Fixes ##1163

pom.xml

@@ -9,7 +9,7 @@
 
     <groupId>org.embl.mobie</groupId>
     <artifactId>mobie-viewer-fiji</artifactId>
-    <version>5.0.9</version>
+    <version>5.0.11</version>
 
     <!-- force javadoc generation to fetch errors:    -->
     <!-- mvn javadoc:javadoc | grep error -->

src/main/java/org/embl/mobie/command/context/AbstractTransformationCommand.java

@@ -66,8 +66,9 @@ public abstract class AbstractTransformationCommand extends DynamicCommand imple
     public String selectedSourceName;
 
     @Parameter ( label = "Transformed image(s) suffix",
-            description = "Upon transformation this suffix will be appended to the moving image(s).\n" +
-                    "Carefully choose a meaningful suffix here that will create a unique new image name.")
+            description = "Upon transformation this suffix will be appended to the moving image name.\n" +
+                    "Carefully choose a meaningful suffix here that will create a unique new image name.\n" +
+                    "If you leave this empty the input image view will be overwritten.")
     public String suffix = "transformed";
 
     // Too complex to maintain right now
@@ -134,7 +135,9 @@ protected void createAndSaveAffineTransformedImages(
     {
         for ( Image< ? > movingImage : movingImages )
         {
-            String transformedImageName = movingImage.getName() + "-" + suffix;
+            String transformedImageName = movingImage.getName();
+            if ( ! suffix.isEmpty() )
+                transformedImageName += "-" + suffix;
 
             AffineTransformation affineTransformation = new AffineTransformation(
                     suffix,

src/main/java/org/embl/mobie/command/context/ManualTransformationCommand.java

@@ -80,7 +80,7 @@ public void startManualTransform()
 		transformationEditor.setActive( true );
 
 		getInfo().getMutableInput( "status", String.class )
-				.setValue( this, "Status: You are transforming " + selectedSourceName + "...");
+				.setValue( this, "Status: You are transforming \"" + selectedSourceName + "\"...");
 	}
 
 	private void acceptManualTransform()

src/main/java/org/embl/mobie/command/open/project/OpenMoBIEProjectCommand.java

@@ -32,11 +32,13 @@
 import org.embl.mobie.MoBIE;
 import org.embl.mobie.MoBIESettings;
 import org.embl.mobie.command.CommandConstants;
+import org.embl.mobie.lib.MoBIEHelper;
 import org.embl.mobie.lib.io.DataFormats;
 import org.scijava.command.Command;
 import org.scijava.plugin.Parameter;
 import org.scijava.plugin.Plugin;
 
+import java.io.File;
 import java.io.IOException;
 
 
@@ -46,7 +48,7 @@ public class OpenMoBIEProjectCommand implements Command
 	static { net.imagej.patcher.LegacyInjector.preinit(); }
 
 	@Parameter ( label = "Project Location" )
-	public String projectLocation = "https://github.com/mobie/platybrowser-datasets";
+	public File projectLocation = new File( "https://github.com/mobie/platybrowser-datasets" );
 
 	@Parameter ( label = "Preferentially Fetch Data From", choices = {"Remote", "Local"} )
 	public String location = "Remote";
@@ -60,7 +62,7 @@ public void run()
 
 		try
 		{
-			new MoBIE( projectLocation, settings );
+			new MoBIE( MoBIEHelper.toURI( projectLocation ), settings );
 		}
 		catch ( IOException e )
 		{

src/main/java/org/embl/mobie/command/open/project/OpenMoBIEProjectExpertCommand.java

@@ -29,20 +29,23 @@
 package org.embl.mobie.command.open.project;
 
 import org.embl.mobie.command.CommandConstants;
+import org.embl.mobie.lib.MoBIEHelper;
 import org.embl.mobie.lib.ThreadHelper;
 import org.embl.mobie.lib.bdv.view.SliceViewer;
 import org.scijava.command.Command;
 import org.scijava.plugin.Parameter;
 import org.scijava.plugin.Plugin;
 
+import java.io.File;
+
 @Plugin(type = Command.class, menuPath = CommandConstants.MOBIE_PLUGIN_OPEN_PROJECT + "Open MoBIE Project Expert Mode..." )
 public class OpenMoBIEProjectExpertCommand extends OpenMoBIEProjectBranchCommand
 {
 	@Parameter ( label = "Image Data Location" )
-	public String imageDataLocation = "https://github.com/platybrowser/platybrowser";
+	public File imageDataLocation = new File( "https://github.com/platybrowser/platybrowser" );
 
