From 22383abc06d0c6ae21c461871e167a88436ff42f Mon Sep 17 00:00:00 2001
From: Christian Tischer <christian.tischer@embl.de>
Date: Fri, 26 Jul 2024 10:58:44 +0200
Subject: [PATCH] Add mobie creation groovy script

---
 .../mobie/lib/create/DatasetSerializer.java   |  4 +--
 .../java/examples/CreateMoBIEProject.groovy   | 35 +++++++++++++++++++
 .../java/examples/CreateMoBIEProject.java     |  1 -
 .../lib/serialize/DatasetJsonParserTest.java  |  3 --
 .../data/blobs/dataset.json                   |  6 ++--
 .../test-project/dataset/dataset.json         |  2 +-
 6 files changed, 41 insertions(+), 10 deletions(-)
 create mode 100644 src/test/java/examples/CreateMoBIEProject.groovy

diff --git a/src/main/java/org/embl/mobie/lib/create/DatasetSerializer.java b/src/main/java/org/embl/mobie/lib/create/DatasetSerializer.java
index 3d5b56d1..3d69178c 100644
--- a/src/main/java/org/embl/mobie/lib/create/DatasetSerializer.java
+++ b/src/main/java/org/embl/mobie/lib/create/DatasetSerializer.java
@@ -233,14 +233,14 @@ private void addNewSegmentationView( Dataset dataset, String imageName, String u
     private void addNewDefaultImageView( Dataset dataset, String imageName, double[] contrastLimits, String colour,
 										 AffineTransform3D sourceTransform )
     {
-        View view = createImageView( imageName, "bookmark", true, contrastLimits, colour,
+        View view = createImageView( imageName, "views", true, contrastLimits, colour,
                 sourceTransform );
         dataset.views().put( View.DEFAULT, view );
     }
 
     private void addNewDefaultSegmentationView( Dataset dataset, String imageName, AffineTransform3D sourceTransform )
     {
-        View view = createSegmentationView( imageName, "bookmark", true, sourceTransform );
+        View view = createSegmentationView( imageName, "views", true, sourceTransform );
         dataset.views().put( View.DEFAULT, view );
     }
 
diff --git a/src/test/java/examples/CreateMoBIEProject.groovy b/src/test/java/examples/CreateMoBIEProject.groovy
new file mode 100644
index 00000000..03538a42
--- /dev/null
+++ b/src/test/java/examples/CreateMoBIEProject.groovy
@@ -0,0 +1,35 @@
+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.lib.create.ProjectCreator
+
+// 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()
\ No newline at end of file
diff --git a/src/test/java/examples/CreateMoBIEProject.java b/src/test/java/examples/CreateMoBIEProject.java
index 453a7ea8..bcb5cff5 100644
--- a/src/test/java/examples/CreateMoBIEProject.java
+++ b/src/test/java/examples/CreateMoBIEProject.java
@@ -5,7 +5,6 @@
 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;
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 4f61d4d6..82202779 100644
--- a/src/test/java/org/embl/mobie/lib/serialize/DatasetJsonParserTest.java
+++ b/src/test/java/org/embl/mobie/lib/serialize/DatasetJsonParserTest.java
@@ -49,11 +49,8 @@
 class DatasetJsonParserTest {
 
     private File tempDir;
-    private static JSONObject datasetSchema;
     private Dataset dataset;
     private final String viewName = View.DEFAULT;
-    private final String uiSelectionGroup = "bookmark";
-    private final boolean isExclusive = true;
     private DatasetJsonParser datasetJsonParser;
     private String datasetJsonName = "dataset.json";
 
diff --git a/src/test/resources/minimal-mobie-project/data/blobs/dataset.json b/src/test/resources/minimal-mobie-project/data/blobs/dataset.json
index 36403992..f0d75917 100644
--- a/src/test/resources/minimal-mobie-project/data/blobs/dataset.json
+++ b/src/test/resources/minimal-mobie-project/data/blobs/dataset.json
@@ -73,7 +73,7 @@
       "description": "blobs, overwrite"
     },
     "default": {
-      "uiSelectionGroup": "bookmark",
+      "uiSelectionGroup": "views",
       "sourceDisplays": [
         {
           "imageDisplay": {
@@ -182,7 +182,7 @@
       "description": ""
     },
     "blobs-transformed": {
-      "uiSelectionGroup": "bookmark",
+      "uiSelectionGroup": "views",
       "sourceDisplays": [
         {
           "imageDisplay": {
@@ -390,7 +390,7 @@
       "description": ""
     },
     "test": {
-      "uiSelectionGroup": "bookmark",
+      "uiSelectionGroup": "views",
       "sourceDisplays": [
         {
           "imageDisplay": {
diff --git a/src/test/resources/test-project/dataset/dataset.json b/src/test/resources/test-project/dataset/dataset.json
index d8d060c4..536bfc1a 100644
--- a/src/test/resources/test-project/dataset/dataset.json
+++ b/src/test/resources/test-project/dataset/dataset.json
@@ -44,7 +44,7 @@
       "isExclusive": false
     },
     "default": {
-      "uiSelectionGroup": "bookmark",
+      "uiSelectionGroup": "views",
       "sourceDisplays": [
         {
           "imageDisplay": {