v.0.5.1

pom.xml

@@ -11,7 +11,7 @@
 
 	<groupId>nl.uu.science.cellbiology</groupId>
 	<artifactId>bigtrace</artifactId>
-	<version>0.5.1-SNAPSHOT</version>
+	<version>0.5.1</version>
 
 	<name>BigTrace</name>
 	<description>Tracing of curvilinear structures in 3D</description>

src/main/java/bigtrace/BigTrace.java

@@ -386,17 +386,17 @@ public void calcShowTraceBox(final LineTrace3D trace, final boolean bRefine)
 
 		if(trace.numVertices() == 1)
 		{
-			rangeTraceBox = VolumeMisc.getTraceBoxCentered(traceIV,btData.lTraceBoxSize, trace.vertices.get(0));
+			rangeTraceBox = VolumeMisc.getTraceBoxCentered(traceIV,btData.nTraceBoxSize, trace.vertices.get(0));
 		}
 		else
 		{
-			rangeTraceBox = getTraceBoxNext(traceIV,btData.lTraceBoxSize, btData.fTraceBoxAdvanceFraction, trace);
+			rangeTraceBox = getTraceBoxNext(traceIV,btData.nTraceBoxSize, btData.fTraceBoxAdvanceFraction, trace);
 		}
 
 		IntervalView<?> traceInterval = Views.interval(traceIV, rangeTraceBox);
 
 		//getCenteredView(traceInterval);
-		viewer.setTransformAnimator(getCenteredViewAnim(traceInterval,btData.dTraceBoxScreenFraction));
+		viewer.setTransformAnimator(getCenteredViewAnim(traceInterval,btData.fTraceBoxScreenFraction));
 		//long start1, end1;
 
 

src/main/java/bigtrace/BigTraceActions.java

@@ -397,7 +397,7 @@ public void actionZoomIn()
 			{
 				if(bt.findPointLocationFromClick(bt.btData.trace_weights,target))
 				{
-					FinalInterval zoomInterval = VolumeMisc.getZoomBoxCentered((long)(bt.btData.lTraceBoxSize*0.5), target);
+					FinalInterval zoomInterval = VolumeMisc.getZoomBoxCentered((long)(bt.btData.nTraceBoxSize*0.5), target);
 
 					bt.viewer.setTransformAnimator(bt.getCenteredViewAnim(zoomInterval,bt.btData.dZoomBoxScreenFraction));
 				}

src/main/java/bigtrace/BigTraceData.java

@@ -235,10 +235,10 @@ public class BigTraceData < T extends RealType< T > & NativeType< T > > {
 	public int nTraceBoxView = 1;
 
 	/** half size of tracing box (for now in all dimensions) **/
-	public long lTraceBoxSize;
+	public int nTraceBoxSize;
 
 	/** fraction of screen occupied by trace box **/
-	public double dTraceBoxScreenFraction;	
+	public float fTraceBoxScreenFraction;	
 
 	/** After advancing tracebox, this parameter defines 
 	 * how much tracebox is going to follow the last direction of trace (with respect to the last added point):
@@ -303,9 +303,9 @@ public BigTraceData(final BigTrace<T> bt_)
 		sigmaTrace[2] = Prefs.get("BigTrace.sigmaTraceZ", 3.0);
 		bTraceOnlyClipped = Prefs.get("BigTrace.bTraceOnlyClipped", false);
 
-		lTraceBoxSize =(long) Prefs.get("BigTrace.lTraceBoxSize", 50);				
+		nTraceBoxSize = (int) Prefs.get("BigTrace.nTraceBoxSize", 50);				
 		fTraceBoxAdvanceFraction = (float) Prefs.get("BigTrace.fTraceBoxAdvanceFraction", 0.9);
-		dTraceBoxScreenFraction = Prefs.get("BigTrace.dTraceBoxScreenFraction", 0.5);
+		fTraceBoxScreenFraction = (float)Prefs.get("BigTrace.fTraceBoxScreenFraction", 0.5);
 		gammaTrace =  Prefs.get("BigTrace.gammaTrace", 0.0);
 
