Resolve trakem2#11 - moved remaining external resources to new legacy…

… package.

src/main/java/de/unihalle/informatik/rhizoTrak/analysis/Compare.java

@@ -137,8 +137,8 @@ as published by the Free Software Foundation (http://www.gnu.org/licenses/gpl.tx
 import ij.process.ByteProcessor;
 import ij3d.Content;
 import ini.trakem2.vector.Editions;
-import ini.trakem2.vector.VectorString3D;
-import mpi.fruitfly.general.MultiThreading;
+import ini.trakem2.vector.VectorString3D;
+import legacy.mpi.fruitfly.general.MultiThreading;
 import mpicbg.imglib.container.cell.Cell;
 import mpicbg.models.AffineModel3D;
 import mpicbg.models.MovingLeastSquaresTransform;

src/main/java/de/unihalle/informatik/rhizoTrak/display/Display.java

@@ -167,8 +167,6 @@ as published by the Free Software Foundation (http://www.gnu.org/licenses/gpl.tx
 import javax.swing.event.DocumentListener;
 import javax.swing.text.Document;
 
-import org.janelia.intensity.MatchIntensities;
-
 import de.unihalle.informatik.rhizoTrak.ControlWindow;
 import de.unihalle.informatik.rhizoTrak.Project;
 import de.unihalle.informatik.rhizoTrak.analysis.Graph;
@@ -219,13 +217,14 @@ as published by the Free Software Foundation (http://www.gnu.org/licenses/gpl.tx
 import ij.measure.Calibration;
 import ij.measure.ResultsTable;
 import ij.process.ImageProcessor;
-import lenscorrection.DistortionCorrectionTask;
-import lenscorrection.NonLinearTransform;
+import legacy.lenscorrection.DistortionCorrectionTask;
+import legacy.lenscorrection.NonLinearTransform;
+import legacy.mpicbg.trakem2.align.AlignLayersTask;
+import legacy.mpicbg.trakem2.align.AlignTask;
+import legacy.mpicbg.trakem2.align.Util;
+import legacy.org.janelia.intensity.MatchIntensities;
 import mpicbg.ij.clahe.Flat;
 import mpicbg.models.PointMatch;
-import mpicbg.trakem2.align.AlignLayersTask;
-import mpicbg.trakem2.align.AlignTask;
-import mpicbg.trakem2.align.Util;
 import mpicbg.trakem2.transform.AffineModel3D;
 import mpicbg.trakem2.transform.CoordinateTransform;
 import mpicbg.trakem2.transform.CoordinateTransformList;

src/main/java/de/unihalle/informatik/rhizoTrak/display/ManualAlignMode.java

@@ -71,8 +71,10 @@ as published by the Free Software Foundation (http://www.gnu.org/licenses/gpl.tx
 
 package de.unihalle.informatik.rhizoTrak.display;
 
-import ij.gui.GenericDialog;
-
+import ij.gui.GenericDialog;
+import legacy.mpicbg.trakem2.align.Align;
+import legacy.mpicbg.trakem2.align.AlignTask;
+
 import java.awt.BasicStroke;
 import java.awt.Color;
 import java.awt.Component;
@@ -104,10 +106,8 @@ as published by the Free Software Foundation (http://www.gnu.org/licenses/gpl.tx
 import mpicbg.models.PointMatch;
 import mpicbg.models.RigidModel2D;
 import mpicbg.models.SimilarityModel2D;
-import mpicbg.models.TranslationModel2D;
-import mpicbg.trakem2.align.Align;
-import mpicbg.trakem2.align.AlignTask;
-
+import mpicbg.models.TranslationModel2D;
+
 import org.xml.sax.Attributes;
 import org.xml.sax.InputSource;
 import org.xml.sax.helpers.DefaultHandler;

