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Merge pull request #10 from ekatrukha/animation
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Animation + imglib2-mesh + anti-aliasing
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@ekatrukha
ekatrukha authored Oct 7, 2024
2 parents 13e09dd + a32ac46 commit 4a68036
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Showing 57 changed files with 4,691 additions and 1,094 deletions.
10 changes: 9 additions & 1 deletion pom.xml
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Expand Up @@ -87,7 +87,7 @@
<dependency>
<groupId>nl.uu.science.cellbiology</groupId>
<artifactId>bvv-playground</artifactId>
<version>0.2.1</version>
<version>0.2.6</version>
</dependency>

<!-- BIOFORMATS -->
Expand Down Expand Up @@ -180,14 +180,22 @@
<groupId>org.joml</groupId>
<artifactId>joml</artifactId>
</dependency>

<!-- BDV dependencies -->
<dependency>
<groupId>sc.fiji</groupId>
<artifactId>bigdataviewer-core</artifactId>
</dependency>
<dependency>
<groupId>sc.fiji</groupId>
<artifactId>bigdataviewer_fiji</artifactId>
</dependency>

<dependency>
<groupId>net.imagej</groupId>
<artifactId>ij</artifactId>
</dependency>

<dependency>
<groupId>gov.nist.math</groupId>
<artifactId>jama</artifactId>
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153 changes: 120 additions & 33 deletions src/main/java/bigtrace/BigTrace.java
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,6 @@
import java.util.List;

import javax.swing.JFrame;
import javax.swing.SwingUtilities;
import javax.swing.UIManager;
import javax.swing.WindowConstants;

Expand Down Expand Up @@ -57,26 +56,29 @@
import bdv.viewer.ViewerState;

import btbvv.vistools.BvvFunctions;
import btbvv.vistools.BvvHandleFrame;
import btbvv.vistools.Bvv;
import btbvv.vistools.BvvStackSource;
import btbvv.core.render.RenderData;
import btbvv.core.render.VolumeRenderer.RepaintType;
import btbvv.btuitools.BvvGamma;
import btbvv.btuitools.GammaConverterSetup;
import btbvv.core.VolumeViewerFrame;
import btbvv.core.VolumeViewerPanel;
import btbvv.core.util.MatrixMath;

import bigtrace.animation.Scene;
import bigtrace.geometry.Cuboid3D;
import bigtrace.geometry.Intersections3D;
import bigtrace.geometry.Line3D;
import bigtrace.gui.AnisotropicTransformAnimator3D;
import bigtrace.gui.GuiMisc;
import bigtrace.math.OneClickTrace;
import bigtrace.math.TraceBoxMath;
import bigtrace.math.TracingBGVect;
import bigtrace.rois.Box3D;
import bigtrace.rois.LineTrace3D;
import bigtrace.rois.RoiManager3D;
import bigtrace.scene.VisPolyLineSimple;
import bigtrace.scene.VisPolyLineAA;
import bigtrace.volume.VolumeMisc;


Expand Down Expand Up @@ -108,12 +110,15 @@ public class BigTrace < T extends RealType< T > & NativeType< T > > implements P

/** Panel of BigVolumeViewer **/
public VolumeViewerPanel viewer;

/** Frame of BigVolumeViewer **/
public VolumeViewerFrame bvvFrame;

/** flag to check if user interface is frozen **/
public volatile boolean bInputLock = false;

/** visualization of coordinates origin axes **/
ArrayList<VisPolyLineSimple> originVis = new ArrayList<>();
ArrayList<VisPolyLineAA> originVis = new ArrayList<>();

/** box around volume **/
Box3D volumeBox;
Expand Down Expand Up @@ -263,8 +268,9 @@ public void initOriginAndBox(double axis_length)
basis.move((-1.0)*axis_length, i);
float [] color_orig = new float[3];
color_orig[i] = 1.0f;
originVis.add(new VisPolyLineSimple( point_coords, 3.0f,new Color(color_orig[0],color_orig[1],color_orig[2])));
originVis.add(new VisPolyLineAA( point_coords, 5.0f,new Color(color_orig[0],color_orig[1],color_orig[2])));
}

float [][] nDimBox = new float [2][3];

for(i=0;i<3;i++)
Expand All @@ -274,9 +280,12 @@ public void initOriginAndBox(double axis_length)
nDimBox[0][i]=btData.nDimIni[0][i]+0.5f;
nDimBox[1][i]=(btData.nDimIni[1][i]-1.0f);
}
volumeBox = new Box3D(nDimBox,0.5f,0.0f,Color.LIGHT_GRAY,Color.LIGHT_GRAY, 0);
clipBox = new Box3D(nDimBox,0.5f,0.0f,Color.LIGHT_GRAY,Color.LIGHT_GRAY, 0);
volumeBox = new Box3D(nDimBox,1.0f,0.0f,Color.WHITE,Color.WHITE, 0);

