Refactor display options

bigdataviewer.properties

@@ -1,8 +1,8 @@
 #
-#Fri Feb 05 10:33:13 CET 2021
+#Fri Apr 30 16:10:12 CEST 2021
 scale-bar-bg-color=-16724788
 show-text-overlay=true
-show-multibox-overlay=true
+show-multibox-overlay=false
 show-scale-bar-in-movie=true
 show-scale-bar=true
 scale-bar-color=-1

plugins/bdvpgsettings/bdvpg.editor.actions.txt

@@ -0,0 +1,23 @@
+[
+  "BDV - Set Number Of Timepoints",
+  "BDV - Show Sources (new Bdv window)",
+  "BDV - Screenshot",
+  "PopupLine",
+  "BDV - Remove Sources From BDV",
+  "Set Sources Color",
+  "Set Sources Brightness",
+  "Make Sources Invisible",
+  "Set Sources Projection Mode",
+  "PopupLine",
+  "Create New Source (Set LUT)",
+  "PopupLine",
+  "Manual Sources Transformation",
+  "Basic Transformation",
+  "Make Global Source Group",
+  "PopupLine",
+  "Inspect Sources",
+  "PopupLine",
+  "Add Metadata To Sources",
+  "PopupLine",
+  "Export Sources to XML/HDF5 Spimdataset"
+]

plugins/bdvpgsettings/bdvpg.editor.actions.txt.default.txt

@@ -1,7 +1,6 @@
 [
   "BDV - Set Number Of Timepoints",
   "BDV - Show Sources (new Bdv window)",
-  "BDV - Screenshot",
   "PopupLine",
   "BDV - Remove Sources From BDV",
   "Set Sources Color",

plugins/bdvpgsettings/bdvpg.tree.actions.txt

@@ -0,0 +1,37 @@
+[
+  "BDV - Show Sources",
+  "BDV - Show Sources (new Bdv window)",
+  "BDV - Zoom to source",
+  "BDV - Show Sources In Multiple BDV Windows",
+  "BDV - Set Number Of Timepoints",
+  "BDV - Create empty BDV window",
+  "BDV - Create Orthogonal Views",
+  "BDV - Screenshot",
+  "BDV - Synchronize Views",
+  "BDV - Remove Sources From BDV",
+  "PopupLine",
+  "Create Empty BVV Frame",
+  "Show Sources in BVV",
+  "PopupLine",
+  "Set Sources Color",
+  "Set Sources Brightness",
+  "Make Sources Invisible",
+  "Make Sources Visible",
+  "Set Sources Projection Mode",
+  "Create New Source (Set LUT)",
+  "Create New Source (Set Color)",
+  "PopupLine",
+  "Manual Sources Transformation",
+  "Basic Transformation",
+  "Make Global Source Group",
+  "PopupLine",
+  "Save BDVDataset",
+  "Inspect Sources",
+  "PopupLine",
+  "Add Metadata To Sources",
+  "Make Metadata Filter Node",
+  "PopupLine",
+  "Export Sources to XML/HDF5 Spimdataset",
+  "Delete Sources",
+  "PopupLine"
+]

plugins/bdvpgsettings/bdvpg.tree.actions.txt.default.txt

@@ -6,7 +6,6 @@
   "BDV - Set Number Of Timepoints",
   "BDV - Create empty BDV window",
   "BDV - Create Orthogonal Views",
-  "BDV - Screenshot",
   "BDV - Synchronize Views",
   "BDV - Remove Sources From BDV",
   "PopupLine",

pom.xml

@@ -11,7 +11,7 @@
 
 	<groupId>sc.fiji</groupId>
 	<artifactId>bigdataviewer-playground</artifactId>
-	<version>0.2.15-SNAPSHOT</version>
+	<version>0.3.0-SNAPSHOT</version>
 
 	<name>bigdataviewer-playground</name>
 	<description>BigDataViewer Actions and GUI</description>
@@ -92,7 +92,6 @@
 		<connection>scm:git:git://github.com/bigdataviewer/bigdataviewer-playground</connection>
 		<developerConnection>scm:git:[email protected]:bigdataviewer/bigdataviewer-playground</developerConnection>
 		<url>https://github.com/bigdataviewer/bigdataviewer-playground/</url>
-    <tag>bigdataviewer-playground-0.2.7</tag>
   </scm>
 
