v.0.3.3

ekatrukha · Nov 20, 2023 · c127fe6 · c127fe6
1 parent 1c9b617
commit c127fe6
Show file tree

Hide file tree

Showing 15 changed files with 95 additions and 128 deletions.
diff --git a/pom.xml b/pom.xml
@@ -5,13 +5,13 @@
 	<parent>
 		<groupId>org.scijava</groupId>
 		<artifactId>pom-scijava</artifactId>
-		<version>33.2.0</version>
+		<version>36.0.0</version>
 		<relativePath />
 	</parent>
 
 	<groupId>sc.fiji</groupId>
 	<artifactId>bigtrace</artifactId>
-	<version>0.3.2</version>
+	<version>0.3.3-SNAPSHOT</version>
 
 	<name>BigTrace</name>
 	<description>Tracing of curvilinear structures in 3D</description>
@@ -96,7 +96,7 @@
 		<dependency>
 		  <groupId>fiji.experimental</groupId>
 		  <artifactId>bvv-playground</artifactId>
-		  <version>0.0.9</version>
+		  <version>0.1.1</version>
 		</dependency>
 		<dependency>
 			<groupId>com.formdev</groupId>
@@ -119,7 +119,6 @@
 		<dependency>
 			<groupId>net.imglib2</groupId>
 			<artifactId>imglib2</artifactId>
-			<version>6.1.0</version>
 		</dependency>
 		<dependency>
 			<groupId>net.imglib2</groupId>

diff --git a/src/main/java/bigtrace/BigTrace.java b/src/main/java/bigtrace/BigTrace.java
@@ -1,9 +1,8 @@
-
 package bigtrace;
 
-
 import java.awt.Color;
 import java.awt.Component;
+import java.awt.Dimension;
 import java.awt.KeyboardFocusManager;
 import java.awt.event.WindowEvent;
 import java.awt.event.WindowListener;
@@ -27,41 +26,14 @@
 import com.formdev.flatlaf.FlatIntelliJLaf;
 import com.jogamp.opengl.GL3;
 
-import bdv.spimdata.SequenceDescriptionMinimal;
-import bdv.spimdata.SpimDataMinimal;
-import bdv.spimdata.XmlIoSpimDataMinimal;
-import bdv.tools.InitializeViewerState;
-import bdv.tools.transformation.TransformedSource;
-import bdv.util.AxisOrder;
-import bdv.util.Bounds;
-import bdv.viewer.Source;
-import bdv.viewer.SourceAndConverter;
-import bdv.viewer.TimePointListener;
-import bdv.viewer.ViewerState;
-import bigtrace.geometry.Cuboid3D;
-import bigtrace.geometry.Intersections3D;
-import bigtrace.geometry.Line3D;
-import bigtrace.gui.AnisotropicTransformAnimator3D;
-import bigtrace.math.OneClickTrace;
-import bigtrace.math.TraceBoxMath;
-import bigtrace.math.TracingBGVect;
-import bigtrace.rois.Box3D;
-import bigtrace.rois.LineTrace3D;
-import bigtrace.rois.Roi3D;
-import bigtrace.rois.RoiManager3D;
-import bigtrace.scene.VisPolyLineSimple;
-import bigtrace.volume.VolumeMisc;
-
-import btbvv.util.BvvStackSource;
 import ij.CompositeImage;
 import ij.IJ;
 import ij.ImageJ;
 import ij.ImagePlus;
 import ij.plugin.PlugIn;
 import ij.process.LUT;
+
 import mpicbg.spim.data.SpimDataException;
-import btbvv.util.BvvFunctions;
-import btbvv.util.Bvv;
 import net.imglib2.AbstractInterval;
 import net.imglib2.FinalInterval;
 import net.imglib2.FinalRealInterval;
@@ -71,7 +43,6 @@
 
 import net.imglib2.img.Img;
 
-import net.imglib2.img.array.ArrayImgs;
 import net.imglib2.img.display.imagej.ImageJFunctions;
 import net.imglib2.realtransform.AffineTransform3D;
 
@@ -83,11 +54,39 @@
 import net.imglib2.view.IntervalView;
 import net.imglib2.view.Views;
 
-import bvvbigtrace.example2.RenderData;
-import bvvbigtrace.example2.VolumeRenderer.RepaintType;
-import bvvbigtrace.example2.VolumeViewerPanel;
-import bvvbigtrace.util.MatrixMath;
+import bdv.spimdata.SequenceDescriptionMinimal;
+import bdv.spimdata.SpimDataMinimal;
+import bdv.spimdata.XmlIoSpimDataMinimal;
+import bdv.tools.InitializeViewerState;
+import bdv.tools.transformation.TransformedSource;
+import bdv.util.Bounds;
+import bdv.viewer.Source;
+import bdv.viewer.SourceAndConverter;
+import bdv.viewer.TimePointListener;
+import bdv.viewer.ViewerState;
 
