Examples with MaskPredicate net.imglib2.roi.MaskPredicate used on opensource projects

Example 1 with MaskPredicate

use of net.imglib2.roi.MaskPredicate 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);
}

Example 2 with MaskPredicate

use of net.imglib2.roi.MaskPredicate in project imagej-omero by imagej.

the class DefaultOMEROService method convertOMEROROI.

@Override
public List<ROIData> convertOMEROROI(final TreeNode<?> dataNodeRois, final Interval interval) {
    final List<ROIData> omeroROIs = new ArrayList<>();
    final List<TreeNode<?>> roiTreeNodes = collectROITreeNodes(dataNodeRois);
    for (final TreeNode<?> dn : roiTreeNodes) {
        ROIData oR;
        // interval if non-null
        if (!(dn.data() instanceof Interval) && !(dn.data() instanceof RealInterval) && dn.data() instanceof MaskPredicate && interval != null)
            oR = convertService.convert(interval((MaskPredicate<?>) dn.data(), interval), ROIData.class);
        else
            // else convert directly
            oR = convertService.convert(dn, ROIData.class);
        if (oR == null)
            throw new IllegalArgumentException("Unsupported type: " + dn.data().getClass());
        omeroROIs.add(oR);
    }
    return omeroROIs;
}

Example 3 with MaskPredicate

use of net.imglib2.roi.MaskPredicate in project imagej-omero by imagej.

the class AbstractTreeNodeToROIData method convert.

@Override
@SuppressWarnings("unchecked")
public <T> T convert(final Object src, final Class<T> dest) {
    if (src == null || dest == null)
        throw new NullPointerException();
    if (!getInputType().isInstance(src)) {
        throw new IllegalArgumentException("Expected: " + getInputType().getSimpleName() + " Received: " + src.getClass().getSimpleName());
    }
    if (!dest.isAssignableFrom(getOutputType())) {
        throw new IllegalArgumentException("Expected: " + getOutputType().getSimpleName() + " Received: " + dest.getSimpleName());
    }
    MaskPredicate<?> mp = null;
    final ROIData r = new ROIData();
    final ShapeData s = convert.convert(((TreeNode<?>) src).data(), ShapeData.class);
    if (src instanceof IntervalView) {
        final RandomAccessible<?> ra = ((IntervalView<?>) src).getSource();
        if (ra instanceof RandomAccessibleOnRealRandomAccessible) {
            final RealRandomAccessible<?> rra = ((RandomAccessibleOnRealRandomAccessible<?>) ra).getSource();
            mp = convert.convert(rra, MaskPredicate.class);
        } else
            mp = convert.convert(ra, MaskPredicate.class);
    }
    if (((TreeNode<?>) src).data() instanceof MaskPredicate)
        mp = (MaskPredicate<?>) ((TreeNode<?>) src).data();
    if (omero.getROIMapping(mp) != null) {
        final ROIData prev = omero.getROIMapping(mp);
        r.setId(prev.getId());
        // Assume there's only one shape, since only ROIData with one ShapeData is
        // equivalent to MaskPredicate
        s.setId(prev.getIterator().next().iterator().next().getId());
    }
    r.addShapeData(s);
    return (T) r;
}