 	<issueManagement>
@@ -118,12 +117,12 @@
 		<releaseProfiles>deploy-to-scijava</releaseProfiles>
 
 		<scijava.deleteOtherVersions>true</scijava.deleteOtherVersions>
-		<scijava.app.directory>C:/Users/nicol/Desktop/fiji-win64-bdv-playground/Fiji.app/</scijava.app.directory>
+		<!-- <scijava.app.directory>C:/Users/nicol/Desktop/fiji-win64-bdv-playground/Fiji.app/</scijava.app.directory> -->
 
 		<bigdataviewer-selector.version>0.1.8</bigdataviewer-selector.version>
 		<bigvolumeviewer.version>0.2.0</bigvolumeviewer.version>
-		<mastodon.version>1.0.0-beta-16</mastodon.version>
-		<bigdataviewer-spimdata-extras.version>0.1.0</bigdataviewer-spimdata-extras.version>
+		<mastodon.version>1.0.0-beta-17</mastodon.version>
+		<bigdataviewer-spimdata-extras.version>0.1.1</bigdataviewer-spimdata-extras.version>
 		<reflections.version>0.9.11</reflections.version>
 
 		<!-- package version below are determined by the parent pom but need to be upgraded -->
@@ -195,12 +194,6 @@
 			<artifactId>imglib2</artifactId>
 		</dependency>
 
-		<dependency>
-			<groupId>ch.epfl.biop</groupId>
-			<artifactId>bigdataviewer-spimdata-extras</artifactId>
-			<version>${bigdataviewer-spimdata-extras.version}</version>
-		</dependency>
-
 		<!-- Test dependencies -->
 		<dependency>
 			<groupId>junit</groupId>

src/main/java/bdv/util/EmptySource.java

@@ -37,6 +37,7 @@
 import net.imglib2.type.numeric.integer.UnsignedShortType;
 import net.imglib2.view.ExtendedRandomAccessibleInterval;
 import net.imglib2.view.Views;
+import sc.fiji.bdvpg.scijava.adapter.source.EmptySourceAdapter;
 
 import java.io.Serializable;
 import java.util.function.BiConsumer;
@@ -48,7 +49,7 @@
  * This source can be thus used to define a template in order to Resample another source
  * with new bounds and voxel size, for instance as a model in {@link ResampledSource}
  *
- * Also this source can be serialized with the gson adapter {@link sc.fiji.bdvpg.services.serializers.plugins.EmptySourceAdapter}
+ * Also this source can be serialized with the gson adapter {@link EmptySourceAdapter}
  * which is helpful to save such source easily.
  *
  */

src/main/java/bdv/util/RAIHelper.java

@@ -49,6 +49,7 @@
 import net.imglib2.util.Util;
 import net.imglib2.view.Views;
 import org.janelia.saalfeldlab.n5.imglib2.RandomAccessibleLoader;
+//import org.janelia.saalfeldlab.n5.imglib2.RandomAccessibleLoader;
 
 import static net.imglib2.img.basictypeaccess.AccessFlags.VOLATILE;
 import static net.imglib2.type.PrimitiveType.*;

src/main/java/sc/fiji/bdvpg/services/serializers/AffineTransform3DAdapter.java → src/main/java/net/imglib2/realtransform/AffineTransform3DAdapter.java

@@ -26,15 +26,16 @@
  * POSSIBILITY OF SUCH DAMAGE.
  * #L%
  */
-package sc.fiji.bdvpg.services.serializers;
+package net.imglib2.realtransform;
 
 import com.google.gson.*;
-import net.imglib2.realtransform.AffineTransform3D;
 import org.scijava.plugin.Plugin;
-import sc.fiji.bdvpg.services.serializers.plugins.IClassAdapter;
-
+import sc.fiji.persist.IClassAdapter;
 import java.lang.reflect.Type;
 
+/**
+ * Affine transform 3D adapter
+ */
 @Plugin(type = IClassAdapter.class)
 public class AffineTransform3DAdapter implements IClassAdapter<AffineTransform3D> {
 
