diff --git a/.travis/build.sh b/.travis/build.sh
new file mode 100644
index 000000000..d20bbdea7
--- /dev/null
+++ b/.travis/build.sh
@@ -0,0 +1,4 @@
+#!/bin/sh
+(cd scijava/scijava-taglets && mvn install)
+curl -fsLO https://raw.githubusercontent.com/scijava/scijava-scripts/master/travis-build.sh
+sh travis-build.sh $encrypted_844f7d2110b9_key $encrypted_844f7d2110b9_iv
diff --git a/imagej/imagej-ops2/pom.xml b/imagej/imagej-ops2/pom.xml
index 5066eb908..164064554 100644
--- a/imagej/imagej-ops2/pom.xml
+++ b/imagej/imagej-ops2/pom.xml
@@ -12,8 +12,8 @@
net.imagej
imagej-ops2
- ImageJ Ops
- ImageJ Operations: a framework for reusable algorithms.
+ ImageJ Ops 2
+ ImageJ Operations 2: a framework for reusable algorithms.
http://imagej.net/ImageJ_Ops
2014
@@ -210,7 +210,8 @@
ImageJ software for multidimensional image processing and analysis.
- org.scijava.*
+ ${scijava.allowedDuplicateClasses}, org.scijava.*,com.github.therapi.runtimejavadoc.repack.com.eclipsesource.json.*
+ ${imagej-ops2.allowedDuplicateClasses}
deploy-to-imagej
@@ -272,7 +273,17 @@
org.scijava
- scijava-ops
+ scijava-ops-api
+ ${project.version}
+
+
+ org.scijava
+ scijava-ops-spi
+ ${project.version}
+
+
+ org.scijava
+ scijava-ops-engine
${project.version}
@@ -297,10 +308,6 @@
-
- com.google.guava
- guava
-
org.apache.commons
commons-math3
@@ -320,18 +327,13 @@
- org.junit.jupiter
- junit-jupiter-api
+ junit
+ junit
test
org.junit.jupiter
- junit-jupiter-engine
- test
-
-
- org.junit.vintage
- junit-vintage-engine
+ junit-jupiter-api
test
diff --git a/imagej/imagej-ops2/src/main/java/module-info.java b/imagej/imagej-ops2/src/main/java/module-info.java
index 421aaf29c..f8f361767 100644
--- a/imagej/imagej-ops2/src/main/java/module-info.java
+++ b/imagej/imagej-ops2/src/main/java/module-info.java
@@ -1,123 +1,120 @@
module net.imagej.ops2 {
+ exports net.imagej.ops2;
// -- Open plugins to scijava-common
- opens net.imagej.ops2.coloc to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.coloc.icq to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.coloc.kendallTau to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.coloc.maxTKendallTau to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.coloc.pearsons to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.coloc.pValue to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.convert to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.convert.clip to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.convert.copy to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.copy to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.create to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.create.img to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.create.kernel to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.deconvolve to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.deconvolve.accelerate to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.eval to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.features.haralick to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.features.haralick.helper to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.features.hog to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.features.lbp2d to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.features.tamura2d to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.features.zernike to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.features.zernike.helper to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.filter to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.filter.addNoise to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.filter.bilateral to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.filter.convolve to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.filter.correlate to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.filter.derivative to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.filter.derivativeGauss to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.filter.dog to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.filter.fft to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.filter.fftSize to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.filter.gauss to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.filter.hessian to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.filter.ifft to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.filter.max to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.filter.mean to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.filter.median to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.filter.min to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.filter.pad to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.filter.sigma to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.filter.sobel to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.filter.tubeness to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.filter.variance to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.filter.vesselness to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.geom to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.geom.geom2d to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.geom.geom3d to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.geom.geom3d.mesh to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.identity to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.image.ascii to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.image.cooccurrenceMatrix to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.image.distancetransform to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.image.equation to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.image.fill to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.image.histogram to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.image.integral to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.image.invert to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.image.normalize to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.image.watershed to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.imagemoments to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.imagemoments.centralmoments to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.imagemoments.hu to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.imagemoments.moments to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.imagemoments.normalizedcentralmoments to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.labeling to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.labeling.cca to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.linalg.rotate to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.logic to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.map.neighborhood to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.math to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.math.multiply to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.morphology to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.morphology.thin to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.project to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.segment.detectJunctions to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.segment.detectRidges to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.slice to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.stats to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.stats.regression.leastSquares to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.thread.chunker to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.threshold to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.threshold.apply to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.threshold.huang to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.threshold.ij1 to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.threshold.intermodes to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.threshold.isoData to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.threshold.li to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.threshold.localBernsen to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.threshold.localContrast to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.threshold.localMean to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.threshold.localMedian to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.threshold.localMidGrey to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.threshold.localNiblack to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.threshold.localPhansalkar to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.threshold.localSauvola to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.threshold.maxEntropy to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.threshold.maxLikelihood to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.threshold.mean to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.threshold.minError to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.threshold.minimum to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.threshold.moments to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.threshold.otsu to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.threshold.percentile to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.threshold.renyiEntropy to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.threshold.rosin to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.threshold.shanbhag to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.threshold.triangle to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.threshold.yen to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.topology to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.topology.eulerCharacteristic to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.transform to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.types to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.types.adapt to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.types.maxValue to org.scijava, org.scijava.ops;
- opens net.imagej.ops2.types.minValue to org.scijava, org.scijava.ops;
+ opens net.imagej.ops2.coloc to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.coloc.icq to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.coloc.kendallTau to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.coloc.maxTKendallTau to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.coloc.pearsons to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.coloc.pValue to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.convert to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.convert.clip to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.convert.copy to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.copy to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.create to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.deconvolve to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.deconvolve.accelerate to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.eval to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.features.haralick to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.features.haralick.helper to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.features.hog to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.features.lbp2d to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.features.tamura2d to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.features.zernike to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.filter to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.filter.addNoise to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.filter.bilateral to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.filter.convolve to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.filter.correlate to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.filter.derivative to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.filter.derivativeGauss to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.filter.dog to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.filter.fft to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.filter.fftSize to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.filter.gauss to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.filter.hessian to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.filter.ifft to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.filter.max to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.filter.mean to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.filter.median to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.filter.min to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.filter.pad to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.filter.sigma to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.filter.sobel to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.filter.tubeness to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.filter.variance to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.filter.vesselness to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.geom to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.geom.geom2d to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.geom.geom3d to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.identity to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.image.ascii to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.image.cooccurrenceMatrix to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.image.distancetransform to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.image.equation to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.image.fill to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.image.histogram to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.image.integral to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.image.invert to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.image.normalize to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.image.watershed to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.imagemoments to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.imagemoments.centralmoments to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.imagemoments.hu to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.imagemoments.moments to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.imagemoments.normalizedcentralmoments to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.labeling to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.labeling.cca to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.linalg.rotate to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.logic to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.map.neighborhood to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.math to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.math.multiply to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.morphology to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.morphology.thin to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.project to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.segment.detectJunctions to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.segment.detectRidges to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.slice to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.stats to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.stats.regression.leastSquares to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.thread.chunker to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.threshold to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.threshold.apply to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.threshold.huang to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.threshold.ij1 to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.threshold.intermodes to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.threshold.isoData to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.threshold.li to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.threshold.localBernsen to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.threshold.localContrast to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.threshold.localMean to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.threshold.localMedian to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.threshold.localMidGrey to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.threshold.localNiblack to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.threshold.localPhansalkar to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.threshold.localSauvola to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.threshold.maxEntropy to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.threshold.maxLikelihood to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.threshold.mean to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.threshold.minError to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.threshold.minimum to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.threshold.moments to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.threshold.otsu to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.threshold.percentile to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.threshold.renyiEntropy to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.threshold.rosin to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.threshold.shanbhag to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.threshold.triangle to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.threshold.yen to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.topology to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.topology.eulerCharacteristic to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.transform to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.types to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.types.adapt to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.types.maxValue to org.scijava, org.scijava.ops.engine;
+ opens net.imagej.ops2.types.minValue to org.scijava, org.scijava.ops.engine;
requires java.desktop;
requires java.scripting;
@@ -128,7 +125,7 @@
requires net.imglib2.roi;
requires org.joml;
requires org.scijava;
- requires org.scijava.ops;
+ requires org.scijava.ops.engine;
requires org.scijava.parsington;
requires org.scijava.types;
@@ -139,5 +136,7 @@
requires imglib2.algorithm.fft;
requires mines.jtk;
requires org.scijava.function;
+ requires org.scijava.ops.api;
+ requires org.scijava.ops.spi;
}
diff --git a/imagej/imagej-ops2/src/main/java/net/imagej/ops2/coloc/icq/LiICQ.java b/imagej/imagej-ops2/src/main/java/net/imagej/ops2/coloc/icq/LiICQ.java
index c7fa99e4d..432a4a14d 100644
--- a/imagej/imagej-ops2/src/main/java/net/imagej/ops2/coloc/icq/LiICQ.java
+++ b/imagej/imagej-ops2/src/main/java/net/imagej/ops2/coloc/icq/LiICQ.java
@@ -38,11 +38,9 @@
import org.scijava.function.Computers;
import org.scijava.function.Functions;
-import org.scijava.ops.OpDependency;
-import org.scijava.ops.core.Op;
-import org.scijava.param.Parameter;
+import org.scijava.ops.spi.Op;
+import org.scijava.ops.spi.OpDependency;
import org.scijava.plugin.Plugin;
-import org.scijava.struct.ItemIO;
/**
* This algorithm calculates Li et al.'s ICQ (intensity correlation quotient).
