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Merge pull request #230 from saalfeldlab/feature/stack-straightening
Feature: Stack straightening
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‎render-ws-java-client/src/main/java/org/janelia/render/client/StackStraighteningClient.java‎

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package org.janelia.render.client;
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import com.beust.jcommander.Parameter;
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import com.beust.jcommander.ParametersDelegate;
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import java.io.IOException;
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import java.util.ArrayList;
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import java.util.HashMap;
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import java.util.List;
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import java.util.Map;
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import mpicbg.trakem2.transform.AffineModel2D;
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import org.janelia.alignment.spec.Bounds;
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import org.janelia.alignment.spec.LeafTransformSpec;
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import org.janelia.alignment.spec.ResolvedTileSpecCollection;
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import org.janelia.alignment.spec.TileSpec;
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import org.janelia.alignment.spec.stack.StackMetaData;
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import org.janelia.render.client.parameter.CommandLineParameters;
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import org.janelia.render.client.parameter.RenderWebServiceParameters;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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/**
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* Java client for straightening a stack by gradually applying an offset
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* computed from the midpoints of the first and last layer bounding boxes.
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* <br>
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* The offset is linearly interpolated across layers:
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* layer z is moved by (z - zmin) / (zmax - zmin) * offset
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*/
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public class StackStraighteningClient {
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public static class Parameters extends CommandLineParameters {
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@ParametersDelegate
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public RenderWebServiceParameters renderWeb = new RenderWebServiceParameters();
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@Parameter(
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names = "--stack",
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description = "Name of source stack",
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required = true)
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public String stack;
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@Parameter(
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names = "--targetStack",
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description = "Name of target stack",
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required = true)
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public String targetStack;
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@Parameter(
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names = "--numberOfZLayersPerChunk",
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description = "Number of Z layers to process per chunk")
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public int numberOfZLayersPerChunk = 1000;
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}
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public static void main(final String[] args) {
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final ClientRunner clientRunner = new ClientRunner(args) {
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@Override
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public void runClient(final String[] args) throws Exception {
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final Parameters parameters = new Parameters();
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parameters.parse(args);
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LOG.info("runClient: entry, parameters={}", parameters);
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final StackStraighteningClient client = new StackStraighteningClient(parameters);
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client.straightenStack();
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}
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};
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clientRunner.run();
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}
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private final Parameters parameters;
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private final RenderDataClient renderDataClient;
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private final List<Double> zValues;
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private final double minZ;
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private final double maxZ;
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private final double zRange;
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private StackStraighteningClient(final Parameters parameters)
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throws IOException {
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this.parameters = parameters;
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this.renderDataClient = parameters.renderWeb.getDataClient();
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this.zValues = renderDataClient.getStackZValues(parameters.stack);
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if (zValues.size() < 2) {
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throw new IllegalArgumentException("Stack must have at least 2 layers for straightening");
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}
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this.minZ = zValues.get(0);
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this.maxZ = zValues.get(zValues.size() - 1);
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this.zRange = maxZ - minZ;
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if (parameters.numberOfZLayersPerChunk < 1) {
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throw new IllegalArgumentException("numberOfZLayersPerChunk must be at least 1");
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}
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}
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private void straightenStack() throws Exception {
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final StackMetaData sourceStackMetaData = renderDataClient.getStackMetaData(parameters.stack);
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renderDataClient.setupDerivedStack(sourceStackMetaData, parameters.targetStack);
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LOG.info("straightenStack: minZ={}, maxZ={}", minZ, maxZ);
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// Get bounding box midpoints for first and last layers
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final double[] firstLayerMidpoint = getLayerBoundingBoxMidpoint(minZ);
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final double[] lastLayerMidpoint = getLayerBoundingBoxMidpoint(maxZ);
