Add Screenshot Stack Command, #1191

mobie · Nov 26, 2024 · cb1aa30 · cb1aa30
1 parent 9d3353c
commit cb1aa30
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Showing 2 changed files with 22 additions and 5 deletions.
diff --git a/pom.xml b/pom.xml
@@ -9,7 +9,7 @@
 
     <groupId>org.embl.mobie</groupId>
     <artifactId>mobie-viewer-fiji</artifactId>
-    <version>5.5.7-SNAPSHOT</version>
+    <version>5.5.7</version>
 
     <!-- mvn clean install -Dmaven.test.skip=true -Dscijava.app.directory=/Users/tischer/Desktop/Fiji/Fiji-MoBIE.app -->
     <!--  ../scijava-scripts/release-version.sh - -skip-version-check - -skip-license-update -->

diff --git a/src/main/java/org/embl/mobie/command/context/ScreenShotStackMakerCommand.java b/src/main/java/org/embl/mobie/command/context/ScreenShotStackMakerCommand.java
@@ -32,6 +32,7 @@
 import ij.IJ;
 import ij.ImagePlus;
 import ij.ImageStack;
+import ij.measure.Calibration;
 import net.imglib2.realtransform.AffineTransform3D;
 import net.imglib2.util.LinAlgHelpers;
 import org.embl.mobie.MoBIE;
@@ -82,14 +83,15 @@ public void run()
         System.out.println( screenToPhysicalScale );
 
         // move viewer to starting point
-        viewerTransform.translate( 0, 0, -numSlices * physicalSliceDistance * screenToPhysicalScale );
+        viewerTransform.translate( 0, 0, - numSlices * physicalSliceDistance * screenToPhysicalScale );
         bdvHandle.getViewerPanel().state().setViewerTransform( viewerTransform );
         bdvHandle.getViewerPanel().requestRepaint();
 
         // collect all slices
         ImageStack rgbStack = new ImageStack();
-        CompositeImage compositeImage = null; // TODO
+        ImageStack compositeStack = new ImageStack();
         numSlices = numSlices * 2 + 1;
+        Calibration calibration = null;
 
         for ( int sliceIndex = 0; sliceIndex < numSlices; sliceIndex++ )
         {
@@ -106,6 +108,13 @@ public void run()
             try
             {
                 rgbStack.addSlice( screenShotMaker.getRGBImagePlus().getProcessor() );
+                ImageStack stack = screenShotMaker.getCompositeImagePlus().getStack();
+                for ( int i = 0; i < stack.size(); i++ )
+                {
+                    compositeStack.addSlice( stack.getProcessor( i + 1 ) );
+                }
+
+                calibration = screenShotMaker.getRGBImagePlus().getCalibration();
             }
             catch ( Exception e )
             {
@@ -118,11 +127,19 @@ public void run()
             }
         }
 
+        bdvHandle.getViewerPanel().state().setViewerTransform( initialViewerTransform );
+        bdvHandle.getViewerPanel().requestRepaint();
+
+        calibration.pixelDepth = physicalSliceDistance;
+
         ImagePlus rgbImage = new ImagePlus( "RGB stack", rgbStack );
         rgbImage.setDimensions( 1, rgbStack.size(), 1 );
+        rgbImage.setCalibration( calibration );
         rgbImage.show();
 
-        bdvHandle.getViewerPanel().state().setViewerTransform( initialViewerTransform );
-        bdvHandle.getViewerPanel().requestRepaint();
+        CompositeImage compositeImage = new CompositeImage( new ImagePlus( "Composite stack", compositeStack ) );
+        compositeImage.setDimensions( compositeStack.size() / rgbStack.size(), rgbStack.size(), 1 );
+        compositeImage.setCalibration( calibration );
+        compositeImage.show();
     }
 }