@@ -53,11 +51,6 @@
* Type of the second image
*/
@Plugin(type = Op.class, name = "coloc.icq")
-@Parameter(key = "image1")
-@Parameter(key = "image2")
-@Parameter(key = "mean1")
-@Parameter(key = "mean2")
-@Parameter(key = "output")
public class LiICQ, U extends RealType, V extends RealType>
implements Functions.Arity4, Iterable, DoubleType, DoubleType, Double> {
@@ -66,6 +59,15 @@ public class LiICQ, U extends RealType, V extends RealT
@OpDependency(name = "stats.mean")
private Computers.Arity1, DoubleType> meanUOp;
+ /**
+ * TODO
+ *
+ * @param image1
+ * @param image2
+ * @param mean1
+ * @param mean2
+ * @return the output
+ */
@Override
public Double apply(final Iterable image1, final Iterable image2, final DoubleType mean1, final DoubleType mean2) {
@@ -120,15 +122,19 @@ private double computeMeanUOf(final Iterable in) {
}
@Plugin(type = Op.class, name = "coloc.icq")
-@Parameter(key = "image1")
-@Parameter(key = "image2")
-@Parameter(key = "output")
class LiICQSimple, U extends RealType, V extends RealType>
implements BiFunction, Iterable, Double> {
@OpDependency(name = "coloc.icq")
private Functions.Arity4, Iterable, DoubleType, DoubleType, Double> colocOp;
+ /**
+ * TODO
+ *
+ * @param image1
+ * @param image2
+ * @return the output
+ */
@Override
public Double apply(Iterable image1, Iterable image2) {
return colocOp.apply(image1, image2, null, null);
diff --git a/imagej/imagej-ops2/src/main/java/net/imagej/ops2/coloc/kendallTau/KendallTauBRank.java b/imagej/imagej-ops2/src/main/java/net/imagej/ops2/coloc/kendallTau/KendallTauBRank.java
index 66c8e620c..feabd2a6e 100644
--- a/imagej/imagej-ops2/src/main/java/net/imagej/ops2/coloc/kendallTau/KendallTauBRank.java
+++ b/imagej/imagej-ops2/src/main/java/net/imagej/ops2/coloc/kendallTau/KendallTauBRank.java
@@ -38,10 +38,8 @@
import net.imglib2.util.IterablePair;
import net.imglib2.util.Pair;
-import org.scijava.ops.core.Op;
-import org.scijava.param.Parameter;
+import org.scijava.ops.spi.Op;
import org.scijava.plugin.Plugin;
-import org.scijava.struct.ItemIO;
/**
* This algorithm calculates Kendall's Tau-b rank correlation coefficient
@@ -76,12 +74,16 @@
* @param
*/
@Plugin(type = Op.class, name = "coloc.kendallTau")
-@Parameter(key = "image1")
-@Parameter(key = "image2")
-@Parameter(key = "output")
public class KendallTauBRank, U extends RealType>
/* extends Algorithm */ implements BiFunction, Iterable, Double> {
+ /**
+ * TODO
+ *
+ * @param image1
+ * @param image2
+ * @return the output
+ */
@Override
public Double apply(Iterable image1, Iterable image2) {
if (!ColocUtil.sameIterationOrder(image1, image2))
diff --git a/imagej/imagej-ops2/src/main/java/net/imagej/ops2/coloc/maxTKendallTau/MTKT.java b/imagej/imagej-ops2/src/main/java/net/imagej/ops2/coloc/maxTKendallTau/MTKT.java
index 522025be0..bffdc2a8c 100644
--- a/imagej/imagej-ops2/src/main/java/net/imagej/ops2/coloc/maxTKendallTau/MTKT.java
+++ b/imagej/imagej-ops2/src/main/java/net/imagej/ops2/coloc/maxTKendallTau/MTKT.java
@@ -49,11 +49,9 @@
import org.scijava.function.Computers;
import org.scijava.function.Functions;
-import org.scijava.ops.OpDependency;
-import org.scijava.ops.core.Op;
-import org.scijava.param.Parameter;
+import org.scijava.ops.spi.Op;
+import org.scijava.ops.spi.OpDependency;
import org.scijava.plugin.Plugin;
-import org.scijava.struct.ItemIO;
import org.scijava.util.IntArray;
/**
@@ -68,10 +66,6 @@
* @author Curtis Rueden
*/
@Plugin(type = Op.class, name = "coloc.maxTKendallTau")
-@Parameter(key = "image1")
-@Parameter(key = "image2")
-@Parameter(key = "seed")
-@Parameter(key = "output")
public class MTKT, U extends RealType>
implements Functions.Arity3, RandomAccessibleInterval, Long, Double>
{
@@ -86,6 +80,14 @@ public class MTKT, U extends RealType>
@OpDependency(name = "threshold.otsu")
private Computers.Arity1, U> thresholdOpU;
+ /**
+ * TODO
+ *
+ * @param image1
+ * @param image2
+ * @param seed
+ * @return the output
+ */
@Override
public Double apply(final RandomAccessibleInterval image1, final RandomAccessibleInterval image2, final Long seed) {
// check image sizes
@@ -248,9 +250,6 @@ static double calculateKendallTau(final double[][] rank,
}
@Plugin(type = Op.class, name = "coloc.maxTKendallTau")
-@Parameter(key = "image1")
-@Parameter(key = "image2")
-@Parameter(key = "output")
class MTKTSimple, U extends RealType>
implements BiFunction, RandomAccessibleInterval, Double>
{
@@ -260,6 +259,13 @@ class MTKTSimple, U extends RealType>
private long seed = 0x89302341;
+ /**
+ * TODO
+ *
+ * @param image1
+ * @param image2
+ * @return the output
+ */
@Override
public Double apply(RandomAccessibleInterval image1, RandomAccessibleInterval image2) {
return colocOp.apply(image1, image2, seed);
diff --git a/imagej/imagej-ops2/src/main/java/net/imagej/ops2/coloc/pValue/DefaultPValue.java b/imagej/imagej-ops2/src/main/java/net/imagej/ops2/coloc/pValue/DefaultPValue.java
index 69be888e1..cd91e8f9a 100644
--- a/imagej/imagej-ops2/src/main/java/net/imagej/ops2/coloc/pValue/DefaultPValue.java
+++ b/imagej/imagej-ops2/src/main/java/net/imagej/ops2/coloc/pValue/DefaultPValue.java
@@ -48,11 +48,9 @@
import net.imglib2.view.Views;
import org.scijava.function.Computers;
-import org.scijava.ops.OpDependency;
-import org.scijava.ops.core.Op;
-import org.scijava.param.Parameter;
+import org.scijava.ops.spi.Op;
+import org.scijava.ops.spi.OpDependency;
import org.scijava.plugin.Plugin;
-import org.scijava.struct.ItemIO;
/**
* This algorithm repeatedly executes a colocalization algorithm, computing a
@@ -62,17 +60,21 @@
* Statistical Approach".
