fix merge conflicts and remove some SOP statements

pom.xml

@@ -121,8 +121,8 @@
 
 		<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 -->

src/main/java/sc/fiji/bdvpg/PlaygroundPrefs.java

@@ -1,3 +1,31 @@
+/*-
+ * #%L
+ * BigDataViewer-Playground
+ * %%
+ * Copyright (C) 2019 - 2021 Nicolas Chiaruttini, EPFL - Robert Haase, MPI CBG - Christian Tischer, EMBL
+ * %%
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ * 
+ * 1. Redistributions of source code must retain the above copyright notice,
+ *    this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright notice,
+ *    this list of conditions and the following disclaimer in the documentation
+ *    and/or other materials provided with the distribution.
+ * 
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ * #L%
+ */
 package sc.fiji.bdvpg;
 
 public abstract class PlaygroundPrefs

src/main/java/sc/fiji/bdvpg/scijava/adapter/AbstractSpimdataAdapter.java

@@ -78,7 +78,7 @@ public JsonElement serialize(AbstractSpimData asd,
     @Override
     public AbstractSpimData deserialize(JsonElement jsonElement, Type type, JsonDeserializationContext jsonDeserializationContext) throws JsonParseException {
         String datalocation = jsonElement.getAsJsonObject().get("datalocation").getAsString();
-        System.out.println("Deserialization of "+datalocation);
+        //System.out.println("Deserialization of "+datalocation);
         if (datalocation.endsWith(".qpath")) {
             System.err.println("qpath project unhandled in deserialization!");
         }

src/main/java/sc/fiji/bdvpg/scijava/adapter/SourceAndConverterAdapter.java

@@ -59,7 +59,7 @@ public SourceAndConverterAdapter(sc.fiji.bdvpg.services.SourceAndConverterAdapte
                     try {
                         ISourceAdapter adapter = pi.createInstance();
                         adapter.setSacSerializer(sacSerializer);
-                        System.out.println("adapter.getSourceClass()= "+adapter.getSourceClass());
+                        //System.out.println("adapter.getSourceClass()= "+adapter.getSourceClass());
                         sourceSerializers.put(adapter.getSourceClass(), adapter);
                         sourceSerializersFromName.put(adapter.getSourceClass().getName(), adapter);
                     } catch (InstantiableException e) {

src/main/java/sc/fiji/bdvpg/scijava/processors/BdvHandlePostprocessor.java

@@ -58,7 +58,7 @@ public class BdvHandlePostprocessor extends AbstractPostprocessorPlugin {
     @Parameter
     SourceAndConverterBdvDisplayService bsds;
 
-    public static Consumer<String> log = (str) -> System.out.println(BdvHandlePostprocessor.class.getSimpleName()+":"+str);
+    public static Consumer<String> log = (str) -> {};//System.out.println(BdvHandlePostprocessor.class.getSimpleName()+":"+str);
 
     @Override
     public void process(Module module) {

src/main/java/sc/fiji/bdvpg/scijava/processors/BvvHandlePostprocessor.java

@@ -60,7 +60,7 @@ public class BvvHandlePostprocessor extends AbstractPostprocessorPlugin {
     @Parameter
     GuavaWeakCacheService cacheService;
 
-    public static Consumer<String> log = (str) -> System.out.println(BvvHandlePostprocessor.class.getSimpleName()+":"+str);
+    public static Consumer<String> log = (str) -> {};//System.out.println(BvvHandlePostprocessor.class.getSimpleName()+":"+str);
 
     @Override
     public void process(Module module) {

src/main/java/sc/fiji/bdvpg/scijava/processors/SpimDataPostprocessor.java

@@ -44,7 +44,7 @@ public class SpimDataPostprocessor extends AbstractPostprocessorPlugin {
     @Parameter
 	SourceAndConverterService bss;
 
-    public static Consumer<String> log = (str) -> System.out.println( SpimDataPostprocessor.class.getSimpleName()+":"+str);
+    public static Consumer<String> log = (str) -> {};//System.out.println( SpimDataPostprocessor.class.getSimpleName()+":"+str);
 
     public static Consumer<String> errlog = (str) -> System.err.println( SpimDataPostprocessor.class.getSimpleName()+":"+str);
 

src/main/java/sc/fiji/bdvpg/scijava/services/SourceAndConverterBdvDisplayService.java

