diff --git a/pom.xml b/pom.xml
index c57caac5..680e8dc7 100644
--- a/pom.xml
+++ b/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 -->
diff --git a/src/main/java/ch/epfl/biop/atlas/aligner/EditLastRegistrationAction.java b/src/main/java/ch/epfl/biop/atlas/aligner/EditLastRegistrationAction.java
index 92d23ee5..e823d89f 100644
--- a/src/main/java/ch/epfl/biop/atlas/aligner/EditLastRegistrationAction.java
+++ b/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;
diff --git a/src/main/java/ch/epfl/biop/atlas/aligner/MultiSlicePositioner.java b/src/main/java/ch/epfl/biop/atlas/aligner/MultiSlicePositioner.java
index b444285e..6331ace2 100644
--- a/src/main/java/ch/epfl/biop/atlas/aligner/MultiSlicePositioner.java
+++ b/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
@@ -1456,7 +1423,7 @@ 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
@@ -1464,7 +1431,7 @@ public SliceInfo(MultiSlicePositioner mp, SliceSources slice) {
* @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);
}
@@ -1472,7 +1439,7 @@ 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);
}
diff --git a/src/main/java/ch/epfl/biop/atlas/aligner/RegisterSliceAction.java b/src/main/java/ch/epfl/biop/atlas/aligner/RegisterSliceAction.java
index 4ee30cbf..8f4418e6 100644
--- a/src/main/java/ch/epfl/biop/atlas/aligner/RegisterSliceAction.java
+++ b/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;
diff --git a/src/main/java/ch/epfl/biop/atlas/aligner/SliceSources.java b/src/main/java/ch/epfl/biop/atlas/aligner/SliceSources.java
index 05cbec9f..5698811d 100644
--- a/src/main/java/ch/epfl/biop/atlas/aligner/SliceSources.java
+++ b/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;
diff --git a/src/main/java/ch/epfl/biop/atlas/aligner/adapter/RegistrationAdapter.java b/src/main/java/ch/epfl/biop/atlas/aligner/adapter/RegistrationAdapter.java
index 550e9789..d4b7fa05 100644
--- a/src/main/java/ch/epfl/biop/atlas/aligner/adapter/RegistrationAdapter.java
+++ b/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());
diff --git a/src/main/java/ch/epfl/biop/atlas/aligner/command/MirrorDoCommand.java b/src/main/java/ch/epfl/biop/atlas/aligner/command/MirrorDoCommand.java
index b7d5be70..0ff46529 100644
--- a/src/main/java/ch/epfl/biop/atlas/aligner/command/MirrorDoCommand.java
+++ b/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);
diff --git a/src/main/java/ch/epfl/biop/atlas/aligner/command/RegisterSlicesBigWarpCommand.java b/src/main/java/ch/epfl/biop/atlas/aligner/command/RegisterSlicesBigWarpCommand.java
index f82f2d87..44c29652 100644
--- a/src/main/java/ch/epfl/biop/atlas/aligner/command/RegisterSlicesBigWarpCommand.java
+++ b/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<>());
}
}
diff --git a/src/main/java/ch/epfl/biop/atlas/aligner/command/RegisterSlicesDeepSliceAbstractCommand.java b/src/main/java/ch/epfl/biop/atlas/aligner/command/RegisterSlicesDeepSliceAbstractCommand.java
index d0fbbda6..4d0c09fd 100644
--- a/src/main/java/ch/epfl/biop/atlas/aligner/command/RegisterSlicesDeepSliceAbstractCommand.java
+++ b/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();
diff --git a/src/main/java/ch/epfl/biop/atlas/aligner/command/RegisterSlicesElastixAffineCommand.java b/src/main/java/ch/epfl/biop/atlas/aligner/command/RegisterSlicesElastixAffineCommand.java
index 9f1c5e3f..7d53c4ee 100644
--- a/src/main/java/ch/epfl/biop/atlas/aligner/command/RegisterSlicesElastixAffineCommand.java
+++ b/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);
diff --git a/src/main/java/ch/epfl/biop/atlas/aligner/command/RegisterSlicesElastixSplineCommand.java b/src/main/java/ch/epfl/biop/atlas/aligner/command/RegisterSlicesElastixSplineCommand.java
index 9d1b026c..f5d4fe28 100644
--- a/src/main/java/ch/epfl/biop/atlas/aligner/command/RegisterSlicesElastixSplineCommand.java
+++ b/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);
diff --git a/src/main/java/ch/epfl/biop/atlas/aligner/gui/bdv/BdvMultislicePositionerView.java b/src/main/java/ch/epfl/biop/atlas/aligner/gui/bdv/BdvMultislicePositionerView.java
index 1702be1c..8747fab8 100644
--- a/src/main/java/ch/epfl/biop/atlas/aligner/gui/bdv/BdvMultislicePositionerView.java
+++ b/src/main/java/ch/epfl/biop/atlas/aligner/gui/bdv/BdvMultislicePositionerView.java
@@ -42,13 +42,17 @@
import ch.epfl.biop.atlas.aligner.command.ImportSliceFromSourcesCommand;
import ch.epfl.biop.atlas.aligner.command.ImportSlicesFromFilesCommand;
import ch.epfl.biop.atlas.aligner.command.ImportSlicesFromQuPathCommand;
+import ch.epfl.biop.atlas.aligner.command.MirrorDoCommand;
import ch.epfl.biop.atlas.aligner.command.MirrorUndoCommand;
import ch.epfl.biop.atlas.aligner.command.RasterSlicesCommand;
import ch.epfl.biop.atlas.aligner.command.RasterSlicesDeformationCommand;
+import ch.epfl.biop.atlas.aligner.command.RegisterSlicesBigWarpCommand;
import ch.epfl.biop.atlas.aligner.command.RegisterSlicesCopyAndApplyCommand;
import ch.epfl.biop.atlas.aligner.command.RegisterSlicesDeepSliceWebCommand;
import ch.epfl.biop.atlas.aligner.command.RegisterSlicesDeepSliceLocalCommand;
import ch.epfl.biop.atlas.aligner.command.RegisterSlicesEditLastCommand;
+import ch.epfl.biop.atlas.aligner.command.RegisterSlicesElastixAffineCommand;
+import ch.epfl.biop.atlas.aligner.command.RegisterSlicesElastixSplineCommand;
import ch.epfl.biop.atlas.aligner.command.RegisterSlicesRemoveLastCommand;
import ch.epfl.biop.atlas.aligner.command.RotateSlicesCommand;
import ch.epfl.biop.atlas.aligner.command.SetSlicesDisplayRangeCommand;
@@ -62,8 +66,6 @@
import ch.epfl.biop.atlas.aligner.gui.bdv.card.NavigationPanel;
import ch.epfl.biop.atlas.aligner.gui.bdv.card.SliceDefineROICommand;
import ch.epfl.biop.atlas.aligner.plugin.ABBACommand;
-import ch.epfl.biop.atlas.aligner.plugin.IABBARegistrationPlugin;
-import ch.epfl.biop.atlas.aligner.plugin.RegistrationPluginHelper;
import ch.epfl.biop.atlas.struct.AtlasNode;
import ch.epfl.biop.bdv.gui.graphicalhandle.GraphicalHandle;
import ch.epfl.biop.bdv.gui.graphicalhandle.GraphicalHandleListener;
@@ -83,7 +85,6 @@
import org.scijava.Context;
import org.scijava.MenuPath;
import org.scijava.cache.CacheService;
-import org.scijava.command.Command;
import org.scijava.command.CommandModule;
import org.scijava.command.CommandService;
import org.scijava.module.Module;
@@ -423,15 +424,11 @@ private void installBdvMenu(int hierarchyLevelsSkipped) {
}
private void installRegistrationPluginUI(int hierarchyLevelsSkipped) {
- PluginService pluginService = msp.getContext().getService(PluginService.class);
- pluginService.getPluginsOfType(IABBARegistrationPlugin.class).forEach(registrationPluginClass -> {
- IABBARegistrationPlugin plugin = pluginService.createInstance(registrationPluginClass);
- for (Class<? extends Command> commandUI: RegistrationPluginHelper.userInterfaces(plugin)) {
- logger.info("Registration plugin "+commandUI.getSimpleName()+" discovered");
- BdvScijavaHelper.addCommandToBdvHandleMenu(bdvh, msp.getContext(), commandUI, hierarchyLevelsSkipped,"mp", msp);
- }
- });
+ BdvScijavaHelper.addCommandToBdvHandleMenu(bdvh, msp.getContext(), RegisterSlicesElastixAffineCommand.class, hierarchyLevelsSkipped,"mp", msp);
+ BdvScijavaHelper.addCommandToBdvHandleMenu(bdvh, msp.getContext(), RegisterSlicesBigWarpCommand.class, hierarchyLevelsSkipped,"mp", msp);
+ BdvScijavaHelper.addCommandToBdvHandleMenu(bdvh, msp.getContext(), RegisterSlicesElastixSplineCommand.class, hierarchyLevelsSkipped,"mp", msp);
+ BdvScijavaHelper.addCommandToBdvHandleMenu(bdvh, msp.getContext(), MirrorDoCommand.class, hierarchyLevelsSkipped,"mp", msp);
BdvScijavaHelper.addCommandToBdvHandleMenu(bdvh, msp.getContext(), MirrorUndoCommand.class, hierarchyLevelsSkipped,"mp", msp);
logger.debug("Installing external registration plugins ui");
diff --git a/src/main/java/ch/epfl/biop/atlas/aligner/plugin/ExternalABBARegistrationPlugin.java b/src/main/java/ch/epfl/biop/atlas/aligner/plugin/ExternalABBARegistrationPlugin.java
deleted file mode 100644
index 95b6bc7e..00000000
--- a/src/main/java/ch/epfl/biop/atlas/aligner/plugin/ExternalABBARegistrationPlugin.java
+++ /dev/null
@@ -1,29 +0,0 @@
-package ch.epfl.biop.atlas.aligner.plugin;
-import org.scijava.command.Command;
-
-/**
- * An registration plugin interface without any annotation - useful
- * mostly useful in order to add a plugin from PyImageJ
- */
-@SuppressWarnings("SameReturnValue")
-public interface ExternalABBARegistrationPlugin extends IABBARegistrationPlugin {
-
- /**
- * Does the registration required an user input ?
- * @return true if some user action is required
- */
- boolean isManual();
-
- /**
- * Can the registration be edited after it has run ?
