Example 1 with Coordinate
use of ini.trakem2.display.Coordinate in project TrakEM2 by trakem2.
the class Segmentation method fastMarching.
public static Bureaucrat fastMarching(final AreaWrapper aw, final Layer layer, final Rectangle srcRect, final int x_p_w, final int y_p_w, final List<Runnable> post_tasks) {
// Capture pointers before they are set to null
final AreaContainer ac = (AreaContainer) aw.getSource();
final AffineTransform source_aff = aw.getSource().getAffineTransform();
final Rectangle box = new Rectangle(x_p_w - Segmentation.fmp.width / 2, y_p_w - Segmentation.fmp.height / 2, Segmentation.fmp.width, Segmentation.fmp.height);
Bureaucrat burro = Bureaucrat.create(new Worker.Task("Fast marching") {
public void exec() {
// Capture image as large as the fmp width,height centered on x_p_w,y_p_w
Utils.log2("fmp box is " + box);
ImagePlus imp = new ImagePlus("", Patch.makeFlatImage(ImagePlus.GRAY8, layer, box, 1.0, (Collection) layer.getDisplayables(Patch.class, new Area(box), true), Color.black));
// Bandpass filter
if (fmp.apply_bandpass_filter) {
IJ.run(imp, "Bandpass Filter...", "filter_large=" + fmp.low_frequency_threshold + " filter_small=" + fmp.high_frequency_threshold + " suppress=None tolerance=5" + (fmp.autoscale_after_filtering ? " autoscale" : "") + (fmp.saturate_when_autoscaling ? " saturate" : ""));
}
// Setup seed point
PointRoi roi = new PointRoi(box.width / 2, box.height / 2);
imp.setRoi(roi);
Utils.log2("imp: " + imp);
Utils.log2("proi: " + imp.getRoi() + " " + Utils.toString(new int[] { x_p_w - srcRect.x, y_p_w - srcRect.y }));
// Setup state
ImageContainer ic = new ImageContainer(imp);
StateContainer state = new StateContainer();
state.setROI(roi, ic.getWidth(), ic.getHeight(), ic.getImageCount(), imp.getCurrentSlice());
state.setExpansionToInside(false);
// Run FastMarching
final FastMarching fm = new FastMarching(ic, null, state, true, fmp.fm_grey, fmp.fm_dist, fmp.apply_grey_value_erosion);
final int max_iterations = fmp.max_iterations;
final int iter_inc = fmp.iter_inc;
for (int i = 0; i < max_iterations; i++) {
if (Thread.currentThread().isInterrupted()) {
return;
}
if (!fm.step(iter_inc))
break;
}
// Extract ROI
setTaskName("Adding area");
final ArrayList<Coordinate> vc = fm.getStateContainer().getXYZ(false);
if (0 == vc.size()) {
Utils.log("No area growth.");
return;
}
final Area area = new Area();
Coordinate first = vc.remove(0);
final Rectangle r = new Rectangle(first.x, first.y, 1, 1);
int count = 0;
// Scan and add line-wise
for (final Coordinate c : vc) {
count++;
if (c.y == r.y && c.x == r.x + 1) {
// same line:
r.width += 1;
continue;
} else {
// add previous one
area.add(new Area(r));
}
// start new line:
r.x = c.x;
r.y = c.y;
r.width = 1;
if (0 == count % 1024 && Thread.currentThread().isInterrupted()) {
return;
}
}
// add last:
area.add(new Area(r));
/*
// Trying from the image mask: JUST AS SLOW
final byte[] b = (byte[]) fm.getStateContainer().getIPMask()[0].getPixels();
final int w = imp.getWidth();
for (int i=0; i<b.length; i++) {
if (0 == b[i]) {
r.x = i%w;
r.y = i/w;
area.add(new Area(r));
}
}
*/
/* // DOESN'T FILL?
// Trying to just get the contour, and then filling holes
for (final Coordinate c : fm.getStateContainer().getXYZ(true)) {
r.x = c.x;
r.y = c.y;
area.add(new Area(r));
}
Polygon pol = new Polygon();
final float[] coords = new float[6];
for (PathIterator pit = area.getPathIterator(null); !pit.isDone(); ) {
switch (pit.currentSegment(coords)) {
case PathIterator.SEG_MOVETO:
case PathIterator.SEG_LINETO:
pol.addPoint((int)coords[0], (int)coords[1]);
break;
case PathIterator.SEG_CLOSE:
area.add(new Area(pol));
// prepare next:
pol = new Polygon();
break;
default:
Utils.log2("WARNING: unhandled seg type.");
break;
}
pit.next();
if (pit.isDone()) {
break;
}
}
*/
// / FAILS because by now AreaWrapper's source is null
// aw.add(area, new AffineTransform(1, 0, 0, 1, box.x, box.y));
// Instead, compose an Area that is local to the AreaWrapper's area
final AffineTransform aff = new AffineTransform(1, 0, 0, 1, box.x, box.y);
try {
aff.preConcatenate(source_aff.createInverse());
} catch (NoninvertibleTransformException nite) {
IJError.print(nite);
return;
}
aw.getArea().add(area.createTransformedArea(aff));
ac.calculateBoundingBox(layer);
Display.repaint(layer);
}
}, layer.getProject());
if (null != post_tasks)
for (Runnable task : post_tasks) burro.addPostTask(task);
burro.goHaveBreakfast();
return burro;
}
Also used :
FastMarching(levelsets.algorithm.FastMarching)
Rectangle(java.awt.Rectangle)
ArrayList(java.util.ArrayList)
Bureaucrat(ini.trakem2.utils.Bureaucrat)
ImagePlus(ij.ImagePlus)
ImageContainer(levelsets.ij.ImageContainer)
NoninvertibleTransformException(java.awt.geom.NoninvertibleTransformException)
Area(java.awt.geom.Area)
StateContainer(levelsets.ij.StateContainer)
Coordinate(levelsets.algorithm.Coordinate)
AreaContainer(ini.trakem2.display.AreaContainer)
AffineTransform(java.awt.geom.AffineTransform)
Worker(ini.trakem2.utils.Worker)
PointRoi(ij.gui.PointRoi)
Example 2 with Coordinate
use of ini.trakem2.display.Coordinate in project TrakEM2 by trakem2.
the class Blending method blendPatches.
public static final void blendPatches(final Set<Patch> patches, final boolean respect_current_mask) {
ExecutorService exe = null;
try {
if (null == patches || patches.size() < 2)
return;
final Layer layer = patches.iterator().next().getLayer();
for (final Patch p : patches) {
if (null != p.getCoordinateTransform()) {
Utils.log("CANNOT blend: at least one image has a coordinate transform.\nBlending of coordinate-transformed images will be enabled in the near future.");
return;
}
if (p.getLayer() != layer) {
Utils.log("CANNOT blend: all images must belong to the same layer!\n Otherwise the overlap cannot be computed.");
return;
}
}
final HashMap<Patch, TransformMesh> meshes = new HashMap<Patch, TransformMesh>();
for (final Patch p : patches) {
meshes.put(p, null == p.getCoordinateTransform() ? null : new TransformMesh(p.getCoordinateTransform(), p.getMeshResolution(), p.getOWidth(), p.getOHeight()));
}
exe = Executors.newFixedThreadPool(Runtime.getRuntime().availableProcessors());
final List<Future<?>> futures = Collections.synchronizedList(new ArrayList<Future<?>>());
final List<Future<?>> futures2 = Collections.synchronizedList(new ArrayList<Future<?>>());
// Cache the indices that determine overlap order within the layer
final HashMap<Patch, Integer> indices = new HashMap<Patch, Integer>();
int i = 0;
for (final Displayable d : layer.getDisplayables()) {
if (d.getClass() == Patch.class && patches.contains((Patch) d)) {
indices.put((Patch) d, i);
}
i += 1;
}
for (final Patch p : patches) {
if (Thread.currentThread().isInterrupted())
break;
futures.add(exe.submit(new Runnable() {
@Override
public void run() {
final int pLayerIndex = indices.get(p);
final Set<Patch> overlapping = new HashSet<Patch>();
for (final Patch op : patches) {
if (indices.get(op) < pLayerIndex)
overlapping.add(op);
}
if (setBlendingMask(p, overlapping, meshes, respect_current_mask)) {
futures2.add(p.updateMipMaps());
}
}
}, null));
}
// join all:
Utils.waitIfAlive(futures, false);
Utils.waitIfAlive(futures2, false);
} catch (final Exception e) {
IJError.print(e);
} finally {
if (null != exe)
exe.shutdown();
Display.repaint();
}
}
Also used :
Displayable(ini.trakem2.display.Displayable)
HashMap(java.util.HashMap)
Layer(ini.trakem2.display.Layer)
NoninvertibleModelException(mpicbg.models.NoninvertibleModelException)
NoninvertibleTransformException(java.awt.geom.NoninvertibleTransformException)
ExecutorService(java.util.concurrent.ExecutorService)
Future(java.util.concurrent.Future)
Patch(ini.trakem2.display.Patch)
TransformMesh(mpicbg.trakem2.transform.TransformMesh)
HashSet(java.util.HashSet)
Example 3 with Coordinate
use of ini.trakem2.display.Coordinate in project TrakEM2 by trakem2.
the class ElasticMontage method exec.
