Dependency version updates

Updated dependencies, including JavaCPP to 1.5. This required changes to all OpenCV-related import statements to become more module-friendly. More information at https://github.com/bytedeco/javacpp-presets/tree/master/opencv Added picocli to parent build.gradle in expectation it will be used soon.
petebankhead · Apr 14, 2019 · a66b6a5 · a66b6a5
1 parent ad8595e
commit a66b6a5
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Showing 43 changed files with 190 additions and 178 deletions.
diff --git a/build.gradle b/build.gradle
@@ -93,6 +93,7 @@ subprojects {
     javafx
     nativeloader
     guava
+    picocli
 
     // Guave tries to bring in extra dependencies not required at runtime
     implementation {
@@ -116,6 +117,8 @@ subprojects {
       javafx "org.openjfx:${fx}:${jfxVersion}:${platform}"
     }
 
+	picocli 'info.picocli:picocli:3.9.6'
+
     richtextfx 'org.fxmisc.richtext:richtextfx:0.9.3'
 
     commonsmath 'org.apache.commons:commons-math3:3.6.1'
@@ -131,12 +134,12 @@ subprojects {
 
     jfxtras 'org.jfxtras:jfxtras-menu:10.0-r1'
 
-    opencv 'org.bytedeco.javacpp-presets:opencv:4.0.1-1.4.4'
+    opencv 'org.bytedeco:opencv:4.0.1-1.5'
     if (nativesCPP != null) {
       if (useGPU)
-        opencv "org.bytedeco.javacpp-presets:opencv:4.0.1-1.4.4:${nativesCPP}-gpu"
+        opencv "org.bytedeco:opencv:4.0.1-1.5:${nativesCPP}-gpu"
       else
-	    opencv "org.bytedeco.javacpp-presets:opencv:4.0.1-1.4.4:${nativesCPP}"
+	    opencv "org.bytedeco:opencv:4.0.1-1.5:${nativesCPP}"
     }
 
     jpen 'net.sourceforge.jpen:jpen:2-150301'
@@ -149,7 +152,7 @@ subprojects {
     if (nativesClassifier != null)
       openslide 'org.openslide:openslide:3.4.1_2:' + nativesClassifier
 
-    nativeloader 'org.scijava:native-lib-loader:2.3.2'
+    nativeloader 'org.scijava:native-lib-loader:2.3.4'
 
     guava 'com.google.guava:guava:27.1-jre'
   }

diff --git a/qupath-core-processing/src/main/java/qupath/opencv/CellCountsCV.java b/qupath-core-processing/src/main/java/qupath/opencv/CellCountsCV.java
@@ -32,8 +32,11 @@
 import java.util.Collection;
 import java.util.List;
 
-import static org.bytedeco.javacpp.opencv_core.*;
-import org.bytedeco.javacpp.opencv_imgproc;
+import static org.bytedeco.opencv.global.opencv_core.*;
+import org.bytedeco.opencv.global.opencv_imgproc;
+import org.bytedeco.opencv.opencv_core.Mat;
+import org.bytedeco.opencv.opencv_core.MatVector;
+import org.bytedeco.opencv.opencv_core.Size;
 import org.bytedeco.javacpp.indexer.FloatIndexer;
 import org.bytedeco.javacpp.indexer.IntIndexer;
 import org.slf4j.Logger;

diff --git a/qupath-core-processing/src/main/java/qupath/opencv/DetectCytokeratinCV.java b/qupath-core-processing/src/main/java/qupath/opencv/DetectCytokeratinCV.java
@@ -34,12 +34,14 @@
 import java.util.Collections;
 import java.util.List;
 
-import static org.bytedeco.javacpp.opencv_core.*;
-import org.bytedeco.javacpp.opencv_imgproc;
+import static org.bytedeco.opencv.global.opencv_core.*;
+import org.bytedeco.opencv.global.opencv_imgproc;
 import org.bytedeco.javacpp.indexer.Indexer;
 import org.bytedeco.javacpp.indexer.IntIndexer;
-import org.bytedeco.javacpp.opencv_core.Mat;
-import org.bytedeco.javacpp.opencv_core.Scalar;
+import org.bytedeco.opencv.opencv_core.Mat;
+import org.bytedeco.opencv.opencv_core.MatVector;
+import org.bytedeco.opencv.opencv_core.Scalar;
+import org.bytedeco.opencv.opencv_core.Size;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 

diff --git a/qupath-core-processing/src/main/java/qupath/opencv/WatershedNucleiCV.java b/qupath-core-processing/src/main/java/qupath/opencv/WatershedNucleiCV.java
@@ -31,8 +31,16 @@
 import java.util.Collection;
 import java.util.List;
 
