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Merged
tferr merged 3 commits into from
Oct 12, 2026
Merged

Extend edit controls to Bdv/Bvv #334

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920bc64
Extend edit controls to Bdv/Bvv
tferr Oct 10, 2026
e035b12
Fix PlausibilityMonitor not picking up changes & extend checks to Bdv…
tferr Oct 11, 2026
8e50ba4
Improve consistency of contextual menus between viewers
tferr Oct 12, 2026
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94 changes: 68 additions & 26 deletions src/main/java/sc/fiji/snt/BookmarkManager.java
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Original file line number Diff line number Diff line change
Expand Up @@ -451,17 +451,14 @@ private void goToRow(final int tableRow) {
// viewer mode: animate camera to marker world position
flyTo(tableRow);
} else {
// Classic mode: move the image windows and any open Bvv/Bdv viewer
final Bookmark b = model.getDataList().get(table.convertRowIndexToModel(tableRow));
final int nViewers = flyOpenViewers(b);
final ImagePlus imp = sntui.plugin.getImagePlus();
if (imp == null) {
noImageOpenError();
if (nViewers == 0) noImageOpenError();
} else {
goTo(tableRow, imp);
if (!sntui.plugin.getSinglePane()) {
final ImagePlus zyImp = sntui.plugin.getImagePlus(SNT.ZY_PLANE);
if (zyImp != null) goTo(tableRow, zyImp, SNT.ZY_PLANE);
final ImagePlus xzImp = sntui.plugin.getImagePlus(SNT.XZ_PLANE);
if (xzImp != null) goTo(tableRow, xzImp, SNT.XZ_PLANE);
}
goToAllPlanes(sntui.plugin, b, false);
}
}
}
Expand Down Expand Up @@ -1303,7 +1300,7 @@ public void actionPerformed(final ActionEvent e) {
viewer.promptGoTo();
return;
}
if (sntui.plugin.getImagePlus() == null) {
if (sntui.plugin.getImagePlus() == null && sntui.getOpenBigViewers().isEmpty()) {
noImageOpenError();
return;
}
Expand All @@ -1317,13 +1314,8 @@ public void actionPerformed(final ActionEvent e) {
final PointInImage pim = SNTPoint.fromString(pos);
final Bookmark b = new Bookmark(String.format("%.2f, %.2f, %.2f", pim.x, pim.y, pim.z),
pim.x, pim.y, pim.z, 1, 1);
goTo(b, sntui.plugin.getImagePlus(), SNT.XY_PLANE);
if (!sntui.plugin.getSinglePane()) {
final ImagePlus zyImp = sntui.plugin.getImagePlus(SNT.ZY_PLANE);
if (zyImp != null) goTo(b, zyImp, SNT.ZY_PLANE);
final ImagePlus xzImp = sntui.plugin.getImagePlus(SNT.XZ_PLANE);
if (xzImp != null) goTo(b, xzImp, SNT.XZ_PLANE);
}
flyOpenViewers(b);
goToAllPlanes(sntui.plugin, b, false);
sntui.showStatus(String.format("Zoomed to %s", b.label), true);
} catch (final Throwable ex) {
getGuiUtils().error("Could not extract a valid location from \"" + pos + "\".");
Expand Down Expand Up @@ -1367,11 +1359,14 @@ private boolean noBookmarksError() {
return false;
}

private void goTo(final int row, final ImagePlus imp, final int plane) {
goTo(model.getDataList().get(table.convertRowIndexToModel(row)), imp, plane);
}

private void goTo(final Bookmark b, final ImagePlus imp, final int plane) {
/**
* Moves the display of an image to a bookmark
*
* @param silent if true, no error is displayed if the bookmark lies outside the image
* @return true if the bookmark is within the image (and the display was moved)
*/
private boolean goTo(final Bookmark b, final ImagePlus imp, final int plane, final boolean silent) {
assert imp != null;

