Merge remote-tracking branch 'origin/master'

saalfeldlab · Jun 11, 2024 · 27e12fe · 27e12fe
2 parents c66a8c1 + a9d3b36
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diff --git a/src/test/java/org/janelia/saalfeldlab/hotknife/MultiSemMovieWafer53_Berlin.java b/src/test/java/org/janelia/saalfeldlab/hotknife/MultiSemMovieWafer53_Berlin.java
@@ -0,0 +1,271 @@
+/**
+ * License: GPL
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 2
+ * as published by the Free Software Foundation.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
+ */
+package org.janelia.saalfeldlab.hotknife;
+
+import java.awt.Graphics2D;
+import java.awt.Window;
+import java.awt.image.BufferedImage;
+import java.io.File;
+import java.io.IOException;
+import java.util.concurrent.Callable;
+import java.util.concurrent.ExecutionException;
+
+import javax.imageio.ImageIO;
+import javax.swing.SwingUtilities;
+
+import bdv.cache.CacheControl;
+import bdv.util.BdvFunctions;
+import bdv.util.BdvOptions;
+import bdv.util.BdvStackSource;
+import bdv.util.RandomAccessibleIntervalMipmapSource;
+import bdv.util.volatiles.SharedQueue;
+import bdv.viewer.Interpolation;
+import bdv.viewer.Source;
+import bdv.viewer.ViewerPanel;
+import bdv.viewer.ViewerState;
+import bdv.viewer.animate.SimilarityTransformAnimator;
+import bdv.viewer.overlay.MultiBoxOverlayRenderer;
+import bdv.viewer.overlay.ScaleBarOverlayRenderer;
+import bdv.viewer.render.MultiResolutionRenderer;
+import bdv.viewer.render.PainterThread;
+import ij.process.ColorProcessor;
+import net.imglib2.multithreading.SimpleMultiThreading;
+import net.imglib2.realtransform.AffineTransform3D;
+import picocli.CommandLine;
+import picocli.CommandLine.Command;
+
+/**
+ *
+ * @author Stephan Saalfeld &lt;[email protected]&gt;
+ */
+@Command
+public class MultiSemMovieWafer53_Berlin implements Callable<Void> {
+
+	/* some parameters */
+	private final int screenWidth = 1280;
+	private final int screenHeight = 800;
+	private final String outDir = "/groups/scicompsoft/home/preibischs/recordMultiSemWafer53-Berlin/";
+	private final String n5Path = "/nrs/hess/data/hess_wafer_53/export/hess_wafer_53_center7.n5/";
+	private final String n5Group = "/wafer-53-align/run_20240604_104500/pass12";//12";//"/wafer-52-align/run_20230329_104500/pass12";
+
+	private final AffineTransform3D viewerScale = new AffineTransform3D();
+	private final AffineTransform3D viewerTranslation = new AffineTransform3D();
+	{
+		viewerScale.set(
+				1.0, 0, 0, 0,
+				0, 1.0, 0, 0,
+				0, 0, 1.0, 0);
+		viewerTranslation.set(
+				1, 0, 0, 0.5 * screenWidth,
+				0, 1, 0, 0.5 * screenHeight,
+				0, 0, 1, 0);
+	}
+
+	private void recordMovie(
+			final ViewerPanel viewer,
+			final int width,
+			final int height,
+			final AffineTransform3D[] transforms,
+			final int[] frames,
+			final int[] accel,
+			final int firstTransformIndex,
+			final String dir) throws IOException {
+
+		final ViewerState renderState = viewer.state();
+		final ScaleBarOverlayRenderer scalebar = new ScaleBarOverlayRenderer();
+		final MultiBoxOverlayRenderer box = new MultiBoxOverlayRenderer(width, height);
+
+		final VNCMovie.Target target = new VNCMovie.Target(width, height);
+
+		final MultiResolutionRenderer renderer = new MultiResolutionRenderer(
+				target,
+				new PainterThread(null),
+				new double[]{1.0},
+				0l,
+				12,
+				null,
+				false,
+				viewer.getOptionValues().getAccumulateProjectorFactory(),
+				new CacheControl.Dummy());
+
+		/* count i up to firstFrame */
+		int i = 0;
+		for (int k = 0; k < firstTransformIndex; ++k)
+			i += frames[k];
+
+		for (int k = firstTransformIndex; k < transforms.length; ++k) {
+			final SimilarityTransformAnimator animator = new SimilarityTransformAnimator(
+					transforms[k - 1],
+					transforms[k],
+					width / 2,
+					height / 2,
+					0);
+
+			for (int d = 0; d < frames[k]; ++d) {
+				final AffineTransform3D tkd = animator.get(VNCMovie.accel((double)d / (double)frames[k], accel[k]));
+				tkd.preConcatenate(viewerTranslation.inverse());
+				tkd.preConcatenate(viewerScale);
