         ImagePlus impTmp = open.openImage(imageStackDir + imageStackName + genNumberString(startingNumber, numberLength) + imageStackExt);
  73         ImageStack stack = new ImageStack(impTmp.getWidth(), impTmp.getHeight());
  74
  75         File f = new File(imageStackDir);
  76         String fileName = "";
  77         int countFiles = 0;
  78
  79         for (int num = startingNumber; num <= endingNumber; num++)
  80         {
  81             fileName = imageStackDir + imageStackName + genNumberString(num, numberLength) + imageStackExt;
  82
  83             try
  84             {
  85                // System.out.print("Reading " + fileName + " ... ");
  86
  87                 stack.addSlice(fileName, open.openImage(fileName).getProcessor());
  88                 countFiles++;
  89
  90                 //System.out.println("done");
  91
  92             } catch (Exception e)
  93             {
  94
  95             };
  96         }
  97
  98
  99         System.out.println(countFiles + " files read.");
 100
 101         return new ImagePlus(imageStackName, stack);
 102     }
 103
 104     private static String genNumberString(int number, int length)
 105     {
 106         String result = "";
 107
 108         result = "" + number;
 109         while (result.length()  < length)
 110             result = "0" + result;
 111
 112         return result;
 113     }
 114
 115     public static BufferedReader openFileRead(String fileName)
 116     {
 117       BufferedReader inputFile;
 118       try
 119       {
 120         inputFile = new BufferedReader(new FileReader(fileName));
 121       }
 122       catch (IOException e)
 123       {
 124         System.err.println("mpi.fruitfly.general.openFileRead(): " + e);
 125         inputFile = null;
 126       }
 127       return(inputFile);
 128     }
 129
 130     public static PrintWriter openFileWrite(String fileName)
 131     {
 132       PrintWriter outputFile;
 133       try
 134       {
 135         outputFile = new PrintWriter(new FileWriter(fileName));
 136       }
 137       catch (IOException e)
 138       {
 139         System.err.println("mpi.fruitfly.general.openFileWrite(): " + e);
 140         outputFile = null;
 141       }
 142       return(outputFile);
 143     }
 144 }