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Merged
mdoube merged 11 commits into from
May 14, 2026
Merged

397 modern table #398

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75eaf86
Mark the legacy ResultInserter as deprecated
mdoube May 11, 2026
04ddef9
Let legacy plugins see the scijava SharedTable and other utilities
mdoube May 12, 2026
c0135c9
Give legacy plugins access to the modern plugin apis
mdoube May 12, 2026
1ae2edf
Put a light scijava wrapper on legacy Connectivity
mdoube May 12, 2026
7a24d31
Remove commented code
mdoube May 12, 2026
ac154bc
Use scijava table for Moments of Inertia
mdoube May 12, 2026
a5ba150
Use scijava SharedTable for SphereFitter
mdoube May 12, 2026
3af3fac
Use scijava SharedTable for Purify
mdoube May 12, 2026
4e1bc00
Use the shared table for particle analyser
mdoube May 12, 2026
156a227
Slice Geometry uses the modern shared table
mdoube May 12, 2026
8bc5094
Remove legacy ResultInserter
mdoube May 13, 2026
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12 changes: 12 additions & 0 deletions Legacy/bonej/pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -105,6 +105,18 @@
<version>${project.version}</version>
</dependency>

<dependency>
<groupId>org.bonej</groupId>
<artifactId>bonej-utilities</artifactId>
<version>${project.version}</version>
</dependency>

<dependency>
<groupId>org.bonej</groupId>
<artifactId>bonej-plugins</artifactId>
<version>${project.version}</version>
</dependency>

<!-- ImageJ dependencies -->
<dependency>
<groupId>net.imagej</groupId>
Expand Down
32 changes: 23 additions & 9 deletions Legacy/bonej/src/main/java/org/bonej/plugins/Connectivity.java
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Expand Up @@ -34,7 +34,10 @@

import org.bonej.util.ImageCheck;
import org.bonej.util.Multithreader;
import org.bonej.util.ResultInserter;
import org.bonej.utilities.SharedTable;
import org.bonej.wrapperPlugins.BoneJCommand;
import org.scijava.command.Command;
import org.scijava.plugin.Plugin;

import ij.IJ;
import ij.ImagePlus;
Expand Down Expand Up @@ -98,7 +101,8 @@
* </p>
*
*/
public class Connectivity implements PlugIn {
@Plugin(type = Command.class, menuPath = "Plugins>BoneJ>Connectivity>Connectivity")
public class Connectivity extends BoneJCommand implements PlugIn {

private final static int[] EULER_LUT = fillEulerLUT();

Expand All @@ -109,8 +113,19 @@ public class Connectivity implements PlugIn {
private int height = 0;

/** working image depth */
private int depth = 0;
private int depth = 0;

/**
* Modern scijava Plugin entry point. Calls the Legacy {@link #run(String)} method
*/
@Override
public void run() {
run("");
}

/**
* Legacy ImageJ1 plugin
*/
@Override
public void run(final String arg) {
final ImagePlus imp = IJ.getImage();
Expand All @@ -132,12 +147,11 @@ public void run(final String arg) {
+ "particles or enclosed cavities.\n\n" + "Try running Purify prior to Connectivity.");
}

final ResultInserter ri = ResultInserter.getInstance();
ri.setResultInRow(imp, "Euler ch.", sumEuler);
ri.setResultInRow(imp, "Δ(χ)", deltaChi);
ri.setResultInRow(imp, "Connectivity", connectivity);
ri.setResultInRow(imp, "Conn.D (" + imp.getCalibration().getUnit() + "^-3)", connDensity);
ri.updateTable();
SharedTable.add(imp.getTitle(), "Euler ch.", sumEuler);
SharedTable.add(imp.getTitle(), "Δ(χ)", deltaChi);
SharedTable.add(imp.getTitle(), "Connectivity", connectivity);
SharedTable.add(imp.getTitle(), "Conn.D (" + imp.getCalibration().getUnit() + "^-3)", connDensity);
resultsTable = SharedTable.getTable();
return;
}

