add scaling of output images according to input image spatial calibra…

…tion
biovoxxel · Feb 3, 2023 · d58e52c · d58e52c
1 parent 3d63b25
commit d58e52c
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Showing 13 changed files with 45 additions and 27 deletions.
diff --git a/BioVoxxel_3D_Box/.classpath b/BioVoxxel_3D_Box/.classpath
@@ -13,7 +13,11 @@
 			<attribute name="test" value="true"/>
 		</attributes>
 	</classpathentry>
-	<classpathentry kind="src" path="src/main/resources/luts"/>
+	<classpathentry excluding="**" kind="src" output="target/classes" path="src/main/resources/luts">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
 	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8">
 		<attributes>
 			<attribute name="maven.pomderived" value="true"/>

diff --git a/BioVoxxel_3D_Box/pom.xml b/BioVoxxel_3D_Box/pom.xml
@@ -2,7 +2,7 @@
 	<modelVersion>4.0.0</modelVersion>
 	<groupId>de.biovoxxel</groupId>
 	<artifactId>bv3dbox</artifactId>
-	<version>1.13.4</version>
+	<version>1.14.2</version>
 
 	<name>BioVoxxel 3D Box</name>
 	<inceptionYear>2021</inceptionYear>

diff --git a/BioVoxxel_3D_Box/src/main/java/de/biovoxxel/bv3dbox/gui/BV_NeighborAnalysisGUI.java b/BioVoxxel_3D_Box/src/main/java/de/biovoxxel/bv3dbox/gui/BV_NeighborAnalysisGUI.java
@@ -80,7 +80,8 @@ public void run() {
 
 		ImagePlus neighborCountMapImp = BV3DBoxUtilities.pullImageFromGPU(neighborAnalysis.getCurrentCLIJ2Instance(), neighbor_image, false, LutNames.GEEN_FIRE_BLUE_LUT);
 		neighborCountMapImp.setTitle(WindowManager.getUniqueName("NeighborCount_" + inputImagePlus.getTitle()));
-
+		System.out.println("Calibration = " + inputImagePlus.getCalibration());
+		neighborCountMapImp.setCalibration(inputImagePlus.getCalibration());
 		neighborCountMapImp.show();
 
 		if (plotNeighborCount) {

diff --git a/BioVoxxel_3D_Box/src/main/java/de/biovoxxel/bv3dbox/gui/BV_ObjectInspectorGUI.java b/BioVoxxel_3D_Box/src/main/java/de/biovoxxel/bv3dbox/gui/BV_ObjectInspectorGUI.java
@@ -91,6 +91,9 @@ public class BV_ObjectInspectorGUI extends DynamicCommand {
 			+ "	 This however introduces a certain bias and error in any analysis and should be used with care or only in test cases.")
 	private Boolean pad_stack_tops = false;
 
+	@Parameter(required = false, label = "Display results tables", description = "")
+	private Boolean display_results_tables = true;
+
 	@Parameter(required = false, label = "Show analysis label map", description = "")
 	private Boolean display_analyzed_label_maps = false;
 
@@ -137,7 +140,8 @@ public void run() {
 		bvoi.setSecondaryVolumeRange(secondary_volume_range);
 		bvoi.setSecondaryMMDTCRRange(secondary_MMER_range);
 		bvoi.setEdgeExclusion(exclude_primary_objects_on_edges);
-		bvoi.setOutputImageFlags(display_analyzed_label_maps, show_count_map);
+		bvoi.padStackTops(pad_stack_tops);
+		bvoi.setOutputImageFlags(display_results_tables, display_analyzed_label_maps, show_count_map);
 
 		bvoi.inspect();
 	}

diff --git a/...3D_Box/src/main/java/de/biovoxxel/bv3dbox/plugins/BV_ConvolutedBackgroundSubtraction.java b/...3D_Box/src/main/java/de/biovoxxel/bv3dbox/plugins/BV_ConvolutedBackgroundSubtraction.java
@@ -2,7 +2,6 @@
 
 import de.biovoxxel.bv3dbox.utilities.BV3DBoxUtilities;
 import ij.ImagePlus;
-import ij.WindowManager;
 import net.haesleinhuepf.clij.clearcl.ClearCLBuffer;
 import net.haesleinhuepf.clij2.CLIJ2;
 

diff --git a/BioVoxxel_3D_Box/src/main/java/de/biovoxxel/bv3dbox/plugins/BV_FlatFieldCorrection.java b/BioVoxxel_3D_Box/src/main/java/de/biovoxxel/bv3dbox/plugins/BV_FlatFieldCorrection.java
@@ -267,7 +267,7 @@ public void flatFieldCorrection() {
 
 			if (showDebugImages) {
 
-				BV3DBoxUtilities.pullAndDisplayImageFromGPU(clij2, corrected_image, false, LutNames.GRAY);
+				BV3DBoxUtilities.pullAndDisplayImageFromGPU(clij2, corrected_image, false, LutNames.GRAY, originalImagePlus.getCalibration());
 