// Bookmark coordinates are always world/calibrated; convert to pixel space, which is
Expand Down Expand Up @@ -1400,33 +1395,80 @@ private void goTo(final Bookmark b, final ImagePlus imp, final int plane) {
}
};

if (viewX > imp.getWidth() || viewY > imp.getHeight()) {
final boolean outsideXY = viewX < 0 || viewY < 0 || viewX > imp.getWidth() || viewY > imp.getHeight();
// Z is only checked on the main XY plane: side views show all Z by definition
final boolean outsideZ = plane == SNT.XY_PLANE && (pz < 0 || pz >= imp.getNSlices());
if (outsideXY || outsideZ) {
// Only show error for the main XY plane
if (plane == SNT.XY_PLANE) {
sntui.guiUtils.error("Location is outside image XY dimensions");
if (plane == SNT.XY_PLANE && !silent) {
final SNT snt = snt();
final String what = (snt != null && snt.isMaterializedCrop()) ? "the materialized crop" : "image";
getGuiUtils().error((outsideXY && outsideZ) ? "Location is outside " + what + " bounds"
: (outsideXY) ? "Location is outside " + what + " XY dimensions"
: "Location is outside " + what + " Z range");
}
return;
return false;
}
if (plane == SNT.XY_PLANE) {
// NB: ImagePlus#setPosition uses 1-based slice indices; pz is 0-based (see worldToPixel)
imp.setPosition(b.c, (int) pz + 1, b.t);
}
// Side views don't need setPosition - they show all Z by definition
ImpUtils.zoomTo(imp, visitingZoom.fraction(), (int) viewX, (int) viewY);
return true;
}

private void goTo(final int row, final ImagePlus imp) {
goTo(row, imp, SNT.XY_PLANE);
/**
* Viewer mode: moves the image windows of a materialized crop (Stream mode), if any, to a bookmark. Bookmarks
* outside the crop, which is only a portion of the streamed data, are skipped with a notice in the viewer
*/
private void goToMaterializedCrop(final Bookmark b) {
final SNT snt = snt();
if (snt == null || !snt.isStreamMode() || !snt.isMaterializedCrop()) return;
if (snt.getImagePlus() == null) return;
if (!goToAllPlanes(snt, b, true)) viewer.showViewerMessage("Bookmark is outside the materialized crop");
}

/**
* Moves the image of the main (XY) view and, if displayed, the side views to a bookmark. Side views are only
* moved if the bookmark lies within the main view
*
* @param silent if true, no error is displayed if the bookmark lies outside the image
* @return true if the bookmark is within the image (and the displays were moved). False if there is no image
*/
private boolean goToAllPlanes(final SNT snt, final Bookmark b, final boolean silent) {
final ImagePlus imp = snt.getImagePlus();
if (imp == null || !goTo(b, imp, SNT.XY_PLANE, silent)) return false;
if (!snt.getSinglePane()) {
final ImagePlus zyImp = snt.getImagePlus(SNT.ZY_PLANE);
if (zyImp != null) goTo(b, zyImp, SNT.ZY_PLANE, silent);
final ImagePlus xzImp = snt.getImagePlus(SNT.XZ_PLANE);
if (xzImp != null) goTo(b, xzImp, SNT.XZ_PLANE, silent);
}
return true;
}

/** Viewer mode: animates the camera to the world position of the selected marker row. */
private void flyTo(final int row) {
flyTo(model.getDataList().get(table.convertRowIndexToModel(row)));
}

/**
* SNT mode: animates every open Bvv/Bdv viewer to the location of the bookmark
*
* @return the number of viewers that were moved
*/
private int flyOpenViewers(final Bookmark b) {
if (sntui == null) return 0;
final java.util.List<AbstractBigViewer> viewers = sntui.getOpenBigViewers();
for (final AbstractBigViewer v : viewers) v.flyTo(b.getX(), b.getY(), b.getZ(), b.t, b.label);
return viewers.size();
}

private void flyTo(final Bookmark b) {
if (viewer == null) return;
viewer.flyTo(b.getX(), b.getY(), b.getZ(), b.t, b.label);
goToMaterializedCrop(b); // Stream mode only
}