@SuppressWarnings("deprecation")
public final void exec(final Param param, final List<Patch> patches, final Set<Patch> fixedPatches) throws Exception {
/* free memory */
patches.get(0).getProject().getLoader().releaseAll();
/* create tiles and models for all patches */
final ArrayList<AbstractAffineTile2D<?>> tiles = new ArrayList<AbstractAffineTile2D<?>>();
final ArrayList<AbstractAffineTile2D<?>> fixedTiles = new ArrayList<AbstractAffineTile2D<?>>();
Align.tilesFromPatches(param.po, patches, fixedPatches, tiles, fixedTiles);
if (!param.isAligned) {
Align.alignTiles(param.po, tiles, fixedTiles, param.tilesAreInPlace, param.maxNumThreads);
/* Apply the estimated affine transform to patches */
for (final AbstractAffineTile2D<?> t : tiles) t.getPatch().setAffineTransform(t.createAffine());
Display.update();
}
/* generate tile pairs for all by now overlapping tiles */
final ArrayList<AbstractAffineTile2D<?>[]> tilePairs = new ArrayList<AbstractAffineTile2D<?>[]>();
AbstractAffineTile2D.pairOverlappingTiles(tiles, tilePairs);
/* check if there was any pair */
if (tilePairs.size() == 0) {
Utils.log("Elastic montage could not find any overlapping patches after pre-montaging.");
return;
}
Utils.log(tilePairs.size() + " pairs of patches will be block-matched...");
/* make pairwise global models local */
final ArrayList<Triple<AbstractAffineTile2D<?>, AbstractAffineTile2D<?>, InvertibleCoordinateTransform>> pairs = new ArrayList<Triple<AbstractAffineTile2D<?>, AbstractAffineTile2D<?>, InvertibleCoordinateTransform>>();
/*
* The following casting madness is necessary to get this code compiled
* with Sun/Oracle Java 6 which otherwise generates an inconvertible
* type exception.
*
* TODO Remove as soon as this bug is fixed in Sun/Oracle javac.
*/
for (final AbstractAffineTile2D<?>[] pair : tilePairs) {
final AbstractAffineModel2D<?> m;
switch(param.po.desiredModelIndex) {
case 0:
final TranslationModel2D t = (TranslationModel2D) (Object) pair[1].getModel().createInverse();
t.concatenate((TranslationModel2D) (Object) pair[0].getModel());
m = t;
break;
case 1:
final RigidModel2D r = (RigidModel2D) (Object) pair[1].getModel().createInverse();
r.concatenate((RigidModel2D) (Object) pair[0].getModel());
m = r;
break;
case 2:
final SimilarityModel2D s = (SimilarityModel2D) (Object) pair[1].getModel().createInverse();
s.concatenate((SimilarityModel2D) (Object) pair[0].getModel());
m = s;
break;
case 3:
final AffineModel2D a = (AffineModel2D) (Object) pair[1].getModel().createInverse();
a.concatenate((AffineModel2D) (Object) pair[0].getModel());
m = a;
break;
default:
m = null;
}
pairs.add(new Triple<AbstractAffineTile2D<?>, AbstractAffineTile2D<?>, InvertibleCoordinateTransform>(pair[0], pair[1], m));
}
/* Elastic alignment */
/* Initialization */
final double springTriangleHeightTwice = 2 * Math.sqrt(0.75 * param.springLengthSpringMesh * param.springLengthSpringMesh);
final ArrayList<SpringMesh> meshes = new ArrayList<SpringMesh>(tiles.size());
final HashMap<AbstractAffineTile2D<?>, SpringMesh> tileMeshMap = new HashMap<AbstractAffineTile2D<?>, SpringMesh>();
for (final AbstractAffineTile2D<?> tile : tiles) {
final double w = tile.getWidth();
final double h = tile.getHeight();
final int numX = Math.max(2, (int) Math.ceil(w / param.springLengthSpringMesh) + 1);
final int numY = Math.max(2, (int) Math.ceil(h / springTriangleHeightTwice) + 1);
final double wMesh = (numX - 1) * param.springLengthSpringMesh;
final double hMesh = (numY - 1) * springTriangleHeightTwice;
final SpringMesh mesh = new SpringMesh(numX, numY, wMesh, hMesh, param.stiffnessSpringMesh, param.maxStretchSpringMesh * param.bmScale, param.dampSpringMesh);
meshes.add(mesh);
tileMeshMap.put(tile, mesh);
}
// final int blockRadius = Math.max( 32, Util.roundPos( param.springLengthSpringMesh / 2 ) );
final int blockRadius = Math.max(Util.roundPos(16 / param.bmScale), param.bmBlockRadius);
/**
* TODO set this something more than the largest error by the approximate model
*/
final int searchRadius = param.bmSearchRadius;
final AbstractModel<?> localSmoothnessFilterModel = mpicbg.trakem2.align.Util.createModel(param.bmLocalModelIndex);
for (final Triple<AbstractAffineTile2D<?>, AbstractAffineTile2D<?>, InvertibleCoordinateTransform> pair : pairs) {
final AbstractAffineTile2D<?> t1 = pair.a;
final AbstractAffineTile2D<?> t2 = pair.b;
final SpringMesh m1 = tileMeshMap.get(t1);
final SpringMesh m2 = tileMeshMap.get(t2);
final ArrayList<PointMatch> pm12 = new ArrayList<PointMatch>();
final ArrayList<PointMatch> pm21 = new ArrayList<PointMatch>();
final ArrayList<Vertex> v1 = m1.getVertices();
final ArrayList<Vertex> v2 = m2.getVertices();
final String patchName1 = patchName(t1.getPatch());
final String patchName2 = patchName(t2.getPatch());
final PatchImage pi1 = t1.getPatch().createTransformedImage();
if (pi1 == null) {
Utils.log("Patch `" + patchName1 + "' failed generating a transformed image. Skipping...");
continue;
}
final PatchImage pi2 = t2.getPatch().createTransformedImage();
if (pi2 == null) {
Utils.log("Patch `" + patchName2 + "' failed generating a transformed image. Skipping...");
continue;
}
final FloatProcessor fp1 = (FloatProcessor) pi1.target.convertToFloat();
final ByteProcessor mask1 = pi1.getMask();
final FloatProcessor fpMask1 = mask1 == null ? null : scaleByte(mask1);
final FloatProcessor fp2 = (FloatProcessor) pi2.target.convertToFloat();
final ByteProcessor mask2 = pi2.getMask();
final FloatProcessor fpMask2 = mask2 == null ? null : scaleByte(mask2);
if (!fixedTiles.contains(t1)) {
BlockMatching.matchByMaximalPMCC(fp1, fp2, fpMask1, fpMask2, param.bmScale, pair.c, blockRadius, blockRadius, searchRadius, searchRadius, param.bmMinR, param.bmRodR, param.bmMaxCurvatureR, v1, pm12, new ErrorStatistic(1));
if (param.bmUseLocalSmoothnessFilter) {
Utils.log("`" + patchName1 + "' > `" + patchName2 + "': found " + pm12.size() + " correspondence candidates.");
localSmoothnessFilterModel.localSmoothnessFilter(pm12, pm12, param.bmLocalRegionSigma, param.bmMaxLocalEpsilon, param.bmMaxLocalTrust);
Utils.log("`" + patchName1 + "' > `" + patchName2 + "': " + pm12.size() + " candidates passed local smoothness filter.");
} else {
Utils.log("`" + patchName1 + "' > `" + patchName2 + "': found " + pm12.size() + " correspondences.");
}
} else {
Utils.log("Skipping fixed patch `" + patchName1 + "'.");
}
if (!fixedTiles.contains(t2)) {
BlockMatching.matchByMaximalPMCC(fp2, fp1, fpMask2, fpMask1, param.bmScale, pair.c.createInverse(), blockRadius, blockRadius, searchRadius, searchRadius, param.bmMinR, param.bmRodR, param.bmMaxCurvatureR, v2, pm21, new ErrorStatistic(1));
if (param.bmUseLocalSmoothnessFilter) {
Utils.log("`" + patchName1 + "' < `" + patchName2 + "': found " + pm21.size() + " correspondence candidates.");
localSmoothnessFilterModel.localSmoothnessFilter(pm21, pm21, param.bmLocalRegionSigma, param.bmMaxLocalEpsilon, param.bmMaxLocalTrust);
Utils.log("`" + patchName1 + "' < `" + patchName2 + "': " + pm21.size() + " candidates passed local smoothness filter.");
} else {
Utils.log("`" + patchName1 + "' < `" + patchName2 + "': found " + pm21.size() + " correspondences.");
}
} else {
Utils.log("Skipping fixed patch `" + patchName2 + "'.");
}
for (final PointMatch pm : pm12) {
final Vertex p1 = (Vertex) pm.getP1();
final Vertex p2 = new Vertex(pm.getP2());
p1.addSpring(p2, new Spring(0, 1.0f));
