Add new arch support

pom.xml

@@ -214,37 +214,97 @@
 			<artifactId>commons-io</artifactId>
 			<version>2.1</version>
 		</dependency>
+
+		<!-- https://mvnrepository.com/artifact/sc.fiji/bigwarp_fiji -->
+		<dependency>
+			<groupId>sc.fiji</groupId>
+			<artifactId>bigwarp_fiji</artifactId>
+			<version>9.3.0</version>
+		</dependency>
+
+		<dependency>
+			<groupId>org.janelia.saalfeldlab</groupId>
+			<artifactId>n5</artifactId>
+			<version>3.3.0</version>
+		</dependency>
+		<dependency>
+			<groupId>org.janelia.saalfeldlab</groupId>
+			<artifactId>n5-blosc</artifactId>
+			<version>1.1.1</version>
+		</dependency>
+		<dependency>
+			<groupId>org.janelia.saalfeldlab</groupId>
+			<artifactId>n5-ij</artifactId>
+			<version>4.2.5</version>
+			<exclusions>
+				<exclusion>
+					<groupId>net.imagej</groupId>
+					<artifactId>imagej</artifactId>
+				</exclusion>
+			</exclusions>
+		</dependency>
+		<dependency>
+			<groupId>org.janelia.saalfeldlab</groupId>
+			<artifactId>n5-imglib2</artifactId>
+			<version>7.0.2</version>
+		</dependency>
+		<dependency>
+			<groupId>org.janelia.saalfeldlab</groupId>
+			<artifactId>n5-aws-s3</artifactId>
+			<version>4.2.1</version>
+		</dependency>
+		<dependency>
+			<groupId>org.janelia.saalfeldlab</groupId>
+			<artifactId>n5-google-cloud</artifactId>
+			<version>3.3.2</version>
+		</dependency>
+		<dependency>
+			<groupId>org.janelia.saalfeldlab</groupId>
+			<artifactId>n5-viewer_fiji</artifactId>
+			<version>6.1.2</version>
+		</dependency>
+		<dependency>
+			<groupId>org.janelia.saalfeldlab</groupId>
+			<artifactId>n5-zarr</artifactId>
+			<version>1.3.5</version>
+		</dependency>
+		<dependency>
+			<groupId>org.janelia.saalfeldlab</groupId>
+			<artifactId>n5-universe</artifactId>
+			<version>1.6.0</version>
+		</dependency>
 	</dependencies>
-<!--
+
 	<build>
 		<plugins>
 			<plugin>
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-shade-plugin</artifactId>
 				<version>3.4.1</version>
-				<artifactId>maven-assembly-plugin</artifactId>
 				<configuration>
 					<appendAssemblyId>false</appendAssemblyId>
 					<archive>
 						<manifest>
 							<mainClass>com.ds4h.imagej.Image_Alignment</mainClass>
 						</manifest>
 					</archive>
+				<!--
 					<descriptorRefs>
 						<descriptorRef>jar-with-dependencies</descriptorRef>
 					</descriptorRefs>
+				-->
 				</configuration>
+
 				<executions>
 					<execution>
-						<id>make-assembly</id>  this is used for inheritance merges
-						<phase>package</phase>  bind to the packaging phase
+						<id>make-assembly</id>
+						<phase>package</phase>
 						<goals>
-							<goal>single</goal>
+							<goal>shade</goal>
 						</goals>
 					</execution>
 				</executions>
 			</plugin>
 		</plugins>
 	</build>
--->
 </project>

src/main/java/com/ds4h/controller/alignmentController/AlignmentControllerInterface.java

@@ -1,10 +1,10 @@
 package com.ds4h.controller.alignmentController;
 
-import com.ds4h.model.alignedImage.AlignedImage;
-import ij.CompositeImage;
+import com.drew.lang.annotations.NotNull;
+import com.ds4h.model.image.alignedImage.AlignedImage;
 import ij.ImagePlus;
+import org.bytedeco.opencv.presets.opencv_core;
 
-import java.awt.*;
 import java.util.List;
 
 /**
@@ -16,6 +16,7 @@ public interface AlignmentControllerInterface {
      * Returns the aligned images.
      * @return the aligned images.
      */
+    @NotNull
     public List<AlignedImage> getAlignedImages();
 
