Merge pull request #204 from BIOP/refactor-register

Big refactoring where registration classes and plugins have been moved in the upstream repo bigdataviewer-biop-tools

The goal was to reuse the nicer registration plugins of ABBA in Warpy instead of creating new ones

pom.xml

@@ -108,8 +108,8 @@
 
 		<!-- bdv playground related dependencies -->
 		<bigdataviewer-playground.version>0.10.1</bigdataviewer-playground.version>
-		<bigdataviewer-image-loaders.version>0.7.1</bigdataviewer-image-loaders.version>
-		<bigdataviewer-biop-tools.version>0.9.4</bigdataviewer-biop-tools.version>
+		<bigdataviewer-image-loaders.version>0.7.2</bigdataviewer-image-loaders.version>
+		<bigdataviewer-biop-tools.version>0.10.0</bigdataviewer-biop-tools.version>
 		<bigdataviewer-selector.version>0.2.6</bigdataviewer-selector.version>
 
 		<!-- maths -->

src/main/java/ch/epfl/biop/atlas/aligner/EditLastRegistrationAction.java

@@ -1,6 +1,6 @@
 package ch.epfl.biop.atlas.aligner;
 
-import ch.epfl.biop.atlas.aligner.plugin.RegistrationPluginHelper;
+import ch.epfl.biop.registration.plugin.RegistrationPluginHelper;
 import ch.epfl.biop.sourceandconverter.processor.SourcesIdentity;
 import ch.epfl.biop.sourceandconverter.processor.SourcesProcessComposer;
 import ch.epfl.biop.sourceandconverter.processor.SourcesProcessor;

src/main/java/ch/epfl/biop/atlas/aligner/MultiSlicePositioner.java

@@ -3,9 +3,9 @@
 import bdv.viewer.SourceAndConverter;
 import ch.epfl.biop.atlas.aligner.action.*;
 import ch.epfl.biop.atlas.aligner.adapter.*;
-import ch.epfl.biop.atlas.aligner.plugin.ExternalABBARegistrationPlugin;
-import ch.epfl.biop.atlas.aligner.plugin.IABBARegistrationPlugin;
-import ch.epfl.biop.atlas.aligner.plugin.RegistrationPluginHelper;
+import ch.epfl.biop.registration.plugin.ExternalRegistrationPlugin;
+import ch.epfl.biop.registration.plugin.IRegistrationPlugin;
+import ch.epfl.biop.registration.plugin.RegistrationPluginHelper;
 import ch.epfl.biop.atlas.struct.Atlas;
 import ch.epfl.biop.registration.Registration;
 import ch.epfl.biop.sourceandconverter.processor.*;
@@ -690,36 +690,6 @@ public static Map<String,String> convertToString(Context ctx, Map<String, Object
         return convertedParams;
     }
 
-    public void registerSelectedSlices(Command command,
-                                       SourcesProcessor preprocessFixed,
-                                       SourcesProcessor preprocessMoving) {
-        registerSelectedSlices(command,
-                preprocessFixed,
-                preprocessMoving,
-                new HashMap<>()
-        );
-    }
-
-    /**
-     * Main function which triggers registration of the selected slices
-     * @param command the ui command
-     * @param preprocessFixed how fixed sources need to be preprocessed before being registered
-     * @param preprocessMoving how moving sources need to be preprocessed before being registered
-     * @param parameters parameters used for the registration - all objects will be converted
-     *                   to String using the scijava {@link ConvertService}. They need to be strings
-     *                   to be serialized
-     */
-    public void registerSelectedSlices(Command command,
-                                       SourcesProcessor preprocessFixed,
-                                       SourcesProcessor preprocessMoving,
-                                       Map<String,Object> parameters) {
-        registerSelectedSlices(RegistrationPluginHelper.registrationFromUI(scijavaCtx,command.getClass()),
-                preprocessFixed,
-                preprocessMoving,
-                parameters
-        );
-    }
-
     /**
      * Main function which triggers registration of the selected slices
      * @param registrationClass the kind of registration which should be started
@@ -729,16 +699,16 @@ public void registerSelectedSlices(Command command,
      *                   to String using the scijava {@link ConvertService}. They need to be strings
      *                   to be serialized
      */
-    public void registerSelectedSlices(Class<? extends IABBARegistrationPlugin> registrationClass,
+    public void registerSelectedSlices(Class<? extends IRegistrationPlugin> registrationClass,
                                        SourcesProcessor preprocessFixed,
                                        SourcesProcessor preprocessMoving,
                                        Map<String,Object> parameters) {
 