 	@Parameter ( label = "Table Data Location" )
-	public String tableDataLocation = "https://github.com/platybrowser/platybrowser";
+	public File tableDataLocation = new File( "https://github.com/platybrowser/platybrowser" );
 
 	@Parameter ( label = "Table Data Branch" )
 	public String tableDataBranch = "master";
@@ -60,8 +63,8 @@ public void run()
 		ThreadHelper.setNumIoThreads( numThreads );
 
 		settings.gitProjectBranch( projectBranch )
-				.imageDataLocation( imageDataLocation )
-				.tableDataLocation( tableDataLocation )
+				.imageDataLocation( MoBIEHelper.toURI( imageDataLocation ) )
+				.tableDataLocation( MoBIEHelper.toURI( tableDataLocation ) )
 				.gitTablesBranch( tableDataBranch );
 
 		super.run();

src/main/java/org/embl/mobie/lib/MoBIEHelper.java

@@ -35,6 +35,8 @@
 import net.imglib2.Cursor;
 import net.imglib2.RandomAccessibleInterval;
 import net.imglib2.type.numeric.RealType;
+import net.imglib2.util.Intervals;
+import net.imglib2.util.ValuePair;
 import net.imglib2.view.Views;
 import org.embl.mobie.io.ImageDataOpener;
 import org.embl.mobie.io.github.GitHubUtils;
@@ -47,10 +49,7 @@
 import java.nio.file.Path;
 import java.nio.file.Paths;
 import java.text.DecimalFormat;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.List;
+import java.util.*;
 import java.util.concurrent.atomic.AtomicInteger;
 import java.util.concurrent.atomic.AtomicLong;
 import java.util.regex.Matcher;
@@ -312,6 +311,25 @@ public static List< String > getFullPaths( String regex, String root )
 		}
 	}
 
+	public static double[] estimateMinMax(
+			RandomAccessibleInterval<? extends RealType<?> > rai)
+	{
+		Cursor<? extends RealType<?>> cursor = Views.iterable(rai).cursor();
+		if (!cursor.hasNext()) return new double[]{0, 255};
+		long stepSize = Intervals.numElements(rai) / 10000 + 1;
+		int randomLimit = (int) Math.min(Integer.MAX_VALUE, stepSize);
+		Random random = new Random(42);
+		double min = cursor.next().getRealDouble();
+		double max = min;
+		while (cursor.hasNext()) {
+			double value = cursor.get().getRealDouble();
+			cursor.jumpFwd(stepSize + random.nextInt(randomLimit));
+			min = Math.min(min, value);
+			max = Math.max(max, value);
+		}
+		return new double[]{min, max};
+	}
+
 	public static <T extends RealType<T> > double[] computeMinMax( RandomAccessibleInterval<T> rai) {
 		Cursor<T> cursor = Views.iterable(rai).cursor();
 

src/main/java/org/embl/mobie/lib/create/ui/ProjectsCreatorUI.java

@@ -336,14 +336,14 @@ private void addButtonsPanel() {
 
         remoteButton.addActionListener( e ->
         {
-            new Thread( () -> { remoteMetadataSettingsDialog(); } ).start();
+            new Thread( this::remoteMetadataSettingsDialog ).start();
         } );
 
         openMoBIEButton.addActionListener( e ->
         {
             new Thread( () -> {
                 OpenMoBIEProjectCommand openMoBIE = new OpenMoBIEProjectCommand();
-                openMoBIE.projectLocation = this.projectCreator.getProjectLocation().getAbsolutePath();
+                openMoBIE.projectLocation = new File( this.projectCreator.getProjectLocation().getAbsolutePath() );
                 openMoBIE.run();
             } ).start();
         } );

src/main/java/org/embl/mobie/lib/files/ImageFileSources.java

@@ -35,6 +35,7 @@
 import net.imglib2.Volatile;
 import net.imglib2.realtransform.AffineTransform3D;
 import org.apache.commons.io.FilenameUtils;
+import org.embl.mobie.DataStore;
 import org.embl.mobie.MoBIE;
 import org.embl.mobie.io.ImageDataOpener;
 import org.embl.mobie.io.imagedata.ImageData;
@@ -51,6 +52,7 @@
 import tech.tablesaw.api.StringColumn;
 import tech.tablesaw.api.Table;
 