- * Considered a manual task by default
- * @return true if the registration can be edited a posteriori
- */
- boolean isEditable();
-
- /**
- * @return the command class the user has to call in order to start a registration
- */
- Class<? extends Command>[] userInterface();
-
-}
diff --git a/src/main/java/ch/epfl/biop/atlas/aligner/plugin/IABBARegistrationPlugin.java b/src/main/java/ch/epfl/biop/atlas/aligner/plugin/IABBARegistrationPlugin.java
deleted file mode 100644
index 344ae1b1..00000000
--- a/src/main/java/ch/epfl/biop/atlas/aligner/plugin/IABBARegistrationPlugin.java
+++ /dev/null
@@ -1,12 +0,0 @@
-package ch.epfl.biop.atlas.aligner.plugin;
-
-import bdv.viewer.SourceAndConverter;
-import ch.epfl.biop.atlas.aligner.MultiSlicePositioner;
-import ch.epfl.biop.registration.Registration;
-import org.scijava.plugin.SciJavaPlugin;
-
-public interface IABBARegistrationPlugin extends SciJavaPlugin, Registration<SourceAndConverter<?>[]> {
-
- void setSliceInfo(MultiSlicePositioner.SliceInfo sliceInfo);
-
-}
diff --git a/src/main/java/ch/epfl/biop/atlas/aligner/plugin/RegistrationPluginHelper.java b/src/main/java/ch/epfl/biop/atlas/aligner/plugin/RegistrationPluginHelper.java
deleted file mode 100644
index 4ce75b41..00000000
--- a/src/main/java/ch/epfl/biop/atlas/aligner/plugin/RegistrationPluginHelper.java
+++ /dev/null
@@ -1,85 +0,0 @@
-package ch.epfl.biop.atlas.aligner.plugin;
-
-import ch.epfl.biop.registration.Registration;
-import org.scijava.Context;
-import org.scijava.command.Command;
-import org.scijava.plugin.PluginService;
-
-import java.util.Arrays;
-
-// Facilitates accessing annotation values
-public class RegistrationPluginHelper {
-
- /**
- * Does the registration required an user input ?
- * @return true if user input is required
- */
- public static boolean isManual(Registration<?> reg) {
- if (reg.getClass().isAnnotationPresent(RegistrationTypeProperties.class)) {
- final RegistrationTypeProperties annotation = reg.getClass()
- .getAnnotation(RegistrationTypeProperties.class);
- return annotation.isManual();
- } else {
- if (reg instanceof ExternalABBARegistrationPlugin) {
- return ((ExternalABBARegistrationPlugin) reg).isManual();
- } else {
- return false; // Default value if no annotation is present
- }
- }
- }
-
- /**
- * Can the registration be edited after it has run ?
- * Considered a manual task by default
- */
- public static boolean isEditable(Registration<?> reg) {
- if (reg.getClass().isAnnotationPresent(RegistrationTypeProperties.class)) {
- final RegistrationTypeProperties annotation = reg.getClass()
- .getAnnotation(RegistrationTypeProperties.class);
- return annotation.isEditable();
- } else {
- if (reg instanceof ExternalABBARegistrationPlugin) {
- return ((ExternalABBARegistrationPlugin) reg).isEditable();
- } else {
- return false; // Default value if no annotation is present
- }
- }
- }
-
- /**
- * @return the command class the user has to call in order to start a registration
- */
- public static Class<? extends Command>[] userInterfaces(Registration<?> reg) {
- if (reg.getClass().isAnnotationPresent(RegistrationTypeProperties.class)) {
- final RegistrationTypeProperties annotation = reg.getClass()
- .getAnnotation(RegistrationTypeProperties.class);
- return annotation.userInterface();
- } else {
- if (reg instanceof ExternalABBARegistrationPlugin) {
- return ((ExternalABBARegistrationPlugin) reg).userInterface();
- } else {
- return new Class[0]; // Default value if no annotation is present
- }
- }
- }
-
- /**
- * Assumes unicity! Find the registration class from a UI class
- * @param queryUIClass the ui class from which the registration is supposed to be found
- * @return null is nothing is found
- */
- public static Class<? extends IABBARegistrationPlugin> registrationFromUI (Context ctx, Class<? extends Command> queryUIClass) {
- PluginService pluginService = ctx.getService(PluginService.class);
-
- // OK... intellij found this alone, let's hope it works
- return pluginService
- .getPluginsOfType(IABBARegistrationPlugin.class)
- .stream().map(pluginService::createInstance)
- .filter(plugin -> Arrays.asList(RegistrationPluginHelper.userInterfaces(plugin)).contains(queryUIClass))
- .findFirst()
- .map(IABBARegistrationPlugin::getClass)
- .orElse(null);
-
- }
-
-}
diff --git a/src/main/java/ch/epfl/biop/atlas/aligner/plugin/RegistrationTypeProperties.java b/src/main/java/ch/epfl/biop/atlas/aligner/plugin/RegistrationTypeProperties.java
deleted file mode 100644
index 74304969..00000000
--- a/src/main/java/ch/epfl/biop/atlas/aligner/plugin/RegistrationTypeProperties.java
+++ /dev/null
@@ -1,29 +0,0 @@
-package ch.epfl.biop.atlas.aligner.plugin;
-
-import org.scijava.command.Command;
-
-import java.lang.annotation.Retention;
-import java.lang.annotation.RetentionPolicy;
-
-@Retention(RetentionPolicy.RUNTIME)
-public @interface RegistrationTypeProperties {
-
- /**
- * Does the registration required an user input ?
- * @return true if the registration requires user input
- */
- boolean isManual();
-
- /**
- * Can the registration be edited after it has run ?
- * Considered a manual task by default
- * @return true if the registration can be edited a posteriori
- */
- boolean isEditable();
-
- /**
- * @return the command class the user has to call in order to start a registration
- */
- Class<? extends Command>[] userInterface();
-}
-
diff --git a/src/main/java/ch/epfl/biop/atlas/aligner/plugin/SimpleABBARegistrationPlugin.java b/src/main/java/ch/epfl/biop/atlas/aligner/plugin/SimpleABBARegistrationPlugin.java
deleted file mode 100644
index 8e708172..00000000
--- a/src/main/java/ch/epfl/biop/atlas/aligner/plugin/SimpleABBARegistrationPlugin.java
+++ /dev/null
@@ -1,32 +0,0 @@
-package ch.epfl.biop.atlas.aligner.plugin;
-
-import ij.ImagePlus;
-import net.imglib2.realtransform.InvertibleRealTransform;
-
-import java.util.Map;
-
-@SuppressWarnings("SameReturnValue")
-public interface SimpleABBARegistrationPlugin {
-
- /**
- * @return Sampling required for the registration, in micrometer
- */
- double getVoxelSizeInMicron();
-
- /**
- * Is called before registration to pass any extra registration parameter
- * argument. Passed as a dictionary of String to preserve serialization
- * capability.
- * @param parameters dictionary of parameters
- */
- void setRegistrationParameters(Map<String,String> parameters);
-
- /**
- *
- * @param fixed image
- * @param moving image
- * @return the transform, result of the registration, in
- * going from fixed to moving coordinates, in pixels
- */
- InvertibleRealTransform register(ImagePlus fixed, ImagePlus moving, ImagePlus fixedMask, ImagePlus movingMask);
-}
diff --git a/src/main/java/ch/epfl/biop/atlas/aligner/plugin/SimpleRegistrationWrapper.java b/src/main/java/ch/epfl/biop/atlas/aligner/plugin/SimpleRegistrationWrapper.java
deleted file mode 100644
index 3bc019e3..00000000
--- a/src/main/java/ch/epfl/biop/atlas/aligner/plugin/SimpleRegistrationWrapper.java
+++ /dev/null
@@ -1,339 +0,0 @@
-package ch.epfl.biop.atlas.aligner.plugin;
-
-import bdv.util.BoundedRealTransform;
-import bdv.viewer.SourceAndConverter;
-import ch.epfl.biop.atlas.aligner.MultiSlicePositioner;
-import ch.epfl.biop.bdv.img.imageplus.ImagePlusHelper;
-import ch.epfl.biop.java.utilities.roi.types.RealPointList;
-import ij.ImagePlus;
-import net.imglib2.RealPoint;
-import net.imglib2.realtransform.AffineTransform3D;
-import net.imglib2.realtransform.InvertibleRealTransform;
-import net.imglib2.realtransform.InvertibleRealTransformSequence;
-import net.imglib2.realtransform.RealTransform;
-import net.imglib2.type.NativeType;
-import net.imglib2.type.numeric.NumericType;
-import org.scijava.Context;
-import org.scijava.command.Command;
-import sc.fiji.bdvpg.sourceandconverter.SourceAndConverterHelper;
-import sc.fiji.bdvpg.sourceandconverter.importer.EmptySourceAndConverterCreator;
-import sc.fiji.bdvpg.sourceandconverter.transform.SourceRealTransformer;
-import sc.fiji.bdvpg.sourceandconverter.transform.SourceResampler;
-import sc.fiji.persist.ScijavaGsonHelper;
-
-import java.util.*;
-import java.util.stream.Collectors;
-
-public class SimpleRegistrationWrapper implements ExternalABBARegistrationPlugin {
-
- public String getRegistrationTypeName() {
- return registrationTypeName;
- }
-
- public SimpleRegistrationWrapper(String registrationTypeName, final SimpleABBARegistrationPlugin simpleRegistration) {
- this.registration = simpleRegistration;
- this.registrationTypeName = registrationTypeName;
- }
-
- final String registrationTypeName;
- final SimpleABBARegistrationPlugin registration;
-
- Context context;
-
- Map<String, String> parameters;
-
- boolean isDone = false;
-
- protected RealTransform rt;
-
- @Override
- public void setSliceInfo(MultiSlicePositioner.SliceInfo sliceInfo) {
-
- }
-
- @Override
- public boolean isManual() {
- return false;
- }
-
- @Override
- public boolean isEditable() {
- return false;
- }
-
- @Override
- public Class<? extends Command>[] userInterface() {
- return new Class[0];
- }
-
- @Override
- public void setScijavaContext(Context context) {
- this.context = context;
- }
-
- @Override
- public void setRegistrationParameters(Map<String, String> parameters) {
- this.parameters = parameters;
- }
-
- @Override
- public Map<String, String> getRegistrationParameters() {
- return parameters;
- }
-
- ImagePlus fixedImage, movingImage, fixedMask, movingMask;
-
- @Override
- public void setFixedImage(SourceAndConverter<?>[] fimg) {
- fixedImage = export("Fixed-", Arrays.asList(fimg),
- (Double.parseDouble(parameters.get("px"))),
- (Double.parseDouble(parameters.get("py"))),
- (Double.parseDouble(parameters.get("sx"))),
- (Double.parseDouble(parameters.get("sy"))),
- registration.getVoxelSizeInMicron()/1000.0,
- 0,
- false
- );
- }
-
- @Override
- public void setMovingImage(SourceAndConverter<?>[] mimg) {
- movingImage = export("Moving-", Arrays.asList(mimg),
- (Double.parseDouble(parameters.get("px"))),
- (Double.parseDouble(parameters.get("py"))),
- (Double.parseDouble(parameters.get("sx"))),
- (Double.parseDouble(parameters.get("sy"))),
- registration.getVoxelSizeInMicron()/1000.0,
- 0,
- false
- );
- }
-
- @Override
- public void setFixedMask(SourceAndConverter<?>[] fimg_mask) {
- fixedMask = export("FixedMask-", Arrays.asList(fimg_mask),
- (Double.parseDouble(parameters.get("px"))),
- (Double.parseDouble(parameters.get("py"))),
- (Double.parseDouble(parameters.get("sx"))),
- (Double.parseDouble(parameters.get("sy"))),
- registration.getVoxelSizeInMicron()/1000.0,
- 0,
- false
- );
- }
-
- @Override
- public void setMovingMask(SourceAndConverter<?>[] mimg_mask) {
- movingMask = export("MovingMask-", Arrays.asList(mimg_mask),
- (Double.parseDouble(parameters.get("px"))),
- (Double.parseDouble(parameters.get("py"))),
- (Double.parseDouble(parameters.get("sx"))),
- (Double.parseDouble(parameters.get("sy"))),
- registration.getVoxelSizeInMicron()/1000.0,
- 0,
- false
- );
- }
-
- @Override
- public void resetRegistration() {
- isDone = false;
- }
-
- @Override
- public void setTimePoint(int timePoint) {
- // ignored: it's 0
- }
-
- @Override
- public boolean register() {
- InvertibleRealTransform inner_rt = registration.register(fixedImage, movingImage, fixedMask, movingMask);
-
- // This transform is for pixel to pixel coordinates -> we need to convert it to physical space.