src/main/java/de/unihalle/informatik/rhizoTrak/display/Patch.java

@@ -146,6 +146,8 @@ as published by the Free Software Foundation (http://www.gnu.org/licenses/gpl.tx
 import ij.process.FloatProcessor;
 import ij.process.ImageProcessor;
 import ij.process.ShortProcessor;
+import legacy.mpicbg.trakem2.transform.ExportUnsignedByte;
+import legacy.mpicbg.trakem2.transform.ExportUnsignedShort;
 import mpicbg.imglib.container.shapelist.ShapeList;
 import mpicbg.imglib.image.display.imagej.ImageJFunctions;
 import mpicbg.imglib.type.numeric.integer.UnsignedByteType;
@@ -154,8 +156,6 @@ as published by the Free Software Foundation (http://www.gnu.org/licenses/gpl.tx
 import mpicbg.trakem2.transform.AffineModel2D;
 import mpicbg.trakem2.transform.CoordinateTransform;
 import mpicbg.trakem2.transform.CoordinateTransformList;
-import mpicbg.trakem2.transform.ExportUnsignedByte;
-import mpicbg.trakem2.transform.ExportUnsignedShort;
 import mpicbg.trakem2.transform.TransformMesh;
 import mpicbg.trakem2.transform.TransformMeshMapping;
 import mpicbg.trakem2.transform.TransformMeshMappingWithMasks.ImageProcessorWithMasks;

src/main/java/de/unihalle/informatik/rhizoTrak/imaging/StitchingTEM.java

@@ -74,8 +74,15 @@ as published by the Free Software Foundation (http://www.gnu.org/licenses/gpl.tx
 import ij.ImagePlus;
 import ij.gui.GenericDialog;
 import ij.gui.Roi;
-import ij.process.ImageProcessor;
-
+import ij.process.ImageProcessor;
+import legacy.mpi.fruitfly.math.datastructures.FloatArray2D;
+import legacy.mpi.fruitfly.registration.CrossCorrelation2D;
+import legacy.mpi.fruitfly.registration.ImageFilter;
+import legacy.mpicbg.trakem2.align.AbstractAffineTile2D;
+import legacy.mpicbg.trakem2.align.Align;
+import legacy.mpicbg.trakem2.align.AlignTask;
+import legacy.mpicbg.trakem2.align.TranslationTile2D;
+
 import java.awt.Image;
 import java.awt.Rectangle;
 import java.awt.geom.AffineTransform;
@@ -93,20 +100,13 @@ as published by the Free Software Foundation (http://www.gnu.org/licenses/gpl.tx
 import de.unihalle.informatik.rhizoTrak.utils.Bureaucrat;
 import de.unihalle.informatik.rhizoTrak.utils.IJError;
 import de.unihalle.informatik.rhizoTrak.utils.Utils;
-import de.unihalle.informatik.rhizoTrak.utils.Worker;
-import mpi.fruitfly.math.datastructures.FloatArray2D;
-import mpi.fruitfly.registration.CrossCorrelation2D;
-import mpi.fruitfly.registration.ImageFilter;
+import de.unihalle.informatik.rhizoTrak.utils.Worker;
 import mpicbg.imglib.algorithm.fft.PhaseCorrelationPeak;
 import mpicbg.models.ErrorStatistic;
 import mpicbg.models.Point;
 import mpicbg.models.PointMatch;
 import mpicbg.models.Tile;
 import mpicbg.models.TranslationModel2D;
-import mpicbg.trakem2.align.AbstractAffineTile2D;
-import mpicbg.trakem2.align.Align;
-import mpicbg.trakem2.align.AlignTask;
-import mpicbg.trakem2.align.TranslationTile2D;
 
 
 /** Given:
@@ -405,7 +405,7 @@ public void run() {
 
 						interestingTiles = new ArrayList< AbstractAffineTile2D< ? > >();
 						for ( final Tile< ? > t : largestGraph )
-							interestingTiles.add( ( AbstractAffineTile2D< ? > )t );
+							interestingTiles.add( (legacy.mpicbg.trakem2.align.AbstractAffineTile2D< ? > )t );
 
 						if ( param.hide_disconnected )
 							for ( final AbstractAffineTile2D< ? > t : al_tiles )

src/main/java/de/unihalle/informatik/rhizoTrak/imaging/filters/RobustNormalizeLocalContrast.java