 			}
 
@@ -288,6 +288,7 @@ public void flatFieldCorrection() {
 
 		correctedImagePlus.setTitle(WindowManager.getUniqueName("FFCorr_" + originalImagePlus.getTitle()));
 		correctedImagePlus.getProcessor().resetMinAndMax();
+		correctedImagePlus.setCalibration(originalImagePlus.getCalibration());
 		correctedImagePlus.show();
 	}
 

diff --git a/BioVoxxel_3D_Box/src/main/java/de/biovoxxel/bv3dbox/plugins/BV_NeighborAnalysis.java b/BioVoxxel_3D_Box/src/main/java/de/biovoxxel/bv3dbox/plugins/BV_NeighborAnalysis.java
@@ -57,7 +57,8 @@ public class BV_NeighborAnalysis {
 
 	private LogService log = new StderrLogService();
 	private PrefService prefs = new DefaultPrefService();
-	private Boolean displayDebugImages = prefs.getBoolean(BV3DBoxSettings.class, "bv_3d_box_settings_display_debug_images", false);
+//	private Boolean displayDebugImages = prefs.getBoolean(BV3DBoxSettings.class, "bv_3d_box_settings_display_debug_images", false);
+	private Boolean displayDebugImages = false;
 	private CLIJ2 clij2;
 	private ClearCLBuffer connectedComponentLabels;
 
@@ -126,7 +127,7 @@ public ClearCLBuffer getNeighborCountMap(ClearCLBuffer input_image, String metho
 
 			clij2.excludeLabelsOutsideSizeRange(size_limited_label_image, input_image, minSize, maxSize);
 
-			if(displayDebugImages) { BV3DBoxUtilities.pullAndDisplayImageFromGPU(clij2, input_image, true, LutNames.GLASBEY_LUT); }
+			if(displayDebugImages) { BV3DBoxUtilities.pullAndDisplayImageFromGPU(clij2, input_image, true, LutNames.GLASBEY_LUT, null); }
 
 			size_limited_label_image.close();
 		} 
@@ -138,7 +139,7 @@ public ClearCLBuffer getNeighborCountMap(ClearCLBuffer input_image, String metho
 
 		clij2.extendLabelingViaVoronoi(input_image, voronoi_image);
 
-		if (displayDebugImages) { BV3DBoxUtilities.pullAndDisplayImageFromGPU(clij2, voronoi_image, false, LutNames.GLASBEY_LUT); }
+		if (displayDebugImages) { BV3DBoxUtilities.pullAndDisplayImageFromGPU(clij2, voronoi_image, false, LutNames.GLASBEY_LUT, null); }
 
 		if (method.equals(NeighborMethods.OBJECTS.method)) {
 
@@ -289,7 +290,7 @@ public static void main(String[] args) {
 
 		ImagePlus neighborCountMapImp = BV3DBoxUtilities.pullImageFromGPU(neighborAnalysis.getCurrentCLIJ2Instance(), neighbor_image, false, LutNames.GEEN_FIRE_BLUE_LUT);
 		neighborCountMapImp.setTitle(WindowManager.getUniqueName("NeighborCount_" + inputImagePlus.getTitle()));
-
+		neighborCountMapImp.setCalibration(inputImagePlus.getCalibration());
 		neighborCountMapImp.show();
 
 		if (plotNeighborCount) {

diff --git a/BioVoxxel_3D_Box/src/main/java/de/biovoxxel/bv3dbox/plugins/BV_ObjectInspector.java b/BioVoxxel_3D_Box/src/main/java/de/biovoxxel/bv3dbox/plugins/BV_ObjectInspector.java
@@ -81,6 +81,7 @@ public class BV_ObjectInspector implements Cancelable {
 	private String secondary_MMER_range = "0.00-1.00";
 	private Boolean exclude_primary_objects_on_edges = true;
 	private Boolean pad_stack_tops = false;
+	private Boolean display_results_tables = true;
 	private Boolean display_analyzed_label_maps = false;
 	private Boolean show_count_map = false;
 