- // Thus adding an AffineTransform to a sequence
-
- InvertibleRealTransformSequence irts = new InvertibleRealTransformSequence();
- AffineTransform3D m = new AffineTransform3D();
-
- double px = (Double.parseDouble(parameters.get("px")));
- double py = (Double.parseDouble(parameters.get("py")));
- double voxSize = registration.getVoxelSizeInMicron();
-
- // We work in millimeters
- m.scale(voxSize/1000.0);
- m.translate(px, py, 0);
-
- // The umbrella trick
- irts.add(m.inverse());
- irts.add(inner_rt);
- irts.add(m);
-
- rt = irts;
-
- isDone = true;
- return true; // no error handling
- }
-
- @Override
- public boolean edit() {
- // TODO : find a way to edit an affine transform -> that shouldn't be so complicated
- throw new UnsupportedOperationException();
- }
-
- @Override
- public boolean isRegistrationDone() {
- return isDone;
- }
-
- @Override
- public SourceAndConverter<?>[] getTransformedImageMovingToFixed(SourceAndConverter<?>[] img) {
- SourceAndConverter[] out = new SourceAndConverter[img.length];
- SourceRealTransformer srt = new SourceRealTransformer(rt);
- for (int idx = 0;idx<img.length;idx++) {
- out[idx] = srt.apply(img[idx]);
- }
- return out;
- }
-
- @Override
- public RealPointList getTransformedPtsFixedToMoving(RealPointList pts) {
- RealTransform innerRT = rt; // To unbox bounded realtransform
-
- // Unbox bounded transform
- if (rt instanceof BoundedRealTransform) {
- innerRT = ((BoundedRealTransform)rt).getTransform().copy();
- }
-
- ArrayList<RealPoint> cvtList = new ArrayList<>();
-
- for (RealPoint p : pts.ptList) {
- RealPoint pt3d = new RealPoint(3);
- pt3d.setPosition(new double[]{p.getDoublePosition(0), p.getDoublePosition(1),0});
- innerRT.apply(pt3d, pt3d);
- RealPoint cpt = new RealPoint(pt3d.getDoublePosition(0), pt3d.getDoublePosition(1));
- cvtList.add(cpt);
- }
-
- return new RealPointList(cvtList);
- }
-
- @Override
- public void abort() {
-
- }
-
- public RealTransform getRealTransform() {
- return rt;
- }
-
- public void setRealTransform(RealTransform transform) {
- this.rt = transform.copy();
- }
-
- @Override
- final public String getTransform() {
- //logger.debug("Serializing transform of class "+rt.getClass().getSimpleName());
- String transform = ScijavaGsonHelper.getGson(context).toJson(rt, RealTransform.class);
- //logger.debug("Serialization result = "+transform);
- return transform;
- }
-
- @Override
- final public void setTransform(String serialized_transform) {
- setRealTransform(ScijavaGsonHelper.getGson(context).fromJson(serialized_transform, RealTransform.class));
- isDone = true;
- }
-
- public RealTransform getTransformAsRealTransform() {
- return rt.copy();
- }
-
-
- public static <T extends NumericType<T> & NativeType<T>> ImagePlus export(String name, List<SourceAndConverter<?>> sourceList,
- double px, double py, double sx, double sy,
- double pixelSizeMillimeter, int timepoint,
- boolean interpolate) {
-
- AffineTransform3D at3D = new AffineTransform3D();
-
- SourceAndConverter model = createModelSource(px, py, sx, sy, pixelSizeMillimeter, at3D);
-
- List<SourceAndConverter<T>> resampledSourceList = sourceList
- .stream()
- .map(sac -> (SourceAndConverter<T>) (new SourceResampler(sac,model,sac.getSpimSource().getName()+"_ResampledLike_"+model.getSpimSource().getName(), true, false, interpolate,0).get()))
- .collect(Collectors.toList());
-
- if ((sourceList.size()>1)) {
-
- Map<SourceAndConverter<T>, Integer> mapMipmap = new HashMap<>();
- sourceList.forEach(src -> {
- int mipmapLevel = SourceAndConverterHelper.bestLevel(src, timepoint, pixelSizeMillimeter);
- //logger.debug("Mipmap level chosen for source ["+src.getSpimSource().getName()+"] : "+mipmapLevel);
- mapMipmap.put(resampledSourceList.get(sourceList.indexOf(src)), mipmapLevel);
- });
-
- ImagePlus resultImage = ImagePlusHelper.wrap(
- resampledSourceList,
- mapMipmap,
- timepoint,
- 1,
- 1);
-
- resultImage.setTitle(name+"-["+px+":"+(px+sx)+" | "+py+":"+(py+sy)+"]");
- ImagePlusHelper.storeExtendedCalibrationToImagePlus(resultImage, at3D.inverse(), "mm", timepoint);
-
- return resultImage;
-
- } else {
- SourceAndConverter source = resampledSourceList.get(0);
- int mipmapLevel = SourceAndConverterHelper.bestLevel(sourceList.get(0), timepoint, pixelSizeMillimeter);
- ImagePlus singleChannel = ImagePlusHelper.wrap(
- source,
- mipmapLevel,
- timepoint,
- 1,
- 1);
- singleChannel.setTitle(source.getSpimSource().getName());
- ImagePlusHelper.storeExtendedCalibrationToImagePlus(singleChannel, at3D.inverse(), "mm", timepoint);
-
- return singleChannel;
- }
-
- }
-
-
- private static SourceAndConverter createModelSource(
- double px, double py,
- double sx, double sy,
- double pixel_size_mm,
- AffineTransform3D transform) {
- // Origin is in fact the point 0,0,0 of the image
- // Get current big dataviewer transformation : source transform and viewer transform
- AffineTransform3D at3D = new AffineTransform3D(); // Empty Transform
- // viewer transform
- // Center on the display center of the viewer ...
- at3D.translate(-px, -py, 0);
-
- at3D.scale(1/pixel_size_mm);
-
- // Getting an image independent of the view scaling unit (not sure)
- long nPx = (long)(sx / pixel_size_mm);
- long nPy = (long)(sy / pixel_size_mm);
- long nPz = 1;
-
- // At least a pixel in all directions
- if (nPz == 0) nPz = 1;
- if (nPx == 0) nPx = 1;
- if (nPy == 0) nPy = 1;
-
- transform.set(at3D);
-
- return new EmptySourceAndConverterCreator("model", at3D.inverse(), nPx, nPy, nPz).get();
- }
-
- @Override
- public String toString() {
- return registrationTypeName;
- }
-
-}
diff --git a/src/main/java/ch/epfl/biop/registration/Registration.java b/src/main/java/ch/epfl/biop/registration/Registration.java
deleted file mode 100644
index adfad215..00000000
--- a/src/main/java/ch/epfl/biop/registration/Registration.java
+++ /dev/null
@@ -1,171 +0,0 @@
-package ch.epfl.biop.registration;
-import ch.epfl.biop.java.utilities.roi.types.RealPointList;
-import net.imglib2.realtransform.RealTransform;
-import org.scijava.Context;
-
-import java.util.Map;
-
-/**
- * Most upstream
- * @param <T> Type of the image to register ( ImagePlus / SourceAndConverter, what else ? )
- */
-
-public interface Registration<T> {
-
- /**
- * Is called just after the Registration object creation to pass
- * the current scijava context
- * is adopted by all registrations
- * @param context
- */
- void setScijavaContext(Context context);
-
- /**
- * Is called before registration to pass any extra registration parameter
- * argument. Passed as a dictionary of String to preserve serialization
- * capability.
- * @param parameters dictionary of parameters
- */
- void setRegistrationParameters(Map<String,String> parameters);
-
- /**
- * For serialization and reproducibility
- * @return parameters that were used for the registration
- */
- Map<String,String> getRegistrationParameters();
-
- /**
- * Sets the fixed image
- * @param fimg fixed image
- */
- void setFixedImage(T fimg);
-
- /**
- * Set the moving image
- * @param mimg moving image
- */
- void setMovingImage(T mimg);
-
- /**
- * Optional - sets the fixed image mask
- * @param fimg_mask fixed image
- */
- void setFixedMask(T fimg_mask);
-
- /**
- * Optional - set the moving image mask
- * @param mimg_mask moving image
- */
- void setMovingMask(T mimg_mask);
-
- /**
- * Sets the state of the registration to not done
- * Called when the registration needs to be rerun for real
- * instead of just restored
- *
- */
- void resetRegistration();
-
- /**
- * Sets the timepoint of the source that should be used for the
- * registration. 0 in most cases
- * @param timePoint
- */
- void setTimePoint(int timePoint);
-
- /**
- * Blocking function which performs the registration
- * @return true if the registration was run succesfully
- */
- boolean register();
-
- /**
- * Can be called after register() return false in order to get
- * a more meaningful explanation
- * @return an error message for a failed registration
- */
- default String getExceptionMessage() {
- return "Unspecified error";
- }
-
- /**
- * Blocking function which is called when the user wants
- * to manually edit the result of the registration
- * @return true is the transform is been edited successfully. If not,
- * the previous state of the registration is restored thanks to the serialization
- * of the transform. An edition cannot occur if the transform has not been set
- * before (either via the run method, or via setting the transform via the
- * {@link Registration#setTransform(String)} method
- */
- boolean edit();
-
- /**
- * Flag functions which serves to know whether the result of the
- * registration is available. Should not be blocking.
- *
- * @return true if the transform is available
- */
- boolean isRegistrationDone();
-
- /**
- * Function which takes an input moving image, transform it
- * according to the result of the registration (transformation),
- * and returns it
- * @param img should not be modified
- * @return the transformed image
- */
- T getTransformedImageMovingToFixed(final T img);
-
- /**
- * Reverse transforms a list of points. This function takes a list
- * of points given in the fixed coordinates system, inverse transform
- * their coordinates according to the result of the registration.
- * The points can be mutated
- * @param pts points to transform from fixed to moving system coordinates
- * @return the transformed points
- */
- RealPointList getTransformedPtsFixedToMoving(RealPointList pts);
-
- /**
- * Function called when a registration is cancelled while being processed
- */
- void abort();
-
- /**
- * This function is used to:
- * - save the registration into a json file
- * - store transiently the state of a registration to cancel the edition of a transform, if needed
- * @return a serialized representation of the transform as a String
- */
- String getTransform();
-
- /**
- * Function used to bypass the real registration process (run)
- * in order to set directly the result of the registration.