     /**
@@ -28,12 +29,14 @@ public interface AlignmentControllerInterface {
      * Returns the name of the algorithm.
      * @return the name of the algorithm.
      */
+    @NotNull
     public String name();
 
     /**
      * Returns all the aligned images as stack.
      * @return all the aligned images as stack,
      */
+    @NotNull
     public ImagePlus getAlignedImagesAsStack();
 
     /**

src/main/java/com/ds4h/controller/alignmentController/AutomaticAlignmentController/AutomaticAlignmentController.java

@@ -1,21 +1,17 @@
 package com.ds4h.controller.alignmentController.AutomaticAlignmentController;
 
+import com.drew.lang.annotations.NotNull;
 import com.ds4h.controller.alignmentController.AlignmentControllerInterface;
-import com.ds4h.controller.pointController.PointController;
-import com.ds4h.model.alignedImage.AlignedImage;
+import com.ds4h.controller.pointController.ImageManagerController;
+import com.ds4h.model.image.alignedImage.AlignedImage;
 import com.ds4h.model.alignment.Alignment;
 import com.ds4h.model.alignment.AlignmentEnum;
 import com.ds4h.model.alignment.alignmentAlgorithm.*;
 import com.ds4h.model.alignment.automatic.pointDetector.Detectors;
-import ij.IJ;
+import com.ds4h.model.util.ImageStackCreator;
 import ij.ImagePlus;
-import ij.ImageStack;
-import ij.process.ByteProcessor;
-import ij.process.ImageConverter;
 
-import java.awt.image.ColorModel;
 import java.util.*;
-import java.util.stream.Collectors;
 
 /**
  * This class is used in order to call all the Model methods of the SURF Alignment inside the view, without
@@ -42,6 +38,7 @@ public AutomaticAlignmentController(){
      * the collection can be empty if the alignment algorithm is not done.
      * @return the list with all the images aligned.
      */
+    @NotNull
     @Override
     public List<AlignedImage> getAlignedImages() {
         return alignment.alignedImages();
@@ -66,12 +63,14 @@ public void releaseImages(){
      * @throws IllegalArgumentException if one of the input is not correct.
      * @throws RuntimeException if during the alignment something happen.
      */
-    public void align(final AlignmentAlgorithm algorithm, final Detectors detector, final PointController pointManager) throws Exception{
+    public void align(@NotNull final AlignmentAlgorithm algorithm,
+                      @NotNull final Detectors detector,
+                      @NotNull final ImageManagerController pointManager) throws Exception{
 
