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Merged
tferr merged 4 commits into from
Apr 23, 2026
Merged

Implement Curation Assistant #284

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e3c955d
Curation Assistance: Implement backbone infrastructure and GUI
tferr Apr 16, 2026
e76851d
Add PlausibilityCalibrator; move curation classes into dedicated package
tferr Apr 20, 2026
e904f19
Curation Assistant: Improve warning mechanism
tferr Apr 23, 2026
03dc4a6
Add template script
tferr Apr 23, 2026
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1,163 changes: 1,163 additions & 0 deletions src/main/java/sc/fiji/snt/CurationAssistantPanel.java
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134 changes: 134 additions & 0 deletions src/main/java/sc/fiji/snt/InteractiveTracerCanvas.java
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Original file line number Diff line number Diff line change
Expand Up @@ -34,6 +34,7 @@
import sc.fiji.snt.analysis.graph.DirectedWeightedGraph;
import sc.fiji.snt.analysis.graph.DirectedWeightedSubgraph;
import sc.fiji.snt.analysis.graph.SWCWeightedEdge;
import sc.fiji.snt.analysis.curation.PlausibilityCheck;
import sc.fiji.snt.gui.GuiUtils;
import sc.fiji.snt.gui.IconFactory;
import sc.fiji.snt.hyperpanes.MultiDThreePanes;
Expand Down Expand Up @@ -98,6 +99,17 @@ class InteractiveTracerCanvas extends TracerCanvas implements MouseWheelListener
// slight mouse/trackpad movement during click, especially on macOS trackpads.
private static final int CLICK_TOLERANCE_SQ = 25;

private List<PointInImage> warningLocations = new ArrayList<>();
private List<Path> warningAffectedPaths = new ArrayList<>();
private PlausibilityCheck.Severity warningMaxSeverity = null;
private boolean warningViewportTint = false;
private long warningFlashStart = 0;
private static final long FLASH_DURATION_MS = 3000;
private static final long TINT_DURATION_MS = 400;
private static final Color WARNING_RING_COLOR = new Color(255, 165, 0); // orange
private static final Color ERROR_RING_COLOR = new Color(255, 80, 80); // red
private static final Color VIEWPORT_TINT_COLOR = new Color(255, 60, 60, 50); // faint red wash

protected InteractiveTracerCanvas(final ImagePlus imp,
final SNT plugin, final int plane,
final PathAndFillManager pathAndFillManager)
Expand Down Expand Up @@ -749,6 +761,46 @@ protected void clickAtMaxPoint(final boolean join_modifier_pressed) {
tracerPlugin.clickAtMaxPoint(x, y, plane, join_modifier_pressed);
}

/**
* Sets the warning overlay state for the canvas.
*
* @param locations spatial locations of warnings (may be null/empty)
* @param affectedPaths paths involved in warnings, highlighted with a thick overlay
* @param maxSeverity the highest severity among the warnings (drives visual tier)
* @param viewportTint whether to flash a brief viewport tint (for ERRORs when panel not visible)
*/
public void setWarningOverlay(final List<PointInImage> locations,
final List<Path> affectedPaths,
final PlausibilityCheck.Severity maxSeverity,
final boolean viewportTint) {
this.warningLocations = (locations != null) ? new ArrayList<>(locations) : new ArrayList<>();
this.warningAffectedPaths = (affectedPaths != null) ? new ArrayList<>(affectedPaths) : new ArrayList<>();
this.warningMaxSeverity = maxSeverity;
this.warningViewportTint = viewportTint;
this.warningFlashStart = System.currentTimeMillis();
repaint();
}

public void clearWarningOverlay() {
warningLocations.clear();
warningAffectedPaths.clear();
warningMaxSeverity = null;
warningViewportTint = false;
repaint();
}

