Fix hardware channel switching, multi-position time points, and channel coordinates

src/main/java/org/micromanager/lightsheetmanager/gui/components/TextField.java

@@ -67,6 +67,17 @@ public void changedUpdate(DocumentEvent e) {
         getDocument().addDocumentListener(docListener);
     }
 
+    /**
+     * Marks the field valid or invalid by setting its background color.
+     * <p>
+     * The caller decides what valid means and owns any tooltip explaining it.
+     *
+     * @param isValid {@code false} to show the error color
+     */
+    public void setValid(final boolean isValid) {
+        setBackground(isValid ? defaultColor_ : ERROR_COLOR);
+    }
+
     /**
      * Returns {@code true} if the filename is valid on Windows.
      *

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

@@ -97,7 +97,7 @@ public void createUserInterface() {
         txtSaveDirectory_ = new TextField();
         txtSaveDirectory_.setEditable(false);
         txtSaveDirectory_.setColumns(18);
-        txtSaveDirectory_.setForeground(Color.BLACK);
+        txtSaveDirectory_.setForeground(Color.WHITE);
         txtSaveDirectory_.setText(acqSettings.saveDirectory());
 
         txtSaveFileName_ = new TextField();
@@ -118,6 +118,7 @@ public void createUserInterface() {
         btnLoadSettings_ = new Button("Load", 60, 20);
         btnConvertSettings_ = new Button("Convert", 72, 20);
 
+        txtSaveDirectory_.setToolTipText("The directory to save images to.");
         btnBrowse_.setToolTipText("Select the save directory with the file browser.");
         btnOpen_.setToolTipText("Open the file explorer to the save directory.");
         btnSaveSettings_.setToolTipText("Save the current acquisition settings to JSON.");
@@ -149,9 +150,13 @@ public void createEventHandlers() {
             if (result != null) {
                 model_.acquisitions().settingsBuilder().saveDirectory(result.toString());
                 txtSaveDirectory_.setText(result.toString());
+                validateSaveDirectory();
             }
         });
 
+        // flag a saved directory that no longer exists as soon as the plugin opens
+        validateSaveDirectory();
+
         // use the text field so we don't need to update settings
         btnOpen_.registerListener(
                 () -> openDirectory(txtSaveDirectory_.getText()));
@@ -214,6 +219,31 @@ public void createEventHandlers() {
         });
     }
 
+    // Colors the save directory field and explains why in its tooltip when the path is unusable.
+    // Only called where the value arrives from outside the field (plugin load, browse, settings
+    // change); this touches the filesystem, and checking a dead network path can block the EDT.
+    private void validateSaveDirectory() {
+        final String path = txtSaveDirectory_.getText();
+        final String problem;
+        if (path == null || path.trim().isEmpty()) {
+            problem = "The save directory is not set.";
+        } else {
+            final File directory = new File(path);
+            if (!directory.exists()) {
+                problem = "This directory does not exist: " + path;
+            } else if (!directory.isDirectory()) {
+                problem = "This is a file, not a directory: " + path;
+            } else if (!directory.canWrite()) {
+                problem = "This directory is not writable: " + path;
+            } else {
+                problem = null;
+            }
+        }
+        txtSaveDirectory_.setValid(problem == null);
+        txtSaveDirectory_.setToolTipText(
+                problem == null ? "The directory to save images to." : problem);
+    }
+
     // Opens the file explorer to the save directory
     private void openDirectory(final String path) {
         final File directory = new File(path);
@@ -223,21 +253,22 @@ private void openDirectory(final String path) {
                 try {
                     desktop.open(directory);
                 } catch (IOException e) {
-                    model_.studio().logs().logError(
-                            "Could not open the save directory.");
+                    model_.studio().logs().showError(
+                            "Could not open the save directory:\n\n" + path);
                 }
             } else {
-                model_.studio().logs().logError(
-                        "Desktop is not supported on this platform.");
+                model_.studio().logs().showError(
+                        "Opening a file explorer is not supported on this platform.");
             }
         } else {
-            model_.studio().logs().logError("Directory does not exist.");
+            model_.studio().logs().showError("The save directory does not exist:\n\n" + path);
         }
     }
 
     @Override
     public void onSettingsChanged(final AcquisitionSettings settings) {
         txtSaveDirectory_.setText(settings.saveDirectory());
+        validateSaveDirectory();
         txtSaveFileName_.setText(settings.saveNamePrefix());
         cbxSaveMode_.setSelected(settings.saveMode());
         cbxSaveWhileAcquiring_.setSelected(settings.isSavingImagesDuringAcquisition());

