update to recent CLIJx-API

README.md

@@ -8,11 +8,11 @@ Right now, this is very preliminary.
 
 ## Installation
 Download the following files, removed the numbers from their file endings and put them all in a folder:
-* [clatlab-0.4.0.jar](https://github.com/clij/clatlab/releases/download/0.4.0/clatlab-0.4.0.jar)
+* [clatlab-0.5.0.jar](https://github.com/clij/clatlab/releases/download/0.5.0/clatlab-0.5.0.jar)
 * [bridj-0.7.0.jar](https://sites.imagej.net/clij/jars/bridj-0.7.0.jar-20181201213334)
-* [clij_1.4.0.jar](https://github.com/clij/clij/releases/download/1.4.0/clij_-1.4.0.jar)
-* [clij-clearcl-0.10.0.jar](https://github.com/clij/clij/releases/download/1.4.0/clij-clearcl-0.10.0.jar)
-* [clij-core-1.4.0.jar](https://github.com/clij/clij/releases/download/1.4.0/clij-core-1.4.0.jar)
+* [clij_1.4.2.jar](https://github.com/clij/clij/releases/download/1.4.2/clij_-1.4.2.jar)
+* [clij-clearcl-0.10.1.jar](https://github.com/clij/clij/releases/download/1.4.2/clij-clearcl-0.10.1.jar)
+* [clij-core-1.4.2.jar](https://github.com/clij/clij/releases/download/1.4.2/clij-core-1.4.2.jar)
 * [clij-coremem-0.6.0.jar](https://github.com/clij/clij/releases/download/1.4.0/clij-coremem-0.6.0.jar)
 * [clij-legacy_-0.1.0.jar](https://github.com/clij/clij-legacy/releases/download/0.1.0/clij-legacy_-0.1.0.jar)
 * [imagej-common-0.28.2.jar](https://sites.imagej.net/Java-8/jars/imagej-common-0.28.2.jar-20190516211613)
@@ -22,7 +22,9 @@ Download the following files, removed the numbers from their file endings and pu
 * [scijava-common-2.77.0.jar](https://sites.imagej.net/Java-8/jars/scijava-common-2.76.1.jar-20181204141527)
 * [ij-1.52p.jar](https://sites.imagej.net/Java-8/jars/ij-1.52p.jar-20190701230425)
 * [imglib2-ij-2.0.0-beta-44.jar](https://sites.imagej.net/Java-8/jars/imglib2-ij-2.0.0-beta-44.jar-20181204141527)
-* [clij-advanced-filters_-0.11.0.jar](https://github.com/clij/clij-advanced-filters/releases/download/0.11.0/clij-advanced-filters_-0.11.0.jar)
+* [clij-advanced-filters_-0.12.4.jar](https://github.com/clij/clij-advanced-filters/releases/download/0.12.4/clij-advanced-filters_-0.12.4.jar)
+* [fiji-lib-2.1.2.jar](https://sites.imagej.net/Java-8/jars/fiji-lib-2.1.2.jar-20170530201750)
+
 
 In your matlab script, specify _every_ individual jar file in this folder using `javaaddpath('folder/jarfile.jar'). 
 It is recommended to do this in a utility function as [demonstrated here](https://github.com/clij/clatlab/blob/master/src/main/matlab/init_clatlab.m).

pom.xml

@@ -12,7 +12,7 @@
 
 	<groupId>net.haesleinhuepf</groupId>
 	<artifactId>clatlab</artifactId>
-	<version>0.4.0</version>
+	<version>0.5.0</version>
 	<name>CLATLAB</name>
 	<description>CLIJ bridge to Matlab</description>
 