-import static org.bytedeco.javacpp.opencv_core.*;
-import org.bytedeco.javacpp.opencv_imgproc;
+import static org.bytedeco.opencv.global.opencv_core.*;
+import org.bytedeco.opencv.global.opencv_imgproc;
+import org.bytedeco.opencv.opencv_core.Mat;
+import org.bytedeco.opencv.opencv_core.MatVector;
+import org.bytedeco.opencv.opencv_core.Point;
+import org.bytedeco.opencv.opencv_core.Rect;
+import org.bytedeco.opencv.opencv_core.RotatedRect;
+import org.bytedeco.opencv.opencv_core.Scalar;
+import org.bytedeco.opencv.opencv_core.Size;
+import org.bytedeco.opencv.opencv_core.Size2f;
 import org.bytedeco.javacpp.indexer.Indexer;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;

diff --git a/qupath-core-processing/src/main/java/qupath/opencv/classify/BayesClassifier.java b/qupath-core-processing/src/main/java/qupath/opencv/classify/BayesClassifier.java
@@ -23,7 +23,7 @@
 
 package qupath.opencv.classify;
 
-import org.bytedeco.javacpp.opencv_ml.NormalBayesClassifier;
+import org.bytedeco.opencv.opencv_ml.NormalBayesClassifier;
 
 /**
  * Wrapper for OpenCV's Normal Bayes classifier.

diff --git a/qupath-core-processing/src/main/java/qupath/opencv/classify/BoostClassifier.java b/qupath-core-processing/src/main/java/qupath/opencv/classify/BoostClassifier.java
@@ -25,8 +25,8 @@
 
 import java.util.List;
 
-import org.bytedeco.javacpp.opencv_ml.Boost;
-import org.bytedeco.javacpp.opencv_core.Mat;
+import org.bytedeco.opencv.opencv_ml.Boost;
+import org.bytedeco.opencv.opencv_core.Mat;
 
 import qupath.lib.objects.PathObject;
 import qupath.lib.objects.classes.PathClass;

diff --git a/qupath-core-processing/src/main/java/qupath/opencv/classify/DTreesClassifier.java b/qupath-core-processing/src/main/java/qupath/opencv/classify/DTreesClassifier.java
@@ -23,7 +23,7 @@
 
 package qupath.opencv.classify;
 
-import org.bytedeco.javacpp.opencv_ml.DTrees;
+import org.bytedeco.opencv.opencv_ml.DTrees;
 
 /**
  * Wrapper for OpenCV's Decision Trees classifier.

diff --git a/qupath-core-processing/src/main/java/qupath/opencv/classify/KNearestClassifier.java b/qupath-core-processing/src/main/java/qupath/opencv/classify/KNearestClassifier.java
@@ -23,7 +23,7 @@
 
 package qupath.opencv.classify;
 
-import org.bytedeco.javacpp.opencv_ml.KNearest;
+import org.bytedeco.opencv.opencv_ml.KNearest;
 
 import qupath.lib.plugins.parameters.ParameterList;
 

diff --git a/qupath-core-processing/src/main/java/qupath/opencv/classify/NeuralNetworksClassifier.java b/qupath-core-processing/src/main/java/qupath/opencv/classify/NeuralNetworksClassifier.java
@@ -23,13 +23,15 @@
 
 package qupath.opencv.classify;
 
-import static org.bytedeco.javacpp.opencv_core.*;
+import static org.bytedeco.opencv.global.opencv_core.*;
+
+import org.bytedeco.opencv.global.opencv_ml;
+import org.bytedeco.opencv.opencv_core.*;
+import org.bytedeco.opencv.opencv_ml.*;
 
 import java.nio.FloatBuffer;
 
-import org.bytedeco.javacpp.opencv_ml.ANN_MLP;
 import org.bytedeco.javacpp.indexer.FloatIndexer;
-import org.bytedeco.javacpp.opencv_ml;
 
 import qupath.lib.plugins.parameters.ParameterList;
 

diff --git a/qupath-core-processing/src/main/java/qupath/opencv/classify/OpenCvClassifier.java b/qupath-core-processing/src/main/java/qupath/opencv/classify/OpenCvClassifier.java
@@ -49,15 +49,17 @@
 import qupath.lib.plugins.parameters.ParameterList;
 import qupath.lib.plugins.parameters.Parameterizable;
 
-import static org.bytedeco.javacpp.opencv_core.*;
-import static org.bytedeco.javacpp.opencv_ml.*;
+import static org.bytedeco.opencv.global.opencv_core.*;
+import static org.bytedeco.opencv.global.opencv_ml.*;
+import org.bytedeco.opencv.opencv_core.*;
+import org.bytedeco.opencv.opencv_ml.*;
 
