Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Find data generalisation #4007

Merged
merged 4 commits into from
Apr 25, 2019
Merged

Find data generalisation #4007

Changes from 1 commit
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
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
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
43 changes: 16 additions & 27 deletions ...ossos-datastore/app/com/scalableminds/webknossos/datastore/services/FindDataService.scala
View file
Open in desktop
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
}
}