Skip to content

Commit

Permalink
Workaround for 3D boxivity failures
Browse files Browse the repository at this point in the history 
It seems that geometric ops do not yet support meshes. This should be reported upstream
Error: No matching 'net.imagej.ops.Ops$Geometric$SmallestEnclosingBoundingBox/net.imagej.ops.special.function.UnaryFunctionOp' op
  • Loading branch information
@tferr
tferr committed Nov 18, 2024
1 parent 33f4cbf commit 65b6621
Show file tree
Hide file tree
Showing 3 changed files with 45 additions and 22 deletions.
31 changes: 23 additions & 8 deletions src/main/java/sc/fiji/snt/analysis/ConvexHullAnalyzer.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -103,7 +103,7 @@ public Map<String, Double> getAnalysis() {
if (isComputable()) {
initHull();
metrics.put(BOUNDARY_SIZE, hull.boundarySize());
metrics.put(BOXIVITY, (tree.is3D()) ? Double.NaN : computeBoxivity(hull));
metrics.put(BOXIVITY, computeBoxivity(hull));
metrics.put(ELONGATION, computeElongation(hull));
metrics.put(ROUNDNESS, computeRoundness(hull));
metrics.put(SIZE, hull.size());
Expand Down Expand Up @@ -185,13 +185,18 @@ else if (hull instanceof ConvexHull2D)
throw new IllegalArgumentException("Unsupported type:" + hull.getClass());
}

protected double computeBoxivity(final AbstractConvexHull hull) { // FIXME this does not work in 3D??
if (hull instanceof ConvexHull3D)
return opService.geom().boxivity(((ConvexHull3D) hull).getMesh()).getRealDouble();
else if (hull instanceof ConvexHull2D)
return opService.geom().boxivity(((ConvexHull2D) hull).getPolygon()).getRealDouble();
else
throw new IllegalArgumentException("Unsupported type:" + hull.getClass());
protected double computeBoxivity(final AbstractConvexHull hull) {
try {
if (hull instanceof ConvexHull3D)
return opService.geom().boxivity(((ConvexHull3D) hull).getMesh()).getRealDouble();
else if (hull instanceof ConvexHull2D)
return opService.geom().boxivity(((ConvexHull2D) hull).getPolygon()).getRealDouble();
} catch (final IllegalArgumentException iae) {
// BUG: No matching 'net.imagej.ops.Ops$Geometric$SmallestEnclosingBoundingBox/net.imagej.ops.special.function.UnaryFunctionOp' op
iae.printStackTrace();
return Double.NaN;
}
throw new IllegalArgumentException("Unsupported type:" + hull.getClass());
}

protected RealLocalizable computeCentroid(final AbstractConvexHull hull) {
Expand Down Expand Up @@ -243,6 +248,16 @@ public Tree getTree() {
return tree;
}

/**
* Returns the physical unit associated with the specified metric.
* @param metric the supported metric to be queried (case-sensitive)
* @return physical unit
* @see #supportedMetrics()
*/
public String getUnit(final String metric) {
return new TreeStatistics(tree).getUnit(metric);
}

public static void main(final String[] args) throws InterruptedException {
final ImageJ ij = new ImageJ();
final SNTService sntService = ij.context().getService(SNTService.class);
Expand Down
4 changes: 4 additions & 0 deletions src/main/java/sc/fiji/snt/gui/MeasureUI.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -720,6 +720,10 @@ private void measureTree(final Tree tree) {
}
final String unit = tStats.getUnit(metric);
final String metricHeader = (unit.length() > 1) ? metric + " (" + unit + ")" : metric;
if (summaryStatistics.getN() < 1) {
table.set(metricHeader, tree.getLabel(), "Err");
continue;
}
if (summaryStatistics.getN() == 1 ) {
table.set(metricHeader + " [Single value]", tree.getLabel(), summaryStatistics.getSum());
continue;
Expand Down
32 changes: 18 additions & 14 deletions src/main/java/sc/fiji/snt/plugin/ConvexHullCmd.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -57,6 +57,7 @@
@Plugin(type = Command.class, visible = false, label = "Convex Hull Analysis...")
public class ConvexHullCmd extends ContextCommand {

private static final String TOOLTIP = "<HTML>See <a href=\"https://imagej.net/plugins/snt/metrics/\">imagej.net/plugins/snt/metrics/</a>";
@Parameter
private SNTService sntService;

