Merge pull request micro-manager#1900 from nicost/acqj

Studo-AcqEngJ: ensure autofocus runs at each new XY stage position.
nicost · Feb 21, 2024 · 1cc660f · 1cc660f
2 parents 170fe24 + 6250d60
commit 1cc660f
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/...dio/src/main/java/org/micromanager/acquisition/internal/acqengjcompat/AcqEngJAdapter.java b/...dio/src/main/java/org/micromanager/acquisition/internal/acqengjcompat/AcqEngJAdapter.java
@@ -271,6 +271,8 @@ private Datastore runAcquisition(SequenceSettings sequenceSettings) {
          }
 
          // These hooks implement Autofocus
+         // TODO: does this give the correct behavior?  This should run after the XY stage
+         // reaches its new position, but before the z stage is moved from its current position
          if (sequenceSettings_.useAutofocus()) {
             currentAcquisition_.addHook(autofocusHookBefore(sequenceSettings_.skipAutofocusCount()),
                   AcquisitionAPI.BEFORE_HARDWARE_HOOK);
@@ -730,8 +732,6 @@ protected AcquisitionHook autofocusHookBefore(int skipFrames) {
          public AcquisitionEvent run(AcquisitionEvent event) {
             if (!event.isAcquisitionFinishedEvent()
                   && (event.getZIndex() == null || event.getZIndex() == 0)
-                  && (event.getAxisPosition(MDAAcqEventModules.POSITION_AXIS) == null
-                        || (Integer) event.getAxisPosition(MDAAcqEventModules.POSITION_AXIS) == 0)
                   && (event.getAxisPosition(AcqEngMetadata.CHANNEL_AXIS) == null
                         || (Integer) event.getAxisPosition(AcqEngMetadata.CHANNEL_AXIS) == 0)) {
                if (event.getTIndex() != null && skipFrames != 0