- * This is used when:
- * - loading a registration from a state file
- * - restore if needed a previous transformed state after an edition
- * a serialized representation of the transform is sent, leading
- * to an immediate registration being done
- * isDone should return true after this function is being called
- * @param serialized_transform
- */
- void setTransform(String serialized_transform);
-
- /**
- * If the transform can be returned as a serializable RealTransform object,
- * this can be used to serialize the successive registrations as a
- * {@link net.imglib2.realtransform.RealTransformSequence} object, or even,
- * if all transformations are invertible, as a {@link net.imglib2.realtransform.InvertibleRealTransformSequence} object
- * @return
- */
- RealTransform getTransformAsRealTransform();
-
- /**
- * Used for serialisation
- * @return
- */
- default String getRegistrationTypeName() {
- return this.getClass().getSimpleName();
- }
-}
diff --git a/src/main/java/ch/epfl/biop/registration/sourceandconverter/SourceAndConverterRegistration.java b/src/main/java/ch/epfl/biop/registration/sourceandconverter/SourceAndConverterRegistration.java
deleted file mode 100644
index d6cded50..00000000
--- a/src/main/java/ch/epfl/biop/registration/sourceandconverter/SourceAndConverterRegistration.java
+++ /dev/null
@@ -1,102 +0,0 @@
-package ch.epfl.biop.registration.sourceandconverter;
-
-import bdv.viewer.SourceAndConverter;
-import ch.epfl.biop.atlas.aligner.MultiSlicePositioner;
-import ch.epfl.biop.atlas.aligner.plugin.IABBARegistrationPlugin;
-import org.scijava.Context;
-import org.scijava.plugin.Parameter;
-
-import java.util.Arrays;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-abstract public class SourceAndConverterRegistration implements IABBARegistrationPlugin {
-
- protected SourceAndConverter<?>[] fimg;
-
- protected SourceAndConverter<?>[] mimg;
-
- protected SourceAndConverter<?>[] fimg_mask;
-
- protected SourceAndConverter<?>[] mimg_mask;
-
- protected int timePoint = 0;
-
- @Parameter
- protected Context context;
-
- @Override
- public void setFixedImage(SourceAndConverter<?>[] fimg) {
- this.fimg = fimg;
- }
-
- @Override
- public void setMovingImage(SourceAndConverter<?>[] mimg) {
- this.mimg = mimg;
- }
-
- @Override
- public void setFixedMask(SourceAndConverter<?>[] fimg) {
- this.fimg_mask = fimg;
- }
-
- @Override
- public void setMovingMask(SourceAndConverter<?>[] mimg) {
- this.mimg_mask = mimg;
- }
-
- @Override
- public void setTimePoint(int timePoint) {
- this.timePoint = timePoint;
- }
-
- /**
- * Is called just after the Registration object creation to pass
- * the current scijava context
- * is adopted by all registrations
- * @param context
- */
- public void setScijavaContext(Context context) {
- this.context = context;
- }
-
- protected boolean isDone = false;
-
- @Override
- public boolean isRegistrationDone() {
- return isDone;
- }
-
- @Override
- public void resetRegistration() {
- isDone = false;
- }
-
- protected Map<String, String> parameters = new HashMap<>();
-
- @Override
- public Map<String, String> getRegistrationParameters() {
- if (parameters!=null) {
- return parameters;
- } else {
- return new HashMap<>();
- }
- }
-
- @Override
- public void setRegistrationParameters(Map<String, String> parameters) {
- this.parameters = parameters;
- }
-
- protected MultiSlicePositioner.SliceInfo sliceInfo;
-
- public void setSliceInfo(MultiSlicePositioner.SliceInfo sliceInfo){
- this.sliceInfo = sliceInfo;
- }
-
- protected static void addToFlatParameters(List<Object> flatParameters, Object... args) {
- flatParameters.addAll(Arrays.asList(args));
- }
-
-}
diff --git a/src/main/java/ch/epfl/biop/registration/sourceandconverter/affine/AffineRegistration.java b/src/main/java/ch/epfl/biop/registration/sourceandconverter/affine/AffineRegistration.java
deleted file mode 100644
index cca0508a..00000000
--- a/src/main/java/ch/epfl/biop/registration/sourceandconverter/affine/AffineRegistration.java
+++ /dev/null
@@ -1,64 +0,0 @@
-package ch.epfl.biop.registration.sourceandconverter.affine;
-
-import bdv.viewer.SourceAndConverter;
-import ch.epfl.biop.atlas.aligner.plugin.IABBARegistrationPlugin;
-import ch.epfl.biop.atlas.aligner.plugin.RegistrationTypeProperties;
-import com.google.gson.Gson;
-import net.imglib2.realtransform.AffineTransform3D;
-import org.scijava.plugin.Plugin;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-/**
- * To make an affine transform programmatically conveniently
- *
- */
-@Plugin(type = IABBARegistrationPlugin.class)
-@RegistrationTypeProperties(
- isManual = false,
- isEditable = false,
- userInterface = {
- })
-
-public class AffineRegistration extends AffineTransformSourceAndConverterRegistration{
-
- protected static Logger logger = LoggerFactory.getLogger(AffineRegistration.class);
-
- @Override
- public void setFixedImage(SourceAndConverter<?>[] fimg) {
- super.setFixedImage(fimg);
- }
-
- @Override
- public void setMovingImage(SourceAndConverter<?>[] mimg) {
- super.setMovingImage(mimg);
- }
-
- public static String affineTransform3DToString(AffineTransform3D transform) {
- return new Gson().toJson(transform.getRowPackedCopy());
- }
-
- public static AffineTransform3D stringToAffineTransform3D(String string) {
- AffineTransform3D transform3D = new AffineTransform3D();
- double[] matrix = new Gson().fromJson(string, double[].class);
- transform3D.set(matrix);
- return transform3D;
- }
-
- @Override
- public boolean register() {
- at3d = stringToAffineTransform3D(parameters.get("transform"));
- isDone = true;
- return true;
- }
-
- @Override
- public void abort() {
-
- }
-
- public String toString() {
- return "Affine";
- }
-
-}
diff --git a/src/main/java/ch/epfl/biop/registration/sourceandconverter/affine/AffineTransformSourceAndConverterRegistration.java b/src/main/java/ch/epfl/biop/registration/sourceandconverter/affine/AffineTransformSourceAndConverterRegistration.java
deleted file mode 100644
index baf57aa6..00000000
--- a/src/main/java/ch/epfl/biop/registration/sourceandconverter/affine/AffineTransformSourceAndConverterRegistration.java
+++ /dev/null
@@ -1,64 +0,0 @@
-package ch.epfl.biop.registration.sourceandconverter.affine;
-
-import bdv.viewer.SourceAndConverter;
-import ch.epfl.biop.java.utilities.roi.types.RealPointList;
-import ch.epfl.biop.registration.sourceandconverter.SourceAndConverterRegistration;
-import net.imglib2.RealPoint;
-import net.imglib2.realtransform.AffineTransform3D;
-import net.imglib2.realtransform.RealTransform;
-import sc.fiji.bdvpg.sourceandconverter.SourceAndConverterAndTimeRange;
-import sc.fiji.bdvpg.sourceandconverter.transform.SourceTransformHelper;
-import sc.fiji.persist.ScijavaGsonHelper;
-
-import java.util.ArrayList;
-
-abstract public class AffineTransformSourceAndConverterRegistration extends SourceAndConverterRegistration {
-
- protected AffineTransform3D at3d = new AffineTransform3D();
-
- @SuppressWarnings("CanBeFinal")
- public int timePoint = 0;
-
- @Override
- public SourceAndConverter<?>[] getTransformedImageMovingToFixed(SourceAndConverter<?>[] img) {
- SourceAndConverter<?>[] out = new SourceAndConverter[img.length];
- for (int idx = 0;idx<img.length;idx++) {
- out[idx] = SourceTransformHelper.createNewTransformedSourceAndConverter(at3d, new SourceAndConverterAndTimeRange<>(img[idx],timePoint));
- }
- return out;
- }
-
- @Override
- public RealPointList getTransformedPtsFixedToMoving(RealPointList pts) {
- ArrayList<RealPoint> cvtList = new ArrayList<>();
- for (RealPoint p : pts.ptList) {
- RealPoint pt3d = new RealPoint(3);
- pt3d.setPosition(new double[]{p.getDoublePosition(0), p.getDoublePosition(1),0});
- at3d.inverse().apply(pt3d, pt3d);
- RealPoint cpt = new RealPoint(pt3d.getDoublePosition(0), pt3d.getDoublePosition(1));
- cvtList.add(cpt);
- }
- return new RealPointList(cvtList);
- }
-
- @Override
- public String getTransform() {
- return ScijavaGsonHelper.getGson(context).toJson(at3d, AffineTransform3D.class);
- }
-
- @Override
- public void setTransform(String serialized_transform) {
- at3d = ScijavaGsonHelper.getGson(context).fromJson(serialized_transform, AffineTransform3D.class);
- isDone = true;
- }
-
- @Override
- public boolean edit() {
- // TODO : find a way to edit an affine transform -> that shouldn't be so complicated
- throw new UnsupportedOperationException();
- }
-
- public RealTransform getTransformAsRealTransform() {
- return at3d.inverse().copy();
- }
-}
diff --git a/src/main/java/ch/epfl/biop/registration/sourceandconverter/affine/AffineTransformedSourceWrapperRegistration.java b/src/main/java/ch/epfl/biop/registration/sourceandconverter/affine/AffineTransformedSourceWrapperRegistration.java
deleted file mode 100644
index a96d64ac..00000000
--- a/src/main/java/ch/epfl/biop/registration/sourceandconverter/affine/AffineTransformedSourceWrapperRegistration.java
+++ /dev/null
@@ -1,71 +0,0 @@
-package ch.epfl.biop.registration.sourceandconverter.affine;
-
-import bdv.viewer.SourceAndConverter;
-import net.imglib2.realtransform.AffineTransform3D;
-import sc.fiji.bdvpg.sourceandconverter.SourceAndConverterAndTimeRange;
-import sc.fiji.bdvpg.sourceandconverter.transform.SourceTransformHelper;
-
-import java.util.HashMap;
-import java.util.Map;
-import java.util.concurrent.ConcurrentHashMap;
-
-/**
- * Fake registration which simply wraps a transform which is used to modify either:
- * - the place of the image in the user GUI, or to
- * TODO : write a bit more clearly what this does
- */
-public class AffineTransformedSourceWrapperRegistration extends AffineTransformSourceAndConverterRegistration {
-
- Map<SourceAndConverter<?>, SourceAndConverter<?>> alreadyTransformedSources = new ConcurrentHashMap<>();
-
- @Override
- public boolean register() {
- isDone = true;
- return true;
- }
-
- /**
- * These function are kept in order to avoid serializing many times
- * unnecessary affinetransform
- * @param at3d_in affine transform
- */
- public synchronized void setAffineTransform(AffineTransform3D at3d_in) {
- this.at3d = at3d_in;
- alreadyTransformedSources.keySet().forEach(sac -> SourceTransformHelper.set(at3d_in, new SourceAndConverterAndTimeRange<>(alreadyTransformedSources.get(sac), timePoint)));
- }
-
- public AffineTransform3D getAffineTransform() {
- return at3d.copy();
- }
-
- /**
- * Overriding to actually mutate SourceAndConverter,
- * it's the only registration which does that, because
- * it's actually not really a registration
- * @param img image
- * @return mutates the transform
- */
- @Override
- public SourceAndConverter<?>[] getTransformedImageMovingToFixed(SourceAndConverter<?>[] img) {
-
- SourceAndConverter<?>[] out = new SourceAndConverter[img.length];
-
- for (int idx = 0;idx<img.length;idx++) {
- if (alreadyTransformedSources.containsKey(img[idx])) {
- out[idx] = alreadyTransformedSources.get(img[idx]);
- SourceTransformHelper.set(at3d, new SourceAndConverterAndTimeRange<>(out[idx], timePoint));
- } else {
- out[idx] = SourceTransformHelper.createNewTransformedSourceAndConverter(at3d, new SourceAndConverterAndTimeRange<>(img[idx], timePoint));
- alreadyTransformedSources.put(img[idx], out[idx]);
- }
- }
-
- return out;
- }
-
- @Override
- public void abort() {
-
- }
-
-}
diff --git a/src/main/java/ch/epfl/biop/registration/sourceandconverter/affine/CenterZeroRegistration.java b/src/main/java/ch/epfl/biop/registration/sourceandconverter/affine/CenterZeroRegistration.java
deleted file mode 100644
index 70eb70dc..00000000
--- a/src/main/java/ch/epfl/biop/registration/sourceandconverter/affine/CenterZeroRegistration.java
+++ /dev/null
@@ -1,54 +0,0 @@
-package ch.epfl.biop.registration.sourceandconverter.affine;
-
-import bdv.viewer.SourceAndConverter;
-import net.imglib2.RealPoint;
-import net.imglib2.realtransform.AffineTransform3D;
-import sc.fiji.bdvpg.sourceandconverter.SourceAndConverterAndTimeRange;
-import sc.fiji.bdvpg.sourceandconverter.SourceAndConverterHelper;
-import sc.fiji.bdvpg.sourceandconverter.transform.SourceTransformHelper;
-
-/**
- * Fake registration : simply centers the image in order to put its center
- * at the origin of the global coordinate system.
