Merge pull request #201 from bls337/main

slicesPerVolume should be slicesPerView
micro-manager · Oct 13, 2023 · 28b42fc · 28b42fc
2 parents 127faaa + 2bd2984
commit 28b42fc
Show file tree

Hide file tree

Showing 5 changed files with 24 additions and 9 deletions.
diff --git a/src/main/java/org/micromanager/lightsheetmanager/api/VolumeSettings.java b/src/main/java/org/micromanager/lightsheetmanager/api/VolumeSettings.java
@@ -30,7 +30,7 @@ interface Builder {
          */
         Builder delayBeforeView(final double viewDelayMs);
 
-        Builder slicesPerVolume(final int n);
+        Builder slicesPerView(final int n);
 
         Builder sliceStepSize(final double um);
 

diff --git a/src/main/java/org/micromanager/lightsheetmanager/api/internal/DefaultVolumeSettings.java b/src/main/java/org/micromanager/lightsheetmanager/api/internal/DefaultVolumeSettings.java
@@ -68,7 +68,7 @@ public VolumeSettings.Builder delayBeforeView(final double viewDelayMs) {
         }
 
         @Override
-        public VolumeSettings.Builder slicesPerVolume(final int n) {
+        public VolumeSettings.Builder slicesPerView(final int n) {
             slicesPerView_ = n;
             return this;
         }

diff --git a/...ain/java/org/micromanager/lightsheetmanager/gui/tabs/acquisition/VolumeSettingsPanel.java b/...ain/java/org/micromanager/lightsheetmanager/gui/tabs/acquisition/VolumeSettingsPanel.java
@@ -118,7 +118,7 @@ private void createEventHandlers() {
 
         spnNumSlices_.registerListener(e -> {
             model_.acquisitions().settingsBuilder().volumeSettingsBuilder()
-                    .slicesPerVolume(spnNumSlices_.getInt());
+                    .slicesPerView(spnNumSlices_.getInt());
         });
 
         spnSliceStepSize_.registerListener(e -> {

diff --git a/src/main/java/org/micromanager/lightsheetmanager/model/XYZGrid.java b/src/main/java/org/micromanager/lightsheetmanager/model/XYZGrid.java
@@ -106,7 +106,7 @@ public void computeGrid() {
             // TODO: update GUI with values, aliases for asb and vsb?
             final double speedFactor = GeometryUtils.DISPIM.getStageGeometricSpeedFactor(true);
             model_.acquisitions().settingsBuilder().volumeSettingsBuilder().sliceStepSize(Math.abs(deltaX_)/speedFactor);
-            model_.acquisitions().settingsBuilder().volumeSettingsBuilder().slicesPerVolume(numX);
+            model_.acquisitions().settingsBuilder().volumeSettingsBuilder().slicesPerView(numX);
             // move to X center if we aren't generating a position list with it
             if (!useY_ && !useZ_) {
                 xyStage.setXYPosition(centerX, xyStage.getXYPosition().y); // TODO: make convenience method?

diff --git a/...in/java/org/micromanager/lightsheetmanager/model/acquisitions/AcquisitionEngineSCAPE.java b/...in/java/org/micromanager/lightsheetmanager/model/acquisitions/AcquisitionEngineSCAPE.java
@@ -16,7 +16,6 @@
 import org.micromanager.data.internal.DefaultSummaryMetadata;
 import org.micromanager.data.internal.ndtiff.NDTiffAdapter;
 import org.micromanager.internal.MMStudio;
-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;
@@ -653,16 +652,32 @@ private boolean doHardwareCalculations(PLogicSCAPE plc) {
                     && (timepointIntervalMs < timepointDuration*1.2)) {
                 //acqSettings_.setHardwareTimesPoints(false);
                 asb_.useHardwareTimePoints(false);
-                // TODO: WARNING
+                // TODO: uncomment when working
+//                studio_.logs().showError("Time point interval may not be sufficient "
+//                        + "depending on actual time required to change positions. "
+//                        + "Proceed at your own risk.");
             }
         }
 
-        // TODO: make sure position updater is turned off!
+//        if (acqSettings_.isUsingHardwareTimePoints()) {
+//            final int numTimePoints = acqSettings_.numTimePoints();
+//            final int numChannels = acqSettings_.numChannels();
+//            final int slicePerView = acqSettings_.volumeSettings().slicesPerView();
+//            // in hardwareTimepoints case we trigger controller once for all timepoints => need to
+//            //   adjust number of frames we expect back from the camera during MM's SequenceAcquisition
+//            if (acqSettings_.cameraMode() == CameraMode.OVERLAP) {
+//                // For overlap mode we are send one extra trigger per channel per side for volume-switching (both PLogic and not)
+//                // This holds for all multichannel modes, just the order in which the extra trigger comes varies
+//                // Very last trigger won't ever return a frame so subtract 1.
+//                final int hardwareSlicesPerView = (slicePerView + 1) * numChannels * numTimePoints;
+//                asb_.volumeSettingsBuilder().slicesPerView(hardwareSlicesPerView - 1);
+//            } else {
+//                asb_.volumeSettingsBuilder().slicesPerView(slicePerView * numTimePoints);
+//            }
+//        }
 
-        // FIXME: what is happening here? getting timing error
         double sliceDuration = asb_.timingSettingsBuilder().sliceDuration();
         if (exposureTime + cameraReadoutTime > sliceDuration) {
-            //System.out.println(sliceDuration);
             // should only possible to mess this up using advanced timing settings
             // or if there are errors in our own calculations
             studio_.logs().showError("Exposure time of " + exposureTime +