Swap Descriptor_based_registration for mvrecon

pom.xml

@@ -140,12 +140,6 @@
         -->
         <n5-version>4.0.1</n5-version>
 
-        <!-- pom-scijava 45 bumps Descriptor_based_registration to 3.0.1, whose SPIM_Registration replacement
-             (net.preibisch:multiview-reconstruction) drops the point-descriptor / DoG API render's geometric
-             descriptor matcher is built on (mpicbg.pointdescriptor.matcher.*, mpicbg.spim.segmentation.*). Porting
-             that matcher is a separate effort, so keep the 2.x line reactor-wide (render-app also pins 2.1.3). -->
-        <Descriptor_based_registration.version>2.1.3</Descriptor_based_registration.version>
-
         <!--
           Keep this in sync with the jackson version bundled with the spark version in
           render-ws-spark-client/pom.xml: spark refuses to start when its jackson-module-scala does not

render-app/pom.xml

@@ -182,7 +182,6 @@
         <dependency>
             <groupId>sc.fiji</groupId>
             <artifactId>Descriptor_based_registration</artifactId>
-            <version>2.1.3</version>
             <exclusions>
                 <!-- filter out slf4j jar so that it does not conflict with jetty version -->
                 <exclusion>

render-app/src/main/java/org/janelia/alignment/match/CanvasPeakMatcher.java

@@ -7,8 +7,8 @@
 import mpicbg.imglib.type.numeric.real.FloatType;
 import mpicbg.models.Model;
 import mpicbg.models.PointMatch;
-import mpicbg.pointdescriptor.matcher.Matcher;
-import mpicbg.pointdescriptor.matcher.SubsetMatcher;
+import net.preibisch.mvrecon.process.pointcloud.pointdescriptor.matcher.Matcher;
+import net.preibisch.mvrecon.process.pointcloud.pointdescriptor.matcher.SubsetMatcher;
 import mpicbg.util.Timer;
 
 import org.janelia.alignment.match.parameters.GeometricDescriptorParameters;

render-app/src/main/java/org/janelia/alignment/match/parameters/GeometricDescriptorParameters.java

@@ -5,7 +5,7 @@
 import java.io.Serializable;
 import java.util.Objects;
 
-import mpicbg.spim.segmentation.InteractiveDoG;
+import net.preibisch.mvrecon.fiji.plugin.interestpointdetection.interactive.HelperFunctions;
 
 import plugin.DescriptorParameters;
 
@@ -149,7 +149,7 @@ public DescriptorParameters toDescriptorParameters() {
         dp.redundancy = redundancy;
         dp.significance = significance;
         dp.sigma1 = sigma;
-        dp.sigma2 = InteractiveDoG.computeSigma2(sigma.floatValue(), InteractiveDoG.standardSensitivity );
+        dp.sigma2 = HelperFunctions.computeSigma2(sigma, 4); // 4 = former InteractiveDoG.standardSensitivity
         dp.threshold = threshold;
         dp.localization = localization.code;
         dp.lookForMinima = lookForMinima;

render-app/src/main/java/process/GeometricDescriptorMatcher.java

@@ -7,7 +7,7 @@
 import mpicbg.imglib.type.numeric.real.FloatType;
 import mpicbg.models.Model;
 import mpicbg.models.PointMatch;
-import mpicbg.pointdescriptor.matcher.Matcher;
+import net.preibisch.mvrecon.process.pointcloud.pointdescriptor.matcher.Matcher;
 
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;

render-app/src/test/java/org/janelia/alignment/match/GeometricDescriptorSIFTMatcherTest.java

@@ -15,7 +15,7 @@
 import mpicbg.models.AffineModel2D;
 import mpicbg.models.Point;
 import mpicbg.models.PointMatch;
-import mpicbg.spim.io.IOFunctions;
+import net.preibisch.legacy.io.IOFunctions;
 import mpicbg.trakem2.transform.TransformMeshMappingWithMasks.ImageProcessorWithMasks;
 
 import org.janelia.alignment.RenderParameters;

render-ws-java-client/pom.xml

@@ -78,7 +78,7 @@
                                     </excludes>
                                 </filter>
                                 <filter>
-                                    <artifact>sc.fiji:SPIM_Registration</artifact>
+                                    <artifact>net.preibisch:multiview-reconstruction</artifact>
                                     <excludes>
                                         <exclude>META-INF/json/**</exclude>
                                     </excludes>

render-ws-java-client/src/main/java/org/janelia/render/client/destreak/StreakCorrection_Plugin.java

@@ -22,7 +22,7 @@
 import org.janelia.render.client.RenderDataClient;
 import org.janelia.render.client.parameter.CommandLineParameters;
 import org.janelia.render.client.parameter.RenderWebServiceParameters;
-import spim.Threads;
+import net.preibisch.mvrecon.Threads;
 
 import javax.swing.SwingUtilities;
 import java.awt.KeyboardFocusManager;

render-ws-java-client/src/main/java/org/janelia/render/client/solver/DistributedSolveMultiThread.java

@@ -17,7 +17,7 @@
 
 import bdv.util.BdvStackSource;
 import mpicbg.models.Affine2D;
-import mpicbg.spim.io.IOFunctions;
+import net.preibisch.legacy.io.IOFunctions;
 import net.imglib2.multithreading.SimpleMultiThreading;
 
 public class DistributedSolveMultiThread extends DistributedSolve

render-ws-spark-client/pom.xml

@@ -75,7 +75,7 @@
                                     </excludes>
                                 </filter>
                                 <filter>
-                                    <artifact>sc.fiji:SPIM_Registration</artifact>
+                                    <artifact>net.preibisch:multiview-reconstruction</artifact>
                                     <excludes>
                                         <exclude>META-INF/json/**</exclude>
                                     </excludes>