v.0.3.1

pom.xml

@@ -11,7 +11,7 @@
 
 	<groupId>sc.fiji</groupId>
 	<artifactId>bigtrace</artifactId>
-	<version>0.3.0</version>
+	<version>0.3.1</version>
 
 	<name>BigTrace</name>
 	<description>Tracing of curvilinear structures in 3D</description>
@@ -119,6 +119,7 @@
 		<dependency>
 			<groupId>net.imglib2</groupId>
 			<artifactId>imglib2</artifactId>
+			<version>6.1.0</version>
 		</dependency>
 		<dependency>
 			<groupId>net.imglib2</groupId>

src/main/java/bigtrace/BigTrace.java

@@ -32,6 +32,7 @@
 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;
@@ -1055,7 +1056,7 @@ public AnisotropicTransformAnimator3D getCenteredViewAnim(final Interval inInter
 		return anim;
 	}
 
-	public void showTraceBox(IntervalView<UnsignedByteType> weights)
+	public void showTraceBox()
 	{
 
 		// there is a trace box already, let's remove it
@@ -1076,7 +1077,8 @@ public void showTraceBox(IntervalView<UnsignedByteType> weights)
 			}
 
 		}
-		bvv_trace = BvvFunctions.show(weights, "weights", Bvv.options().addTo(bvv_main));
+
+		bvv_trace = BvvFunctions.show(btdata.trace_weights, "weights", Bvv.options().addTo(bvv_main));
 		bvv_trace.setCurrent();
 		bvv_trace.setRenderType(btdata.nRenderMethod);
 		bvv_trace.setDisplayRangeBounds(0, 255);
@@ -1100,8 +1102,7 @@ public void showTraceBox(IntervalView<UnsignedByteType> weights)
 	public void removeTraceBox()
 	{
 
-
-		if(bvv_trace!=null)
+		if(bvv_trace != null)
 		{
 			btdata.bcTraceBox.storeBC(bvv_trace);
 			bvv_trace.removeFromBdv();

src/main/java/bigtrace/BigTraceData.java

@@ -19,7 +19,7 @@
 public class BigTraceData < T extends RealType< T > > {
 
 	/** current plugin version **/
-	public static String sVersion = "0.3.0";
+	public static String sVersion = "0.3.1";
 
 	/** plugin instanse **/
 	BigTrace<T> bt;

src/main/java/bigtrace/BigTraceRenderSettings.java

@@ -7,7 +7,7 @@
 import ij.Prefs;
 
 
-@Plugin(type = Command.class, menuPath = "Plugins>BigTrace 0.3.0>Render Settings")
+@Plugin(type = Command.class, menuPath = "Plugins>BigTrace 0.3.1>Render Settings")
 public class BigTraceRenderSettings implements Command {
 
 	@Parameter( label = "Render width" )

src/main/java/bigtrace/math/TraceBoxMath.java

@@ -1,6 +1,7 @@
 package bigtrace.math;
 
 
+import java.util.concurrent.ExecutionException;
 import java.util.concurrent.ExecutorService;
 import java.util.concurrent.Executors;
 
@@ -84,7 +85,7 @@ protected Void doInBackground() throws Exception {
 				nDerivOrder[d2]++;
 				kernels = DerivConvolutionKernels.convolve_derive_kernel(bt.btdata.sigmaTrace, nDerivOrder );
 				derivKernel = Kernel1D.centralAsymmetric(kernels);
-				convObj=SeparableKernelConvolution.convolution( derivKernel );
+				convObj = SeparableKernelConvolution.convolution( derivKernel );
 				convObj.setExecutor(es);
 				convObj.process(Views.extendBorder(input), hs2 );
 				//SeparableKernelConvolution.convolution( derivKernel ).process( input, hs2 );
@@ -112,11 +113,15 @@ protected Void doInBackground() throws Exception {
 
