From dba08ec39fe6f22b04fcb7ba5f4c48af34123740 Mon Sep 17 00:00:00 2001 From: leowe Date: Thu, 22 Sep 2022 15:50:22 +0200 Subject: [PATCH 01/63] refactor Hdf5Access --- .../datastore/services/MeshFileService.scala | 66 +++++++++---------- .../datastore/storage/Hdf5FileCache.scala | 8 ++- 2 files changed, 36 insertions(+), 38 deletions(-) diff --git a/webknossos-datastore/app/com/scalableminds/webknossos/datastore/services/MeshFileService.scala b/webknossos-datastore/app/com/scalableminds/webknossos/datastore/services/MeshFileService.scala index d8942ad1bed..eba3ead2034 100644 --- a/webknossos-datastore/app/com/scalableminds/webknossos/datastore/services/MeshFileService.scala +++ b/webknossos-datastore/app/com/scalableminds/webknossos/datastore/services/MeshFileService.scala @@ -1,21 +1,21 @@ package com.scalableminds.webknossos.datastore.services -import java.nio.file.{Path, Paths} - import com.scalableminds.util.geometry.Vec3Int import com.scalableminds.util.io.PathUtils import com.scalableminds.util.tools.{Fox, FoxImplicits} import com.scalableminds.webknossos.datastore.DataStoreConfig import com.scalableminds.webknossos.datastore.storage.{CachedHdf5File, Hdf5FileCache} import com.typesafe.scalalogging.LazyLogging -import javax.inject.Inject import net.liftweb.common.Box import net.liftweb.util.Helpers.tryo import org.apache.commons.io.FilenameUtils import play.api.libs.json.{Json, OFormat} +import java.nio.file.{Path, Paths} +import javax.inject.Inject import scala.collection.JavaConverters._ import scala.concurrent.ExecutionContext +import scala.util.Using trait GenericJsonFormat[T] {} @@ -84,14 +84,11 @@ class MeshFileService @Inject()(config: DataStoreConfig)(implicit ec: ExecutionC Note that null is a valid value here for once. Meshfiles with no information about the meshFilePath will return Fox.empty, while meshfiles with one marked as empty, will return Fox.successful(null) */ + def mappingNameForMeshFile(meshFilePath: Path): Fox[String] = - for { - cachedMeshFile <- tryo { meshFileCache.withCache(meshFilePath)(CachedHdf5File.fromPath) } ?~> "mesh.file.open.failed" - mappingName <- tryo { _: Throwable => - cachedMeshFile.finishAccess() - } { cachedMeshFile.reader.string().getAttr("/", "metadata/mapping_name") } ?~> "mesh.file.readEncoding.failed" - _ = cachedMeshFile.finishAccess() - } yield mappingName + safeExecute(meshFilePath) { cachedMeshFile => + cachedMeshFile.reader.string().getAttr("/", "metadata/mapping_name") + } ?~> "mesh.file.readEncoding.failed" def listMeshChunksForSegment(organizationName: String, dataSetName: String, @@ -105,20 +102,14 @@ class MeshFileService @Inject()(config: DataStoreConfig)(implicit ec: ExecutionC .resolve(meshesDir) .resolve(s"${listMeshChunksRequest.meshFile}.$meshFileExtension") - for { - cachedMeshFile <- tryo { meshFileCache.withCache(meshFilePath)(CachedHdf5File.fromPath) } ?~> "mesh.file.open.failed" - chunkPositionLiterals <- tryo { _: Throwable => - cachedMeshFile.finishAccess() - } { - cachedMeshFile.reader - .`object`() - .getAllGroupMembers(s"/${listMeshChunksRequest.segmentId}/$defaultLevelOfDetail") - .asScala - .toList - }.toFox - _ = cachedMeshFile.finishAccess() - positions <- Fox.serialCombined(chunkPositionLiterals)(parsePositionLiteral) - } yield positions + safeExecute(meshFilePath) { cachedMeshFile => + val chunkPositionLiterals = cachedMeshFile.reader + .`object`() + .getAllGroupMembers(s"/${listMeshChunksRequest.segmentId}/$defaultLevelOfDetail") + .asScala + .toList + Fox.serialCombined(chunkPositionLiterals)(parsePositionLiteral) + }.flatten ?~> "mesh.file.open.failed" } def readMeshChunk(organizationName: String, @@ -131,19 +122,24 @@ class MeshFileService @Inject()(config: DataStoreConfig)(implicit ec: ExecutionC .resolve(dataLayerName) .resolve(meshesDir) .resolve(s"${meshChunkDataRequest.meshFile}.$meshFileExtension") - for { - cachedMeshFile <- tryo { meshFileCache.withCache(meshFilePath)(CachedHdf5File.fromPath) } ?~> "mesh.file.open.failed" - encoding <- tryo { _: Throwable => - cachedMeshFile.finishAccess() - } { cachedMeshFile.reader.string().getAttr("/", "metadata/encoding") } ?~> "mesh.file.readEncoding.failed" - key = s"/${meshChunkDataRequest.segmentId}/$defaultLevelOfDetail/${positionLiteral(meshChunkDataRequest.position)}" - data <- tryo { _: Throwable => - cachedMeshFile.finishAccess() - } { cachedMeshFile.reader.readAsByteArray(key) } ?~> "mesh.file.readData.failed" - _ = cachedMeshFile.finishAccess() - } yield (data, encoding) + + safeExecute(meshFilePath) { cachedMeshFile => + val encoding = cachedMeshFile.reader.string().getAttr("/", "metadata/encoding") + val key = + s"/${meshChunkDataRequest.segmentId}/$defaultLevelOfDetail/${positionLiteral(meshChunkDataRequest.position)}" + val data = cachedMeshFile.reader.readAsByteArray(key) + (data, encoding) + } ?~> "mesh.file.readData.failed" } + private def safeExecute[T](filePath: Path)(block: CachedHdf5File => T): Fox[T] = + for { + _ <- bool2Fox(filePath.toFile.exists()) ?~> "mesh.file.open.failed" + result <- Using(meshFileCache.withCache(filePath)(CachedHdf5File.fromPath)) { + block + }.toFox + } yield result + private def positionLiteral(position: Vec3Int) = s"${position.x}_${position.y}_${position.z}" diff --git a/webknossos-datastore/app/com/scalableminds/webknossos/datastore/storage/Hdf5FileCache.scala b/webknossos-datastore/app/com/scalableminds/webknossos/datastore/storage/Hdf5FileCache.scala index bab2be48413..7a76d160306 100644 --- a/webknossos-datastore/app/com/scalableminds/webknossos/datastore/storage/Hdf5FileCache.scala +++ b/webknossos-datastore/app/com/scalableminds/webknossos/datastore/storage/Hdf5FileCache.scala @@ -1,13 +1,15 @@ package com.scalableminds.webknossos.datastore.storage -import java.nio.file.Path - import ch.systemsx.cisd.hdf5.{HDF5FactoryProvider, IHDF5Reader} import com.scalableminds.util.cache.LRUConcurrentCache import com.scalableminds.webknossos.datastore.dataformats.SafeCachable -case class CachedHdf5File(reader: IHDF5Reader) extends SafeCachable { +import java.nio.file.Path + +case class CachedHdf5File(reader: IHDF5Reader) extends SafeCachable with AutoCloseable { override protected def onFinalize(): Unit = reader.close() + + override def close(): Unit = this.finishAccess() } object CachedHdf5File { From c9aecb77d72d9963fc69c92aa41b028de2f676b9 Mon Sep 17 00:00:00 2001 From: leowe Date: Thu, 22 Sep 2022 19:30:15 +0200 Subject: [PATCH 02/63] add first new mesh file functionality --- .../datastore/services/MeshFileService.scala | 104 ++++++++++++++++++ 1 file changed, 104 insertions(+) diff --git a/webknossos-datastore/app/com/scalableminds/webknossos/datastore/services/MeshFileService.scala b/webknossos-datastore/app/com/scalableminds/webknossos/datastore/services/MeshFileService.scala index eba3ead2034..67f3bba5647 100644 --- a/webknossos-datastore/app/com/scalableminds/webknossos/datastore/services/MeshFileService.scala +++ b/webknossos-datastore/app/com/scalableminds/webknossos/datastore/services/MeshFileService.scala @@ -1,5 +1,6 @@ package com.scalableminds.webknossos.datastore.services +import com.google.common.io.LittleEndianDataInputStream import com.scalableminds.util.geometry.Vec3Int import com.scalableminds.util.io.PathUtils import com.scalableminds.util.tools.{Fox, FoxImplicits} @@ -11,6 +12,7 @@ import net.liftweb.util.Helpers.tryo import org.apache.commons.io.FilenameUtils import play.api.libs.json.{Json, OFormat} +import java.io.ByteArrayInputStream import java.nio.file.{Path, Paths} import javax.inject.Inject import scala.collection.JavaConverters._ @@ -55,6 +57,7 @@ class MeshFileService @Inject()(config: DataStoreConfig)(implicit ec: ExecutionC private val meshesDir = "meshes" private val meshFileExtension = "hdf5" private val defaultLevelOfDetail = 0 + private def hashFn: Long => Long = identity private lazy val meshFileCache = new Hdf5FileCache(30) @@ -112,6 +115,107 @@ class MeshFileService @Inject()(config: DataStoreConfig)(implicit ec: ExecutionC }.flatten ?~> "mesh.file.open.failed" } + def listMeshChunksForSegmentNewFormat(organizationName: String, + dataSetName: String, + dataLayerName: String, + listMeshChunksRequest: ListMeshChunksRequest): Fox[List[Vec3Int]] = { + val meshFilePath = + dataBaseDir + .resolve(organizationName) + .resolve(dataSetName) + .resolve(dataLayerName) + .resolve(meshesDir) + .resolve(s"${listMeshChunksRequest.meshFile}.$meshFileExtension") + + safeExecute(meshFilePath) { cachedMeshFile => +// val chunkPositionLiterals = cachedMeshFile.reader +// .`object`() +// .getAllGroupMembers(s"/${listMeshChunksRequest.segmentId}/$defaultLevelOfDetail") +// .asScala +// .toList +// Fox.serialCombined(chunkPositionLiterals)(parsePositionLiteral) + val segmentId = listMeshChunksRequest.segmentId + val (neuroglancerStart, neuroglancerEnd) = getNeuroglancerOffsets(segmentId, cachedMeshFile) + val manifest = cachedMeshFile.reader + .uint8() + .readArrayBlockWithOffset("neuroglancer", (neuroglancerEnd - neuroglancerStart).toInt, neuroglancerStart) + val byteInput = new ByteArrayInputStream(manifest) + val dis = new LittleEndianDataInputStream(byteInput) + // todo use vec3int + val chunkShape = new Array[Float](3) + for (d <- 0 until 3) { + chunkShape(d) = dis.readFloat + } + // todo use vec3int + val gridOrigin = new Array[Float](3) + for (d <- 0 until 3) { + gridOrigin(d) = dis.readFloat + } + // TODO should uint + val numLods = dis.readInt() + val lodScales = new Array[Float](numLods) + for (d <- 0 until numLods) { + lodScales(d) = dis.readFloat() + } + // TODO use vec3int + val vertexOffsets = new Array[Array[Float]](numLods) + for (d <- 0 until numLods) { + for (x <- 0 until 3) { + vertexOffsets(d)(x) = dis.readFloat() + } + } + // TODO should be uint + val numFragmentsPerLod = new Array[Int](numLods) + for (lod <- 0 until numLods) { + numFragmentsPerLod(lod) = dis.readInt() + } + // TODO should be uint + val fragmentPositions = new Array[Array[Array[Int]]](numLods) + val fragmentPositionsVec3 = new Array[Array[Vec3Int]](numLods) + val fragmentOffsets = new Array[Array[Int]](numLods) + for (lod <- 0 until numLods) { + // TODO is that the right order?? + for (row <- 0 until 3) { + for (col <- 0 until numFragmentsPerLod(lod)) { + fragmentPositions(lod)(row)(col) = dis.readInt() + } + } + // TODO make functional, this is a mess + for (col <- 0 until numFragmentsPerLod(lod)) { + fragmentPositionsVec3(lod)(col) = + Vec3Int(fragmentPositions(lod)(0)(col), fragmentPositions(lod)(1)(col), fragmentPositions(lod)(2)(col)) + } + + for (row <- 0 until numFragmentsPerLod(lod)) { + fragmentOffsets(lod)(row) = dis.readInt() + } + } + val DEFAULT_LOD = 1 + fragmentPositionsVec3(DEFAULT_LOD).toList + } + } + + private def getNeuroglancerOffsets(segmentId: Long, cachedMeshFile: CachedHdf5File): (Long, Long) = { + val nBuckets = cachedMeshFile.reader.uint64().getAttr("/", "metadata/n_buckets") + // TODO get hashfunction from metadata + val bucketIndex = hashFn(segmentId) % nBuckets + val cappedBucketIndex = bucketIndex.toInt + val bucketOffsets = cachedMeshFile.reader.uint64().readArrayBlockWithOffset("bucket_offsets", 2, bucketIndex) + val bucketStart = bucketOffsets(cappedBucketIndex) + val cappedBucketStart = bucketStart.toInt + val bucketEnd = bucketOffsets(cappedBucketIndex + 1) + val cappedBucketEnd = bucketEnd.toInt + // TODO is this access correct? + val buckets = cachedMeshFile.reader + .uint64() + .readMatrixBlockWithOffset("buckets", cappedBucketEnd - cappedBucketStart + 1, 3, bucketStart, 0) + // TODO does this work as intended? + val bucketLocalOffset = buckets.map(_(0)).indexOf(segmentId) + val neuroglancerStart = buckets(bucketLocalOffset)(1) + val neuroglancerEnd = buckets(bucketLocalOffset)(2) + (neuroglancerStart, neuroglancerEnd) + } + def readMeshChunk(organizationName: String, dataSetName: String, dataLayerName: String, From 1f60390e30b3c6abcc350fc6c9a8e2382d3163a1 Mon Sep 17 00:00:00 2001 From: leowe Date: Fri, 23 Sep 2022 16:38:58 +0200 Subject: [PATCH 03/63] finished basic functionality --- .../util/geometry/Vec3Float.scala | 9 + .../scalableminds/util/geometry/Vec3Int.scala | 2 + .../datastore/services/MeshFileService.scala | 182 ++++++++++++------ 3 files changed, 137 insertions(+), 56 deletions(-) create mode 100644 util/src/main/scala/com/scalableminds/util/geometry/Vec3Float.scala diff --git a/util/src/main/scala/com/scalableminds/util/geometry/Vec3Float.scala b/util/src/main/scala/com/scalableminds/util/geometry/Vec3Float.scala new file mode 100644 index 00000000000..cc645bea0be --- /dev/null +++ b/util/src/main/scala/com/scalableminds/util/geometry/Vec3Float.scala @@ -0,0 +1,9 @@ +package com.scalableminds.util.geometry; + +case class Vec3Float(x: Float, y: Float, z: Float) { + def scale(s: Float): Vec3Float = Vec3Float(x * s, y * s, z * s) + + def *(s: Float): Vec3Float = scale(s) + def *(that: Vec3Float): Vec3Float = Vec3Float(x * that.x, y * that.y, z * that.z) + def +(that: Vec3Float): Vec3Float = Vec3Float(x + that.x, y + that.y, z + that.y) +} diff --git a/util/src/main/scala/com/scalableminds/util/geometry/Vec3Int.scala b/util/src/main/scala/com/scalableminds/util/geometry/Vec3Int.scala index 87e5754d949..6c3c8f65e6f 100644 --- a/util/src/main/scala/com/scalableminds/util/geometry/Vec3Int.scala +++ b/util/src/main/scala/com/scalableminds/util/geometry/Vec3Int.scala @@ -32,6 +32,8 @@ case class Vec3Int(x: Int, y: Int, z: Int) { def toList: List[Int] = List(x, y, z) + def toVec3Float: Vec3Float = Vec3Float(x.toFloat, y.toFloat, z.toFloat) + def move(dx: Int, dy: Int, dz: Int): Vec3Int = Vec3Int(x + dx, y + dy, z + dz) diff --git a/webknossos-datastore/app/com/scalableminds/webknossos/datastore/services/MeshFileService.scala b/webknossos-datastore/app/com/scalableminds/webknossos/datastore/services/MeshFileService.scala index 67f3bba5647..11df7ae12b6 100644 --- a/webknossos-datastore/app/com/scalableminds/webknossos/datastore/services/MeshFileService.scala +++ b/webknossos-datastore/app/com/scalableminds/webknossos/datastore/services/MeshFileService.scala @@ -1,7 +1,7 @@ package com.scalableminds.webknossos.datastore.services import com.google.common.io.LittleEndianDataInputStream -import com.scalableminds.util.geometry.Vec3Int +import com.scalableminds.util.geometry.{Vec3Float, Vec3Int} import com.scalableminds.util.io.PathUtils import com.scalableminds.util.tools.{Fox, FoxImplicits} import com.scalableminds.webknossos.datastore.DataStoreConfig @@ -49,6 +49,21 @@ object MeshFileNameWithMappingName { implicit val jsonFormat: OFormat[MeshFileNameWithMappingName] = Json.format[MeshFileNameWithMappingName] } +case class NeuroglancerSegmentInfo(chunkShape: Vec3Float, + gridOrigin: Vec3Float, + numLods: Int, + lodScales: Array[Float], + vertexOffsets: Array[Vec3Float], + numFragmentsPerLod: Array[Int], + fragmentPositions: Array[Array[Vec3Int]], + fragmentOffsets: Array[Array[Int]]) + +case class MeshfileFragment(position: Vec3Float, byteOffset: Int, byteSize: Int) + +case class MeshfileLod(scale: Int, vertexOffset: Vec3Float, chunkShape: Vec3Float, fragments: List[MeshfileFragment]) + +case class Meshfile(chunkShape: Vec3Float, gridOrigin: Vec3Float, lods: List[MeshfileLod]) + class MeshFileService @Inject()(config: DataStoreConfig)(implicit ec: ExecutionContext) extends FoxImplicits with LazyLogging { @@ -128,71 +143,107 @@ class MeshFileService @Inject()(config: DataStoreConfig)(implicit ec: ExecutionC .resolve(s"${listMeshChunksRequest.meshFile}.$meshFileExtension") safeExecute(meshFilePath) { cachedMeshFile => -// val chunkPositionLiterals = cachedMeshFile.reader -// .`object`() -// .getAllGroupMembers(s"/${listMeshChunksRequest.segmentId}/$defaultLevelOfDetail") -// .asScala -// .toList -// Fox.serialCombined(chunkPositionLiterals)(parsePositionLiteral) val segmentId = listMeshChunksRequest.segmentId val (neuroglancerStart, neuroglancerEnd) = getNeuroglancerOffsets(segmentId, cachedMeshFile) + // TODO transform is actually a matrix + val transform = cachedMeshFile.reader.float32().getAttr("/", "metadata/transform") val manifest = cachedMeshFile.reader .uint8() .readArrayBlockWithOffset("neuroglancer", (neuroglancerEnd - neuroglancerStart).toInt, neuroglancerStart) - val byteInput = new ByteArrayInputStream(manifest) - val dis = new LittleEndianDataInputStream(byteInput) - // todo use vec3int - val chunkShape = new Array[Float](3) - for (d <- 0 until 3) { - chunkShape(d) = dis.readFloat - } - // todo use vec3int - val gridOrigin = new Array[Float](3) - for (d <- 0 until 3) { - gridOrigin(d) = dis.readFloat - } - // TODO should uint - val numLods = dis.readInt() - val lodScales = new Array[Float](numLods) - for (d <- 0 until numLods) { - lodScales(d) = dis.readFloat() - } - // TODO use vec3int - val vertexOffsets = new Array[Array[Float]](numLods) - for (d <- 0 until numLods) { - for (x <- 0 until 3) { - vertexOffsets(d)(x) = dis.readFloat() - } - } - // TODO should be uint - val numFragmentsPerLod = new Array[Int](numLods) - for (lod <- 0 until numLods) { - numFragmentsPerLod(lod) = dis.readInt() - } - // TODO should be uint - val fragmentPositions = new Array[Array[Array[Int]]](numLods) - val fragmentPositionsVec3 = new Array[Array[Vec3Int]](numLods) - val fragmentOffsets = new Array[Array[Int]](numLods) - for (lod <- 0 until numLods) { - // TODO is that the right order?? - for (row <- 0 until 3) { - for (col <- 0 until numFragmentsPerLod(lod)) { - fragmentPositions(lod)(row)(col) = dis.readInt() - } - } - // TODO make functional, this is a mess + val segmentInfo = parseNeuroglancerManifest(manifest) + val meshfile = getFragmentsFromSegmentInfo(segmentInfo, transform, neuroglancerStart) + // TODO we need more info than just this, frontend probably needs also quantization bit + segmentInfo.fragmentPositions(defaultLevelOfDetail).toList + } + } + + private def getFragmentsFromSegmentInfo(segmentInfo: NeuroglancerSegmentInfo, + transform: Float, + neuroglancerOffsetStart: Long): Meshfile = { + val totalMeshSize = segmentInfo.fragmentOffsets.reduce((a, b) => a.sum + b.sum) + val meshByteStartOffset = neuroglancerOffsetStart - totalMeshSize + val fragmentByteOffsets = segmentInfo.fragmentOffsets.map(_.scanLeft(0)(_ + _)) + + def computeGlobalPositionAndOffset(lod: Int, currentFragment: Int): MeshfileFragment = { + val globalPosition = segmentInfo.gridOrigin + segmentInfo + .fragmentPositions(lod)(currentFragment) + .toVec3Float * segmentInfo.chunkShape * segmentInfo.lodScales(lod) + + MeshfileFragment( + position = globalPosition * transform, + byteOffset = meshByteStartOffset.toInt + fragmentByteOffsets(lod)(currentFragment), + byteSize = segmentInfo.fragmentOffsets(lod)(currentFragment), + ) + } + + val lods = for (lod <- 0 until segmentInfo.numLods) yield lod + + def fragmentNums(lod: Int): IndexedSeq[(Int, Int)] = + for (currentFragment <- 0 until segmentInfo.numFragmentsPerLod(lod)) + yield (lod, currentFragment) + val fragments = lods.map(lod => fragmentNums(lod).map(x => computeGlobalPositionAndOffset(x._1, x._2)).toList) + + val meshfileLods = lods.map( + lod => + MeshfileLod(scale = segmentInfo.lodScales(lod).toInt, + vertexOffset = segmentInfo.vertexOffsets(lod), + chunkShape = segmentInfo.chunkShape, + fragments = fragments(lod))).toList + Meshfile(chunkShape = segmentInfo.chunkShape, gridOrigin = segmentInfo.gridOrigin, lods = meshfileLods) + } + private def parseNeuroglancerManifest(manifest: Array[Byte]): NeuroglancerSegmentInfo = { + // All Ints here should be UInt32 per spec. + // But they all are used to index into Arrays and JVM doesn't allow for Long Array Indexes, + // we can't convert them. + // TODO Check whether limit exceeded for the Ints. + val byteInput = new ByteArrayInputStream(manifest) + val dis = new LittleEndianDataInputStream(byteInput) + + val chunkShape = Vec3Float(x = dis.readFloat, y = dis.readFloat, z = dis.readFloat) + val gridOrigin = Vec3Float(x = dis.readFloat, y = dis.readFloat, z = dis.readFloat) + + val numLods = dis.readInt + + val lodScales = new Array[Float](numLods) + for (d <- 0 until numLods) { + lodScales(d) = dis.readFloat + } + + val vertexOffsets = new Array[Vec3Float](numLods) + for (d <- 0 until numLods) { + vertexOffsets(d) = Vec3Float(x = dis.readFloat, y = dis.readFloat, z = dis.readFloat) + } + + val numFragmentsPerLod = new Array[Int](numLods) + for (lod <- 0 until numLods) { + numFragmentsPerLod(lod) = dis.readInt() + } + + val fragmentPositions = new Array[Array[Array[Int]]](numLods) + val fragmentPositionsVec3 = new Array[Array[Vec3Int]](numLods) + val fragmentSizes = new Array[Array[Int]](numLods) + for (lod <- 0 until numLods) { + for (row <- 0 until 3) { for (col <- 0 until numFragmentsPerLod(lod)) { - fragmentPositionsVec3(lod)(col) = - Vec3Int(fragmentPositions(lod)(0)(col), fragmentPositions(lod)(1)(col), fragmentPositions(lod)(2)(col)) + fragmentPositions(lod)(row)(col) = dis.readInt } + } - for (row <- 0 until numFragmentsPerLod(lod)) { - fragmentOffsets(lod)(row) = dis.readInt() - } + fragmentPositionsVec3(lod) = fragmentPositions(lod).transpose.map(xs => Vec3Int(xs(0), xs(1), xs(2))) + + for (fragmentNum <- 0 until numFragmentsPerLod(lod)) { + fragmentSizes(lod)(fragmentNum) = dis.readInt } - val DEFAULT_LOD = 1 - fragmentPositionsVec3(DEFAULT_LOD).toList } + + NeuroglancerSegmentInfo(chunkShape, + gridOrigin, + numLods, + lodScales, + vertexOffsets, + numFragmentsPerLod, + fragmentPositionsVec3, + fragmentSizes) } private def getNeuroglancerOffsets(segmentId: Long, cachedMeshFile: CachedHdf5File): (Long, Long) = { @@ -236,6 +287,25 @@ class MeshFileService @Inject()(config: DataStoreConfig)(implicit ec: ExecutionC } ?~> "mesh.file.readData.failed" } + + def readMeshChunkNewFormat(organizationName: String, + dataSetName: String, + dataLayerName: String, + meshChunkDataRequest: MeshChunkDataRequest, fragmentStartOffset: Long, fragmentSize: Int): Fox[(Array[Byte], String)] = { + val meshFilePath = dataBaseDir + .resolve(organizationName) + .resolve(dataSetName) + .resolve(dataLayerName) + .resolve(meshesDir) + .resolve(s"${meshChunkDataRequest.meshFile}.$meshFileExtension") + + safeExecute(meshFilePath) { cachedMeshFile => + val meshFormat = cachedMeshFile.reader.string().getAttr("/", "metadata/mesh_format") + val data = cachedMeshFile.reader.uint8().readArrayBlockWithOffset("neuroglancer", fragmentSize, fragmentStartOffset) + (data, meshFormat) + } ?~> "mesh.file.readData.failed" + } + private def safeExecute[T](filePath: Path)(block: CachedHdf5File => T): Fox[T] = for { _ <- bool2Fox(filePath.toFile.exists()) ?~> "mesh.file.open.failed" From 41904404d014871b8cbd5906e7dff6139aa67bbc Mon Sep 17 00:00:00 2001 From: leowe Date: Mon, 26 Sep 2022 18:45:06 +0200 Subject: [PATCH 04/63] write new routes --- .../util/geometry/Vec3Float.scala | 19 +- .../controllers/DataSourceController.scala | 60 ++++- .../datastore/services/MeshFileService.scala | 209 ++++++++++++------ ....scalableminds.webknossos.datastore.routes | 7 +- 4 files changed, 214 insertions(+), 81 deletions(-) diff --git a/util/src/main/scala/com/scalableminds/util/geometry/Vec3Float.scala b/util/src/main/scala/com/scalableminds/util/geometry/Vec3Float.scala index cc645bea0be..f9557fb68e6 100644 --- a/util/src/main/scala/com/scalableminds/util/geometry/Vec3Float.scala +++ b/util/src/main/scala/com/scalableminds/util/geometry/Vec3Float.scala @@ -1,4 +1,6 @@ -package com.scalableminds.util.geometry; +package com.scalableminds.util.geometry + +import play.api.libs.json.{Json, OFormat}; case class Vec3Float(x: Float, y: Float, z: Float) { def scale(s: Float): Vec3Float = Vec3Float(x * s, y * s, z * s) @@ -6,4 +8,19 @@ case class Vec3Float(x: Float, y: Float, z: Float) { def *(s: Float): Vec3Float = scale(s) def *(that: Vec3Float): Vec3Float = Vec3Float(x * that.x, y * that.y, z * that.z) def +(that: Vec3Float): Vec3Float = Vec3Float(x + that.x, y + that.y, z + that.y) + + def toList: List[Float] = List(x, y, z) + def matmul(that: Array[Array[Float]]): Option[Vec3Float] = { + val l: Array[Float] = this.toList.toArray ++ Array[Float](1.0.toFloat) + val result: Array[Array[Float]] = that.map(xs => xs.zip(l).map{case (x,y) => x * y}) + + if (that.length < 3 || that(0).length < 3) + None + else + Some(Vec3Float(result(0).sum, result(1).sum, result(2).sum)) + } +} + +object Vec3Float { + implicit val jsonFormat: OFormat[Vec3Float] = Json.format[Vec3Float] } diff --git a/webknossos-datastore/app/com/scalableminds/webknossos/datastore/controllers/DataSourceController.scala b/webknossos-datastore/app/com/scalableminds/webknossos/datastore/controllers/DataSourceController.scala index 63a9db7e333..7ed93fc8abd 100644 --- a/webknossos-datastore/app/com/scalableminds/webknossos/datastore/controllers/DataSourceController.scala +++ b/webknossos-datastore/app/com/scalableminds/webknossos/datastore/controllers/DataSourceController.scala @@ -415,15 +415,15 @@ Expects: } @ApiOperation(hidden = true, value = "") - def listMeshChunksForSegment(token: Option[String], - organizationName: String, - dataSetName: String, - dataLayerName: String): Action[ListMeshChunksRequest] = + def listMeshChunksForSegmentV0(token: Option[String], + organizationName: String, + dataSetName: String, + dataLayerName: String): Action[ListMeshChunksRequest] = Action.async(validateJson[ListMeshChunksRequest]) { implicit request => accessTokenService.validateAccess(UserAccessRequest.readDataSources(DataSourceId(dataSetName, organizationName)), urlOrHeaderToken(token, request)) { for { - positions <- meshFileService.listMeshChunksForSegment(organizationName, + positions <- meshFileService.listMeshChunksForSegmentV0(organizationName, dataSetName, dataLayerName, request.body) ?~> Messages( @@ -435,15 +435,53 @@ Expects: } @ApiOperation(hidden = true, value = "") - def readMeshChunk(token: Option[String], - organizationName: String, - dataSetName: String, - dataLayerName: String): Action[MeshChunkDataRequest] = - Action.async(validateJson[MeshChunkDataRequest]) { implicit request => + def listMeshChunksForSegmentV1(token: Option[String], + organizationName: String, + dataSetName: String, + dataLayerName: String): Action[ListMeshChunksRequest] = + Action.async(validateJson[ListMeshChunksRequest]) { implicit request => + accessTokenService.validateAccess(UserAccessRequest.readDataSources(DataSourceId(dataSetName, organizationName)), + urlOrHeaderToken(token, request)) { + for { + positions <- meshFileService.listMeshChunksForSegmentV1(organizationName, + dataSetName, + dataLayerName, + request.body) ?~> Messages( + "mesh.file.listChunks.failed", + request.body.segmentId.toString, + request.body.meshFile) ?~> Messages("mesh.file.load.failed", request.body.segmentId.toString) ~> BAD_REQUEST + } yield Ok(Json.toJson(positions)) + } + } + + @ApiOperation(hidden = true, value = "") + def readMeshChunkV0(token: Option[String], + organizationName: String, + dataSetName: String, + dataLayerName: String): Action[MeshChunkDataRequestV0] = + Action.async(validateJson[MeshChunkDataRequestV0]) { implicit request => accessTokenService.validateAccess(UserAccessRequest.readDataSources(DataSourceId(dataSetName, organizationName)), urlOrHeaderToken(token, request)) { for { - (data, encoding) <- meshFileService.readMeshChunk(organizationName, dataSetName, dataLayerName, request.body) ?~> "mesh.file.loadChunk.failed" + (data, encoding) <- meshFileService.readMeshChunkV0(organizationName, dataSetName, dataLayerName, request.body) ?~> "mesh.file.loadChunk.failed" + } yield { + if (encoding.contains("gzip")) { + Ok(data).withHeaders("Content-Encoding" -> "gzip") + } else Ok(data) + } + } + } + + @ApiOperation(hidden = true, value = "") + def readMeshChunkV1(token: Option[String], + organizationName: String, + dataSetName: String, + dataLayerName: String): Action[MeshChunkDataRequestV1] = + Action.async(validateJson[MeshChunkDataRequestV1]) { implicit request => + accessTokenService.validateAccess(UserAccessRequest.readDataSources(DataSourceId(dataSetName, organizationName)), + urlOrHeaderToken(token, request)) { + for { + (data, encoding) <- meshFileService.readMeshChunkV1(organizationName, dataSetName, dataLayerName, request.body) ?~> "mesh.file.loadChunk.failed" } yield { if (encoding.contains("gzip")) { Ok(data).withHeaders("Content-Encoding" -> "gzip") diff --git a/webknossos-datastore/app/com/scalableminds/webknossos/datastore/services/MeshFileService.scala b/webknossos-datastore/app/com/scalableminds/webknossos/datastore/services/MeshFileService.scala index 11df7ae12b6..3821a82d881 100644 --- a/webknossos-datastore/app/com/scalableminds/webknossos/datastore/services/MeshFileService.scala +++ b/webknossos-datastore/app/com/scalableminds/webknossos/datastore/services/MeshFileService.scala @@ -7,16 +7,18 @@ import com.scalableminds.util.tools.{Fox, FoxImplicits} import com.scalableminds.webknossos.datastore.DataStoreConfig import com.scalableminds.webknossos.datastore.storage.{CachedHdf5File, Hdf5FileCache} import com.typesafe.scalalogging.LazyLogging -import net.liftweb.common.Box +import net.liftweb.common.{Box, Empty, Full} import net.liftweb.util.Helpers.tryo +import org.apache.commons.codec.digest.MurmurHash3 import org.apache.commons.io.FilenameUtils import play.api.libs.json.{Json, OFormat} import java.io.ByteArrayInputStream +import java.nio.ByteBuffer import java.nio.file.{Path, Paths} import javax.inject.Inject import scala.collection.JavaConverters._ -import scala.concurrent.ExecutionContext +import scala.concurrent.{ExecutionContext} import scala.util.Using trait GenericJsonFormat[T] {} @@ -30,23 +32,34 @@ object ListMeshChunksRequest { implicit val jsonFormat: OFormat[ListMeshChunksRequest] = Json.format[ListMeshChunksRequest] } -case class MeshChunkDataRequest( +case class MeshChunkDataRequestV0( meshFile: String, position: Vec3Int, segmentId: Long ) -object MeshChunkDataRequest { - implicit val jsonFormat: OFormat[MeshChunkDataRequest] = Json.format[MeshChunkDataRequest] +case class MeshChunkDataRequestV1( + meshFile: String, + fragmentStartOffset: Long, + fragmentSize: Int +) + +object MeshChunkDataRequestV0 { + implicit val jsonFormat: OFormat[MeshChunkDataRequestV0] = Json.format[MeshChunkDataRequestV0] +} + +object MeshChunkDataRequestV1 { + implicit val jsonFormat: OFormat[MeshChunkDataRequestV1] = Json.format[MeshChunkDataRequestV1] } -case class MeshFileNameWithMappingName( +case class MeshFileInfo( meshFileName: String, - mappingName: Option[String] + mappingName: Option[String], + formatVersion: Int ) -object MeshFileNameWithMappingName { - implicit val jsonFormat: OFormat[MeshFileNameWithMappingName] = Json.format[MeshFileNameWithMappingName] +object MeshFileInfo { + implicit val jsonFormat: OFormat[MeshFileInfo] = Json.format[MeshFileInfo] } case class NeuroglancerSegmentInfo(chunkShape: Vec3Float, @@ -58,11 +71,26 @@ case class NeuroglancerSegmentInfo(chunkShape: Vec3Float, fragmentPositions: Array[Array[Vec3Int]], fragmentOffsets: Array[Array[Int]]) -case class MeshfileFragment(position: Vec3Float, byteOffset: Int, byteSize: Int) +case class MeshFragment(position: Vec3Float, byteOffset: Int, byteSize: Int) -case class MeshfileLod(scale: Int, vertexOffset: Vec3Float, chunkShape: Vec3Float, fragments: List[MeshfileFragment]) +object MeshFragment { + implicit val jsonFormat: OFormat[MeshFragment] = Json.format[MeshFragment] +} +case class MeshLodInfo(scale: Int, vertexOffset: Vec3Float, chunkShape: Vec3Float, fragments: List[MeshFragment]) + +object MeshLodInfo { + implicit val jsonFormat: OFormat[MeshLodInfo] = Json.format[MeshLodInfo] +} +case class MeshSegmentInfo(chunkShape: Vec3Float, gridOrigin: Vec3Float, lods: List[MeshLodInfo]) -case class Meshfile(chunkShape: Vec3Float, gridOrigin: Vec3Float, lods: List[MeshfileLod]) +object MeshSegmentInfo { + implicit val jsonFormat: OFormat[MeshSegmentInfo] = Json.format[MeshSegmentInfo] +} +case class WebknossosSegmentInfo(transform: Array[Array[Float]], meshFormat: String, chunks: MeshSegmentInfo) + +object WebknossosSegmentInfo { + implicit val jsonFormat: OFormat[WebknossosSegmentInfo] = Json.format[WebknossosSegmentInfo] +} class MeshFileService @Inject()(config: DataStoreConfig)(implicit ec: ExecutionContext) extends FoxImplicits @@ -72,13 +100,16 @@ class MeshFileService @Inject()(config: DataStoreConfig)(implicit ec: ExecutionC private val meshesDir = "meshes" private val meshFileExtension = "hdf5" private val defaultLevelOfDetail = 0 - private def hashFn: Long => Long = identity + private def getHashFunction(name: String): Long => Long = name match { + case "identity" => identity + case "murmurhash3_x64_128" => + x: Long => + Math.abs(MurmurHash3.hash128x64(ByteBuffer.allocate(8).putLong(x).array())(1)) + } private lazy val meshFileCache = new Hdf5FileCache(30) - def exploreMeshFiles(organizationName: String, - dataSetName: String, - dataLayerName: String): Fox[Set[MeshFileNameWithMappingName]] = { + def exploreMeshFiles(organizationName: String, dataSetName: String, dataLayerName: String): Fox[Set[MeshFileInfo]] = { val layerDir = dataBaseDir.resolve(organizationName).resolve(dataSetName).resolve(dataLayerName) val meshFileNames = PathUtils .listFiles(layerDir.resolve(meshesDir), PathUtils.fileExtensionFilter(meshFileExtension)) @@ -91,27 +122,38 @@ class MeshFileService @Inject()(config: DataStoreConfig)(implicit ec: ExecutionC val meshFilePath = layerDir.resolve(meshesDir).resolve(s"$fileName.$meshFileExtension") mappingNameForMeshFile(meshFilePath) } + + val mappingVersions = meshFileNames.map { fileName => + val meshFilePath = layerDir.resolve(meshesDir).resolve(s"$fileName.$meshFileExtension") + mappingVersionForMeshFile(meshFilePath) + } + for { mappingNameBoxes: Seq[Box[String]] <- Fox.sequence(mappingNameFoxes) + mappingNameOptions = mappingNameBoxes.map(_.toOption) - zipped = meshFileNames.zip(mappingNameOptions).toSet - } yield zipped.map(tuple => MeshFileNameWithMappingName(tuple._1, tuple._2)) + zipped = (meshFileNames, mappingNameOptions, mappingVersions).zipped + } yield zipped.map(MeshFileInfo(_, _, _)).toSet } /* Note that null is a valid value here for once. Meshfiles with no information about the meshFilePath will return Fox.empty, while meshfiles with one marked as empty, will return Fox.successful(null) */ - def mappingNameForMeshFile(meshFilePath: Path): Fox[String] = safeExecute(meshFilePath) { cachedMeshFile => cachedMeshFile.reader.string().getAttr("/", "metadata/mapping_name") } ?~> "mesh.file.readEncoding.failed" - def listMeshChunksForSegment(organizationName: String, - dataSetName: String, - dataLayerName: String, - listMeshChunksRequest: ListMeshChunksRequest): Fox[List[Vec3Int]] = { + def mappingVersionForMeshFile(meshFilePath: Path): Int = + safeExecuteBox(meshFilePath) { cachedMeshFile => + cachedMeshFile.reader.int32().getAttr("/", "metadata/version") + }.toOption.getOrElse(0) + + def listMeshChunksForSegmentV0(organizationName: String, + dataSetName: String, + dataLayerName: String, + listMeshChunksRequest: ListMeshChunksRequest): Fox[List[Vec3Int]] = { val meshFilePath = dataBaseDir .resolve(organizationName) @@ -130,10 +172,12 @@ class MeshFileService @Inject()(config: DataStoreConfig)(implicit ec: ExecutionC }.flatten ?~> "mesh.file.open.failed" } - def listMeshChunksForSegmentNewFormat(organizationName: String, - dataSetName: String, - dataLayerName: String, - listMeshChunksRequest: ListMeshChunksRequest): Fox[List[Vec3Int]] = { + def listMeshChunksForSegmentV1(organizationName: String, + dataSetName: String, + dataLayerName: String, + listMeshChunksRequest: ListMeshChunksRequest): Fox[WebknossosSegmentInfo] = { + // TODO neue routen bauen und entsprechende datentypen zurückgeben + val meshFilePath = dataBaseDir .resolve(organizationName) @@ -145,35 +189,42 @@ class MeshFileService @Inject()(config: DataStoreConfig)(implicit ec: ExecutionC safeExecute(meshFilePath) { cachedMeshFile => val segmentId = listMeshChunksRequest.segmentId val (neuroglancerStart, neuroglancerEnd) = getNeuroglancerOffsets(segmentId, cachedMeshFile) - // TODO transform is actually a matrix - val transform = cachedMeshFile.reader.float32().getAttr("/", "metadata/transform") + val transform = cachedMeshFile.reader.float32().readMatrixBlockWithOffset("metadata/transform", 4, 3, 0, 0) + val encoding = cachedMeshFile.reader.string().getAttr("/", "metadata/mesh_format") + + val lodScaleMultiplier = cachedMeshFile.reader.float32().getAttr("", "metadata/lod_scale_multiplier") val manifest = cachedMeshFile.reader .uint8() - .readArrayBlockWithOffset("neuroglancer", (neuroglancerEnd - neuroglancerStart).toInt, neuroglancerStart) + .readArrayBlockWithOffset("neuroglancer", (neuroglancerEnd - neuroglancerStart + 1).toInt, neuroglancerStart) val segmentInfo = parseNeuroglancerManifest(manifest) - val meshfile = getFragmentsFromSegmentInfo(segmentInfo, transform, neuroglancerStart) - // TODO we need more info than just this, frontend probably needs also quantization bit - segmentInfo.fragmentPositions(defaultLevelOfDetail).toList - } + val meshfile = getFragmentsFromSegmentInfo(segmentInfo, transform, lodScaleMultiplier, neuroglancerStart) + meshfile + .map(meshInfo => WebknossosSegmentInfo(transform = transform, meshFormat = encoding, chunks = meshInfo)) + .toFox + }.flatten } private def getFragmentsFromSegmentInfo(segmentInfo: NeuroglancerSegmentInfo, - transform: Float, - neuroglancerOffsetStart: Long): Meshfile = { - val totalMeshSize = segmentInfo.fragmentOffsets.reduce((a, b) => a.sum + b.sum) + transform: Array[Array[Float]], + lodScaleMultiplier: Float, + neuroglancerOffsetStart: Long): Option[MeshSegmentInfo] = { + val totalMeshSize = segmentInfo.fragmentOffsets.map(_.sum).sum val meshByteStartOffset = neuroglancerOffsetStart - totalMeshSize - val fragmentByteOffsets = segmentInfo.fragmentOffsets.map(_.scanLeft(0)(_ + _)) + val fragmentByteOffsets = segmentInfo.fragmentOffsets.map(_.scanLeft(0)(_ + _)) // This builds a cumulative sum - def computeGlobalPositionAndOffset(lod: Int, currentFragment: Int): MeshfileFragment = { + def computeGlobalPositionAndOffset(lod: Int, currentFragment: Int): Option[MeshFragment] = { val globalPosition = segmentInfo.gridOrigin + segmentInfo .fragmentPositions(lod)(currentFragment) - .toVec3Float * segmentInfo.chunkShape * segmentInfo.lodScales(lod) - - MeshfileFragment( - position = globalPosition * transform, - byteOffset = meshByteStartOffset.toInt + fragmentByteOffsets(lod)(currentFragment), - byteSize = segmentInfo.fragmentOffsets(lod)(currentFragment), - ) + .toVec3Float * segmentInfo.chunkShape * segmentInfo.lodScales(lod) * lodScaleMultiplier + val transformedPosition = globalPosition.matmul(transform) + + transformedPosition.map( + position => + MeshFragment( + position = position, + byteOffset = meshByteStartOffset.toInt + fragmentByteOffsets(lod)(currentFragment), + byteSize = segmentInfo.fragmentOffsets(lod)(currentFragment), + )) } val lods = for (lod <- 0 until segmentInfo.numLods) yield lod @@ -183,13 +234,20 @@ class MeshFileService @Inject()(config: DataStoreConfig)(implicit ec: ExecutionC yield (lod, currentFragment) val fragments = lods.map(lod => fragmentNums(lod).map(x => computeGlobalPositionAndOffset(x._1, x._2)).toList) - val meshfileLods = lods.map( - lod => - MeshfileLod(scale = segmentInfo.lodScales(lod).toInt, - vertexOffset = segmentInfo.vertexOffsets(lod), - chunkShape = segmentInfo.chunkShape, - fragments = fragments(lod))).toList - Meshfile(chunkShape = segmentInfo.chunkShape, gridOrigin = segmentInfo.gridOrigin, lods = meshfileLods) + if (fragments.contains(None)) + None + else { + val meshfileLods = lods + .map( + lod => + MeshLodInfo(scale = segmentInfo.lodScales(lod).toInt, + vertexOffset = segmentInfo.vertexOffsets(lod), + chunkShape = segmentInfo.chunkShape, + fragments = fragments(lod).flatten)) + .toList + Some( + MeshSegmentInfo(chunkShape = segmentInfo.chunkShape, gridOrigin = segmentInfo.gridOrigin, lods = meshfileLods)) + } } private def parseNeuroglancerManifest(manifest: Array[Byte]): NeuroglancerSegmentInfo = { // All Ints here should be UInt32 per spec. @@ -248,29 +306,29 @@ class MeshFileService @Inject()(config: DataStoreConfig)(implicit ec: ExecutionC private def getNeuroglancerOffsets(segmentId: Long, cachedMeshFile: CachedHdf5File): (Long, Long) = { val nBuckets = cachedMeshFile.reader.uint64().getAttr("/", "metadata/n_buckets") - // TODO get hashfunction from metadata - val bucketIndex = hashFn(segmentId) % nBuckets + val hashName = cachedMeshFile.reader.string().getAttr("/", "metadata/hash_function") + + val bucketIndex = getHashFunction(hashName)(segmentId) % nBuckets val cappedBucketIndex = bucketIndex.toInt val bucketOffsets = cachedMeshFile.reader.uint64().readArrayBlockWithOffset("bucket_offsets", 2, bucketIndex) val bucketStart = bucketOffsets(cappedBucketIndex) val cappedBucketStart = bucketStart.toInt val bucketEnd = bucketOffsets(cappedBucketIndex + 1) val cappedBucketEnd = bucketEnd.toInt - // TODO is this access correct? val buckets = cachedMeshFile.reader .uint64() .readMatrixBlockWithOffset("buckets", cappedBucketEnd - cappedBucketStart + 1, 3, bucketStart, 0) - // TODO does this work as intended? + val bucketLocalOffset = buckets.map(_(0)).indexOf(segmentId) val neuroglancerStart = buckets(bucketLocalOffset)(1) val neuroglancerEnd = buckets(bucketLocalOffset)(2) (neuroglancerStart, neuroglancerEnd) } - def readMeshChunk(organizationName: String, - dataSetName: String, - dataLayerName: String, - meshChunkDataRequest: MeshChunkDataRequest): Fox[(Array[Byte], String)] = { + def readMeshChunkV0(organizationName: String, + dataSetName: String, + dataLayerName: String, + meshChunkDataRequest: MeshChunkDataRequestV0): Fox[(Array[Byte], String)] = { val meshFilePath = dataBaseDir .resolve(organizationName) .resolve(dataSetName) @@ -287,11 +345,11 @@ class MeshFileService @Inject()(config: DataStoreConfig)(implicit ec: ExecutionC } ?~> "mesh.file.readData.failed" } - - def readMeshChunkNewFormat(organizationName: String, - dataSetName: String, - dataLayerName: String, - meshChunkDataRequest: MeshChunkDataRequest, fragmentStartOffset: Long, fragmentSize: Int): Fox[(Array[Byte], String)] = { + def readMeshChunkV1(organizationName: String, + dataSetName: String, + dataLayerName: String, + meshChunkDataRequest: MeshChunkDataRequestV1, + ): Fox[(Array[Byte], String)] = { val meshFilePath = dataBaseDir .resolve(organizationName) .resolve(dataSetName) @@ -301,7 +359,12 @@ class MeshFileService @Inject()(config: DataStoreConfig)(implicit ec: ExecutionC safeExecute(meshFilePath) { cachedMeshFile => val meshFormat = cachedMeshFile.reader.string().getAttr("/", "metadata/mesh_format") - val data = cachedMeshFile.reader.uint8().readArrayBlockWithOffset("neuroglancer", fragmentSize, fragmentStartOffset) + val data = + cachedMeshFile.reader + .uint8() + .readArrayBlockWithOffset("neuroglancer", + meshChunkDataRequest.fragmentSize, + meshChunkDataRequest.fragmentStartOffset) (data, meshFormat) } ?