| Batch_Folder.java |
package vnt;
/**
* Batch_Folder.java - v1.0
* Began: April 23, 2006
* Last Updated: April 23, 2006
*
* Copyright (C) 2005-2006 - Michael D. Miller - mdm162@truman.edu
* Truman State University
* 100 E. Normal
* Kirksville, MO - 63501
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
*/
import ij.*;
import ij.gui.*;
import java.awt.*;
import java.awt.Color.*;
import ij.plugin.PlugIn;
import ij.process.*;
import java.io.*;
import ij.io.*;
import java.lang.String.*;
import java.lang.Math.*;
/**
* <p>Batch processes an entire folder of images.
* Batch_Folder will do the following:</p>
* <ol>
* <li>grayscale</li>
* <li>lighting correction</li>
* <li>segmentation</li>
* <li>skeletonization</li>
* <li>endpoint pruning and outline generation</li>
* <li>perform graph theoretic analysis on the skeleton</li>
* </ol>
*
* <p>After it is complete, Batch_Folder closes all images.
* An alternative is Batch_Filde, which will perform this process on only one
* specific image, but it will leave all the images generated by the process
* open for user inspection.</p>
*
* @author Michael Miller - Truman State University
* @version 1.0
* @since 1.0
* @see Batch_File
*/
public class Batch_Folder extends VascularNetworkToolkit implements PlugIn {
/**
* This is called at the beginning of the PlugIn.
*
* <p>Pre: ImageJ is open and the plugin was called.
* <br />Post: A batch process is performed on a selected folder.
* @param arg Required by the interface. The argument, if any (may be blank).
*/
public void run(String arg){
// check the ImageJ version
// if (!IJ.versionLessThan("1.35l")) {
if (IJ.versionLessThan("1.32")) {
// ImageJ needs to be updated.
IJ.showMessage("ImageJ Version Update Needed", "ImageJ needs to be updated to run this plugin.");
return;
}
// create an Open dialogue for the user
String directoryName = IJ.getDirectory("");
if (directoryName.length() == 0) {
// user closed the dialogue
return;
}
// process the folder
recursiveProcessFolder(directoryName, true);
return;
}
private void recursiveProcessFolder(String directoryName, boolean goDeeper) {
File directory = new File(directoryName);
FilenameFilter filter = new FilenameFilter() {
public boolean accept(File directory, String name) {
if (name.startsWith("."))
return false;
if (name.endsWith(".txt"))
return false;
return true;
}
};
String[] contents = directory.list(filter);
if (contents == null) {
// Either dir does not exist or is not a directory.
return;
}
String filename;
for (int i=0; i<contents.length; i++) {
// Get filename of file or directory
filename = directoryName+contents[i];
// check if the content is a file or a folder
if ((new File(filename)).isDirectory()) {
// if content is a folder, should we recursively explore it?
if (goDeeper)
recursiveProcessFolder(filename+"/", goDeeper);
} else {
// content is a file, is it an image?
// if (getFileInformation(IJ.openImage(filename))) {
IJ.open(filename);
if (getFileInformation(IJ.getImage())) {
// we now have an open image and we extracted its settings, analyze it!
mainProcess();
cleanUpAfterProcess();
}
}
}
// all done with this folder!
}
/**
* This is called when a particular image is open and it needs to be processed.
*
* <p>Pre: An image is open and ready to be processed by the VNT.
* <br />Post: A batch process is performed on a currently active image.
