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GUI: Yet more menu ~~tectonics~~ re-organization
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@tferr
tferr committed Jun 29, 2024
1 parent 907acc9 commit 6ccb96b
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Showing 4 changed files with 164 additions and 139 deletions.
14 changes: 1 addition & 13 deletions src/main/java/sc/fiji/snt/PathManagerUI.java
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Original file line number Diff line number Diff line change
Expand Up @@ -487,19 +487,7 @@ private JMenu getTimeSequenceMenu(final MultiPathActionListener multiPathListene
final JMenu menu = new JMenu("Time-lapse Utilities");
final String tooltip = "Assumes selected path(s) belong to a time-lapse series";
menu.setIcon(IconFactory.getMenuIcon(IconFactory.GLYPH.VIDEO));
JMenuItem jmi = new JMenuItem("Apply 3D Drift Corrections...");
jmi.setToolTipText("<HTML>Assumes loaded image is a time-lapse series. Should be run <i>before</i> tracing operations");
jmi.addActionListener( e-> {
if (!plugin.accessToValidImageData() || plugin.getImagePlus().getNFrames() == 1) {
guiUtils.error("A timelapse is required but none seems to be loaded.");
}
else if (!ScriptInstaller.runScript("Plugins/Registration/Correct_3D_drift.py")) {
guiUtils.error("Could not find 'Correct 3D Drift'. " +
"Make sure no files are missing from your Fiji install.");
}
});
menu.add(jmi);
jmi = new JMenuItem(MultiPathActionListener.MATCH_PATHS_ACROSS_TIME_CMD);
JMenuItem jmi = new JMenuItem(MultiPathActionListener.MATCH_PATHS_ACROSS_TIME_CMD);
jmi.setToolTipText(tooltip);
jmi.addActionListener(multiPathListener);
menu.add(jmi);
Expand Down
220 changes: 128 additions & 92 deletions src/main/java/sc/fiji/snt/SNTUI.java
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Original file line number Diff line number Diff line change
Expand Up @@ -113,7 +113,6 @@ public class SNTUI extends JDialog {
private JButton showOrHidePathList;
private JButton showOrHideFillList = new JButton(); // must be initialized
private JMenuItem saveMenuItem;
private JMenuItem exportCSVMenuItem;
private JMenuItem quitMenuItem;
private JMenuItem sendToTrakEM2;
private JLabel statusText;
Expand Down Expand Up @@ -880,7 +879,6 @@ public void changeState(final int newState) {
fmUI.setEnabledWhileNotFilling();
saveMenuItem.setEnabled(true);

exportCSVMenuItem.setEnabled(true);
sendToTrakEM2.setEnabled(plugin.anyListeners());
quitMenuItem.setEnabled(true);
showPathsSelected.setEnabled(true);
Expand All @@ -902,7 +900,6 @@ public void changeState(final int newState) {
// setFillListVisible(false);
saveMenuItem.setEnabled(true);

exportCSVMenuItem.setEnabled(true);
sendToTrakEM2.setEnabled(plugin.anyListeners());
quitMenuItem.setEnabled(true);
showPathsSelected.setEnabled(true);
Expand Down Expand Up @@ -1085,7 +1082,8 @@ private JPanel sourcePanel(final ImagePlus imp) {
positionPanel.add(applyPositionButton);

final JCheckBox autoCTcheckbox = new JCheckBox("Auto-load CT position of new paths", plugin.autoCT);
commandFinder.register(autoCTcheckbox, "Main Tab", "Data Source");
commandFinder.register(autoCTcheckbox, "Toggle Auto-load CT Position of New Paths",
"Main Tab", "Data Source");
GuiUtils.addTooltip(autoCTcheckbox, "Automatically loads the active channel and frame of the starting " +
"node of newly created paths.<br>" +
"NB: This option may be incompatible with secondary layers and Z-projection overlays.");
Expand Down Expand Up @@ -1181,7 +1179,7 @@ private JPanel viewsPanel() {

final CheckboxSpinner mipCS = new CheckboxSpinner(new JCheckBox("Overlay MIP(s) at"),
GuiUtils.integerSpinner(20, 10, 80, 1, true));
registerInCommandFinder(mipCS.getCheckBox(), "Overlay MIP(s)", "Options Tab");
registerInCommandFinder(mipCS.getCheckBox(), "Toggle Overlay MIP(s)", "Options Tab");
mipCS.getSpinner().addChangeListener(e -> mipCS.setSelected(false));
mipCS.appendLabel(" % opacity");
mipCS.getCheckBox().addActionListener(e -> {
Expand All @@ -1201,6 +1199,8 @@ private JPanel viewsPanel() {

