Merge pull request #256 from bls337/main

switch to scape settings as default for now
micro-manager · Mar 14, 2024 · e3027a7 · e3027a7
2 parents 36ea964 + 9905cf3
commit e3027a7
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Showing 17 changed files with 102 additions and 105 deletions.
diff --git a/src/main/java/org/micromanager/lightsheetmanager/gui/tabs/AcquisitionTab.java b/src/main/java/org/micromanager/lightsheetmanager/gui/tabs/AcquisitionTab.java
@@ -6,6 +6,7 @@
 import javax.swing.SwingUtilities;
 import org.micromanager.Studio;
 import org.micromanager.lightsheetmanager.api.internal.DefaultAcquisitionSettingsDISPIM;
+import org.micromanager.lightsheetmanager.api.internal.DefaultAcquisitionSettingsSCAPE;
 import org.micromanager.lightsheetmanager.gui.components.ListeningPanel;
 import org.micromanager.lightsheetmanager.gui.data.Icons;
 import org.micromanager.lightsheetmanager.gui.tabs.acquisition.AdvancedTimingPanel;
@@ -81,7 +82,7 @@ public AcquisitionTab(final LightSheetManagerModel model) {
 
     private void createUserInterface() {
 
-        final DefaultAcquisitionSettingsDISPIM acqSettings =
+        final DefaultAcquisitionSettingsSCAPE acqSettings =
                 model_.acquisitions().settings();
 
         Panel.setMigLayoutDefault(

diff --git a/src/main/java/org/micromanager/lightsheetmanager/gui/tabs/AutofocusTab.java b/src/main/java/org/micromanager/lightsheetmanager/gui/tabs/AutofocusTab.java
@@ -3,7 +3,7 @@
 import org.micromanager.lightsheetmanager.api.data.AutofocusFitType;
 import org.micromanager.lightsheetmanager.api.data.AutofocusMode;
 import org.micromanager.lightsheetmanager.api.data.AutofocusType;
-import org.micromanager.lightsheetmanager.api.internal.DefaultAcquisitionSettingsDISPIM;
+import org.micromanager.lightsheetmanager.api.internal.DefaultAcquisitionSettingsSCAPE;
 import org.micromanager.lightsheetmanager.gui.components.CheckBox;
 import org.micromanager.lightsheetmanager.gui.components.ComboBox;
 import org.micromanager.lightsheetmanager.gui.components.Label;
@@ -52,7 +52,7 @@ public AutofocusTab(final LightSheetManagerModel model) {
     }
 
     public void createUserInterface() {
-        final DefaultAcquisitionSettingsDISPIM acqSettings =
+        final DefaultAcquisitionSettingsSCAPE acqSettings =
                 model_.acquisitions().settings();
 
         final Label lblTitle = new Label("Autofocus Settings", Font.BOLD, 18);

diff --git a/src/main/java/org/micromanager/lightsheetmanager/gui/tabs/DataTab.java b/src/main/java/org/micromanager/lightsheetmanager/gui/tabs/DataTab.java
@@ -5,7 +5,7 @@
 import java.util.EventObject;
 
 import org.micromanager.internal.utils.FileDialogs;
-import org.micromanager.lightsheetmanager.api.internal.DefaultAcquisitionSettingsDISPIM;
+import org.micromanager.lightsheetmanager.api.internal.DefaultAcquisitionSettingsSCAPE;
 import org.micromanager.lightsheetmanager.gui.LightSheetManagerFrame;
 import org.micromanager.lightsheetmanager.gui.components.*;
 import org.micromanager.lightsheetmanager.gui.components.Button;
@@ -54,7 +54,7 @@ private void createUserInterface() {
         final Label lblTitle = new Label("Data Settings", Font.BOLD, 18);
 
 
-        final DefaultAcquisitionSettingsDISPIM acqSettings =
+        final DefaultAcquisitionSettingsSCAPE acqSettings =
                 model_.acquisitions().settings();
 
         final Panel pnlSave = new Panel("Image Save Settings");

diff --git a/src/main/java/org/micromanager/lightsheetmanager/gui/tabs/SettingsTab.java b/src/main/java/org/micromanager/lightsheetmanager/gui/tabs/SettingsTab.java
@@ -1,6 +1,6 @@
 package org.micromanager.lightsheetmanager.gui.tabs;
 
