diff --git a/pom.xml b/pom.xml index b11899651..88fb27992 100644 --- a/pom.xml +++ b/pom.xml @@ -140,12 +140,6 @@ --> 4.0.1 - - 2.1.3 - diff --git a/render-app/src/main/java/org/janelia/alignment/match/CanvasPeakMatcher.java b/render-app/src/main/java/org/janelia/alignment/match/CanvasPeakMatcher.java index 0300c2129..ebba4c1d8 100644 --- a/render-app/src/main/java/org/janelia/alignment/match/CanvasPeakMatcher.java +++ b/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; diff --git a/render-app/src/main/java/org/janelia/alignment/match/parameters/GeometricDescriptorParameters.java b/render-app/src/main/java/org/janelia/alignment/match/parameters/GeometricDescriptorParameters.java index 23bd38dff..50e9ae365 100644 --- a/render-app/src/main/java/org/janelia/alignment/match/parameters/GeometricDescriptorParameters.java +++ b/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; diff --git a/render-app/src/main/java/process/GeometricDescriptorMatcher.java b/render-app/src/main/java/process/GeometricDescriptorMatcher.java index bade81e44..d4031145a 100644 --- a/render-app/src/main/java/process/GeometricDescriptorMatcher.java +++ b/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; diff --git a/render-app/src/test/java/org/janelia/alignment/match/GeometricDescriptorSIFTMatcherTest.java b/render-app/src/test/java/org/janelia/alignment/match/GeometricDescriptorSIFTMatcherTest.java index 89a67dea7..18539b1d4 100644 --- a/render-app/src/test/java/org/janelia/alignment/match/GeometricDescriptorSIFTMatcherTest.java +++ b/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; diff --git a/render-ws-java-client/pom.xml b/render-ws-java-client/pom.xml index ce9ef8d82..e5656b18c 100644 --- a/render-ws-java-client/pom.xml +++ b/render-ws-java-client/pom.xml @@ -78,7 +78,7 @@ - sc.fiji:SPIM_Registration + net.preibisch:multiview-reconstruction META-INF/json/** diff --git a/render-ws-java-client/src/main/java/org/janelia/render/client/destreak/StreakCorrection_Plugin.java b/render-ws-java-client/src/main/java/org/janelia/render/client/destreak/StreakCorrection_Plugin.java index 29cd73a50..952b117c1 100644 --- a/render-ws-java-client/src/main/java/org/janelia/render/client/destreak/StreakCorrection_Plugin.java +++ b/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; diff --git a/render-ws-java-client/src/main/java/org/janelia/render/client/solver/DistributedSolveMultiThread.java b/render-ws-java-client/src/main/java/org/janelia/render/client/solver/DistributedSolveMultiThread.java index 9d69da039..fd2418f8d 100644 --- a/render-ws-java-client/src/main/java/org/janelia/render/client/solver/DistributedSolveMultiThread.java +++ b/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 diff --git a/render-ws-spark-client/pom.xml b/render-ws-spark-client/pom.xml index 1d5945f74..cbdf09bac 100644 --- a/render-ws-spark-client/pom.xml +++ b/render-ws-spark-client/pom.xml @@ -75,7 +75,7 @@ - sc.fiji:SPIM_Registration + net.preibisch:multiview-reconstruction META-INF/json/**