Merge branch 'main' into feature/make-critvol-settable

Author: Jannetty

.github/config/checks.xml

@@ -28,11 +28,17 @@
     <module name="Translation" />
 
     <!-- Checks for size violations -->
-    <module name="FileLength" />
-    <module name="LineLength">
-        <property name="id" value="LineLength"/>
-        <property name="fileExtensions" value="java" />
-        <property name="max" value="100"/>
+    <!-- Error-level FileLength (for src files) -->
+    <module name="FileLength">
+        <property name="id" value="FileLengthError"/>
+        <property name="max" value="2000"/>
+        <property name="severity" value="error"/>
+    </module>
+    <!-- Warning-level FileLength (for test files) -->
+    <module name="FileLength">
+        <property name="id" value="FileLengthWarn"/>
+        <property name="max" value="2000"/>
+        <property name="severity" value="warning"/>
     </module>
     <module name="LineLength">
         <property name="id" value="LineLengthTest"/>
@@ -183,7 +189,11 @@
         <!-- Miscellaneous other checks -->
         <module name="ArrayTypeStyle" />
         <module name="CommentsIndentation" />
-        <module name="TodoComment" />
         <module name="UpperEll" />
+
+        <!-- TODO comments raise warnings but don't throw errors -->
+        <module name="TodoComment">
+            <property name="severity" value="warning" />
+        </module>
     </module>
 </module>

.github/config/suppressions.xml

@@ -10,6 +10,7 @@
 
     <!-- Checks for size violations -->
     <suppress checks="LineLength" files="test/*" id="LineLength" />
+    <suppress checks="LineLengthTest" files="src/*" id="LineLength" />
 
     <!-- Checks for Javadoc comments -->
     <suppress checks="JavadocVariable" files="test/*" />
@@ -21,4 +22,14 @@
 
     <!-- Checks for class design-->
     <suppress checks="VisibilityModifier" files="/sim/*" />
+
+
+    <!-- Checks for filelengths -->
+    <suppress checks="FileLength"
+              id="FileLengthError"
+              files="test/*" />
+    <!-- Suppress warning-level FileLength in non-test files -->
+    <suppress checks="FileLength"
+              id="FileLengthWarn"
+              files="src/*" />
 </suppressions>

.github/workflows/lint.yml

@@ -15,12 +15,12 @@ jobs:
         fetch-depth: 0
 
     - name: Lint code base
-      uses: dbelyaev/action-checkstyle@v0.9.5
+      uses: dbelyaev/action-checkstyle@v3.0.0
       with:
         github_token: ${{ secrets.GITHUB_TOKEN }}
         reporter: github-check
         checkstyle_config: .github/config/checks.xml
-        fail_on_error: true
+        fail_level: error
 
   update-lint-badges:
     if: ${{ always() && github.ref == 'refs/heads/main' }}

src/arcade/core/gui/GUI.java

@@ -371,7 +371,7 @@ public File getPath() {
     }
 
     /** Custom file filter for XML files. */
-    private static class XMLFileFilter extends FileFilter {
+    private static final class XMLFileFilter extends FileFilter {
         /**
          * Determines if the file is an XML file.
          *

src/arcade/potts/env/location/PottsLocation.java

@@ -10,6 +10,9 @@
 import arcade.core.env.location.LocationContainer;
 import arcade.core.util.Plane;
 import arcade.core.util.Utilities;
+import arcade.core.util.Vector;
+import arcade.potts.util.PottsEnums.Direction;
+import arcade.potts.util.PottsEnums.Region;
 import static arcade.potts.util.PottsEnums.Direction;
 import static arcade.potts.util.PottsEnums.Region;
 
@@ -605,6 +608,16 @@ void updateCenter(int x, int y, int z, int change) {
      */
     abstract ArrayList<Voxel> getSelected(Voxel focus, double n);
 
+    /**
+     * Gets the voxel at specified percentage offsets along the location's axes with the provided
+     * ApicalAxis considered to be pointing up the Y axis.
+     *
+     * @param offsets the percent offsets along the location's axes
+     * @param apicalAxis the axis considered to be pointing up along the Y axis
+     * @return the voxel at the specified offset in the frame of the apical axis
+     */
+    abstract Voxel getOffsetInApicalFrame(ArrayList<Integer> offsets, Vector apicalAxis);
+
     /**
      * Gets the direction of the slice orthagonal to the direction with the smallest diameter.
      *

src/arcade/potts/env/location/PottsLocation2D.java

@@ -1,7 +1,10 @@
 package arcade.potts.env.location;
 
 import java.util.ArrayList;
+import java.util.Collections;
+import java.util.Comparator;
 import java.util.HashMap;
+import arcade.core.util.Vector;
 import static arcade.potts.util.PottsEnums.Direction;
 