@@ -27,12 +27,12 @@
 		<dependency>
 			<groupId>net.haesleinhuepf</groupId>
 			<artifactId>clij-core</artifactId>
-			<version>1.4.0</version>
+			<version>1.4.2</version>
 		</dependency>
 		<dependency>
 			<groupId>net.haesleinhuepf</groupId>
 			<artifactId>clij-advanced-filters_</artifactId>
-			<version>0.11.0</version>
+			<version>0.12.4</version>
 		</dependency>
 	</dependencies>
 

src/main/matlab/init_clatlab.m

@@ -17,11 +17,11 @@
     if (exist('net.haesleinhuepf.clatlab.CLATLAB') ~= 8)
         clatlab_folder = '../../../classpath/';
         javaaddpath(strcat(clatlab_folder, 'ij-1.52p.jar'));
-        javaaddpath(strcat(clatlab_folder, 'clatlab-0.4.0.jar'));
+        javaaddpath(strcat(clatlab_folder, 'clatlab-0.5.0.jar'));
         javaaddpath(strcat(clatlab_folder, 'bridj-0.7.0.jar'));
-        javaaddpath(strcat(clatlab_folder, 'clij_-1.4.0.jar'));
-        javaaddpath(strcat(clatlab_folder, 'clij-clearcl-0.10.0.jar'));
-        javaaddpath(strcat(clatlab_folder, 'clij-core-1.4.0.jar'));
+        javaaddpath(strcat(clatlab_folder, 'clij_-1.4.2.jar'));
+        javaaddpath(strcat(clatlab_folder, 'clij-clearcl-0.10.1.jar'));
+        javaaddpath(strcat(clatlab_folder, 'clij-core-1.4.2.jar'));
         javaaddpath(strcat(clatlab_folder, 'clij-coremem-0.6.0.jar'));
         javaaddpath(strcat(clatlab_folder, 'clij-legacy_-0.1.0.jar'));
         javaaddpath(strcat(clatlab_folder, 'imagej-common-0.28.2.jar'));
@@ -30,8 +30,8 @@
         javaaddpath(strcat(clatlab_folder, 'jocl-2.0.1.jar'));
         javaaddpath(strcat(clatlab_folder, 'scijava-common-2.76.1.jar'));
         javaaddpath(strcat(clatlab_folder, 'imglib2-ij-2.0.0-beta-44.jar'));
-        javaaddpath(strcat(clatlab_folder, 'clij-advanced-filters_-0.11.0.jar'));
-
+        javaaddpath(strcat(clatlab_folder, 'clij-advanced-filters_-0.12.4.jar'));
+        javaaddpath(strcat(clatlab_folder, 'fiji-lib-2.1.2.jar'));
         % import and initialize CLATLAB
 
 

src/main/matlab/segmentation.m

@@ -38,15 +38,16 @@
 blurred = clijx.create(input);
 thresholded = clijx.create(input);
 labelled = clijx.create(input);
+labelled_without_edges = clijx.create(input);
 
 % blur, threshold and label the image
 clijx.blur(input, blurred, 5, 5, 0);
 clijx.automaticThreshold(blurred, thresholded, "Otsu");
 clijx.connectedComponentsLabeling(thresholded, labelled);
-
+clijx.excludeLabelsOnEdges(labelled, labelled_without_edges);
 
 % pull result back from GPU and show it next to input
-result = clijx.pullMat(labelled);
+result = clijx.pullMat(labelled_without_edges);
 number_of_found_objects = clijx.maximumOfAllPixels(labelled);
 lookuptable = rand(number_of_found_objects, 3);
 subplot(1,2,2), imshow(result, lookuptable);
@@ -57,3 +58,5 @@
 thresholded.close();
 labelled.close();
 
+
+

src/main/matlab/spotDetection3D.m

@@ -92,7 +92,7 @@
 scatter3(points(1,:), points(2,:), points(3,:))
 
 % visualise data set as maximum projection
-maximumProjected = clx.create(processingSize(1:2), backgroundSubtracted.getNativeType());
+maximumProjected = clijx.create(processingSize(1:2), backgroundSubtracted.getNativeType());
 clijx.maximumZProjection(backgroundSubtracted, maximumProjected);
 figure
 imshow(clijx.pullMat(maximumProjected), [0 250]);
@@ -111,5 +111,6 @@
 z = points(3,:);
 tri = delaunay(x, y, z)
 %trimesh(tri, x, y, z);
+figure;
 trisurf(tri, x, y, z,'FaceAlpha',0.3)