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cleanup 1.4 port leftovers #460

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Merged
bls337 merged 3 commits into from
Jul 28, 2026
Merged

cleanup 1.4 port leftovers #460

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1d08569
remove left overs from the 1.4 port
Jul 28, 2026
4f05542
remove left overs from the 1.4 port; diSPIM
Jul 28, 2026
8c057ac
More 1.4 port cleanup
Jul 28, 2026
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48 changes: 0 additions & 48 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 @@ -53,19 +53,11 @@ public class PLogicDispim {
private double scanDistance_; // in microns; cached value from last call to prepareControllerForAcquisition()
private double actualStepSizeUm_; // cached value from last call to prepareControllerForAcquisition()
private boolean zSpeedZero_; // cached value from last call to prepareStageScanForAcquisition()
private String lastDistanceStr_; // cached value from last call to prepareControllerForAcquisition()
private String lastPosStr_; // cached value from last call to prepareControllerForAcquisition()

// PLC
private static final int triggerStepDurationTics = 10; // 2.5ms with 0.25ms tics
private static final int acquisitionFlagAddr = 1;
private static final int counterLSBAddr = 3;
private static final int counterMSBAddr = 4;
private static final int triggerStepEdgeAddr = 6;
private static final int triggerStepPulseAddr = 7;
private static final int triggerStepOutputAddr = 40; // BNC #8
private static final int triggerInAddr = 35; // BNC #3
private static final int triggerSPIMAddr = 46; // backplane signal, same as XY card's TTL output
private static final int laserTriggerAddress = 10; // this should be set to (42 || 8) = (TTL1 || manual laser on)

private final DispimAcquisitionSettings acqSettings_;
Expand All @@ -86,8 +78,6 @@ public PLogicDispim(final LightSheetManager model) {
scanDistance_ = 0;
actualStepSizeUm_ = 0;
zSpeedZero_ = true;
lastDistanceStr_ = "";
lastPosStr_ = "";

final GeometryType geometryType = model_.devices().adapter().geometry();

Expand Down Expand Up @@ -952,31 +942,6 @@ public boolean triggerControllerStartAcquisition(final AcquisitionMode acqMode,
return true;
}

public boolean triggerControllerStartAcquisitionSCAPE(final AcquisitionMode acqMode, int side) {
switch (acqMode) {
case STAGE_SCAN:
case STAGE_SCAN_INTERLEAVED:
case STAGE_SCAN_UNIDIRECTIONAL:
// for stage scan we send trigger to stage card, which sends
// hardware trigger to the micro-mirror card
scanner_.setSPIMState(ASIScanner.SPIMState.ARMED);
xyStage_.setScanState(ASIXYStage.ScanState.RUNNING);
break;
case PIEZO_SLICE_SCAN:
case SLICE_SCAN_ONLY:
case PIEZO_SCAN_ONLY:
case NO_SCAN:
// in actuality only matters which device we trigger if there are
// two micro-mirror cards, which hasn't ever been done in practice yet
scanner_.setSPIMState(ASIScanner.SPIMState.RUNNING);
break;
default:
studio_.logs().showError("Unknown acquisition mode");
return false;
}
return true;
}

// TODO: "output 5 only" needs to be added to ASIPLogic
private int getPLogicOutputFromChannel(final ChannelSpec channel, final String channelGroup) {
try {
Expand Down Expand Up @@ -1164,19 +1129,6 @@ public void stopSPIMStateMachines() {
}
}

// private void stopSPIMStateMachines(DefaultAcquisitionSettingsDISPIM acqSettings) {
// final int numViews = acqSettings_.volumeSettings().numViews();
// if (numViews == 1) {
// ASIScanner scanner = model_.devices().getDevice("IllumBeam");
// scanner.setSPIMState(ASIScanner.SPIMState.IDLE);
// }
// for (int i = 1; i <= numViews; i++) {
// ASIScanner scanner = model_.devices().getDevice("Illum" + i + "Beam");
// scanner.setSPIMState(ASIScanner.SPIMState.IDLE);
// }
// // TODO: ASI stage scanning conditionals
// }

}


80 changes: 3 additions & 77 deletions src/main/java/org/micromanager/lightsheetmanager/model/PLogicScape.java
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Original file line number Diff line number Diff line change
Expand Up @@ -43,19 +43,11 @@ public class PLogicScape {
private double scanDistance_; // in microns; cached value from last call to prepareControllerForAcquisition()
private double actualStepSizeUm_; // cached value from last call to prepareControllerForAcquisition()
private boolean zSpeedZero_; // cached value from last call to prepareStageScanForAcquisition()
private String lastDistanceStr_; // cached value from last call to prepareControllerForAcquisition()
private String lastPosStr_; // cached value from last call to prepareControllerForAcquisition()

// PLC
private static final int triggerStepDurationTics = 10; // 2.5ms with 0.25ms tics
private static final int acquisitionFlagAddr = 1;
private static final int counterLSBAddr = 3;
private static final int counterMSBAddr = 4;
private static final int triggerStepEdgeAddr = 6;
private static final int triggerStepPulseAddr = 7;
private static final int triggerStepOutputAddr = 40; // BNC #8
private static final int triggerInAddr = 35; // BNC #3
private static final int triggerSPIMAddr = 46; // backplane signal, same as XY card's TTL output
private static final int laserTriggerAddress = 10; // this should be set to (42 || 8) = (TTL1 || manual laser on)

private final ScapeAcquisitionSettings acqSettings_;
Expand All @@ -74,8 +66,6 @@ public PLogicScape(final LightSheetManager model) {
scanDistance_ = 0;
actualStepSizeUm_ = 0;
zSpeedZero_ = true;
lastDistanceStr_ = "";
lastPosStr_ = "";

