set useStageScanning_ through acquisitionMode method, improve API

src/main/java/org/micromanager/lightsheetmanager/api/AcquisitionSettingsSCAPE.java

@@ -75,13 +75,6 @@ interface Builder<T extends AcquisitionSettings.Builder<T>> extends AcquisitionS
          */
         T useHardwareTimePoints(final boolean state);
 
-        /**
-         * Sets the acquisition to use stage scanning.
-         *
-         * @param state true to use stage scanning.
-         */
-        T useStageScanning(final boolean state);
-
         /**
          * Sets the acquisition to use advanced timing settings.
          *
@@ -131,6 +124,11 @@ interface Builder<T extends AcquisitionSettings.Builder<T>> extends AcquisitionS
          */
         T channels(final ChannelSpec[] channels);
 
+        /**
+         * Sets the live scan period.
+         *
+         * @param liveScanPeriod the channel array
+         */
         T liveScanPeriod(final double liveScanPeriod);
 
         /**

src/main/java/org/micromanager/lightsheetmanager/api/internal/DefaultAcquisitionSettingsSCAPE.java

@@ -76,13 +76,21 @@ public Builder(final DefaultAcquisitionSettingsSCAPE acqSettings) {
         }
 
         /**
-         * Sets the acquisition mode.
+         * Set the mode for the acquisition.
+         * <p>
+         * If the mode is a stage scanning mode,
+         * set internal stage scanning flag.
          *
          * @param acqMode the acquisition mode
          */
         @Override
         public Builder acquisitionMode(final AcquisitionMode acqMode) {
             acquisitionMode_ = acqMode;
+            if (acqMode == AcquisitionMode.STAGE_SCAN
+                    || acqMode == AcquisitionMode.STAGE_SCAN_INTERLEAVED
+                    || acqMode == AcquisitionMode.STAGE_SCAN_UNIDIRECTIONAL) {
+                useStageScanning_ = true;
+            }
             return this;
         }
 
@@ -163,17 +171,6 @@ public Builder useHardwareTimePoints(final boolean state) {
             return this;
         }
 
-        /**
-         * Sets the acquisition to use stage scanning.
-         *
-         * @param state true to use stage scanning.
-         */
-        @Override
-        public Builder useStageScanning(final boolean state) {
-            useStageScanning_ = state;
-            return this;
-        }
-
         /**
          * Sets the acquisition to use advanced timing settings.
          *

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

@@ -289,6 +289,7 @@ private void createEventHandlers() {
             pnlChannelTable_.setItemsEnabled(state);
         });
 
+        // select the acquisition mode
         cmbAcquisitionModes_.registerListener(e -> {
             final int index = cmbAcquisitionModes_.getSelectedIndex();
             model_.acquisitions().settingsBuilder().acquisitionMode(AcquisitionMode.getByIndex(index));

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

@@ -53,11 +53,10 @@ boolean setup() {
 
     @Override
     boolean run() {
-        // TODO: make this happen for all acq types
         final boolean isPolling = frame_.getNavigationPanel().isPolling();
         if (isPolling) {
-            studio_.logs().logMessage("stopped position polling");
             frame_.getNavigationPanel().stopPolling();
+            studio_.logs().logMessage("stopped position polling");
         }
 
         asb_.sheetCalibrationBuilder(1).useAutoSheetWidth(true);
@@ -82,7 +81,6 @@ boolean run() {
 
         // initialize stage scanning so we can restore state
         Point2D.Double xyPosUm = new Point2D.Double();
-        double xSupPosUm = 0.0;
         double origXSpeed = 1.0; // don't want 0 in case something goes wrong
         double origXAccel = 1.0; // don't want 0 in case something goes wrong
 
@@ -101,17 +99,16 @@ boolean run() {
                     return false;
                 }
 
-                // second part: initialize stage scanning so we can restore state
+                // second part: initialize stage scanning, so we can restore state later
                 xyPosUm = xyStage.getXYPosition();
                 origXSpeed = xyStage.getSpeedX();
                 origXAccel = xyStage.getAccelerationX();
 
-                // TODO: add more checks from orignal plugin here...
+                // TODO: add more checks from original plugin here...
                 //  if (origXSpeed < 0.2 && resetXaxisSpeed_) { etc...
             }
         }
 
-
         PLogicSCAPE controller = null;
 
         // Assume demo mode if default camera is DemoCamera