Revert "In Data Loading, Clip to Layer BoundingBox (#8551)"

CHANGELOG.unreleased.md

@@ -19,7 +19,6 @@ For upgrade instructions, please check the [migration guide](MIGRATIONS.released
 - Adjusted the names of custom model inference jobs and train model jobs to match the worker's naming. [#8524](https://github.com/scalableminds/webknossos/pull/8524)
 - Updated screenshot tests to use `vitest` framework instead of `ava`. [#8553](https://github.com/scalableminds/webknossos/pull/8553)
 - The mapping dropdown for segmentation is wider now so that mapping names are fully readable. [#8570](https://github.com/scalableminds/webknossos/pull/8570)
-- When loading data from a data layer that has data stored beyond the bounding box specified in the datasource-properties.json, data outside of the bounding box is now zeroed. (the layer is “clipped”). [#8551](https://github.com/scalableminds/webknossos/pull/8551)
 
 ### Fixed
 - Fixed a bug in the trees tab where the color change of a tree would affect the tree on which the context menu was previously opened. [#8562](https://github.com/scalableminds/webknossos/pull/8562)

util/src/main/scala/com/scalableminds/util/geometry/BoundingBox.scala

@@ -6,7 +6,7 @@ import play.api.libs.json.{JsObject, Json}
 
 case class BoundingBox(topLeft: Vec3Int, width: Int, height: Int, depth: Int) {
 
-  lazy val bottomRight: Vec3Int = topLeft.move(width, height, depth)
+  val bottomRight: Vec3Int = topLeft.move(width, height, depth)
 
   def intersects(other: BoundingBox): Boolean =
     math.max(topLeft.x, other.topLeft.x) < math.min(bottomRight.x, other.bottomRight.x) &&
@@ -45,9 +45,6 @@ case class BoundingBox(topLeft: Vec3Int, width: Int, height: Int, depth: Int) {
     BoundingBox(Vec3Int(x, y, z), w, h, d)
   }
 
-  def isFullyContainedIn(other: BoundingBox): Boolean =
-    this.intersection(other).contains(this)
-
   def isEmpty: Boolean =
     width <= 0 || height <= 0 || depth <= 0
 
@@ -64,9 +61,6 @@ case class BoundingBox(topLeft: Vec3Int, width: Int, height: Int, depth: Int) {
     // Since floorDiv is used for topLeft, ceilDiv is used for the size to avoid voxels being lost at the border
     BoundingBox(topLeft / that, ceilDiv(width, that.x), ceilDiv(height, that.y), ceilDiv(depth, that.z))
 
-  def move(delta: Vec3Int): BoundingBox =
-    this.copy(topLeft = this.topLeft + delta)
-
   def toSql: List[Int] =
     List(topLeft.x, topLeft.y, topLeft.z, width, height, depth)
 

util/src/main/scala/com/scalableminds/util/geometry/Vec3Int.scala

@@ -23,9 +23,6 @@ case class Vec3Int(x: Int, y: Int, z: Int) {
   def /(that: Vec3Int): Vec3Int =
     Vec3Int(x / that.x, y / that.y, z / that.z)
 
-  def unary_- : Vec3Int =
-    Vec3Int(-x, -y, -z)
-
   def scale(s: Float): Vec3Int =
     Vec3Int((x * s).toInt, (y * s).toInt, (z * s).toInt)
 
@@ -56,6 +53,8 @@ case class Vec3Int(x: Int, y: Int, z: Int) {
   def move(other: Vec3Int): Vec3Int =
     move(other.x, other.y, other.z)
 
+  def negate: Vec3Int = Vec3Int(-x, -y, -z)
+
   def to(bottomRight: Vec3Int): Seq[Vec3Int] =
     range(bottomRight, _ to _)
 

webknossos-datastore/app/com/scalableminds/webknossos/datastore/models/requests/Cuboid.scala

@@ -1,6 +1,6 @@
 package com.scalableminds.webknossos.datastore.models.requests
 
-import com.scalableminds.util.geometry.{BoundingBox, Vec3Int}
+import com.scalableminds.util.geometry.Vec3Int
 import com.scalableminds.webknossos.datastore.models.{BucketPosition, VoxelPosition}
 
 /**
@@ -51,10 +51,4 @@ case class Cuboid(topLeft: VoxelPosition, width: Int, height: Int, depth: Int) {
     height * mag.y,
     depth * mag.z
   )
-
-  def toBoundingBoxInMag: BoundingBox =
-    BoundingBox(Vec3Int(topLeft.voxelXInMag, topLeft.voxelYInMag, topLeft.voxelZInMag), width, height, depth)
-
-  def toMag1BoundingBox: BoundingBox =
-    toMag1.toBoundingBoxInMag
 }

webknossos-datastore/app/com/scalableminds/webknossos/datastore/models/requests/DataServiceRequests.scala