@Override
public void repaint() {
super.repaint();
// Schedule repaints for pulsing animation while flash is active
if (!warningLocations.isEmpty() || !warningAffectedPaths.isEmpty()) {
final long elapsed = System.currentTimeMillis() - warningFlashStart;
if (elapsed < FLASH_DURATION_MS) {
super.repaint(50);
}
}
}

protected void startShollAnalysis() {
PointInImage centerScaled = null;
if (pathAndFillManager.anySelected()) {
Expand Down Expand Up @@ -1261,6 +1313,88 @@ protected void drawOverlay(final Graphics2D g) {
if (tracerPlugin.manualRadius > 0 && last_x_in_pane_precise != Double.MIN_VALUE) {
drawManualRadiusCursor(g);
}

// Warning overlay (tiered by severity)
drawWarningOverlay(g);
}

private void drawWarningOverlay(final Graphics2D g) {
if (warningLocations.isEmpty() && warningAffectedPaths.isEmpty()) return;
final long elapsed = System.currentTimeMillis() - warningFlashStart;
if (elapsed >= FLASH_DURATION_MS) return;

final Stroke savedStroke = g.getStroke();
final Color savedColor = g.getColor();
final Composite savedComposite = g.getComposite();

// Pulsing alpha: 600ms cycle, sinusoidal
final double phase = (elapsed % 600) / 600.0;
final float pulseAlpha = (float) (0.4 + 0.6 * Math.abs(Math.sin(phase * Math.PI)));
final Color baseColor = (warningMaxSeverity == PlausibilityCheck.Severity.ERROR)
? ERROR_RING_COLOR : WARNING_RING_COLOR;

// Tier 1 (all severities): Affected path highlights (simplified thick lines)
if (!warningAffectedPaths.isEmpty()) {
g.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER, pulseAlpha * 0.5f));
g.setStroke(new BasicStroke(5f, BasicStroke.CAP_ROUND, BasicStroke.JOIN_ROUND));
g.setColor(baseColor);
for (final Path path : warningAffectedPaths) {
drawPathSimplified(g, path);
}
}

// Tier 1 (all severities): Pulsing rings at warning locations
if (!warningLocations.isEmpty()) {
final int ringRadius = Math.max(10, (int) (12 * getMagnification() / 4));
g.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER, pulseAlpha));
for (final PointInImage loc : warningLocations) {
final int sx = myScreenXD(loc.x / tracerPlugin.x_spacing);
final int sy = myScreenYD(loc.y / tracerPlugin.y_spacing);
// Dark outline ring
g.setColor(Color.BLACK);
g.setStroke(new BasicStroke(3f));
g.drawOval(sx - ringRadius, sy - ringRadius, ringRadius * 2, ringRadius * 2);
// Colored ring
g.setColor(baseColor);
g.setStroke(new BasicStroke(2f));
g.drawOval(sx - ringRadius, sy - ringRadius, ringRadius * 2, ringRadius * 2);
}
}

// Tier 3 (ERROR + panel not visible): Brief viewport tint
if (warningViewportTint && elapsed < TINT_DURATION_MS) {
final float tintAlpha = 1f - (float) elapsed / TINT_DURATION_MS; // fade out
g.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER, tintAlpha));
g.setColor(VIEWPORT_TINT_COLOR);
g.fillRect(0, 0, getWidth(), getHeight());
}
g.setStroke(savedStroke);
g.setColor(savedColor);
g.setComposite(savedComposite);
}

/** Draws a path as connected line segments without delegating to Path's own drawing logic. */
private void drawPathSimplified(final Graphics2D g, final Path path) {
if (path == null || path.size() < 2) return;
final int sliceZeroIndexed = imp.getZ() - 1;
final double xSpacing = tracerPlugin.x_spacing;
final double ySpacing = tracerPlugin.y_spacing;
final double zSpacing = tracerPlugin.z_spacing;
int prevSx = Integer.MIN_VALUE, prevSy = Integer.MIN_VALUE;
for (int i = 0; i < path.size(); i++) {
final PointInImage p = path.getNodeWithoutChecks(i);
// Skip nodes far from current Z slice (tolerance: ±2 slices)
final int nodeSlice = (int) Math.round(p.z / zSpacing);
if (just_near_slices && Math.abs(nodeSlice - sliceZeroIndexed) > Math.max(eitherSide, 2))
continue;
final int sx = myScreenXD(p.x / xSpacing);
final int sy = myScreenYD(p.y / ySpacing);
if (prevSx != Integer.MIN_VALUE) {
g.drawLine(prevSx, prevSy, sx, sy);
}
prevSx = sx;
prevSy = sy;
}
}

