From 735cac238ea305391abb1319464940ab2853ae32 Mon Sep 17 00:00:00 2001
From: Akhilesh Halageri <akhilesh@zetta.ai>
Date: Wed, 8 Nov 2023 09:15:58 -0600
Subject: [PATCH] fix: handle skip connection missing lods

---
 src/neuroglancer/datasource/graphene/backend.ts |  4 ++++
 src/neuroglancer/mesh/multiscale.ts             | 11 ++++++-----
 2 files changed, 10 insertions(+), 5 deletions(-)

diff --git a/src/neuroglancer/datasource/graphene/backend.ts b/src/neuroglancer/datasource/graphene/backend.ts
index b05598b3b..4f84fa977 100644
--- a/src/neuroglancer/datasource/graphene/backend.ts
+++ b/src/neuroglancer/datasource/graphene/backend.ts
@@ -150,6 +150,10 @@ function decodeMultiscaleManifestChunk(chunk: GrapheneMultiscaleManifestChunk, r
     clipUpperBound: vec3.clone(response.clipUpperBound),
   }
   chunk.fragmentIds = response.fragments;
+  chunk.manifest.clipLowerBound.fill(0);
+  chunk.manifest.clipUpperBound.fill(100000);
+  chunk.manifest.octree[5*(response.fragments.length-1) + 4] &= 0x7FFFFFFF;
+  chunk.manifest.octree[5*(response.fragments.length-1) + 3] |= 0x80000000;
 }
 
 async function decodeMultiscaleFragmentChunk(
diff --git a/src/neuroglancer/mesh/multiscale.ts b/src/neuroglancer/mesh/multiscale.ts
index 0cd31b060..64250efbb 100644
--- a/src/neuroglancer/mesh/multiscale.ts
+++ b/src/neuroglancer/mesh/multiscale.ts
@@ -153,12 +153,13 @@ export function getDesiredMultiscaleMeshChunks(
 
       if (priorLodScale === 0 || pixelSize * detailCutoff < priorLodScale) {
         let lodScale = lodScales[lod];
-        if ((childBeginAndVirtual & (1 << 31)) !== 0) {
-          lodScale = 0;
-        }
-
         if (lodScale !== 0) {
-          callback(lod, row, lodScale / pixelSize, (childEndAndEmpty >>> 31));
+          const virtual = (childBeginAndVirtual >>> 31);
+          if (virtual) {
+            lodScale = 0;
+          }
+          const empty = (childEndAndEmpty >>> 31);
+          callback(lod, row, lodScale / pixelSize, empty | virtual);
         }
 
         if (lod > 0 && (lodScale === 0 || pixelSize * detailCutoff < lodScale)) {