start the saving and loading of acq settings

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

@@ -12,7 +12,7 @@ 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 = "0.6.0";
+    public static final String version = "0.6.1";
 
     private Studio studio_;
     private LightSheetManager model_;

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

@@ -11,6 +11,7 @@
 import org.micromanager.lightsheetmanager.gui.components.TextField;
 import org.micromanager.lightsheetmanager.gui.data.Icons;
 import org.micromanager.lightsheetmanager.model.DataStorage;
+import org.micromanager.lightsheetmanager.model.utils.FileUtils;
 
 import javax.swing.JLabel;
 import java.awt.Color;
@@ -30,7 +31,12 @@ public class SavePanel extends Panel {
     private ComboBox<DataStorage.SaveMode> cbxSaveMode_;
     private CheckBox cbxSaveWhileAcquiring_;
 
+    private Button btnSaveSettings_;
+    private Button btnLoadSettings_;
+
     private final FileDialogs.FileType directorySelect_;
+    private final FileDialogs.FileType jsonFileSave_;
+    private final FileDialogs.FileType jsonFileLoad_;
 
     private final LightSheetManager model_;
     private final LightSheetManagerFrame frame_;
@@ -40,7 +46,6 @@ public SavePanel(final LightSheetManager model, final LightSheetManagerFrame fra
         model_ = Objects.requireNonNull(model);
         frame_ = Objects.requireNonNull(frame);
 
-        // file type filter
         directorySelect_ = new FileDialogs.FileType(
                 "SAVE_DIRECTORY",
                 "All Directories",
@@ -49,6 +54,22 @@ public SavePanel(final LightSheetManager model, final LightSheetManagerFrame fra
                 ""
         );
 
+        jsonFileSave_ = new FileDialogs.FileType(
+                "SAVE_FILE",
+                "JSON Files",
+                "acq_settings.json",
+                false,
+                "json"
+        );
+
+        jsonFileLoad_ = new FileDialogs.FileType(
+                "OPEN_FILE",
+                "JSON Files",
+                "acq_settings.json",
+                false,
+                "json"
+        );
+
         createUserInterface();
         createEventHandlers();
     }
@@ -86,6 +107,9 @@ public void createUserInterface() {
         cbxSaveWhileAcquiring_ = new CheckBox("Save images during acquisition",
                 acqSettings.isSavingImagesDuringAcquisition());
 
+        btnSaveSettings_ = new Button("Save", 60, 20);
+        btnLoadSettings_ = new Button("Load", 60, 20);
+
         add(lblSaveDirectory, "");
         add(txtSaveDirectory_, "");
         add(btnBrowse_, "");
@@ -95,6 +119,9 @@ public void createUserInterface() {
         add(lblSaveMode, "");
         add(cbxSaveMode_, "split 2, wrap");
         add(cbxSaveWhileAcquiring_, "span 2, wrap");
+        add(new JLabel("Acq Settings:"), "");
+        add(btnSaveSettings_, "split 2");
+        add(btnLoadSettings_, "");
     }
 
     public void createEventHandlers() {
@@ -123,8 +150,33 @@ public void createEventHandlers() {
         cbxSaveMode_.registerListener(e ->
                 model_.acquisitions().settingsBuilder().saveMode(cbxSaveMode_.getSelected()));
 
+        btnSaveSettings_.registerListener(e -> {
+            final File file = FileDialogs.save(frame_,
+                    "Save the acquisition settings to JSON...", jsonFileSave_
+            );
+            if (file != null) {
+                // TODO: prompt if file exists
+                FileUtils.writeStringToFile(file.toString(), model_.acquisitions().settings().toPrettyJson());
+                model_.studio().logs().logMessage("Acquisition settings saved to: " + file);
+            }
+        });
+
+        btnLoadSettings_.registerListener(e -> {
+            final File file = FileDialogs.openFile(frame_,
+                    "Load the acquisition settings from JSON...", jsonFileLoad_
+            );
+            if (file != null) {
+                // TODO: prompt to overwrite settings
+                final String json = FileUtils.readFileToString(file.toString());
+                model_.acquisitions().setAcquisitionSettingsAndBuilder(
+                        ScapeAcquisitionSettings.fromJson(json, ScapeAcquisitionSettings.class));
+                model_.studio().logs().logMessage("Acquisition settings loaded from: " + file);
+            }
+        });
+
     }
 