@@ -191,7 +192,8 @@ public void padStackTops(boolean pad_stack_tops) {
 	 * @param display_analyzed_label_maps
 	 * @param show_count_map
 	 */
-	public void setOutputImageFlags(boolean display_analyzed_label_maps, boolean show_count_map) {
+	public void setOutputImageFlags(boolean display_results_tables, boolean display_analyzed_label_maps, boolean show_count_map) {
+		this.display_results_tables = display_results_tables;
 		this.display_analyzed_label_maps = display_analyzed_label_maps;
 		this.show_count_map = show_count_map;
 	}
@@ -215,6 +217,7 @@ public void inspect() {
 		log.debug("secondary_MMDTCR_range = " + secondary_MMER_range);
 		log.debug("exclude_primary_objects_on_edges = " + exclude_primary_objects_on_edges);
 		log.debug("pad_stack_tops = " + pad_stack_tops);
+		log.debug("display_results_tables = " + display_results_tables);
 		log.debug("display_analyzed_label_maps = " + display_analyzed_label_maps);
 		log.debug("show_count_map = " + show_count_map);
 		log.debug("------------------------------------------------------");
@@ -474,7 +477,7 @@ public void inspect() {
 		final_primary_results_table.setColumn("SEC_OBJECT_COUNT", secondaryObjectCountArray);
 
 		if (show_count_map) {
-			BV3DBoxUtilities.pullAndDisplayImageFromGPU(clij2, overlapCountMap, true, LutNames.GEEN_FIRE_BLUE_LUT);	//test output			
+			BV3DBoxUtilities.pullAndDisplayImageFromGPU(clij2, overlapCountMap, true, LutNames.GEEN_FIRE_BLUE_LUT, voxel_calibration);	//test output			
 		}
 		overlapCountMap.close();
 
@@ -585,8 +588,8 @@ public void inspect() {
 
 
 		if (display_analyzed_label_maps) {
-			BV3DBoxUtilities.pullAndDisplayImageFromGPU(clij2, finalLabels_1, true, LutNames.GLASBEY_LUT);
-			BV3DBoxUtilities.pullAndDisplayImageFromGPU(clij2, finalLabels_2, true, LutNames.GLASBEY_LUT);
+			BV3DBoxUtilities.pullAndDisplayImageFromGPU(clij2, finalLabels_1, true, LutNames.GLASBEY_LUT, voxel_calibration);
+			BV3DBoxUtilities.pullAndDisplayImageFromGPU(clij2, finalLabels_2, true, LutNames.GLASBEY_LUT, voxel_calibration);
 		}
 		finalLabels_1.close();
 		finalLabels_2.close();
@@ -677,8 +680,10 @@ public void inspect() {
 
 		secondary_original_measurements_table = null;
 
-		final_primary_results_table.show(PRIMARY_RESULTS_TABLE_NAME);	
-		final_secondary_results_table.show(SECONDARY_RESULTS_TABLE_NAME);
+		if (display_results_tables) {
+			final_primary_results_table.show(PRIMARY_RESULTS_TABLE_NAME);	
+			final_secondary_results_table.show(SECONDARY_RESULTS_TABLE_NAME);			
+		}
 
 		clij2.clear();
 	}

diff --git a/BioVoxxel_3D_Box/src/main/java/de/biovoxxel/bv3dbox/plugins/BV_OverlapExtractor.java b/BioVoxxel_3D_Box/src/main/java/de/biovoxxel/bv3dbox/plugins/BV_OverlapExtractor.java
@@ -227,7 +227,7 @@ public void extract() {
 			ClearCLBuffer percent_volume_vector = clij2.push(percent_volume_image);
 			percent_volume_map.setName("%volume_" + image_plus_2.getTitle());
 			clij2.generateParametricImage(image_1_CCL, percent_volume_vector, percent_volume_map);
-			BV3DBoxUtilities.pullAndDisplayImageFromGPU(clij2, percent_volume_map, true, LutNames.GEEN_FIRE_BLUE_LUT);
+			BV3DBoxUtilities.pullAndDisplayImageFromGPU(clij2, percent_volume_map, true, LutNames.GEEN_FIRE_BLUE_LUT, image_plus_1.getCalibration());
 			percent_volume_map.close();
 			percent_volume_vector.close();
 		}
@@ -237,7 +237,7 @@ public void extract() {
 			ClearCLBuffer kept_image_1_CCL = clij2.create(image_1_CCL);
 			kept_image_1_CCL.setName("extracted_" + image_plus_1.getTitle());
 			clij2.excludeLabels(flag_list_vector, image_1_CCL, kept_image_1_CCL);		
-			BV3DBoxUtilities.pullAndDisplayImageFromGPU(clij2, kept_image_1_CCL, true, LutNames.GEEN_FIRE_BLUE_LUT);
+			BV3DBoxUtilities.pullAndDisplayImageFromGPU(clij2, kept_image_1_CCL, true, LutNames.GEEN_FIRE_BLUE_LUT, image_plus_1.getCalibration());
 			flag_list_vector.close();
 			kept_image_1_CCL.close();
 

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
@@ -62,7 +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();
+//	private BV_LabelSeparator bvls = new BV_LabelSeparator();
 