+import btbvv.vistools.BvvFunctions;
+import btbvv.vistools.Bvv;
+import btbvv.vistools.BvvStackSource;
+import btbvv.core.render.RenderData;
+import btbvv.core.render.VolumeRenderer.RepaintType;
+import btbvv.btuitools.BvvGamma;
+import btbvv.core.VolumeViewerPanel;
+import btbvv.core.util.MatrixMath;
+
+import bigtrace.geometry.Cuboid3D;
+import bigtrace.geometry.Intersections3D;
+import bigtrace.geometry.Line3D;
+import bigtrace.gui.AnisotropicTransformAnimator3D;
+import bigtrace.math.OneClickTrace;
+import bigtrace.math.TraceBoxMath;
+import bigtrace.math.TracingBGVect;
+import bigtrace.rois.Box3D;
+import bigtrace.rois.LineTrace3D;
+import bigtrace.rois.Roi3D;
+import bigtrace.rois.RoiManager3D;
+import bigtrace.scene.VisPolyLineSimple;
+import bigtrace.volume.VolumeMisc;
 
 public class BigTrace < T extends RealType< T > > implements PlugIn, WindowListener, TimePointListener
 {
@@ -207,7 +206,6 @@ public void run(String arg)
 		} catch( Exception ex ) {
 		    System.err.println( "Failed to initialize LaF" );
 		}
-
 		//not sure we really need it, but anyway
         javax.swing.SwingUtilities.invokeLater(new Runnable() {
             public void run() {
@@ -772,10 +770,12 @@ public void actionToggleRender()
 		if(btdata.nRenderMethod==0)
 		{
 			btpanel.renderMethodPanel.cbRenderMethod.setSelectedIndex(1);
+			panel.showMessage("volumetric");
 		}
 		else
 		{
 			btpanel.renderMethodPanel.cbRenderMethod.setSelectedIndex(0);
+			panel.showMessage("maximum intensity");
 		}
 	}
 	public void installActions(final Actions actions)
@@ -791,7 +791,7 @@ public void installActions(final Actions actions)
 		actions.runnableAction(() -> actionZoomToPoint(),			"zoom in to click", "D" );
 		actions.runnableAction(() -> actionZoomOut(),				"center view (zoom out)", "C" );
 		actions.runnableAction(() -> actionResetCrop(),				"reset crop", "X" );
-		actions.runnableAction(() -> actionToggleRender(),			"toggle render mode", "P" );
+		actions.runnableAction(() -> actionToggleRender(),			"toggle render mode", "O" );
 		actions.runnableAction(() -> actionSelectRoi(),	            "select ROI", "E" );
 
 
@@ -1247,43 +1247,7 @@ public void initBVVSourcesImageJ()
 		Path p = Paths.get(btdata.sFileNameFullImg);
 		String filename = p.getFileName().toString();
 
-		/// "dummy" interval to init BVV
-		RandomAccessibleInterval< UnsignedByteType > empty_view;
-		// init bigvolumeviewer
-		final Img< UnsignedByteType > imgx = ArrayImgs.unsignedBytes( new long[]{ 2, 2, 2 } );
-		empty_view =				 
-				 Views.interval( imgx, new long[] { 0, 0, 0 }, new long[]{ 1, 1, 1 } );
-		/*
-		bvv_main = BvvFunctions.show( all_ch_RAI, "empty" ,Bvv.options().
-				dCam(btdata.dCam).
-				dClipNear(btdata.dClipNear).
-				dClipFar(btdata.dClipFar).				
-				renderWidth( BigTraceData.renderParams.nRenderW).
-				renderHeight( BigTraceData.renderParams.nRenderH).
-				numDitherSamples( BigTraceData.renderParams.numDitherSamples ).
-				cacheBlockSize( BigTraceData.renderParams.cacheBlockSize ).
-				maxCacheSizeInMB( BigTraceData.renderParams.maxCacheSizeInMB ).
-				ditherWidth(BigTraceData.renderParams.ditherWidth).
-				frameTitle(filename)
-				);*/
-		/*
-		bvv_main = BvvFunctions.show( all_ch_RAI, "empty" ,Bvv.options().
-				dCam(btdata.dCam).
-				dClipNear(btdata.dClipNear).
-				dClipFar(btdata.dClipFar).				
-				renderWidth( BigTraceData.renderParams.nRenderW).
-				renderHeight( BigTraceData.renderParams.nRenderH).
-				numDitherSamples( BigTraceData.renderParams.numDitherSamples ).
-				cacheBlockSize( BigTraceData.renderParams.cacheBlockSize ).
-				maxCacheSizeInMB( BigTraceData.renderParams.maxCacheSizeInMB ).
-				ditherWidth(BigTraceData.renderParams.ditherWidth).
-				frameTitle(filename)
-				);
-		
-		*/
-		//imgx
-		bvv_main = BvvFunctions.show( imgx, "empty" ,Bvv.options().
-		//bvv_main = BvvFunctions.show( empty_view, "empty" ,Bvv.options().
+		Bvv Tempbvv = BvvFunctions.show( Bvv.options().
 				dCam(btdata.dCam).
 				dClipNear(btdata.dClipNear).
 				dClipFar(btdata.dClipFar).				
@@ -1299,10 +1263,8 @@ public void initBVVSourcesImageJ()
 