m2.addPassiveVertex(p2);
}
for (final PointMatch pm : pm21) {
final Vertex p1 = (Vertex) pm.getP1();
final Vertex p2 = new Vertex(pm.getP2());
p1.addSpring(p2, new Spring(0, 1.0f));
m1.addPassiveVertex(p2);
}
}
/* initialize */
for (final Map.Entry<AbstractAffineTile2D<?>, SpringMesh> entry : tileMeshMap.entrySet()) entry.getValue().init(entry.getKey().getModel());
/* optimize the meshes */
try {
final long t0 = System.currentTimeMillis();
IJ.log("Optimizing spring meshes...");
if (param.useLegacyOptimizer) {
Utils.log(" ...using legacy optimizer...");
SpringMesh.optimizeMeshes2(meshes, param.po.maxEpsilon, param.maxIterationsSpringMesh, param.maxPlateauwidthSpringMesh, param.visualize);
} else {
SpringMesh.optimizeMeshes(meshes, param.po.maxEpsilon, param.maxIterationsSpringMesh, param.maxPlateauwidthSpringMesh, param.visualize);
}
IJ.log("Done optimizing spring meshes. Took " + (System.currentTimeMillis() - t0) + " ms");
} catch (final NotEnoughDataPointsException e) {
Utils.log("There were not enough data points to get the spring mesh optimizing.");
e.printStackTrace();
return;
}
/* apply */
for (final Map.Entry<AbstractAffineTile2D<?>, SpringMesh> entry : tileMeshMap.entrySet()) {
final AbstractAffineTile2D<?> tile = entry.getKey();
if (!fixedTiles.contains(tile)) {
final Patch patch = tile.getPatch();
final SpringMesh mesh = entry.getValue();
final Set<PointMatch> matches = mesh.getVA().keySet();
Rectangle box = patch.getCoordinateTransformBoundingBox();
/* compensate for existing coordinate transform bounding box */
for (final PointMatch pm : matches) {
final Point p1 = pm.getP1();
final double[] l = p1.getL();
l[0] += box.x;
l[1] += box.y;
}
final ThinPlateSplineTransform mlt = ElasticLayerAlignment.makeTPS(matches);
patch.appendCoordinateTransform(mlt);
box = patch.getCoordinateTransformBoundingBox();
patch.getAffineTransform().setToTranslation(box.x, box.y);
patch.updateInDatabase("transform");
patch.updateBucket();
patch.updateMipMaps();
}
}
Utils.log("Done.");
}
Also used :
ByteProcessor(ij.process.ByteProcessor)
NotEnoughDataPointsException(mpicbg.models.NotEnoughDataPointsException)
Vertex(mpicbg.models.Vertex)
SpringMesh(mpicbg.models.SpringMesh)
ThinPlateSplineTransform(mpicbg.trakem2.transform.ThinPlateSplineTransform)
HashMap(java.util.HashMap)
ArrayList(java.util.ArrayList)
Rectangle(java.awt.Rectangle)
RigidModel2D(mpicbg.models.RigidModel2D)
AbstractAffineModel2D(mpicbg.models.AbstractAffineModel2D)
AffineModel2D(mpicbg.models.AffineModel2D)
SimilarityModel2D(mpicbg.models.SimilarityModel2D)
FloatProcessor(ij.process.FloatProcessor)
Point(mpicbg.models.Point)
Spring(mpicbg.models.Spring)
Point(mpicbg.models.Point)
Triple(mpicbg.trakem2.util.Triple)
PointMatch(mpicbg.models.PointMatch)
PatchImage(ini.trakem2.display.Patch.PatchImage)
InvertibleCoordinateTransform(mpicbg.models.InvertibleCoordinateTransform)
ErrorStatistic(mpicbg.models.ErrorStatistic)
TranslationModel2D(mpicbg.models.TranslationModel2D)
HashMap(java.util.HashMap)
Map(java.util.Map)
Patch(ini.trakem2.display.Patch)
Example 4 with Coordinate
use of ini.trakem2.display.Coordinate in project TrakEM2 by trakem2.
the class AbstractAffineTile2D method pairOverlappingTiles.
/**
* Search a {@link List} of {@link AbstractAffineTile2D Tiles} for
* overlapping pairs. Adds the pairs into tilePairs.
*
* @param tiles
* @param tilePairs
*/
public static final <AAT extends AbstractAffineTile2D<?>> void pairOverlappingTiles(final List<AAT> tiles, final List<AbstractAffineTile2D<?>[]> tilePairs, final boolean sloppyOverlapTest) {
final HashSet<Patch> visited = new HashSet<Patch>();
final ArrayList<AbstractAffineTile2D<?>[]> tilePairCandidates = new ArrayList<AbstractAffineTile2D<?>[]>();
/* LUT for tiles */
final Hashtable<Patch, AAT> lut = new Hashtable<Patch, AAT>();
for (final AAT tile : tiles) lut.put(tile.patch, tile);
for (int a = 0; a < tiles.size(); ++a) {
final AbstractAffineTile2D<?> ta = tiles.get(a);
final Patch pa = ta.patch;
visited.add(pa);
final Layer la = pa.getLayer();
for (final Displayable d : la.getDisplayables(Patch.class, pa.getBoundingBox())) {
final Patch pb = (Patch) d;
if (visited.contains(pb))
continue;
final AAT tb = lut.get(pb);
if (tb == null)
continue;
tilePairCandidates.add(new AbstractAffineTile2D<?>[] { ta, tb });
}
}
if (sloppyOverlapTest)
tilePairs.addAll(tilePairCandidates);
else {
// TODO Fix this and use what the user wants to provide
final ExecutorService exec = Executors.newFixedThreadPool(Runtime.getRuntime().availableProcessors());
final ArrayList<Future<?>> futures = new ArrayList<Future<?>>();
for (final AbstractAffineTile2D<?>[] tatb : tilePairCandidates) {
futures.add(exec.submit(new Runnable() {
@Override
public void run() {
if (tatb[0].intersects(tatb[1]))
synchronized (tilePairs) {
tilePairs.add(tatb);
}
}
}));
}
try {
for (final Future<?> f : futures) f.get();
} catch (final InterruptedException e) {
e.printStackTrace();
} catch (final ExecutionException e) {
e.printStackTrace();
} finally {
exec.shutdown();
}
}
// // 1. Precompute the Area of each tile's Patch
// final HashMap< Patch, Pair< AAT, Area > > m = new HashMap< Patch, Pair< AAT, Area > >();
// // A lazy collection of pairs, computed in parallel ahead of consumption
// final Iterable< Pair< AAT, Area > > ts =
// new ParallelMapping< AAT, Pair< AAT, Area > >(
// tiles,
// new TaskFactory< AAT, Pair< AAT, Area > >() {
// @Override
// public Pair< AAT, Area > process( final AAT tile ) {
// return new Pair< AAT, Area >( tile, tile.patch.getArea() );
// }
// }
// );
// for ( final Pair< AAT, Area > t : ts) {
// m.put( t.a.patch, t );
// }
//
// // 2. Obtain the list of tile pairs, at one list per tile
// final Iterable< List<AbstractAffineTile2D< ? >[]> > pairsList =
// new ParallelMapping< AAT, List<AbstractAffineTile2D< ? >[]> >(
// tiles,
// new TaskFactory< AAT, List<AbstractAffineTile2D< ? >[]> >() {
// @Override
// public List<AbstractAffineTile2D< ? >[]> process( final AAT ta ) {
// final Area a;
// synchronized (m) {
// a = m.get( ta.patch ).b;
// }
// final ArrayList<AbstractAffineTile2D< ? >[]> seq = new ArrayList<AbstractAffineTile2D< ? >[]>();
// for ( final Patch p : ta.patch.getLayer().getIntersecting( ta.patch, Patch.class ) ) {
// if ( p == ta.patch )
// continue;
// final Pair< AAT, Area > pair;
// synchronized (m) {
// pair = m.get(p);
// }
// // Check that the Patch is among those to consider in the alignment
// if ( null != pair ) {
// // Check that the Patch visible pixels overlap -- may not if it has an alpha mask or coordinate transform
// if ( M.intersects( a, pair.b ) ) {
// seq.add( new AbstractAffineTile2D< ? >[]{ ta, pair.a });
// }
// }
// }
// return seq;
// }
// }
// );
//
// for (final List<AbstractAffineTile2D<?>[]> list: pairsList) {
// tilePairs.addAll(list);
// }
}
Also used :
Displayable(ini.trakem2.display.Displayable)
Hashtable(java.util.Hashtable)
ArrayList(java.util.ArrayList)
Layer(ini.trakem2.display.Layer)
Point(mpicbg.models.Point)
ExecutorService(java.util.concurrent.ExecutorService)
Future(java.util.concurrent.Future)
ExecutionException(java.util.concurrent.ExecutionException)
Patch(ini.trakem2.display.Patch)
HashSet(java.util.HashSet)
Example 5 with Coordinate
use of ini.trakem2.display.Coordinate in project TrakEM2 by trakem2.
the class Display method getPopupMenu.
/**
* Return a context-sensitive popup menu.