-import org.micromanager.lightsheetmanager.api.internal.DefaultAcquisitionSettingsDISPIM;
+import org.micromanager.lightsheetmanager.api.internal.DefaultAcquisitionSettingsSCAPE;
 import org.micromanager.lightsheetmanager.gui.components.CheckBox;
 import org.micromanager.lightsheetmanager.gui.components.ListeningPanel;
 import org.micromanager.lightsheetmanager.gui.components.Panel;
@@ -41,7 +41,7 @@ public SettingsTab(final LightSheetManagerModel model) {
     }
 
     private void createUserInterface() {
-        final DefaultAcquisitionSettingsDISPIM acqSettings =
+        final DefaultAcquisitionSettingsSCAPE acqSettings =
                 model_.acquisitions().settings();
 
         isUsingPLogic_ = model_.devices().isUsingPLogic();

diff --git a/...main/java/org/micromanager/lightsheetmanager/gui/tabs/acquisition/MultiPositionPanel.java b/...main/java/org/micromanager/lightsheetmanager/gui/tabs/acquisition/MultiPositionPanel.java
@@ -1,6 +1,6 @@
 package org.micromanager.lightsheetmanager.gui.tabs.acquisition;
 
-import org.micromanager.lightsheetmanager.api.internal.DefaultAcquisitionSettingsDISPIM;
+import org.micromanager.lightsheetmanager.api.internal.DefaultAcquisitionSettingsSCAPE;
 import org.micromanager.lightsheetmanager.gui.components.Button;
 import org.micromanager.lightsheetmanager.gui.components.CheckBox;
 import org.micromanager.lightsheetmanager.gui.components.Label;
@@ -30,7 +30,7 @@ public MultiPositionPanel(final LightSheetManagerModel model, final CheckBox cbx
     }
 
     private void createUserInterface() {
-        final DefaultAcquisitionSettingsDISPIM acqSettings =
+        final DefaultAcquisitionSettingsSCAPE acqSettings =
                 model_.acquisitions().settings();
 
         Spinner.setDefaultSize(7);

diff --git a/src/main/java/org/micromanager/lightsheetmanager/gui/tabs/acquisition/TimePointsPanel.java b/src/main/java/org/micromanager/lightsheetmanager/gui/tabs/acquisition/TimePointsPanel.java
@@ -1,6 +1,6 @@
 package org.micromanager.lightsheetmanager.gui.tabs.acquisition;
 
-import org.micromanager.lightsheetmanager.api.internal.DefaultAcquisitionSettingsDISPIM;
+import org.micromanager.lightsheetmanager.api.internal.DefaultAcquisitionSettingsSCAPE;
 import org.micromanager.lightsheetmanager.gui.components.CheckBox;
 import org.micromanager.lightsheetmanager.gui.components.Label;
 import org.micromanager.lightsheetmanager.gui.components.Panel;
@@ -26,7 +26,7 @@ public TimePointsPanel(final LightSheetManagerModel model, final CheckBox cbxUse
     }
 
     private void createUserInterface() {
-        final DefaultAcquisitionSettingsDISPIM acqSettings =
+        final DefaultAcquisitionSettingsSCAPE acqSettings =
                 model_.acquisitions().settings();
 
         setMigLayout(

diff --git a/src/main/java/org/micromanager/lightsheetmanager/gui/tabs/setup/BeamSheetControlPanel.java b/src/main/java/org/micromanager/lightsheetmanager/gui/tabs/setup/BeamSheetControlPanel.java
@@ -2,7 +2,7 @@
 
 import org.micromanager.lightsheetmanager.api.data.CameraMode;
 import org.micromanager.lightsheetmanager.api.data.GeometryType;
-import org.micromanager.lightsheetmanager.api.internal.DefaultAcquisitionSettingsDISPIM;
+import org.micromanager.lightsheetmanager.api.internal.DefaultAcquisitionSettingsSCAPE;
 import org.micromanager.lightsheetmanager.gui.components.Button;
 import org.micromanager.lightsheetmanager.gui.components.CheckBox;
 import org.micromanager.lightsheetmanager.gui.components.Panel;
@@ -66,7 +66,7 @@ private void createUserInterface() {
         final GeometryType geometryType = model_.devices()
                 .getDeviceAdapter().getMicroscopeGeometry();
 
