start implementing deformation field difference

Author: StephanPreibisch

src/main/java/org/janelia/saalfeldlab/hotknife/SparkViewDeformationFieldDifference.java

@@ -0,0 +1,109 @@
+package org.janelia.saalfeldlab.hotknife;
+
+import java.io.IOException;
+import java.io.Serializable;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.concurrent.ExecutionException;
+
+import org.janelia.saalfeldlab.hotknife.util.Transform;
+import org.janelia.saalfeldlab.n5.N5FSReader;
+import org.janelia.saalfeldlab.n5.N5Reader;
+import org.kohsuke.args4j.CmdLineException;
+import org.kohsuke.args4j.CmdLineParser;
+import org.kohsuke.args4j.Option;
+
+import net.imglib2.realtransform.RealTransform;
+
+public class SparkViewDeformationFieldDifference
+{
+	/*
+	--n5Path=/nrs/hess/data/hess_wafer_53/export/hess_wafer_53_center7.n5/
+	--scaleIndex=5
+	--n5Group=/surface-align/run_20240517_200443/pass04
+	--saveDir='/home/[email protected]/workspace/hot-knife/tmp'
+	*/
+	@SuppressWarnings("serial")
+	public static class Options extends AbstractOptions implements Serializable {
+
+		@Option(name = "--n5Path", required = true, usage = "N5 path, e.g. /nrs/hess/data/hess_wafer_53/export/hess_wafer_53_center7.n5")
+		private String n5Path;
+
+		@Option(name = "--n5Group", required = false, usage = "N5 group, e.g. /surface-align/run_20240517_200443/pass04")
+		private String group = "/";
+
+		@Option(name = "--scaleIndex", required = true, usage = "scale index for visualization, e.g. 4 (means scale = 1.0 / 2^4)")
+		private int transformScaleIndex;
+
+		@Option(name = "-a", required = false, usage = "list of transformation fields (sorted as pairs with 'b'), e.g. -a flat_mask.s281_m206.bot4_clahe.face OR -a pass04/flat_mask.s281_m206.bot4_clahe.face")
+		private ArrayList<String> a = new ArrayList<>();
+
+		@Option(name = "-b", required = false, usage = "list of transformation fields (sorted as pairs with 'a'), e.g. -a flat_mask.s281_m206.top4_clahe.face")
+		private ArrayList<String> b = new ArrayList<>();
+
+		@Option(name = "-o", aliases = {"--saveDir"}, required = true, usage = "directory for saving differences in transformation fields")
+		private String saveDir;
+
+		@Option(name = "--localSparkBindAddress", required = false, usage = "specify Spark bind address as localhost")
+		private boolean localSparkBindAddress = false;
+
+		public Options(final String[] args) {
+
+			final CmdLineParser parser = new CmdLineParser(this);
+			try {
+				parser.parseArgument(args);
+
+				parsedSuccessfully = true;
+
+			} catch (final CmdLineException e) {
+				System.err.println(e.getMessage());
+				parser.printUsage(System.err);
+			}
+		}
+
+		public String getN5Path() { return n5Path; }
+		public int getScaleIndex() { return transformScaleIndex; }
+		public String saveDir() { return saveDir; }
+		public String getGroup() { return group; }
+	}
+
+	public static void main(final String... args) throws IOException, InterruptedException, ExecutionException
+	{
+
+		final SparkViewDeformationFieldDifference.Options options = new SparkViewDeformationFieldDifference.Options(args);
+		if (! options.parsedSuccessfully) {
+			throw new IllegalArgumentException("Options were not parsed successfully");
+		}
+
+		if ( options.a.size() != options.b.size() )
+			throw new RuntimeException( "size of a and b not equal." );
+
+		if ( options.a.size() == 0 )
+			throw new RuntimeException( "a and b not specified." );
+
+		final String n5Path = options.getN5Path();
+		final String n5Group = options.getGroup();
+		final int scaleIndex = options.getScaleIndex();
+		final ArrayList< String > transformANames = options.a;
+		final ArrayList< String > transformBNames = options.b;
+
+		for ( int i = 0; i < options.a.size(); ++ i )
+		{
+			final N5Reader n5 = new N5FSReader(n5Path);
+
+			final String transformA = transformANames.get( i );
+			final String transformB = transformBNames.get( i );
+
+			final double[] boundsMin = n5.getAttribute(transformA, "boundsMin", double[].class);
+			final double transformScale = n5.getAttribute(transformA, "scale", double.class);
+
+			final RealTransform tA = Transform.loadScaledTransform(n5, n5Group + "/" + transformA );
+			final RealTransform tB = Transform.loadScaledTransform(n5, n5Group + "/" + transformB );
+
+			final RealTransform sTA = Transform.createScaledRealTransform( tA, scaleIndex );
+			final RealTransform sTB = Transform.createScaledRealTransform( tB, scaleIndex );
+
+
+		}
+	}
+}