 	for(int i=0;i<sources.size();i++)
 		{
-		//bvv_main.getSources()
-
-			//bvv_sources.add(BvvFunctions.show( sources.get(i), "ch_"+Integer.toString(i+1), Bvv.options().addTo(bvv_main)));
-			bvv_sources.add(BvvFunctions.show( Views.hyperSlice(all_ch_RAI,4,i), "ch_"+Integer.toString(i+1), Bvv.options().addTo(bvv_main)));			
+
+			bvv_sources.add(BvvFunctions.show( Views.hyperSlice(all_ch_RAI,4,i), "ch_"+Integer.toString(i+1), Bvv.options().addTo(Tempbvv)));
 			if(nBitDepth<=8)
 			{
 				bvv_sources.get(i).setDisplayRangeBounds(0, 255);
@@ -1319,9 +1281,9 @@ public void initBVVSourcesImageJ()
 			bvv_sources.get(i).setRenderType(btdata.nRenderMethod);
 
 		}
-		bvv_main.removeFromBdv();
+
 		bvv_main = bvv_sources.get(0);
-		//
+
 		panel = bvv_main.getBvvHandle().getViewerPanel();
 	}
 
@@ -1369,14 +1331,11 @@ public void initBVVSourcesHDF5()
 			}
 			(( TransformedSource< ? > ) source.getSpimSource() ).setIncrementalTransform(transform);	 
 		}
+
 		BigTraceData.dMinVoxelSize = Math.min(Math.min(BigTraceData.globCal[0], BigTraceData.globCal[1]), BigTraceData.globCal[2]);
-		double [] minmaxBrightness = initBrightnessBVV( 0.001, 0.999, panel.state() );
+
+		BvvGamma.initBrightness( 0.001, 0.999, panel.state(), panel.getConverterSetups());
 
-		for(int i=0;i<bvv_sources.size();i++)
-		{
-			bvv_sources.get(i).setDisplayRange(minmaxBrightness[0], minmaxBrightness[1]);
-			bvv_sources.get(i).setAlphaRange(minmaxBrightness[0], minmaxBrightness[1]);
-		}
 	}
 
 	public void setInitialTransform()

diff --git a/src/main/java/bigtrace/BigTraceControlPanel.java b/src/main/java/bigtrace/BigTraceControlPanel.java
@@ -36,7 +36,7 @@
 import bigtrace.measure.RoiMeasure3D;
 import bigtrace.rois.RoiManager3D;
 import bigtrace.BigTraceData;
-import btbvv.util.BvvStackSource;
+import btbvv.vistools.BvvStackSource;
 import ij.Prefs;
 import net.imglib2.FinalRealInterval;
 import net.imglib2.realtransform.AffineTransform3D;

diff --git a/src/main/java/bigtrace/BigTraceData.java b/src/main/java/bigtrace/BigTraceData.java
@@ -19,7 +19,7 @@
 public class BigTraceData < T extends RealType< T > > {
 
 	/** current plugin version **/
-	public static String sVersion = "0.3.2";
+	public static String sVersion = "0.3.3";
 
 	/** plugin instanse **/
 	BigTrace<T> bt;

diff --git a/src/main/java/bigtrace/BigTraceRenderSettings.java b/src/main/java/bigtrace/BigTraceRenderSettings.java
@@ -7,7 +7,7 @@
 import ij.Prefs;
 
 
-@Plugin(type = Command.class, menuPath = "Plugins>BigTrace 0.3.2>Render Settings")
+@Plugin(type = Command.class, menuPath = "Plugins>BigTrace 0.3.3>Render Settings")
 public class BigTraceRenderSettings implements Command {
 
 	@Parameter( label = "Render width" )

diff --git a/src/main/java/bigtrace/gui/BCsettings.java b/src/main/java/bigtrace/gui/BCsettings.java
@@ -1,7 +1,7 @@
 package bigtrace.gui;
 
