diff --git a/.gitignore b/.gitignore index 11a95077c..63555d8ba 100644 --- a/.gitignore +++ b/.gitignore @@ -17,7 +17,7 @@ hs_err_*.log pom.xml.releaseBackup -src/test/java/projects +src/test/java/projects/ mobie-files diff --git a/pom.xml b/pom.xml index 914c63cde..d5f87e243 100644 --- a/pom.xml +++ b/pom.xml @@ -9,7 +9,7 @@ org.embl.mobie mobie-viewer-fiji - 5.2.4-SNAPSHOT + 5.3.0-SNAPSHOT @@ -84,7 +84,7 @@ EMBL true - 3.0.2 + 3.0.3 0.7.0 0.9.0 diff --git a/src/main/java/org/embl/mobie/MoBIE.java b/src/main/java/org/embl/mobie/MoBIE.java index e47f426cc..7c6abcbc3 100644 --- a/src/main/java/org/embl/mobie/MoBIE.java +++ b/src/main/java/org/embl/mobie/MoBIE.java @@ -120,7 +120,7 @@ public MoBIE( String uri, MoBIESettings settings ) throws IOException initImageJAndMoBIE(); initProject( IOHelper.getFileName( uri ) ); - CollectionTableDataSetter dataSetter = new CollectionTableDataSetter( table ); + CollectionTableDataSetter dataSetter = new CollectionTableDataSetter( table, settings.values.getDataRoot() ); dataSetter.addToDataset( dataset ); dataset.is2D( false ); // TODO: determine from data?! diff --git a/src/main/java/org/embl/mobie/MoBIESettings.java b/src/main/java/org/embl/mobie/MoBIESettings.java index eb91ad16a..563d79982 100644 --- a/src/main/java/org/embl/mobie/MoBIESettings.java +++ b/src/main/java/org/embl/mobie/MoBIESettings.java @@ -108,12 +108,6 @@ public MoBIESettings setVoxelDimensions( VoxelDimensions voxelDimensions ) return this; } - public MoBIESettings appendGroovyCode( String groovyCode ) - { - this.values.groovyScript += groovyCode; - return this; - } - public MoBIESettings openedFromCLI( Boolean cli ) { this.values.openedFromCLI = cli; @@ -126,6 +120,12 @@ public MoBIESettings projectType( ProjectType projectType ) return this; } + public MoBIESettings dataRoot( String dataRoot ) + { + this.values.dataRoot = dataRoot; + return this; + } + public static class Values { @@ -141,7 +141,12 @@ public static class Values private VoxelDimensions voxelDimensions = null; private Boolean openedFromCLI = false; // started from CLI private ProjectType projectType = ProjectType.MoBIEJSON; - private String groovyScript = ""; + private String dataRoot = null; + + public String getDataRoot() + { + return dataRoot; + } public VoxelDimensions getVoxelDimensions() { diff --git a/src/main/java/org/embl/mobie/cmd/ProjectCmd.java b/src/main/java/org/embl/mobie/cmd/ProjectCmd.java index 2d1281d71..2ab514fe3 100644 --- a/src/main/java/org/embl/mobie/cmd/ProjectCmd.java +++ b/src/main/java/org/embl/mobie/cmd/ProjectCmd.java @@ -28,7 +28,6 @@ */ package org.embl.mobie.cmd; -import net.imagej.ImageJ; import org.embl.mobie.MoBIE; import org.embl.mobie.MoBIESettings; import picocli.CommandLine; diff --git a/src/main/java/org/embl/mobie/command/open/OpenCollectionTableCommand.java b/src/main/java/org/embl/mobie/command/open/OpenCollectionTableCommand.java index fb9ef67e3..a15af6074 100644 --- a/src/main/java/org/embl/mobie/command/open/OpenCollectionTableCommand.java +++ b/src/main/java/org/embl/mobie/command/open/OpenCollectionTableCommand.java @@ -33,19 +33,13 @@ import org.embl.mobie.MoBIESettings; import org.embl.mobie.ProjectType; import org.embl.mobie.command.CommandConstants; -import org.embl.mobie.command.SpatialCalibration; import org.embl.mobie.lib.MoBIEHelper; -import org.embl.mobie.lib.transform.GridType; import org.scijava.command.Command; import org.scijava.plugin.Parameter; import org.scijava.plugin.Plugin; import java.io.File; import java.io.IOException; -import java.util.ArrayList; -import java.util.Arrays; -import java.util.List; -import java.util.stream.Collectors; @Plugin(type = Command.class, menuPath = CommandConstants.MOBIE_PLUGIN_OPEN + "Open Collection Table..." ) public class OpenCollectionTableCommand implements Command { @@ -55,16 +49,24 @@ public class OpenCollectionTableCommand implements Command { @Parameter( label = "Table Path", required = true ) public File table; + @Parameter( label = "Data Root Folder", + style = "directory", + description = "Use this is if the paths to the images and labels in the table are relative.", + required = false ) + public File dataRoot; + @Override public void run() { DebugTools.setRootLevel( "OFF" ); final MoBIESettings settings = new MoBIESettings() - .projectType( ProjectType.CollectionTable ); + .projectType( ProjectType.CollectionTable ) + .dataRoot( dataRoot.getAbsolutePath() ); try { + String rootPath = dataRoot == null ? null : dataRoot.getAbsolutePath(); new MoBIE( MoBIEHelper.toURI( table ), settings ); } catch ( IOException e ) diff --git a/src/main/java/org/embl/mobie/command/open/OpenTableCommand.java b/src/main/java/org/embl/mobie/command/open/OpenTableCommand.java index 42c6bdbcf..bf8342923 100644 --- a/src/main/java/org/embl/mobie/command/open/OpenTableCommand.java +++ b/src/main/java/org/embl/mobie/command/open/OpenTableCommand.java @@ -60,9 +60,9 @@ public class OpenTableCommand implements Command { @Parameter( label = "Labels Path Columns (Comma Separated)", required = false ) public String labels; - @Parameter( label = "Images & Labels Root Folder", + @Parameter( label = "Data Root Folder", style = "directory", - description = "Use this is if the images and labels paths in the table are relative.", + description = "Use this is if the paths to the images and labels in the table are relative.", required = false ) public File root; diff --git a/src/main/java/org/embl/mobie/command/open/project/OpenMoBIEProjectCommand.java b/src/main/java/org/embl/mobie/command/open/project/OpenMoBIEProjectCommand.java index 68461c047..82fe28113 100644 --- a/src/main/java/org/embl/mobie/command/open/project/OpenMoBIEProjectCommand.java +++ b/src/main/java/org/embl/mobie/command/open/project/OpenMoBIEProjectCommand.java @@ -31,15 +31,12 @@ 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.IOException; -import java.net.URI; -import java.net.URL; @Plugin(type = Command.class, menuPath = CommandConstants.MOBIE_PLUGIN_OPEN_PROJECT + "Open MoBIE Project..." ) diff --git a/src/main/java/org/embl/mobie/command/open/project/OpenPlatyBrowserCommand.java b/src/main/java/org/embl/mobie/command/open/project/OpenPlatyBrowserCommand.java index b3663486b..440825617 100644 --- a/src/main/java/org/embl/mobie/command/open/project/OpenPlatyBrowserCommand.java +++ b/src/main/java/org/embl/mobie/command/open/project/OpenPlatyBrowserCommand.java @@ -49,7 +49,7 @@ public void run() try { - new MoBIE( "https://github.com/mobie/platybrowser-project", settings ); + new MoBIE( "https://github.com/mobie/platybrowser-project", settings ); } catch ( IOException e ) { diff --git a/src/main/java/org/embl/mobie/lib/ImageDataAdder.java b/src/main/java/org/embl/mobie/lib/ImageDataAdder.java index bf73796c0..5018bd9af 100644 --- a/src/main/java/org/embl/mobie/lib/ImageDataAdder.java +++ b/src/main/java/org/embl/mobie/lib/ImageDataAdder.java @@ -28,7 +28,6 @@ */ package org.embl.mobie.lib; -import mpicbg.spim.data.generic.sequence.BasicViewSetup; import org.apache.commons.io.FilenameUtils; import org.embl.mobie.MoBIESettings; import org.embl.mobie.io.ImageDataFormat; @@ -44,8 +43,6 @@ import org.embl.mobie.lib.serialize.display.SegmentationDisplay; import org.embl.mobie.lib.table.TableDataFormat; import org.janelia.saalfeldlab.n5.universe.metadata.canonical.CanonicalDatasetMetadata; -import org.janelia.saalfeldlab.n5.universe.metadata.canonical.CanonicalSpatialDatasetMetadata; -import spimdata.util.Displaysettings; import java.io.File; import java.util.Arrays; @@ -110,7 +107,7 @@ private void addData( ImageData< ? > imageData, boolean isSegmentation ) } dataSource.preInit( true ); - dataset.addDataSource( dataSource ); + dataset.putDataSource( dataSource ); dataset.is2D( MoBIEHelper.is2D( imageData, datasetIndex ) ); } } diff --git a/src/main/java/org/embl/mobie/lib/annotation/DefaultAnnotationAdapter.java b/src/main/java/org/embl/mobie/lib/annotation/DefaultAnnotationAdapter.java index c4ac294ec..8f67e4527 100644 --- a/src/main/java/org/embl/mobie/lib/annotation/DefaultAnnotationAdapter.java +++ b/src/main/java/org/embl/mobie/lib/annotation/DefaultAnnotationAdapter.java @@ -32,30 +32,39 @@ import java.util.Iterator; import java.util.Map; -import java.util.Set; import java.util.concurrent.ConcurrentHashMap; import java.util.concurrent.atomic.AtomicBoolean; -import java.util.stream.Collectors; public class DefaultAnnotationAdapter< A extends Annotation > implements AnnotationAdapter< A > { private final AtomicBoolean throwError = new AtomicBoolean( true ); private final AnnData< A > annData; private final String source; + private final A annotation; private Map< String, A > stlToAnnotation; // source, timepoint, label public DefaultAnnotationAdapter( AnnData< A > annData ) { this.annData = annData; this.source = null; + this.annotation = null; } public DefaultAnnotationAdapter( AnnData< A > annData, String source ) { this.annData = annData; this.source = source; + this.annotation = null; } + public DefaultAnnotationAdapter( AnnData< A > annData, String source, A annotation ) + { + this.annData = annData; + this.source = source; + this.annotation = annotation; + } + + // FIXME: Can we get rid of this? Currently not used... @Override public A createVariable() { @@ -87,6 +96,7 @@ public synchronized A getAnnotation( String source, final int timePoint, final i if ( annotation == null ) { + // FIXME: Check whether this could be done lazy? if ( throwError.get() ) { System.err.println( "AnnotationAdapter: Missing annotation: " + source+ "; time point = " + timePoint + "; label = " + label + "\nSuppressing further errors of that kind." ); diff --git a/src/main/java/org/embl/mobie/lib/bdv/MobieBdvSupplier.java b/src/main/java/org/embl/mobie/lib/bdv/MobieBdvSupplier.java index aea3c37f7..d4e973020 100644 --- a/src/main/java/org/embl/mobie/lib/bdv/MobieBdvSupplier.java +++ b/src/main/java/org/embl/mobie/lib/bdv/MobieBdvSupplier.java @@ -91,7 +91,7 @@ public BdvHandle get() JFrame bdvFrame = (JFrame) SwingUtilities.getWindowAncestor(bdvHandle.getViewerPanel()); // Get the existing menu bar - // Here we could add or remove stuff... + // TODO: Here we could add or remove stuff... JMenuBar menuBar = bdvFrame.getJMenuBar(); setTimepointTextColor( bdvHandle ); diff --git a/src/main/java/org/embl/mobie/lib/data/CollectionTableDataSetter.java b/src/main/java/org/embl/mobie/lib/data/CollectionTableDataSetter.java index 325f0a21e..47ed580a8 100644 --- a/src/main/java/org/embl/mobie/lib/data/CollectionTableDataSetter.java +++ b/src/main/java/org/embl/mobie/lib/data/CollectionTableDataSetter.java @@ -31,10 +31,12 @@ public class CollectionTableDataSetter { private final Table table; + private final String rootPath; - public CollectionTableDataSetter( Table table ) + public CollectionTableDataSetter( Table table, String rootPath ) { this.table = table; + this.rootPath = rootPath; } public void addToDataset( Dataset dataset ) @@ -45,10 +47,12 @@ public void addToDataset( Dataset dataset ) for ( Row row : table ) { final StorageLocation storageLocation = new StorageLocation(); + storageLocation.absolutePath = getUri( row ); + if ( rootPath != null ) + storageLocation.absolutePath = IOHelper.combinePath( rootPath, storageLocation.absolutePath ); + ImageDataFormat imageDataFormat = ImageDataFormat.fromPath( storageLocation.absolutePath ); - // FIXME: how to decide? - //imageDataFormat = ImageDataFormat.BioFormats; storageLocation.setChannel( getChannel( row ) ); // TODO: Fetch from table or URI? https://forum.image.sc/t/loading-only-one-channel-from-an-ome-zarr/97798 String imageName = getName( row ); String pixelType = getPixelType( row ); @@ -65,7 +69,7 @@ public void addToDataset( Dataset dataset ) ); segmentationDataSource.preInit( false ); - dataset.addDataSource( segmentationDataSource ); + dataset.putDataSource( segmentationDataSource ); display = createSegmentationDisplay( imageName, @@ -75,7 +79,7 @@ public void addToDataset( Dataset dataset ) { final ImageDataSource imageDataSource = new ImageDataSource( imageName, imageDataFormat, storageLocation ); imageDataSource.preInit( false ); - dataset.addDataSource( imageDataSource ); + dataset.putDataSource( imageDataSource ); display = createImageDisplay( imageName, @@ -84,7 +88,8 @@ public void addToDataset( Dataset dataset ) addDisplayToViews( dataset, display, row ); - IJ.log("## " + imageName ); + IJ.log(" " ); + IJ.log("Name: " + imageName ); IJ.log("URI: " + storageLocation.absolutePath ); IJ.log("Opener: " + imageDataFormat ); IJ.log("Type: " + pixelType ); @@ -147,7 +152,7 @@ private static void addDisplayToViews( Dataset dataset, Display< ? > display, Ro { final View newView = new View( viewName, - getGroup( display ), + getGroup( display, row ), displays, transforms, // asserting that display name == image name null, @@ -160,10 +165,21 @@ private static void addDisplayToViews( Dataset dataset, Display< ? > display, Ro } @NotNull - private static String getGroup( Display< ? > display ) + private static String getGroup( Display< ? > display, Row row ) { - // TODO: fetch from table - return "views"; + try + { + String name = row.getString( CollectionTableConstants.GROUP ); + + if ( name.isEmpty() ) + return "views"; + + return name; + } + catch ( Exception e ) + { + return "views"; + } } private static String getViewName( Display< ? > display, Row row ) diff --git a/src/main/java/org/embl/mobie/lib/data/GridSourcesDataSetter.java b/src/main/java/org/embl/mobie/lib/data/GridSourcesDataSetter.java index 9680ebad7..40cebefb3 100644 --- a/src/main/java/org/embl/mobie/lib/data/GridSourcesDataSetter.java +++ b/src/main/java/org/embl/mobie/lib/data/GridSourcesDataSetter.java @@ -103,13 +103,13 @@ public void addDataAndDisplaysAndViews( Dataset dataset ) final TableSource tableSource = ( ( LabelGridSources ) sources ).getLabelTable( imageName ); SegmentationDataSource segmentationDataSource = SegmentationDataSource.create( imageName, imageDataFormat, storageLocation, tableSource ); segmentationDataSource.preInit( false ); - dataset.addDataSource( segmentationDataSource ); + dataset.putDataSource( segmentationDataSource ); } else { final ImageDataSource imageDataSource = new ImageDataSource( imageName, imageDataFormat, storageLocation ); imageDataSource.preInit( false ); - dataset.addDataSource( imageDataSource ); + dataset.putDataSource( imageDataSource ); } } } diff --git a/src/main/java/org/embl/mobie/lib/hcs/HCSPlateAdder.java b/src/main/java/org/embl/mobie/lib/hcs/HCSPlateAdder.java index 5137d12f1..cd60b866b 100644 --- a/src/main/java/org/embl/mobie/lib/hcs/HCSPlateAdder.java +++ b/src/main/java/org/embl/mobie/lib/hcs/HCSPlateAdder.java @@ -145,7 +145,7 @@ public void addPlateToDataset( Dataset dataset ) // String siteID = getSiteID( plate, channel, well, site ); ImageDataSource imageDataSource = createImageDataSource( channel, site, siteID ); - dataset.addDataSource( imageDataSource ); + dataset.putDataSource( imageDataSource ); // add site image source to site grid siteGrid.sources.add( imageDataSource.getName() ); @@ -166,7 +166,7 @@ public void addPlateToDataset( Dataset dataset ) // the one site is the well // ImageDataSource imageDataSource = createImageDataSource( channel, site, wellID ); - dataset.addDataSource( imageDataSource ); + dataset.putDataSource( imageDataSource ); } } diff --git a/src/main/java/org/embl/mobie/lib/image/AnnotationLabelImage.java b/src/main/java/org/embl/mobie/lib/image/AnnotationLabelImage.java index 6af878687..820241b65 100644 --- a/src/main/java/org/embl/mobie/lib/image/AnnotationLabelImage.java +++ b/src/main/java/org/embl/mobie/lib/image/AnnotationLabelImage.java @@ -30,9 +30,11 @@ import net.imglib2.type.numeric.IntegerType; import org.embl.mobie.lib.annotation.Annotation; +import org.embl.mobie.lib.annotation.AnnotationAdapter; public interface AnnotationLabelImage< A extends Annotation > extends AnnotationImage< A > { - // Label image corresponding to {@code annotation.label()} Image< ? extends IntegerType< ? > > getLabelImage(); + + AnnotationAdapter< A > getAnnotationAdapter(); } diff --git a/src/main/java/org/embl/mobie/lib/image/DefaultAnnotationLabelImage.java b/src/main/java/org/embl/mobie/lib/image/DefaultAnnotationLabelImage.java index 6734efbba..1d697937b 100644 --- a/src/main/java/org/embl/mobie/lib/image/DefaultAnnotationLabelImage.java +++ b/src/main/java/org/embl/mobie/lib/image/DefaultAnnotationLabelImage.java @@ -119,4 +119,9 @@ public AnnData< A > getAnnData() return labelImage; } + @Override + public AnnotationAdapter< A > getAnnotationAdapter() + { + return annotationAdapter; + } } diff --git a/src/main/java/org/embl/mobie/lib/serialize/Dataset.java b/src/main/java/org/embl/mobie/lib/serialize/Dataset.java index 871555699..551b8082f 100644 --- a/src/main/java/org/embl/mobie/lib/serialize/Dataset.java +++ b/src/main/java/org/embl/mobie/lib/serialize/Dataset.java @@ -73,7 +73,7 @@ public Map< String, DataSource > sources() return sources; } - public void addDataSource( DataSource dataSource ) + public void putDataSource( DataSource dataSource ) { sources.put( dataSource.getName(), dataSource ); } diff --git a/src/main/java/org/embl/mobie/lib/source/AnnotatedLabelSource.java b/src/main/java/org/embl/mobie/lib/source/AnnotatedLabelSource.java index 69b5cc173..2789d9f07 100644 --- a/src/main/java/org/embl/mobie/lib/source/AnnotatedLabelSource.java +++ b/src/main/java/org/embl/mobie/lib/source/AnnotatedLabelSource.java @@ -58,7 +58,7 @@ public RandomAccessibleInterval< AnnotationType< A > > getSource( final int t, f { return Converters.convert( source.getSource( t, level ), ( input, output ) -> { setOutput( input, t, output ); - }, new AnnotationType( annotationAdapter.createVariable() ) ); + }, new AnnotationType() ); // annotationAdapter.createVariable() } @Override @@ -82,6 +82,7 @@ private void setOutput( T input, int t, AnnotationType< A > output ) @Override public AnnotationType< A > getType() { - return new AnnotationType( annotationAdapter.createVariable() ); + //return new AnnotationType( annotationAdapter.createVariable() ); + return new AnnotationType( null ); } } diff --git a/src/main/java/org/embl/mobie/lib/source/VolatileAnnotatedLabelSource.java b/src/main/java/org/embl/mobie/lib/source/VolatileAnnotatedLabelSource.java index 2d22488ea..5459465bb 100644 --- a/src/main/java/org/embl/mobie/lib/source/VolatileAnnotatedLabelSource.java +++ b/src/main/java/org/embl/mobie/lib/source/VolatileAnnotatedLabelSource.java @@ -91,6 +91,6 @@ public VolatileAnnotationType< A > getType() private VolatileAnnotationType< A > createVariable() { - return new VolatileAnnotationType( annotationAdapter.createVariable(), true ); + return new VolatileAnnotationType( new AnnotationType<>() , true ); // annotationAdapter.createVariable() } } diff --git a/src/main/java/org/embl/mobie/lib/table/columns/CollectionTableConstants.java b/src/main/java/org/embl/mobie/lib/table/columns/CollectionTableConstants.java index d5170a906..da63fbc7d 100644 --- a/src/main/java/org/embl/mobie/lib/table/columns/CollectionTableConstants.java +++ b/src/main/java/org/embl/mobie/lib/table/columns/CollectionTableConstants.java @@ -140,9 +140,8 @@ public class CollectionTableConstants /** * The "view" column MAY be present. * - * The value will determine to which view this image will be added. - * Note that each image will be anyway visible via its own view, - * whose name is determined by the "name" column. + * The value will determine to which view this image will be added, + * i.e. at which name it can be accessed in the MoBIE UI. * * Supported values: * - Free text @@ -153,7 +152,7 @@ public class CollectionTableConstants * - the value is empty. * * Use cases: - * - One can add data from an URI a second time, but + * - One can add data from the same URI a second time, but * with a different "affine" transform, or a different "channel" * - One can combine several images into the same view, e.g. * different channels of the same image, or an image and a corresponding @@ -162,14 +161,11 @@ public class CollectionTableConstants */ public static final String VIEW = "view"; - /** * The "group" column MAY be present. * * The value will create a UI selection group in the MoBIE user interface * to which the view of this image will be added. - * Note that each image will be anyway visible via its own view, - * whose name is determined by the "name" column. * * Supported values: * - Free text @@ -180,12 +176,8 @@ public class CollectionTableConstants * - the table cell is empty. * * Use cases: - * - One can add data from an URI a second time, but - * with a different "affine" transform, or a different "channel" - * - One can combine several images into the same view, e.g. - * different channels of the same image, or an image and a corresponding - * label mask (segmentation) image, or several (registered) images of - * a CLEM experiment. + * - If you have a lot of data it can be helpful to + * divide the views into groups. */ public static final String GROUP = "group"; } diff --git a/src/main/java/org/embl/mobie/lib/transform/ImageTransformer.java b/src/main/java/org/embl/mobie/lib/transform/ImageTransformer.java index 79486e74e..f291bc6eb 100644 --- a/src/main/java/org/embl/mobie/lib/transform/ImageTransformer.java +++ b/src/main/java/org/embl/mobie/lib/transform/ImageTransformer.java @@ -32,7 +32,9 @@ import net.imglib2.type.numeric.IntegerType; import org.embl.mobie.lib.ThreadHelper; import org.embl.mobie.lib.annotation.Annotation; +import org.embl.mobie.lib.annotation.AnnotationAdapter; import org.embl.mobie.lib.annotation.DefaultAnnotationAdapter; +import org.embl.mobie.lib.annotation.LazyAnnotatedSegmentAdapter; import org.embl.mobie.lib.image.*; import org.embl.mobie.lib.serialize.transformation.AffineTransformation; import org.embl.mobie.lib.serialize.transformation.InterpolatedAffineTransformation; @@ -113,23 +115,36 @@ else if ( image instanceof AnnotationImage ) return realTransformedImage; } - private static < A extends Annotation, TA extends A > DefaultAnnotationLabelImage< TA > createTransformedAnnotatedLabelImage( + private static < A extends Annotation, TA extends A > DefaultAnnotationLabelImage< ? > createTransformedAnnotatedLabelImage( AnnotationLabelImage< A > annotatedLabelImage, AffineTransformation affineTransformation ) { final Image< ? extends IntegerType< ? > > labelImage = annotatedLabelImage.getLabelImage(); - + final Image< ? extends IntegerType< ? > > transformedLabelImage = ( Image< ? extends IntegerType< ? > > ) affineTransform( labelImage, affineTransformation ); final AnnData< A > annData = annotatedLabelImage.getAnnData(); - final AnnotationAffineTransformer< A, TA > affineTransformer = new AnnotationAffineTransformer<>( affineTransformation.getAffineTransform3D() ); + AnnotationAdapter< A > annotationAdapter = annotatedLabelImage.getAnnotationAdapter(); - TransformedAnnData< A, TA > transformedAnnData = new TransformedAnnData<>( annData, affineTransformer ); + if ( annotationAdapter instanceof LazyAnnotatedSegmentAdapter ) + { + // There are no annotations with coordinates, + // thus we do not need to transform them. + return new DefaultAnnotationLabelImage< A >( transformedLabelImage, annData, annotationAdapter ); + } + else + { + final AnnotationAffineTransformer< A, TA > affineTransformer = + new AnnotationAffineTransformer<>( affineTransformation.getAffineTransform3D() ); - final DefaultAnnotationAdapter< TA > annotationAdapter = new DefaultAnnotationAdapter<>( transformedAnnData, annotatedLabelImage.getName() ); + TransformedAnnData< A, TA > transformedAnnData = new TransformedAnnData<>( annData, affineTransformer ); - final Image< ? extends IntegerType< ? > > transformedLabelImage = ( Image< ? extends IntegerType< ? > > ) affineTransform( labelImage, affineTransformation ); + AnnotationAdapter< TA > newAnnotationAdapter = + new DefaultAnnotationAdapter<>( + transformedAnnData, + annotatedLabelImage.getName() ); - return new DefaultAnnotationLabelImage< TA >( transformedLabelImage, transformedAnnData, annotationAdapter ); + return new DefaultAnnotationLabelImage< TA >( transformedLabelImage, transformedAnnData, newAnnotationAdapter ); + } } public static List< ? extends Image< ? > > gridTransform( List< List< ? extends Image< ? > > > nestedImages, @Nullable List< List< String > > nestedTransformedNames, List< int[] > positions, double[] tileRealDimensions, boolean centerAtOrigin, double[] withinTileOffset ) diff --git a/src/main/java/org/embl/mobie/lib/view/ViewManager.java b/src/main/java/org/embl/mobie/lib/view/ViewManager.java index 3f593e907..e43b02ef9 100644 --- a/src/main/java/org/embl/mobie/lib/view/ViewManager.java +++ b/src/main/java/org/embl/mobie/lib/view/ViewManager.java @@ -239,6 +239,8 @@ public synchronized void show( View view ) { final long startTime = System.currentTimeMillis(); + IJ.log("Opening view \"" + view.getName() + "\"..." ); + if ( view.isExclusive() ) { removeAllSourceDisplays( true ); @@ -306,7 +308,7 @@ public synchronized void show( View view ) userInterface.setImageNameOverlay( imageNameOverlay ); imageNameOverlay.setActive( view.overlayNames() ); - IJ.log("Opened view \"" + view.getName() + "\" in " + (System.currentTimeMillis() - startTime) + " ms." ); + IJ.log("...done in " + (System.currentTimeMillis() - startTime) + " ms." ); if ( view.getDescription() != null ) IJ.log( "View description: \"" + view.getDescription() + "\"" ); @@ -327,7 +329,11 @@ public void initData( View view ) // if a view is created on the fly in a running project, e.g. due to an image registration // the data sources may already be present and thus do not need to be instantiated - dataSources = dataSources.stream().filter( ds -> ! DataStore.containsImage( ds.getName() ) ).collect( Collectors.toList() ); + // FIXME: the issue here is that then an image may exist already and a transformation is applied twice (see below) + // example: public class OpenPaoloFirstTable => view the first image twice + // dataSources = dataSources.stream() + // .filter( ds -> ! DataStore.containsImage( ds.getName() ) ) + // .collect( Collectors.toList() ); for ( DataSource dataSource : dataSources ) { @@ -363,6 +369,7 @@ public void initData( View view ) final List< Transformation > transformations = view.transformations(); if ( transformations != null ) { + // FIXME: the issue here is that then an image may exist already and a transformation is applied twice (see above) for ( Transformation transformation : transformations ) { if ( transformation instanceof ImageTransformation ) diff --git a/src/main/java/org/embl/mobie/ui/UserInterfaceHelper.java b/src/main/java/org/embl/mobie/ui/UserInterfaceHelper.java index a2f320a20..5bbee352e 100644 --- a/src/main/java/org/embl/mobie/ui/UserInterfaceHelper.java +++ b/src/main/java/org/embl/mobie/ui/UserInterfaceHelper.java @@ -1238,7 +1238,7 @@ public static JButton createFocusButton( AbstractDisplay< ? > sourceDisplay, List< Source< ? > > sources ) { JButton button = getIconButton( "focus.png" ); - button.setToolTipText( "Show whole dataset" ); + button.setToolTipText( "Fit image to viewer" ); button.addActionListener( e -> { diff --git a/src/test/java/debug/DebugIssue1096.java b/src/test/java/debug/DebugIssue1096.java index 1d95fbc07..7fa4c2962 100644 --- a/src/test/java/debug/DebugIssue1096.java +++ b/src/test/java/debug/DebugIssue1096.java @@ -43,6 +43,6 @@ public static void main( String[] args ) throws IOException final ImageJ imageJ = new ImageJ(); imageJ.ui().showUI(); - new MoBIE("/Volumes/kreshuk/hellgoth/mobie_project_shared/culture-collections", MoBIESettings.settings() ); + new MoBIE("/Volumes/kreshuk/hellgoth/mobie_project_shared/culture-collections",MoBIESettings.settings() ); } } diff --git a/src/test/java/develop/DevelopNormalisedViewerTransforms.java b/src/test/java/develop/DevelopNormalisedViewerTransforms.java index b4a019116..e7aa60d66 100644 --- a/src/test/java/develop/DevelopNormalisedViewerTransforms.java +++ b/src/test/java/develop/DevelopNormalisedViewerTransforms.java @@ -28,7 +28,6 @@ */ package develop; -import org.embl.mobie.io.ImageDataFormat; import org.embl.mobie.MoBIE; import org.embl.mobie.MoBIESettings; import net.imagej.ImageJ; @@ -47,8 +46,7 @@ public static void main( String[] args ) testNormalisationAndReversion(); try { - final MoBIE moBIE = new MoBIE("https://github.com/mobie-org/covid-em-datasets", - MoBIESettings.settings() ); + final MoBIE moBIE = new MoBIE("https://github.com/mobie-org/covid-em-datasets", MoBIESettings.settings() ); } catch (IOException e) { e.printStackTrace(); } diff --git a/src/test/java/develop/OpenPaoloFirstTable.java b/src/test/java/develop/OpenPaoloFirstTable.java index 2947cb1a7..0bc34cc07 100644 --- a/src/test/java/develop/OpenPaoloFirstTable.java +++ b/src/test/java/develop/OpenPaoloFirstTable.java @@ -12,11 +12,13 @@ public static void main( String[] args ) final ImageJ imageJ = new ImageJ(); imageJ.ui().showUI(); - String tablePath = "/Users/tischer/Desktop/Paolo.txt"; - File tableFile = new File( tablePath ); +// OpenCollectionTableCommand command = new OpenCollectionTableCommand(); +// command.table = new File( "/Users/tischer/Desktop/Paolo.txt" ); +// command.run(); OpenCollectionTableCommand command = new OpenCollectionTableCommand(); - command.table = tableFile; + command.table = new File( "/Users/tischer/Desktop/Paolo-relative.txt" ); + command.dataRoot = new File( "/Volumes/emcf/ronchi/MRC-MM/aligned" ); command.run(); } } diff --git a/src/test/java/examples/OpenCollectionTable.java b/src/test/java/examples/OpenBlobsCollectionTable.java similarity index 58% rename from src/test/java/examples/OpenCollectionTable.java rename to src/test/java/examples/OpenBlobsCollectionTable.java index d80b0741c..533ef8812 100644 --- a/src/test/java/examples/OpenCollectionTable.java +++ b/src/test/java/examples/OpenBlobsCollectionTable.java @@ -1,24 +1,20 @@ package examples; import net.imagej.ImageJ; -import org.embl.mobie.MoBIE; -import org.embl.mobie.MoBIESettings; import org.embl.mobie.command.open.OpenCollectionTableCommand; import java.io.File; -public class OpenCollectionTable +public class OpenBlobsCollectionTable { public static void main( String[] args ) { final ImageJ imageJ = new ImageJ(); imageJ.ui().showUI(); - String tablePath = "src/test/resources/collections/blobs-table.txt"; - File tableFile = new File( tablePath ); - OpenCollectionTableCommand command = new OpenCollectionTableCommand(); - command.table = tableFile; + command.table = new File( "src/test/resources/collections/blobs-table.txt" ); + command.dataRoot = new File( "/Users/tischer/Documents/mobie-viewer-fiji/src/test/resources" ); command.run(); } } diff --git a/src/test/java/examples/OpenPlatybrowser.java b/src/test/java/examples/OpenPlatybrowser.java index 72e35704a..3dfbaa34b 100644 --- a/src/test/java/examples/OpenPlatybrowser.java +++ b/src/test/java/examples/OpenPlatybrowser.java @@ -42,6 +42,6 @@ public static void main( String[] args ) throws IOException imageJ.ui().showUI(); final MoBIE moBIE = new MoBIE( "https://github.com/mobie/covid-if-project", - MoBIESettings.settings().gitProjectBranch( "main" ).view( "default" ) ); + MoBIESettings.settings().gitProjectBranch( "main" ).view( "default" ) ); } } diff --git a/src/test/java/org/embl/mobie/lib/serialize/DatasetJsonParserTest.java b/src/test/java/org/embl/mobie/lib/serialize/DatasetJsonParserTest.java index effe23d01..4f61d4d6b 100644 --- a/src/test/java/org/embl/mobie/lib/serialize/DatasetJsonParserTest.java +++ b/src/test/java/org/embl/mobie/lib/serialize/DatasetJsonParserTest.java @@ -79,7 +79,7 @@ public void savePlatyView() throws IOException final ImageJ imageJ = new ImageJ(); imageJ.ui().showUI(); - final MoBIE moBIE = new MoBIE("https://github.com/mobie/platybrowser-project", MoBIESettings.settings()); + final MoBIE moBIE = new MoBIE("https://github.com/mobie/platybrowser-project",MoBIESettings.settings()); // show a view with a segmentation and // selected cells that loads fast, to test saving diff --git a/src/test/java/projects/OmeZarrS3V4Opener.java b/src/test/java/projects/OmeZarrS3V4Opener.java index ee634717b..a95034166 100644 --- a/src/test/java/projects/OmeZarrS3V4Opener.java +++ b/src/test/java/projects/OmeZarrS3V4Opener.java @@ -29,7 +29,6 @@ package projects; import net.imagej.ImageJ; -import org.embl.mobie.io.ImageDataFormat; import org.embl.mobie.MoBIE; import org.embl.mobie.MoBIESettings; @@ -43,6 +42,6 @@ public static void main(String[] args) throws IOException { public static void showYX() throws IOException { final ImageJ imageJ = new ImageJ(); imageJ.ui().showUI(); - final MoBIE moBIE = new MoBIE("https://s3.embl.de/i2k-2020/ngff-example-data/v0.4/yx.ome.zarr", MoBIESettings.settings()); + final MoBIE moBIE = new MoBIE("https://s3.embl.de/i2k-2020/ngff-example-data/v0.4/yx.ome.zarr",MoBIESettings.settings()); } } diff --git a/src/test/java/projects/OmeZarrV4FSOpener.java b/src/test/java/projects/OmeZarrV4FSOpener.java index e5646952b..2fece31d8 100644 --- a/src/test/java/projects/OmeZarrV4FSOpener.java +++ b/src/test/java/projects/OmeZarrV4FSOpener.java @@ -29,7 +29,6 @@ package projects; import net.imagej.ImageJ; -import org.embl.mobie.io.ImageDataFormat; import org.embl.mobie.MoBIE; import org.embl.mobie.MoBIESettings; @@ -43,6 +42,6 @@ public static void main(String[] args) throws IOException { public static void showYX() throws IOException { final ImageJ imageJ = new ImageJ(); imageJ.ui().showUI(); - new MoBIE("/home/katerina/Documents/embl/mnt/kreshuk2/kreshuk/pape/Work/mobie/ngff/ome-ngff-prototypes/single_image/v0.4/yx.ome.zarr", MoBIESettings.settings()); + new MoBIE("/home/katerina/Documents/embl/mnt/kreshuk2/kreshuk/pape/Work/mobie/ngff/ome-ngff-prototypes/single_image/v0.4/yx.ome.zarr",MoBIESettings.settings()); } } diff --git a/src/test/java/projects/OpenLocalAutophagosomesEM.java b/src/test/java/projects/OpenLocalAutophagosomesEM.java index bd18d9ac1..f1f976efd 100644 --- a/src/test/java/projects/OpenLocalAutophagosomesEM.java +++ b/src/test/java/projects/OpenLocalAutophagosomesEM.java @@ -28,7 +28,6 @@ */ package projects; -import org.embl.mobie.io.ImageDataFormat; import org.embl.mobie.MoBIE; import