Merge pull request micro-manager#99 from henrypinkard/main

Clean up behavior related to non core-focus z drives

pom.xml

@@ -2,7 +2,7 @@
     <modelVersion>4.0.0</modelVersion>
     <groupId>org.micro-manager.acqengj</groupId>
     <artifactId>AcqEngJ</artifactId>
-    <version>0.29.3</version>
+    <version>0.30.0</version>
     <packaging>jar</packaging>
      <name>AcqEngJ</name>
     <description>Java-based Acquisition engine for Micro-Manager</description>

src/main/java/org/micromanager/acqj/main/AcqEngMetadata.java

@@ -51,6 +51,8 @@ public class AcqEngMetadata {
    public static final String X_UM_INTENDED = "XPosition_um_Intended";
    public static final String Y_UM_INTENDED = "YPosition_um_Intended";
    public static final String Z_UM_INTENDED = "ZPosition_um_Intended";
+   public static final String GENERIC_UM_INTENDED_SUFFIX = "Position_um_Intended";
+
    public static final String X_UM = "XPosition_um";
    public static final String Y_UM = "YPosition_um";
    public static final String Z_UM = "ZPosition_um";
@@ -114,37 +116,44 @@ public static void addImageMetadata(JSONObject tags, AcquisitionEvent event,
          //AcqEngMetadata.setZPositionUm(tags, Engine.getCore().getPosition());
 
 
-         //Axes (i.e. channel. z, t, or arbitray other indices)
+         //Axes (i.e. channel. z, t, or arbitrary other indices)
          AcqEngMetadata.createAxes(tags);
+         ////// Axes positions /////
+         for (String s : event.getDefinedAxes()) {
+            AcqEngMetadata.setAxisPosition(tags, s, event.getAxisPosition(s));
+         }
+
 
          /////////  XY Stage Positions (with optional support for grid layout) ////////
          if (event.getXPosition() != null && event.getYPosition() != null) {
             //infer Stage position index at acquisition time to support on the fly modification
 //            AcqEngMetadata.setPositionIndex(tags, event.acquisition_.getPositionIndexFromName(event.getXY()));
             AcqEngMetadata.setStageXIntended(tags, event.getXPosition());
             AcqEngMetadata.setStageYIntended(tags, event.getYPosition());
-
          }
+         if (event.getPositionName() != null) {
+            AcqEngMetadata.setPositionName(tags, event.getPositionName());
+         }
+
+
          if (event.getZPosition() != null) {
             AcqEngMetadata.setStageZIntended(tags, event.getZPosition());
+         } else if (event.getStageSingleAxisStagePosition(Engine.getCore().getFocusDevice()) != null) {
+            AcqEngMetadata.setStageZIntended(tags, event.getStageSingleAxisStagePosition(Engine.getCore().getFocusDevice()));
          }
-         if (event.getPositionName() != null) {
-            AcqEngMetadata.setPositionName(tags, event.getPositionName());
+         // Other non-coreFocusZ positions
+         for (String name : event.getStageDeviceNames()) {
+            if (!name.equals(Engine.getCore().getFocusDevice())) {
+               AcqEngMetadata.setStagePositionIntended(tags, name, event.getStageSingleAxisStagePosition(name));
+            }
          }
 
+
          if (event.getSequence() != null) {
             //Dont add the event to image metadata if it is a sequence, because it could potentially be very large
-            // Could probably pop out the individual event in the squence this corresponds to
+            // Could probably pop out the individual event in the sequence this corresponds to
             AcqEngMetadata.addAcquisitionEvent(tags, event);
          }
-
-         ////// Generic image coordinate axes //////
-         // Position and channel indices are inferred at acquisition time
-         //All other axes (including T and Z) must be explicitly defined in the 
-         //acquisition event and get added here
-         for (String s : event.getDefinedAxes()) {
-            AcqEngMetadata.setAxisPosition(tags, s, event.getAxisPosition(s));
-         }
 
          AcqEngMetadata.setExposure(tags, exposure);
 
@@ -841,6 +850,15 @@ public static double getStageZIntended(JSONObject smd) {
       }
    }
 
+   public static void setStagePositionIntended(JSONObject tags,
+                                               String name, Double stageSingleAxisStagePosition) {
+      try {
+         tags.put(name + GENERIC_UM_INTENDED_SUFFIX, stageSingleAxisStagePosition);
+      } catch (JSONException ex) {
+         throw new RuntimeException("Couldnt set stage y");
+      }
+   }
+
    public static void setStageX(JSONObject smd, double x) {
       try {
          smd.put(X_UM, x);

src/main/java/org/micromanager/acqj/main/AcquisitionEvent.java

@@ -493,6 +493,9 @@ public void setStageCoordinate(String deviceName, double v, String axisName) {
 
 
    public Double getStageSingleAxisStagePosition(String deviceName) {
+      if (deviceName == null) {
+         return null;
+      }
       if (!stageCoordinates_.containsKey(deviceName)) {
          return null;
       }

src/main/java/org/micromanager/acqj/util/AcqEventModules.java

@@ -134,8 +134,19 @@ public AcquisitionEvent next() {
                channelEvent.setChannelName(channelList.get(index).config_);
                boolean hasZOffsets = channelList.stream().map(t -> t.offset_).
                        filter(t -> t != 0).collect(Collectors.toList()).size() > 0;
-               Double zPos;
-               if (channelEvent.getZPosition() == null) {
+               Double zPos = null;
+               if (channelEvent.getZPosition() != null) {
+                  zPos = channelEvent.getZPosition();
+               }
+               if (channelEvent.getStageSingleAxisStagePosition(Engine.getCore().getFocusDevice()) != null) {
+                  if (zPos != null) {
+                     throw new RuntimeException("Can't have both a z position and a named axis focus position");
+                  } else {
+                     zPos = channelEvent.getStageSingleAxisStagePosition(Engine.getCore().getFocusDevice());
+                  }
+               }
+
+               if (zPos == null) {
                   if (hasZOffsets) {
                      try {
                         zPos = Engine.getCore().getPosition() + channelList.get(index).offset_;
@@ -146,20 +157,17 @@ public AcquisitionEvent next() {
                      zPos = null;
                   }
                } else {
-                  zPos = channelEvent.getZPosition() + channelList.get(index).offset_;
+                  zPos += hasZOffsets ? channelList.get(index).offset_ : 0;
                }
-               channelEvent.setZ(channelEvent.getZIndex(), zPos);
-
-//               try {
-//                  channelEvent.setZ(channelEvent.getZIndex(),
-//                          channelEvent.getZPosition() == null ?
-//                                  hasZOffsets ?
-//                                          Engine.getCore().getPosition() + channelList.get(index).offset_ : null
-//                                  : channelEvent.getZPosition() + channelList.get(index).offset_
-//                  );
-//               } catch (Exception e) {
-//                  throw new RuntimeException(e);
-//               }
+               if (zPos != null) {
+                  // Its either stored as a named stage or as "z", keep it con
+                  if (channelEvent.getStageSingleAxisStagePosition(Engine.getCore().getFocusDevice()) != null) {
+                     channelEvent.setStageCoordinate(Engine.getCore().getFocusDevice(), zPos);
+                  } else {
+                     channelEvent.setZ(channelEvent.getZIndex(), zPos);
+                  }
+               }
+
                channelEvent.setExposure(channelList.get(index).exposure_);
                index++;
                return channelEvent;