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Keep controller errors out of dialogs in quiet mode, and start the filter frequency spinners from the scanner #534

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Merged
bls337 merged 6 commits into from
Oct 11, 2026
Merged

Keep controller errors out of dialogs in quiet mode, and start the filter frequency spinners from the scanner #534

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09f8c3e
start the filter frequency spinners from the scanner and allow 10 kHz…
Oct 11, 2026
a3de793
log a Tiger stage whose label is not recognised
Oct 11, 2026
593b033
load the delay before camera and laser duration from their own fields
Oct 11, 2026
e9eeb31
log a trigger shutter the plugin cannot use
Oct 11, 2026
f224506
log the scape controller errors when acquisition failures are quiet
Oct 11, 2026
5cf8229
log the dispim controller errors when acquisition failures are quiet
Oct 11, 2026
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30 changes: 27 additions & 3 deletions src/main/java/org/micromanager/lightsheetmanager/gui/tabs/SettingsTab.java
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Original file line number Diff line number Diff line change
Expand Up @@ -114,9 +114,33 @@ private void createUserInterface() {
final JLabel lblSliceAxisFilterFreq = new JLabel("Filter freq, slice axis [kHz]:");
final JLabel lblLiveScanPeriod = new JLabel("Live scan period [ms]:");

// TODO: increase max filter freq based on build (to 10.0)
spnSheetAxisFilterFreq_ = Spinner.createDoubleSpinner(0.4, 0.1, 1.0, 0.1);
spnSliceAxisFilterFreq_ = Spinner.createDoubleSpinner(0.4, 0.1, 1.0, 0.1);
// start the filter spinners from the scanner, because a run uses the scanner's values
double maxFilterFreq = 1.0;
double sheetAxisFilterFreq = 0.8;
double sliceAxisFilterFreq = 0.4;
if (isUsingPLogic_) {
final ASIScanner scanner = model_.devices().device("IllumSlice");
if (scanner != null) {
// the galvo firmware builds can filter up to 10 kHz
final String build = scanner.getFirmwareBuild();
if (build.equals("GALVO_SPIM") || build.equals("GALVO_SPIM_SLAVE")) {
maxFilterFreq = 10.0;
}
// a failed read returns 0, so keep the default
final double sheetAxis = scanner.getFilterFreqX();
if (sheetAxis > 0.0) {
sheetAxisFilterFreq = sheetAxis;
}
final double sliceAxis = scanner.getFilterFreqY();
if (sliceAxis > 0.0) {
sliceAxisFilterFreq = sliceAxis;
}
}
}
spnSheetAxisFilterFreq_ = Spinner.createDoubleSpinner(
sheetAxisFilterFreq, 0.1, maxFilterFreq, 0.1);
spnSliceAxisFilterFreq_ = Spinner.createDoubleSpinner(
sliceAxisFilterFreq, 0.1, maxFilterFreq, 0.1);
spnLiveScanPeriod_ = Spinner.createIntegerSpinner(20, 2, 10000, 100);

