diff --git a/pom.xml b/pom.xml index 94c4822e9..470d92e97 100644 --- a/pom.xml +++ b/pom.xml @@ -88,7 +88,7 @@ 0.7.0 0.9.0 - 9.1.2 + 9.1.3 1.0.2 16.0.2 diff --git a/src/main/java/org/embl/mobie/command/context/BigWarpRegistrationCommand.java b/src/main/java/org/embl/mobie/command/context/BigWarpRegistrationCommand.java index 8ffba857c..2bfbe9342 100644 --- a/src/main/java/org/embl/mobie/command/context/BigWarpRegistrationCommand.java +++ b/src/main/java/org/embl/mobie/command/context/BigWarpRegistrationCommand.java @@ -34,6 +34,7 @@ import bdv.viewer.SourceAndConverter; import bdv.viewer.TransformListener; import bigwarp.BigWarp; +import bigwarp.transforms.BigWarpTransform; import jj2000.j2k.codestream.HeaderInfo; import org.embl.mobie.command.CommandConstants; import org.embl.mobie.lib.transform.TransformHelper; @@ -115,7 +116,7 @@ public void launchBigWarp() final AffineTransform3D normalisedViewerTransform = TransformHelper.createNormalisedViewerTransform( bdvHandle.getViewerPanel() ); applyViewerTransform( normalisedViewerTransform, bigWarp.getViewerFrameQ().getViewerPanel() ); applyViewerTransform( normalisedViewerTransform, bigWarp.getViewerFrameP().getViewerPanel() ); - bigWarp.setTransformType( TransformTypeSelectDialog.AFFINE ); + bigWarp.setTransformType( BigWarpTransform.AFFINE ); bigWarp.addTransformListener( this ); } @@ -136,9 +137,9 @@ public void cancel() public void transformChanged( InvertibleRealTransform transform ) { final String transformType = bigWarp.getTransformType(); - if ( transformType.equals( TransformTypeSelectDialog.TPS ) ) + if ( transformType.equals( BigWarpTransform.TPS ) ) { - System.err.println( TransformTypeSelectDialog.TPS + "is currently not supported by MoBIE please choose any of the other transform types by selecting one of the BigWarp windows and pressing F2."); + System.err.println( BigWarpTransform.TPS + "is currently not supported by MoBIE please choose any of the other transform types by selecting one of the BigWarp windows and pressing F2."); } } diff --git a/src/test/java/examples/CreateMoBIEProject.java b/src/test/java/examples/CreateMoBIEProject.java new file mode 100644 index 000000000..453a7ea8d --- /dev/null +++ b/src/test/java/examples/CreateMoBIEProject.java @@ -0,0 +1,47 @@ +package examples; + +import ij.IJ; +import ij.ImagePlus; +import net.imagej.ImageJ; +import net.imglib2.realtransform.AffineTransform3D; +import org.embl.mobie.command.open.project.OpenMoBIEProjectCommand; +import org.embl.mobie.io.ImageDataFormat; +import org.embl.mobie.lib.create.ProjectCreator; + +import java.io.File; +import java.io.IOException; + +public class CreateMoBIEProject +{ + public static void main( String[] args ) throws IOException + { + // Init the project + // Please CHANGE the below path to point to location on your computer + String projectPath = "/Users/tischer/Documents/mobie-viewer-fiji/src/test/resources/test-project"; + + ProjectCreator creator = new ProjectCreator( new File( projectPath ) ); + creator.getDatasetsCreator().addDataset( + "dataset", + false // say whether the data is only 2D (false = 3D) + ); + + // Add one image + ImagePlus imagePlus = IJ.openImage( "http://imagej.net/images/mri-stack.zip" ); + creator.getImagesCreator().addImage( + imagePlus, + "MRI", + "dataset", + ProjectCreator.ImageType.Image, + new AffineTransform3D(), + "views", + false, // view is exclusive + true // overwrite + ); + + // Open the project to check whether it worked + new ImageJ().ui().showUI(); + OpenMoBIEProjectCommand openMoBIE = new OpenMoBIEProjectCommand(); + openMoBIE.uri = creator.getProjectLocation().getAbsolutePath(); + openMoBIE.run(); + } +} 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 deleted file mode 100644 index a0cf06ba8..000000000 Binary files a/src/test/resources/collections/Opening images for image analysis through MoBIE.docx and /dev/null differ diff --git a/src/test/resources/test-project/dataset/dataset.json b/src/test/resources/test-project/dataset/dataset.json new file mode 100644 index 000000000..d8d060c44 --- /dev/null +++ b/src/test/resources/test-project/dataset/dataset.json @@ -0,0 +1,70 @@ +{ + "is2D": false, + "defaultLocation": { + "position": [ + 0.0, + 0.0, + 0.0 + ], + "timepoint": 0 + }, + "sources": { + "MRI": { + "image": { + "imageData": { + "ome.zarr": { + "relativePath": "images/MRI.ome.zarr" + } + } + } + } + }, + "views": { + "MRI": { + "uiSelectionGroup": "views", + "sourceDisplays": [ + { + "imageDisplay": { + "sources": [ + "MRI" + ], + "color": "r255-g255-b255-a255", + "contrastLimits": [ + 0.0, + 255.0 + ], + "showImagesIn3d": false, + "invert": false, + "name": "MRI", + "opacity": 1.0, + "visible": true + } + } + ], + "isExclusive": false + }, + "default": { + "uiSelectionGroup": "bookmark", + "sourceDisplays": [ + { + "imageDisplay": { + "sources": [ + "MRI" + ], + "color": "r255-g255-b255-a255", + "contrastLimits": [ + 0.0, + 255.0 + ], + "showImagesIn3d": false, + "invert": false, + "name": "MRI", + "opacity": 1.0, + "visible": true + } + } + ], + "isExclusive": true + } + } +} \ No newline at end of file diff --git a/src/test/resources/test-project/dataset/images/MRI.ome.zarr/.zattrs b/src/test/resources/test-project/dataset/images/MRI.ome.zarr/.zattrs new file mode 100644 index 000000000..a11aea9e8 --- /dev/null +++ b/src/test/resources/test-project/dataset/images/MRI.ome.zarr/.zattrs @@ -0,0 +1 @@ +{"multiscales":[{"name":"","type":"Average","version":"0.4","axes":[{"type":"space","name":"z","unit":"pixel"},{"type":"space","name":"y","unit":"pixel"},{"type":"space","name":"x","unit":"pixel"}],"datasets":[{"path":"s0","coordinateTransformations":[{"scale":[1.0,1.0,1.0],"type":"scale"},{"translation":[0.0,0.0,0.0],"type":"translation"}]}],"coordinateTransformations":[]}]} \ No newline at end of file diff --git a/src/test/resources/test-project/dataset/images/MRI.ome.zarr/.zgroup b/src/test/resources/test-project/dataset/images/MRI.ome.zarr/.zgroup new file mode 100644 index 000000000..c71fe9d0b --- /dev/null +++ b/src/test/resources/test-project/dataset/images/MRI.ome.zarr/.zgroup @@ -0,0 +1 @@ +{"zarr_format":2} \ No newline at end of file diff --git a/src/test/resources/test-project/dataset/images/MRI.ome.zarr/s0/.zarray b/src/test/resources/test-project/dataset/images/MRI.ome.zarr/s0/.zarray new file mode 100644 index 