-        final DefaultAcquisitionSettingsDISPIM acqSettings = model_.acquisitions()
+        final DefaultAcquisitionSettingsSCAPE acqSettings = model_.acquisitions()
                 .settings();
 
         pnlFirst_ = new Panel();

diff --git a/src/main/java/org/micromanager/lightsheetmanager/gui/tabs/setup/PiezoCalibrationPanel.java b/src/main/java/org/micromanager/lightsheetmanager/gui/tabs/setup/PiezoCalibrationPanel.java
@@ -2,7 +2,7 @@
 
 
 import org.micromanager.lightsheetmanager.api.data.GeometryType;
-import org.micromanager.lightsheetmanager.api.internal.DefaultAcquisitionSettingsDISPIM;
+import org.micromanager.lightsheetmanager.api.internal.DefaultAcquisitionSettingsSCAPE;
 import org.micromanager.lightsheetmanager.gui.data.Icons;
 import org.micromanager.lightsheetmanager.gui.components.Button;
 import org.micromanager.lightsheetmanager.gui.components.Panel;
@@ -76,7 +76,7 @@ private void createUserInterface() {
         }
         btnRunAutofocus_ = new Button("Run Autofocus", 120, 26);
 
-        final DefaultAcquisitionSettingsDISPIM acqSettings =
+        final DefaultAcquisitionSettingsSCAPE acqSettings =
                 model_.acquisitions().settings();
 
         txtSlope_ = new TextField(7);

diff --git a/src/main/java/org/micromanager/lightsheetmanager/model/LightSheetManagerModel.java b/src/main/java/org/micromanager/lightsheetmanager/model/LightSheetManagerModel.java
@@ -9,6 +9,7 @@
 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;

diff --git a/src/main/java/org/micromanager/lightsheetmanager/model/PLogicDISPIM.java b/src/main/java/org/micromanager/lightsheetmanager/model/PLogicDISPIM.java
@@ -77,7 +77,10 @@ public PLogicDISPIM(final LightSheetManagerModel model) {
         devices_ = model_.devices();
         core_ = studio_.core();
 
-        acqSettings_ = model_.acquisitions().settings();
+
+        // TODO: remove this when a more generic method is available and get from model
+        //acqSettings_ = model_.acquisitions().settings();
+        acqSettings_ = new DefaultAcquisitionSettingsDISPIM.Builder().build();
 
         scanDistance_ = 0;
         actualStepSizeUm_ = 0;

diff --git a/src/main/java/org/micromanager/lightsheetmanager/model/PLogicSCAPE.java b/src/main/java/org/micromanager/lightsheetmanager/model/PLogicSCAPE.java
@@ -3,12 +3,11 @@
 import mmcorej.CMMCore;
 import mmcorej.Configuration;
 import org.micromanager.Studio;
-import org.micromanager.lightsheetmanager.api.AcquisitionSettingsDISPIM;
 import org.micromanager.lightsheetmanager.api.data.AcquisitionMode;
 import org.micromanager.lightsheetmanager.api.data.CameraMode;
 import org.micromanager.lightsheetmanager.api.data.GeometryType;
 import org.micromanager.lightsheetmanager.api.data.MultiChannelMode;
-import org.micromanager.lightsheetmanager.api.internal.DefaultAcquisitionSettingsDISPIM;
+import org.micromanager.lightsheetmanager.api.internal.DefaultAcquisitionSettingsSCAPE;
 import org.micromanager.lightsheetmanager.api.internal.DefaultTimingSettings;
 import org.micromanager.lightsheetmanager.model.channels.ChannelSpec;
 import org.micromanager.lightsheetmanager.model.devices.cameras.CameraBase;
@@ -57,7 +56,7 @@ public class PLogicSCAPE {
     private static final int triggerSPIMAddr = 46;  // backplane signal, same as XY card's TTL output
     private static final int laserTriggerAddress = 10;  // this should be set to (42 || 8) = (TTL1 || manual laser on)
 
-    private final DefaultAcquisitionSettingsDISPIM acqSettings_;
+    private final DefaultAcquisitionSettingsSCAPE acqSettings_;
 
     private final LightSheetManagerModel model_;
 
@@ -93,7 +92,7 @@ public PLogicSCAPE(final LightSheetManagerModel model) {
      * @return
      */
     public boolean prepareControllerForAcquisitionOffsetOnly(
-            final DefaultAcquisitionSettingsDISPIM settings,
+            final DefaultAcquisitionSettingsSCAPE settings,
             final double channelOffset) {
 
         final int numViews = settings.volumeSettings().numViews();
@@ -264,7 +263,7 @@ public boolean prepareControllerForAcquisitionOffsetOnly(
 //    }
 
     public boolean prepareControllerForAcquisitionSCAPE(
-            final DefaultAcquisitionSettingsDISPIM settings,
+            final DefaultAcquisitionSettingsSCAPE settings,
             final double channelOffset) {
         // turn off beam and scan on both sides (they are turned off by SPIM state machine anyway)
         // also ensures that properties match reality at end of acquisition
@@ -317,7 +316,7 @@ public boolean prepareControllerForAcquisitionSCAPE(
     }
 