~> "mesh.file.readData.failed" } @@ -314,6 +377,18 @@ class MeshFileService @Inject()(config: DataStoreConfig)(implicit ec: ExecutionC }.toFox } yield result + private def safeExecuteBox[T](filePath: Path)(block: CachedHdf5File => T): Box[T] = + for { + _ <- if (filePath.toFile.exists()) { + new Full + } else { + Empty ~> "mesh.file.open.failed" + } + result <- Using(meshFileCache.withCache(filePath)(CachedHdf5File.fromPath)) { + block + }.toOption + } yield result + private def positionLiteral(position: Vec3Int) = s"${position.x}_${position.y}_${position.z}" diff --git a/webknossos-datastore/conf/com.scalableminds.webknossos.datastore.routes b/webknossos-datastore/conf/com.scalableminds.webknossos.datastore.routes index 4848e40ac6f..7ef4caa6bd7 100644 --- a/webknossos-datastore/conf/com.scalableminds.webknossos.datastore.routes +++ b/webknossos-datastore/conf/com.scalableminds.webknossos.datastore.routes @@ -56,8 +56,11 @@ POST /datasets/:organizationName/:dataSetName/layers/:dataLayerName/agg # Mesh files GET /datasets/:organizationName/:dataSetName/layers/:dataLayerName/meshes @com.scalableminds.webknossos.datastore.controllers.DataSourceController.listMeshFiles(token: Option[String], organizationName: String, dataSetName: String, dataLayerName: String) -POST /datasets/:organizationName/:dataSetName/layers/:dataLayerName/meshes/chunks @com.scalableminds.webknossos.datastore.controllers.DataSourceController.listMeshChunksForSegment(token: Option[String], organizationName: String, dataSetName: String, dataLayerName: String) -POST /datasets/:organizationName/:dataSetName/layers/:dataLayerName/meshes/chunks/data @com.scalableminds.webknossos.datastore.controllers.DataSourceController.readMeshChunk(token: Option[String], organizationName: String, dataSetName: String, dataLayerName: String) +POST /datasets/:organizationName/:dataSetName/layers/:dataLayerName/meshes/chunks @com.scalableminds.webknossos.datastore.controllers.DataSourceController.listMeshChunksForSegmentV0(token: Option[String], organizationName: String, dataSetName: String, dataLayerName: String) +POST /datasets/:organizationName/:dataSetName/layers/:dataLayerName/meshes/chunks/data @com.scalableminds.webknossos.datastore.controllers.DataSourceController.readMeshChunkV0(token: Option[String], organizationName: String, dataSetName: String, dataLayerName: String) +POST /datasets/:organizationName/:dataSetName/layers/:dataLayerName/v1/meshes/chunks @com.scalableminds.webknossos.datastore.controllers.DataSourceController.listMeshChunksForSegmentV1(token: Option[String], organizationName: String, dataSetName: String, dataLayerName: String) +POST /datasets/:organizationName/:dataSetName/layers/:dataLayerName/v1/meshes/chunks/data @com.scalableminds.webknossos.datastore.controllers.DataSourceController.readMeshChunkV1(token: Option[String], organizationName: String, dataSetName: String, dataLayerName: String) + # Connectome files GET /datasets/:organizationName/:dataSetName/layers/:dataLayerName/connectomes @com.scalableminds.webknossos.datastore.controllers.DataSourceController.listConnectomeFiles(token: Option[String], organizationName: String, dataSetName: String, dataLayerName: String) From ca0690c74c5f8835ed3f977b8887c914bd428340 Mon Sep 17 00:00:00 2001 From: leowe Date: Mon, 26 Sep 2022 19:08:07 +0200 Subject: [PATCH 05/63] add small todo --- .../webknossos/datastore/services/MeshFileService.scala | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/webknossos-datastore/app/com/scalableminds/webknossos/datastore/services/MeshFileService.scala b/webknossos-datastore/app/com/scalableminds/webknossos/datastore/services/MeshFileService.scala index 3821a82d881..e52b953688f 100644 --- a/webknossos-datastore/app/com/scalableminds/webknossos/datastore/services/MeshFileService.scala +++ b/webknossos-datastore/app/com/scalableminds/webknossos/datastore/services/MeshFileService.scala @@ -55,7 +55,7 @@ object MeshChunkDataRequestV1 { case class MeshFileInfo( meshFileName: String, mappingName: Option[String], - formatVersion: Int + formatVersion: Long ) object MeshFileInfo { @@ -216,6 +216,7 @@ class MeshFileService @Inject()(config: DataStoreConfig)(implicit ec: ExecutionC val globalPosition = segmentInfo.gridOrigin + segmentInfo .fragmentPositions(lod)(currentFragment) .toVec3Float * segmentInfo.chunkShape * segmentInfo.lodScales(lod) * lodScaleMultiplier + // todo this is still the wrong way around val transformedPosition = globalPosition.matmul(transform) transformedPosition.map( From 0865d99ec8f2be7ecda42ee4a4a8fb60728043bb Mon Sep 17 00:00:00 2001 From: leowe Date: Tue, 27 Sep 2022 13:37:32 +0200 Subject: [PATCH 06/63] add dummy draco route --- binaryData/draco_file.bin | Bin 0 -> 251 bytes .../util/geometry/Vec3Float.scala | 10 +- .../controllers/DataSourceController.scala | 6 + .../datastore/services/MeshFileService.scala | 106 ++++++++++-------- ....scalableminds.webknossos.datastore.routes | 2 +- 5 files changed, 67 insertions(+), 57 deletions(-) create mode 100644 binaryData/draco_file.bin diff --git a/binaryData/draco_file.bin b/binaryData/draco_file.bin new file mode 100644 index 0000000000000000000000000000000000000000..96ec360ddbfef72332e9fde2f3bd34fa2ca6357d GIT binary patch literal 251 zcmV)B3}%UkOd?Jr8rgk~f~*4|bojJJO?w9xUW0^R z3@`#C*tQ#hN(6s|!VKUE+ChjrKt6sRiT;SkGr%vQ0OT2P z4>WH*xZ&j)8oLrO(-Mej0RZS9k%A#c*ra}V%gCn5Vd+#I4)}zbCxAUIlr|Fp5#K=r zD)LgeR*z(>1BSso@%I7L1|#h_yQgXe000000RIC30I#64LN8J}LwdNFLtsh!K?(<^ BTtNT; literal 0 HcmV?d00001 diff --git a/util/src/main/scala/com/scalableminds/util/geometry/Vec3Float.scala b/util/src/main/scala/com/scalableminds/util/geometry/Vec3Float.scala index f9557fb68e6..40de93c024f 100644 --- a/util/src/main/scala/com/scalableminds/util/geometry/Vec3Float.scala +++ b/util/src/main/scala/com/scalableminds/util/geometry/Vec3Float.scala @@ -6,19 +6,11 @@ case class Vec3Float(x: Float, y: Float, z: Float) { def scale(s: Float): Vec3Float = Vec3Float(x * s, y * s, z * s) def *(s: Float): Vec3Float = scale(s) + def *(s: Double): Vec3Float = scale(s.toFloat) def *(that: Vec3Float): Vec3Float = Vec3Float(x * that.x, y * that.y, z * that.z) def +(that: Vec3Float): Vec3Float = Vec3Float(x + that.x, y + that.y, z + that.y) def toList: List[Float] = List(x, y, z) - def matmul(that: Array[Array[Float]]): Option[Vec3Float] = { - val l: Array[Float] = this.toList.toArray ++ Array[Float](1.0.toFloat) - val result: Array[Array[Float]] = that.map(xs => xs.zip(l).map{case (x,y) => x * y}) - - if (that.length < 3 || that(0).length < 3) - None - else - Some(Vec3Float(result(0).sum, result(1).sum, result(2).sum)) - } } object Vec3Float { diff --git a/webknossos-datastore/app/com/scalableminds/webknossos/datastore/controllers/DataSourceController.scala b/webknossos-datastore/app/com/scalableminds/webknossos/datastore/controllers/DataSourceController.scala index 7ed93fc8abd..541fd47c1b9 100644 --- a/webknossos-datastore/app/com/scalableminds/webknossos/datastore/controllers/DataSourceController.scala +++ b/webknossos-datastore/app/com/scalableminds/webknossos/datastore/controllers/DataSourceController.scala @@ -400,6 +400,12 @@ Expects: } } + def dummyDracoFile(): Action[AnyContent] = Action.async { implicit request => + for { + draco <- meshFileService.readDummyDraco() + } yield Ok(Json.toJson(draco)) + } + @ApiOperation(hidden = true, value = "") def listMeshFiles(token: Option[String], organizationName: String, diff --git a/webknossos-datastore/app/com/scalableminds/webknossos/datastore/services/MeshFileService.scala b/webknossos-datastore/app/com/scalableminds/webknossos/datastore/services/MeshFileService.scala index e52b953688f..2f6a6fcb5f6 100644 --- a/webknossos-datastore/app/com/scalableminds/webknossos/datastore/services/MeshFileService.scala +++ b/webknossos-datastore/app/com/scalableminds/webknossos/datastore/services/MeshFileService.scala @@ -15,10 +15,10 @@ import play.api.libs.json.{Json, OFormat} import java.io.ByteArrayInputStream import java.nio.ByteBuffer -import java.nio.file.{Path, Paths} +import java.nio.file.{Files, Path, Paths} import javax.inject.Inject import scala.collection.JavaConverters._ -import scala.concurrent.{ExecutionContext} +import scala.concurrent.ExecutionContext import scala.util.Using trait GenericJsonFormat[T] {} @@ -86,7 +86,7 @@ case class MeshSegmentInfo(chunkShape: Vec3Float, gridOrigin: Vec3Float, lods: L object MeshSegmentInfo { implicit val jsonFormat: OFormat[MeshSegmentInfo] = Json.format[MeshSegmentInfo] } -case class WebknossosSegmentInfo(transform: Array[Array[Float]], meshFormat: String, chunks: MeshSegmentInfo) +case class WebknossosSegmentInfo(transform: Array[Array[Double]], meshFormat: String, chunks: MeshSegmentInfo) object WebknossosSegmentInfo { implicit val jsonFormat: OFormat[WebknossosSegmentInfo] = Json.format[WebknossosSegmentInfo] @@ -109,6 +109,11 @@ class MeshFileService @Inject()(config: DataStoreConfig)(implicit ec: ExecutionC private lazy val meshFileCache = new Hdf5FileCache(30) + def readDummyDraco(): Fox[Array[Byte]] = { + val path = dataBaseDir.resolve("draco_file.bin") + tryo(Files.readAllBytes(path)).toOption.toFox + } + def exploreMeshFiles(organizationName: String, dataSetName: String, dataLayerName: String): Fox[Set[MeshFileInfo]] = { val layerDir = dataBaseDir.resolve(organizationName).resolve(dataSetName).resolve(dataLayerName) val meshFileNames = PathUtils @@ -118,21 +123,22 @@ class MeshFileService @Inject()(config: DataStoreConfig)(implicit ec: ExecutionC } .toOption .getOrElse(Nil) - val mappingNameFoxes = meshFileNames.map { fileName => + + val meshFileVersions = meshFileNames.map { fileName => val meshFilePath = layerDir.resolve(meshesDir).resolve(s"$fileName.$meshFileExtension") - mappingNameForMeshFile(meshFilePath) + mappingVersionForMeshFile(meshFilePath) } - val mappingVersions = meshFileNames.map { fileName => + val mappingNameFoxes = (meshFileNames, meshFileVersions).zipped.map { (fileName, fileVersion) => val meshFilePath = layerDir.resolve(meshesDir).resolve(s"$fileName.$meshFileExtension") - mappingVersionForMeshFile(meshFilePath) + mappingNameForMeshFile(meshFilePath, fileVersion) } for { mappingNameBoxes: Seq[Box[String]] <- Fox.sequence(mappingNameFoxes) mappingNameOptions = mappingNameBoxes.map(_.toOption) - zipped = (meshFileNames, mappingNameOptions, mappingVersions).zipped + zipped = (meshFileNames, mappingNameOptions, meshFileVersions).zipped } yield zipped.map(MeshFileInfo(_, _, _)).toSet } @@ -140,14 +146,21 @@ class MeshFileService @Inject()(config: DataStoreConfig)(implicit ec: ExecutionC Note that null is a valid value here for once. Meshfiles with no information about the meshFilePath will return Fox.empty, while meshfiles with one marked as empty, will return Fox.successful(null) */ - def mappingNameForMeshFile(meshFilePath: Path): Fox[String] = - safeExecute(meshFilePath) { cachedMeshFile => - cachedMeshFile.reader.string().getAttr("/", "metadata/mapping_name") - } ?~> "mesh.file.readEncoding.failed" + def mappingNameForMeshFile(meshFilePath: Path, meshFileVersion: Long): Fox[String] = { + if (meshFileVersion == 0) { + safeExecute(meshFilePath) { cachedMeshFile => + cachedMeshFile.reader.string().getAttr("/", "metadata/mapping_name") + } ?~> "mesh.file.readEncoding.failed" + } else { + safeExecute(meshFilePath) { cachedMeshFile => + cachedMeshFile.reader.string().getAttr("/", "mapping_name") + } ?~> "mesh.file.readEncoding.failed" + } + } - def mappingVersionForMeshFile(meshFilePath: Path): Int = + def mappingVersionForMeshFile(meshFilePath: Path): Long = safeExecuteBox(meshFilePath) { cachedMeshFile => - cachedMeshFile.reader.int32().getAttr("/", "metadata/version") + cachedMeshFile.reader.int64().getAttr("/", "version") }.toOption.getOrElse(0) def listMeshChunksForSegmentV0(organizationName: String, @@ -176,8 +189,6 @@ class MeshFileService @Inject()(config: DataStoreConfig)(implicit ec: ExecutionC dataSetName: String, dataLayerName: String, listMeshChunksRequest: ListMeshChunksRequest): Fox[WebknossosSegmentInfo] = { - // TODO neue routen bauen und entsprechende datentypen zurückgeben - val meshFilePath = dataBaseDir .resolve(organizationName) @@ -186,18 +197,25 @@ class MeshFileService @Inject()(config: DataStoreConfig)(implicit ec: ExecutionC .resolve(meshesDir) .resolve(s"${listMeshChunksRequest.meshFile}.$meshFileExtension") + println(s"Reading $meshFilePath") + safeExecute(meshFilePath) { cachedMeshFile => val segmentId = listMeshChunksRequest.segmentId + println(s"Reading $segmentId") + val encoding = cachedMeshFile.reader.string().getAttr("/", "mesh_format") + val lodScaleMultiplier = cachedMeshFile.reader.float64().getAttr("/", "lod_scale_multiplier") + println(s"encoding: $encoding") + val transform = cachedMeshFile.reader.float64().readMatrixBlockWithOffset("/transform", 3, 4, 0, 0) + println(s"transform: ${transform.mkString("Array(", ", ", ")")}") + val (neuroglancerStart, neuroglancerEnd) = getNeuroglancerOffsets(segmentId, cachedMeshFile) - val transform = cachedMeshFile.reader.float32().readMatrixBlockWithOffset("metadata/transform", 4, 3, 0, 0) - val encoding = cachedMeshFile.reader.string().getAttr("/", "metadata/mesh_format") + println(s"from $neuroglancerStart to $neuroglancerEnd") - val lodScaleMultiplier = cachedMeshFile.reader.float32().getAttr("", "metadata/lod_scale_multiplier") val manifest = cachedMeshFile.reader .uint8() - .readArrayBlockWithOffset("neuroglancer", (neuroglancerEnd - neuroglancerStart + 1).toInt, neuroglancerStart) + .readArrayBlockWithOffset("/neuroglancer", (neuroglancerEnd - neuroglancerStart + 1).toInt, neuroglancerStart) val segmentInfo = parseNeuroglancerManifest(manifest) - val meshfile = getFragmentsFromSegmentInfo(segmentInfo, transform, lodScaleMultiplier, neuroglancerStart) + val meshfile = getFragmentsFromSegmentInfo(segmentInfo, lodScaleMultiplier, neuroglancerStart) meshfile .map(meshInfo => WebknossosSegmentInfo(transform = transform, meshFormat = encoding, chunks = meshInfo)) .toFox @@ -205,27 +223,22 @@ class MeshFileService @Inject()(config: DataStoreConfig)(implicit ec: ExecutionC } private def getFragmentsFromSegmentInfo(segmentInfo: NeuroglancerSegmentInfo, - transform: Array[Array[Float]], - lodScaleMultiplier: Float, + lodScaleMultiplier: Double, neuroglancerOffsetStart: Long): Option[MeshSegmentInfo] = { val totalMeshSize = segmentInfo.fragmentOffsets.map(_.sum).sum val meshByteStartOffset = neuroglancerOffsetStart - totalMeshSize val fragmentByteOffsets = segmentInfo.fragmentOffsets.map(_.scanLeft(0)(_ + _)) // This builds a cumulative sum - def computeGlobalPositionAndOffset(lod: Int, currentFragment: Int): Option[MeshFragment] = { + def computeGlobalPositionAndOffset(lod: Int, currentFragment: Int): MeshFragment = { val globalPosition = segmentInfo.gridOrigin + segmentInfo .fragmentPositions(lod)(currentFragment) .toVec3Float * segmentInfo.chunkShape * segmentInfo.lodScales(lod) * lodScaleMultiplier - // todo this is still the wrong way around - val transformedPosition = globalPosition.matmul(transform) - transformedPosition.map( - position => MeshFragment( - position = position, + position = globalPosition, // This position is in Voxel Space byteOffset = meshByteStartOffset.toInt + fragmentByteOffsets(lod)(currentFragment), byteSize = segmentInfo.fragmentOffsets(lod)(currentFragment), - )) + ) } val lods = for (lod <- 0 until segmentInfo.numLods) yield lod @@ -235,20 +248,16 @@ class MeshFileService @Inject()(config: DataStoreConfig)(implicit ec: ExecutionC yield (lod, currentFragment) val fragments = lods.map(lod => fragmentNums(lod).map(x => computeGlobalPositionAndOffset(x._1, x._2)).toList) - if (fragments.contains(None)) - None - else { - val meshfileLods = lods - .map( - lod => - MeshLodInfo(scale = segmentInfo.lodScales(lod).toInt, - vertexOffset = segmentInfo.vertexOffsets(lod), - chunkShape = segmentInfo.chunkShape, - fragments = fragments(lod).flatten)) - .toList - Some( - MeshSegmentInfo(chunkShape = segmentInfo.chunkShape, gridOrigin = segmentInfo.gridOrigin, lods = meshfileLods)) - } + val meshfileLods = lods + .map( + lod => + MeshLodInfo(scale = segmentInfo.lodScales(lod).toInt, + vertexOffset = segmentInfo.vertexOffsets(lod), + chunkShape = segmentInfo.chunkShape, + fragments = fragments(lod))) + .toList + Some( + MeshSegmentInfo(chunkShape = segmentInfo.chunkShape, gridOrigin = segmentInfo.gridOrigin, lods = meshfileLods)) } private def parseNeuroglancerManifest(manifest: Array[Byte]): NeuroglancerSegmentInfo = { // All Ints here should be UInt32 per spec. @@ -306,8 +315,11 @@ class MeshFileService @Inject()(config: DataStoreConfig)(implicit ec: ExecutionC } private def getNeuroglancerOffsets(segmentId: Long, cachedMeshFile: CachedHdf5File): (Long, Long) = { - val nBuckets = cachedMeshFile.reader.uint64().getAttr("/", "metadata/n_buckets") - val hashName = cachedMeshFile.reader.string().getAttr("/", "metadata/hash_function") + val nBuckets = cachedMeshFile.reader.uint64().getAttr("/", "n_buckets") + val hashName = cachedMeshFile.reader.string().getAttr("/", "hash_function") + + println(s"nBuckets: $nBuckets") + println(s"hashName: $hashName") val bucketIndex = getHashFunction(hashName)(segmentId) % nBuckets val cappedBucketIndex = bucketIndex.toInt @@ -359,7 +371,7 @@ class MeshFileService @Inject()(config: DataStoreConfig)(implicit ec: ExecutionC .resolve(s"${meshChunkDataRequest.meshFile}.$meshFileExtension") safeExecute(meshFilePath) { cachedMeshFile => - val meshFormat = cachedMeshFile.reader.string().getAttr("/", "metadata/mesh_format") + val meshFormat = cachedMeshFile.reader.string().getAttr("/", "mesh_format") val data = cachedMeshFile.reader .uint8() diff --git a/webknossos-datastore/conf/com.scalableminds.webknossos.datastore.routes b/webknossos-datastore/conf/com.scalableminds.webknossos.datastore.routes index 7ef4caa6bd7..b92f4d95825 100644 --- a/webknossos-datastore/conf/com.scalableminds.webknossos.datastore.routes +++ b/webknossos-datastore/conf/com.scalableminds.webknossos.datastore.routes @@ -60,7 +60,7 @@ POST /datasets/:organizationName/:dataSetName/layers/:dataLayerName/mes POST /datasets/:organizationName/:dataSetName/layers/:dataLayerName/meshes/chunks/data @com.scalableminds.webknossos.datastore.controllers.DataSourceController.readMeshChunkV0(token: Option[String], organizationName: String, dataSetName: String, dataLayerName: String) POST /datasets/:organizationName/:dataSetName/layers/:dataLayerName/v1/meshes/chunks @com.scalableminds.webknossos.datastore.controllers.DataSourceController.listMeshChunksForSegmentV1(token: Option[String], organizationName: String, dataSetName: String, dataLayerName: String) POST /datasets/:organizationName/:dataSetName/layers/:dataLayerName/v1/meshes/chunks/data @com.scalableminds.webknossos.datastore.controllers.DataSourceController.readMeshChunkV1(token: Option[String], organizationName: String, dataSetName: String, dataLayerName: String) - +GET /datasets/dummyDraco @com.scalableminds.webknossos.datastore.controllers.DataSourceController.dummyDracoFile() # Connectome files GET /datasets/:organizationName/:dataSetName/layers/:dataLayerName/connectomes @com.scalableminds.webknossos.datastore.controllers.DataSourceController.listConnectomeFiles(token: Option[String], organizationName: String, dataSetName: String, dataLayerName: String) From 56cd3f7c772be2c8bff890dc94f195d6dc3334fb Mon Sep 17 00:00:00 2001 From: leowe Date: Tue, 27 Sep 2022 14:12:57 +0200 Subject: [PATCH 07/63] remove draco file from binaryData --- binaryData/draco_file.bin | Bin 251 -> 0 bytes 1 file changed, 0 insertions(+), 0 deletions(-) delete mode 100644 binaryData/draco_file.bin diff --git a/binaryData/draco_file.bin b/binaryData/draco_file.bin deleted file mode 100644 index 96ec360ddbfef72332e9fde2f3bd34fa2ca6357d..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 251 zcmV)B3}%UkOd?Jr8rgk~f~*4|bojJJO?w9xUW0^R z3@`#C*tQ#hN(6s|!VKUE+ChjrKt6sRiT;SkGr%vQ0OT2P z4>WH*xZ&j)8oLrO(-Mej0RZS9k%A#c*ra}V%gCn5Vd+#I4)}zbCxAUIlr|Fp5#K=r zD)LgeR*z(>1BSso@%I7L1|#h_yQgXe000000RIC30I#64LN8J}LwdNFLtsh!K?(<^ BTtNT; From 786129c912cd7afc4826af4ffaa1f29c19c911b1 Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Tue, 27 Sep 2022 15:54:26 +0200 Subject: [PATCH 08/63] add dummy loading of draco encoded file --- frontend/javascripts/admin/admin_rest_api.ts | 17 ++++++++ .../oxalis/model/sagas/isosurface_saga.ts | 40 +++++++++++++++++++ .../oxalis/view/action_bar_view.tsx | 5 +++ package.json | 1 + yarn.lock | 5 +++ 5 files changed, 68 insertions(+) diff --git a/frontend/javascripts/admin/admin_rest_api.ts b/frontend/javascripts/admin/admin_rest_api.ts index d1949635572..45c4016a254 100644 --- a/frontend/javascripts/admin/admin_rest_api.ts +++ b/frontend/javascripts/admin/admin_rest_api.ts @@ -2165,6 +2165,23 @@ export function getMeshfileChunkData( }); } +export function getDummyDraco(): Promise { + return doWithToken(async (token) => { + const data = await Request.receiveArraybuffer(`/assets/draco_file.bin`, { + // const data = await Request.receiveArraybuffer(`/data/datasets/dummyDraco?token=${token}`, { + useWebworkerForArrayBuffer: false, + }); + + console.log("works", data, new Uint8Array(data)); + + const data2 = await Request.receiveArraybuffer(`/data/datasets/dummyDraco?token=${token}`, { + useWebworkerForArrayBuffer: false, + }); + console.log("doesnt work", data2, new Uint8Array(data2)); + return data2; + }); +} + // ### Connectomes export function getConnectomeFilesForDatasetLayer( dataStoreUrl: string, diff --git a/frontend/javascripts/oxalis/model/sagas/isosurface_saga.ts b/frontend/javascripts/oxalis/model/sagas/isosurface_saga.ts index 9ed29a8afd7..f000cf2081d 100644 --- a/frontend/javascripts/oxalis/model/sagas/isosurface_saga.ts +++ b/frontend/javascripts/oxalis/model/sagas/isosurface_saga.ts @@ -4,6 +4,8 @@ import { V3 } from "libs/mjs"; import { sleep } from "libs/utils"; import ErrorHandling from "libs/error_handling"; import type { APIDataLayer } from "types/api_flow_types"; +import "libs/DRACOLoader.js"; + import { ResolutionInfo, getResolutionInfo, @@ -42,6 +44,7 @@ import { sendAnalyticsEvent, getMeshfileChunksForSegment, getMeshfileChunkData, + getDummyDraco, } from "admin/admin_rest_api"; import { getFlooredPosition } from "oxalis/model/accessors/flycam_accessor"; import { setImportingMeshStateAction } from "oxalis/model/actions/ui_actions"; @@ -60,6 +63,8 @@ import messages from "messages"; import processTaskWithPool from "libs/task_pool"; import { getBaseSegmentationName } from "oxalis/view/right-border-tabs/segments_tab/segments_view_helper"; import { UpdateSegmentAction } from "../actions/volumetracing_actions"; +import * as THREE from "three"; + const MAX_RETRY_COUNT = 5; const RETRY_WAIT_TIME = 5000; const MESH_CHUNK_THROTTLE_DELAY = 500; @@ -602,6 +607,40 @@ function* loadPrecomputedMeshForSegmentId( yield* put(finishedLoadingIsosurfaceAction(layerName, id)); } +function* addDummyDraco() { + const buffer = yield* call(getDummyDraco); + console.log("buffer", buffer); + + const loader = new THREE.DRACOLoader(); + console.log("THREE.DRACOLoader", loader); + + loader.setDecoderPath( + "https://raw.githubusercontent.com/mrdoob/three.js/dev/examples/js/libs/draco/", + ); + loader.setDecoderConfig({ type: "js" }); + + const sceneController = yield* call(getSceneController); + + // const url = "/data/datasets/dummyDraco"; + const url = "/assets/draco_file.bin"; + // const url = "http://localhost:9000/assets/bunny.drc"; + // loader.load(url, (geometry) => { + loader.decodeDracoFile(buffer, (geometry) => { + // geometry.computeVertexNormals(); + + // todo: use correct id + sceneController.addIsosurfaceFromGeometry(geometry, 2347819234); + + // Release decoder resources. + loader.dispose(); + }); + + // const decoderModule = yield* call(() => draco3d.createDecoderModule({})); + // let decoder = new decoderModule.Decoder(); + // console.log("decoder"); + // const geometry = yield* call(parseStlBuffer, stlData); +} + /* * * Ad Hoc and Precomputed Meshes @@ -689,4 +728,5 @@ export default function* isosurfaceSaga(): Saga { yield* takeEvery("UPDATE_ISOSURFACE_VISIBILITY", handleIsosurfaceVisibilityChange); yield* takeEvery(["START_EDITING", "COPY_SEGMENTATION_LAYER"], markEditedCellAsDirty); yield* takeEvery(["UPDATE_SEGMENT"], handleIsosurfaceColorChange); + yield* takeEvery(["ADD_DUMMY_DRACO"], addDummyDraco); } diff --git a/frontend/javascripts/oxalis/view/action_bar_view.tsx b/frontend/javascripts/oxalis/view/action_bar_view.tsx index 7370f1d9794..bdcc58c0de4 100644 --- a/frontend/javascripts/oxalis/view/action_bar_view.tsx +++ b/frontend/javascripts/oxalis/view/action_bar_view.tsx @@ -28,6 +28,7 @@ import { getVisibleSegmentationLayer, } from "oxalis/model/accessors/dataset_accessor"; import { AsyncButton } from "components/async_clickables"; +import ButtonComponent from "./components/button_component"; const VersionRestoreWarning = ( { {!isReadOnly && constants.MODES_PLANE.indexOf(viewMode) > -1 ? : null} {isArbitrarySupported && !is2d ? : null} {isViewMode ? this.renderStartTracingButton() : null} + + Store.dispatch({ type: "ADD_DUMMY_DRACO" })}> + ADD_DUMMY_DRACO + Date: Tue, 27 Sep 2022 15:54:39 +0200 Subject: [PATCH 09/63] add dummy draco file --- public/draco_file.bin | Bin 0 -> 251 bytes 1 file changed, 0 insertions(+), 0 deletions(-) create mode 100644 public/draco_file.bin diff --git a/public/draco_file.bin b/public/draco_file.bin new file mode 100644 index 0000000000000000000000000000000000000000..96ec360ddbfef72332e9fde2f3bd34fa2ca6357d GIT binary patch literal 251 zcmV)B3}%UkOd?Jr8rgk~f~*4|bojJJO?w9xUW0^R z3@`#C*tQ#hN(6s|!VKUE+ChjrKt6sRiT;SkGr%vQ0OT2P z4>WH*xZ&j)8oLrO(-Mej0RZS9k%A#c*ra}V%gCn5Vd+#I4)}zbCxAUIlr|Fp5#K=r zD)LgeR*z(>1BSso@%I7L1|#h_yQgXe000000RIC30I#64LN8J}LwdNFLtsh!K?(<^ BTtNT; literal 0 HcmV?d00001 From 220a97a4a759ff3dd0347661eba861089d0d1993 Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Tue, 27 Sep 2022 16:13:40 +0200 Subject: [PATCH 10/63] add draco loader --- frontend/javascripts/libs/DRACOLoader.js | 467 +++++++++++++++++++++++ 1 file changed, 467 insertions(+) create mode 100644 frontend/javascripts/libs/DRACOLoader.js diff --git a/frontend/javascripts/libs/DRACOLoader.js b/frontend/javascripts/libs/DRACOLoader.js new file mode 100644 index 00000000000..c04219bf122 --- /dev/null +++ b/frontend/javascripts/libs/DRACOLoader.js @@ -0,0 +1,467 @@ +import * as THREE from "three"; + +(function () { + const _taskCache = new WeakMap(); + + class DRACOLoader extends THREE.Loader { + constructor(manager) { + super(manager); + this.decoderPath = ""; + this.decoderConfig = {}; + this.decoderBinary = null; + this.decoderPending = null; + this.workerLimit = 4; + this.workerPool = []; + this.workerNextTaskID = 1; + this.workerSourceURL = ""; + this.defaultAttributeIDs = { + position: "POSITION", + normal: "NORMAL", + color: "COLOR", + uv: "TEX_COORD", + }; + this.defaultAttributeTypes = { + position: "Float32Array", + normal: "Float32Array", + color: "Float32Array", + uv: "Float32Array", + }; + } + + setDecoderPath(path) { + this.decoderPath = path; + return this; + } + + setDecoderConfig(config) { + this.decoderConfig = config; + return this; + } + + setWorkerLimit(workerLimit) { + this.workerLimit = workerLimit; + return this; + } + + load(url, onLoad, onProgress, onError) { + const loader = new THREE.FileLoader(this.manager); + loader.setPath(this.path); + loader.setResponseType("arraybuffer"); + loader.setRequestHeader(this.requestHeader); + loader.setWithCredentials(this.withCredentials); + loader.load( + url, + (buffer) => { + this.decodeDracoFile(buffer, onLoad).catch(onError); + }, + onProgress, + onError, + ); + } + + decodeDracoFile(buffer, callback, attributeIDs, attributeTypes) { + const taskConfig = { + attributeIDs: attributeIDs || this.defaultAttributeIDs, + attributeTypes: attributeTypes || this.defaultAttributeTypes, + useUniqueIDs: !!attributeIDs, + }; + return this.decodeGeometry(buffer, taskConfig).then(callback); + } + + decodeGeometry(buffer, taskConfig) { + const taskKey = JSON.stringify(taskConfig); // Check for an existing task using this buffer. A transferred buffer cannot be transferred + // again from this thread. + + if (_taskCache.has(buffer)) { + const cachedTask = _taskCache.get(buffer); + + if (cachedTask.key === taskKey) { + return cachedTask.promise; + } else if (buffer.byteLength === 0) { + // Technically, it would be possible to wait for the previous task to complete, + // transfer the buffer back, and decode again with the second configuration. That + // is complex, and I don't know of any reason to decode a Draco buffer twice in + // different ways, so this is left unimplemented. + throw new Error( + "THREE.DRACOLoader: Unable to re-decode a buffer with different " + + "settings. Buffer has already been transferred.", + ); + } + } // + + let worker; + const taskID = this.workerNextTaskID++; + const taskCost = buffer.byteLength; // Obtain a worker and assign a task, and construct a geometry instance + // when the task completes. + + const geometryPending = this._getWorker(taskID, taskCost) + .then((_worker) => { + worker = _worker; + return new Promise((resolve, reject) => { + worker._callbacks[taskID] = { + resolve, + reject, + }; + worker.postMessage( + { + type: "decode", + id: taskID, + taskConfig, + buffer, + }, + [buffer], + ); // this.debug(); + }); + }) + .then((message) => this._createGeometry(message.geometry)); // Remove task from the task list. + // Note: replaced '.finally()' with '.catch().then()' block - iOS 11 support (#19416) + + geometryPending + .catch(() => true) + .then(() => { + if (worker && taskID) { + this._releaseTask(worker, taskID); // this.debug(); + } + }); // Cache the task result. + + _taskCache.set(buffer, { + key: taskKey, + promise: geometryPending, + }); + + return geometryPending; + } + + _createGeometry(geometryData) { + const geometry = new THREE.BufferGeometry(); + + if (geometryData.index) { + geometry.setIndex(new THREE.BufferAttribute(geometryData.index.array, 1)); + } + + for (let i = 0; i < geometryData.attributes.length; i++) { + const attribute = geometryData.attributes[i]; + const name = attribute.name; + const array = attribute.array; + const itemSize = attribute.itemSize; + geometry.setAttribute(name, new THREE.BufferAttribute(array, itemSize)); + } + + return geometry; + } + + _loadLibrary(url, responseType) { + const loader = new THREE.FileLoader(this.manager); + loader.setPath(this.decoderPath); + loader.setResponseType(responseType); + loader.setWithCredentials(this.withCredentials); + return new Promise((resolve, reject) => { + loader.load(url, resolve, undefined, reject); + }); + } + + preload() { + this._initDecoder(); + + return this; + } + + _initDecoder() { + if (this.decoderPending) return this.decoderPending; + const useJS = typeof WebAssembly !== "object" || this.decoderConfig.type === "js"; + const librariesPending = []; + + if (useJS) { + librariesPending.push(this._loadLibrary("draco_decoder.js", "text")); + } else { + librariesPending.push(this._loadLibrary("draco_wasm_wrapper.js", "text")); + librariesPending.push(this._loadLibrary("draco_decoder.wasm", "arraybuffer")); + } + + this.decoderPending = Promise.all(librariesPending).then((libraries) => { + const jsContent = libraries[0]; + + if (!useJS) { + this.decoderConfig.wasmBinary = libraries[1]; + } + + const fn = DRACOWorker.toString(); + const body = [ + "/* draco decoder */", + jsContent, + "", + "/* worker */", + fn.substring(fn.indexOf("{") + 1, fn.lastIndexOf("}")), + ].join("\n"); + this.workerSourceURL = URL.createObjectURL(new Blob([body])); + }); + return this.decoderPending; + } + + _getWorker(taskID, taskCost) { + return this._initDecoder().then(() => { + if (this.workerPool.length < this.workerLimit) { + const worker = new Worker(this.workerSourceURL); + worker._callbacks = {}; + worker._taskCosts = {}; + worker._taskLoad = 0; + worker.postMessage({ + type: "init", + decoderConfig: this.decoderConfig, + }); + + worker.onmessage = function (e) { + const message = e.data; + + switch (message.type) { + case "decode": + worker._callbacks[message.id].resolve(message); + + break; + + case "error": + worker._callbacks[message.id].reject(message); + + break; + + default: + console.error('THREE.DRACOLoader: Unexpected message, "' + message.type + '"'); + } + }; + + this.workerPool.push(worker); + } else { + this.workerPool.sort(function (a, b) { + return a._taskLoad > b._taskLoad ? -1 : 1; + }); + } + + const worker = this.workerPool[this.workerPool.length - 1]; + worker._taskCosts[taskID] = taskCost; + worker._taskLoad += taskCost; + return worker; + }); + } + + _releaseTask(worker, taskID) { + worker._taskLoad -= worker._taskCosts[taskID]; + delete worker._callbacks[taskID]; + delete worker._taskCosts[taskID]; + } + + debug() { + console.log( + "Task load: ", + this.workerPool.map((worker) => worker._taskLoad), + ); + } + + dispose() { + for (let i = 0; i < this.workerPool.length; ++i) { + this.workerPool[i].terminate(); + } + + this.workerPool.length = 0; + return this; + } + } + /* WEB WORKER */ + + function DRACOWorker() { + let decoderConfig; + let decoderPending; + + onmessage = function (e) { + const message = e.data; + + switch (message.type) { + case "init": + decoderConfig = message.decoderConfig; + decoderPending = new Promise(function ( + resolve, + /*, reject*/ + ) { + decoderConfig.onModuleLoaded = function (draco) { + // Module is Promise-like. Wrap before resolving to avoid loop. + resolve({ + draco: draco, + }); + }; + + DracoDecoderModule(decoderConfig); // eslint-disable-line no-undef + }); + break; + + case "decode": + const buffer = message.buffer; + const taskConfig = message.taskConfig; + decoderPending.then((module) => { + const draco = module.draco; + const decoder = new draco.Decoder(); + const decoderBuffer = new draco.DecoderBuffer(); + decoderBuffer.Init(new Int8Array(buffer), buffer.byteLength); + + try { + const geometry = decodeGeometry(draco, decoder, decoderBuffer, taskConfig); + const buffers = geometry.attributes.map((attr) => attr.array.buffer); + if (geometry.index) buffers.push(geometry.index.array.buffer); + self.postMessage( + { + type: "decode", + id: message.id, + geometry, + }, + buffers, + ); + } catch (error) { + console.error(error); + self.postMessage({ + type: "error", + id: message.id, + error: error.message, + }); + } finally { + draco.destroy(decoderBuffer); + draco.destroy(decoder); + } + }); + break; + } + }; + + function decodeGeometry(draco, decoder, decoderBuffer, taskConfig) { + const attributeIDs = taskConfig.attributeIDs; + const attributeTypes = taskConfig.attributeTypes; + let dracoGeometry; + let decodingStatus; + const geometryType = decoder.GetEncodedGeometryType(decoderBuffer); + + if (geometryType === draco.TRIANGULAR_MESH) { + dracoGeometry = new draco.Mesh(); + decodingStatus = decoder.DecodeBufferToMesh(decoderBuffer, dracoGeometry); + } else if (geometryType === draco.POINT_CLOUD) { + dracoGeometry = new draco.PointCloud(); + decodingStatus = decoder.DecodeBufferToPointCloud(decoderBuffer, dracoGeometry); + } else { + throw new Error("THREE.DRACOLoader: Unexpected geometry type."); + } + + if (!decodingStatus.ok() || dracoGeometry.ptr === 0) { + throw new Error("THREE.DRACOLoader: Decoding failed: " + decodingStatus.error_msg()); + } + + const geometry = { + index: null, + attributes: [], + }; // Gather all vertex attributes. + + for (const attributeName in attributeIDs) { + const attributeType = self[attributeTypes[attributeName]]; + let attribute; + let attributeID; // A Draco file may be created with default vertex attributes, whose attribute IDs + // are mapped 1:1 from their semantic name (POSITION, NORMAL, ...). Alternatively, + // a Draco file may contain a custom set of attributes, identified by known unique + // IDs. glTF files always do the latter, and `.drc` files typically do the former. + + if (taskConfig.useUniqueIDs) { + attributeID = attributeIDs[attributeName]; + attribute = decoder.GetAttributeByUniqueId(dracoGeometry, attributeID); + } else { + attributeID = decoder.GetAttributeId(dracoGeometry, draco[attributeIDs[attributeName]]); + if (attributeID === -1) continue; + attribute = decoder.GetAttribute(dracoGeometry, attributeID); + } + + geometry.attributes.push( + decodeAttribute(draco, decoder, dracoGeometry, attributeName, attributeType, attribute), + ); + } // Add index. + + if (geometryType === draco.TRIANGULAR_MESH) { + geometry.index = decodeIndex(draco, decoder, dracoGeometry); + } + + draco.destroy(dracoGeometry); + return geometry; + } + + function decodeIndex(draco, decoder, dracoGeometry) { + const numFaces = dracoGeometry.num_faces(); + const numIndices = numFaces * 3; + const byteLength = numIndices * 4; + + const ptr = draco._malloc(byteLength); + + decoder.GetTrianglesUInt32Array(dracoGeometry, byteLength, ptr); + const index = new Uint32Array(draco.HEAPF32.buffer, ptr, numIndices).slice(); + + draco._free(ptr); + + return { + array: index, + itemSize: 1, + }; + } + + function decodeAttribute( + draco, + decoder, + dracoGeometry, + attributeName, + attributeType, + attribute, + ) { + const numComponents = attribute.num_components(); + const numPoints = dracoGeometry.num_points(); + const numValues = numPoints * numComponents; + const byteLength = numValues * attributeType.BYTES_PER_ELEMENT; + const dataType = getDracoDataType(draco, attributeType); + + const ptr = draco._malloc(byteLength); + + decoder.GetAttributeDataArrayForAllPoints( + dracoGeometry, + attribute, + dataType, + byteLength, + ptr, + ); + const array = new attributeType(draco.HEAPF32.buffer, ptr, numValues).slice(); + + draco._free(ptr); + + return { + name: attributeName, + array: array, + itemSize: numComponents, + }; + } + + function getDracoDataType(draco, attributeType) { + switch (attributeType) { + case Float32Array: + return draco.DT_FLOAT32; + + case Int8Array: + return draco.DT_INT8; + + case Int16Array: + return draco.DT_INT16; + + case Int32Array: + return draco.DT_INT32; + + case Uint8Array: + return draco.DT_UINT8; + + case Uint16Array: + return draco.DT_UINT16; + + case Uint32Array: + return draco.DT_UINT32; + } + } + } + + THREE.DRACOLoader = DRACOLoader; +})(); From b931cda0ce2557ea277ab6b2964725468d647419 Mon Sep 17 00:00:00 2001 From: leowe Date: Tue, 27 Sep 2022 16:14:56 +0200 Subject: [PATCH 11/63] change response from dummyDracoFile --- .../controllers/DataSourceController.scala | 2 +- .../datastore/services/MeshFileService.scala | 81 ++++++++++++------- 2 files changed, 55 insertions(+), 28 deletions(-) diff --git a/webknossos-datastore/app/com/scalableminds/webknossos/datastore/controllers/DataSourceController.scala b/webknossos-datastore/app/com/scalableminds/webknossos/datastore/controllers/DataSourceController.scala index 541fd47c1b9..e08e20837f6 100644 --- a/webknossos-datastore/app/com/scalableminds/webknossos/datastore/controllers/DataSourceController.scala +++ b/webknossos-datastore/app/com/scalableminds/webknossos/datastore/controllers/DataSourceController.scala @@ -403,7 +403,7 @@ Expects: def dummyDracoFile(): Action[AnyContent] = Action.async { implicit request => for { draco <- meshFileService.readDummyDraco() - } yield Ok(Json.toJson(draco)) + } yield Ok(draco) } @ApiOperation(hidden = true, value = "") diff --git a/webknossos-datastore/app/com/scalableminds/webknossos/datastore/services/MeshFileService.scala b/webknossos-datastore/app/com/scalableminds/webknossos/datastore/services/MeshFileService.scala index 2f6a6fcb5f6..94560b1dd99 100644 --- a/webknossos-datastore/app/com/scalableminds/webknossos/datastore/services/MeshFileService.scala +++ b/webknossos-datastore/app/com/scalableminds/webknossos/datastore/services/MeshFileService.scala @@ -18,6 +18,7 @@ import java.nio.ByteBuffer import java.nio.file.{Files, Path, Paths} import javax.inject.Inject import scala.collection.JavaConverters._ +import scala.collection.mutable.ListBuffer import scala.concurrent.ExecutionContext import scala.util.Using @@ -68,8 +69,8 @@ case class NeuroglancerSegmentInfo(chunkShape: Vec3Float, lodScales: Array[Float], vertexOffsets: Array[Vec3Float], numFragmentsPerLod: Array[Int], - fragmentPositions: Array[Array[Vec3Int]], - fragmentOffsets: Array[Array[Int]]) + fragmentPositions: List[List[Vec3Int]], + fragmentOffsets: List[List[Int]]) case class MeshFragment(position: Vec3Float, byteOffset: Int, byteSize: Int) @@ -129,7 +130,7 @@ class MeshFileService @Inject()(config: DataStoreConfig)(implicit ec: ExecutionC mappingVersionForMeshFile(meshFilePath) } - val mappingNameFoxes = (meshFileNames, meshFileVersions).zipped.map { (fileName, fileVersion) => + val mappingNameFoxes = (meshFileNames, meshFileVersions).zipped.map { (fileName, fileVersion) => val meshFilePath = layerDir.resolve(meshesDir).resolve(s"$fileName.$meshFileExtension") mappingNameForMeshFile(meshFilePath, fileVersion) } @@ -146,7 +147,7 @@ class MeshFileService @Inject()(config: DataStoreConfig)(implicit ec: ExecutionC Note that null is a valid value here for once. Meshfiles with no information about the meshFilePath will return Fox.empty, while meshfiles with one marked as empty, will return Fox.successful(null) */ - def mappingNameForMeshFile(meshFilePath: Path, meshFileVersion: Long): Fox[String] = { + def mappingNameForMeshFile(meshFilePath: Path, meshFileVersion: Long): Fox[String] = if (meshFileVersion == 0) { safeExecute(meshFilePath) { cachedMeshFile => cachedMeshFile.reader.string().getAttr("/", "metadata/mapping_name") @@ -156,7 +157,6 @@ class MeshFileService @Inject()(config: DataStoreConfig)(implicit ec: ExecutionC cachedMeshFile.reader.string().getAttr("/", "mapping_name") } ?