protected void interpolateSurface(LinkedList<Point3d> points) throws InterruptedException {
double pixSize = MMStudio.getInstance().getCore().getPixelSizeUm();
// provide interpolator with current list of data points
Point_dt triangulationPoints[] = new Point_dt[points.size()];
for (int i = 0; i < points.size(); i++) {
triangulationPoints[i] = new Point_dt(points.get(i).x, points.get(i).y, points.get(i).z);
}
Delaunay_Triangulation dTri = new Delaunay_Triangulation(triangulationPoints);
int maxPixelDimension =
(int) (Math.max(boundXMax_ - boundXMin_, boundYMax_ - boundYMin_) / pixSize);
// Start with at least 20 interp points and go smaller and smaller until every pixel interped?
int pixelsPerInterpPoint = 1;
while (maxPixelDimension / (pixelsPerInterpPoint + 1) > 20) {
pixelsPerInterpPoint *= 2;
}
if (Thread.interrupted()) {
throw new InterruptedException();
}
while (pixelsPerInterpPoint >= MIN_PIXELS_PER_INTERP_POINT) {
int numInterpPointsX = (int) (((boundXMax_ - boundXMin_) / pixSize) / pixelsPerInterpPoint);
int numInterpPointsY = (int) (((boundYMax_ - boundYMin_) / pixSize) / pixelsPerInterpPoint);
double dx = (boundXMax_ - boundXMin_) / (numInterpPointsX - 1);
double dy = (boundYMax_ - boundYMin_) / (numInterpPointsY - 1);
Double[][] interpVals = new Double[numInterpPointsY][numInterpPointsX];
for (int yInd = 0; yInd < interpVals.length; yInd++) {
for (int xInd = 0; xInd < interpVals[0].length; xInd++) {
if (Thread.interrupted()) {
throw new InterruptedException();
}
double xVal = boundXMin_ + dx * xInd;
double yVal = boundYMin_ + dy * yInd;
boolean inHull =
convexHullRegion_.checkPoint(new Vector2D(xVal, yVal)) == Region.Location.INSIDE;
if (inHull) {
Triangle_dt tri = dTri.find(new Point_dt(xVal, yVal));
// convert to apache commons coordinates to make a plane
Vector3D v1 = new Vector3D(tri.p1().x(), tri.p1().y(), tri.p1().z());
Vector3D v2 = new Vector3D(tri.p2().x(), tri.p2().y(), tri.p2().z());
Vector3D v3 = new Vector3D(tri.p3().x(), tri.p3().y(), tri.p3().z());
Plane plane = new Plane(v1, v2, v3);
Vector3D pointInPlane =
(Vector3D)
plane.intersection(
new Line(new Vector3D(xVal, yVal, 0), new Vector3D(xVal, yVal, 1)));
double zVal = (double) pointInPlane.getZ();
interpVals[yInd][xInd] = zVal;
} else {
interpVals[yInd][xInd] = null;
}
}
}
if (Thread.interrupted()) {
throw new InterruptedException();
}
synchronized (interpolationLock_) {
currentInterpolation_ =
new SingleResolutionInterpolation(
pixelsPerInterpPoint,
interpVals,
boundXMin_,
boundXMax_,
boundYMin_,
boundYMax_,
convexHullRegion_,
convexHullVertices_,
getPoints());
interpolationLock_.notifyAll();
}
pixelsPerInterpPoint /= 2;
}
}
public PagePanel() {
super();
title_ = new String();
MMStudio mmf = MMStudio.getInstance();
if (mmf != null) setBackground(MMStudio.getInstance().getBackgroundColor());
}
/**
* Creates the ASIdiSPIM plugin frame
*
* @param gui - Micro-Manager script interface
* @throws ASIdiSPIMException
*/
public ASIdiSPIMFrame(ScriptInterface gui) throws ASIdiSPIMException {
// create interface objects used by panels
gui_ = gui;
prefs_ = new Prefs(Preferences.userNodeForPackage(this.getClass()));
devices_ = new Devices(gui_, prefs_);
props_ = new Properties(gui_, devices_, prefs_);
