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Animation duration ref #569

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4 changes: 2 additions & 2 deletions pom.xml
Original file line number Diff line number Diff line change
Expand Up @@ -93,7 +93,7 @@

<!-- EMBL CBA -->
<imagej-utils.version>0.6.4</imagej-utils.version>
<mobie-io.version>1.0.8</mobie-io.version>
<mobie-io.version>1.0.9-SNAPSHOT</mobie-io.version>

<!-- Version 1.6.0-scijava-3-SNAPSHOT of j3dcore addresses a minor issue
https://github.com/fiji/3D_Viewer/issues/26
Expand Down Expand Up @@ -162,7 +162,7 @@
<dependency>
<groupId>org.embl.mobie</groupId>
<artifactId>mobie-io</artifactId>
<version>${mobie-io.version}</version>
<version>1.0.9</version>
</dependency>
<dependency>
<groupId>org.janelia.saalfeldlab</groupId>
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4 changes: 2 additions & 2 deletions src/main/java/org/embl/mobie/viewer/MoBIE.java
Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,8 @@
import bdv.viewer.Source;
import bdv.viewer.SourceAndConverter;
import de.embl.cba.bdv.utils.Logger;
import org.embl.mobie.io.n5.openers.SpimDataOpener;
import org.embl.mobie.io.n5.util.ImageDataFormat;
import org.embl.mobie.io.ome.zarr.loaders.N5OMEZarrImageLoader;
import org.embl.mobie.viewer.display.SegmentationSourceDisplay;
import org.embl.mobie.viewer.display.AnnotatedIntervalDisplay;
Expand All @@ -12,10 +14,8 @@
import org.embl.mobie.viewer.playground.BdvPlaygroundUtils;
import org.embl.mobie.viewer.serialize.DatasetJsonParser;
import org.embl.mobie.viewer.serialize.ProjectJsonParser;
import org.embl.mobie.viewer.source.ImageDataFormat;
import org.embl.mobie.viewer.source.ImageSource;
import org.embl.mobie.viewer.source.SegmentationSource;
import org.embl.mobie.viewer.source.SpimDataOpener;
import org.embl.mobie.viewer.table.TableDataFormat;
import org.embl.mobie.viewer.ui.UserInterface;
import org.embl.mobie.viewer.ui.WindowArrangementHelper;
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3 changes: 2 additions & 1 deletion src/main/java/org/embl/mobie/viewer/MoBIESettings.java
Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
package org.embl.mobie.viewer;

import org.embl.mobie.viewer.source.ImageDataFormat;

import org.embl.mobie.io.n5.util.ImageDataFormat;

public class MoBIESettings
{
Expand Down
3 changes: 2 additions & 1 deletion src/main/java/org/embl/mobie/viewer/Project.java
Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
package org.embl.mobie.viewer;

import org.embl.mobie.viewer.source.ImageDataFormat;

import org.embl.mobie.io.n5.util.ImageDataFormat;

import java.util.List;

Expand Down
Original file line number Diff line number Diff line change
@@ -1,8 +1,8 @@
package org.embl.mobie.viewer.command;

import org.embl.mobie.io.n5.util.ImageDataFormat;
import org.embl.mobie.viewer.MoBIE;
import org.embl.mobie.viewer.MoBIESettings;
import org.embl.mobie.viewer.source.ImageDataFormat;
import org.scijava.command.Command;
import org.scijava.plugin.Parameter;
import org.scijava.plugin.Plugin;
Expand Down
Original file line number Diff line number Diff line change
@@ -1,8 +1,8 @@
package org.embl.mobie.viewer.command;

import mpicbg.spim.data.SpimData;
import org.embl.mobie.io.ome.zarr.OMEZarrViewer;
import org.embl.mobie.io.ome.zarr.openers.OMEZarrOpener;
import org.embl.mobie.viewer.view.OMEZarrViewer;
import org.scijava.command.Command;
import org.scijava.plugin.Parameter;
import org.scijava.plugin.Plugin;
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Original file line number Diff line number Diff line change
@@ -1,8 +1,8 @@
package org.embl.mobie.viewer.command;

import org.embl.mobie.io.n5.util.ImageDataFormat;
import org.embl.mobie.viewer.MoBIE;
import org.embl.mobie.viewer.MoBIESettings;
import org.embl.mobie.viewer.source.ImageDataFormat;
import org.scijava.command.Command;
import org.scijava.plugin.Plugin;