// volumeBox = new Box3D(nDimBox,1.0f,0.0f,Color.LIGHT_GRAY,Color.LIGHT_GRAY, 0);
clipBox = new Box3D(nDimBox,1.0f,0.0f,Color.LIGHT_GRAY,Color.LIGHT_GRAY, 0);
}

public void initSourcesCanvas(double origin_axis_length)
{

Expand All @@ -293,6 +302,7 @@ public void initSourcesCanvas(double origin_axis_length)

viewer = bvv_main.getBvvHandle().getViewerPanel();
viewer.setRenderScene(this::renderScene);

btActions = new BigTraceActions<>(this);
setInitialTransform();
viewer.addTimePointListener(this);
Expand All @@ -303,23 +313,27 @@ private void createAndShowGUI()
{
btPanel = new BigTraceControlPanel<>(this, btData,roiManager);
btPanel.finFrame = new JFrame("BigTrace");

btPanel.bvv_frame=(JFrame) SwingUtilities.getWindowAncestor(viewer);

btPanel.finFrame.setDefaultCloseOperation(WindowConstants.DO_NOTHING_ON_CLOSE);
btPanel.bvv_frame.setDefaultCloseOperation(WindowConstants.DO_NOTHING_ON_CLOSE);


bvvFrame = ((BvvHandleFrame)bvv_main.getBvvHandle()).getBigVolumeViewer().getViewerFrame();

bvvFrame.setDefaultCloseOperation(WindowConstants.DO_NOTHING_ON_CLOSE);


btPanel.finFrame.add(btPanel);

//Display the window.
btPanel.finFrame.setSize(400,600);
btPanel.finFrame.setVisible(true);
java.awt.Point bvv_p = btPanel.bvv_frame.getLocationOnScreen();
java.awt.Dimension bvv_d = btPanel.bvv_frame.getSize();
java.awt.Point bvv_p = bvvFrame.getLocationOnScreen();
java.awt.Dimension bvv_d = bvvFrame.getSize();

btPanel.finFrame.setLocation(bvv_p.x+bvv_d.width, bvv_p.y);
btPanel.finFrame.addWindowListener(this);
btPanel.bvv_frame.addWindowListener(this);
bvvFrame.addWindowListener(this);


bInputLock = false;
}

Expand Down Expand Up @@ -416,6 +430,20 @@ public IntervalView<T> getTraceInterval(boolean bClippedInterval)
return Views.interval(full_int, full_int);
}

public synchronized void setLockMode(boolean bLockMode)
{

boolean bState = !bLockMode;

GuiMisc.setPanelStatusAllComponents(roiManager, bState);
GuiMisc.setPanelStatusAllComponents(btPanel.roiMeasure, bState);
GuiMisc.setPanelStatusAllComponents(btPanel.btTracksPanel, bState);
GuiMisc.setPanelStatusAllComponents(btPanel.btAniPanel, bState);
btPanel.voxelSizePanel.allowVoxelSizeChange(bState);
btPanel.clipPanel.butExtractClipped.setEnabled( bState );
//keep it on
roiManager.butShowAll.setEnabled(true);
}
/** calculate optimal path **/
public void getSemiAutoTrace(RealPoint target)
{
Expand Down Expand Up @@ -659,7 +687,7 @@ public void removeTraceBox()
public void setTraceBoxMode(boolean bStatus)
{
bTraceMode = bStatus;
roiManager.setLockMode(bStatus);
setLockMode(bStatus);
//entering trace mode,
//let's save current view
if(bStatus)
Expand Down Expand Up @@ -710,6 +738,8 @@ public void renderScene(final GL3 gl, final RenderData data)
{
originVis.get(i).draw(gl, pvm);
}


}

//render a box around the volume
Expand Down Expand Up @@ -818,9 +848,43 @@ public void initBVVSourcesSpimData()
bvv_main = bvv_sources.get(0);
viewer = bvv_main.getBvvHandle().getViewerPanel();

//AffineTransform3D transformfin = new AffineTransform3D();
//translate all sources so they are at the zero
AffineTransform3D transformTranslation = new AffineTransform3D();
double [] shiftTR = new double [3];
for (int d=0;d<3;d++)
{
shiftTR[d]=Double.MAX_VALUE;
}

for ( SourceAndConverter< ? > source : viewer.state().getSources() )
{
AffineTransform3D transformSource = new AffineTransform3D();

for(int nTP=0;nTP<BigTraceData.nNumTimepoints;nTP++)
{
if(source.getSpimSource().isPresent( nTP ))
{
(( TransformedSource< ? > ) source.getSpimSource() ).getSourceTransform(nTP, 0, transformSource);

for(int d=0;d<3;d++)
{
if(transformSource.get(d, 3)<shiftTR[d])
{
shiftTR[d]=transformSource.get(d, 3);
}
}
}
}
}
for (int d=0;d<3;d++)
{
shiftTR[d]*=(-1);
}
transformTranslation.identity();
transformTranslation.translate(shiftTR);