@@ -1,6 +1,5 @@
 package com.scalableminds.webknossos.datastore.models.requests
 
-import com.scalableminds.util.geometry.Vec3Int
 import com.scalableminds.webknossos.datastore.models.{AdditionalCoordinate, BucketPosition}
 import com.scalableminds.webknossos.datastore.models.datasource.{DataLayer, DataSource, SegmentationLayer}
 
@@ -22,7 +21,6 @@ case class DataServiceDataRequest(
     settings: DataServiceRequestSettings
 ) {
   def isSingleBucket: Boolean = cuboid.isSingleBucket(DataLayer.bucketLength)
-  def mag: Vec3Int = cuboid.mag
 }
 
 case class DataReadInstruction(

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

@@ -108,52 +108,16 @@ class BinaryDataService(val dataBaseDir: Path,
                                                   conversionFunc(inputArray))
     else Fox.successful(inputArray)
 
-  /*
-   * Everything outside of the layer bounding box is set to black (zero) so data outside of the specified
-   *  bounding box is not exposed to the user
-   */
-  private def clipToLayerBoundingBox(request: DataServiceDataRequest)(inputArray: Array[Byte]): Box[Array[Byte]] = {
-    val bytesPerElement = request.dataLayer.bytesPerElement
-    val requestBboxInMag = request.cuboid.toBoundingBoxInMag
-    val layerBboxInMag = request.dataLayer.boundingBox / request.mag // Note that this div is implemented to round to the bigger bbox so we don’t lose voxels inside.
-    val intersectionOpt = requestBboxInMag.intersection(layerBboxInMag).map(_.move(-requestBboxInMag.topLeft))
-    val outputArray = Array.fill[Byte](inputArray.length)(0)
-    intersectionOpt.foreach { intersection =>
-      for {
-        z <- intersection.topLeft.z until intersection.bottomRight.z
-        y <- intersection.topLeft.y until intersection.bottomRight.y
-        // We can bulk copy a row of voxels and do not need to iterate in the x dimension
-      } {
-        val offset =
-          (intersection.topLeft.x +
-            y * requestBboxInMag.width +
-            z * requestBboxInMag.width * requestBboxInMag.height) * bytesPerElement
-        System.arraycopy(inputArray,
-                         offset,
-                         outputArray,
-                         offset,
-                         (intersection.bottomRight.x - intersection.topLeft.x) * bytesPerElement)
-      }
-    }
-    Full(outputArray)
-  }
-
   private def convertAccordingToRequest(request: DataServiceDataRequest, inputArray: Array[Byte]): Fox[Array[Byte]] =
     for {
-      clippedData <- convertIfNecessary(
-        !request.cuboid.toMag1BoundingBox.isFullyContainedIn(request.dataLayer.boundingBox),
-        inputArray,
-        data => clipToLayerBoundingBox(request)(data).toFox,
-        request
-      )
       mappedDataFox <- agglomerateServiceOpt.map { agglomerateService =>
         convertIfNecessary(
           request.settings.appliedAgglomerate.isDefined && request.dataLayer.category == Category.segmentation && request.cuboid.mag.maxDim <= MaxMagForAgglomerateMapping,
-          clippedData,
+          inputArray,
           data => agglomerateService.applyAgglomerate(request)(data).toFox,
           request
         )
-      }.toFox.fillEmpty(Fox.successful(clippedData)) ?~> "Failed to apply agglomerate mapping"
+      }.toFox.fillEmpty(Fox.successful(inputArray)) ?~> "Failed to apply agglomerate mapping"
       mappedData <- mappedDataFox
       resultData <- convertIfNecessary(request.settings.halfByte, mappedData, convertToHalfByte, request)
     } yield resultData
@@ -204,6 +168,7 @@ class BinaryDataService(val dataBaseDir: Path,
   private def cutOutCuboid(request: DataServiceDataRequest, rs: List[(BucketPosition, Array[Byte])]): Array[Byte] = {
     val bytesPerElement = request.dataLayer.bytesPerElement
     val cuboid = request.cuboid
+    val subsamplingStrides = Vec3Int.ones
 
     val resultShape = Vec3Int(cuboid.width, cuboid.height, cuboid.depth)
     val result = new Array[Byte](cuboid.volume * bytesPerElement)
@@ -229,9 +194,9 @@ class BinaryDataService(val dataBaseDir: Path,
               y % bucketLength * bucketLength +
               z % bucketLength * bucketLength * bucketLength) * bytesPerElement
 
-          val rx = xMin - cuboid.topLeft.voxelXInMag
-          val ry = y - cuboid.topLeft.voxelYInMag
-          val rz = z - cuboid.topLeft.voxelZInMag
+          val rx = (xMin - cuboid.topLeft.voxelXInMag) / subsamplingStrides.x
+          val ry = (y - cuboid.topLeft.voxelYInMag) / subsamplingStrides.y
+          val rz = (z - cuboid.topLeft.voxelZInMag) / subsamplingStrides.z
 
           val resultOffset = (rx + ry * resultShape.x + rz * resultShape.x * resultShape.y) * bytesPerElement
           System.arraycopy(data, dataOffset, result, resultOffset, (xMax - xMin) * bytesPerElement)