Merge branch 'master' of https://github.com/Bobafotz/clijx-1

Author: Bobafotz

pom.xml

@@ -8,13 +8,13 @@
 	<parent>
 		<groupId>net.haesleinhuepf</groupId>
 		<artifactId>clij-parent-pom</artifactId>
-		<version>2.1.4.0</version>
+		<version>2.1.4.10</version>
 		<relativePath />
 	</parent>
 
 	<groupId>net.haesleinhuepf</groupId>
 	<artifactId>clijx_</artifactId>
-	<version>0.29.4.7</version>
+	<version>0.29.4.10</version>
 
 	<name>clijx_</name>
 	<description>clijx</description>

src/main/java/net/haesleinhuepf/clijx/jython/CLIJxAutoComplete.java

@@ -2,8 +2,11 @@
 
 import ij.IJ;
 import ij.ImagePlus;
+import ij.ImageStack;
 import ij.gui.Overlay;
+import ij.gui.PolygonRoi;
 import ij.gui.Roi;
+import ij.gui.TextRoi;
 import ij.macro.Interpreter;
 import ij.measure.ResultsTable;
 import ij.plugin.frame.RoiManager;
@@ -87,19 +90,24 @@ private ScriptingAutoCompleteProvider() {
             addCompletion(basicCompletion);
         }
 
-        addClassToAutoCompletion(CLIJOps.class, "clij.op().");
-        addClassToAutoCompletion(CLIJ.class, "clij.");
+        //addClassToAutoCompletion(CLIJOps.class, "clij.op().");
+        //addClassToAutoCompletion(CLIJ.class, "clij.");
         addClassToAutoCompletion(ClearCLBuffer.class, "buffer.");
 
         addClassToAutoCompletion(ImagePlus.class, "imp.");
+        addClassToAutoCompletion(ImageStack.class, "is.");
         addClassToAutoCompletion(ImageProcessor.class, "ip.");
         addClassToAutoCompletion(IJ.class, "IJ.");
         addClassToAutoCompletion(Roi.class, "roi.");
+        addClassToAutoCompletion(TextRoi.class, "textroi.");
+        addClassToAutoCompletion(PolygonRoi.class, "polygonroi.");
+
         addClassToAutoCompletion(RoiManager.class, "rm.");
         addClassToAutoCompletion(Color.class, "Color.");
         addClassToAutoCompletion(Overlay.class, "overlay.");
         addClassToAutoCompletion(ResultsTable.class, "table.");
 
+        addClassToAutoCompletion(List.class, "list.");
 
         addClassToAutoCompletion(ArrayImgs.class, "ArrayImgs.");
         addClassToAutoCompletion(Cursor.class, "cursor.");
@@ -109,6 +117,9 @@ private ScriptingAutoCompleteProvider() {
         addClassToAutoCompletion(Views.class, "Views.");
         addClassToAutoCompletion(Regions.class, "Regions.");
         addClassToAutoCompletion(ImageJFunctions.class, "ImageJFunctions.");
+
+
+
     }
 
     private void addClassToAutoCompletion(Class c, String prefix) {

src/main/java/net/haesleinhuepf/clijx/jython/ScriptingAutoCompleteProvider.java

@@ -0,0 +1,8 @@
+package net.haesleinhuepf.clijx.legacy;
+
+public class FallBackCLIJMacroPluginService extends net.haesleinhuepf.clij2.legacy.FallBackCLIJMacroPluginService {
+
+    public FallBackCLIJMacroPluginService() {
+        FallBackCLIJMacroPluginServiceInitializer.initialize(this);
+    }
+}

src/main/java/net/haesleinhuepf/clijx/legacy/FallBackCLIJMacroPluginService.java

@@ -13,7 +13,7 @@
  * Author: @haesleinhuepf
  *         November 2019
  */
-
+@Deprecated
 @Plugin(type = CLIJMacroPlugin.class, name = "CLIJx_absoluteInplace")
 public class AbsoluteInplace extends AbstractCLIJxPlugin implements CLIJMacroPlugin, CLIJOpenCLProcessor, OffersDocumentation {
 
@@ -22,6 +22,7 @@ public boolean executeCL() {
         return absoluteInplace(getCLIJx(), (ClearCLBuffer) args[0]);
     }
 
