improve ui swap between advanced and standard timing

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

@@ -79,6 +79,9 @@ public AcquisitionTab(final LightSheetManagerModel model) {
         createEventHandlers();
     }
 
+    /**
+     * Create the user interface.
+     */
     private void createUserInterface() {
 
         final DefaultAcquisitionSettingsSCAPE acqSettings =
@@ -207,56 +210,25 @@ private void createUserInterface() {
         add(pnlButtons_, "span 3, gaptop 60");
     }
 
-    private void acqFinishedCallback() {
-        try {
-            SwingUtilities.invokeAndWait(() -> {
-                btnRunAcquisition_.setState(false);
-                btnPauseAcquisition_.setEnabled(false);
-                btnSpeedTest_.setEnabled(true);
-            });
-        } catch (InterruptedException e) {
-            e.printStackTrace();
-        } catch (InvocationTargetException e) {
-            e.printStackTrace();
-        }
-    }
-
-    private void runAcquisition(boolean speedTest) {
-        btnPauseAcquisition_.setEnabled(true);
-        btnSpeedTest_.setEnabled(false);
-        Future<?> acqFinished = model_.acquisitions().requestRun(speedTest);
-        // Launch new thread to update the button when the acquisition is complete
-        new Thread(() -> {
-            try {
-                acqFinished.get();
-            } catch (Exception e) {
-                e.printStackTrace();
-            }
-            // update the GUI when acquisition complete
-            acqFinishedCallback();
-        }).start();
-    }
-
+    /**
+     * Create event handlers for the user interface.
+     */
     private void createEventHandlers() {
 
         // start/stop acquisitions
         btnRunAcquisition_.registerListener(e -> {
             if (btnRunAcquisition_.isSelected()) {
                 runAcquisition(false);
-                System.out.println("request run");
             } else {
                 model_.acquisitions().requestStop();
-                System.out.println("request stop");
             }
         });
 
         btnPauseAcquisition_.registerListener(e -> {
             if (btnPauseAcquisition_.isSelected()) {
                 model_.acquisitions().requestPause();
-                System.out.println("request pause");
             } else {
                 model_.acquisitions().requestResume();
-                System.out.println("request resume");
             }
         });
 
@@ -265,7 +237,6 @@ private void createEventHandlers() {
 
         btnSpeedTest_.registerListener(e -> runAcquisition(true));
         btnRunOverviewAcq_.registerListener(e -> {
-            System.out.println("run overview acquisition");
             // TODO: run the overview acq
         });
 
@@ -295,27 +266,29 @@ private void createEventHandlers() {
         cmbAcquisitionModes_.registerListener(e -> {
             final int index = cmbAcquisitionModes_.getSelectedIndex();
             model_.acquisitions().settingsBuilder().acquisitionMode(AcquisitionMode.getByIndex(index));
-            //System.out.println("getAcquisitionMode: " + model_.acquisitions().getAcquisitionSettings().getAcquisitionMode());
         });
 
+        // TODO: should timing recalc be part of setting use advanced timing value in model?
         // switches timing panels based on check box
         cbxUseAdvancedTiming_.registerListener(e -> {
-            final boolean state = cbxUseAdvancedTiming_.isSelected();
-            model_.acquisitions().settingsBuilder().useAdvancedTiming(state);
-            switchTimingSettings(state);
+            final boolean useAdvTiming = cbxUseAdvancedTiming_.isSelected();
+            model_.acquisitions().settingsBuilder().useAdvancedTiming(useAdvTiming);
+            swapTimingSettingsPanels(useAdvTiming);
+            if (useAdvTiming) {
+                pnlAdvancedTiming_.updateSpinners();
+            } else {
+                model_.acquisitions().updateAcquisitionSettings();
+                model_.acquisitions().recalculateSliceTiming();
+            }
         });
     }
 
-    public SliceSettingsPanel getSliceSettingsPanel() {
-        return pnlSliceSettings_;
-    }
-
     /**
      * Switch between slice timing panel and advanced timing panel.
      *
      * @param state the state of the CheckBox
      */
-    private void switchTimingSettings(final boolean state) {
+    private void swapTimingSettingsPanels(final boolean state) {
         pnlRight_.removeAll();
         if (state) {
             pnlRight_.add(pnlVolumeSettings_, "growx, wrap");
@@ -330,6 +303,40 @@ private void switchTimingSettings(final boolean state) {
         pnlRight_.repaint();
     }
 
