Examples with ImagePlus ij.ImagePlus used on opensource projects

Example 16 with ImagePlus

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

the class ConfigurationTemplate method displayTemplate.

/**
	 * Display the template image in an image window with the specified title. If the window exists it will be reused
	 * and the appropriate properties updated.
	 *
	 * @param title
	 *            the title
	 * @param templateImp
	 *            the template image
	 * @return the image plus
	 */
public static ImagePlus displayTemplate(String title, ImagePlus templateImp) {
    ImagePlus imp = Utils.display(title, templateImp.getStack());
    imp.setOverlay(templateImp.getOverlay());
    imp.setProperty("Info", templateImp.getProperty("Info"));
    imp.setCalibration(templateImp.getCalibration());
    return imp;
}

Example 17 with ImagePlus

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

the class BenchmarkFilterAnalysis method createBounds.

private synchronized int[] createBounds() {
    if (bounds == null) {
        ImagePlus imp = CreateData.getImage();
        if (imp != null) {
            return new int[] { imp.getWidth(), imp.getHeight() };
        }
        Rectangle bounds = results.getBounds(true);
        int maxx = bounds.x + bounds.width;
        int maxy = bounds.y + bounds.height;
        return new int[] { maxx, maxy };
    }
    return bounds;
}

Example 18 with ImagePlus

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

the class SeriesImageSource method getFrame.

/*
	 * (non-Javadoc)
	 * 
	 * @see gdsc.smlm.results.ImageSource#getFrame(int, java.awt.Rectangle)
	 */
@Override
protected float[] getFrame(int frame, Rectangle bounds) {
    if (maxz == 0 || frame < 1)
        return null;
    // Calculate the required image and slice
    int image = (frame - 1) / maxz;
    int slice = (frame - 1) % maxz;
    // Return from the cache if it exists
    if (image != lastImage || lastImageArray == null) {
        lastImageArray = null;
        lastImageSize = 0;
        if (image < images.size()) {
            ImagePlus imp = IJ.openImage(images.get(image++));
            if (imp != null) {
                lastImageArray = imp.getImageStack().getImageArray();
                lastImageSize = imp.getStackSize();
            }
        }
    }
    lastImage = image;
    if (lastImageArray != null) {
        if (slice < lastImageSize) {
            return ImageConverter.getData(lastImageArray[slice], width, height, bounds, null);
        }
    }
    return null;
}

Example 19 with ImagePlus

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

the class PSFDrift method createImageList.

public static List<String> createImageList() {
    List<String> titles = new LinkedList<String>();
    int[] ids = WindowManager.getIDList();
    if (ids != null) {
        for (int id : ids) {
            ImagePlus imp = WindowManager.getImage(id);
            if (imp != null) {
                // Image must be greyscale
                if (imp.getType() == ImagePlus.GRAY8 || imp.getType() == ImagePlus.GRAY16 || imp.getType() == ImagePlus.GRAY32) {
                    // Image must be square and a stack of a single channel
                    if (imp.getWidth() == imp.getHeight() && imp.getNChannels() == 1) {
                        // Check if these are PSF images created by the SMLM plugins
                        PSFSettings psfSettings = getPSFSettings(imp);
                        if (psfSettings != null) {
                            if (psfSettings.zCentre <= 0) {
                                Utils.log(TITLE + ": Unknown PSF z-centre setting for image: " + imp.getTitle());
                                continue;
                            }
                            if (psfSettings.nmPerPixel <= 0) {
                                Utils.log(TITLE + ": Unknown PSF nm/pixel setting for image: " + imp.getTitle());
                                continue;
                            }
                            if (psfSettings.nmPerSlice <= 0) {
                                Utils.log(TITLE + ": Unknown PSF nm/slice setting for image: " + imp.getTitle());
                                continue;
                            }
                            if (psfSettings.fwhm <= 0) {
                                Utils.log(TITLE + ": Unknown PSF FWHM setting for image: " + imp.getTitle());
                                continue;
                            }
                            titles.add(imp.getTitle());
                        }
                    }
                }
            }
        }
    }
    return titles;
}

Example 20 with ImagePlus

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

the class PSFCombiner method createImageList.

public static List<String> createImageList() {
    List<String> titles = new LinkedList<String>();
    int[] ids = WindowManager.getIDList();
    if (ids != null) {
        for (int id : ids) {
            ImagePlus imp = WindowManager.getImage(id);
            if (imp != null) {
                // Image must be greyscale
                if (imp.getType() == ImagePlus.GRAY8 || imp.getType() == ImagePlus.GRAY16 || imp.getType() == ImagePlus.GRAY32) {
                    // Image must be square and a stack of a single channel
                    if (imp.getWidth() == imp.getHeight() && imp.getNChannels() == 1) {
                        // Check if these are PSF images created by the SMLM plugins
                        if (containsPSF(imp))
                            titles.add(imp.getTitle());
                    }
                }
            }
        }
    }
    return titles;
}