private void drawManualRadiusCursor(final Graphics2D g) {
Expand Down
21 changes: 21 additions & 0 deletions src/main/java/sc/fiji/snt/Path.java
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Original file line number Diff line number Diff line change
Expand Up @@ -733,6 +733,27 @@ private double getExtensionAngle(final int view) {
return Math.toDegrees(angle); // return angle in 0-360 degrees
}

/**
* Returns a (non-normalized) direction vector from the first node to the
* node at index {@code min(maxNodes, size()-1)}. This is useful for
* measuring the initial heading of a child path near a fork point.
*
* @param maxNodes the maximum node index to use as the end point
* @return a 3-element array {@code [dx, dy, dz]}, or {@code null} if the
* path has fewer than 2 nodes or the resulting vector is zero-length
*/
public double[] getInitialDirection(final int maxNodes) {
final int end = Math.min(maxNodes, size() - 1);
if (end < 1) return null;
final PointInImage p0 = getNodeWithoutChecks(0);
final PointInImage pN = getNodeWithoutChecks(end);
final double dx = pN.x - p0.x;
final double dy = pN.y - p0.y;
final double dz = pN.z - p0.z;
if (dx == 0 && dy == 0 && dz == 0) return null;
return new double[]{ dx, dy, dz };
}

/**
* Returns the 3D extension direction vector of this path using linear regression.
* The vector represents the overall direction from start to end of the path, fitted through all its nodes.
Expand Down
15 changes: 15 additions & 0 deletions src/main/java/sc/fiji/snt/SNT.java
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Original file line number Diff line number Diff line change
Expand Up @@ -1233,6 +1233,10 @@ public void finished(final SearchInterface source, final boolean success) {
return;
}
setTemporaryPath(result);
// Hook 2: Run plausibility checks on candidate segment
if (ui != null && ui.getPlausibilityMonitor().isEnabled() && currentPath != null) {
ui.getPlausibilityMonitor().onSegmentCompleted(result);
}
if (rubberBandTracing) {
// In rubber band mode: show preview, stay in PARTIAL_PATH.
// The user clicks to accept; no Y confirmation needed.
Expand Down Expand Up @@ -2464,6 +2468,10 @@ protected synchronized void finishedPath() {
}
if (pathAndFillManager.getPathFromID(currentPath.getID()) == null) {
pathAndFillManager.addPath(currentPath, true, false, false);
// Hook 3: Run holistic plausibility check on completed path
if (ui != null && ui.getPlausibilityMonitor().isEnabled()) {
ui.getPlausibilityMonitor().onPathFinalized(currentPath);
}
}
lastStartPointSet = false;
if (activateFinishedPath) selectPath(currentPath, false);
Expand Down Expand Up @@ -2646,12 +2654,19 @@ synchronized void startPath(final double world_x, final double world_y,
real_last_start_y = world_y;
real_last_start_z = world_z;
ballColor = getXYCanvas().getTemporaryPathColor();
// Clear fork context: this is a root path, not a fork
if (ui != null) ui.getPlausibilityMonitor().clearForkContext();
}
else {
real_last_start_x = joinPoint.x;
real_last_start_y = joinPoint.y;
real_last_start_z = joinPoint.z;
path.setBranchFrom(joinPoint.onPath, joinPoint);
// Hook 1: Notify plausibility monitor of fork initiation
if (ui != null && ui.getPlausibilityMonitor().isEnabled()) {
final int branchIdx = path.getBranchPointIndex();
ui.getPlausibilityMonitor().onForkInitiated(joinPoint.onPath, branchIdx);
}
ballColor = Color.GREEN;
}
// offset is irrelevant: newly created paths always have canvasOffset = (0,0,0)
Expand Down
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