feat/tes: ApplyBigwarpPlugin expose show option

* dont try to show results in BigWarpApplyTests
saalfeldlab · Oct 3, 2024 · a71d024 · a71d024
1 parent 7ce37da
commit a71d024
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Showing 2 changed files with 97 additions and 43 deletions.
diff --git a/src/main/java/bdv/ij/ApplyBigwarpPlugin.java b/src/main/java/bdv/ij/ApplyBigwarpPlugin.java
@@ -69,7 +69,6 @@
 import net.imglib2.Interval;
 import net.imglib2.RandomAccessibleInterval;
 import net.imglib2.RealInterval;
-import net.imglib2.RealPoint;
 import net.imglib2.RealRandomAccessible;
 import net.imglib2.realtransform.AffineGet;
 import net.imglib2.realtransform.AffineRandomAccessible;
@@ -907,6 +906,32 @@ public static <T> List<ImagePlus> apply(
 			final boolean wait,
 			final WriteDestinationOptions writeOpts) {
 
+		final boolean show = ( writeOpts == null || writeOpts.pathOrN5Root == null || writeOpts.pathOrN5Root.isEmpty());
+		return apply(bwData, landmarks, invXfm,
+				tranformTypeOption, fieldOfViewOption, fieldOfViewPointFilter, bboxEst,
+				resolutionOption, resolutionSpec, fovSpec, offsetSpec, 
+				interp, isVirtual, nThreads, wait, writeOpts, show);
+	}
+
+	public static <T> List<ImagePlus> apply(
+			final BigWarpData<T> bwData,
+			final LandmarkTableModel landmarks,
+			final InvertibleRealTransform invXfm,
+			final String tranformTypeOption,
+			final String fieldOfViewOption,
+			final String fieldOfViewPointFilter,
+			final BoundingBoxEstimation bboxEst,
+			final String resolutionOption,
+			final double[] resolutionSpec,
+			final double[] fovSpec,
+			final double[] offsetSpec,
+			final Interpolation interp,
+			final boolean isVirtual,
+			final int nThreads,
+			final boolean wait,
+			final WriteDestinationOptions writeOpts,
+			final boolean show) {
+
 		final int numChannels = bwData.numMovingSources();
 		for ( int i = 0; i < numChannels; i++ )
 		{
@@ -955,11 +980,7 @@ public static <T> List<ImagePlus> apply(
 		}
 		else
 		{
-			final boolean show;
-			if( writeOpts == null || writeOpts.pathOrN5Root == null || writeOpts.pathOrN5Root.isEmpty())
-				show = true;
-			else
-				show = false;
+
 
 			return runExport( bwData, bwData.sources, fieldOfViewOption,
 					outputIntervalList, matchedPtNames, interp,

diff --git a/src/test/java/bigwarp/apply/BigWarpApplyTests.java b/src/test/java/bigwarp/apply/BigWarpApplyTests.java
@@ -17,10 +17,11 @@
 import bigwarp.landmarks.LandmarkTableModel;
 import bigwarp.transforms.BigWarpTransform;
 import ij.ImagePlus;
-import net.imglib2.Cursor;
 import net.imglib2.img.Img;
 import net.imglib2.img.display.imagej.ImageJFunctions;
 import net.imglib2.iterator.RealIntervalIterator;
+import net.imglib2.realtransform.BoundingBoxEstimation;
+import net.imglib2.realtransform.InvertibleRealTransform;
 import net.imglib2.type.numeric.integer.UnsignedByteType;
 import net.imglib2.util.Intervals;
 
@@ -201,58 +202,90 @@ private static void assertOriginsEqual(double[] expected, ImagePlus actual) {
 
 	private static List<ImagePlus> transformToTarget(ImagePlus mvg, ImagePlus tgt, LandmarkTableModel ltm) {
 