add(lblGeometryType, "wrap");
Expand Down
4 changes: 1 addition & 3 deletions ...ain/java/org/micromanager/lightsheetmanager/gui/tabs/acquisition/AdvancedTimingPanel.java
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Original file line number Diff line number Diff line change
Expand Up @@ -253,9 +253,7 @@ public void onSettingsChanged(final AcquisitionSettings settings) {
spnScanDuration_.setValue(settingsScape.timing().scanDurationMs());
spnDelayBeforeLaser_.setValue(settingsScape.timing().delayBeforeLaserMs());
spnLaserTriggerDuration_.setValue(settingsScape.timing().laserTriggerDurationMs());
spnDelayBeforeCamera_.setValue(settingsScape.timing().cameraTriggerDurationMs());
spnLaserTriggerDuration_.setValue(settingsScape.timing().cameraTriggerDurationMs());
spnDelayBeforeCamera_.setDouble(settingsScape.timing().cameraTriggerDurationMs());
spnDelayBeforeCamera_.setValue(settingsScape.timing().delayBeforeCameraMs());
spnCameraTriggerDuration_.setDouble(settingsScape.timing().cameraTriggerDurationMs());
spnCameraExposure_.setValue(settingsScape.timing().cameraExposureMs());
cbxAlternateScanDirection_.setSelected(settingsScape.timing().useAlternateScanDirection());
Expand Down
12 changes: 10 additions & 2 deletions src/main/java/org/micromanager/lightsheetmanager/model/DeviceManager.java
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Original file line number Diff line number Diff line change
Expand Up @@ -148,11 +148,14 @@ public void setup() {
ASIPiezo piezo = new ASIPiezo(studio_, deviceName);
addDevice(propertyName, deviceName, piezo);
devicesAdded.put(deviceName, piezo);
}
if (deviceName.contains("ZStage")) {
} else if (deviceName.contains("ZStage")) {
ASIZStage zStage = new ASIZStage(studio_, deviceName);
addDevice(propertyName, deviceName, zStage);
devicesAdded.put(deviceName, zStage);
} else {
studio_.logs().logError("DeviceManager: " + propertyName + " names "
+ deviceName + ", a Tiger stage whose label has neither Piezo "
+ "nor ZStage in it, so it is ignored");
}
} else {
// generic stage device
Expand Down Expand Up @@ -181,6 +184,11 @@ public void setup() {
NIDAQ nidaq = new NIDAQ(studio_, deviceName);
addDevice(propertyName, deviceName, nidaq);
devicesAdded.put(deviceName, nidaq);
} else {
studio_.logs().logError("DeviceManager: " + propertyName + " names "
+ deviceName + ", a shutter from the " + deviceLibrary
+ " library, which is neither an ASI PLogic card nor a NIDAQ board, "
+ "so it is ignored");
}
} else if (deviceType == DeviceType.CameraDevice) {
createCameraDevice(propertyName, deviceName,
Expand Down
50 changes: 25 additions & 25 deletions src/main/java/org/micromanager/lightsheetmanager/model/PLogicDispim.java
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Original file line number Diff line number Diff line change
Expand Up @@ -181,11 +181,11 @@ public boolean prepareControllerForAcquisition(
if (settings.stageScan().enabled()
&& settings.acquisitionMode() == AcquisitionMode.STAGE_SCAN_INTERLEAVED) {
if (numViews != 2) {
studio_.logs().showError("Interleaved stage scan only possible for 2-sided acquisition.");
model_.logging().reportError("Interleaved stage scan only possible for 2-sided acquisition.");
return false;
}
if (settings.cameraMode() == CameraMode.OVERLAP) {
studio_.logs().showError("Interleaved stage scan not compatible with overlap camera mode");
model_.logging().reportError("Interleaved stage scan not compatible with overlap camera mode");
return false;
}
}
Expand All @@ -198,7 +198,7 @@ public boolean prepareControllerForAcquisition(
try {
core_.setShutterDevice(plcLaser_.getDeviceName());
} catch (Exception e) {
studio_.logs().showError("could not set shutter to " + plcLaser_.getDeviceName());
model_.logging().reportError("could not set shutter to " + plcLaser_.getDeviceName());
}

if (settings.stageScan().enabled()) {
Expand Down Expand Up @@ -229,13 +229,13 @@ public boolean prepareControllerForAcquisition(
final double maxSpeed = xyStage_.getMaxSpeedX();
if (requestedMotorSpeed > maxSpeed * 0.8) {
// trying to go near max speed smooth scanning will be compromised
studio_.logs().showError("Required stage speed is too fast, please reduce step size or increase sample exposure.");
model_.logging().reportError("Required stage speed is too fast, please reduce step size or increase sample exposure.");
return false;
}
if (requestedMotorSpeed < maxSpeed / 2000) {
// 1/2000 of the max speed is approximate place where smooth scanning breaks down (speed quantum is ~1/12000 max speed);
// this also prevents setting to 0 which the controller rejects
studio_.logs().showError("Required stage speed is too slow, please increase step size or decrease sample exposure.");
model_.logging().reportError("Required stage speed is too slow, please increase step size or decrease sample exposure.");
return false;
}
xyStage_.setSpeedX(requestedMotorSpeed);
Expand All @@ -258,7 +258,7 @@ public boolean prepareControllerForAcquisition(
xyStage_.setScanPattern(isStageScan2Sided ? ASIXYStage.ScanPattern.SERPENTINE : ASIXYStage.ScanPattern.RASTER);