 /** Concrete implementation of {@link PottsLocation} for 2D. */
@@ -64,4 +67,57 @@ Direction getSlice(Direction direction, HashMap<Direction, Integer> diameters) {
     ArrayList<Voxel> getSelected(Voxel focus, double n) {
         return Location2D.getSelected(voxels, focus, n);
     }
+
+    /**
+     * Gets the voxel at specified percentage offsets along the location's X and Y axes with the
+     * provided apicalAxis considered to be pointing up the Y axis. Returns null if this
+     * PottsLocation2D contains no voxels.
+     *
+     * @param offsets the percent offsets along the location's X and Y axes
+     * @param apicalAxis the axis considered to be pointing up along the Y axis
+     * @return the voxel through which the plane of division will pass
+     */
+    @Override
+    public Voxel getOffsetInApicalFrame(ArrayList<Integer> offsets, Vector apicalAxis) {
+        if (voxels.isEmpty()) {
+            return null;
+        }
+        if (offsets == null || offsets.size() != 2) {
+            throw new IllegalArgumentException("Offsets must be 2 integers.");
+        }
+
+        // Normalize axes
+        Vector yAxis = Vector.normalizeVector(apicalAxis);
+        Vector xAxis = Vector.normalizeVector(new Vector(apicalAxis.getY(), -apicalAxis.getX(), 0));
+
+        // Project voxels onto apical axis and group by rounded projection
+        HashMap<Integer, ArrayList<Voxel>> apicalBands = new HashMap<>();
+        ArrayList<Integer> apicalKeys = new ArrayList<>();
+
+        for (Voxel v : voxels) {
+            Vector pos = new Vector(v.x, v.y, 0);
+            double apicalProj = Vector.dotProduct(pos, yAxis);
+            int roundedProj = (int) Math.round(apicalProj);
+            apicalBands.computeIfAbsent(roundedProj, k -> new ArrayList<>()).add(v);
+            apicalKeys.add(roundedProj);
+        }
+
+        // Sort apical keys and choose percentile
+        Collections.sort(apicalKeys);
+        int yIndex =
+                Math.min(
+                        apicalKeys.size() - 1,
+                        (int) ((offsets.get(1) / 100.0) * apicalKeys.size()));
+        int targetApicalKey = apicalKeys.get(yIndex);
+
+        ArrayList<Voxel> band = apicalBands.get(targetApicalKey);
+        if (band == null || band.isEmpty()) {
+            return null;
+        }
+        // Project to orthogonal axis within the band and sort
+        band.sort(
+                Comparator.comparingDouble(v -> Vector.dotProduct(new Vector(v.x, v.y, 0), xAxis)));
+        int xIndex = Math.min(band.size() - 1, (int) ((offsets.get(0) / 100.0) * band.size()));
+        return band.get(xIndex);
+    }
 }

src/arcade/potts/env/location/PottsLocation3D.java

@@ -2,6 +2,8 @@
 
 import java.util.ArrayList;
 import java.util.HashMap;
+import arcade.core.util.Vector;
+import arcade.potts.util.PottsEnums.Direction;
 import static arcade.potts.util.PottsEnums.Direction;
 
 /** Concrete implementation of {@link PottsLocation} for 3D. */
@@ -64,4 +66,10 @@ Direction getSlice(Direction direction, HashMap<Direction, Integer> diameters) {
     ArrayList<Voxel> getSelected(Voxel focus, double n) {
         return Location3D.getSelected(voxels, focus, n);
     }
+
+    @Override
+    Voxel getOffsetInApicalFrame(ArrayList<Integer> offsets, Vector apicalAxis) {
+        throw new UnsupportedOperationException(
+                "getOffsetInApicalFrame is not implemented for PottsLocation3D");
+    }
 }

src/arcade/potts/env/location/PottsLocations.java

@@ -6,6 +6,8 @@
 import ec.util.MersenneTwisterFast;
 import arcade.core.env.location.Location;
 import arcade.core.env.location.LocationContainer;
+import arcade.core.util.Vector;
+import arcade.potts.util.PottsEnums.Region;
 import static arcade.potts.util.PottsEnums.Region;
 
 /**
@@ -286,4 +288,10 @@ Location separateVoxels(
 
         return splitLocation;
     }
+
+    @Override
+    Voxel getOffsetInApicalFrame(ArrayList<Integer> offsets, Vector apicalAxis) {
+        throw new UnsupportedOperationException(
+                "getOffsetInApicalFrame is not implemented for PottsLocations");
+    }
 }

src/arcade/potts/env/location/PottsLocations2D.java

@@ -2,6 +2,9 @@
 
 import java.util.ArrayList;
 import java.util.HashMap;
+import arcade.core.util.Vector;
+import arcade.potts.util.PottsEnums.Direction;
+import arcade.potts.util.PottsEnums.Region;
 import static arcade.potts.util.PottsEnums.Direction;
 import static arcade.potts.util.PottsEnums.Region;
 
@@ -70,4 +73,10 @@ Direction getSlice(Direction direction, HashMap<Direction, Integer> diameters) {
     ArrayList<Voxel> getSelected(Voxel focus, double n) {
         return Location2D.getSelected(locations.get(Region.DEFAULT).voxels, focus, n);
     }
+
+    @Override
+    Voxel getOffsetInApicalFrame(ArrayList<Integer> offsets, Vector apicalAxis) {
+        throw new UnsupportedOperationException(
+                "getOffsetInApicalFrame is not implemented for PottsLocations2D");
+    }
 }