Examples with Position net.imagej.Position used on opensource projects

Example 1 with Position

use of net.imagej.Position in project imagej-ui-swing by imagej.

the class DefaultJHotDrawAdapter method updateFigure.

@Override
public void updateFigure(final OverlayView overlay, final ImageFigure figure) {
    super.updateFigure(overlay, figure);
    // Override the base: set the fill color to transparent.
    figure.set(AttributeKeys.FILL_COLOR, new Color(0, 0, 0, 0));
    final RegionOfInterest roi = overlay.getData().getRegionOfInterest();
    if (roi != null) {
        final long minX = (long) Math.floor(roi.realMin(0));
        final long maxX = (long) Math.ceil(roi.realMax(0)) + 1;
        final long minY = (long) Math.floor(roi.realMin(1));
        final long maxY = (long) Math.ceil(roi.realMax(1)) + 1;
        final ColorRGB color = overlay.getData().getFillColor();
        final IndexColorModel cm = new IndexColorModel(1, 2, new byte[] { 0, (byte) color.getRed() }, new byte[] { 0, (byte) color.getGreen() }, new byte[] { 0, (byte) color.getBlue() }, new byte[] { 0, (byte) overlay.getData().getAlpha() });
        final int w = (int) (maxX - minX);
        final int h = (int) (maxY - minY);
        final BufferedImage img = new BufferedImage(w, h, BufferedImage.TYPE_BYTE_INDEXED, cm);
        final SampleModel sm = new SinglePixelPackedSampleModel(DataBuffer.TYPE_BYTE, w, h, new int[] { 1 });
        final DataBuffer dbuncast = sm.createDataBuffer();
        assert dbuncast instanceof DataBufferByte;
        final DataBufferByte db = (DataBufferByte) dbuncast;
        final byte[] bankData = db.getData();
        final RealRandomAccess<BitType> ra = roi.realRandomAccess();
        final Position planePos = overlay.getPlanePosition();
        for (int i = 0; i < planePos.numDimensions(); i++) {
            final long position = planePos.getLongPosition(i);
            ra.setPosition(position, i + 2);
        }
        int index = 0;
        for (int j = 0; j < h; j++) {
            ra.setPosition(minY + j, 1);
            for (int i = 0; i < w; i++) {
                ra.setPosition(minX + i, 0);
                if (ra.get().get())
                    bankData[index] = -1;
                index++;
            }
        }
        final Raster raster = Raster.createRaster(sm, db, new java.awt.Point(0, 0));
        img.setData(raster);
        figure.setBounds(new Rectangle2D.Double(minX, minY, w, h));
        figure.setBufferedImage(img);
    }
}

Example 2 with Position

use of net.imagej.Position in project imagej-plugins-commands by imagej.

the class XYFlipper method process.

/**
 * Fills the output image from the input image doing coordinate
 * transformations as needed
 */
@Override
public boolean process() {
    final Img<? extends RealType<?>> inputImage = dataset.getImgPlus();
    inputAccessor = inputImage.randomAccess();
    outputAccessor = outputImage.randomAccess();
    final long width = inputDimensions[0];
    final long height = inputDimensions[1];
    long rx, ry, rw, rh;
    if (flipper.isShapePreserving() && (bounds.width > 0) && (bounds.height > 0)) {
        rx = (long) bounds.x;
        ry = (long) bounds.y;
        rw = (long) bounds.width;
        rh = (long) bounds.height;
    } else {
        rx = 0;
        ry = 0;
        rw = width;
        rh = height;
    }
    final long[] planeDims = new long[inputImage.numDimensions() - 2];
    for (int i = 0; i < planeDims.length; i++) planeDims[i] = inputDimensions[i + 2];
    final Extents extents = new Extents(planeDims);
    final Position planePos = extents.createPosition();
    if (planeDims.length == 0) {
        // 2d Dataset
        processPlane(planePos, rx, ry, rw, rh);
    } else {
        // more than two dimensions
        while (planePos.hasNext()) {
            planePos.fwd();
            processPlane(planePos, rx, ry, rw, rh);
        }
    }
    return true;
}

Example 3 with Position

use of net.imagej.Position in project imagej-plugins-commands by imagej.

the class ShowLUTAsTable method run.

// -- Command methods --
@Override
public void run() {
    final DatasetView view = imgDispService.getActiveDatasetView(display);
    final List<ColorTable> colorTables = view.getColorTables();
    final Position planePos = view.getPlanePosition();
    long pos = planePos.getIndex();
    if (pos < 0 || pos >= colorTables.size())
        pos = 0;
    final ColorTable colorTable = colorTables.get((int) pos);
    final int rowCount = colorTable.getLength();
    final int componentCount = colorTable.getComponentCount();
    final int colCount = componentCount + 1;
    table = new DefaultResultsTable(colCount, rowCount);
    table.setColumnHeader(0, "Index");
    // use here.
    for (int x = 0; x < componentCount; x++) {
        table.setColumnHeader(x + 1, "CH" + x);
    }
    // fill in values
    for (int y = 0; y < rowCount; y++) {
        table.setValue(0, y, y);
        for (int x = 0; x < componentCount; x++) {
            final double value = colorTable.get(x, y);
            table.setValue(x + 1, y, value);
        }
    }
}

Example 4 with Position

use of net.imagej.Position in project imagej-plugins-commands by imagej.

the class AddNoiseToDataValues method run.

// -- public interface --
@Override
public void run() {
    Dataset dataset = displayService.getActiveDataset(display);
    Overlay overlay = overlayService.getActiveOverlay(display);
    DatasetView view = displayService.getActiveDatasetView(display);
    Position planePos = (allPlanes) ? null : view.getPlanePosition();
    NoiseAdder<T> noiseAdder = new NoiseAdder<T>(dataset, overlay, planePos);
    noiseAdder.setStdDev(25.0);
    noiseAdder.run();
}

Example 5 with Position

use of net.imagej.Position in project imagej-plugins-commands by imagej.

the class AddSpecifiedNoiseToDataValues method run.

// -- public interface --
@Override
public void run() {
    Dataset dataset = displayService.getActiveDataset(display);
    Overlay overlay = overlayService.getActiveOverlay(display);
    DatasetView view = displayService.getActiveDatasetView(display);
    Position planePos = (allPlanes) ? null : view.getPlanePosition();
    NoiseAdder<T> noiseAdder = new NoiseAdder<T>(dataset, overlay, planePos);
    noiseAdder.setStdDev(stdDev);
    noiseAdder.run();
}