~> "mesh.file.readEncoding.failed" } - } def mappingVersionForMeshFile(meshFilePath: Path): Long = safeExecuteBox(meshFilePath) { cachedMeshFile => @@ -205,7 +205,7 @@ class MeshFileService @Inject()(config: DataStoreConfig)(implicit ec: ExecutionC val encoding = cachedMeshFile.reader.string().getAttr("/", "mesh_format") val lodScaleMultiplier = cachedMeshFile.reader.float64().getAttr("/", "lod_scale_multiplier") println(s"encoding: $encoding") - val transform = cachedMeshFile.reader.float64().readMatrixBlockWithOffset("/transform", 3, 4, 0, 0) + val transform = cachedMeshFile.reader.float64().getMatrixAttr("/", "transform") println(s"transform: ${transform.mkString("Array(", ", ", ")")}") val (neuroglancerStart, neuroglancerEnd) = getNeuroglancerOffsets(segmentId, cachedMeshFile) @@ -213,7 +213,8 @@ class MeshFileService @Inject()(config: DataStoreConfig)(implicit ec: ExecutionC val manifest = cachedMeshFile.reader .uint8() - .readArrayBlockWithOffset("/neuroglancer", (neuroglancerEnd - neuroglancerStart + 1).toInt, neuroglancerStart) + .readArrayBlockWithOffset("/neuroglancer", (neuroglancerEnd - neuroglancerStart).toInt, neuroglancerStart) + println(s"""manifest: ${manifest.mkString("Array(", ", ", ")")}""") val segmentInfo = parseNeuroglancerManifest(manifest) val meshfile = getFragmentsFromSegmentInfo(segmentInfo, lodScaleMultiplier, neuroglancerStart) meshfile @@ -229,16 +230,19 @@ class MeshFileService @Inject()(config: DataStoreConfig)(implicit ec: ExecutionC val meshByteStartOffset = neuroglancerOffsetStart - totalMeshSize val fragmentByteOffsets = segmentInfo.fragmentOffsets.map(_.scanLeft(0)(_ + _)) // This builds a cumulative sum + println(s"totalMeshSize: $totalMeshSize") + println(s"meshByteStartOffset: $meshByteStartOffset") + println(s"fragmentByteOffsets: ${fragmentByteOffsets.mkString("Array(", ", ", ")")}") def computeGlobalPositionAndOffset(lod: Int, currentFragment: Int): MeshFragment = { val globalPosition = segmentInfo.gridOrigin + segmentInfo .fragmentPositions(lod)(currentFragment) .toVec3Float * segmentInfo.chunkShape * segmentInfo.lodScales(lod) * lodScaleMultiplier - MeshFragment( - position = globalPosition, // This position is in Voxel Space - byteOffset = meshByteStartOffset.toInt + fragmentByteOffsets(lod)(currentFragment), - byteSize = segmentInfo.fragmentOffsets(lod)(currentFragment), - ) + MeshFragment( + position = globalPosition, // This position is in Voxel Space + byteOffset = meshByteStartOffset.toInt + fragmentByteOffsets(lod)(currentFragment), + byteSize = segmentInfo.fragmentOffsets(lod)(currentFragment), + ) } val lods = for (lod <- 0 until segmentInfo.numLods) yield lod @@ -256,8 +260,7 @@ class MeshFileService @Inject()(config: DataStoreConfig)(implicit ec: ExecutionC chunkShape = segmentInfo.chunkShape, fragments = fragments(lod))) .toList - Some( - MeshSegmentInfo(chunkShape = segmentInfo.chunkShape, gridOrigin = segmentInfo.gridOrigin, lods = meshfileLods)) + Some(MeshSegmentInfo(chunkShape = segmentInfo.chunkShape, gridOrigin = segmentInfo.gridOrigin, lods = meshfileLods)) } private def parseNeuroglancerManifest(manifest: Array[Byte]): NeuroglancerSegmentInfo = { // All Ints here should be UInt32 per spec. @@ -272,6 +275,10 @@ class MeshFileService @Inject()(config: DataStoreConfig)(implicit ec: ExecutionC val numLods = dis.readInt + println(s"chunkShape: $chunkShape") + println(s"gridOrigin: $gridOrigin") + println(s"numLods: $numLods") + val lodScales = new Array[Float](numLods) for (d <- 0 until numLods) { lodScales(d) = dis.readFloat @@ -282,26 +289,35 @@ class MeshFileService @Inject()(config: DataStoreConfig)(implicit ec: ExecutionC vertexOffsets(d) = Vec3Float(x = dis.readFloat, y = dis.readFloat, z = dis.readFloat) } + println(s"lodScales: ${lodScales.mkString("Array(", ", ", ")")}") + println(s"vertexOffsets: ${lodScales.mkString("Array(", ", ", ")")}") + val numFragmentsPerLod = new Array[Int](numLods) for (lod <- 0 until numLods) { numFragmentsPerLod(lod) = dis.readInt() } - val fragmentPositions = new Array[Array[Array[Int]]](numLods) - val fragmentPositionsVec3 = new Array[Array[Vec3Int]](numLods) - val fragmentSizes = new Array[Array[Int]](numLods) + println(s"numFragmentsPerLod: ${numFragmentsPerLod.mkString("Array(", ", ", ")")}") + // TODO what if there are no fragments? + val fragmentPositionsList = new ListBuffer[List[Vec3Int]] + val fragmentSizes = new ListBuffer[List[Int]] for (lod <- 0 until numLods) { - for (row <- 0 until 3) { - for (col <- 0 until numFragmentsPerLod(lod)) { - fragmentPositions(lod)(row)(col) = dis.readInt + val currentFragmentPositions = (ListBuffer[Int](), ListBuffer[Int](), ListBuffer[Int]()) + for (row <- 0 until 3; _ <- 0 until numFragmentsPerLod(lod)) { + row match { + case 0 => currentFragmentPositions._1.append(dis.readInt) + case 1 => currentFragmentPositions._2.append(dis.readInt) + case 2 => currentFragmentPositions._3.append(dis.readInt) } } - fragmentPositionsVec3(lod) = fragmentPositions(lod).transpose.map(xs => Vec3Int(xs(0), xs(1), xs(2))) + fragmentPositionsList.append(currentFragmentPositions.zipped.map(Vec3Int(_, _, _)).toList) - for (fragmentNum <- 0 until numFragmentsPerLod(lod)) { - fragmentSizes(lod)(fragmentNum) = dis.readInt + val currentFragmentSizes = ListBuffer[Int]() + for (_ <- 0 until numFragmentsPerLod(lod)) { + currentFragmentSizes.append(dis.readInt) } + fragmentSizes.append(currentFragmentSizes.toList) } NeuroglancerSegmentInfo(chunkShape, @@ -310,8 +326,8 @@ class MeshFileService @Inject()(config: DataStoreConfig)(implicit ec: ExecutionC lodScales, vertexOffsets, numFragmentsPerLod, - fragmentPositionsVec3, - fragmentSizes) + fragmentPositionsList.toList, + fragmentSizes.toList) } private def getNeuroglancerOffsets(segmentId: Long, cachedMeshFile: CachedHdf5File): (Long, Long) = { @@ -324,17 +340,28 @@ class MeshFileService @Inject()(config: DataStoreConfig)(implicit ec: ExecutionC val bucketIndex = getHashFunction(hashName)(segmentId) % nBuckets val cappedBucketIndex = bucketIndex.toInt val bucketOffsets = cachedMeshFile.reader.uint64().readArrayBlockWithOffset("bucket_offsets", 2, bucketIndex) - val bucketStart = bucketOffsets(cappedBucketIndex) + println(s"bucketOffsets: ${bucketOffsets.mkString("Array(", ", ", ")")}") + println(s"cappedBucketIndex: $cappedBucketIndex") + val bucketStart = bucketOffsets(0) val cappedBucketStart = bucketStart.toInt - val bucketEnd = bucketOffsets(cappedBucketIndex + 1) + val bucketEnd = bucketOffsets(1) val cappedBucketEnd = bucketEnd.toInt + + println(s"bucketStart: ${cappedBucketStart}, bucketEnd: ${cappedBucketEnd}") val buckets = cachedMeshFile.reader .uint64() .readMatrixBlockWithOffset("buckets", cappedBucketEnd - cappedBucketStart + 1, 3, bucketStart, 0) + println(s"buckets: ${buckets.mkString("Array(", ", ", ")")}") + println(s"buckets0: ${buckets(0).mkString("Array(", ", ", ")")}") + println(s"buckets1: ${buckets(1).mkString("Array(", ", ", ")")}") + println(s"buckets2: ${buckets(2).mkString("Array(", ", ", ")")}") + // TODO what if you don't find segment val bucketLocalOffset = buckets.map(_(0)).indexOf(segmentId) val neuroglancerStart = buckets(bucketLocalOffset)(1) val neuroglancerEnd = buckets(bucketLocalOffset)(2) + + println(s"neuroglancerStart: $neuroglancerStart, neurglancerEnd: $neuroglancerEnd") (neuroglancerStart, neuroglancerEnd) } From e214ee0a66a9c9893e5f5746791bd1c083268a04 Mon Sep 17 00:00:00 2001 From: leowe Date: Tue, 27 Sep 2022 16:52:23 +0200 Subject: [PATCH 12/63] remove println --- .../datastore/services/MeshFileService.scala | 31 +------------------ 1 file changed, 1 insertion(+), 30 deletions(-) diff --git a/webknossos-datastore/app/com/scalableminds/webknossos/datastore/services/MeshFileService.scala b/webknossos-datastore/app/com/scalableminds/webknossos/datastore/services/MeshFileService.scala index 94560b1dd99..c50f4d9a91d 100644 --- a/webknossos-datastore/app/com/scalableminds/webknossos/datastore/services/MeshFileService.scala +++ b/webknossos-datastore/app/com/scalableminds/webknossos/datastore/services/MeshFileService.scala @@ -201,20 +201,15 @@ class MeshFileService @Inject()(config: DataStoreConfig)(implicit ec: ExecutionC safeExecute(meshFilePath) { cachedMeshFile => val segmentId = listMeshChunksRequest.segmentId - println(s"Reading $segmentId") val encoding = cachedMeshFile.reader.string().getAttr("/", "mesh_format") val lodScaleMultiplier = cachedMeshFile.reader.float64().getAttr("/", "lod_scale_multiplier") - println(s"encoding: $encoding") val transform = cachedMeshFile.reader.float64().getMatrixAttr("/", "transform") - println(s"transform: ${transform.mkString("Array(", ", ", ")")}") val (neuroglancerStart, neuroglancerEnd) = getNeuroglancerOffsets(segmentId, cachedMeshFile) - println(s"from $neuroglancerStart to $neuroglancerEnd") val manifest = cachedMeshFile.reader .uint8() .readArrayBlockWithOffset("/neuroglancer", (neuroglancerEnd - neuroglancerStart).toInt, neuroglancerStart) - println(s"""manifest: ${manifest.mkString("Array(", ", ", ")")}""") val segmentInfo = parseNeuroglancerManifest(manifest) val meshfile = getFragmentsFromSegmentInfo(segmentInfo, lodScaleMultiplier, neuroglancerStart) meshfile @@ -230,9 +225,6 @@ class MeshFileService @Inject()(config: DataStoreConfig)(implicit ec: ExecutionC val meshByteStartOffset = neuroglancerOffsetStart - totalMeshSize val fragmentByteOffsets = segmentInfo.fragmentOffsets.map(_.scanLeft(0)(_ + _)) // This builds a cumulative sum - println(s"totalMeshSize: $totalMeshSize") - println(s"meshByteStartOffset: $meshByteStartOffset") - println(s"fragmentByteOffsets: ${fragmentByteOffsets.mkString("Array(", ", ", ")")}") def computeGlobalPositionAndOffset(lod: Int, currentFragment: Int): MeshFragment = { val globalPosition = segmentInfo.gridOrigin + segmentInfo .fragmentPositions(lod)(currentFragment) @@ -275,10 +267,6 @@ class MeshFileService @Inject()(config: DataStoreConfig)(implicit ec: ExecutionC val numLods = dis.readInt - println(s"chunkShape: $chunkShape") - println(s"gridOrigin: $gridOrigin") - println(s"numLods: $numLods") - val lodScales = new Array[Float](numLods) for (d <- 0 until numLods) { lodScales(d) = dis.readFloat @@ -289,15 +277,11 @@ class MeshFileService @Inject()(config: DataStoreConfig)(implicit ec: ExecutionC vertexOffsets(d) = Vec3Float(x = dis.readFloat, y = dis.readFloat, z = dis.readFloat) } - println(s"lodScales: ${lodScales.mkString("Array(", ", ", ")")}") - println(s"vertexOffsets: ${lodScales.mkString("Array(", ", ", ")")}") - val numFragmentsPerLod = new Array[Int](numLods) for (lod <- 0 until numLods) { numFragmentsPerLod(lod) = dis.readInt() } - println(s"numFragmentsPerLod: ${numFragmentsPerLod.mkString("Array(", ", ", ")")}") // TODO what if there are no fragments? val fragmentPositionsList = new ListBuffer[List[Vec3Int]] val fragmentSizes = new ListBuffer[List[Int]] @@ -334,34 +318,21 @@ class MeshFileService @Inject()(config: DataStoreConfig)(implicit ec: ExecutionC val nBuckets = cachedMeshFile.reader.uint64().getAttr("/", "n_buckets") val hashName = cachedMeshFile.reader.string().getAttr("/", "hash_function") - println(s"nBuckets: $nBuckets") - println(s"hashName: $hashName") - val bucketIndex = getHashFunction(hashName)(segmentId) % nBuckets val cappedBucketIndex = bucketIndex.toInt val bucketOffsets = cachedMeshFile.reader.uint64().readArrayBlockWithOffset("bucket_offsets", 2, bucketIndex) - println(s"bucketOffsets: ${bucketOffsets.mkString("Array(", ", ", ")")}") - println(s"cappedBucketIndex: $cappedBucketIndex") val bucketStart = bucketOffsets(0) - val cappedBucketStart = bucketStart.toInt val bucketEnd = bucketOffsets(1) - val cappedBucketEnd = bucketEnd.toInt - println(s"bucketStart: ${cappedBucketStart}, bucketEnd: ${cappedBucketEnd}") val buckets = cachedMeshFile.reader .uint64() - .readMatrixBlockWithOffset("buckets", cappedBucketEnd - cappedBucketStart + 1, 3, bucketStart, 0) + .readMatrixBlockWithOffset("buckets", (bucketEnd - bucketStart + 1).toInt, 3, bucketStart, 0) - println(s"buckets: ${buckets.mkString("Array(", ", ", ")")}") - println(s"buckets0: ${buckets(0).mkString("Array(", ", ", ")")}") - println(s"buckets1: ${buckets(1).mkString("Array(", ", ", ")")}") - println(s"buckets2: ${buckets(2).mkString("Array(", ", ", ")")}") // TODO what if you don't find segment val bucketLocalOffset = buckets.map(_(0)).indexOf(segmentId) val neuroglancerStart = buckets(bucketLocalOffset)(1) val neuroglancerEnd = buckets(bucketLocalOffset)(2) - println(s"neuroglancerStart: $neuroglancerStart, neurglancerEnd: $neuroglancerEnd") (neuroglancerStart, neuroglancerEnd) } From 610a331e035e38e8730bcf163fe2981ffd421d6b Mon Sep 17 00:00:00 2001 From: leowe Date: Wed, 28 Sep 2022 11:16:48 +0200 Subject: [PATCH 13/63] reformat --- .../controllers/DataSourceController.scala | 32 +++++++++++-------- .../datastore/services/MeshFileService.scala | 5 +-- 2 files changed, 20 insertions(+), 17 deletions(-) diff --git a/webknossos-datastore/app/com/scalableminds/webknossos/datastore/controllers/DataSourceController.scala b/webknossos-datastore/app/com/scalableminds/webknossos/datastore/controllers/DataSourceController.scala index e08e20837f6..c8b6aedf82d 100644 --- a/webknossos-datastore/app/com/scalableminds/webknossos/datastore/controllers/DataSourceController.scala +++ b/webknossos-datastore/app/com/scalableminds/webknossos/datastore/controllers/DataSourceController.scala @@ -401,9 +401,9 @@ Expects: } def dummyDracoFile(): Action[AnyContent] = Action.async { implicit request => - for { - draco <- meshFileService.readDummyDraco() - } yield Ok(draco) + for { + draco <- meshFileService.readDummyDraco() + } yield Ok(draco) } @ApiOperation(hidden = true, value = "") @@ -430,9 +430,9 @@ Expects: urlOrHeaderToken(token, request)) { for { positions <- meshFileService.listMeshChunksForSegmentV0(organizationName, - dataSetName, - dataLayerName, - request.body) ?~> Messages( + dataSetName, + dataLayerName, + request.body) ?~> Messages( "mesh.file.listChunks.failed", request.body.segmentId.toString, request.body.meshFile) ?~> Messages("mesh.file.load.failed", request.body.segmentId.toString) ~> BAD_REQUEST @@ -447,12 +447,12 @@ Expects: dataLayerName: String): Action[ListMeshChunksRequest] = Action.async(validateJson[ListMeshChunksRequest]) { implicit request => accessTokenService.validateAccess(UserAccessRequest.readDataSources(DataSourceId(dataSetName, organizationName)), - urlOrHeaderToken(token, request)) { + urlOrHeaderToken(token, request)) { for { positions <- meshFileService.listMeshChunksForSegmentV1(organizationName, - dataSetName, - dataLayerName, - request.body) ?~> Messages( + dataSetName, + dataLayerName, + request.body) ?~> Messages( "mesh.file.listChunks.failed", request.body.segmentId.toString, request.body.meshFile) ?~> Messages("mesh.file.load.failed", request.body.segmentId.toString) ~> BAD_REQUEST @@ -469,7 +469,10 @@ Expects: accessTokenService.validateAccess(UserAccessRequest.readDataSources(DataSourceId(dataSetName, organizationName)), urlOrHeaderToken(token, request)) { for { - (data, encoding) <- meshFileService.readMeshChunkV0(organizationName, dataSetName, dataLayerName, request.body) ?~> "mesh.file.loadChunk.failed" + (data, encoding) <- meshFileService.readMeshChunkV0(organizationName, + dataSetName, + dataLayerName, + request.body) ?~> "mesh.file.loadChunk.failed" } yield { if (encoding.contains("gzip")) { Ok(data).withHeaders("Content-Encoding" -> "gzip") @@ -485,9 +488,12 @@ Expects: dataLayerName: String): Action[MeshChunkDataRequestV1] = Action.async(validateJson[MeshChunkDataRequestV1]) { implicit request => accessTokenService.validateAccess(UserAccessRequest.readDataSources(DataSourceId(dataSetName, organizationName)), - urlOrHeaderToken(token, request)) { + urlOrHeaderToken(token, request)) { for { - (data, encoding) <- meshFileService.readMeshChunkV1(organizationName, dataSetName, dataLayerName, request.body) ?~> "mesh.file.loadChunk.failed" + (data, encoding) <- meshFileService.readMeshChunkV1(organizationName, + dataSetName, + dataLayerName, + request.body) ?~> "mesh.file.loadChunk.failed" } yield { if (encoding.contains("gzip")) { Ok(data).withHeaders("Content-Encoding" -> "gzip") diff --git a/webknossos-datastore/app/com/scalableminds/webknossos/datastore/services/MeshFileService.scala b/webknossos-datastore/app/com/scalableminds/webknossos/datastore/services/MeshFileService.scala index c50f4d9a91d..86545c24255 100644 --- a/webknossos-datastore/app/com/scalableminds/webknossos/datastore/services/MeshFileService.scala +++ b/webknossos-datastore/app/com/scalableminds/webknossos/datastore/services/MeshFileService.scala @@ -197,8 +197,6 @@ class MeshFileService @Inject()(config: DataStoreConfig)(implicit ec: ExecutionC .resolve(meshesDir) .resolve(s"${listMeshChunksRequest.meshFile}.$meshFileExtension") - println(s"Reading $meshFilePath") - safeExecute(meshFilePath) { cachedMeshFile => val segmentId = listMeshChunksRequest.segmentId val encoding = cachedMeshFile.reader.string().getAttr("/", "mesh_format") @@ -319,7 +317,6 @@ class MeshFileService @Inject()(config: DataStoreConfig)(implicit ec: ExecutionC val hashName = cachedMeshFile.reader.string().getAttr("/", "hash_function") val bucketIndex = getHashFunction(hashName)(segmentId) % nBuckets - val cappedBucketIndex = bucketIndex.toInt val bucketOffsets = cachedMeshFile.reader.uint64().readArrayBlockWithOffset("bucket_offsets", 2, bucketIndex) val bucketStart = bucketOffsets(0) val bucketEnd = bucketOffsets(1) @@ -391,7 +388,7 @@ class MeshFileService @Inject()(config: DataStoreConfig)(implicit ec: ExecutionC private def safeExecuteBox[T](filePath: Path)(block: CachedHdf5File => T): Box[T] = for { _ <- if (filePath.toFile.exists()) { - new Full + Full(true) } else { Empty ~> "mesh.file.open.failed" } From ef11d686fd8633d83274a666b618a6a5d7737884 Mon Sep 17 00:00:00 2001 From: leowe Date: Thu, 29 Sep 2022 10:52:20 +0200 Subject: [PATCH 14/63] add changelog entry --- CHANGELOG.unreleased.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.unreleased.md b/CHANGELOG.unreleased.md index 55dd5449149..7bc9dc15a38 100644 --- a/CHANGELOG.unreleased.md +++ b/CHANGELOG.unreleased.md @@ -11,6 +11,7 @@ For upgrade instructions, please check the [migration guide](MIGRATIONS.released [Commits](https://github.com/scalableminds/webknossos/compare/22.10.0...HEAD) ### Added +- Support for a new mesh file format which allows up to billions of meshes. [#6491](https://github.com/scalableminds/webknossos/pull/6491) ### Changed - Creating tasks in bulk now also supports referencing task types by their summary instead of id. [#6486](https://github.com/scalableminds/webknossos/pull/6486) From 877a85e73973adeaa1b8938ac0ba0465803dbd4a Mon Sep 17 00:00:00 2001 From: leowe Date: Thu, 29 Sep 2022 13:36:50 +0200 Subject: [PATCH 15/63] add formatVersion als parameter in URL --- .../com/scalableminds/util/tools/Fox.scala | 2 +- .../controllers/DataSourceController.scala | 44 +++--- .../datastore/services/MeshFileService.scala | 66 +++------ .../datastore/storage/Hdf5FileCache.scala | 28 ++++ ....scalableminds.webknossos.datastore.routes | 130 +++++++++--------- 5 files changed, 139 insertions(+), 131 deletions(-) diff --git a/util/src/main/scala/com/scalableminds/util/tools/Fox.scala b/util/src/main/scala/com/scalableminds/util/tools/Fox.scala index f862bf9f285..eb0ef55f6cf 100644 --- a/util/src/main/scala/com/scalableminds/util/tools/Fox.scala +++ b/util/src/main/scala/com/scalableminds/util/tools/Fox.scala @@ -33,7 +33,7 @@ trait FoxImplicits { implicit def try2Fox[T](t: Try[T])(implicit ec: ExecutionContext): Fox[T] = t match { case Success(result) => Fox.successful(result) - case scala.util.Failure(e) => Fox.failure(e.getMessage) + case scala.util.Failure(e) => Fox.failure(s"${e.toString}") } implicit def fox2FutureBox[T](f: Fox[T]): Future[Box[T]] = diff --git a/webknossos-datastore/app/com/scalableminds/webknossos/datastore/controllers/DataSourceController.scala b/webknossos-datastore/app/com/scalableminds/webknossos/datastore/controllers/DataSourceController.scala index c8b6aedf82d..b400eea832b 100644 --- a/webknossos-datastore/app/com/scalableminds/webknossos/datastore/controllers/DataSourceController.scala +++ b/webknossos-datastore/app/com/scalableminds/webknossos/datastore/controllers/DataSourceController.scala @@ -441,21 +441,23 @@ Expects: } @ApiOperation(hidden = true, value = "") - def listMeshChunksForSegmentV1(token: Option[String], - organizationName: String, - dataSetName: String, - dataLayerName: String): Action[ListMeshChunksRequest] = + def listMeshChunksForSegmentForVersion(token: Option[String], + organizationName: String, + dataSetName: String, + dataLayerName: String, + formatVersion: Int): Action[ListMeshChunksRequest] = Action.async(validateJson[ListMeshChunksRequest]) { implicit request => accessTokenService.validateAccess(UserAccessRequest.readDataSources(DataSourceId(dataSetName, organizationName)), urlOrHeaderToken(token, request)) { for { - positions <- meshFileService.listMeshChunksForSegmentV1(organizationName, - dataSetName, - dataLayerName, - request.body) ?~> Messages( - "mesh.file.listChunks.failed", - request.body.segmentId.toString, - request.body.meshFile) ?~> Messages("mesh.file.load.failed", request.body.segmentId.toString) ~> BAD_REQUEST + positions <- formatVersion match { + case 3 => + meshFileService.listMeshChunksForSegmentV3(organizationName, dataSetName, dataLayerName, request.body) ?~> Messages( + "mesh.file.listChunks.failed", + request.body.segmentId.toString, + request.body.meshFile) ?~> Messages("mesh.file.load.failed", request.body.segmentId.toString) ~> BAD_REQUEST + case _ => Fox.failure("Wrong format version") ~> BAD_REQUEST + } } yield Ok(Json.toJson(positions)) } } @@ -482,18 +484,20 @@ Expects: } @ApiOperation(hidden = true, value = "") - def readMeshChunkV1(token: Option[String], - organizationName: String, - dataSetName: String, - dataLayerName: String): Action[MeshChunkDataRequestV1] = - Action.async(validateJson[MeshChunkDataRequestV1]) { implicit request => + def readMeshChunkForVersion(token: Option[String], + organizationName: String, + dataSetName: String, + dataLayerName: String, + formatVersion: Int): Action[MeshChunkDataRequestV3] = + Action.async(validateJson[MeshChunkDataRequestV3]) { implicit request => accessTokenService.validateAccess(UserAccessRequest.readDataSources(DataSourceId(dataSetName, organizationName)), urlOrHeaderToken(token, request)) { for { - (data, encoding) <- meshFileService.readMeshChunkV1(organizationName, - dataSetName, - dataLayerName, - request.body) ?~> "mesh.file.loadChunk.failed" + (data, encoding) <- formatVersion match { + case 3 => + meshFileService.readMeshChunkV3(organizationName, dataSetName, dataLayerName, request.body) ?~> "mesh.file.loadChunk.failed" + case _ => Fox.failure("Wrong format version") ~> BAD_REQUEST + } } yield { if (encoding.contains("gzip")) { Ok(data).withHeaders("Content-Encoding" -> "gzip") diff --git a/webknossos-datastore/app/com/scalableminds/webknossos/datastore/services/MeshFileService.scala b/webknossos-datastore/app/com/scalableminds/webknossos/datastore/services/MeshFileService.scala index 86545c24255..5ca3eaf546a 100644 --- a/webknossos-datastore/app/com/scalableminds/webknossos/datastore/services/MeshFileService.scala +++ b/webknossos-datastore/app/com/scalableminds/webknossos/datastore/services/MeshFileService.scala @@ -5,9 +5,10 @@ import com.scalableminds.util.geometry.{Vec3Float, Vec3Int} import com.scalableminds.util.io.PathUtils import com.scalableminds.util.tools.{Fox, FoxImplicits} import com.scalableminds.webknossos.datastore.DataStoreConfig +import com.scalableminds.webknossos.datastore.storage.CachedHdf5Utils.{safeExecute, safeExecuteBox} import com.scalableminds.webknossos.datastore.storage.{CachedHdf5File, Hdf5FileCache} import com.typesafe.scalalogging.LazyLogging -import net.liftweb.common.{Box, Empty, Full} +import net.liftweb.common.Box import net.liftweb.util.Helpers.tryo import org.apache.commons.codec.digest.MurmurHash3 import org.apache.commons.io.FilenameUtils @@ -20,7 +21,6 @@ import javax.inject.Inject import scala.collection.JavaConverters._ import scala.collection.mutable.ListBuffer import scala.concurrent.ExecutionContext -import scala.util.Using trait GenericJsonFormat[T] {} @@ -39,7 +39,7 @@ case class MeshChunkDataRequestV0( segmentId: Long ) -case class MeshChunkDataRequestV1( +case class MeshChunkDataRequestV3( meshFile: String, fragmentStartOffset: Long, fragmentSize: Int @@ -49,8 +49,8 @@ object MeshChunkDataRequestV0 { implicit val jsonFormat: OFormat[MeshChunkDataRequestV0] = Json.format[MeshChunkDataRequestV0] } -object MeshChunkDataRequestV1 { - implicit val jsonFormat: OFormat[MeshChunkDataRequestV1] = Json.format[MeshChunkDataRequestV1] +object MeshChunkDataRequestV3 { + implicit val jsonFormat: OFormat[MeshChunkDataRequestV3] = Json.format[MeshChunkDataRequestV3] } case class MeshFileInfo( @@ -72,6 +72,7 @@ case class NeuroglancerSegmentInfo(chunkShape: Vec3Float, fragmentPositions: List[List[Vec3Int]], fragmentOffsets: List[List[Int]]) +// TODO position als Vec3Int case class MeshFragment(position: Vec3Float, byteOffset: Int, byteSize: Int) object MeshFragment { @@ -149,17 +150,17 @@ class MeshFileService @Inject()(config: DataStoreConfig)(implicit ec: ExecutionC */ def mappingNameForMeshFile(meshFilePath: Path, meshFileVersion: Long): Fox[String] = if (meshFileVersion == 0) { - safeExecute(meshFilePath) { cachedMeshFile => + safeExecute(meshFilePath, meshFileCache) { cachedMeshFile => cachedMeshFile.reader.string().getAttr("/", "metadata/mapping_name") } ?~> "mesh.file.readEncoding.failed" } else { - safeExecute(meshFilePath) { cachedMeshFile => + safeExecute(meshFilePath, meshFileCache) { cachedMeshFile => cachedMeshFile.reader.string().getAttr("/", "mapping_name") } ?~> "mesh.file.readEncoding.failed" } def mappingVersionForMeshFile(meshFilePath: Path): Long = - safeExecuteBox(meshFilePath) { cachedMeshFile => + safeExecuteBox(meshFilePath, meshFileCache) { cachedMeshFile => cachedMeshFile.reader.int64().getAttr("/", "version") }.toOption.getOrElse(0) @@ -175,7 +176,7 @@ class MeshFileService @Inject()(config: DataStoreConfig)(implicit ec: ExecutionC .resolve(meshesDir) .resolve(s"${listMeshChunksRequest.meshFile}.$meshFileExtension") - safeExecute(meshFilePath) { cachedMeshFile => + safeExecute(meshFilePath, meshFileCache) { cachedMeshFile => val chunkPositionLiterals = cachedMeshFile.reader .`object`() .getAllGroupMembers(s"/${listMeshChunksRequest.segmentId}/$defaultLevelOfDetail") @@ -185,7 +186,7 @@ class MeshFileService @Inject()(config: DataStoreConfig)(implicit ec: ExecutionC }.flatten ?~> "mesh.file.open.failed" } - def listMeshChunksForSegmentV1(organizationName: String, + def listMeshChunksForSegmentV3(organizationName: String, dataSetName: String, dataLayerName: String, listMeshChunksRequest: ListMeshChunksRequest): Fox[WebknossosSegmentInfo] = { @@ -197,7 +198,7 @@ class MeshFileService @Inject()(config: DataStoreConfig)(implicit ec: ExecutionC .resolve(meshesDir) .resolve(s"${listMeshChunksRequest.meshFile}.$meshFileExtension") - safeExecute(meshFilePath) { cachedMeshFile => + safeExecute(meshFilePath, meshFileCache) { cachedMeshFile => val segmentId = listMeshChunksRequest.segmentId val encoding = cachedMeshFile.reader.string().getAttr("/", "mesh_format") val lodScaleMultiplier = cachedMeshFile.reader.float64().getAttr("/", "lod_scale_multiplier") @@ -210,15 +211,13 @@ class MeshFileService @Inject()(config: DataStoreConfig)(implicit ec: ExecutionC .readArrayBlockWithOffset("/neuroglancer", (neuroglancerEnd - neuroglancerStart).toInt, neuroglancerStart) val segmentInfo = parseNeuroglancerManifest(manifest) val meshfile = getFragmentsFromSegmentInfo(segmentInfo, lodScaleMultiplier, neuroglancerStart) - meshfile - .map(meshInfo => WebknossosSegmentInfo(transform = transform, meshFormat = encoding, chunks = meshInfo)) - .toFox - }.flatten + WebknossosSegmentInfo(transform = transform, meshFormat = encoding, chunks = meshfile) + } } private def getFragmentsFromSegmentInfo(segmentInfo: NeuroglancerSegmentInfo, lodScaleMultiplier: Double, - neuroglancerOffsetStart: Long): Option[MeshSegmentInfo] = { + neuroglancerOffsetStart: Long): MeshSegmentInfo = { val totalMeshSize = segmentInfo.fragmentOffsets.map(_.sum).sum val meshByteStartOffset = neuroglancerOffsetStart - totalMeshSize val fragmentByteOffsets = segmentInfo.fragmentOffsets.map(_.scanLeft(0)(_ + _)) // This builds a cumulative sum @@ -250,13 +249,12 @@ class MeshFileService @Inject()(config: DataStoreConfig)(implicit ec: ExecutionC chunkShape = segmentInfo.chunkShape, fragments = fragments(lod))) .toList - Some(MeshSegmentInfo(chunkShape = segmentInfo.chunkShape, gridOrigin = segmentInfo.gridOrigin, lods = meshfileLods)) + MeshSegmentInfo(chunkShape = segmentInfo.chunkShape, gridOrigin = segmentInfo.gridOrigin, lods = meshfileLods) } private def parseNeuroglancerManifest(manifest: Array[Byte]): NeuroglancerSegmentInfo = { - // All Ints here should be UInt32 per spec. + // All Ints here should be UInt32 per spec. We assume that the sign bit is not necessary (the encoded values are at most 2^31). // But they all are used to index into Arrays and JVM doesn't allow for Long Array Indexes, // we can't convert them. - // TODO Check whether limit exceeded for the Ints. val byteInput = new ByteArrayInputStream(manifest) val dis = new LittleEndianDataInputStream(byteInput) @@ -280,7 +278,6 @@ class MeshFileService @Inject()(config: DataStoreConfig)(implicit ec: ExecutionC numFragmentsPerLod(lod) = dis.readInt() } - // TODO what if there are no fragments? val fragmentPositionsList = new ListBuffer[List[Vec3Int]] val fragmentSizes = new ListBuffer[List[Int]] for (lod <- 0 until numLods) { @@ -325,7 +322,6 @@ class MeshFileService @Inject()(config: DataStoreConfig)(implicit ec: ExecutionC .uint64() .readMatrixBlockWithOffset("buckets", (bucketEnd - bucketStart + 1).toInt, 3, bucketStart, 0) - // TODO what if you don't find segment val bucketLocalOffset = buckets.map(_(0)).indexOf(segmentId) val neuroglancerStart = buckets(bucketLocalOffset)(1) val neuroglancerEnd = buckets(bucketLocalOffset)(2) @@ -344,7 +340,7 @@ class MeshFileService @Inject()(config: DataStoreConfig)(implicit ec: ExecutionC .resolve(meshesDir) .resolve(s"${meshChunkDataRequest.meshFile}.$meshFileExtension") - safeExecute(meshFilePath) { cachedMeshFile => + safeExecute(meshFilePath, meshFileCache) { cachedMeshFile => val encoding = cachedMeshFile.reader.string().getAttr("/", "metadata/encoding") val key = s"/${meshChunkDataRequest.segmentId}/$defaultLevelOfDetail/${positionLiteral(meshChunkDataRequest.position)}" @@ -353,10 +349,10 @@ class MeshFileService @Inject()(config: DataStoreConfig)(implicit ec: ExecutionC } ?~> "mesh.file.readData.failed" } - def readMeshChunkV1(organizationName: String, + def readMeshChunkV3(organizationName: String, dataSetName: String, dataLayerName: String, - meshChunkDataRequest: MeshChunkDataRequestV1, + meshChunkDataRequest: MeshChunkDataRequestV3, ): Fox[(Array[Byte], String)] = { val meshFilePath = dataBaseDir .resolve(organizationName) @@ -365,7 +361,7 @@ class MeshFileService @Inject()(config: DataStoreConfig)(implicit ec: ExecutionC .resolve(meshesDir) .resolve(s"${meshChunkDataRequest.meshFile}.$meshFileExtension") - safeExecute(meshFilePath) { cachedMeshFile => + safeExecute(meshFilePath, meshFileCache) { cachedMeshFile => val meshFormat = cachedMeshFile.reader.string().getAttr("/", "mesh_format") val data = cachedMeshFile.reader @@ -377,26 +373,6 @@ class MeshFileService @Inject()(config: DataStoreConfig)(implicit ec: ExecutionC } ?~> "mesh.file.readData.failed" } - private def safeExecute[T](filePath: Path)(block: CachedHdf5File => T): Fox[T] = - for { - _ <- bool2Fox(filePath.toFile.exists()) ?~> "mesh.file.open.failed" - result <- Using(meshFileCache.withCache(filePath)(CachedHdf5File.fromPath)) { - block - }.toFox - } yield result - - private def safeExecuteBox[T](filePath: Path)(block: CachedHdf5File => T): Box[T] = - for { - _ <- if (filePath.toFile.exists()) { - Full(true) - } else { - Empty ~> "mesh.file.open.failed" - } - result <- Using(meshFileCache.withCache(filePath)(CachedHdf5File.fromPath)) { - block - }.toOption - } yield result - private def positionLiteral(position: Vec3Int) = s"${position.x}_${position.y}_${position.z}" diff --git a/webknossos-datastore/app/com/scalableminds/webknossos/datastore/storage/Hdf5FileCache.scala b/webknossos-datastore/app/com/scalableminds/webknossos/datastore/storage/Hdf5FileCache.scala index 7a76d160306..00569aa1c35 100644 --- a/webknossos-datastore/app/com/scalableminds/webknossos/datastore/storage/Hdf5FileCache.scala +++ b/webknossos-datastore/app/com/scalableminds/webknossos/datastore/storage/Hdf5FileCache.scala @@ -2,9 +2,14 @@ package com.scalableminds.webknossos.datastore.storage import ch.systemsx.cisd.hdf5.{HDF5FactoryProvider, IHDF5Reader} import com.scalableminds.util.cache.LRUConcurrentCache +import com.scalableminds.util.tools.Fox +import com.scalableminds.util.tools.Fox.{bool2Fox, try2Fox} import com.scalableminds.webknossos.datastore.dataformats.SafeCachable +import net.liftweb.common.{Box, Full, Empty} import java.nio.file.Path +import scala.concurrent.ExecutionContext +import scala.util.Using case class CachedHdf5File(reader: IHDF5Reader) extends SafeCachable with AutoCloseable { override protected def onFinalize(): Unit = reader.close() @@ -43,3 +48,26 @@ class Hdf5FileCache(val maxEntries: Int) extends LRUConcurrentCache[String, Cach } } } + +object CachedHdf5Utils { + def safeExecute[T](filePath: Path, meshFileCache: Hdf5FileCache)(block: CachedHdf5File => T)( + implicit ec: ExecutionContext): Fox[T] = + for { + _ <- bool2Fox(filePath.toFile.exists()) ?~> "mesh.file.open.failed" + result <- Using(meshFileCache.withCache(filePath)(CachedHdf5File.fromPath)) { + block + }.toFox + } yield result + + def safeExecuteBox[T](filePath: Path, meshFileCache: Hdf5FileCache)(block: CachedHdf5File => T): Box[T] = + for { + _ <- if (filePath.toFile.exists()) { + Full(true) + } else { + Empty ~> "mesh.file.open.failed" + } + result <- Using(meshFileCache.withCache(filePath)(CachedHdf5File.fromPath)) { + block + }.toOption + } yield result +} diff --git a/webknossos-datastore/conf/com.scalableminds.webknossos.datastore.routes b/webknossos-datastore/conf/com.scalableminds.webknossos.datastore.routes index b92f4d95825..c647910ae95 100644 --- a/webknossos-datastore/conf/com.scalableminds.webknossos.datastore.routes +++ b/webknossos-datastore/conf/com.scalableminds.webknossos.datastore.routes @@ -2,92 +2,92 @@ # Health endpoint -GET /health @com.scalableminds.webknossos.datastore.controllers.Application.health +GET /health @com.scalableminds.webknossos.datastore.controllers.Application.health # Read image data -POST /datasets/:organizationName/:dataSetName/layers/:dataLayerName/data @com.scalableminds.webknossos.datastore.controllers.BinaryDataController.requestViaWebKnossos(token: Option[String], organizationName: String, dataSetName: String, dataLayerName: String) -GET /datasets/:organizationName/:dataSetName/layers/:dataLayerName/data @com.scalableminds.webknossos.datastore.controllers.BinaryDataController.requestRawCuboid(token: Option[String], organizationName: String, dataSetName: String, dataLayerName: String, x: Int, y: Int, z: Int, width: Int, height: Int, depth: Int, mag: String, halfByte: Boolean ?= false, mappingName: Option[String]) -GET /datasets/:organizationName/:dataSetName/layers/:dataLayerName/thumbnail.jpg @com.scalableminds.webknossos.datastore.controllers.BinaryDataController.thumbnailJpeg(token: Option[String], organizationName: String, dataSetName: String, dataLayerName: String, width: Int, height: Int, centerX: Option[Int], centerY: Option[Int], centerZ: Option[Int], zoom: Option[Double]) -GET /datasets/:organizationName/:dataSetName/layers/:dataLayerName/findData @com.scalableminds.webknossos.datastore.controllers.BinaryDataController.findData(token: Option[String], organizationName: String, dataSetName: String, dataLayerName: String) -GET /datasets/:organizationName/:dataSetName/layers/:dataLayerName/colorStatistics @com.scalableminds.webknossos.datastore.controllers.BinaryDataController.colorStatistics(token: Option[String], organizationName: String, dataSetName: String, dataLayerName: String) -GET /datasets/:organizationName/:dataSetName/layers/:dataLayerName/histogram @com.scalableminds.webknossos.datastore.controllers.BinaryDataController.histogram(token: Option[String], organizationName: String, dataSetName: String, dataLayerName: String) +POST /datasets/:organizationName/:dataSetName/layers/:dataLayerName/data @com.scalableminds.webknossos.datastore.controllers.BinaryDataController.requestViaWebKnossos(token: Option[String], organizationName: String, dataSetName: String, dataLayerName: String) +GET /datasets/:organizationName/:dataSetName/layers/:dataLayerName/data @com.scalableminds.webknossos.datastore.controllers.BinaryDataController.requestRawCuboid(token: Option[String], organizationName: String, dataSetName: String, dataLayerName: String, x: Int, y: Int, z: Int, width: Int, height: Int, depth: Int, mag: String, halfByte: Boolean ?= false, mappingName: Option[String]) +GET /datasets/:organizationName/:dataSetName/layers/:dataLayerName/thumbnail.jpg @com.scalableminds.webknossos.datastore.controllers.BinaryDataController.thumbnailJpeg(token: Option[String], organizationName: String, dataSetName: String, dataLayerName: String, width: Int, height: Int, centerX: Option[Int], centerY: Option[Int], centerZ: Option[Int], zoom: Option[Double]) +GET /datasets/:organizationName/:dataSetName/layers/:dataLayerName/findData @com.scalableminds.webknossos.datastore.controllers.BinaryDataController.findData(token: Option[String], organizationName: String, dataSetName: String, dataLayerName: String) +GET /datasets/:organizationName/:dataSetName/layers/:dataLayerName/colorStatistics @com.scalableminds.webknossos.datastore.controllers.BinaryDataController.colorStatistics(token: Option[String], organizationName: String, dataSetName: String, dataLayerName: String) +GET /datasets/:organizationName/:dataSetName/layers/:dataLayerName/histogram @com.scalableminds.webknossos.datastore.controllers.BinaryDataController.histogram(token: Option[String], organizationName: String, dataSetName: String, dataLayerName: String) # Knossos compatible routes -GET /datasets/:organizationName/:dataSetName/layers/:dataLayerName/mag:resolution/x:x/y:y/z:z/bucket.raw @com.scalableminds.webknossos.datastore.controllers.BinaryDataController.requestViaKnossos(token: Option[String], organizationName: String, dataSetName: String, dataLayerName: String, resolution: Int, x: Int, y: Int, z: Int, cubeSize: Int) +GET /datasets/:organizationName/:dataSetName/layers/:dataLayerName/mag:resolution/x:x/y:y/z:z/bucket.raw @com.scalableminds.webknossos.datastore.controllers.BinaryDataController.requestViaKnossos(token: Option[String], organizationName: String, dataSetName: String, dataLayerName: String, resolution: Int, x: Int, y: Int, z: Int, cubeSize: Int) # Zarr compatible routes -GET /zarr/:organizationName/:dataSetName @com.scalableminds.webknossos.datastore.controllers.ZarrStreamingController.requestDataSourceFolderContents(token: Option[String], organizationName: String, dataSetName: String) -GET /zarr/:organizationName/:dataSetName/ @com.scalableminds.webknossos.datastore.controllers.ZarrStreamingController.requestDataSourceFolderContents(token: Option[String], organizationName: String, dataSetName: String) -GET /zarr/:organizationName/:dataSetName/.zgroup @com.scalableminds.webknossos.datastore.controllers.ZarrStreamingController.requestZGroup(token: Option[String], organizationName: String, dataSetName: String, dataLayerName="") -GET /zarr/:organizationName/:dataSetName/datasource-properties.json @com.scalableminds.webknossos.datastore.controllers.ZarrStreamingController.requestDataSource(token: Option[String], organizationName: String, dataSetName: String) -GET /zarr/:organizationName/:dataSetName/:dataLayerName @com.scalableminds.webknossos.datastore.controllers.ZarrStreamingController.requestDataLayerFolderContents(token: Option[String], organizationName: String, dataSetName: String, dataLayerName: String) -GET /zarr/:organizationName/:dataSetName/:dataLayerName/ @com.scalableminds.webknossos.datastore.controllers.ZarrStreamingController.requestDataLayerFolderContents(token: Option[String], organizationName: String, dataSetName: String, dataLayerName: String) -GET /zarr/:organizationName/:dataSetName/:dataLayerName/.zattrs @com.scalableminds.webknossos.datastore.controllers.ZarrStreamingController.requestZAttrs(token: Option[String], organizationName: String, dataSetName: String, dataLayerName: String) -GET /zarr/:organizationName/:dataSetName/:dataLayerName/.zgroup @com.scalableminds.webknossos.datastore.controllers.ZarrStreamingController.requestZGroup(token: Option[String], organizationName: String, dataSetName: String, dataLayerName: String) -GET /zarr/:organizationName/:dataSetName/:dataLayerName/:mag @com.scalableminds.webknossos.datastore.controllers.ZarrStreamingController.requestDataLayerMagFolderContents(token: Option[String], organizationName: String, dataSetName: String, dataLayerName: String, mag: String) -GET /zarr/:organizationName/:dataSetName/:dataLayerName/:mag/ @com.scalableminds.webknossos.datastore.controllers.ZarrStreamingController.requestDataLayerMagFolderContents(token: Option[String], organizationName: String, dataSetName: String, dataLayerName: String, mag: String) -GET /zarr/:organizationName/:dataSetName/:dataLayerName/:mag/.zarray @com.scalableminds.webknossos.datastore.controllers.ZarrStreamingController.requestZArray(token: Option[String], organizationName: String, dataSetName: String, dataLayerName: String, mag: String) -GET /zarr/:organizationName/:dataSetName/:dataLayerName/:mag/:cxyz @com.scalableminds.webknossos.datastore.controllers.ZarrStreamingController.requestRawZarrCube(token: Option[String], organizationName: String, dataSetName: String, dataLayerName: String, mag: String, cxyz: String) +GET /zarr/:organizationName/:dataSetName @com.scalableminds.webknossos.datastore.controllers.ZarrStreamingController.requestDataSourceFolderContents(token: Option[String], organizationName: String, dataSetName: String) +GET /zarr/:organizationName/:dataSetName/ @com.scalableminds.webknossos.datastore.controllers.ZarrStreamingController.requestDataSourceFolderContents(token: Option[String], organizationName: String, dataSetName: String) +GET /zarr/:organizationName/:dataSetName/.zgroup @com.scalableminds.webknossos.datastore.controllers.ZarrStreamingController.requestZGroup(token: Option[String], organizationName: String, dataSetName: String, dataLayerName="") +GET /zarr/:organizationName/:dataSetName/datasource-properties.json @com.scalableminds.webknossos.datastore.controllers.ZarrStreamingController.requestDataSource(token: Option[String], organizationName: String, dataSetName: String) +GET /zarr/:organizationName/:dataSetName/:dataLayerName @com.scalableminds.webknossos.datastore.controllers.ZarrStreamingController.requestDataLayerFolderContents(token: Option[String], organizationName: String, dataSetName: String, dataLayerName: String) +GET /zarr/:organizationName/:dataSetName/:dataLayerName/ @com.scalableminds.webknossos.datastore.controllers.ZarrStreamingController.requestDataLayerFolderContents(token: Option[String], organizationName: String, dataSetName: String, dataLayerName: String) +GET /zarr/:organizationName/:dataSetName/:dataLayerName/.zattrs @com.scalableminds.webknossos.datastore.controllers.ZarrStreamingController.requestZAttrs(token: Option[String], organizationName: String, dataSetName: String, dataLayerName: String) +GET /zarr/:organizationName/:dataSetName/:dataLayerName/.zgroup @com.scalableminds.webknossos.datastore.controllers.ZarrStreamingController.requestZGroup(token: Option[String], organizationName: String, dataSetName: String, dataLayerName: String) +GET /zarr/:organizationName/:dataSetName/:dataLayerName/:mag @com.scalableminds.webknossos.datastore.controllers.ZarrStreamingController.requestDataLayerMagFolderContents(token: Option[String], organizationName: String, dataSetName: String, dataLayerName: String, mag: String) +GET /zarr/:organizationName/:dataSetName/:dataLayerName/:mag/ @com.scalableminds.webknossos.datastore.controllers.ZarrStreamingController.requestDataLayerMagFolderContents(token: Option[String], organizationName: String, dataSetName: String, dataLayerName: String, mag: String) +GET /zarr/:organizationName/:dataSetName/:dataLayerName/:mag/.zarray @com.scalableminds.webknossos.datastore.controllers.ZarrStreamingController.requestZArray(token: Option[String], organizationName: String, dataSetName: String, dataLayerName: String, mag: String) +GET /zarr/:organizationName/:dataSetName/:dataLayerName/:mag/:cxyz @com.scalableminds.webknossos.datastore.controllers.ZarrStreamingController.requestRawZarrCube(token: Option[String], organizationName: String, dataSetName: String, dataLayerName: String, mag: String, cxyz: String) -GET /annotations/zarr/:accessTokenOrId @com.scalableminds.webknossos.datastore.controllers.ZarrStreamingController.dataSourceFolderContentsPrivateLink(token: Option[String], accessTokenOrId: String) -GET /annotations/zarr/:accessTokenOrId/ @com.scalableminds.webknossos.datastore.controllers.ZarrStreamingController.dataSourceFolderContentsPrivateLink(token: Option[String], accessTokenOrId: String) -GET /annotations/zarr/:accessTokenOrId/.zgroup @com.scalableminds.webknossos.datastore.controllers.ZarrStreamingController.zGroupPrivateLink(token: Option[String], accessTokenOrId: String, dataLayerName="") -GET /annotations/zarr/:accessTokenOrId/datasource-properties.json @com.scalableminds.webknossos.datastore.controllers.ZarrStreamingController.dataSourceWithAnnotationPrivateLink(token: Option[String], accessTokenOrId: String) -GET /annotations/zarr/:accessTokenOrId/:dataLayerName @com.scalableminds.webknossos.datastore.controllers.ZarrStreamingController.dataLayerFolderContentsPrivateLink(token: Option[String], accessTokenOrId: String, dataLayerName: String) -GET /annotations/zarr/:accessTokenOrId/:dataLayerName/ @com.scalableminds.webknossos.datastore.controllers.ZarrStreamingController.dataLayerFolderContentsPrivateLink(token: Option[String], accessTokenOrId: String, dataLayerName: String) -GET /annotations/zarr/:accessTokenOrId/:dataLayerName/.zattrs @com.scalableminds.webknossos.datastore.controllers.ZarrStreamingController.zAttrsWithAnnotationPrivateLink(token: Option[String], accessTokenOrId: String, dataLayerName: String) -GET /annotations/zarr/:accessTokenOrId/:dataLayerName/.zgroup @com.scalableminds.webknossos.datastore.controllers.ZarrStreamingController.zGroupPrivateLink(token: Option[String], accessTokenOrId: String, dataLayerName: String) -GET /annotations/zarr/:accessTokenOrId/:dataLayerName/:mag @com.scalableminds.webknossos.datastore.controllers.ZarrStreamingController.dataLayerMagFolderContentsPrivateLink(token: Option[String], accessTokenOrId: String, dataLayerName: String, mag: String) -GET /annotations/zarr/:accessTokenOrId/:dataLayerName/:mag/ @com.scalableminds.webknossos.datastore.controllers.ZarrStreamingController.dataLayerMagFolderContentsPrivateLink(token: Option[String], accessTokenOrId: String, dataLayerName: String, mag: String) -GET /annotations/zarr/:accessTokenOrId/:dataLayerName/:mag/.zarray @com.scalableminds.webknossos.datastore.controllers.ZarrStreamingController.zArrayPrivateLink(token: Option[String], accessTokenOrId: String, dataLayerName: String, mag: String) -GET /annotations/zarr/:accessTokenOrId/:dataLayerName/:mag/:cxyz @com.scalableminds.webknossos.datastore.controllers.ZarrStreamingController.rawZarrCubePrivateLink(token: Option[String], accessTokenOrId: String, dataLayerName: String, mag: String, cxyz: String) +GET /annotations/zarr/:accessTokenOrId @com.scalableminds.webknossos.datastore.controllers.ZarrStreamingController.dataSourceFolderContentsPrivateLink(token: Option[String], accessTokenOrId: String) +GET /annotations/zarr/:accessTokenOrId/ @com.scalableminds.webknossos.datastore.controllers.ZarrStreamingController.dataSourceFolderContentsPrivateLink(token: Option[String], accessTokenOrId: String) +GET /annotations/zarr/:accessTokenOrId/.zgroup @com.scalableminds.webknossos.datastore.controllers.ZarrStreamingController.zGroupPrivateLink(token: Option[String], accessTokenOrId: String, dataLayerName="") +GET /annotations/zarr/:accessTokenOrId/datasource-properties.json @com.scalableminds.webknossos.datastore.controllers.ZarrStreamingController.dataSourceWithAnnotationPrivateLink(token: Option[String], accessTokenOrId: String) +GET /annotations/zarr/:accessTokenOrId/:dataLayerName @com.scalableminds.webknossos.datastore.controllers.ZarrStreamingController.dataLayerFolderContentsPrivateLink(token: Option[String], accessTokenOrId: String, dataLayerName: String) +GET /annotations/zarr/:accessTokenOrId/:dataLayerName/ @com.scalableminds.webknossos.datastore.controllers.ZarrStreamingController.dataLayerFolderContentsPrivateLink(token: Option[String], accessTokenOrId: String, dataLayerName: String) +GET /annotations/zarr/:accessTokenOrId/:dataLayerName/.zattrs @com.scalableminds.webknossos.datastore.controllers.ZarrStreamingController.zAttrsWithAnnotationPrivateLink(token: Option[String], accessTokenOrId: String, dataLayerName: String) +GET /annotations/zarr/:accessTokenOrId/:dataLayerName/.zgroup @com.scalableminds.webknossos.datastore.controllers.ZarrStreamingController.zGroupPrivateLink(token: Option[String], accessTokenOrId: String, dataLayerName: String) +GET /annotations/zarr/:accessTokenOrId/:dataLayerName/:mag @com.scalableminds.webknossos.datastore.controllers.ZarrStreamingController.dataLayerMagFolderContentsPrivateLink(token: Option[String], accessTokenOrId: String, dataLayerName: String, mag: String) +GET /annotations/zarr/:accessTokenOrId/:dataLayerName/:mag/ @com.scalableminds.webknossos.datastore.controllers.ZarrStreamingController.dataLayerMagFolderContentsPrivateLink(token: Option[String], accessTokenOrId: String, dataLayerName: String, mag: String) +GET /annotations/zarr/:accessTokenOrId/:dataLayerName/:mag/.zarray @com.scalableminds.webknossos.datastore.controllers.ZarrStreamingController.zArrayPrivateLink(token: Option[String], accessTokenOrId: String, dataLayerName: String, mag: String) +GET /annotations/zarr/:accessTokenOrId/:dataLayerName/:mag/:cxyz @com.scalableminds.webknossos.datastore.controllers.ZarrStreamingController.rawZarrCubePrivateLink(token: Option[String], accessTokenOrId: String, dataLayerName: String, mag: String, cxyz: String) # Segmentation mappings -GET /datasets/:organizationName/:dataSetName/layers/:dataLayerName/mappings/:mappingName @com.scalableminds.webknossos.datastore.controllers.BinaryDataController.mappingJson(token: Option[String], organizationName: String, dataSetName: String, dataLayerName: String, mappingName: String) -GET /datasets/:organizationName/:dataSetName/layers/:dataLayerName/mappings @com.scalableminds.webknossos.datastore.controllers.DataSourceController.listMappings(token: Option[String], organizationName: String, dataSetName: String, dataLayerName: String) +GET /datasets/:organizationName/:dataSetName/layers/:dataLayerName/mappings/:mappingName @com.scalableminds.webknossos.datastore.controllers.BinaryDataController.mappingJson(token: Option[String], organizationName: String, dataSetName: String, dataLayerName: String, mappingName: String) +GET /datasets/:organizationName/:dataSetName/layers/:dataLayerName/mappings @com.scalableminds.webknossos.datastore.controllers.DataSourceController.listMappings(token: Option[String], organizationName: String, dataSetName: String, dataLayerName: String) # Agglomerate files -GET /datasets/:organizationName/:dataSetName/layers/:dataLayerName/agglomerates @com.scalableminds.webknossos.datastore.controllers.DataSourceController.listAgglomerates(token: Option[String], organizationName: String, dataSetName: String, dataLayerName: String) -GET /datasets/:organizationName/:dataSetName/layers/:dataLayerName/agglomerates/:mappingName/skeleton/:agglomerateId @com.scalableminds.webknossos.datastore.controllers.DataSourceController.generateAgglomerateSkeleton(token: Option[String], organizationName: String, dataSetName: String, dataLayerName: String, mappingName: String, agglomerateId: Long) -GET /datasets/:organizationName/:dataSetName/layers/:dataLayerName/agglomerates/:mappingName/agglomerateGraph/:agglomerateId @com.scalableminds.webknossos.datastore.controllers.DataSourceController.agglomerateGraph(token: Option[String], organizationName: String, dataSetName: String, dataLayerName: String, mappingName: String, agglomerateId: Long) -GET /datasets/:organizationName/:dataSetName/layers/:dataLayerName/agglomerates/:mappingName/largestAgglomerateId @com.scalableminds.webknossos.datastore.controllers.DataSourceController.largestAgglomerateId(token: Option[String], organizationName: String, dataSetName: String, dataLayerName: String, mappingName: String) -POST /datasets/:organizationName/:dataSetName/layers/:dataLayerName/agglomerates/:mappingName/agglomeratesForSegments @com.scalableminds.webknossos.datastore.controllers.DataSourceController.agglomerateIdsForSegmentIds(token: Option[String], organizationName: String, dataSetName: String, dataLayerName: String, mappingName: String) +GET /datasets/:organizationName/:dataSetName/layers/:dataLayerName/agglomerates @com.scalableminds.webknossos.datastore.controllers.DataSourceController.listAgglomerates(token: Option[String], organizationName: String, dataSetName: String, dataLayerName: String) +GET /datasets/:organizationName/:dataSetName/layers/:dataLayerName/agglomerates/:mappingName/skeleton/:agglomerateId @com.scalableminds.webknossos.datastore.controllers.DataSourceController.generateAgglomerateSkeleton(token: Option[String], organizationName: String, dataSetName: String, dataLayerName: String, mappingName: String, agglomerateId: Long) +GET /datasets/:organizationName/:dataSetName/layers/:dataLayerName/agglomerates/:mappingName/agglomerateGraph/:agglomerateId @com.scalableminds.webknossos.datastore.controllers.DataSourceController.agglomerateGraph(token: Option[String], organizationName: String, dataSetName: String, dataLayerName: String, mappingName: String, agglomerateId: Long) +GET /datasets/:organizationName/:dataSetName/layers/:dataLayerName/agglomerates/:mappingName/largestAgglomerateId @com.scalableminds.webknossos.datastore.controllers.DataSourceController.largestAgglomerateId(token: Option[String], organizationName: String, dataSetName: String, dataLayerName: String, mappingName: String) +POST /datasets/:organizationName/:dataSetName/layers/:dataLayerName/agglomerates/:mappingName/agglomeratesForSegments @com.scalableminds.webknossos.datastore.controllers.DataSourceController.agglomerateIdsForSegmentIds(token: Option[String], organizationName: String, dataSetName: String, dataLayerName: String, mappingName: String) # Mesh files -GET /datasets/:organizationName/:dataSetName/layers/:dataLayerName/meshes @com.scalableminds.webknossos.datastore.controllers.DataSourceController.listMeshFiles(token: Option[String], organizationName: String, dataSetName: String, dataLayerName: String) -POST /datasets/:organizationName/:dataSetName/layers/:dataLayerName/meshes/chunks @com.scalableminds.webknossos.datastore.controllers.DataSourceController.listMeshChunksForSegmentV0(token: Option[String], organizationName: String, dataSetName: String, dataLayerName: String) -POST /datasets/:organizationName/:dataSetName/layers/:dataLayerName/meshes/chunks/data @com.scalableminds.webknossos.datastore.controllers.DataSourceController.readMeshChunkV0(token: Option[String], organizationName: String, dataSetName: String, dataLayerName: String) -POST /datasets/:organizationName/:dataSetName/layers/:dataLayerName/v1/meshes/chunks @com.scalableminds.webknossos.datastore.controllers.DataSourceController.listMeshChunksForSegmentV1(token: Option[String], organizationName: String, dataSetName: String, dataLayerName: String) -POST /datasets/:organizationName/:dataSetName/layers/:dataLayerName/v1/meshes/chunks/data @com.scalableminds.webknossos.datastore.controllers.DataSourceController.readMeshChunkV1(token: Option[String], organizationName: String, dataSetName: String, dataLayerName: String) -GET /datasets/dummyDraco @com.scalableminds.webknossos.datastore.controllers.DataSourceController.dummyDracoFile() +GET /datasets/:organizationName/:dataSetName/layers/:dataLayerName/meshes @com.scalableminds.webknossos.datastore.controllers.DataSourceController.listMeshFiles(token: Option[String], organizationName: String, dataSetName: String, dataLayerName: String) +POST /datasets/:organizationName/:dataSetName/layers/:dataLayerName/meshes/chunks @com.scalableminds.webknossos.datastore.controllers.DataSourceController.listMeshChunksForSegmentV0(token: Option[String], organizationName: String, dataSetName: String, dataLayerName: String) +POST /datasets/:organizationName/:dataSetName/layers/:dataLayerName/meshes/chunks/data @com.scalableminds.webknossos.datastore.controllers.DataSourceController.readMeshChunkV0(token: Option[String], organizationName: String, dataSetName: String, dataLayerName: String) +POST /datasets/:organizationName/:dataSetName/layers/:dataLayerName/meshes/formatVersion/:formatVersion/chunks @com.scalableminds.webknossos.datastore.controllers.DataSourceController.listMeshChunksForSegmentForVersion(token: Option[String], organizationName: String, dataSetName: String, dataLayerName: String, formatVersion: Int) +POST /datasets/:organizationName/:dataSetName/layers/:dataLayerName/meshes/formatVersion/:formatVersion/chunks/data @com.scalableminds.webknossos.datastore.controllers.DataSourceController.readMeshChunkForVersion(token: Option[String], organizationName: String, dataSetName: String, dataLayerName: String, formatVersion: Int) +GET /datasets/dummyDraco @com.scalableminds.webknossos.datastore.controllers.DataSourceController.dummyDracoFile() # Connectome files -GET /datasets/:organizationName/:dataSetName/layers/:dataLayerName/connectomes @com.scalableminds.webknossos.datastore.controllers.DataSourceController.listConnectomeFiles(token: Option[String], organizationName: String, dataSetName: String, dataLayerName: String) -POST /datasets/:organizationName/:dataSetName/layers/:dataLayerName/connectomes/synapses/positions @com.scalableminds.webknossos.datastore.controllers.DataSourceController.getSynapsePositions(token: Option[String], organizationName: String, dataSetName: String, dataLayerName: String) -POST /datasets/:organizationName/:dataSetName/layers/:dataLayerName/connectomes/synapses/types @com.scalableminds.webknossos.datastore.controllers.DataSourceController.getSynapseTypes(token: Option[String], organizationName: String, dataSetName: String, dataLayerName: String) -POST /datasets/:organizationName/:dataSetName/layers/:dataLayerName/connectomes/synapses/:direction @com.scalableminds.webknossos.datastore.controllers.DataSourceController.getSynapticPartnerForSynapses(token: Option[String], organizationName: String, dataSetName: String, dataLayerName: String, direction: String) -POST /datasets/:organizationName/:dataSetName/layers/:dataLayerName/connectomes/synapses @com.scalableminds.webknossos.datastore.controllers.DataSourceController.getSynapsesForAgglomerates(token: Option[String], organizationName: String, dataSetName: String, dataLayerName: String) +GET /datasets/:organizationName/:dataSetName/layers/:dataLayerName/connectomes @com.scalableminds.webknossos.datastore.controllers.DataSourceController.listConnectomeFiles(token: Option[String], organizationName: String, dataSetName: String, dataLayerName: String) +POST /datasets/:organizationName/:dataSetName/layers/:dataLayerName/connectomes/synapses/positions @com.scalableminds.webknossos.datastore.controllers.DataSourceController.getSynapsePositions(token: Option[String], organizationName: String, dataSetName: String, dataLayerName: String) +POST /datasets/:organizationName/:dataSetName/layers/:dataLayerName/connectomes/synapses/types @com.scalableminds.webknossos.datastore.controllers.DataSourceController.getSynapseTypes(token: Option[String], organizationName: String, dataSetName: String, dataLayerName: String) +POST /datasets/:organizationName/:dataSetName/layers/:dataLayerName/connectomes/synapses/:direction @com.scalableminds.webknossos.datastore.controllers.DataSourceController.getSynapticPartnerForSynapses(token: Option[String], organizationName: String, dataSetName: String, dataLayerName: String, direction: String) +POST /datasets/:organizationName/:dataSetName/layers/:dataLayerName/connectomes/synapses @com.scalableminds.webknossos.datastore.controllers.DataSourceController.getSynapsesForAgglomerates(token: Option[String], organizationName: String, dataSetName: String, dataLayerName: String) # Isosurfaces -POST /datasets/:organizationName/:dataSetName/layers/:dataLayerName/isosurface @com.scalableminds.webknossos.datastore.controllers.BinaryDataController.requestIsosurface(token: Option[String], organizationName: String, dataSetName: String, dataLayerName: String) +POST /datasets/:organizationName/:dataSetName/layers/:dataLayerName/isosurface @com.scalableminds.webknossos.datastore.controllers.BinaryDataController.requestIsosurface(token: Option[String], organizationName: String, dataSetName: String, dataLayerName: String) # DataSource management -POST /datasets @com.scalableminds.webknossos.datastore.controllers.DataSourceController.uploadChunk(token: Option[String]) -POST /datasets/reserveUpload @com.scalableminds.webknossos.datastore.controllers.DataSourceController.reserveUpload(token: Option[String]) -POST /datasets/finishUpload @com.scalableminds.webknossos.datastore.controllers.DataSourceController.finishUpload(token: Option[String]) -POST /datasets/cancelUpload @com.scalableminds.webknossos.datastore.controllers.DataSourceController.cancelUpload(token: Option[String]) -GET /datasets/:organizationName/:dataSetName/readInboxDataSourceLike @com.scalableminds.webknossos.datastore.controllers.DataSourceController.read(token: Option[String], organizationName: String, dataSetName: String, returnFormatLike: Boolean ?= true) -GET /datasets/:organizationName/:dataSetName/readInboxDataSource @com.scalableminds.webknossos.datastore.controllers.DataSourceController.read(token: Option[String], organizationName: String, dataSetName: String, returnFormatLike: Boolean ?= false) -POST /datasets/:organizationName/:dataSetName @com.scalableminds.webknossos.datastore.controllers.DataSourceController.update(token: Option[String], organizationName: String, dataSetName: String) -PUT /datasets/:organizationName/:dataSetName @com.scalableminds.webknossos.datastore.controllers.DataSourceController.add(token: Option[String], organizationName: String, dataSetName: String) -GET /datasets/:organizationName/:dataSetName @com.scalableminds.webknossos.datastore.controllers.DataSourceController.explore(token: Option[String], organizationName: String, dataSetName: String) -DELETE /datasets/:organizationName/:dataSetName/deleteOnDisk @com.scalableminds.webknossos.datastore.controllers.DataSourceController.deleteOnDisk(token: Option[String], organizationName: String, dataSetName: String) +POST /datasets @com.scalableminds.webknossos.datastore.controllers.DataSourceController.uploadChunk(token: Option[String]) +POST /datasets/reserveUpload @com.scalableminds.webknossos.datastore.controllers.DataSourceController.reserveUpload(token: Option[String]) +POST /datasets/finishUpload @com.scalableminds.webknossos.datastore.controllers.DataSourceController.finishUpload(token: Option[String]) +POST /datasets/cancelUpload @com.scalableminds.webknossos.datastore.controllers.DataSourceController.cancelUpload(token: Option[String]) +GET /datasets/:organizationName/:dataSetName/readInboxDataSourceLike @com.scalableminds.webknossos.datastore.controllers.DataSourceController.read(token: Option[String], organizationName: String, dataSetName: String, returnFormatLike: Boolean ?= true) +GET /datasets/:organizationName/:dataSetName/readInboxDataSource @com.scalableminds.webknossos.datastore.controllers.DataSourceController.read(token: Option[String], organizationName: String, dataSetName: String, returnFormatLike: Boolean ?= false) +POST /datasets/:organizationName/:dataSetName @com.scalableminds.webknossos.datastore.controllers.DataSourceController.update(token: Option[String], organizationName: String, dataSetName: String) +PUT /datasets/:organizationName/:dataSetName @com.scalableminds.webknossos.datastore.controllers.DataSourceController.add(token: Option[String], organizationName: String, dataSetName: String) +GET /datasets/:organizationName/:dataSetName @com.scalableminds.webknossos.datastore.controllers.DataSourceController.explore(token: Option[String], organizationName: String, dataSetName: String) +DELETE /datasets/:organizationName/:dataSetName/deleteOnDisk @com.scalableminds.webknossos.datastore.controllers.DataSourceController.deleteOnDisk(token: Option[String], organizationName: String, dataSetName: String) # Actions -POST /triggers/checkInboxBlocking @com.scalableminds.webknossos.datastore.controllers.DataSourceController.triggerInboxCheckBlocking(token: Option[String]) -POST /triggers/newOrganizationFolder @com.scalableminds.webknossos.datastore.controllers.DataSourceController.createOrganizationDirectory(token: Option[String], organizationName: String) -POST /triggers/reload/:organizationName/:dataSetName @com.scalableminds.webknossos.datastore.controllers.DataSourceController.reload(token: Option[String], organizationName: String, dataSetName: String, layerName: Option[String]) +POST /triggers/checkInboxBlocking @com.scalableminds.webknossos.datastore.controllers.DataSourceController.triggerInboxCheckBlocking(token: Option[String]) +POST /triggers/newOrganizationFolder @com.scalableminds.webknossos.datastore.controllers.DataSourceController.createOrganizationDirectory(token: Option[String], organizationName: String) +POST /triggers/reload/:organizationName/:dataSetName @com.scalableminds.webknossos.datastore.controllers.DataSourceController.reload(token: Option[String], organizationName: String, dataSetName: String, layerName: Option[String]) # Exports -GET /exports/:jobId/download @com.scalableminds.webknossos.datastore.controllers.ExportsController.download(token: Option[String], jobId: String) +GET /exports/:jobId/download @com.scalableminds.webknossos.datastore.controllers.ExportsController.download(token: Option[String], jobId: String) From 8e60a9d2e71b096882c43faa6943d3348c6e4153 Mon Sep 17 00:00:00 2001 From: leowe Date: Thu, 29 Sep 2022 14:31:50 +0200 Subject: [PATCH 16/63] rename chunkdatarequest and add custom writes to vec3float --- .../util/geometry/Vec3Float.scala | 23 +++++++++++++++++-- .../datastore/services/MeshFileService.scala | 8 +++---- 2 files changed, 25 insertions(+), 6 deletions(-) diff --git a/util/src/main/scala/com/scalableminds/util/geometry/Vec3Float.scala b/util/src/main/scala/com/scalableminds/util/geometry/Vec3Float.scala index 40de93c024f..170a6afdc33 100644 --- a/util/src/main/scala/com/scalableminds/util/geometry/Vec3Float.scala +++ b/util/src/main/scala/com/scalableminds/util/geometry/Vec3Float.scala @@ -1,6 +1,7 @@ package com.scalableminds.util.geometry -import play.api.libs.json.{Json, OFormat}; +import play.api.libs.json.Json.{fromJson, toJson} +import play.api.libs.json.{JsArray, JsError, JsPath, JsResult, JsSuccess, JsValue, JsonValidationError, Reads, Writes}; case class Vec3Float(x: Float, y: Float, z: Float) { def scale(s: Float): Vec3Float = Vec3Float(x * s, y * s, z * s) @@ -14,5 +15,23 @@ case class Vec3Float(x: Float, y: Float, z: Float) { } object Vec3Float { - implicit val jsonFormat: OFormat[Vec3Float] = Json.format[Vec3Float] + implicit object Vec3FloatReads extends Reads[Vec3Float] { + def reads(json: JsValue): JsResult[Vec3Float] = json match { + case JsArray(ts) if ts.size == 3 => + val c = ts.map(fromJson[Float](_)).flatMap(_.asOpt) + if (c.size != 3) + JsError(Seq(JsPath() -> Seq(JsonValidationError("validate.error.array.invalidContent")))) + else + JsSuccess(Vec3Float(c(0), c(1), c(2))) + case _ => + JsError(Seq(JsPath() -> Seq(JsonValidationError("validate.error.expected.vec3FloatArray")))) + } + } + + implicit object Vec3FloatWrites extends Writes[Vec3Float] { + def writes(v: Vec3Float): JsArray = { + val l = List(v.x, v.y, v.z) + JsArray(l.map(toJson(_))) + } + } } diff --git a/webknossos-datastore/app/com/scalableminds/webknossos/datastore/services/MeshFileService.scala b/webknossos-datastore/app/com/scalableminds/webknossos/datastore/services/MeshFileService.scala index 5ca3eaf546a..bc87fcfce21 100644 --- a/webknossos-datastore/app/com/scalableminds/webknossos/datastore/services/MeshFileService.scala +++ b/webknossos-datastore/app/com/scalableminds/webknossos/datastore/services/MeshFileService.scala @@ -41,8 +41,8 @@ case class MeshChunkDataRequestV0( case class MeshChunkDataRequestV3( meshFile: String, - fragmentStartOffset: Long, - fragmentSize: Int + byteOffset: Long, + byteSize: Int ) object MeshChunkDataRequestV0 { @@ -367,8 +367,8 @@ class MeshFileService @Inject()(config: DataStoreConfig)(implicit ec: ExecutionC cachedMeshFile.reader .uint8() .readArrayBlockWithOffset("neuroglancer", - meshChunkDataRequest.fragmentSize, - meshChunkDataRequest.fragmentStartOffset) + meshChunkDataRequest.byteSize, + meshChunkDataRequest.byteOffset) (data, meshFormat) } ?~> "mesh.file.readData.failed" } From 72e325d6fe3ba252b270fc0d6e9ed4477473867d Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Thu, 29 Sep 2022 16:32:13 +0200 Subject: [PATCH 17/63] use new mesh v3 api --- frontend/javascripts/admin/admin_rest_api.ts | 102 +-------------- frontend/javascripts/libs/DRACOLoader.js | 6 +- .../oxalis/controller/scene_controller.ts | 10 ++ .../oxalis/model/sagas/isosurface_saga.ts | 123 ++++++++++++------ .../segments_tab/segments_view_helper.tsx | 8 +- 5 files changed, 111 insertions(+), 138 deletions(-) diff --git a/frontend/javascripts/admin/admin_rest_api.ts b/frontend/javascripts/admin/admin_rest_api.ts index 1e29007d453..41e8804146d 100644 --- a/frontend/javascripts/admin/admin_rest_api.ts +++ b/frontend/javascripts/admin/admin_rest_api.ts @@ -91,9 +91,14 @@ import messages from "messages"; import window, { location } from "libs/window"; import { SaveQueueType } from "oxalis/model/actions/save_actions"; import { DatasourceConfiguration } from "types/schemas/datasource.types"; +import { doWithToken } from "./api/token"; const MAX_SERVER_ITEMS_PER_RESPONSE = 1000; +export * from "./api/token"; +export * as meshV3 from "./api/mesh_v3"; +export * as meshV0 from "./api/mesh_v0"; + type NewTeam = { readonly name: string; }; @@ -107,58 +112,6 @@ function assertResponseLimit(collection: unknown[]) { } // ### Do with userToken -let tokenRequestPromise: Promise | null; - -function requestUserToken(): Promise { - if (tokenRequestPromise) { - return tokenRequestPromise; - } - - tokenRequestPromise = Request.receiveJSON("/api/userToken/generate", { - method: "POST", - }).then((tokenObj) => { - tokenRequestPromise = null; - return tokenObj.token as string; - }); - - return tokenRequestPromise; -} - -export function getSharingTokenFromUrlParameters(): string | null | undefined { - if (location != null) { - const params = Utils.getUrlParamsObject(); - - if (params != null && params.token != null) { - return params.token; - } - } - - return null; -} - -let tokenPromise: Promise; -export function doWithToken(fn: (token: string) => Promise, tries: number = 1): Promise { - const sharingToken = getSharingTokenFromUrlParameters(); - - if (sharingToken != null) { - return fn(sharingToken); - } - - if (!tokenPromise) tokenPromise = requestUserToken(); - return tokenPromise.then(fn).catch((error) => { - if (error.status === 403) { - console.warn("Token expired. Requesting new token..."); - tokenPromise = requestUserToken(); - - // If three new tokens did not fix the 403, abort, otherwise we'll get into an endless loop here - if (tries < 3) { - return doWithToken(fn, tries + 1); - } - } - - throw error; - }); -} export function sendAnalyticsEvent(eventType: string, eventProperties: {} = {}): void { // Note that the Promise from sendJSONReceiveJSON is not awaited or returned here, @@ -2130,51 +2083,6 @@ export function getMeshfilesForDatasetLayer( ); } -export function getMeshfileChunksForSegment( - dataStoreUrl: string, - datasetId: APIDatasetId, - layerName: string, - meshFile: string, - segmentId: number, -): Promise> { - return doWithToken((token) => - Request.sendJSONReceiveJSON( - `${dataStoreUrl}/data/datasets/${datasetId.owningOrganization}/${datasetId.name}/layers/${layerName}/meshes/chunks?token=${token}`, - { - data: { - meshFile, - segmentId, - }, - showErrorToast: false, - }, - ), - ); -} - -export function getMeshfileChunkData( - dataStoreUrl: string, - datasetId: APIDatasetId, - layerName: string, - meshFile: string, - segmentId: number, - position: Vector3, -): Promise { - return doWithToken(async (token) => { - const data = await Request.sendJSONReceiveArraybufferWithHeaders( - `${dataStoreUrl}/data/datasets/${datasetId.owningOrganization}/${datasetId.name}/layers/${layerName}/meshes/chunks/data?token=${token}`, - { - data: { - meshFile, - segmentId, - position, - }, - useWebworkerForArrayBuffer: false, - }, - ); - return data; - }); -} - export function getDummyDraco(): Promise { return doWithToken(async (token) => { const data = await Request.receiveArraybuffer(`/assets/draco_file.bin`, { diff --git a/frontend/javascripts/libs/DRACOLoader.js b/frontend/javascripts/libs/DRACOLoader.js index c04219bf122..d39552db1cf 100644 --- a/frontend/javascripts/libs/DRACOLoader.js +++ b/frontend/javascripts/libs/DRACOLoader.js @@ -65,7 +65,11 @@ import * as THREE from "three"; attributeTypes: attributeTypes || this.defaultAttributeTypes, useUniqueIDs: !!attributeIDs, }; - return this.decodeGeometry(buffer, taskConfig).then(callback); + const promise = this.decodeGeometry(buffer, taskConfig); + if (callback == null) { + return promise; + } + return promise.then(callback); } decodeGeometry(buffer, taskConfig) { diff --git a/frontend/javascripts/oxalis/controller/scene_controller.ts b/frontend/javascripts/oxalis/controller/scene_controller.ts index 0c34490a033..904f7b095d2 100644 --- a/frontend/javascripts/oxalis/controller/scene_controller.ts +++ b/frontend/javascripts/oxalis/controller/scene_controller.ts @@ -272,6 +272,8 @@ class SceneController { geometry: THREE.BufferGeometry, segmentationId: number, passive: boolean = false, + offset: Vector3 | null = null, + useDatasetScale: boolean = false, ): void { if (this.isosurfacesGroupsPerSegmentationId[segmentationId] == null) { const newGroup = new THREE.Group(); @@ -281,8 +283,16 @@ class SceneController { newGroup.cellId = segmentationId; // @ts-ignore newGroup.passive = passive; + if (useDatasetScale) { + newGroup.scale.copy(new THREE.Vector3(...Store.getState().dataset.dataSource.scale)); + } } const mesh = this.constructIsosurfaceMesh(segmentationId, geometry, passive); + if (offset) { + mesh.translateX(offset[0]); + mesh.translateY(offset[1]); + mesh.translateZ(offset[2]); + } this.isosurfacesGroupsPerSegmentationId[segmentationId].add(mesh); } diff --git a/frontend/javascripts/oxalis/model/sagas/isosurface_saga.ts b/frontend/javascripts/oxalis/model/sagas/isosurface_saga.ts index f000cf2081d..e2387bb8fd8 100644 --- a/frontend/javascripts/oxalis/model/sagas/isosurface_saga.ts +++ b/frontend/javascripts/oxalis/model/sagas/isosurface_saga.ts @@ -1,7 +1,7 @@ import { saveAs } from "file-saver"; import _ from "lodash"; import { V3 } from "libs/mjs"; -import { sleep } from "libs/utils"; +import { point3ToVector3, sleep } from "libs/utils"; import ErrorHandling from "libs/error_handling"; import type { APIDataLayer } from "types/api_flow_types"; import "libs/DRACOLoader.js"; @@ -42,9 +42,9 @@ import { stlIsosurfaceConstants } from "oxalis/view/right-border-tabs/segments_t import { computeIsosurface, sendAnalyticsEvent, - getMeshfileChunksForSegment, - getMeshfileChunkData, getDummyDraco, + meshV0, + meshV3, } from "admin/admin_rest_api"; import { getFlooredPosition } from "oxalis/model/accessors/flycam_accessor"; import { setImportingMeshStateAction } from "oxalis/model/actions/ui_actions"; @@ -551,17 +551,30 @@ function* loadPrecomputedMeshForSegmentId( yield* put(addPrecomputedIsosurfaceAction(layerName, id, seedPosition, meshFileName)); yield* put(startedLoadingIsosurfaceAction(layerName, id)); const dataset = yield* select((state) => state.dataset); - let availableChunks = null; + let availableChunks = null; + const version = 3; try { - availableChunks = yield* call( - getMeshfileChunksForSegment, - dataset.dataStore.url, - dataset, - getBaseSegmentationName(segmentationLayer), - meshFileName, - id, - ); + if (version === 3) { + const segmentInfo = yield* call( + meshV3.getMeshfileChunksForSegment, + dataset.dataStore.url, + dataset, + getBaseSegmentationName(segmentationLayer), + meshFileName, + id, + ); + availableChunks = _.first(segmentInfo.chunks.lods)?.fragments || []; + } else { + availableChunks = yield* call( + meshV0.getMeshfileChunksForSegment, + dataset.dataStore.url, + dataset, + getBaseSegmentationName(segmentationLayer), + meshFileName, + id, + ); + } } catch (exception) { console.warn("Mesh chunk couldn't be loaded due to", exception); Toast.warning(messages["tracing.mesh_listing_failed"]); @@ -571,29 +584,54 @@ function* loadPrecomputedMeshForSegmentId( } // Sort the chunks by distance to the seedPosition, so that the mesh loads from the inside out - const sortedAvailableChunks = _.sortBy(availableChunks, (chunkPosition) => - V3.length(V3.sub(seedPosition, chunkPosition)), - ); + const sortedAvailableChunks = _.sortBy(availableChunks, (chunk: Vector3 | meshV3.MeshFragment) => + V3.length(V3.sub(seedPosition, "position" in chunk ? point3ToVector3(chunk.position) : chunk)), + ) as Array | Array; const tasks = sortedAvailableChunks.map( - (chunkPosition) => + (chunk) => function* loadChunk() { - const stlData = yield* call( - getMeshfileChunkData, - dataset.dataStore.url, - dataset, - getBaseSegmentationName(segmentationLayer), - meshFileName, - id, - chunkPosition, - ); - const geometry = yield* call(parseStlBuffer, stlData); const sceneController = yield* call(getSceneController); - yield* call( - { context: sceneController, fn: sceneController.addIsosurfaceFromGeometry }, - geometry, - id, - ); + + if ("position" in chunk) { + const dracoData = yield* call( + meshV3.getMeshfileChunkData, + dataset.dataStore.url, + dataset, + getBaseSegmentationName(segmentationLayer), + meshFileName, + chunk.byteOffset, + chunk.byteSize, + ); + const loader = getDracoLoader(); + + const geometry = yield* call(loader.decodeDracoFile.bind(loader), dracoData); + yield* call( + { context: sceneController, fn: sceneController.addIsosurfaceFromGeometry }, + geometry, + id, + false, + point3ToVector3(chunk.position), + true, + ); + } else { + const stlData = yield* call( + meshV0.getMeshfileChunkData, + dataset.dataStore.url, + dataset, + getBaseSegmentationName(segmentationLayer), + meshFileName, + id, + chunk, + ); + const geometry = yield* call(parseStlBuffer, stlData); + yield* call( + { context: sceneController, fn: sceneController.addIsosurfaceFromGeometry }, + geometry, + id, + false, + ); + } }, ); @@ -607,18 +645,25 @@ function* loadPrecomputedMeshForSegmentId( yield* put(finishedLoadingIsosurfaceAction(layerName, id)); } -function* addDummyDraco() { - const buffer = yield* call(getDummyDraco); - console.log("buffer", buffer); - - const loader = new THREE.DRACOLoader(); - console.log("THREE.DRACOLoader", loader); +let _dracoLoader; +function getDracoLoader() { + if (_dracoLoader) { + return _dracoLoader; + } + _dracoLoader = new THREE.DRACOLoader(); - loader.setDecoderPath( + _dracoLoader.setDecoderPath( "https://raw.githubusercontent.com/mrdoob/three.js/dev/examples/js/libs/draco/", ); - loader.setDecoderConfig({ type: "js" }); + _dracoLoader.setDecoderConfig({ type: "js" }); + return _dracoLoader; +} + +function* addDummyDraco() { + const buffer = yield* call(getDummyDraco); + console.log("buffer", buffer); + const loader = getDracoLoader(); const sceneController = yield* call(getSceneController); // const url = "/data/datasets/dummyDraco"; diff --git a/frontend/javascripts/oxalis/view/right-border-tabs/segments_tab/segments_view_helper.tsx b/frontend/javascripts/oxalis/view/right-border-tabs/segments_tab/segments_view_helper.tsx index 721a109ae4c..5512f158db6 100644 --- a/frontend/javascripts/oxalis/view/right-border-tabs/segments_tab/segments_view_helper.tsx +++ b/frontend/javascripts/oxalis/view/right-border-tabs/segments_tab/segments_view_helper.tsx @@ -84,7 +84,13 @@ export function withMappingActivationConfirmation> // If the mapping name is undefined, no mapping is specified. In that case never show the activation modal. // In contrast, if the mapping name is null, this indicates that all mappings should be specifically disabled. - if (mappingName === undefined || layerName == null || mappingName === enabledMappingName) { + // todo: remove last condition + if ( + mappingName === undefined || + layerName == null || + mappingName === enabledMappingName || + mappingName == "" + ) { // @ts-expect-error ts-migrate(2322) FIXME: Type 'Omit, ... Remove this comment to see the full error message return ; } From de2c466ea85e37ba75b57b3df85dad9d9b14d373 Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Thu, 29 Sep 2022 16:32:26 +0200 Subject: [PATCH 18/63] temporary workaround for mapping name with empty string --- frontend/javascripts/oxalis/api/api_latest.ts | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/frontend/javascripts/oxalis/api/api_latest.ts b/frontend/javascripts/oxalis/api/api_latest.ts index c2762f3df2c..3bafa75c9dc 100644 --- a/frontend/javascripts/oxalis/api/api_latest.ts +++ b/frontend/javascripts/oxalis/api/api_latest.ts @@ -1841,7 +1841,8 @@ class DataApi { const { mappingName, meshFileName } = currentMeshFile; - if (mappingName != null) { + // todo: remove second condition + if (mappingName != null && mappingName != "") { const activeMapping = this.getActiveMapping(effectiveLayerName); if (mappingName !== activeMapping) { From 8b55ab46cd059fe75ea318270ab9cbca8607632f Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Thu, 29 Sep 2022 16:37:17 +0200 Subject: [PATCH 19/63] adapt frontend to backend changes --- frontend/javascripts/oxalis/model/sagas/isosurface_saga.ts | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/frontend/javascripts/oxalis/model/sagas/isosurface_saga.ts b/frontend/javascripts/oxalis/model/sagas/isosurface_saga.ts index e2387bb8fd8..446177787de 100644 --- a/frontend/javascripts/oxalis/model/sagas/isosurface_saga.ts +++ b/frontend/javascripts/oxalis/model/sagas/isosurface_saga.ts @@ -1,7 +1,7 @@ import { saveAs } from "file-saver"; import _ from "lodash"; import { V3 } from "libs/mjs"; -import { point3ToVector3, sleep } from "libs/utils"; +import { sleep } from "libs/utils"; import ErrorHandling from "libs/error_handling"; import type { APIDataLayer } from "types/api_flow_types"; import "libs/DRACOLoader.js"; @@ -585,7 +585,7 @@ function* loadPrecomputedMeshForSegmentId( // Sort the chunks by distance to the seedPosition, so that the mesh loads from the inside out const sortedAvailableChunks = _.sortBy(availableChunks, (chunk: Vector3 | meshV3.MeshFragment) => - V3.length(V3.sub(seedPosition, "position" in chunk ? point3ToVector3(chunk.position) : chunk)), + V3.length(V3.sub(seedPosition, "position" in chunk ? chunk.position : chunk)), ) as Array | Array; const tasks = sortedAvailableChunks.map( @@ -611,7 +611,7 @@ function* loadPrecomputedMeshForSegmentId( geometry, id, false, - point3ToVector3(chunk.position), + chunk.position, true, ); } else { From a8bfbac20f55db9375d59cc4c882c55eb3e726bd Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Thu, 29 Sep 2022 16:37:35 +0200 Subject: [PATCH 20/63] add new api modules --- frontend/javascripts/admin/api/mesh_v0.ts | 49 ++++++++++++++++ frontend/javascripts/admin/api/mesh_v3.ts | 70 +++++++++++++++++++++++ frontend/javascripts/admin/api/token.ts | 56 ++++++++++++++++++ 3 files changed, 175 insertions(+) create mode 100644 frontend/javascripts/admin/api/mesh_v0.ts create mode 100644 frontend/javascripts/admin/api/mesh_v3.ts create mode 100644 frontend/javascripts/admin/api/token.ts diff --git a/frontend/javascripts/admin/api/mesh_v0.ts b/frontend/javascripts/admin/api/mesh_v0.ts new file mode 100644 index 00000000000..933d2187d9f --- /dev/null +++ b/frontend/javascripts/admin/api/mesh_v0.ts @@ -0,0 +1,49 @@ +import Request from "libs/request"; +import { Vector3 } from "oxalis/constants"; +import { APIDatasetId } from "types/api_flow_types"; +import { doWithToken } from "./token"; + +export function getMeshfileChunksForSegment( + dataStoreUrl: string, + datasetId: APIDatasetId, + layerName: string, + meshFile: string, + segmentId: number, +): Promise> { + return doWithToken((token) => + Request.sendJSONReceiveJSON( + `${dataStoreUrl}/data/datasets/${datasetId.owningOrganization}/${datasetId.name}/layers/${layerName}/meshes/chunks?token=${token}`, + { + data: { + meshFile, + segmentId, + }, + showErrorToast: false, + }, + ), + ); +} + +export function getMeshfileChunkData( + dataStoreUrl: string, + datasetId: APIDatasetId, + layerName: string, + meshFile: string, + segmentId: number, + position: Vector3, +): Promise { + return doWithToken(async (token) => { + const data = await Request.sendJSONReceiveArraybufferWithHeaders( + `${dataStoreUrl}/data/datasets/${datasetId.owningOrganization}/${datasetId.name}/layers/${layerName}/meshes/chunks/data?token=${token}`, + { + data: { + meshFile, + segmentId, + position, + }, + useWebworkerForArrayBuffer: false, + }, + ); + return data; + }); +} diff --git a/frontend/javascripts/admin/api/mesh_v3.ts b/frontend/javascripts/admin/api/mesh_v3.ts new file mode 100644 index 00000000000..0cb80696b83 --- /dev/null +++ b/frontend/javascripts/admin/api/mesh_v3.ts @@ -0,0 +1,70 @@ +import Request from "libs/request"; +import { Vector3 } from "oxalis/constants"; +import { APIDatasetId } from "types/api_flow_types"; +import { doWithToken } from "./token"; + +export type MeshFragment = { position: Vector3; byteOffset: number; byteSize: number }; + +type MeshLodInfo = { + scale: number; + vertexOffset: Vector3; + chunkShape: Vector3; + fragments: Array; +}; + +type MeshSegmentInfo = { + chunkShape: Vector3; + gridOrigin: Vector3; + lods: Array; +}; + +type SegmentInfo = { + transform: number[][]; // 3x3 matrix + meshFormat: "draco"; + chunks: MeshSegmentInfo; +}; + +export function getMeshfileChunksForSegment( + dataStoreUrl: string, + datasetId: APIDatasetId, + layerName: string, + meshFile: string, + segmentId: number, +): Promise { + return doWithToken((token) => + Request.sendJSONReceiveJSON( + `${dataStoreUrl}/data/datasets/${datasetId.owningOrganization}/${datasetId.name}/layers/${layerName}/meshes/formatVersion/3/chunks?token=${token}`, + { + data: { + meshFile, + segmentId, + }, + showErrorToast: false, + }, + ), + ); +} + +export function getMeshfileChunkData( + dataStoreUrl: string, + datasetId: APIDatasetId, + layerName: string, + meshFile: string, + byteOffset: number, + byteSize: number, +): Promise { + return doWithToken(async (token) => { + const data = await Request.sendJSONReceiveArraybufferWithHeaders( + `${dataStoreUrl}/data/datasets/${datasetId.owningOrganization}/${datasetId.name}/layers/${layerName}/meshes/formatVersion/3/chunks/data?token=${token}`, + { + data: { + meshFile, + byteOffset, + byteSize, + }, + useWebworkerForArrayBuffer: false, + }, + ); + return data; + }); +} diff --git a/frontend/javascripts/admin/api/token.ts b/frontend/javascripts/admin/api/token.ts new file mode 100644 index 00000000000..4424ca662c6 --- /dev/null +++ b/frontend/javascripts/admin/api/token.ts @@ -0,0 +1,56 @@ +import Request from "libs/request"; +import * as Utils from "libs/utils"; + +let tokenPromise: Promise; + +let tokenRequestPromise: Promise | null; + +function requestUserToken(): Promise { + if (tokenRequestPromise) { + return tokenRequestPromise; + } + + tokenRequestPromise = Request.receiveJSON("/api/userToken/generate", { + method: "POST", + }).then((tokenObj) => { + tokenRequestPromise = null; + return tokenObj.token as string; + }); + + return tokenRequestPromise; +} + +export function getSharingTokenFromUrlParameters(): string | null | undefined { + if (location != null) { + const params = Utils.getUrlParamsObject(); + + if (params != null && params.token != null) { + return params.token; + } + } + + return null; +} + +export function doWithToken(fn: (token: string) => Promise, tries: number = 1): Promise { + const sharingToken = getSharingTokenFromUrlParameters(); + + if (sharingToken != null) { + return fn(sharingToken); + } + + if (!tokenPromise) tokenPromise = requestUserToken(); + return tokenPromise.then(fn).catch((error) => { + if (error.status === 403) { + console.warn("Token expired. Requesting new token..."); + tokenPromise = requestUserToken(); + + // If three new tokens did not fix the 403, abort, otherwise we'll get into an endless loop here + if (tries < 3) { + return doWithToken(fn, tries + 1); + } + } + + throw error; + }); +} From 65081e97714312e217ae4e631b85e88b0e8cf293 Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Thu, 29 Sep 2022 16:39:21 +0200 Subject: [PATCH 21/63] remove the dummy draco file code again --- frontend/javascripts/admin/admin_rest_api.ts | 17 --------- .../oxalis/model/sagas/isosurface_saga.ts | 38 ++----------------- .../oxalis/view/action_bar_view.tsx | 4 -- 3 files changed, 4 insertions(+), 55 deletions(-) diff --git a/frontend/javascripts/admin/admin_rest_api.ts b/frontend/javascripts/admin/admin_rest_api.ts index 41e8804146d..6e560f3b50e 100644 --- a/frontend/javascripts/admin/admin_rest_api.ts +++ b/frontend/javascripts/admin/admin_rest_api.ts @@ -2083,23 +2083,6 @@ export function getMeshfilesForDatasetLayer( ); } -export function getDummyDraco(): Promise { - return doWithToken(async (token) => { - const data = await Request.receiveArraybuffer(`/assets/draco_file.bin`, { - // const data = await Request.receiveArraybuffer(`/data/datasets/dummyDraco?token=${token}`, { - useWebworkerForArrayBuffer: false, - }); - - console.log("works", data, new Uint8Array(data)); - - const data2 = await Request.receiveArraybuffer(`/data/datasets/dummyDraco?token=${token}`, { - useWebworkerForArrayBuffer: false, - }); - console.log("doesnt work", data2, new Uint8Array(data2)); - return data2; - }); -} - // ### Connectomes export function getConnectomeFilesForDatasetLayer( dataStoreUrl: string, diff --git a/frontend/javascripts/oxalis/model/sagas/isosurface_saga.ts b/frontend/javascripts/oxalis/model/sagas/isosurface_saga.ts index 446177787de..9959fd6adac 100644 --- a/frontend/javascripts/oxalis/model/sagas/isosurface_saga.ts +++ b/frontend/javascripts/oxalis/model/sagas/isosurface_saga.ts @@ -39,13 +39,7 @@ import type { Saga } from "oxalis/model/sagas/effect-generators"; import { select } from "oxalis/model/sagas/effect-generators"; import { actionChannel, takeEvery, call, take, race, put } from "typed-redux-saga"; import { stlIsosurfaceConstants } from "oxalis/view/right-border-tabs/segments_tab/segments_view"; -import { - computeIsosurface, - sendAnalyticsEvent, - getDummyDraco, - meshV0, - meshV3, -} from "admin/admin_rest_api"; +import { computeIsosurface, sendAnalyticsEvent, meshV0, meshV3 } from "admin/admin_rest_api"; import { getFlooredPosition } from "oxalis/model/accessors/flycam_accessor"; import { setImportingMeshStateAction } from "oxalis/model/actions/ui_actions"; import { zoomedAddressToAnotherZoomStepWithInfo } from "oxalis/model/helpers/position_converter"; @@ -656,34 +650,11 @@ function getDracoLoader() { "https://raw.githubusercontent.com/mrdoob/three.js/dev/examples/js/libs/draco/", ); _dracoLoader.setDecoderConfig({ type: "js" }); - return _dracoLoader; -} - -function* addDummyDraco() { - const buffer = yield* call(getDummyDraco); - console.log("buffer", buffer); - - const loader = getDracoLoader(); - const sceneController = yield* call(getSceneController); - // const url = "/data/datasets/dummyDraco"; - const url = "/assets/draco_file.bin"; - // const url = "http://localhost:9000/assets/bunny.drc"; - // loader.load(url, (geometry) => { - loader.decodeDracoFile(buffer, (geometry) => { - // geometry.computeVertexNormals(); + // todo: never dispose? + // loader.dispose(); - // todo: use correct id - sceneController.addIsosurfaceFromGeometry(geometry, 2347819234); - - // Release decoder resources. - loader.dispose(); - }); - - // const decoderModule = yield* call(() => draco3d.createDecoderModule({})); - // let decoder = new decoderModule.Decoder(); - // console.log("decoder"); - // const geometry = yield* call(parseStlBuffer, stlData); + return _dracoLoader; } /* @@ -773,5 +744,4 @@ export default function* isosurfaceSaga(): Saga { yield* takeEvery("UPDATE_ISOSURFACE_VISIBILITY", handleIsosurfaceVisibilityChange); yield* takeEvery(["START_EDITING", "COPY_SEGMENTATION_LAYER"], markEditedCellAsDirty); yield* takeEvery(["UPDATE_SEGMENT"], handleIsosurfaceColorChange); - yield* takeEvery(["ADD_DUMMY_DRACO"], addDummyDraco); } diff --git a/frontend/javascripts/oxalis/view/action_bar_view.tsx b/frontend/javascripts/oxalis/view/action_bar_view.tsx index bdcc58c0de4..11a6ec0519e 100644 --- a/frontend/javascripts/oxalis/view/action_bar_view.tsx +++ b/frontend/javascripts/oxalis/view/action_bar_view.tsx @@ -160,10 +160,6 @@ class ActionBarView extends React.PureComponent { {!isReadOnly && constants.MODES_PLANE.indexOf(viewMode) > -1 ? : null} {isArbitrarySupported && !is2d ? : null} {isViewMode ? this.renderStartTracingButton() : null} - - Store.dispatch({ type: "ADD_DUMMY_DRACO" })}> - ADD_DUMMY_DRACO - Date: Thu, 29 Sep 2022 16:45:21 +0200 Subject: [PATCH 22/63] fix addition --- .../main/scala/com/scalableminds/util/geometry/Vec3Float.scala | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/util/src/main/scala/com/scalableminds/util/geometry/Vec3Float.scala b/util/src/main/scala/com/scalableminds/util/geometry/Vec3Float.scala index 170a6afdc33..7b2fe6ef557 100644 --- a/util/src/main/scala/com/scalableminds/util/geometry/Vec3Float.scala +++ b/util/src/main/scala/com/scalableminds/util/geometry/Vec3Float.scala @@ -9,7 +9,7 @@ case class Vec3Float(x: Float, y: Float, z: Float) { def *(s: Float): Vec3Float = scale(s) def *(s: Double): Vec3Float = scale(s.toFloat) def *(that: Vec3Float): Vec3Float = Vec3Float(x * that.x, y * that.y, z * that.z) - def +(that: Vec3Float): Vec3Float = Vec3Float(x + that.x, y + that.y, z + that.y) + def +(that: Vec3Float): Vec3Float = Vec3Float(x + that.x, y + that.y, z + that.z) def toList: List[Float] = List(x, y, z) } From d269280a35e71327f84a58c15ec149e83e8854c3 Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Thu, 29 Sep 2022 16:58:06 +0200 Subject: [PATCH 23/63] use DRACOLoader from threejs package --- frontend/javascripts/libs/DRACOLoader.js | 471 ------------------ .../oxalis/model/sagas/isosurface_saga.ts | 18 +- public/draco_file.bin | Bin 251 -> 0 bytes 3 files changed, 15 insertions(+), 474 deletions(-) delete mode 100644 frontend/javascripts/libs/DRACOLoader.js delete mode 100644 public/draco_file.bin diff --git a/frontend/javascripts/libs/DRACOLoader.js b/frontend/javascripts/libs/DRACOLoader.js deleted file mode 100644 index d39552db1cf..00000000000 --- a/frontend/javascripts/libs/DRACOLoader.js +++ /dev/null @@ -1,471 +0,0 @@ -import * as THREE from "three"; - -(function () { - const _taskCache = new WeakMap(); - - class DRACOLoader extends THREE.Loader { - constructor(manager) { - super(manager); - this.decoderPath = ""; - this.decoderConfig = {}; - this.decoderBinary = null; - this.decoderPending = null; - this.workerLimit = 4; - this.workerPool = []; - this.workerNextTaskID = 1; - this.workerSourceURL = ""; - this.defaultAttributeIDs = { - position: "POSITION", - normal: "NORMAL", - color: "COLOR", - uv: "TEX_COORD", - }; - this.defaultAttributeTypes = { - position: "Float32Array", - normal: "Float32Array", - color: "Float32Array", - uv: "Float32Array", - }; - } - - setDecoderPath(path) { - this.decoderPath = path; - return this; - } - - setDecoderConfig(config) { - this.decoderConfig = config; - return this; - } - - setWorkerLimit(workerLimit) { - this.workerLimit = workerLimit; - return this; - } - - load(url, onLoad, onProgress, onError) { - const loader = new THREE.FileLoader(this.manager); - loader.setPath(this.path); - loader.setResponseType("arraybuffer"); - loader.setRequestHeader(this.requestHeader); - loader.setWithCredentials(this.withCredentials); - loader.load( - url, - (buffer) => { - this.decodeDracoFile(buffer, onLoad).catch(onError); - }, - onProgress, - onError, - ); - } - - decodeDracoFile(buffer, callback, attributeIDs, attributeTypes) { - const taskConfig = { - attributeIDs: attributeIDs || this.defaultAttributeIDs, - attributeTypes: attributeTypes || this.defaultAttributeTypes, - useUniqueIDs: !!attributeIDs, - }; - const promise = this.decodeGeometry(buffer, taskConfig); - if (callback == null) { - return promise; - } - return promise.then(callback); - } - - decodeGeometry(buffer, taskConfig) { - const taskKey = JSON.stringify(taskConfig); // Check for an existing task using this buffer. A transferred buffer cannot be transferred - // again from this thread. - - if (_taskCache.has(buffer)) { - const cachedTask = _taskCache.get(buffer); - - if (cachedTask.key === taskKey) { - return cachedTask.promise; - } else if (buffer.byteLength === 0) { - // Technically, it would be possible to wait for the previous task to complete, - // transfer the buffer back, and decode again with the second configuration. That - // is complex, and I don't know of any reason to decode a Draco buffer twice in - // different ways, so this is left unimplemented. - throw new Error( - "THREE.DRACOLoader: Unable to re-decode a buffer with different " + - "settings. Buffer has already been transferred.", - ); - } - } // - - let worker; - const taskID = this.workerNextTaskID++; - const taskCost = buffer.byteLength; // Obtain a worker and assign a task, and construct a geometry instance - // when the task completes. - - const geometryPending = this._getWorker(taskID, taskCost) - .then((_worker) => { - worker = _worker; - return new Promise((resolve, reject) => { - worker._callbacks[taskID] = { - resolve, - reject, - }; - worker.postMessage( - { - type: "decode", - id: taskID, - taskConfig, - buffer, - }, - [buffer], - ); // this.debug(); - }); - }) - .then((message) => this._createGeometry(message.geometry)); // Remove task from the task list. - // Note: replaced '.finally()' with '.catch().then()' block - iOS 11 support (#19416) - - geometryPending - .catch(() => true) - .then(() => { - if (worker && taskID) { - this._releaseTask(worker, taskID); // this.debug(); - } - }); // Cache the task result. - - _taskCache.set(buffer, { - key: taskKey, - promise: geometryPending, - }); - - return geometryPending; - } - - _createGeometry(geometryData) { - const geometry = new THREE.BufferGeometry(); - - if (geometryData.index) { - geometry.setIndex(new THREE.BufferAttribute(geometryData.index.array, 1)); - } - - for (let i = 0; i < geometryData.attributes.length; i++) { - const attribute = geometryData.attributes[i]; - const name = attribute.name; - const array = attribute.array; - const itemSize = attribute.itemSize; - geometry.setAttribute(name, new THREE.BufferAttribute(array, itemSize)); - } - - return geometry; - } - - _loadLibrary(url, responseType) { - const loader = new THREE.FileLoader(this.manager); - loader.setPath(this.decoderPath); - loader.setResponseType(responseType); - loader.setWithCredentials(this.withCredentials); - return new Promise((resolve, reject) => { - loader.load(url, resolve, undefined, reject); - }); - } - - preload() { - this._initDecoder(); - - return this; - } - - _initDecoder() { - if (this.decoderPending) return this.decoderPending; - const useJS = typeof WebAssembly !