*/
protected JPopupMenu getPopupMenu() {
// get the job canceling dialog
if (!canvas.isInputEnabled()) {
return project.getLoader().getJobsPopup(this);
}
// create new
this.popup = new JPopupMenu();
JMenuItem item = null;
JMenu menu = null;
if (mode instanceof InspectPatchTrianglesMode) {
item = new JMenuItem("Exit inspection");
item.addActionListener(this);
popup.add(item);
item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_ESCAPE, 0, true));
return popup;
} else if (canvas.isTransforming()) {
item = new JMenuItem("Apply transform");
item.addActionListener(this);
popup.add(item);
// dummy, for I don't add a MenuKeyListener, but "works" through the normal key listener. It's here to provide a visual cue
item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_ENTER, 0, true));
item = new JMenuItem("Apply transform propagating to last layer");
item.addActionListener(this);
popup.add(item);
if (layer.getParent().indexOf(layer) == layer.getParent().size() - 1)
item.setEnabled(false);
if (!(getMode().getClass() == AffineTransformMode.class || getMode().getClass() == NonLinearTransformMode.class))
item.setEnabled(false);
item = new JMenuItem("Apply transform propagating to first layer");
item.addActionListener(this);
popup.add(item);
if (0 == layer.getParent().indexOf(layer))
item.setEnabled(false);
if (!(getMode().getClass() == AffineTransformMode.class || getMode().getClass() == NonLinearTransformMode.class))
item.setEnabled(false);
item = new JMenuItem("Cancel transform");
item.addActionListener(this);
popup.add(item);
item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_ESCAPE, 0, true));
item = new JMenuItem("Specify transform...");
item.addActionListener(this);
popup.add(item);
if (getMode().getClass() != AffineTransformMode.class)
item.setEnabled(false);
if (getMode().getClass() == ManualAlignMode.class) {
final JMenuItem lexport = new JMenuItem("Export landmarks");
popup.add(lexport);
final JMenuItem limport = new JMenuItem("Import landmarks");
popup.add(limport);
final ActionListener a = new ActionListener() {
@Override
public void actionPerformed(final ActionEvent ae) {
final ManualAlignMode mam = (ManualAlignMode) getMode();
final Object source = ae.getSource();
if (lexport == source) {
mam.exportLandmarks();
} else if (limport == source) {
mam.importLandmarks();
}
}
};
lexport.addActionListener(a);
limport.addActionListener(a);
}
return popup;
}
final Class<?> aclass = null == active ? null : active.getClass();
if (null != active) {
if (Profile.class == aclass) {
item = new JMenuItem("Duplicate, link and send to next layer");
item.addActionListener(this);
popup.add(item);
Layer nl = layer.getParent().next(layer);
if (nl == layer)
item.setEnabled(false);
item = new JMenuItem("Duplicate, link and send to previous layer");
item.addActionListener(this);
popup.add(item);
nl = layer.getParent().previous(layer);
if (nl == layer)
item.setEnabled(false);
menu = new JMenu("Duplicate, link and send to");
int i = 1;
for (final Layer la : layer.getParent().getLayers()) {
// TODO should label which layers contain Profile instances linked to the one being duplicated
item = new JMenuItem(i + ": z = " + la.getZ());
// TODO should label which layers contain Profile instances linked to the one being duplicated
item.addActionListener(this);
// TODO should label which layers contain Profile instances linked to the one being duplicated
menu.add(item);
if (la == this.layer)
item.setEnabled(false);
i++;
}
popup.add(menu);
item = new JMenuItem("Duplicate, link and send to...");
item.addActionListener(this);
popup.add(item);
popup.addSeparator();
item = new JMenuItem("Unlink from images");
item.addActionListener(this);
popup.add(item);
// isLinked() checks if it's linked to a Patch in its own layer
if (!active.isLinked())
item.setEnabled(false);
item = new JMenuItem("Show in 3D");
item.addActionListener(this);
popup.add(item);
popup.addSeparator();
} else if (Patch.class == aclass) {
final JMenu m = new JMenu("Patch");
item = new JMenuItem("Fill ROI in alpha mask");
item.addActionListener(this);
m.add(item);
item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_F, 0));
item.setEnabled(null != getRoi());
item = new JMenuItem("Fill inverse ROI in alpha mask");
item.addActionListener(this);
m.add(item);
item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_F, Event.SHIFT_MASK));
item.setEnabled(null != getRoi());
item = new JMenuItem("Remove alpha mask");
item.addActionListener(this);
m.add(item);
if (!((Patch) active).hasAlphaMask())
item.setEnabled(false);
item = new JMenuItem("Unlink from images");
item.addActionListener(this);
m.add(item);
if (!active.isLinked(Patch.class))
item.setEnabled(false);
if (((Patch) active).isStack()) {
item = new JMenuItem("Unlink slices");
item.addActionListener(this);
m.add(item);
}
final int n_sel_patches = selection.getSelected(Patch.class).size();
item = new JMenuItem("Snap");
item.addActionListener(this);
m.add(item);
item.setEnabled(1 == n_sel_patches);
item = new JMenuItem("Montage");
item.addActionListener(this);
m.add(item);
item.setEnabled(n_sel_patches > 1);
item = new JMenuItem("Lens correction");
item.addActionListener(this);
m.add(item);
item.setEnabled(n_sel_patches > 1);
item = new JMenuItem("Blend");
item.addActionListener(this);
m.add(item);
item.setEnabled(n_sel_patches > 1);
item = new JMenuItem("Open image");
item.addActionListener(new ActionListener() {
@Override
public void actionPerformed(final ActionEvent e) {
for (final Patch p : selection.get(Patch.class)) {
p.getImagePlus().show();
}
}
});
m.add(item);
item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_D, KeyEvent.SHIFT_MASK, true));
item = new JMenuItem("Open original image");
item.addActionListener(new ActionListener() {
@Override
public void actionPerformed(final ActionEvent e) {
for (final Patch p : selection.get(Patch.class)) {
p.getProject().getLoader().releaseToFit(p.getOWidth(), p.getOHeight(), p.getType(), 5);
p.getProject().getLoader().openImagePlus(p.getImageFilePath()).show();
}
}
});
item = new JMenuItem("View volume");
item.addActionListener(this);
m.add(item);
final HashSet<Displayable> hs = active.getLinked(Patch.class);
if (null == hs || 0 == hs.size())
item.setEnabled(false);
item = new JMenuItem("View orthoslices");
item.addActionListener(this);
m.add(item);
// if no Patch instances among the directly linked, then it's not a stack
if (null == hs || 0 == hs.size())
item.setEnabled(false);
popup.add(m);
popup.addSeparator();
} else {
item = new JMenuItem("Unlink");
item.addActionListener(this);
popup.add(item);
item = new JMenuItem("Show in 3D");
item.addActionListener(this);
popup.add(item);
popup.addSeparator();
}
if (AreaList.class == aclass) {
final ArrayList<?> al = selection.getSelected();
int n = 0;
for (final Iterator<?> it = al.iterator(); it.hasNext(); ) {
if (it.next().getClass() == AreaList.class)
n++;
}
item = new JMenuItem("Merge");
item.addActionListener(this);
popup.add(item);
if (n < 2)
item.setEnabled(false);
item = new JMenuItem("Split");
item.addActionListener(this);
popup.add(item);
if (n < 1)
item.setEnabled(false);
addAreaListAreasMenu(popup, active);
popup.addSeparator();
} else if (Pipe.class == aclass) {
item = new JMenuItem("Reverse point order");
item.addActionListener(this);
popup.add(item);
popup.addSeparator();
} else if (Treeline.class == aclass || AreaTree.class == aclass) {
if (AreaTree.class == aclass)
addAreaTreeAreasMenu(popup, (AreaTree) active);
item = new JMenuItem("Reroot");
item.addActionListener(this);
popup.add(item);
item = new JMenuItem("Part subtree");
item.addActionListener(this);
popup.add(item);
item = new JMenuItem("Join");
item.addActionListener(this);
popup.add(item);
item = new JMenuItem("Show tabular view");
item.addActionListener(this);
popup.add(item);
final Collection<Tree> trees = selection.get(Tree.class);
//
final JMenu nodeMenu = new JMenu("Nodes");
item = new JMenuItem("Mark");
item.addActionListener(this);
nodeMenu.add(item);
item = new JMenuItem("Clear marks (selected Trees)");
item.addActionListener(this);
nodeMenu.add(item);
final JMenuItem nodeColor = new JMenuItem("Color...");
nodeMenu.add(nodeColor);
nodeColor.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_C, KeyEvent.SHIFT_MASK, true));
final JMenuItem nodePairColor = new JMenuItem("Color path between two nodes tagged as...");
nodeMenu.add(nodePairColor);
final JMenuItem nodeRadius = active instanceof Treeline ? new JMenuItem("Radius...") : null;
if (null != nodeRadius) {
nodeMenu.add(nodeRadius);
nodeRadius.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_O, 0, true));
}
final JMenuItem removeAllTags = new JMenuItem("Drop all tags (selected trees)");
nodeMenu.add(removeAllTags);
final JMenuItem removeTag = new JMenuItem("Drop all occurrences of tag...");
nodeMenu.add(removeTag);
final JMenuItem colorizeByNodeCentrality = new JMenuItem("Colorize by node betweenness centrality");
nodeMenu.add(colorizeByNodeCentrality);
final JMenuItem colorizeByBranchCentrality = new JMenuItem("Colorize by branch betweenness centrality");
nodeMenu.add(colorizeByBranchCentrality);
popup.add(nodeMenu);
final ActionListener ln = new ActionListener() {
@Override
public void actionPerformed(final ActionEvent ae) {
if (null == active) {
Utils.showMessage("No tree selected!");
return;
}
if (!(active instanceof Tree)) {
Utils.showMessage("The selected object is not a Tree!");
return;
}
final Tree tree = (Tree) active;
final Object src = ae.getSource();
//
if (src == nodeColor) {
final Node nd = tree.getLastVisited();
if (null == nd) {
Utils.showMessage("Select a node first by clicking on it\nor moving the mouse over it and pushing 'g'.");
return;
}
// sets an undo step
tree.adjustNodeColors(nd);
} else if (src == nodePairColor) {
final TreeMap<String, Tag> sm = getTags(tree);
if (null == sm)
return;
if (1 == sm.size()) {
Utils.showMessage("Need at least two different tags in the tree!");
return;
}
final Color color = tree.getColor();
final GenericDialog gd = new GenericDialog("Node colors");
gd.addSlider("Red: ", 0, 255, color.getRed());
gd.addSlider("Green: ", 0, 255, color.getGreen());
gd.addSlider("Blue: ", 0, 255, color.getBlue());
final String[] stags = asStrings(sm);
sm.keySet().toArray(stags);
gd.addChoice("Upstream tag:", stags, stags[0]);
gd.addChoice("Downstream tag:", stags, stags[1]);
gd.showDialog();
if (gd.wasCanceled())
return;
final Color newColor = new Color((int) gd.getNextNumber(), (int) gd.getNextNumber(), (int) gd.getNextNumber());
final Tag upstreamTag = sm.get(gd.getNextChoice());
final Tag downstreamTag = sm.get(gd.getNextChoice());
final List<Tree<?>.NodePath> pairs = tree.findTaggedPairs(upstreamTag, downstreamTag);
if (null == pairs || pairs.isEmpty()) {
Utils.showMessage("No pairs found for '" + upstreamTag + "' and '" + downstreamTag + "'");
return;
}
getLayerSet().addDataEditStep(tree);
for (final Tree<?>.NodePath pair : pairs) {
for (final Node<?> nd : pair.path) {
nd.setColor(newColor);
}
}
getLayerSet().addDataEditStep(tree);
Display.repaint();
} else if (src == nodeRadius) {
if (!(tree instanceof Treeline))
return;
final Node nd = tree.getLastVisited();
if (null == nd) {
Utils.showMessage("Select a node first by clicking on it\nor moving the mouse over it and pushing 'g'.");
return;
}
// sets an undo step
((Treeline) tree).askAdjustRadius(nd);
} else if (src == removeAllTags) {
if (!Utils.check("Really remove all tags from all selected trees?"))