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
 /**
  * Abstract base class for OpenCV classifiers.
- * 
+ * <p>
  * Note: We cannot directly serialize an OpenCV classifier, so instead the training data is serialized and the classifier
  * rebuilt as required.  This means that potentially if a classifier is reloaded with a different version of the OpenCV library,
  * if the training algorithm has changed then there may be a different result.

diff --git a/...core-processing/src/main/java/qupath/opencv/classify/ParameterizableOpenCvClassifier.java b/...core-processing/src/main/java/qupath/opencv/classify/ParameterizableOpenCvClassifier.java
@@ -27,16 +27,16 @@
 import java.io.ObjectInput;
 import java.io.ObjectOutput;
 
-import org.bytedeco.javacpp.opencv_ml.StatModel;
-import org.bytedeco.javacpp.opencv_core.TermCriteria;
+import org.bytedeco.opencv.opencv_ml.StatModel;
+import org.bytedeco.opencv.opencv_core.TermCriteria;
 
 import qupath.lib.plugins.parameters.ParameterList;
 import qupath.lib.plugins.parameters.Parameterizable;
 
 /**
  * Abstract base class useful for creating OpenCV classifiers that can be modified depending 
  * on the values of several parameters.
- * 
+ * <p>
  * This takes care of some of the effort involved in representing and storing the parameters.
  * 
  * @author Pete Bankhead

diff --git a/qupath-core-processing/src/main/java/qupath/opencv/classify/RTreesClassifier.java b/qupath-core-processing/src/main/java/qupath/opencv/classify/RTreesClassifier.java
@@ -25,9 +25,9 @@
 
 import java.util.List;
 
-import org.bytedeco.javacpp.opencv_ml.RTrees;
-import org.bytedeco.javacpp.opencv_core.Mat;
-import org.bytedeco.javacpp.opencv_core.TermCriteria;
+import org.bytedeco.opencv.opencv_ml.RTrees;
+import org.bytedeco.opencv.opencv_core.Mat;
+import org.bytedeco.opencv.opencv_core.TermCriteria;
 
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;

diff --git a/qupath-core-processing/src/main/java/qupath/opencv/classify/SVMClassifier.java b/qupath-core-processing/src/main/java/qupath/opencv/classify/SVMClassifier.java
@@ -23,7 +23,7 @@
 
 package qupath.opencv.classify;
 
-import org.bytedeco.javacpp.opencv_ml.SVM;
+import org.bytedeco.opencv.opencv_ml.SVM;
 
 import qupath.lib.plugins.parameters.ParameterList;
 

diff --git a/qupath-core-processing/src/main/java/qupath/opencv/features/DelaunayTriangulation.java b/qupath-core-processing/src/main/java/qupath/opencv/features/DelaunayTriangulation.java
@@ -35,8 +35,9 @@
 import java.util.Set;
 import java.util.stream.Collectors;
 
-import static org.bytedeco.javacpp.opencv_core.*;
-import static org.bytedeco.javacpp.opencv_imgproc.Subdiv2D;
+import org.bytedeco.opencv.opencv_core.Point2f;
+import org.bytedeco.opencv.opencv_core.Rect;
+import org.bytedeco.opencv.opencv_imgproc.Subdiv2D;
 
 import qupath.lib.analysis.stats.RunningStatistics;
 import qupath.lib.classifiers.PathClassificationLabellingHelper;

diff --git a/qupath-core-processing/src/main/java/qupath/opencv/processing/OpenCVTools.java b/qupath-core-processing/src/main/java/qupath/opencv/processing/OpenCVTools.java
@@ -30,8 +30,8 @@
 import java.awt.image.Raster;
 import java.awt.image.WritableRaster;
 import java.nio.FloatBuffer;
-import static org.bytedeco.javacpp.opencv_core.*;
-import org.bytedeco.javacpp.opencv_imgproc;
+import static org.bytedeco.opencv.global.opencv_core.*;
+import org.bytedeco.opencv.global.opencv_imgproc;
 import org.bytedeco.javacpp.indexer.ByteIndexer;
 import org.bytedeco.javacpp.indexer.DoubleIndexer;
 import org.bytedeco.javacpp.indexer.FloatIndexer;
@@ -41,8 +41,10 @@
 import org.bytedeco.javacpp.indexer.UShortIndexer;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
-import org.bytedeco.javacpp.opencv_core.Mat;
-import org.bytedeco.javacpp.opencv_core.Scalar;
+import org.bytedeco.opencv.opencv_core.Mat;
+import org.bytedeco.opencv.opencv_core.MatVector;
+import org.bytedeco.opencv.opencv_core.Point;
+import org.bytedeco.opencv.opencv_core.Scalar;
 
 import qupath.lib.common.ColorTools;
 

diff --git a/qupath-core-processing/src/main/java/qupath/opencv/processing/PixelImageCV.java b/qupath-core-processing/src/main/java/qupath/opencv/processing/PixelImageCV.java
@@ -23,10 +23,13 @@
 
 package qupath.opencv.processing;
 