+    @Deprecated
     public static boolean absoluteInplace(CLIJx clijx, ClearCLBuffer input_output) {
         ClearCLBuffer buffer = clijx.create(input_output);
         clijx.copy(input_output, buffer);
@@ -38,7 +39,8 @@ public String getParameterHelpText() {
 
     @Override
     public String getDescription() {
-        return "Computes the absolute value of every individual pixel x in a given image.\n\n<pre>f(x) = |x| </pre>";
+        return "Computes the absolute value of every individual pixel x in a given image.\n\n<pre>f(x) = |x| </pre>\n\n" +
+                "Deprecated: Use absolute() instead.";
     }
 
     @Override

src/main/java/net/haesleinhuepf/clijx/legacy/FallBackCLIJMacroPluginServiceInitializer.java

@@ -18,6 +18,7 @@
  * Author: @haesleinhuepf
  *         November 2019
  */
+@Deprecated
 @Plugin(type = CLIJMacroPlugin.class, name = "CLIJx_automaticThresholdInplace")
 public class AutomaticThresholdInplace extends AbstractCLIJxPlugin implements CLIJMacroPlugin, CLIJOpenCLProcessor, OffersDocumentation {
 
@@ -31,6 +32,7 @@ public boolean executeCL() {
         return true;
     }
 
+    @Deprecated
     public static boolean automaticThresholdInplace(CLIJx clijx, ClearCLBuffer src_dst, String userSelectedMethod) {
         ClearCLBuffer buffer = clijx.create(src_dst);
         clijx.copy(src_dst, buffer);
@@ -46,7 +48,8 @@ public String getDescription() {
         doc.append("The automatic thresholder utilizes the threshold methods from ImageJ on a histogram determined on \n" +
                 "the GPU to create binary images as similar as possible to ImageJ 'Apply Threshold' method. Enter one \n" +
                 "of these methods in the method text field:\n" +
-                Arrays.toString(AutoThresholder.getMethods()) );
+                Arrays.toString(AutoThresholder.getMethods()) + "\n\n" +
+                "Deprecated: Use threshold* instead.");
         return doc.toString();
     }
 

src/main/java/net/haesleinhuepf/clijx/plugins/AbsoluteInplace.java

@@ -17,6 +17,7 @@
 
 import java.util.HashMap;
 
+@Deprecated
 @Plugin(type = CLIJMacroPlugin.class, name = "CLIJx_bilateral")
 public class Bilateral extends AbstractCLIJxPlugin implements CLIJMacroPlugin, CLIJOpenCLProcessor, OffersDocumentation, HasAuthor, IsCategorized {
 
@@ -31,6 +32,7 @@ public boolean executeCL() {
         return result;
     }
 
+    @Deprecated
     public static boolean bilateral(CLIJ2 clij2, ClearCLBuffer input, ClearCLBuffer output, Integer radiusX, Integer radiusY, Integer radiusZ, Float sigma_intensity, Float sigma_space) {
         HashMap<String, Object> parameters = new HashMap<>();
         parameters.put("input", input);
@@ -50,7 +52,8 @@ public static boolean bilateral(CLIJ2 clij2, ClearCLBuffer input, ClearCLBuffer
 
     @Override
     public String getDescription() {
-        return "Applies a bilateral filter using a box neighborhood with sigma weights for space and intensity to the input image.";
+        return "Applies a bilateral filter using a box neighborhood with sigma weights for space and intensity to the input image.\n\n" +
+                "Deprecated: Use SimpleITK bilateral() instead.";
     }
 
     @Override

src/main/java/net/haesleinhuepf/clijx/plugins/AutomaticThresholdInplace.java

@@ -12,6 +12,7 @@
  * Author: @haesleinhuepf
  * 12 2018
  */
+@Deprecated
 @Plugin(type = CLIJMacroPlugin.class, name = "CLIJx_blurBuffers3D")
 public class BlurBuffers3D extends AbstractCLIJPlugin implements CLIJMacroPlugin, CLIJOpenCLProcessor, OffersDocumentation {
 

