add plugin for applying a transform

See #42

src/main/java/bdv/ij/ApplyBigwarpPlugin.java

@@ -0,0 +1,163 @@
+package bdv.ij;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.ArrayList;
+
+import bdv.img.TpsTransformWrapper;
+import bdv.img.WarpedSource;
+import bdv.viewer.Interpolation;
+import bdv.viewer.SourceAndConverter;
+import bigwarp.BigWarp.BigWarpData;
+import bigwarp.BigWarp;
+import bigwarp.BigWarpARGBExporter;
+import bigwarp.BigWarpExporter;
+import bigwarp.BigWarpInit;
+import bigwarp.BigWarpRealExporter;
+import bigwarp.landmarks.LandmarkTableModel;
+import ij.IJ;
+import ij.ImageJ;
+import ij.ImagePlus;
+import ij.gui.GenericDialog;
+import ij.plugin.PlugIn;
+import jitk.spline.ThinPlateR2LogRSplineKernelTransform;
+import mpicbg.spim.data.sequence.VoxelDimensions;
+import net.imglib2.realtransform.InverseRealTransform;
+import net.imglib2.type.numeric.ARGBType;
+import net.imglib2.type.numeric.integer.ByteType;
+import net.imglib2.type.numeric.integer.IntType;
+import net.imglib2.type.numeric.integer.UnsignedByteType;
+import net.imglib2.type.numeric.integer.UnsignedShortType;
+import net.imglib2.type.numeric.real.DoubleType;
+import net.imglib2.type.numeric.real.FloatType;
+
+/**
+ * 
+ * Apply a bigwarp transform to a 2d or 3d ImagePlus
+ *
+ */
+public class ApplyBigwarpPlugin implements PlugIn
+{
+	public static void main( String[] args ) throws IOException
+	{
+		new ImageJ();
+		new ApplyBigwarpPlugin().run( "" );
+	}
+
+	public static ImagePlus apply(
+			final ImagePlus movingIp,
+			final ImagePlus targetIp,
+			final LandmarkTableModel landmarks,
+			final Interpolation interp,
+			final int nThreads )
+	{
+		int numChannels = movingIp.getNChannels();
+		BigWarpData bwData = BigWarpInit.createBigWarpDataFromImages( movingIp, targetIp );
+
+		BigWarpExporter< ? > exporter = null;
+		ArrayList< SourceAndConverter< ? > > sources = bwData.sources;
+		int[] movingSourceIndexList = bwData.movingSourceIndices;
+		int[] targetSourceIndexList = bwData.targetSourceIndices;
+		VoxelDimensions voxdim = sources.get( targetSourceIndexList[ 0 ] ).getSpimSource().getVoxelDimensions();
+
+		ArrayList< SourceAndConverter< ? >> sourcesxfm = BigWarp.wrapSourcesAsTransformed(
+				sources, 
+				landmarks.getNumdims(),
+				movingSourceIndexList );
+
+		ThinPlateR2LogRSplineKernelTransform xfm = landmarks.getTransform();
+
+		for ( int i = 0; i < numChannels; i++ )
+		{
+			InverseRealTransform irXfm = new InverseRealTransform( new TpsTransformWrapper( 3, xfm ) );
+			((WarpedSource< ? >) (sourcesxfm.get( i ).getSpimSource())).updateTransform( irXfm );
+			((WarpedSource< ? >) (sourcesxfm.get( i ).getSpimSource())).setIsTransformed( true );
+		}
+
+		if ( BigWarpRealExporter.isTypeListFullyConsistent( sources, movingSourceIndexList ) )
+		{
+			Object baseType = sourcesxfm.get( movingSourceIndexList[ 0 ] ).getSpimSource().getType();
+			if ( ByteType.class.isInstance( baseType ) )
+				exporter = new BigWarpRealExporter< ByteType >( sourcesxfm, movingSourceIndexList, targetSourceIndexList, interp, ( ByteType ) baseType );
+			else if ( UnsignedByteType.class.isInstance( baseType ) )
+				exporter = new BigWarpRealExporter< UnsignedByteType >( sourcesxfm, movingSourceIndexList, targetSourceIndexList, interp, ( UnsignedByteType ) baseType );