-import btbvv.tools.RealARGBColorGammaConverterSetup;
-import btbvv.util.BvvStackSource;
+import btbvv.btuitools.RealARGBColorGammaConverterSetup;
+import btbvv.vistools.BvvStackSource;
 
 /** class to store and apply broghtness and contrast settings **/
 public class BCsettings {

diff --git a/src/main/java/bigtrace/math/OneClickTrace.java b/src/main/java/bigtrace/math/OneClickTrace.java
@@ -24,7 +24,6 @@
 import net.imglib2.img.array.ArrayImgs;
 import net.imglib2.img.basictypeaccess.array.FloatArray;
 import net.imglib2.type.numeric.RealType;
-import net.imglib2.type.numeric.integer.UnsignedByteType;
 import net.imglib2.type.numeric.real.FloatType;
 import net.imglib2.util.Intervals;
 import net.imglib2.util.LinAlgHelpers;

diff --git a/src/main/java/bigtrace/rois/Box3D.java b/src/main/java/bigtrace/rois/Box3D.java
@@ -14,7 +14,6 @@
 import bigtrace.scene.VisPointsScaled;
 import bigtrace.scene.VisPolyLineSimple;
 import net.imglib2.AbstractInterval;
-import net.imglib2.FinalInterval;
 import net.imglib2.Interval;
 import net.imglib2.RealPoint;
 

diff --git a/src/main/java/bigtrace/rois/RoiManager3D.java b/src/main/java/bigtrace/rois/RoiManager3D.java
@@ -1,7 +1,5 @@
 package bigtrace.rois;
 
-
-
 import java.awt.Color;
 
 import java.awt.Dimension;
@@ -42,22 +40,25 @@
 import com.jogamp.opengl.GL3;
 
 import bdv.tools.brightness.ColorIcon;
+
+import ij.Prefs;
+import ij.io.OpenDialog;
+import ij.io.SaveDialog;
+import net.imglib2.RealPoint;
+
 import bigtrace.BigTrace;
 import bigtrace.BigTraceData;
 import bigtrace.geometry.Line3D;
 import bigtrace.gui.GuiMisc;
 import bigtrace.gui.NumberField;
 import bigtrace.gui.PanelTitle;
 import bigtrace.measure.RoiMeasure3D;
-import ij.Prefs;
-import ij.io.OpenDialog;
-import ij.io.SaveDialog;
-import net.imglib2.RealPoint;
 
 
 public class RoiManager3D extends JPanel implements ListSelectionListener, ActionListener {
 
 
+	 @SuppressWarnings("rawtypes")
 	 BigTrace bt;
 
 	 private static final long serialVersionUID = -2843907862066423151L;
@@ -81,7 +82,8 @@ public class RoiManager3D extends JPanel implements ListSelectionListener, Actio
 	 public boolean bShowAll = true;
 
 	 //MEASURE OBJECT
-	 public RoiMeasure3D roiMeasure = null;
+	 @SuppressWarnings("rawtypes")
+	public RoiMeasure3D roiMeasure = null;
 
 	 //GUI
 	 public DefaultListModel<String> listModel; 
@@ -558,8 +560,13 @@ public void draw(final GL3 gl, final Matrix4fc pvm,  final int[] screen_size)
 	       int nShift;
 	       float fOpacityScale = 1.0f;
 	       float fOpacitySave = 1.0f;
-	       final int nMinF = (int)Math.min(0,BigTraceData.timeFade);
-	       final int nMaxF = (int)Math.max(0,BigTraceData.timeFade);
+	       int nMinF = (int)Math.min(0,BigTraceData.timeFade);
+	       int nMaxF = (int)Math.max(0,BigTraceData.timeFade);
+	       if(BigTraceData.timeRender==0)
+	       {
+		       nMinF = 0;
+		       nMaxF = 0;
+	       }
 
 	       for (i=0;i<rois.size();i++) 
 	       {
@@ -843,6 +850,7 @@ private void fireActiveRoiChanged(int nRoi)
 			l.activeRoiChanged(nRoi);
 	}
 
+	@SuppressWarnings("unchecked")
 	@Override
 	public void valueChanged(ListSelectionEvent e) 
 	{
@@ -876,6 +884,7 @@ public void valueChanged(ListSelectionEvent e)
     }
 
 	//buttons
+	@SuppressWarnings("unchecked")
 	@Override
 	public void actionPerformed(ActionEvent e) 
 	{
@@ -1622,6 +1631,7 @@ public void dialProperties()
 	}
 
 	/** Save ROIS dialog and saving **/
+	@SuppressWarnings("unchecked")
 	public void diagSaveROIs()
 	{
 		String filename;