*/
@Plugin(type = Op.class, name = "coloc.pValue")
-@Parameter(key = "image1")
-@Parameter(key = "image2")
-@Parameter(key = "op")
-@Parameter(key = "nrRandomizations")
-@Parameter(key = "psfSize")
-@Parameter(key = "seed")
-@Parameter(key = "executorService")
-@Parameter(key = "output")
public class DefaultPValue, U extends RealType> implements
Computers.Arity7, RandomAccessibleInterval, BiFunction, RandomAccessibleInterval, Double>, Integer, Dimensions, Long, ExecutorService, PValueResult> {
+ /**
+ * TODO
+ *
+ * @param image1
+ * @param image2
+ * @param op
+ * @param nrRandomizations
+ * @param psfSize
+ * @param seed
+ * @param executorService
+ * @param output
+ */
@Override
public void compute(final RandomAccessibleInterval image1, final RandomAccessibleInterval image2,
final BiFunction, RandomAccessibleInterval, Double> op,
@@ -191,18 +193,22 @@ private static RandomAccessibleInterval trim(final RandomAccessibleInterv
}
@Plugin(type = Op.class, name = "coloc.pValue")
-@Parameter(key = "image1")
-@Parameter(key = "image2")
-@Parameter(key = "op")
-@Parameter(key = "nrRandomizations")
-@Parameter(key = "executorService")
-@Parameter(key = "output")
class PValueSimpleWithRandomizations, U extends RealType> implements
Computers.Arity5, RandomAccessibleInterval, BiFunction, RandomAccessibleInterval, Double>, Integer, ExecutorService, PValueResult> {
@OpDependency(name = "coloc.pValue")
private Computers.Arity7, RandomAccessibleInterval, BiFunction, RandomAccessibleInterval, Double>, Integer, Dimensions, Long, ExecutorService, PValueResult> pValueOp;
+ /**
+ * TODO
+ *
+ * @param image1
+ * @param image2
+ * @param op
+ * @param nrRandomizations
+ * @param executorService
+ * @param output
+ */
@Override
public void compute(RandomAccessibleInterval in1, RandomAccessibleInterval in2,
BiFunction, RandomAccessibleInterval, Double> in3, Integer in4,
@@ -214,17 +220,21 @@ public void compute(RandomAccessibleInterval in1, RandomAccessibleInterval
}
@Plugin(type = Op.class, name = "coloc.pValue")
-@Parameter(key = "image1")
-@Parameter(key = "image2")
-@Parameter(key = "op")
-@Parameter(key = "executorService")
-@Parameter(key = "output")
class PValueSimple, U extends RealType> implements
Computers.Arity4, RandomAccessibleInterval, BiFunction, RandomAccessibleInterval, Double>, ExecutorService, PValueResult> {
@OpDependency(name = "coloc.pValue")
private Computers.Arity5, RandomAccessibleInterval, BiFunction, RandomAccessibleInterval, Double>, Integer, ExecutorService, PValueResult> pValueOp;
+ /**
+ * TODO
+ *
+ * @param image1
+ * @param image2
+ * @param op
+ * @param executorService
+ * @param output
+ */
@Override
public void compute(RandomAccessibleInterval in1, RandomAccessibleInterval in2,
BiFunction, RandomAccessibleInterval, Double> in3, ExecutorService in4,
diff --git a/imagej/imagej-ops2/src/main/java/net/imagej/ops2/coloc/pearsons/DefaultPearsons.java b/imagej/imagej-ops2/src/main/java/net/imagej/ops2/coloc/pearsons/DefaultPearsons.java
index 726f4d7dc..721c851f3 100644
--- a/imagej/imagej-ops2/src/main/java/net/imagej/ops2/coloc/pearsons/DefaultPearsons.java
+++ b/imagej/imagej-ops2/src/main/java/net/imagej/ops2/coloc/pearsons/DefaultPearsons.java
@@ -35,10 +35,8 @@
import net.imglib2.util.IterablePair;
import net.imglib2.util.Pair;
-import org.scijava.ops.core.Op;
-import org.scijava.param.Parameter;
+import org.scijava.ops.spi.Op;
import org.scijava.plugin.Plugin;
-import org.scijava.struct.ItemIO;
/**
* A class that represents the mean calculation of the two source images in the
@@ -47,13 +45,17 @@
* @author Ellen T Arena
*/
@Plugin(type = Op.class, name = "coloc.pearsons")
-@Parameter(key = "image1")
-@Parameter(key = "image2")
-@Parameter(key = "output")
public class DefaultPearsons, U extends RealType> implements
BiFunction, Iterable, Double>
{
+ /**
+ * TODO
+ *
+ * @param image1
+ * @param image2
+ * @return the output
+ */
@Override
public Double apply(final Iterable image1,
final Iterable image2)
diff --git a/imagej/imagej-ops2/src/main/java/net/imagej/ops2/convert/ConvertTypes.java b/imagej/imagej-ops2/src/main/java/net/imagej/ops2/convert/ConvertTypes.java
index aa5315bba..c5927c551 100644
--- a/imagej/imagej-ops2/src/main/java/net/imagej/ops2/convert/ConvertTypes.java
+++ b/imagej/imagej-ops2/src/main/java/net/imagej/ops2/convert/ConvertTypes.java
@@ -52,11 +52,9 @@
import net.imglib2.type.numeric.real.FloatType;
import org.scijava.function.Computers;
-import org.scijava.ops.OpField;
-import org.scijava.ops.core.OpCollection;
-import org.scijava.param.Parameter;
+import org.scijava.ops.spi.OpCollection;
+import org.scijava.ops.spi.OpField;
import org.scijava.plugin.Plugin;
-import org.scijava.struct.ItemIO;
/**
* Converters for converting between Complex types
diff --git a/imagej/imagej-ops2/src/main/java/net/imagej/ops2/convert/Converters.java b/imagej/imagej-ops2/src/main/java/net/imagej/ops2/convert/Converters.java
index be0838cf0..19f5f8e75 100644
--- a/imagej/imagej-ops2/src/main/java/net/imagej/ops2/convert/Converters.java
+++ b/imagej/imagej-ops2/src/main/java/net/imagej/ops2/convert/Converters.java
@@ -6,11 +6,9 @@
import net.imglib2.type.Type;
import org.scijava.function.Functions;
-import org.scijava.ops.OpField;
-import org.scijava.ops.core.OpCollection;
-import org.scijava.param.Parameter;
+import org.scijava.ops.spi.OpCollection;
+import org.scijava.ops.spi.OpField;
import org.scijava.plugin.Plugin;
-import org.scijava.struct.ItemIO;
@Plugin(type = OpCollection.class)
public class Converters> {
diff --git a/imagej/imagej-ops2/src/main/java/net/imagej/ops2/convert/clip/ClipRealTypes.java b/imagej/imagej-ops2/src/main/java/net/imagej/ops2/convert/clip/ClipRealTypes.java
index 41d852383..88354ef31 100644
--- a/imagej/imagej-ops2/src/main/java/net/imagej/ops2/convert/clip/ClipRealTypes.java
+++ b/imagej/imagej-ops2/src/main/java/net/imagej/ops2/convert/clip/ClipRealTypes.java
@@ -32,10 +32,8 @@
import net.imglib2.type.numeric.RealType;
import org.scijava.function.Computers;
-import org.scijava.ops.core.Op;
-import org.scijava.param.Parameter;
+import org.scijava.ops.spi.Op;
import org.scijava.plugin.Plugin;
-import org.scijava.struct.ItemIO;
/**
* Copies the value of one {@link RealType} to another, and clips values which