if (xyStage_.getAxisPolarityX() != ASIXYStage.AxisPolarity.NORMAL) {
studio_.logs().showError(
model_.logging().reportError(
"Stage scanning requires X axis polarity set to " + ASIXYStage.AxisPolarity.NORMAL);
return false;
}
Expand Down Expand Up @@ -323,7 +323,7 @@ public boolean prepareControllerForAcquisitionSCAPE(
try {
core_.setShutterDevice(plcLaser_.getDeviceName());
} catch (Exception e) {
studio_.logs().showError("could not set shutter to " + plcLaser_.getDeviceName());
model_.logging().reportError("could not set shutter to " + plcLaser_.getDeviceName());
}

scanDistance_ = 0;
Expand Down Expand Up @@ -490,7 +490,7 @@ public boolean prepareControllerForAcquisitionSide(
piezo = piezo2_;
break;
default:
studio_.logs().showError("does not support numViews > 2!");
model_.logging().reportError("does not support numViews > 2!");
break;
}

Expand Down Expand Up @@ -583,7 +583,7 @@ public boolean prepareControllerForAcquisitionSide(
final double slope2 = settings.sliceCalibration(2).slope();
double sliceRate = (view == 1) ? slope1 : slope2;
if (NumberUtils.doublesEqual(sliceRate, 0.0)) {
studio_.logs().showError("Calibration slope for view " + view + " cannot be zero. Re-do calibration on Setup tab.");
model_.logging().reportError("Calibration slope for view " + view + " cannot be zero. Re-do calibration on Setup tab.");
return false;
}
final double offset1 = settings.sliceCalibration(1).offset() + channelOffset;
Expand All @@ -609,11 +609,11 @@ public boolean prepareControllerForAcquisitionSide(
// so an unreadable scanner refuses the sweep rather than passing it through.
final double halfSweep = Math.abs(sliceAmplitude) / 2;
if (sliceCenter + halfSweep > scanner.getMaxDeflectionY()) {
studio_.logs().showError("Scanner will exceed allowed range in positive direction.");
model_.logging().reportError("Scanner will exceed allowed range in positive direction.");
return false;
}
if (sliceCenter - halfSweep < scanner.getMinDeflectionY()) {
studio_.logs().showError("Scanner will exceed allowed range in negative direction.");
model_.logging().reportError("Scanner will exceed allowed range in negative direction.");
return false;
}

Expand Down Expand Up @@ -665,7 +665,7 @@ public boolean prepareControllerForAcquisitionSide(

if (NumberUtils.outsideRange(piezoCenter - piezoAmplitude / 2, piezoMin, piezoMax)
|| NumberUtils.outsideRange(piezoCenter + piezoAmplitude / 2, piezoMin, piezoMax)) {
studio_.logs().showError("Imaging piezo for view " + view +
model_.logging().reportError("Imaging piezo for view " + view +
" would travel outside the piezo limits during acquisition.");
return false;
}
Expand Down Expand Up @@ -780,7 +780,7 @@ public boolean setupHardwareChannelSwitching(final DispimAcquisitionSettings set
// PLogic can only handle up to 4 channels
if ((settings.channels().count() > 4) &&
(channelMode == ChannelMode.VOLUME_HW || channelMode == ChannelMode.SLICE_HW)) {
studio_.logs().showError("PLogic card cannot handle more than 4 channels for hardware switching.");
model_.logging().reportError("PLogic card cannot handle more than 4 channels for hardware switching.");
return false;
}

Expand All @@ -797,7 +797,7 @@ public boolean setupHardwareChannelSwitching(final DispimAcquisitionSettings set
}
break;
default:
studio_.logs().showError("Unknown multichannel mode for hardware switching.");
model_.logging().reportError("Unknown multichannel mode for hardware switching.");
return false;
}

Expand All @@ -816,7 +816,7 @@ public boolean setupHardwareChannelSwitching(final DispimAcquisitionSettings set
plcLaser_.setPreset(15); // mod4 counter
break;
default:
studio_.logs().showError("Hardware channel switching only supports 1-4 channels");
model_.logging().reportError("Hardware channel switching only supports 1-4 channels");
return false;
}

Expand All @@ -841,7 +841,7 @@ public boolean setupHardwareChannelSwitching(final DispimAcquisitionSettings set
if (plcLaser_.getNumCells() < 24) {
// restore update setting
plcLaser_.setAutoUpdateCells(editCellUpdates);
studio_.logs().showError("Require 24-cell PLC firmware to use hardware channel switching with 7-channel shutter");
model_.logging().reportError("Require 24-cell PLC firmware to use hardware channel switching with 7-channel shutter");
return false;
}

