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
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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
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diff --git a/src/test/resources/collections/mri-stack/mri-stack-0001.tif b/src/test/resources/collections/mri-stack/mri-stack-0001.tif
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diff --git a/src/test/resources/collections/mri-stack/mri-stack-0002.tif b/src/test/resources/collections/mri-stack/mri-stack-0002.tif
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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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