Change SegmentationPlugins to take ImgPlus

src/main/java/com/indago/io/DoubleTypeImgLoader.java

@@ -9,11 +9,13 @@
 
 import ij.IJ;
 import ij.ImagePlus;
+import net.imagej.ImgPlus;
 import net.imglib2.IterableInterval;
 import net.imglib2.RandomAccessibleInterval;
 import net.imglib2.img.ImagePlusAdapter;
 import net.imglib2.img.Img;
 import net.imglib2.img.array.ArrayImgFactory;
+import net.imglib2.type.numeric.RealType;
 import net.imglib2.type.numeric.real.DoubleType;
 import net.imglib2.view.Views;
 
@@ -40,26 +42,34 @@ public static Img< DoubleType > loadTiff( final File file ) {
 	public static RandomAccessibleInterval< DoubleType > loadTiffEnsureType( final File file ) {
 		final Img< DoubleType > img = loadTiff( file );
 
-		final long dims[] = new long[ img.numDimensions() ];
-		img.dimensions( dims );
-		final RandomAccessibleInterval< DoubleType > ret =
-				new ArrayImgFactory< DoubleType >().create( dims, new DoubleType() );
-		final IterableInterval< DoubleType > iterRet = Views.iterable( ret );
-		try {
-			DataMover.convertAndCopy( Views.extendZero( img ), iterRet );
-		} catch ( final Exception e ) {
-			e.printStackTrace();
-		}
+		final RandomAccessibleInterval< DoubleType > ret = copyToDouble( img );
 		return ret;
 	}
 
+	public static ImgPlus< DoubleType > wrapEnsureType( final ImgPlus< ? extends RealType > imgPlus ) {
+		final Img< DoubleType > newImg = copyToDouble( imgPlus.getImg() );
+		final ImgPlus< DoubleType > result = new ImgPlus<>( newImg, imgPlus.getName() );
+		for ( int i = 0; i < result.numDimensions(); i++ )
+			result.setAxis( imgPlus.axis( i ), i );
+		return result;
+	}
+
 	public static RandomAccessibleInterval< DoubleType > wrapEnsureType( final ImagePlus imagePlus ) {
 		final Img< DoubleType > img =
 				ImagePlusAdapter.wrapReal( imagePlus );
 
+		final RandomAccessibleInterval< DoubleType > ret = copyToDouble( img );
+		return ret;
+	}
+
+	/**
+	 * @param img
+	 * @return
+	 */
+	private static Img< DoubleType > copyToDouble( final Img< ? extends RealType > img ) {
 		final long dims[] = new long[ img.numDimensions() ];
 		img.dimensions( dims );
-		final RandomAccessibleInterval< DoubleType > ret =
+		final Img< DoubleType > ret =
 				new ArrayImgFactory< DoubleType >().create( dims, new DoubleType() );
 		final IterableInterval< DoubleType > iterRet = Views.iterable( ret );
 		try {

src/main/java/com/indago/plugins/seg/IndagoSegmentationPlugin.java

@@ -12,6 +12,7 @@
 import com.indago.io.ProjectFolder;
 
 import net.imagej.ImageJPlugin;
+import net.imagej.ImgPlus;
 import net.imglib2.RandomAccessibleInterval;
 import net.imglib2.type.numeric.integer.IntType;
 import net.imglib2.type.numeric.real.DoubleType;
@@ -25,7 +26,7 @@ public interface IndagoSegmentationPlugin extends ImageJPlugin, AutoCloseable {
 
 	List< RandomAccessibleInterval< IntType > > getOutputs();
 
-	void setProjectFolderAndData( ProjectFolder projectFolder, RandomAccessibleInterval< DoubleType > rawData );
+	void setProjectFolderAndData( ProjectFolder projectFolder, ImgPlus< DoubleType > rawData );
 
 	String getUiName();
 

src/main/java/com/indago/plugins/seg/IndagoSegmentationPluginService.java

@@ -12,7 +12,7 @@
 import com.indago.io.ProjectFolder;
 
 import net.imagej.ImageJService;
-import net.imglib2.RandomAccessibleInterval;
+import net.imagej.ImgPlus;
 import net.imglib2.type.numeric.real.DoubleType;
 
 @Plugin(type = Service.class)
@@ -24,7 +24,7 @@ public class IndagoSegmentationPluginService extends AbstractPTService< IndagoSe
 	/**
 	 * Gets the list of available plugin types.
 	 * The names on this list can be passed to
-	 * {@link #createPlugin(String, ProjectFolder, RandomAccessibleInterval, Logger)}
+	 * {@link #createPlugin(String, ProjectFolder, ImgPlus, Logger)}
 	 * to create instances of that animal.
 	 *
 	 * @return a set of plugin names
@@ -36,7 +36,7 @@ public Set< String > getPluginNames() {
 	public IndagoSegmentationPlugin createPlugin(
 			final String name,
 			final ProjectFolder projectFolder,
-			final RandomAccessibleInterval< DoubleType > raiData,
+			final ImgPlus< DoubleType > imgPlus,
 			final Logger logger ) {
 		// First, we get the animal plugin with the given name.
 		final PluginInfo< IndagoSegmentationPlugin > info = plugins.get( name );
@@ -46,7 +46,7 @@ public IndagoSegmentationPlugin createPlugin(
 		// Next, we use the plugin service to create an animal of that kind.
 		final IndagoSegmentationPlugin segPlugin = getPluginService().createInstance( info );
 		segPlugin.setLogger( logger );
-		segPlugin.setProjectFolderAndData( projectFolder, raiData );
+		segPlugin.setProjectFolderAndData( projectFolder, imgPlus );
 
 		return segPlugin;
 	}