positions_ = new Positions(gui_, devices_);
joystick_ = new Joystick(devices_, props_);
cameras_ = new Cameras(gui_, devices_, props_, prefs_);
controller_ = new ControllerUtils(gui_, props_, prefs_, devices_, positions_);
// make sure Live mode is turned off (panels assume it can manipulate
// cameras which requires live mode to be turned off)
boolean liveModeOriginally = gui_.isLiveModeOn();
String cameraOriginal = gui_.getMMCore().getCameraDevice();
if (liveModeOriginally) {
gui_.enableLiveMode(false);
}
// create the panels themselves
// in some cases dependencies create required ordering
devicesPanel_ = new DevicesPanel(gui_, devices_, props_);
stagePosUpdater_ =
new StagePositionUpdater(positions_, props_); // needed for setup and navigation
autofocus_ =
new AutofocusUtils(
gui_, devices_, props_, prefs_, cameras_, stagePosUpdater_, positions_, controller_);
acquisitionPanel_ =
new AcquisitionPanel(
gui_,
devices_,
props_,
cameras_,
prefs_,
stagePosUpdater_,
positions_,
controller_,
autofocus_);
setupPanelA_ =
new SetupPanel(
gui_,
devices_,
props_,
joystick_,
Devices.Sides.A,
positions_,
cameras_,
prefs_,
stagePosUpdater_,
autofocus_);
if (!ASIdiSPIM.oSPIM) {
setupPanelB_ =
new SetupPanel(
gui_,
devices_,
props_,
joystick_,
Devices.Sides.B,
positions_,
cameras_,
prefs_,
stagePosUpdater_,
autofocus_);
} else {
setupPanelB_ = null;
}
navigationPanel_ =
new NavigationPanel(
gui_, devices_, props_, joystick_, positions_, prefs_, cameras_, stagePosUpdater_);
dataAnalysisPanel_ = new DataAnalysisPanel(gui_, prefs_);
autofocusPanel_ = new AutofocusPanel(gui_, devices_, props_, prefs_, autofocus_);
settingsPanel_ = new SettingsPanel(gui_, devices_, props_, prefs_, stagePosUpdater_);
stagePosUpdater_.oneTimeUpdate(); // needed for NavigationPanel
helpPanel_ = new HelpPanel();
statusSubPanel_ = new StatusSubPanel(devices_, props_, positions_, stagePosUpdater_);
// now add tabs to GUI
// all added tabs must be of type ListeningJPanel
// only use addLTab, not addTab to guarantee this
tabbedPane_ = new ListeningJTabbedPane();
if (isMac()) {
tabbedPane_.setTabPlacement(JTabbedPane.TOP);
} else {
tabbedPane_.setTabPlacement(JTabbedPane.LEFT);
}
tabbedPane_.addLTab(navigationPanel_); // tabIndex = 0
tabbedPane_.addLTab(setupPanelA_); // tabIndex = 1
if (!ASIdiSPIM.oSPIM) {
tabbedPane_.addLTab(setupPanelB_); // tabIndex = 2
}
tabbedPane_.addLTab(acquisitionPanel_); // tabIndex = 3
tabbedPane_.addLTab(dataAnalysisPanel_); // tabIndex = 4
tabbedPane_.addLTab(devicesPanel_); // tabIndex = 5
final int deviceTabIndex = tabbedPane_.getTabCount() - 1;
tabbedPane_.addLTab(autofocusPanel_); // tabIndex = 6
tabbedPane_.addLTab(settingsPanel_); // tabIndex = 7
tabbedPane_.addLTab(helpPanel_); // tabIndex = 8
final int helpTabIndex = tabbedPane_.getTabCount() - 1;
// make taller tabs for easier navigation between them
// we create own labels instead of having JTabbedPane do it from titles
final Border paddingBorder = BorderFactory.createEmptyBorder(4, 0, 4, 0);
for (int i = 0; i < tabbedPane_.getTabCount(); i++) {
JLabel lab = new JLabel(((ListeningJPanel) tabbedPane_.getComponentAt(i)).getPanelName());
lab.setBorder(paddingBorder);
tabbedPane_.setTabComponentAt(i, lab);