+    // Opens the file explorer to the save directory
     private void openDirectory(final String path) {
         final File directory = new File(path);
         if (directory.exists()) {

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

@@ -286,23 +286,7 @@ public <T extends DeviceBase> T requiredDevice(final String name, final Class<T>
     }
 
     public CameraBase firstImagingCamera() {
-        String deviceKey;
-        //if (model_.acquisitions().settings().isUsingSimultaneousCameras()) {
-        if (true) {
-            deviceKey =  firstActiveCameraName();
-        } else {
-            final DeviceAdapter adapter = model_.devices().adapter();
-            if (adapter.numSimultaneousCameras() > 1 && adapter.numImagingPaths() == 1) {
-                deviceKey = "ImagingCamera1";
-            } else if (adapter.numSimultaneousCameras() > 1) {
-                deviceKey = "Imaging1Camera1";
-            } else if (adapter.numImagingPaths() > 1) {
-                deviceKey = "Imaging1Camera";
-            } else {
-                deviceKey = "ImagingCamera";
-            }
-        }
-        return (CameraBase) deviceMap_.get(deviceKey);
+        return (CameraBase) deviceMap_.get(firstActiveCameraName());
     }
 
     // For simultaneous cameras
@@ -352,19 +336,14 @@ public String[] imagingCameraNames() {
 
     public CameraBase[] imagingCameras() {
         String[] cameraNames;
-        //if (model_.acquisitions().settings().isUsingSimultaneousCameras()) {
-        if (true) {
-            ArrayList<String> names = new ArrayList<>();
-            final CameraData[] cameras = model_.acquisitions().settings().imagingCameraOrder();
-            for (CameraData camera : cameras) {
-                if (camera.isActive()) {
-                    names.add(camera.name());
-                }
+        ArrayList<String> names = new ArrayList<>();
+        final CameraData[] cameras = model_.acquisitions().settings().imagingCameraOrder();
+        for (CameraData camera : cameras) {
+            if (camera.isActive()) {
+                names.add(camera.name());
             }
-            cameraNames = names.toArray(String[]::new);
-        } else {
-            cameraNames = imagingCameraNames();
         }
+        cameraNames = names.toArray(String[]::new);
         return Arrays.stream(cameraNames)
                 .map(name -> (CameraBase)deviceMap_.get(name))
                 .filter(Objects::nonNull)

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

@@ -36,6 +36,8 @@
  */
 public class AcquisitionEngineDispim extends AcquisitionEngine {
 
+    private boolean isPolling_; // true if polling was enabled at the start of an acquisition
+
 //    private DefaultAcquisitionSettingsDISPIM.Builder asb_;
    // TODO: remove this when a more generic method is available and get from base class
     private DispimAcquisitionSettings acqSettings_;
@@ -46,33 +48,23 @@ public AcquisitionEngineDispim(final LightSheetManager model) {
         acqSettings_ = DispimAcquisitionSettings.builder().build();
     }
 
-//    @Override
-//    public DefaultAcquisitionSettingsDISPIM settings() {
-//        return acqSettings_;
-//    }
-//
-//    @Override
-//    public DefaultAcquisitionSettingsDISPIM.Builder settingsBuilder() {
-//        return asb_;
-//    }
-
     @Override
     boolean setup() {
-        return true;
-    }
-
-    @Override
-    boolean run() {
-
-        final boolean isPolling = model_.positions().isPolling();
-        if (isPolling) {
-            studio_.logs().logMessage("stopped position polling");
+        isPolling_ = model_.positions().isPolling();
+        if (isPolling_) {
             model_.positions().stopPolling();
+            studio_.logs().logMessage("stopped position polling");
         }
 
         // make settings current
         updateAcquisitionSettings();
 
+        return true;
+    }
+
+    @Override
+    boolean run() {
+
         final boolean isLiveModeOn = studio_.live().isLiveModeOn();
         if (isLiveModeOn) {
             studio_.live().setLiveModeOn(false);
@@ -497,20 +489,16 @@ public void close() {
 //            }
 //        }
 