Expand Down
Original file line number Diff line number Diff line change
@@ -1,9 +1,9 @@
package org.embl.mobie.viewer.command;

import org.embl.mobie.io.n5.util.DownsampleBlock;
import org.embl.mobie.io.n5.util.ImageDataFormat;
import org.embl.mobie.io.ome.zarr.writers.imgplus.WriteImgPlusToN5OmeZarr;
import org.embl.mobie.viewer.projectcreator.ui.ManualExportPanel;
import org.embl.mobie.viewer.source.ImageDataFormat;
import ij.ImagePlus;
import net.imglib2.realtransform.AffineTransform3D;
import org.janelia.saalfeldlab.n5.GzipCompression;
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Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
package org.embl.mobie.viewer.projectcreator;

import org.embl.mobie.io.n5.util.ImageDataFormat;
import org.embl.mobie.viewer.TableColumnNames;
import org.embl.mobie.viewer.Dataset;
import org.embl.mobie.viewer.display.ImageSourceDisplay;
Expand Down Expand Up @@ -28,8 +29,8 @@ public DatasetJsonCreator( ProjectCreator projectCreator ) {
}

public void addImageToDatasetJson( String imageName, String datasetName,
String uiSelectionGroup, boolean is2D, int nTimepoints,
ImageDataFormat imageDataFormat, double[] contrastLimits, String colour ) {
String uiSelectionGroup, boolean is2D, int nTimepoints,
ImageDataFormat imageDataFormat, double[] contrastLimits, String colour ) {
Dataset dataset = fetchDataset( datasetName, is2D, nTimepoints );

addNewImageSource( dataset, imageName, imageDataFormat );
Expand Down
Original file line number Diff line number Diff line change
@@ -1,8 +1,8 @@
package org.embl.mobie.viewer.projectcreator;

import org.embl.mobie.io.n5.util.ImageDataFormat;
import org.embl.mobie.viewer.Project;
import org.embl.mobie.viewer.serialize.ProjectJsonParser;
import org.embl.mobie.viewer.source.ImageDataFormat;
import de.embl.cba.tables.FileAndUrlUtils;
import ij.IJ;

Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -7,16 +7,16 @@
import bdv.viewer.SourceAndConverter;
import ij.process.LUT;
import org.embl.mobie.io.n5.loaders.N5FSImageLoader;
import org.embl.mobie.io.n5.openers.SpimDataOpener;
import org.embl.mobie.io.n5.util.DownsampleBlock;
import org.embl.mobie.io.n5.util.ImageDataFormat;
import org.embl.mobie.io.n5.writers.WriteImgPlusToN5;
import org.embl.mobie.io.ome.zarr.loaders.N5OMEZarrImageLoader;
import org.embl.mobie.io.ome.zarr.readers.N5OmeZarrReader;
import org.embl.mobie.io.ome.zarr.writers.imgplus.WriteImgPlusToN5BdvOmeZarr;
import org.embl.mobie.io.ome.zarr.writers.imgplus.WriteImgPlusToN5OmeZarr;

