optimized CC

ekatrukha · May 1, 2024 · 0f12c2d · 0f12c2d
1 parent ecaf13f
commit 0f12c2d
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Showing 11 changed files with 526 additions and 26 deletions.
diff --git a/src/main/java/averagingND/GenNormCC.java b/src/main/java/averagingND/GenNormCC.java
@@ -27,7 +27,7 @@
 import net.imglib2.util.Intervals;
 import net.imglib2.view.IntervalView;
 import net.imglib2.view.Views;
-
+@Deprecated
 public class GenNormCC {
 
 	/** dimensionality of images **/	
@@ -59,7 +59,9 @@ public class GenNormCC {
 	 * the boundaries are always strange **/
 	final double max_fraction_shift = 0.9;	
 
-	/** 
+	/** 		//ImagePlus imageIn = IJ.openVirtual("/home/eugene/Desktop/projects/UnequalTiffs/BB/001f.tif");
+		//Img< FloatType >img = FloatTiffImgWrap.wrapVirtualFloat(imageIn, MiscUtils.getDimensionsTextImageJ(imageIn));
+		//ImageJFunctions.show(img, "test_raw");
 	 * @param image
 	 * @param template
 	 */

diff --git a/src/main/java/averagingND/ImageSet.java b/src/main/java/averagingND/ImageSet.java
@@ -15,10 +15,7 @@
 import ij.ImagePlus;
 import ij.WindowManager;
 import ij.measure.Calibration;
-import io.scif.config.SCIFIOConfig;
-import io.scif.config.SCIFIOConfig.ImgMode;
-import io.scif.img.ImgOpener;
-import io.scif.img.SCIFIOImgPlus;
+
 import net.imglib2.Cursor;
 import net.imglib2.RandomAccessibleInterval;
 import net.imglib2.converter.Converter;
@@ -27,10 +24,6 @@
 import net.imglib2.img.imageplus.ImagePlusImg;
 import net.imglib2.img.imageplus.ImagePlusImgFactory;
 import net.imglib2.type.Type;
-import net.imglib2.type.numeric.ARGBType;
-import net.imglib2.type.numeric.ComplexType;
-import net.imglib2.type.numeric.integer.UnsignedByteType;
-import net.imglib2.type.numeric.integer.UnsignedShortType;
 import net.imglib2.type.numeric.real.FloatType;
 import net.imglib2.view.Views;
 
@@ -153,8 +146,6 @@ boolean initializeFromOpenWindows()
 		return true;
 	}
 
-
-	@SuppressWarnings("unchecked")
 	boolean loadAllImages()
 	{
 		int i;

diff --git a/src/main/java/averagingND/IterativeAveraging.java b/src/main/java/averagingND/IterativeAveraging.java
@@ -202,7 +202,8 @@ public void run(String paramString) {
 			processIntermediate(0);
 		}
 
-		GenNormCC normCC = new GenNormCC();
+		//GenNormCC normCC = new GenNormCC();
+		MaskedNormCC normCC = new MaskedNormCC();
 		normCC.bVerbose = false;
 		normCC.bZeroMask = bZeroMask;
 		normCC.lim_fractions = lim_fractions;
@@ -268,7 +269,8 @@ public void run(String paramString) {
 				//currAverageImg = removeOneAverage(sumAndCount,imgs_shift.get(i));
 				//ImageJFunctions.show(currAverageImg, "aver"+Integer.toString(i+1));
 				//removeOneAverage
-				normCC.caclulateGenNormCC(Views.zeroMin(currAverageImg), imageSet.imgs.get(i), false);
+				//normCC.caclulateGenNormCC(Views.zeroMin(currAverageImg), imageSet.imgs.get(i), false);
+				normCC.caclulateMaskedNormCC(Views.zeroMin(currAverageImg), imageSet.imgs.get(i), false);
 
 				avrgCC+=normCC.dMaxCC;
 				listCC[i]=normCC.dMaxCC;

diff --git a/src/main/java/averagingND/LogPolarToCartesianTransform2D.java b/src/main/java/averagingND/LogPolarToCartesianTransform2D.java
@@ -4,7 +4,7 @@
 import net.imglib2.RealPositionable;
 import net.imglib2.realtransform.InverseRealTransform;
 import net.imglib2.realtransform.InvertibleRealTransform;
-import net.imglib2.realtransform.PolarToCartesianTransform2D;
+
 
 public class LogPolarToCartesianTransform2D implements InvertibleRealTransform
 {