From 6b40984ea2ffaa7029c09e927d113f79d7f5f277 Mon Sep 17 00:00:00 2001
From: Caleb Hulbert <cmhulbert@gmail.com>
Date: Tue, 17 Oct 2023 14:36:25 -0400
Subject: [PATCH] refactor,fix: move BundleView to non-overloaded package

---
 .../bdv/fx/viewer/project/VolatileHierarchyProjector.java  | 2 +-
 .../project/VolatileHierarchyProjectorPreMultiply.java     | 2 +-
 .../saalfeldlab/paintera/data/mask/MaskedSource.java       | 2 +-
 .../janelia/saalfeldlab/paintera/data/mask/SourceMask.java | 2 +-
 .../janelia/saalfeldlab/paintera/meshes/MarchingCubes.java | 2 +-
 .../java/{ => paintera}/net/imglib2/view/BundleView.java   | 7 ++++++-
 .../paintera/control/actions/paint/SmoothAction.kt         | 2 +-
 .../saalfeldlab/paintera/control/paint/ViewerMask.kt       | 2 +-
 .../saalfeldlab/paintera/control/tools/paint/SamTool.kt    | 2 +-
 .../janelia/saalfeldlab/paintera/PainteraBaseViewTest.java | 2 +-
 10 files changed, 15 insertions(+), 10 deletions(-)
 rename src/main/java/{ => paintera}/net/imglib2/view/BundleView.java (94%)

diff --git a/src/main/java/bdv/fx/viewer/project/VolatileHierarchyProjector.java b/src/main/java/bdv/fx/viewer/project/VolatileHierarchyProjector.java
index 5982942d0..2cb7057f7 100644
--- a/src/main/java/bdv/fx/viewer/project/VolatileHierarchyProjector.java
+++ b/src/main/java/bdv/fx/viewer/project/VolatileHierarchyProjector.java
@@ -44,7 +44,7 @@
 import net.imglib2.type.operators.SetZero;
 import net.imglib2.util.Intervals;
 import net.imglib2.util.StopWatch;
-import net.imglib2.view.BundleView;
+import paintera.net.imglib2.view.BundleView;
 import net.imglib2.view.Views;
 
 import java.util.ArrayList;
diff --git a/src/main/java/bdv/fx/viewer/project/VolatileHierarchyProjectorPreMultiply.java b/src/main/java/bdv/fx/viewer/project/VolatileHierarchyProjectorPreMultiply.java
index 2d2142e9c..bfd28d1dd 100644
--- a/src/main/java/bdv/fx/viewer/project/VolatileHierarchyProjectorPreMultiply.java
+++ b/src/main/java/bdv/fx/viewer/project/VolatileHierarchyProjectorPreMultiply.java
@@ -9,7 +9,7 @@
 import net.imglib2.parallel.TaskExecutor;
 import net.imglib2.type.numeric.ARGBType;
 import net.imglib2.type.numeric.integer.ByteType;
-import net.imglib2.view.BundleView;
+import paintera.net.imglib2.view.BundleView;
 import net.imglib2.view.Views;
 
 import java.util.List;
diff --git a/src/main/java/org/janelia/saalfeldlab/paintera/data/mask/MaskedSource.java b/src/main/java/org/janelia/saalfeldlab/paintera/data/mask/MaskedSource.java
index 3e3287e8d..a6ced8582 100644
--- a/src/main/java/org/janelia/saalfeldlab/paintera/data/mask/MaskedSource.java
+++ b/src/main/java/org/janelia/saalfeldlab/paintera/data/mask/MaskedSource.java
@@ -86,7 +86,7 @@
 import net.imglib2.util.ConstantUtils;
 import net.imglib2.util.IntervalIndexer;
 import net.imglib2.util.Intervals;
-import net.imglib2.view.BundleView;
+import paintera.net.imglib2.view.BundleView;
 import net.imglib2.view.ExtendedRealRandomAccessibleRealInterval;
 import net.imglib2.view.IntervalView;
 import net.imglib2.view.RealRandomAccessibleTriple;
diff --git a/src/main/java/org/janelia/saalfeldlab/paintera/data/mask/SourceMask.java b/src/main/java/org/janelia/saalfeldlab/paintera/data/mask/SourceMask.java
index 48ab5e90c..9b4e26add 100644
--- a/src/main/java/org/janelia/saalfeldlab/paintera/data/mask/SourceMask.java
+++ b/src/main/java/org/janelia/saalfeldlab/paintera/data/mask/SourceMask.java
@@ -8,7 +8,7 @@
 import net.imglib2.type.numeric.IntegerType;
 import net.imglib2.type.numeric.integer.UnsignedLongType;
 import net.imglib2.type.volatiles.VolatileUnsignedLongType;
-import net.imglib2.view.BundleView;
+import paintera.net.imglib2.view.BundleView;
 import net.imglib2.view.IntervalView;
 import net.imglib2.view.Views;
 