-import static org.bytedeco.javacpp.opencv_core.*;
+import static org.bytedeco.opencv.global.opencv_core.*;
 
 import java.nio.FloatBuffer;
 
+import org.bytedeco.opencv.opencv_core.Mat;
+import org.bytedeco.opencv.opencv_core.Scalar;
+
 import qupath.lib.analysis.algorithms.SimpleModifiableImage;
 
 /**

diff --git a/qupath-core-processing/src/main/java/qupath/opencv/processing/ProcessingCV.java b/qupath-core-processing/src/main/java/qupath/opencv/processing/ProcessingCV.java
@@ -23,7 +23,7 @@
 
 package qupath.opencv.processing;
 
-import org.bytedeco.javacpp.opencv_core.Mat;
+import org.bytedeco.opencv.opencv_core.Mat;
 
 import qupath.lib.analysis.algorithms.MorphologicalReconstruction;
 import qupath.lib.analysis.algorithms.Watershed;

diff --git a/qupath-core-processing/src/main/java/qupath/opencv/processing/TypeAdaptersCV.java b/qupath-core-processing/src/main/java/qupath/opencv/processing/TypeAdaptersCV.java
@@ -2,21 +2,9 @@
 
 import java.io.IOException;
 
-import org.bytedeco.javacpp.opencv_core;
-import org.bytedeco.javacpp.opencv_core.FileStorage;
-import org.bytedeco.javacpp.opencv_core.Mat;
-import org.bytedeco.javacpp.opencv_core.SparseMat;
-import org.bytedeco.javacpp.opencv_ml.ANN_MLP;
-import org.bytedeco.javacpp.opencv_ml.Boost;
-import org.bytedeco.javacpp.opencv_ml.DTrees;
-import org.bytedeco.javacpp.opencv_ml.EM;
-import org.bytedeco.javacpp.opencv_ml.KNearest;
-import org.bytedeco.javacpp.opencv_ml.LogisticRegression;
-import org.bytedeco.javacpp.opencv_ml.NormalBayesClassifier;
-import org.bytedeco.javacpp.opencv_ml.RTrees;
-import org.bytedeco.javacpp.opencv_ml.SVM;
-import org.bytedeco.javacpp.opencv_ml.SVMSGD;
-import org.bytedeco.javacpp.opencv_ml.StatModel;
+import org.bytedeco.opencv.global.opencv_core;
+import org.bytedeco.opencv.opencv_core.*;
+import org.bytedeco.opencv.opencv_ml.*;
 
 import com.google.gson.Gson;
 import com.google.gson.GsonBuilder;

diff --git a/qupath-core-processing/src/test/java/qupath/opencv/processing/TypeAdaptersCVTest.java b/qupath-core-processing/src/test/java/qupath/opencv/processing/TypeAdaptersCVTest.java
@@ -3,13 +3,13 @@
 import static org.junit.Assert.*;
 
 import org.bytedeco.javacpp.PointerScope;
-import org.bytedeco.javacpp.opencv_core;
-import org.bytedeco.javacpp.opencv_core.Mat;
-import org.bytedeco.javacpp.opencv_core.Scalar;
-import org.bytedeco.javacpp.opencv_core.SparseMat;
-import org.bytedeco.javacpp.opencv_ml.EM;
-import org.bytedeco.javacpp.opencv_ml.StatModel;
-import org.bytedeco.javacpp.opencv_core.TermCriteria;
+import org.bytedeco.opencv.global.opencv_core;
+import org.bytedeco.opencv.opencv_core.Mat;
+import org.bytedeco.opencv.opencv_core.Scalar;
+import org.bytedeco.opencv.opencv_core.SparseMat;
+import org.bytedeco.opencv.opencv_ml.EM;
+import org.bytedeco.opencv.opencv_ml.StatModel;
+import org.bytedeco.opencv.opencv_core.TermCriteria;
 import org.junit.Test;
 
 import com.google.gson.GsonBuilder;

diff --git a/qupath-experimental/src/main/java/qupath/lib/classifiers/gui/PixelClassifierHelper.java b/qupath-experimental/src/main/java/qupath/lib/classifiers/gui/PixelClassifierHelper.java
@@ -1,9 +1,9 @@
 package qupath.lib.classifiers.gui;
 
