Merge pull request #91 from nicost/tags

Add tags in events that will be added to metadata.

pom.xml

@@ -2,7 +2,7 @@
     <modelVersion>4.0.0</modelVersion>
     <groupId>org.micro-manager.acqengj</groupId>
     <artifactId>AcqEngJ</artifactId>
-    <version>0.27.0</version>
+    <version>0.28.0</version>
     <packaging>jar</packaging>
      <name>AcqEngJ</name>
     <description>Java-based Acquisition engine for Micro-Manager</description>

src/main/java/org/micromanager/acqj/internal/Engine.java

@@ -19,6 +19,7 @@
 import java.util.concurrent.FutureTask;
 import java.util.concurrent.TimeUnit;
 import java.util.concurrent.TimeoutException;
+import mmcorej.org.json.JSONException;
 import org.micromanager.acqj.api.AcquisitionAPI;
 import org.micromanager.acqj.main.AcquisitionEvent;
 import org.micromanager.acqj.api.AcquisitionHook;
@@ -534,6 +535,12 @@ private void acquireImages(final AcquisitionEvent event) throws HardwareControlE
             //add metadata
             AcqEngMetadata.addImageMetadata(ti.tags, correspondingEvent,
                     currentTime - correspondingEvent.acquisition_.getStartTime_ms(), exposure);
+            try {
+               correspondingEvent.acquisition_.addTagsToTaggedImage(ti.tags,
+                     correspondingEvent.getTags());
+            } catch (JSONException jse) {
+               core_.logMessage("Error adding tags to image metadata", false);
+            }
             correspondingEvent.acquisition_.addToImageMetadata(ti.tags);
 
             correspondingEvent.acquisition_.addToOutput(ti);

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

@@ -77,10 +77,11 @@ public class AcqEngMetadata {
    public static final String CORE_XYSTAGE = "Core-XYStage";
    public static final String CORE_FOCUS = "Core-Focus";
    public static final String AXES = "Axes";
-
    public static final String CHANNEL_AXIS = "channel";
    public static final String TIME_AXIS = "time";
    public static final String Z_AXIS = "z";
+   public static final String TAGS = "tags";
+
    private static final String ACQUISITION_EVENT = "Event";
 
 

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

@@ -16,7 +16,9 @@
 //
 package org.micromanager.acqj.main;
 
+import java.util.HashMap;
 import java.util.Iterator;
+import java.util.Map;
 import java.util.concurrent.*;
 import java.util.function.Consumer;
 
@@ -156,11 +158,35 @@ public void addToImageMetadata(JSONObject tags) {
       }
    }
 
+   /**
+    * Add provided tags (Key-Value pairs of type String) to the Tagged Image tags.
+    * These will appear as JSONObjects under the key:
+    * {@link org.micromanager.acqj.main.AcqEngMetadata#TAGS "Tags"}.
+    *
+    * @param tags Tagged Image tags
+    * @param moreTags User-provided tags as Key-Value pairs
+    */
+   public void addTagsToTaggedImage(JSONObject tags, HashMap<String, String> moreTags)
+         throws JSONException {
+      if (moreTags.isEmpty()) {
+         return;
+      }
+      JSONObject moreTagsObject = new JSONObject();
+      for (Map.Entry<String, String> entry : moreTags.entrySet()) {
+         try {
+            moreTagsObject.put(entry.getKey(), entry.getValue());
+         } catch (JSONException e) {
+            e.printStackTrace();
+         }
+      }
+      tags.put(AcqEngMetadata.TAGS, moreTagsObject);
+   }
+
    @Override
    public Future submitEventIterator(Iterator<AcquisitionEvent> evt) {
       if (!started_) {
          start();
-      }
+       }
       return Engine.getInstance().submitEventIterator(evt);
    }
 
@@ -283,19 +309,21 @@ public void waitForCompletion() {
     * 3) Initialize data sink.
     */
    protected void initialize() {
-      JSONObject summaryMetadata = AcqEngMetadata.makeSummaryMD(this);
-      addToSummaryMetadata(summaryMetadata);
+      if (core_ != null) {
+         JSONObject summaryMetadata = AcqEngMetadata.makeSummaryMD(this);
+         addToSummaryMetadata(summaryMetadata);
 
-      try {
-         // Make a local in copy in case something else modifies it
-         summaryMetadata_ = new JSONObject(summaryMetadata.toString());
-      } catch (JSONException ex) {
-         System.err.print("Couldn't copy summaary metadata");
-         ex.printStackTrace();
-      }
-      if (dataSink_ != null) {
-         //It could be null if not using saving and viewing and diverting with custom processor
-         dataSink_.initialize(this, summaryMetadata);
+         try {
+            // Make a local in copy in case something else modifies it
+            summaryMetadata_ = new JSONObject(summaryMetadata.toString());
+         } catch (JSONException ex) {
+            System.err.print("Couldn't copy summaary metadata");
+            ex.printStackTrace();
+         }
+         if (dataSink_ != null) {
+            //It could be null if not using saving and viewing and diverting with custom processor
+            dataSink_.initialize(this, summaryMetadata);
+         }
       }
    }
 