Expand Down
65 changes: 38 additions & 27 deletions Legacy/bonej/src/main/java/org/bonej/plugins/Moments.java
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Original file line number Diff line number Diff line change
Expand Up @@ -43,10 +43,13 @@
import org.bonej.util.ImageCheck;
import org.bonej.util.MatrixUtils;
import org.bonej.util.Multithreader;
import org.bonej.util.ResultInserter;
import org.bonej.util.ThresholdGuesser;
import org.jogamp.vecmath.Color3f;
import org.jogamp.vecmath.Point3f;
import org.bonej.utilities.SharedTable;
import org.bonej.wrapperPlugins.BoneJCommand;
import org.scijava.command.Command;
import org.scijava.plugin.Plugin;

import Jama.EigenvalueDecomposition;
import Jama.Matrix;
Expand All @@ -71,7 +74,8 @@
*
* @author Michael Doube
*/
public class Moments implements PlugIn, DialogListener {
@Plugin(type = Command.class, menuPath = "Plugins>BoneJ>Moments of Inertia")
public class Moments extends BoneJCommand implements PlugIn, DialogListener {

private boolean fieldUpdated;
private Calibration cal;
Expand Down Expand Up @@ -110,6 +114,14 @@ public boolean dialogItemChanged(final GenericDialog gd, final AWTEvent e) {
// conversion coefficient from mm^5 to kg.m² = 1.8*10^-12
// double cc = 1.8*Math.pow(10, -12);

/**
* Modern scijava Plugin entry point. Calls the Legacy {@link #run(String)} method
*/
@Override
public void run() {
run("");
}

@Override
public void run(final String arg) {
final ImagePlus imp = IJ.getImage();
Expand Down Expand Up @@ -187,33 +199,32 @@ public void run(final String arg) {
final double[] moments = (double[]) momentResults[1];

final String units = imp.getCalibration().getUnits();
final ResultInserter ri = ResultInserter.getInstance();
ri.setResultInRow(imp, "Xc (" + units + ")", centroid[0]);
ri.setResultInRow(imp, "Yc (" + units + ")", centroid[1]);
ri.setResultInRow(imp, "Zc (" + units + ")", centroid[2]);
ri.setResultInRow(imp, "Vol (" + units + "³)", moments[0]);
ri.setResultInRow(imp, "Mass (g)", moments[1]);
ri.setResultInRow(imp, "Icxx (kg.m²)", moments[2]);
ri.setResultInRow(imp, "Icyy (kg.m²)", moments[3]);
ri.setResultInRow(imp, "Iczz (kg.m²)", moments[4]);
ri.setResultInRow(imp, "Icxy (kg.m²)", moments[5]);
ri.setResultInRow(imp, "Icxz (kg.m²)", moments[6]);
ri.setResultInRow(imp, "Icyz (kg.m²)", moments[7]);
ri.setResultInRow(imp, "I1 (kg.m²)", E.getD().get(2, 2));
ri.setResultInRow(imp, "I2 (kg.m²)", E.getD().get(1, 1));
ri.setResultInRow(imp, "I3 (kg.m²)", E.getD().get(0, 0));
SharedTable.add(imp.getTitle(), "Xc (" + units + ")", centroid[0]);
SharedTable.add(imp.getTitle(), "Yc (" + units + ")", centroid[1]);
SharedTable.add(imp.getTitle(), "Zc (" + units + ")", centroid[2]);
SharedTable.add(imp.getTitle(), "Vol (" + units + "³)", moments[0]);
SharedTable.add(imp.getTitle(), "Mass (g)", moments[1]);
SharedTable.add(imp.getTitle(), "Icxx (kg.m²)", moments[2]);
SharedTable.add(imp.getTitle(), "Icyy (kg.m²)", moments[3]);
SharedTable.add(imp.getTitle(), "Iczz (kg.m²)", moments[4]);
SharedTable.add(imp.getTitle(), "Icxy (kg.m²)", moments[5]);
SharedTable.add(imp.getTitle(), "Icxz (kg.m²)", moments[6]);
SharedTable.add(imp.getTitle(), "Icyz (kg.m²)", moments[7]);
SharedTable.add(imp.getTitle(), "I1 (kg.m²)", E.getD().get(2, 2));
SharedTable.add(imp.getTitle(), "I2 (kg.m²)", E.getD().get(1, 1));
SharedTable.add(imp.getTitle(), "I3 (kg.m²)", E.getD().get(0, 0));
if (doVerboseUnitVectors) {
ri.setResultInRow(imp, "vX0", E.getV().get(0, 0));
ri.setResultInRow(imp, "vY0", E.getV().get(1, 0));
ri.setResultInRow(imp, "vZ0", E.getV().get(2, 0));
ri.setResultInRow(imp, "vX1", E.getV().get(0, 1));
ri.setResultInRow(imp, "vY1", E.getV().get(1, 1));
ri.setResultInRow(imp, "vZ1", E.getV().get(2, 1));
ri.setResultInRow(imp, "vX2", E.getV().get(0, 2));
ri.setResultInRow(imp, "vY2", E.getV().get(1, 2));
ri.setResultInRow(imp, "vZ2", E.getV().get(2, 2));
SharedTable.add(imp.getTitle(), "vX0", E.getV().get(0, 0));
SharedTable.add(imp.getTitle(), "vY0", E.getV().get(1, 0));
SharedTable.add(imp.getTitle(), "vZ0", E.getV().get(2, 0));
SharedTable.add(imp.getTitle(), "vX1", E.getV().get(0, 1));
SharedTable.add(imp.getTitle(), "vY1", E.getV().get(1, 1));
SharedTable.add(imp.getTitle(), "vZ1", E.getV().get(2, 1));
SharedTable.add(imp.getTitle(), "vX2", E.getV().get(0, 2));
SharedTable.add(imp.getTitle(), "vY2", E.getV().get(1, 2));
SharedTable.add(imp.getTitle(), "vZ2", E.getV().get(2, 2));
}
ri.updateTable();
resultsTable = SharedTable.getTable();