// Remove voxel scale and any translation transforms for all sources.
// Remove voxel scale for all sources.
// We needed it, because later voxel size transform is applied to the general ViewerPanel.
for ( SourceAndConverter< ? > source : viewer.state().getSources() )
{
Expand All @@ -829,23 +893,15 @@ public void initBVVSourcesSpimData()
(( TransformedSource< ? > ) source.getSpimSource() ).getSourceTransform(0, 0, transformSource);

AffineTransform3D transformScale = new AffineTransform3D();
AffineTransform3D transformTranslation = new AffineTransform3D();
transformTranslation.identity();
double [] shiftTR = new double [3];

for(int j=0;j<3;j++)
{
//BigTraceData.globCal[j] = transformSource.get(j, j);
{
transformScale.set(1.0/BigTraceData.globCal[j], j, j);
shiftTR[j]= (-1.0)*transformSource.get(j, 3);
}
transformTranslation.identity();
transformTranslation.translate(shiftTR);
//AffineTransform3D transformFinal = transformScale.concatenate(transformTranslation);

AffineTransform3D transformFinal = transformScale.concatenate(transformTranslation);
(( TransformedSource< ? > ) source.getSpimSource() ).setFixedTransform(transformFinal);
// (( TransformedSource< ? > ) source.getSpimSource() ).setIncrementalTransform(transformFinal);

//(( TransformedSource< ? > ) source.getSpimSource() ).getSourceTransform(0, 0, transformfin);

}

if(bApplyLLSTransform)
Expand Down Expand Up @@ -1458,6 +1514,38 @@ public void timePointChanged(int timePointIndex)
}
}

/** get current scene (view transform + crop for now) **/
public Scene getCurrentScene()
{
final AffineTransform3D transform = new AffineTransform3D();
viewer.state().getViewerTransform(transform);
int canvasW = viewer.getWidth();
int canvasH = viewer.getHeight();
transform.set( transform.get( 0, 3 ) - canvasW / 2, 0, 3 );
transform.set( transform.get( 1, 3 ) - canvasH / 2, 1, 3 );
transform.scale( 1.0/ canvasW );

return new Scene(transform, BigTraceData.nDimCurr, btData.nCurrTimepoint);
}

public void setScene(final Scene scene)
{
final AffineTransform3D affine = new AffineTransform3D();
affine.set( scene.getViewerTransform());
int width = viewer.getWidth();
int height = viewer.getHeight();
affine.scale( width );
affine.set( affine.get( 0, 3 ) + width / 2, 0, 3 );
affine.set( affine.get( 1, 3 ) + height / 2, 1, 3 );
viewer.state().setViewerTransform( affine );
int nTimePoint = scene.getTimeFrame();
if(nTimePoint<BigTraceData.nNumTimepoints)
{
viewer.state().setCurrentTimepoint(nTimePoint);
}
btPanel.clipPanel.setBoundingBox( scene.getClipBox());
}


@Override
public void windowActivated(WindowEvent arg0) {
Expand Down Expand Up @@ -1504,9 +1592,8 @@ public void windowOpened(WindowEvent arg0) {

public void closeWindows()
{

viewer.stop();
btPanel.bvv_frame.dispose();
bvvFrame.dispose();
btPanel.finFrame.dispose();
}

Expand Down Expand Up @@ -1585,8 +1672,8 @@ public static void main(String... args) throws Exception

testI.run("");
//testI.run("/home/eugene/Desktop/projects/BigTrace/BigTrace_data/ExM_MT.tif");
//testI.run("/home/eugene/Desktop/projects/BigTrace/BT_tracks/Snejana_small_example.tif");

///testI.run("/home/eugene/Desktop/projects/BigTrace/BT_tracks/Snejana_small_example.tif");
//testI.run("/home/eugene/Desktop/bend/test_bend_2ch/output/trace1514947168.xml");

///macros test
// testI.run("/home/eugene/Desktop/projects/BigTrace/BigTrace_data/ExM_MT_8bit.tif");
Expand Down
2 changes: 1 addition & 1 deletion src/main/java/bigtrace/BigTraceActions.java
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Original file line number Diff line number Diff line change
Expand Up @@ -154,7 +154,7 @@ public void actionAddPoint()
}
}

bt.roiManager.setLockMode(true);
bt.setLockMode(true);
bt.runOneClickTrace(target, bMakeNewTrace);
break;
default:
Expand Down
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