final JCheckBox zoomAllPanesCheckBox = new JCheckBox("Apply zoom changes to all views",
!plugin.isZoomAllPanesDisabled());
registerInCommandFinder(zoomAllPanesCheckBox, "Toggle Apply Zoom Changes to All Views'",
"Options Tab");
zoomAllPanesCheckBox
.addItemListener(e -> plugin.disableZoomAllPanes(e.getStateChange() == ItemEvent.DESELECTED));
viewsPanel.add(zoomAllPanesCheckBox, gdb);
Expand Down Expand Up @@ -1353,7 +1353,8 @@ private JPanel tracingPanel() {

final JCheckBox confirmTemporarySegmentsCheckbox = new JCheckBox("Confirm temporary segments",
confirmTemporarySegments);
registerInCommandFinder(confirmTemporarySegmentsCheckbox, null, "Options Tab");
registerInCommandFinder(confirmTemporarySegmentsCheckbox, "Toggle Confirm Temporary Segments",
"Options Tab");
tPanel.add(confirmTemporarySegmentsCheckbox, gdb);
++gdb.gridy;

Expand All @@ -1376,13 +1377,16 @@ private JPanel tracingPanel() {

final JCheckBox activateFinishedPathCheckbox = new JCheckBox("Finishing a path selects it",
plugin.activateFinishedPath);
registerInCommandFinder(activateFinishedPathCheckbox, null, "Options Tab");
registerInCommandFinder(activateFinishedPathCheckbox, "Toggle Finishing a Path Selects It",
"Options Tab");
GuiUtils.addTooltip(activateFinishedPathCheckbox, "Whether the path being traced should automatically be selected once finished.");
activateFinishedPathCheckbox.addItemListener(e -> plugin.enableAutoSelectionOfFinishedPath(e.getStateChange() == ItemEvent.SELECTED));
tPanel.add(activateFinishedPathCheckbox, gdb);
++gdb.gridy;

final JCheckBox requireShiftToForkCheckbox = new JCheckBox("Require 'Shift' to branch off a path", plugin.requireShiftToFork);
registerInCommandFinder(requireShiftToForkCheckbox, "Toggle Require 'Shift' to Branch Off a Path",
"Options Tab");
GuiUtils.addTooltip(requireShiftToForkCheckbox, "When branching off a path: Use Shift+Alt+click or Alt+click at the forking node? "
+ "NB: Alt+click is a common trigger for window dragging on Linux. Use Super+Alt+click to circumvent OS conflics.");
requireShiftToForkCheckbox.addItemListener(e ->plugin.requireShiftToFork = e.getStateChange() == ItemEvent.SELECTED);
Expand All @@ -1395,7 +1399,7 @@ private JPanel pathOptionsPanel() {
final JPanel intPanel = new JPanel(new GridBagLayout());
final GridBagConstraints gdb = GuiUtils.defaultGbc();
final JCheckBox diametersCheckBox = new JCheckBox("Draw diameters", plugin.getDrawDiameters());
registerInCommandFinder(diametersCheckBox, null, "Options Tab");
registerInCommandFinder(diametersCheckBox, "Toggle Draw Diameters", "Options Tab");
diametersCheckBox.addItemListener(e -> plugin.setDrawDiameters(e.getStateChange() == ItemEvent.SELECTED));
intPanel.add(diametersCheckBox, gdb);
++gdb.gridy;
Expand Down Expand Up @@ -1618,12 +1622,16 @@ private JPanel miscPanel() {
++gdb.gridy;
final JCheckBox canvasCheckBox = new JCheckBox("Activate canvas on mouse hovering",
plugin.autoCanvasActivation);
registerInCommandFinder(canvasCheckBox, "Toggle Activate Canvas on Mouse Hovering",
"Options Tab");
GuiUtils.addTooltip(canvasCheckBox, "Whether the image window should be brought to front as soon as the mouse "
+ "pointer enters it. This may be needed to ensure single key shortcuts work as expected when tracing.");
canvasCheckBox.addItemListener(e -> plugin.enableAutoActivation(e.getStateChange() == ItemEvent.SELECTED));
miscPanel.add(canvasCheckBox, gdb);
++gdb.gridy;
final JCheckBox askUserConfirmationCheckBox = new JCheckBox("Skip confirmation dialogs", !askUserConfirmation);
registerInCommandFinder(askUserConfirmationCheckBox, "Toggle Skip Confirmation Dialogs",
"Options Tab");
GuiUtils.addTooltip(askUserConfirmationCheckBox,
"Whether \"Are you sure?\" type of prompts should precede major operations");
askUserConfirmationCheckBox
Expand Down Expand Up @@ -2286,7 +2294,8 @@ private JPanel secondaryDataPanel() {
c.insets.left *= 2;
secLayerImgOverlayCSpinner = new CheckboxSpinner(new JCheckBox("Render in overlay at "),
GuiUtils.integerSpinner(20, 10, 80, 1, true));
registerInCommandFinder(secLayerImgOverlayCSpinner.getCheckBox(), "Toggle secondary layer overlay", "Main Tab");
registerInCommandFinder(secLayerImgOverlayCSpinner.getCheckBox(), "Toggle Secondary Layer Overlay",
"Main Tab");
secLayerImgOverlayCSpinner.getSpinner().addChangeListener(e -> {
secLayerImgOverlayCSpinner.setSelected(false);
});
Expand Down Expand Up @@ -2658,17 +2667,10 @@ private JMenuBar createMenuBar() {
getPathManager().quickMeasurementsCmdError(guiUtils);
}
});
final JMenuItem plotMenuItem = new JMenuItem("Reconstruction Plotter...", IconFactory.getMenuIcon(IconFactory.GLYPH.DRAFT));
plotMenuItem.setToolTipText("Renders traced paths as vector graphics (2D)");
plotMenuItem.addActionListener( e -> {
if (noPathsError()) return;
final Tree tree = getPathManager().getSingleTree();
if (tree == null) return;
final Map<String, Object> input = new HashMap<>();
input.put("tree", tree);
final CommandService cmdService = plugin.getContext().getService(CommandService.class);
cmdService.run(PlotterCmd.class, true, input);
});