@@ -58,4 +59,5 @@ public JsonElement serialize(AffineTransform3D affineTransform3D, Type type, Jso
     public Class<? extends AffineTransform3D> getAdapterClass() {
         return AffineTransform3D.class;
     }
+
 }

src/main/java/sc/fiji/bdvpg/services/serializers/plugins/BdvPlaygroundObjectAdapterService.java → src/main/java/net/imglib2/realtransform/AffineTransform3DRunTimeAdapter.java

@@ -26,17 +26,30 @@
  * POSSIBILITY OF SUCH DAMAGE.
  * #L%
  */
-package sc.fiji.bdvpg.services.serializers.plugins;
+package net.imglib2.realtransform;
 
-import org.scijava.plugin.PTService;
-import org.scijava.plugin.PluginInfo;
-import org.scijava.service.SciJavaService;
+import org.scijava.plugin.Plugin;
+import sc.fiji.persist.IClassRuntimeAdapter;
 
-import java.util.List;
+/**
+ * Runtime adapter for RealTransform
+ */
+@Plugin(type = IClassRuntimeAdapter.class)
+public class AffineTransform3DRunTimeAdapter implements IClassRuntimeAdapter<RealTransform, AffineTransform3D> {
+
+    @Override
+    public Class<? extends RealTransform> getBaseClass() {
+        return RealTransform.class;
+    }
 
-public interface BdvPlaygroundObjectAdapterService extends PTService<IBdvPlaygroundObjectAdapter>, SciJavaService {
+    @Override
+    public Class<? extends AffineTransform3D> getRunTimeClass() {
+        return AffineTransform3D.class;
+    }
 
-    //List<PluginInfo<IBdvPlaygroundObjectAdapter>> getAdapters(Class<? extends IBdvPlaygroundObjectAdapter> adapterClass);
+    @Override
+    public boolean useCustomAdapter() {
+        return false;
+    }
 
-    <PT extends IBdvPlaygroundObjectAdapter> List<PluginInfo<PT>> getAdapters(Class<PT> adapterClass);
 }

src/main/java/net/imglib2/realtransform/InvertibleRealTransformSequenceAdapter.java

@@ -30,7 +30,7 @@
 
 import com.google.gson.*;
 import org.scijava.plugin.Plugin;
-import sc.fiji.bdvpg.services.serializers.plugins.IClassRuntimeAdapter;
+import sc.fiji.persist.IClassRuntimeAdapter;
 
 import java.lang.reflect.Type;
 
@@ -57,6 +57,11 @@ public Class<? extends InvertibleRealTransformSequence> getRunTimeClass() {
         return InvertibleRealTransformSequence.class;
     }
 
+    @Override
+    public boolean useCustomAdapter() {
+        return true;
+    }
+
     @Override
     public InvertibleRealTransformSequence deserialize(JsonElement jsonElement, Type type, JsonDeserializationContext jsonDeserializationContext) throws JsonParseException {
         JsonObject obj = jsonElement.getAsJsonObject();
@@ -77,7 +82,7 @@ public InvertibleRealTransformSequence deserialize(JsonElement jsonElement, Type
                 if (transform instanceof InvertibleRealTransform) {
                     irts.add((InvertibleRealTransform) transform);
                 } else {
-                    System.err.println("Deserialization eroor: "+transform+" of class "+transform.getClass().getSimpleName()+" is not invertible!");
+                    System.err.println("Deserialization error: "+transform+" of class "+transform.getClass().getSimpleName()+" is not invertible!");
                     return null;
                 }
             }
@@ -89,15 +94,10 @@ public InvertibleRealTransformSequence deserialize(JsonElement jsonElement, Type
     @Override
     public JsonElement serialize(InvertibleRealTransformSequence irts, Type type, JsonSerializationContext jsonSerializationContext) {
         JsonObject obj = new JsonObject();
-
-        obj.addProperty("type", InvertibleRealTransformSequence.class.getSimpleName());
-
         obj.addProperty("size", irts.transforms.size());
-
         for (int iTransform = 0; iTransform<irts.transforms.size(); iTransform++) {
-            obj.add("realTransform_"+iTransform, jsonSerializationContext.serialize(irts.transforms.get(iTransform)));
+            obj.add("realTransform_"+iTransform, jsonSerializationContext.serialize(irts.transforms.get(iTransform), RealTransform.class));
         }
-
         return obj;
     }
 }