diff --git a/src/main/java/org/janelia/saalfeldlab/paintera/meshes/MarchingCubes.java b/src/main/java/org/janelia/saalfeldlab/paintera/meshes/MarchingCubes.java
index faf77d93a..8a3d009cd 100644
--- a/src/main/java/org/janelia/saalfeldlab/paintera/meshes/MarchingCubes.java
+++ b/src/main/java/org/janelia/saalfeldlab/paintera/meshes/MarchingCubes.java
@@ -8,7 +8,7 @@
 import net.imglib2.loops.LoopBuilder;
 import net.imglib2.type.BooleanType;
 import net.imglib2.util.Intervals;
-import net.imglib2.view.BundleView;
+import paintera.net.imglib2.view.BundleView;
 import net.imglib2.view.IntervalView;
 import net.imglib2.view.Views;
 import org.slf4j.Logger;
diff --git a/src/main/java/net/imglib2/view/BundleView.java b/src/main/java/paintera/net/imglib2/view/BundleView.java
similarity index 94%
rename from src/main/java/net/imglib2/view/BundleView.java
rename to src/main/java/paintera/net/imglib2/view/BundleView.java
index ff61fce6b..d1dde9764 100644
--- a/src/main/java/net/imglib2/view/BundleView.java
+++ b/src/main/java/paintera/net/imglib2/view/BundleView.java
@@ -31,7 +31,7 @@
  * POSSIBILITY OF SUCH DAMAGE.
  * #L%
  */
-package net.imglib2.view;
+package paintera.net.imglib2.view;
 
 import net.imglib2.Interval;
 import net.imglib2.RandomAccess;
@@ -51,6 +51,11 @@
  * {@link RandomAccess RandomAccess&lt;RandomAccess&lt;T&gt;&gt;} will preserve
  * this relative offset while absolute positioning will reset it, so, you can
  * do that, but you should know why :).</p>
+ * <p>
+ * NOTE: Copied from imglib2 to expose as public while
+ * <a href="https://github.com/imglib/imglib2/issues/351">Imglib2 Issue #351</a>
+ * is being resolved.
+ * </p>
  *
  * @param <T>
  * @author Stephan Saalfeld &lt;saalfelds@janelia.hhmi.org&gt;
diff --git a/src/main/kotlin/org/janelia/saalfeldlab/paintera/control/actions/paint/SmoothAction.kt b/src/main/kotlin/org/janelia/saalfeldlab/paintera/control/actions/paint/SmoothAction.kt
index cdb0e30a5..886088adc 100644
--- a/src/main/kotlin/org/janelia/saalfeldlab/paintera/control/actions/paint/SmoothAction.kt
+++ b/src/main/kotlin/org/janelia/saalfeldlab/paintera/control/actions/paint/SmoothAction.kt
@@ -40,7 +40,7 @@ import net.imglib2.realtransform.AffineTransform3D
 import net.imglib2.type.numeric.integer.UnsignedLongType
 import net.imglib2.type.numeric.real.DoubleType
 import net.imglib2.util.Intervals
-import net.imglib2.view.BundleView
+import paintera.net.imglib2.view.BundleView
 import org.janelia.saalfeldlab.fx.Tasks
 import org.janelia.saalfeldlab.fx.UtilityTask
 import org.janelia.saalfeldlab.fx.actions.Action
diff --git a/src/main/kotlin/org/janelia/saalfeldlab/paintera/control/paint/ViewerMask.kt b/src/main/kotlin/org/janelia/saalfeldlab/paintera/control/paint/ViewerMask.kt
index e26a66a48..03f97d2d1 100644
--- a/src/main/kotlin/org/janelia/saalfeldlab/paintera/control/paint/ViewerMask.kt
+++ b/src/main/kotlin/org/janelia/saalfeldlab/paintera/control/paint/ViewerMask.kt
@@ -17,7 +17,7 @@ import net.imglib2.type.numeric.integer.UnsignedLongType
 import net.imglib2.type.volatiles.VolatileUnsignedLongType
 import net.imglib2.util.Intervals
 import net.imglib2.util.LinAlgHelpers
-import net.imglib2.view.BundleView
+import paintera.net.imglib2.view.BundleView
 import net.imglib2.view.Views
 import org.janelia.saalfeldlab.fx.extensions.component1
 import org.janelia.saalfeldlab.fx.extensions.component2
diff --git a/src/main/kotlin/org/janelia/saalfeldlab/paintera/control/tools/paint/SamTool.kt b/src/main/kotlin/org/janelia/saalfeldlab/paintera/control/tools/paint/SamTool.kt
index f7bcf47a8..6a6f8ad9f 100644
--- a/src/main/kotlin/org/janelia/saalfeldlab/paintera/control/tools/paint/SamTool.kt
+++ b/src/main/kotlin/org/janelia/saalfeldlab/paintera/control/tools/paint/SamTool.kt
@@ -46,7 +46,7 @@ import net.imglib2.type.numeric.integer.UnsignedLongType
 import net.imglib2.type.numeric.real.FloatType
 import net.imglib2.type.volatiles.VolatileUnsignedLongType
 import net.imglib2.util.Intervals
-import net.imglib2.view.BundleView
+import paintera.net.imglib2.view.BundleView
 import net.imglib2.view.Views
 import org.apache.http.HttpException
 import org.apache.http.client.methods.HttpPost
diff --git a/src/test/java/org/janelia/saalfeldlab/paintera/PainteraBaseViewTest.java b/src/test/java/org/janelia/saalfeldlab/paintera/PainteraBaseViewTest.java
index d100433e8..579ce9612 100644
--- a/src/test/java/org/janelia/saalfeldlab/paintera/PainteraBaseViewTest.java
+++ b/src/test/java/org/janelia/saalfeldlab/paintera/PainteraBaseViewTest.java
@@ -15,7 +15,7 @@
 import net.imglib2.type.numeric.integer.UnsignedLongType;
 import net.imglib2.util.Intervals;
 import net.imglib2.util.LinAlgHelpers;
-import net.imglib2.view.BundleView;
+import paintera.net.imglib2.view.BundleView;
 import net.imglib2.view.IntervalView;
 import net.imglib2.view.Views;
 import org.janelia.saalfeldlab.fx.util.InvokeOnJavaFXApplicationThread;