add maxima sphere label splitting

biovoxxel · May 1, 2022 · 8d4aa44 · 8d4aa44
1 parent 84a50e2
commit 8d4aa44
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Showing 4 changed files with 30 additions and 14 deletions.
diff --git a/BioVoxxel_3D_Box/src/main/java/de/biovoxxel/bv3dbox/gui/BV_PostProcessorGUI.java b/BioVoxxel_3D_Box/src/main/java/de/biovoxxel/bv3dbox/gui/BV_PostProcessorGUI.java
@@ -14,6 +14,7 @@
 import ij.WindowManager;
 import net.haesleinhuepf.clij.clearcl.ClearCLBuffer;
 import net.haesleinhuepf.clij2.CLIJ2;
+import net.imagej.updater.UpdateService;
 
 /*
  * BSD 3-Clause License
@@ -88,8 +89,8 @@ public void run() {
 
 	private void setupImage() {
 
-		//BV3DBoxUtilities.displayMissingDependencyWarning(getContext().service(UpdateService.class), "clij,clij2");
-
+		BV3DBoxUtilities.displayMissingDependencyWarning(getContext().service(UpdateService.class), "clij,clij2,clijx-assistant,clijx-assistant-extensions,3D ImageJ Suite");
+				
 		bvpp = new BV_PostProcessor(inputImagePlus);
 
 		outputImageName = "BVPP_" + inputImagePlus.getTitle();
@@ -123,6 +124,8 @@ public void processImage() {
 		outputImagePlus.setTitle("BVPP_" + inputImagePlus.getTitle());
 		outputImagePlus.getProcessor().resetMinAndMax();
 		outputImagePlus.show();
+
+		BV3DBoxUtilities.adaptImageDisplay(inputImagePlus, outputImagePlus);
 	}
 
 	@SuppressWarnings("unused")

diff --git a/BioVoxxel_3D_Box/src/main/java/de/biovoxxel/bv3dbox/gui/BV_VoronoiThresholdLabelingGUI.java b/BioVoxxel_3D_Box/src/main/java/de/biovoxxel/bv3dbox/gui/BV_VoronoiThresholdLabelingGUI.java
@@ -80,7 +80,7 @@ public class BV_VoronoiThresholdLabelingGUI extends DynamicCommand {
 	@Parameter(label = "Threshold method", initializer = "thresholdMethodList", callback = "processImage")
 	private String thresholdMethod = "Default";
 
-	@Parameter(label = "Separation method", choices = {"None", "Maxima", "Eroded Maxima", "EDM Maxima", "DoG Seeds", "Eroded box", "Eroded sphere"}, callback = "processImage")
+	@Parameter(label = "Separation method", choices = {"None", "Maxima", "Eroded Maxima", "EDM Maxima", "Maxima Spheres", "DoG Seeds", "Eroded box", "Eroded sphere"}, callback = "processImage")
 	private String separationMethod = "Maxima";
 
 	@Parameter(label = "Spot sigma / Erosion", min = "0f", callback = "processImage")
@@ -137,7 +137,7 @@ public void run() {
 
 	private void setupImage() {
 
-		BV3DBoxUtilities.displayMissingDependencyWarning(getContext().service(UpdateService.class), "clij,clij2");
+		BV3DBoxUtilities.displayMissingDependencyWarning(getContext().service(UpdateService.class), "clij,clij2,clijx-assistant,clijx-assistant-extensions,3D ImageJ Suite");
 
 		bvvtl.setupInputImage(inputImagePlus);
 		input_image = bvvtl.getInputImageAsClearClBuffer();
@@ -280,6 +280,9 @@ private void processImage() {
 		case "EDM Maxima":
 			seed_image = labelSplitter.detectDistanceMapMaxima(thresholded_image, maximaRadius);
 			break;
+		case "Maxima Spheres":
+			seed_image = labelSplitter.createMaximaSpheres(thresholded_image, spotSigma, maximaRadius);
+			break;
 		case "DoG Seeds":
 			CLIJ2 clij2 = bvvtl.getCurrentCLIJ2Instance();
 			ClearCLBuffer binary_8_bit_image = clij2.create(thresholded_image);