== "object" || this.decoderConfig.type === "js"; - const librariesPending = []; - - if (useJS) { - librariesPending.push(this._loadLibrary("draco_decoder.js", "text")); - } else { - librariesPending.push(this._loadLibrary("draco_wasm_wrapper.js", "text")); - librariesPending.push(this._loadLibrary("draco_decoder.wasm", "arraybuffer")); - } - - this.decoderPending = Promise.all(librariesPending).then((libraries) => { - const jsContent = libraries[0]; - - if (!useJS) { - this.decoderConfig.wasmBinary = libraries[1]; - } - - const fn = DRACOWorker.toString(); - const body = [ - "/* draco decoder */", - jsContent, - "", - "/* worker */", - fn.substring(fn.indexOf("{") + 1, fn.lastIndexOf("}")), - ].join("\n"); - this.workerSourceURL = URL.createObjectURL(new Blob([body])); - }); - return this.decoderPending; - } - - _getWorker(taskID, taskCost) { - return this._initDecoder().then(() => { - if (this.workerPool.length < this.workerLimit) { - const worker = new Worker(this.workerSourceURL); - worker._callbacks = {}; - worker._taskCosts = {}; - worker._taskLoad = 0; - worker.postMessage({ - type: "init", - decoderConfig: this.decoderConfig, - }); - - worker.onmessage = function (e) { - const message = e.data; - - switch (message.type) { - case "decode": - worker._callbacks[message.id].resolve(message); - - break; - - case "error": - worker._callbacks[message.id].reject(message); - - break; - - default: - console.error('THREE.DRACOLoader: Unexpected message, "' + message.type + '"'); - } - }; - - this.workerPool.push(worker); - } else { - this.workerPool.sort(function (a, b) { - return a._taskLoad > b._taskLoad ? -1 : 1; - }); - } - - const worker = this.workerPool[this.workerPool.length - 1]; - worker._taskCosts[taskID] = taskCost; - worker._taskLoad += taskCost; - return worker; - }); - } - - _releaseTask(worker, taskID) { - worker._taskLoad -= worker._taskCosts[taskID]; - delete worker._callbacks[taskID]; - delete worker._taskCosts[taskID]; - } - - debug() { - console.log( - "Task load: ", - this.workerPool.map((worker) => worker._taskLoad), - ); - } - - dispose() { - for (let i = 0; i < this.workerPool.length; ++i) { - this.workerPool[i].terminate(); - } - - this.workerPool.length = 0; - return this; - } - } - /* WEB WORKER */ - - function DRACOWorker() { - let decoderConfig; - let decoderPending; - - onmessage = function (e) { - const message = e.data; - - switch (message.type) { - case "init": - decoderConfig = message.decoderConfig; - decoderPending = new Promise(function ( - resolve, - /*, reject*/ - ) { - decoderConfig.onModuleLoaded = function (draco) { - // Module is Promise-like. Wrap before resolving to avoid loop. - resolve({ - draco: draco, - }); - }; - - DracoDecoderModule(decoderConfig); // eslint-disable-line no-undef - }); - break; - - case "decode": - const buffer = message.buffer; - const taskConfig = message.taskConfig; - decoderPending.then((module) => { - const draco = module.draco; - const decoder = new draco.Decoder(); - const decoderBuffer = new draco.DecoderBuffer(); - decoderBuffer.Init(new Int8Array(buffer), buffer.byteLength); - - try { - const geometry = decodeGeometry(draco, decoder, decoderBuffer, taskConfig); - const buffers = geometry.attributes.map((attr) => attr.array.buffer); - if (geometry.index) buffers.push(geometry.index.array.buffer); - self.postMessage( - { - type: "decode", - id: message.id, - geometry, - }, - buffers, - ); - } catch (error) { - console.error(error); - self.postMessage({ - type: "error", - id: message.id, - error: error.message, - }); - } finally { - draco.destroy(decoderBuffer); - draco.destroy(decoder); - } - }); - break; - } - }; - - function decodeGeometry(draco, decoder, decoderBuffer, taskConfig) { - const attributeIDs = taskConfig.attributeIDs; - const attributeTypes = taskConfig.attributeTypes; - let dracoGeometry; - let decodingStatus; - const geometryType = decoder.GetEncodedGeometryType(decoderBuffer); - - if (geometryType === draco.TRIANGULAR_MESH) { - dracoGeometry = new draco.Mesh(); - decodingStatus = decoder.DecodeBufferToMesh(decoderBuffer, dracoGeometry); - } else if (geometryType === draco.POINT_CLOUD) { - dracoGeometry = new draco.PointCloud(); - decodingStatus = decoder.DecodeBufferToPointCloud(decoderBuffer, dracoGeometry); - } else { - throw new Error("THREE.DRACOLoader: Unexpected geometry type."); - } - - if (!decodingStatus.ok() || dracoGeometry.ptr === 0) { - throw new Error("THREE.DRACOLoader: Decoding failed: " + decodingStatus.error_msg()); - } - - const geometry = { - index: null, - attributes: [], - }; // Gather all vertex attributes. - - for (const attributeName in attributeIDs) { - const attributeType = self[attributeTypes[attributeName]]; - let attribute; - let attributeID; // A Draco file may be created with default vertex attributes, whose attribute IDs - // are mapped 1:1 from their semantic name (POSITION, NORMAL, ...). Alternatively, - // a Draco file may contain a custom set of attributes, identified by known unique - // IDs. glTF files always do the latter, and `.drc` files typically do the former. - - if (taskConfig.useUniqueIDs) { - attributeID = attributeIDs[attributeName]; - attribute = decoder.GetAttributeByUniqueId(dracoGeometry, attributeID); - } else { - attributeID = decoder.GetAttributeId(dracoGeometry, draco[attributeIDs[attributeName]]); - if (attributeID === -1) continue; - attribute = decoder.GetAttribute(dracoGeometry, attributeID); - } - - geometry.attributes.push( - decodeAttribute(draco, decoder, dracoGeometry, attributeName, attributeType, attribute), - ); - } // Add index. - - if (geometryType === draco.TRIANGULAR_MESH) { - geometry.index = decodeIndex(draco, decoder, dracoGeometry); - } - - draco.destroy(dracoGeometry); - return geometry; - } - - function decodeIndex(draco, decoder, dracoGeometry) { - const numFaces = dracoGeometry.num_faces(); - const numIndices = numFaces * 3; - const byteLength = numIndices * 4; - - const ptr = draco._malloc(byteLength); - - decoder.GetTrianglesUInt32Array(dracoGeometry, byteLength, ptr); - const index = new Uint32Array(draco.HEAPF32.buffer, ptr, numIndices).slice(); - - draco._free(ptr); - - return { - array: index, - itemSize: 1, - }; - } - - function decodeAttribute( - draco, - decoder, - dracoGeometry, - attributeName, - attributeType, - attribute, - ) { - const numComponents = attribute.num_components(); - const numPoints = dracoGeometry.num_points(); - const numValues = numPoints * numComponents; - const byteLength = numValues * attributeType.BYTES_PER_ELEMENT; - const dataType = getDracoDataType(draco, attributeType); - - const ptr = draco._malloc(byteLength); - - decoder.GetAttributeDataArrayForAllPoints( - dracoGeometry, - attribute, - dataType, - byteLength, - ptr, - ); - const array = new attributeType(draco.HEAPF32.buffer, ptr, numValues).slice(); - - draco._free(ptr); - - return { - name: attributeName, - array: array, - itemSize: numComponents, - }; - } - - function getDracoDataType(draco, attributeType) { - switch (attributeType) { - case Float32Array: - return draco.DT_FLOAT32; - - case Int8Array: - return draco.DT_INT8; - - case Int16Array: - return draco.DT_INT16; - - case Int32Array: - return draco.DT_INT32; - - case Uint8Array: - return draco.DT_UINT8; - - case Uint16Array: - return draco.DT_UINT16; - - case Uint32Array: - return draco.DT_UINT32; - } - } - } - - THREE.DRACOLoader = DRACOLoader; -})(); diff --git a/frontend/javascripts/oxalis/model/sagas/isosurface_saga.ts b/frontend/javascripts/oxalis/model/sagas/isosurface_saga.ts index 9959fd6adac..f2725d561e4 100644 --- a/frontend/javascripts/oxalis/model/sagas/isosurface_saga.ts +++ b/frontend/javascripts/oxalis/model/sagas/isosurface_saga.ts @@ -4,7 +4,7 @@ import { V3 } from "libs/mjs"; import { sleep } from "libs/utils"; import ErrorHandling from "libs/error_handling"; import type { APIDataLayer } from "types/api_flow_types"; -import "libs/DRACOLoader.js"; +import { DRACOLoader } from "three/examples/jsm/loaders/DRACOLoader.js"; import { ResolutionInfo, @@ -599,7 +599,7 @@ function* loadPrecomputedMeshForSegmentId( ); const loader = getDracoLoader(); - const geometry = yield* call(loader.decodeDracoFile.bind(loader), dracoData); + const geometry = yield* call(loader.decodeDracoFileAsync, dracoData); yield* call( { context: sceneController, fn: sceneController.addIsosurfaceFromGeometry }, geometry, @@ -644,13 +644,25 @@ function getDracoLoader() { if (_dracoLoader) { return _dracoLoader; } - _dracoLoader = new THREE.DRACOLoader(); + _dracoLoader = new DRACOLoader(); _dracoLoader.setDecoderPath( "https://raw.githubusercontent.com/mrdoob/three.js/dev/examples/js/libs/draco/", ); _dracoLoader.setDecoderConfig({ type: "js" }); + _dracoLoader.decodeDracoFileAsync = (buffer, ...args) => + new Promise((resolve, reject) => + _dracoLoader.decodeDracoFile( + buffer, + (x) => { + debugger; + resolve(x); + }, + ...args, + ), + ); + // todo: never dispose? // loader.dispose(); diff --git a/public/draco_file.bin b/public/draco_file.bin deleted file mode 100644 index 96ec360ddbfef72332e9fde2f3bd34fa2ca6357d..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 251 zcmV)B3}%UkOd?Jr8rgk~f~*4|bojJJO?w9xUW0^R z3@`#C*tQ#hN(6s|!VKUE+ChjrKt6sRiT;SkGr%vQ0OT2P z4>WH*xZ&j)8oLrO(-Mej0RZS9k%A#c*ra}V%gCn5Vd+#I4)}zbCxAUIlr|Fp5#K=r zD)LgeR*z(>1BSso@%I7L1|#h_yQgXe000000RIC30I#64LN8J}LwdNFLtsh!K?(<^ BTtNT; From d506a52feeaf0981a7314aa84d1becdb82717297 Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Thu, 29 Sep 2022 16:58:52 +0200 Subject: [PATCH 24/63] use wasm for draco decoding --- frontend/javascripts/oxalis/model/sagas/isosurface_saga.ts | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/frontend/javascripts/oxalis/model/sagas/isosurface_saga.ts b/frontend/javascripts/oxalis/model/sagas/isosurface_saga.ts index f2725d561e4..2c865e28eaf 100644 --- a/frontend/javascripts/oxalis/model/sagas/isosurface_saga.ts +++ b/frontend/javascripts/oxalis/model/sagas/isosurface_saga.ts @@ -649,7 +649,7 @@ function getDracoLoader() { _dracoLoader.setDecoderPath( "https://raw.githubusercontent.com/mrdoob/three.js/dev/examples/js/libs/draco/", ); - _dracoLoader.setDecoderConfig({ type: "js" }); + _dracoLoader.setDecoderConfig({ type: "wasm" }); _dracoLoader.decodeDracoFileAsync = (buffer, ...args) => new Promise((resolve, reject) => From dbdd895e8be91621a5966f6e1ba9260f9fd72599 Mon Sep 17 00:00:00 2001 From: leowe Date: Thu, 29 Sep 2022 17:10:57 +0200 Subject: [PATCH 25/63] reformat and rename fragment to chunk --- .../datastore/services/MeshFileService.scala | 84 +++++++++---------- 1 file changed, 41 insertions(+), 43 deletions(-) diff --git a/webknossos-datastore/app/com/scalableminds/webknossos/datastore/services/MeshFileService.scala b/webknossos-datastore/app/com/scalableminds/webknossos/datastore/services/MeshFileService.scala index bc87fcfce21..083c4b93c55 100644 --- a/webknossos-datastore/app/com/scalableminds/webknossos/datastore/services/MeshFileService.scala +++ b/webknossos-datastore/app/com/scalableminds/webknossos/datastore/services/MeshFileService.scala @@ -68,17 +68,17 @@ case class NeuroglancerSegmentInfo(chunkShape: Vec3Float, numLods: Int, lodScales: Array[Float], vertexOffsets: Array[Vec3Float], - numFragmentsPerLod: Array[Int], - fragmentPositions: List[List[Vec3Int]], - fragmentOffsets: List[List[Int]]) + numChunksPerLod: Array[Int], + chunkPositions: List[List[Vec3Int]], + chunkByteOffsets: List[List[Int]]) // TODO position als Vec3Int -case class MeshFragment(position: Vec3Float, byteOffset: Int, byteSize: Int) +case class MeshChunk(position: Vec3Float, byteOffset: Int, byteSize: Int) -object MeshFragment { - implicit val jsonFormat: OFormat[MeshFragment] = Json.format[MeshFragment] +object MeshChunk { + implicit val jsonFormat: OFormat[MeshChunk] = Json.format[MeshChunk] } -case class MeshLodInfo(scale: Int, vertexOffset: Vec3Float, chunkShape: Vec3Float, fragments: List[MeshFragment]) +case class MeshLodInfo(scale: Int, vertexOffset: Vec3Float, chunkShape: Vec3Float, chunks: List[MeshChunk]) object MeshLodInfo { implicit val jsonFormat: OFormat[MeshLodInfo] = Json.format[MeshLodInfo] @@ -210,36 +210,36 @@ class MeshFileService @Inject()(config: DataStoreConfig)(implicit ec: ExecutionC .uint8() .readArrayBlockWithOffset("/neuroglancer", (neuroglancerEnd - neuroglancerStart).toInt, neuroglancerStart) val segmentInfo = parseNeuroglancerManifest(manifest) - val meshfile = getFragmentsFromSegmentInfo(segmentInfo, lodScaleMultiplier, neuroglancerStart) + val meshfile = getChunksFromSegmentInfo(segmentInfo, lodScaleMultiplier, neuroglancerStart) WebknossosSegmentInfo(transform = transform, meshFormat = encoding, chunks = meshfile) } } - private def getFragmentsFromSegmentInfo(segmentInfo: NeuroglancerSegmentInfo, - lodScaleMultiplier: Double, - neuroglancerOffsetStart: Long): MeshSegmentInfo = { - val totalMeshSize = segmentInfo.fragmentOffsets.map(_.sum).sum + private def getChunksFromSegmentInfo(segmentInfo: NeuroglancerSegmentInfo, + lodScaleMultiplier: Double, + neuroglancerOffsetStart: Long): MeshSegmentInfo = { + val totalMeshSize = segmentInfo.chunkByteOffsets.map(_.sum).sum val meshByteStartOffset = neuroglancerOffsetStart - totalMeshSize - val fragmentByteOffsets = segmentInfo.fragmentOffsets.map(_.scanLeft(0)(_ + _)) // This builds a cumulative sum + val chunkByteOffsets = segmentInfo.chunkByteOffsets.map(_.scanLeft(0)(_ + _)) // This builds a cumulative sum - def computeGlobalPositionAndOffset(lod: Int, currentFragment: Int): MeshFragment = { + def computeGlobalPositionAndOffset(lod: Int, currentChunk: Int): MeshChunk = { val globalPosition = segmentInfo.gridOrigin + segmentInfo - .fragmentPositions(lod)(currentFragment) + .chunkPositions(lod)(currentChunk) .toVec3Float * segmentInfo.chunkShape * segmentInfo.lodScales(lod) * lodScaleMultiplier - MeshFragment( + MeshChunk( position = globalPosition, // This position is in Voxel Space - byteOffset = meshByteStartOffset.toInt + fragmentByteOffsets(lod)(currentFragment), - byteSize = segmentInfo.fragmentOffsets(lod)(currentFragment), + byteOffset = meshByteStartOffset.toInt + chunkByteOffsets(lod)(currentChunk), + byteSize = segmentInfo.chunkByteOffsets(lod)(currentChunk), ) } val lods = for (lod <- 0 until segmentInfo.numLods) yield lod - def fragmentNums(lod: Int): IndexedSeq[(Int, Int)] = - for (currentFragment <- 0 until segmentInfo.numFragmentsPerLod(lod)) - yield (lod, currentFragment) - val fragments = lods.map(lod => fragmentNums(lod).map(x => computeGlobalPositionAndOffset(x._1, x._2)).toList) + def chunkNums(lod: Int): IndexedSeq[(Int, Int)] = + for (currentChunk <- 0 until segmentInfo.numChunksPerLod(lod)) + yield (lod, currentChunk) + val chunks = lods.map(lod => chunkNums(lod).map(x => computeGlobalPositionAndOffset(x._1, x._2)).toList) val meshfileLods = lods .map( @@ -247,7 +247,7 @@ class MeshFileService @Inject()(config: DataStoreConfig)(implicit ec: ExecutionC MeshLodInfo(scale = segmentInfo.lodScales(lod).toInt, vertexOffset = segmentInfo.vertexOffsets(lod), chunkShape = segmentInfo.chunkShape, - fragments = fragments(lod))) + chunks = chunks(lod))) .toList MeshSegmentInfo(chunkShape = segmentInfo.chunkShape, gridOrigin = segmentInfo.gridOrigin, lods = meshfileLods) } @@ -273,30 +273,30 @@ class MeshFileService @Inject()(config: DataStoreConfig)(implicit ec: ExecutionC vertexOffsets(d) = Vec3Float(x = dis.readFloat, y = dis.readFloat, z = dis.readFloat) } - val numFragmentsPerLod = new Array[Int](numLods) + val numChunksPerLod = new Array[Int](numLods) for (lod <- 0 until numLods) { - numFragmentsPerLod(lod) = dis.readInt() + numChunksPerLod(lod) = dis.readInt() } - val fragmentPositionsList = new ListBuffer[List[Vec3Int]] - val fragmentSizes = new ListBuffer[List[Int]] + val chunkPositionsList = new ListBuffer[List[Vec3Int]] + val chunkSizes = new ListBuffer[List[Int]] for (lod <- 0 until numLods) { - val currentFragmentPositions = (ListBuffer[Int](), ListBuffer[Int](), ListBuffer[Int]()) - for (row <- 0 until 3; _ <- 0 until numFragmentsPerLod(lod)) { + val currentChunkPositions = (ListBuffer[Int](), ListBuffer[Int](), ListBuffer[Int]()) + for (row <- 0 until 3; _ <- 0 until numChunksPerLod(lod)) { row match { - case 0 => currentFragmentPositions._1.append(dis.readInt) - case 1 => currentFragmentPositions._2.append(dis.readInt) - case 2 => currentFragmentPositions._3.append(dis.readInt) + case 0 => currentChunkPositions._1.append(dis.readInt) + case 1 => currentChunkPositions._2.append(dis.readInt) + case 2 => currentChunkPositions._3.append(dis.readInt) } } - fragmentPositionsList.append(currentFragmentPositions.zipped.map(Vec3Int(_, _, _)).toList) + chunkPositionsList.append(currentChunkPositions.zipped.map(Vec3Int(_, _, _)).toList) - val currentFragmentSizes = ListBuffer[Int]() - for (_ <- 0 until numFragmentsPerLod(lod)) { - currentFragmentSizes.append(dis.readInt) + val currentChunkSizes = ListBuffer[Int]() + for (_ <- 0 until numChunksPerLod(lod)) { + currentChunkSizes.append(dis.readInt) } - fragmentSizes.append(currentFragmentSizes.toList) + chunkSizes.append(currentChunkSizes.toList) } NeuroglancerSegmentInfo(chunkShape, @@ -304,9 +304,9 @@ class MeshFileService @Inject()(config: DataStoreConfig)(implicit ec: ExecutionC numLods, lodScales, vertexOffsets, - numFragmentsPerLod, - fragmentPositionsList.toList, - fragmentSizes.toList) + numChunksPerLod, + chunkPositionsList.toList, + chunkSizes.toList) } private def getNeuroglancerOffsets(segmentId: Long, cachedMeshFile: CachedHdf5File): (Long, Long) = { @@ -366,9 +366,7 @@ class MeshFileService @Inject()(config: DataStoreConfig)(implicit ec: ExecutionC val data = cachedMeshFile.reader .uint8() - .readArrayBlockWithOffset("neuroglancer", - meshChunkDataRequest.byteSize, - meshChunkDataRequest.byteOffset) + .readArrayBlockWithOffset("neuroglancer", meshChunkDataRequest.byteSize, meshChunkDataRequest.byteOffset) (data, meshFormat) } ?~> "mesh.file.readData.failed" } From 56ba4e2574267b3240a71a13c3c8a2b4552a7c59 Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Thu, 29 Sep 2022 17:47:36 +0200 Subject: [PATCH 26/63] clean up typing for draco loader --- .eslintrc.json | 1 + frontend/javascripts/libs/draco.ts | 34 +++++++++++++++++++ frontend/javascripts/oxalis/api/api_latest.ts | 2 +- .../oxalis/model/sagas/isosurface_saga.ts | 33 +----------------- .../oxalis/view/action_bar_view.tsx | 2 +- .../segments_tab/segments_view_helper.tsx | 2 +- 6 files changed, 39 insertions(+), 35 deletions(-) create mode 100644 frontend/javascripts/libs/draco.ts diff --git a/.eslintrc.json b/.eslintrc.json index 6faa372de9f..61974196b5b 100644 --- a/.eslintrc.json +++ b/.eslintrc.json @@ -40,6 +40,7 @@ "eslint-comments/no-unused-disable": "error", "flowtype/no-types-missing-file-annotation": "off", "import/extensions": ["warn", { "js": "never", "jsx": "always" }], + "import/prefer-default-export": ["warn"], "import/no-cycle": "off", "import/no-extraneous-dependencies": [ "error", diff --git a/frontend/javascripts/libs/draco.ts b/frontend/javascripts/libs/draco.ts new file mode 100644 index 00000000000..e0af0bc3b43 --- /dev/null +++ b/frontend/javascripts/libs/draco.ts @@ -0,0 +1,34 @@ +import { BufferGeometry } from "three"; +import { DRACOLoader } from "three/examples/jsm/loaders/DRACOLoader.js"; + +let _dracoLoader: CustomDRACOLoader | null; + +class CustomDRACOLoader extends DRACOLoader { + // Subclass to create a promise-based API and add typing + decodeDracoFileAsync = (buffer: ArrayBuffer, ...args: any[]): Promise => + new Promise((resolve) => { + if (_dracoLoader == null) { + throw new Error("DracoLoader not instantiated."); + } + // @ts-ignore + _dracoLoader.decodeDracoFile(buffer, resolve, ...args); + }); +} + +export function getDracoLoader(): CustomDRACOLoader { + if (_dracoLoader) { + return _dracoLoader; + } + _dracoLoader = new CustomDRACOLoader(); + + _dracoLoader.setDecoderPath( + "https://raw.githubusercontent.com/mrdoob/three.js/dev/examples/js/libs/draco/", + ); + _dracoLoader.setDecoderConfig({ type: "wasm" }); + // The loader could theoretically be disposed like this: + // _dracoLoader.dispose(); + // However, it's probably okay to not release the resources, + // since the loader might be used again soon, anyway. + + return _dracoLoader; +} diff --git a/frontend/javascripts/oxalis/api/api_latest.ts b/frontend/javascripts/oxalis/api/api_latest.ts index 3bafa75c9dc..38be03d21fa 100644 --- a/frontend/javascripts/oxalis/api/api_latest.ts +++ b/frontend/javascripts/oxalis/api/api_latest.ts @@ -1842,7 +1842,7 @@ class DataApi { const { mappingName, meshFileName } = currentMeshFile; // todo: remove second condition - if (mappingName != null && mappingName != "") { + if (mappingName != null && mappingName !== "") { const activeMapping = this.getActiveMapping(effectiveLayerName); if (mappingName !== activeMapping) { diff --git a/frontend/javascripts/oxalis/model/sagas/isosurface_saga.ts b/frontend/javascripts/oxalis/model/sagas/isosurface_saga.ts index 2c865e28eaf..5c64a27b872 100644 --- a/frontend/javascripts/oxalis/model/sagas/isosurface_saga.ts +++ b/frontend/javascripts/oxalis/model/sagas/isosurface_saga.ts @@ -4,7 +4,6 @@ import { V3 } from "libs/mjs"; import { sleep } from "libs/utils"; import ErrorHandling from "libs/error_handling"; import type { APIDataLayer } from "types/api_flow_types"; -import { DRACOLoader } from "three/examples/jsm/loaders/DRACOLoader.js"; import { ResolutionInfo, @@ -53,11 +52,11 @@ import window from "libs/window"; import { getActiveSegmentationTracing } from "oxalis/model/accessors/volumetracing_accessor"; import { saveNowAction } from "oxalis/model/actions/save_actions"; import Toast from "libs/toast"; +import { getDracoLoader } from "libs/draco"; import messages from "messages"; import processTaskWithPool from "libs/task_pool"; import { getBaseSegmentationName } from "oxalis/view/right-border-tabs/segments_tab/segments_view_helper"; import { UpdateSegmentAction } from "../actions/volumetracing_actions"; -import * as THREE from "three"; const MAX_RETRY_COUNT = 5; const RETRY_WAIT_TIME = 5000; @@ -639,36 +638,6 @@ function* loadPrecomputedMeshForSegmentId( yield* put(finishedLoadingIsosurfaceAction(layerName, id)); } -let _dracoLoader; -function getDracoLoader() { - if (_dracoLoader) { - return _dracoLoader; - } - _dracoLoader = new DRACOLoader(); - - _dracoLoader.setDecoderPath( - "https://raw.githubusercontent.com/mrdoob/three.js/dev/examples/js/libs/draco/", - ); - _dracoLoader.setDecoderConfig({ type: "wasm" }); - - _dracoLoader.decodeDracoFileAsync = (buffer, ...args) => - new Promise((resolve, reject) => - _dracoLoader.decodeDracoFile( - buffer, - (x) => { - debugger; - resolve(x); - }, - ...args, - ), - ); - - // todo: never dispose? - // loader.dispose(); - - return _dracoLoader; -} - /* * * Ad Hoc and Precomputed Meshes diff --git a/frontend/javascripts/oxalis/view/action_bar_view.tsx b/frontend/javascripts/oxalis/view/action_bar_view.tsx index 11a6ec0519e..36d544dc4a7 100644 --- a/frontend/javascripts/oxalis/view/action_bar_view.tsx +++ b/frontend/javascripts/oxalis/view/action_bar_view.tsx @@ -28,7 +28,7 @@ import { getVisibleSegmentationLayer, } from "oxalis/model/accessors/dataset_accessor"; import { AsyncButton } from "components/async_clickables"; -import ButtonComponent from "./components/button_component"; + const VersionRestoreWarning = ( > mappingName === undefined || layerName == null || mappingName === enabledMappingName || - mappingName == "" + mappingName === "" ) { // @ts-expect-error ts-migrate(2322) FIXME: Type 'Omit, ... Remove this comment to see the full error message return ; From 44951071b9e1ff69fa8fd77d36d5344c9aaa6aba Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Thu, 29 Sep 2022 17:48:31 +0200 Subject: [PATCH 27/63] remove unused draco3d image --- package.json | 3 +-- yarn.lock | 5 ----- 2 files changed, 1 insertion(+), 7 deletions(-) diff --git a/package.json b/package.json index 58e2bf943bb..e4fa20735aa 100644 --- a/package.json +++ b/package.json @@ -176,7 +176,6 @@ "deep-freeze": "0.0.1", "dice-coefficient": "^2.1.0", "distance-transform": "^1.0.2", - "draco3d": "^1.5.3", "eslint-plugin-ava": "^13.2.0", "file-saver": "^2.0.1", "flexlayout-react": "^0.5.5", @@ -201,8 +200,8 @@ "process": "^0.11.10", "protobufjs": "^6.10.3", "react": "^16.12.0", - "react-colorful": "^5.6.1", "react-ansi": "^3.0.2", + "react-colorful": "^5.6.1", "react-debounce-render": "^8.0.1", "react-dnd": "^11.1.3", "react-dnd-html5-backend": "^11.1.3", diff --git a/yarn.lock b/yarn.lock index 1c647e424c4..19687b5ca92 100644 --- a/yarn.lock +++ b/yarn.lock @@ -5540,11 +5540,6 @@ dotgitignore@^2.1.0: find-up "^3.0.0" minimatch "^3.0.4" -draco3d@^1.5.3: - version "1.5.3" - resolved "https://registry.yarnpkg.com/draco3d/-/draco3d-1.5.3.tgz#75dfb3da7d1420571b1ab999191c49fdc2a74571" - integrity sha512-Ahum6SewAd1oVMm6Fk8T/zCE0qbzjohhO5pl1Xp5Outl4JKv7jYicfd5vNtkzImx94XE35fhNXVqHk9ajt+6Tg== - draft-js@^0.10.0, draft-js@~0.10.0: version "0.10.5" resolved "https://registry.yarnpkg.com/draft-js/-/draft-js-0.10.5.tgz#bfa9beb018fe0533dbb08d6675c371a6b08fa742" From 39596a1cfa924bbb8a86684ac70de4e69183df8b Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Thu, 29 Sep 2022 17:50:19 +0200 Subject: [PATCH 28/63] pin URI to WASM in GH repo --- frontend/javascripts/libs/draco.ts | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/frontend/javascripts/libs/draco.ts b/frontend/javascripts/libs/draco.ts index e0af0bc3b43..f464f632db5 100644 --- a/frontend/javascripts/libs/draco.ts +++ b/frontend/javascripts/libs/draco.ts @@ -22,7 +22,7 @@ export function getDracoLoader(): CustomDRACOLoader { _dracoLoader = new CustomDRACOLoader(); _dracoLoader.setDecoderPath( - "https://raw.githubusercontent.com/mrdoob/three.js/dev/examples/js/libs/draco/", + "https://raw.githubusercontent.com/mrdoob/three.js/r145/examples/js/libs/draco/", ); _dracoLoader.setDecoderConfig({ type: "wasm" }); // The loader could theoretically be disposed like this: From 97facd43f505c9ec9cdaf1b9e8a498c91ab4457a Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Thu, 29 Sep 2022 17:54:33 +0200 Subject: [PATCH 29/63] rename fragment to chunk like the back-end did it --- frontend/javascripts/admin/api/mesh_v3.ts | 4 ++-- frontend/javascripts/oxalis/model/sagas/isosurface_saga.ts | 6 +++--- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/frontend/javascripts/admin/api/mesh_v3.ts b/frontend/javascripts/admin/api/mesh_v3.ts index 0cb80696b83..db3ae0c0537 100644 --- a/frontend/javascripts/admin/api/mesh_v3.ts +++ b/frontend/javascripts/admin/api/mesh_v3.ts @@ -3,13 +3,13 @@ import { Vector3 } from "oxalis/constants"; import { APIDatasetId } from "types/api_flow_types"; import { doWithToken } from "./token"; -export type MeshFragment = { position: Vector3; byteOffset: number; byteSize: number }; +export type MeshChunk = { position: Vector3; byteOffset: number; byteSize: number }; type MeshLodInfo = { scale: number; vertexOffset: Vector3; chunkShape: Vector3; - fragments: Array; + chunks: Array; }; type MeshSegmentInfo = { diff --git a/frontend/javascripts/oxalis/model/sagas/isosurface_saga.ts b/frontend/javascripts/oxalis/model/sagas/isosurface_saga.ts index 5c64a27b872..77760fe9058 100644 --- a/frontend/javascripts/oxalis/model/sagas/isosurface_saga.ts +++ b/frontend/javascripts/oxalis/model/sagas/isosurface_saga.ts @@ -557,7 +557,7 @@ function* loadPrecomputedMeshForSegmentId( meshFileName, id, ); - availableChunks = _.first(segmentInfo.chunks.lods)?.fragments || []; + availableChunks = _.first(segmentInfo.chunks.lods)?.chunks || []; } else { availableChunks = yield* call( meshV0.getMeshfileChunksForSegment, @@ -577,9 +577,9 @@ function* loadPrecomputedMeshForSegmentId( } // Sort the chunks by distance to the seedPosition, so that the mesh loads from the inside out - const sortedAvailableChunks = _.sortBy(availableChunks, (chunk: Vector3 | meshV3.MeshFragment) => + const sortedAvailableChunks = _.sortBy(availableChunks, (chunk: Vector3 | meshV3.MeshChunk) => V3.length(V3.sub(seedPosition, "position" in chunk ? chunk.position : chunk)), - ) as Array | Array; + ) as Array | Array; const tasks = sortedAvailableChunks.map( (chunk) => From 7b7764a1943b9f636655c9a812d2410db383bd9a Mon Sep 17 00:00:00 2001 From: leowe Date: Thu, 29 Sep 2022 18:29:57 +0200 Subject: [PATCH 30/63] NOW ALL NEW: THE GREAT NEW MESHCONTROLLER --- .../controllers/DataSourceController.scala | 107 --------------- .../controllers/MeshController.scala | 125 ++++++++++++++++++ .../datastore/services/MeshFileService.scala | 5 - ....scalableminds.webknossos.datastore.routes | 11 +- 4 files changed, 130 insertions(+), 118 deletions(-) create mode 100644 webknossos-datastore/app/com/scalableminds/webknossos/datastore/controllers/MeshController.scala diff --git a/webknossos-datastore/app/com/scalableminds/webknossos/datastore/controllers/DataSourceController.scala b/webknossos-datastore/app/com/scalableminds/webknossos/datastore/controllers/DataSourceController.scala index b400eea832b..958188dc1cf 100644 --- a/webknossos-datastore/app/com/scalableminds/webknossos/datastore/controllers/DataSourceController.scala +++ b/webknossos-datastore/app/com/scalableminds/webknossos/datastore/controllers/DataSourceController.scala @@ -29,7 +29,6 @@ class DataSourceController @Inject()( remoteWebKnossosClient: DSRemoteWebKnossosClient, accessTokenService: DataStoreAccessTokenService, binaryDataServiceHolder: BinaryDataServiceHolder, - meshFileService: MeshFileService, connectomeFileService: ConnectomeFileService, uploadService: UploadService )(implicit bodyParsers: PlayBodyParsers) @@ -400,112 +399,6 @@ Expects: } } - def dummyDracoFile(): Action[AnyContent] = Action.async { implicit request => - for { - draco <- meshFileService.readDummyDraco() - } yield Ok(draco) - } - - @ApiOperation(hidden = true, value = "") - def listMeshFiles(token: Option[String], - organizationName: String, - dataSetName: String, - dataLayerName: String): Action[AnyContent] = - Action.async { implicit request => - accessTokenService.validateAccess(UserAccessRequest.readDataSources(DataSourceId(dataSetName, organizationName)), - urlOrHeaderToken(token, request)) { - for { - meshFiles <- meshFileService.exploreMeshFiles(organizationName, dataSetName, dataLayerName) - } yield Ok(Json.toJson(meshFiles)) - } - } - - @ApiOperation(hidden = true, value = "") - def listMeshChunksForSegmentV0(token: Option[String], - organizationName: String, - dataSetName: String, - dataLayerName: String): Action[ListMeshChunksRequest] = - Action.async(validateJson[ListMeshChunksRequest]) { implicit request => - accessTokenService.validateAccess(UserAccessRequest.readDataSources(DataSourceId(dataSetName, organizationName)), - urlOrHeaderToken(token, request)) { - for { - positions <- meshFileService.listMeshChunksForSegmentV0(organizationName, - dataSetName, - dataLayerName, - request.body) ?~> Messages( - "mesh.file.listChunks.failed", - request.body.segmentId.toString, - request.body.meshFile) ?~> Messages("mesh.file.load.failed", request.body.segmentId.toString) ~> BAD_REQUEST - } yield Ok(Json.toJson(positions)) - } - } - - @ApiOperation(hidden = true, value = "") - def listMeshChunksForSegmentForVersion(token: Option[String], - organizationName: String, - dataSetName: String, - dataLayerName: String, - formatVersion: Int): Action[ListMeshChunksRequest] = - Action.async(validateJson[ListMeshChunksRequest]) { implicit request => - accessTokenService.validateAccess(UserAccessRequest.readDataSources(DataSourceId(dataSetName, organizationName)), - urlOrHeaderToken(token, request)) { - for { - positions <- formatVersion match { - case 3 => - meshFileService.listMeshChunksForSegmentV3(organizationName, dataSetName, dataLayerName, request.body) ?~> Messages( - "mesh.file.listChunks.failed", - request.body.segmentId.toString, - request.body.meshFile) ?~> Messages("mesh.file.load.failed", request.body.segmentId.toString) ~> BAD_REQUEST - case _ => Fox.failure("Wrong format version") ~> BAD_REQUEST - } - } yield Ok(Json.toJson(positions)) - } - } - - @ApiOperation(hidden = true, value = "") - def readMeshChunkV0(token: Option[String], - organizationName: String, - dataSetName: String, - dataLayerName: String): Action[MeshChunkDataRequestV0] = - Action.async(validateJson[MeshChunkDataRequestV0]) { implicit request => - accessTokenService.validateAccess(UserAccessRequest.readDataSources(DataSourceId(dataSetName, organizationName)), - urlOrHeaderToken(token, request)) { - for { - (data, encoding) <- meshFileService.readMeshChunkV0(organizationName, - dataSetName, - dataLayerName, - request.body) ?~> "mesh.file.loadChunk.failed" - } yield { - if (encoding.contains("gzip")) { - Ok(data).withHeaders("Content-Encoding" -> "gzip") - } else Ok(data) - } - } - } - - @ApiOperation(hidden = true, value = "") - def readMeshChunkForVersion(token: Option[String], - organizationName: String, - dataSetName: String, - dataLayerName: String, - formatVersion: Int): Action[MeshChunkDataRequestV3] = - Action.async(validateJson[MeshChunkDataRequestV3]) { implicit request => - accessTokenService.validateAccess(UserAccessRequest.readDataSources(DataSourceId(dataSetName, organizationName)), - urlOrHeaderToken(token, request)) { - for { - (data, encoding) <- formatVersion match { - case 3 => - meshFileService.readMeshChunkV3(organizationName, dataSetName, dataLayerName, request.body) ?~> "mesh.file.loadChunk.failed" - case _ => Fox.failure("Wrong format version") ~> BAD_REQUEST - } - } yield { - if (encoding.contains("gzip")) { - Ok(data).withHeaders("Content-Encoding" -> "gzip") - } else Ok(data) - } - } - } - @ApiOperation(hidden = true, value = "") def update(token: Option[String], organizationName: String, dataSetName: String): Action[DataSource] = Action.async(validateJson[DataSource]) { implicit request => diff --git a/webknossos-datastore/app/com/scalableminds/webknossos/datastore/controllers/MeshController.scala b/webknossos-datastore/app/com/scalableminds/webknossos/datastore/controllers/MeshController.scala new file mode 100644 index 00000000000..c2e9131932d --- /dev/null +++ b/webknossos-datastore/app/com/scalableminds/webknossos/datastore/controllers/MeshController.scala @@ -0,0 +1,125 @@ +package com.scalableminds.webknossos.datastore.controllers + +import com.google.inject.Inject +import com.scalableminds.util.tools.{Fox, FoxImplicits} +import com.scalableminds.webknossos.datastore.controllers.Controller +import com.scalableminds.webknossos.datastore.models.datasource.DataSourceId +import com.scalableminds.webknossos.datastore.services._ +import play.api.i18n.Messages +import play.api.libs.json.Json +import play.api.mvc.{Action, AnyContent, PlayBodyParsers} + +import io.swagger.annotations.{Api, ApiOperation} + +import scala.concurrent.ExecutionContext.Implicits.global + +@Api(tags = Array("datastore")) +class MeshController @Inject()( + accessTokenService: DataStoreAccessTokenService, + meshFileService: MeshFileService, +)(implicit bodyParsers: PlayBodyParsers) + extends Controller + with FoxImplicits { + + override def allowRemoteOrigin: Boolean = true + + @ApiOperation(hidden = true, value = "") + def listMeshFiles(token: Option[String], + organizationName: String, + dataSetName: String, + dataLayerName: String): Action[AnyContent] = + Action.async { implicit request => + accessTokenService.validateAccess(UserAccessRequest.readDataSources(DataSourceId(dataSetName, organizationName)), + urlOrHeaderToken(token, request)) { + for { + meshFiles <- meshFileService.exploreMeshFiles(organizationName, dataSetName, dataLayerName) + } yield Ok(Json.toJson(meshFiles)) + } + } + + @ApiOperation(hidden = true, value = "") + def listMeshChunksForSegmentV0(token: Option[String], + organizationName: String, + dataSetName: String, + dataLayerName: String): Action[ListMeshChunksRequest] = + Action.async(validateJson[ListMeshChunksRequest]) { implicit request => + accessTokenService.validateAccess(UserAccessRequest.readDataSources(DataSourceId(dataSetName, organizationName)), + urlOrHeaderToken(token, request)) { + for { + positions <- meshFileService.listMeshChunksForSegmentV0(organizationName, + dataSetName, + dataLayerName, + request.body) ?~> Messages( + "mesh.file.listChunks.failed", + request.body.segmentId.toString, + request.body.meshFile) ?~> Messages("mesh.file.load.failed", request.body.segmentId.toString) ~> BAD_REQUEST + } yield Ok(Json.toJson(positions)) + } + } + + @ApiOperation(hidden = true, value = "") + def listMeshChunksForSegmentForVersion(token: Option[String], + organizationName: String, + dataSetName: String, + dataLayerName: String, + formatVersion: Int): Action[ListMeshChunksRequest] = + Action.async(validateJson[ListMeshChunksRequest]) { implicit request => + accessTokenService.validateAccess(UserAccessRequest.readDataSources(DataSourceId(dataSetName, organizationName)), + urlOrHeaderToken(token, request)) { + for { + positions <- formatVersion match { + case 3 => + meshFileService.listMeshChunksForSegmentV3(organizationName, dataSetName, dataLayerName, request.body) ?~> Messages( + "mesh.file.listChunks.failed", + request.body.segmentId.toString, + request.body.meshFile) ?~> Messages("mesh.file.load.failed", request.body.segmentId.toString) ~> BAD_REQUEST + case _ => Fox.failure("Wrong format version") ~> BAD_REQUEST + } + } yield Ok(Json.toJson(positions)) + } + } + + @ApiOperation(hidden = true, value = "") + def readMeshChunkV0(token: Option[String], + organizationName: String, + dataSetName: String, + dataLayerName: String): Action[MeshChunkDataRequestV0] = + Action.async(validateJson[MeshChunkDataRequestV0]) { implicit request => + accessTokenService.validateAccess(UserAccessRequest.readDataSources(DataSourceId(dataSetName, organizationName)), + urlOrHeaderToken(token, request)) { + for { + (data, encoding) <- meshFileService.readMeshChunkV0(organizationName, + dataSetName, + dataLayerName, + request.body) ?~> "mesh.file.loadChunk.failed" + } yield { + if (encoding.contains("gzip")) { + Ok(data).withHeaders("Content-Encoding" -> "gzip") + } else Ok(data) + } + } + } + + @ApiOperation(hidden = true, value = "") + def readMeshChunkForVersion(token: Option[String], + organizationName: String, + dataSetName: String, + dataLayerName: String, + formatVersion: Int): Action[MeshChunkDataRequestV3] = + Action.async(validateJson[MeshChunkDataRequestV3]) { implicit request => + accessTokenService.validateAccess(UserAccessRequest.readDataSources(DataSourceId(dataSetName, organizationName)), + urlOrHeaderToken(token, request)) { + for { + (data, encoding) <- formatVersion match { + case 3 => + meshFileService.readMeshChunkV3(organizationName, dataSetName, dataLayerName, request.body) ?~> "mesh.file.loadChunk.failed" + case _ => Fox.failure("Wrong format version") ~> BAD_REQUEST + } + } yield { + if (encoding.contains("gzip")) { + Ok(data).withHeaders("Content-Encoding" -> "gzip") + } else Ok(data) + } + } + } +} diff --git a/webknossos-datastore/app/com/scalableminds/webknossos/datastore/services/MeshFileService.scala b/webknossos-datastore/app/com/scalableminds/webknossos/datastore/services/MeshFileService.scala index 083c4b93c55..881dd13ed3c 100644 --- a/webknossos-datastore/app/com/scalableminds/webknossos/datastore/services/MeshFileService.scala +++ b/webknossos-datastore/app/com/scalableminds/webknossos/datastore/services/MeshFileService.scala @@ -111,11 +111,6 @@ class MeshFileService @Inject()(config: DataStoreConfig)(implicit ec: ExecutionC private lazy val meshFileCache = new Hdf5FileCache(30) - def readDummyDraco(): Fox[Array[Byte]] = { - val path = dataBaseDir.resolve("draco_file.bin") - tryo(Files.readAllBytes(path)).toOption.toFox - } - def exploreMeshFiles(organizationName: String, dataSetName: String, dataLayerName: String): Fox[Set[MeshFileInfo]] = { val layerDir = dataBaseDir.resolve(organizationName).resolve(dataSetName).resolve(dataLayerName) val meshFileNames = PathUtils diff --git a/webknossos-datastore/conf/com.scalableminds.webknossos.datastore.routes b/webknossos-datastore/conf/com.scalableminds.webknossos.datastore.routes index c647910ae95..4efb8744b76 100644 --- a/webknossos-datastore/conf/com.scalableminds.webknossos.datastore.routes +++ b/webknossos-datastore/conf/com.scalableminds.webknossos.datastore.routes @@ -55,12 +55,11 @@ POST /datasets/:organizationName/:dataSetName/layers/:dataLayerName/agg # Mesh files -GET /datasets/:organizationName/:dataSetName/layers/:dataLayerName/meshes @com.scalableminds.webknossos.datastore.controllers.DataSourceController.listMeshFiles(token: Option[String], organizationName: String, dataSetName: String, dataLayerName: String) -POST /datasets/:organizationName/:dataSetName/layers/:dataLayerName/meshes/chunks @com.scalableminds.webknossos.datastore.controllers.DataSourceController.listMeshChunksForSegmentV0(token: Option[String], organizationName: String, dataSetName: String, dataLayerName: String) -POST /datasets/:organizationName/:dataSetName/layers/:dataLayerName/meshes/chunks/data @com.scalableminds.webknossos.datastore.controllers.DataSourceController.readMeshChunkV0(token: Option[String], organizationName: String, dataSetName: String, dataLayerName: String) -POST /datasets/:organizationName/:dataSetName/layers/:dataLayerName/meshes/formatVersion/:formatVersion/chunks @com.scalableminds.webknossos.datastore.controllers.DataSourceController.listMeshChunksForSegmentForVersion(token: Option[String], organizationName: String, dataSetName: String, dataLayerName: String, formatVersion: Int) -POST /datasets/:organizationName/:dataSetName/layers/:dataLayerName/meshes/formatVersion/:formatVersion/chunks/data @com.scalableminds.webknossos.datastore.controllers.DataSourceController.readMeshChunkForVersion(token: Option[String], organizationName: String, dataSetName: String, dataLayerName: String, formatVersion: Int) -GET /datasets/dummyDraco @com.scalableminds.webknossos.datastore.controllers.DataSourceController.dummyDracoFile() +GET /datasets/:organizationName/:dataSetName/layers/:dataLayerName/meshes @com.scalableminds.webknossos.datastore.controllers.MeshController.listMeshFiles(token: Option[String], organizationName: String, dataSetName: String, dataLayerName: String) +POST /datasets/:organizationName/:dataSetName/layers/:dataLayerName/meshes/chunks @com.scalableminds.webknossos.datastore.controllers.MeshController.listMeshChunksForSegmentV0(token: Option[String], organizationName: String, dataSetName: String, dataLayerName: String) +POST /datasets/:organizationName/:dataSetName/layers/:dataLayerName/meshes/chunks/data @com.scalableminds.webknossos.datastore.controllers.MeshController.readMeshChunkV0(token: Option[String], organizationName: String, dataSetName: String, dataLayerName: String) +POST /datasets/:organizationName/:dataSetName/layers/:dataLayerName/meshes/formatVersion/:formatVersion/chunks @com.scalableminds.webknossos.datastore.controllers.MeshController.listMeshChunksForSegmentForVersion(token: Option[String], organizationName: String, dataSetName: String, dataLayerName: String, formatVersion: Int) +POST /datasets/:organizationName/:dataSetName/layers/:dataLayerName/meshes/formatVersion/:formatVersion/chunks/data @com.scalableminds.webknossos.datastore.controllers.MeshController.readMeshChunkForVersion(token: Option[String], organizationName: String, dataSetName: String, dataLayerName: String, formatVersion: Int) # Connectome files GET /datasets/:organizationName/:dataSetName/layers/:dataLayerName/connectomes @com.scalableminds.webknossos.datastore.controllers.DataSourceController.listConnectomeFiles(token: Option[String], organizationName: String, dataSetName: String, dataLayerName: String) From e9f26c66c77efd3208cc6d853367d191597a27c9 Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Thu, 29 Sep 2022 19:01:31 +0200 Subject: [PATCH 31/63] fix colors by computing vertex normals --- frontend/javascripts/oxalis/controller/scene_controller.ts | 3 ++- frontend/javascripts/oxalis/model/sagas/isosurface_saga.ts | 6 +++++- 2 files changed, 7 insertions(+), 2 deletions(-) diff --git a/frontend/javascripts/oxalis/controller/scene_controller.ts b/frontend/javascripts/oxalis/controller/scene_controller.ts index 904f7b095d2..d7074f48d18 100644 --- a/frontend/javascripts/oxalis/controller/scene_controller.ts +++ b/frontend/javascripts/oxalis/controller/scene_controller.ts @@ -200,8 +200,9 @@ class SceneController { constructIsosurfaceMesh(cellId: number, geometry: THREE.BufferGeometry, passive: boolean) { const color = this.getColorObjectForSegment(cellId); - const meshMaterial = new THREE.MeshLambertMaterial({ + const meshMaterial = new THREE.MeshStandardMaterial({ color, + // flatShading: true, }); meshMaterial.side = THREE.FrontSide; meshMaterial.transparent = true; diff --git a/frontend/javascripts/oxalis/model/sagas/isosurface_saga.ts b/frontend/javascripts/oxalis/model/sagas/isosurface_saga.ts index 77760fe9058..62c49df9b4a 100644 --- a/frontend/javascripts/oxalis/model/sagas/isosurface_saga.ts +++ b/frontend/javascripts/oxalis/model/sagas/isosurface_saga.ts @@ -546,7 +546,9 @@ function* loadPrecomputedMeshForSegmentId( const dataset = yield* select((state) => state.dataset); let availableChunks = null; - const version = 3; + + // todo: dont hardcode + const version = meshFileName.includes("4-4") ? 