--wip-- [skip ci]

Author: frcroth

.gitignore

@@ -82,7 +82,7 @@ errorShots/
 flow-coverage/
 
 
-# Sublime 
+# Sublime
 *.sublime-project
 *.sublime-workspace
 
@@ -102,7 +102,7 @@ metals.sbt
 **/screenshots/*.diff.png
 **/screenshots/*.new.png
 
-# Yarn 
+# Yarn
 .yarn/*
 !.yarn/cache
 !.yarn/patches

docker-compose.yml

@@ -3,12 +3,7 @@ version: "2.2"
 services:
   # Production
   webknossos:
-    build:
-      context: .
-      dockerfile: Dockerfile
-      cache_from:
-        - scalableminds/webknossos
-        - scalableminds/webknossos:${DEV_CACHE:-master}
+    build: .
     image: scalableminds/webknossos:${DOCKER_TAG:-master}
     ports:
       - "9000:9000"
@@ -105,8 +100,6 @@ services:
       - CERTIFICATE_PUBLIC_KEY
       - TZ=${TZ:-Europe/Berlin}
       - POSTGRES_URL=jdbc:postgresql://postgres/webknossos
-      - POSTGRES_USER=webknossos_user
-      - POSTGRES_PASSWORD=secret_password
       - HOME=/root
       - CIRCLE_TAG=${CIRCLE_TAG}
       - CIRCLE_BUILD_NUM=${CIRCLE_BUILD_NUM}
@@ -205,7 +198,7 @@ services:
           -Ddatastore.redis.address=redis
           -Ddatastore.watchFileSystem.enabled=false"
     volumes:
-      - ./binaryData/Organization_X:/home/${USER_NAME:-sbt-user}/webknossos/binaryData/Organization_X
+      - ./binaryData/Connectomics department:/home/${USER_NAME:-sbt-user}/webknossos/binaryData/Organization_X
 
   screenshot-tests:
     image: scalableminds/puppeteer:master
@@ -218,6 +211,12 @@ services:
       - ".:/home/pptruser/webknossos"
     user: ${USER_UID:-1000}:${USER_GID:-1000}
 
+  # webKnossos-connect
+  webknossos-connect:
+    image: scalableminds/webknossos-connect:master__205
+    volumes:
+      - "./conf/connect:/app/data"
+
   # Postgres
   postgres:
     image: postgres:10-alpine
@@ -226,7 +225,7 @@ services:
       - POSTGRES_USER=webknossos_user
       - POSTGRES_PASSWORD=secret_password
     healthcheck:
-      test: ["CMD-SHELL", "pg_isready -d webknossos -U webknossos_user -h 127.0.0.1 -p 5432"]
+      test: ["CMD-SHELL", "pg_isready -U postgres -h 127.0.0.1 -p 5432"]
       interval: 2s
       timeout: 5s
       retries: 30
@@ -237,7 +236,7 @@ services:
     ports:
       - "5434:5432"
     volumes:
-      - "./pg/db:/var/lib/postgresql/data/"
+      - "./pg.old/db:/var/lib/postgresql/data/"
 
   postgres-dev:
     extends:
@@ -249,7 +248,7 @@ services:
 
   psql:
     extends: postgres
-    command: psql -h postgres -U webknossos_user webknossos
+    command: psql -h postgres -U postgres webknossos
     links:
       - "postgres-persisted:postgres"
     depends_on:
@@ -262,7 +261,7 @@ services:
 
   drop-db:
     extends: postgres
-    command: psql -h postgres -U webknossos_user postgres -c "DROP DATABASE webknossos"
+    command: psql -h postgres -U postgres postgres -c "DROP DATABASE webknossos"
     links:
       - "postgres-persisted:postgres"
     depends_on:
@@ -284,8 +283,8 @@ services:
     extends:
       service: fossildb
     volumes:
-      - "./fossildb/data:/fossildb/data"
-      - "./fossildb/backup:/fossildb/backup"
+      - "./fossildb-old/data:/fossildb/data"
+      - "./fossildb-old/backup:/fossildb/backup"
 