src/main/java/net/haesleinhuepf/clijx/plugins/Bilateral.java

@@ -13,6 +13,7 @@
  * Author: @haesleinhuepf
  * 12 2018
  */
+@Deprecated
 @Plugin(type = CLIJMacroPlugin.class, name = "CLIJx_blurImages3D")
 public class BlurImages3D extends AbstractCLIJPlugin implements CLIJMacroPlugin, CLIJOpenCLProcessor, OffersDocumentation {
 

src/main/java/net/haesleinhuepf/clijx/plugins/BlurBuffers3D.java

@@ -13,6 +13,7 @@
  * Author: @haesleinhuepf
  * 12 2018
  */
+@Deprecated
 @Plugin(type = CLIJMacroPlugin.class, name = "CLIJx_blurInplace3D")
 public class BlurInplace3D extends AbstractCLIJPlugin implements CLIJMacroPlugin, CLIJOpenCLProcessor, OffersDocumentation {
 

src/main/java/net/haesleinhuepf/clijx/plugins/BlurImages3D.java

@@ -28,6 +28,7 @@
  * Author: @haesleinhuepf
  * 06 2019
  */
+@Deprecated
 @Plugin(type = CLIJMacroPlugin.class, name = "CLIJx_connectedComponentsLabelingInplace")
 public class ConnectedComponentsLabelingInplace extends AbstractCLIJxPlugin implements CLIJMacroPlugin, CLIJOpenCLProcessor, OffersDocumentation {
 
@@ -41,6 +42,7 @@ public boolean executeCL() {
         return result;
     }
 
+    @Deprecated
     public static boolean connectedComponentsLabelingInplace(CLIJx clijx, ClearCLBuffer output) {
         ClearCLImage temp1 = clijx.create(output.getDimensions(), ImageChannelDataType.Float);
         ClearCLImage temp2 = clijx.create(output.getDimensions(), ImageChannelDataType.Float);
@@ -121,7 +123,8 @@ public String getParameterHelpText() {
 
     @Override
     public String getDescription() {
-        return "Performs connected components analysis to a binary image and generates a label map.";
+        return "Performs connected components analysis to a binary image and generates a label map.\n\n" +
+                "Deprecated: Use connectedComponentsLabelingBox() instead.";
     }
 
     @Override

src/main/java/net/haesleinhuepf/clijx/plugins/BlurInplace3D.java

@@ -16,7 +16,7 @@
  * Author: @haesleinhuepf
  *         March 2020
  */
-
+@Deprecated
 @Plugin(type = CLIJMacroPlugin.class, name = "CLIJx_customBinaryOperation")
 public class CustomBinaryOperation extends AbstractCLIJxPlugin implements CLIJMacroPlugin, CLIJOpenCLProcessor, OffersDocumentation {
 
@@ -25,6 +25,7 @@ public boolean executeCL() {
         return customBinaryOperation(getCLIJx(), (ClearCLBuffer) args[0], (ClearCLBuffer) args[1], (String)args[2]);
     }
 
+    @Deprecated
     private static boolean customBinaryOperation(CLIJx clijx, ClearCLImageInterface image1, ClearCLImageInterface image2, String openCLCode) {
         HashMap<String, Object> parameters = new HashMap<>();
         parameters.put("image1", image1);
@@ -52,7 +53,8 @@ public String getParameterHelpText() {
 
     @Override
     public String getDescription() {
-        return "Executes custom OpenCL code on a pair of images.";
+        return "Executes custom OpenCL code on a pair of images.\n\n" +
+                "Deprecated: Use customOperation() instead.";
     }
 
     @Override

src/main/java/net/haesleinhuepf/clijx/plugins/ConnectedComponentsLabelingInplace.java

@@ -8,7 +8,7 @@
 import net.haesleinhuepf.clij.macro.CLIJOpenCLProcessor;
 import net.haesleinhuepf.clij.macro.documentation.OffersDocumentation;
 import org.scijava.plugin.Plugin;
-
+@Deprecated
 @Plugin(type = CLIJMacroPlugin.class, name = "CLIJx_differenceOfGaussianInplace3D")
 public class DifferenceOfGaussianInplace3D extends AbstractCLIJPlugin implements CLIJMacroPlugin, CLIJOpenCLProcessor, OffersDocumentation {
 