@@ -44,12 +42,16 @@
* @author Martin Horn (University of Konstanz)
*/
@Plugin(type = Op.class, name = "convert.clip")
-@Parameter(key = "input")
-@Parameter(key = "output")
public class ClipRealTypes, O extends RealType>
implements Computers.Arity1
{
+ /**
+ * TODO
+ *
+ * @param input
+ * @param output
+ */
@Override
public void compute(final I input, final O output) {
final double v = input.getRealDouble();
diff --git a/imagej/imagej-ops2/src/main/java/net/imagej/ops2/convert/copy/CopyRealTypes.java b/imagej/imagej-ops2/src/main/java/net/imagej/ops2/convert/copy/CopyRealTypes.java
index 2484c13f7..0185f6300 100644
--- a/imagej/imagej-ops2/src/main/java/net/imagej/ops2/convert/copy/CopyRealTypes.java
+++ b/imagej/imagej-ops2/src/main/java/net/imagej/ops2/convert/copy/CopyRealTypes.java
@@ -32,10 +32,8 @@
import net.imglib2.type.numeric.RealType;
import org.scijava.function.Computers;
-import org.scijava.ops.core.Op;
-import org.scijava.param.Parameter;
+import org.scijava.ops.spi.Op;
import org.scijava.plugin.Plugin;
-import org.scijava.struct.ItemIO;
/**
* Copies the value of one {@link RealType} into another using {@code double}
@@ -44,12 +42,16 @@
* @author Martin Horn (University of Konstanz)
*/
@Plugin(type = Op.class, name = "convert.copy")
-@Parameter(key = "input")
-@Parameter(key = "output")
public class CopyRealTypes, O extends RealType>
implements Computers.Arity1
{
+ /**
+ * TODO
+ *
+ * @param input
+ * @param output
+ */
@Override
public void compute(final I input, final O output) {
output.setReal(input.getRealDouble());
diff --git a/imagej/imagej-ops2/src/main/java/net/imagej/ops2/copy/CopyArrayImg.java b/imagej/imagej-ops2/src/main/java/net/imagej/ops2/copy/CopyArrayImg.java
index 1edce1c98..47b5789c5 100644
--- a/imagej/imagej-ops2/src/main/java/net/imagej/ops2/copy/CopyArrayImg.java
+++ b/imagej/imagej-ops2/src/main/java/net/imagej/ops2/copy/CopyArrayImg.java
@@ -39,11 +39,9 @@
import org.scijava.Priority;
import org.scijava.function.Computers;
-import org.scijava.ops.OpDependency;
-import org.scijava.ops.core.Op;
-import org.scijava.param.Parameter;
+import org.scijava.ops.spi.Op;
+import org.scijava.ops.spi.OpDependency;
import org.scijava.plugin.Plugin;
-import org.scijava.struct.ItemIO;
/**
* Copying {@link ArrayImg} into another {@link ArrayImg}
@@ -52,10 +50,14 @@
* @param
*/
@Plugin(type = Op.class, name = "copy, copy.img", priority = Priority.VERY_HIGH)
-@Parameter(key = "input")
-@Parameter(key = "copy")
public class CopyArrayImg, A extends ArrayDataAccess>
implements Computers.Arity1, ArrayImg> {
+ /**
+ * TODO
+ *
+ * @param input
+ * @param copy
+ */
@Override
public void compute(final ArrayImg input, final ArrayImg output) {
@@ -69,14 +71,18 @@ public void compute(final ArrayImg input, final ArrayImg output) {
}
@Plugin(type = Op.class, name = "copy, copy.img", priority = Priority.VERY_HIGH)
-@Parameter(key = "input")
-@Parameter(key = "copy")
class CopyArrayImgFunction, A extends ArrayDataAccess>
implements Function, ArrayImg> {
@OpDependency(name = "copy.img")
private Computers.Arity1, ArrayImg> copyOp;
+ /**
+ * TODO
+ *
+ * @param input
+ * @param copy
+ */
@Override
public ArrayImg apply(ArrayImg input) {
// NB: Workaround for ArrayImgFactory not overriding create(Dimensions, T).
diff --git a/imagej/imagej-ops2/src/main/java/net/imagej/ops2/copy/CopyII.java b/imagej/imagej-ops2/src/main/java/net/imagej/ops2/copy/CopyII.java
index 6033bf832..937519f6c 100644
--- a/imagej/imagej-ops2/src/main/java/net/imagej/ops2/copy/CopyII.java
+++ b/imagej/imagej-ops2/src/main/java/net/imagej/ops2/copy/CopyII.java
@@ -36,12 +36,10 @@
import net.imglib2.IterableInterval;
import org.scijava.function.Computers;
-import org.scijava.ops.OpDependency;
-import org.scijava.ops.core.Op;
-import org.scijava.ops.util.Maps;
-import org.scijava.param.Parameter;
+import org.scijava.ops.engine.util.Maps;
+import org.scijava.ops.spi.Op;
+import org.scijava.ops.spi.OpDependency;
import org.scijava.plugin.Plugin;
-import org.scijava.struct.ItemIO;
/**
* Copies an {@link IterableInterval} into another {@link IterableInterval}
@@ -50,8 +48,6 @@
* @param
*/
@Plugin(type = Op.class, name = "copy, copy.iterableInterval", priority = 1.0)
-@Parameter(key = "input")
-@Parameter(key = "output")
public class CopyII implements Computers.Arity1, IterableInterval> {
// used internally
@@ -59,6 +55,12 @@ public class CopyII implements Computers.Arity1, Iterable
@OpDependency(name = "copy.type")
private Computers.Arity1 copyOp;
+ /**
+ * TODO
+ *
+ * @param input
+ * @param output
+ */
@Override
public void compute(final IterableInterval input, final IterableInterval output) {
if (!input.iterationOrder().equals(output.iterationOrder()))
@@ -69,8 +71,6 @@ public void compute(final IterableInterval input, final IterableInterval o
}
@Plugin(type = Op.class, name = "copy, copy.iterableInterval", priority = 1.0)
-@Parameter(key = "input")
-@Parameter(key = "output")
class CopyIIFunction implements Function, IterableInterval> {
@OpDependency(name = "create.img")
@@ -78,6 +78,12 @@ class CopyIIFunction implements Function, IterableInterva
@OpDependency(name = "copy.iterableInterval")
private Computers.Arity1, IterableInterval> copyOp;
+ /**
+ * TODO
+ *
+ * @param input
+ * @return the output
+ */
@Override
public IterableInterval apply(IterableInterval input) {
IterableInterval output = imgCreator.apply(input, input.firstElement());
diff --git a/imagej/imagej-ops2/src/main/java/net/imagej/ops2/copy/CopyImg.java b/imagej/imagej-ops2/src/main/java/net/imagej/ops2/copy/CopyImg.java
index 947ac5b29..72ae90b20 100644
--- a/imagej/imagej-ops2/src/main/java/net/imagej/ops2/copy/CopyImg.java
+++ b/imagej/imagej-ops2/src/main/java/net/imagej/ops2/copy/CopyImg.java
@@ -35,11 +35,9 @@
import net.imglib2.type.NativeType;
import org.scijava.function.Computers;
-import org.scijava.ops.OpDependency;
-import org.scijava.ops.core.Op;
-import org.scijava.param.Parameter;
+import org.scijava.ops.spi.Op;
+import org.scijava.ops.spi.OpDependency;
import org.scijava.plugin.Plugin;
-import org.scijava.struct.ItemIO;
/**
* Copying {@link Img} into another {@link Img}. Exists mainly for convenience
@@ -49,13 +47,17 @@
* @param
*/
@Plugin(type = Op.class, name = "copy, copy.img")