+import javax.xml.crypto.Data;
 import java.io.File;
 import java.util.*;
 
@@ -180,17 +182,19 @@ protected static boolean isCellProfilerColumn( String column, Table table )
 	private void setMetadata( Integer channelIndex )
 	{
 		metadataSource = nameToFullPath.keySet().iterator().next();
-		IJ.log( "Fetching metadata from " + nameToFullPath.get( metadataSource ) );
+		IJ.log( "Fetching metadata for channel " + channelIndex + "..." );
+		IJ.log( "...from image file " + nameToFullPath.get( metadataSource ) );
+		// FIXME: Cache the image data, because for multiple images it is now reloaded!
 		ImageData< ? > imageData = ImageDataOpener.open( nameToFullPath.get( metadataSource ) );
 		CanonicalDatasetMetadata canonicalDatasetMetadata = imageData.getMetadata( channelIndex );
 		metadata = new Metadata( canonicalDatasetMetadata );
 		Source< ? > source = imageData.getSourcePair( channelIndex ).getA();
 		metadata.numZSlices = (int) source.getSource( 0, 0  ).dimension( 2 );
 		metadata.numTimePoints = SourceHelper.getNumTimePoints( source );
-		metadata.contrastLimits = MoBIEHelper.computeMinMax( ( RandomAccessibleInterval ) source.getSource( 0, source.getNumMipmapLevels() -1 ) );
+		metadata.contrastLimits = MoBIEHelper.estimateMinMax( ( RandomAccessibleInterval ) source.getSource( 0, source.getNumMipmapLevels() -1 ) );
 		IJ.log( "Slices: " + metadata.numZSlices );
 		IJ.log( "Frames: " + metadata.numTimePoints );
-		IJ.log( "Min, max: " + Arrays.toString( metadata.contrastLimits ) );
+		IJ.log( "Contrast limits: " + Arrays.toString( metadata.contrastLimits ) );
 	}
 
 	private static String applyPathMapping( String pathMapping, String path )

src/main/java/org/embl/mobie/lib/source/SourceHelper.java

@@ -38,19 +38,18 @@
 import bdv.viewer.Source;
 import mpicbg.spim.data.sequence.FinalVoxelDimensions;
 import mpicbg.spim.data.sequence.VoxelDimensions;
-import net.imglib2.FinalRealInterval;
-import net.imglib2.Interval;
-import net.imglib2.Point;
-import net.imglib2.RandomAccessibleInterval;
-import net.imglib2.RealInterval;
-import net.imglib2.RealPoint;
+import net.imglib2.*;
 import net.imglib2.realtransform.AffineTransform3D;
 import net.imglib2.roi.RealMaskRealInterval;
 import net.imglib2.roi.geom.GeomMasks;
 import net.imglib2.roi.geom.real.WritableBox;
+import net.imglib2.type.numeric.RealType;
 import net.imglib2.util.Intervals;
+import net.imglib2.util.ValuePair;
+import net.imglib2.view.Views;
 import org.embl.mobie.lib.bdv.CalibratedMousePositionProvider;
 import org.jetbrains.annotations.NotNull;
+import sc.fiji.bdvpg.sourceandconverter.SourceAndConverterHelper;
 
 import java.lang.reflect.Field;
 import java.util.*;
@@ -60,7 +59,6 @@
 
 public abstract class SourceHelper
 {
-
 	public static < T > T unwrapSource( Source source, Class< T > clazz )
 	{
 		if ( source == null )
@@ -375,4 +373,5 @@ public static boolean isPositionWithinSourceInterval( Source< ? > source, RealPo
 //		}
 //		else {
 	}
+
 }

src/main/java/org/embl/mobie/ui/UserInterfaceHelper.java

@@ -37,13 +37,15 @@
 import de.embl.cba.tables.SwingUtils;
 import ij.IJ;
 import ij.gui.GenericDialog;
+import net.imglib2.RandomAccessibleInterval;
 import net.imglib2.converter.Converter;
 import net.imglib2.display.ColorConverter;
 import net.imglib2.realtransform.AffineTransform3D;
 import net.imglib2.type.numeric.ARGBType;
 import org.embl.mobie.command.context.ConfigureSegmentRenderingCommand;
 import org.embl.mobie.io.util.IOHelper;
 import org.embl.mobie.MoBIE;
+import org.embl.mobie.lib.MoBIEHelper;
 import org.embl.mobie.lib.io.FileLocation;
 import org.embl.mobie.lib.MoBIEInfo;
 import org.embl.mobie.lib.Services;
@@ -488,7 +490,6 @@ public static JFrame showOpacityAndContrastLimitsDialog(
 		selection.setUpdateListener( opacityUpdateListener );
 		panel.add( opacitySlider );
 