-		return ApplyBigwarpPlugin.apply(mvg, tgt,
+		final BigWarpData<?> bwData = BigWarpInit.createBigWarpDataFromImages(mvg, tgt);
+		bwData.wrapMovingSources();
+		final BoundingBoxEstimation bboxEst = new BoundingBoxEstimation(BoundingBoxEstimation.Method.CORNERS);
+		final InvertibleRealTransform invXfm = new BigWarpTransform( ltm, BigWarpTransform.AFFINE ).getTransformation();
+
+		 return ApplyBigwarpPlugin.apply(
+				bwData,
 				ltm,
-				BigWarpTransform.AFFINE,
-				ApplyBigwarpPlugin.TARGET,
-				null, // fov pt filter
+				invXfm,
+				BigWarpTransform.AFFINE, // tform type
+				ApplyBigwarpPlugin.TARGET, // fov option 
+				null,
+				bboxEst,
 				ApplyBigwarpPlugin.TARGET,
-				null, // res option
-				null, // fov spac
-				null, // offset spac
+				null,
+				null,
+				null,
 				Interpolation.NEARESTNEIGHBOR,
-				false, // virtual
-				true, // wait
-				1); // nThreads
+				false, // virtual 
+				1, // nThreads
+				true,
+				null, // writeOpts
+				false);
 	}
 
 	private static List<ImagePlus> transformToSpec(final ImagePlus mvg,
 			final double[] offset, final double[] fov, final double[] res,
 			final LandmarkTableModel ltm) {
 
-		return ApplyBigwarpPlugin.apply(mvg, null,
-				ltm,
-				BigWarpTransform.AFFINE,
-				ApplyBigwarpPlugin.SPECIFIED_PHYSICAL,
-				null, // fov pt filter
-				ApplyBigwarpPlugin.SPECIFIED,
-				res, // res option
-				fov, // fov spac
-				offset, // offset spac
-				Interpolation.NEARESTNEIGHBOR,
-				false, // virtual
-				true, // wait
-				1); // nThreads
+		ImagePlus tgt = null;
+		final BigWarpData<?> bwData = BigWarpInit.createBigWarpDataFromImages(mvg, tgt);
+		bwData.wrapMovingSources();
+		final BoundingBoxEstimation bboxEst = new BoundingBoxEstimation(BoundingBoxEstimation.Method.CORNERS);
+		final InvertibleRealTransform invXfm = new BigWarpTransform( ltm, BigWarpTransform.AFFINE ).getTransformation();
+
+		 return ApplyBigwarpPlugin.apply(
+					bwData,
+					ltm,
+					invXfm,
+					BigWarpTransform.AFFINE, // tform type
+					ApplyBigwarpPlugin.SPECIFIED_PHYSICAL, // fov option 
+					null,
+					bboxEst,
+					ApplyBigwarpPlugin.SPECIFIED,
+					res,
+					fov,
+					offset,
+					Interpolation.NEARESTNEIGHBOR,
+					false, // virtual 
+					1, // nThreads
+					true,
+					null, // writeOpts
+					false);
 	}
 
 	private static List<ImagePlus> transformToPtsSpec(final ImagePlus mvg,
 			final double[] res,
 			final LandmarkTableModel ltm,
 			final String fieldOfViewPointFilter) {
 
-		return ApplyBigwarpPlugin.apply(mvg, null,
-				ltm,
-				BigWarpTransform.AFFINE,
-				ApplyBigwarpPlugin.LANDMARK_POINTS,
-				fieldOfViewPointFilter, // fov pt filter
-				ApplyBigwarpPlugin.SPECIFIED,
-				res, // res option
-				null, // fov spec
-				null, // offset spac
-				Interpolation.NEARESTNEIGHBOR,
-				false, // virtual
-				true, // wait
-				1); // nThreads
+		ImagePlus tgt = null;
+		final BigWarpData<?> bwData = BigWarpInit.createBigWarpDataFromImages(mvg, tgt);
+		bwData.wrapMovingSources();
+		final BoundingBoxEstimation bboxEst = new BoundingBoxEstimation(BoundingBoxEstimation.Method.CORNERS);
+		final InvertibleRealTransform invXfm = new BigWarpTransform( ltm, BigWarpTransform.AFFINE ).getTransformation();
+
+		 return ApplyBigwarpPlugin.apply(
+					bwData,
+					ltm,
+					invXfm,
+					BigWarpTransform.AFFINE, // tform type
+					ApplyBigwarpPlugin.LANDMARK_POINTS, // fov option 
+					fieldOfViewPointFilter,
+					bboxEst,
+					ApplyBigwarpPlugin.SPECIFIED,
+					res,
+					null, // fov
+					null, // offset
+					Interpolation.NEARESTNEIGHBOR,
+					false, // virtual 
+					1, // nThreads
+					true,
+					null, // writeOpts
+					false);
 	}
 
 }