@@ -107,7 +107,7 @@ public RobustNormalizeLocalContrast(final Map<String,String> params) {
 	@Override
 	public ImageProcessor process(final ImageProcessor ip) {
 		try {
-			mpicbg.trakem2.util.RobustNormalizeLocalContrast.run(
+			legacy.mpicbg.trakem2.util.RobustNormalizeLocalContrast.run(
 					ip, scaleLevel, brx1, bry1, stds1, brx2, bry2, stds2);
 		} catch (final Exception e) {
 			e.printStackTrace();

src/main/java/de/unihalle/informatik/rhizoTrak/io/AmiraImporter.java

@@ -84,8 +84,9 @@ as published by the Free Software Foundation (http://www.gnu.org/licenses/gpl.tx
 import ij.ImageStack;
 import ij.io.FileInfo;
 import ij.io.OpenDialog;
-import ij.process.ImageProcessor;
-
+import ij.process.ImageProcessor;
+import legacy.mpi.fruitfly.general.MultiThreading;
+
 import java.awt.Color;
 import java.awt.Rectangle;
 import java.awt.geom.Area;
@@ -94,8 +95,6 @@ as published by the Free Software Foundation (http://www.gnu.org/licenses/gpl.tx
 import java.util.Map;
 import java.util.concurrent.atomic.AtomicInteger;
 
-import mpi.fruitfly.general.MultiThreading;
-
 /** Parses an amira labelfield and imports the labels as AreaList instances into the project tree.*/
 public class AmiraImporter {
 

src/main/java/de/unihalle/informatik/rhizoTrak/persistence/FSLoader.java

@@ -86,6 +86,7 @@ TrakEM2 plugin for ImageJ(C).
 import ij.process.ColorProcessor;
 import ij.process.FloatProcessor;
 import ij.process.ImageProcessor;
+import legacy.org.janelia.intensity.LinearIntensityMap;
 
 import java.awt.Image;
 import java.awt.event.ActionEvent;
@@ -133,7 +134,6 @@ TrakEM2 plugin for ImageJ(C).
 import net.imglib2.img.imageplus.ImagePlusImgs;
 import net.imglib2.type.numeric.real.FloatType;
 
-import org.janelia.intensity.LinearIntensityMap;
 import org.jfree.chart.plot.CategoryCrosshairState;
 import org.xml.sax.InputSource;
 

src/main/java/de/unihalle/informatik/rhizoTrak/persistence/Loader.java

@@ -182,13 +182,13 @@ as published by the Free Software Foundation (http://www.gnu.org/licenses/gpl.tx
 import ij.process.ImageProcessor;
 import ij.process.ImageStatistics;
 import ij.process.StackStatistics;
+import legacy.mpi.fruitfly.general.MultiThreading;
+import legacy.mpi.fruitfly.math.datastructures.FloatArray2D;
+import legacy.mpi.fruitfly.registration.ImageFilter;
+import legacy.mpicbg.trakem2.transform.ExportUnsignedShort;
 import loci.formats.ChannelSeparator;
 import loci.formats.FormatException;
 import loci.formats.IFormatReader;
-import mpi.fruitfly.general.MultiThreading;
-import mpi.fruitfly.math.datastructures.FloatArray2D;
-import mpi.fruitfly.registration.ImageFilter;
-import mpicbg.trakem2.transform.ExportUnsignedShort;
 import mpicbg.trakem2.util.Triple;
 
 /** Handle all data-related issues with a virtualization engine, including load/unload and saving, saving as and overwriting. */

src/main/java/de/unihalle/informatik/rhizoTrak/persistence/ProjectTiler.java

@@ -50,8 +50,9 @@
 package de.unihalle.informatik.rhizoTrak.persistence;
 
 import ij.ImagePlus;
-import ij.io.FileSaver;
-
+import ij.io.FileSaver;
+import legacy.mpicbg.trakem2.transform.ExportUnsignedShort;
+
 import java.awt.Color;
 import java.awt.Rectangle;
 import java.io.File;
@@ -76,8 +77,7 @@
 import de.unihalle.informatik.rhizoTrak.tree.ProjectThing;
 import de.unihalle.informatik.rhizoTrak.tree.TemplateThing;
 import de.unihalle.informatik.rhizoTrak.utils.IJError;
-import de.unihalle.informatik.rhizoTrak.utils.Utils;
-import mpicbg.trakem2.transform.ExportUnsignedShort;
+import de.unihalle.informatik.rhizoTrak.utils.Utils;
 import mpicbg.trakem2.transform.ExportedTile;
 
 public class ProjectTiler {

src/main/java/de/unihalle/informatik/rhizoTrak/tree/ProjectTree.java

@@ -72,8 +72,9 @@ as published by the Free Software Foundation (http://www.gnu.org/licenses/gpl.tx
 package de.unihalle.informatik.rhizoTrak.tree;
 
