Create skeleton for background correction tool

render-ws-java-client/src/main/java/org/janelia/render/client/BackgroundComputationClient.java

@@ -0,0 +1,106 @@
+package org.janelia.render.client;
+
+import com.beust.jcommander.Parameter;
+import com.beust.jcommander.ParametersDelegate;
+import org.janelia.alignment.spec.ResolvedTileSpecCollection;
+import org.janelia.render.client.parameter.CommandLineParameters;
+import org.janelia.render.client.parameter.RenderWebServiceParameters;
+import org.janelia.render.client.parameter.ZRangeParameters;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.awt.Rectangle;
+import java.io.IOException;
+
+/**
+ * Create and store a background image that can be used to subtract a
+ * spatially varying background from a set of images.
+ */
+public class BackgroundComputationClient {
+
+	private final Parameters params;
+	private final RenderDataClient renderClient;
+
+	public static class Parameters extends CommandLineParameters {
+		@ParametersDelegate
+		private final RenderWebServiceParameters renderParams = new RenderWebServiceParameters();
+		@ParametersDelegate
+		private final ZRangeParameters zRangeParams = new ZRangeParameters();
+		@Parameter(names = "--stack", description = "Stack for which to compute background", required = true)
+		private String stack;
+		@Parameter(names = "--regex", description = "Regular expression for matching tiles to use for background computation; all tiles are used if not given")
+		private String regex = null;
+		@Parameter(names = "--fileName", description = "Name of file to write background image to (default: background_<stack>.png)")
+		private String fileName = null;
+
+		public String getFileName() {
+			if (fileName == null) {
+				fileName = "background_" + stack + ".png";
+			}
+			return fileName;
+		}
+	}
+
+	public static void main(String[] args) {
+
+		if (args.length == 0) {
+			args = new String[] {
+					"--baseDataUrl", "http://renderer-dev.int.janelia.org:8080/render-ws/v1",
+					"--owner", "cellmap",
+					"--project", "jrc_mus_thymus_1",
+					"--stack", "v2_acquire_align",
+					"--minZ", "1250",
+					"--maxZ", "1253",
+					"--regex", ".*_0-[01]-1.*",
+					"--fileName", "background_test.png"
+			};
+		}
+
+		final ClientRunner clientRunner = new ClientRunner(args) {
+			@Override
+			public void runClient(final String[] args) {
+
+				final Parameters parameters = new Parameters();
+				parameters.parse(args);
+				LOG.info("runClient: entry, parameters={}", parameters);
+
+				final BackgroundComputationClient client = new BackgroundComputationClient(parameters);
+				client.computeBackground();
+			}
+		};
+		clientRunner.run();
+	}
+
+	public BackgroundComputationClient(final Parameters parameters) {
+		this.params = parameters;
+		this.renderClient = new RenderDataClient(parameters.renderParams.baseDataUrl, parameters.renderParams.owner, parameters.renderParams.project);
+	}
+
+	public void computeBackground() {
+		final ResolvedTileSpecCollection tileSpecs = getTileSpecs();
+		final Rectangle backgroundBounds = tileSpecs.toBounds().toRectangle();
+
+		System.out.println("Fetched " + tileSpecs.getTileCount() + " tile specs, bounds: " + backgroundBounds);
+	}
+
+	private ResolvedTileSpecCollection getTileSpecs() {
+		ResolvedTileSpecCollection tileSpecs = null;
+		try {
+			tileSpecs = renderClient.getResolvedTiles(params.stack,
+													  params.zRangeParams.minZ,
+													  params.zRangeParams.maxZ,
+													  null,
+													  null,
+													  null,
+													  null,
+													  null,
+													  params.regex);
+		} catch (final IOException e) {
+			LOG.error("Could not get tile specs: ", e);
+			System.exit(1);
+		}
+		return tileSpecs;
+	}
+
+	private static final Logger LOG = LoggerFactory.getLogger(BackgroundComputationClient.class);
+}