         PluginService ps = scijavaCtx.getService(PluginService.class);
-        Supplier<? extends IABBARegistrationPlugin> pluginSupplier =
+        Supplier<? extends IRegistrationPlugin> pluginSupplier =
                 () -> {
                     try {
-                        return (IABBARegistrationPlugin) ps.getPlugin(registrationClass).createInstance();
+                        return (IRegistrationPlugin) ps.getPlugin(registrationClass).createInstance();
                     } catch (InstantiableException e) {
                         e.printStackTrace();
                         return null;
@@ -780,7 +750,7 @@ public void registerSelectedSlices(String registrationPluginName,
      *                   to String using the scijava {@link ConvertService}. They need to be strings
      *                   to be serialized
      */
-    public void registerSelectedSlices(Supplier<? extends IABBARegistrationPlugin> registrationPluginSupplier,
+    public void registerSelectedSlices(Supplier<? extends IRegistrationPlugin> registrationPluginSupplier,
                                        SourcesProcessor preprocessFixed,
                                        SourcesProcessor preprocessMoving,
                                        Map<String,Object> parameters) {
@@ -797,14 +767,11 @@ public void registerSelectedSlices(Supplier<? extends IABBARegistrationPlugin> r
 
             for (SliceSources slice : getSelectedSlices()) {
                 logger.debug("Starting slice registration for "+slice.getName());
-                IABBARegistrationPlugin registration = registrationPluginSupplier.get();
+                IRegistrationPlugin registration = registrationPluginSupplier.get();
                 if (registration!=null) {
                     logger.debug("\t slice registration for "+slice.getName()+"- set context");
                     registration.setScijavaContext(scijavaCtx);
 
-                    logger.debug("\t slice registration for "+slice.getName()+"- setSliceInfo");
-                    registration.setSliceInfo(new SliceInfo(this, slice));
-
                     // Sends parameters to the registration
                     logger.debug("\t slice registration for "+slice.getName()+"- setRegistrationParameters");
                     registration.setRegistrationParameters(convertToString(scijavaCtx, parameters));
@@ -915,15 +882,15 @@ public Gson getGsonStateSerializer(List<SourceAndConverter> serialized_sources)
         PluginService pluginService = scijavaCtx.getService(PluginService.class);
 
         // Creates adapter for all registration plugins
-        RegistrationAdapter registrationAdapter = new RegistrationAdapter(scijavaCtx, this);
-        pluginService.getPluginsOfType(IABBARegistrationPlugin.class).forEach(registrationPluginClass -> {
-            IABBARegistrationPlugin plugin = pluginService.createInstance(registrationPluginClass);
+        RegistrationAdapter registrationAdapter = new RegistrationAdapter(scijavaCtx);
+        pluginService.getPluginsOfType(IRegistrationPlugin.class).forEach(registrationPluginClass -> {
+            IRegistrationPlugin plugin = pluginService.createInstance(registrationPluginClass);
             factoryRegistrations.registerSubtype(plugin.getClass());
             gsonbuilder.registerTypeHierarchyAdapter(plugin.getClass(), registrationAdapter);
         });
 
-        factoryRegistrations.registerSubtype(ExternalABBARegistrationPlugin.class);
-        gsonbuilder.registerTypeHierarchyAdapter(ExternalABBARegistrationPlugin.class, registrationAdapter);
+        factoryRegistrations.registerSubtype(ExternalRegistrationPlugin.class);
+        gsonbuilder.registerTypeHierarchyAdapter(ExternalRegistrationPlugin.class, registrationAdapter);
 