- */
-
-public class CenterZeroRegistration extends AffineTransformSourceAndConverterRegistration {
-
- @Override
- public boolean register() {
-
- SourceAndConverter<?> sac = mimg[0];
-
- RealPoint center = SourceAndConverterHelper.getSourceAndConverterCenterPoint(sac,0);
-
- at3d = new AffineTransform3D();
-
- at3d.translate(
- -center.getDoublePosition(0),
- -center.getDoublePosition(1),
- -center.getDoublePosition(2));
-
- isDone = true;
-
- return true;
- }
-
- /**
- * @param img image
- * @return transformed images (new source created)
- */
- @Override
- public SourceAndConverter<?>[] getTransformedImageMovingToFixed(SourceAndConverter<?>[] img) {
- SourceAndConverter<?>[] out = new SourceAndConverter[img.length];
- for (int idx = 0;idx<img.length;idx++) {
- out[idx] = SourceTransformHelper.createNewTransformedSourceAndConverter(at3d, new SourceAndConverterAndTimeRange<>(img[idx], timePoint));
- }
- return out;
- }
-
- @Override
- public void abort() {
- // Cannot be aborted - is very fast anyway
- }
-
-}
diff --git a/src/main/java/ch/epfl/biop/registration/sourceandconverter/affine/Elastix2DAffineRegistration.java b/src/main/java/ch/epfl/biop/registration/sourceandconverter/affine/Elastix2DAffineRegistration.java
deleted file mode 100644
index 4090d734..00000000
--- a/src/main/java/ch/epfl/biop/registration/sourceandconverter/affine/Elastix2DAffineRegistration.java
+++ /dev/null
@@ -1,150 +0,0 @@
-package ch.epfl.biop.registration.sourceandconverter.affine;
-
-import bdv.viewer.SourceAndConverter;
-import ch.epfl.biop.atlas.aligner.command.RegisterSlicesElastixAffineCommand;
-import ch.epfl.biop.atlas.aligner.plugin.IABBARegistrationPlugin;
-import ch.epfl.biop.atlas.aligner.plugin.RegistrationTypeProperties;
-import ch.epfl.biop.scijava.command.source.register.Elastix2DAffineRegisterCommand;
-import net.imglib2.realtransform.AffineTransform3D;
-import org.scijava.command.Command;
-import org.scijava.command.CommandModule;
-import org.scijava.command.CommandService;
-import org.scijava.plugin.Plugin;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-import sc.fiji.bdvpg.sourceandconverter.SourceAndConverterHelper;
-
-import java.util.ArrayList;
-import java.util.List;
-import java.util.concurrent.Future;
-
-/**
- * Uses Elastix backend to perform an affine transform registration
- *
- */
-@Plugin(type = IABBARegistrationPlugin.class)
-@RegistrationTypeProperties(
- isManual = false,
- isEditable = false,
- userInterface = {
- RegisterSlicesElastixAffineCommand.class
- //RegistrationElastixAffineRemoteCommand.class
- })
-
-public class Elastix2DAffineRegistration extends AffineTransformSourceAndConverterRegistration{
-
-
- protected static final Logger logger = LoggerFactory.getLogger(Elastix2DAffineRegistration.class);
-
- @Override
- public void setFixedImage(SourceAndConverter[] fimg) {
- if (fimg.length==0) {
- logger.error("Error, no fixed image set in class "+this.getClass().getSimpleName());
- }
- super.setFixedImage(fimg);
- }
-
- @Override
- public void setMovingImage(SourceAndConverter[] mimg) {
- if (mimg.length==0) {
- logger.error("Error, no fixed image set in class "+this.getClass().getSimpleName());
- }
- super.setMovingImage(mimg);
- }
-
- Future<CommandModule> task;
-
- @Override
- public boolean register() {
- try {
- Class<? extends Command> registrationCommandClass;
- // Is it supposed to be done on a server ?
- registrationCommandClass = Elastix2DAffineRegisterCommand.class;
-
- // Registration success flag
- boolean success = true;
-
- // Transforms map into flat String : key1, value1, key2, value2, etc.
- // Necessary for CommandService
- List<Object> flatParameters = new ArrayList<>(parameters.size()*2+4);
-
- double voxSizeInMm = Double.parseDouble(parameters.get("pxSizeInCurrentUnit"));
-
- parameters.keySet().forEach(k -> {
- flatParameters.add(k);
- flatParameters.add(parameters.get(k));
- });
-
- addToFlatParameters(flatParameters,
- // Fixed image
- "sacs_fixed", fimg,
- // Moving image
- "sacs_moving", mimg,
- // No interpolation in resampling
- "interpolate", false,
- // Start registration with a 4x4 pixel image
- "minPixSize",4,
- // 100 iteration steps
- "maxIterationNumberPerScale",100,
- // Do not write anything
- "verbose", false,
- // Centers centers of mass of both images before starting registration
- "automaticTransformInitialization", true,
- // Atlas image : a single timepoint
- "tpFixed", 0,
- // Level 2 for the atlas
- "levelFixedSource", SourceAndConverterHelper.bestLevel(fimg[0], timePoint, voxSizeInMm),
- // Timepoint moving source (normally 0)
- "tpMoving", timePoint,
- // Tries to be clever for the moving source sampling
- "levelMovingSource", SourceAndConverterHelper.bestLevel(mimg[0], timePoint, voxSizeInMm)
- );
-
- task = context
- .getService(CommandService.class)
- .run(registrationCommandClass, false,
- flatParameters.toArray(new Object[0])
- );
-
- CommandModule module = task.get();
-
- if (module.getOutputs().containsKey("success")) {
- success = (boolean) module.getOutput("success");
- }
- if (success) {
- at3d = (AffineTransform3D) module.getOutput("at3D");
- } else {
- if (module.getOutputs().containsKey("error")) {
- errorMessage = (String) module.getOutput("error");
- }
- }
-
- isDone = true;
- return success;
- } catch (Exception e) {
- errorMessage = e.getMessage();
- e.printStackTrace();
- return false;
- }
- }
-
- String errorMessage = "";
-
- @Override
- public String getExceptionMessage() {
- return errorMessage;
- }
-
- @Override
- public void abort() {
- if (task!=null) {
- logger.info(this.getClass().getSimpleName()+": Attempt to interrupt registration...");
- task.cancel(true);
- }
- }
-
- public String toString() {
- return "Elastix 2D Affine";
- }
-
-}
diff --git a/src/main/java/ch/epfl/biop/registration/sourceandconverter/bigwarp/SacBigWarp2DRegistration.java b/src/main/java/ch/epfl/biop/registration/sourceandconverter/bigwarp/SacBigWarp2DRegistration.java
deleted file mode 100644
index 7eb5e7b3..00000000
--- a/src/main/java/ch/epfl/biop/registration/sourceandconverter/bigwarp/SacBigWarp2DRegistration.java
+++ /dev/null
@@ -1,128 +0,0 @@
-package ch.epfl.biop.registration.sourceandconverter.bigwarp;
-
-import bdv.gui.TransformTypeSelectDialog;
-import bdv.tools.brightness.ConverterSetup;
-import bdv.util.BdvHandle;
-import bdv.viewer.DisplayMode;
-import bdv.viewer.SourceAndConverter;
-import ch.epfl.biop.atlas.aligner.command.RegisterSlicesBigWarpCommand;
-import ch.epfl.biop.atlas.aligner.plugin.IABBARegistrationPlugin;
-import ch.epfl.biop.atlas.aligner.plugin.RegistrationTypeProperties;
-import ch.epfl.biop.registration.sourceandconverter.spline.RealTransformSourceAndConverterRegistration;
-import ij.gui.WaitForUserDialog;
-import org.scijava.plugin.Plugin;
-import sc.fiji.bdvpg.bdv.BdvHandleHelper;
-import sc.fiji.bdvpg.services.SourceAndConverterServices;
-import sc.fiji.bdvpg.sourceandconverter.register.BigWarpLauncher;
-
-import java.util.Arrays;
-import java.util.List;
-import java.util.stream.Collectors;
-
-import static bdv.util.RealTransformHelper.BigWarpFileFromRealTransform;
-
-@Plugin(type = IABBARegistrationPlugin.class)
-@RegistrationTypeProperties(
- isManual = true,
- isEditable = true,
- userInterface = {
- RegisterSlicesBigWarpCommand.class
- }
-)
-
-public class SacBigWarp2DRegistration extends RealTransformSourceAndConverterRegistration {
-
- BigWarpLauncher bwl;
-
- Runnable waitForUser = () -> {
- WaitForUserDialog dialog = new WaitForUserDialog("Big Warp registration","Please perform carefully your registration then press ok. Do not forget to press 't' when 4 landmarks are placed.");
- dialog.show();
- };
-
- public void setWaitForUserMethod(Runnable r) {
- waitForUser = r;
- }
-
- @Override
- public boolean register() {
- {
-
- List<SourceAndConverter<?>> movingSacs = Arrays.stream(mimg).collect(Collectors.toList());
-
- List<SourceAndConverter<?>> fixedSacs = Arrays.stream(fimg).collect(Collectors.toList());
-
- List<ConverterSetup> converterSetups = Arrays.stream(mimg).map(src -> SourceAndConverterServices.getSourceAndConverterService().getConverterSetup(src)).collect(Collectors.toList());
-
- converterSetups.addAll(Arrays.stream(fimg).map(src -> SourceAndConverterServices.getSourceAndConverterService().getConverterSetup(src)).collect(Collectors.toList()));
-
- // Launch BigWarp
- bwl = new BigWarpLauncher(movingSacs, fixedSacs, "Big Warp", converterSetups);
- bwl.set2d();
- bwl.run();
-
- // Output bdvh handles -> will be put in the object service
- BdvHandle bdvhQ = bwl.getBdvHandleQ();
- BdvHandle bdvhP = bwl.getBdvHandleP();
-
- bdvhQ.getViewerPanel().state().setDisplayMode(DisplayMode.FUSED);
- bdvhP.getViewerPanel().state().setDisplayMode(DisplayMode.FUSED);
-
- bdvhP.getViewerPanel().state().setViewerTransform(BdvHandleHelper.getViewerTransformWithNewCenter(bdvhP, new double[]{0,0,0}));
- bdvhQ.getViewerPanel().state().setViewerTransform(BdvHandleHelper.getViewerTransformWithNewCenter(bdvhQ, new double[]{0,0,0}));
-
- SourceAndConverterServices.getBdvDisplayService().pairClosing(bdvhQ,bdvhP);
-
- bdvhP.getViewerPanel().requestRepaint();
- bdvhQ.getViewerPanel().requestRepaint();
-
- bwl.getBigWarp().getLandmarkFrame().repaint();
-
- // Restores landmarks if some were already defined
- if (rt!=null) {
- String bigWarpFile = BigWarpFileFromRealTransform(rt);
- if (bigWarpFile!=null) { // If the transform is not a spline, no landmarks are saved, the user has to redo his job
- bwl.getBigWarp().loadLandmarks(bigWarpFile);