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// Compute the total offset between first and last layer midpoints
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final double totalOffsetX = lastLayerMidpoint[0] - firstLayerMidpoint[0];
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final double totalOffsetY = lastLayerMidpoint[1] - firstLayerMidpoint[1];
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LOG.info("straightenStack: firstLayerMidpoint=({}, {}), lastLayerMidpoint=({}, {}), totalOffset=({}, {})",
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firstLayerMidpoint[0], firstLayerMidpoint[1],
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lastLayerMidpoint[0], lastLayerMidpoint[1],
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totalOffsetX, totalOffsetY);
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for (int start = 0; start < zValues.size(); start += parameters.numberOfZLayersPerChunk) {
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final int end = Math.min(start + parameters.numberOfZLayersPerChunk, zValues.size());
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final List<Double> zLayersChunk = zValues.subList(start, end);
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straightenLayers(zLayersChunk, totalOffsetX, totalOffsetY);
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}
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renderDataClient.setStackState(parameters.targetStack, StackMetaData.StackState.COMPLETE);
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LOG.info("straightenStack: exit, processed {} layers", zValues.size());
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}
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private double[] getLayerBoundingBoxMidpoint(final double z) throws Exception {
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final Bounds layerBounds = renderDataClient.getLayerBounds(parameters.stack, z);
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if (layerBounds == null || layerBounds.getMinX() == null) {
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throw new IllegalArgumentException("Cannot compute bounding box for layer z=" + z);
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}
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final double midX = (layerBounds.getMinX() + layerBounds.getMaxX()) / 2.0;
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final double midY = (layerBounds.getMinY() + layerBounds.getMaxY()) / 2.0;
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LOG.info("getLayerBoundingBoxMidpoint: z={}, bounds={}, midpoint=({}, {})",
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z, layerBounds, midX, midY);
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return new double[] { midX, midY };
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}
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private void straightenLayers(final List<Double> zLayersChunk,
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final double totalOffsetX,
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final double totalOffsetY)
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throws Exception {
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final Double firstZ = zLayersChunk.get(0);
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final Double lastZ = zLayersChunk.get(zLayersChunk.size() - 1);
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LOG.info("straightenLayers: entry, firstZ={}, lastZ={}", firstZ, lastZ);
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final ResolvedTileSpecCollection resolvedTiles = renderDataClient.getResolvedTiles(parameters.stack,
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firstZ,
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lastZ,
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null,
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null,
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null,
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null,
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null,
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null);
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final Map<Double, List<TileSpec>> zToTileSpecs = new HashMap<>();
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final Map<Double, LeafTransformSpec> zToTranslation = new HashMap<>();
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for (final TileSpec tileSpec : resolvedTiles.getTileSpecs()) {
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final List<TileSpec> tileSpecsForZ = zToTileSpecs.computeIfAbsent(tileSpec.getZ(),
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k -> new ArrayList<>());
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tileSpecsForZ.add(tileSpec);
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if (! zToTranslation.containsKey(tileSpec.getZ())) {
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final Double z = tileSpec.getZ();
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// Compute the interpolation factor for this layer
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// At zMin, factor = 0 (no movement)
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// At zMax, factor = 1 (full offset applied, but negated to bring it back to first layer position)
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final double factor = (z - minZ) / zRange;
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// The translation needed to straighten this layer
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final double translateX = -factor * totalOffsetX;
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final double translateY = -factor * totalOffsetY;
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final AffineModel2D translationModel = new AffineModel2D();
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translationModel.set(1, 0, 0, 1, translateX, translateY);
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zToTranslation.put(z, new LeafTransformSpec(translationModel.getClass().getName(),
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translationModel.toDataString()));
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}
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}
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for (final Double z : zLayersChunk) {
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final List<TileSpec> layerTileSpecs = zToTileSpecs.get(z);
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final LeafTransformSpec transformSpec = zToTranslation.get(z);
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for (final TileSpec tileSpec : layerTileSpecs) {
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resolvedTiles.addTransformSpecToTile(tileSpec.getTileId(),
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transformSpec,
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ResolvedTileSpecCollection.TransformApplicationMethod.PRE_CONCATENATE_LAST);
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}
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LOG.debug("straightenLayers: applied affine transform {} to {} tiles for z={}",
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transformSpec.getDataString(), layerTileSpecs.size(), z);
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}
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renderDataClient.saveResolvedTiles(resolvedTiles, parameters.targetStack, null);
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LOG.info("straightenLayers: exit, saved {} tiles for z {} to {}", resolvedTiles.getTileCount(), firstZ, lastZ);
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}
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private static final Logger LOG = LoggerFactory.getLogger(StackStraighteningClient.class);
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}

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