@@ -26,6 +26,7 @@ public boolean executeCL() {
         return result;
     }
 
+    @Deprecated
     public static boolean differenceOfGaussianInplace3D(CLIJ clij, ClearCLBuffer input_output, Float sigma1x, Float sigma1y, Float sigma1z, Float sigma2x, Float sigma2y, Float sigma2z) {
 
         ClearCLBuffer temp1 = clij.create(input_output);
@@ -44,7 +45,8 @@ public static boolean differenceOfGaussianInplace3D(CLIJ clij, ClearCLBuffer inp
     @Override
     public String getDescription() {
         return "Applies Gaussian blur to the input image twice with different sigma values resulting in two images which are then subtracted from each other.\n\n" +
-                "It is recommended to apply this operation to images of type Float (32 bit) as results might be negative.";
+                "It is recommended to apply this operation to images of type Float (32 bit) as results might be negative.\n\n" +
+                "Deprecated: Use differenceOfGaussian3D instead.";
     }
 
     @Override

src/main/java/net/haesleinhuepf/clijx/plugins/CustomBinaryOperation.java

@@ -16,7 +16,7 @@
 
 import java.util.HashMap;
 
-
+@Deprecated
 @Plugin(type = CLIJMacroPlugin.class, name = "CLIJx_gaussJordan")
 public class GaussJordan extends AbstractCLIJPlugin implements CLIJMacroPlugin, CLIJOpenCLProcessor, OffersDocumentation, HasAuthor, HasLicense, IsCategorized {
 

src/main/java/net/haesleinhuepf/clijx/plugins/DifferenceOfGaussianInplace3D.java

@@ -31,15 +31,18 @@ public boolean executeCL() {
 
     public static boolean rigidTransform(CLIJ2 clij2, ClearCLBuffer pushed, ClearCLBuffer result, Float translation_x, Float translation_y, Float translation_z, Float rotation_x, Float rotation_y, Float rotation_z) {
 
-        String transform = getTransform(translation_x, translation_y, translation_z, rotation_x, rotation_y, rotation_z);
-
-        clij2.affineTransform3D(pushed, result, transform);
-
+        if (pushed.getDimension() == 2) {
+            String transform = getTransform2D(translation_x, translation_y, translation_z, rotation_x, rotation_y, rotation_z);
+            clij2.affineTransform2D(pushed, result, transform);
+        } else {
+            String transform = getTransform3D(translation_x, translation_y, translation_z, rotation_x, rotation_y, rotation_z);
+            clij2.affineTransform3D(pushed, result, transform);
+        }
         return true;
     }
 
 
-    public static String getTransform(Float translation_x, Float translation_y, Float translation_z, Float rotation_x, Float rotation_y, Float rotation_z) {
+    public static String getTransform3D(Float translation_x, Float translation_y, Float translation_z, Float rotation_x, Float rotation_y, Float rotation_z) {
             return
                     "-center" +
                             " translateX=" + translation_x +
@@ -51,6 +54,15 @@ public static String getTransform(Float translation_x, Float translation_y, Floa
                             " center";
     }
 
+    public static String getTransform2D(Float translation_x, Float translation_y, Float translation_z, Float rotation_x, Float rotation_y, Float rotation_z) {
+        return
+                "-center" +
+                        " translateX=" + translation_x +
+                        " translateY=" + translation_y +
+                        " rotate=" + rotation_z +
+                        " center";
+    }
+
     @Override
     public String getDescription() {
         return "Applies a rigid transform using linear interpolation to an image stack.";

src/main/java/net/haesleinhuepf/clijx/plugins/GaussJordan.java

@@ -23,6 +23,7 @@
  * Author: @haesleinhuepf
  *         March 2020
  */
+@Deprecated
 @Plugin(type = CLIJMacroPlugin.class, name = "CLIJx_skeletonize")
 public class Skeletonize extends AbstractCLIJ2Plugin implements CLIJMacroPlugin, CLIJOpenCLProcessor, OffersDocumentation, HasAuthor, HasLicense, IsCategorized {
 
@@ -31,6 +32,7 @@ public boolean executeCL() {
         return skeletonize(getCLIJ2(), (ClearCLBuffer)( args[0]), (ClearCLBuffer)(args[1]));
     }
 