+				tkd.preConcatenate(viewerTranslation);
+				viewer.state().setViewerTransform(tkd);
+				renderState.setViewerTransform(tkd);
+				renderer.requestRepaint();
+				try {
+					renderer.paint(renderState);
+				} catch (final Exception e) {
+					e.printStackTrace();
+					return;
+				}
+
+				/* clahe */
+				final BufferedImage bi = target.renderResult.getBufferedImage();
+				final ColorProcessor ip = new ColorProcessor(bi);
+//				final ImagePlus imp = new ImagePlus("", ip);
+//				Flat.getFastInstance().run(imp, 128, 256, 1.5f, null, false);
+
+				final Graphics2D g2 = bi.createGraphics();
+				g2.drawImage(ip.createImage(), 0, 0, null);
+
+				/* scalebar */
+				g2.setClip(0, 0, width, height);
+				scalebar.setViewerState(renderState);
+				scalebar.paint(g2);
+				box.setViewerState(renderState);
+				box.paint(g2);
+
+				/* save image */
+				ImageIO.write(bi, "png", new File(String.format("%s/img-%04d.png", dir, i++)));
+
+				System.out.println(String.format("%s/img-%04d.png", dir, i));
+			}
+		}
+	}
+
+	public static final void main(final String... args) throws IOException, InterruptedException, ExecutionException {
+
+		new CommandLine(new MultiSemMovieWafer53_Berlin()).execute(args);
+	}
+
+	@Override
+	public final Void call() throws IOException, InterruptedException, ExecutionException {
+
+		final RandomAccessibleIntervalMipmapSource<?> mipmapSource = VNCMovie.createMipmapSource( n5Path, n5Group, false, true, false );
+
+		boolean setUpTransforms = false;
+		final BdvStackSource<?> bdv;
+
+		if ( setUpTransforms )
+		{
+			// volatile for setting up transformations
+			bdv = BdvFunctions.show((Source)mipmapSource.asVolatile(new SharedQueue(Math.max(1, Runtime.getRuntime().availableProcessors() - 1))));
+			bdv.getBdvHandle().getViewerPanel().setInterpolation(Interpolation.NLINEAR);
+			bdv.getBdvHandle().getViewerPanel().setCanvasSize(screenWidth, screenHeight);
+			final Window frame = SwingUtilities.getWindowAncestor(bdv.getBdvHandle().getViewerPanel());
+			frame.setSize(screenWidth, screenHeight);
+			SimpleMultiThreading.threadHaltUnClean();
+		}
+		else
+		{
+			// non-volatile for movie
+			bdv = BdvFunctions.show(mipmapSource, BdvOptions.options().numRenderingThreads((Runtime.getRuntime().availableProcessors() - 1)));
+			bdv.getBdvHandle().getViewerPanel().setInterpolation(Interpolation.NLINEAR);
+			bdv.getBdvHandle().getViewerPanel().setCanvasSize(screenWidth, screenHeight);
+			final Window frame = SwingUtilities.getWindowAncestor(bdv.getBdvHandle().getViewerPanel());
+			frame.setSize(screenWidth, screenHeight);
+
+			Thread.sleep(2000);
+		}
+
+		/* animate */
+		final AffineTransform3D[] transforms = new AffineTransform3D[10];
+		final int[] frames = new int[transforms.length];
+		final int[] accel  = new int[transforms.length];
+
+		transforms[0] = new AffineTransform3D();
+		transforms[0].set(0.0122538061665851, 0.0, 0.0, -474.67919207417896, 0.0, 0.012253806166585099, 4.0813373236309525E-18, -463.19387309691666, 0.0, -4.0813373236309525E-18, 0.012253806166585099, 0.005);
+		frames[0] = 0;
+		accel[0] = 0;
+
+		transforms[1] = new AffineTransform3D(); // z=0
+		transforms[1].set(0.0122538061665851, 0.0, 0.0, -474.67919207417896, 0.0, 0.012253806166585099, 4.0813373236309525E-18, -463.19387309691666, 0.0, -4.0813373236309525E-18, 0.012253806166585099, 0.005);
+		frames[1] = 0;
+		accel[1] = 0;
+
+		transforms[2] = new AffineTransform3D(); // z=end
+		transforms[2].set(0.0122538061665851, 0.0, 0.0, -474.67919207417896, 0.0, 0.012253806166585099, 4.0813373236309525E-18, -463.19387309691666, 0.0, -4.0813373236309525E-18, 0.012253806166585099, -159.16833904313424);
+		frames[2] = 160;
+		accel[2] = 0;
+
+		transforms[3] = new AffineTransform3D(); // z=middle+zoom-in
+		transforms[3].set(6.579532889242826E-17, 0.6376821067782059, 1.4159387146732836E-16, -22266.147865369756, -0.6376821067782059, 6.579532889242826E-17, 0.0, 23708.05356588698, 0.0, -1.415938714673285E-16, 0.6376821067782059, -3993.4537357004856);
+		frames[3] = 120;
+		accel[3] = 0;
+