// populate devices
scanner_ = devices_.device("IllumSlice");
Expand Down Expand Up @@ -627,28 +617,11 @@ private boolean cleanUpControllerAfterAcquisitionSide(
final boolean movePiezo,
final double piezoPosition) {

// TODO: skip scanner warnings?
// ASIScanner scanner = null;
// ASIPiezo piezo = null;
// switch (view) {
// case 1:
// scanner = scanner1_;
// piezo = piezo1_;
// break;
// case 2:
// scanner = scanner2_;
// piezo = piezo2_;
// default:
// break;
// }

// make sure SPIM state machine is stopped
scanner_.setSPIMState(ASIScanner.SPIMState.IDLE);

// restore sheet width and offset in case they got clobbered by the code implementing light sheet mode
// TODO: reset light sheet properties
final double saAmplitudeXDegrees = scanner_.sa().getAmplitudeX();
final double saOffsetXDegrees = scanner_.sa().getOffsetX();
// NB: no sheet width/offset to restore here — SCAPE never writes the galvo x-axis
// (see prepareControllerForAcquisitionSide), so nothing can have clobbered it.

// move piezo back to desired position
if (movePiezo) {
Expand Down Expand Up @@ -853,7 +826,7 @@ public boolean setupHardwareChannelSwitching(final ScapeAcquisitionSettings sett
return true;
}

public boolean triggerControllerStartAcquisition(final AcquisitionMode acqMode, int side) {
public boolean triggerControllerStartAcquisition(final AcquisitionMode acqMode) {
switch (acqMode) {
case STAGE_SCAN:
case STAGE_SCAN_INTERLEAVED:
Expand All @@ -865,8 +838,6 @@ public boolean triggerControllerStartAcquisition(final AcquisitionMode acqMode,
break;
case GALVO_SCAN:
case NO_SCAN:
// in actuality only matters which device we trigger if there are
// two micro-mirror cards, which hasn't ever been done in practice yet
scanner_.setSPIMState(ASIScanner.SPIMState.RUNNING);
break;
default:
Expand Down Expand Up @@ -1025,38 +996,6 @@ public double getActualStepSizeUm() {
return actualStepSizeUm_;
}

// TODO: maybe make this work with any number of PathConfig variables...?
/**
* Sets the side-specific preset from the selected group. Blocks until all involved devices are not busy.
* Put in this class for convenience though it isn't necessarily about the controller.
* @param side
*/
public void setPathPreset(int side) {
// set preset requested on Settings tab
String sideKey = "PathConfig1";
switch (side) {
case 1:
sideKey = "PathConfig1";
break;
case 2:
sideKey = "PathConfig2";
break;
default:
studio_.logs().showError("unknown side when setting up path presets");
break;
}
final String preset = "PathConfig1";///props_.getPropValueString(Devices.Keys.PLUGIN, sideKey); // TODO: get from plugin!
final String group = "PathGroup"; //props_.getPropValueString(Devices.Keys.PLUGIN, Properties.Keys.PLUGIN_PATH_GROUP); // TODO: get from plugin!
try {
if (!preset.equals("")) {
core_.setConfig(group, preset);
core_.waitForConfig(group, preset);
}
} catch (Exception e) {
studio_.logs().showError("Couldn't set the path config " + preset + " of group " + group);
}
}

public void stopSPIMStateMachines() {
scanner_.setSPIMState(ASIScanner.SPIMState.IDLE);
if (acqSettings_.stageScan().enabled()) {
Expand Down Expand Up @@ -1084,17 +1023,4 @@ public void stopSPIMStateMachines() {
}
}

// private void stopSPIMStateMachines(DefaultAcquisitionSettingsDISPIM acqSettings) {
// final int numViews = acqSettings_.volumeSettings().numViews();
// if (numViews == 1) {
// ASIScanner scanner = model_.devices().getDevice("IllumBeam");
// scanner.setSPIMState(ASIScanner.SPIMState.IDLE);
// }
// for (int i = 1; i <= numViews; i++) {
// ASIScanner scanner = model_.devices().getDevice("Illum" + i + "Beam");
// scanner.setSPIMState(ASIScanner.SPIMState.IDLE);
// }
// // TODO: ASI stage scanning conditionals
// }

}
6 changes: 2 additions & 4 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 @@ -475,8 +475,7 @@ public AcquisitionEvent run(AcquisitionEvent event) {
xyStage.setSpeedX(scanSpeedX_);
xyStage.setAccelerationX(scanAccelX_);
controllerInstance.prepareStageScanForAcquisition(pos.x, pos.y, acqSettings_);
controllerInstance.triggerControllerStartAcquisition(acqSettings_.acquisitionMode(),
acqSettings_.volume().firstView());
controllerInstance.triggerControllerStartAcquisition(acqSettings_.acquisitionMode());
return event;
}

Expand All @@ -500,11 +499,10 @@ public AcquisitionEvent run(AcquisitionEvent event) {
}
}

int side = 0;
// NOTE: not sure why this is being triggered twice with only 1 camera; so we need guard
// TODO: enable 2 sided acquisition
if (scanner.getSPIMState().equals(ASIScanner.SPIMState.IDLE)) {
controllerInstance.triggerControllerStartAcquisition(acqSettings_.acquisitionMode(), side);
controllerInstance.triggerControllerStartAcquisition(acqSettings_.acquisitionMode());
}
}
return event;
Expand Down
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