return;
final List<Tree> sel = selection.get(Tree.class);
getLayerSet().addDataEditStep(new HashSet<Displayable>(sel));
try {
for (final Tree t : sel) {
t.dropAllTags();
}
// current state
getLayerSet().addDataEditStep(new HashSet<Displayable>(sel));
} catch (final Exception e) {
getLayerSet().undoOneStep();
IJError.print(e);
}
Display.repaint();
} else if (src == removeTag) {
final TreeMap<String, Tag> tags = getTags(tree);
final String[] ts = asStrings(tags);
final GenericDialog gd = new GenericDialog("Remove tags");
gd.addChoice("Tag:", ts, ts[0]);
final String[] c = new String[] { "Active tree", "All selected trees and connectors", "All trees and connectors" };
gd.addChoice("From: ", c, c[0]);
gd.showDialog();
if (gd.wasCanceled())
return;
final HashSet<Displayable> ds = new HashSet<Displayable>();
final Tag tag = tags.get(gd.getNextChoice());
switch(gd.getNextChoiceIndex()) {
case 0:
ds.add(tree);
break;
case 1:
ds.addAll(selection.get(Tree.class));
case 2:
ds.addAll(getLayerSet().getZDisplayables(Tree.class, true));
}
getLayerSet().addDataEditStep(ds);
try {
for (final Displayable d : ds) {
final Tree t = (Tree) d;
t.removeTag(tag);
}
getLayerSet().addDataEditStep(ds);
} catch (final Exception e) {
getLayerSet().undoOneStep();
IJError.print(e);
}
Display.repaint();
} else if (src == colorizeByNodeCentrality) {
final List<Tree> ts = selection.get(Tree.class);
final HashSet<Tree> ds = new HashSet<Tree>(ts);
getLayerSet().addDataEditStep(ds);
try {
for (final Tree t : ts) {
t.colorizeByNodeBetweennessCentrality();
}
getLayerSet().addDataEditStep(ds);
Display.repaint();
} catch (final Exception e) {
getLayerSet().undoOneStep();
IJError.print(e);
}
} else if (src == colorizeByBranchCentrality) {
final List<Tree> ts = selection.get(Tree.class);
final HashSet<Tree> ds = new HashSet<Tree>(ts);
getLayerSet().addDataEditStep(ds);
try {
for (final Tree t : ts) {
t.colorizeByBranchBetweennessCentrality(2);
}
getLayerSet().addDataEditStep(ds);
Display.repaint();
} catch (final Exception e) {
getLayerSet().undoOneStep();
IJError.print(e);
}
}
}
};
for (final JMenuItem a : new JMenuItem[] { nodeColor, nodePairColor, nodeRadius, removeAllTags, removeTag, colorizeByNodeCentrality, colorizeByBranchCentrality }) {
if (null == a)
continue;
a.addActionListener(ln);
}
//
final JMenu review = new JMenu("Review");
final JMenuItem tgenerate = new JMenuItem("Generate review stacks (selected Trees)");
review.add(tgenerate);
tgenerate.setEnabled(trees.size() > 0);
final JMenuItem tslab = new JMenuItem("Generate review stack for current slab");
review.add(tslab);
final JMenuItem tsubtree = new JMenuItem("Generate review stacks for subtree");
review.add(tsubtree);
final JMenuItem tremove = new JMenuItem("Remove reviews (selected Trees)");
review.add(tremove);
tremove.setEnabled(trees.size() > 0);
final JMenuItem tconnectors = new JMenuItem("View table of outgoing/incoming connectors");
review.add(tconnectors);
final ActionListener l = new ActionListener() {
@Override
public void actionPerformed(final ActionEvent ae) {
if (!Utils.check("Really " + ae.getActionCommand())) {
return;
}
dispatcher.exec(new Runnable() {
@Override
public void run() {
int count = 0;
for (final Tree<?> t : trees) {
Utils.log("Processing " + (++count) + "/" + trees.size());
Bureaucrat bu = null;
if (ae.getSource() == tgenerate)
bu = t.generateAllReviewStacks();
else if (ae.getSource() == tremove)
bu = t.removeReviews();
else if (ae.getSource() == tslab) {
final Point po = canvas.consumeLastPopupPoint();
Utils.log2(po, layer, 1.0);
bu = t.generateReviewStackForSlab(po.x, po.y, Display.this.layer, 1.0);
} else if (ae.getSource() == tsubtree) {
final Point po = canvas.consumeLastPopupPoint();
bu = t.generateSubtreeReviewStacks(po.x, po.y, Display.this.layer, 1.0);
}
if (null != bu)
try {
bu.getWorker().join();
} catch (final InterruptedException ie) {
return;
}
}
}
});
}
};
for (final JMenuItem c : new JMenuItem[] { tgenerate, tslab, tsubtree, tremove }) c.addActionListener(l);
tconnectors.addActionListener(new ActionListener() {
@Override
public void actionPerformed(final ActionEvent ae) {
for (final Tree<?> t : trees) TreeConnectorsView.create(t);
}
});
popup.add(review);
final JMenu go = new JMenu("Go");
item = new JMenuItem("Previous branch node or start");
item.addActionListener(this);
go.add(item);
item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_B, 0, true));
item = new JMenuItem("Next branch node or end");
item.addActionListener(this);
go.add(item);
item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_N, 0, true));
item = new JMenuItem("Root");
item.addActionListener(this);
go.add(item);
item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_R, 0, true));
go.addSeparator();
item = new JMenuItem("Last added node");
item.addActionListener(this);
go.add(item);
item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_L, 0, true));
item = new JMenuItem("Last edited node");
item.addActionListener(this);
go.add(item);
item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_E, 0, true));
popup.add(go);
final JMenu tmeasure = new JMenu("Measure");
final JMenuItem dist_to_root = new JMenuItem("Distance from this node to root");
tmeasure.add(dist_to_root);
final JMenuItem dist_to_tag = new JMenuItem("Distance from this node to all nodes tagged as...");
tmeasure.add(dist_to_tag);
final JMenuItem dist_to_mark = new JMenuItem("Distance from this node to the marked node");
tmeasure.add(dist_to_mark);
final JMenuItem dist_pairs = new JMenuItem("Shortest distances between all pairs of nodes tagged as...");
tmeasure.add(dist_pairs);
final ActionListener tma = getTreePathMeasureListener((Tree<?>) active);
for (final JMenuItem mi : new JMenuItem[] { dist_to_root, dist_to_tag, dist_to_mark, dist_pairs }) {
mi.addActionListener(tma);
}
popup.add(tmeasure);
final String[] name = new String[] { AreaTree.class.getSimpleName(), Treeline.class.getSimpleName() };
if (Treeline.class == aclass) {
final String a = name[0];
name[0] = name[1];
name[1] = a;
}
item = new JMenuItem("Duplicate " + name[0] + " as " + name[1]);
item.addActionListener(new ActionListener() {
@Override
public void actionPerformed(final ActionEvent e) {
Bureaucrat.createAndStart(new Worker.Task("Converting") {
@Override
public void exec() {
try {
getLayerSet().addChangeTreesStep();
final Map<Tree<?>, Tree<?>> m = Tree.duplicateAs(selection.getSelected(), (Class<Tree<?>>) (Treeline.class == aclass ? AreaTree.class : Treeline.class));
if (m.isEmpty()) {
getLayerSet().removeLastUndoStep();
} else {
getLayerSet().addChangeTreesStep();
}
} catch (final Exception e) {
IJError.print(e);
}
}
}, getProject());
}
});
popup.add(item);
popup.addSeparator();
} else if (Connector.class == aclass) {
item = new JMenuItem("Merge");
item.addActionListener(new ActionListener() {
@Override
public void actionPerformed(final ActionEvent ae) {
if (null == getActive() || getActive().getClass() != Connector.class) {
Utils.log("Active object must be a Connector!");
return;
}
final List<Connector> col = selection.get(Connector.class);
if (col.size() < 2) {
Utils.log("Select more than one Connector!");
return;
}
if (col.get(0) != getActive()) {
if (col.remove(getActive())) {
col.add(0, (Connector) getActive());
} else {
Utils.log("ERROR: cannot find active object in selection list!");
return;
}
}
Bureaucrat.createAndStart(new Worker.Task("Merging connectors") {
@Override
public void exec() {
getLayerSet().addChangeTreesStep();
Connector base = null;
try {
base = Connector.merge(col);
} catch (final Exception e) {
IJError.print(e);
}
if (null == base) {
Utils.log("ERROR: could not merge connectors!");
getLayerSet().undoOneStep();
} else {
getLayerSet().addChangeTreesStep();
}
Display.repaint();
}
}, getProject());
}
});
popup.add(item);
item.setEnabled(selection.getSelected(Connector.class).size() > 1);
popup.addSeparator();
}
item = new JMenuItem("Duplicate");
item.addActionListener(this);
popup.add(item);
item = new JMenuItem("Color...");
item.addActionListener(this);
popup.add(item);
if (active instanceof LayerSet)
item.setEnabled(false);
if (active.isLocked()) {
item = new JMenuItem("Unlock");
item.addActionListener(this);
popup.add(item);
} else {
item = new JMenuItem("Lock");
item.addActionListener(this);
popup.add(item);
}
menu = new JMenu("Move");
popup.addSeparator();
final LayerSet ls = layer.getParent();
item = new JMenuItem("Move to top");
item.addActionListener(this);
menu.add(item);
// this is just to draw the key name by the menu; it does not incur on any event being generated (that I know if), and certainly not any event being listened to by TrakEM2.