         // For sources processor
 
@@ -1456,23 +1423,23 @@ public SliceInfo(MultiSlicePositioner mp, SliceSources slice) {
 
     //---------------------- For PyImageJ extensions
 
-    static final Map<String, Supplier<? extends IABBARegistrationPlugin>> externalRegistrationPlugins = new HashMap<>();
+    static final Map<String, Supplier<? extends IRegistrationPlugin>> externalRegistrationPlugins = new HashMap<>();
 
     /**
      * Register an external registration plugin, for instance performed by a python function
      * through PyImageJ
      * @param name of the registration plugin
      * @param pluginSupplier the thing that makes a new plugin of this kind
      */
-    public static void registerRegistrationPlugin(String name, Supplier<? extends IABBARegistrationPlugin> pluginSupplier) {
+    public static void registerRegistrationPlugin(String name, Supplier<? extends IRegistrationPlugin> pluginSupplier) {
         externalRegistrationPlugins.put(name, pluginSupplier);
     }
 
     public static boolean isExternalRegistrationPlugin(String name) {
         return externalRegistrationPlugins.containsKey(name);
     }
 
-    public static Supplier<? extends IABBARegistrationPlugin> getExternalRegistrationPluginSupplier(String name) {
+    public static Supplier<? extends IRegistrationPlugin> getExternalRegistrationPluginSupplier(String name) {
         return externalRegistrationPlugins.get(name);
     }
 

src/main/java/ch/epfl/biop/atlas/aligner/RegisterSliceAction.java

@@ -1,7 +1,7 @@
 package ch.epfl.biop.atlas.aligner;
 
 import bdv.viewer.SourceAndConverter;
-import ch.epfl.biop.atlas.aligner.plugin.RegistrationPluginHelper;
+import ch.epfl.biop.registration.plugin.RegistrationPluginHelper;
 import ch.epfl.biop.registration.Registration;
 import ch.epfl.biop.sourceandconverter.processor.SourcesProcessor;
 import org.slf4j.Logger;

src/main/java/ch/epfl/biop/atlas/aligner/SliceSources.java

@@ -15,7 +15,7 @@
 import bdv.viewer.Interpolation;
 import bdv.viewer.Source;
 import bdv.viewer.SourceAndConverter;
-import ch.epfl.biop.atlas.aligner.plugin.RegistrationPluginHelper;
+import ch.epfl.biop.registration.plugin.RegistrationPluginHelper;
 import ch.epfl.biop.atlas.mouse.allen.ccfv3.command.AllenBrainAdultMouseAtlasCCF2017Command;
 import ch.epfl.biop.atlas.struct.AtlasHelper;
 import ch.epfl.biop.atlas.struct.AtlasNode;
@@ -61,7 +61,6 @@
 import net.imglib2.img.display.imagej.ImageJFunctions;
 import net.imglib2.position.FunctionRandomAccessible;
 import net.imglib2.realtransform.AffineTransform3D;
-import net.imglib2.realtransform.BoundingBoxEstimation;
 import net.imglib2.realtransform.InvertibleRealTransform;
 import net.imglib2.realtransform.InvertibleRealTransformSequence;
 import net.imglib2.realtransform.RealTransform;
@@ -113,10 +112,6 @@
 import java.util.concurrent.ForkJoinPool;
 import java.util.stream.Collectors;
 
-import static net.imglib2.realtransform.BoundingBoxEstimation.Method.CORNERS;
-import static net.imglib2.realtransform.BoundingBoxEstimation.Method.FACES;
-import static net.imglib2.realtransform.BoundingBoxEstimation.Method.VOLUME;
-
 
 /**
  * Class which contains the current registered SourceAndConverter array
@@ -1827,7 +1822,7 @@ public void popRasterSlice() {
         registered_sacs = sourcesNonRasterized.pop();
     }
 
