update methods to imglib v7

ekatrukha · Jan 28, 2025 · 55f2060 · 55f2060
1 parent 9c0f1b3
commit 55f2060
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Showing 7 changed files with 18 additions and 19 deletions.
diff --git a/src/main/java/bigtrace/animation/UnCoilAnimation.java b/src/main/java/bigtrace/animation/UnCoilAnimation.java
@@ -505,7 +505,7 @@ public IntervalView<T> generateSingleVolumeSetup(int nInd, int nChannel)
 
 		RandomAccessibleInterval<T> all_RAI =  bt.btData.getAllDataRAI();
 
-		Img<T> outImg = Util.getSuitableImgFactory(roiIntervBox, Util.getTypeFromInterval(all_RAI) ).create(roiIntervBox);
+		Img<T> outImg = Util.getSuitableImgFactory(roiIntervBox, all_RAI.getType() ).create(roiIntervBox);
 
 		IntervalView<T> outInterval = Views.translate( outImg, roiIntervBox.minAsLongArray() );
 
@@ -614,7 +614,7 @@ public boolean loadTemplate(String sTemplateTIF)
 		final ImagePlus imp = IJ.openImage( sTemplateTIF );
 
 		int nBitD = imp.getBitDepth();
-		T ff = Util.getTypeFromInterval( bt.btData.getAllDataRAI() );
+		T ff =  bt.btData.getAllDataRAI().getType();
 
 		if(ff instanceof UnsignedByteType)
 		{

diff --git a/src/main/java/bigtrace/io/UnCoilFrameImgLoader.java b/src/main/java/bigtrace/io/UnCoilFrameImgLoader.java
@@ -10,7 +10,6 @@
 import net.imglib2.type.numeric.integer.UnsignedByteType;
 import net.imglib2.type.numeric.integer.UnsignedShortType;
 import net.imglib2.type.numeric.real.FloatType;
-import net.imglib2.util.Util;
 import net.imglib2.view.Views;
 
 import bigtrace.BigTrace;
@@ -44,11 +43,11 @@ public RandomAccessibleInterval< UnsignedShortType > getImage( int timepointId,
 			{
 				final RandomAccessibleInterval< ? > raiXYZ
 				= Views.zeroMin(unCoil.generateSingleVolumeSetup( timepointId, setupId ));
-				if ( Util.getTypeFromInterval( raiXYZ ) instanceof UnsignedShortType )
+				if ( raiXYZ.getType() instanceof UnsignedShortType )
 				{
 					return (RandomAccessibleInterval <UnsignedShortType >) raiXYZ;
 				}
-				else if ( Util.getTypeFromInterval( raiXYZ ) instanceof UnsignedByteType )
+				else if ( raiXYZ.getType() instanceof UnsignedByteType )
 				{
 					return Converters.convert(
 							raiXYZ,

diff --git a/src/main/java/bigtrace/math/EigenValVecSymmDecomposition.java b/src/main/java/bigtrace/math/EigenValVecSymmDecomposition.java
@@ -87,9 +87,9 @@ private void computeVWRAIthreaded( final RandomAccessibleInterval< T > RAIin,
    }
    public void computeVWRAI( final RandomAccessibleInterval< T > RAIin, final RandomAccessibleInterval< T > eVector, final RandomAccessibleInterval< T > eWeight)
    {
-	   final Cursor< RealComposite< T > > m = Views.iterable( Views.collapseReal( RAIin ) ).cursor();
-	   final Cursor< RealComposite< T > > eV = Views.iterable( Views.collapseReal( eVector ) ).cursor();
-	   final Cursor<  T > eW = Views.iterable(  eWeight  ).cursor();
+	   final Cursor< RealComposite< T > > m =  Views.collapseReal( RAIin ).cursor();
+	   final Cursor< RealComposite< T > > eV =  Views.collapseReal( eVector ).cursor();
+	   final Cursor<  T > eW =   eWeight.cursor();
 
 	   while ( m.hasNext() )
 	   {
@@ -179,10 +179,10 @@ public void computeVWRAI( final RandomAccessibleInterval< T > tensor,
 