0 : 3; try { if (version === 3) { const segmentInfo = yield* call( @@ -599,6 +601,8 @@ function* loadPrecomputedMeshForSegmentId( const loader = getDracoLoader(); const geometry = yield* call(loader.decodeDracoFileAsync, dracoData); + geometry.computeVertexNormals(); + yield* call( { context: sceneController, fn: sceneController.addIsosurfaceFromGeometry }, geometry, From 233f03e7e0937ff18efb7f02c9c1c04e19221573 Mon Sep 17 00:00:00 2001 From: leowe Date: Thu, 29 Sep 2022 19:14:41 +0200 Subject: [PATCH 32/63] remove todo --- .../webknossos/datastore/services/MeshFileService.scala | 1 - 1 file changed, 1 deletion(-) diff --git a/webknossos-datastore/app/com/scalableminds/webknossos/datastore/services/MeshFileService.scala b/webknossos-datastore/app/com/scalableminds/webknossos/datastore/services/MeshFileService.scala index 881dd13ed3c..b4b597ba659 100644 --- a/webknossos-datastore/app/com/scalableminds/webknossos/datastore/services/MeshFileService.scala +++ b/webknossos-datastore/app/com/scalableminds/webknossos/datastore/services/MeshFileService.scala @@ -72,7 +72,6 @@ case class NeuroglancerSegmentInfo(chunkShape: Vec3Float, chunkPositions: List[List[Vec3Int]], chunkByteOffsets: List[List[Int]]) -// TODO position als Vec3Int case class MeshChunk(position: Vec3Float, byteOffset: Int, byteSize: Int) object MeshChunk { From 562da591be31c1826f7807a1a5a8db977f2b335d Mon Sep 17 00:00:00 2001 From: leowe Date: Thu, 29 Sep 2022 19:44:59 +0200 Subject: [PATCH 33/63] what we don't need we don't keep --- .../webknossos/datastore/controllers/MeshController.scala | 1 - .../webknossos/datastore/services/MeshFileService.scala | 2 +- 2 files changed, 1 insertion(+), 2 deletions(-) diff --git a/webknossos-datastore/app/com/scalableminds/webknossos/datastore/controllers/MeshController.scala b/webknossos-datastore/app/com/scalableminds/webknossos/datastore/controllers/MeshController.scala index c2e9131932d..ad05c79ac87 100644 --- a/webknossos-datastore/app/com/scalableminds/webknossos/datastore/controllers/MeshController.scala +++ b/webknossos-datastore/app/com/scalableminds/webknossos/datastore/controllers/MeshController.scala @@ -2,7 +2,6 @@ package com.scalableminds.webknossos.datastore.controllers import com.google.inject.Inject import com.scalableminds.util.tools.{Fox, FoxImplicits} -import com.scalableminds.webknossos.datastore.controllers.Controller import com.scalableminds.webknossos.datastore.models.datasource.DataSourceId import com.scalableminds.webknossos.datastore.services._ import play.api.i18n.Messages diff --git a/webknossos-datastore/app/com/scalableminds/webknossos/datastore/services/MeshFileService.scala b/webknossos-datastore/app/com/scalableminds/webknossos/datastore/services/MeshFileService.scala index b4b597ba659..290d0f0947e 100644 --- a/webknossos-datastore/app/com/scalableminds/webknossos/datastore/services/MeshFileService.scala +++ b/webknossos-datastore/app/com/scalableminds/webknossos/datastore/services/MeshFileService.scala @@ -16,7 +16,7 @@ import play.api.libs.json.{Json, OFormat} import java.io.ByteArrayInputStream import java.nio.ByteBuffer -import java.nio.file.{Files, Path, Paths} +import java.nio.file.{Path, Paths} import javax.inject.Inject import scala.collection.JavaConverters._ import scala.collection.mutable.ListBuffer From 5c71d4bdf454d8927196ac79f7a30594b305130b Mon Sep 17 00:00:00 2001 From: leowe <13684843+leowe@users.noreply.github.com> Date: Fri, 30 Sep 2022 10:47:11 +0200 Subject: [PATCH 34/63] Update util/src/main/scala/com/scalableminds/util/tools/Fox.scala Co-authored-by: Florian M --- util/src/main/scala/com/scalableminds/util/tools/Fox.scala | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/util/src/main/scala/com/scalableminds/util/tools/Fox.scala b/util/src/main/scala/com/scalableminds/util/tools/Fox.scala index eb0ef55f6cf..842e41fe7bb 100644 --- a/util/src/main/scala/com/scalableminds/util/tools/Fox.scala +++ b/util/src/main/scala/com/scalableminds/util/tools/Fox.scala @@ -33,7 +33,7 @@ trait FoxImplicits { implicit def try2Fox[T](t: Try[T])(implicit ec: ExecutionContext): Fox[T] = t match { case Success(result) => Fox.successful(result) - case scala.util.Failure(e) => Fox.failure(s"${e.toString}") + case scala.util.Failure(e) => Fox.failure(e.toString) } implicit def fox2FutureBox[T](f: Fox[T]): Future[Box[T]] = From 947a4c873edbc5aaa8e59ee299bd33ff40a1cf6e Mon Sep 17 00:00:00 2001 From: leowe <13684843+leowe@users.noreply.github.com> Date: Fri, 30 Sep 2022 10:47:31 +0200 Subject: [PATCH 35/63] Update webknossos-datastore/app/com/scalableminds/webknossos/datastore/services/MeshFileService.scala Co-authored-by: Florian M --- .../datastore/services/MeshFileService.scala | 12 ++++-------- 1 file changed, 4 insertions(+), 8 deletions(-) diff --git a/webknossos-datastore/app/com/scalableminds/webknossos/datastore/services/MeshFileService.scala b/webknossos-datastore/app/com/scalableminds/webknossos/datastore/services/MeshFileService.scala index 290d0f0947e..a7ffaf86f78 100644 --- a/webknossos-datastore/app/com/scalableminds/webknossos/datastore/services/MeshFileService.scala +++ b/webknossos-datastore/app/com/scalableminds/webknossos/datastore/services/MeshFileService.scala @@ -143,14 +143,10 @@ class MeshFileService @Inject()(config: DataStoreConfig)(implicit ec: ExecutionC meshFilePath will return Fox.empty, while meshfiles with one marked as empty, will return Fox.successful(null) */ def mappingNameForMeshFile(meshFilePath: Path, meshFileVersion: Long): Fox[String] = - if (meshFileVersion == 0) { - safeExecute(meshFilePath, meshFileCache) { cachedMeshFile => - cachedMeshFile.reader.string().getAttr("/", "metadata/mapping_name") - } ?~> "mesh.file.readEncoding.failed" - } else { - safeExecute(meshFilePath, meshFileCache) { cachedMeshFile => - cachedMeshFile.reader.string().getAttr("/", "mapping_name") - } ?~> "mesh.file.readEncoding.failed" + val attributeName = if (meshFileVersion == 0) "metadata/mapping_name" else "mapping_name" + safeExecute(meshFilePath, meshFileCache) { cachedMeshFile => + cachedMeshFile.reader.string().getAttr("/", attributeName) + } ?~> "mesh.file.readEncoding.failed" } def mappingVersionForMeshFile(meshFilePath: Path): Long = From c76c090a556323f795bace2aff998f652f6c3c17 Mon Sep 17 00:00:00 2001 From: leowe <13684843+leowe@users.noreply.github.com> Date: Fri, 30 Sep 2022 10:47:42 +0200 Subject: [PATCH 36/63] Update webknossos-datastore/app/com/scalableminds/webknossos/datastore/storage/Hdf5FileCache.scala Co-authored-by: Florian M --- .../webknossos/datastore/storage/Hdf5FileCache.scala | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/webknossos-datastore/app/com/scalableminds/webknossos/datastore/storage/Hdf5FileCache.scala b/webknossos-datastore/app/com/scalableminds/webknossos/datastore/storage/Hdf5FileCache.scala index 00569aa1c35..f2c61d800b8 100644 --- a/webknossos-datastore/app/com/scalableminds/webknossos/datastore/storage/Hdf5FileCache.scala +++ b/webknossos-datastore/app/com/scalableminds/webknossos/datastore/storage/Hdf5FileCache.scala @@ -64,7 +64,7 @@ object CachedHdf5Utils { _ <- if (filePath.toFile.exists()) { Full(true) } else { - Empty ~> "mesh.file.open.failed" + Failure("mesh.file.open.failed") } result <- Using(meshFileCache.withCache(filePath)(CachedHdf5File.fromPath)) { block From 5ab2f836aabfae1fa064334821203cf1bcf088b2 Mon Sep 17 00:00:00 2001 From: leowe Date: Fri, 30 Sep 2022 11:31:10 +0200 Subject: [PATCH 37/63] incorporate pr feedback (move methods, renaming) --- .../controllers/MeshController.scala | 8 - .../datastore/services/MeshFileService.scala | 141 +++++++++--------- .../datastore/storage/Hdf5FileCache.scala | 23 ++- 3 files changed, 81 insertions(+), 91 deletions(-) diff --git a/webknossos-datastore/app/com/scalableminds/webknossos/datastore/controllers/MeshController.scala b/webknossos-datastore/app/com/scalableminds/webknossos/datastore/controllers/MeshController.scala index ad05c79ac87..7c3e9e4b920 100644 --- a/webknossos-datastore/app/com/scalableminds/webknossos/datastore/controllers/MeshController.scala +++ b/webknossos-datastore/app/com/scalableminds/webknossos/datastore/controllers/MeshController.scala @@ -8,11 +8,8 @@ import play.api.i18n.Messages import play.api.libs.json.Json import play.api.mvc.{Action, AnyContent, PlayBodyParsers} -import io.swagger.annotations.{Api, ApiOperation} - import scala.concurrent.ExecutionContext.Implicits.global -@Api(tags = Array("datastore")) class MeshController @Inject()( accessTokenService: DataStoreAccessTokenService, meshFileService: MeshFileService, @@ -22,7 +19,6 @@ class MeshController @Inject()( override def allowRemoteOrigin: Boolean = true - @ApiOperation(hidden = true, value = "") def listMeshFiles(token: Option[String], organizationName: String, dataSetName: String, @@ -36,7 +32,6 @@ class MeshController @Inject()( } } - @ApiOperation(hidden = true, value = "") def listMeshChunksForSegmentV0(token: Option[String], organizationName: String, dataSetName: String, @@ -56,7 +51,6 @@ class MeshController @Inject()( } } - @ApiOperation(hidden = true, value = "") def listMeshChunksForSegmentForVersion(token: Option[String], organizationName: String, dataSetName: String, @@ -78,7 +72,6 @@ class MeshController @Inject()( } } - @ApiOperation(hidden = true, value = "") def readMeshChunkV0(token: Option[String], organizationName: String, dataSetName: String, @@ -99,7 +92,6 @@ class MeshController @Inject()( } } - @ApiOperation(hidden = true, value = "") def readMeshChunkForVersion(token: Option[String], organizationName: String, dataSetName: String, diff --git a/webknossos-datastore/app/com/scalableminds/webknossos/datastore/services/MeshFileService.scala b/webknossos-datastore/app/com/scalableminds/webknossos/datastore/services/MeshFileService.scala index a7ffaf86f78..f9c4fea07db 100644 --- a/webknossos-datastore/app/com/scalableminds/webknossos/datastore/services/MeshFileService.scala +++ b/webknossos-datastore/app/com/scalableminds/webknossos/datastore/services/MeshFileService.scala @@ -5,7 +5,7 @@ import com.scalableminds.util.geometry.{Vec3Float, Vec3Int} import com.scalableminds.util.io.PathUtils import com.scalableminds.util.tools.{Fox, FoxImplicits} import com.scalableminds.webknossos.datastore.DataStoreConfig -import com.scalableminds.webknossos.datastore.storage.CachedHdf5Utils.{safeExecute, safeExecuteBox} +import com.scalableminds.webknossos.datastore.storage.CachedHdf5Utils.executeWithCachedHdf5 import com.scalableminds.webknossos.datastore.storage.{CachedHdf5File, Hdf5FileCache} import com.typesafe.scalalogging.LazyLogging import net.liftweb.common.Box @@ -72,6 +72,66 @@ case class NeuroglancerSegmentInfo(chunkShape: Vec3Float, chunkPositions: List[List[Vec3Int]], chunkByteOffsets: List[List[Int]]) +object NeuroglancerSegmentInfo { + def fromBytes(manifest: Array[Byte]): NeuroglancerSegmentInfo = { + // All Ints here should be UInt32 per spec. We assume that the sign bit is not necessary (the encoded values are at most 2^31). + // But they all are used to index into Arrays and JVM doesn't allow for Long Array Indexes, + // we can't convert them. + val byteInput = new ByteArrayInputStream(manifest) + val dis = new LittleEndianDataInputStream(byteInput) + + val chunkShape = Vec3Float(x = dis.readFloat, y = dis.readFloat, z = dis.readFloat) + val gridOrigin = Vec3Float(x = dis.readFloat, y = dis.readFloat, z = dis.readFloat) + + val numLods = dis.readInt + + val lodScales = new Array[Float](numLods) + for (d <- 0 until numLods) { + lodScales(d) = dis.readFloat + } + + val vertexOffsets = new Array[Vec3Float](numLods) + for (d <- 0 until numLods) { + vertexOffsets(d) = Vec3Float(x = dis.readFloat, y = dis.readFloat, z = dis.readFloat) + } + + val numChunksPerLod = new Array[Int](numLods) + for (lod <- 0 until numLods) { + numChunksPerLod(lod) = dis.readInt() + } + + val chunkPositionsList = new ListBuffer[List[Vec3Int]] + val chunkSizes = new ListBuffer[List[Int]] + for (lod <- 0 until numLods) { + val currentChunkPositions = (ListBuffer[Int](), ListBuffer[Int](), ListBuffer[Int]()) + for (row <- 0 until 3; _ <- 0 until numChunksPerLod(lod)) { + row match { + case 0 => currentChunkPositions._1.append(dis.readInt) + case 1 => currentChunkPositions._2.append(dis.readInt) + case 2 => currentChunkPositions._3.append(dis.readInt) + } + } + + chunkPositionsList.append(currentChunkPositions.zipped.map(Vec3Int(_, _, _)).toList) + + val currentChunkSizes = ListBuffer[Int]() + for (_ <- 0 until numChunksPerLod(lod)) { + currentChunkSizes.append(dis.readInt) + } + chunkSizes.append(currentChunkSizes.toList) + } + + NeuroglancerSegmentInfo(chunkShape, + gridOrigin, + numLods, + lodScales, + vertexOffsets, + numChunksPerLod, + chunkPositionsList.toList, + chunkSizes.toList) + } +} + case class MeshChunk(position: Vec3Float, byteOffset: Int, byteSize: Int) object MeshChunk { @@ -142,15 +202,15 @@ class MeshFileService @Inject()(config: DataStoreConfig)(implicit ec: ExecutionC Note that null is a valid value here for once. Meshfiles with no information about the meshFilePath will return Fox.empty, while meshfiles with one marked as empty, will return Fox.successful(null) */ - def mappingNameForMeshFile(meshFilePath: Path, meshFileVersion: Long): Fox[String] = + def mappingNameForMeshFile(meshFilePath: Path, meshFileVersion: Long): Fox[String] = { val attributeName = if (meshFileVersion == 0) "metadata/mapping_name" else "mapping_name" - safeExecute(meshFilePath, meshFileCache) { cachedMeshFile => + executeWithCachedHdf5(meshFilePath, meshFileCache) { cachedMeshFile => cachedMeshFile.reader.string().getAttr("/", attributeName) } ?~> "mesh.file.readEncoding.failed" - } + } def mappingVersionForMeshFile(meshFilePath: Path): Long = - safeExecuteBox(meshFilePath, meshFileCache) { cachedMeshFile => + executeWithCachedHdf5(meshFilePath, meshFileCache) { cachedMeshFile => cachedMeshFile.reader.int64().getAttr("/", "version") }.toOption.getOrElse(0) @@ -166,7 +226,7 @@ class MeshFileService @Inject()(config: DataStoreConfig)(implicit ec: ExecutionC .resolve(meshesDir) .resolve(s"${listMeshChunksRequest.meshFile}.$meshFileExtension") - safeExecute(meshFilePath, meshFileCache) { cachedMeshFile => + executeWithCachedHdf5(meshFilePath, meshFileCache) { cachedMeshFile => val chunkPositionLiterals = cachedMeshFile.reader .`object`() .getAllGroupMembers(s"/${listMeshChunksRequest.segmentId}/$defaultLevelOfDetail") @@ -188,7 +248,7 @@ class MeshFileService @Inject()(config: DataStoreConfig)(implicit ec: ExecutionC .resolve(meshesDir) .resolve(s"${listMeshChunksRequest.meshFile}.$meshFileExtension") - safeExecute(meshFilePath, meshFileCache) { cachedMeshFile => + executeWithCachedHdf5(meshFilePath, meshFileCache) { cachedMeshFile => val segmentId = listMeshChunksRequest.segmentId val encoding = cachedMeshFile.reader.string().getAttr("/", "mesh_format") val lodScaleMultiplier = cachedMeshFile.reader.float64().getAttr("/", "lod_scale_multiplier") @@ -199,9 +259,9 @@ class MeshFileService @Inject()(config: DataStoreConfig)(implicit ec: ExecutionC val manifest = cachedMeshFile.reader .uint8() .readArrayBlockWithOffset("/neuroglancer", (neuroglancerEnd - neuroglancerStart).toInt, neuroglancerStart) - val segmentInfo = parseNeuroglancerManifest(manifest) - val meshfile = getChunksFromSegmentInfo(segmentInfo, lodScaleMultiplier, neuroglancerStart) - WebknossosSegmentInfo(transform = transform, meshFormat = encoding, chunks = meshfile) + val segmentInfo = NeuroglancerSegmentInfo.fromBytes(manifest) + val processedSegmentInfo = getChunksFromSegmentInfo(segmentInfo, lodScaleMultiplier, neuroglancerStart) + WebknossosSegmentInfo(transform = transform, meshFormat = encoding, chunks = processedSegmentInfo) } } @@ -241,63 +301,6 @@ class MeshFileService @Inject()(config: DataStoreConfig)(implicit ec: ExecutionC .toList MeshSegmentInfo(chunkShape = segmentInfo.chunkShape, gridOrigin = segmentInfo.gridOrigin, lods = meshfileLods) } - private def parseNeuroglancerManifest(manifest: Array[Byte]): NeuroglancerSegmentInfo = { - // All Ints here should be UInt32 per spec. We assume that the sign bit is not necessary (the encoded values are at most 2^31). - // But they all are used to index into Arrays and JVM doesn't allow for Long Array Indexes, - // we can't convert them. - val byteInput = new ByteArrayInputStream(manifest) - val dis = new LittleEndianDataInputStream(byteInput) - - val chunkShape = Vec3Float(x = dis.readFloat, y = dis.readFloat, z = dis.readFloat) - val gridOrigin = Vec3Float(x = dis.readFloat, y = dis.readFloat, z = dis.readFloat) - - val numLods = dis.readInt - - val lodScales = new Array[Float](numLods) - for (d <- 0 until numLods) { - lodScales(d) = dis.readFloat - } - - val vertexOffsets = new Array[Vec3Float](numLods) - for (d <- 0 until numLods) { - vertexOffsets(d) = Vec3Float(x = dis.readFloat, y = dis.readFloat, z = dis.readFloat) - } - - val numChunksPerLod = new Array[Int](numLods) - for (lod <- 0 until numLods) { - numChunksPerLod(lod) = dis.readInt() - } - - val chunkPositionsList = new ListBuffer[List[Vec3Int]] - val chunkSizes = new ListBuffer[List[Int]] - for (lod <- 0 until numLods) { - val currentChunkPositions = (ListBuffer[Int](), ListBuffer[Int](), ListBuffer[Int]()) - for (row <- 0 until 3; _ <- 0 until numChunksPerLod(lod)) { - row match { - case 0 => currentChunkPositions._1.append(dis.readInt) - case 1 => currentChunkPositions._2.append(dis.readInt) - case 2 => currentChunkPositions._3.append(dis.readInt) - } - } - - chunkPositionsList.append(currentChunkPositions.zipped.map(Vec3Int(_, _, _)).toList) - - val currentChunkSizes = ListBuffer[Int]() - for (_ <- 0 until numChunksPerLod(lod)) { - currentChunkSizes.append(dis.readInt) - } - chunkSizes.append(currentChunkSizes.toList) - } - - NeuroglancerSegmentInfo(chunkShape, - gridOrigin, - numLods, - lodScales, - vertexOffsets, - numChunksPerLod, - chunkPositionsList.toList, - chunkSizes.toList) - } private def getNeuroglancerOffsets(segmentId: Long, cachedMeshFile: CachedHdf5File): (Long, Long) = { val nBuckets = cachedMeshFile.reader.uint64().getAttr("/", "n_buckets") @@ -330,7 +333,7 @@ class MeshFileService @Inject()(config: DataStoreConfig)(implicit ec: ExecutionC .resolve(meshesDir) .resolve(s"${meshChunkDataRequest.meshFile}.$meshFileExtension") - safeExecute(meshFilePath, meshFileCache) { cachedMeshFile => + executeWithCachedHdf5(meshFilePath, meshFileCache) { cachedMeshFile => val encoding = cachedMeshFile.reader.string().getAttr("/", "metadata/encoding") val key = s"/${meshChunkDataRequest.segmentId}/$defaultLevelOfDetail/${positionLiteral(meshChunkDataRequest.position)}" @@ -351,7 +354,7 @@ class MeshFileService @Inject()(config: DataStoreConfig)(implicit ec: ExecutionC .resolve(meshesDir) .resolve(s"${meshChunkDataRequest.meshFile}.$meshFileExtension") - safeExecute(meshFilePath, meshFileCache) { cachedMeshFile => + executeWithCachedHdf5(meshFilePath, meshFileCache) { cachedMeshFile => val meshFormat = cachedMeshFile.reader.string().getAttr("/", "mesh_format") val data = cachedMeshFile.reader diff --git a/webknossos-datastore/app/com/scalableminds/webknossos/datastore/storage/Hdf5FileCache.scala b/webknossos-datastore/app/com/scalableminds/webknossos/datastore/storage/Hdf5FileCache.scala index f2c61d800b8..1bb024dd7f0 100644 --- a/webknossos-datastore/app/com/scalableminds/webknossos/datastore/storage/Hdf5FileCache.scala +++ b/webknossos-datastore/app/com/scalableminds/webknossos/datastore/storage/Hdf5FileCache.scala @@ -5,7 +5,7 @@ import com.scalableminds.util.cache.LRUConcurrentCache import com.scalableminds.util.tools.Fox import com.scalableminds.util.tools.Fox.{bool2Fox, try2Fox} import com.scalableminds.webknossos.datastore.dataformats.SafeCachable -import net.liftweb.common.{Box, Full, Empty} +import net.liftweb.common.{Box, Failure, Full} import java.nio.file.Path import scala.concurrent.ExecutionContext @@ -50,24 +50,19 @@ class Hdf5FileCache(val maxEntries: Int) extends LRUConcurrentCache[String, Cach } object CachedHdf5Utils { - def safeExecute[T](filePath: Path, meshFileCache: Hdf5FileCache)(block: CachedHdf5File => T)( - implicit ec: ExecutionContext): Fox[T] = - for { - _ <- bool2Fox(filePath.toFile.exists()) ?~> "mesh.file.open.failed" - result <- Using(meshFileCache.withCache(filePath)(CachedHdf5File.fromPath)) { - block - }.toFox - } yield result - - def safeExecuteBox[T](filePath: Path, meshFileCache: Hdf5FileCache)(block: CachedHdf5File => T): Box[T] = + def executeWithCachedHdf5[T](filePath: Path, meshFileCache: Hdf5FileCache)(block: CachedHdf5File => T): Box[T] = for { _ <- if (filePath.toFile.exists()) { Full(true) } else { Failure("mesh.file.open.failed") } - result <- Using(meshFileCache.withCache(filePath)(CachedHdf5File.fromPath)) { + result = Using(meshFileCache.withCache(filePath)(CachedHdf5File.fromPath)) { block - }.toOption - } yield result + } + boxedResult <- result match { + case scala.util.Success(result) => Full(result) + case scala.util.Failure(e) => Failure(e.toString) + } + } yield boxedResult } From 57ad538b10d38dddb6f097000e559076ee74dc97 Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Fri, 30 Sep 2022 13:17:02 +0200 Subject: [PATCH 38/63] make all meshes smooth --- .../oxalis/controller/scene_controller.ts | 10 ++++------ frontend/javascripts/oxalis/default_state.ts | 1 + .../oxalis/model/sagas/isosurface_saga.ts | 15 ++++++++++++++- frontend/javascripts/oxalis/store.ts | 1 + .../segments_tab/segments_view.tsx | 17 ++++++++++++++++- 5 files changed, 36 insertions(+), 8 deletions(-) diff --git a/frontend/javascripts/oxalis/controller/scene_controller.ts b/frontend/javascripts/oxalis/controller/scene_controller.ts index d7074f48d18..dc61fb827da 100644 --- a/frontend/javascripts/oxalis/controller/scene_controller.ts +++ b/frontend/javascripts/oxalis/controller/scene_controller.ts @@ -39,6 +39,7 @@ import constants, { import window from "libs/window"; import { setSceneController } from "oxalis/controller/scene_controller_provider"; import { getSegmentColorAsHSL } from "oxalis/model/accessors/volumetracing_accessor"; +import { mergeVertices } from "three/examples/jsm/utils/BufferGeometryUtils.js"; const CUBE_COLOR = 0x999999; @@ -200,9 +201,8 @@ class SceneController { constructIsosurfaceMesh(cellId: number, geometry: THREE.BufferGeometry, passive: boolean) { const color = this.getColorObjectForSegment(cellId); - const meshMaterial = new THREE.MeshStandardMaterial({ + const meshMaterial = new THREE.MeshLambertMaterial({ color, - // flatShading: true, }); meshMaterial.side = THREE.FrontSide; meshMaterial.transparent = true; @@ -259,10 +259,8 @@ class SceneController { let bufferGeometry = new THREE.BufferGeometry(); bufferGeometry.setAttribute("position", new THREE.BufferAttribute(vertices, 3)); - // @ts-ignore - if (window.__isosurfaceMergeVertices) { - // @ts-ignore mergeVertices - bufferGeometry = THREE.BufferGeometryUtils.mergeVertices(bufferGeometry); + if (Store.getState().userConfiguration.useSmoothMeshes) { + bufferGeometry = mergeVertices(bufferGeometry); } bufferGeometry.computeVertexNormals(); diff --git a/frontend/javascripts/oxalis/default_state.ts b/frontend/javascripts/oxalis/default_state.ts index fd5f91ceb4d..c0480b58feb 100644 --- a/frontend/javascripts/oxalis/default_state.ts +++ b/frontend/javascripts/oxalis/default_state.ts @@ -78,6 +78,7 @@ const defaultState: OxalisState = { fillMode: FillModeEnum._2D, interpolationMode: InterpolationModeEnum.INTERPOLATE, useLegacyBindings: false, + useSmoothMeshes: true, }, temporaryConfiguration: { viewMode: Constants.MODE_PLANE_TRACING, diff --git a/frontend/javascripts/oxalis/model/sagas/isosurface_saga.ts b/frontend/javascripts/oxalis/model/sagas/isosurface_saga.ts index 62c49df9b4a..67d8b1d40f7 100644 --- a/frontend/javascripts/oxalis/model/sagas/isosurface_saga.ts +++ b/frontend/javascripts/oxalis/model/sagas/isosurface_saga.ts @@ -4,6 +4,7 @@ import { V3 } from "libs/mjs"; import { sleep } from "libs/utils"; import ErrorHandling from "libs/error_handling"; import type { APIDataLayer } from "types/api_flow_types"; +import { mergeVertices } from "three/examples/jsm/utils/BufferGeometryUtils.js"; import { ResolutionInfo, @@ -589,6 +590,7 @@ function* loadPrecomputedMeshForSegmentId( const sceneController = yield* call(getSceneController); if ("position" in chunk) { + // V3 const dracoData = yield* call( meshV3.getMeshfileChunkData, dataset.dataStore.url, @@ -601,6 +603,7 @@ function* loadPrecomputedMeshForSegmentId( const loader = getDracoLoader(); const geometry = yield* call(loader.decodeDracoFileAsync, dracoData); + // Compute vertex normals to achieve smooth shading geometry.computeVertexNormals(); yield* call( @@ -612,6 +615,7 @@ function* loadPrecomputedMeshForSegmentId( true, ); } else { + // V0 const stlData = yield* call( meshV0.getMeshfileChunkData, dataset.dataStore.url, @@ -621,7 +625,16 @@ function* loadPrecomputedMeshForSegmentId( id, chunk, ); - const geometry = yield* call(parseStlBuffer, stlData); + let geometry = yield* call(parseStlBuffer, stlData); + + // Delete existing vertex normals (since these are not interpolated + // across faces). + geometry.deleteAttribute("normal"); + // Ensure that vertices of adjacent faces are shared. + geometry = mergeVertices(geometry); + // Recompute normals to achieve smooth shading + geometry.computeVertexNormals(); + yield* call( { context: sceneController, fn: sceneController.addIsosurfaceFromGeometry }, geometry, diff --git a/frontend/javascripts/oxalis/store.ts b/frontend/javascripts/oxalis/store.ts index 56519199dc6..fde163e83cf 100644 --- a/frontend/javascripts/oxalis/store.ts +++ b/frontend/javascripts/oxalis/store.ts @@ -325,6 +325,7 @@ export type UserConfiguration = { readonly fillMode: FillMode; readonly interpolationMode: InterpolationMode; readonly useLegacyBindings: boolean; + readonly useSmoothMeshes: boolean; }; export type RecommendedConfiguration = Partial< UserConfiguration & diff --git a/frontend/javascripts/oxalis/view/right-border-tabs/segments_tab/segments_view.tsx b/frontend/javascripts/oxalis/view/right-border-tabs/segments_tab/segments_view.tsx index 40412e120f8..ccf1b37527f 100644 --- a/frontend/javascripts/oxalis/view/right-border-tabs/segments_tab/segments_view.tsx +++ b/frontend/javascripts/oxalis/view/right-border-tabs/segments_tab/segments_view.tsx @@ -31,7 +31,10 @@ import { } from "oxalis/view/right-border-tabs/segments_tab/segments_view_helper"; import { setPositionAction } from "oxalis/model/actions/flycam_actions"; import { startComputeMeshFileJob, getJobs } from "admin/admin_rest_api"; -import { updateTemporarySettingAction } from "oxalis/model/actions/settings_actions"; +import { + updateTemporarySettingAction, + updateUserSettingAction, +} from "oxalis/model/actions/settings_actions"; import { updateSegmentAction, setActiveCellAction, @@ -51,6 +54,7 @@ import type { import Store from "oxalis/store"; import Toast from "libs/toast"; import features from "features"; +import { SwitchSetting } from "oxalis/view/components/setting_input_views"; const { Option } = Select; // Interval in ms to check for running mesh file computation jobs for this dataset @@ -83,6 +87,7 @@ type StateProps = { preferredQualityForMeshPrecomputation: number; preferredQualityForMeshAdHocComputation: number; resolutionInfoOfVisibleSegmentationLayer: ResolutionInfo; + useSmoothMeshes: boolean; }; const mapStateToProps = (state: OxalisState): StateProps => { @@ -124,6 +129,7 @@ const mapStateToProps = (state: OxalisState): StateProps => { preferredQualityForMeshAdHocComputation: state.temporaryConfiguration.preferredQualityForMeshAdHocComputation, resolutionInfoOfVisibleSegmentationLayer: getResolutionInfoOfVisibleSegmentationLayer(state), + useSmoothMeshes: state.userConfiguration.useSmoothMeshes, }; }; @@ -425,9 +431,18 @@ class SegmentsView extends React.Component { const { preferredQualityForMeshAdHocComputation, resolutionInfoOfVisibleSegmentationLayer: datasetResolutionInfo, + useSmoothMeshes, } = this.props; return (
+ { + Store.dispatch(updateUserSettingAction("useSmoothMeshes", value)); + }} + labelSpan={18} + />
Quality for Ad-Hoc Mesh Computation:
 From 2710f81b4092f86df01cc9e66d450983e656f5ad Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Fri, 30 Sep 2022 13:17:30 +0200 Subject: [PATCH 39/63] generalize switch setting to allow for different width of label --- .../oxalis/view/components/setting_input_views.tsx | 11 ++++++++--- 1 file changed, 8 insertions(+), 3 deletions(-) diff --git a/frontend/javascripts/oxalis/view/components/setting_input_views.tsx b/frontend/javascripts/oxalis/view/components/setting_input_views.tsx index da964db2a78..7901b0f7133 100644 --- a/frontend/javascripts/oxalis/view/components/setting_input_views.tsx +++ b/frontend/javascripts/oxalis/view/components/setting_input_views.tsx @@ -9,6 +9,8 @@ import messages from "messages"; const ROW_GUTTER = 1; +const ANTD_TOTAL_SPAN = 24; + // Always the left part: export const SETTING_LEFT_SPAN = 10; @@ -187,6 +189,7 @@ type SwitchSettingProps = { disabled: boolean; tooltipText: string | null | undefined; loading: boolean; + labelSpan?: number | null; }; export class SwitchSetting extends React.PureComponent { static defaultProps = { @@ -196,13 +199,15 @@ export class SwitchSetting extends React.PureComponent { }; render() { - const { label, onChange, value, disabled, tooltipText, loading } = this.props; + const { label, onChange, value, disabled, tooltipText, loading, labelSpan } = this.props; + const leftSpanValue = labelSpan || SETTING_LEFT_SPAN; + const rightSpanValue = labelSpan != null ? ANTD_TOTAL_SPAN - leftSpanValue : SETTING_RIGHT_SPAN; return ( - + - + {/* This div is necessary for the tooltip to be displayed */}
Date: Fri, 30 Sep 2022 13:19:05 +0200 Subject: [PATCH 40/63] remove setting for smooth meshes again (always use smooth meshes) --- .../javascripts/oxalis/controller/scene_controller.ts | 6 ++---- frontend/javascripts/oxalis/default_state.ts | 1 - frontend/javascripts/oxalis/store.ts | 1 - .../right-border-tabs/segments_tab/segments_view.tsx | 11 ----------- 4 files changed, 2 insertions(+), 17 deletions(-) diff --git a/frontend/javascripts/oxalis/controller/scene_controller.ts b/frontend/javascripts/oxalis/controller/scene_controller.ts index dc61fb827da..3ea94d45345 100644 --- a/frontend/javascripts/oxalis/controller/scene_controller.ts +++ b/frontend/javascripts/oxalis/controller/scene_controller.ts @@ -259,11 +259,9 @@ class SceneController { let bufferGeometry = new THREE.BufferGeometry(); bufferGeometry.setAttribute("position", new THREE.BufferAttribute(vertices, 3)); - if (Store.getState().userConfiguration.useSmoothMeshes) { - bufferGeometry = mergeVertices(bufferGeometry); - } - + bufferGeometry = mergeVertices(bufferGeometry); bufferGeometry.computeVertexNormals(); + this.addIsosurfaceFromGeometry(bufferGeometry, segmentationId, passive); } diff --git a/frontend/javascripts/oxalis/default_state.ts b/frontend/javascripts/oxalis/default_state.ts index c0480b58feb..fd5f91ceb4d 100644 --- a/frontend/javascripts/oxalis/default_state.ts +++ b/frontend/javascripts/oxalis/default_state.ts @@ -78,7 +78,6 @@ const defaultState: OxalisState = { fillMode: FillModeEnum._2D, interpolationMode: InterpolationModeEnum.INTERPOLATE, useLegacyBindings: false, - useSmoothMeshes: true, }, temporaryConfiguration: { viewMode: Constants.MODE_PLANE_TRACING, diff --git a/frontend/javascripts/oxalis/store.ts b/frontend/javascripts/oxalis/store.ts index fde163e83cf..56519199dc6 100644 --- a/frontend/javascripts/oxalis/store.ts +++ b/frontend/javascripts/oxalis/store.ts @@ -325,7 +325,6 @@ export type UserConfiguration = { readonly fillMode: FillMode; readonly interpolationMode: InterpolationMode; readonly useLegacyBindings: boolean; - readonly useSmoothMeshes: boolean; }; export type RecommendedConfiguration = Partial< UserConfiguration & diff --git a/frontend/javascripts/oxalis/view/right-border-tabs/segments_tab/segments_view.tsx b/frontend/javascripts/oxalis/view/right-border-tabs/segments_tab/segments_view.tsx index ccf1b37527f..297152f1bc7 100644 --- a/frontend/javascripts/oxalis/view/right-border-tabs/segments_tab/segments_view.tsx +++ b/frontend/javascripts/oxalis/view/right-border-tabs/segments_tab/segments_view.tsx @@ -87,7 +87,6 @@ type StateProps = { preferredQualityForMeshPrecomputation: number; preferredQualityForMeshAdHocComputation: number; resolutionInfoOfVisibleSegmentationLayer: ResolutionInfo; - useSmoothMeshes: boolean; }; const mapStateToProps = (state: OxalisState): StateProps => { @@ -129,7 +128,6 @@ const mapStateToProps = (state: OxalisState): StateProps => { preferredQualityForMeshAdHocComputation: state.temporaryConfiguration.preferredQualityForMeshAdHocComputation, resolutionInfoOfVisibleSegmentationLayer: getResolutionInfoOfVisibleSegmentationLayer(state), - useSmoothMeshes: state.userConfiguration.useSmoothMeshes, }; }; @@ -431,18 +429,9 @@ class SegmentsView extends React.Component { const { preferredQualityForMeshAdHocComputation, resolutionInfoOfVisibleSegmentationLayer: datasetResolutionInfo, - useSmoothMeshes, } = this.props; return (
- { - Store.dispatch(updateUserSettingAction("useSmoothMeshes", value)); - }} - labelSpan={18} - />
Quality for Ad-Hoc Mesh Computation:
 From c6ddc483279aaeca1c39e3fb396dafd7652627fa Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Fri, 30 Sep 2022 13:19:23 +0200 Subject: [PATCH 41/63] improve lighting and expose window.testLights method for tuning parameters in dev --- .../oxalis/controller/scene_controller.ts | 64 +++++++++++++++++-- 1 file changed, 59 insertions(+), 5 deletions(-) diff --git a/frontend/javascripts/oxalis/controller/scene_controller.ts b/frontend/javascripts/oxalis/controller/scene_controller.ts index 3ea94d45345..386e435e701 100644 --- a/frontend/javascripts/oxalis/controller/scene_controller.ts +++ b/frontend/javascripts/oxalis/controller/scene_controller.ts @@ -309,12 +309,66 @@ class SceneController { // At the moment, we only attach an AmbientLight for the isosurfaces group. // The PlaneView attaches a directional light directly to the TD camera, // so that the light moves along the cam. - const ambientLightForIsosurfaces = new THREE.AmbientLight(0x404040, 15); // soft white light - - this.isosurfacesRootGroup.add(ambientLightForIsosurfaces); - const ambientLightForMeshes = new THREE.AmbientLight(0x404040, 15); // soft white light + // const ambientLightForIsosurfaces = new THREE.AmbientLight(0x404040, 15); // soft white light + // this.isosurfacesRootGroup.add(ambientLightForIsosurfaces); + + // const ambientLightForMeshes = new THREE.AmbientLight(0x404040, 5); // soft white light + // this.meshesRootGroup.add(ambientLightForMeshes); + + let unsubscribe = () => {}; + const testLights = (a: number, b: number, c: number, d: number) => { + unsubscribe(); + const ambientLight = new THREE.AmbientLight(2105376, a); + + const directionalLight = new THREE.DirectionalLight(16777215, b); + directionalLight.position.x = 1; + directionalLight.position.y = 1; + directionalLight.position.z = 1; + directionalLight.position.normalize(); + + // const max = 10000000000; + + const directionalLight2 = new THREE.DirectionalLight(16777215, c); + directionalLight2.position.x = -1; + directionalLight2.position.y = -1; + directionalLight2.position.z = -1; + directionalLight2.position.normalize(); + + const pointLight = new THREE.PointLight(16777215, d); + pointLight.position.x = 0; + pointLight.position.y = -25; + pointLight.position.z = 10; + + this.isosurfacesRootGroup.add(ambientLight); + this.isosurfacesRootGroup.add(directionalLight); + this.isosurfacesRootGroup.add(directionalLight2); + this.isosurfacesRootGroup.add(pointLight); + + unsubscribe = () => { + this.isosurfacesRootGroup.remove(ambientLight); + this.isosurfacesRootGroup.remove(directionalLight); + this.isosurfacesRootGroup.remove(directionalLight2); + this.isosurfacesRootGroup.remove(pointLight); + }; + }; - this.meshesRootGroup.add(ambientLightForMeshes); + testLights(30, 5, 5, 5); + // @ts-ignore + window.testLights = testLights; + // directionalLight.position.x = 2 * max; + // directionalLight.position.y = 0; + // directionalLight.position.z = 2 * max; + // pointLight.position.x = max / 2; + // pointLight.position.y = max / 2; + // pointLight.position.z = 2 * max; + + // const light1 = new THREE.DirectionalLight(0xefefff, 12); + // light1.position.set(1, 1, 1).normalize(); + // this.isosurfacesRootGroup.add(light1); + + // const light2 = new THREE.DirectionalLight(0xffefef, 8); + // light2.position.set(-1, -1, -1).normalize(); + // this.isosurfacesRootGroup.add(light2); } removeSTL(id: string): void { From 5c2d8663297827d4914a4aa4c229c04ef7338db4 Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Fri, 30 Sep 2022 13:19:58 +0200 Subject: [PATCH 42/63] remove unused imports --- .../view/right-border-tabs/segments_tab/segments_view.tsx | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/frontend/javascripts/oxalis/view/right-border-tabs/segments_tab/segments_view.tsx b/frontend/javascripts/oxalis/view/right-border-tabs/segments_tab/segments_view.tsx index 297152f1bc7..40412e120f8 100644 --- a/frontend/javascripts/oxalis/view/right-border-tabs/segments_tab/segments_view.tsx +++ b/frontend/javascripts/oxalis/view/right-border-tabs/segments_tab/segments_view.tsx @@ -31,10 +31,7 @@ import { } from "oxalis/view/right-border-tabs/segments_tab/segments_view_helper"; import { setPositionAction } from "oxalis/model/actions/flycam_actions"; import { startComputeMeshFileJob, getJobs } from "admin/admin_rest_api"; -import { - updateTemporarySettingAction, - updateUserSettingAction, -} from "oxalis/model/actions/settings_actions"; +import { updateTemporarySettingAction } from "oxalis/model/actions/settings_actions"; import { updateSegmentAction, setActiveCellAction, @@ -54,7 +51,6 @@ import type { import Store from "oxalis/store"; import Toast from "libs/toast"; import features from "features"; -import { SwitchSetting } from "oxalis/view/components/setting_input_views"; const { Option } = Select; // Interval in ms to check for running mesh file computation jobs for this dataset From 9f5a4eb31e83ec2fac729f8b48a4ee39469e14aa Mon Sep 17 00:00:00 2001 From: leowe Date: Fri, 30 Sep 2022 13:42:34 +0200 Subject: [PATCH 43/63] remove unused imports --- .../webknossos/datastore/storage/Hdf5FileCache.scala | 3 --- 1 file changed, 3 deletions(-) diff --git a/webknossos-datastore/app/com/scalableminds/webknossos/datastore/storage/Hdf5FileCache.scala b/webknossos-datastore/app/com/scalableminds/webknossos/datastore/storage/Hdf5FileCache.scala index 1bb024dd7f0..799f6c5785d 100644 --- a/webknossos-datastore/app/com/scalableminds/webknossos/datastore/storage/Hdf5FileCache.scala +++ b/webknossos-datastore/app/com/scalableminds/webknossos/datastore/storage/Hdf5FileCache.scala @@ -2,13 +2,10 @@ package com.scalableminds.webknossos.datastore.storage import ch.systemsx.cisd.hdf5.{HDF5FactoryProvider, IHDF5Reader} import com.scalableminds.util.cache.LRUConcurrentCache -import com.scalableminds.util.tools.Fox -import com.scalableminds.util.tools.Fox.{bool2Fox, try2Fox} import com.scalableminds.webknossos.datastore.dataformats.SafeCachable import net.liftweb.common.{Box, Failure, Full} import java.nio.file.Path -import scala.concurrent.ExecutionContext import scala.util.Using case class CachedHdf5File(reader: IHDF5Reader) extends SafeCachable with AutoCloseable { From d5fc95a729ffdbc65a60eb1dc46ec5d36d08fb03 Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Fri, 30 Sep 2022 13:52:37 +0200 Subject: [PATCH 44/63] use formatVersion of mesh file to decide which routes to use --- frontend/javascripts/admin/admin_rest_api.ts | 12 ++++++++++-- frontend/javascripts/oxalis/api/api_latest.ts | 3 +-- .../oxalis/model/sagas/isosurface_saga.ts | 16 +++++++++++++--- .../segments_tab/segments_view_helper.tsx | 8 +------- frontend/javascripts/types/api_flow_types.ts | 4 ++++ 5 files changed, 29 insertions(+), 14 deletions(-) diff --git a/frontend/javascripts/admin/admin_rest_api.ts b/frontend/javascripts/admin/admin_rest_api.ts index 6e560f3b50e..c8065cf160e 100644 --- a/frontend/javascripts/admin/admin_rest_api.ts +++ b/frontend/javascripts/admin/admin_rest_api.ts @@ -2071,16 +2071,24 @@ export function getEditableAgglomerateSkeleton( ); } -export function getMeshfilesForDatasetLayer( +export async function getMeshfilesForDatasetLayer( dataStoreUrl: string, datasetId: APIDatasetId, layerName: string, ): Promise> { - return doWithToken((token) => + const meshFiles: Array = await doWithToken((token) => Request.receiveJSON( `${dataStoreUrl}/data/datasets/${datasetId.owningOrganization}/${datasetId.name}/layers/${layerName}/meshes?token=${token}`, ), ); + + for (const file of meshFiles) { + if (file.mappingName === "") { + file.mappingName = undefined; + } + } + + return meshFiles; } // ### Connectomes diff --git a/frontend/javascripts/oxalis/api/api_latest.ts b/frontend/javascripts/oxalis/api/api_latest.ts index 38be03d21fa..c2762f3df2c 100644 --- a/frontend/javascripts/oxalis/api/api_latest.ts +++ b/frontend/javascripts/oxalis/api/api_latest.ts @@ -1841,8 +1841,7 @@ class DataApi { const { mappingName, meshFileName } = currentMeshFile; - // todo: remove second condition - if (mappingName != null && mappingName !== "") { + if (mappingName != null) { const activeMapping = this.getActiveMapping(effectiveLayerName); if (mappingName !== activeMapping) { diff --git a/frontend/javascripts/oxalis/model/sagas/isosurface_saga.ts b/frontend/javascripts/oxalis/model/sagas/isosurface_saga.ts index 67d8b1d40f7..a07078d7610 100644 --- a/frontend/javascripts/oxalis/model/sagas/isosurface_saga.ts +++ b/frontend/javascripts/oxalis/model/sagas/isosurface_saga.ts @@ -548,10 +548,20 @@ function* loadPrecomputedMeshForSegmentId( let availableChunks = null; - // todo: dont hardcode - const version = meshFileName.includes("4-4") ? 