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

@@ -484,9 +484,9 @@ public boolean prepareControllerForAcquisitionSide(
         // The galvo/sheet offset must always land on the true imaging plane. For a stage scan the
         // piezo convention parks piezoCenter at home (~0); using that here would place the sheet on
         // the home plane instead of the imaging center, so the acquired volume is offset from the
-        // stage sweep -- the #404 "scan not centered" symptom. diSPIM 1.4 SCOPE never writes the
-        // galvo offset during a stage scan (it holds the value the Setup tab computed from the
-        // imaging center); LSM writes it at acq time, so derive it from the imaging center here.
+        // stage sweep. diSPIM 1.4 SCOPE never writes the galvo offset during a stage scan (it holds
+        // the value the Setup tab computed from the imaging center); LSM writes it at acq time, so
+        // derive it from the imaging center here.
         final double galvoCenter = settings.stageScan().enabled() ? imagingCenter : piezoCenter;
         double sliceCenter = (galvoCenter - sliceOffset) / sliceRate;
 
@@ -727,7 +727,7 @@ public boolean setupHardwareChannelSwitching(final ScapeAcquisitionSettings sett
         // 2. (newer) with 7-channel TTL-triggered on PLogic card shared with single camera trigger output (i.e. not dual-view system)
         // however they share some things like using cells 17-24 and building a 3-input LUT which code is just copy/paste right now
         final boolean isSevenChannelShutter = plcLaser_.getShutterMode() == ASIPLogic.ShutterMode.SEVEN_CHANNEL_SHUTTER;
-        final boolean isSevenChannelShutterTTL = plcLaser_.getShutterMode() == ASIPLogic.ShutterMode.SEVEN_CHANNEL_SHUTTER;
+        final boolean isSevenChannelShutterTTL = plcLaser_.getShutterMode() == ASIPLogic.ShutterMode.SEVEN_CHANNEL_TTL_SHUTTER;
 
         if (isSevenChannelShutter) {
             // original special 7-channel case

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

@@ -24,6 +24,7 @@
 import org.micromanager.lightsheetmanager.model.channels.ChannelSpec;
 import org.micromanager.lightsheetmanager.model.devices.cameras.CameraBase;
 
+import java.io.File;
 import java.util.ArrayList;
 import java.util.List;
 import java.util.Objects;
@@ -56,6 +57,64 @@ public abstract class AcquisitionEngine implements AcquisitionManager, MMAcquist
 
     protected final LightSheetManager model_;
 
+    /**
+     * Validates that the acquisition can actually be written to disk, before anything is acquired.
+     * <p>
+     * The images are written by {@code finish()}, i.e. only AFTER the run completes, so without this
+     * check an unusable save location is discovered at the very end and the data is lost. Observed
+     * 2026-07-27: a 41 s dual-camera run ended in "could not save the acquisition data to:
+     * D:\SCOPE\test\Test" because {@code D:\SCOPE\test} did not exist. The same path also silently
+     * drops {@code acq_settings.json} and {@code position_list.pos}, which are written up front.
+     * <p>
+     * Called from both geometry engines' {@code setup()} before any hardware is touched, so a failure
+     * costs nothing and leaves the microscope untouched.
+     *
+     * @return true if saving is off, or the save location is usable; false to abort setup
+     */
+    protected boolean validateSaveLocation() {
+        if (!acqSettings_.isSavingImagesDuringAcquisition()) {
+            return true; // not saving => nothing to validate
+        }
+
+        final String saveNamePrefix = acqSettings_.saveNamePrefix();
+        if (saveNamePrefix == null || saveNamePrefix.trim().isEmpty()) {
+            studio_.logs().showError("The save name prefix is empty.\n\n"
+                    + "Set a name on the Datastore panel, or uncheck \"Save images during acquisition\".");
+            return false;
+        }
+
+        final String saveDirectory = acqSettings_.saveDirectory();
+        if (saveDirectory == null || saveDirectory.trim().isEmpty()) {
+            studio_.logs().showError("The save directory is not set.\n\n"
+                    + "Set a directory on the Datastore panel, or uncheck "
+                    + "\"Save images during acquisition\".");
+            return false;
+        }
+
+        final File directory = new File(saveDirectory);
+        if (!directory.exists()) {
+            studio_.logs().showError("The save directory does not exist:\n\n" + saveDirectory
+                    + "\n\nCreate it, or choose another directory on the Datastore panel.");
+            return false;
+        }
+        if (!directory.isDirectory()) {
+            studio_.logs().showError("The save directory is a file, not a directory:\n\n"
+                    + saveDirectory);
+            return false;
+        }
+        // canWrite() is advisory on Windows (it reports the read-only attribute, not the ACL), so it
+        // catches the common cases without being authoritative; a real write failure still surfaces
+        // at finish(). Cheap enough to be worth keeping.
+        if (!directory.canWrite()) {
+            studio_.logs().showError("The save directory is not writable:\n\n" + saveDirectory);
+            return false;
+        }
+
+        studio_.logs().logMessage("save location validated: " + saveDirectory
+                + File.separator + saveNamePrefix);
+        return true;
+    }
+
     public AcquisitionEngine(final LightSheetManager model) {
         model_ = Objects.requireNonNull(model);
         studio_ = model.studio();
@@ -146,7 +205,9 @@ public Future<?> requestRun(boolean speedTest) {
 
