more durations improvements

src/main/java/org/micromanager/lightsheetmanager/LightSheetManagerPlugin.java

@@ -14,7 +14,7 @@ public class LightSheetManagerPlugin implements MenuPlugin, SciJavaPlugin {
     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 = "0.6.1";
+    public static final String version = "0.6.3";
 
     private Studio studio_;
     private LightSheetManager model_;

src/main/java/org/micromanager/lightsheetmanager/gui/tabs/AcquisitionTab.java

@@ -177,8 +177,11 @@ private void createUserInterface() {
                 settings.acquisitionMode(),
                 180, 24);
 
+        final boolean isUsingAdvancedTiming = settings.isUsingAdvancedTiming();
         cbxUseAdvancedTiming_ = new CheckBox("Use advanced timing settings",
-                12, settings.isUsingAdvancedTiming(), CheckBox.RIGHT);
+                12, isUsingAdvancedTiming, CheckBox.RIGHT);
+        // initial enabled or disabled state
+        swapTimingSettingsPanels(isUsingAdvancedTiming);
 
         btnRunOverviewAcq_.setEnabled(false); // TODO: re-enable when these features are put in
         btnTestAcquisition_.setEnabled(false);
@@ -275,9 +278,11 @@ private void createEventHandlers() {
         });
 
         // select the acquisition mode
-        cmbAcquisitionModes_.registerListener(
-                () -> model_.acquisitions().settingsBuilder()
-                        .acquisitionMode(cmbAcquisitionModes_.getSelected()));
+        cmbAcquisitionModes_.registerListener(() -> {
+            model_.acquisitions().settingsBuilder()
+                    .acquisitionMode(cmbAcquisitionModes_.getSelected());
+            model_.acquisitions().updateDurationLabels();
+        });
 
         // switches timing panels based on check box
         cbxUseAdvancedTiming_.registerListener(() -> {

src/main/java/org/micromanager/lightsheetmanager/gui/tabs/SettingsTab.java

@@ -156,10 +156,10 @@ private void createUserInterface() {
 
         add(pnlScanSettings, "wrap");
         if (isUsingPLogic_) {
-            add(pnlLightSheet, "growx");
+            add(pnlLightSheet, "growx, wrap");
         }
 
-        add(btnCreateConfigGroup_, "gaptop 40");
+        add(btnCreateConfigGroup_, "");
     }
 
     private void createEventHandlers() {

src/main/java/org/micromanager/lightsheetmanager/gui/tabs/acquisition/SavePanel.java

@@ -118,6 +118,13 @@ public void createUserInterface() {
         btnLoadSettings_ = new Button("Load", 60, 20);
         btnConvertSettings_ = new Button("Convert", 72, 20);
 
+        btnBrowse_.setToolTipText("Select the save directory with the file browser.");
+        btnOpen_.setToolTipText("Open the file explorer to the save directory.");
+        btnSaveSettings_.setToolTipText("Save the current acquisition settings to JSON.");
+        btnLoadSettings_.setToolTipText("Load acquisitions settings from a JSON file.");
+        btnConvertSettings_.setToolTipText("Convert \"AcqSettings.txt\" from the " +
+                "Micro-Manager 1.4 plugin into Light Sheet Manager settings.");
+
         add(lblSaveDirectory, "");
         add(txtSaveDirectory_, "");
         add(btnBrowse_, "");

src/main/java/org/micromanager/lightsheetmanager/gui/tabs/setup/PiezoCalibrationPanel.java

@@ -173,6 +173,8 @@ private void createEventHandlers() {
                           .sliceCalibrationBuilder().offset(newOffset);
                     model_.studio().logs().logMessage("updated offset for view " + pathNum_ + "; new value is " +
                             newOffset + " (with channel offset of " + channelOffset + ")");
+                } else {
+                    model_.studio().logs().showError("The beam must be enabled to update the offset.", btnUpdate_);
                 }
             });
         }

src/main/java/org/micromanager/lightsheetmanager/gui/tabs/setup/SetupPanel.java

@@ -7,8 +7,6 @@
 
 import java.util.Objects;
 