 		//one-click

src/main/java/bigtrace/io/ROIsExportSWC.java

@@ -58,6 +58,21 @@ protected Void doInBackground() throws Exception {
 				String sRadius;
 				writer.write("#raw "+ bt.btData.sFileNameFullImg+"\n");
 				writer.write("#original_source BigTrace_ver_" +BigTraceData.sVersion+"\n");
+				writer.write( "#roi_shape_interpolation " );
+				switch (BigTraceData.shapeInterpolation)
+				{
+				case BigTraceData.SHAPE_Voxel:
+					writer.write("voxel\n");
+					break;
+				case BigTraceData.SHAPE_Smooth:
+					writer.write("smooth\n");
+					break;
+				case BigTraceData.SHAPE_Spline:
+					writer.write("spline\n");
+					break;
+				}
+				writer.write( "#smooth_window "+Integer.toString( BigTraceData.nSmoothWindow )+"\n" );
+
 				for(nRoi=0; nRoi<nRoiN; nRoi++)
 				{
 
@@ -96,7 +111,7 @@ protected Void doInBackground() throws Exception {
 				writer.close();
 			}
 			setProgress(100);
-			setProgressState("exporting curve ROIs done.");
+			setProgressState("SWC export curve ROIs done.");
 		} catch (IOException e) {	
 			IJ.log(e.getMessage());
 			//e.printStackTrace();
@@ -113,7 +128,7 @@ public void done()
     	bt.bInputLock = false;
     	bt.setLockMode(false);
 		setProgress(100);
-		setProgressState("export traces to SWC done.");
+		setProgressState("SWC export curve ROI done.");
     }
 
 

src/main/java/bigtrace/io/ROIsLoadBG.java

@@ -20,6 +20,7 @@
 import bigtrace.rois.Roi3D;
 import bigtrace.rois.Roi3DGroup;
 import bigtrace.rois.Roi3DGroupManager;
+import ij.Prefs;
 
 import net.imglib2.RealPoint;
 import net.imglib2.type.NativeType;
@@ -161,7 +162,28 @@ protected Void doInBackground() throws Exception {
 					  break;
 				  case "FrameInterval":
 					  bt.btData.dFrameInterval = Double.parseDouble(line_array[1]);
-					  break;					  
+					  break;	
+				  case "Intensity Interpolation":
+					  BigTraceData.intensityInterpolation =  Integer.parseInt( line_array[1] );
+					  Prefs.set("BigTrace.IntInterpolation",BigTraceData.intensityInterpolation);
+					  bt.btData.setInterpolationFactory();
+					  break;
+				  case "ROI Shape Interpolation":
+					  BigTraceData.shapeInterpolation =  Integer.parseInt( line_array[1] );
+					  Prefs.set("BigTrace.ShapeInterpolation",BigTraceData.shapeInterpolation);
+					  break;
+				  case "Rotation min frame type":
+					  BigTraceData.rotationMinFrame = Integer.parseInt( line_array[1] );
+					  Prefs.set("BigTrace.RotationMinFrame",BigTraceData.rotationMinFrame);
+					  break;
+				  case "Smooth window":
+					  BigTraceData.nSmoothWindow = Integer.parseInt( line_array[1] );
+					  Prefs.set("BigTrace.nSmoothWindow", BigTraceData.nSmoothWindow);
+					  break;
+				  case "Sector number":
+					  BigTraceData.sectorN = Integer.parseInt( line_array[1] );
+					  Prefs.set("BigTrace.nSectorN", BigTraceData.sectorN);
+					  break;	  
 				  case "BT_Roi":
 					  //Sleep for up to one second.
 					  try {

src/main/java/bigtrace/io/ROIsSaveBG.java

@@ -63,6 +63,11 @@ protected Void doInBackground() throws Exception {
 				writer.write("ImageVoxelDepth," + df3.format(BigTraceData.globCal[2]) + "\n");
 				writer.write("TimeUnits," + bt.btData.sTimeUnit + "\n");
 				writer.write("FrameInterval," + df3.format(bt.btData.dFrameInterval) + "\n");
+				writer.write("Intensity Interpolation,"+Integer.toString( BigTraceData.intensityInterpolation )+"\n");
+				writer.write("ROI Shape Interpolation,"+Integer.toString( BigTraceData.shapeInterpolation )+"\n");
+				writer.write("Rotation min frame type,"+Integer.toString( BigTraceData.rotationMinFrame )+"\n");
+				writer.write("Smooth window,"+Integer.toString( BigTraceData.nSmoothWindow )+"\n");
+
 				nRoiN = bt.roiManager.rois.size();
 				writer.write("ROIsNumber," + Integer.toString(nRoiN)+"\n");
 				for(nRoi=0;nRoi<nRoiN;nRoi++)