-        if (!this.alignment.isAlive() && Objects.nonNull(pointManager) && Objects.nonNull(pointManager.getPointManager())) {
-            if (pointManager.getPointManager().getPointImages().size() > 1 && detector.getScaling() >= 1) {
+        if (!this.alignment.isAlive() && Objects.nonNull(pointManager) && Objects.nonNull(pointManager.getImageManager())) {
+            if (pointManager.getImageManager().getPointImages().size() > 1 && detector.getScaling() >= 1) {
                 try{
-                    this.alignment.alignImages(pointManager.getPointManager(), algorithm,
+                    this.alignment.alignImages(pointManager.getImageManager(), algorithm,
                             AlignmentEnum.AUTOMATIC,
                             Objects.requireNonNull(detector.pointDetector()),
                             detector.getThresholdFactor(),
@@ -100,6 +99,7 @@ public boolean isAlive(){
      * Returns the alignment name.
      * @return the alignment name.
      */
+    @NotNull
     @Override
     public String name() {
         return "AUTOMATIC";
@@ -110,36 +110,11 @@ public String name() {
      * @return all the aligned images as stack.
      * @throws RuntimeException if something goes wrong (there are no images, etc, etc..).
      */
+    @NotNull
     @Override
     public ImagePlus getAlignedImagesAsStack() throws RuntimeException{
         if(!this.getAlignedImages().isEmpty()){
-            final ImageStack stack = new ImageStack(this.getAlignedImages().get(0).getAlignedImage().getWidth(),
-                    this.getAlignedImages().get(0).getAlignedImage().getHeight(), ColorModel.getRGBdefault());
-            System.gc();
-            final List<AlignedImage> images = this.getAlignedImages();
-            //final LUT[] luts = new LUT[images.size()];
-            //int index = 0;
-            final int bitDepth = images.stream()
-                    .min(Comparator.comparingInt(img -> img.getAlignedImage().getBitDepth())).get().getAlignedImage().getBitDepth();
-            IJ.log("[ALIGNED STACK] Bit Depth: " + bitDepth);
-            for (final AlignedImage image : images) {
-                if(!(image.getAlignedImage().getProcessor() instanceof ByteProcessor)) {
-                    final ImageConverter imageConverter = new ImageConverter(image.getAlignedImage());
-                    imageConverter.convertToGray8();
-                    IJ.log("[STACK] " + (image.getAlignedImage().getProcessor() instanceof ByteProcessor));
-                }
-                //luts[index] = image.getAlignedImage().getProcessor().getLut();
-                IJ.log("[NAME] " + image.getName());
-                stack.addSlice(image.getName(), image.getAlignedImage().getProcessor());
-                //index++;
-            }
-            try {
-                //final CompositeImage composite = new CompositeImage(new ImagePlus("Aligned Stack", stack));
-                //composite.setLuts(luts);
-                return new ImagePlus("AlignedStack", stack);
-            }catch (Exception e){
-                throw new RuntimeException("Something went wrong with the creation of the stack.");
-            }
+            return ImageStackCreator.createImageStack(this.getAlignedImages());
         }
         throw new RuntimeException("The detection has failed, the number of points found can not be used with the selected \"Algorithm\".\n" +
                 "Please consider to expand the memory (by going to Edit > Options > Memory & Threads)\n" +
@@ -159,6 +134,7 @@ public int getStatus() {
      * Returns the algorithm.
      * @return the algorithm
      */
+    @NotNull
     public AlignmentAlgorithm getAlgorithm() {
         return this.algorithm;
     }
@@ -167,18 +143,17 @@ public AlignmentAlgorithm getAlgorithm() {
      * Set the algorithm to use.
      * @param algorithm the algorithm to use.
      */
-    public void setAlgorithm(final AlignmentAlgorithm algorithm){
-        if(Objects.nonNull(algorithm)) {
-            this.algorithm = algorithm;
-        }
+    public void setAlgorithm(@NotNull final AlignmentAlgorithm algorithm){
+        this.algorithm = algorithm;
     }
 
     /**
      * Returns the alignment algorithm.
      * @param algorithmEnum the selected algorithm.
      * @return the alignment algorithm.
      */
-    public AlignmentAlgorithm getAlgorithmFromEnum(final AlignmentAlgorithmEnum algorithmEnum){
+    @NotNull
+    public AlignmentAlgorithm getAlgorithmFromEnum(@NotNull final AlignmentAlgorithmEnum algorithmEnum){
         switch (algorithmEnum){
             case TRANSLATIONAL:
                 return this.translational;
@@ -189,10 +164,8 @@ public AlignmentAlgorithm getAlgorithmFromEnum(final AlignmentAlgorithmEnum algo
         }
         throw new IllegalArgumentException("Algorithm not present");
     }
+    @NotNull
     public Detectors[] getDetectors(){
-        if(System.getProperty("os.name").toLowerCase().contains("mac")){
-            return Arrays.stream(Detectors.values()).filter(d -> d != Detectors.SIFT).collect(Collectors.toList()).toArray(new Detectors[0]);
-        }
         return Detectors.values();
     }
-}
+}

src/main/java/com/ds4h/controller/alignmentController/ManualAlignmentController/ManualAlignmentController.java

@@ -1,18 +1,15 @@
 package com.ds4h.controller.alignmentController.ManualAlignmentController;
 