0 : 3; + const meshFile = yield* select((state) => + (state.localSegmentationData[layerName].availableMeshFiles || []).find( + (file) => file.meshFileName === meshFileName, + ), + ); + if (!meshFile) { + throw new Error("Could not find requested mesh file."); + } + + const version = meshFile.formatVersion; try { - if (version === 3) { + // todo: should actually check against 3, but some new mesh files + // still have version 2 ? + if (version >= 2) { const segmentInfo = yield* call( meshV3.getMeshfileChunksForSegment, dataset.dataStore.url, diff --git a/frontend/javascripts/oxalis/view/right-border-tabs/segments_tab/segments_view_helper.tsx b/frontend/javascripts/oxalis/view/right-border-tabs/segments_tab/segments_view_helper.tsx index 2420e928aab..721a109ae4c 100644 --- a/frontend/javascripts/oxalis/view/right-border-tabs/segments_tab/segments_view_helper.tsx +++ b/frontend/javascripts/oxalis/view/right-border-tabs/segments_tab/segments_view_helper.tsx @@ -84,13 +84,7 @@ export function withMappingActivationConfirmation> // If the mapping name is undefined, no mapping is specified. In that case never show the activation modal. // In contrast, if the mapping name is null, this indicates that all mappings should be specifically disabled. - // todo: remove last condition - if ( - mappingName === undefined || - layerName == null || - mappingName === enabledMappingName || - mappingName === "" - ) { + if (mappingName === undefined || layerName == null || mappingName === enabledMappingName) { // @ts-expect-error ts-migrate(2322) FIXME: Type 'Omit, ... Remove this comment to see the full error message return ; } diff --git a/frontend/javascripts/types/api_flow_types.ts b/frontend/javascripts/types/api_flow_types.ts index 863936f9f0d..8754552544d 100644 --- a/frontend/javascripts/types/api_flow_types.ts +++ b/frontend/javascripts/types/api_flow_types.ts @@ -693,6 +693,10 @@ export type ServerEditableMapping = { export type APIMeshFile = { meshFileName: string; mappingName?: string | null | undefined; + // 0 - is the first mesh file version + // 1-2 - skipped for consistency with VX artifact versioning + // 3 - (some artifacts might have used 2, too) is the newer version with draco encoding. + formatVersion: number; }; export type APIConnectomeFile = { connectomeFileName: string; From 4dab4a43d361a02604e4056492d4ba0c8248f33a Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Fri, 30 Sep 2022 16:02:46 +0200 Subject: [PATCH 45/63] fix failing tests by simply copying DracoLoader and BufferGeometryUtils from threejs package to repo, because of ERR_REQUIRE_ESM error --- frontend/javascripts/admin/api/token.ts | 1 + .../javascripts/libs/BufferGeometryUtils.ts | 839 ++++++++++++++++++ frontend/javascripts/libs/DRACOLoader.ts | 470 ++++++++++ frontend/javascripts/libs/draco.ts | 3 +- .../oxalis/controller/scene_controller.ts | 2 +- .../oxalis/model/sagas/isosurface_saga.ts | 2 +- 6 files changed, 1314 insertions(+), 3 deletions(-) create mode 100644 frontend/javascripts/libs/BufferGeometryUtils.ts create mode 100644 frontend/javascripts/libs/DRACOLoader.ts diff --git a/frontend/javascripts/admin/api/token.ts b/frontend/javascripts/admin/api/token.ts index 4424ca662c6..9b0de025484 100644 --- a/frontend/javascripts/admin/api/token.ts +++ b/frontend/javascripts/admin/api/token.ts @@ -1,3 +1,4 @@ +import { location } from "libs/window"; import Request from "libs/request"; import * as Utils from "libs/utils"; diff --git a/frontend/javascripts/libs/BufferGeometryUtils.ts b/frontend/javascripts/libs/BufferGeometryUtils.ts new file mode 100644 index 00000000000..7b51c73a324 --- /dev/null +++ b/frontend/javascripts/libs/BufferGeometryUtils.ts @@ -0,0 +1,839 @@ +// @ts-nocheck +// Copied from three/examples/js/utils/BufferGeometryUtils.js to fix ERR_REQUIRE_ESM error. +import { + BufferAttribute, + BufferGeometry, + Float32BufferAttribute, + InterleavedBuffer, + InterleavedBufferAttribute, + TriangleFanDrawMode, + TriangleStripDrawMode, + TrianglesDrawMode, + Vector3, +} from "three"; + +function computeTangents(geometry) { + geometry.computeTangents(); + console.warn( + "THREE.BufferGeometryUtils: .computeTangents() has been removed. Use BufferGeometry.computeTangents() instead.", + ); +} + +/** + * @param {Array} geometries + * @param {Boolean} useGroups + * @return {BufferGeometry} + */ +function mergeBufferGeometries(geometries, useGroups = false) { + const isIndexed = geometries[0].index !== null; + + const attributesUsed = new Set(Object.keys(geometries[0].attributes)); + const morphAttributesUsed = new Set(Object.keys(geometries[0].morphAttributes)); + + const attributes = {}; + const morphAttributes = {}; + + const morphTargetsRelative = geometries[0].morphTargetsRelative; + + const mergedGeometry = new BufferGeometry(); + + let offset = 0; + + for (let i = 0; i < geometries.length; ++i) { + const geometry = geometries[i]; + let attributesCount = 0; + + // ensure that all geometries are indexed, or none + + if (isIndexed !== (geometry.index !== null)) { + console.error( + "THREE.BufferGeometryUtils: .mergeBufferGeometries() failed with geometry at index " + + i + + ". All geometries must have compatible attributes; make sure index attribute exists among all geometries, or in none of them.", + ); + return null; + } + + // gather attributes, exit early if they're different + + for (const name in geometry.attributes) { + if (!attributesUsed.has(name)) { + console.error( + "THREE.BufferGeometryUtils: .mergeBufferGeometries() failed with geometry at index " + + i + + '. All geometries must have compatible attributes; make sure "' + + name + + '" attribute exists among all geometries, or in none of them.', + ); + return null; + } + + if (attributes[name] === undefined) attributes[name] = []; + + attributes[name].push(geometry.attributes[name]); + + attributesCount++; + } + + // ensure geometries have the same number of attributes + + if (attributesCount !== attributesUsed.size) { + console.error( + "THREE.BufferGeometryUtils: .mergeBufferGeometries() failed with geometry at index " + + i + + ". Make sure all geometries have the same number of attributes.", + ); + return null; + } + + // gather morph attributes, exit early if they're different + + if (morphTargetsRelative !== geometry.morphTargetsRelative) { + console.error( + "THREE.BufferGeometryUtils: .mergeBufferGeometries() failed with geometry at index " + + i + + ". .morphTargetsRelative must be consistent throughout all geometries.", + ); + return null; + } + + for (const name in geometry.morphAttributes) { + if (!morphAttributesUsed.has(name)) { + console.error( + "THREE.BufferGeometryUtils: .mergeBufferGeometries() failed with geometry at index " + + i + + ". .morphAttributes must be consistent throughout all geometries.", + ); + return null; + } + + if (morphAttributes[name] === undefined) morphAttributes[name] = []; + + morphAttributes[name].push(geometry.morphAttributes[name]); + } + + // gather .userData + + mergedGeometry.userData.mergedUserData = mergedGeometry.userData.mergedUserData || []; + mergedGeometry.userData.mergedUserData.push(geometry.userData); + + if (useGroups) { + let count; + + if (isIndexed) { + count = geometry.index.count; + } else if (geometry.attributes.position !== undefined) { + count = geometry.attributes.position.count; + } else { + console.error( + "THREE.BufferGeometryUtils: .mergeBufferGeometries() failed with geometry at index " + + i + + ". The geometry must have either an index or a position attribute", + ); + return null; + } + + mergedGeometry.addGroup(offset, count, i); + + offset += count; + } + } + + // merge indices + + if (isIndexed) { + let indexOffset = 0; + const mergedIndex = []; + + for (let i = 0; i < geometries.length; ++i) { + const index = geometries[i].index; + + for (let j = 0; j < index.count; ++j) { + mergedIndex.push(index.getX(j) + indexOffset); + } + + indexOffset += geometries[i].attributes.position.count; + } + + mergedGeometry.setIndex(mergedIndex); + } + + // merge attributes + + for (const name in attributes) { + const mergedAttribute = mergeBufferAttributes(attributes[name]); + + if (!mergedAttribute) { + console.error( + "THREE.BufferGeometryUtils: .mergeBufferGeometries() failed while trying to merge the " + + name + + " attribute.", + ); + return null; + } + + mergedGeometry.setAttribute(name, mergedAttribute); + } + + // merge morph attributes + + for (const name in morphAttributes) { + const numMorphTargets = morphAttributes[name][0].length; + + if (numMorphTargets === 0) break; + + mergedGeometry.morphAttributes = mergedGeometry.morphAttributes || {}; + mergedGeometry.morphAttributes[name] = []; + + for (let i = 0; i < numMorphTargets; ++i) { + const morphAttributesToMerge = []; + + for (let j = 0; j < morphAttributes[name].length; ++j) { + morphAttributesToMerge.push(morphAttributes[name][j][i]); + } + + const mergedMorphAttribute = mergeBufferAttributes(morphAttributesToMerge); + + if (!mergedMorphAttribute) { + console.error( + "THREE.BufferGeometryUtils: .mergeBufferGeometries() failed while trying to merge the " + + name + + " morphAttribute.", + ); + return null; + } + + mergedGeometry.morphAttributes[name].push(mergedMorphAttribute); + } + } + + return mergedGeometry; +} + +/** + * @param {Array} attributes + * @return {BufferAttribute} + */ +function mergeBufferAttributes(attributes) { + let TypedArray; + let itemSize; + let normalized; + let arrayLength = 0; + + for (let i = 0; i < attributes.length; ++i) { + const attribute = attributes[i]; + + if (attribute.isInterleavedBufferAttribute) { + console.error( + "THREE.BufferGeometryUtils: .mergeBufferAttributes() failed. InterleavedBufferAttributes are not supported.", + ); + return null; + } + + if (TypedArray === undefined) TypedArray = attribute.array.constructor; + if (TypedArray !== attribute.array.constructor) { + console.error( + "THREE.BufferGeometryUtils: .mergeBufferAttributes() failed. BufferAttribute.array must be of consistent array types across matching attributes.", + ); + return null; + } + + if (itemSize === undefined) itemSize = attribute.itemSize; + if (itemSize !== attribute.itemSize) { + console.error( + "THREE.BufferGeometryUtils: .mergeBufferAttributes() failed. BufferAttribute.itemSize must be consistent across matching attributes.", + ); + return null; + } + + if (normalized === undefined) normalized = attribute.normalized; + if (normalized !== attribute.normalized) { + console.error( + "THREE.BufferGeometryUtils: .mergeBufferAttributes() failed. BufferAttribute.normalized must be consistent across matching attributes.", + ); + return null; + } + + arrayLength += attribute.array.length; + } + + const array = new TypedArray(arrayLength); + let offset = 0; + + for (let i = 0; i < attributes.length; ++i) { + array.set(attributes[i].array, offset); + + offset += attributes[i].array.length; + } + + return new BufferAttribute(array, itemSize, normalized); +} + +/** + * @param {Array} attributes + * @return {Array} + */ +function interleaveAttributes(attributes) { + // Interleaves the provided attributes into an InterleavedBuffer and returns + // a set of InterleavedBufferAttributes for each attribute + let TypedArray; + let arrayLength = 0; + let stride = 0; + + // calculate the the length and type of the interleavedBuffer + for (let i = 0, l = attributes.length; i < l; ++i) { + const attribute = attributes[i]; + + if (TypedArray === undefined) TypedArray = attribute.array.constructor; + if (TypedArray !== attribute.array.constructor) { + console.error("AttributeBuffers of different types cannot be interleaved"); + return null; + } + + arrayLength += attribute.array.length; + stride += attribute.itemSize; + } + + // Create the set of buffer attributes + const interleavedBuffer = new InterleavedBuffer(new TypedArray(arrayLength), stride); + let offset = 0; + const res = []; + const getters = ["getX", "getY", "getZ", "getW"]; + const setters = ["setX", "setY", "setZ", "setW"]; + + for (let j = 0, l = attributes.length; j < l; j++) { + const attribute = attributes[j]; + const itemSize = attribute.itemSize; + const count = attribute.count; + const iba = new InterleavedBufferAttribute( + interleavedBuffer, + itemSize, + offset, + attribute.normalized, + ); + res.push(iba); + + offset += itemSize; + + // Move the data for each attribute into the new interleavedBuffer + // at the appropriate offset + for (let c = 0; c < count; c++) { + for (let k = 0; k < itemSize; k++) { + iba[setters[k]](c, attribute[getters[k]](c)); + } + } + } + + return res; +} + +/** + * @param {Array} geometry + * @return {number} + */ +function estimateBytesUsed(geometry) { + // Return the estimated memory used by this geometry in bytes + // Calculate using itemSize, count, and BYTES_PER_ELEMENT to account + // for InterleavedBufferAttributes. + let mem = 0; + for (const name in geometry.attributes) { + const attr = geometry.getAttribute(name); + mem += attr.count * attr.itemSize * attr.array.BYTES_PER_ELEMENT; + } + + const indices = geometry.getIndex(); + mem += indices ? indices.count * indices.itemSize * indices.array.BYTES_PER_ELEMENT : 0; + return mem; +} + +/** + * @param {BufferGeometry} geometry + * @param {number} tolerance + * @return {BufferGeometry>} + */ +function mergeVertices(geometry, tolerance = 1e-4) { + tolerance = Math.max(tolerance, Number.EPSILON); + + // Generate an index buffer if the geometry doesn't have one, or optimize it + // if it's already available. + const hashToIndex = {}; + const indices = geometry.getIndex(); + const positions = geometry.getAttribute("position"); + const vertexCount = indices ? indices.count : positions.count; + + // next value for triangle indices + let nextIndex = 0; + + // attributes and new attribute arrays + const attributeNames = Object.keys(geometry.attributes); + const attrArrays = {}; + const morphAttrsArrays = {}; + const newIndices = []; + const getters = ["getX", "getY", "getZ", "getW"]; + + // initialize the arrays + for (let i = 0, l = attributeNames.length; i < l; i++) { + const name = attributeNames[i]; + + attrArrays[name] = []; + + const morphAttr = geometry.morphAttributes[name]; + if (morphAttr) { + morphAttrsArrays[name] = new Array(morphAttr.length).fill().map(() => []); + } + } + + // convert the error tolerance to an amount of decimal places to truncate to + const decimalShift = Math.log10(1 / tolerance); + const shiftMultiplier = Math.pow(10, decimalShift); + for (let i = 0; i < vertexCount; i++) { + const index = indices ? indices.getX(i) : i; + + // Generate a hash for the vertex attributes at the current index 'i' + let hash = ""; + for (let j = 0, l = attributeNames.length; j < l; j++) { + const name = attributeNames[j]; + const attribute = geometry.getAttribute(name); + const itemSize = attribute.itemSize; + + for (let k = 0; k < itemSize; k++) { + // double tilde truncates the decimal value + hash += `${~~(attribute[getters[k]](index) * shiftMultiplier)},`; + } + } + + // Add another reference to the vertex if it's already + // used by another index + if (hash in hashToIndex) { + newIndices.push(hashToIndex[hash]); + } else { + // copy data to the new index in the attribute arrays + for (let j = 0, l = attributeNames.length; j < l; j++) { + const name = attributeNames[j]; + const attribute = geometry.getAttribute(name); + const morphAttr = geometry.morphAttributes[name]; + const itemSize = attribute.itemSize; + const newarray = attrArrays[name]; + const newMorphArrays = morphAttrsArrays[name]; + + for (let k = 0; k < itemSize; k++) { + const getterFunc = getters[k]; + newarray.push(attribute[getterFunc](index)); + + if (morphAttr) { + for (let m = 0, ml = morphAttr.length; m < ml; m++) { + newMorphArrays[m].push(morphAttr[m][getterFunc](index)); + } + } + } + } + + hashToIndex[hash] = nextIndex; + newIndices.push(nextIndex); + nextIndex++; + } + } + + // Generate typed arrays from new attribute arrays and update + // the attributeBuffers + const result = geometry.clone(); + for (let i = 0, l = attributeNames.length; i < l; i++) { + const name = attributeNames[i]; + const oldAttribute = geometry.getAttribute(name); + + const buffer = new oldAttribute.array.constructor(attrArrays[name]); + const attribute = new BufferAttribute(buffer, oldAttribute.itemSize, oldAttribute.normalized); + + result.setAttribute(name, attribute); + + // Update the attribute arrays + if (name in morphAttrsArrays) { + for (let j = 0; j < morphAttrsArrays[name].length; j++) { + const oldMorphAttribute = geometry.morphAttributes[name][j]; + + const buffer = new oldMorphAttribute.array.constructor(morphAttrsArrays[name][j]); + const morphAttribute = new BufferAttribute( + buffer, + oldMorphAttribute.itemSize, + oldMorphAttribute.normalized, + ); + result.morphAttributes[name][j] = morphAttribute; + } + } + } + + // indices + + result.setIndex(newIndices); + + return result; +} + +/** + * @param {BufferGeometry} geometry + * @param {number} drawMode + * @return {BufferGeometry>} + */ +function toTrianglesDrawMode(geometry, drawMode) { + if (drawMode === TrianglesDrawMode) { + console.warn( + "THREE.BufferGeometryUtils.toTrianglesDrawMode(): Geometry already defined as triangles.", + ); + return geometry; + } + + if (drawMode === TriangleFanDrawMode || drawMode === TriangleStripDrawMode) { + let index = geometry.getIndex(); + + // generate index if not present + + if (index === null) { + const indices = []; + + const position = geometry.getAttribute("position"); + + if (position !== undefined) { + for (let i = 0; i < position.count; i++) { + indices.push(i); + } + + geometry.setIndex(indices); + index = geometry.getIndex(); + } else { + console.error( + "THREE.BufferGeometryUtils.toTrianglesDrawMode(): Undefined position attribute. Processing not possible.", + ); + return geometry; + } + } + + // + + const numberOfTriangles = index.count - 2; + const newIndices = []; + + if (drawMode === TriangleFanDrawMode) { + // gl.TRIANGLE_FAN + + for (let i = 1; i <= numberOfTriangles; i++) { + newIndices.push(index.getX(0)); + newIndices.push(index.getX(i)); + newIndices.push(index.getX(i + 1)); + } + } else { + // gl.TRIANGLE_STRIP + + for (let i = 0; i < numberOfTriangles; i++) { + if (i % 2 === 0) { + newIndices.push(index.getX(i)); + newIndices.push(index.getX(i + 1)); + newIndices.push(index.getX(i + 2)); + } else { + newIndices.push(index.getX(i + 2)); + newIndices.push(index.getX(i + 1)); + newIndices.push(index.getX(i)); + } + } + } + + if (newIndices.length / 3 !== numberOfTriangles) { + console.error( + "THREE.BufferGeometryUtils.toTrianglesDrawMode(): Unable to generate correct amount of triangles.", + ); + } + + // build final geometry + + const newGeometry = geometry.clone(); + newGeometry.setIndex(newIndices); + newGeometry.clearGroups(); + + return newGeometry; + } else { + console.error("THREE.BufferGeometryUtils.toTrianglesDrawMode(): Unknown draw mode:", drawMode); + return geometry; + } +} + +/** + * Calculates the morphed attributes of a morphed/skinned BufferGeometry. + * Helpful for Raytracing or Decals. + * @param {Mesh | Line | Points} object An instance of Mesh, Line or Points. + * @return {Object} An Object with original position/normal attributes and morphed ones. + */ +function computeMorphedAttributes(object) { + if (object.geometry.isBufferGeometry !== true) { + console.error("THREE.BufferGeometryUtils: Geometry is not of type BufferGeometry."); + return null; + } + + const _vA = new Vector3(); + const _vB = new Vector3(); + const _vC = new Vector3(); + + const _tempA = new Vector3(); + const _tempB = new Vector3(); + const _tempC = new Vector3(); + + const _morphA = new Vector3(); + const _morphB = new Vector3(); + const _morphC = new Vector3(); + + function _calculateMorphedAttributeData( + object, + material, + attribute, + morphAttribute, + morphTargetsRelative, + a, + b, + c, + modifiedAttributeArray, + ) { + _vA.fromBufferAttribute(attribute, a); + _vB.fromBufferAttribute(attribute, b); + _vC.fromBufferAttribute(attribute, c); + + const morphInfluences = object.morphTargetInfluences; + + if (material.morphTargets && morphAttribute && morphInfluences) { + _morphA.set(0, 0, 0); + _morphB.set(0, 0, 0); + _morphC.set(0, 0, 0); + + for (let i = 0, il = morphAttribute.length; i < il; i++) { + const influence = morphInfluences[i]; + const morph = morphAttribute[i]; + + if (influence === 0) continue; + + _tempA.fromBufferAttribute(morph, a); + _tempB.fromBufferAttribute(morph, b); + _tempC.fromBufferAttribute(morph, c); + + if (morphTargetsRelative) { + _morphA.addScaledVector(_tempA, influence); + _morphB.addScaledVector(_tempB, influence); + _morphC.addScaledVector(_tempC, influence); + } else { + _morphA.addScaledVector(_tempA.sub(_vA), influence); + _morphB.addScaledVector(_tempB.sub(_vB), influence); + _morphC.addScaledVector(_tempC.sub(_vC), influence); + } + } + + _vA.add(_morphA); + _vB.add(_morphB); + _vC.add(_morphC); + } + + if (object.isSkinnedMesh) { + object.boneTransform(a, _vA); + object.boneTransform(b, _vB); + object.boneTransform(c, _vC); + } + + modifiedAttributeArray[a * 3 + 0] = _vA.x; + modifiedAttributeArray[a * 3 + 1] = _vA.y; + modifiedAttributeArray[a * 3 + 2] = _vA.z; + modifiedAttributeArray[b * 3 + 0] = _vB.x; + modifiedAttributeArray[b * 3 + 1] = _vB.y; + modifiedAttributeArray[b * 3 + 2] = _vB.z; + modifiedAttributeArray[c * 3 + 0] = _vC.x; + modifiedAttributeArray[c * 3 + 1] = _vC.y; + modifiedAttributeArray[c * 3 + 2] = _vC.z; + } + + const geometry = object.geometry; + const material = object.material; + + let a, b, c; + const index = geometry.index; + const positionAttribute = geometry.attributes.position; + const morphPosition = geometry.morphAttributes.position; + const morphTargetsRelative = geometry.morphTargetsRelative; + const normalAttribute = geometry.attributes.normal; + const morphNormal = geometry.morphAttributes.position; + + const groups = geometry.groups; + const drawRange = geometry.drawRange; + let i, j, il, jl; + let group, groupMaterial; + let start, end; + + const modifiedPosition = new Float32Array(positionAttribute.count * positionAttribute.itemSize); + const modifiedNormal = new Float32Array(normalAttribute.count * normalAttribute.itemSize); + + if (index !== null) { + // indexed buffer geometry + + if (Array.isArray(material)) { + for (i = 0, il = groups.length; i < il; i++) { + group = groups[i]; + groupMaterial = material[group.materialIndex]; + + start = Math.max(group.start, drawRange.start); + end = Math.min(group.start + group.count, drawRange.start + drawRange.count); + + for (j = start, jl = end; j < jl; j += 3) { + a = index.getX(j); + b = index.getX(j + 1); + c = index.getX(j + 2); + + _calculateMorphedAttributeData( + object, + groupMaterial, + positionAttribute, + morphPosition, + morphTargetsRelative, + a, + b, + c, + modifiedPosition, + ); + + _calculateMorphedAttributeData( + object, + groupMaterial, + normalAttribute, + morphNormal, + morphTargetsRelative, + a, + b, + c, + modifiedNormal, + ); + } + } + } else { + start = Math.max(0, drawRange.start); + end = Math.min(index.count, drawRange.start + drawRange.count); + + for (i = start, il = end; i < il; i += 3) { + a = index.getX(i); + b = index.getX(i + 1); + c = index.getX(i + 2); + + _calculateMorphedAttributeData( + object, + material, + positionAttribute, + morphPosition, + morphTargetsRelative, + a, + b, + c, + modifiedPosition, + ); + + _calculateMorphedAttributeData( + object, + material, + normalAttribute, + morphNormal, + morphTargetsRelative, + a, + b, + c, + modifiedNormal, + ); + } + } + } else if (positionAttribute !== undefined) { + // non-indexed buffer geometry + + if (Array.isArray(material)) { + for (i = 0, il = groups.length; i < il; i++) { + group = groups[i]; + groupMaterial = material[group.materialIndex]; + + start = Math.max(group.start, drawRange.start); + end = Math.min(group.start + group.count, drawRange.start + drawRange.count); + + for (j = start, jl = end; j < jl; j += 3) { + a = j; + b = j + 1; + c = j + 2; + + _calculateMorphedAttributeData( + object, + groupMaterial, + positionAttribute, + morphPosition, + morphTargetsRelative, + a, + b, + c, + modifiedPosition, + ); + + _calculateMorphedAttributeData( + object, + groupMaterial, + normalAttribute, + morphNormal, + morphTargetsRelative, + a, + b, + c, + modifiedNormal, + ); + } + } + } else { + start = Math.max(0, drawRange.start); + end = Math.min(positionAttribute.count, drawRange.start + drawRange.count); + + for (i = start, il = end; i < il; i += 3) { + a = i; + b = i + 1; + c = i + 2; + + _calculateMorphedAttributeData( + object, + material, + positionAttribute, + morphPosition, + morphTargetsRelative, + a, + b, + c, + modifiedPosition, + ); + + _calculateMorphedAttributeData( + object, + material, + normalAttribute, + morphNormal, + morphTargetsRelative, + a, + b, + c, + modifiedNormal, + ); + } + } + } + + const morphedPositionAttribute = new Float32BufferAttribute(modifiedPosition, 3); + const morphedNormalAttribute = new Float32BufferAttribute(modifiedNormal, 3); + + return { + positionAttribute: positionAttribute, + normalAttribute: normalAttribute, + morphedPositionAttribute: morphedPositionAttribute, + morphedNormalAttribute: morphedNormalAttribute, + }; +} + +export { + computeTangents, + mergeBufferGeometries, + mergeBufferAttributes, + interleaveAttributes, + estimateBytesUsed, + mergeVertices, + toTrianglesDrawMode, + computeMorphedAttributes, +}; diff --git a/frontend/javascripts/libs/DRACOLoader.ts b/frontend/javascripts/libs/DRACOLoader.ts new file mode 100644 index 00000000000..5ddac61fa87 --- /dev/null +++ b/frontend/javascripts/libs/DRACOLoader.ts @@ -0,0 +1,470 @@ +// @ts-nocheck +// Copied from node_modules/three/examples/jsm/loaders/DRACOLoader.js to fix ERR_REQUIRE_ESM error. +import { BufferAttribute, BufferGeometry, FileLoader, Loader } from "three"; + +const _taskCache = new WeakMap(); + +class DRACOLoader extends Loader { + constructor(manager) { + super(manager); + + this.decoderPath = ""; + this.decoderConfig = {}; + this.decoderBinary = null; + this.decoderPending = null; + + this.workerLimit = 4; + this.workerPool = []; + this.workerNextTaskID = 1; + this.workerSourceURL = ""; + + this.defaultAttributeIDs = { + position: "POSITION", + normal: "NORMAL", + color: "COLOR", + uv: "TEX_COORD", + }; + this.defaultAttributeTypes = { + position: "Float32Array", + normal: "Float32Array", + color: "Float32Array", + uv: "Float32Array", + }; + } + + setDecoderPath(path) { + this.decoderPath = path; + + return this; + } + + setDecoderConfig(config) { + this.decoderConfig = config; + + return this; + } + + setWorkerLimit(workerLimit) { + this.workerLimit = workerLimit; + + return this; + } + + load(url, onLoad, onProgress, onError) { + const loader = new FileLoader(this.manager); + + loader.setPath(this.path); + loader.setResponseType("arraybuffer"); + loader.setRequestHeader(this.requestHeader); + loader.setWithCredentials(this.withCredentials); + + loader.load( + url, + (buffer) => { + const taskConfig = { + attributeIDs: this.defaultAttributeIDs, + attributeTypes: this.defaultAttributeTypes, + useUniqueIDs: false, + }; + + this.decodeGeometry(buffer, taskConfig).then(onLoad).catch(onError); + }, + onProgress, + onError, + ); + } + + /** @deprecated Kept for backward-compatibility with previous DRACOLoader versions. */ + decodeDracoFile(buffer, callback, attributeIDs, attributeTypes) { + const taskConfig = { + attributeIDs: attributeIDs || this.defaultAttributeIDs, + attributeTypes: attributeTypes || this.defaultAttributeTypes, + useUniqueIDs: !!attributeIDs, + }; + + this.decodeGeometry(buffer, taskConfig).then(callback); + } + + decodeGeometry(buffer, taskConfig) { + // TODO: For backward-compatibility, support 'attributeTypes' objects containing + // references (rather than names) to typed array constructors. These must be + // serialized before sending them to the worker. + for (const attribute in taskConfig.attributeTypes) { + const type = taskConfig.attributeTypes[attribute]; + + if (type.BYTES_PER_ELEMENT !== undefined) { + taskConfig.attributeTypes[attribute] = type.name; + } + } + + // + + const taskKey = JSON.stringify(taskConfig); + + // Check for an existing task using this buffer. A transferred buffer cannot be transferred + // again from this thread. + if (_taskCache.has(buffer)) { + const cachedTask = _taskCache.get(buffer); + + if (cachedTask.key === taskKey) { + return cachedTask.promise; + } else if (buffer.byteLength === 0) { + // Technically, it would be possible to wait for the previous task to complete, + // transfer the buffer back, and decode again with the second configuration. That + // is complex, and I don't know of any reason to decode a Draco buffer twice in + // different ways, so this is left unimplemented. + throw new Error( + "THREE.DRACOLoader: Unable to re-decode a buffer with different " + + "settings. Buffer has already been transferred.", + ); + } + } + + // + + let worker; + const taskID = this.workerNextTaskID++; + const taskCost = buffer.byteLength; + + // Obtain a worker and assign a task, and construct a geometry instance + // when the task completes. + const geometryPending = this._getWorker(taskID, taskCost) + .then((_worker) => { + worker = _worker; + + return new Promise((resolve, reject) => { + worker._callbacks[taskID] = { resolve, reject }; + + worker.postMessage({ type: "decode", id: taskID, taskConfig, buffer }, [buffer]); + + // this.debug(); + }); + }) + .then((message) => this._createGeometry(message.geometry)); + + // Remove task from the task list. + // Note: replaced '.finally()' with '.catch().then()' block - iOS 11 support (#19416) + geometryPending + .catch(() => true) + .then(() => { + if (worker && taskID) { + this._releaseTask(worker, taskID); + + // this.debug(); + } + }); + + // Cache the task result. + _taskCache.set(buffer, { + key: taskKey, + promise: geometryPending, + }); + + return geometryPending; + } + + _createGeometry(geometryData) { + const geometry = new BufferGeometry(); + + if (geometryData.index) { + geometry.setIndex(new BufferAttribute(geometryData.index.array, 1)); + } + + for (let i = 0; i < geometryData.attributes.length; i++) { + const attribute = geometryData.attributes[i]; + const name = attribute.name; + const array = attribute.array; + const itemSize = attribute.itemSize; + + geometry.setAttribute(name, new BufferAttribute(array, itemSize)); + } + + return geometry; + } + + _loadLibrary(url, responseType) { + const loader = new FileLoader(this.manager); + loader.setPath(this.decoderPath); + loader.setResponseType(responseType); + loader.setWithCredentials(this.withCredentials); + + return new Promise((resolve, reject) => { + loader.load(url, resolve, undefined, reject); + }); + } + + preload() { + this._initDecoder(); + + return this; + } + + _initDecoder() { + if (this.decoderPending) return this.decoderPending; + + const useJS = typeof WebAssembly !== "object" || this.decoderConfig.type === "js"; + const librariesPending = []; + + if (useJS) { + librariesPending.push(this._loadLibrary("draco_decoder.js", "text")); + } else { + librariesPending.push(this._loadLibrary("draco_wasm_wrapper.js", "text")); + librariesPending.push(this._loadLibrary("draco_decoder.wasm", "arraybuffer")); + } + + this.decoderPending = Promise.all(librariesPending).then((libraries) => { + const jsContent = libraries[0]; + + if (!useJS) { + this.decoderConfig.wasmBinary = libraries[1]; + } + + const fn = DRACOWorker.toString(); + + const body = [ + "/* draco decoder */", + jsContent, + "", + "/* worker */", + fn.substring(fn.indexOf("{") + 1, fn.lastIndexOf("}")), + ].join("\n"); + + this.workerSourceURL = URL.createObjectURL(new Blob([body])); + }); + + return this.decoderPending; + } + + _getWorker(taskID, taskCost) { + return this._initDecoder().then(() => { + if (this.workerPool.length < this.workerLimit) { + const worker = new Worker(this.workerSourceURL); + + worker._callbacks = {}; + worker._taskCosts = {}; + worker._taskLoad = 0; + + worker.postMessage({ type: "init", decoderConfig: this.decoderConfig }); + + worker.onmessage = function (e) { + const message = e.data; + + switch (message.type) { + case "decode": + worker._callbacks[message.id].resolve(message); + break; + + case "error": + worker._callbacks[message.id].reject(message); + break; + + default: + console.error('THREE.DRACOLoader: Unexpected message, "' + message.type + '"'); + } + }; + + this.workerPool.push(worker); + } else { + this.workerPool.sort(function (a, b) { + return a._taskLoad > b._taskLoad ? -1 : 1; + }); + } + + const worker = this.workerPool[this.workerPool.length - 1]; + worker._taskCosts[taskID] = taskCost; + worker._taskLoad += taskCost; + return worker; + }); + } + + _releaseTask(worker, taskID) { + worker._taskLoad -= worker._taskCosts[taskID]; + delete worker._callbacks[taskID]; + delete worker._taskCosts[taskID]; + } + + debug() { + console.log( + "Task load: ", + this.workerPool.map((worker) => worker._taskLoad), + ); + } + + dispose() { + for (let i = 0; i < this.workerPool.length; ++i) { + this.workerPool[i].terminate(); + } + + this.workerPool.length = 0; + + return this; + } +} + +/* WEB WORKER */ + +function DRACOWorker() { + let decoderConfig; + let decoderPending; + + onmessage = function (e) { + const message = e.data; + + switch (message.type) { + case "init": + decoderConfig = message.decoderConfig; + decoderPending = new Promise(function (resolve /*, reject*/) { + decoderConfig.onModuleLoaded = function (draco) { + // Module is Promise-like. Wrap before resolving to avoid loop. + resolve({ draco: draco }); + }; + + DracoDecoderModule(decoderConfig); // eslint-disable-line no-undef + }); + break; + + case "decode": + const buffer = message.buffer; + const taskConfig = message.taskConfig; + decoderPending.then((module) => { + const draco = module.draco; + const decoder = new draco.Decoder(); + const decoderBuffer = new draco.DecoderBuffer(); + decoderBuffer.Init(new Int8Array(buffer), buffer.byteLength); + + try { + const geometry = decodeGeometry(draco, decoder, decoderBuffer, taskConfig); + + const buffers = geometry.attributes.map((attr) => attr.array.buffer); + + if (geometry.index) buffers.push(geometry.index.array.buffer); + + self.postMessage({ type: "decode", id: message.id, geometry }, buffers); + } catch (error) { + console.error(error); + + self.postMessage({ type: "error", id: message.id, error: error.message }); + } finally { + draco.destroy(decoderBuffer); + draco.destroy(decoder); + } + }); + break; + } + }; + + function decodeGeometry(draco, decoder, decoderBuffer, taskConfig) { + const attributeIDs = taskConfig.attributeIDs; + const attributeTypes = taskConfig.attributeTypes; + + let dracoGeometry; + let decodingStatus; + + const geometryType = decoder.GetEncodedGeometryType(decoderBuffer); + + if (geometryType === draco.TRIANGULAR_MESH) { + dracoGeometry = new draco.Mesh(); + decodingStatus = decoder.DecodeBufferToMesh(decoderBuffer, dracoGeometry); + } else if (geometryType === draco.POINT_CLOUD) { + dracoGeometry = new draco.PointCloud(); + decodingStatus = decoder.DecodeBufferToPointCloud(decoderBuffer, dracoGeometry); + } else { + throw new Error("THREE.DRACOLoader: Unexpected geometry type."); + } + + if (!decodingStatus.ok() || dracoGeometry.ptr === 0) { + throw new Error("THREE.DRACOLoader: Decoding failed: " + decodingStatus.error_msg()); + } + + const geometry = { index: null, attributes: [] }; + + // Gather all vertex attributes. + for (const attributeName in attributeIDs) { + const attributeType = self[attributeTypes[attributeName]]; + + let attribute; + let attributeID; + + // A Draco file may be created with default vertex attributes, whose attribute IDs + // are mapped 1:1 from their semantic name (POSITION, NORMAL, ...). Alternatively, + // a Draco file may contain a custom set of attributes, identified by known unique + // IDs. glTF files always do the latter, and `.drc` files typically do the former. + if (taskConfig.useUniqueIDs) { + attributeID = attributeIDs[attributeName]; + attribute = decoder.GetAttributeByUniqueId(dracoGeometry, attributeID); + } else { + attributeID = decoder.GetAttributeId(dracoGeometry, draco[attributeIDs[attributeName]]); + + if (attributeID === -1) continue; + + attribute = decoder.GetAttribute(dracoGeometry, attributeID); + } + + geometry.attributes.push( + decodeAttribute(draco, decoder, dracoGeometry, attributeName, attributeType, attribute), + ); + } + + // Add index. + if (geometryType === draco.TRIANGULAR_MESH) { + geometry.index = decodeIndex(draco, decoder, dracoGeometry); + } + + draco.destroy(dracoGeometry); + + return geometry; + } + + function decodeIndex(draco, decoder, dracoGeometry) { + const numFaces = dracoGeometry.num_faces(); + const numIndices = numFaces * 3; + const byteLength = numIndices * 4; + + const ptr = draco._malloc(byteLength); + decoder.GetTrianglesUInt32Array(dracoGeometry, byteLength, ptr); + const index = new Uint32Array(draco.HEAPF32.buffer, ptr, numIndices).slice(); + draco._free(ptr); + + return { array: index, itemSize: 1 }; + } + + function decodeAttribute(draco, decoder, dracoGeometry, attributeName, attributeType, attribute) { + const numComponents = attribute.num_components(); + const numPoints = dracoGeometry.num_points(); + const numValues = numPoints * numComponents; + const byteLength = numValues * attributeType.BYTES_PER_ELEMENT; + const dataType = getDracoDataType(draco, attributeType); + + const ptr = draco._malloc(byteLength); + decoder.GetAttributeDataArrayForAllPoints(dracoGeometry, attribute, dataType, byteLength, ptr); + const array = new attributeType(draco.HEAPF32.buffer, ptr, numValues).slice(); + draco._free(ptr); + + return { + name: attributeName, + array: array, + itemSize: numComponents, + }; + } + + function getDracoDataType(draco, attributeType) { + switch (attributeType) { + case Float32Array: + return draco.DT_FLOAT32; + case Int8Array: + return draco.DT_INT8; + case Int16Array: + return draco.DT_INT16; + case Int32Array: + return draco.DT_INT32; + case Uint8Array: + return draco.DT_UINT8; + case Uint16Array: + return draco.DT_UINT16; + case Uint32Array: + return draco.DT_UINT32; + } + } +} + +export { DRACOLoader }; diff --git a/frontend/javascripts/libs/draco.ts b/frontend/javascripts/libs/draco.ts index f464f632db5..09cd247b177 100644 --- a/frontend/javascripts/libs/draco.ts +++ b/frontend/javascripts/libs/draco.ts @@ -1,5 +1,5 @@ import { BufferGeometry } from "three"; -import { DRACOLoader } from "three/examples/jsm/loaders/DRACOLoader.js"; +import { DRACOLoader } from "libs/DRACOLoader.js"; let _dracoLoader: CustomDRACOLoader | null; @@ -19,6 +19,7 @@ export function getDracoLoader(): CustomDRACOLoader { if (_dracoLoader) { return _dracoLoader; } + // @ts-ignore _dracoLoader = new CustomDRACOLoader(); _dracoLoader.setDecoderPath( diff --git a/frontend/javascripts/oxalis/controller/scene_controller.ts b/frontend/javascripts/oxalis/controller/scene_controller.ts index 386e435e701..418a8fe1b8a 100644 --- a/frontend/javascripts/oxalis/controller/scene_controller.ts +++ b/frontend/javascripts/oxalis/controller/scene_controller.ts @@ -39,7 +39,7 @@ import constants, { import window from "libs/window"; import { setSceneController } from "oxalis/controller/scene_controller_provider"; import { getSegmentColorAsHSL } from "oxalis/model/accessors/volumetracing_accessor"; -import { mergeVertices } from "three/examples/jsm/utils/BufferGeometryUtils.js"; +import { mergeVertices } from "libs/BufferGeometryUtils"; const CUBE_COLOR = 0x999999; diff --git a/frontend/javascripts/oxalis/model/sagas/isosurface_saga.ts b/frontend/javascripts/oxalis/model/sagas/isosurface_saga.ts index a07078d7610..262ea1587cb 100644 --- a/frontend/javascripts/oxalis/model/sagas/isosurface_saga.ts +++ b/frontend/javascripts/oxalis/model/sagas/isosurface_saga.ts @@ -4,7 +4,7 @@ import { V3 } from "libs/mjs"; import { sleep } from "libs/utils"; import ErrorHandling from "libs/error_handling"; import type { APIDataLayer } from "types/api_flow_types"; -import { mergeVertices } from "three/examples/jsm/utils/BufferGeometryUtils.js"; +import { mergeVertices } from "libs/BufferGeometryUtils"; import { ResolutionInfo, From 616bf50269ac08bc5eeb6c657161fe12bcf85b0f Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Tue, 4 Oct 2022 09:32:36 +0200 Subject: [PATCH 46/63] fix linting --- frontend/javascripts/libs/BufferGeometryUtils.ts | 2 ++ frontend/javascripts/libs/DRACOLoader.ts | 3 +++ 2 files changed, 5 insertions(+) diff --git a/frontend/javascripts/libs/BufferGeometryUtils.ts b/frontend/javascripts/libs/BufferGeometryUtils.ts index 7b51c73a324..f379d5ed519 100644 --- a/frontend/javascripts/libs/BufferGeometryUtils.ts +++ b/frontend/javascripts/libs/BufferGeometryUtils.ts @@ -1,4 +1,6 @@ // @ts-nocheck +/* eslint-disable eslint-comments/no-unlimited-disable */ +/* eslint-disable */ // Copied from three/examples/js/utils/BufferGeometryUtils.js to fix ERR_REQUIRE_ESM error. import { BufferAttribute, diff --git a/frontend/javascripts/libs/DRACOLoader.ts b/frontend/javascripts/libs/DRACOLoader.ts index 5ddac61fa87..dc6b8dd7e31 100644 --- a/frontend/javascripts/libs/DRACOLoader.ts +++ b/frontend/javascripts/libs/DRACOLoader.ts @@ -1,4 +1,7 @@ // @ts-nocheck +/* eslint-disable eslint-comments/no-unlimited-disable */ +/* eslint-disable eslint-comments/no-unused-disable */ +/* eslint-disable */ // Copied from node_modules/three/examples/jsm/loaders/DRACOLoader.js to fix ERR_REQUIRE_ESM error. import { BufferAttribute, BufferGeometry, FileLoader, Loader } from "three"; From 0c95492a08c6c9534bd0a2a1a240553422cbf6cf Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Tue, 4 Oct 2022 10:11:19 +0200 Subject: [PATCH 47/63] fix import --- frontend/javascripts/libs/draco.ts | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/frontend/javascripts/libs/draco.ts b/frontend/javascripts/libs/draco.ts index 09cd247b177..27531720e5c 100644 --- a/frontend/javascripts/libs/draco.ts +++ b/frontend/javascripts/libs/draco.ts @@ -1,5 +1,5 @@ import { BufferGeometry } from "three"; -import { DRACOLoader } from "libs/DRACOLoader.js"; +import { DRACOLoader } from "libs/DRACOLoader"; let _dracoLoader: CustomDRACOLoader | null; From 45182257c0e85ec154d1971766ee63c7ea0e9b3d Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Tue, 4 Oct 2022 10:45:07 +0200 Subject: [PATCH 48/63] fix linting --- frontend/javascripts/libs/DRACOLoader.ts | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/frontend/javascripts/libs/DRACOLoader.ts b/frontend/javascripts/libs/DRACOLoader.ts index dc6b8dd7e31..cfbd3ff285c 100644 --- a/frontend/javascripts/libs/DRACOLoader.ts +++ b/frontend/javascripts/libs/DRACOLoader.ts @@ -1,6 +1,5 @@ // @ts-nocheck /* eslint-disable eslint-comments/no-unlimited-disable */ -/* eslint-disable eslint-comments/no-unused-disable */ /* eslint-disable */ // Copied from node_modules/three/examples/jsm/loaders/DRACOLoader.js to fix ERR_REQUIRE_ESM error. import { BufferAttribute, BufferGeometry, FileLoader, Loader } from "three"; @@ -322,7 +321,7 @@ function DRACOWorker() { resolve({ draco: draco }); }; - DracoDecoderModule(decoderConfig); // eslint-disable-line no-undef + DracoDecoderModule(decoderConfig); }); break; From 126f2ccfa4cb868a6f6618f74289fe03d25a544e Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Tue, 4 Oct 2022 16:41:41 +0200 Subject: [PATCH 49/63] fix error when sharing link with meshes --- .../oxalis/model/sagas/isosurface_saga.ts | 20 +++++++++++++------ 1 file changed, 14 insertions(+), 6 deletions(-) diff --git a/frontend/javascripts/oxalis/model/sagas/isosurface_saga.ts b/frontend/javascripts/oxalis/model/sagas/isosurface_saga.ts index 262ea1587cb..76dba7eb710 100644 --- a/frontend/javascripts/oxalis/model/sagas/isosurface_saga.ts +++ b/frontend/javascripts/oxalis/model/sagas/isosurface_saga.ts @@ -56,7 +56,10 @@ import Toast from "libs/toast"; import { getDracoLoader } from "libs/draco"; import messages from "messages"; import processTaskWithPool from "libs/task_pool"; -import { getBaseSegmentationName } from "oxalis/view/right-border-tabs/segments_tab/segments_view_helper"; +import { + getBaseSegmentationName, + maybeFetchMeshFiles, +} from "oxalis/view/right-border-tabs/segments_tab/segments_view_helper"; import { UpdateSegmentAction } from "../actions/volumetracing_actions"; const MAX_RETRY_COUNT = 5; @@ -548,13 +551,18 @@ function* loadPrecomputedMeshForSegmentId( let availableChunks = null; - const meshFile = yield* select((state) => - (state.localSegmentationData[layerName].availableMeshFiles || []).find( - (file) => file.meshFileName === meshFileName, - ), + const availableMeshFiles = yield* call( + maybeFetchMeshFiles, + segmentationLayer, + dataset, + false, + false, ); + + const meshFile = availableMeshFiles.find((file) => file.meshFileName === meshFileName); if (!meshFile) { - throw new Error("Could not find requested mesh file."); + Toast.error("Could not load mesh, since the requested mesh file was not found."); + return; } const version = meshFile.formatVersion; From 9e4bd5447d5264b04abff1412d9676e86194fcb5 Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Tue, 4 Oct 2022 17:06:33 +0200 Subject: [PATCH 50/63] refactor maybeFetchMeshFiles to be a saga --- frontend/javascripts/oxalis/api/api_latest.ts | 10 ++- .../model/actions/annotation_actions.ts | 42 +++++++++++++ .../oxalis/model/sagas/isosurface_saga.ts | 61 ++++++++++++++++--- .../javascripts/oxalis/view/context_menu.tsx | 10 +-- .../segments_tab/segments_view.tsx | 34 ++++++++--- .../segments_tab/segments_view_helper.tsx | 36 ----------- 6 files changed, 132 