000000000..2aeba983f --- /dev/null +++ b/src/test/resources/test-project/dataset/images/MRI.ome.zarr/s0/.zarray @@ -0,0 +1 @@ +{"zarr_format":2,"shape":[27,226,186],"chunks":[96,96,96],"dtype":"|u1","compressor":{"id":"gzip","level":-1},"fill_value":0,"filters":[],"order":"C","dimension_separator":"/"} \ No newline at end of file diff --git a/src/test/resources/test-project/dataset/images/MRI.ome.zarr/s0/.zattrs b/src/test/resources/test-project/dataset/images/MRI.ome.zarr/s0/.zattrs new file mode 100644 index 000000000..463fae2a9 --- /dev/null +++ b/src/test/resources/test-project/dataset/images/MRI.ome.zarr/s0/.zattrs @@ -0,0 +1 @@ +{"path":"s0","axes":[{"type":"space","name":"x","unit":"pixel"},{"type":"space","name":"y","unit":"pixel"},{"type":"space","name":"z","unit":"pixel"}],"coordinateTransformations":[{"scale":[1.0,1.0,1.0],"type":"scale"},{"translation":[0.0,0.0,0.0],"type":"translation"}]} \ No newline at end of file diff --git a/src/test/resources/test-project/dataset/images/MRI.ome.zarr/s0/0/0/0 b/src/test/resources/test-project/dataset/images/MRI.ome.zarr/s0/0/0/0 new file mode 100644 index 000000000..b10aae8d6 Binary files /dev/null and b/src/test/resources/test-project/dataset/images/MRI.ome.zarr/s0/0/0/0 differ diff --git a/src/test/resources/test-project/dataset/images/MRI.ome.zarr/s0/0/0/1 b/src/test/resources/test-project/dataset/images/MRI.ome.zarr/s0/0/0/1 new file mode 100644 index 000000000..c2c9120fb Binary files /dev/null and b/src/test/resources/test-project/dataset/images/MRI.ome.zarr/s0/0/0/1 differ diff --git a/src/test/resources/test-project/dataset/images/MRI.ome.zarr/s0/0/1/0 b/src/test/resources/test-project/dataset/images/MRI.ome.zarr/s0/0/1/0 new file mode 100644 index 000000000..04bec0985 Binary files /dev/null and b/src/test/resources/test-project/dataset/images/MRI.ome.zarr/s0/0/1/0 differ diff --git a/src/test/resources/test-project/dataset/images/MRI.ome.zarr/s0/0/1/1 b/src/test/resources/test-project/dataset/images/MRI.ome.zarr/s0/0/1/1 new file mode 100644 index 000000000..d28b33d28 Binary files /dev/null and b/src/test/resources/test-project/dataset/images/MRI.ome.zarr/s0/0/1/1 differ diff --git a/src/test/resources/test-project/dataset/images/MRI.ome.zarr/s0/0/2/0 b/src/test/resources/test-project/dataset/images/MRI.ome.zarr/s0/0/2/0 new file mode 100644 index 000000000..5dc010f00 Binary files /dev/null and b/src/test/resources/test-project/dataset/images/MRI.ome.zarr/s0/0/2/0 differ diff --git a/src/test/resources/test-project/dataset/images/MRI.ome.zarr/s0/0/2/1 b/src/test/resources/test-project/dataset/images/MRI.ome.zarr/s0/0/2/1 new file mode 100644 index 000000000..147e329b8 Binary files /dev/null and b/src/test/resources/test-project/dataset/images/MRI.ome.zarr/s0/0/2/1 differ diff --git a/src/test/resources/test-project/project.json b/src/test/resources/test-project/project.json new file mode 100644 index 000000000..1a055e995 --- /dev/null +++ b/src/test/resources/test-project/project.json @@ -0,0 +1,8 @@ +{ + "datasets": [ + "dataset" + ], + "defaultDataset": "dataset", + "specVersion": "0.3.0", + "references": [] +} \ No newline at end of file diff --git