- bwl.getBigWarp().setInLandmarkMode(true);
- bwl.getBigWarp().setIsMovingDisplayTransformed(true);
- }
- }
-
- waitForUser.run();
-
- switch (bwl.getBigWarp().getBwTransform().getTransformType()) {
- case (TransformTypeSelectDialog.TPS) :
- // Thin plate spline transform
- rt = bwl.getBigWarp().getBwTransform().getTransformation();
- break;
- default:
- // Any other transform, currently Affine 3D
- rt = bwl.getBigWarp().getBwTransform().affine3d();
- }
-
- bwl.getBigWarp().closeAll();
-
- isDone = true;
-
- return true;
-
- }
- }
-
- @Override
- public boolean edit() {
- // Just launching again BigWarp
- this.register();
- return true;
- }
-
- @Override
- public void abort() {
-
- }
-
-
- public String toString() {
- return "Big Warp";
- }
-
-}
diff --git a/src/main/java/ch/epfl/biop/registration/sourceandconverter/mirror/MirrorXRegistration.java b/src/main/java/ch/epfl/biop/registration/sourceandconverter/mirror/MirrorXRegistration.java
deleted file mode 100644
index 71c31fe3..00000000
--- a/src/main/java/ch/epfl/biop/registration/sourceandconverter/mirror/MirrorXRegistration.java
+++ /dev/null
@@ -1,51 +0,0 @@
-package ch.epfl.biop.registration.sourceandconverter.mirror;
-
-import ch.epfl.biop.atlas.aligner.command.MirrorDoCommand;
-import ch.epfl.biop.atlas.aligner.plugin.IABBARegistrationPlugin;
-import ch.epfl.biop.atlas.aligner.plugin.RegistrationTypeProperties;
-import ch.epfl.biop.registration.sourceandconverter.spline.RealTransformSourceAndConverterRegistration;
-import org.scijava.plugin.Plugin;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-@Plugin(type = IABBARegistrationPlugin.class)
-@RegistrationTypeProperties(
- isManual = false,
- isEditable = true,
- userInterface = {
- MirrorDoCommand.class
- }
-)
-
-public class MirrorXRegistration extends RealTransformSourceAndConverterRegistration {
-
- protected static Logger logger = LoggerFactory.getLogger(MirrorXRegistration.class);
-
- @Override
- public boolean register() {
- String mirrorSide = parameters.get("mirror_side");
- if (mirrorSide.equals("Left")) {
- rt = new MirrorXTransform(-1);
- } else {
- rt = new MirrorXTransform(1);
- }
- isDone = true;
- return true;
- }
-
- @Override
- public boolean edit() {
- return false;
- }
-
- @Override
- public void abort() {
-
- }
-
- final public static String MIRROR_X_REGISTRATION_NAME = "Mirror X";
- public String toString() {
- return MIRROR_X_REGISTRATION_NAME;
- }
-
-}
\ No newline at end of file
diff --git a/src/main/java/ch/epfl/biop/registration/sourceandconverter/mirror/MirrorXTransform.java b/src/main/java/ch/epfl/biop/registration/sourceandconverter/mirror/MirrorXTransform.java
deleted file mode 100644
index 6de805ee..00000000
--- a/src/main/java/ch/epfl/biop/registration/sourceandconverter/mirror/MirrorXTransform.java
+++ /dev/null
@@ -1,64 +0,0 @@
-package ch.epfl.biop.registration.sourceandconverter.mirror;
-
-import net.imglib2.RealLocalizable;
-import net.imglib2.RealPositionable;
-import net.imglib2.realtransform.AffineTransform3D;
-import net.imglib2.realtransform.InvertibleRealTransform;
-
-public class MirrorXTransform implements InvertibleRealTransform {
-
- final double xFactor;
-
- public MirrorXTransform(double xFactor) {
- this.xFactor = xFactor;
- }
-
- @Override
- public int numSourceDimensions() {
- return 3;
- }
-
- @Override
- public int numTargetDimensions() {
- return 3;
- }
-
- @Override
- public void apply(double[] source, double[] target) {
- target[0] = source[0]*xFactor>0 ? source[0]:-source[0];
- target[1] = source[1];
- target[2] = source[2];
- }
-
- @Override
- public void apply(RealLocalizable realLocalizable, RealPositionable realPositionable) {
- double xPos = realLocalizable.getDoublePosition(0);
- realPositionable.setPosition(xPos*xFactor>0 ? xPos:-xPos,0);
- realPositionable.setPosition(realLocalizable.getDoublePosition(1),1);
- realPositionable.setPosition(realLocalizable.getDoublePosition(2),2);
- }
-
- @Override
- public void applyInverse(double[] source, double[] target) {
- target[0] = source[0];
- target[1] = source[1];
- target[2] = source[2];
- }
-
- @Override
- public void applyInverse(RealPositionable realPositionable, RealLocalizable realLocalizable) {
- realPositionable.setPosition(realLocalizable.getDoublePosition(0),0);
- realPositionable.setPosition(realLocalizable.getDoublePosition(1),1);
- realPositionable.setPosition(realLocalizable.getDoublePosition(2),2);
- }
-
- @Override
- public InvertibleRealTransform inverse() {
- return new AffineTransform3D();
- }
-
- @Override
- public InvertibleRealTransform copy() {
- return new MirrorXTransform(xFactor);
- }
-}
diff --git a/src/main/java/ch/epfl/biop/registration/sourceandconverter/mirror/MirrorXTransformAdapter.java b/src/main/java/ch/epfl/biop/registration/sourceandconverter/mirror/MirrorXTransformAdapter.java
deleted file mode 100644
index 2eb20869..00000000
--- a/src/main/java/ch/epfl/biop/registration/sourceandconverter/mirror/MirrorXTransformAdapter.java
+++ /dev/null
@@ -1,44 +0,0 @@
-package ch.epfl.biop.registration.sourceandconverter.mirror;
-
-
-import com.google.gson.JsonDeserializationContext;
-import com.google.gson.JsonElement;
-import com.google.gson.JsonObject;
-import com.google.gson.JsonParseException;
-import com.google.gson.JsonSerializationContext;
-import net.imglib2.realtransform.RealTransform;
-import org.scijava.plugin.Plugin;
-import sc.fiji.persist.IClassRuntimeAdapter;
-
-import java.lang.reflect.Type;
-@Plugin(type = IClassRuntimeAdapter.class)
-public class MirrorXTransformAdapter implements IClassRuntimeAdapter<RealTransform, MirrorXTransform> {
- @Override
- public Class<? extends RealTransform> getBaseClass() {
- return RealTransform.class;
- }
-
- @Override
- public Class<? extends MirrorXTransform> getRunTimeClass() {
- return MirrorXTransform.class;
- }
-
- @Override
- public boolean useCustomAdapter() {
- return true;
- }
-
- @Override
- public MirrorXTransform deserialize(JsonElement jsonElement, Type type, JsonDeserializationContext jsonDeserializationContext) throws JsonParseException {
- JsonObject obj = jsonElement.getAsJsonObject();
- double xFactor = obj.getAsJsonPrimitive("xFactor").getAsDouble();
- return new MirrorXTransform(xFactor);
- }
-
- @Override
- public JsonElement serialize(MirrorXTransform transform, Type type, JsonSerializationContext jsonSerializationContext) {
- JsonObject obj = new JsonObject();
- obj.addProperty("xFactor", transform.xFactor);
- return obj;
- }
-}
diff --git a/src/main/java/ch/epfl/biop/registration/sourceandconverter/spline/Elastix2DSplineRegistration.java b/src/main/java/ch/epfl/biop/registration/sourceandconverter/spline/Elastix2DSplineRegistration.java
deleted file mode 100644
index adca3631..00000000
--- a/src/main/java/ch/epfl/biop/registration/sourceandconverter/spline/Elastix2DSplineRegistration.java
+++ /dev/null
@@ -1,322 +0,0 @@
-package ch.epfl.biop.registration.sourceandconverter.spline;
-
-import bdv.tools.brightness.ConverterSetup;
-import bdv.util.BdvHandle;
-import bdv.viewer.DisplayMode;
-import bdv.viewer.Interpolation;
-import bdv.viewer.SourceAndConverter;
-import ch.epfl.biop.atlas.aligner.command.RegisterSlicesElastixSplineCommand;
-import ch.epfl.biop.atlas.aligner.plugin.IABBARegistrationPlugin;
-import ch.epfl.biop.atlas.aligner.plugin.RegistrationTypeProperties;
-import ch.epfl.biop.scijava.command.source.register.Elastix2DSplineRegisterCommand;
-import ij.gui.WaitForUserDialog;
-import jitk.spline.ThinPlateR2LogRSplineKernelTransform;
-import net.imglib2.RealPoint;
-import net.imglib2.RealRandomAccessible;
-import net.imglib2.realtransform.*;
-import net.imglib2.realtransform.inverse.WrappedIterativeInvertibleRealTransform;
-import net.imglib2.type.numeric.IntegerType;
-import org.scijava.command.Command;
-import org.scijava.command.CommandModule;
-import org.scijava.command.CommandService;
-import org.scijava.plugin.Plugin;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-import sc.fiji.bdvpg.bdv.BdvHandleHelper;
-import sc.fiji.bdvpg.services.SourceAndConverterServices;
-import sc.fiji.bdvpg.sourceandconverter.SourceAndConverterHelper;
-import sc.fiji.bdvpg.sourceandconverter.register.BigWarpLauncher;
-
-import java.util.*;
-import java.util.concurrent.Future;
-import java.util.stream.Collectors;
-
-import static bdv.util.RealTransformHelper.BigWarpFileFromRealTransform;
-
-@Plugin(type = IABBARegistrationPlugin.class)
-@RegistrationTypeProperties(
- isManual = false,
- isEditable = true,
- userInterface = {
- RegisterSlicesElastixSplineCommand.class
- //RegistrationElastixSplineRemoteCommand.class
- }
-)
-
-public class Elastix2DSplineRegistration extends RealTransformSourceAndConverterRegistration {
-
- protected static final Logger logger = LoggerFactory.getLogger(Elastix2DSplineRegistration.class);
-
- Future<CommandModule> task;
-
- @Override
- public void setFixedImage(SourceAndConverter[] fimg) {
- if (fimg.length==0) {
- logger.error("Error, no fixed image set in class "+this.getClass().getSimpleName());
- }
- super.setFixedImage(fimg);
- }
-
- @Override
- public void setMovingImage(SourceAndConverter[] mimg) {
- if (mimg.length==0) {
- logger.error("Error, no fixed image set in class "+this.getClass().getSimpleName());
- }
- super.setMovingImage(mimg);
- }
-
- @Override
- public boolean register() {
- try {
- boolean success = true;
- Class<? extends Command> registrationCommandClass;
- registrationCommandClass = Elastix2DSplineRegisterCommand.class;
-
- // Transforms map into flat String : key1, value1, key2, value2, etc.