import org.embl.mobie.viewer.projectcreator.ui.ManualExportPanel;
import org.embl.mobie.viewer.source.ImageDataFormat;
import org.embl.mobie.viewer.source.SpimDataOpener;
import de.embl.cba.tables.FileAndUrlUtils;
import de.embl.cba.tables.Tables;
import ij.IJ;
Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -3,11 +3,11 @@
import bdv.img.n5.N5ImageLoader;
import org.embl.mobie.io.n5.loaders.N5FSImageLoader;
import org.embl.mobie.io.n5.loaders.N5S3ImageLoader;
import org.embl.mobie.io.n5.util.ImageDataFormat;
import org.embl.mobie.io.ome.zarr.loaders.N5OMEZarrImageLoader;
import org.embl.mobie.io.ome.zarr.loaders.N5S3OMEZarrImageLoader;
import org.embl.mobie.io.ome.zarr.readers.N5OmeZarrReader;
import org.embl.mobie.viewer.Dataset;
import org.embl.mobie.viewer.source.ImageDataFormat;
import org.embl.mobie.viewer.view.View;
import org.embl.mobie.viewer.view.additionalviews.AdditionalViews;
import de.embl.cba.tables.FileAndUrlUtils;
Expand Down
Original file line number Diff line number Diff line change
@@ -1,11 +1,11 @@
package org.embl.mobie.viewer.projectcreator;

import org.embl.mobie.io.n5.loaders.xml.XmlIoN5S3ImageLoader;
import org.embl.mobie.io.n5.openers.SpimDataOpener;
import org.embl.mobie.io.n5.util.ImageDataFormat;
import org.embl.mobie.io.ome.zarr.loaders.xml.XmlN5S3OmeZarrImageLoader;
import org.embl.mobie.viewer.Dataset;
import org.embl.mobie.viewer.source.ImageDataFormat;
import org.embl.mobie.viewer.source.ImageSource;
import org.embl.mobie.viewer.source.SpimDataOpener;
import org.embl.mobie.viewer.source.StorageLocation;
import de.embl.cba.tables.FileAndUrlUtils;
import ij.IJ;
Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -2,10 +2,10 @@

import bdv.ij.util.PluginHelper;
import org.embl.mobie.io.n5.util.DownsampleBlock;
import org.embl.mobie.io.n5.util.ImageDataFormat;
import org.embl.mobie.io.n5.writers.WriteImgPlusToN5;
import org.embl.mobie.io.ome.zarr.writers.imgplus.WriteImgPlusToN5BdvOmeZarr;
import org.embl.mobie.io.ome.zarr.writers.imgplus.WriteImgPlusToN5OmeZarr;
import org.embl.mobie.viewer.source.ImageDataFormat;

import fiji.util.gui.GenericDialogPlus;
import ij.IJ;
Expand Down
Original file line number Diff line number Diff line change
@@ -1,12 +1,12 @@
package org.embl.mobie.viewer.projectcreator.ui;

import org.embl.mobie.io.n5.util.ImageDataFormat;
import org.embl.mobie.viewer.Dataset;
import org.embl.mobie.viewer.MoBIE;
import org.embl.mobie.viewer.Project;
import org.embl.mobie.viewer.MoBIEUtils;
import org.embl.mobie.viewer.command.OpenMoBIEProjectCommand;
import org.embl.mobie.viewer.projectcreator.ProjectCreator;
import org.embl.mobie.viewer.source.ImageDataFormat;
import de.embl.cba.tables.FileAndUrlUtils;
import de.embl.cba.tables.SwingUtils;
import ij.IJ;
Expand Down
111 changes: 0 additions & 111 deletions src/main/java/org/embl/mobie/viewer/source/ImageDataFormat.java

This file was deleted.

4 changes: 3 additions & 1 deletion src/main/java/org/embl/mobie/viewer/source/ImageSource.java
Original file line number Diff line number Diff line change
@@ -1,8 +1,10 @@
package org.embl.mobie.viewer.source;

import org.embl.mobie.io.n5.util.ImageDataFormat;

import java.util.Map;

public class ImageSource
{
public Map< ImageDataFormat, StorageLocation > imageData;
public Map<ImageDataFormat, StorageLocation > imageData;
}
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