-@Parameter(key = "input")
-@Parameter(key = "output")
public class CopyImg> implements Computers.Arity1
, Img> {
@OpDependency(name = "copy.iterableInterval")
private Computers.Arity1, Iterable> copyComputer;
+ /**
+ * TODO
+ *
+ * @param input
+ * @param output
+ */
@Override
public void compute(final Img input, final Img output) {
if (!input.iterationOrder().equals(output.iterationOrder()))
@@ -65,8 +67,6 @@ public void compute(final Img input, final Img output) {
}
@Plugin(type = Op.class, name = "copy, copy.img")
-@Parameter(key = "input")
-@Parameter(key = "output")
class CopyImgFunction> implements Function
, Img> {
@OpDependency(name = "copy.img")
@@ -75,6 +75,12 @@ class CopyImgFunction> implements Function
, Img, Img> createFunc;
+ /**
+ * TODO
+ *
+ * @param input
+ * @return the output
+ */
@Override
public Img apply(Img input) {
Img output = createFunc.apply(input);
diff --git a/imagej/imagej-ops2/src/main/java/net/imagej/ops2/copy/CopyImgLabeling.java b/imagej/imagej-ops2/src/main/java/net/imagej/ops2/copy/CopyImgLabeling.java
index ec5a60eac..d314183ec 100644
--- a/imagej/imagej-ops2/src/main/java/net/imagej/ops2/copy/CopyImgLabeling.java
+++ b/imagej/imagej-ops2/src/main/java/net/imagej/ops2/copy/CopyImgLabeling.java
@@ -38,11 +38,9 @@
import net.imglib2.util.Util;
import org.scijava.function.Computers;
-import org.scijava.ops.OpDependency;
-import org.scijava.ops.core.Op;
-import org.scijava.param.Parameter;
+import org.scijava.ops.spi.Op;
+import org.scijava.ops.spi.OpDependency;
import org.scijava.plugin.Plugin;
-import org.scijava.struct.ItemIO;
/**
* Copying {@link ImgLabeling} into another {@link ImgLabeling}
@@ -51,8 +49,6 @@
* @param
*/
@Plugin(type = Op.class, name = "copy, copy.imgLabeling")
-@Parameter(key = "input")
-@Parameter(key = "output")
public class CopyImgLabeling & NativeType, L>
implements Computers.Arity1, ImgLabeling> {
@@ -61,6 +57,12 @@ public class CopyImgLabeling & NativeType, L>
@OpDependency(name = "copy.labelingMapping")
private Computers.Arity1, LabelingMapping> mappingCopyOp;
+ /**
+ * TODO
+ *
+ * @param input
+ * @param output
+ */
@Override
public void compute(final ImgLabeling input, final ImgLabeling output) {
if (!Intervals.equalDimensions(input, output))
diff --git a/imagej/imagej-ops2/src/main/java/net/imagej/ops2/copy/CopyLabelingMapping.java b/imagej/imagej-ops2/src/main/java/net/imagej/ops2/copy/CopyLabelingMapping.java
index 9185783db..c9ff90b42 100644
--- a/imagej/imagej-ops2/src/main/java/net/imagej/ops2/copy/CopyLabelingMapping.java
+++ b/imagej/imagej-ops2/src/main/java/net/imagej/ops2/copy/CopyLabelingMapping.java
@@ -37,10 +37,8 @@
import org.scijava.Priority;
import org.scijava.function.Computers;
-import org.scijava.ops.core.Op;
-import org.scijava.param.Parameter;
+import org.scijava.ops.spi.Op;
import org.scijava.plugin.Plugin;
-import org.scijava.struct.ItemIO;
/**
* Copies a {@link LabelingMapping} into another {@link LabelingMapping}
@@ -49,10 +47,14 @@
* @param
*/
@Plugin(type = Op.class, name = "copy, copy.labelingMapping", priority = Priority.VERY_HIGH)
-@Parameter(key = "input")
-@Parameter(key = "output")
public class CopyLabelingMapping implements Computers.Arity1, LabelingMapping> {
+ /**
+ * TODO
+ *
+ * @param input
+ * @param output
+ */
@Override
public void compute(final LabelingMapping input, final LabelingMapping output) {
@@ -63,8 +65,6 @@ public void compute(final LabelingMapping input, final LabelingMapping out
}
//@Plugin(type = Op.class, name = "copy.labelingMapping", priority = Priority.VERY_HIGH)
-//@Parameter(key = "input")
-//@Parameter(key = "output")
//class CopyLabelingMappingFunction implements Function, LabelingMapping> {
//
// @OpDependency(name = "copy.labelingMapping")
diff --git a/imagej/imagej-ops2/src/main/java/net/imagej/ops2/copy/CopyRAI.java b/imagej/imagej-ops2/src/main/java/net/imagej/ops2/copy/CopyRAI.java
index c00fb770e..69ad36566 100644
--- a/imagej/imagej-ops2/src/main/java/net/imagej/ops2/copy/CopyRAI.java
+++ b/imagej/imagej-ops2/src/main/java/net/imagej/ops2/copy/CopyRAI.java
@@ -35,11 +35,9 @@
import net.imglib2.view.Views;
import org.scijava.function.Computers;
-import org.scijava.ops.OpDependency;
-import org.scijava.ops.core.Op;
-import org.scijava.param.Parameter;
+import org.scijava.ops.spi.Op;
+import org.scijava.ops.spi.OpDependency;
import org.scijava.plugin.Plugin;
-import org.scijava.struct.ItemIO;
/**
* Copies a {@link RandomAccessibleInterval} into another
@@ -49,13 +47,17 @@
* @param
*/
@Plugin(type = Op.class, name = "copy, copy.rai", priority = 1.0)
-@Parameter(key = "input")
-@Parameter(key = "copy")
public class CopyRAI implements Computers.Arity1, RandomAccessibleInterval> {
@OpDependency(name = "copy")
private Computers.Arity1 mapComputer;
+ /**
+ * TODO
+ *
+ * @param input
+ * @param copy
+ */
@Override
public void compute(final RandomAccessibleInterval input, final RandomAccessibleInterval output) {
if (!Intervals.equalDimensions(input, output))
diff --git a/imagej/imagej-ops2/src/main/java/net/imagej/ops2/copy/CopyType.java b/imagej/imagej-ops2/src/main/java/net/imagej/ops2/copy/CopyType.java
index 3c45565df..a1f37fec3 100644
--- a/imagej/imagej-ops2/src/main/java/net/imagej/ops2/copy/CopyType.java
+++ b/imagej/imagej-ops2/src/main/java/net/imagej/ops2/copy/CopyType.java
@@ -32,10 +32,8 @@
import net.imglib2.type.Type;
import org.scijava.function.Computers;
-import org.scijava.ops.core.Op;
-import org.scijava.param.Parameter;
+import org.scijava.ops.spi.Op;
import org.scijava.plugin.Plugin;
-import org.scijava.struct.ItemIO;
/**
* Copy {@link Type} to another {@link Type}
@@ -44,10 +42,14 @@
* @param
*/
@Plugin(type = Op.class, name = "copy, copy.type")
-@Parameter(key = "input")
-@Parameter(key = "copy")
public class CopyType> implements Computers.Arity1 {
+ /**
+ * TODO
+ *
+ * @param input
+ * @param copy
+ */
@Override
public void compute(final T input, final T output) {
output.set(input);
diff --git a/imagej/imagej-ops2/src/main/java/net/imagej/ops2/create/CreateTypes.java b/imagej/imagej-ops2/src/main/java/net/imagej/ops2/create/CreateTypes.java
index e92f27c8c..40ea1adfd 100644
--- a/imagej/imagej-ops2/src/main/java/net/imagej/ops2/create/CreateTypes.java
+++ b/imagej/imagej-ops2/src/main/java/net/imagej/ops2/create/CreateTypes.java