item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_HOME, 0, true));
if (ls.isTop(active))
item.setEnabled(false);
item = new JMenuItem("Move up");
item.addActionListener(this);
menu.add(item);
item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_PAGE_UP, 0, true));
if (ls.isTop(active))
item.setEnabled(false);
item = new JMenuItem("Move down");
item.addActionListener(this);
menu.add(item);
item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_PAGE_DOWN, 0, true));
if (ls.isBottom(active))
item.setEnabled(false);
item = new JMenuItem("Move to bottom");
item.addActionListener(this);
menu.add(item);
item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_END, 0, true));
if (ls.isBottom(active))
item.setEnabled(false);
popup.add(menu);
popup.addSeparator();
item = new JMenuItem("Delete...");
item.addActionListener(this);
popup.add(item);
try {
if (Patch.class == aclass) {
if (!active.isOnlyLinkedTo(Patch.class)) {
item.setEnabled(false);
}
}
} catch (final Exception e) {
IJError.print(e);
item.setEnabled(false);
}
if (Patch.class == aclass) {
item = new JMenuItem("Revert");
item.addActionListener(this);
popup.add(item);
if (null == ((Patch) active).getOriginalPath())
item.setEnabled(false);
popup.addSeparator();
}
item = new JMenuItem("Properties...");
item.addActionListener(this);
popup.add(item);
item = new JMenuItem("Show centered");
item.addActionListener(this);
popup.add(item);
popup.addSeparator();
if (!(active instanceof ZDisplayable)) {
final int i_layer = layer.getParent().indexOf(layer);
final int n_layers = layer.getParent().size();
item = new JMenuItem("Send to previous layer");
item.addActionListener(this);
popup.add(item);
if (1 == n_layers || 0 == i_layer || active.isLinked())
item.setEnabled(false);
else // check if the active is a profile and contains a link to another profile in the layer it is going to be sent to, or it is linked
if (active instanceof Profile && !active.canSendTo(layer.getParent().previous(layer)))
item.setEnabled(false);
item = new JMenuItem("Send to next layer");
item.addActionListener(this);
popup.add(item);
if (1 == n_layers || n_layers - 1 == i_layer || active.isLinked())
item.setEnabled(false);
else if (active instanceof Profile && !active.canSendTo(layer.getParent().next(layer)))
item.setEnabled(false);
menu = new JMenu("Send linked group to...");
if (active.hasLinkedGroupWithinLayer(this.layer)) {
int i = 1;
for (final Layer la : ls.getLayers()) {
String layer_title = i + ": " + la.getTitle();
if (-1 == layer_title.indexOf(' '))
layer_title += " ";
item = new JMenuItem(layer_title);
item.addActionListener(this);
menu.add(item);
if (la == this.layer)
item.setEnabled(false);
i++;
}
popup.add(menu);
} else {
menu.setEnabled(false);
// Utils.log("Active's linked group not within layer.");
}
popup.add(menu);
popup.addSeparator();
}
}
item = new JMenuItem("Undo");
item.addActionListener(this);
popup.add(item);
if (!layer.getParent().canUndo() || canvas.isTransforming())
item.setEnabled(false);
item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_Z, Utils.getControlModifier(), true));
item = new JMenuItem("Redo");
item.addActionListener(this);
popup.add(item);
if (!layer.getParent().canRedo() || canvas.isTransforming())
item.setEnabled(false);
item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_Z, Event.SHIFT_MASK | Utils.getControlModifier(), true));
popup.addSeparator();
try {
menu = new JMenu("Hide/Unhide");
item = new JMenuItem("Hide deselected");
item.addActionListener(this);
menu.add(item);
item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_H, Event.SHIFT_MASK, true));
boolean none = 0 == selection.getNSelected();
if (none)
item.setEnabled(false);
item = new JMenuItem("Hide deselected except images");
item.addActionListener(this);
menu.add(item);
item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_H, Event.SHIFT_MASK | Event.ALT_MASK, true));
if (none)
item.setEnabled(false);
item = new JMenuItem("Hide selected");
item.addActionListener(this);
menu.add(item);
item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_H, 0, true));
if (none)
item.setEnabled(false);
none = !layer.getParent().containsDisplayable(DLabel.class);
item = new JMenuItem("Hide all labels");
item.addActionListener(this);
menu.add(item);
if (none)
item.setEnabled(false);
item = new JMenuItem("Unhide all labels");
item.addActionListener(this);
menu.add(item);
if (none)
item.setEnabled(false);
none = !layer.getParent().contains(AreaList.class);
item = new JMenuItem("Hide all arealists");
item.addActionListener(this);
menu.add(item);
if (none)
item.setEnabled(false);
item = new JMenuItem("Unhide all arealists");
item.addActionListener(this);
menu.add(item);
if (none)
item.setEnabled(false);
none = !layer.contains(Profile.class);
item = new JMenuItem("Hide all profiles");
item.addActionListener(this);
menu.add(item);
if (none)
item.setEnabled(false);
item = new JMenuItem("Unhide all profiles");
item.addActionListener(this);
menu.add(item);
if (none)
item.setEnabled(false);
none = !layer.getParent().contains(Pipe.class);
item = new JMenuItem("Hide all pipes");
item.addActionListener(this);
menu.add(item);
if (none)
item.setEnabled(false);
item = new JMenuItem("Unhide all pipes");
item.addActionListener(this);
menu.add(item);
if (none)
item.setEnabled(false);
none = !layer.getParent().contains(Polyline.class);
item = new JMenuItem("Hide all polylines");
item.addActionListener(this);
menu.add(item);
if (none)
item.setEnabled(false);
item = new JMenuItem("Unhide all polylines");
item.addActionListener(this);
menu.add(item);
if (none)
item.setEnabled(false);
none = !layer.getParent().contains(Treeline.class);
item = new JMenuItem("Hide all treelines");
item.addActionListener(this);
menu.add(item);
if (none)
item.setEnabled(false);
item = new JMenuItem("Unhide all treelines");
item.addActionListener(this);
menu.add(item);
if (none)
item.setEnabled(false);
none = !layer.getParent().contains(AreaTree.class);
item = new JMenuItem("Hide all areatrees");
item.addActionListener(this);
menu.add(item);
if (none)
item.setEnabled(false);
item = new JMenuItem("Unhide all areatrees");
item.addActionListener(this);
menu.add(item);
if (none)
item.setEnabled(false);
none = !layer.getParent().contains(Ball.class);
item = new JMenuItem("Hide all balls");
item.addActionListener(this);
menu.add(item);
if (none)
item.setEnabled(false);
item = new JMenuItem("Unhide all balls");
item.addActionListener(this);
menu.add(item);
if (none)
item.setEnabled(false);
none = !layer.getParent().contains(Connector.class);
item = new JMenuItem("Hide all connectors");
item.addActionListener(this);
menu.add(item);
if (none)
item.setEnabled(false);
item = new JMenuItem("Unhide all connectors");
item.addActionListener(this);
menu.add(item);
if (none)
item.setEnabled(false);
none = !layer.getParent().containsDisplayable(Patch.class);
item = new JMenuItem("Hide all images");
item.addActionListener(this);
menu.add(item);
if (none)
item.setEnabled(false);
item = new JMenuItem("Unhide all images");
item.addActionListener(this);
menu.add(item);
if (none)
item.setEnabled(false);
item = new JMenuItem("Hide all but images");
item.addActionListener(this);
menu.add(item);
item = new JMenuItem("Unhide all");
item.addActionListener(this);
menu.add(item);
item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_H, Event.ALT_MASK, true));
popup.add(menu);
} catch (final Exception e) {
IJError.print(e);
}
// plugins, if any
Utils.addPlugIns(popup, "Display", project, new Callable<Displayable>() {
@Override
public Displayable call() {
return Display.this.getActive();
}
});
final JMenu align_menu = new JMenu("Align");
item = new JMenuItem("Align stack slices");
item.addActionListener(this);
align_menu.add(item);
if (selection.isEmpty() || !(getActive().getClass() == Patch.class && ((Patch) getActive()).isStack()))
item.setEnabled(false);
item = new JMenuItem("Align layers");
item.addActionListener(this);
align_menu.add(item);
if (1 == layer.getParent().size())
item.setEnabled(false);
item = new JMenuItem("Align layers manually with landmarks");
item.addActionListener(this);
align_menu.add(item);
if (1 == layer.getParent().size())
item.setEnabled(false);
item = new JMenuItem("Align multi-layer mosaic");
item.addActionListener(this);
align_menu.add(item);
if (1 == layer.getParent().size())
item.setEnabled(false);