org.embl.mobie.MoBIESettings; import net.imagej.ImageJ; @@ -42,7 +41,7 @@ public static void main( String[] args ) new ImageJ().ui().showUI(); try { new MoBIE("/g/kreshuk/pape/work/my_projects/autophagosoms-clem/data", - MoBIESettings.settings() ); + MoBIESettings.settings() ); } catch (IOException e) { e.printStackTrace(); } diff --git a/src/test/java/projects/OpenLocalBdvOmeZarr.java b/src/test/java/projects/OpenLocalBdvOmeZarr.java index 7b2f01633..47bcf7ed9 100644 --- a/src/test/java/projects/OpenLocalBdvOmeZarr.java +++ b/src/test/java/projects/OpenLocalBdvOmeZarr.java @@ -28,7 +28,6 @@ */ package projects; -import org.embl.mobie.io.ImageDataFormat; import net.imagej.ImageJ; import org.embl.mobie.MoBIE; import org.embl.mobie.MoBIESettings; @@ -40,6 +39,6 @@ public static void main( String[] args ) throws IOException { final ImageJ imageJ = new ImageJ(); imageJ.ui().showUI(); - final MoBIE moBIE = new MoBIE("/home/katerina/Documents/embl/mnt/kreshuk/pape/Work/mobie/covid-em-datasets/ngff-example/data", MoBIESettings.settings()); + final MoBIE moBIE = new MoBIE("/home/katerina/Documents/embl/mnt/kreshuk/pape/Work/mobie/covid-em-datasets/ngff-example/data",MoBIESettings.settings()); } } diff --git a/src/test/java/projects/OpenLocalBeckwith.java b/src/test/java/projects/OpenLocalBeckwith.java index 092c37ca3..01f697e8f 100644 --- a/src/test/java/projects/OpenLocalBeckwith.java +++ b/src/test/java/projects/OpenLocalBeckwith.java @@ -41,7 +41,7 @@ public static void main( String[] args ) throws IOException final ImageJ imageJ = new ImageJ(); imageJ.ui().showUI(); - final MoBIE moBIE = new MoBIE("/g/cba/exchange/marianne-beckwidth/220509_MSB26_sample2_MoBIE", new MoBIESettings().view( "default" ) ); + final MoBIE moBIE = new MoBIE("/g/cba/exchange/marianne-beckwidth/220509_MSB26_sample2_MoBIE", new MoBIESettings().view( "default" ) ); } } diff --git a/src/test/java/projects/OpenLocalConstantinNoTables.java b/src/test/java/projects/OpenLocalConstantinNoTables.java index e3a44f3f3..1dd4a8109 100644 --- a/src/test/java/projects/OpenLocalConstantinNoTables.java +++ b/src/test/java/projects/OpenLocalConstantinNoTables.java @@ -29,7 +29,6 @@ package projects; import net.imagej.ImageJ; -import org.embl.mobie.io.ImageDataFormat; import org.embl.mobie.MoBIE; import org.embl.mobie.MoBIESettings; @@ -41,6 +40,6 @@ public static void main( String[] args ) throws IOException { final ImageJ imageJ = new ImageJ(); imageJ.ui().showUI(); - final MoBIE moBIE = new MoBIE("/Volumes/emcf/pape/jil", MoBIESettings.settings()); + final MoBIE moBIE = new MoBIE("/Volumes/emcf/pape/jil",MoBIESettings.settings()); } } diff --git a/src/test/java/projects/OpenLocalCovid2.java b/src/test/java/projects/OpenLocalCovid2.java index 3310c5af9..68eae11c5 100644 --- a/src/test/java/projects/OpenLocalCovid2.java +++ b/src/test/java/projects/OpenLocalCovid2.java @@ -42,7 +42,7 @@ public static void main( String[] args ) imageJ.ui().showUI(); try { - new MoBIE("/g/kreshuk/pape/Work/data/mobie/covid-if-2", MoBIESettings.settings().view( "segmentations" ) );//.getViewManager().show( "cell-segmentation" ); + new MoBIE("/g/kreshuk/pape/Work/data/mobie/covid-if-2",MoBIESettings.settings().view( "segmentations" ) );//.getViewManager().show( "cell-segmentation" ); } catch (IOException e) { e.printStackTrace(); } diff --git a/src/test/java/projects/OpenLocalCovidEMCF.java b/src/test/java/projects/OpenLocalCovidEMCF.java index aee8063ba..012c887bb 100644 --- a/src/test/java/projects/OpenLocalCovidEMCF.java +++ b/src/test/java/projects/OpenLocalCovidEMCF.java @@ -28,7 +28,6 @@ */ package projects; -import org.embl.mobie.io.ImageDataFormat; import org.embl.mobie.MoBIE; import org.embl.mobie.MoBIESettings; import net.imagej.ImageJ; @@ -43,7 +42,7 @@ public static void main( String[] args ) imageJ.ui().showUI(); try { new MoBIE("/Volumes/emcf/common/5792_Sars-Cov-2/covid-em/data", - MoBIESettings.settings() ); + MoBIESettings.settings() ); } catch (IOException e) { e.printStackTrace(); } diff --git a/src/test/java/projects/OpenLocalCovidPlate.java b/src/test/java/projects/OpenLocalCovidPlate.java index ddc4c0919..ddf7a0d71 100644 --- a/src/test/java/projects/OpenLocalCovidPlate.java +++ b/src/test/java/projects/OpenLocalCovidPlate.java @@ -28,7 +28,6 @@ */ package projects; -import org.embl.mobie.io.ImageDataFormat; import org.embl.mobie.MoBIE; import org.embl.mobie.MoBIESettings; import net.imagej.ImageJ; @@ -43,7 +42,7 @@ public static void main( String[] args ) imageJ.ui().showUI(); try { - new MoBIE("/g/kreshuk/pape/Work/mobie/covid-if-project/data", MoBIESettings.settings() ); + new MoBIE("/g/kreshuk/pape/Work/mobie/covid-if-project/data",MoBIESettings.settings() ); } catch (IOException e) { e.printStackTrace(); } diff --git a/src/test/java/projects/OpenLocalCovidTomos.java b/src/test/java/projects/OpenLocalCovidTomos.java index 0fd200f10..98c213533 100644 --- a/src/test/java/projects/OpenLocalCovidTomos.java +++ b/src/test/java/projects/OpenLocalCovidTomos.java @@ -28,7 +28,6 @@ */ package projects; -import org.embl.mobie.io.ImageDataFormat; import org.embl.mobie.MoBIE; import org.embl.mobie.MoBIESettings; import net.imagej.ImageJ; @@ -42,7 +41,7 @@ public static void main( String[] args ) final ImageJ imageJ = new ImageJ(); imageJ.ui().showUI(); try { - new MoBIE("/Volumes/kreshuk/pape/Work/mobie/covid-tomo-datasets", MoBIESettings.settings() ); + new MoBIE("/Volumes/kreshuk/pape/Work/mobie/covid-tomo-datasets",MoBIESettings.settings() ); } catch (IOException e) { e.printStackTrace(); } diff --git a/src/test/java/projects/OpenLocalGiuliaCLEM.java b/src/test/java/projects/OpenLocalGiuliaCLEM.java index 7b42841fb..bd41094ac 100644 --- a/src/test/java/projects/OpenLocalGiuliaCLEM.java +++ b/src/test/java/projects/OpenLocalGiuliaCLEM.java @@ -42,6 +42,6 @@ public static void main( String[] args ) throws IOException imageJ.ui().showUI(); // Move 62 towards 63 appears in wrong place - new MoBIE("/Volumes/emcf/mizzon/projects/2024/HEV_vCLEM/HEV_D7/HEV_D7-1_oRblended_sec5-8/mobie_backup_2", MoBIESettings.settings() ); + new MoBIE("/Volumes/emcf/mizzon/projects/2024/HEV_vCLEM/HEV_D7/HEV_D7-1_oRblended_sec5-8/mobie_backup_2",MoBIESettings.settings() ); } } diff --git a/src/test/java/projects/OpenLocalGiuliaMartinCLEM.java b/src/test/java/projects/OpenLocalGiuliaMartinCLEM.java index cfeb286fb..602473246 100644 --- a/src/test/java/projects/OpenLocalGiuliaMartinCLEM.java +++ b/src/test/java/projects/OpenLocalGiuliaMartinCLEM.java @@ -29,7 +29,6 @@ package projects; import net.imagej.ImageJ; -import org.embl.mobie.io.ImageDataFormat; import org.embl.mobie.MoBIE; import org.embl.mobie.MoBIESettings; @@ -41,6 +40,6 @@ public static void main( String[] args ) throws IOException { final ImageJ imageJ = new ImageJ(); imageJ.ui().showUI(); - new MoBIE("/g/emcf/pape/clem-example-project", MoBIESettings.settings() ); + new MoBIE("/g/emcf/pape/clem-example-project",MoBIESettings.settings() ); } } diff --git a/src/test/java/projects/OpenLocalJulianNoTables.java b/src/test/java/projects/OpenLocalJulianNoTables.java index 2be7e0fc6..5936418ce 100644 --- a/src/test/java/projects/OpenLocalJulianNoTables.java +++ b/src/test/java/projects/OpenLocalJulianNoTables.java @@ -40,7 +40,7 @@ public static void main( String[] args ) throws IOException { final ImageJ imageJ = new ImageJ(); imageJ.ui().showUI(); - final MoBIE moBIE = new MoBIE("/Volumes/emcf/hennies/for_constantin/mobie_no_table_test/", new MoBIESettings() ); + final MoBIE moBIE = new MoBIE("/Volumes/emcf/hennies/for_constantin/mobie_no_table_test/", new MoBIESettings() ); moBIE.getViewManager().show( "seg-test" ); } } diff --git a/src/test/java/projects/OpenLocalKarel.java b/src/test/java/projects/OpenLocalKarel.java index 5fb40d579..14caac5b3 100644 --- a/src/test/java/projects/OpenLocalKarel.java +++ b/src/test/java/projects/OpenLocalKarel.java @@ -39,6 +39,6 @@ public class OpenLocalKarel public static void main(String[] args) throws IOException { final ImageJ imageJ = new ImageJ(); imageJ.ui().showUI(); - new MoBIE( "/Volumes/schwab/Karel/MOBIE/MOBIE1_bc", new MoBIESettings() ); + new MoBIE( "/Volumes/schwab/Karel/MOBIE/MOBIE1_bc", new MoBIESettings() ); } } diff --git a/src/test/java/projects/OpenLocalMalariaXRayHDF5.java b/src/test/java/projects/OpenLocalMalariaXRayHDF5.java index 0505f6a81..eb5543fb6 100644 --- a/src/test/java/projects/OpenLocalMalariaXRayHDF5.java +++ b/src/test/java/projects/OpenLocalMalariaXRayHDF5.java @@ -42,7 +42,7 @@ public static void main( String[] args ) imageJ.ui().showUI(); try { - new