}
// add the testing panel explicitly by uncommenting following lines
// intended to only be done in short term for testing
// TestingPanel testingPanel = new TestingPanel();
// tabbedPane_.addLTab(testingPanel);
// attach position updaters
stagePosUpdater_.addPanel(setupPanelA_);
if (!ASIdiSPIM.oSPIM) {
stagePosUpdater_.addPanel(setupPanelB_);
}
stagePosUpdater_.addPanel(navigationPanel_);
stagePosUpdater_.addPanel(statusSubPanel_);
piezoSleepPreventer_ = new PiezoSleepPreventer(gui_, devices_, props_);
// attach live mode listeners
MMStudio.getInstance()
.getSnapLiveManager()
.addLiveModeListener((LiveModeListener) setupPanelA_);
if (!ASIdiSPIM.oSPIM) {
MMStudio.getInstance()
.getSnapLiveManager()
.addLiveModeListener((LiveModeListener) setupPanelB_);
}
MMStudio.getInstance()
.getSnapLiveManager()
.addLiveModeListener((LiveModeListener) navigationPanel_);
MMStudio.getInstance()
.getSnapLiveManager()
.addLiveModeListener(
new LiveModeListener() {
// make sure to "wake up" any piezos with autosleep enabled before we start imaging
@Override
public void liveModeEnabled(boolean enabled) {
if (enabled) {
piezoSleepPreventer_.start();
} else {
piezoSleepPreventer_.stop();
}
}
});
// set scan for live mode to be triangle (now live mode setting not affected by SPIM setting)
props_.setPropValue(
new Devices.Keys[] {Devices.Keys.GALVOA, Devices.Keys.GALVOB},
Properties.Keys.SA_PATTERN_X,
Properties.Values.SAM_TRIANGLE,
true);
// make sure gotDeSelected() and gotSelected() get called whenever we switch tabs
tabbedPane_.addChangeListener(
new ChangeListener() {
int lastSelectedIndex_ = tabbedPane_.getSelectedIndex();
@Override
public void stateChanged(ChangeEvent e) {
((ListeningJPanel) tabbedPane_.getComponentAt(lastSelectedIndex_)).gotDeSelected();
((ListeningJPanel) tabbedPane_.getSelectedComponent()).gotSelected();
lastSelectedIndex_ = tabbedPane_.getSelectedIndex();
}
});
// put frame back where it was last time
this.loadAndRestorePosition(100, 100);
// clear any previous joystick settings
joystick_.unsetAllJoysticks();
// gotSelected will be called because we put this after adding the ChangeListener
tabbedPane_.setSelectedIndex(
helpTabIndex); // setSelectedIndex(0) just after initialization doesn't fire ChangeListener,
// so switch to help panel first
tabbedPane_.setSelectedIndex(
prefs_.getInt(
MAIN_PREF_NODE,
Prefs.Keys.TAB_INDEX,
deviceTabIndex)); // default to devicesPanel_ on first run
// set up the window
add(tabbedPane_); // add the pane to the GUI window
setTitle(ASIdiSPIM.menuName + " Control");
pack(); // shrinks the window as much as it can
setResizable(false);
// take care of shutdown tasks when window is closed
setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE);
// add status panel as an overlay that is visible from all tabs
Container glassPane = (Container) getGlassPane();
glassPane.setVisible(true);
glassPane.setLayout(
new MigLayout("", "[" + this.getWidth() + "]", "[" + this.getHeight() + "]"));
glassPane.add(statusSubPanel_, "dock south");
// restore live mode and camera
if (liveModeOriginally) {
gui_.enableLiveMode(true);
}
try {
gui_.getMMCore().setCameraDevice(cameraOriginal);
} catch (Exception ex) {
// do nothing
}
}