+		transforms[4] = new AffineTransform3D(); // step through z
+		transforms[4].set(1.4159387146732836E-16, 0.6376821067782059, 2.0784318863440765E-16, -22266.147865369756, -0.6376821067782059, 1.4159387146732836E-16, -6.374851374646151E-17, 23708.05356588698, -6.374851374646156E-17, -2.078431886344076E-16, 0.6376821067782059, -4502.453735700481);
+		frames[4] = 240;
+		accel[4] = 0;
+
+		transforms[5] = new AffineTransform3D(); // all slabs orthogonal 
+		transforms[5].set(1.0512578058281057E-18, 1.6517096550903686E-17, 0.0951089894453882, -620.619890088475, -5.2796094965550275E-18, 0.0951089894453882, -1.6517096550903683E-17, -3233.723408947371, -0.0951089894453882, -1.0559218993110087E-17, 6.330867302383132E-18, 3523.330399871545);
+		frames[5] = 30;
+		accel[5] = 0;
+
+		/*
+		transforms[6] = new AffineTransform3D(); // go through slabs  
+		transforms[6].set(1.0512578058281057E-18, 1.6517096550903686E-17, 0.0951089894453882, -620.619890088475, -5.2796094965550275E-18, 0.0951089894453882, -1.6517096550903683E-17, -3233.723408947371, -0.0951089894453882, -1.0559218993110087E-17, 6.330867302383132E-18, 3363.330399871545 );
+		frames[6] = 150;
+		accel[6] = 0;
+
+		transforms[7] = new AffineTransform3D(); // turn around axis
+		transforms[7].set( 0.09510898944538818 -1.5407439555097887E-33, 1.0559218993110086E-17, -3310.3303998715437, 1.5407439555097887E-33, 0.09510898944538819, 1.9845370556821E-33, -3233.72340894737, -1.0559218993110086E-17, -4.3543850344344235E-34, 0.09510898944538818, -673.6198900884727 );
+		frames[7] = 60;
+		accel[7] = 0;
+		*/
+
+		transforms[6] = new AffineTransform3D(); // go through slabs and zoom in at the same time 
+		transforms[6].set(3.0908166389664937E-16, 2.031029209420573E-16, 1.391980066352003, -11217.100597845474, -1.1590562396124324E-16, 1.391980066352003, -2.031029209420573E-16, -46183.47172595864, -1.391980066352003, -1.159056239612432E-16, 3.0908166389664937E-16, 49224.462382340185 );
+		frames[6] = 240;
+		accel[6] = 0;
+
+		transforms[7] = new AffineTransform3D(); // turn around axis
+		transforms[7].set( 1.391980066352003, 4.930380657631324E-32, 0.0, -49182.46238234019, -2.465190328815662E-32, 1.391980066352003, -2.5736218481063475E-32, -46183.47172595865, 0.0, -1.0843151929068615E-33, 1.391980066352003, -11259.100597845456 );
+		frames[7] = 30;
+		accel[7] = 0;
+
+		transforms[8] = new AffineTransform3D(); // back to start
+		transforms[8].set(0.0122538061665851, 0.0, 0.0, -474.67919207417896, 0.0, 0.012253806166585099, 4.0813373236309525E-18, -463.19387309691666, 0.0, -4.0813373236309525E-18, 0.012253806166585099, 0.005);
+		frames[8] = 60;
+		accel[8] = 0;
+
+		transforms[9] = new AffineTransform3D();
+		transforms[9].set(0.0122538061665851, 0.0, 0.0, -474.67919207417896, 0.0, 0.012253806166585099, 4.0813373236309525E-18, -463.19387309691666, 0.0, -4.0813373236309525E-18, 0.012253806166585099, 0.005);
+		frames[9] = 3;
+		accel[9] = 0;
+
+		recordMovie(
+				bdv.getBdvHandle().getViewerPanel(),
+				screenWidth,
+				screenHeight,
+				transforms,
+				frames,
+				accel,
+				1,
+				outDir);
+
+		return null;
+	}
+}
diff --git a/src/test/java/org/janelia/saalfeldlab/hotknife/VNCMovie.java b/src/test/java/org/janelia/saalfeldlab/hotknife/VNCMovie.java
@@ -273,7 +273,19 @@ public static RandomAccessibleIntervalMipmapSource<UnsignedByteType> createMipma
 
 			if ( invert )
 			{
-				img = Converters.convertRAI( img, (in,out) -> { if (in.get() == 0) { out.set( 0 ); } else { out.set( 255 - in.get() );} }, new UnsignedByteType() );
+				final RandomAccessibleInterval< UnsignedByteType > imgFinal = img;
+
+				img = Lazy.process(
+						imgFinal,
+						new int[] {128, 128, 128},
+						new UnsignedByteType(),
+						AccessFlags.setOf(AccessFlags.VOLATILE),
+						out -> {
+							Views.flatIterable(Views.interval(Views.pair(imgFinal, out), out)).forEach(
+									//pair -> { if (pair.getA().get() == 0) { pair.getB().set( 0 ); } else { pair.getB().set( 255 - pair.getA().get() );} }
+									pair -> pair.getB().set(255 - pair.getA().get())
+							);
+						});
 			}
 
 			if ( normalizeContrast )