MoBIE("/Volumes/cba/exchange/Nedal_Jonas_XrayImaging/mobie/test_hdf5/", MoBIESettings.settings() );//.getViewManager().show( "cell-segmentation" ); + new MoBIE("/Volumes/cba/exchange/Nedal_Jonas_XrayImaging/mobie/test_hdf5/",MoBIESettings.settings() );//.getViewManager().show( "cell-segmentation" ); } catch (IOException e) { e.printStackTrace(); } diff --git a/src/test/java/projects/OpenLocalMalariaXRayZarr.java b/src/test/java/projects/OpenLocalMalariaXRayZarr.java index eac061891..8c25e19f5 100644 --- a/src/test/java/projects/OpenLocalMalariaXRayZarr.java +++ b/src/test/java/projects/OpenLocalMalariaXRayZarr.java @@ -42,7 +42,7 @@ public static void main( String[] args ) imageJ.ui().showUI(); try { - new MoBIE("/Volumes/cba/exchange/Nedal_Jonas_XrayImaging/mobie/test_zarr/", MoBIESettings.settings() );//.getViewManager().show( "cell-segmentation" ); + new MoBIE("/Volumes/cba/exchange/Nedal_Jonas_XrayImaging/mobie/test_zarr/",MoBIESettings.settings() );//.getViewManager().show( "cell-segmentation" ); } catch (IOException e) { e.printStackTrace(); } diff --git a/src/test/java/projects/OpenLocalMarianne.java b/src/test/java/projects/OpenLocalMarianne.java index 902510d90..4ad16721b 100644 --- a/src/test/java/projects/OpenLocalMarianne.java +++ b/src/test/java/projects/OpenLocalMarianne.java @@ -39,6 +39,6 @@ public class OpenLocalMarianne public static void main(String[] args) throws IOException { final ImageJ imageJ = new ImageJ(); imageJ.ui().showUI(); - new MoBIE( "/Volumes/cba/exchange/marianne-beckwidth/220509_MSB26_sample2_MoBIE", new MoBIESettings() ); + new MoBIE( "/Volumes/cba/exchange/marianne-beckwidth/220509_MSB26_sample2_MoBIE", new MoBIESettings() ); } } diff --git a/src/test/java/projects/OpenLocalOmeZarr.java b/src/test/java/projects/OpenLocalOmeZarr.java index 91af5b4d5..c30bde1df 100644 --- a/src/test/java/projects/OpenLocalOmeZarr.java +++ b/src/test/java/projects/OpenLocalOmeZarr.java @@ -28,7 +28,6 @@ */ package projects; -import org.embl.mobie.io.ImageDataFormat; import org.embl.mobie.MoBIE; import org.embl.mobie.MoBIESettings; import net.imagej.ImageJ; @@ -39,6 +38,6 @@ public class OpenLocalOmeZarr { public static void main(String[] args) throws IOException { final ImageJ imageJ = new ImageJ(); imageJ.ui().showUI(); - new MoBIE( "/g/kreshuk/pape/Work/mobie/covid-if-project/data", MoBIESettings.settings() ); + new MoBIE( "/g/kreshuk/pape/Work/mobie/covid-if-project/data",MoBIESettings.settings() ); } } diff --git a/src/test/java/projects/OpenLocalPlankton.java b/src/test/java/projects/OpenLocalPlankton.java index 6c11d1138..e7efcf982 100644 --- a/src/test/java/projects/OpenLocalPlankton.java +++ b/src/test/java/projects/OpenLocalPlankton.java @@ -33,7 +33,6 @@ import net.imagej.ImageJ; import java.io.IOException; -import org.embl.mobie.io.ImageDataFormat; public class OpenLocalPlankton { @@ -42,7 +41,7 @@ public static void main( String[] args ) new ImageJ().ui().showUI(); try { new MoBIE("/Volumes/emcf/pape/plankton-fibsem-project", - MoBIESettings.settings().dataset( "galdieria" ) ); + MoBIESettings.settings().dataset( "galdieria" ) ); } catch (IOException e) { e.printStackTrace(); } diff --git a/src/test/java/projects/OpenLocalShila.java b/src/test/java/projects/OpenLocalShila.java index e31648a20..4008dc97d 100644 --- a/src/test/java/projects/OpenLocalShila.java +++ b/src/test/java/projects/OpenLocalShila.java @@ -41,7 +41,7 @@ public static void main( String[] args ) final ImageJ imageJ = new ImageJ(); imageJ.ui().showUI(); try { - new MoBIE("/Volumes/kreshuk/data/marioni/shila/mouse-atlas-2020/ngff/", new MoBIESettings() ); + new MoBIE("/Volumes/kreshuk/data/marioni/shila/mouse-atlas-2020/ngff/", new MoBIESettings() ); } catch (IOException e) { e.printStackTrace(); } diff --git a/src/test/java/projects/OpenLocalSpatialOmics.java b/src/test/java/projects/OpenLocalSpatialOmics.java index eb5215150..7f4357f92 100644 --- a/src/test/java/projects/OpenLocalSpatialOmics.java +++ b/src/test/java/projects/OpenLocalSpatialOmics.java @@ -40,7 +40,7 @@ public static void main( String[] args ) { new ImageJ().ui().showUI(); try { - new MoBIE("/g/kreshuk/data/marioni/shila/mouse-atlas-2020/ngff", MoBIESettings.settings().view( "gene-clustering-example" ).dataset( "embryo3" ) ); + new MoBIE("/g/kreshuk/data/marioni/shila/mouse-atlas-2020/ngff",MoBIESettings.settings().view( "gene-clustering-example" ).dataset( "embryo3" ) ); // "stitched-full" "stitched-small" "only_spots" } catch (IOException e) { e.printStackTrace(); diff --git a/src/test/java/projects/OpenLocalTobias.java b/src/test/java/projects/OpenLocalTobias.java index b43150bcd..7deb19b41 100644 --- a/src/test/java/projects/OpenLocalTobias.java +++ b/src/test/java/projects/OpenLocalTobias.java @@ -33,7 +33,6 @@ import net.imagej.ImageJ; import java.io.IOException; -import org.embl.mobie.io.ImageDataFormat; public class OpenLocalTobias { @@ -43,7 +42,7 @@ public static void main( String[] args ) imageJ.ui().showUI(); try { new MoBIE("/g/schwab/Tobias/MoBIE", - MoBIESettings.settings() ); + MoBIESettings.settings() ); } catch (IOException e) { e.printStackTrace(); } diff --git a/src/test/java/projects/OpenLocalXRay.java b/src/test/java/projects/OpenLocalXRay.java index 808857c62..cdfb56f38 100644 --- a/src/test/java/projects/OpenLocalXRay.java +++ b/src/test/java/projects/OpenLocalXRay.java @@ -39,6 +39,6 @@ public class OpenLocalXRay public static void main(String[] args) throws IOException { final ImageJ imageJ = new ImageJ(); imageJ.ui().showUI(); - new MoBIE( "/Volumes/emcf/Hamburg_XRay/20220522/mobie_demo", new MoBIESettings() ); + new MoBIE( "/Volumes/emcf/Hamburg_XRay/20220522/mobie_demo", new MoBIESettings() ); } } diff --git a/src/test/java/projects/OpenMinimalProjectLocalBlobs.java b/src/test/java/projects/OpenMinimalProjectLocalBlobs.java index 8decd72c4..aeb5497bd 100644 --- a/src/test/java/projects/OpenMinimalProjectLocalBlobs.java +++ b/src/test/java/projects/OpenMinimalProjectLocalBlobs.java @@ -42,6 +42,6 @@ public static void main( String[] args ) throws IOException imageJ.ui().showUI(); new MoBIE( "/Users/tischer/Documents/mobie-viewer-fiji/src/test/resources/minimal-mobie-project" - , new MoBIESettings() ); + , new MoBIESettings() ); } } \ No newline at end of file diff --git a/src/test/java/projects/OpenRemoteArabidopsis.java b/src/test/java/projects/OpenRemoteArabidopsis.java index d276bdde6..df489bb95 100644 --- a/src/test/java/projects/OpenRemoteArabidopsis.java +++ b/src/test/java/projects/OpenRemoteArabidopsis.java @@ -40,6 +40,6 @@ public static void main( String[] args ) throws IOException { final ImageJ imageJ = new ImageJ(); imageJ.ui().showUI(); - new MoBIE("https://github.com/mobie/arabidopsis-root-lm-datasets", new MoBIESettings() ); + new MoBIE("https://github.com/mobie/arabidopsis-root-lm-datasets", new MoBIESettings() ); } } diff --git a/src/test/java/projects/OpenRemoteAutophagosomesCLEM.java b/src/test/java/projects/OpenRemoteAutophagosomesCLEM.java index 7679f5a24..23b9cc588 100644 --- a/src/test/java/projects/OpenRemoteAutophagosomesCLEM.java +++ b/src/test/java/projects/OpenRemoteAutophagosomesCLEM.java @@ -33,7 +33,6 @@ import net.imagej.ImageJ; import java.io.IOException; -import org.embl.mobie.io.ImageDataFormat; public class OpenRemoteAutophagosomesCLEM { @@ -43,7 +42,7 @@ public static void main( String[] args ) imageJ.ui().showUI(); try { new MoBIE("https://github.com/mobie-org/autophagosomes-clem-datasets", - MoBIESettings.settings() ); + MoBIESettings.settings() ); } catch (IOException e) { e.printStackTrace(); } diff --git a/src/test/java/projects/OpenRemoteBdvOmeZarr.java b/src/test/java/projects/OpenRemoteBdvOmeZarr.java index 60a783968..f81178e86 100644 --- a/src/test/java/projects/OpenRemoteBdvOmeZarr.java +++ b/src/test/java/projects/OpenRemoteBdvOmeZarr.java @@ -28,7 +28,6 @@ */ package projects; -import org.embl.mobie.io.ImageDataFormat; import org.embl.mobie.MoBIE; import org.embl.mobie.MoBIESettings; import net.imagej.ImageJ; @@ -39,6 +38,6 @@ public class OpenRemoteBdvOmeZarr { public static void main(String[] args) throws IOException { final ImageJ imageJ = new ImageJ(); imageJ.ui().showUI(); - new MoBIE("https://s3.embl.de/i2k-2020/project-bdv-ome-zarr", MoBIESettings.settings()); + new MoBIE("https://s3.embl.de/i2k-2020/project-bdv-ome-zarr",MoBIESettings.settings()); } } diff --git a/src/test/java/projects/OpenRemoteCLEMExample.java b/src/test/java/projects/OpenRemoteCLEMExample.java index ff7dc37b8..9f2777ee1 100644 --- a/src/test/java/projects/OpenRemoteCLEMExample.java +++ b/src/test/java/projects/OpenRemoteCLEMExample.java @@ -42,6 +42,6 @@ public static void main( String[] args ) throws IOException imageJ.ui().showUI(); new MoBIE("https://github.com/mobie/clem-example-project/", - MoBIESettings.settings().gitProjectBranch( "main" ).view( "SupplFig1a" )); + MoBIESettings.settings().gitProjectBranch( "main" ).view( "SupplFig1a" )); } } diff --git a/src/test/java/projects/OpenRemoteCOMULIS.java b/src/test/java/projects/OpenRemoteCOMULIS.java index ce490d16b..5a1b72066 100644 --- a/src/test/java/projects/OpenRemoteCOMULIS.java +++ b/src/test/java/projects/OpenRemoteCOMULIS.java @@ -33,7 +33,6 @@ import org.embl.mobie.MoBIESettings; import java.io.IOException; -import org.embl.mobie.io.ImageDataFormat; public class OpenRemoteCOMULIS { @@ -41,6 +40,6 @@ public static void main( String[] args ) throws IOException { final ImageJ imageJ = new ImageJ(); imageJ.ui().showUI(); - new MoBIE("https://s3.embl.de/comulis", MoBIESettings.settings().s3AccessAndSecretKey( new String[]{"UYP3FNN3V5F0P86DR2O3","3EL7Czzg0vVwx2L4v27GQiX0Ct1GkMHS+tbcJR3D"} ) ); + new MoBIE("https://s3.embl.de/comulis",MoBIESettings.settings().s3AccessAndSecretKey( new String[]{"UYP3FNN3V5F0P86DR2O3","3EL7Czzg0vVwx2L4v27GQiX0Ct1GkMHS+tbcJR3D"} ) ); } } diff --git a/src/test/java/projects/OpenRemoteCentriolesBranch.java b/src/test/java/projects/OpenRemoteCentriolesBranch.java index 902369ac1..e136599ab 100644 --- a/src/test/java/projects/OpenRemoteCentriolesBranch.java +++ b/src/test/java/projects/OpenRemoteCentriolesBranch.java @@ -33,7 +33,6 @@ import org.embl.mobie.MoBIESettings; import java.io.IOException; -import org.embl.mobie.io.ImageDataFormat; public class OpenRemoteCentriolesBranch { @@ -44,7 +43,7 @@ public static void main( String[] args ) try { new MoBIE("https://github.com/mobie/centrioles-tomo-datasets", - MoBIESettings.settings().gitProjectBranch( "grid-test-tomo" ) ); + MoBIESettings.settings().gitProjectBranch( "grid-test-tomo" ) ); } catch (IOException e) { e.printStackTrace(); } diff --git a/src/test/java/projects/OpenRemoteCovidEM.java b/src/test/java/projects/OpenRemoteCovidEM.java index 3c865453f..39501c265 100644 --- a/src/test/java/projects/OpenRemoteCovidEM.java +++ b/src/test/java/projects/OpenRemoteCovidEM.java @@ -43,7 +43,7 @@ public static void main( String[] args ) try { new MoBIE("https://github.com/mobie/covid-em-project", - MoBIESettings.settings().gitProjectBranch( "mobie3" ).view( "s5_mock_segmentation" ) ); + MoBIESettings.settings().gitProjectBranch( "mobie3" ).view( "s5_mock_segmentation" ) ); } catch (IOException e) { e.printStackTrace(); } diff --git a/src/test/java/projects/OpenRemoteCovidIF.java b/src/test/java/projects/OpenRemoteCovidIF.java index 0129db268..0ce09077f 100644 --- a/src/test/java/projects/OpenRemoteCovidIF.java +++ b/src/test/java/projects/OpenRemoteCovidIF.java @@ -41,6 +41,6 @@ public static void main( String[] args ) throws IOException final ImageJ imageJ = new ImageJ(); imageJ.ui().showUI(); - final MoBIE moBIE = new MoBIE( "https://github.com/mobie/covid-if-project", MoBIESettings.settings().gitProjectBranch( "main" ).view( "default" ) ); //"full_grid" + final MoBIE moBIE = new MoBIE( "https://github.com/mobie/covid-if-project",MoBIESettings.settings().gitProjectBranch( "main" ).view( "default" ) ); //"full_grid" } } diff --git a/src/test/java/projects/OpenRemoteCovidTomogramsBranch.java b/src/test/java/projects/OpenRemoteCovidTomogramsBranch.java index a9081ccfe..2d6f5e4a4 100644 --- a/src/test/java/projects/OpenRemoteCovidTomogramsBranch.java +++ b/src/test/java/projects/OpenRemoteCovidTomogramsBranch.java @@ -43,7 +43,7 @@ public static void main( String[] args ) try { new MoBIE("https://github.com/mobie/covid-tomo-datasets", - MoBIESettings.settings().gitProjectBranch( "mobie3" ).view( "s5_mock_segmentation" ) ); + MoBIESettings.settings().gitProjectBranch( "mobie3" ).view( "s5_mock_segmentation" ) ); } catch (IOException e) { e.printStackTrace(); } diff --git a/src/test/java/projects/OpenRemoteDynoflagellate.java b/src/test/java/projects/OpenRemoteDynoflagellate.java index aba4c86fc..03cde88b8 100644 --- a/src/test/java/projects/OpenRemoteDynoflagellate.java +++ b/src/test/java/projects/OpenRemoteDynoflagellate.java @@ -40,6 +40,6 @@ public static void main( String[] args ) throws IOException { final ImageJ imageJ = new ImageJ(); imageJ.ui().showUI(); - new MoBIE( "https://github.com/mobie/environmental-dinoflagellate-vCLEM", new MoBIESettings() ); + new MoBIE( "https://github.com/mobie/environmental-dinoflagellate-vCLEM", new MoBIESettings() ); } } diff --git a/src/test/java/projects/OpenRemoteMalariaWithCredentials.java b/src/test/java/projects/OpenRemoteMalariaWithCredentials.java index 74be849c0..496bd9c5b 100644 --- a/src/test/java/projects/OpenRemoteMalariaWithCredentials.java +++ b/src/test/java/projects/OpenRemoteMalariaWithCredentials.java @@ -43,7 +43,7 @@ public static void main( String[] args ) try { new MoBIE("https://s3.embl.de/plasmodium-oocysts/mobie", - MoBIESettings.settings().s3AccessAndSecretKey( new String[]{ "DstL6Ju", "r4bqZzZsyJde9"} ) ); + MoBIESettings.settings().s3AccessAndSecretKey( new String[]{ "DstL6Ju", "r4bqZzZsyJde9"} ) ); } catch (IOException e) { e.printStackTrace(); } diff --git a/src/test/java/projects/OpenRemoteOpenOrganelle.java b/src/test/java/projects/OpenRemoteOpenOrganelle.java index 4b0a72cff..dc0543992 100644 --- a/src/test/java/projects/OpenRemoteOpenOrganelle.java +++ b/src/test/java/projects/OpenRemoteOpenOrganelle.java @@ -33,7 +33,6 @@ import net.imagej.ImageJ; import java.io.IOException; -import org.embl.mobie.io.ImageDataFormat; public class OpenRemoteOpenOrganelle { @@ -42,7 +41,7 @@ public static void main( String[] args ) final ImageJ imageJ = new ImageJ(); imageJ.ui().showUI(); try { - new MoBIE("https://github.com/mobie/open-organelle-test", MoBIESettings.settings() ); + new MoBIE("https://github.com/mobie/open-organelle-test",MoBIESettings.settings() ); } catch (IOException e) { e.printStackTrace(); } diff --git a/src/test/java/projects/OpenRemotePagDapex2FIBSEM.java b/src/test/java/projects/OpenRemotePagDapex2FIBSEM.java index 35edf2b23..ec942a3a6 100644 --- a/src/test/java/projects/OpenRemotePagDapex2FIBSEM.java +++ b/src/test/java/projects/OpenRemotePagDapex2FIBSEM.java @@ -41,7 +41,7 @@ public static void main( String[] args ) final ImageJ imageJ = new ImageJ(); imageJ.ui().showUI(); try { - new MoBIE("https://github.com/mobie/pag-dapex2-fibsem", MoBIESettings.settings().gitProjectBranch( "mobie3" ) ); + new MoBIE("https://github.com/mobie/pag-dapex2-fibsem",MoBIESettings.settings().gitProjectBranch( "mobie3" ) ); } catch (IOException e) { e.printStackTrace(); } diff --git a/src/test/java/projects/OpenRemotePlankton.java b/src/test/java/projects/OpenRemotePlankton.java index dbdb20e18..962ca7c0d 100644 --- a/src/test/java/projects/OpenRemotePlankton.java +++ b/src/test/java/projects/OpenRemotePlankton.java @@ -41,7 +41,7 @@ public static void main( String[] args ) final ImageJ imageJ = new ImageJ(); imageJ.ui().showUI(); try { - new MoBIE("https://github.com/mobie/plankton-fibsem-project", MoBIESettings.settings().gitProjectBranch( "mobie3" ).dataset( "micromonas" ).view( "all-cells" ) ); + new MoBIE("https://github.com/mobie/plankton-fibsem-project",MoBIESettings.settings().gitProjectBranch( "mobie3" ).dataset( "micromonas" ).view( "all-cells" ) ); } catch (IOException e) { e.printStackTrace(); } diff --git a/src/test/java/projects/OpenRemotePlatynereis.java b/src/test/java/projects/OpenRemotePlatynereis.java index ae0f1d156..555e2dae8 100644 --- a/src/test/java/projects/OpenRemotePlatynereis.java +++ b/src/test/java/projects/OpenRemotePlatynereis.java @@ -42,6 +42,6 @@ public static void main( String[] args ) throws IOException imageJ.ui().showUI(); final MoBIE moBIE = new MoBIE( "https://github.com/mobie/covid-if-project", - MoBIESettings.settings().gitProjectBranch( "main" ).view( "default" ) ); + MoBIESettings.settings().gitProjectBranch( "main" ).view( "default" ) ); } } diff --git a/src/test/java/projects/OpenRemoteSponge.java b/src/test/java/projects/OpenRemoteSponge.java index 35730401f..6af8e601e 100644 --- a/src/test/java/projects/OpenRemoteSponge.java +++ b/src/test/java/projects/OpenRemoteSponge.java @@ -41,6 +41,6 @@ public static void main( String[] args ) throws IOException final ImageJ imageJ = new ImageJ(); imageJ.ui().showUI(); - final MoBIE moBIE = new MoBIE( "https://github.com/mobie/sponge-fibsem-project", MoBIESettings.settings().gitProjectBranch( "mobie3" ).view( "fibsem-cell" ) ); + final