a/test-project/dataset/dataset.json b/test-project/dataset/dataset.json new file mode 100644 index 000000000..1f7f6ce34 --- /dev/null +++ b/test-project/dataset/dataset.json @@ -0,0 +1,13 @@ +{ + "is2D": false, + "defaultLocation": { + "position": [ + 0.0, + 0.0, + 0.0 + ], + "timepoint": 0 + }, + "sources": {}, + "views": {} +} \ No newline at end of file diff --git a/test-project/dataset/images/MRI.ome.zarr/.zattrs b/test-project/dataset/images/MRI.ome.zarr/.zattrs new file mode 100644 index 000000000..a11aea9e8 --- /dev/null +++ b/test-project/dataset/images/MRI.ome.zarr/.zattrs @@ -0,0 +1 @@ +{"multiscales":[{"name":"","type":"Average","version":"0.4","axes":[{"type":"space","name":"z","unit":"pixel"},{"type":"space","name":"y","unit":"pixel"},{"type":"space","name":"x","unit":"pixel"}],"datasets":[{"path":"s0","coordinateTransformations":[{"scale":[1.0,1.0,1.0],"type":"scale"},{"translation":[0.0,0.0,0.0],"type":"translation"}]}],"coordinateTransformations":[]}]} \ No newline at end of file diff --git a/test-project/dataset/images/MRI.ome.zarr/.zgroup b/test-project/dataset/images/MRI.ome.zarr/.zgroup new file mode 100644 index 000000000..c71fe9d0b --- /dev/null +++ b/test-project/dataset/images/MRI.ome.zarr/.zgroup @@ -0,0 +1 @@ +{"zarr_format":2} \ No newline at end of file diff --git a/test-project/dataset/images/MRI.ome.zarr/s0/.zarray b/test-project/dataset/images/MRI.ome.zarr/s0/.zarray new file mode 100644 index 000000000..2aeba983f --- /dev/null +++ b/test-project/dataset/images/MRI.ome.zarr/s0/.zarray @@ -0,0 +1 @@ +{"zarr_format":2,"shape":[27,226,186],"chunks":[96,96,96],"dtype":"|u1","compressor":{"id":"gzip","level":-1},"fill_value":0,"filters":[],"order":"C","dimension_separator":"/"} \ No newline at end of file diff --git a/test-project/dataset/images/MRI.ome.zarr/s0/.zattrs b/test-project/dataset/images/MRI.ome.zarr/s0/.zattrs new file mode 100644 index 000000000..463fae2a9 --- /dev/null +++ b/test-project/dataset/images/MRI.ome.zarr/s0/.zattrs @@ -0,0 +1 @@ +{"path":"s0","axes":[{"type":"space","name":"x","unit":"pixel"},{"type":"space","name":"y","unit":"pixel"},{"type":"space","name":"z","unit":"pixel"}],"coordinateTransformations":[{"scale":[1.0,1.0,1.0],"type":"scale"},{"translation":[0.0,0.0,0.0],"type":"translation"}]} \ No newline at end of file diff --git a/test-project/dataset/images/MRI.ome.zarr/s0/0/0/0 b/test-project/dataset/images/MRI.ome.zarr/s0/0/0/0 new file mode 100644 index 000000000..b10aae8d6 Binary files /dev/null and b/test-project/dataset/images/MRI.ome.zarr/s0/0/0/0 differ diff --git a/test-project/dataset/images/MRI.ome.zarr/s0/0/0/1 b/test-project/dataset/images/MRI.ome.zarr/s0/0/0/1 new file mode 100644 index 000000000..c2c9120fb Binary files /dev/null and b/test-project/dataset/images/MRI.ome.zarr/s0/0/0/1 differ diff --git a/test-project/dataset/images/MRI.ome.zarr/s0/0/1/0 b/test-project/dataset/images/MRI.ome.zarr/s0/0/1/0 new file mode 100644 index 000000000..04bec0985 Binary files /dev/null and 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[ + "dataset" + ], + "defaultDataset": "dataset", + "specVersion": "0.3.0", + "references": [] +} \ No newline at end of file