Expand Down Expand Up @@ -893,7 +893,7 @@ public boolean setupHardwareChannelSwitching(final DispimAcquisitionSettings set
if (hardwareChannelUsed[outputNum - 5]) {
// restore update setting
plcLaser_.setAutoUpdateCells(editCellUpdates);
studio_.logs().showError("Multiple channels cannot use same laser for PLogic triggering");
model_.logging().reportError("Multiple channels cannot use same laser for PLogic triggering");
return false;
} else {
hardwareChannelUsed[outputNum - 5] = true;
Expand Down Expand Up @@ -950,7 +950,7 @@ public boolean triggerControllerStartAcquisition(final AcquisitionMode acqMode,
scanner.setSPIMState(ASIScanner.SPIMState.RUNNING);
break;
default:
studio_.logs().showError("Unknown acquisition mode");
model_.logging().reportError("Unknown acquisition mode");
return false;
}
return true;
Expand All @@ -961,7 +961,7 @@ private int getPLogicOutputFromChannel(final ChannelSpec channel, final String c
try {
Configuration configData = core_.getConfigData(channelGroup, channel.getName());
if (!configData.isPropertyIncluded(plcLaser_.getDeviceName(), "OutputChannel")) {
studio_.logs().showError("Channel preset \"" + channel.getName() + "\" (group \""
model_.logging().reportError("Channel preset \"" + channel.getName() + "\" (group \""
+ channelGroup + "\") must include the PLogic \"OutputChannel\" property to use "
+ "hardware channel switching. Edit the preset in the main Micro-Manager window and "
+ "set \"OutputChannel\" to one of \"output 5 only\" through \"output 8 only\".");
Expand All @@ -977,14 +977,14 @@ private int getPLogicOutputFromChannel(final ChannelSpec channel, final String c
} else if (setting.equals("output 8 only")) {
return 8;
} else {
studio_.logs().showError("Channel preset \"" + channel.getName() + "\" (group \""
model_.logging().reportError("Channel preset \"" + channel.getName() + "\" (group \""
+ channelGroup + "\") has PLogic \"OutputChannel\" set to \"" + setting + "\"; it "
+ "must be one of \"output 5 only\" through \"output 8 only\" (each channel a "
+ "distinct output 5-8). Edit the preset in the main Micro-Manager window.");
return 0;
}
} catch (Exception e) {
studio_.logs().showError(e, "Could not get PLogic output from channel");
model_.logging().reportError(e, "Could not get PLogic output from channel");
return 0;
}
}
Expand All @@ -994,13 +994,13 @@ private boolean doesPLogicChannelIncludeLaser(final int laserNum, final ChannelS
try {
Configuration configData = core_.getConfigData(channelGroup, channel.getName());
if (!configData.isPropertyIncluded(plcLaser_.getDeviceName(), "OutputChannel")) {
studio_.logs().showError("Must include PLogic \"OutputChannel\" in preset for hardware switching");
model_.logging().reportError("Must include PLogic \"OutputChannel\" in preset for hardware switching");
return false;
}
String setting = configData.getSetting(plcLaser_.getDeviceName(), "OutputChannel").getPropertyValue();
return setting.contains(String.valueOf(laserNum));
} catch (Exception e) {
studio_.logs().showError(e, "Could not get PLogic output from channel");
model_.logging().reportError(e, "Could not get PLogic output from channel");
return false;
}
}
Expand Down Expand Up @@ -1120,7 +1120,7 @@ public void setPathPreset(int side) {
sideKey = "PathConfig2";
break;
default:
studio_.logs().showError("unknown side when setting up path presets");
model_.logging().reportError("unknown side when setting up path presets");
break;
}
final String preset = "PathConfig1";///props_.getPropValueString(Devices.Keys.PLUGIN, sideKey); // TODO: get from plugin!
Expand All @@ -1131,7 +1131,7 @@ public void setPathPreset(int side) {
core_.waitForConfig(group, preset);
}
} catch (Exception e) {
studio_.logs().showError("Couldn't set the path config " + preset + " of group " + group);
model_.logging().reportError("Couldn't set the path config " + preset + " of group " + group);
}
}

Expand Down
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