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

@@ -21,7 +21,9 @@
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.HashSet;
+import java.util.Iterator;
 import java.util.List;
+import java.util.Map;
 import java.util.Set;
 import java.util.TreeSet;
 import mmcorej.org.json.JSONArray;
@@ -64,6 +66,8 @@ enum SpecialFlag {
    private HashMap<String, Double> stageCoordinates_ = new HashMap<String, Double>();
    // Mapping from device names to axis names
    private HashMap<String, String> stageDeviceNamesToAxisNames_ = new HashMap<String, String>();
+   // tags to be added to the acquired image
+   private final HashMap<String, String> tags_ = new HashMap<String, String>();
 
    //Option to not acquire an image for SLM events
    private Boolean acquireImage_ = null;
@@ -142,6 +146,7 @@ public AcquisitionEvent copy() {
       e.acquireImage_ = acquireImage_;
       e.properties_ = new TreeSet<ThreeTuple>(this.properties_);
       e.camera_ = camera_;
+      e.setTags(tags_);
       return e;
    }
 
@@ -213,6 +218,14 @@ private static JSONObject eventToJSON(AcquisitionEvent e) {
             json.put("camera", e.camera_);
          }
 
+         if (e.getTags() != null) {
+            JSONObject jsonTags = new JSONObject();
+            for (Map.Entry<String, String> entry : e.getTags().entrySet()) {
+               jsonTags.put(entry.getKey(), entry.getValue());
+            }
+            json.put("tags", jsonTags);
+         }
+
          //TODO: galvo
          //TODO: more support for imperative API calls (i.e. SLM set image)
          //Arbitrary extra properties
@@ -223,7 +236,7 @@ private static JSONObject eventToJSON(AcquisitionEvent e) {
             prop.put(t.prop);
             prop.put(t.val);
             props.put(prop);
-         }
+          }
          if (props.length() > 0) {
             json.put("properties", props);
          }
@@ -318,6 +331,17 @@ private static AcquisitionEvent eventFromJSON(JSONObject json, AcquisitionAPI ac
             event.camera_ = json.getString("camera");
          }
 
+         if (json.has("tags")) {
+            HashMap<String, String> tags = new HashMap<>();
+            JSONObject jsonTags = json.getJSONObject("tags");
+            Iterator<String> keys = jsonTags.keys();
+            while (keys.hasNext()) {
+               String key = keys.next();
+               tags.put(key, jsonTags.getString(key));
+            }
+            event.setTags(tags);
+         }
+
          //TODO: galvo, etc (i.e. other aspects of imperative API)
 
 
@@ -434,9 +458,9 @@ public void setProperty(String device, String property, String value) {
    }
 
    /**
-    * Set the minimum start time in ms relative to when the acq started
+    * Set the minimum start time in ms relative to when the acq started.
     *
-    * @param l
+    * @param l Minimum start time in ms.
     */
    public void setMinimumStartTime(Long l) {
       miniumumStartTime_ms_ = l;
@@ -544,7 +568,7 @@ public Double getZPosition() {
    }
 
    /**
-    * get the minimum start timein system time
+    * Get the minimum start time in system time.
     *
     * @return
     */
@@ -621,6 +645,18 @@ public void setY(double y) {
       yPosition_ = y;
    }
 
+   public void setTags(HashMap<String, String> tags)  {
+      tags_.clear();
+      if (tags != null) {
+         tags_.putAll(tags);
+      }
+   }
+   public HashMap<String, String> getTags () {
+      HashMap<String, String> tags = new HashMap<>(tags_.size());
+      tags.putAll(tags_);
+      return tags;
+   }
+
 
    //For debugging
    @Override

tests/org/micromanager/acqj/main/TestAcquisitionEvent.java

@@ -0,0 +1,41 @@
+package org.micromanager.acqj.main;
+
+import java.util.HashMap;
+import mmcorej.org.json.JSONObject;
+import org.junit.Assert;
+import org.junit.Test;
+import org.micromanager.acqj.example.BlackHoleDataSink;
+
+public class TestAcquisitionEvent {
+   @Test
+   public void testSetupIsSane() {
+      Assert.assertTrue("must be true", true);
+   }
+
+   @Test
+   public void testEventSerialization() {
+      BlackHoleDataSink bhds = new BlackHoleDataSink();
+      Acquisition acq = new Acquisition(bhds);
+      AcquisitionEvent event = new AcquisitionEvent(acq);
+      final int z = 2;
+      event.setZ(z, z * 0.5);
+      final int t = 3;
+      event.setTimeIndex(t);
+      final long minimumStartTime = 892567265;
+      event.setMinimumStartTime(minimumStartTime);
+      HashMap<String, String> tags = new HashMap<>();
+      tags.put("test", "test");
+      tags.put("test2", "test2");
+
+      JSONObject eventSerial = event.toJSON();
+      AcquisitionEvent eventCopy = AcquisitionEvent.fromJSON(eventSerial, acq);
+
+      Assert.assertTrue(eventCopy.getZIndex() == z);
+      Assert.assertEquals(eventCopy.getZPosition(), z * 0.5, 0.0000001);
+      Assert.assertTrue(eventCopy.getTIndex() == t);
+      Assert.assertEquals(eventCopy.getMinimumStartTimeAbsolute(), minimumStartTime, 2000);
+      Assert.assertEquals(eventCopy.getTags().get("test"), event.getTags().get("test"));
+      Assert.assertEquals(eventCopy.getTags().get("test2"), event.getTags().get("test2"));
+   }
+}
+