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Find data generalisation #4007

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merged 4 commits into from
Apr 25, 2019
Merged

Find data generalisation #4007

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1be6b33
dont rely on type conversion in find data #3936
Apr 11, 2019
3622d5d
Merge branch 'master' into find-data-generalisation
Apr 18, 2019
b741737
Merge branch 'master' into find-data-generalisation
youri-k Apr 18, 2019
1b98ae4
Merge branch 'master' into find-data-generalisation
fm3 Apr 25, 2019
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43 changes: 16 additions & 27 deletions ...ossos-datastore/app/com/scalableminds/webknossos/datastore/services/FindDataService.scala
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Original file line number Diff line number Diff line change
Expand Up @@ -25,42 +25,22 @@ class FindDataService @Inject()(dataServicesHolder: BinaryDataServiceHolder)(imp
positionAndResolutionOpt <- checkAllPositionsForData(dataSource, dataLayer)
} yield positionAndResolutionOpt

private def convertData(data: Array[Byte],
elementClass: ElementClass.Value): Array[_ >: Byte with Short with Int with Long] =
elementClass match {
case ElementClass.uint8 =>
convertDataImpl[Byte, ByteBuffer](data, DataTypeFunctors[Byte, ByteBuffer](identity, _.get(_), _.toByte))
case ElementClass.uint16 =>
convertDataImpl[Short, ShortBuffer](data,
DataTypeFunctors[Short, ShortBuffer](_.asShortBuffer, _.get(_), _.toShort))
case ElementClass.uint32 =>
convertDataImpl[Int, IntBuffer](data, DataTypeFunctors[Int, IntBuffer](_.asIntBuffer, _.get(_), _.toInt))
case ElementClass.uint64 =>
convertDataImpl[Long, LongBuffer](data, DataTypeFunctors[Long, LongBuffer](_.asLongBuffer, _.get(_), identity))
}

private def convertDataImpl[T: ClassTag, B <: Buffer](data: Array[Byte],
dataTypeFunctor: DataTypeFunctors[T, B]): Array[T] = {
val srcBuffer = dataTypeFunctor.getTypedBufferFn(ByteBuffer.wrap(data).order(ByteOrder.LITTLE_ENDIAN))
srcBuffer.rewind()
val dstArray = Array.ofDim[T](srcBuffer.remaining())
dataTypeFunctor.copyDataFn(srcBuffer, dstArray)
dstArray
}

private def checkAllPositionsForData(dataSource: DataSource,
dataLayer: DataLayer): Fox[Option[(Point3D, Point3D)]] = {

def getExactDataOffset(data: Array[Byte]): Point3D = {
val cubeLength = DataLayer.bucketLength / dataLayer.bytesPerElement
val convertedData = convertData(data, dataLayer.elementClass)
val bytesPerElement = dataLayer.bytesPerElement
val cubeLength = DataLayer.bucketLength / bytesPerElement
for {
z <- 0 until cubeLength
y <- 0 until cubeLength
x <- 0 until cubeLength
scaledX = x * bytesPerElement
scaledY = y * bytesPerElement
scaledZ = z * bytesPerElement
} {
val voxelOffset = x + y * cubeLength + z * cubeLength * cubeLength
if (convertedData(voxelOffset) != 0) return Point3D(x, y, z)
val voxelOffset = scaledX + scaledY * cubeLength + scaledZ * cubeLength * cubeLength
if (data.slice(voxelOffset, voxelOffset + bytesPerElement).exists(_ != 0)) return Point3D(x, y, z)
}
Point3D(0, 0, 0)
}
Expand Down Expand Up @@ -204,4 +184,13 @@ class FindDataService @Inject()(dataServicesHolder: BinaryDataServiceHolder)(imp
dataLayer.resolutions.minBy(_.maxDim))
} yield meanAndStdDev
}

private def convertDataImpl[T: ClassTag, B <: Buffer](data: Array[Byte],
dataTypeFunctor: DataTypeFunctors[T, B]): Array[T] = {
val srcBuffer = dataTypeFunctor.getTypedBufferFn(ByteBuffer.wrap(data).order(ByteOrder.LITTLE_ENDIAN))
srcBuffer.rewind()
val dstArray = Array.ofDim[T](srcBuffer.remaining())
dataTypeFunctor.copyDataFn(srcBuffer, dstArray)
dstArray
}
}