Merge pull request micro-manager#33 from micro-manager/internal_reorg

Internal refactor of NDViewer + fix contrast bugs
mehta-lab · Aug 1, 2023 · 6da0576 · 6da0576
2 parents 76481b7 + 30950db
commit 6da0576
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Showing 19 changed files with 931 additions and 558 deletions.
diff --git a/pom.xml b/pom.xml
@@ -2,7 +2,7 @@
     <modelVersion>4.0.0</modelVersion>
     <groupId>org.micro-manager.ndviewer</groupId>
     <artifactId>NDViewer</artifactId>
-    <version>0.9.1</version>
+    <version>0.10.0</version>
     <packaging>jar</packaging>
     <name>NDViewer image viewer</name>
     <description>Java-based multidimensional image viewer</description>

diff --git a/src/main/java/org/micromanager/ndviewer/api/NDViewerAPI.java b/src/main/java/org/micromanager/ndviewer/api/NDViewerAPI.java
@@ -71,6 +71,7 @@ public interface NDViewerAPI {
     * @param axisMins map of axis names to miniumum extents (can be negative)
     * @param axisMaxs map of axis names to maximum extents
     */
+   @Deprecated
     void initializeViewerToLoaded(List<String> channelNames,
               JSONObject displaySettings,
               HashMap<String, Object> axisMins,

diff --git a/src/main/java/org/micromanager/ndviewer/api/NDViewerDataSource.java b/src/main/java/org/micromanager/ndviewer/api/NDViewerDataSource.java
@@ -17,6 +17,12 @@
  */
 public interface NDViewerDataSource {
 
+
+   /**
+    * Is the dataset still acquiring data/be written
+    */
+   public boolean isFinished();
+
    /**
     * The minimal and maximal pixel coordinates of the image to be viewed
     * 

diff --git a/src/main/java/org/micromanager/ndviewer/internal/gui/BaseOverlayer.java b/src/main/java/org/micromanager/ndviewer/internal/gui/BaseOverlayer.java
@@ -190,7 +190,7 @@ private void addTextBox(String[] text, Overlay overlay) {
 
    private Overlay createDefaultOverlay(DataViewCoords viewCoords) {
       Overlay overlay = new Overlay();
-      if (display_.isImageXYBounded()) {
+      if (display_.getDataSource().getBounds() != null) {
          drawZoomIndicator(overlay, viewCoords);
       }
       if (showScalebar_) {

diff --git a/src/main/java/org/micromanager/ndviewer/internal/gui/DataViewCoords.java b/src/main/java/org/micromanager/ndviewer/internal/gui/DataViewCoords.java
@@ -9,6 +9,7 @@
 import java.util.HashMap;
 
 import org.micromanager.ndviewer.api.NDViewerDataSource;
+import org.micromanager.ndviewer.main.NDViewer;
 
 /**
  *
@@ -23,16 +24,16 @@ public class DataViewCoords {
    private double xView_, yView_; //top left pixel in full res coordinates
    private HashMap<String, Object> axes_ = new HashMap<String, Object>();
    private int resolutionIndex_;
-   private NDViewerDataSource cache_;
+   private NDViewerDataSource data_;
    private boolean rgb_;
    private boolean sourceDataWidthInitialized_ = false;
 
    //Parameters that track what part of the dataset is being viewed
    public int xMax_, yMax_, xMin_, yMin_;
 
-   public DataViewCoords(NDViewerDataSource cache, double xView, double yView,
+   public DataViewCoords(NDViewerDataSource data, double xView, double yView,
                          Double initialWidth, Double initialHeight, int[] imageBounds, boolean rgb) {
-      cache_ = cache;
+      data_ = data;
       xView_ = 0;
       yView_ = 0;
       if (initialWidth == null) {
@@ -108,13 +109,15 @@ public double getMagnification() {
 
    private void updateResIndex() {
       double resIndexFloat = Math.log(sourceDataFullResWidth_ / (double) displayImageWidth_) / Math.log(2);
-      resolutionIndex_ = (int) Math.max(0, Math.ceil(resIndexFloat));
+      int newResIndex = (int) Math.max(0, Math.ceil(resIndexFloat));
 
       // Let the storage know the viewer will be requesting data at this resolution
-      int currentMaxResIndex = cache_.getMaxResolutionIndex();
-      if (resolutionIndex_ > currentMaxResIndex) {
-         cache_.increaseMaxResolutionLevel(resolutionIndex_);
+      int currentMaxResIndex = data_.getMaxResolutionIndex();
+      if (newResIndex > currentMaxResIndex && !data_.isFinished()) {
+         // Try to increase max resolution level, though not guarenteed it will happen
+         data_.increaseMaxResolutionLevel(newResIndex);
       }
+      resolutionIndex_ = Math.min(newResIndex, data_.getMaxResolutionIndex());
    }
 
    /**
@@ -158,7 +161,7 @@ public Object getAxisPosition(String axis) {
    }
 
    public DataViewCoords copy() {
-      DataViewCoords view = new DataViewCoords(cache_, xView_, yView_,
+      DataViewCoords view = new DataViewCoords(data_, xView_, yView_,
               sourceDataFullResWidth_, sourceDataFullResHeight_, new int[]{xMin_, yMin_, xMax_, yMax_}, rgb_);
       for (String axisName : axes_.keySet()) {
          view.axes_.put(axisName, axes_.get(axisName));
@@ -174,17 +177,17 @@ public DataViewCoords copy() {
       return view;
    }
 
-   public String getActiveChannel() {
-      return axes_.get("channel") != null ? "" + axes_.get("channel") : "" ;
-   }
+//   public String getActiveChannel() {
+//      return axes_.get("channel") != null ? "" + axes_.get("channel") : "" ;
+//   }
 
    public HashMap<String, Object> getAxesPositions() {
       return axes_;
    }
 
-   public void setActiveChannel(String channelName) {
-      axes_.put("channel", channelName);
-   }
+//   public void setActiveChannel(String channelName) {
+//      axes_.put(NDViewer.CHANNEL_AXIS, channelName);
+//   }
 
    public int[] getBounds() {
       return new int[]{xMin_, yMin_, xMax_, yMax_};