if (doAlign) alignToPrincipalAxes(imp, E.getV(), centroid, startSlice,
endSlice, min, max, doAxes).show();
Expand Down
128 changes: 68 additions & 60 deletions Legacy/bonej/src/main/java/org/bonej/plugins/ParticleCounter.java
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Original file line number Diff line number Diff line change
Expand Up @@ -40,7 +40,11 @@
import org.bonej.menuWrappers.ThicknessHelper;
import org.bonej.util.DialogModifier;
import org.bonej.util.ImageCheck;
import org.bonej.utilities.SharedTable;
import org.bonej.wrapperPlugins.BoneJCommand;
import org.jogamp.vecmath.Point3f;
import org.scijava.command.Command;
import org.scijava.plugin.Plugin;

import Jama.EigenvalueDecomposition;

Expand All @@ -49,7 +53,6 @@
import ij.gui.DialogListener;
import ij.gui.GenericDialog;
import ij.measure.Calibration;
import ij.measure.ResultsTable;
import ij.plugin.PlugIn;
import ij3d.Image3DUniverse;
import sc.fiji.analyzeSkeleton.SkeletonResult;
Expand All @@ -64,9 +67,9 @@
*
* @author Michael Doube
*/
public class ParticleCounter implements PlugIn, DialogListener {
@Plugin(type = Command.class, menuPath = "Plugins>BoneJ>Analyze>Particle Analyser")
public class ParticleCounter extends BoneJCommand implements PlugIn, DialogListener {


/* (non-Javadoc)
* @see ij.gui.DialogListener#dialogItemChanged(ij.gui.GenericDialog, java.awt.AWTEvent)
*/
Expand Down Expand Up @@ -96,6 +99,14 @@ public boolean dialogItemChanged(final GenericDialog gd, final AWTEvent e) {
return true;
}

/**
* Modern scijava Plugin entry point. Calls the Legacy {@link #run(String)} method
*/
@Override
public void run() {
run("");
}

/* (non-Javadoc)
* @see ij.plugin.PlugIn#run(java.lang.String)
*/
Expand Down Expand Up @@ -292,54 +303,52 @@ public void run(final String arg) {
}