     // Compute appropriate motor speed in mm/s for the given stage scanning settings
-    public double computeScanSpeed(DefaultAcquisitionSettingsDISPIM settings, final int numScansPerSlice) {
+    public double computeScanSpeed(DefaultAcquisitionSettingsSCAPE settings, final int numScansPerSlice) {
         //double sliceDuration = settings.timingSettings().sliceDuration();
         //double sliceDuration = 0.0; // TODO: get from SliceTiming
         double sliceDuration = getSliceDuration(settings.timingSettings(), numScansPerSlice); // TODO: ???
@@ -333,7 +332,7 @@ public double computeScanSpeed(DefaultAcquisitionSettingsDISPIM settings, final
     }
 
     // compute how many channels we do in each one-way scan
-    private int computeScanChannelsPerPass(DefaultAcquisitionSettingsDISPIM settings) {
+    private int computeScanChannelsPerPass(DefaultAcquisitionSettingsSCAPE settings) {
         return settings.channelMode() == MultiChannelMode.SLICE_HW ? settings.numChannels() : 1;
     }
 
@@ -343,7 +342,7 @@ private int computeScanChannelsPerPass(DefaultAcquisitionSettingsDISPIM settings
      * @param motorSpeed
      * @return
      */
-    public double computeScanAcceleration(final double motorSpeed, DefaultAcquisitionSettingsDISPIM settings) {
+    public double computeScanAcceleration(final double motorSpeed, DefaultAcquisitionSettingsSCAPE settings) {
         return (10 + 100 * (motorSpeed / xyStage_.getMaxSpeedX())) * settings.scanSettings().scanAccelerationFactor();
     }
 
@@ -376,7 +375,7 @@ public double computeScanAcceleration(final double motorSpeed, final double maxM
         return (10 + 100 * (motorSpeed / maxMotorSpeed)) * stageScanAccelFactor;
     }
 
-    public boolean prepareStageScanForAcquisition(final double x, final double y, DefaultAcquisitionSettingsDISPIM settings) {
+    public boolean prepareStageScanForAcquisition(final double x, final double y, DefaultAcquisitionSettingsSCAPE settings) {
         final boolean scanFromCurrent = settings.scanSettings().scanFromCurrentPosition();
         final boolean scanNegative = settings.scanSettings().scanFromNegativeDirection();
         double xStartUm;
@@ -415,7 +414,7 @@ public boolean prepareStageScanForAcquisition(final double x, final double y, De
      * @param centerPiezos true to move piezos to center position
      * @return false if there is a fatal error, true if successful
      */
-    public boolean cleanUpControllerAfterAcquisition(final DefaultAcquisitionSettingsDISPIM settings, final boolean centerPiezos) {
+    public boolean cleanUpControllerAfterAcquisition(final DefaultAcquisitionSettingsSCAPE settings, final boolean centerPiezos) {
         // clear "acquisition running" flag on PLC
         plcCamera_.setPreset(2);
         plcLaser_.setPreset(2);
@@ -447,7 +446,7 @@ public boolean cleanUpControllerAfterAcquisition(final DefaultAcquisitionSetting
     }
 
     public boolean prepareControllerForAcquisitionSide(
-            final AcquisitionSettingsDISPIM settings,
+            final DefaultAcquisitionSettingsSCAPE settings,
             final int view,
             final double channelOffset,
             final boolean offsetOnly) {
@@ -686,7 +685,7 @@ private boolean cleanUpControllerAfterAcquisitionSide(
         return true;
     }
 
-    public boolean setupHardwareChannelSwitching(final DefaultAcquisitionSettingsDISPIM settings) {
+    public boolean setupHardwareChannelSwitching(final DefaultAcquisitionSettingsSCAPE settings) {
 