-    public static class RegistrationAndSources {
+    private static class RegistrationAndSources {
 
         final Registration reg;
         final SourceAndConverter[] sacs;

src/main/java/ch/epfl/biop/atlas/aligner/adapter/RegistrationAdapter.java

@@ -1,7 +1,7 @@
 package ch.epfl.biop.atlas.aligner.adapter;
 
 import ch.epfl.biop.atlas.aligner.MultiSlicePositioner;
-import ch.epfl.biop.atlas.aligner.plugin.ExternalABBARegistrationPlugin;
+import ch.epfl.biop.registration.plugin.ExternalRegistrationPlugin;
 import ch.epfl.biop.registration.Registration;
 import com.google.gson.*;
 import org.scijava.Context;
@@ -20,10 +20,8 @@ public class RegistrationAdapter implements JsonSerializer<Registration>,
 
     final Context scijavacontext;
 
-    final MultiSlicePositioner msp;
-    public RegistrationAdapter(Context context, MultiSlicePositioner mp) {
+    public RegistrationAdapter(Context context) {
         this.scijavacontext = context;
-        this.msp = mp;
     }
 
     @Override
@@ -32,7 +30,7 @@ public Registration deserialize(JsonElement json, Type typeOfT, JsonDeserializat
             Registration registration;
 
             logger.debug("Fetching registration plugin "+typeOfT.getTypeName());
-            if (typeOfT.getTypeName().equals(ExternalABBARegistrationPlugin.class.getName())) {
+            if (typeOfT.getTypeName().equals(ExternalRegistrationPlugin.class.getName())) {
                 String registrationTypeName = json
                         .getAsJsonObject()
                         .get("external_type")
@@ -50,7 +48,7 @@ public Registration deserialize(JsonElement json, Type typeOfT, JsonDeserializat
             registration.setRegistrationParameters(context.deserialize(json.getAsJsonObject().get("parameters"), Map.class));
             return registration;
         } catch (InstantiableException e) {
-            msp.errlog.accept("Unrecognized registration plugin "+typeOfT.getTypeName());
+            logger.error("Unrecognized registration plugin "+typeOfT.getTypeName());
             e.printStackTrace();
             return null;
         }
@@ -64,7 +62,7 @@ public JsonElement serialize(Registration registration, Type typeOfSrc, JsonSeri
         logger.debug("With transform "+registration.getTransform());
         logger.debug("And parameters "+registration.getRegistrationParameters());
         if (MultiSlicePositioner.isExternalRegistrationPlugin(registration.getRegistrationTypeName())) {
-            obj.addProperty("type", ExternalABBARegistrationPlugin.class.getSimpleName());
+            obj.addProperty("type", ExternalRegistrationPlugin.class.getSimpleName());
             obj.addProperty("external_type", registration.getRegistrationTypeName());
         } else {
             obj.addProperty("type", registration.getRegistrationTypeName());

src/main/java/ch/epfl/biop/atlas/aligner/command/MirrorDoCommand.java

@@ -3,6 +3,7 @@
 import ch.epfl.biop.atlas.aligner.MultiSlicePositioner;
 import ch.epfl.biop.atlas.aligner.SliceSources;
 import ch.epfl.biop.atlas.aligner.action.MarkActionSequenceBatchAction;
+import ch.epfl.biop.registration.sourceandconverter.mirror.MirrorXRegistration;
 import ch.epfl.biop.sourceandconverter.processor.SourcesIdentity;
 import org.scijava.command.Command;
 import org.scijava.plugin.Parameter;
@@ -38,7 +39,7 @@ public void run() {
         parameters.put("mirror_side", mirror_side);
 
         new MarkActionSequenceBatchAction(mp).runRequest();
-        mp.registerSelectedSlices(this,
+        mp.registerSelectedSlices(MirrorXRegistration.class,
                 new SourcesIdentity(),
                 new SourcesIdentity(),
                 parameters);

src/main/java/ch/epfl/biop/atlas/aligner/command/RegisterSlicesBigWarpCommand.java

@@ -1,15 +1,18 @@
 package ch.epfl.biop.atlas.aligner.command;
 
+import ch.epfl.biop.registration.sourceandconverter.bigwarp.SacBigWarp2DRegistration;
 import org.scijava.command.Command;
 import org.scijava.plugin.Plugin;
 