private void loadBookmarksFromFile(final File file) {
Expand Down
17 changes: 15 additions & 2 deletions src/main/java/sc/fiji/snt/CurationManager.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -676,14 +676,15 @@ private JPanel buildLiveParamsPanel() {
angleCheck != null && angleCheck.isEnabled());
branchAngleMinCheckbox.setToolTipText("Warns when a child path emerges nearly parallel to its parent");
branchAngleMinSpinner = new JSpinner(new SpinnerNumberModel(
angleCheck != null ? angleCheck.getMinAngleDeg() : 10.0, 0.0, 90.0, 5.0));
angleCheck != null ? angleCheck.getMinAngleDeg() : 10.0, 0.0, 180.0, 5.0));
branchAngleMinCheckbox.addActionListener(e -> {
if (angleCheck != null) angleCheck.setEnabled(
branchAngleMinCheckbox.isSelected() || branchAngleMaxCheckbox.isSelected());
branchAngleMinSpinner.setEnabled(branchAngleMinCheckbox.isSelected());
});
branchAngleMinSpinner.addChangeListener(e -> {
if (angleCheck != null) angleCheck.setMinAngleDeg((Double) branchAngleMinSpinner.getValue());
coupleBranchAngleBounds();
});
// Histogram button: both BranchAngle spinners share the same OUTSIDE-flagged
// distribution. Clicking either button opens the same chart with both markers.
Expand All @@ -701,14 +702,15 @@ private JPanel buildLiveParamsPanel() {
angleCheck != null && angleCheck.isEnabled());
branchAngleMaxCheckbox.setToolTipText("Warns when a child path doubles back, nearly anti-parallel to its parent");
branchAngleMaxSpinner = new JSpinner(new SpinnerNumberModel(
angleCheck != null ? angleCheck.getMaxAngleDeg() : 170.0, 90.0, 180.0, 5.0));
angleCheck != null ? angleCheck.getMaxAngleDeg() : 170.0, 0.0, 180.0, 5.0));
branchAngleMaxCheckbox.addActionListener(e -> {
if (angleCheck != null) angleCheck.setEnabled(
branchAngleMinCheckbox.isSelected() || branchAngleMaxCheckbox.isSelected());
branchAngleMaxSpinner.setEnabled(branchAngleMaxCheckbox.isSelected());
});
branchAngleMaxSpinner.addChangeListener(e -> {
if (angleCheck != null) angleCheck.setMaxAngleDeg((Double) branchAngleMaxSpinner.getValue());
coupleBranchAngleBounds();
});
final JButton branchAngleMaxHist = (angleCheck == null) ? null
: CurationHistograms.button("Fork angle", null,
Expand All @@ -718,6 +720,7 @@ private JPanel buildLiveParamsPanel() {
() -> ((Number) branchAngleMinSpinner.getValue()).doubleValue(),
CurationHistograms.Side.OUTSIDE_FLAGGED, p);
addCheckRow(p, c, branchAngleMaxCheckbox, spinnerWithHistogram(branchAngleMaxSpinner, branchAngleMaxHist));
coupleBranchAngleBounds();

// Direction continuity
final PlausibilityCheck.DirectionContinuity dirCheck =
Expand Down Expand Up @@ -1906,6 +1909,16 @@ private JComponent spinnerWithHistogram(final JSpinner spinner, final JButton hi
return p;
}

/** Keeps min <= max: each fork angle spinner is bounded by the other's value */
private void coupleBranchAngleBounds() {
if (branchAngleMinSpinner == null || branchAngleMaxSpinner == null) return;
if (branchAngleMinSpinner.getModel() instanceof SpinnerNumberModel minModel
&& branchAngleMaxSpinner.getModel() instanceof SpinnerNumberModel maxModel) {
minModel.setMaximum(((Number) maxModel.getValue()).doubleValue());
maxModel.setMinimum(((Number) minModel.getValue()).doubleValue());
}
}

/**
* Reduces a spinner's editor to a compact column count. All curation
* spinners hold short numeric values (typically 3-5 characters); the
Expand Down
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