    public void computeVWCRAI( final RandomAccessibleInterval< T > RAIin, final RandomAccessibleInterval< T > eVector, final RandomAccessibleInterval< T > eWeight,final RandomAccessibleInterval< T > eCorners)
    {
-	   final Cursor< RealComposite< T > > m = Views.iterable( Views.collapseReal( RAIin ) ).cursor();
-	   final Cursor< RealComposite< T > > eV = Views.iterable( Views.collapseReal( eVector ) ).cursor();
-	   final Cursor<  T > eW = Views.iterable(  eWeight  ).cursor();
-	   final Cursor<  T > eC = Views.iterable(  eCorners  ).cursor();
+	   final Cursor< RealComposite< T > > m = Views.collapseReal( RAIin ).cursor();
+	   final Cursor< RealComposite< T > > eV = Views.collapseReal( eVector ).cursor();
+	   final Cursor<  T > eW = eWeight.cursor();
+	   final Cursor<  T > eC =   eCorners.cursor();
 
 	   while ( m.hasNext() )
 	   {

diff --git a/src/main/java/bigtrace/measure/RoiMeasure3D.java b/src/main/java/bigtrace/measure/RoiMeasure3D.java
@@ -1090,7 +1090,7 @@ void measureEndsDirection(final Roi3D roi, final MeasureValues val)
 
 	public static double getMeanDoubleArray(final double [] values)
 	{
-		final RealSum realSum = new RealSum(values.length);
+		final RealSum realSum = new RealSum();
 
 		for(int i=0;i<values.length;i++)
 		{
@@ -1102,7 +1102,7 @@ public static double getMeanDoubleArray(final double [] values)
 
 	public static double getSDDoubleArray(final double mean, final double [] values)
 	{
-		final RealSum realSum = new RealSum(values.length);
+		final RealSum realSum = new RealSum();
 		for(int i=0;i<values.length;i++)
 		{
 			realSum.add((values[i]-mean)*(values[i]-mean));
@@ -1116,7 +1116,7 @@ public static double getSDDoubleArray(final double mean, final double [] values)
 
 	public static double getSumDoubleArray(final double [] values)
 	{
-		final RealSum realSum = new RealSum(values.length);
+		final RealSum realSum = new RealSum();
 
 		for(int i=0;i<values.length;i++)
 		{

diff --git a/src/main/java/bigtrace/volume/ExtractROIBox.java b/src/main/java/bigtrace/volume/ExtractROIBox.java
@@ -219,7 +219,7 @@ IntervalView<T> extractBoxRoiVolumeShape(final Roi3D roiIn, final RandomAccessib
 
 		IntervalView<T> bboxMeasure = Views.interval(Views.extendZero(all_RAI),finBoxInt);
 
-		Img<T> out1 =  Util.getSuitableImgFactory(bboxMeasure, Util.getTypeFromInterval(bboxMeasure)).create(bboxMeasure);
+		Img<T> out1 =  Util.getSuitableImgFactory(bboxMeasure, bboxMeasure.getType()).create(bboxMeasure);
 
 		IntervalView< T > trans = Views.translate( out1, bboxMeasure.minAsLongArray() );
 

diff --git a/src/main/java/bigtrace/volume/SplitVolumePlane.java b/src/main/java/bigtrace/volume/SplitVolumePlane.java
@@ -78,10 +78,10 @@ protected Void doInBackground() throws Exception {
 		//(for now)
 		//make two copies
 
-		Img<T> out1 =  Util.getSuitableImgFactory(all_RAI, Util.getTypeFromInterval(all_RAI)).create(all_RAI);
+		Img<T> out1 =  Util.getSuitableImgFactory(all_RAI, all_RAI.getType()).create(all_RAI);
 		LoopBuilder.setImages(out1,all_RAI).forEachPixel(Type::set);
 
-		Img<T> out2 =  Util.getSuitableImgFactory(all_RAI, Util.getTypeFromInterval(all_RAI)).create(all_RAI);
+		Img<T> out2 =  Util.getSuitableImgFactory(all_RAI, all_RAI.getType()).create(all_RAI);
 		LoopBuilder.setImages(out2, all_RAI).forEachPixel(Type::set);
 
 		final long [] nTotPixArr = all_RAI.dimensionsAsLongArray();

diff --git a/src/main/java/bigtrace/volume/StraightenCurve.java b/src/main/java/bigtrace/volume/StraightenCurve.java
@@ -210,7 +210,7 @@ IntervalView<T> extractCurveRAI(final AbstractCurve3D curveROI, final RandomAcce
 		nChannelN = dimS[4];
 
 		//this is where we store straightened volume
-		Img<T> out1 = Util.getSuitableImgFactory(all_RAI, Util.getTypeFromInterval(all_RAI)).create(new FinalInterval(dimS));
+		Img<T> out1 = Util.getSuitableImgFactory(all_RAI, all_RAI.getType()).create(new FinalInterval(dimS));
 
 
 		//get a frame around line