Add first version of BackgroundCorrectedImageUrlClient

This client points tile specs to background-corrected images

render-ws-java-client/src/main/java/org/janelia/render/client/multisem/BackgroundCorrectedImageUrlClient.java

@@ -0,0 +1,126 @@
+package org.janelia.render.client.multisem;
+
+import com.beust.jcommander.Parameter;
+import com.beust.jcommander.ParametersDelegate;
+import org.janelia.alignment.ImageAndMask;
+import org.janelia.alignment.spec.ChannelSpec;
+import org.janelia.alignment.spec.ResolvedTileSpecCollection;
+import org.janelia.alignment.spec.TileSpec;
+import org.janelia.alignment.spec.stack.StackMetaData;
+import org.janelia.render.client.ClientRunner;
+import org.janelia.render.client.RenderDataClient;
+import org.janelia.render.client.parameter.CommandLineParameters;
+import org.janelia.render.client.parameter.RenderWebServiceParameters;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.io.File;
+import java.util.List;
+import java.util.Map;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
+/**
+ * Java client to copy a stack's tiles, changing the image URL paths for all tiles in the resulting stack.
+ * In this case, the image URLs are changed to point to images that have been contrast-adjusted using the Hayworth
+ * pipeline.
+ */
+public class BackgroundCorrectedImageUrlClient {
+
+    public static class Parameters extends CommandLineParameters {
+
+        @ParametersDelegate
+        public RenderWebServiceParameters renderWeb = new RenderWebServiceParameters();
+
+        @Parameter(
+                names = "--stack",
+                description = "Name of stack from which tile specs should be read",
+                required = true)
+        private String stack;
+
+        @Parameter(
+                names = "--targetStack",
+                description = "Name of stack to which updated tile specs should be written",
+                required = true)
+        private String targetStack;
+    }
+
+    public static void main(final String[] args) {
+
+        final ClientRunner clientRunner = new ClientRunner(args) {
+            @Override
+            public void runClient(final String[] args)
+                    throws Exception {
+
+                final Parameters parameters = new Parameters();
+                parameters.parse(args);
+
+                LOG.info("runClient: entry, parameters={}", parameters);
+
+                final BackgroundCorrectedImageUrlClient client = new BackgroundCorrectedImageUrlClient(parameters);
+                client.fixStackData();
+            }
+        };
+        clientRunner.run();
+    }
+
+    private final Parameters parameters;
+
+    private final RenderDataClient renderDataClient;
+
+    private BackgroundCorrectedImageUrlClient(final Parameters parameters) {
+        this.parameters = parameters;
+        this.renderDataClient = parameters.renderWeb.getDataClient();
+    }
+
+    private void fixStackData() throws Exception {
+        final StackMetaData fromStackMetaData = renderDataClient.getStackMetaData(parameters.stack);
+
+        // remove mipmap path builder if it is defined since we did not generate mipmaps for the hacked source images
+        fromStackMetaData.setCurrentMipmapPathBuilder(null);
+
+        renderDataClient.setupDerivedStack(fromStackMetaData, parameters.targetStack);
+
+        for (final Double z : renderDataClient.getStackZValues(parameters.stack)) {
+            final ResolvedTileSpecCollection resolvedTiles = renderDataClient.getResolvedTiles(parameters.stack, z);
+            for (final TileSpec tileSpec : resolvedTiles.getTileSpecs()) {
+                fixTileSpec(tileSpec);
+            }
+            renderDataClient.saveResolvedTiles(resolvedTiles, parameters.targetStack, z);
+        }
+
+        renderDataClient.setStackState(parameters.targetStack, StackMetaData.StackState.COMPLETE);
+    }
+
+    private void fixTileSpec(final TileSpec tileSpec) {
+
+        final Integer zeroLevelKey = 0;
+
+        for (final ChannelSpec channelSpec : tileSpec.getAllChannels()) {
+
+            final Map.Entry<Integer, ImageAndMask> entry = channelSpec.getFirstMipmapEntry();
+
+            if ((entry != null) && zeroLevelKey.equals(entry.getKey())) {
+
+                final ImageAndMask sourceImageAndMask = entry.getValue();
+
+                // file:/nrs/hess/ibeammsem/system_02/wafers/wafer_60/acquisition/background_corrected/scans/scan_004/slabs/slab_0399/mfovs/mfov_0000/sfov_001.png
+                final String imageUrl = sourceImageAndMask.getImageUrl();
+                final String newUrl = imageUrl.substring(5, 62) + "/background_corrected" + imageUrl.substring(62);
+
+                final File newFile = new File(newUrl);
+                if (! newFile.exists()) {
+                    throw new IllegalArgumentException("file does not exist: " + newFile);
+                }
+
+                final ImageAndMask newImageAndMask =
+                        sourceImageAndMask.copyWithDerivedUrls("file:" + newFile.getAbsolutePath(),
+                                                               sourceImageAndMask.getMaskUrl());
+
+                channelSpec.putMipmap(zeroLevelKey, newImageAndMask);
+            }
+        }
+    }
+
+    private static final Logger LOG = LoggerFactory.getLogger(BackgroundCorrectedImageUrlClient.class);
+}

render-ws-java-client/src/main/java/org/janelia/render/client/multisem/HackImageUrlPathClient.java

@@ -22,6 +22,8 @@
 
 /**
  * Java client to copy a stack's tiles, changing the image URL paths for all tiles in the resulting stack.
+ * In this case, the image URLs are changed to point to images that have been contrast-adjusted using the Hayworth
+ * pipeline.
  *
  * @author Eric Trautman
  */