analysisMenu.add(getBrainAnnotationMenu());
analysisMenu.add(getPathAnalysisMenu());
analysisMenu.addSeparator();

final JMenuItem convexHullMenuItem = GuiUtils.MenuItems.convexHull();
convexHullMenuItem.addActionListener(e -> {
Expand All @@ -2682,36 +2684,6 @@ private JMenuBar createMenuBar() {
(new CmdRunner(ConvexHullCmd.class, inputs, getState())).execute();
});
analysisMenu.add(convexHullMenuItem);
analysisMenu.addSeparator();

final JMenuItem pathOrderAnalysis = new JMenuItem("Path Order Analysis",
IconFactory.getMenuIcon(IconFactory.GLYPH.BRANCH_CODE));
pathOrderAnalysis.setToolTipText("Horton-Strahler-like analysis based on paths rather than branches");
pathOrderAnalysis.addActionListener(e -> {
if (noPathsError()) return;
final Tree tree = getPathManager().getSingleTree();
if (tree == null) return;
final PathOrderAnalysisCmd pa = new PathOrderAnalysisCmd(tree);
pa.setContext(plugin.getContext());
pa.setTable(new SNTTable(), "SNT: Path Order Analysis");
pa.run();
});
analysisMenu.add(pathOrderAnalysis);
exportCSVMenuItem = new JMenuItem("Path Properties: Export CSV...", IconFactory.getMenuIcon(IconFactory.GLYPH.CSV));
exportCSVMenuItem.setToolTipText("Export details (metrics, relationships, ...) of existing paths as tabular data");
exportCSVMenuItem.addActionListener(listener);
analysisMenu.add(exportCSVMenuItem);
analysisMenu.addSeparator();
final JMenuItem brainMenuItem = GuiUtils.MenuItems.brainAreaAnalysis();
brainMenuItem.addActionListener(e -> {
if (noPathsError()) return;
final Tree tree = getPathManager().getSingleTree();
if (tree == null) return;
final HashMap<String, Object> inputs = new HashMap<>();
inputs.put("tree", tree);
new DynamicCmdRunner(BrainAnnotationCmd.class, inputs).run();
});
analysisMenu.add(brainMenuItem);
final JMenuItem tmdMenuItem = GuiUtils.MenuItems.persistenceAnalysis();
tmdMenuItem.addActionListener(e -> {
if (noPathsError()) return;
Expand Down Expand Up @@ -2785,19 +2757,8 @@ private JMenuBar createMenuBar() {
(new DynamicCmdRunner(GroupAnalyzerCmd.class, null)).run();
}
});
utilitiesMenu.add(plotMenuItem);
utilitiesMenu.add(getRecPlotterMenuItem());
utilitiesMenu.addSeparator();