+import com.drew.lang.annotations.NotNull;
 import com.ds4h.controller.alignmentController.AlignmentControllerInterface;
-import com.ds4h.controller.pointController.PointController;
-import com.ds4h.model.alignedImage.AlignedImage;
+import com.ds4h.controller.pointController.ImageManagerController;
+import com.ds4h.model.image.alignedImage.AlignedImage;
 import com.ds4h.model.alignment.Alignment;
 import com.ds4h.model.alignment.AlignmentEnum;
 import com.ds4h.model.alignment.alignmentAlgorithm.*;
-import ij.IJ;
+import com.ds4h.model.util.ImageStackCreator;
 import ij.ImagePlus;
-import ij.ImageStack;
-import ij.process.ByteProcessor;
-import ij.process.ImageConverter;
 
-import java.awt.image.ColorModel;
 import java.util.LinkedList;
 import java.util.List;
 import java.util.Objects;
@@ -39,6 +36,7 @@ public ManualAlignmentController(){
      * Returns all the aligned images.
      * @return all the aligned images.
      */
+    @NotNull
     @Override
     public List<AlignedImage> getAlignedImages(){
         return new LinkedList<>(alignment.alignedImages());
@@ -48,26 +46,10 @@ public List<AlignedImage> getAlignedImages(){
      * Returns all the aligned images as stack.
      * @return all the aligned images as stack.
      */
+    @NotNull
     public ImagePlus getAlignedImagesAsStack(){
         if(!this.getAlignedImages().isEmpty()){
-            final ImageStack stack = new ImageStack(this.getAlignedImages().get(0).getAlignedImage().getWidth(), this.getAlignedImages().get(0).getAlignedImage().getHeight(), ColorModel.getRGBdefault());
-            System.gc();
-            final List<AlignedImage> images = this.getAlignedImages();
-            //LUT[] luts = new LUT[images.size()];
-            //int index = 0;
-            for (final AlignedImage image : images) {
-                if(!(image.getAlignedImage().getProcessor() instanceof ByteProcessor)) {
-                    final ImageConverter imageConverter = new ImageConverter(image.getAlignedImage());
-                    imageConverter.convertToGray8();
-                    IJ.log("[STACK] " + (image.getAlignedImage().getProcessor() instanceof ByteProcessor));
-                }
-                //luts[index] = image.getAlignedImage().getProcessor().getLut();
-                stack.addSlice(image.getName(),image.getAlignedImage().getProcessor());
-                //index++;
-            }
-            //final CompositeImage composite = new CompositeImage(new ImagePlus("Aligned_Stack", stack));
-            //composite.setLuts(luts);
-            return new ImagePlus("AlignedStack", stack);
+            return ImageStackCreator.createImageStack(this.getAlignedImages());
         }
         throw new RuntimeException("The detection has failed, the number of points found can not be used with the selected \"Algorithm\".\n" +
                 "Please consider to expand the memory (by going to Edit > Options > Memory & Threads)\n" +
@@ -96,6 +78,7 @@ public boolean isAlive() {
      * Returns the algorithm name.
      * @return the algorithm name.
      */
+    @NotNull
     @Override
     public String name() {
         return "MANUAL";
@@ -108,10 +91,10 @@ public String name() {
      * @param pointManager where all the images are stored.
      * @throws IllegalArgumentException if one of the parameters is not correct.
      */
-    public void align(final AlignmentAlgorithm algorithm, final PointController pointManager) throws IllegalArgumentException{
-        if(!this.alignment.isAlive() && Objects.nonNull(pointManager) && Objects.nonNull(pointManager.getPointManager())) {
-            if(pointManager.getPointManager().getPointImages().size() > 1) {
-                this.alignment.alignImages(pointManager.getPointManager(), algorithm, AlignmentEnum.MANUAL);
+    public void align(final AlignmentAlgorithm algorithm, final ImageManagerController pointManager) throws IllegalArgumentException{
+        if(!this.alignment.isAlive() && Objects.nonNull(pointManager) && Objects.nonNull(pointManager.getImageManager())) {
+            if(pointManager.getImageManager().getPointImages().size() > 1) {
+                this.alignment.alignImages(pointManager.getImageManager(), algorithm, AlignmentEnum.MANUAL);
             }else{
                 throw new IllegalArgumentException("For the alignment are needed at least TWO images.");
             }
@@ -176,4 +159,4 @@ public void setPointOverload(final PointOverloadEnum overload) {
     public void releaseImages(){
         this.alignment.clearList();
     }
-}
+}