 
-import ij.gui.GenericDialog;
-
+import ij.gui.GenericDialog;
+import legacy.mpicbg.trakem2.align.AlignTask;
+
 import java.awt.Choice;
 import java.awt.Color;
 import java.awt.Component;
@@ -130,7 +131,6 @@ as published by the Free Software Foundation (http://www.gnu.org/licenses/gpl.tx
 import de.unihalle.informatik.rhizoTrak.utils.IJError;
 import de.unihalle.informatik.rhizoTrak.utils.Utils;
 import de.unihalle.informatik.rhizoTrak.utils.Worker;
-import mpicbg.trakem2.align.AlignTask;
 
 /** A class to hold a tree of Thing nodes */
 public final class ProjectTree extends DNDTree implements MouseListener, ActionListener {

src/main/java/bunwarpj/trakem2/transform/CubicBSplineTransform.java → src/main/java/legacy/bunwarpj/trakem2/transform/CubicBSplineTransform.java

@@ -14,7 +14,7 @@
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
  */
-package bunwarpj.trakem2.transform;
+package legacy.bunwarpj.trakem2.transform;
 
 import java.util.Collection;
 import java.util.Stack;

src/main/java/lenscorrection/DistortionCorrectionTask.java → src/main/java/legacy/lenscorrection/DistortionCorrectionTask.java

@@ -1,7 +1,7 @@
 /**
  *
  */
-package lenscorrection;
+package legacy.lenscorrection;
 
 import java.awt.Rectangle;
 import java.awt.geom.AffineTransform;
@@ -23,15 +23,15 @@
 import de.unihalle.informatik.rhizoTrak.utils.Worker;
 import ij.IJ;
 import ij.gui.GenericDialog;
-import lenscorrection.Distortion_Correction.BasicParam;
-import lenscorrection.Distortion_Correction.PointMatchCollectionAndAffine;
+import legacy.lenscorrection.Distortion_Correction.BasicParam;
+import legacy.lenscorrection.Distortion_Correction.PointMatchCollectionAndAffine;
+import legacy.mpicbg.trakem2.align.AbstractAffineTile2D;
+import legacy.mpicbg.trakem2.align.Align;
+import legacy.mpicbg.trakem2.align.RegularizedAffineLayerAlignment.Param;
 import mpicbg.ij.SIFT;
 import mpicbg.models.Point;
 import mpicbg.models.PointMatch;
 import mpicbg.models.Tile;
-import mpicbg.trakem2.align.AbstractAffineTile2D;
-import mpicbg.trakem2.align.Align;
-import mpicbg.trakem2.align.RegularizedAffineLayerAlignment.Param;
 import mpicbg.trakem2.transform.CoordinateTransform;
 
 /**
@@ -472,7 +472,7 @@ final static public void run( final CorrectDistortionFromSelectionParam p, final
 
 		interestingTiles = new ArrayList< AbstractAffineTile2D< ? > >();
 		for ( final Tile< ? > t : largestGraph )
-			interestingTiles.add( ( AbstractAffineTile2D< ? > )t );
+			interestingTiles.add( (legacy.mpicbg.trakem2.align.AbstractAffineTile2D< ? > )t );
 
 		if ( Thread.currentThread().isInterrupted() ) return;
 

src/main/java/lenscorrection/Distortion_Correction.java → src/main/java/legacy/lenscorrection/Distortion_Correction.java

@@ -37,7 +37,7 @@ as published by the Free Software Foundation (http://www.gnu.org/licenses/gpl.tx
  *  SIFT implementation: Stephan Saalfeld                                       *
  * **************************************************************************** */
 