+import java.util.HashMap;
+
 @Plugin(type = Command.class,
         menuPath = "Plugins>BIOP>Atlas>Multi Image To Atlas>Align>ABBA - BigWarp Registration",
         description = "Uses BigWarp for in plane registration of selected slices")
 public class RegisterSlicesBigWarpCommand extends RegistrationMultiChannelCommand {
 
     public void runValidated() {
-        mp.registerSelectedSlices(this, getFixedFilter(), getMovingFilter());
+        mp.registerSelectedSlices(SacBigWarp2DRegistration.class, getFixedFilter(), getMovingFilter(), new HashMap<>());
     }
 
 }

src/main/java/ch/epfl/biop/atlas/aligner/command/RegisterSlicesDeepSliceAbstractCommand.java

@@ -8,7 +8,7 @@
 import ch.epfl.biop.atlas.aligner.RegisterSliceAction;
 import ch.epfl.biop.atlas.aligner.SliceSources;
 import ch.epfl.biop.atlas.aligner.action.MarkActionSequenceBatchAction;
-import ch.epfl.biop.atlas.aligner.plugin.IABBARegistrationPlugin;
+import ch.epfl.biop.registration.plugin.IRegistrationPlugin;
 import ch.epfl.biop.java.utilities.TempDirectory;
 import ch.epfl.biop.quicknii.QuickNIIExporter;
 import ch.epfl.biop.quicknii.QuickNIISeries;
@@ -392,11 +392,9 @@ protected void  affineTransformInPlane(final List<SliceSources> slices, double n
 
             //logger.debug("Slice QuickNii "+i+" correspond to initial slice "+iSliceSource);
 
-            IABBARegistrationPlugin registration = (IABBARegistrationPlugin)
+            IRegistrationPlugin registration = (IRegistrationPlugin)
                     pluginService.getPlugin(AffineRegistration.class).createInstance();
             registration.setScijavaContext(ctx);
-
-            registration.setSliceInfo(new MultiSlicePositioner.SliceInfo(mp, slices.get(iSliceSource)));
             Map<String,Object> parameters = new HashMap<>();
 
             AffineTransform3D inPlaneTransform = new AffineTransform3D();

src/main/java/ch/epfl/biop/atlas/aligner/command/RegisterSlicesElastixAffineCommand.java

@@ -1,5 +1,6 @@
 package ch.epfl.biop.atlas.aligner.command;
 
+import ch.epfl.biop.registration.sourceandconverter.affine.Elastix2DAffineRegistration;
 import ch.epfl.biop.scijava.command.source.register.ElastixHelper;
 import org.scijava.command.Command;
 import org.scijava.plugin.Parameter;
@@ -40,7 +41,7 @@ public void runValidated() {
         parameters.put("background_offset_value_fixed", background_offset_value_fixed);
         parameters.put("pxSizeInCurrentUnit", pixel_size_micrometer/1000.0);
 
-        mp.registerSelectedSlices(this,
+        mp.registerSelectedSlices(Elastix2DAffineRegistration.class,
                 getFixedFilter(),
                 getMovingFilter(),
                 parameters);

src/main/java/ch/epfl/biop/atlas/aligner/command/RegisterSlicesElastixSplineCommand.java

@@ -1,5 +1,6 @@
 package ch.epfl.biop.atlas.aligner.command;
 
+import ch.epfl.biop.registration.sourceandconverter.spline.Elastix2DSplineRegistration;
 import ch.epfl.biop.scijava.command.source.register.ElastixHelper;
 import org.scijava.command.Command;
 import org.scijava.plugin.Parameter;
@@ -51,7 +52,7 @@ public void runValidated() {
         parameters.put("background_offset_value_fixed", background_offset_value_fixed);
         parameters.put("pxSizeInCurrentUnit", pixel_size_micrometer/1000.0);
 
-        mp.registerSelectedSlices(this,
+        mp.registerSelectedSlices(Elastix2DSplineRegistration.class,
                 getFixedFilter(),
                 getMovingFilter(),
                 parameters);