diff --git a/BioVoxxel_3D_Box/src/main/java/de/biovoxxel/bv3dbox/plugins/BV_PostProcessor.java b/BioVoxxel_3D_Box/src/main/java/de/biovoxxel/bv3dbox/plugins/BV_PostProcessor.java
@@ -62,6 +62,7 @@ public class BV_PostProcessor extends DynamicCommand {
 	private final PrefService prefs = new DefaultPrefService();
 	private static CLIJ2 clij2;
 	private ClearCLBuffer input_image;
+	private BV_LabelSeparator bvls = new BV_LabelSeparator();
 
 	/**
 	 * 
@@ -136,7 +137,24 @@ public ClearCLBuffer postProcessor(String method, int iteration) {
 				clij2.dilateLabels(temp_eroded, output_image, iteration);
 				temp_eroded.close();
 				break;
-
+
+//			case "Close Label":
+//				ClearCLBuffer temp_dilated = clij2.create(input_image);
+//				
+//				clij2.dilateLabels(input_image, temp_dilated, iteration);
+//				
+//				ClearCLBuffer temp_splitted_labels = clij2.create(input_image);
+//				bvls.splitLabels(clij2, temp_dilated, temp_splitted_labels);
+//				temp_dilated.close();
+//				
+//				if (is3D) {
+//					clij2.minimum3DSphere(temp_splitted_labels, output_image, iteration, iteration, iteration);					
+//				} else {
+//					clij2.minimum2DSphere(temp_splitted_labels, output_image, iteration, iteration);
+//				}
+//				temp_splitted_labels.close();
+//				break;
+
 			case "Minimum (sphere)":
 				if (is3D) {
 					clij2.minimum3DSphere(input_image, output_image, iteration, iteration, iteration);					

diff --git a/BioVoxxel_3D_Box/src/main/java/de/biovoxxel/bv3dbox/plugins/BV_VoronoiThresholdLabeling.java b/BioVoxxel_3D_Box/src/main/java/de/biovoxxel/bv3dbox/plugins/BV_VoronoiThresholdLabeling.java
@@ -391,7 +391,6 @@ public ClearCLBuffer thresholdImage(ClearCLBuffer background_subtracted_image, S
 
 
 
-	//TODO: Outlines does not work as intended, since the gray LUT is not applied to the output image
 	public void createOutputImage(ClearCLBuffer output_image, String outputType) {
 		ImagePlus tempOutputImagePlus = null;
 
@@ -403,7 +402,7 @@ public void createOutputImage(ClearCLBuffer output_image, String outputType) {
 
 			ClearCLBuffer temp_output_image = clij2.create(input_image);
 			clij2.visualizeOutlinesOnOriginal(input_image, output_image, temp_output_image);
-			tempOutputImagePlus = BV3DBoxUtilities.pullImageFromGPU(clij2, temp_output_image, true, LutNames.GRAY);
+			tempOutputImagePlus = BV3DBoxUtilities.pullImageFromGPU(clij2, temp_output_image, true, LutNames.OUTLINE);
 			temp_output_image.close();
 		}
 
@@ -415,13 +414,6 @@ public void createOutputImage(ClearCLBuffer output_image, String outputType) {
 
 		outputImagePlus.setImage(tempOutputImagePlus);
 		outputImagePlus.setTitle(outputImageName);
-
-		if (outputType.equals("Binary") || outputType.equals("Outlines")) {
-			outputImagePlus.setLut(grays);
-		} else {
-			outputImagePlus.setLut(glasbey);
-		}
-
 		outputImagePlus.show();
 
 		BV3DBoxUtilities.adaptImageDisplay(inputImagePlus, outputImagePlus);