Fix issue with DeepSlice not appearing in GUI

Author: NicoKiaru

src/main/java/ch/epfl/biop/atlas/aligner/DeepSliceHelper.java

@@ -16,6 +16,15 @@
 
 public class DeepSliceHelper {
 
+    public static void addJavaAtlases() {
+        DeepSliceHelper.addMouseCompatibleAtlas("Adult Mouse Brain - Allen Brain Atlas V3");
+        DeepSliceHelper.addMouseCompatibleAtlas("Adult Mouse Brain - Allen Brain Atlas V3p1");
+        DeepSliceHelper.addMouseCompatibleAtlas("allen_mouse_10um_java");
+        DeepSliceHelper.addRatCompatibleAtlas("Rat - Waxholm Sprague Dawley V4");
+        DeepSliceHelper.addRatCompatibleAtlas("Rat - Waxholm Sprague Dawley V4p2");
+        DeepSliceHelper.addRatCompatibleAtlas("whs_sd_rat_39um_java");
+    }
+
     final private static List<String> atlasNameMouseCompatible = new ArrayList<>();
     final private static List<String> atlasNameRatCompatible = new ArrayList<>();
 

src/main/java/ch/epfl/biop/atlas/aligner/MultiSlicePositioner.java

@@ -199,6 +199,8 @@ public List<SliceSources> getSlices() { // synchronized ??
      */
     public MultiSlicePositioner(Atlas biopAtlas, ReslicedAtlas reslicedAtlas, Context ctx) {
 
+        DeepSliceHelper.addJavaAtlases();
+
         logger.info("Creating MultiSlicePositioner instance");
         this.reslicedAtlas = reslicedAtlas;
         this.biopAtlas = biopAtlas;

src/main/java/ch/epfl/biop/atlas/aligner/command/RegisterSlicesDeepSliceAbstractCommand.java

@@ -113,12 +113,7 @@ abstract public class RegisterSlicesDeepSliceAbstractCommand implements Command
 
     public void run() {
 
-        DeepSliceHelper.addMouseCompatibleAtlas("Adult Mouse Brain - Allen Brain Atlas V3");
-        DeepSliceHelper.addMouseCompatibleAtlas("Adult Mouse Brain - Allen Brain Atlas V3p1");
-        DeepSliceHelper.addMouseCompatibleAtlas("allen_mouse_10um_java");
-        DeepSliceHelper.addRatCompatibleAtlas("Rat - Waxholm Sprague Dawley V4");
-        DeepSliceHelper.addRatCompatibleAtlas("Rat - Waxholm Sprague Dawley V4p2");
-        DeepSliceHelper.addRatCompatibleAtlas("whs_sd_rat_39um_java");
+        DeepSliceHelper.addJavaAtlases();
 
         List<SliceSources> iniList = mp.getSlices().stream().filter(SliceSources::isSelected)
                 .collect(Collectors.toList());

src/main/java/ch/epfl/biop/atlas/aligner/gui/bdv/BdvMultislicePositionerView.java

@@ -399,6 +399,8 @@ private void installBdvMenu(int hierarchyLevelsSkipped) {
             if (this.mode == POSITIONING_MODE_INT) msp.equalSpacingSelectedSlices();
         });
 
+        DeepSliceHelper.addJavaAtlases();
+
         if (DeepSliceHelper.isDeepSliceMouseCompatible(msp.getReslicedAtlas().ba.getName())) {
 
             logger.debug("Installing DeepSlice Command for Mouse");