From a89b2e0f16bb7e22e7ddb05307b86a2180e98cc6 Mon Sep 17 00:00:00 2001
From: Brandon <brandon@asiimaging.com>
Date: Wed, 1 May 2024 16:16:02 -0700
Subject: [PATCH] fix negative scan direction stage scanning

---
 .../lightsheetmanager/model/PLogicSCAPE.java  |  3 +-
 .../acquisitions/AcquisitionEngineSCAPE.java  | 43 +++++++++++--------
 .../model/devices/vendor/ASIXYStage.java      |  9 ++++
 3 files changed, 35 insertions(+), 20 deletions(-)

diff --git a/src/main/java/org/micromanager/lightsheetmanager/model/PLogicSCAPE.java b/src/main/java/org/micromanager/lightsheetmanager/model/PLogicSCAPE.java
index d87257f..db18900 100644
--- a/src/main/java/org/micromanager/lightsheetmanager/model/PLogicSCAPE.java
+++ b/src/main/java/org/micromanager/lightsheetmanager/model/PLogicSCAPE.java
@@ -230,6 +230,7 @@ public boolean prepareControllerForAcquisition(
 
             xyStage_.setScanPattern(isStageScan2Sided ?
                     ASIXYStage.ScanPattern.SERPENTINE : ASIXYStage.ScanPattern.RASTER);
+            xyStage_.setScanSettlingTime(acqSettings_.volumeSettings().delayBeforeView());
 
             if (xyStage_.getAxisPolarityX() != ASIXYStage.AxisPolarity.NORMAL) {
                 studio_.logs().showError(
@@ -351,7 +352,7 @@ public boolean prepareStageScanForAcquisition(final double x, final double y, De
         xyStage_.setSlowAxisStop(y / 1000);
 
         zSpeedZero_ = true;  // will turn false if we are doing planar correction
-        return false;
+        return true;
         // return preparePlanarCorrectionForAcquisition(); TODO: add planar correction later
     }
 
diff --git a/src/main/java/org/micromanager/lightsheetmanager/model/acquisitions/AcquisitionEngineSCAPE.java b/src/main/java/org/micromanager/lightsheetmanager/model/acquisitions/AcquisitionEngineSCAPE.java
index e3c3bc9..301436b 100644
--- a/src/main/java/org/micromanager/lightsheetmanager/model/acquisitions/AcquisitionEngineSCAPE.java
+++ b/src/main/java/org/micromanager/lightsheetmanager/model/acquisitions/AcquisitionEngineSCAPE.java
@@ -40,6 +40,7 @@
 import java.io.IOException;
 import java.util.ArrayList;
 
+
 public class AcquisitionEngineSCAPE extends AcquisitionEngine {
 
     private double origSpeedX_;
@@ -149,29 +150,33 @@ boolean run() {
         }
 
             // --- testing code below ---
-//            String plcName = "Scanner:AB:33";
-//            StrVector propertyNames;
-//            try {
-//                propertyNames = core_.getDevicePropertyNames(plcName);
-//            } catch (Exception e) {
-//                propertyNames = null;
-//            }
-//
-//            Gson gsonObj = new Gson();
-//            HashMap<String, String> deviceProps = new HashMap<>();
-//            for (String propName : propertyNames) {
-//                String propValue;
+//            StrVector deviceNames = core_.getLoadedDevices();
+//            for (String deviceName : deviceNames) {
+//                System.out.println("deviceName: " + deviceName);
+//                StrVector propertyNames;
 //                try {
-//                    propValue = core_.getProperty(plcName, propName);
+//                    propertyNames = core_.getDevicePropertyNames(deviceName);
 //                } catch (Exception e) {
-//                    propValue = "";
-//                    System.out.println("failed!");
+//                    propertyNames = null;
 //                }
-//                deviceProps.put(propName, propValue);
-//                //System.out.println(propName);
+//
+//                Gson gsonObj = new Gson();
+//                HashMap<String, String> deviceProps = new HashMap<>();
+//                for (String propName : propertyNames) {
+//                    String propValue;
+//                    try {
+//                        propValue = core_.getProperty(deviceName, propName);
+//                    } catch (Exception e) {
+//                        propValue = "";
+//                        System.out.println("failed!");
+//                    }
+//                    deviceProps.put(propName, propValue);
+//                    //System.out.println(propName);
+//                }
+//
+//                String jsonStr = gsonObj.toJson(deviceProps);
+//                System.out.println(jsonStr);
 //            }
-//            String jsonStr = gsonObj.toJson(deviceProps);
-//            System.out.println(jsonStr);
 
         setAcquisitionSettings(asb_.build());
 
diff --git a/src/main/java/org/micromanager/lightsheetmanager/model/devices/vendor/ASIXYStage.java b/src/main/java/org/micromanager/lightsheetmanager/model/devices/vendor/ASIXYStage.java
index 47da0a2..f5fe38e 100644
--- a/src/main/java/org/micromanager/lightsheetmanager/model/devices/vendor/ASIXYStage.java
+++ b/src/main/java/org/micromanager/lightsheetmanager/model/devices/vendor/ASIXYStage.java
@@ -158,6 +158,14 @@ public ScanState getScanState() {
         return ScanState.fromString(getProperty(Properties.SCAN_STATE));
     }
 
+    public void setScanSettlingTime(final double milliseconds) {
+        setPropertyFloat(Properties.SCAN_SETTLING_TIME, milliseconds);
+    }
+
+    public double getScanSettlingTime() {
+        return getPropertyFloat(Properties.SCAN_SETTLING_TIME);
+    }
+
     public static class Properties {
         public static final String AXIS_POLARITY_X = "AxisPolarityX";
         public static final String AXIS_POLARITY_Y = "AxisPolarityY";
@@ -173,6 +181,7 @@ public static class Properties {
         public static final String SCAN_NUM_LINES = "ScanNumLines";
         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_FAST_AXIS_START_POSITION = "ScanFastAxisStartPosition(mm)";
         public static final String SCAN_FAST_AXIS_STOP_POSITION = "ScanFastAxisStopPosition(mm)";