/**
* This main method is used for testing. It starts ImageJ, loads a test image and starts the
* plugin.
*
* <p>User interaction is necessary, as the plugin uses a GUI.
*
* <p><a href=
* "https://github.com/imagej/minimal-ij1-plugin/blob/master/src/main/java/Process_Pixels.java"
* >see minimal-ij1-plugin on GitHub</a>
*
* @param args
*/
public static void main(final String[] args) {
EFTEMj_Debug.setDebugLevel(EFTEMj_Debug.DEBUG_FULL);
/*
* start ImageJ
*/
new ImageJ();
String baseFolder = "C:/Temp/";
final String os = System.getProperty("os.name").toLowerCase();
if (os.indexOf("nix") >= 0 || os.indexOf("nux") >= 0 || os.indexOf("aix") > 0) {
final String userHome = System.getProperty("user.home");
baseFolder = userHome + "/Downloads/";
}
/*
* Check if the test image is available. Otherwise prompt a message with
* the download link.
*/
final File testImage =
new File(baseFolder + "20140106 SM125 -20%/20140106_SR-EELS_TestImage_small.tif");
if (!testImage.exists()) {
final String url = "http://eftemj.entrup.com.de/SR-EELS_TestImage.zip";
/*
* IJ.showMessage("Test image not found", "<html>" +
* "Please download the file" + "<br />" + "<a href='" + url +
* "'>SR-EELS_TestImage.zip</a> from" + "<br/>" + url + "<br />" +
* "and extract it to 'C:\\temp\\'." + "</html>");
*/
final GenericDialog gd = new GenericDialog("Test image not found");
gd.addMessage(
"Please download the file 'SR-EELS_TestImage.zip' and extract it to '"
+ baseFolder
+ "'.");
gd.addMessage("Copy the following link, or click Ok to open it with your default browser.");
gd.addStringField("", url, url.length());
gd.showDialog();
if (gd.wasOKed()) {
try {
final URI link = new URI(url);
final Desktop desktop = Desktop.getDesktop();
desktop.browse(link);
} catch (final Exception exc) {
IJ.showMessage("An Exception occured", exc.getMessage());
return;
}
}
return;
}
/*
* open the test image
*/
final ImagePlus image =
IJ.openImage(baseFolder + "20140106 SM125 -20%/20140106_SR-EELS_TestImage_small.tif");
image.show();
/*
* run the plugin
*/
final Class<?> clazz = SR_EELS_CorrectionPlugin.class;
IJ.runPlugIn(clazz.getName(), "");
}
/*
* (non-Javadoc)
*
* @see ij.plugin.filter.PlugInFilter#run(ij.process.ImageProcessor)
*/
@Override
public void run(final ImageProcessor ip) {
/*
* Each correction contains of implementations of the abstract classes
* CoordinateCorrector and a IntensityCorrector that can be can be
* combined as you want.
*
* By using getFunctionWidth() and getFunctionBorders() the
* characterisation results are loaded and an implementation of the
* Levenberg–Marquardt algorithm (LMA) is used to fit functions to the
* discrete values.
*/
IJ.showStatus("Preparing correction...");
importer = new DataImporter(pathResults, false);
final SR_EELS_Polynomial_2D widthFunction = getFunctionWidth();
inputProcessor.setWidthFunction(widthFunction);
final SR_EELS_Polynomial_2D borderFunction = getFunctionBorders();
inputProcessor.setBorderFunction(borderFunction);
/*
* TODO: Add the used correction methods to the image title.
*/
outputProcessor = widthFunction.createOutputImage();
outputImage = new ImagePlus(title + "_corrected", outputProcessor);
final Calibration cal = new Calibration(inputImp);
cal.pixelHeight = widthFunction.getPixelHeight();
outputImage.setCalibration(cal);
final CoordinateCorrector coordinateCorrection =
new FullCoordinateCorrection(inputProcessor, outputProcessor);
final IntensityCorrector intensityCorrection =
new SimpleIntensityCorrection(inputProcessor, coordinateCorrection);
/*
* Each line of the image is a step that is visualise by the progress
* bar of ImageJ.
*/
setupProgress(outputProcessor.getHeight());
if (EFTEMj_Debug.getDebugLevel() == EFTEMj_Debug.DEBUG_FULL) {
for (int x2 = 0; x2 < outputProcessor.getHeight(); x2++) {
for (int x1 = 0; x1 < outputProcessor.getWidth(); x1++) {
final float intensity = intensityCorrection.getIntensity(x1, x2);
outputProcessor.setf(x1, x2, intensity);
}
updateProgress();
}
} else {
/*
* The ExecutorService is used to handle the multithreading. see
* http://www.vogella.com/tutorials/JavaConcurrency/article.html#
* threadpools
*/
final ExecutorService executorService =
Executors.newFixedThreadPool(Runtime.getRuntime().availableProcessors());
for (int x2 = 0; x2 < outputProcessor.getHeight(); x2++) {
final int x2Temp = x2;
executorService.execute(
new Runnable() {
@Override
public void run() {
for (int x1 = 0; x1 < outputProcessor.getWidth(); x1++) {
final float intensity = intensityCorrection.getIntensity(x1, x2Temp);
outputProcessor.setf(x1, x2Temp, intensity);
}
updateProgress();
}
});
}
executorService.shutdown();
try {
executorService.awaitTermination(30, TimeUnit.MINUTES);
} catch (final InterruptedException e) {
e.printStackTrace();
}
}
}