MoBIE moBIE = new MoBIE( "https://github.com/mobie/sponge-fibsem-project",MoBIESettings.settings().gitProjectBranch( "mobie3" ).view( "fibsem-cell" ) ); } } diff --git a/src/test/java/projects/OpenRemoteTomograms.java b/src/test/java/projects/OpenRemoteTomograms.java index d240ecfad..4aeae9753 100644 --- a/src/test/java/projects/OpenRemoteTomograms.java +++ b/src/test/java/projects/OpenRemoteTomograms.java @@ -33,7 +33,6 @@ import net.imagej.ImageJ; import java.io.IOException; -import org.embl.mobie.io.ImageDataFormat; public class OpenRemoteTomograms { @@ -44,7 +43,7 @@ public static void main( String[] args ) try { new MoBIE("https://github.com/mobie/covid-tomo-datasets", - MoBIESettings.settings() ); + MoBIESettings.settings() ); } catch (IOException e) { e.printStackTrace(); } diff --git a/src/test/java/projects/OpenRemoteZebrafish.java b/src/test/java/projects/OpenRemoteZebrafish.java index 6fceeec18..6d0de050e 100644 --- a/src/test/java/projects/OpenRemoteZebrafish.java +++ b/src/test/java/projects/OpenRemoteZebrafish.java @@ -40,6 +40,6 @@ public static void main( String[] args ) throws IOException { final ImageJ imageJ = new ImageJ(); imageJ.ui().showUI(); - new MoBIE("https://github.com/mobie/zebrafish-lm-datasets", new MoBIESettings() ); + new MoBIE("https://github.com/mobie/zebrafish-lm-datasets", new MoBIESettings() ); } } diff --git a/src/test/java/projects/drosophila_synthetic_locus/DrosophilaSyntheticLocus.java b/src/test/java/projects/drosophila_synthetic_locus/DrosophilaSyntheticLocus.java index da03915d6..30fc56d6d 100644 --- a/src/test/java/projects/drosophila_synthetic_locus/DrosophilaSyntheticLocus.java +++ b/src/test/java/projects/drosophila_synthetic_locus/DrosophilaSyntheticLocus.java @@ -1,9 +1,23 @@ package projects.drosophila_synthetic_locus; +import net.imagej.ImageJ; +import org.embl.mobie.command.SpatialCalibration; +import org.embl.mobie.command.open.OpenTableCommand; +import org.embl.mobie.lib.transform.GridType; + +import java.io.File; + public class DrosophilaSyntheticLocus { public static void main( String[] args ) { - "/Volumes/Image_analysis/stage_8_image_analysis/20240624-stage8/summary_.txt"; + new ImageJ().ui().showUI(); + OpenTableCommand command = new OpenTableCommand(); + command.table = new File( "/Volumes/Image_analysis/stage_8_image_analysis/20240624-stage8/summary_.txt" ); + command.gridType = GridType.Transformed; + command.spatialCalibration = SpatialCalibration.FromImage; + command.images ="FileName_Result.Image_IMG"; + command.root = new File("/Volumes/Image_analysis/stage_8_image_analysis/20240624-stage8" ); + command.run(); } } diff --git a/src/test/java/projects/em_xray_alignment/OpenEMXRAY.java b/src/test/java/projects/em_xray_alignment/OpenEMXRAY.java index 274d2b307..881818ef8 100644 --- a/src/test/java/projects/em_xray_alignment/OpenEMXRAY.java +++ b/src/test/java/projects/em_xray_alignment/OpenEMXRAY.java @@ -42,6 +42,6 @@ public static void main( String[] args ) throws IOException final ImageJ imageJ = new ImageJ(); imageJ.ui().showUI(); MoBIESettings settings = new MoBIESettings(); //.view( "em-invert-sift-similarity_iat" ); - new MoBIE("/Volumes/cba/exchange/em-xray-alignment/mobie", settings ); + new MoBIE("/Volumes/cba/exchange/em-xray-alignment/mobie", settings ); } } diff --git a/src/test/java/projects/platybrowser/OpenLocalPlatynereis.java b/src/test/java/projects/platybrowser/OpenLocalPlatynereis.java index 19917843f..0b982ff32 100644 --- a/src/test/java/projects/platybrowser/OpenLocalPlatynereis.java +++ b/src/test/java/projects/platybrowser/OpenLocalPlatynereis.java @@ -41,6 +41,6 @@ public static void main( String[] args ) throws IOException final ImageJ imageJ = new ImageJ(); imageJ.ui().showUI(); - final MoBIE moBIE = new MoBIE( "/Volumes/cba/exchange/buglakova/platybrowser-smfish-project", new MoBIESettings() ); + final MoBIE moBIE = new MoBIE( "/Volumes/cba/exchange/buglakova/platybrowser-smfish-project", new MoBIESettings() ); } } diff --git a/src/test/java/projects/platybrowser/OpenRemotePlatynereisBranch.java b/src/test/java/projects/platybrowser/OpenRemotePlatynereisBranch.java index 9dd601090..256536d35 100644 --- a/src/test/java/projects/platybrowser/OpenRemotePlatynereisBranch.java +++ b/src/test/java/projects/platybrowser/OpenRemotePlatynereisBranch.java @@ -40,6 +40,6 @@ public static void main( String[] args ) throws IOException { final ImageJ imageJ = new ImageJ(); imageJ.ui().showUI(); - new MoBIE( "https://github.com/mobie/platybrowser-datasets", MoBIESettings.settings().gitProjectBranch( "main" ).view( "cells" ) ); //"Figure 3B: Morphology clustering full body" + new MoBIE( "https://github.com/mobie/platybrowser-datasets",MoBIESettings.settings().gitProjectBranch( "main" ).view( "cells" ) ); //"Figure 3B: Morphology clustering full body" } } diff --git a/src/test/java/projects/platybrowser/OpenRemotePlatynereisFigure2B.java b/src/test/java/projects/platybrowser/OpenRemotePlatynereisFigure2B.java index d176e71de..e41cf9fd8 100644 --- a/src/test/java/projects/platybrowser/OpenRemotePlatynereisFigure2B.java +++ b/src/test/java/projects/platybrowser/OpenRemotePlatynereisFigure2B.java @@ -41,6 +41,6 @@ public static void main( String[] args ) throws IOException final ImageJ imageJ = new ImageJ(); imageJ.ui().showUI(); - final MoBIE moBIE = new MoBIE( "https://github.com/platybrowser/platybrowser", new MoBIESettings().view( "Figure 2B: Epithelial cell segmentation" ) ); + final MoBIE moBIE = new MoBIE( "https://github.com/platybrowser/platybrowser", new MoBIESettings().view( "Figure 2B: Epithelial cell segmentation" ) ); } } diff --git a/src/test/java/projects/rafael/CreateRafaelProject.java b/src/test/java/projects/rafael/CreateRafaelProject.java index db2b5da6f..cf7d1c0f9 100644 --- a/src/test/java/projects/rafael/CreateRafaelProject.java +++ b/src/test/java/projects/rafael/CreateRafaelProject.java @@ -110,7 +110,7 @@ public static void main( String[] args ) throws IOException, SpimDataException } // Show the project in MoBIE - new MoBIE( projectDirectory, new MoBIESettings() ); + new MoBIE( projectDirectory, new MoBIESettings() ); } private static ImagePlus cropAndClearOutside( ImagePlus imp, Roi roi ) diff --git a/src/test/resources/collections/Opening images for image analysis through MoBIE.docx b/src/test/resources/collections/Opening images for image analysis through MoBIE.docx new file mode 100644 index 000000000..a0cf06ba8 Binary files /dev/null and b/src/test/resources/collections/Opening images for image analysis through MoBIE.docx differ diff --git a/src/test/resources/collections/blobs-table.txt b/src/test/resources/collections/blobs-table.txt index bf610147d..f816ebdcd 100644 --- a/src/test/resources/collections/blobs-table.txt +++ b/src/test/resources/collections/blobs-table.txt @@ -1,4 +1,4 @@ uri type affine color view -/Users/tischer/Documents/mobie-viewer-fiji/src/test/resources/collections/blobs.tif intensities (1,0,0,-80,0,1,0,0,0,0,1,0) green -/Users/tischer/Documents/mobie-viewer-fiji/src/test/resources/collections/blobs.tif intensities segmented blobs -/Users/tischer/Documents/mobie-viewer-fiji/src/test/resources/collections/blobs-labels.tif labels segmented blobs \ No newline at end of file +collections/blobs.tif intensities (10,0,0,0,0,10,0,0,0,0,1,0) segmented blobs +collections/blobs-labels.tif labels (10,0,0,0,0,10,0,0,0,0,1,0) segmented blobs +collections/mri-stack intensities (10,0,0,0,0,10,0,0,0,0,100,0) mri \ No newline at end of file diff --git a/src/test/resources/collections/mri-stack/mri-stack-0000.tif b/src/test/resources/collections/mri-stack/mri-stack-0000.tif new file mode 100644 index 000000000..811c6240f Binary files /dev/null and b/src/test/resources/collections/mri-stack/mri-stack-0000.tif differ diff --git a/src/test/resources/collections/mri-stack/mri-stack-0001.tif b/src/test/resources/collections/mri-stack/mri-stack-0001.tif new file mode 100644 index 000000000..dce7c2cf7 Binary files /dev/null and b/src/test/resources/collections/mri-stack/mri-stack-0001.tif differ diff --git a/src/test/resources/collections/mri-stack/mri-stack-0002.tif b/src/test/resources/collections/mri-stack/mri-stack-0002.tif new file mode 100644 index 000000000..f1064937b Binary files /dev/null and b/src/test/resources/collections/mri-stack/mri-stack-0002.tif differ diff --git a/src/test/resources/collections/mri-stack/mri-stack-0003.tif b/src/test/resources/collections/mri-stack/mri-stack-0003.tif 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