virtualstack

ekatrukha · May 1, 2024 · ecaf13f · ecaf13f
1 parent f258cd9
commit ecaf13f
Show file tree

Hide file tree

Showing 5 changed files with 311 additions and 57 deletions.
diff --git a/src/main/java/averagingND/FloatTiffImgWrap.java b/src/main/java/averagingND/FloatTiffImgWrap.java
@@ -0,0 +1,117 @@
+package averagingND;
+
+import ij.ImagePlus;
+import net.imglib2.cache.img.CellLoader;
+import net.imglib2.cache.img.ReadOnlyCachedCellImgFactory;
+import net.imglib2.cache.img.ReadOnlyCachedCellImgOptions;
+import net.imglib2.cache.img.SingleCellArrayImg;
+import net.imglib2.img.Img;
+import net.imglib2.type.numeric.real.FloatType;
+
+public class FloatTiffImgWrap {
+
+
+	public static Img< FloatType > wrapVirtualFloat(final ImagePlus imp, String sDims_)
+	{
+		String sDims = sDims_;
+		final int nDims = sDims.length();
+		final long[] dimensions = new long[nDims];
+		final int nBitD = imp.getBitDepth();
+		for(int i=0;i<nDims;i++)
+		{
+			if(sDims.charAt(i)=='X')
+			{
+				dimensions[i]=imp.getWidth();
+			}
+			if(sDims.charAt(i)=='Y')
+			{
+				dimensions[i]=imp.getHeight();
+			}
+			if(sDims.charAt(i)=='Z')
+			{
+				dimensions[i]=imp.getNSlices();
+			}
+			if(sDims.charAt(i)=='C')
+			{
+				dimensions[i]=imp.getNChannels();				
+			}
+			if(sDims.charAt(i)=='T')
+			{
+				dimensions[i]=imp.getNFrames();
+			}
+		}
+
+		// set up cell size such that one cell is one plane
+		final int[] cellDimensions = new int[] {
+				imp.getStack().getWidth(),
+				imp.getStack().getHeight(),
+				1
+		};
+		// make a CellLoader that copies one plane of data from the virtual stack
+		final CellLoader< FloatType > loader = new CellLoader< FloatType  >()
+		{
+			@Override
+			public void load( final SingleCellArrayImg< FloatType , ? > cell ) throws Exception
+			{
+				//final int z = ( int ) cell.min( 2 );
+				int nCh = 1;
+				int nSl = 1;
+				int nTp = 1;
+				for(int i=2;i<nDims;i++)
+				{
+					if(sDims.charAt(i)=='C')
+					{
+						nCh = (int)cell.min(i)+1;
+					}
+					if(sDims.charAt(i)=='Z')
+					{
+						nSl = (int)cell.min(i)+1;
+					}
+					if(sDims.charAt(i)=='T')
+					{
+						nTp = (int)cell.min(i)+1;
+					}
+
+				}
+
+				final int stInd = imp.getStackIndex(nCh, nSl, nTp);
+				//final short[] impdata = ( short[] ) imp.getStack().getProcessor( 1 + z ).getPixels();
+				final float[] celldata = ( float[] ) cell.getStorageArray();
+				if(nBitD == 32)
+				{
+					final float[] impdata = ( float[] ) imp.getStack().getProcessor(stInd).getPixels();
+					System.arraycopy( impdata, 0, celldata, 0, celldata.length );
+				}
+				if(nBitD == 16)
+				{
+					final short[] impdata = ( short[] ) imp.getStack().getProcessor( stInd ).getPixels();
+					for(int i=0;i<celldata.length;i++)
+					{
+						celldata[i]=impdata[i]&0xffff;
+					}
+				}
+				if(nBitD == 8)
+				{
+					final byte[] impdata = ( byte[] ) imp.getStack().getProcessor( stInd ).getPixels();
+					for(int i=0;i<celldata.length;i++)
+					{
+						celldata[i]=impdata[i]&0xff;
+					}
+				}
+				//System.arraycopy( impdata, 0, celldata, 0, celldata.length );
+			}
+		};
+		// create a CellImg with that CellLoader
+//		final Img< FloatType > img = new ReadOnlyCachedCellImgFactory().create(
+//				dimensions,
+//				new FloatType(),
+//				loader,
+//				ReadOnlyCachedCellImgOptions.options().cellDimensions( cellDimensions ) );
+		return new ReadOnlyCachedCellImgFactory().create(
+				dimensions,
+				new FloatType(),
+				loader,
+				ReadOnlyCachedCellImgOptions.options().cellDimensions( cellDimensions ) );
+	}
+	//static long[]
+}
diff --git a/src/main/java/averagingND/GenNormCC.java b/src/main/java/averagingND/GenNormCC.java
@@ -9,6 +9,8 @@
 import net.imglib2.RandomAccessibleInterval;
 import net.imglib2.algorithm.fft2.FFT;
 import net.imglib2.algorithm.fft2.FFTMethods;
+import net.imglib2.converter.Converter;
+import net.imglib2.converter.Converters;
 import net.imglib2.img.Img;
 import net.imglib2.img.ImgFactory;
 import net.imglib2.img.ImgView;
@@ -17,6 +19,9 @@
 import net.imglib2.img.array.ArrayImgs;
 import net.imglib2.img.basictypeaccess.array.FloatArray;
 import net.imglib2.img.display.imagej.ImageJFunctions;
+import net.imglib2.img.imageplus.ImagePlusImg;
+import net.imglib2.img.imageplus.ImagePlusImgFactory;
+import net.imglib2.type.Type;
 import net.imglib2.type.numeric.complex.ComplexFloatType;
 import net.imglib2.type.numeric.real.FloatType;
 import net.imglib2.util.Intervals;
@@ -170,12 +175,13 @@ public boolean caclulateGenNormCC(final RandomAccessibleInterval< FloatType > im
 		//ImageJFunctions.show(padUnitTem).setTitle( "unipadded2" );
 