-package lenscorrection;
+package legacy.lenscorrection;
 
 import java.awt.Color;
 import java.awt.geom.AffineTransform;
@@ -67,7 +67,7 @@ as published by the Free Software Foundation (http://www.gnu.org/licenses/gpl.tx
 import ij.plugin.PlugIn;
 import ij.process.ColorProcessor;
 import ij.process.ImageProcessor;
-import mpi.fruitfly.general.MultiThreading;
+import legacy.mpi.fruitfly.general.MultiThreading;
 import mpicbg.ij.SIFT;
 import mpicbg.imagefeatures.Feature;
 import mpicbg.imagefeatures.FloatArray2DSIFT;

src/main/java/lenscorrection/NonLinearTransform.java → src/main/java/legacy/lenscorrection/NonLinearTransform.java

@@ -32,7 +32,7 @@ as published by the Free Software Foundation (http://www.gnu.org/licenses/gpl.tx
  *
  * ****************************************************************  */
 
-package lenscorrection;
+package legacy.lenscorrection;
 
 import ij.ImagePlus;
 import ij.io.FileSaver;

src/main/java/lenscorrection/PolynomialModel2D.java → src/main/java/legacy/lenscorrection/PolynomialModel2D.java

@@ -14,7 +14,7 @@
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
  */
-package lenscorrection;
+package legacy.lenscorrection;
 
 import java.util.Collection;
 

src/main/java/mpi/fruitfly/general/ArrayConverter.java → src/main/java/legacy/mpi/fruitfly/general/ArrayConverter.java

@@ -1,4 +1,4 @@
-package mpi.fruitfly.general;
+package legacy.mpi.fruitfly.general;
 
 /**
  * <p>Title: </p>

src/main/java/mpi/fruitfly/general/ImageArrayConverter.java → src/main/java/legacy/mpi/fruitfly/general/ImageArrayConverter.java

@@ -1,33 +1,20 @@
-package mpi.fruitfly.general;
-
-/**
- * <p>Title: </p>
- *
- * <p>Description: </p>
- *
- * <p>Copyright: Copyright (c) 2006</p>
- *
- * <p>Company: </p>
- *
- * @author not attributable
- * @version 1.0
- */
-
-import static mpi.fruitfly.math.General.max;
+package legacy.mpi.fruitfly.general;
+
 import ij.IJ;
 import ij.ImagePlus;
 import ij.ImageStack;
 import ij.process.ByteProcessor;
 import ij.process.FloatProcessor;
 import ij.process.ImageProcessor;
 import ij.process.ShortProcessor;
+import legacy.mpi.fruitfly.math.datastructures.FloatArray;
+import legacy.mpi.fruitfly.math.datastructures.FloatArray2D;
+import legacy.mpi.fruitfly.math.datastructures.FloatArray3D;
+import legacy.mpi.fruitfly.math.datastructures.FloatArray4D;
 
-import java.awt.Point;
+import static legacy.mpi.fruitfly.math.General.max;
 
-import mpi.fruitfly.math.datastructures.FloatArray;
-import mpi.fruitfly.math.datastructures.FloatArray2D;
-import mpi.fruitfly.math.datastructures.FloatArray3D;
-import mpi.fruitfly.math.datastructures.FloatArray4D;
+import java.awt.Point;
 
 
 public class ImageArrayConverter

src/main/java/mpi/fruitfly/general/MultiThreading.java → src/main/java/legacy/mpi/fruitfly/general/MultiThreading.java

@@ -1,4 +1,4 @@
-package mpi.fruitfly.general;
+package legacy.mpi.fruitfly.general;
 
 /**
  * <p>Title: MultiThreading </p>

src/main/java/mpi/fruitfly/math/General.java → src/main/java/legacy/mpi/fruitfly/math/General.java

@@ -1,4 +1,4 @@
-package mpi.fruitfly.math;
+package legacy.mpi.fruitfly.math;
 
 /**
  * <p>Title: </p>

src/main/java/mpi/fruitfly/math/Quicksortable.java → src/main/java/legacy/mpi/fruitfly/math/Quicksortable.java

@@ -1,4 +1,4 @@
-package mpi.fruitfly.math;
+package legacy.mpi.fruitfly.math;
 
 /**
  * <p>Title: </p>

src/main/java/mpi/fruitfly/math/datastructures/FloatArray.java → src/main/java/legacy/mpi/fruitfly/math/datastructures/FloatArray.java

@@ -1,4 +1,4 @@
-package mpi.fruitfly.math.datastructures;
+package legacy.mpi.fruitfly.math.datastructures;
 
 /**
  * <p>Title: </p>