-import org.bytedeco.javacpp.opencv_core;
-import org.bytedeco.javacpp.opencv_imgproc;
-import org.bytedeco.javacpp.opencv_ml;
-import org.bytedeco.javacpp.opencv_ml.TrainData;
+import org.bytedeco.opencv.global.opencv_core;
+import org.bytedeco.opencv.global.opencv_imgproc;
+import org.bytedeco.opencv.global.opencv_ml;
+import org.bytedeco.opencv.opencv_ml.TrainData;
 import org.bytedeco.javacpp.indexer.UByteIndexer;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -16,8 +16,10 @@
 import qupath.lib.images.servers.ImageChannel;
 import qupath.lib.images.servers.ImageServer;
 
-import org.bytedeco.javacpp.opencv_core.Mat;
-import org.bytedeco.javacpp.opencv_core.MatVector;
+import org.bytedeco.opencv.opencv_core.Mat;
+import org.bytedeco.opencv.opencv_core.MatVector;
+import org.bytedeco.opencv.opencv_core.Scalar;
+import org.bytedeco.opencv.opencv_core.Size;
 
 import qupath.lib.objects.PathAnnotationObject;
 import qupath.lib.objects.PathObject;
@@ -401,7 +403,7 @@ else if (boundaryStrategy == BoundaryStrategy.CLASSIFY_IGNORE) {
                         int heightFeatures = matFeaturesFull.rows();
                         int widthFeatures = matFeaturesFull.cols();
                         if (heightFeatures != matMask.rows() || widthFeatures != matMask.cols()) {
-                            opencv_imgproc.resize(matMask, matMask, new opencv_core.Size(widthFeatures, heightFeatures));
+                            opencv_imgproc.resize(matMask, matMask, new Size(widthFeatures, heightFeatures));
                         }
                         // Reshape mask to a column matrix
                         matMask.put(matMask.reshape(1, matMask.rows()*matMask.cols()));
@@ -427,7 +429,7 @@ else if (isArea)
                 }
                 if (matFeatures != null && !matFeatures.empty()) {
                     allFeatures.add(matFeatures.clone()); // Clone to be careful... not sure if normalization could impact this under adverse conditions
-                    Mat targets = new Mat(matFeatures.rows(), 1, opencv_core.CV_32SC1, opencv_core.Scalar.all(label));
+                    Mat targets = new Mat(matFeatures.rows(), 1, opencv_core.CV_32SC1, Scalar.all(label));
                     allTargets.add(targets);
                 }
             }

diff --git a/qupath-experimental/src/main/java/qupath/lib/classifiers/gui/PixelClassifierStatic.java b/qupath-experimental/src/main/java/qupath/lib/classifiers/gui/PixelClassifierStatic.java
@@ -10,12 +10,12 @@
 import org.bytedeco.javacpp.indexer.FloatIndexer;
 import org.bytedeco.javacpp.indexer.UByteIndexer;
 import org.bytedeco.javacpp.indexer.UShortIndexer;
-import org.bytedeco.javacpp.opencv_core;
-import org.bytedeco.javacpp.opencv_core.Mat;
-import org.bytedeco.javacpp.opencv_core.MatVector;
-import org.bytedeco.javacpp.opencv_core.Scalar;
-import org.bytedeco.javacpp.opencv_core.Size;
-import org.bytedeco.javacpp.opencv_imgproc;
+import org.bytedeco.opencv.global.opencv_core;
+import org.bytedeco.opencv.opencv_core.Mat;
+import org.bytedeco.opencv.opencv_core.MatVector;
+import org.bytedeco.opencv.opencv_core.Scalar;
+import org.bytedeco.opencv.opencv_core.Size;
+import org.bytedeco.opencv.global.opencv_imgproc;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 

diff --git a/qupath-experimental/src/main/java/qupath/lib/classifiers/opencv/Normalizer.java b/qupath-experimental/src/main/java/qupath/lib/classifiers/opencv/Normalizer.java
@@ -2,8 +2,8 @@
 
 import java.util.Arrays;
 
-import org.bytedeco.javacpp.opencv_core;
-import org.bytedeco.javacpp.opencv_core.Mat;
+import org.bytedeco.opencv.global.opencv_core;
+import org.bytedeco.opencv.opencv_core.Mat;
 import qupath.lib.analysis.stats.RunningStatistics;
 import qupath.lib.classifiers.Normalization;