+    public SliceSettingsPanel getSliceSettingsPanel() {
+        return pnlSliceSettings_;
+    }
+
+    private void acqFinishedCallback() {
+        try {
+            SwingUtilities.invokeAndWait(() -> {
+                btnRunAcquisition_.setState(false);
+                btnPauseAcquisition_.setEnabled(false);
+                btnSpeedTest_.setEnabled(true);
+            });
+        } catch (InterruptedException e) {
+            e.printStackTrace();
+        } catch (InvocationTargetException e) {
+            e.printStackTrace();
+        }
+    }
+
+    private void runAcquisition(boolean speedTest) {
+        btnPauseAcquisition_.setEnabled(true);
+        btnSpeedTest_.setEnabled(false);
+        Future<?> acqFinished = model_.acquisitions().requestRun(speedTest);
+        // Launch new thread to update the button when the acquisition is complete
+        new Thread(() -> {
+            try {
+                acqFinished.get();
+            } catch (Exception e) {
+                studio_.logs().logError("error in runAcquisition");
+            }
+            // update the GUI when acquisition complete
+            acqFinishedCallback();
+        }).start();
+    }
+
     @Override
     public void selected() {
 

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

@@ -136,4 +136,21 @@ private void createEventHandlers() {
                     .timingSettingsBuilder().useAlternateScanDirection(cbxAlternateScanDirection_.isSelected());
         });
     }
+
+    /**
+     * Updates the spinner values from the timing settings builder.
+     */
+    public void updateSpinners() {
+        final DefaultTimingSettings timingSettings = model_.acquisitions()
+                .settingsBuilder().timingSettingsBuilder().build();
+        spnDelayBeforeScan_.setDouble(timingSettings.delayBeforeScan());
+        spnScansPerSlice_.setInt(timingSettings.scansPerSlice());
+        spnScanDuration_.setDouble(timingSettings.scanDuration());
+        spnDelayBeforeLaser_.setDouble(timingSettings.delayBeforeLaser());
+        spnLaserTriggerDuration_.setDouble(timingSettings.laserTriggerDuration());
+        spnDelayBeforeCamera_.setDouble(timingSettings.delayBeforeCamera());
+        spnCameraTriggerDuration_.setDouble(timingSettings.cameraTriggerDuration());
+        spnCameraExposure_.setDouble(timingSettings.cameraExposure());
+        cbxAlternateScanDirection_.setSelected(timingSettings.useAlternateScanDirection());
+    }
 }

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

@@ -94,16 +94,25 @@ private void createEventHandlers() {
             spnSlicePeriod_.setEnabled(!selected);
             model_.acquisitions().settingsBuilder()
                     .sliceSettingsBuilder().minimizeSlicePeriod(selected);
+            // update slice timing
+            model_.acquisitions().updateAcquisitionSettings();
+            model_.acquisitions().recalculateSliceTiming();
         });
 
         spnSlicePeriod_.registerListener(e -> {
             model_.acquisitions().settingsBuilder()
                     .sliceSettingsBuilder().slicePeriod(spnSlicePeriod_.getDouble());
+            // update slice timing
+            model_.acquisitions().updateAcquisitionSettings();
+            model_.acquisitions().recalculateSliceTiming();
         });
 
         spnSampleExposure_.registerListener(e -> {
             model_.acquisitions().settingsBuilder()
                     .sliceSettingsBuilder().sampleExposure(spnSampleExposure_.getDouble());
+            // update slice timing
+            model_.acquisitions().updateAcquisitionSettings();
+            model_.acquisitions().recalculateSliceTiming();
         });
 
         // virtual slit panel

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

@@ -1,15 +1,13 @@
 package org.micromanager.lightsheetmanager.model;
 
 import mmcorej.CMMCore;
-import org.micromanager.LogManager;
 import org.micromanager.Studio;
 import org.micromanager.lightsheetmanager.api.AutofocusSettings;
 import org.micromanager.lightsheetmanager.api.LightSheetManager;
 import org.micromanager.lightsheetmanager.api.TimingSettings;
 import org.micromanager.lightsheetmanager.api.VolumeSettings;
 import org.micromanager.lightsheetmanager.api.data.GeometryType;
 import org.micromanager.lightsheetmanager.model.acquisitions.AcquisitionEngine;
-//import org.micromanager.lightsheetmanager.model.acquisitions.AcquisitionEngineDISPIM;
 import org.micromanager.lightsheetmanager.model.acquisitions.AcquisitionEngineDISPIM;
 import org.micromanager.lightsheetmanager.model.acquisitions.AcquisitionEngineSCAPE;
 import org.micromanager.lightsheetmanager.model.playlist.AcquisitionTableData;
@@ -23,7 +21,6 @@ public class LightSheetManagerModel implements LightSheetManager {
 
     private final Studio studio_;
     private final CMMCore core_;
-    private final LogManager logs_;
 
     private String errorText_;
 