Expand Down Expand Up @@ -88,16 +89,19 @@ public class ConvexHullCmd extends ContextCommand {
@Parameter(label = "<HTML><b>Measurements:", required = false, visibility = ItemVisibility.MESSAGE)
private String HEADER2;

@Parameter(label = "Boundary Size")
@Parameter(label = "Boundary Size", description = TOOLTIP)
private boolean doBoundarySize;

@Parameter(label = "Main Elongation")
@Parameter(label = "Boxivity", description = TOOLTIP)
private boolean doBoxivity;

@Parameter(label = "Main Elongation", description = TOOLTIP)
private boolean doMainElongation;

@Parameter(label = "Roundness")
@Parameter(label = "Roundness", description = TOOLTIP)
private boolean doRoundness;

@Parameter(label = "Size")
@Parameter(label = "Size", description = TOOLTIP)
private boolean doSize;

@Override
Expand Down Expand Up @@ -132,7 +136,7 @@ private void run(final Tree tree) {
if (splitByType) {
axon = tree.subTree("axon");
dendrite = tree.subTree("dendrite");
if (axon.isEmpty() && dendrite.isEmpty()) {
if ( (axon == null || axon.isEmpty()) && (dendrite == null || dendrite.isEmpty()) ) {
splitByType = false;
axon = tree;
}
Expand Down Expand Up @@ -191,7 +195,7 @@ private void run(final Tree tree) {
if (!table.isEmpty()) {
final List<Display<?>> displays = displayService.getDisplays(table);
if (displays != null && !displays.isEmpty()) {
displays.forEach(d -> d.update());
displays.forEach(Display::update);
} else {
displayService.createDisplay("SNT Measurements", table);
}
Expand All @@ -215,19 +219,19 @@ private void addHullToRecViewer(final AbstractConvexHull hull, final String iden
private void measure(final ConvexHullAnalyzer analyzer, final SNTTable table, final String rowLabel) {
try {
table.insertRow(rowLabel);
final String unit = (String) analyzer.getTree().getProperties().getOrDefault(Tree.KEY_SPATIAL_UNIT,
"? units");
final boolean is3D = analyzer.getHull() instanceof ConvexHull3D;
if (doSize)
table.appendToLastRow("Convex hull: Size (" + unit + ((is3D) ? "^3" : "^2") + ")", analyzer.getSize());
table.appendToLastRow(String.format("Convex hull: Size (%s)", analyzer.getUnit("Convex hull: Size")),
analyzer.getSize());
if (doBoundarySize)
table.appendToLastRow("Convex hull: Boundary size (" + unit + ((is3D) ? "^2" : "") + ")",
analyzer.getBoundarySize());
table.appendToLastRow(String.format("Convex hull: Boundary size (%s)", analyzer.getUnit("Convex hull: Boundary size")),
analyzer.getBoundarySize());
if (doBoxivity)
table.appendToLastRow("Convex hull: Boxivity", analyzer.getBoxivity());
if (doRoundness)
table.appendToLastRow("Convex hull: Roundness", analyzer.getRoundness());
if (doMainElongation)
table.appendToLastRow("Convex hull: Boundary size (" + unit + ")",
analyzer.getElongation());
table.appendToLastRow(String.format("Convex hull: Elongation (%s)", analyzer.getUnit("Convex hull: Elongation")),
analyzer.getElongation());
} catch (final IndexOutOfBoundsException | IllegalArgumentException ex) {
ex.printStackTrace();
}
Expand Down

0 comments on commit 65b6621

Please sign in to comment.