src/main/java/bigtrace/io/ViewsIO.java

@@ -70,7 +70,19 @@ public static < T extends RealType< T > & NativeType< T > > void saveView(final
 				writer.write("wireAntiAliasing,"+Integer.toString( BigTraceData.wireAntiAliasing ? 1 : 0)+"\n");
 				writer.write("timeRender,"+Integer.toString( BigTraceData.timeRender )+"\n");
 				writer.write("timeFade,"+Integer.toString( BigTraceData.timeFade )+"\n");
-
+				//tracing parameters
+				writer.write("nTraceBoxSize,"+Integer.toString( bt.btData.nTraceBoxSize )+"\n");
+				writer.write("fTraceBoxScreenFraction,"+df3.format(bt.btData.fTraceBoxScreenFraction)+"\n");
+				writer.write("fTraceBoxAdvanceFraction,"+df3.format(bt.btData.fTraceBoxAdvanceFraction)+"\n");
+				writer.write("nVertexPlacementPointN,"+Integer.toString( bt.btData.nVertexPlacementPointN )+"\n");
+				writer.write("dDirectionalityOneClick,"+df3.format(bt.btData.dDirectionalityOneClick)+"\n");
+				writer.write("bOCIntensityStop,"+Integer.toString(bt.btData.bOCIntensityStop ? 1 : 0)+"\n");
+				writer.write("dOCIntensityThreshold,"+df3.format(bt.btData.dOCIntensityThreshold)+"\n");
+				for (int d=0;d<3;d++)
+				{
+					writer.write("Trace sigma,"+Integer.toString( d )+ ","+ df3.format(bt.btData.sigmaTrace[d])+"\n");					
+				}
+
 				writer.write("Scene, current\n");
 				bt.getCurrentScene().save( writer );
 				int nSourcesN = bt.bvv_sources.size();
@@ -145,6 +157,8 @@ public static < T extends RealType< T > & NativeType< T > > void loadView(final
         bt.bInputLock = true;
         bt.setLockMode(true);
         int nSourcesN = bt.bvv_sources.size();
+
+        String [] sigmaTraceName = new String [] {"sigmaTraceX", "sigmaTraceY", "sigmaTraceZ"};
 		try ( BufferedReader br = new BufferedReader(new FileReader(sFilename));) 
 		{			       
 			String line = "";
@@ -265,6 +279,40 @@ public static < T extends RealType< T > & NativeType< T > > void loadView(final
 					BigTraceData.timeFade = Integer.parseInt( line_array[1] );
 					Prefs.set("BigTrace.timeFade", BigTraceData.timeFade);
 					break;
+				case "nTraceBoxSize":
+					bt.btData.nTraceBoxSize = Integer.parseInt( line_array[1] );
+					Prefs.set("BigTrace.nTraceBoxSize", bt.btData.nTraceBoxSize);
+					break;	
+				case "fTraceBoxScreenFraction":
+					bt.btData.fTraceBoxScreenFraction = Float.parseFloat( line_array[1] );
+					Prefs.set("BigTrace.fTraceBoxScreenFraction", bt.btData.fTraceBoxScreenFraction);
+					break;	
+				case "fTraceBoxAdvanceFraction":
+					bt.btData.fTraceBoxAdvanceFraction = Float.parseFloat( line_array[1] );
+					Prefs.set("BigTrace.fTraceBoxAdvanceFraction", bt.btData.fTraceBoxAdvanceFraction);
+					break;						
+				case "nVertexPlacementPointN":
+					bt.btData.nVertexPlacementPointN = Integer.parseInt( line_array[1] );
+					Prefs.set("BigTrace.nVertexPlacementPointN", bt.btData.nVertexPlacementPointN);
+					break;	
+				case "dDirectionalityOneClick":
+					bt.btData.dDirectionalityOneClick = Double.parseDouble( line_array[1] );
+					Prefs.set("BigTrace.dDirectionalityOneClick", bt.btData.dDirectionalityOneClick);
+					break;					
+				case "bOCIntensityStop":
+					bt.btData.bOCIntensityStop = line_array[1].equals( "1" )? true : false;
+					Prefs.set("BigTrace.bOCIntensityStop", bt.btData.bOCIntensityStop);
+					break;
+				case "dOCIntensityThreshold":
+					bt.btData.dOCIntensityThreshold = Double.parseDouble( line_array[1] );
+					Prefs.set("BigTrace.dOCIntensityThreshold", bt.btData.dOCIntensityThreshold);
+					break;	
+				case "Trace sigma":
+					int dA = Integer.parseInt( line_array[1]);
+					bt.btData.sigmaTrace[dA] = Double.parseDouble( line_array[2] ) ;
+					Prefs.set("BigTrace."+sigmaTraceName[dA], bt.btData.sigmaTrace[dA]);
+					break;	
+
 				case "Scene":
 					 final Scene scLoad = new Scene();
 					 scLoad.load( br );