                 try {
                     if (!setup()) {
-                        studio_.logs().showError("Error during setup!");
+                        // every setup() failure path already showed its own specific error,
+                        // so log this rather than stacking a second dialog on top of it
+                        studio_.logs().logMessage("Error during setup!");
                         return; // early exit => stop acquisition
                     }
                 } catch (Exception e) {

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

@@ -65,6 +65,12 @@ boolean setup() {
         // make settings current
         updateSettings();
 
+        // fail before touching any hardware: the datastore is written by finish(), so an unusable
+        // save location would otherwise cost a full acquisition before it is discovered
+        if (!validateSaveLocation()) {
+            return false; // early exit => save location unusable
+        }
+
         return true;
     }
 
@@ -248,7 +254,7 @@ boolean run() {
 
         ////////////  Acquisition hooks ////////////////////
         // These functions will be run on different threads during the acquisition process
-        //    Hooks will run on the Acquisition Engine thread--the one that controls all hardware
+        //    Hooks will run on the Acquisition Engine thread, the one that controls all hardware
 
         // TODO add any code that needs to be executed on the acquisition thread (i.e. the one
         //  that controls hardware)

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

@@ -81,6 +81,12 @@ boolean setup() {
         // make settings current
         updateSettings();
 
+        // fail before touching any hardware: the datastore is written by finish(), so an unusable
+        // save location would otherwise cost a full acquisition before it is discovered
+        if (!validateSaveLocation()) {
+            return false; // early exit => save location unusable
+        }
+
 //        // check pixel size
 //        if (core_.getPixelSizeUm() < 1e-6) {
 //            studio_.logs().showError(
@@ -321,7 +327,7 @@ boolean run() {
 
         ////////////  Acquisition hooks ////////////////////
         // These functions will be run on different threads during the acquisition process
-        //    Hooks will run on the Acquisition Engine thread--the one that controls all hardware
+        //    Hooks will run on the Acquisition Engine thread, the one that controls all hardware
 
         // TODO add any code that needs to be executed on the acquisition thread (i.e. the one
         //  that controls hardware)
@@ -628,7 +634,7 @@ public void close() {
                             // software "Every Volume" multichannel submits ONE event
                             // iterator PER channel, so AcqEngJ flushes a SequenceEnd between
                             // channels (Engine.java:187) and the controller re-fires once per
-                            // channel-volume -- mirroring 1.4's per-channel loop and LSM's own
+                            // channel-volume, mirroring 1.4's per-channel loop and LSM's own
                             // per-timepoint loop. Submitting all channels in a single iterator lets
                             // AcqEngJ merge identical-preset channels into one sequence that fires the
                             // controller once, collapsing the channel dimension (hang on hardware,
@@ -643,7 +649,7 @@ public void close() {
                         } else {
                             // Hardware channel modes (SLICE_HW / VOLUME_HW with hardware timepoints
                             // off): the controller emits all channels in one trigger, so a single
-                            // merged iterator is correct here -- unchanged.
+                            // merged iterator is correct here, unchanged.
                             currentAcquisition_.submitEventIterator(
                                     LightSheetEventAdapter.createChannelAcqEvents(
                                             baseEvent.copy(), acqSettings_, cameraNames, null));
@@ -959,20 +965,22 @@ private boolean doHardwareCalculations(PLogicScape plc) {
         // TODO: implement multiple positions using hardware time points, currently
         //  set hardware time points to false if using multiple positions
         if (acqSettings_.isUsingMultiplePositions()) {
-            if (acqSettings_.isUsingHardwareTimePoints()) {
+            if (isUsingHardwareTimePoints) {
 //                    || acqSettings_.numTimePoints() > 1)
 //                    && (timepointIntervalMs < timepointDuration*1.2)) {
                 asb_.useHardwareTimePoints(false);
+                isUsingHardwareTimePoints = false;
 //                studio_.logs().showError("Time point interval may not be sufficient "
 //                        + "depending on actual time required to change positions. "
 //                        + "Proceed at your own risk.");
             }
         }
 
         // only use hardware time points when use time points is checked
-        if (acqSettings_.isUsingHardwareTimePoints()) {
+        if (isUsingHardwareTimePoints) {
             if (!acqSettings_.isUsingTimePoints()) {
                 asb_.useHardwareTimePoints(false);
+                isUsingHardwareTimePoints = false;
             }
         }