+    @Deprecated
     public static boolean skeletonize(CLIJ2 clij2, ClearCLBuffer src, ClearCLBuffer dst) {
         assertDifferent(src, dst);
         if (!checkDimensions(src.getDimension(), src.getDimension(), dst.getDimension())) {
@@ -111,7 +113,8 @@ public String getParameterHelpText() {
 
     @Override
     public String getDescription() {
-        return "Erodes a binary image until just its skeleton is left. \n\nThe result is similar to Skeletonize3D in Fiji.";
+        return "Erodes a binary image until just its skeleton is left. \n\nThe result is similar to Skeletonize3D in Fiji.\n\n" +
+                "Deprecated: Use SimpleITK binaryThinning() instead.";
     }
 
     @Override

src/main/java/net/haesleinhuepf/clijx/plugins/RigidTransform.java

@@ -10,6 +10,7 @@
 import net.haesleinhuepf.clijx.utilities.AbstractCLIJxPlugin;
 import org.scijava.plugin.Plugin;
 
+@Deprecated
 @Plugin(type = CLIJMacroPlugin.class, name = "CLIJx_subtractBackground2D")
 public class SubtractBackground2D extends AbstractCLIJxPlugin implements CLIJMacroPlugin, CLIJOpenCLProcessor, OffersDocumentation {
 
@@ -44,7 +45,8 @@ public static boolean subtractBackground(CLIJx clijx, ClearCLImageInterface inpu
 
     @Override
     public String getDescription() {
-        return "Applies Gaussian blur to the input image and subtracts the result from the original image.";
+        return "Applies Gaussian blur to the input image and subtracts the result from the original image.\n\n" +
+                "Deprecated: Use topHat() or differenceOfGaussian() instead.";
     }
 
     @Override

src/main/java/net/haesleinhuepf/clijx/plugins/Skeletonize.java

@@ -10,6 +10,7 @@
 import net.haesleinhuepf.clijx.utilities.AbstractCLIJxPlugin;
 import org.scijava.plugin.Plugin;
 
+@Deprecated
 @Plugin(type = CLIJMacroPlugin.class, name = "CLIJx_subtractBackground3D")
 public class SubtractBackground3D extends AbstractCLIJxPlugin implements CLIJMacroPlugin, CLIJOpenCLProcessor, OffersDocumentation {
 
@@ -44,7 +45,8 @@ public static boolean subtractBackground(CLIJx clijx, ClearCLImageInterface inpu
 
     @Override
     public String getDescription() {
-        return "Applies Gaussian blur to the input image and subtracts the result from the original image.";
+        return "Applies Gaussian blur to the input image and subtracts the result from the original image.\n\n" +
+                "Deprecated: Use topHat() or differenceOfGaussian() instead.";
     }
 
     @Override

src/main/java/net/haesleinhuepf/clijx/plugins/SubtractBackground2D.java

@@ -12,6 +12,7 @@
 import net.haesleinhuepf.clijx.CLIJx;
 import org.scijava.plugin.Plugin;
 
+@Deprecated
 @Plugin(type = CLIJMacroPlugin.class, name = "CLIJx_subtractGaussianBackground")
 public class SubtractGaussianBackground extends AbstractCLIJ2Plugin implements CLIJMacroPlugin, CLIJOpenCLProcessor, OffersDocumentation, IsCategorized {
     @Override
@@ -39,7 +40,8 @@ public static boolean subtractGaussianBackground(CLIJ2 clij2, ClearCLImageInterf
 
     @Override
     public String getDescription() {
-        return "Applies Gaussian blur to the input image and subtracts the result from the original image.";
+        return "Applies Gaussian blur to the input image and subtracts the result from the original image.\n\n" +
+                "Deprecated: Use differenceOfGaussian() instead.";
     }
 
     @Override

src/main/java/net/haesleinhuepf/clijx/plugins/SubtractBackground3D.java

@@ -21,6 +21,7 @@
  * Author: @haesleinhuepf
  *         December 2019
  */
+@Deprecated
 @Plugin(type = CLIJMacroPlugin.class, name = "CLIJx_topHatOctagon")
 public class TopHatOctagon extends AbstractCLIJxPlugin implements CLIJMacroPlugin, CLIJOpenCLProcessor, OffersDocumentation, IsCategorized {