-
 		if ( addContrastLimitUI )
 		{
 			// Contrast Limits
@@ -503,7 +504,6 @@ public static JFrame showOpacityAndContrastLimitsDialog(
 					.map( sac -> sac.getConverter() )
 					.collect( Collectors.toList() );
 
-
 			final double currentContrastLimitsMin = converterSetups.get( 0 ).getDisplayRangeMin();
 			final double currentContrastLimitsMax = converterSetups.get( 0 ).getDisplayRangeMax();
 			final double absCurrentRange = Math.abs( currentContrastLimitsMax - currentContrastLimitsMin );
@@ -548,6 +548,18 @@ public static JFrame showOpacityAndContrastLimitsDialog(
 			panel.add( minSlider );
 			panel.add( maxSlider );
 
+			JButton autoButton = new JButton("Auto Min Max");
+			autoButton.addActionListener( e ->
+			{
+				Source< ? > source = sacs.get( 0 ).getSpimSource();
+				RandomAccessibleInterval< ? > rai = source.getSource( bdvHandle.getViewerPanel().state().getCurrentTimepoint(),
+						source.getNumMipmapLevels() - 1 );
+				double[] minMax = MoBIEHelper.estimateMinMax( ( RandomAccessibleInterval ) rai );
+				min.setCurrentValue( minMax[ 0 ] );
+				max.setCurrentValue( minMax[ 1 ] );
+			});
+			panel.add( autoButton );
+
 			boolean isInvert = false;
 			for ( Converter< ?, ARGBType > converter : converters )
 			{

src/test/java/projects/muscle_patterning_drosophila/OpenTeresaData.java

@@ -41,15 +41,37 @@ public static void main( String[] args )
         final ImageJ imageJ = new ImageJ();
         imageJ.ui().showUI();
 
+//        OpenTableCommand command = new OpenTableCommand();
+//        command.table = new File( "/Users/tischer/Desktop/teresa/summary_calculated1_subset.txt" );
+//        command.root = command.table.getParentFile();
+//        command.images = "FileName_Result.Image_IMG"; // Result.Image.Zarr
+//        command.gridType = GridType.Transformed; // TODO: not working with Stitched!
+//        command.run();
+
         OpenTableCommand command = new OpenTableCommand();
-        //command.table = new File( "/Volumes/almf/group/Aliaksandr/User_data/Furlong_CrispR/test_data_20231018/20231004/20231004-172458/summary_calculated1.txt" );
-        //command.table = new File( "/Volumes/almf/group/Aliaksandr/User_data/Furlong_CrispR/test_data_20231018/20231004/20231004-172458/summary_calculated1_subset.txt" );
-        command.table = new File( "/Users/tischer/Desktop/teresa/summary_calculated1_subset.txt" );
-        //command.table = new File( "/Volumes/cba/exchange/furlong_test/summary_calculated1_subset_zarr.txt" );
-        //command.images = "Result.Image.Zarr"; // Result.Image.Zarr
+        command.table = new File( "/Volumes/CRISPR_project_data/test_data_new/20231122-170451/summary_new.txt" );
         command.root = command.table.getParentFile();
-        command.images = "FileName_Result.Image_IMG"; // Result.Image.Zarr
+        command.images = "FileName_Result.Image_IMG";
         command.gridType = GridType.Transformed; // TODO: not working with Stitched!
         command.run();
+
+        /*
+        TODO:
+
+        Why is it fetching so much metadata?? It is opening the same data again for all channels.
+
+        Also initialisation is slow...
+
+        Min, max: [6.0, 2608.0]
+        Fetching metadata from /Volumes/CRISPR_project_data/test_data_new/20231122-170451/Result-Image/Result-Image--WA01--P0001--T0001.oir
+        Slices: 11
+        Frames: 1
+        Min, max: [13.0, 981.0]
+        Fetching metadata from /Volumes/CRISPR_project_data/test_data_new/20231122-170451/Result-Image/Result-Image--WA01--P0001--T0001.oir
+        Slices: 11
+        Frames: 1
+        Min, max: [7.0, 2060.0]
+         */
+
     }
 }