@@ -39,7 +36,6 @@ public class LightSheetManagerModel implements LightSheetManager {
     public LightSheetManagerModel(final Studio studio) {
         studio_ = Objects.requireNonNull(studio);
         core_ = studio_.core();
-        logs_ = studio_.logs();
 
         settings_ = new UserSettings(this);
         xyzGrid_ = new XYZGrid(this);

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

@@ -16,7 +16,6 @@
 import org.micromanager.data.internal.PropertyKey;
 import org.micromanager.lightsheetmanager.LightSheetManagerPlugin;
 import org.micromanager.lightsheetmanager.api.AcquisitionManager;
-import org.micromanager.lightsheetmanager.api.internal.DefaultAcquisitionSettingsDISPIM;
 import org.micromanager.lightsheetmanager.api.internal.DefaultAcquisitionSettingsSCAPE;
 import org.micromanager.lightsheetmanager.gui.LightSheetManagerFrame;
 import org.micromanager.lightsheetmanager.model.autofocus.AutofocusRunner;
@@ -69,7 +68,6 @@ public AcquisitionEngine(final LightSheetManagerModel model) {
         acqSettings_ = asb_.build();
     }
 
-
     //public abstract DefaultAcquisitionSettingsDISPIM settings();
 
     //public abstract <T extends DefaultAcquisitionSettings.Builder<Builder>> T settingsBuilder();
@@ -80,6 +78,8 @@ public AcquisitionEngine(final LightSheetManagerModel model) {
 
     abstract boolean finish();
 
+    public abstract void recalculateSliceTiming();
+
     public void setFrame(final LightSheetManagerFrame frame) {
         frame_ = Objects.requireNonNull(frame);
     }
@@ -94,6 +94,10 @@ public void setAcquisitionSettings(final DefaultAcquisitionSettingsSCAPE acqSett
         acqSettings_ = acqSettings;
     }
 
+    public void updateAcquisitionSettings() {
+        acqSettings_ = asb_.build();
+    }
+
     @Override
     public Future<?> requestRun(boolean speedTest) {
         // Run on a new thread, so it doesn't block the EDT

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

@@ -680,6 +680,7 @@ private void doHardwareCalculationsNIDAQ() {
         //daq.setProperty("PropertyName", "1");
     }
 
+    @Override
     public void recalculateSliceTiming() {
         // don't change timing settings if user is using advanced timing
         if (acqSettings_.isUsingAdvancedTiming()) {

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

@@ -89,7 +89,7 @@ boolean run() {
         setAcquisitionSettings(asb_.build());
 
         // TODO: delete later, this is the settings before everything is set up in doHardwareCalculations (used to debug)
-        studio_.logs().logMessage("debug info:\n" + acqSettings_.toPrettyJson());
+        //studio_.logs().logMessage("debug info:\n" + acqSettings_.toPrettyJson());
 
         final boolean isLiveModeOn = studio_.live().isLiveModeOn();
         if (isLiveModeOn) {
@@ -913,6 +913,7 @@ private void doHardwareCalculationsNIDAQ() {
         //daq.setProperty("PropertyName", "1");
     }
 
+    @Override
     public void recalculateSliceTiming() {
         // update timing settings if not using advanced timing
         if (!acqSettings_.isUsingAdvancedTiming()) {
@@ -921,8 +922,14 @@ public void recalculateSliceTiming() {
         }
         final double sliceDuration = getSliceDuration(asb_.timingSettingsBuilder());
         asb_.timingSettingsBuilder().sliceDuration(sliceDuration);
+        //System.out.println(asb_.timingSettingsBuilder());
     }
 
+    /**
+     * Single objective timing settings.
+     *
+     * @return a builder for DefaultTimingSettings
+     */
     public DefaultTimingSettings.Builder getTimingFromExposure() {
         // Note: sliceDuration is computed in recalculateSliceTiming
         DefaultTimingSettings.Builder tsb = new DefaultTimingSettings.Builder();
@@ -942,7 +949,6 @@ public DefaultTimingSettings.Builder getTimingFromExposure() {
         final double slicePeriod = Math.max(Math.max(laserDuration, cameraTotalTime),
                 isSlicePeriodMinimized ? 0 : desiredSlicePeriod);
         final double sliceDeadTime = NumberUtils.roundToQuarterMs(slicePeriod - laserDuration);
-
         switch (cameraMode) {
             case PSEUDO_OVERLAP: // e.g. Kinetix
                 tsb.scansPerSlice(1);