@@ -19,11 +19,9 @@
import net.imglib2.type.numeric.real.FloatType;
import org.scijava.function.Producer;
-import org.scijava.ops.OpField;
-import org.scijava.ops.core.OpCollection;
-import org.scijava.param.Parameter;
+import org.scijava.ops.spi.OpCollection;
+import org.scijava.ops.spi.OpField;
import org.scijava.plugin.Plugin;
-import org.scijava.struct.ItemIO;
@Plugin(type = OpCollection.class)
public class CreateTypes {
diff --git a/imagej/imagej-ops2/src/main/java/net/imagej/ops2/create/Creators.java b/imagej/imagej-ops2/src/main/java/net/imagej/ops2/create/Creators.java
index 1c3357e06..cb2fdb56b 100644
--- a/imagej/imagej-ops2/src/main/java/net/imagej/ops2/create/Creators.java
+++ b/imagej/imagej-ops2/src/main/java/net/imagej/ops2/create/Creators.java
@@ -6,14 +6,6 @@
import net.imagej.ImgPlus;
import net.imagej.ImgPlusMetadata;
-import net.imagej.ops2.create.img.Imgs;
-import net.imagej.ops2.create.kernel.DefaultCreateKernel2ndDerivBiGauss;
-import net.imagej.ops2.create.kernel.DefaultCreateKernelBiGauss;
-import net.imagej.ops2.create.kernel.DefaultCreateKernelGabor;
-import net.imagej.ops2.create.kernel.DefaultCreateKernelGauss;
-import net.imagej.ops2.create.kernel.DefaultCreateKernelGibsonLanni;
-import net.imagej.ops2.create.kernel.DefaultCreateKernelLog;
-import net.imagej.ops2.create.kernel.DefaultCreateKernelSobel;
import net.imglib2.Cursor;
import net.imglib2.Dimensions;
import net.imglib2.FinalDimensions;
@@ -50,8 +42,8 @@
import org.scijava.Priority;
import org.scijava.function.Functions;
import org.scijava.function.Producer;
-import org.scijava.ops.OpField;
-import org.scijava.ops.core.OpCollection;
+import org.scijava.ops.spi.OpCollection;
+import org.scijava.ops.spi.OpField;
import org.scijava.plugin.Plugin;
@Plugin(type = OpCollection.class)
diff --git a/imagej/imagej-ops2/src/main/java/net/imagej/ops2/create/kernel/DefaultCreateKernel2ndDerivBiGauss.java b/imagej/imagej-ops2/src/main/java/net/imagej/ops2/create/DefaultCreateKernel2ndDerivBiGauss.java
similarity index 99%
rename from imagej/imagej-ops2/src/main/java/net/imagej/ops2/create/kernel/DefaultCreateKernel2ndDerivBiGauss.java
rename to imagej/imagej-ops2/src/main/java/net/imagej/ops2/create/DefaultCreateKernel2ndDerivBiGauss.java
index e34a382e5..64333421a 100644
--- a/imagej/imagej-ops2/src/main/java/net/imagej/ops2/create/kernel/DefaultCreateKernel2ndDerivBiGauss.java
+++ b/imagej/imagej-ops2/src/main/java/net/imagej/ops2/create/DefaultCreateKernel2ndDerivBiGauss.java
@@ -27,7 +27,7 @@
* #L%
*/
-package net.imagej.ops2.create.kernel;
+package net.imagej.ops2.create;
import java.util.function.BiFunction;
diff --git a/imagej/imagej-ops2/src/main/java/net/imagej/ops2/create/kernel/DefaultCreateKernelBiGauss.java b/imagej/imagej-ops2/src/main/java/net/imagej/ops2/create/DefaultCreateKernelBiGauss.java
similarity index 99%
rename from imagej/imagej-ops2/src/main/java/net/imagej/ops2/create/kernel/DefaultCreateKernelBiGauss.java
rename to imagej/imagej-ops2/src/main/java/net/imagej/ops2/create/DefaultCreateKernelBiGauss.java
index f78a025b5..671cfdc39 100644
--- a/imagej/imagej-ops2/src/main/java/net/imagej/ops2/create/kernel/DefaultCreateKernelBiGauss.java
+++ b/imagej/imagej-ops2/src/main/java/net/imagej/ops2/create/DefaultCreateKernelBiGauss.java
@@ -27,7 +27,7 @@
* #L%
*/
-package net.imagej.ops2.create.kernel;
+package net.imagej.ops2.create;
import java.util.function.BiFunction;
diff --git a/imagej/imagej-ops2/src/main/java/net/imagej/ops2/create/kernel/DefaultCreateKernelGabor.java b/imagej/imagej-ops2/src/main/java/net/imagej/ops2/create/DefaultCreateKernelGabor.java
similarity index 99%
rename from imagej/imagej-ops2/src/main/java/net/imagej/ops2/create/kernel/DefaultCreateKernelGabor.java
rename to imagej/imagej-ops2/src/main/java/net/imagej/ops2/create/DefaultCreateKernelGabor.java
index 532eedcdb..88ccc1e1c 100644
--- a/imagej/imagej-ops2/src/main/java/net/imagej/ops2/create/kernel/DefaultCreateKernelGabor.java
+++ b/imagej/imagej-ops2/src/main/java/net/imagej/ops2/create/DefaultCreateKernelGabor.java
@@ -27,7 +27,7 @@
* #L%
*/
-package net.imagej.ops2.create.kernel;
+package net.imagej.ops2.create;
import java.util.function.BiFunction;
diff --git a/imagej/imagej-ops2/src/main/java/net/imagej/ops2/create/kernel/DefaultCreateKernelGauss.java b/imagej/imagej-ops2/src/main/java/net/imagej/ops2/create/DefaultCreateKernelGauss.java
similarity index 98%
rename from imagej/imagej-ops2/src/main/java/net/imagej/ops2/create/kernel/DefaultCreateKernelGauss.java
rename to imagej/imagej-ops2/src/main/java/net/imagej/ops2/create/DefaultCreateKernelGauss.java
index 29dd6b65d..4f0eaff9e 100644
--- a/imagej/imagej-ops2/src/main/java/net/imagej/ops2/create/kernel/DefaultCreateKernelGauss.java
+++ b/imagej/imagej-ops2/src/main/java/net/imagej/ops2/create/DefaultCreateKernelGauss.java
@@ -27,7 +27,7 @@
* #L%
*/
-package net.imagej.ops2.create.kernel;
+package net.imagej.ops2.create;
import java.util.function.BiFunction;
diff --git a/imagej/imagej-ops2/src/main/java/net/imagej/ops2/create/kernel/DefaultCreateKernelGibsonLanni.java b/imagej/imagej-ops2/src/main/java/net/imagej/ops2/create/DefaultCreateKernelGibsonLanni.java
similarity index 99%
rename from imagej/imagej-ops2/src/main/java/net/imagej/ops2/create/kernel/DefaultCreateKernelGibsonLanni.java
rename to imagej/imagej-ops2/src/main/java/net/imagej/ops2/create/DefaultCreateKernelGibsonLanni.java
index 9d3106593..c13b66a9b 100644
--- a/imagej/imagej-ops2/src/main/java/net/imagej/ops2/create/kernel/DefaultCreateKernelGibsonLanni.java
+++ b/imagej/imagej-ops2/src/main/java/net/imagej/ops2/create/DefaultCreateKernelGibsonLanni.java
@@ -27,7 +27,7 @@
* #L%
*/
-package net.imagej.ops2.create.kernel;
+package net.imagej.ops2.create;
import java.util.function.BiFunction;
diff --git a/imagej/imagej-ops2/src/main/java/net/imagej/ops2/create/kernel/DefaultCreateKernelLog.java b/imagej/imagej-ops2/src/main/java/net/imagej/ops2/create/DefaultCreateKernelLog.java
similarity index 99%
rename from imagej/imagej-ops2/src/main/java/net/imagej/ops2/create/kernel/DefaultCreateKernelLog.java
rename to imagej/imagej-ops2/src/main/java/net/imagej/ops2/create/DefaultCreateKernelLog.java
index 016da987e..0c1298498 100644