-// Note: changes based on camera trigger mode
-
 /**
  * A setup panel for diSPIM.
  */

src/main/java/org/micromanager/lightsheetmanager/model/PLogicScape.java

@@ -4,7 +4,6 @@
 import mmcorej.Configuration;
 import org.micromanager.Studio;
 import org.micromanager.lightsheetmanager.LightSheetManager;
-import org.micromanager.lightsheetmanager.api.TimingSettings;
 import org.micromanager.lightsheetmanager.api.data.AcquisitionMode;
 import org.micromanager.lightsheetmanager.api.data.CameraMode;
 import org.micromanager.lightsheetmanager.api.data.GeometryType;
@@ -193,7 +192,7 @@ public boolean prepareControllerForAcquisition(
             final boolean isInterleaved = (settings.acquisitionMode() == AcquisitionMode.STAGE_SCAN_INTERLEAVED);
 
             // figure out the speed we should be going according to slice period, slice spacing, geometry, etc.
-            final double requestedMotorSpeed = computeScanSpeed(settings, scanner_.getSPIMNumScansPerSlice());  // in mm/sec
+            final double requestedMotorSpeed = computeScanSpeed(settings);  // in mm/sec
 
             final double maxSpeed = xyStage_.getMaxSpeedX();
             if (requestedMotorSpeed > (maxSpeed * 0.8)) {
@@ -265,10 +264,8 @@ public boolean prepareControllerForAcquisition(
     }
 
     // Compute appropriate motor speed in mm/s for the given stage scanning settings
-    public double computeScanSpeed(ScapeAcquisitionSettings settings, final int numScansPerSlice) {
-        //double sliceDuration = settings.timingSettings().sliceDuration();
-        // TODO: getSliceDuration only used here, but maybe should be computed elsewhere, and get with method above?
-        double sliceDuration = getSliceDuration(settings.timing(), numScansPerSlice);
+    public double computeScanSpeed(final ScapeAcquisitionSettings settings) {
+        double sliceDuration = settings.timing().sliceDuration();
         if (settings.acquisitionMode() == AcquisitionMode.STAGE_SCAN_INTERLEAVED) {
             // pretend like our slice takes twice as long so that we move the correct speed
             // this has the effect of halving the motor speed, but keeping the scan distance the same
@@ -291,25 +288,10 @@ private int computeScanChannelsPerPass(ScapeAcquisitionSettings settings) {
      * @param motorSpeed
      * @return
      */
-    public double computeScanAcceleration(final double motorSpeed, ScapeAcquisitionSettings settings) {
+    public double computeScanAcceleration(final double motorSpeed, final ScapeAcquisitionSettings settings) {
         return (10 + 100 * (motorSpeed / xyStage_.getMaxSpeedX())) * settings.stageScan().accelerationFactor();
     }
 
-    // TODO: scanNum was part of SliceSettings (now TimingSettings)
-    // scanNum was populated from numScansPerSlice_ which is the scanner SPIM_NUM_SCANSPERSLICE("SPIMNumScansPerSlice")
-    // labeled "Lines scans per slice:" in advanced timing tab
-    //    * gets the correct value for the slice timing's sliceDuration field based on other values of slice timing
-
-    // slice duration is the max out of the scan time, laser time, and camera time
-    public double getSliceDuration(final TimingSettings s, final int scanNum) {
-        return Math.max(Math.max(
-                        s.delayBeforeScan() + (s.scanDuration() * scanNum), // scan time
-                        s.delayBeforeLaser() + s.laserTriggerDuration()     // laser time
-                ),
-                s.delayBeforeCamera() + s.cameraTriggerDuration()   // camera time
-        );
-    }
-
     /**
      * Compute appropriate acceleration time in ms for the specified motor speed.
      * Set to be 10ms + 0-100ms depending on relative speed to max, all scaled by factor specified on the settings panel
@@ -487,7 +469,8 @@ public boolean prepareControllerForAcquisitionSide(
         //final double slope2 = settings.sliceCalibration(2).sliceSlope();
         double sliceRate = settings.sliceCalibration().slope();//(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.");
+            studio_.logs().showError("The \"Galvo constant\" is not set, it must not be 0.\n" +
+                    "Please update the value on the setup tab.");
             return false;
         }
         //final double offset1 = settings.sliceCalibration(1).sliceOffset() + channelOffset;

src/main/java/org/micromanager/lightsheetmanager/model/acquisitions/AcquisitionEngineDispim.java