- // Necessary for CommandService
- List<Object> flatParameters = new ArrayList<>(parameters.size()*2+4);
-
- double voxSizeInMm = Double.parseDouble(parameters.get("pxSizeInCurrentUnit"));
-
- parameters.keySet().forEach(k -> {
- flatParameters.add(k);
- flatParameters.add(parameters.get(k));
- });
-
- addToFlatParameters(flatParameters,
- // Fixed image
- "sacs_fixed",fimg,
- // Moving image
- "sacs_moving", mimg,
- // Interpolation in resampling
- "interpolate", true,
- // Start registration with a 32x32 pixel image
- "minPixSize", 32,
- // 100 iteration steps
- "maxIterationNumberPerScale",100,
- // Do not write anything
- "verbose", false,
- // Do not center centers of mass of both images before starting registration
- "automaticTransformInitialization", false,
- // Atlas image : a single timepoint
- "tpFixed", 0,
- // Level 2 for the atlas
- "levelFixedSource", SourceAndConverterHelper.bestLevel(fimg[0], timePoint, voxSizeInMm),
- // Timepoint moving source (normally 0)
- "tpMoving", timePoint,
- // Tries to be clever for the moving source sampling
- "levelMovingSource", SourceAndConverterHelper.bestLevel(mimg[0], timePoint, voxSizeInMm)
- );
-
- task = context
- .getService(CommandService.class)
- .run(registrationCommandClass, false,
- flatParameters.toArray(new Object[0]));
-
- CommandModule module = task.get();
-
- if (module.getOutputs().containsKey("success")) {
- success = (boolean) module.getOutput("success");
- }
-
- if (success) {
- rt = (RealTransform) module.getOutput("rt");
- rt = pruneLandMarksOutsideAtlas(rt);
- } else {
- if (module.getOutputs().containsKey("error")) {
- errorMessage = (String) module.getOutput("error");
- }
- }
-
-
- isDone = true;
- return success;
- } catch (Exception e) {
- errorMessage = e.getMessage();
- e.printStackTrace();
- return false;
- }
- }
-
- String errorMessage = "";
-
- @Override
- public String getExceptionMessage() {
- return errorMessage;
- }
-
- /**
- * This function removes the landmarks located outside the atlas,
- * meaning where the atlas 3d image value is zero
- * 4 landmarks are kept
- * @param rt_in the realtransfrom spline to prune
- * @return same transform with landmarks pruned
- */
- private RealTransform pruneLandMarksOutsideAtlas(RealTransform rt_in) {
-
- RealTransform input = rt_in;
- boolean wrapped2d3d = false;
- boolean wrappedInvertible = false;
- if (rt_in instanceof Wrapped2DTransformAs3D) {
- rt_in = ((Wrapped2DTransformAs3D)rt_in).transform;
- wrapped2d3d = true;
- }
-
- if (rt_in instanceof WrappedIterativeInvertibleRealTransform) {
- rt_in = ((WrappedIterativeInvertibleRealTransform)rt_in).getTransform();
- wrappedInvertible = true;
- }
-
- if (!(rt_in instanceof ThinplateSplineTransform)) {
- System.err.println("Cannot edit the transform : it's not of class thinplatesplinetransform");
- return input;
- } else {
- if (fimg_mask !=null) {
- ThinplateSplineTransform tst = (ThinplateSplineTransform) rt_in;
- ThinPlateR2LogRSplineKernelTransform kernel = ThinPlateSplineTransformAdapter.getKernel(tst);
- double[][] srcPts = ThinPlateSplineTransformAdapter.getSrcPts(kernel);
- double[][] tgtPts = ThinPlateSplineTransformAdapter.getTgtPts(kernel);
- int nbLandmarks = kernel.getNumLandmarks();
- int nbDimensions = kernel.getNumDims();
-
- List<RealPoint> ptsSource = new ArrayList<>();
- List<RealPoint> ptsTarget = new ArrayList<>();
-
- for (int i = 0; i < nbLandmarks; ++i) {
- RealPoint ptSource = new RealPoint(3);
- RealPoint ptTarget = new RealPoint(3);
- int d;
- for (d = 0; d < nbDimensions; ++d) {
- ptTarget.setPosition(tgtPts[d][i], d);
- }
- ptTarget.setPosition(0,2); // 0 position in z
-
- for (d = 0; d < nbDimensions; ++d) {
- ptSource.setPosition(srcPts[d][i], d);
- }
- ptSource.setPosition(0,2); // 0 position in z
-
- ptsSource.add(ptSource);
- ptsTarget.add(ptTarget);
- }
-
- RealRandomAccessible rawMask = fimg_mask[0].getSpimSource().getInterpolatedSource(timePoint,0, Interpolation.NEARESTNEIGHBOR);
-
- RealRandomAccessible<IntegerType> mask = (RealRandomAccessible<IntegerType>) rawMask;
-
- AffineTransform3D at3D = new AffineTransform3D();
- fimg_mask[0].getSpimSource().getSourceTransform(timePoint,0,at3D);
-
- List<Integer> landMarksToKeep = new ArrayList<>();
- for (int i = 0; i < nbLandmarks; ++i) {
- at3D.inverse().apply(ptsTarget.get(i), ptsTarget.get(i));
- at3D.inverse().apply(ptsSource.get(i), ptsSource.get(i));
-
- if ((mask.getAt(ptsSource.get(i)).getInteger() == 0) && (mask.getAt(ptsTarget.get(i)).getInteger() == 0)) {
-
- } else {
- landMarksToKeep.add(i);
- }
- }
-
- if (landMarksToKeep.size()<4) {
- // Too many landmarks removed
- System.err.println("Too few landmarks after pruning - skip pruning");
- return input;
- }
-
- // Ok, now let's reconstruct the transform
-
- double[][] srcPtsKept = new double[nbDimensions][landMarksToKeep.size()];
- double[][] tgtPtsKept = new double[nbDimensions][landMarksToKeep.size()];
-
- for (int i = 0;i<landMarksToKeep.size();i++) {
- for (int d = 0; d < nbDimensions; ++d) {
- srcPtsKept[d][i] = srcPts[d][landMarksToKeep.get(i)];
- tgtPtsKept[d][i] = tgtPts[d][landMarksToKeep.get(i)];
- }
- }
-
- RealTransform pruned = new ThinplateSplineTransform(srcPtsKept, tgtPtsKept);
-
- if (wrappedInvertible) {
- pruned = new WrappedIterativeInvertibleRealTransform<>(pruned);
- }
-
- if (wrapped2d3d) {
- pruned = new Wrapped2DTransformAs3D((InvertibleRealTransform) pruned);
- }
-
- return pruned;
-
- } else return input;
- }
- }
-
- Runnable waitForUser = () -> {
- WaitForUserDialog dialog = new WaitForUserDialog("Choose slice","Please perform carefully your registration then press ok.");
- dialog.show();
- };
-
- @Override
- public boolean edit() {
-
- List<SourceAndConverter<?>> movingSacs = Arrays.stream(mimg).collect(Collectors.toList());
-
- List<SourceAndConverter<?>> fixedSacs = Arrays.stream(fimg).collect(Collectors.toList());
-
- List<ConverterSetup> converterSetups = Arrays.stream(mimg).map(src -> SourceAndConverterServices.getSourceAndConverterService().getConverterSetup(src)).collect(Collectors.toList());
-
- converterSetups.addAll(Arrays.stream(fimg).map(src -> SourceAndConverterServices.getSourceAndConverterService().getConverterSetup(src)).collect(Collectors.toList()));
-
- // Launch BigWarp
- BigWarpLauncher bwl = new BigWarpLauncher(movingSacs, fixedSacs, "Big Warp", converterSetups);
- bwl.set2d();
- bwl.run();
-
- // Output bdvh handles -> will be put in the object service
- BdvHandle bdvhQ = bwl.getBdvHandleQ();
- BdvHandle bdvhP = bwl.getBdvHandleP();
-
- bdvhP.getViewerPanel().state().setViewerTransform(BdvHandleHelper.getViewerTransformWithNewCenter(bdvhP, new double[]{0,0,0}));
- bdvhQ.getViewerPanel().state().setViewerTransform(BdvHandleHelper.getViewerTransformWithNewCenter(bdvhQ, new double[]{0,0,0}));
-
- bdvhQ.getViewerPanel().state().setDisplayMode(DisplayMode.FUSED);
- bdvhP.getViewerPanel().state().setDisplayMode(DisplayMode.FUSED);
-
- SourceAndConverterServices.getBdvDisplayService().pairClosing(bdvhQ,bdvhP);
-
- bdvhP.getViewerPanel().requestRepaint();
- bdvhQ.getViewerPanel().requestRepaint();
-
- bwl.getBigWarp().getLandmarkFrame().repaint();
-
- if (rt!=null) {
- bwl.getBigWarp().loadLandmarks(BigWarpFileFromRealTransform(rt));
- bwl.getBigWarp().setIsMovingDisplayTransformed(true);
- }
-
- waitForUser.run();
-
- rt = bwl.getBigWarp().getBwTransform().getTransformation();
-
- bwl.getBigWarp().closeAll();
-
- isDone = true;
-
- return true;
-
- }
-
- @Override
- public void abort() {
- if (task!=null) {
- task.cancel(true);
- }
- }
-
- public String toString() {
- return "Elastix 2D Spline";
- }
-
-}
diff --git a/src/main/java/ch/epfl/biop/registration/sourceandconverter/spline/RealTransformSourceAndConverterRegistration.java b/src/main/java/ch/epfl/biop/registration/sourceandconverter/spline/RealTransformSourceAndConverterRegistration.java
deleted file mode 100644
index 8c7e0f18..00000000
--- a/src/main/java/ch/epfl/biop/registration/sourceandconverter/spline/RealTransformSourceAndConverterRegistration.java
+++ /dev/null
@@ -1,79 +0,0 @@
-package ch.epfl.biop.registration.sourceandconverter.spline;
-
-import bdv.util.BoundedRealTransform;
-import bdv.viewer.SourceAndConverter;
-import ch.epfl.biop.java.utilities.roi.types.RealPointList;
-import ch.epfl.biop.registration.sourceandconverter.SourceAndConverterRegistration;
-import net.imglib2.RealPoint;
-import net.imglib2.realtransform.RealTransform;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-import sc.fiji.bdvpg.sourceandconverter.transform.SourceRealTransformer;
-import sc.fiji.persist.ScijavaGsonHelper;
-
-import java.util.ArrayList;
-
-abstract public class RealTransformSourceAndConverterRegistration extends SourceAndConverterRegistration {
-
- final static Logger logger = LoggerFactory.getLogger(RealTransformSourceAndConverterRegistration.class);