insertions(+), 61 deletions(-) diff --git a/frontend/javascripts/oxalis/api/api_latest.ts b/frontend/javascripts/oxalis/api/api_latest.ts index c2762f3df2c..24ee26839d2 100644 --- a/frontend/javascripts/oxalis/api/api_latest.ts +++ b/frontend/javascripts/oxalis/api/api_latest.ts @@ -83,7 +83,6 @@ import { loadPrecomputedMeshAction, } from "oxalis/model/actions/segmentation_actions"; import { loadAgglomerateSkeletonForSegmentId } from "oxalis/controller/combinations/segmentation_handlers"; -import { maybeFetchMeshFiles } from "oxalis/view/right-border-tabs/segments_tab/segments_view_helper"; import { overwriteAction } from "oxalis/model/helpers/overwrite_action_middleware"; import { parseNml } from "oxalis/model/helpers/nml_helpers"; import { rotate3DViewTo } from "oxalis/controller/camera_controller"; @@ -95,6 +94,7 @@ import { refreshIsosurfacesAction, updateIsosurfaceVisibilityAction, removeIsosurfaceAction, + dispatchMaybeFetchMeshFilesAsync, } from "oxalis/model/actions/annotation_actions"; import { updateUserSettingAction, @@ -1733,7 +1733,13 @@ class DataApi { const state = Store.getState(); const { dataset } = state; - const meshFiles = await maybeFetchMeshFiles(effectiveLayer, dataset, true, false); + const meshFiles = await dispatchMaybeFetchMeshFilesAsync( + Store.dispatch, + effectiveLayer, + dataset, + true, + false, + ); return meshFiles.map((meshFile) => meshFile.meshFileName); } diff --git a/frontend/javascripts/oxalis/model/actions/annotation_actions.ts b/frontend/javascripts/oxalis/model/actions/annotation_actions.ts index ca6546fe6ba..20716be25c1 100644 --- a/frontend/javascripts/oxalis/model/actions/annotation_actions.ts +++ b/frontend/javascripts/oxalis/model/actions/annotation_actions.ts @@ -1,6 +1,8 @@ import type { APIAnnotation, APIAnnotationVisibility, + APIDataLayer, + APIDataset, APIMeshFile, EditableLayerProperties, LocalMeshMetaData, @@ -14,6 +16,9 @@ import type { UserBoundingBoxWithoutIdMaybe, } from "oxalis/store"; import type { Vector3 } from "oxalis/constants"; +import _ from "lodash"; +import { Dispatch } from "redux"; +import Deferred from "libs/deferred"; type InitializeAnnotationAction = ReturnType; type SetAnnotationNameAction = ReturnType; @@ -35,6 +40,7 @@ export type UpdateIsosurfaceVisibilityAction = ReturnType; export type DeleteMeshAction = ReturnType; export type CreateMeshFromBufferAction = ReturnType; +export type MaybeFetchMeshFilesAction = ReturnType; export type TriggerIsosurfaceDownloadAction = ReturnType; export type RefreshIsosurfacesAction = ReturnType; export type RefreshIsosurfaceAction = ReturnType; @@ -67,6 +73,7 @@ export type AnnotationActionTypes = | AddMeshMetadataAction | DeleteMeshAction | CreateMeshFromBufferAction + | MaybeFetchMeshFilesAction | UpdateLocalMeshMetaDataAction | UpdateIsosurfaceVisibilityAction | TriggerIsosurfaceDownloadAction @@ -228,6 +235,22 @@ export const createMeshFromBufferAction = (name: string, buffer: ArrayBuffer) => name, } as const); +export const maybeFetchMeshFilesAction = ( + segmentationLayer: APIDataLayer | null | undefined, + dataset: APIDataset, + mustRequest: boolean, + autoActivate: boolean = true, + callback: (meshes: Array) => void = _.noop, +) => + ({ + type: "MAYBE_FETCH_MESH_FILES", + segmentationLayer, + dataset, + mustRequest, + autoActivate, + callback, + } as const); + export const triggerIsosurfaceDownloadAction = (cellName: string, cellId: number) => ({ type: "TRIGGER_ISOSURFACE_DOWNLOAD", @@ -327,3 +350,22 @@ export const setOthersMayEditForAnnotationAction = (othersMayEdit: boolean) => type: "SET_OTHERS_MAY_EDIT_FOR_ANNOTATION", othersMayEdit, } as const); + +export const dispatchMaybeFetchMeshFilesAsync = async ( + dispatch: Dispatch, + segmentationLayer: APIDataLayer | null | undefined, + dataset: APIDataset, + mustRequest: boolean, + autoActivate: boolean = true, +): Promise> => { + const readyDeferred = new Deferred(); + const action = maybeFetchMeshFilesAction( + segmentationLayer, + dataset, + mustRequest, + autoActivate, + (meshes) => readyDeferred.resolve(meshes), + ); + dispatch(action); + return await readyDeferred.promise(); +}; diff --git a/frontend/javascripts/oxalis/model/sagas/isosurface_saga.ts b/frontend/javascripts/oxalis/model/sagas/isosurface_saga.ts index 76dba7eb710..2566f501934 100644 --- a/frontend/javascripts/oxalis/model/sagas/isosurface_saga.ts +++ b/frontend/javascripts/oxalis/model/sagas/isosurface_saga.ts @@ -6,6 +6,7 @@ import ErrorHandling from "libs/error_handling"; import type { APIDataLayer } from "types/api_flow_types"; import { mergeVertices } from "libs/BufferGeometryUtils"; +import Store from "oxalis/store"; import { ResolutionInfo, getResolutionInfo, @@ -21,12 +22,16 @@ import type { import type { Action } from "oxalis/model/actions/actions"; import type { Vector3 } from "oxalis/constants"; import { MappingStatusEnum } from "oxalis/constants"; -import type { +import { ImportIsosurfaceFromStlAction, UpdateIsosurfaceVisibilityAction, RemoveIsosurfaceAction, RefreshIsosurfaceAction, TriggerIsosurfaceDownloadAction, + MaybeFetchMeshFilesAction, + updateMeshFileListAction, + updateCurrentMeshFileAction, + dispatchMaybeFetchMeshFilesAsync, } from "oxalis/model/actions/annotation_actions"; import { removeIsosurfaceAction, @@ -39,7 +44,13 @@ import type { Saga } from "oxalis/model/sagas/effect-generators"; import { select } from "oxalis/model/sagas/effect-generators"; import { actionChannel, takeEvery, call, take, race, put } from "typed-redux-saga"; import { stlIsosurfaceConstants } from "oxalis/view/right-border-tabs/segments_tab/segments_view"; -import { computeIsosurface, sendAnalyticsEvent, meshV0, meshV3 } from "admin/admin_rest_api"; +import { + computeIsosurface, + sendAnalyticsEvent, + meshV0, + meshV3, + getMeshfilesForDatasetLayer, +} from "admin/admin_rest_api"; import { getFlooredPosition } from "oxalis/model/accessors/flycam_accessor"; import { setImportingMeshStateAction } from "oxalis/model/actions/ui_actions"; import { zoomedAddressToAnotherZoomStepWithInfo } from "oxalis/model/helpers/position_converter"; @@ -56,10 +67,7 @@ import Toast from "libs/toast"; import { getDracoLoader } from "libs/draco"; import messages from "messages"; import processTaskWithPool from "libs/task_pool"; -import { - getBaseSegmentationName, - maybeFetchMeshFiles, -} from "oxalis/view/right-border-tabs/segments_tab/segments_view_helper"; +import { getBaseSegmentationName } from "oxalis/view/right-border-tabs/segments_tab/segments_view_helper"; import { UpdateSegmentAction } from "../actions/volumetracing_actions"; const MAX_RETRY_COUNT = 5; @@ -508,6 +516,43 @@ function* _refreshIsosurfaceWithMap( * Precomputed Meshes * */ + +function* maybeFetchMeshFiles(action: MaybeFetchMeshFilesAction): Saga { + const { segmentationLayer, dataset, mustRequest, autoActivate, callback } = action; + + if (!segmentationLayer) { + callback([]); + return; + } + + const layerName = segmentationLayer.name; + const files = yield* select((state) => state.localSegmentationData[layerName].availableMeshFiles); + + // Only send new get request, if it hasn't happened before (files in store are null) + // else return the stored files (might be empty array). Or if we force a reload. + if (!files || mustRequest) { + const availableMeshFiles = yield* call( + getMeshfilesForDatasetLayer, + dataset.dataStore.url, + dataset, + getBaseSegmentationName(segmentationLayer), + ); + yield* put(updateMeshFileListAction(layerName, availableMeshFiles)); + + const currentMeshFile = yield* select( + (state) => state.localSegmentationData[layerName].currentMeshFile, + ); + if (!currentMeshFile && availableMeshFiles.length > 0 && autoActivate) { + yield* put(updateCurrentMeshFileAction(layerName, availableMeshFiles[0].meshFileName)); + } + + callback(availableMeshFiles); + return; + } + + callback(files); +} + function* loadPrecomputedMesh(action: LoadPrecomputedMeshAction) { const { cellId, seedPosition, meshFileName, layerName } = action; const layer = yield* select((state) => @@ -552,7 +597,8 @@ function* loadPrecomputedMeshForSegmentId( let availableChunks = null; const availableMeshFiles = yield* call( - maybeFetchMeshFiles, + dispatchMaybeFetchMeshFilesAsync, + Store.dispatch, segmentationLayer, dataset, false, @@ -750,6 +796,7 @@ export default function* isosurfaceSaga(): Saga { const loadPrecomputedMeshActionChannel = yield* actionChannel("LOAD_PRECOMPUTED_MESH_ACTION"); yield* take("SCENE_CONTROLLER_READY"); yield* take("WK_READY"); + yield* takeEvery("MAYBE_FETCH_MESH_FILES", maybeFetchMeshFiles); yield* takeEvery(loadAdHocMeshActionChannel, loadAdHocIsosurfaceFromAction); yield* takeEvery(loadPrecomputedMeshActionChannel, loadPrecomputedMesh); yield* takeEvery("TRIGGER_ISOSURFACE_DOWNLOAD", downloadIsosurfaceCell); diff --git a/frontend/javascripts/oxalis/view/context_menu.tsx b/frontend/javascripts/oxalis/view/context_menu.tsx index 517d6ea5cf1..53f2308bce1 100644 --- a/frontend/javascripts/oxalis/view/context_menu.tsx +++ b/frontend/javascripts/oxalis/view/context_menu.tsx @@ -35,6 +35,7 @@ import { addUserBoundingBoxAction, deleteUserBoundingBoxAction, changeUserBoundingBoxAction, + maybeFetchMeshFilesAction, } from "oxalis/model/actions/annotation_actions"; import { deleteEdgeAction, @@ -66,10 +67,7 @@ import { loadSynapsesOfAgglomerateAtPosition, } from "oxalis/controller/combinations/segmentation_handlers"; import { isBoundingBoxUsableForMinCut } from "oxalis/model/sagas/min_cut_saga"; -import { - maybeFetchMeshFiles, - withMappingActivationConfirmation, -} from "oxalis/view/right-border-tabs/segments_tab/segments_view_helper"; +import { withMappingActivationConfirmation } from "oxalis/view/right-border-tabs/segments_tab/segments_view_helper"; import { maybeGetSomeTracing } from "oxalis/model/accessors/tracing_accessor"; import { performMinCutAction, @@ -679,9 +677,7 @@ function NoNodeContextMenuOptions(props: NoNodeContextMenuProps): JSX.Element { const isConnectomeMappingEnabled = useSelector(hasConnectomeFile); useEffect(() => { - (async () => { - await maybeFetchMeshFiles(visibleSegmentationLayer, dataset, false); - })(); + dispatch(maybeFetchMeshFilesAction(visibleSegmentationLayer, dataset, false)); }, [visibleSegmentationLayer, dataset]); const loadPrecomputedMesh = async () => { diff --git a/frontend/javascripts/oxalis/view/right-border-tabs/segments_tab/segments_view.tsx b/frontend/javascripts/oxalis/view/right-border-tabs/segments_tab/segments_view.tsx index 40412e120f8..fb84aea48e3 100644 --- a/frontend/javascripts/oxalis/view/right-border-tabs/segments_tab/segments_view.tsx +++ b/frontend/javascripts/oxalis/view/right-border-tabs/segments_tab/segments_view.tsx @@ -12,7 +12,10 @@ import { loadAdHocMeshAction, loadPrecomputedMeshAction, } from "oxalis/model/actions/segmentation_actions"; -import { updateCurrentMeshFileAction } from "oxalis/model/actions/annotation_actions"; +import { + maybeFetchMeshFilesAction, + updateCurrentMeshFileAction, +} from "oxalis/model/actions/annotation_actions"; import { getActiveSegmentationTracing, getVisibleSegments, @@ -25,10 +28,7 @@ import { getMappingInfo, ResolutionInfo, } from "oxalis/model/accessors/dataset_accessor"; -import { - maybeFetchMeshFiles, - getBaseSegmentationName, -} from "oxalis/view/right-border-tabs/segments_tab/segments_view_helper"; +import { getBaseSegmentationName } from "oxalis/view/right-border-tabs/segments_tab/segments_view_helper"; import { setPositionAction } from "oxalis/model/actions/flycam_actions"; import { startComputeMeshFileJob, getJobs } from "admin/admin_rest_api"; import { updateTemporarySettingAction } from "oxalis/model/actions/settings_actions"; @@ -211,7 +211,9 @@ class SegmentsView extends React.Component { }; componentDidMount() { - maybeFetchMeshFiles(this.props.visibleSegmentationLayer, this.props.dataset, false); + Store.dispatch( + maybeFetchMeshFilesAction(this.props.visibleSegmentationLayer, this.props.dataset, false), + ); if (features().jobsEnabled) { this.pollJobData(); @@ -220,7 +222,9 @@ class SegmentsView extends React.Component { componentDidUpdate(prevProps: Props) { if (prevProps.visibleSegmentationLayer !== this.props.visibleSegmentationLayer) { - maybeFetchMeshFiles(this.props.visibleSegmentationLayer, this.props.dataset, false); + Store.dispatch( + maybeFetchMeshFilesAction(this.props.visibleSegmentationLayer, this.props.dataset, false), + ); } } @@ -251,7 +255,13 @@ class SegmentsView extends React.Component { }); // maybeFetchMeshFiles will fetch the new mesh file and also activate it if no other mesh file // currently exists. - maybeFetchMeshFiles(this.props.visibleSegmentationLayer, this.props.dataset, true); + Store.dispatch( + maybeFetchMeshFilesAction( + this.props.visibleSegmentationLayer, + this.props.dataset, + true, + ), + ); break; } @@ -558,7 +568,13 @@ class SegmentsView extends React.Component { - maybeFetchMeshFiles(this.props.visibleSegmentationLayer, this.props.dataset, true) + Store.dispatch( + maybeFetchMeshFilesAction( + this.props.visibleSegmentationLayer, + this.props.dataset, + true, + ), + ) } style={{ marginLeft: 8, diff --git a/frontend/javascripts/oxalis/view/right-border-tabs/segments_tab/segments_view_helper.tsx b/frontend/javascripts/oxalis/view/right-border-tabs/segments_tab/segments_view_helper.tsx index 721a109ae4c..d79450b3164 100644 --- a/frontend/javascripts/oxalis/view/right-border-tabs/segments_tab/segments_view_helper.tsx +++ b/frontend/javascripts/oxalis/view/right-border-tabs/segments_tab/segments_view_helper.tsx @@ -20,42 +20,6 @@ export function getBaseSegmentationName(segmentationLayer: APIDataLayer) { // @ts-expect-error ts-migrate(2339) FIXME: Property 'fallbackLayer' does not exist on type 'A... Remove this comment to see the full error message return segmentationLayer.fallbackLayer || segmentationLayer.name; } -export async function maybeFetchMeshFiles( - segmentationLayer: APIDataLayer | null | undefined, - dataset: APIDataset, - mustRequest: boolean, - autoActivate: boolean = true, -): Promise> { - if (!segmentationLayer) { - return []; - } - - const layerName = segmentationLayer.name; - const files = Store.getState().localSegmentationData[layerName].availableMeshFiles; - - // Only send new get request, if it hasn't happened before (files in store are null) - // else return the stored files (might be empty array). Or if we force a reload. - if (!files || mustRequest) { - const availableMeshFiles = await getMeshfilesForDatasetLayer( - dataset.dataStore.url, - dataset, - getBaseSegmentationName(segmentationLayer), - ); - Store.dispatch(updateMeshFileListAction(layerName, availableMeshFiles)); - - if ( - !Store.getState().localSegmentationData[layerName].currentMeshFile && - availableMeshFiles.length > 0 && - autoActivate - ) { - Store.dispatch(updateCurrentMeshFileAction(layerName, availableMeshFiles[0].meshFileName)); - } - - return availableMeshFiles; - } - - return files; -} type MappingActivationConfirmationProps = R & { mappingName: string | null | undefined; From e658ada307a387b3beafabccb740c63f0caf21bf Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Tue, 4 Oct 2022 17:36:57 +0200 Subject: [PATCH 51/63] avoid redundant fetches of mesh files for the same layer --- .../model/actions/annotation_actions.ts | 2 +- .../oxalis/model/sagas/isosurface_saga.ts | 40 ++++++++++++++----- .../segments_tab/segments_view_helper.tsx | 7 +--- 3 files changed, 33 insertions(+), 16 deletions(-) diff --git a/frontend/javascripts/oxalis/model/actions/annotation_actions.ts b/frontend/javascripts/oxalis/model/actions/annotation_actions.ts index 20716be25c1..409eddd9778 100644 --- a/frontend/javascripts/oxalis/model/actions/annotation_actions.ts +++ b/frontend/javascripts/oxalis/model/actions/annotation_actions.ts @@ -367,5 +367,5 @@ export const dispatchMaybeFetchMeshFilesAsync = async ( (meshes) => readyDeferred.resolve(meshes), ); dispatch(action); - return await readyDeferred.promise(); + return readyDeferred.promise(); }; diff --git a/frontend/javascripts/oxalis/model/sagas/isosurface_saga.ts b/frontend/javascripts/oxalis/model/sagas/isosurface_saga.ts index 2566f501934..84a1500556b 100644 --- a/frontend/javascripts/oxalis/model/sagas/isosurface_saga.ts +++ b/frontend/javascripts/oxalis/model/sagas/isosurface_saga.ts @@ -3,8 +3,9 @@ import _ from "lodash"; import { V3 } from "libs/mjs"; import { sleep } from "libs/utils"; import ErrorHandling from "libs/error_handling"; -import type { APIDataLayer } from "types/api_flow_types"; +import type { APIDataLayer, APIMeshFile } from "types/api_flow_types"; import { mergeVertices } from "libs/BufferGeometryUtils"; +import Deferred from "libs/deferred"; import Store from "oxalis/store"; import { @@ -32,8 +33,6 @@ import { updateMeshFileListAction, updateCurrentMeshFileAction, dispatchMaybeFetchMeshFilesAsync, -} from "oxalis/model/actions/annotation_actions"; -import { removeIsosurfaceAction, addAdHocIsosurfaceAction, addPrecomputedIsosurfaceAction, @@ -517,6 +516,9 @@ function* _refreshIsosurfaceWithMap( * */ +// Avoid redundant fetches of mesh files for the same layer by +// storing Deferreds per layer lazily. +const fetchDeferredsPerLayer: Record, unknown>> = {}; function* maybeFetchMeshFiles(action: MaybeFetchMeshFilesAction): Saga { const { segmentationLayer, dataset, mustRequest, autoActivate, callback } = action; @@ -526,6 +528,30 @@ function* maybeFetchMeshFiles(action: MaybeFetchMeshFilesAction): Saga { } const layerName = segmentationLayer.name; + + function* maybeActivateMeshFile(availableMeshFiles: APIMeshFile[]) { + const currentMeshFile = yield* select( + (state) => state.localSegmentationData[layerName].currentMeshFile, + ); + if (!currentMeshFile && availableMeshFiles.length > 0 && autoActivate) { + yield* put(updateCurrentMeshFileAction(layerName, availableMeshFiles[0].meshFileName)); + } + } + + // If a deferred already exists, the one can be awaited (regardless of + // whether it's finished or not) and its content used to call the callback. + // If mustRequest was set to true, a new deferred will be created which + // replaces the old one (old references to the first Deferred will still + // work and will be resolved by the corresponding saga execution). + if (fetchDeferredsPerLayer[layerName] && !mustRequest) { + const meshes = yield* call(() => fetchDeferredsPerLayer[layerName].promise()); + yield* maybeActivateMeshFile(meshes); + callback(meshes); + return; + } + const deferred = new Deferred, unknown>(); + fetchDeferredsPerLayer[layerName] = deferred; + const files = yield* select((state) => state.localSegmentationData[layerName].availableMeshFiles); // Only send new get request, if it hasn't happened before (files in store are null) @@ -538,13 +564,9 @@ function* maybeFetchMeshFiles(action: MaybeFetchMeshFilesAction): Saga { getBaseSegmentationName(segmentationLayer), ); yield* put(updateMeshFileListAction(layerName, availableMeshFiles)); + deferred.resolve(availableMeshFiles); - const currentMeshFile = yield* select( - (state) => state.localSegmentationData[layerName].currentMeshFile, - ); - if (!currentMeshFile && availableMeshFiles.length > 0 && autoActivate) { - yield* put(updateCurrentMeshFileAction(layerName, availableMeshFiles[0].meshFileName)); - } + yield* maybeActivateMeshFile(availableMeshFiles); callback(availableMeshFiles); return; diff --git a/frontend/javascripts/oxalis/view/right-border-tabs/segments_tab/segments_view_helper.tsx b/frontend/javascripts/oxalis/view/right-border-tabs/segments_tab/segments_view_helper.tsx index d79450b3164..2ccf7659df9 100644 --- a/frontend/javascripts/oxalis/view/right-border-tabs/segments_tab/segments_view_helper.tsx +++ b/frontend/javascripts/oxalis/view/right-border-tabs/segments_tab/segments_view_helper.tsx @@ -1,14 +1,9 @@ import type { ComponentType } from "react"; import React from "react"; import { Modal } from "antd"; -import { getMeshfilesForDatasetLayer } from "admin/admin_rest_api"; -import type { APIDataset, APIDataLayer, APIMeshFile } from "types/api_flow_types"; +import type { APIDataLayer } from "types/api_flow_types"; import type { ActiveMappingInfo } from "oxalis/store"; import Store from "oxalis/store"; -import { - updateMeshFileListAction, - updateCurrentMeshFileAction, -} from "oxalis/model/actions/annotation_actions"; import { MappingStatusEnum } from "oxalis/constants"; import { setMappingAction, setMappingEnabledAction } from "oxalis/model/actions/settings_actions"; import { waitForCondition } from "libs/utils"; From 286325bfd34103604e17f4d612b8a0769b8978c5 Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Tue, 4 Oct 2022 19:06:54 +0200 Subject: [PATCH 52/63] add draco decoder wasm to repo and use that instead of depending on github --- frontend/javascripts/libs/draco.ts | 4 +- public/wasm/draco_decoder.wasm | Bin 0 -> 281481 bytes public/wasm/draco_wasm_wrapper.js | 104 +++++++++++++++++++++++++++++ 3 files changed, 105 insertions(+), 3 deletions(-) create mode 100644 public/wasm/draco_decoder.wasm create mode 100644 public/wasm/draco_wasm_wrapper.js diff --git a/frontend/javascripts/libs/draco.ts b/frontend/javascripts/libs/draco.ts index 27531720e5c..65189d2f57b 100644 --- a/frontend/javascripts/libs/draco.ts +++ b/frontend/javascripts/libs/draco.ts @@ -22,9 +22,7 @@ export function getDracoLoader(): CustomDRACOLoader { // @ts-ignore _dracoLoader = new CustomDRACOLoader(); - _dracoLoader.setDecoderPath( - "https://raw.githubusercontent.com/mrdoob/three.js/r145/examples/js/libs/draco/", - ); + _dracoLoader.setDecoderPath("/assets/wasm/"); _dracoLoader.setDecoderConfig({ type: "wasm" }); // The loader could theoretically be disposed like this: // _dracoLoader.dispose(); diff --git a/public/wasm/draco_decoder.wasm b/public/wasm/draco_decoder.wasm new file mode 100644 index 0000000000000000000000000000000000000000..3f0ba9ce8ee46caf5822a61235c9c271b79c9fdd GIT binary patch literal 281481 zcmeFa3xHi$UGKm5+IyclGiN3_Ndtr?-0pMCg%nx|w6+!MHM>pQggz460M(2CX=nq@ zOq%B;g0`8cpa?!dK|u@ldeLfW6?ut>S`d+os8uPVq82Ou8C*k*=yXa{>HP>HOZ`f<$?bm zT@&#p<*7>8XLLXscM`q(A*Nj*RHJ#2LIl@QzfWmZq zgbznS56?}Zno%?2X?cEbadfoD`XRbf6_j{sj;(K-+ z+%)FPiuzxypv7GW_U@THxa)g&9-Msf z&Y39gFVQMX*gHXx?Reqd12a)e-ygs8hJ)80*tKtF=bp&}JJrbK^*eX$^PoPi_VR|E 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a.asm.dynCall_iiiiiii.apply(null,arguments)};a.dynCall_iidiiii=function(){return a.asm.dynCall_iidiiii.apply(null,arguments)};a.dynCall_jiji=function(){return a.asm.dynCall_jiji.apply(null,arguments)};a.dynCall_viiiiii=function(){return a.asm.dynCall_viiiiii.apply(null,arguments)};a.dynCall_viiiii=function(){return a.asm.dynCall_viiiii.apply(null,arguments)};a.asm=La;var fa;a.then=function(e){if(fa)e(a); +else{var c=a.onRuntimeInitialized;a.onRuntimeInitialized=function(){c&&c();e(a)}}return a};ja=function c(){fa||ma();fa||(ja=c)};a.run=ma;if(a.preInit)for("function"==typeof a.preInit&&(a.preInit=[a.preInit]);0=n.size?(t(0>=1;break;case 4:d>>=2;break;case 8:d>>=3}for(var c=0;c Date: Wed, 5 Oct 2022 10:54:39 +0200 Subject: [PATCH 53/63] integrate some PR feedback --- frontend/javascripts/oxalis/model/sagas/isosurface_saga.ts | 6 +++--- public/wasm/draco_wasm_wrapper.js | 1 + 2 files changed, 4 insertions(+), 3 deletions(-) diff --git a/frontend/javascripts/oxalis/model/sagas/isosurface_saga.ts b/frontend/javascripts/oxalis/model/sagas/isosurface_saga.ts index 84a1500556b..8e04453dead 100644 --- a/frontend/javascripts/oxalis/model/sagas/isosurface_saga.ts +++ b/frontend/javascripts/oxalis/model/sagas/isosurface_saga.ts @@ -544,9 +544,9 @@ function* maybeFetchMeshFiles(action: MaybeFetchMeshFilesAction): Saga { // replaces the old one (old references to the first Deferred will still // work and will be resolved by the corresponding saga execution). if (fetchDeferredsPerLayer[layerName] && !mustRequest) { - const meshes = yield* call(() => fetchDeferredsPerLayer[layerName].promise()); - yield* maybeActivateMeshFile(meshes); - callback(meshes); + const availableMeshFiles = yield* call(() => fetchDeferredsPerLayer[layerName].promise()); + yield* maybeActivateMeshFile(availableMeshFiles); + callback(availableMeshFiles); return; } const deferred = new Deferred, unknown>(); diff --git a/public/wasm/draco_wasm_wrapper.js b/public/wasm/draco_wasm_wrapper.js index d12278ef53e..60a3b94fdda 100644 --- a/public/wasm/draco_wasm_wrapper.js +++ b/public/wasm/draco_wasm_wrapper.js @@ -1,3 +1,4 @@ +// copied from node_modules/three/examples/js/libs/draco/ var $jscomp=$jscomp||{};$jscomp.scope={};$jscomp.arrayIteratorImpl=function(f){var m=0;return function(){return m Date: Wed, 5 Oct 2022 11:37:16 +0200 Subject: [PATCH 54/63] simplify maybeFetchMeshFiles saga --- .../oxalis/model/sagas/isosurface_saga.ts | 42 ++++++++----------- 1 file changed, 18 insertions(+), 24 deletions(-) diff --git a/frontend/javascripts/oxalis/model/sagas/isosurface_saga.ts b/frontend/javascripts/oxalis/model/sagas/isosurface_saga.ts index 8e04453dead..3fefa8d5527 100644 --- a/frontend/javascripts/oxalis/model/sagas/isosurface_saga.ts +++ b/frontend/javascripts/oxalis/model/sagas/isosurface_saga.ts @@ -538,41 +538,35 @@ function* maybeFetchMeshFiles(action: MaybeFetchMeshFilesAction): Saga { } } - // If a deferred already exists, the one can be awaited (regardless of - // whether it's finished or not) and its content used to call the callback. - // If mustRequest was set to true, a new deferred will be created which - // replaces the old one (old references to the first Deferred will still - // work and will be resolved by the corresponding saga execution). + // If a deferred already exists (and mustRequest is not true), the deferred + // can be awaited (regardless of whether it's finished or not) and its + // content used to call the callback. if (fetchDeferredsPerLayer[layerName] && !mustRequest) { const availableMeshFiles = yield* call(() => fetchDeferredsPerLayer[layerName].promise()); yield* maybeActivateMeshFile(availableMeshFiles); callback(availableMeshFiles); return; } + // A request has to be made (either because none was made before or because + // it is enforced by mustRequest). + // If mustRequest is true and an old deferred exists, a new deferred will be created which + // replaces the old one (old references to the first Deferred will still + // work and will be resolved by the corresponding saga execution). const deferred = new Deferred, unknown>(); fetchDeferredsPerLayer[layerName] = deferred; - const files = yield* select((state) => state.localSegmentationData[layerName].availableMeshFiles); - - // Only send new get request, if it hasn't happened before (files in store are null) - // else return the stored files (might be empty array). Or if we force a reload. - if (!files || mustRequest) { - const availableMeshFiles = yield* call( - getMeshfilesForDatasetLayer, - dataset.dataStore.url, - dataset, - getBaseSegmentationName(segmentationLayer), - ); - yield* put(updateMeshFileListAction(layerName, availableMeshFiles)); - deferred.resolve(availableMeshFiles); - - yield* maybeActivateMeshFile(availableMeshFiles); + const availableMeshFiles = yield* call( + getMeshfilesForDatasetLayer, + dataset.dataStore.url, + dataset, + getBaseSegmentationName(segmentationLayer), + ); + yield* put(updateMeshFileListAction(layerName, availableMeshFiles)); + deferred.resolve(availableMeshFiles); - callback(availableMeshFiles); - return; - } + yield* maybeActivateMeshFile(availableMeshFiles); - callback(files); + callback(availableMeshFiles); } function* loadPrecomputedMesh(action: LoadPrecomputedMeshAction) { From fb33b560d4f3c6e66b5ec31c1146bb9a490b2784 Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Wed, 5 Oct 2022 14:04:56 +0200 Subject: [PATCH 55/63] clean up version handling --- .../javascripts/oxalis/model/sagas/isosurface_saga.ts | 9 ++++++--- frontend/javascripts/types/api_flow_types.ts | 4 ++-- 2 files changed, 8 insertions(+), 5 deletions(-) diff --git a/frontend/javascripts/oxalis/model/sagas/isosurface_saga.ts b/frontend/javascripts/oxalis/model/sagas/isosurface_saga.ts index 3fefa8d5527..62e89f99218 100644 --- a/frontend/javascripts/oxalis/model/sagas/isosurface_saga.ts +++ b/frontend/javascripts/oxalis/model/sagas/isosurface_saga.ts @@ -629,9 +629,7 @@ function* loadPrecomputedMeshForSegmentId( const version = meshFile.formatVersion; try { - // todo: should actually check against 3, but some new mesh files - // still have version 2 ? - if (version >= 2) { + if (version >= 3) { const segmentInfo = yield* call( meshV3.getMeshfileChunksForSegment, dataset.dataStore.url, @@ -641,6 +639,11 @@ function* loadPrecomputedMeshForSegmentId( id, ); availableChunks = _.first(segmentInfo.chunks.lods)?.chunks || []; + } else if (version > 0) { + Toast.error( + `Mesh file with invalid version found (version=${version}). Recompute the mesh file.`, + ); + return; } else { availableChunks = yield* call( meshV0.getMeshfileChunksForSegment, diff --git a/frontend/javascripts/types/api_flow_types.ts b/frontend/javascripts/types/api_flow_types.ts index 8754552544d..d9eb8e495ab 100644 --- a/frontend/javascripts/types/api_flow_types.ts +++ b/frontend/javascripts/types/api_flow_types.ts @@ -694,8 +694,8 @@ export type APIMeshFile = { meshFileName: string; mappingName?: string | null | undefined; // 0 - is the first mesh file version - // 1-2 - skipped for consistency with VX artifact versioning - // 3 - (some artifacts might have used 2, too) is the newer version with draco encoding. + // 1-2 - skipped/not used for consistency with VX artifact versioning + // 3 - is the newer version with draco encoding. formatVersion: number; }; export type APIConnectomeFile = { From e8902f5a564f9bb03c4679bd4fdfd48dff6bd851 Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Wed, 5 Oct 2022 15:14:11 +0200 Subject: [PATCH 56/63] read artifact_schema_version from mesh files instead of version property (the latter won't exist for newer mesh files, as it was redundant) --- .../webknossos/datastore/services/MeshFileService.scala | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/webknossos-datastore/app/com/scalableminds/webknossos/datastore/services/MeshFileService.scala b/webknossos-datastore/app/com/scalableminds/webknossos/datastore/services/MeshFileService.scala index f9c4fea07db..e8806c048b3 100644 --- a/webknossos-datastore/app/com/scalableminds/webknossos/datastore/services/MeshFileService.scala +++ b/webknossos-datastore/app/com/scalableminds/webknossos/datastore/services/MeshFileService.scala @@ -211,7 +211,7 @@ class MeshFileService @Inject()(config: DataStoreConfig)(implicit ec: ExecutionC def mappingVersionForMeshFile(meshFilePath: Path): Long = executeWithCachedHdf5(meshFilePath, meshFileCache) { cachedMeshFile => - cachedMeshFile.reader.int64().getAttr("/", "version") + cachedMeshFile.reader.int64().getAttr("/", "artifact_schema_version") }.toOption.getOrElse(0) def listMeshChunksForSegmentV0(organizationName: String, From 122b1bd3b2115724a4cbb3075dba8936b366dd15 Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Wed, 5 Oct 2022 15:23:25 +0200 Subject: [PATCH 57/63] re-add support for v1 and v2 mesh files --- frontend/javascripts/oxalis/model/sagas/isosurface_saga.ts | 5 ----- frontend/javascripts/types/api_flow_types.ts | 2 +- 2 files changed, 1 insertion(+), 6 deletions(-) diff --git a/frontend/javascripts/oxalis/model/sagas/isosurface_saga.ts b/frontend/javascripts/oxalis/model/sagas/isosurface_saga.ts index 62e89f99218..8be037f49b1 100644 --- a/frontend/javascripts/oxalis/model/sagas/isosurface_saga.ts +++ b/frontend/javascripts/oxalis/model/sagas/isosurface_saga.ts @@ -639,11 +639,6 @@ function* loadPrecomputedMeshForSegmentId( id, ); availableChunks = _.first(segmentInfo.chunks.lods)?.chunks || []; - } else if (version > 0) { - Toast.error( - `Mesh file with invalid version found (version=${version}). Recompute the mesh file.`, - ); - return; } else { availableChunks = yield* call( meshV0.getMeshfileChunksForSegment, diff --git a/frontend/javascripts/types/api_flow_types.ts b/frontend/javascripts/types/api_flow_types.ts index d9eb8e495ab..cb6c5a59673 100644 --- a/frontend/javascripts/types/api_flow_types.ts +++ b/frontend/javascripts/types/api_flow_types.ts @@ -694,7 +694,7 @@ export type APIMeshFile = { meshFileName: string; mappingName?: string | null | undefined; // 0 - is the first mesh file version - // 1-2 - skipped/not used for consistency with VX artifact versioning + // 1-2 - the format should behave as v0 (refer to voxelytics for actual differences) // 3 - is the newer version with draco encoding. formatVersion: number; }; From 2c2e23a53dee992b3cfb1ca7b34123acd387a26e Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Wed, 5 Oct 2022 15:38:10 +0200 Subject: [PATCH 58/63] clean up lighting --- .../oxalis/controller/scene_controller.ts | 89 ++++++------------- 1 file changed, 28 insertions(+), 61 deletions(-) diff --git a/frontend/javascripts/oxalis/controller/scene_controller.ts b/frontend/javascripts/oxalis/controller/scene_controller.ts index 418a8fe1b8a..39af8ac1880 100644 --- a/frontend/javascripts/oxalis/controller/scene_controller.ts +++ b/frontend/javascripts/oxalis/controller/scene_controller.ts @@ -306,69 +306,36 @@ class SceneController { } addLights(): void { - // At the moment, we only attach an AmbientLight for the isosurfaces group. - // The PlaneView attaches a directional light directly to the TD camera, + // Note that the PlaneView also attaches a directional light directly to the TD camera, // so that the light moves along the cam. - // const ambientLightForIsosurfaces = new THREE.AmbientLight(0x404040, 15); // soft white light - // this.isosurfacesRootGroup.add(ambientLightForIsosurfaces); - - // const ambientLightForMeshes = new THREE.AmbientLight(0x404040, 5); // soft white light - // this.meshesRootGroup.add(ambientLightForMeshes); - - let unsubscribe = () => {}; - const testLights = (a: number, b: number, c: number, d: number) => { - unsubscribe(); - const ambientLight = new THREE.AmbientLight(2105376, a); - - const directionalLight = new THREE.DirectionalLight(16777215, b); - directionalLight.position.x = 1; - directionalLight.position.y = 1; - directionalLight.position.z = 1; - directionalLight.position.normalize(); - - // const max = 10000000000; - - const directionalLight2 = new THREE.DirectionalLight(16777215, c); - directionalLight2.position.x = -1; - directionalLight2.position.y = -1; - directionalLight2.position.z = -1; - directionalLight2.position.normalize(); - - const pointLight = new THREE.PointLight(16777215, d); - pointLight.position.x = 0; - pointLight.position.y = -25; - pointLight.position.z = 10; - - this.isosurfacesRootGroup.add(ambientLight); - this.isosurfacesRootGroup.add(directionalLight); - this.isosurfacesRootGroup.add(directionalLight2); - this.isosurfacesRootGroup.add(pointLight); - - unsubscribe = () => { - this.isosurfacesRootGroup.remove(ambientLight); - this.isosurfacesRootGroup.remove(directionalLight); - this.isosurfacesRootGroup.remove(directionalLight2); - this.isosurfacesRootGroup.remove(pointLight); - }; - }; - testLights(30, 5, 5, 5); - // @ts-ignore - window.testLights = testLights; - // directionalLight.position.x = 2 * max; - // directionalLight.position.y = 0; - // directionalLight.position.z = 2 * max; - // pointLight.position.x = max / 2; - // pointLight.position.y = max / 2; - // pointLight.position.z = 2 * max; - - // const light1 = new THREE.DirectionalLight(0xefefff, 12); - // light1.position.set(1, 1, 1).normalize(); - // this.isosurfacesRootGroup.add(light1); - - // const light2 = new THREE.DirectionalLight(0xffefef, 8); - // light2.position.set(-1, -1, -1).normalize(); - // this.isosurfacesRootGroup.add(light2); + const AMBIENT_INTENSITY = 30; + const DIRECTIONAL_INTENSITRY = 5; + const POINT_INTENSITY = 5; + + const ambientLight = new THREE.AmbientLight(2105376, AMBIENT_INTENSITY); + + const directionalLight = new THREE.DirectionalLight(16777215, DIRECTIONAL_INTENSITRY); + directionalLight.position.x = 1; + directionalLight.position.y = 1; + directionalLight.position.z = 1; + directionalLight.position.normalize(); + + const directionalLight2 = new THREE.DirectionalLight(16777215, DIRECTIONAL_INTENSITRY); + directionalLight2.position.x = -1; + directionalLight2.position.y = -1; + directionalLight2.position.z = -1; + directionalLight2.position.normalize(); + + const pointLight = new THREE.PointLight(16777215, POINT_INTENSITY); + pointLight.position.x = 0; + pointLight.position.y = -25; + pointLight.position.z = 10; + + this.isosurfacesRootGroup.add(ambientLight); + this.isosurfacesRootGroup.add(directionalLight); + this.isosurfacesRootGroup.add(directionalLight2); + this.isosurfacesRootGroup.add(pointLight); } removeSTL(id: string): void { From 378b29a957c6b20ff890df9d8a18f02c517289fb Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Wed, 5 Oct 2022 15:59:28 +0200 Subject: [PATCH 59/63] fix enabling of corresponding mesh file when loading meshes specified in sharing link --- .../javascripts/oxalis/model/sagas/isosurface_saga.ts | 4 +++- frontend/javascripts/oxalis/model_initialization.ts | 9 +++++++-- 2 files changed, 10 insertions(+), 3 deletions(-) diff --git a/frontend/javascripts/oxalis/model/sagas/isosurface_saga.ts b/frontend/javascripts/oxalis/model/sagas/isosurface_saga.ts index 8be037f49b1..ce65dec30bc 100644 --- a/frontend/javascripts/oxalis/model/sagas/isosurface_saga.ts +++ b/frontend/javascripts/oxalis/model/sagas/isosurface_saga.ts @@ -808,9 +808,11 @@ export default function* isosurfaceSaga(): Saga { // Buffer actions since they might be dispatched before WK_READY const loadAdHocMeshActionChannel = yield* actionChannel("LOAD_AD_HOC_MESH_ACTION"); const loadPrecomputedMeshActionChannel = yield* actionChannel("LOAD_PRECOMPUTED_MESH_ACTION"); + const maybeFetchMeshFilesActionChannel = yield* actionChannel("MAYBE_FETCH_MESH_FILES"); + yield* take("SCENE_CONTROLLER_READY"); yield* take("WK_READY"); - yield* takeEvery("MAYBE_FETCH_MESH_FILES", maybeFetchMeshFiles); + yield* takeEvery(maybeFetchMeshFilesActionChannel, maybeFetchMeshFiles); yield* takeEvery(loadAdHocMeshActionChannel, loadAdHocIsosurfaceFromAction); yield* takeEvery(loadPrecomputedMeshActionChannel, loadPrecomputedMesh); yield* takeEvery("TRIGGER_ISOSURFACE_DOWNLOAD", downloadIsosurfaceCell); diff --git a/frontend/javascripts/oxalis/model_initialization.ts b/frontend/javascripts/oxalis/model_initialization.ts index 2cce1012406..25a7d9aff4f 100644 --- a/frontend/javascripts/oxalis/model_initialization.ts +++ b/frontend/javascripts/oxalis/model_initialization.ts @@ -29,6 +29,7 @@ import { isSegmentationLayer, getSegmentationLayers, getSegmentationLayerByNameOrFallbackName, + getSegmentationLayerByName, } from "oxalis/model/accessors/dataset_accessor"; import { getNullableSkeletonTracing } from "oxalis/model/accessors/skeletontracing_accessor"; import { getServerVolumeTracings } from "oxalis/model/accessors/volumetracing_accessor"; @@ -45,6 +46,7 @@ import { getAnnotationCompoundInformation, } from "admin/admin_rest_api"; import { + dispatchMaybeFetchMeshFilesAsync, initializeAnnotationAction, updateCurrentMeshFileAction, } from "oxalis/model/actions/annotation_actions"; @@ -660,13 +662,13 @@ export function applyState(state: PartialUrlManagerState, ignoreZoom: boolean = } } -function applyLayerState(stateByLayer: UrlStateByLayer) { +async function applyLayerState(stateByLayer: UrlStateByLayer) { for (const layerName of Object.keys(stateByLayer)) { const layerState = stateByLayer[layerName]; let effectiveLayerName; + const { dataset } = Store.getState(); try { - const { dataset } = Store.getState(); // The name of the layer could have changed if a volume tracing was created from a viewed annotation effectiveLayerName = getSegmentationLayerByNameOrFallbackName(dataset, layerName).name; } catch (e) { @@ -715,6 +717,9 @@ function applyLayerState(stateByLayer: UrlStateByLayer) { const { meshFileName: currentMeshFileName, meshes } = layerState.meshInfo; if (currentMeshFileName != null) { + // ensure mesh files are loaded, so that the given mesh file name can be activated + const segmentationLayer = getSegmentationLayerByName(dataset, effectiveLayerName); + await dispatchMaybeFetchMeshFilesAsync(Store.dispatch, segmentationLayer, dataset, false); Store.dispatch(updateCurrentMeshFileAction(effectiveLayerName, currentMeshFileName)); } From 6ef6faf0baa24ae75f4ccf40b2be50091c6f1566 Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Wed, 5 Oct 2022 16:04:08 +0200 Subject: [PATCH 60/63] fix linting --- frontend/javascripts/oxalis/model_initialization.ts | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/frontend/javascripts/oxalis/model_initialization.ts b/frontend/javascripts/oxalis/model_initialization.ts index 25a7d9aff4f..557ed06baf3 100644 --- a/frontend/javascripts/oxalis/model_initialization.ts +++ b/frontend/javascripts/oxalis/model_initialization.ts @@ -717,8 +717,11 @@ async function applyLayerState(stateByLayer: UrlStateByLayer) { const { meshFileName: currentMeshFileName, meshes } = layerState.meshInfo; if (currentMeshFileName != null) { - // ensure mesh files are loaded, so that the given mesh file name can be activated const segmentationLayer = getSegmentationLayerByName(dataset, effectiveLayerName); + // Ensure mesh files are loaded, so that the given mesh file name can be activated. + // Doing this in a loop is fine, since it can only happen once (maximum) and there + // are not many other iterations (== layers) which are blocked by this. + // eslint-disable-next-line no-await-in-loop await dispatchMaybeFetchMeshFilesAsync(Store.dispatch, segmentationLayer, dataset, false); Store.dispatch(updateCurrentMeshFileAction(effectiveLayerName, currentMeshFileName)); } From 978b493ed3715ae38f4641a60416daf6d7bc7e70 Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Wed, 5 Oct 2022 16:18:14 +0200 Subject: [PATCH 61/63] set opacity to 100% for non-passive meshes --- frontend/javascripts/oxalis/controller/scene_controller.ts | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/frontend/javascripts/oxalis/controller/scene_controller.ts b/frontend/javascripts/oxalis/controller/scene_controller.ts index 39af8ac1880..2f992d9ed09 100644 --- a/frontend/javascripts/oxalis/controller/scene_controller.ts +++ b/frontend/javascripts/oxalis/controller/scene_controller.ts @@ -217,7 +217,7 @@ class SceneController { tweenAnimation .to( { - opacity: passive ? 0.4 : 0.9, + opacity: passive ? 0.4 : 1, }, 500, ) From 466a12ff6e42a7f6baae95221f2f90c91646c297 Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Wed, 5 Oct 2022 16:24:01 +0200 Subject: [PATCH 62/63] fix typo --- frontend/javascripts/oxalis/controller/scene_controller.ts | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/frontend/javascripts/oxalis/controller/scene_controller.ts b/frontend/javascripts/oxalis/controller/scene_controller.ts index 2f992d9ed09..188eeb95658 100644 --- a/frontend/javascripts/oxalis/controller/scene_controller.ts +++ b/frontend/javascripts/oxalis/controller/scene_controller.ts @@ -310,18 +310,18 @@ class SceneController { // so that the light moves along the cam. const AMBIENT_INTENSITY = 30; - const DIRECTIONAL_INTENSITRY = 5; + const DIRECTIONAL_INTENSITY = 5; const POINT_INTENSITY = 5; const ambientLight = new THREE.AmbientLight(2105376, AMBIENT_INTENSITY); - const directionalLight = new THREE.DirectionalLight(16777215, DIRECTIONAL_INTENSITRY); + const directionalLight = new THREE.DirectionalLight(16777215, DIRECTIONAL_INTENSITY); directionalLight.position.x = 1; directionalLight.position.y = 1; directionalLight.position.z = 1; directionalLight.position.normalize(); - const directionalLight2 = new THREE.DirectionalLight(16777215, DIRECTIONAL_INTENSITRY); + const directionalLight2 = new THREE.DirectionalLight(16777215, DIRECTIONAL_INTENSITY); directionalLight2.position.x = -1; directionalLight2.position.y = -1; directionalLight2.position.z = -1; From c08a8a9dc5ea3b3fb738e314cecc788c86907794 Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Wed, 5 Oct 2022 16:46:08 +0200 Subject: [PATCH 63/63] always add an isosurface object when loading ad-hoc (will simply overwrite the existing key), as this is important when an existing precomputed mesh is changed to an ad-hoc one (the same was already done when adding precomputed meshes) --- .../javascripts/oxalis/model/sagas/isosurface_saga.ts | 11 +---------- 1 file changed, 1 insertion(+), 10 deletions(-) diff --git a/frontend/javascripts/oxalis/model/sagas/isosurface_saga.ts b/frontend/javascripts/oxalis/model/sagas/isosurface_saga.ts index ce65dec30bc..469d8455e06 100644 --- a/frontend/javascripts/oxalis/model/sagas/isosurface_saga.ts +++ b/frontend/javascripts/oxalis/model/sagas/isosurface_saga.ts @@ -290,16 +290,7 @@ function* loadIsosurfaceWithNeighbors( const { mappingName, mappingType } = isosurfaceExtraInfo; const clippedPosition = clipPositionToCubeBoundary(position); let positionsToRequest = [clippedPosition]; - const hasIsosurface = yield* select( - (state) => - state.localSegmentationData[layer.name].isosurfaces != null && - state.localSegmentationData[layer.name].isosurfaces[segmentId] != null, - ); - - if (!hasIsosurface) { - yield* put(addAdHocIsosurfaceAction(layer.name, segmentId, position, mappingName, mappingType)); - } - + yield* put(addAdHocIsosurfaceAction(layer.name, segmentId, position, mappingName, mappingType)); yield* put(startedLoadingIsosurfaceAction(layer.name, segmentId)); while (positionsToRequest.length > 0) {