@@ -885,17 +885,6 @@ public double getSliceDuration(
         );
     }
 
-    private double getSliceDuration(DefaultTimingSettings.Builder tsb) {
-        DefaultTimingSettings s = tsb.build();
-        // slice duration is the max out of the scan time, laser time, and camera time
-        return Math.max(Math.max(
-                        s.delayBeforeScan() + (s.scanDuration() * s.scansPerSlice()),   // scan time
-                        s.delayBeforeLaser() + s.laserTriggerDuration()                 // laser time
-                ),
-                s.delayBeforeCamera() + s.cameraTriggerDuration()                      // camera time
-        );
-    }
-
     private double computeTimePointDuration() {
         final double volumeDuration = computeActualVolumeDuration(acqSettings_);
         if (acqSettings_.isUsingMultiplePositions()) {

src/main/java/org/micromanager/lightsheetmanager/model/acquisitions/AcquisitionEngineScape.java

@@ -21,6 +21,7 @@
 import org.micromanager.lightsheetmanager.api.data.CameraMode;
 import org.micromanager.lightsheetmanager.api.data.ChannelMode;
 import org.micromanager.lightsheetmanager.api.internal.DefaultTimingSettings;
+import org.micromanager.lightsheetmanager.api.internal.ScapeAcquisitionSettings;
 import org.micromanager.lightsheetmanager.gui.utils.DialogUtils;
 import org.micromanager.lightsheetmanager.model.DataStorage;
 import org.micromanager.lightsheetmanager.LightSheetManager;
@@ -36,6 +37,7 @@
 import org.micromanager.lightsheetmanager.model.devices.vendor.ASIScanner;
 import org.micromanager.lightsheetmanager.model.devices.vendor.ASIXYStage;
 import org.micromanager.lightsheetmanager.model.utils.FileUtils;
+import org.micromanager.lightsheetmanager.model.utils.GeometryUtils;
 import org.micromanager.lightsheetmanager.model.utils.NumberUtils;
 
 import javax.swing.JLabel;
@@ -754,11 +756,14 @@ boolean finish() {
             studio_.logs().logError("Couldn't restore shutter to original state");
         }
 
-        // Check if acquisition ended due to an exception and show error to user if it did
-        try {
-            currentAcquisition_.checkForExceptions();
-        } catch (Exception e) {
-            studio_.logs().logError(e);
+        // check if acquisition ended due to an exception and show error
+        // currentAcquisition_ can be null if an error occurred during setup
+        if (currentAcquisition_ != null) {
+            try {
+                currentAcquisition_.checkForExceptions();
+            } catch (Exception e) {
+                studio_.logs().logError(e);
+            }
         }
 
         // TODO: execute any end-acquisition runnables
@@ -992,8 +997,7 @@ private boolean doHardwareCalculations(PLogicScape plc) {
         }
 
         double extraChannelOffset = 0.0;
-        plc.prepareControllerForAcquisition(acqSettings_, extraChannelOffset);
-        return true;
+        return plc.prepareControllerForAcquisition(acqSettings_, extraChannelOffset);
     }
 
     private void doHardwareCalculationsNIDAQ() {
@@ -1125,7 +1129,7 @@ public DefaultTimingSettings.Builder getTimingFromExposure() {
             // only true when user has specified period that is unattainable
             if (globalDelay < 0) {
                 globalDelay = 0;
-                studio_.logs().showError("Increasing slice period to meet laser exposure constraint\n"
+                studio_.logs().logDebugMessage("Increasing slice period to meet laser exposure constraint\n"
                         + "(time required for camera readout; readout time depends on ROI).");
             }
             delayBeforeCamera += globalDelay;
@@ -1310,7 +1314,7 @@ public DefaultTimingSettings.Builder getTimingFromPeriodAndLightExposure() {
             // only true when user has specified period that is unattainable
             if (globalDelay < 0) {
                 globalDelay = 0;
-                studio_.logs().showError("Increasing slice period to meet laser exposure constraint\n"
+                studio_.logs().logDebugMessage("Increasing slice period to meet laser exposure constraint\n"
                         + "(time required for camera readout; readout time depends on ROI).");
             }
             delayBeforeCamera += globalDelay;
@@ -1432,8 +1436,8 @@ public double computeVolumeDuration() {
         final double stackDuration = numCameraTriggers * acqSettings_.timing().sliceDuration();
 