--- a/imagej/imagej-ops2/src/main/java/net/imagej/ops2/create/kernel/DefaultCreateKernelLog.java
+++ b/imagej/imagej-ops2/src/main/java/net/imagej/ops2/create/DefaultCreateKernelLog.java
@@ -27,7 +27,7 @@
* #L%
*/
-package net.imagej.ops2.create.kernel;
+package net.imagej.ops2.create;
import java.util.function.BiFunction;
diff --git a/imagej/imagej-ops2/src/main/java/net/imagej/ops2/create/kernel/DefaultCreateKernelSobel.java b/imagej/imagej-ops2/src/main/java/net/imagej/ops2/create/DefaultCreateKernelSobel.java
similarity index 98%
rename from imagej/imagej-ops2/src/main/java/net/imagej/ops2/create/kernel/DefaultCreateKernelSobel.java
rename to imagej/imagej-ops2/src/main/java/net/imagej/ops2/create/DefaultCreateKernelSobel.java
index e3993b740..ececfd61c 100644
--- a/imagej/imagej-ops2/src/main/java/net/imagej/ops2/create/kernel/DefaultCreateKernelSobel.java
+++ b/imagej/imagej-ops2/src/main/java/net/imagej/ops2/create/DefaultCreateKernelSobel.java
@@ -26,7 +26,7 @@
* #L%
*/
-package net.imagej.ops2.create.kernel;
+package net.imagej.ops2.create;
import java.util.function.BiFunction;
diff --git a/imagej/imagej-ops2/src/main/java/net/imagej/ops2/create/img/Imgs.java b/imagej/imagej-ops2/src/main/java/net/imagej/ops2/create/Imgs.java
similarity index 99%
rename from imagej/imagej-ops2/src/main/java/net/imagej/ops2/create/img/Imgs.java
rename to imagej/imagej-ops2/src/main/java/net/imagej/ops2/create/Imgs.java
index fb2b9fc88..6e3c0190a 100644
--- a/imagej/imagej-ops2/src/main/java/net/imagej/ops2/create/img/Imgs.java
+++ b/imagej/imagej-ops2/src/main/java/net/imagej/ops2/create/Imgs.java
@@ -26,7 +26,7 @@
* POSSIBILITY OF SUCH DAMAGE.
* #L%
*/
-package net.imagej.ops2.create.img;
+package net.imagej.ops2.create;
import net.imglib2.Dimensions;
import net.imglib2.Interval;
diff --git a/imagej/imagej-ops2/src/main/java/net/imagej/ops2/deconvolve/NonCirculantFirstGuess.java b/imagej/imagej-ops2/src/main/java/net/imagej/ops2/deconvolve/NonCirculantFirstGuess.java
index 88c0a5a43..6dcdb1e99 100644
--- a/imagej/imagej-ops2/src/main/java/net/imagej/ops2/deconvolve/NonCirculantFirstGuess.java
+++ b/imagej/imagej-ops2/src/main/java/net/imagej/ops2/deconvolve/NonCirculantFirstGuess.java
@@ -42,11 +42,9 @@
import org.scijava.Priority;
import org.scijava.function.Computers;
import org.scijava.function.Functions;
-import org.scijava.ops.OpDependency;
-import org.scijava.ops.core.Op;
-import org.scijava.param.Parameter;
+import org.scijava.ops.spi.Op;
+import org.scijava.ops.spi.OpDependency;
import org.scijava.plugin.Plugin;
-import org.scijava.struct.ItemIO;
/**
* Calculate non-circulant first guess. This is used as part of the Boundary
@@ -61,10 +59,6 @@
*/
@Plugin(type = Op.class, name = "deconvolve.firstGuess", priority = Priority.LOW)
-@Parameter(key = "input")
-@Parameter(key = "outType")
-@Parameter(key = "k")
-@Parameter(key = "output")
public class NonCirculantFirstGuess, O extends RealType, K extends RealType, C extends ComplexType>
implements
Functions.Arity3, O, Dimensions, RandomAccessibleInterval>
@@ -82,6 +76,14 @@ public class NonCirculantFirstGuess, O extends RealType
* image before extension, k is required to calculate the non-circulant
* normalization factor
*/
+ /**
+ * TODO
+ *
+ * @param input
+ * @param outType
+ * @param k
+ * @return the output
+ */
@Override
public RandomAccessibleInterval apply(RandomAccessibleInterval in, final O outType, final Dimensions k) {
diff --git a/imagej/imagej-ops2/src/main/java/net/imagej/ops2/deconvolve/NonCirculantNormalizationFactor.java b/imagej/imagej-ops2/src/main/java/net/imagej/ops2/deconvolve/NonCirculantNormalizationFactor.java
index a14c92da2..b4aa48903 100644
--- a/imagej/imagej-ops2/src/main/java/net/imagej/ops2/deconvolve/NonCirculantNormalizationFactor.java
+++ b/imagej/imagej-ops2/src/main/java/net/imagej/ops2/deconvolve/NonCirculantNormalizationFactor.java
@@ -50,11 +50,9 @@
import org.scijava.Priority;
import org.scijava.function.Computers;
import org.scijava.function.Inplaces;
-import org.scijava.ops.OpDependency;
-import org.scijava.ops.core.Op;
-import org.scijava.param.Parameter;
+import org.scijava.ops.spi.Op;
+import org.scijava.ops.spi.OpDependency;
import org.scijava.plugin.Plugin;
-import org.scijava.struct.ItemIO;
/**
* Calculate non-circulant normalization factor. This is used as part of the
@@ -70,12 +68,6 @@
@Plugin(type = Op.class, name = "deconvolve.normalizationFactor",
priority = Priority.LOW)
-@Parameter(key = "io")
-@Parameter(key = "k")
-@Parameter(key = "l")
-@Parameter(key = "fftInput")
-@Parameter(key = "fftKernel")
-@Parameter(key = "executorService")
public class NonCirculantNormalizationFactor, O extends RealType, K extends RealType, C extends ComplexType>
implements Inplaces.Arity6_1, Dimensions, Dimensions, RandomAccessibleInterval, RandomAccessibleInterval, ExecutorService>
{
@@ -123,6 +115,13 @@ public class NonCirculantNormalizationFactor, O extends Re
/**
* apply the normalization image needed for semi noncirculant model see
* http://bigwww.epfl.ch/deconvolution/challenge2013/index.html?p=doc_math_rl
+ *
+ * @param io
+ * @param k
+ * @param l
+ * @param fftInput
+ * @param fftKernel
+ * @param executorService
*/
@Override
public void mutate(RandomAccessibleInterval arg, final Dimensions k, final Dimensions l, final RandomAccessibleInterval fftInput, final RandomAccessibleInterval fftKernel, final ExecutorService es) {
diff --git a/imagej/imagej-ops2/src/main/java/net/imagej/ops2/deconvolve/RichardsonLucyC.java b/imagej/imagej-ops2/src/main/java/net/imagej/ops2/deconvolve/RichardsonLucyC.java
index d887a24f0..0dbe2ab9f 100644
--- a/imagej/imagej-ops2/src/main/java/net/imagej/ops2/deconvolve/RichardsonLucyC.java
+++ b/imagej/imagej-ops2/src/main/java/net/imagej/ops2/deconvolve/RichardsonLucyC.java
@@ -45,11 +45,9 @@
import org.scijava.Priority;
import org.scijava.function.Computers;
import org.scijava.function.Inplaces;
-import org.scijava.ops.OpDependency;
-import org.scijava.ops.core.Op;
-import org.scijava.param.Parameter;
+import org.scijava.ops.spi.Op;
+import org.scijava.ops.spi.OpDependency;
import org.scijava.plugin.Plugin;
-import org.scijava.struct.ItemIO;
/**
* Richardson Lucy algorithm for (@link RandomAccessibleInterval) (Lucy, L. B.
