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improve error handling for acq failures #348

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Merged
bls337 merged 1 commit into from
Dec 18, 2025
Merged

improve error handling for acq failures #348

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8 changes: 4 additions & 4 deletions src/main/java/org/micromanager/lightsheetmanager/model/acquisitions/AcquisitionEngine.java
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Original file line number Diff line number Diff line change
Expand Up @@ -120,8 +120,7 @@ public Future<?> requestRun(boolean speedTest) {
}

try {
// make sure AcquisitionSettings are up-to-date
acqSettings_ = asb_.build();
updateAcquisitionSettings(); // make sure settings are current

if (speedTest) {
try {
Expand All @@ -133,16 +132,17 @@ public Future<?> requestRun(boolean speedTest) {
}
} else {
studio_.logs().logMessage("Preparing Acquisition: plugin version " + LightSheetManagerPlugin.version);
// run abstract methods implemented by acquisition engine geometry types
// run methods implemented by acquisition engine geometry types
if (!setup()) {
studio_.logs().logError("error during setup!");
return; // early exit => stop acquisition
}
run(); // run the acquisition and block until complete
finish(); // cleanup any resources
}
} catch (Exception e) {
studio_.logs().showError(e);
} finally {
finish(); // cleanup any resources
}
});
return acqFinished;
Expand Down
70 changes: 35 additions & 35 deletions ...in/java/org/micromanager/lightsheetmanager/model/acquisitions/AcquisitionEngineSCAPE.java
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Original file line number Diff line number Diff line change
Expand Up @@ -22,9 +22,6 @@
import org.micromanager.lightsheetmanager.api.data.MultiChannelMode;
import org.micromanager.lightsheetmanager.api.internal.DefaultAcquisitionSettingsSCAPE;
import org.micromanager.lightsheetmanager.api.internal.DefaultTimingSettings;



import org.micromanager.lightsheetmanager.gui.utils.DialogUtils;
import org.micromanager.lightsheetmanager.model.DataStorage;
import org.micromanager.lightsheetmanager.LightSheetManager;
Expand All @@ -50,10 +47,16 @@

public class AcquisitionEngineSCAPE extends AcquisitionEngine {

PLogicSCAPE controller_;
ArrayList<Double> savedExposures_;
Point2D.Double xyPosUm_;
private double origSpeedX_;
private double origAccelX_;
private double scanSpeedX_;
private double scanAccelX_;
private boolean isShutterOpen_;
private boolean autoShutter_;
private boolean isPolling_; // true if polling was enabled at the start of an acquisition

public AcquisitionEngineSCAPE(final LightSheetManager model) {
super(model);
Expand Down Expand Up @@ -91,8 +94,8 @@ boolean setup() {

@Override
boolean run() {
final boolean isPolling = model_.positions().isPolling();
if (isPolling) {
isPolling_ = model_.positions().isPolling();
if (isPolling_) {
model_.positions().stopPolling();
studio_.logs().logMessage("stopped position polling");
}
Expand All @@ -117,16 +120,16 @@ boolean run() {

// save current exposure to restore later
CameraBase[] cameras = model_.devices().getImagingCameras();
ArrayList<Double> savedExposures = new ArrayList<>();
savedExposures_ = new ArrayList<>();
for (CameraBase camera : cameras) {
savedExposures.add(camera.getExposure());
savedExposures_.add(camera.getExposure());
}

// used to detect if the plugin is using ASI hardware
final boolean isUsingPLC = model_.devices().isUsingPLogic();

// initialize stage scanning so we can restore state
Point2D.Double xyPosUm = new Point2D.Double();
xyPosUm_ = new Point2D.Double();
origSpeedX_ = 1.0; // don't want 0 in case something goes wrong
origAccelX_ = 1.0; // don't want 0 in case something goes wrong

Expand All @@ -146,7 +149,7 @@ boolean run() {
}

// second part: initialize stage scanning, so we can restore state later
xyPosUm = xyStage.getXYPosition();
xyPosUm_ = xyStage.getXYPosition();
origSpeedX_ = xyStage.getSpeedX();
origAccelX_ = xyStage.getAccelerationX();

Expand All @@ -163,8 +166,6 @@ boolean run() {
}
}

PLogicSCAPE controller = null;

