Attempt at creating a way to import an atlas from an imageplus

pom.xml

@@ -107,6 +107,7 @@
 		<license.licenseName>gpl_v3</license.licenseName>
 		<license.copyrightOwners>EPFL</license.copyrightOwners>
 		<bigdataviewer-playground.version>0.10.4</bigdataviewer-playground.version>
+		<bigdataviewer-image-loaders.version>0.8.6</bigdataviewer-image-loaders.version>
 
 		<!-- NB: Deploy releases to the SciJava Maven repository. -->
 		<releaseProfiles>sign,deploy-to-scijava</releaseProfiles>
@@ -144,5 +145,18 @@
 			<version>${bigdataviewer-playground.version}</version>
 		</dependency>
 
+		<dependency>
+			<groupId>ch.epfl.biop</groupId>
+			<artifactId>bigdataviewer-image-loaders</artifactId>
+			<version>${bigdataviewer-image-loaders.version}</version>
+		</dependency>
+
+		<dependency>
+			<groupId>ch.epfl.biop</groupId>
+			<artifactId>ImageToAtlasRegister</artifactId>
+			<version>0.9.8</version>
+			<scope>test</scope>
+		</dependency>
+
 	</dependencies>
 </project>

src/main/java/ch/epfl/biop/atlas/custom/AtlasFromImagePlusCommand.java

@@ -0,0 +1,54 @@
+package ch.epfl.biop.atlas.custom;
+
+import ch.epfl.biop.atlas.scijava.AtlasChooserCommand;
+import ch.epfl.biop.atlas.struct.Atlas;
+import ch.epfl.biop.atlas.struct.AtlasHelper;
+import com.google.gson.GsonBuilder;
+import ij.ImagePlus;
+import org.scijava.command.Command;
+import org.scijava.object.ObjectService;
+import org.scijava.plugin.Parameter;
+import org.scijava.plugin.Plugin;
+
+
+@Plugin(type = Command.class,
+        menuPath = "Plugins>BIOP>Atlas>Create Atlas from Images",
+        description = "A simple way to create an atlas.")
+public class AtlasFromImagePlusCommand implements Command {
+
+    @Parameter
+    String atlas_name;
+
+    @Parameter
+    ImagePlus structural_images;
+
+    @Parameter(label = "Label Image (optional)", required = false)
+    ImagePlus label_image;
+
+    @Parameter
+    Double atlas_precision_mm;
+
+    @Parameter
+    ObjectService os;
+
+    @Override
+    public void run() {
+        Atlas atlas = AtlasFromSourcesHelper.fromImagePlus(atlas_name, structural_images, label_image, atlas_precision_mm);
+        try {
+            atlas.initialize(null, null);
+            atlas.getOntology().initialize();
+            os.addObject(atlas, atlas_name);
+            AtlasChooserCommand.registerAtlas(atlas.getName(), () -> atlas);
+
+            //AtlasHelper.saveOntologyToJsonFile(atlas.getOntology(), ontology.getAbsolutePath());
+
+            System.out.println(
+            new GsonBuilder()
+                    .setPrettyPrinting()
+                    .create()
+                    .toJson(new AtlasHelper.SerializableOntology(atlas.getOntology())));
+        } catch (Exception e) {
+            throw new RuntimeException(e);
+        }
+    }
+}