@@ -64,20 +62,6 @@
*/
@Plugin(type = Op.class, name = "deconvolve.richardsonLucy", priority = Priority.HIGH)
-@Parameter(key = "input")
-@Parameter(key = "kernel")
-@Parameter(key = "fftInput")
-@Parameter(key = "fftKernel")
-@Parameter(key = "performInputFFT")
-@Parameter(key = "performKernelFFT")
-@Parameter(key = "complexType")
-@Parameter(key = "maxIterations")
-@Parameter(key = "accelerator")
-@Parameter(key = "updateOp", description = "by default, this should be RichardsonLucyUpdate")
-@Parameter(key = "raiExtendedEstimate")
-@Parameter(key = "iterativePostProcessingOps")
-@Parameter(key = "executorService")
-@Parameter(key = "output")
public class RichardsonLucyC, O extends RealType, K extends RealType, C extends ComplexType>
implements Computers.Arity13, RandomAccessibleInterval, RandomAccessibleInterval, //
RandomAccessibleInterval, Boolean, Boolean, C, Integer, Inplaces.Arity1>, //
@@ -134,6 +118,24 @@ public class RichardsonLucyC, O extends RealType, K ext
@OpDependency(name = "copy.rai")
private Computers.Arity1, RandomAccessibleInterval> copy2Op;
+ /**
+ * TODO
+ *
+ * @param input
+ * @param kernel
+ * @param fftInput
+ * @param fftKernel
+ * @param performInputFFT
+ * @param performKernelFFT
+ * @param complexType
+ * @param maxIterations
+ * @param accelerator
+ * @param updateOp by default, this should be RichardsonLucyUpdate
+ * @param raiExtendedEstimate
+ * @param iterativePostProcessingOps
+ * @param executorService
+ * @param output
+ */
@Override
public void compute(RandomAccessibleInterval in, RandomAccessibleInterval kernel,
RandomAccessibleInterval fftInput, RandomAccessibleInterval fftKernel, Boolean performInputFFT,
diff --git a/imagej/imagej-ops2/src/main/java/net/imagej/ops2/deconvolve/RichardsonLucyCorrection.java b/imagej/imagej-ops2/src/main/java/net/imagej/ops2/deconvolve/RichardsonLucyCorrection.java
index 4420bedb1..dce9f4dc0 100644
--- a/imagej/imagej-ops2/src/main/java/net/imagej/ops2/deconvolve/RichardsonLucyCorrection.java
+++ b/imagej/imagej-ops2/src/main/java/net/imagej/ops2/deconvolve/RichardsonLucyCorrection.java
@@ -44,11 +44,9 @@
import org.scijava.Priority;
import org.scijava.function.Computers;
-import org.scijava.ops.OpDependency;
-import org.scijava.ops.core.Op;
-import org.scijava.param.Parameter;
+import org.scijava.ops.spi.Op;
+import org.scijava.ops.spi.OpDependency;
import org.scijava.plugin.Plugin;
-import org.scijava.struct.ItemIO;
/**
* Computes Richardson Lucy correction factor for (@link
@@ -62,12 +60,6 @@
*/
@Plugin(type = Op.class, name = "deconvolve.richardsonLucyCorrection",
priority = Priority.HIGH)
-@Parameter(key = "input")
-@Parameter(key = "reblurred")
-@Parameter(key = "fftBuffer")
-@Parameter(key = "fftKernel")
-@Parameter(key = "executorService")
-@Parameter(key = "output")
public class RichardsonLucyCorrection, O extends RealType, C extends ComplexType>
implements
Computers.Arity5, RandomAccessibleInterval, RandomAccessibleInterval, RandomAccessibleInterval, ExecutorService, RandomAccessibleInterval>
@@ -105,6 +97,13 @@ public class RichardsonLucyCorrection, O extends RealType<
/**
* computes the correction factor of the Richardson Lucy Algorithm
+ *
+ * @param input
+ * @param reblurred
+ * @param fftBuffer
+ * @param fftKernel
+ * @param executorService
+ * @param output
*/
@Override
public void compute(RandomAccessibleInterval observed,
diff --git a/imagej/imagej-ops2/src/main/java/net/imagej/ops2/deconvolve/RichardsonLucyF.java b/imagej/imagej-ops2/src/main/java/net/imagej/ops2/deconvolve/RichardsonLucyF.java
index 61ec30465..13e2a8dcd 100644
--- a/imagej/imagej-ops2/src/main/java/net/imagej/ops2/deconvolve/RichardsonLucyF.java
+++ b/imagej/imagej-ops2/src/main/java/net/imagej/ops2/deconvolve/RichardsonLucyF.java
@@ -47,11 +47,9 @@
import org.scijava.function.Computers;
import org.scijava.function.Functions;
import org.scijava.function.Inplaces;
-import org.scijava.ops.OpDependency;
-import org.scijava.ops.core.Op;
-import org.scijava.param.Parameter;
+import org.scijava.ops.spi.Op;
+import org.scijava.ops.spi.OpDependency;
import org.scijava.plugin.Plugin;
-import org.scijava.struct.ItemIO;
/**
* Richardson Lucy function op that operates on (@link RandomAccessibleInterval)
@@ -65,18 +63,6 @@
* @param
*/
@Plugin(type = Op.class, name = "deconvolve.richardsonLucy", priority = Priority.HIGH)
-@Parameter(key = "input")
-@Parameter(key = "kernel")
-@Parameter(key = "borderSize")
-@Parameter(key = "obfInput")
-@Parameter(key = "obfKernel")
-@Parameter(key = "outType")
-@Parameter(key = "fftType")
-@Parameter(key = "maxIterations", description = "max number of iterations")
-@Parameter(key = "nonCirculant", description = "indicates whether to use non-circulant edge handling")
-@Parameter(key = "accelerate", description = "indicates whether or not to use acceleration")
-@Parameter(key = "executorService")
-@Parameter(key = "output")
public class RichardsonLucyF & NativeType, O extends RealType & NativeType, K extends RealType & NativeType, C extends ComplexType & NativeType>
implements
Functions.Arity11, RandomAccessibleInterval, long[], OutOfBoundsFactory>, OutOfBoundsFactory>, O, C, Integer, Boolean, Boolean, ExecutorService, RandomAccessibleInterval> {
@@ -194,6 +180,22 @@ private void computeFilter(final RandomAccessibleInterval input,
filter.compute(paddedInput, paddedKernel, output);
}
+ /**
+ * TODO
+ *
+ * @param input
+ * @param kernel
+ * @param borderSize
+ * @param obfInput
+ * @param obfKernel
+ * @param outType
+ * @param fftType
+ * @param maxIterations max number of iterations
+ * @param nonCirculant indicates whether to use non-circulant edge handling
+ * @param accelerate indicates whether or not to use acceleration
+ * @param executorService
+ * @return the output
+ */
@Override
public RandomAccessibleInterval apply(RandomAccessibleInterval