 		//squared image values
-		Img< FloatType > sqImg = ImgView.wrap(image).copy();
-		Img< FloatType > sqTem = ImgView.wrap(template).copy();
-
-		sqImg.forEach(t-> t.mul(t.get()));
-		sqTem.forEach(t-> t.mul(t.get()));
-
+		//Img< FloatType > sqImg = ImgView.wrap(image).copy();
+		//Img< FloatType > sqTem = ImgView.wrap(template).copy();
+		//sqImg.forEach(t-> t.mul(t.get()));
+		//sqTem.forEach(t-> t.mul(t.get()));
+		RandomAccessibleInterval< FloatType > sqImg = Converters.convert(image, ( in,out )-> {out.set(in.get()*in.get());}, new FloatType()); 
+		RandomAccessibleInterval< FloatType > sqTem =  Converters.convert(template, ( in,out )-> {out.set(in.get()*in.get());}, new FloatType()); 
+
 		//padded squared images
 		IntervalView< FloatType > padSqImg = Views.interval(Views.extendZero(sqImg),imgIntPad);
 		IntervalView< FloatType > padSqTem = Views.interval(Views.extendZero(sqTem),temIntPad);
@@ -200,12 +206,14 @@ public boolean caclulateGenNormCC(final RandomAccessibleInterval< FloatType > im
 		FFTMethods.complexConjugate(sqTemplateFFT2);	
 
 		//multiplications
+	    final Img< ComplexFloatType > I1F2F2 = multCompl(unImageFFT2,sqTemplateFFT2);
+
 		final Img< ComplexFloatType > deNOM = multCompl(unImageFFT2,unTemplateFFT2);
 	    final Img< ComplexFloatType > F1F2 = multCompl(imageFFT2,templateFFT2);
 	    final Img< ComplexFloatType > F1I2 = multCompl(imageFFT2,unTemplateFFT2);
 	    final Img< ComplexFloatType > I1F2 = multCompl(unImageFFT2,templateFFT2);
 	    final Img< ComplexFloatType > F1F1I2 = multCompl(sqImageFFT2,unTemplateFFT2);
-	    final Img< ComplexFloatType > I1F2F2 = multCompl(unImageFFT2,sqTemplateFFT2);
+
 
 	    //inverse FFT
 		final Img< FloatType > invdeNOM = FFT.complexToReal(deNOM, factoryFloat, new FloatType());	
@@ -458,4 +466,5 @@ public static Img< ComplexFloatType > multCompl(final Img< ComplexFloatType > im
 
 	    return output;
 	}
+
 }