Merge pull request #219 from bigdataviewer/refactor_display_options

Refactor display options

Heaving refactoring. A lot of the display customization is removed from this repository and goes into https://github.com/NicoKiaru/bigdataviewer_playground_display. We get a better separation of tasks, the same functionalities as before, and an easier and more flexible to extend them.

This PR allows to solve, or provide an easier way to fix:

    #199 -> done in bigdataviewer_playground_display
    #196 -> done in bigdataviewer_playground_display with more flexibility
    #140
    #136
    #131
    #117
    #95
    #94

Two main mecahnisms used to separates concerns:
* using more scijava plugins extensibility mechanism
* using gson serialization, in combination with scijava plugins

This  allows in particular  the serialization of the suppliers of Bdv windows. User prefs (and dev prefs) are stored conveniently in the class that builds bdv windows, and is stored through serialization.

Another kind of plugin is added, which allows to handle any sourceandconverter operation based on a tag of xml of spimdata objects, when spimdata objects are loaded or saved ( think displaysettings, projection, and also custom converters for label images).

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;
     }
 }