         if (acqSettings_.stageScan().enabled()) {
-            final double rampDuration = 1; //getStageRampDuration(acqSettings);
-            final double retraceTime = 1; //getStageRetraceDuration(acqSettings);
+            final double rampDuration = getStageRampDuration(acqSettings_);
+            final double retraceTime = getStageRetraceDuration(acqSettings_);
             // TODO(Jon): double-check these calculations below, at least they are better than before ;-)
             if (acqSettings_.acquisitionMode() == AcquisitionMode.STAGE_SCAN) {
                 if (channelMode == ChannelMode.SLICE_HW) {
@@ -1468,4 +1472,42 @@ public double computeVolumeDuration() {
         }
     }
 
+    private double getStageRampDuration(final ScapeAcquisitionSettings settings) {
+        final double rampDuration = settings.volume().delayBeforeView() + getScanStageAcceleration(settings);
+        model_.studio().logs().logDebugMessage("stage ramp duration is " + rampDuration + " milliseconds");
+        return rampDuration;
+    }
+
+    private double getScanStageAcceleration(final ScapeAcquisitionSettings settings) {
+        // TODO: remove this and find a better way
+        if (controller_ == null) {
+            controller_ = new PLogicScape(model_);
+        }
+        // extra 1 for rounding up that often happens in controller
+        return controller_.computeScanAcceleration(controller_.computeScanSpeed(settings), settings) + 1;
+    }
+
+    private double getStageRetraceDuration(final ScapeAcquisitionSettings settings) {
+        final ASIXYStage stage = model_.devices().device("SampleXY");
+        if (stage == null) {
+            studio_.logs().showError("could not find XY stage!");
+            return 0.0; // early exit => error
+        }
+        final double retraceRelativeSpeedPercent;
+        if (stage.hasProperty(ASIXYStage.Properties.SCAN_RETRACE_SPEED)) {
+            // this added in firmware v3.30; if not present then we set to firmware default hardcoded previously
+            retraceRelativeSpeedPercent = stage.getScanRetraceSpeed();
+        } else {
+            retraceRelativeSpeedPercent = 67.0;
+        }
+        final double retraceSpeed = retraceRelativeSpeedPercent / 100 * stage.getMaxSpeedX();
+        final double speedFactor = GeometryUtils.getStageGeometricSpeedFactor(
+                settings.stageScan().firstViewAngle(), settings.volume().firstView() == 1);
+        final double scanDistance = settings.volume().slicesPerView() * settings.volume().sliceStepSize() * speedFactor;
+        final double accelerationX = getScanStageAcceleration(settings);
+        final double retraceDuration = scanDistance / retraceSpeed + accelerationX * 2;
+        studio_.logs().logDebugMessage("stage retrace duration is " + retraceDuration + " milliseconds");
+        return retraceDuration;
+    }
+
 }

src/main/java/org/micromanager/lightsheetmanager/model/devices/vendor/ASIXYStage.java

@@ -166,6 +166,11 @@ public double getScanSettlingTime() {
         return getPropertyFloat(Properties.SCAN_SETTLING_TIME);
     }
 
+    // TODO: should this be an int?
+    public double getScanRetraceSpeed() {
+        return getPropertyFloat(Properties.SCAN_RETRACE_SPEED);
+    }
+
     public static class Properties {
         public static final String AXIS_POLARITY_X = "AxisPolarityX";
         public static final String AXIS_POLARITY_Y = "AxisPolarityY";
@@ -182,7 +187,7 @@ public static class Properties {
         public static final String SCAN_PATTERN = "ScanPattern";
         public static final String SCAN_STATE = "ScanState";
         public static final String SCAN_SETTLING_TIME = "ScanSettlingTime(ms)";
-
+        public static final String SCAN_RETRACE_SPEED = "ScanRetraceSpeedPercent(%)";
         public static final String SCAN_FAST_AXIS_START_POSITION = "ScanFastAxisStartPosition(mm)";
         public static final String SCAN_FAST_AXIS_STOP_POSITION = "ScanFastAxisStopPosition(mm)";
         public static final String SCAN_SLOW_AXIS_START_POSITION = "ScanSlowAxisStartPosition(mm)";