         MultiChannelMode channelMode = settings.channelMode();
 

diff --git a/src/main/java/org/micromanager/lightsheetmanager/model/UserSettings.java b/src/main/java/org/micromanager/lightsheetmanager/model/UserSettings.java
@@ -4,7 +4,7 @@
 import mmcorej.org.json.JSONObject;
 import org.micromanager.UserProfile;
 import org.micromanager.lightsheetmanager.api.data.GeometryType;
-import org.micromanager.lightsheetmanager.api.internal.DefaultAcquisitionSettingsDISPIM;
+import org.micromanager.lightsheetmanager.api.internal.DefaultAcquisitionSettingsSCAPE;
 import org.micromanager.propertymap.MutablePropertyMapView;
 
 import java.util.Iterator;
@@ -77,8 +77,8 @@ public void load() {
             JSONObject loadedJson = validateUserSettings(json);
             if (loadedJson != null) {
                 // TODO: switch this based on microscope geometry type
-                DefaultAcquisitionSettingsDISPIM acqSettings = DefaultAcquisitionSettingsDISPIM.fromJson(
-                        loadedJson.toString(), DefaultAcquisitionSettingsDISPIM.class);
+                DefaultAcquisitionSettingsSCAPE acqSettings = DefaultAcquisitionSettingsSCAPE.fromJson(
+                        loadedJson.toString(), DefaultAcquisitionSettingsSCAPE.class);
                 model_.acquisitions().setAcquisitionSettings(acqSettings);
                 //System.out.println("loadedJson: " + loadedJson);
             }
@@ -115,7 +115,7 @@ public void save() {
     private JSONObject validateUserSettings(final String loadedSettings) {
         // get default settings from builder
         final String defaultSettings =
-                new DefaultAcquisitionSettingsDISPIM.Builder().build().toJson();
+                new DefaultAcquisitionSettingsSCAPE.Builder().build().toJson();
         // validate json strings and count the number of keys
         int numLoadedKeys, numDefaultKeys;
         JSONObject loadedJson, defaultJson;

diff --git a/src/main/java/org/micromanager/lightsheetmanager/model/acquisitions/AcquisitionEngine.java b/src/main/java/org/micromanager/lightsheetmanager/model/acquisitions/AcquisitionEngine.java
@@ -17,6 +17,7 @@
 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;
 import org.micromanager.lightsheetmanager.model.DataStorage;
@@ -35,8 +36,8 @@ public abstract class AcquisitionEngine implements AcquisitionManager, MMAcquist
     protected final Studio studio_;
     protected final CMMCore core_;
 
-    protected DefaultAcquisitionSettingsDISPIM.Builder asb_;
-    protected DefaultAcquisitionSettingsDISPIM acqSettings_;
+    protected DefaultAcquisitionSettingsSCAPE.Builder asb_;
+    protected DefaultAcquisitionSettingsSCAPE acqSettings_;
 
     private final ExecutorService acquisitionExecutor_ = Executors.newSingleThreadExecutor(
             r -> new Thread(r, "Acquisition Thread"));
@@ -64,7 +65,7 @@ public AcquisitionEngine(final LightSheetManagerModel model) {
         autofocusRunner_ = new AutofocusRunner(model_);
 
         // default settings
-        asb_ = new DefaultAcquisitionSettingsDISPIM.Builder();
+        asb_ = new DefaultAcquisitionSettingsSCAPE.Builder();
         acqSettings_ = asb_.build();
     }
 
@@ -88,8 +89,8 @@ public void setFrame(final LightSheetManagerFrame frame) {
      *
      * @param acqSettings the acquisition settings to set
      */
-    public void setAcquisitionSettings(final DefaultAcquisitionSettingsDISPIM acqSettings) {
-        asb_ = new DefaultAcquisitionSettingsDISPIM.Builder(acqSettings);
+    public void setAcquisitionSettings(final DefaultAcquisitionSettingsSCAPE acqSettings) {
+        asb_ = new DefaultAcquisitionSettingsSCAPE.Builder(acqSettings);
         acqSettings_ = acqSettings;
     }
 
@@ -232,15 +233,15 @@ protected DefaultSummaryMetadata addMMSummaryMetadata(JSONObject summaryMetadata
 
     // TODO: keep long method name versions or just use aliases?
 
-    public DefaultAcquisitionSettingsDISPIM settings() {
+    public DefaultAcquisitionSettingsSCAPE settings() {
         return acqSettings_;
     }
 //
 //    public DefaultAcquisitionSettingsDISPIM getAcquisitionSettings() {
 //        return acqSettings_;
 //    }
 //
-    public DefaultAcquisitionSettingsDISPIM.Builder settingsBuilder() {
+    public DefaultAcquisitionSettingsSCAPE.Builder settingsBuilder() {
         return asb_;
     }
 //