item = new JMenuItem("Montage all images in this layer");
item.addActionListener(this);
align_menu.add(item);
if (layer.getDisplayables(Patch.class).size() < 2)
item.setEnabled(false);
item = new JMenuItem("Montage selected images");
item.addActionListener(this);
align_menu.add(item);
if (selection.getSelected(Patch.class).size() < 2)
item.setEnabled(false);
item = new JMenuItem("Montage multiple layers");
item.addActionListener(this);
align_menu.add(item);
popup.add(align_menu);
final JMenuItem st = new JMenu("Transform");
final StartTransformMenuListener tml = new StartTransformMenuListener();
item = new JMenuItem("Transform (affine)");
item.addActionListener(tml);
st.add(item);
item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_T, 0, true));
if (null == active)
item.setEnabled(false);
item = new JMenuItem("Transform (non-linear)");
item.addActionListener(tml);
st.add(item);
if (null == active)
item.setEnabled(false);
item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_T, Event.SHIFT_MASK, true));
item = new JMenuItem("Cancel transform");
st.add(item);
item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_ESCAPE, 0, true));
// just added as a self-documenting cue; no listener
item.setEnabled(false);
item = new JMenuItem("Remove rotation, scaling and shear (selected images)");
item.addActionListener(tml);
st.add(item);
if (null == active)
item.setEnabled(false);
item = new JMenuItem("Remove rotation, scaling and shear layer-wise");
item.addActionListener(tml);
st.add(item);
item = new JMenuItem("Remove coordinate transforms (selected images)");
item.addActionListener(tml);
st.add(item);
if (null == active)
item.setEnabled(false);
item = new JMenuItem("Remove coordinate transforms layer-wise");
item.addActionListener(tml);
st.add(item);
item = new JMenuItem("Adjust mesh resolution (selected images)");
item.addActionListener(tml);
st.add(item);
if (null == active)
item.setEnabled(false);
item = new JMenuItem("Adjust mesh resolution layer-wise");
item.addActionListener(tml);
st.add(item);
item = new JMenuItem("Set coordinate transform of selected image to other selected images");
item.addActionListener(tml);
st.add(item);
if (null == active)
item.setEnabled(false);
item = new JMenuItem("Set coordinate transform of selected image layer-wise");
item.addActionListener(tml);
st.add(item);
if (null == active)
item.setEnabled(false);
item = new JMenuItem("Set affine transform of selected image to other selected images");
item.addActionListener(tml);
st.add(item);
if (null == active)
item.setEnabled(false);
item = new JMenuItem("Set affine transform of selected image layer-wise");
item.addActionListener(tml);
st.add(item);
if (null == active)
item.setEnabled(false);
popup.add(st);
final JMenu link_menu = new JMenu("Link");
item = new JMenuItem("Link images...");
item.addActionListener(this);
link_menu.add(item);
item = new JMenuItem("Unlink all selected images");
item.addActionListener(this);
link_menu.add(item);
item.setEnabled(selection.getSelected(Patch.class).size() > 0);
item = new JMenuItem("Unlink all");
item.addActionListener(this);
link_menu.add(item);
popup.add(link_menu);
final JMenu adjust_menu = new JMenu("Adjust images");
item = new JMenuItem("Enhance contrast layer-wise...");
item.addActionListener(this);
adjust_menu.add(item);
item = new JMenuItem("Enhance contrast (selected images)...");
item.addActionListener(this);
adjust_menu.add(item);
if (selection.isEmpty())
item.setEnabled(false);
item = new JMenuItem("Adjust image filters (selected images)");
item.addActionListener(this);
adjust_menu.add(item);
if (selection.isEmpty())
item.setEnabled(false);
item = new JMenuItem("Set Min and Max layer-wise...");
item.addActionListener(this);
adjust_menu.add(item);
item = new JMenuItem("Set Min and Max (selected images)...");
item.addActionListener(this);
adjust_menu.add(item);
if (selection.isEmpty())
item.setEnabled(false);
item = new JMenuItem("Adjust min and max (selected images)...");
item.addActionListener(this);
adjust_menu.add(item);
item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_J, 0));
if (selection.isEmpty())
item.setEnabled(false);
item = new JMenuItem("Mask image borders (layer-wise)...");
item.addActionListener(this);
adjust_menu.add(item);
item = new JMenuItem("Mask image borders (selected images)...");
item.addActionListener(this);
adjust_menu.add(item);
if (selection.isEmpty())
item.setEnabled(false);
item = new JMenuItem("Remove alpha masks (layer-wise)...");
item.addActionListener(this);
adjust_menu.add(item);
item = new JMenuItem("Remove alpha masks (selected images)...");
item.addActionListener(this);
adjust_menu.add(item);
if (selection.isEmpty())
item.setEnabled(false);
item = new JMenuItem("Split images under polyline ROI");
item.addActionListener(this);
adjust_menu.add(item);
final Roi roi = canvas.getFakeImagePlus().getRoi();
if (null == roi || !(roi.getType() == Roi.POLYLINE || roi.getType() == Roi.FREELINE))
item.setEnabled(false);
item = new JMenuItem("Blend (layer-wise)...");
item.addActionListener(this);
adjust_menu.add(item);
item = new JMenuItem("Blend (selected images)...");
item.addActionListener(this);
adjust_menu.add(item);
if (selection.isEmpty())
item.setEnabled(false);
item = new JMenuItem("Match intensities (layer-wise)...");
item.addActionListener(this);
adjust_menu.add(item);
item = new JMenuItem("Remove intensity maps (layer-wise)...");
item.addActionListener(this);
adjust_menu.add(item);
popup.add(adjust_menu);
final JMenu script = new JMenu("Script");
final MenuScriptListener msl = new MenuScriptListener();
item = new JMenuItem("Set preprocessor script layer-wise...");
item.addActionListener(msl);
script.add(item);
item = new JMenuItem("Set preprocessor script (selected images)...");
item.addActionListener(msl);
script.add(item);
if (selection.isEmpty())
item.setEnabled(false);
item = new JMenuItem("Remove preprocessor script layer-wise...");
item.addActionListener(msl);
script.add(item);
item = new JMenuItem("Remove preprocessor script (selected images)...");
item.addActionListener(msl);
script.add(item);
if (selection.isEmpty())
item.setEnabled(false);
popup.add(script);
menu = new JMenu("Import");
item = new JMenuItem("Import image");
item.addActionListener(this);
menu.add(item);
item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_I, Event.ALT_MASK & Event.SHIFT_MASK, true));
item = new JMenuItem("Import stack...");
item.addActionListener(this);
menu.add(item);
item = new JMenuItem("Import stack with landmarks...");
item.addActionListener(this);
menu.add(item);
item = new JMenuItem("Import grid...");
item.addActionListener(this);
menu.add(item);
item = new JMenuItem("Import sequence as grid...");
item.addActionListener(this);
menu.add(item);
item = new JMenuItem("Import from text file...");
item.addActionListener(this);
menu.add(item);
item = new JMenuItem("Import labels as arealists...");
item.addActionListener(this);
menu.add(item);
item = new JMenuItem("Tags ...");
item.addActionListener(this);
menu.add(item);
popup.add(menu);
menu = new JMenu("Export");
final boolean has_arealists = layer.getParent().contains(AreaList.class);
item = new JMenuItem("Make flat image...");
item.addActionListener(this);
menu.add(item);
item = new JMenuItem("Arealists as labels (tif)");
item.addActionListener(this);
menu.add(item);
item.setEnabled(has_arealists);
item = new JMenuItem("Arealists as labels (amira)");
item.addActionListener(this);
menu.add(item);
item.setEnabled(has_arealists);
item = new JMenuItem("Image stack under selected Arealist");
item.addActionListener(this);
menu.add(item);
item.setEnabled(null != active && AreaList.class == active.getClass());
item = new JMenuItem("Fly through selected Treeline/AreaTree");
item.addActionListener(this);
menu.add(item);
item.setEnabled(null != active && Tree.class.isInstance(active));
item = new JMenuItem("Tags...");
item.addActionListener(this);
menu.add(item);
item = new JMenuItem("Connectivity graph...");
item.addActionListener(this);
menu.add(item);
item = new JMenuItem("NeuroML...");
item.addActionListener(this);
menu.add(item);
popup.add(menu);
menu = new JMenu("Display");
item = new JMenuItem("Resize canvas/LayerSet...");
item.addActionListener(this);
menu.add(item);
item = new JMenuItem("Autoresize canvas/LayerSet");
item.addActionListener(this);
menu.add(item);
item = new JMenuItem("Resize canvas/LayerSet to ROI");
