Examples with DatasetView net.imagej.display.DatasetView used on opensource projects

Example 11 with DatasetView

use of net.imagej.display.DatasetView in project imagej-plugins-commands by imagej.

the class ExpDataValues method run.

// -- public interface --
@Override
public void run() {
    Dataset dataset = imgDispService.getActiveDataset(display);
    Overlay overlay = overlayService.getActiveOverlay(display);
    DatasetView view = imgDispService.getActiveDatasetView(display);
    final RealExp<DoubleType, DoubleType> op = new RealExp<DoubleType, DoubleType>();
    final InplaceUnaryTransform<T, DoubleType> transform;
    if (allPlanes)
        transform = new InplaceUnaryTransform<T, DoubleType>(op, new DoubleType(), dataset, overlay);
    else
        transform = new InplaceUnaryTransform<T, DoubleType>(op, new DoubleType(), dataset, overlay, view.getPlanePosition());
    transform.run();
}

Example 12 with DatasetView

use of net.imagej.display.DatasetView in project imagej-plugins-commands by imagej.

the class InvertDataValues method run.

// -- public interface --
@Override
public void run() {
    Dataset dataset = imgDispService.getActiveDataset(display);
    Overlay overlay = overlayService.getActiveOverlay(display);
    DatasetView view = imgDispService.getActiveDatasetView(display);
    OptionsCompatibility options = optionsService.getOptions(OptionsCompatibility.class);
    if (options.isInvertModeLegacy() && dataset.isInteger() && !dataset.isSigned() && dataset.getType().getBitsPerPixel() == 8) {
        min = 0;
        max = 255;
    } else
        calcValueRange(dataset);
    final RealInvert<DoubleType, DoubleType> op = new RealInvert<DoubleType, DoubleType>(min, max);
    final InplaceUnaryTransform<T, DoubleType> transform;
    if (allPlanes)
        transform = new InplaceUnaryTransform<T, DoubleType>(op, new DoubleType(), dataset, overlay);
    else
        transform = new InplaceUnaryTransform<T, DoubleType>(op, new DoubleType(), dataset, overlay, view.getPlanePosition());
    transform.run();
}

Example 13 with DatasetView

use of net.imagej.display.DatasetView in project imagej-plugins-commands by imagej.

the class AbsDataValues method run.

// -- public interface --
@Override
public void run() {
    Dataset dataset = imgDispService.getActiveDataset(display);
    Overlay overlay = overlayService.getActiveOverlay(display);
    DatasetView view = imgDispService.getActiveDatasetView(display);
    final RealAbs<DoubleType, DoubleType> op = new RealAbs<DoubleType, DoubleType>();
    final InplaceUnaryTransform<T, DoubleType> transform;
    if (allPlanes)
        transform = new InplaceUnaryTransform<T, DoubleType>(op, new DoubleType(), dataset, overlay);
    else
        transform = new InplaceUnaryTransform<T, DoubleType>(op, new DoubleType(), dataset, overlay, view.getPlanePosition());
    transform.run();
}

Example 14 with DatasetView

use of net.imagej.display.DatasetView 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 15 with DatasetView

use of net.imagej.display.DatasetView in project imagej-omero by imagej.

the class DefaultOMEROService method toOMERO.

@Override
public Object toOMERO(final omero.client client, final Object value) throws omero.ServerError, IOException, ExecutionException, DSOutOfServiceException, DSAccessException, NumberFormatException, URISyntaxException {
    if (value == null)
        return null;
    if (value instanceof Dataset) {
        // upload image to OMERO, returning the resultant image ID
        final Dataset d = (Dataset) value;
        final long imageID = uploadImage(client, d);
        // TODO: upload or update?
        if (d.getProperties().get("rois") != null)
            uploadROIs(createCredentials(client), (TreeNode<?>) d.getProperties().get("rois"), imageID);
        // TODO: Modify tables to implement Named??
        if (d.getProperties().get("tables") != null) {
            @SuppressWarnings("unchecked") final List<Table<?, ?>> tables = (List<Table<?, ?>>) d.getProperties().get("tables");
            final OMEROLocation cred = createCredentials(client);
            for (final Table<?, ?> table : tables) uploadTable(cred, d.getName() + "-table", table, imageID);
        }
        return toOMERO(client, imageID);
    }
    if (convertService.supports(value, Dataset.class))
        return toOMERO(client, convertService.convert(value, Dataset.class));
    if (value instanceof DatasetView) {
        final DatasetView datasetView = (DatasetView) value;
        // TODO: Verify whether any view-specific metadata can be preserved.
        return toOMERO(client, datasetView.getData());
    }
    if (value instanceof ImageDisplay) {
        final ImageDisplay imageDisplay = (ImageDisplay) value;
        // TODO: Support more aspects of image displays; e.g., multiple datasets.
        return toOMERO(client, imageDisplayService.getActiveDataset(imageDisplay));
    }
    if (value instanceof Table)
        return convertOMEROTable((Table<?, ?>) value);
    if (value instanceof TableDisplay)
        return toOMERO(client, ((TableDisplay) value).get(0));
    if (convertService.supports(value, Table.class))
        return toOMERO(client, convertService.convert(value, Table.class));
    if (value instanceof TreeNode) {
        return convertOMEROROI((TreeNode<?>) value, null);
    }
    if (value instanceof MaskPredicate) {
        final Object o = toOMERO(client, new DefaultTreeNode<>(value, null));
        return ((List<?>) o).get(0);
    }
    if (convertService.supports(value, TreeNode.class))
        return toOMERO(client, convertService.convert(value, TreeNode.class));
    if (convertService.supports(value, MaskPredicate.class))
        return toOMERO(client, convertService.convert(value, MaskPredicate.class));
    return toOMERO(value);
}