src/main/java/bigtrace/rois/RoiManager3DDialogs.java

@@ -104,8 +104,8 @@ public void dialSemiAutoProperties()
 		NumberField nfTraceBoxScreenFraction = new NumberField(4);
 		NumberField nfTBAdvance = new NumberField(4);
 
-		nfTraceBoxSize.setText(Integer.toString((int)(2.0*bt.btData.lTraceBoxSize)));
-		nfTraceBoxScreenFraction.setText(df.format(bt.btData.dTraceBoxScreenFraction));
+		nfTraceBoxSize.setText(Integer.toString((int)(2.0*bt.btData.nTraceBoxSize)));
+		nfTraceBoxScreenFraction.setText(df.format(bt.btData.fTraceBoxScreenFraction));
 		nfGammaTrace.setText(df.format(bt.btData.gammaTrace));
 		nfTBAdvance.setText(df.format(bt.btData.fTraceBoxAdvanceFraction));
 
@@ -145,12 +145,9 @@ public void dialSemiAutoProperties()
 
 		if (reply == JOptionPane.OK_OPTION) 
 		{
-
-			bt.btData.lTraceBoxSize=(long)(Integer.parseInt(nfTraceBoxSize.getText())*0.5);
-			Prefs.set("BigTrace.lTraceBoxSize", bt.btData.lTraceBoxSize);
-
-			bt.btData.lTraceBoxSize=(long)(Integer.parseInt(nfTraceBoxSize.getText())*0.5);
-			Prefs.set("BigTrace.lTraceBoxSize", bt.btData.lTraceBoxSize);
+
+			bt.btData.nTraceBoxSize = (int)(Integer.parseInt(nfTraceBoxSize.getText())*0.5);
+			Prefs.set("BigTrace.lTraceBoxSize", bt.btData.nTraceBoxSize);
 
 			//TRACING OPTIONS
 
@@ -166,11 +163,8 @@ public void dialSemiAutoProperties()
 			bt.btData.bTraceOnlyClipped = cbTraceOnlyClipped.isSelected();
 			Prefs.set("BigTrace.bTraceOnlyClipped", bt.btData.bTraceOnlyClipped);			
 
-			bt.btData.lTraceBoxSize=(long)(Integer.parseInt(nfTraceBoxSize.getText())*0.5);
-			Prefs.set("BigTrace.lTraceBoxSize", bt.btData.lTraceBoxSize);
-
-			bt.btData.dTraceBoxScreenFraction = Double.parseDouble(nfTraceBoxScreenFraction.getText());
-			Prefs.set("BigTrace.dTraceBoxScreenFraction", bt.btData.dTraceBoxScreenFraction);
+			bt.btData.fTraceBoxScreenFraction = Float.parseFloat(nfTraceBoxScreenFraction.getText());
+			Prefs.set("BigTrace.dTraceBoxScreenFraction", bt.btData.fTraceBoxScreenFraction);
 
 			bt.btData.fTraceBoxAdvanceFraction = Float.parseFloat(nfTBAdvance.getText());
 			Prefs.set("BigTrace.fTraceBoxAdvanceFraction", bt.btData.fTraceBoxAdvanceFraction);