   fossildb-dev:
     extends:

frontend/javascripts/oxalis/controller/segment_mesh_controller.ts

@@ -167,6 +167,7 @@ export default class SegmentMeshController {
       } else {
         this.meshesLODRootGroup.addLODMesh(targetGroup, lod);
       }
+      console.log("Mesh using scale and offset with lod ", scale, offset, lod);
       targetGroup.segmentId = segmentId;
       if (scale != null) {
         targetGroup.scale.copy(new THREE.Vector3(...scale));

webknossos-datastore/app/com/scalableminds/webknossos/datastore/services/MeshFileService.scala

@@ -414,9 +414,7 @@ class MeshFileService @Inject()(config: DataStoreConfig, dataVaultService: DataV
       bytesPerLod.take(lod).sum + chunkByteOffsetsInLod(lod)(currentChunk)
 
     def computeGlobalPositionAndOffset(lod: Int, currentChunk: Int): MeshChunk = {
-      val globalPosition = segmentInfo.gridOrigin + segmentInfo
-        .chunkPositions(lod)(currentChunk)
-        .toVec3Float * segmentInfo.chunkShape * Math.pow(2, lod) * segmentInfo.lodScales(lod) * lodScaleMultiplier
+      val globalPosition = segmentInfo.chunkPositions(lod)(currentChunk).toVec3Float
 
       MeshChunk(
         position = globalPosition, // This position is in Voxel Space
@@ -479,11 +477,26 @@ class MeshFileService @Inject()(config: DataStoreConfig, dataVaultService: DataV
       chunkRange <- mesh.getChunkRange(segmentId, minishardIndex)
       chunk <- mesh.getChunk(chunkRange, shardUrl)
       segmentManifest = NeuroglancerSegmentManifest.fromBytes(chunk)
+      _ = logger.info(s"Chunk Position 0 ${segmentManifest.chunkPositions(0)}")
       meshSegmentInfo = enrichSegmentInfo(segmentManifest, meshInfo.lod_scale_multiplier, chunkRange.start, segmentId)
-      transform = meshInfo.transform2DArray // Something is going wrong here, the meshes are far outside the other data
-      //transform = Array(Array(2.0, 0.0, 0.0, 0.0), Array(0.0, 2.0, 0.0, 0.0), Array(0.0, 0.0, 2.0, 0.0))
+      meshSegmentInfoc = meshSegmentInfo.copy(lods = List(meshSegmentInfo.lods(0)))
+      scale = segmentManifest.chunkShape * meshInfo.lod_scale_multiplier
+      _ = logger.info(s"segment info $meshSegmentInfo")
+      transform = Array(
+        Array(scale.x * meshInfo.transform(0), 0.0, 0.0, 0.0),
+        Array(0.0, scale.y * meshInfo.transform(5), 0.0, 0.0),
+        Array(0.0, 0.0, scale.z * meshInfo.transform(10), 0.0),
+        Array(0.0, 0.0, 0.0, 1.0)
+      )
+      //transform = meshInfo.transform2DArray // Something is going wrong here, the meshes are far outside the other data
+      //
+      // This works for precomputed-fafb with ds scale 4,4,40
+      //transform = Array(Array(2.0, 0.0, 0.0, 0.0),
+      //                  Array(0.0, 2.0, 0.0, 0.0),
+      //                  Array(0.0, 0.0, 2.5, 0.0),
+      //                  Array(0.0, 0.0, 0.0, 1.0))
       encoding = "draco"
-      wkChunkInfos <- WebknossosSegmentInfo.fromMeshInfosAndMetadata(List(meshSegmentInfo), encoding, transform)
+      wkChunkInfos <- WebknossosSegmentInfo.fromMeshInfosAndMetadata(List(meshSegmentInfoc), encoding, transform)
     } yield wkChunkInfos
 
   def readMeshChunk(organizationId: String,