Add example code for creating a MOBIE project

pom.xml

@@ -88,7 +88,7 @@
         <imagej-utils.version>0.7.0</imagej-utils.version>
 
         <bigdataviewer-playground.version>0.9.0</bigdataviewer-playground.version>
-        <bigwarp_fiji.version>9.1.2</bigwarp_fiji.version>
+        <bigwarp_fiji.version>9.1.3</bigwarp_fiji.version>
 
         <trove.version>1.0.2</trove.version>
         <annotations.version>16.0.2</annotations.version>

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.");
 		}
 	}
 

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();
+    }
+}

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
+    }
+  }
+}

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":[]}]}

src/test/resources/test-project/dataset/images/MRI.ome.zarr/.zgroup

@@ -0,0 +1 @@
+{"zarr_format":2}

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":"/"}

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"}]}

src/test/resources/test-project/project.json

@@ -0,0 +1,8 @@
+{
+	"datasets": [
+		"dataset"
+	],
+	"defaultDataset": "dataset",
+	"specVersion": "0.3.0",
+	"references": []
+}

test-project/dataset/dataset.json

@@ -0,0 +1,13 @@
+{
+  "is2D": false,
+  "defaultLocation": {
+    "position": [
+      0.0,
+      0.0,
+      0.0
+    ],
+    "timepoint": 0
+  },
+  "sources": {},
+  "views": {}
+}

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":[]}]}

test-project/dataset/images/MRI.ome.zarr/.zgroup

@@ -0,0 +1 @@
+{"zarr_format":2}

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":"/"}

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"}]}

test-project/project.json

@@ -0,0 +1,8 @@
+{
+	"datasets": [
+		"dataset"
+	],
+	"defaultDataset": "dataset",
+	"specVersion": "0.3.0",
+	"references": []
+}