item.addActionListener(this);
menu.add(item);
item.setEnabled(null != canvas.getFakeImagePlus().getRoi());
item = new JMenuItem("Properties ...");
item.addActionListener(this);
menu.add(item);
item = new JMenuItem("Calibration...");
item.addActionListener(this);
menu.add(item);
item = new JMenuItem("Grid overlay...");
item.addActionListener(this);
menu.add(item);
item = new JMenuItem("Adjust snapping parameters...");
item.addActionListener(this);
menu.add(item);
item = new JMenuItem("Adjust fast-marching parameters...");
item.addActionListener(this);
menu.add(item);
item = new JMenuItem("Adjust arealist paint parameters...");
item.addActionListener(this);
menu.add(item);
item = new JMenuItem("Show current 2D position in 3D");
item.addActionListener(this);
menu.add(item);
item = new JMenuItem("Show layers as orthoslices in 3D");
item.addActionListener(this);
menu.add(item);
item = new JMenuItem("Inspect image mesh triangles");
item.addActionListener(this);
menu.add(item);
popup.add(menu);
menu = new JMenu("Project");
this.project.getLoader().setupMenuItems(menu, this.getProject());
item = new JMenuItem("Project properties...");
item.addActionListener(this);
menu.add(item);
item = new JMenuItem("Create subproject");
item.addActionListener(this);
menu.add(item);
item = new JMenuItem("Create sibling project with retiled layers");
item.addActionListener(this);
menu.add(item);
item = new JMenuItem("Release memory...");
item.addActionListener(this);
menu.add(item);
item = new JMenuItem("Flush image cache");
item.addActionListener(this);
menu.add(item);
item = new JMenuItem("Regenerate all mipmaps");
item.addActionListener(this);
menu.add(item);
item = new JMenuItem("Regenerate mipmaps (selected images)");
item.addActionListener(this);
menu.add(item);
menu.addSeparator();
item = new JMenuItem("Measurement options...");
item.addActionListener(this);
menu.add(item);
popup.add(menu);
menu = new JMenu("Selection");
item = new JMenuItem("Select all");
item.addActionListener(this);
menu.add(item);
item = new JMenuItem("Select all visible");
item.addActionListener(this);
menu.add(item);
item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_A, Utils.getControlModifier(), true));
if (0 == layer.getDisplayableList().size() && 0 == layer.getParent().getDisplayableList().size())
item.setEnabled(false);
item = new JMenuItem("Select all that match...");
item.addActionListener(this);
menu.add(item);
item = new JMenuItem("Select none");
item.addActionListener(this);
menu.add(item);
if (0 == selection.getNSelected())
item.setEnabled(false);
item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_ESCAPE, 0, true));
final JMenu bytype = new JMenu("Select all by type");
item = new JMenuItem("AreaList");
item.addActionListener(bytypelistener);
bytype.add(item);
item = new JMenuItem("AreaTree");
item.addActionListener(bytypelistener);
bytype.add(item);
item = new JMenuItem("Ball");
item.addActionListener(bytypelistener);
bytype.add(item);
item = new JMenuItem("Connector");
item.addActionListener(bytypelistener);
bytype.add(item);
item = new JMenuItem("Dissector");
item.addActionListener(bytypelistener);
bytype.add(item);
item = new JMenuItem("Image");
item.addActionListener(bytypelistener);
bytype.add(item);
item = new JMenuItem("Pipe");
item.addActionListener(bytypelistener);
bytype.add(item);
item = new JMenuItem("Polyline");
item.addActionListener(bytypelistener);
bytype.add(item);
item = new JMenuItem("Profile");
item.addActionListener(bytypelistener);
bytype.add(item);
item = new JMenuItem("Text");
item.addActionListener(bytypelistener);
bytype.add(item);
item = new JMenuItem("Treeline");
item.addActionListener(bytypelistener);
bytype.add(item);
menu.add(bytype);
item = new JMenuItem("Restore selection");
item.addActionListener(this);
menu.add(item);
item = new JMenuItem("Select under ROI");
item.addActionListener(this);
menu.add(item);
if (canvas.getFakeImagePlus().getRoi() == null)
item.setEnabled(false);
final JMenu graph = new JMenu("Graph");
final GraphMenuListener gl = new GraphMenuListener();
item = new JMenuItem("Select outgoing Connectors");
item.addActionListener(gl);
graph.add(item);
item = new JMenuItem("Select incoming Connectors");
item.addActionListener(gl);
graph.add(item);
item = new JMenuItem("Select downstream targets");
item.addActionListener(gl);
graph.add(item);
item = new JMenuItem("Select upstream targets");
item.addActionListener(gl);
graph.add(item);
graph.setEnabled(!selection.isEmpty());
menu.add(graph);
item = new JMenuItem("Measure");
item.addActionListener(this);
menu.add(item);
item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_M, 0, true));
item.setEnabled(!selection.isEmpty());
popup.add(menu);
menu = new JMenu("Tool");
item = new JMenuItem("Rectangular ROI");
item.addActionListener(new SetToolListener(Toolbar.RECTANGLE));
menu.add(item);
item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_F1, 0, true));
item = new JMenuItem("Polygon ROI");
item.addActionListener(new SetToolListener(Toolbar.POLYGON));
menu.add(item);
item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_F2, 0, true));
item = new JMenuItem("Freehand ROI");
item.addActionListener(new SetToolListener(Toolbar.FREEROI));
menu.add(item);
item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_F3, 0, true));
item = new JMenuItem("Text");
item.addActionListener(new SetToolListener(Toolbar.TEXT));
menu.add(item);
item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_F4, 0, true));
item = new JMenuItem("Magnifier glass");
item.addActionListener(new SetToolListener(Toolbar.MAGNIFIER));
menu.add(item);
item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_F5, 0, true));
item = new JMenuItem("Hand");
item.addActionListener(new SetToolListener(Toolbar.HAND));
menu.add(item);
item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_F6, 0, true));
item = new JMenuItem("Select");
item.addActionListener(new SetToolListener(ProjectToolbar.SELECT));
menu.add(item);
item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_F9, 0, true));
item = new JMenuItem("Pencil");
item.addActionListener(new SetToolListener(ProjectToolbar.PENCIL));
menu.add(item);
item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_F10, 0, true));
item = new JMenuItem("Pen");
item.addActionListener(new SetToolListener(ProjectToolbar.PEN));
menu.add(item);
item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_F11, 0, true));
popup.add(menu);
item = new JMenuItem("Search...");
item.addActionListener(this);
popup.add(item);
item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_F, Utils.getControlModifier(), true));
// canvas.add(popup);
return popup;
}
Also used :
AlignTask(mpicbg.trakem2.align.AlignTask)
AlignLayersTask(mpicbg.trakem2.align.AlignLayersTask)
DistortionCorrectionTask(lenscorrection.DistortionCorrectionTask)
ActionEvent(java.awt.event.ActionEvent)
Bureaucrat(ini.trakem2.utils.Bureaucrat)
ArrayList(java.util.ArrayList)
List(java.util.List)
CoordinateTransformList(mpicbg.trakem2.transform.CoordinateTransformList)
HashSet(java.util.HashSet)
Color(java.awt.Color)
PolygonRoi(ij.gui.PolygonRoi)
ShapeRoi(ij.gui.ShapeRoi)
Roi(ij.gui.Roi)
ActionListener(java.awt.event.ActionListener)
DBObject(ini.trakem2.persistence.DBObject)
InspectPatchTrianglesMode(ini.trakem2.display.inspect.InspectPatchTrianglesMode)
GenericDialog(ij.gui.GenericDialog)
Worker(ini.trakem2.utils.Worker)
JMenuItem(javax.swing.JMenuItem)
Point(java.awt.Point)
TreeMap(java.util.TreeMap)
JPopupMenu(javax.swing.JPopupMenu)
Point(java.awt.Point)
NoninvertibleTransformException(java.awt.geom.NoninvertibleTransformException)
JMenu(javax.swing.JMenu)
Aggregations
ArrayList (java.util.ArrayList)14
Layer (ini.trakem2.display.Layer)10
HashMap (java.util.HashMap)10
Rectangle (java.awt.Rectangle)9
Patch (ini.trakem2.display.Patch)8
AffineTransform (java.awt.geom.AffineTransform)7
Map (java.util.Map)7
Displayable (ini.trakem2.display.Displayable)6
NoninvertibleTransformException (java.awt.geom.NoninvertibleTransformException)6
TreeMap (java.util.TreeMap)6
Worker (ini.trakem2.utils.Worker)5
Area (java.awt.geom.Area)5
HashSet (java.util.HashSet)5
GenericDialog (ij.gui.GenericDialog)4
Calibration (ij.measure.Calibration)4
ByteProcessor (ij.process.ByteProcessor)4
File (java.io.File)4
Future (java.util.concurrent.Future)4
ImagePlus (ij.ImagePlus)3
ColorProcessor (ij.process.ColorProcessor)3
