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fix timing settings for stage scan acq mode #338

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Merged
bls337 merged 1 commit into from
Dec 3, 2025
Merged

fix timing settings for stage scan acq mode #338

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6 changes: 3 additions & 3 deletions src/main/java/org/micromanager/lightsheetmanager/LightSheetManagerPlugin.java
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Original file line number Diff line number Diff line change
Expand Up @@ -9,18 +9,18 @@

@Plugin(type = MenuPlugin.class)
public class LightSheetManagerPlugin implements MenuPlugin, SciJavaPlugin {
public static final String copyright = "Applied Scientific Instrumentation (ASI), 2022-2025";
public static final String copyright = "Applied Scientific Instrumentation (ASI), 2022-2026";
public static final String description = "A plugin to control various types of light sheet microscopes.";
public static final String menuName = "Light Sheet Manager";
public static final String version = "0.5.1";
public static final String version = "0.5.2";

private Studio studio_;
private LightSheetManager model_;
private LightSheetManagerFrame frame_;

@Override
public void setContext(final Studio studio) {
this.studio_ = studio;
studio_ = studio;
}

@Override
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50 changes: 30 additions & 20 deletions ...in/java/org/micromanager/lightsheetmanager/model/acquisitions/AcquisitionEngineSCAPE.java
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Expand Up @@ -1003,16 +1003,21 @@ public DefaultTimingSettings.Builder getTimingFromExposure() {
//final double desiredSlicePeriod = acqSettings_.sliceSettings().slicePeriod();
// final double slicePeriod = Math.max(Math.max(laserDuration, cameraTotalTime),
// isSlicePeriodMinimized ? 0 : desiredSlicePeriod);

// the delays may need to be increased by the global delay
double delayBeforeCamera = 0.0;
double delayBeforeLaser = 0.0;
double delayBeforeScan = 0.0;
switch (cameraMode) {
case PSEUDO_OVERLAP: // e.g. Kinetix
tsb.scansPerSlice(1);
tsb.scanDuration(0.25);
tsb.cameraExposure(laserDuration);
tsb.laserTriggerDuration(laserDuration);
tsb.cameraTriggerDuration(laserDuration);
tsb.delayBeforeCamera(0.25);
tsb.delayBeforeLaser(sliceDeadTime);
tsb.delayBeforeScan(0.0);
delayBeforeCamera = 0.25;
delayBeforeLaser = sliceDeadTime;
delayBeforeScan = 0.0;
break;
case OVERLAP: // e.g.
if (acqSettings_.isUsingChannels() && acqSettings_.channelSettings().numChannels() > 1
Expand All @@ -1023,19 +1028,19 @@ public DefaultTimingSettings.Builder getTimingFromExposure() {
tsb.cameraExposure(0.25);
tsb.laserTriggerDuration(laserDuration);
tsb.cameraTriggerDuration(0.0);
tsb.delayBeforeCamera(0.25);
tsb.delayBeforeLaser(sliceDeadTime + NumberUtils.ceilToQuarterMs(cameraResetTime));
tsb.delayBeforeScan(0.0);
delayBeforeCamera = 0.25;
delayBeforeLaser = sliceDeadTime + NumberUtils.ceilToQuarterMs(cameraResetTime);
delayBeforeScan = 0.0;
} else {
// the usual case
tsb.scansPerSlice(1);
tsb.scanDuration(1.0);
tsb.cameraExposure(0.25);
tsb.laserTriggerDuration(laserDuration);
tsb.cameraTriggerDuration(1.0);
tsb.delayBeforeCamera(0.0);
tsb.delayBeforeLaser(sliceDeadTime + sliceLaserInterleaved);
tsb.delayBeforeScan(0.0);
delayBeforeCamera = 0.0;
delayBeforeLaser = sliceDeadTime + sliceLaserInterleaved;
delayBeforeScan = 0.0;
}
break;
case EDGE:
Expand All @@ -1046,38 +1051,43 @@ public DefaultTimingSettings.Builder getTimingFromExposure() {
tsb.cameraExposure(laserDuration - NumberUtils.ceilToQuarterMs(actualCameraResetTime + cameraReadoutTime));
tsb.laserTriggerDuration(laserDuration);
tsb.cameraTriggerDuration(1.0);
tsb.delayBeforeCamera(sliceLaserInterleaved);
tsb.delayBeforeLaser(sliceDeadTime + sliceLaserInterleaved);
tsb.delayBeforeScan(0.0);
delayBeforeCamera = sliceLaserInterleaved;
delayBeforeLaser = sliceDeadTime + sliceLaserInterleaved;
delayBeforeScan = 0.0;
break;
default:
studio_.logs().showError("Invalid camera mode");
break;
}

// FIXME: needs delay
if (!acqSettings_.sliceSettings().isSlicePeriodMinimized()) {
double globalDelay = acqSettings_.sliceSettings().slicePeriod() - getSliceDuration(tsb);
if (cameraMode == CameraMode.VIRTUAL_SLIT) {
globalDelay = 0;
}
if (globalDelay < 0) {
globalDelay = 0;
studio_.logs().showError(
"Increasing slice period to meet laser exposure constraint\n"
+ "(time required for camera readout; readout time depends on ROI).");
}
// tsb.delayBeforeScan();
// tsb.delayBeforeCamera();
// tsb.delayBeforeLaser();
delayBeforeCamera += globalDelay;
delayBeforeLaser += globalDelay;
delayBeforeScan += globalDelay;
}

// FIXME: needs delay
final double cameraExposure = model_.acquisitions().settings().sliceSettings().sampleExposure();
double globalDelay = NumberUtils.ceilToQuarterMs(cameraExposure + cameraReadoutTime);
if (globalDelay > 0) {
// tsb.delayBeforeScan();
// tsb.delayBeforeCamera();
// tsb.delayBeforeLaser();
delayBeforeCamera += globalDelay;
delayBeforeLaser += globalDelay;
delayBeforeScan += globalDelay;
}

tsb.delayBeforeCamera(delayBeforeCamera);
tsb.delayBeforeLaser(delayBeforeLaser);
tsb.delayBeforeScan(delayBeforeScan);

// update the slice duration based on our new values
tsb.sliceDuration(getSliceDuration(tsb));
return tsb;
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