From 934142697af74cdf18d654696beffd6edd53543b Mon Sep 17 00:00:00 2001
From: Ulrik Guenther <hello@ulrik.is>
Date: Fri, 16 Oct 2020 20:46:57 +0200
Subject: [PATCH 1/4] POM: Bump to latest scenery repository version

---
 pom.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pom.xml b/pom.xml
index b23729dc..b82188d4 100644
--- a/pom.xml
+++ b/pom.xml
@@ -108,7 +108,7 @@
 		<!-- NB: Deploy releases to the SciJava Maven repository. -->
 		<releaseProfiles>deploy-to-scijava</releaseProfiles>
 
-		<scenery.version>b9c44a2</scenery.version>
+		<scenery.version>242d9cf</scenery.version>
 <!--		<scijava-common.version>2.84.0</scijava-common.version>-->
 
 		<kotlin.version>1.4.10</kotlin.version>

From e8f7c9f0b11bfe73c3b9ea1cee2d88ce5d0e1939 Mon Sep 17 00:00:00 2001
From: Ulrik Guenther <hello@ulrik.is>
Date: Fri, 16 Oct 2020 20:47:42 +0200
Subject: [PATCH 2/4] SciView: Use duplicate buffers for accessing geometry
 when writing STL files

---
 src/main/java/sc/iview/SciView.java | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/main/java/sc/iview/SciView.java b/src/main/java/sc/iview/SciView.java
index bf4a415a..9eee42f9 100644
--- a/src/main/java/sc/iview/SciView.java
+++ b/src/main/java/sc/iview/SciView.java
@@ -1269,8 +1269,8 @@ public void writeSCMesh( String filename, Mesh scMesh ) {
             out = new BufferedOutputStream( new FileOutputStream( f ) );
             out.write( "solid STL generated by FIJI\n".getBytes() );
 
-            FloatBuffer normalsFB = scMesh.getNormals();
-            FloatBuffer verticesFB = scMesh.getVertices();
+            FloatBuffer normalsFB = scMesh.getNormals().duplicate();
+            FloatBuffer verticesFB = scMesh.getVertices().duplicate();
 
             while( verticesFB.hasRemaining() && normalsFB.hasRemaining() ) {
                 out.write( ( "facet normal " + normalsFB.get() + " " + normalsFB.get() + " " + normalsFB.get() +

From 67dc3e16f7ba30d53f33ba0ef373a31c5bd11fe6 Mon Sep 17 00:00:00 2001
From: Ulrik Guenther <hello@ulrik.is>
Date: Fri, 16 Oct 2020 20:48:39 +0200
Subject: [PATCH 3/4] Isosurface: Recalculate normals and use same
 pixel-to-world ratio as Volume

---
 src/main/java/sc/iview/commands/process/Isosurface.java | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/src/main/java/sc/iview/commands/process/Isosurface.java b/src/main/java/sc/iview/commands/process/Isosurface.java
index 0da844e7..f25604d3 100644
--- a/src/main/java/sc/iview/commands/process/Isosurface.java
+++ b/src/main/java/sc/iview/commands/process/Isosurface.java
@@ -28,6 +28,7 @@
  */
 package sc.iview.commands.process;
 
+import graphics.scenery.HasGeometry;
 import graphics.scenery.Node;
 import net.imagej.mesh.Mesh;
 import net.imagej.ops.OpService;
@@ -36,6 +37,7 @@
 import net.imglib2.img.Img;
 import net.imglib2.type.logic.BitType;
 import net.imglib2.type.numeric.RealType;
+import org.joml.Vector3f;
 import org.scijava.command.Command;
 import org.scijava.plugin.Menu;
 import org.scijava.plugin.Parameter;
@@ -82,7 +84,8 @@ public void run() {
         Mesh m = ops.geom().marchingCubes(bitImg, 1, new BitTypeVertexInterpolator());
 
         Node scMesh = sciView.addMesh(m);
-
+        ((HasGeometry)scMesh).recalculateNormals();
+        scMesh.setScale(new Vector3f(0.001f, 0.001f, 0.001f));
     }
 
 }

From 17cade6169f1fe5d568092b989461ef787606572 Mon Sep 17 00:00:00 2001
From: Ulrik Guenther <hello@ulrik.is>
Date: Fri, 16 Oct 2020 21:56:59 +0200
Subject: [PATCH 4/4] Travis CI: Disable shallow cloning

---
 .travis.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.travis.yml b/.travis.yml
index fa17be5f..ee5b1533 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -5,6 +5,8 @@ branches:
   - master
   - "/.*-[0-9]+\\..*/"
 install: true
+git:
+  depth: false
 script:
 #- ".travis/build.sh"
 - "python3 .travis/pre_ci.py"