Examples with ImagePlus ij.ImagePlus used on opensource projects

Example 71 with ImagePlus

use of ij.ImagePlus in project TrakEM2 by trakem2.

the class PatchStack method createColor256Copy.

// WARNING This method will fail if the stack has slices of different dimensions
/**
 * Does not respect local transform of the patches, this is intended for confocal stacks.
 */
public ImagePlus createColor256Copy() {
    final Rectangle box = patch[0].getBoundingBox();
    final int width = box.width;
    final int height = box.height;
    Loader loader = patch[0].getProject().getLoader();
    // the montage, in RGB
    patch[0].getProject().getLoader().releaseToFit(4 * patch.length * width * height);
    final ColorProcessor montage = new ColorProcessor(width * patch.length, height);
    for (int i = 0; i < patch.length; i++) {
        montage.insert(this.stack.getProcessor(i + 1), i * width, 0);
    }
    final MedianCut mc = new MedianCut(montage);
    loader.releaseToFit(patch.length * width * height);
    ImageProcessor m2 = mc.convertToByte(256);
    final ImageStack st = new ImageStack(width, height);
    for (int i = 0; i < patch.length; i++) {
        m2.setRoi(i * width, 0, width, height);
        loader.releaseToFit(width * height);
        st.addSlice(null, m2.crop());
    }
    ImagePlus imp = new ImagePlus("color256", st);
    imp.setCalibration(patch[0].getLayer().getParent().getCalibrationCopy());
    // imp.getCalibration().pixelDepth = patch[0].getLayer().getThickness();
    return imp;
}

Example 72 with ImagePlus

use of ij.ImagePlus in project TrakEM2 by trakem2.

the class PatchStack method getMask.

public ImageProcessor getMask() {
    ImagePlus imp = patch[currentSlice - 1].getProject().getLoader().fetchImagePlus(patch[currentSlice - 1]);
    ImageProcessor ip = imp.getProcessor();
    Roi roi = getRoi();
    if (null == roi) {
        ip.resetRoi();
        return null;
    }
    ImageProcessor mask = roi.getMask();
    if (null == mask)
        return null;
    ip.setMask(mask);
    ip.setRoi(roi.getBounds());
    return mask;
}

Example 73 with ImagePlus

use of ij.ImagePlus in project TrakEM2 by trakem2.

the class PatchStack method setRoi.

public void setRoi(Rectangle r) {
    if (null == r) {
        killRoi();
        return;
    }
    killRoi();
    this.roi = new Roi(r.x, r.y, r.width, r.height);
    this.roi.setImage(this);
    ImagePlus imp = patch[currentSlice - 1].getProject().getLoader().fetchImagePlus(patch[currentSlice - 1]);
    ImageProcessor ip = imp.getProcessor();
    if (null != ip) {
        ip.setMask(null);
        ip.setRoi(r);
    }
// draw(); // not needed
}

Example 74 with ImagePlus

use of ij.ImagePlus in project TrakEM2 by trakem2.

the class PatchStack method trimProcessor.

public synchronized void trimProcessor() {
    if (!locked) {
        try {
            ImagePlus imp = patch[currentSlice - 1].getProject().getLoader().fetchImagePlus(patch[currentSlice - 1]);
            imp.trimProcessor();
        } catch (Exception e) {
            e.printStackTrace();
        }
    }
}

Example 75 with ImagePlus

use of ij.ImagePlus in project TrakEM2 by trakem2.

the class PatchStack method createGray8Copy.

// WARNING This method will fail if the stack has slices of different dimensions
/**
 * Does not respect local transform of the patches, this is intended for confocal stacks.
 */
public ImagePlus createGray8Copy() {
    final Rectangle box = patch[0].getBoundingBox();
    final int width = box.width;
    final int height = box.height;
    // compute minimum bounding box
    ImageStack st = new ImageStack(width, height);
    Loader loader = patch[0].getProject().getLoader();
    for (int i = 1; i < patch.length; i++) {
        loader.releaseToFit(width * height);
        st.addSlice(Integer.toString(i), this.stack.getProcessor(i).convertToByte(true));
    }
    ImagePlus imp = new ImagePlus("byte", st);
    imp.setCalibration(patch[0].getLayer().getParent().getCalibrationCopy());
    // imp.getCalibration().pixelDepth = patch[0].getLayer().getThickness();
    return imp;
}