-
- protected RealTransform rt;
-
- @Override
- public SourceAndConverter[] getTransformedImageMovingToFixed(SourceAndConverter[] img) {
- SourceAndConverter[] out = new SourceAndConverter[img.length];
- SourceRealTransformer srt = new SourceRealTransformer(rt);
- for (int idx = 0;idx<img.length;idx++) {
- out[idx] = srt.apply(img[idx]);
- }
- return out;
- }
-
- @Override
- public RealPointList getTransformedPtsFixedToMoving(RealPointList pts) {
- RealTransform innerRT = rt; // To unbox bounded realtransform
-
- // Unbox bounded transform
- if (rt instanceof BoundedRealTransform) {
- innerRT = ((BoundedRealTransform)rt).getTransform().copy();
- }
-
- ArrayList<RealPoint> cvtList = new ArrayList<>();
- for (RealPoint p : pts.ptList) {
- RealPoint pt3d = new RealPoint(3);
- pt3d.setPosition(new double[]{p.getDoublePosition(0), p.getDoublePosition(1),0});
- innerRT.apply(pt3d, pt3d);
- RealPoint cpt = new RealPoint(pt3d.getDoublePosition(0), pt3d.getDoublePosition(1));
- cvtList.add(cpt);
- }
-
- return new RealPointList(cvtList);
- }
-
- public RealTransform getRealTransform() {
- return rt;
- }
-
- public void setRealTransform(RealTransform transform) {
- this.rt = transform.copy();
- }
-
- @Override
- final public String getTransform() {
- //logger.debug("Serializing transform of class "+rt.getClass().getSimpleName());
- String transform = ScijavaGsonHelper.getGson(context).toJson(rt, RealTransform.class);
- //logger.debug("Serialization result = "+transform);
- return transform;
- }
-
- @Override
- final public void setTransform(String serialized_transform) {
- setRealTransform(ScijavaGsonHelper.getGson(context).fromJson(serialized_transform, RealTransform.class));
- isDone = true;
- }
-
- public RealTransform getTransformAsRealTransform() {
- return rt.copy();
- }
-
-}
diff --git a/src/test/java/ch/epfl/biop/abba/pluginexample/IdentityRegistrationCommand.java b/src/test/java/ch/epfl/biop/abba/pluginexample/IdentityRegistrationCommand.java
index ee64da1d..74d847b1 100644
--- a/src/test/java/ch/epfl/biop/abba/pluginexample/IdentityRegistrationCommand.java
+++ b/src/test/java/ch/epfl/biop/abba/pluginexample/IdentityRegistrationCommand.java
@@ -6,6 +6,8 @@
import org.scijava.plugin.Parameter;
import org.scijava.plugin.Plugin;
+import java.util.HashMap;
+
@Plugin(type = Command.class, menuPath = "Plugins>BIOP>Atlas>Multi Image To Atlas>Align>[ABBA Dev] - Your Registration Here!")
public class IdentityRegistrationCommand implements Command {
@@ -14,7 +16,7 @@ public class IdentityRegistrationCommand implements Command {
@Override
public void run() {
- mp.registerSelectedSlices(this, SourcesProcessorHelper.Identity(),
- SourcesProcessorHelper.Identity());
+ mp.registerSelectedSlices(IdentityRegistrationPluginExample.class, SourcesProcessorHelper.Identity(),
+ SourcesProcessorHelper.Identity(), new HashMap<>());
}
}
diff --git a/src/test/java/ch/epfl/biop/abba/pluginexample/IdentityRegistrationPluginExample.java b/src/test/java/ch/epfl/biop/abba/pluginexample/IdentityRegistrationPluginExample.java
index 29abd2e7..0903ebef 100644
--- a/src/test/java/ch/epfl/biop/abba/pluginexample/IdentityRegistrationPluginExample.java
+++ b/src/test/java/ch/epfl/biop/abba/pluginexample/IdentityRegistrationPluginExample.java
@@ -1,9 +1,8 @@
package ch.epfl.biop.abba.pluginexample;
import bdv.viewer.SourceAndConverter;
-import ch.epfl.biop.atlas.aligner.MultiSlicePositioner;
-import ch.epfl.biop.atlas.aligner.plugin.IABBARegistrationPlugin;
-import ch.epfl.biop.atlas.aligner.plugin.RegistrationTypeProperties;
+import ch.epfl.biop.registration.plugin.IRegistrationPlugin;
+import ch.epfl.biop.registration.plugin.RegistrationTypeProperties;
import ch.epfl.biop.java.utilities.roi.types.RealPointList;
import net.imglib2.realtransform.RealTransform;
import org.scijava.Context;
@@ -21,13 +20,12 @@
* is an array of SourceAndConverter, each element of the array being a single channel.
*
*/
-@Plugin(type = IABBARegistrationPlugin.class)
+@Plugin(type = IRegistrationPlugin.class)
@RegistrationTypeProperties(
isEditable = false,
- isManual = false,
- userInterface = {IdentityRegistrationCommand.class}
+ isManual = false
)
-public class IdentityRegistrationPluginExample implements IABBARegistrationPlugin{
+public class IdentityRegistrationPluginExample implements IRegistrationPlugin {
public static final Consumer<String> defaultLog = (string) -> System.out.println(IdentityRegistrationPluginExample.class.getSimpleName()+":"+string);
@@ -59,7 +57,7 @@ public void setScijavaContext(Context context) {
/**
* Any parameter of a registration method has to be set as a String to String dictionnary
- * this same dictionnary needs to be returned in {@link IABBARegistrationPlugin#getRegistrationParameters()}
+ * this same dictionnary needs to be returned in {@link IRegistrationPlugin#getRegistrationParameters()}
* for a correct serialization
* @param parameters dictionary of parameters
*/
@@ -69,7 +67,7 @@ public void setRegistrationParameters(Map<String, String> parameters) {
}
/**
- * see {@link IABBARegistrationPlugin#setRegistrationParameters(Map)}
+ * see {@link IRegistrationPlugin#setRegistrationParameters(Map)}
* @return the dictionnary containing the parameters for this registration
*/
@Override
@@ -198,11 +196,6 @@ public RealTransform getTransformAsRealTransform() {
return null; // unsupported, but in fact in this case
}
- @Override
- public void setSliceInfo(MultiSlicePositioner.SliceInfo sliceInfo) {
- // Can be used to retrieve some info about the slice being registered
- }
-
String errorMessage = "No error";
@Override
diff --git a/src/test/java/ch/epfl/biop/abba/pluginexample/py/ExternalIdentityRegistrationPlugin.java b/src/test/java/ch/epfl/biop/abba/pluginexample/py/ExternalIdentityRegistrationPlugin.java
index 5b0319f3..ee738ced 100644
--- a/src/test/java/ch/epfl/biop/abba/pluginexample/py/ExternalIdentityRegistrationPlugin.java
+++ b/src/test/java/ch/epfl/biop/abba/pluginexample/py/ExternalIdentityRegistrationPlugin.java
@@ -1,8 +1,7 @@
package ch.epfl.biop.abba.pluginexample.py;
import bdv.viewer.SourceAndConverter;
-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.java.utilities.roi.types.RealPointList;
import net.imglib2.realtransform.AffineTransform3D;
import net.imglib2.realtransform.RealTransform;
@@ -12,7 +11,7 @@
import java.util.HashMap;
import java.util.Map;
-public class ExternalIdentityRegistrationPlugin implements ExternalABBARegistrationPlugin {
+public class ExternalIdentityRegistrationPlugin implements ExternalRegistrationPlugin {
Map<String, String> params = new HashMap<>();
@@ -20,11 +19,6 @@ public String getRegistrationTypeName() {
return "PyIdentity";
}
- @Override
- public void setSliceInfo(MultiSlicePositioner.SliceInfo sliceInfo) {
- // Do nothing
- }
-
@Override
public boolean isManual() {
return false;
diff --git a/src/test/java/ch/epfl/biop/abba/pluginexample/py/ExternalSimpleRotationRegistrationPlugin.java b/src/test/java/ch/epfl/biop/abba/pluginexample/py/ExternalSimpleRotationRegistrationPlugin.java
index cc2417bd..4eee8114 100644
--- a/src/test/java/ch/epfl/biop/abba/pluginexample/py/ExternalSimpleRotationRegistrationPlugin.java
+++ b/src/test/java/ch/epfl/biop/abba/pluginexample/py/ExternalSimpleRotationRegistrationPlugin.java
@@ -1,13 +1,13 @@
package ch.epfl.biop.abba.pluginexample.py;
-import ch.epfl.biop.atlas.aligner.plugin.SimpleABBARegistrationPlugin;
+import ch.epfl.biop.registration.plugin.SimpleRegistrationPlugin;
import ij.ImagePlus;
import net.imglib2.realtransform.AffineTransform3D;
import net.imglib2.realtransform.InvertibleRealTransform;
import java.util.Map;
-public class ExternalSimpleRotationRegistrationPlugin implements SimpleABBARegistrationPlugin {
+public class ExternalSimpleRotationRegistrationPlugin implements SimpleRegistrationPlugin {
@Override
public double getVoxelSizeInMicron() {
diff --git a/src/test/java/ch/epfl/biop/abba/pluginexample/py/TestExternalRegistrationPlugin.java b/src/test/java/ch/epfl/biop/abba/pluginexample/py/TestExternalRegistrationPlugin.java
index ec32a2f8..863829d1 100644
--- a/src/test/java/ch/epfl/biop/abba/pluginexample/py/TestExternalRegistrationPlugin.java
+++ b/src/test/java/ch/epfl/biop/abba/pluginexample/py/TestExternalRegistrationPlugin.java
@@ -6,7 +6,7 @@
import ch.epfl.biop.atlas.aligner.SliceSources;
import ch.epfl.biop.atlas.aligner.command.ABBAStartCommand;
import ch.epfl.biop.atlas.aligner.gui.bdv.BdvMultislicePositionerView;
-import ch.epfl.biop.atlas.aligner.plugin.SimpleRegistrationWrapper;
+import ch.epfl.biop.registration.plugin.SimpleRegistrationWrapper;
import ch.epfl.biop.atlas.mouse.allen.ccfv3p1.command.AllenBrainAdultMouseAtlasCCF2017v3p1Command;
import ch.epfl.biop.atlas.struct.Atlas;
import ch.epfl.biop.scijava.command.spimdata.SourceFromImagePlusCommand;