@@ -123,7 +123,7 @@ public void setDefaultBdvSupplier(IBdvSupplier bdvSupplier) {
         log.accept(" --- Serializing to save default bdv window of class "+bdvSupplier.getClass().getSimpleName());
         Gson gson = ScijavaGsonHelper.getGson(ctx, true);
         String bdvSupplierSerialized = gson.toJson(bdvSupplier, IBdvSupplier.class);
-        System.out.println("Bdv Supplier serialized into : "+bdvSupplierSerialized);
+        log.accept("Bdv Supplier serialized into : "+bdvSupplierSerialized);
         // Saved in prefs for next session
         Prefs.set("bigdataviewer.playground.supplier", bdvSupplierSerialized);
     }
@@ -139,10 +139,10 @@ public BdvHandle getNewBdv() {
                 bdvSupplier = gson.fromJson(bdvSupplierJson, IBdvSupplier.class);
             } catch (Exception e) {
                 e.printStackTrace();
-                System.err.println("Restoring default bdv supplier");
+                errlog.accept("Restoring default bdv supplier");
                 bdvSupplier = new DefaultBdvSupplier(new SerializableBdvOptions());
                 String bdvSupplierSerialized = gson.toJson(bdvSupplier, IBdvSupplier.class);
-                System.out.println("Bdv Supplier serialized into : "+bdvSupplierSerialized);
+                log.accept("Bdv Supplier serialized into : "+bdvSupplierSerialized);
                 // Saved in prefs for next session
                 Prefs.set("bigdataviewer.playground.supplier", bdvSupplierSerialized);
             }

src/main/java/sc/fiji/bdvpg/scijava/services/SourceAndConverterService.java

@@ -360,7 +360,6 @@ public synchronized void register(AbstractSpimData asd) {
         this.register(setupIdToSourceAndConverter.values()); // Necessary ? Yes!
 
         setupIdToSourceAndConverter.keySet().forEach(id -> {
-            System.out.println("id = "+id);
             linkToSpimData(setupIdToSourceAndConverter.get(id), asd, id);
         });
 
@@ -542,7 +541,7 @@ public static String getCommandName(Class<? extends Command> c) {
     void registerDefaultActions() {
         this.registerAction("Display names", (srcs) -> {
             for (SourceAndConverter src:srcs){
-                System.out.println(src.getSpimSource().getName());
+                log.accept(src.getSpimSource().getName());
             }});
 
         context().getService(PluginService.class)

src/main/java/sc/fiji/bdvpg/scijava/services/ui/SourceAndConverterInspector.java

@@ -269,20 +269,20 @@ public static LinkedList<SourceAndConverter> getListToRootSourceAndConverter(Sou
         DefaultMutableTreeNode current = nodeSac;
 
         while (current.getChildCount() > 0) {
-            System.out.println(">>>>");
+            //System.out.println(">>>>");
             current = (DefaultMutableTreeNode) current.getFirstChild();
             if (current.getUserObject() instanceof RenamableSourceAndConverter) {
 
-                System.out.println("RSAC");
+                //System.out.println("RSAC");
                 chain.add(((RenamableSourceAndConverter) (current.getUserObject())).sac);
-                System.out.println("Renamable SourceAndConverter found");
-                System.out.println(">"+chain.getLast());
+                //System.out.println("Renamable SourceAndConverter found");
+                //System.out.println(">"+chain.getLast());
             } else {
-                System.out.println("NO RSAC");
-                System.out.println("RenamableSourceAndConverter not contained " +
-                        "in first node of inspector result");
-                System.out.println("Class found = "+current.getUserObject().getClass().getSimpleName());
-                System.out.println("Object found = "+current.getUserObject());
+                //System.out.println("NO RSAC");
+                //System.out.println("RenamableSourceAndConverter not contained " +
+                //        "in first node of inspector result");
+                //System.out.println("Class found = "+current.getUserObject().getClass().getSimpleName());
+                //System.out.println("Object found = "+current.getUserObject());
 
                 //return null;
             }

src/main/java/sc/fiji/bdvpg/services/SourceAndConverterServiceLoader.java

@@ -75,7 +75,7 @@ public void run() {
 
             Gson gson = new Gson();
             JsonArray rawSacsArray = gson.fromJson(fileReader, JsonArray.class);
-            System.out.println(rawSacsArray.size());
+            //System.out.println(rawSacsArray.size());
 
             for (int i = 0;i<rawSacsArray.size();i++) {
                 if (rawSacsArray.get(i).isJsonObject()) {

src/main/java/sc/fiji/bdvpg/sourceandconverter/importer/SourceAndConverterFromSpimDataCreator.java

@@ -1,3 +1,31 @@
+/*-
+ * #%L
+ * BigDataViewer-Playground
+ * %%
+ * Copyright (C) 2019 - 2021 Nicolas Chiaruttini, EPFL - Robert Haase, MPI CBG - Christian Tischer, EMBL
+ * %%
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ * 
+ * 1. Redistributions of source code must retain the above copyright notice,
+ *    this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright notice,
+ *    this list of conditions and the following disclaimer in the documentation
+ *    and/or other materials provided with the distribution.
+ * 
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ * #L%
+ */
 package sc.fiji.bdvpg.sourceandconverter.importer;
 
 import bdv.SpimSource;

src/main/java/sc/fiji/bdvpg/spimdata/exporter/XmlFromSpimDataExporter.java

@@ -88,7 +88,7 @@ public void run() {
         try {
 
             if (context!=null) {
-                System.out.println(" Handling scijava extra attributes");
+                //System.out.println(" Handling scijava extra attributes");
                 // We can handle the extra attributes, see {@link IEntityHandlerService}
                 Map<Class<? extends Entity>, EntityHandler> entityClassToHandler = new HashMap<>();