Examples with ImagePlus ij.ImagePlus used on opensource projects

Example 41 with ImagePlus

use of ij.ImagePlus in project GDSC-SMLM by aherbert.

the class SpotAnalysis method imageUpdated.

/*
	 * (non-Javadoc)
	 * 
	 * @see ij.ImageListener#imageUpdated(ij.ImagePlus)
	 */
public void imageUpdated(ImagePlus imp) {
    ImagePlus from = null, to = null;
    if (imp == rawImp) {
        from = rawImp;
        to = blurImp;
    } else if (imp == blurImp) {
        from = blurImp;
        to = rawImp;
    }
    if (from != null) {
        int slice = from.getCurrentSlice();
        updateCurrentSlice(slice);
        if (to != null) {
            if (to.getCurrentSlice() != slice) {
                //System.out.println("updating image");
                to.setSlice(slice);
            //to.resetDisplayRange();
            }
        }
    }
}

Example 42 with ImagePlus

use of ij.ImagePlus in project GDSC-SMLM by aherbert.

the class PulseActivationAnalysis method displayComposite.

private void displayComposite(ImageProcessor[] images, String name) {
    // We do not yet know the size
    ImageStack stack = null;
    for (int i = 0; i < images.length; i++) {
        ImageProcessor ip = images[i];
        if (stack == null)
            stack = new ImageStack(ip.getWidth(), ip.getHeight());
        ip.setColorModel(null);
        stack.addSlice("C" + (i + 1), ip);
    }
    // Create a composite
    ImagePlus imp = new ImagePlus(name, stack);
    imp.setDimensions(images.length, 1, 1);
    CompositeImage ci = new CompositeImage(imp, IJ.COMPOSITE);
    // Make it easier to see
    //ij.plugin.ContrastEnhancerce = new ij.plugin.ContrastEnhancer();
    //double saturated = 0.35;
    //ce.stretchHistogram(ci, saturated);
    autoAdjust(ci, ci.getProcessor());
    imp = WindowManager.getImage(name);
    if (imp != null && imp.isComposite()) {
        ci.setMode(imp.getCompositeMode());
        imp.setImage(ci);
        imp.getWindow().toFront();
    } else {
        ci.show();
        imp = ci;
    }
    if (WindowManager.getWindow("Channels") == null) {
        IJ.run("Channels Tool...");
        Window w = WindowManager.getWindow("Channels");
        if (w == null)
            return;
        Window w2 = imp.getWindow();
        if (w2 == null)
            return;
        java.awt.Point p = w2.getLocation();
        p.x += w2.getWidth();
        w.setLocation(p);
    }
}

Example 43 with ImagePlus

use of ij.ImagePlus in project GDSC-SMLM by aherbert.

the class ConfigurationTemplateTest method canLoadTemplateImageFromFile.

@Test
public void canLoadTemplateImageFromFile() throws IOException {
    ConfigurationTemplate.clearTemplates();
    Assert.assertEquals(0, ConfigurationTemplate.getTemplateNamesWithImage().length);
    // Create a dummy image
    int size = 20;
    float[] pixels = new float[size * size];
    RandomGenerator r = new Well19937c();
    for (int i = pixels.length; i-- > 0; ) pixels[i] = r.nextFloat();
    ImagePlus imp = new ImagePlus("test", new FloatProcessor(size, size, pixels));
    File tmpFile = File.createTempFile("tmp", ".tif");
    tmpFile.deleteOnExit();
    IJ.save(imp, tmpFile.getPath());
    String name = "canLoadTemplateImageFromFile";
    File file = new File(Utils.replaceExtension(tmpFile.getPath(), ".xml"));
    ConfigurationTemplate.saveTemplate(name, new GlobalSettings(), file);
    Assert.assertEquals(1, ConfigurationTemplate.getTemplateNamesWithImage().length);
    ImagePlus imp2 = ConfigurationTemplate.getTemplateImage(name);
    Assert.assertNotNull(imp2);
    float[] data = (float[]) imp2.getProcessor().toFloat(0, null).getPixels();
    Assert.assertArrayEquals(pixels, data, 0);
}

Example 44 with ImagePlus

use of ij.ImagePlus in project GDSC-SMLM by aherbert.

the class BatchPeakFit method runBatch.

/**
	 * Reads the batch configuration file. For each parameter variation, create a fitting configuration. Then run the
	 * fit engine on each input image using each configuration.
	 * 
	 * @param configurationFilename
	 */
private void runBatch(String configurationFilename) {
    BatchSettings settings = loadSettings(configurationFilename);
    if (settings == null || settings.parameters.isEmpty()) {
        IJ.log("No settings for the fitting engine");
        return;
    }
    if (!new File(settings.resultsDirectory).exists()) {
        if (!new File(settings.resultsDirectory).mkdirs()) {
            IJ.log("Unable to create the results directory: " + settings.resultsDirectory);
            return;
        }
    }
    Document doc = getDefaultSettingsXmlDocument();
    if (doc == null)
        return;
    // Create XML for each variation
    ArrayList<String> xmlSettings = new ArrayList<String>();
    setParameters(settings.parameters, 0, doc, xmlSettings);
    // Run all the variants on the input images
    for (String imageFilename : settings.images) {
        ImagePlus imp = IJ.openImage(imageFilename);
        if (imp == null) {
            IJ.log("Unable to load image: " + imageFilename);
            continue;
        }
        processImage(settings, imp, xmlSettings);
    }
}

Example 45 with ImagePlus

use of ij.ImagePlus in project GDSC-SMLM by aherbert.

the class FIRE method showInputDialog.

private boolean showInputDialog() {
    ExtendedGenericDialog gd = new ExtendedGenericDialog(TITLE);
    gd.addMessage("Compute the resolution using Fourier Ring Correlation");
    gd.addHelp(About.HELP_URL);
    // Build a list of all images with a region ROI
    List<String> titles = new LinkedList<String>();
    if (WindowManager.getWindowCount() > 0) {
        for (int imageID : WindowManager.getIDList()) {
            ImagePlus imp = WindowManager.getImage(imageID);
            if (imp != null && imp.getRoi() != null && imp.getRoi().isArea())
                titles.add(imp.getTitle());
        }
    }
    ResultsManager.addInput(gd, inputOption, InputSource.MEMORY);
    ResultsManager.addInput(gd, "Input2", inputOption2, InputSource.NONE, InputSource.MEMORY);
    if (!titles.isEmpty())
        gd.addCheckbox((titles.size() == 1) ? "Use_ROI" : "Choose_ROI", chooseRoi);
    gd.showDialog();
    if (gd.wasCanceled())
        return false;
    inputOption = ResultsManager.getInputSource(gd);
    inputOption2 = ResultsManager.getInputSource(gd);
    if (!titles.isEmpty())
        chooseRoi = gd.getNextBoolean();
    if (!titles.isEmpty() && chooseRoi) {
        if (titles.size() == 1) {
            roiImage = titles.get(0);
            Recorder.recordOption("Image", roiImage);
        } else {
            String[] items = titles.toArray(new String[titles.size()]);
            gd = new ExtendedGenericDialog(TITLE);
            gd.addMessage("Select the source image for the ROI");
            gd.addChoice("Image", items, roiImage);
            gd.showDialog();
            if (gd.wasCanceled())
                return false;
            roiImage = gd.getNextChoice();
        }
        ImagePlus imp = WindowManager.getImage(roiImage);
        roiBounds = imp.getRoi().getBounds();
        roiImageWidth = imp.getWidth();
        roiImageHeight = imp.getHeight();
    } else {
        roiBounds = null;
    }
    return true;
}