+			else if ( IntType.class.isInstance( baseType ) )
+				exporter = new BigWarpRealExporter< IntType >( sourcesxfm, movingSourceIndexList, targetSourceIndexList, interp, ( IntType ) baseType );
+			else if ( UnsignedShortType.class.isInstance( baseType ) )
+				exporter = new BigWarpRealExporter< UnsignedShortType >( sourcesxfm, movingSourceIndexList, targetSourceIndexList, interp, ( UnsignedShortType ) baseType );
+			else if ( FloatType.class.isInstance( baseType ) )
+				exporter = new BigWarpRealExporter< FloatType >( sourcesxfm, movingSourceIndexList, targetSourceIndexList, interp, ( FloatType ) baseType );
+			else if ( DoubleType.class.isInstance( baseType ) )
+				exporter = new BigWarpRealExporter< DoubleType >( sourcesxfm, movingSourceIndexList, targetSourceIndexList, interp, ( DoubleType ) baseType );
+			else if ( ARGBType.class.isInstance( baseType ) )
+				exporter = new BigWarpARGBExporter( sourcesxfm, movingSourceIndexList, targetSourceIndexList );
+			else
+			{
+				System.err.println( "Can't export type " + baseType.getClass() );
+				exporter = null;
+				return null;
+			}
+		}
+
+		ImagePlus warpedIp = exporter.exportMovingImagePlus( false, nThreads );
+
+		// Note: need to get number of channels and frames from moving image
+		// but get the number of slices form the target
+		warpedIp.setDimensions( movingIp.getNChannels(), targetIp.getNSlices(),
+				movingIp.getNFrames() );
+
+		warpedIp.getCalibration().pixelWidth = 1.0 / voxdim.dimension( 0 );
+		warpedIp.getCalibration().pixelHeight = 1.0 / voxdim.dimension( 1 );
+		warpedIp.getCalibration().pixelDepth = voxdim.dimension( 2 );
+		warpedIp.getCalibration().setUnit( voxdim.unit() );
+		warpedIp.setTitle( movingIp.getTitle() + "_bigwarped" );
+
+		return warpedIp;
+	}
+
+	@Override
+	public void run( String arg )
+	{
+		if ( IJ.versionLessThan( "1.40" ) )
+			return;
+
+		final GenericDialog gd = new GenericDialog( "Apply Big Warp transform" );
+		gd.addMessage( "File Selection:" );
+		gd.addStringField( "landmarks_image_file", "" );
+		gd.addStringField( "moving_image_file", "" );
+		gd.addStringField( "target_space_file", "" );
+		System.out.println( "cow" );
+		gd.showDialog();
+
+		if ( gd.wasCanceled() )
+			return;
+
+		String landmarksPath = gd.getNextString();
+		String movingPath = gd.getNextString();
+		String targetPath = gd.getNextString();
+
+		ImagePlus movingIp = IJ.openImage( movingPath );
+		ImagePlus targetIp = movingIp;
+
+		if ( !targetPath.isEmpty() )
+			targetIp = IJ.openImage( targetPath );
+
+		int nd = 2;
+		if ( movingIp.getNSlices() > 1 )
+			nd = 3;
+
+		LandmarkTableModel ltm = new LandmarkTableModel( nd );
+		try
+		{
+			ltm.load( new File( landmarksPath ) );
+		} catch ( IOException e )
+		{
+			e.printStackTrace();
+			return;
+		}
+
+		ImagePlus warpedIp = apply( movingIp, targetIp, ltm, Interpolation.NLINEAR, 8 );
+		warpedIp.show();
+	}
+
+}

src/main/resources/plugins.config

@@ -9,4 +9,5 @@
 # If something like ("<arg>") is appended to the class name, the setup() method
 # will get that as arg parameter; otherwise arg is simply the empty string.
 
-Plugins>BigDataViewer, "Big Warp", bdv.ij.BigWarpImagePlusPlugIn
+Plugins>BigDataViewer, "Big Warp", bdv.ij.BigWarpImagePlusPlugIn
+Plugins>BigDataViewer, "Big Warp Apply", bdv.ij.ApplyBigwarpPlugin