// Show numerical results
final ResultsTable rt = new ResultsTable();
SharedTable.reset();
for (int i = 1; i < volumes.length; i++) {
if (volumes[i] > 0) {
rt.incrementCounter();
rt.addLabel(imp.getTitle());
rt.addValue("ID", i);
rt.addValue("Vol. (" + units + "³)", volumes[i]);
rt.addValue("x Cent (" + units + ")", centroids[i][0]);
rt.addValue("y Cent (" + units + ")", centroids[i][1]);
rt.addValue("z Cent (" + units + ")", centroids[i][2]);
SharedTable.add(imp.getTitle(),"ID", i);
SharedTable.add(imp.getTitle(),"Vol. (" + units + "³)", volumes[i]);
SharedTable.add(imp.getTitle(),"x Cent (" + units + ")", centroids[i][0]);
SharedTable.add(imp.getTitle(),"y Cent (" + units + ")", centroids[i][1]);
SharedTable.add(imp.getTitle(),"z Cent (" + units + ")", centroids[i][2]);
if (doAlignedBoxes) {
rt.addValue("Box x (" + units + ")", alignedBoxes[i][0]);
rt.addValue("Box y (" + units + ")", alignedBoxes[i][1]);
rt.addValue("Box z (" + units + ")", alignedBoxes[i][2]);
rt.addValue("Box l0 (" + units + ")", alignedBoxes[i][3]);
rt.addValue("Box l1 (" + units + ")", alignedBoxes[i][4]);
rt.addValue("Box l2 (" + units + ")", alignedBoxes[i][5]);
SharedTable.add(imp.getTitle(),"Box x (" + units + ")", alignedBoxes[i][0]);
SharedTable.add(imp.getTitle(),"Box y (" + units + ")", alignedBoxes[i][1]);
SharedTable.add(imp.getTitle(),"Box z (" + units + ")", alignedBoxes[i][2]);
SharedTable.add(imp.getTitle(),"Box l0 (" + units + ")", alignedBoxes[i][3]);
SharedTable.add(imp.getTitle(),"Box l1 (" + units + ")", alignedBoxes[i][4]);
SharedTable.add(imp.getTitle(),"Box l2 (" + units + ")", alignedBoxes[i][5]);
}
if (doSurfaceArea) {
rt.addValue("SA (" + units + "²)", surfaceAreas[i]);
SharedTable.add(imp.getTitle(),"SA (" + units + "²)", surfaceAreas[i]);
}
if (doFeret) {
rt.addValue("Feret (" + units + ")", ferets[i][0]);
rt.addValue("FeretAx (" + units + ")", ferets[i][1]);
rt.addValue("FeretAy (" + units + ")", ferets[i][2]);
rt.addValue("FeretAz (" + units + ")", ferets[i][3]);
rt.addValue("FeretBx (" + units + ")", ferets[i][4]);
rt.addValue("FeretBy (" + units + ")", ferets[i][5]);
rt.addValue("FeretBz (" + units + ")", ferets[i][6]);
SharedTable.add(imp.getTitle(),"Feret (" + units + ")", ferets[i][0]);
SharedTable.add(imp.getTitle(),"FeretAx (" + units + ")", ferets[i][1]);
SharedTable.add(imp.getTitle(),"FeretAy (" + units + ")", ferets[i][2]);
SharedTable.add(imp.getTitle(),"FeretAz (" + units + ")", ferets[i][3]);
SharedTable.add(imp.getTitle(),"FeretBx (" + units + ")", ferets[i][4]);
SharedTable.add(imp.getTitle(),"FeretBy (" + units + ")", ferets[i][5]);
SharedTable.add(imp.getTitle(),"FeretBz (" + units + ")", ferets[i][6]);
}
if (doSurfaceVolume) {
rt.addValue("Encl. Vol. (" + units + "³)", surfaceVolumes[i]);
SharedTable.add(imp.getTitle(),"Encl. Vol. (" + units + "³)", surfaceVolumes[i]);
}
if (doMoments) {
final EigenvalueDecomposition E = eigens[i];
rt.addValue("I1", E.getD().get(2, 2));
rt.addValue("I2", E.getD().get(1, 1));
rt.addValue("I3", E.getD().get(0, 0));
rt.addValue("vX", E.getV().get(0, 0));
rt.addValue("vY", E.getV().get(1, 0));
rt.addValue("vZ", E.getV().get(2, 0));
SharedTable.add(imp.getTitle(),"I1", E.getD().get(2, 2));
SharedTable.add(imp.getTitle(),"I2", E.getD().get(1, 1));
SharedTable.add(imp.getTitle(),"I3", E.getD().get(0, 0));
SharedTable.add(imp.getTitle(),"vX", E.getV().get(0, 0));
SharedTable.add(imp.getTitle(),"vY", E.getV().get(1, 0));