final JMenuItem annotGenerator = GuiUtils.MenuItems.createAnnotionGraph();
utilitiesMenu.add(annotGenerator);
annotGenerator.addActionListener(e -> {
if (noPathsError()) return;
final Collection<Tree> trees = getPathManager().getMultipleTrees();
if (trees == null) return;
final HashMap<String, Object> inputs = new HashMap<>();
inputs.put("trees", trees);
(new DynamicCmdRunner(AnnotationGraphGeneratorCmd.class, inputs)).run();
});
final JMenuItem graphGenerator = GuiUtils.MenuItems.createDendrogram();
utilitiesMenu.add(graphGenerator);
graphGenerator.addActionListener(e -> {
Expand All @@ -2820,6 +2781,7 @@ private JMenuBar createMenuBar() {
utilitiesMenu.add(figureGenerator);
utilitiesMenu.addSeparator();

utilitiesMenu.add(getDriftCorrectionMenuItem());
// similar to File>Autotrace Segmented Image File... but assuming current image as source,
// which does not require file validations etc.
final JMenuItem autotraceJMI = new JMenuItem("Autotrace Segmented Image...",
Expand All @@ -2828,7 +2790,6 @@ private JMenuBar createMenuBar() {
utilitiesMenu.add(autotraceJMI);
ScriptRecorder.setRecordingCall(autotraceJMI, "snt.getUI().runAutotracingWizard(false)");
autotraceJMI.addActionListener(e -> runAutotracingOnImage(false));

// View menu
final JMenuItem arrangeDialogsMenuItem = new JMenuItem("Arrange Dialogs",
IconFactory.getMenuIcon(IconFactory.GLYPH.WINDOWS2));
Expand Down Expand Up @@ -2905,6 +2866,109 @@ private JMenuBar createMenuBar() {
return menuBar;
}

private JMenuItem getDriftCorrectionMenuItem() {
final JMenuItem driftJMI = new JMenuItem("Apply 3D Drift Corrections...", IconFactory.getMenuIcon(GLYPH.VIDEO));
driftJMI.setToolTipText("<HTML>Assumes loaded image is a time-lapse series. Should be run <i>before</i> tracing operations");
driftJMI.addActionListener( e-> {
if (!plugin.accessToValidImageData() || plugin.getImagePlus().getNFrames() == 1) {
guiUtils.error("A timelapse is required but none seems to be loaded.");
}
else if (!ScriptInstaller.runScript("Plugins/Registration/Correct_3D_drift.py")) {
guiUtils.error("Could not find 'Correct 3D Drift'. " +
"Make sure no files are missing from your Fiji install.");
}
});
return driftJMI;
}

private JMenuItem getRecPlotterMenuItem() {
final JMenuItem plotMenuItem = new JMenuItem("Reconstruction Plotter...", IconFactory.getMenuIcon(IconFactory.GLYPH.DRAFT));
plotMenuItem.setToolTipText("Renders traced paths as vector graphics (2D)");
plotMenuItem.addActionListener( e -> {
if (noPathsError()) return;
final Tree tree = getPathManager().getSingleTree();
if (tree == null) return;
final Map<String, Object> input = new HashMap<>();
input.put("tree", tree);
final CommandService cmdService = plugin.getContext().getService(CommandService.class);
cmdService.run(PlotterCmd.class, true, input);
});
return plotMenuItem;
}

private JMenu getBrainAnnotationMenu() {
final JMenu menu = new JMenu("Atlas-based");
menu.setIcon(IconFactory.getMenuIcon(GLYPH.ATLAS));
JMenuItem mi = GuiUtils.MenuItems.createAnnotionGraph();
mi.addActionListener(e -> {
if (noPathsError()) return;
final Collection<Tree> trees = getPathManager().getMultipleTrees();
if (trees == null) return;
final HashMap<String, Object> inputs = new HashMap<>();
inputs.put("trees", trees);
(new DynamicCmdRunner(AnnotationGraphGeneratorCmd.class, inputs)).run();
});
menu.add(mi);
mi = GuiUtils.MenuItems.brainAreaAnalysis();
mi.addActionListener(e -> {
if (noPathsError()) return;
final Tree tree = getPathManager().getSingleTree();
if (tree == null) return;
final HashMap<String, Object> inputs = new HashMap<>();
inputs.put("tree", tree);
new DynamicCmdRunner(BrainAnnotationCmd.class, inputs).run();
});
menu.add(mi);
return menu;
}