*/
private void mainProcess() {
////////////////////
// 0) Grayscaling // (and TIFF conversion)
////////////////////
String extlessName = name.substring(0,name.lastIndexOf('.'));
if (!name.equalsIgnoreCase(extlessName+".tif")) {
IJ.run("RGB Color");
IJ.saveAs("tiff", directory+name);
}
IJ.run("8-bit");
IJ.saveAs("tiff", directory+"gray_"+name);
////////////////////////
// 1) Light Correction//
////////////////////////
if (performPolynomialLightingCorrection)
IJ.run("Lighting Correction");
// Note: This plugin saves a new image as "lightcorrected_"+filename
////////////////////
// 2) Segmentation//
////////////////////
if (useHighLowSegmentation)
IJ.run("Basic Segment");
else
IJ.run("FindEdges Segment");
// Note: This plugin saves a new image as "segmented_"+filename
///////////////////////
// 3) Skeletonization//
///////////////////////
IJ.run("DistanceMap Skeleton");
// Note: This plugin saves a new image as "skeleton_"+filename
///////////////
// 4) Pruning//
///////////////
IJ.run("Endpoint Prune");
// Note: This plugin saves a new image as "pruned_"+filename
////////////////////////////
// 4.5) Outline Generation//
////////////////////////////
IJ.run("DistanceMap Outline");
// Note: This plugin saves a new image as "outline_"+filename
IJ.run("Close");
////////////////
// 5) Analysis//
////////////////
IJ.run("Node Analysis");
// Note: This plugin saves a new image as "nodes_"+filename
// Note: This plugin saves a new image as "graph_"+filename
/////////////////////////////
// 6) Additional Operations//
/////////////////////////////
if (performEyeCandy)
IJ.run("Eye Candy");
}
/**
* This is called after a particular image has been processed by the VNT.
*
* <p>Pre: An image has been opened and processed by the VNT.
* <br />Post: All open files are closed, and [temp files may be deleted].
*/
private void cleanUpAfterProcess() {
////////////////////
// 0) Grayscaling // (and TIF conversion)
////////////////////
IJ.runMacro("close();");
////////////////////////
// 1) Light Correction//
////////////////////////
if (performPolynomialLightingCorrection) {
IJ.runMacro("close();");
IJ.runMacro("close();");
}
////////////////////
// 2) Segmentation//
////////////////////
if (useHighLowSegmentation) {
IJ.runMacro("close();");
IJ.runMacro("close();");
IJ.runMacro("close();");
} else {
IJ.runMacro("close();");
IJ.runMacro("close();");
}
///////////////////////
// 3) Skeletonization//
///////////////////////
IJ.runMacro("close();");
IJ.runMacro("close();");
IJ.runMacro("close();");
///////////////
// 4) Pruning//
///////////////
IJ.runMacro("close();");
////////////////////////////
// 4.5) Outline Generation//
////////////////////////////
////////////////
// 5) Analysis//
////////////////
IJ.runMacro("close();");
IJ.runMacro("close();");
IJ.runMacro("close();");
/////////////////////////////
// 6) Additional Operations//
/////////////////////////////
if (performEyeCandy) {
IJ.runMacro("close();");
}
// compute an extensionless filename
String extlessName = name.substring(0,name.lastIndexOf('.'));
// delete all temporary image files
if (keepTemporaryImageFiles == false) {
if (!name.equalsIgnoreCase(extlessName+".tif"))
(new File(directory+extlessName+".tif")).delete();
(new File(directory+"gray_"+extlessName+".tif")).delete();
(new File(directory+"lightcorrected_"+extlessName+".tif")).delete();
if (generateLightingCorrectionSurfaceEyeCandy)
(new File(directory+"surface_"+extlessName+".tif")).delete();
(new File(directory+"segmented_"+extlessName+".tif")).delete();
(new File(directory+"skeleton_"+extlessName+".tif")).delete();
(new File(directory+"pruned_"+extlessName+".tif")).delete();
(new File(directory+"outline_"+extlessName+".tif")).delete();
(new File(directory+"nodes_"+extlessName+".tif")).delete();
(new File(directory+"graph_"+extlessName+".tif")).delete();
(new File(directory+"merged_"+extlessName+".tif")).delete();
}
// delete all graph text files
if (keepGraphTextFiles == false) {
(new File(directory+"coord"+extlessName+".txt")).delete();
(new File(directory+"skel"+extlessName+".txt")).delete();
}
// all done cleaning!
}
}