// Assume demo mode if default camera is DemoCamera
boolean demoMode = false;
try {
Expand All @@ -176,9 +177,9 @@ boolean run() {
if (!demoMode) {

if (isUsingPLC) {
controller = new PLogicSCAPE(model_);
controller_ = new PLogicSCAPE(model_);

final boolean success = doHardwareCalculations(controller);
final boolean success = doHardwareCalculations(controller_);
if (!success) {
return false; // early exit => could not set up hardware
}
Expand Down Expand Up @@ -443,7 +444,7 @@ public void close() {
// }
// }, Acquisition.AFTER_HARDWARE_HOOK);

final PLogicSCAPE controllerInstance = controller;
final PLogicSCAPE controllerInstance = controller_;
// TODO This after camera hook is called after the camera has been readied to acquire a
// sequence. I assume we want to tell the Tiger to start sending TTLs etc here
currentAcquisition_.addHook(new AcquisitionHook() {
Expand Down Expand Up @@ -489,19 +490,18 @@ public void close() {
}, Acquisition.AFTER_CAMERA_HOOK);

///////////// Turn off autoshutter /////////////////
final boolean isShutterOpen;
try {
isShutterOpen = core_.getShutterOpen();
isShutterOpen_ = core_.getShutterOpen();
} catch (Exception e) {
throw new RuntimeException(e);
}

// TODO: should the shutter be left open for the full duration of acquisition?
// because that's what this code currently does
boolean autoShutter = core_.getAutoShutter();
if (autoShutter) {
autoShutter_ = core_.getAutoShutter();
if (autoShutter_) {
core_.setAutoShutter(false);
if (!isShutterOpen) {
if (!isShutterOpen_) {
try {
core_.setShutterOpen(true);
} catch (Exception e) {
Expand Down Expand Up @@ -668,14 +668,18 @@ public void close() {
final long elapsedTimeMs = System.currentTimeMillis() - acqButtonStart;
studio_.logs().logMessage("SCAPE plugin acquisition took: " + elapsedTimeMs + " milliseconds");

return true;
}

@Override
boolean finish() {
// clean up controller settings after acquisition
// want to do this, even with demo cameras, so we can test everything else
// TODO: figure out if we really want to return piezos to 0 position (maybe center position,
// maybe not at all since we move when we switch to setup tab, something else??)
if (isUsingPLC) {
controller.cleanUpControllerAfterAcquisition(acqSettings_, true);
controller.stopSPIMStateMachines();
if (model_.devices().isUsingPLogic()) {
controller_.cleanUpControllerAfterAcquisition(acqSettings_, true);
controller_.stopSPIMStateMachines();
}

// if we did stage scanning restore the original position and speed
Expand All @@ -691,14 +695,14 @@ public void close() {
xyStage.setAccelerationX(origAccelX_);

if (returnToOriginalPosition) {
xyStage.setXYPosition(xyPosUm.x, xyPosUm.y);
xyStage.setXYPosition(xyPosUm_.x, xyPosUm_.y);
}
}

// Restore shutter/autoshutter to original state
try {
core_.setShutterOpen(isShutterOpen);
core_.setAutoShutter(autoShutter);
core_.setShutterOpen(isShutterOpen_);
core_.setAutoShutter(autoShutter_);
} catch (Exception e) {
throw new RuntimeException("Couldn't restore shutter to original state");
}
Expand All @@ -713,40 +717,36 @@ public void close() {
// TODO: execute any end-acquisition runnables

// set the camera trigger modes back to internal for live mode
CameraBase[] cameras = model_.devices().getImagingCameras();
for (int i = 0; i < cameras.length; i++) {
CameraBase camera = cameras[i];
camera.setTriggerMode(CameraMode.INTERNAL);
camera.setExposure(savedExposures.get(i));
camera.setExposure(savedExposures_.get(i));
}

currentAcquisition_ = null;

if (acqSettings_.isSavingImagesDuringAcquisition()) {
final String savePath = FileUtils.createUniquePath(saveDir, saveName);
//System.out.println("savePath: " + savePath);
final String savePath = FileUtils.createUniquePath(
acqSettings_.saveDirectory(), acqSettings_.saveNamePrefix());
try {
// convert from DataStorage.SaveMode to Datastore.SaveMode
final Datastore.SaveMode saveMode =
DataStorage.SaveMode.convert(acqSettings_.saveMode());
DataStorage.SaveMode.convert(acqSettings_.saveMode());
curStore_.save(saveMode, savePath);
} catch (IOException e) {
model_.studio().logs().showError("could not save the acquisition data to: \n" + savePath);
}
}

// start polling for navigation panel
if (isPolling) {
if (isPolling_) {
studio_.logs().logMessage("started position polling after acquisition");
model_.positions().startPolling();
}
return true;
}

@Override
boolean finish() {
return true;
}

private boolean doHardwareCalculations(PLogicSCAPE plc) {

// TODO: find a better place to set the camera trigger mode for SCAPE
Expand Down
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