 		mEV.computeVWCRAI(hessian, directionVectors,salWeights, lineCorners,nThreads,es);
 		es.shutdown();
+
 		setProgress(100);
 		setProgressState("trace box done.");
-		bt.btdata.trace_weights=VolumeMisc.convertFloatToUnsignedByte(salWeights,false);
+
+		bt.btdata.trace_weights = VolumeMisc.convertFloatToUnsignedByte(salWeights,false);
+
+
 		//bt.btdata.jump_points =VolumeMisc.localMaxPointList(VolumeMisc.convertFloatToUnsignedByte(lineCorners,false), 50);
-		bt.btdata.jump_points =VolumeMisc.localMaxPointList(VolumeMisc.convertFloatToUnsignedByte(lineCorners,false), 10);
+		bt.btdata.jump_points = VolumeMisc.localMaxPointList(VolumeMisc.convertFloatToUnsignedByte(lineCorners,false), 10);
 		bt.btdata.trace_vectors = directionVectors;
 		//bt.showCorners(bt.btdata.jump_points);
 		return null;
@@ -127,7 +132,19 @@ protected Void doInBackground() throws Exception {
     @Override
     public void done() 
     {
-    	bt.showTraceBox(bt.btdata.trace_weights);
+    	//see if we have some errors
+    	 try {
+             get();
+         	} 
+    	 catch (ExecutionException e) {
+             e.getCause().printStackTrace();
+             String msg = String.format("Unexpected problem during Hessian calculations: %s", 
+                            e.getCause().toString());
+             System.out.println(msg);
+         } catch (InterruptedException e) {
+             // Process e here
+         }
+    	bt.showTraceBox();
 
 		//unlock user interaction
     	bt.bInputLock = false;

src/main/java/bigtrace/volume/VolumeMisc.java

@@ -21,6 +21,7 @@
 import net.imglib2.algorithm.neighborhood.RectangleShape;
 import net.imglib2.algorithm.neighborhood.Shape;
 import net.imglib2.algorithm.region.BresenhamLine;
+import net.imglib2.converter.Converters;
 import net.imglib2.converter.RealUnsignedByteConverter;
 import net.imglib2.converter.RealUnsignedShortConverter;
 import net.imglib2.converter.read.ConvertedRandomAccessibleInterval;
@@ -183,18 +184,21 @@ public static IntervalView< UnsignedByteType > localMax(final IntervalView< Unsi
 			return output;
 		}
 
-	public static IntervalView<UnsignedByteType> convertFloatToUnsignedByte(IntervalView<FloatType> input, boolean inverse)
+	public static IntervalView<UnsignedByteType> convertFloatToUnsignedByte(RandomAccessibleInterval<FloatType> input, boolean inverse)
 	{
+
+
 		float minVal = Float.MAX_VALUE;
 		float maxVal = -Float.MAX_VALUE;
-		for ( final FloatType h : input )
+		IntervalView<FloatType> inInt = Views.interval(input,input.minAsLongArray(),input.maxAsLongArray());
+		for ( final FloatType h : inInt )
 		{
 			final float dd = h.get();
 			minVal = Math.min( dd, minVal );
 			maxVal = Math.max( dd, maxVal );
 		}
 
-		
+
 		//final RealUnsignedByteConverter<FloatType> cvU = new RealUnsignedByteConverter<FloatType>(minVal,maxVal);
 		final RealUnsignedByteConverter<FloatType> cvU;
 		if (inverse)
@@ -205,9 +209,16 @@ public static IntervalView<UnsignedByteType> convertFloatToUnsignedByte(Interval
 		{
 			cvU = new RealUnsignedByteConverter<FloatType>(minVal, maxVal);
 		}
-		final ConvertedRandomAccessibleInterval< FloatType, UnsignedByteType > inputScaled = new ConvertedRandomAccessibleInterval<>( input, ( s, t ) -> {
-			cvU.convert(s,t);
+
+
+
+		RandomAccessibleInterval<UnsignedByteType> inputScaled = Converters.convert(input, cvU, new UnsignedByteType());
+
+		/*
+		final ConvertedRandomAccessibleInterval< FloatType, UnsignedByteType > inputScaled = new ConvertedRandomAccessibleInterval<FloatType, UnsignedByteType>( input, ( s, t ) -> {
+			cvU.convert(s, t);
 		}, new UnsignedByteType() );	
+		*/
 		return Views.interval(inputScaled,inputScaled.minAsLongArray(),inputScaled.maxAsLongArray());
 
 	}

src/main/resources/plugins.config

@@ -1 +1 @@
-Plugins>BigTrace 0.3.0, "Open TIF/BDV(xml) volume", bigtrace.BigTrace
+Plugins>BigTrace 0.3.1, "Open TIF/BDV(xml) volume", bigtrace.BigTrace