private JMenu getPathAnalysisMenu() {
final JMenu menu = new JMenu("Path-based");
menu.setIcon(IconFactory.getMenuIcon(GLYPH.ROUTE));
JMenuItem mi = new JMenuItem("Path Order Analysis", IconFactory.getMenuIcon(IconFactory.GLYPH.BRANCH_CODE));
mi.setToolTipText("Horton-Strahler-like analysis based on paths rather than branches");
mi.addActionListener(e -> {
if (noPathsError()) return;
final Tree tree = getPathManager().getSingleTree();
if (tree == null) return;
final PathOrderAnalysisCmd pa = new PathOrderAnalysisCmd(tree);
pa.setContext(plugin.getContext());
pa.setTable(new SNTTable(), "SNT: Path Order Analysis");
pa.run();
});
menu.add(mi);
mi = new JMenuItem("Path Properties: Export CSV...", IconFactory.getMenuIcon(IconFactory.GLYPH.CSV));
mi.setToolTipText("Export details (metrics, relationships, ...) of existing paths as tabular data");
mi.addActionListener(e -> {
final File saveFile = saveFile("Export All Paths as CSV...", "CSV_Properties.csv", "csv");
if (saveFile == null)
return; // user pressed cancel
if (saveFile.exists() && !guiUtils.getConfirmation(
"The file " + saveFile.getAbsolutePath() + " already exists. " + "Do you want to replace it?",
"Override CSV file?")) {
return;
}
final String savePath = saveFile.getAbsolutePath();
showStatus("Exporting as CSV to " + savePath, false);
final int preExportingState = currentState;
changeState(SAVING);
// Export here...
try {
pathAndFillManager.exportToCSV(saveFile);
} catch (final IOException ioe) {
showStatus("Exporting failed.", true);
guiUtils.error("Writing traces to '" + savePath + "' failed. See Console for details.");
changeState(preExportingState);
ioe.printStackTrace();
return;
}
showStatus("Export complete.", true);
changeState(preExportingState);
});
menu.add(mi);
return menu;
}

private JMenuItem getExportSWCMenuItem() {
final JMenuItem exportAllSWCMenuItem = new JMenuItem("Export As SWC...");
exportAllSWCMenuItem.addActionListener( e -> {
Expand Down Expand Up @@ -3037,7 +3101,7 @@ private JPanel colorOptionsPanel() {
GuiUtils.addTooltip(jcheckbox,
"Whether default colors above should be used even when color tags have been applied in the Path Manager.<br><br>" +
"NB: This option does not affect color-coded paths, or paths with multi-color nodes");
registerInCommandFinder(jcheckbox, "Enforce Default Colors", "Main Tab");
registerInCommandFinder(jcheckbox, "Toggle Enforce Default Colors", "Main Tab");
jcheckbox.addActionListener(e -> {
plugin.displayCustomPathColors = !jcheckbox.isSelected();
plugin.updateTracingViewers(true);
Expand Down Expand Up @@ -4077,34 +4141,6 @@ public void actionPerformed(final ActionEvent e) {
plugin.enableSecondaryLayerTracing(false);
}

} else if (source == exportCSVMenuItem && !noPathsError()) {

final File saveFile = saveFile("Export All Paths as CSV...", "CSV_Properties.csv", "csv");
if (saveFile == null)
return; // user pressed cancel
if (saveFile.exists() && !guiUtils.getConfirmation(
"The file " + saveFile.getAbsolutePath() + " already exists. " + "Do you want to replace it?",
"Override CSV file?")) {
return;
}
final String savePath = saveFile.getAbsolutePath();
showStatus("Exporting as CSV to " + savePath, false);

final int preExportingState = currentState;
changeState(SAVING);
// Export here...
try {
pathAndFillManager.exportToCSV(saveFile);
} catch (final IOException ioe) {
showStatus("Exporting failed.", true);
guiUtils.error("Writing traces to '" + savePath + "' failed. See Console for details.");
changeState(preExportingState);
ioe.printStackTrace();
return;
}
showStatus("Export complete.", true);
changeState(preExportingState);

} else if (source == keepSegment) {

plugin.confirmTemporary(true);
Expand Down
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