SharedTable.add(imp.getTitle(),"vZ", E.getV().get(2, 0));
if (doVerboseUnitVectors) {
rt.addValue("vX1", E.getV().get(0, 1));
rt.addValue("vY1", E.getV().get(1, 1));
rt.addValue("vZ1", E.getV().get(2, 1));
rt.addValue("vX2", E.getV().get(0, 2));
rt.addValue("vY2", E.getV().get(1, 2));
rt.addValue("vZ2", E.getV().get(2, 2));
SharedTable.add(imp.getTitle(),"vX1", E.getV().get(0, 1));
SharedTable.add(imp.getTitle(),"vY1", E.getV().get(1, 1));
SharedTable.add(imp.getTitle(),"vZ1", E.getV().get(2, 1));
SharedTable.add(imp.getTitle(),"vX2", E.getV().get(0, 2));
SharedTable.add(imp.getTitle(),"vY2", E.getV().get(1, 2));
SharedTable.add(imp.getTitle(),"vZ2", E.getV().get(2, 2));
}
}
if (doSkeletons) {
Expand All @@ -353,18 +362,18 @@ public void run(final String arg) {
branchesLength = skeletonResults[i].getAverageBranchLength()[0]
* nBranches;
}
rt.addValue("n Branches", nBranches);
rt.addValue("Branches length ("+units+")", branchesLength);
SharedTable.add(imp.getTitle(),"n Branches", nBranches);
SharedTable.add(imp.getTitle(),"Branches length ("+units+")", branchesLength);
}
if (doEulerCharacters) {
rt.addValue("Euler (χ)", eulerCharacters[i][0]);
rt.addValue("Holes (β1)", eulerCharacters[i][1]);
rt.addValue("Cavities (β2)", eulerCharacters[i][2]);
SharedTable.add(imp.getTitle(),"Euler (χ)", eulerCharacters[i][0]);
SharedTable.add(imp.getTitle(),"Holes (β1)", eulerCharacters[i][1]);
SharedTable.add(imp.getTitle(),"Cavities (β2)", eulerCharacters[i][2]);
}
if (doThickness) {
rt.addValue("Thickness (" + units + ")", thick[i][0]);
rt.addValue("SD Thickness (" + units + ")", thick[i][1]);
rt.addValue("Max Thickness (" + units + ")", thick[i][2]);
SharedTable.add(imp.getTitle(),"Thickness (" + units + ")", thick[i][0]);
SharedTable.add(imp.getTitle(),"SD Thickness (" + units + ")", thick[i][1]);
SharedTable.add(imp.getTitle(),"Max Thickness (" + units + ")", thick[i][2]);
}
if (doEllipsoids) {
final double[] rad;
Expand All @@ -380,25 +389,24 @@ public void run(final String arg) {
rad = (double[]) el[1];
unitV = (double[][]) el[2];
}
rt.addValue("Major radius (" + units + ")", rad[0]);
rt.addValue("Int. radius (" + units + ")", rad[1]);
rt.addValue("Minor radius (" + units + ")", rad[2]);
SharedTable.add(imp.getTitle(),"Major radius (" + units + ")", rad[0]);
SharedTable.add(imp.getTitle(),"Int. radius (" + units + ")", rad[1]);
SharedTable.add(imp.getTitle(),"Minor radius (" + units + ")", rad[2]);
if (doVerboseUnitVectors) {
rt.addValue("V00", unitV[0][0]);
rt.addValue("V01", unitV[0][1]);
rt.addValue("V02", unitV[0][2]);
rt.addValue("V10", unitV[1][0]);
rt.addValue("V11", unitV[1][1]);
rt.addValue("V12", unitV[1][2]);
rt.addValue("V20", unitV[2][0]);
rt.addValue("V21", unitV[2][1]);
rt.addValue("V22", unitV[2][2]);
SharedTable.add(imp.getTitle(),"V00", unitV[0][0]);
SharedTable.add(imp.getTitle(),"V01", unitV[0][1]);
SharedTable.add(imp.getTitle(),"V02", unitV[0][2]);
SharedTable.add(imp.getTitle(),"V10", unitV[1][0]);
SharedTable.add(imp.getTitle(),"V11", unitV[1][1]);
SharedTable.add(imp.getTitle(),"V12", unitV[1][2]);
SharedTable.add(imp.getTitle(),"V20", unitV[2][0]);
SharedTable.add(imp.getTitle(),"V21", unitV[2][1]);
SharedTable.add(imp.getTitle(),"V22", unitV[2][2]);
}
}
rt.updateResults();
}
}
rt.show("Results");
resultsTable = SharedTable.getTable();

// Show resulting image stacks
if (doParticleImage) {
Expand Down
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