-
-
         // No more instructions (i.e. AcquisitionEvents); tell the acquisition to initiate shutdown
         // once everything finishes
         currentAcquisition_.finish();
 
-
         currentAcquisition_.waitForCompletion();
 
         // cleanup
         studio_.logs().logMessage("diSPIM plugin acquisition " +
                 " took: " + (System.currentTimeMillis() - acqButtonStart) + "ms");
 
-
         // clean up controller settings after acquisition
         // want to do this, even with demo cameras, so we can test everything else
         // TODO: figure out if we really want to return piezos to 0 position (maybe center position,
@@ -542,6 +530,12 @@ public void close() {
 
     @Override
     boolean finish() {
+
+        // start polling for navigation panel
+        if (isPolling_) {
+            studio_.logs().logMessage("started position polling after acquisition");
+            model_.positions().startPolling();
+        }
         return true;
     }
 

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

@@ -40,6 +40,7 @@
 
 import javax.swing.JLabel;
 import java.awt.geom.Point2D;
+import java.io.File;
 import java.io.IOException;
 import java.util.ArrayList;
 
@@ -230,11 +231,26 @@ boolean run() {
 
         updateAcquisitionSettings();
 
-        studio_.logs().logMessage("Starting Acquisition with settings:\n" + acqSettings_.toPrettyJson());
+        final String settingsJson = acqSettings_.toPrettyJson();
+        studio_.logs().logMessage("Starting Acquisition with settings:\n" + settingsJson);
 
         String saveDir = acqSettings_.saveDirectory();
         String saveName = acqSettings_.saveNamePrefix();
 
+        // TODO: put this in AcquisitionEngine base class, between setup and run once structure is better
+        // save settings as JSON to the save directory
+        FileUtils.writeStringToFile(saveDir + File.separator + "acq_settings.json", settingsJson);
+        final PositionList positionList = model_.studio().positions().getPositionList();
+        if (positionList.getNumberOfPositions() > 0) {
+            try {
+                final String path = saveDir + File.separator + "position_list.pos";
+                positionList.save(path);
+                model_.studio().logs().logMessage("Position list saved to " + path);
+            } catch (Exception e) {
+                model_.studio().logs().logError(e, "Could not save position list.");
+            }
+        }
+
         // This sets the preferred save mode for DefaultDatastore, this value
         // is used in the MMAcquisition constructor to set the Storage object.
         if (acqSettings_.saveMode() == DataStorage.SaveMode.ND_TIFF) {
@@ -550,26 +566,15 @@ public void close() {
             }
             cameraNames = cameraDeviceNames.toArray(new String[0]);
         } else {
-            // TODO(Brandon): account for > 2 simultaneous cameras
             final DeviceAdapter adapter = model_.devices().adapter();
             if (adapter.numSimultaneousCameras() > 1 && adapter.numImagingPaths() == 1) {
-               // multiple simultaneous cameras
-                //if (model_.acquisitions().settings().isUsingSimultaneousCameras()) {
-                if (true) {
-                    // use 2 cameras
-                    final ArrayList<String> names = new ArrayList<>();
-                    final CameraBase[] cameraList = model_.devices().imagingCameras();
-                    for (CameraBase camera: cameraList) {
-                        names.add(camera.getDeviceName());
-                    }
-                    cameraNames = names.toArray(String[]::new);
-                } else {
-                    // use 1 camera
-                    final String camera = "ImagingCamera1"; // model_.acquisitions().settings().primaryCamera();
-                    cameraNames = new String[] {
-                            model_.devices().device(camera).getDeviceName(),
-                    };
+                // multiple simultaneous cameras
+                final ArrayList<String> names = new ArrayList<>();
+                final CameraBase[] cameraList = model_.devices().imagingCameras();
+                for (CameraBase camera: cameraList) {
+                    names.add(camera.getDeviceName());
                 }
+                cameraNames = names.toArray(String[]::new);
             } else {
                // standard camera setup
                if (acqSettings_.volume().numViews() > 1) {