 	/**
 	 * 

diff --git a/...oxxel_3D_Box/src/main/java/de/biovoxxel/bv3dbox/plugins/BV_PseudoFlatFieldCorrection.java b/...oxxel_3D_Box/src/main/java/de/biovoxxel/bv3dbox/plugins/BV_PseudoFlatFieldCorrection.java
@@ -1,7 +1,5 @@
 package de.biovoxxel.bv3dbox.plugins;
 
-import java.awt.Point;
-
 import org.scijava.Cancelable;
 import org.scijava.log.LogLevel;
 import org.scijava.log.LogService;
@@ -14,7 +12,6 @@
 import de.biovoxxel.bv3dbox.utilities.BV3DBoxUtilities.LutNames;
 import ij.ImagePlus;
 import ij.WindowManager;
-import ij.gui.ImageWindow;
 import ij.measure.Calibration;
 import net.haesleinhuepf.clij.clearcl.ClearCLBuffer;
 import net.haesleinhuepf.clij.coremem.enums.NativeTypeEnum;
@@ -165,8 +162,7 @@ public void runCorrection(float radius, boolean force2D, boolean showBackgroundI
 
 		outputImagePlus.setImage(tempOutputImagePlus);
 		outputImagePlus.setTitle(outputImageName);
-		//ImageWindow inputImageWindow = inputImagePlus.getWindow();
-		//Point inputImageLocation = inputImageWindow.getLocationOnScreen();
+		outputImagePlus.setCalibration(inputImagePlus.getCalibration());
 		outputImagePlus.show();
 		//outputImagePlus.getWindow().setLocation(inputImageLocation.x + inputImageWindow.getWidth() + 10, inputImageLocation.y);
 		BV3DBoxUtilities.adaptImageDisplay(inputImagePlus, outputImagePlus);

diff --git a/BioVoxxel_3D_Box/src/main/java/de/biovoxxel/bv3dbox/plugins/BV_ThresholdCheck.java b/BioVoxxel_3D_Box/src/main/java/de/biovoxxel/bv3dbox/plugins/BV_ThresholdCheck.java
@@ -233,19 +233,20 @@ public void applyThreshold(double thresholdValue) {
 
 			ImagePlus outputImagePlus = clij2.pullBinary(outputImage);
 			outputImagePlus.setTitle(outputImageName);
+			outputImagePlus.setCalibration(inputImagePlus.getCalibration());
 			outputImagePlus.show();
 
 		} else if (outputImageStyle.equals("0/1")) {
 
 			outputImage.setName(outputImageName);
-			BV3DBoxUtilities.pullAndDisplayImageFromGPU(clij2, outputImage, true, LutNames.GRAY);
+			BV3DBoxUtilities.pullAndDisplayImageFromGPU(clij2, outputImage, true, LutNames.GRAY, inputImagePlus.getCalibration());
 
 		} else {
 
 			ClearCLBuffer labelOutputImage = clij2.create(outputImage.getDimensions(), NativeTypeEnum.Float);
 			clij2.connectedComponentsLabelingBox(outputImage, labelOutputImage);
 			labelOutputImage.setName(outputImageName);
-			BV3DBoxUtilities.pullAndDisplayImageFromGPU(clij2, labelOutputImage, true, LutNames.GLASBEY_LUT);
+			BV3DBoxUtilities.pullAndDisplayImageFromGPU(clij2, labelOutputImage, true, LutNames.GLASBEY_LUT, inputImagePlus.getCalibration());
 			labelOutputImage.close();
 
 		}

diff --git a/BioVoxxel_3D_Box/src/main/java/de/biovoxxel/bv3dbox/utilities/BV3DBoxUtilities.java b/BioVoxxel_3D_Box/src/main/java/de/biovoxxel/bv3dbox/utilities/BV3DBoxUtilities.java
@@ -174,7 +174,7 @@ public static String[] extendImageTitleListWithNone() {
 	}
 
 
-	public static void pullAndDisplayImageFromGPU(CLIJ2 clij2, ClearCLBuffer imageToShow, boolean autoContrast, LutNames lutName) {
+	public static void pullAndDisplayImageFromGPU(CLIJ2 clij2, ClearCLBuffer imageToShow, boolean autoContrast, LutNames lutName, Calibration cal) {
 
 		ImagePlus imagePlusToBePulled = clij2.pull(imageToShow);
 		imagePlusToBePulled.setTitle(imageToShow.getName());
@@ -198,6 +198,12 @@ public static void pullAndDisplayImageFromGPU(CLIJ2 clij2, ClearCLBuffer imageTo
 		} else {
 			imagePlusToBePulled.resetDisplayRange();			
 		}
+
+		System.out.println("Calubration = " + cal);
+		if (cal != null) {
+			imagePlusToBePulled.setCalibration(cal);
+		}
+
 		imagePlusToBePulled.show();
 
 	}