Bugfix for getRoi on single slice objects

mianalysis · Nov 15, 2023 · cd4aae1 · cd4aae1
1 parent 2333637
commit cd4aae1
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Showing 16 changed files with 5 additions and 1,249 deletions.
diff --git a/src/main/java/io/github/mianalysis/mia/module/objects/detect/ManuallyIdentifyObjects.java b/src/main/java/io/github/mianalysis/mia/module/objects/detect/ManuallyIdentifyObjects.java
@@ -583,7 +583,7 @@ public Category getCategory() {
 
     @Override
     public String getVersionNumber() {
-        return "1.0.1";
+        return "1.0.2";
     }
 
     @Override

diff --git a/src/main/java/io/github/mianalysis/mia/module/script/RunScript.java b/src/main/java/io/github/mianalysis/mia/module/script/RunScript.java
@@ -31,6 +31,7 @@
 import io.github.mianalysis.mia.module.Modules;
 import io.github.mianalysis.mia.module.system.GlobalVariables;
 import io.github.mianalysis.mia.object.Workspace;
+import io.github.mianalysis.mia.object.coordinates.Point;
 import io.github.mianalysis.mia.object.coordinates.volume.PointOutOfRangeException;
 import io.github.mianalysis.mia.object.coordinates.volume.SpatCal;
 import io.github.mianalysis.mia.object.coordinates.volume.VolumeType;
@@ -201,7 +202,7 @@ public Category getCategory() {
 
     @Override
     public String getVersionNumber() {
-        return "1.0.1";
+        return "1.0.2";
     }
 
     @Override
@@ -249,6 +250,7 @@ String redirectImports(String scriptText, String extension) {
         movedClasses.put("io.github.sjcross.common.object.volume.PointOutOfRangeException",
                 PointOutOfRangeException.class.getName());
         movedClasses.put("io.github.sjcross.common.object.volume.SpatCal", SpatCal.class.getName());
+        movedClasses.put("io.github.sjcross.common.object.Point", Point.class.getName());
         movedClasses.put("io.github.sjcross.common.object.volume.VolumeType", VolumeType.class.getName());
 
         for (String oldLocation : movedClasses.keySet()) {

diff --git a/src/main/java/io/github/mianalysis/mia/object/coordinates/volume/Volume.java b/src/main/java/io/github/mianalysis/mia/object/coordinates/volume/Volume.java
@@ -160,7 +160,7 @@ public Volume getSlice(int slice) {
                 break;
         }
 
-        Volume sliceVol = new Volume(outputType, spatCal.width, spatCal.height, 1, spatCal.dppXY, spatCal.dppZ,
+        Volume sliceVol = new Volume(outputType, spatCal.width, spatCal.height, spatCal.nSlices, spatCal.dppXY, spatCal.dppZ,
                 spatCal.units);
         sliceVol.setCoordinateSet(coordinateSet.getSlice(slice));
 
@@ -226,7 +226,6 @@ public long getNumberOfElements() {
 
     public boolean is2D() {
         return spatCal.nSlices == 1;
-
     }
 
     @Deprecated