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|
{-# LANGUAGE ForeignFunctionInterface #-}
{-# LANGUAGE UnicodeSyntax #-}
module Hkl.H5
( Dataset
, File
, H5
, H5Path
, check_ndims
, closeDataset
, closeFile
, get_position
, get_position_new
, get_ub
, lenH5Dataspace
, nxEntries
, openDataset
, openH5
, withH5File
)
where
import Bindings.HDF5.Core ( HSize(HSize)
, IndexType(ByName)
, IterOrder(Native)
, hid
, hSize
, indexTypeCode
, iterOrderCode
)
import Bindings.HDF5.File ( File
, AccFlags(ReadOnly)
, openFile
, closeFile
)
import Bindings.HDF5.Dataset ( Dataset
, openDataset
, closeDataset
, getDatasetSpace
, readDataset
, readDatasetInto
)
import Bindings.HDF5.Dataspace ( Dataspace
, SelectionOperator(Set)
, closeDataspace
, createSimpleDataspace
, getSimpleDataspaceExtentNDims
, getSimpleDataspaceExtentNPoints
, selectHyperslab
)
import Bindings.HDF5.Raw ( HErr_t(HErr_t)
, HId_t(HId_t)
, H5L_info_t
, h5l_iterate
)
import Control.Exception (bracket)
import Data.Array.Repa (Shape, listOfShape)
import Data.ByteString.Char8 ( pack )
import Data.IORef ( newIORef, readIORef, writeIORef )
import Data.Vector.Storable (Vector, freeze)
import Data.Vector.Storable.Mutable (replicate)
import Foreign.StablePtr ( castPtrToStablePtr
, castStablePtrToPtr
, deRefStablePtr
, freeStablePtr
, newStablePtr
)
import Foreign.Ptr ( FunPtr, freeHaskellFunPtr )
import Foreign.Ptr.Conventions ( In(In)
, InOut(InOut)
, castWrappedPtr
, withInOut_
)
import Foreign.C.String ( CString, peekCString )
import Foreign.C.Types (CInt(CInt))
import Numeric.LinearAlgebra (Matrix, reshape)
{-# ANN module "HLint: ignore Use camelCase" #-}
data H5
type H5Path = String
check_ndims :: Dataset -> Int -> IO Bool
check_ndims d expected = do
space_id <- getDatasetSpace d
(CInt ndims) <- getSimpleDataspaceExtentNDims space_id
return $ expected == fromEnum ndims
toHyperslab :: Shape sh => sh -> [(HSize, Maybe HSize, HSize, Maybe HSize)]
toHyperslab s = [(HSize (fromIntegral n), Just (HSize 1), HSize 1, Just (HSize 1)) | n <- listOfShape s]
get_position_new :: Shape sh => Dataset -> sh -> IO (Vector Double)
get_position_new dataset s =
withDataspace dataset $ \dataspace -> do
selectHyperslab dataspace Set (toHyperslab s)
withDataspace' $ \memspace -> do
data_out <- Data.Vector.Storable.Mutable.replicate 1 (0.0 :: Double)
readDatasetInto dataset (Just memspace) (Just dataspace) Nothing data_out
freeze data_out
get_position :: Dataset -> Int -> IO (Vector Double)
get_position dataset n =
withDataspace dataset $ \dataspace -> do
let start = HSize (fromIntegral n)
let stride = Just (HSize 1)
let count = HSize 1
let block = Just (HSize 1)
selectHyperslab dataspace Set [(start, stride, count, block)]
withDataspace' $ \memspace -> do
data_out <- Data.Vector.Storable.Mutable.replicate 1 (0.0 :: Double)
readDatasetInto dataset (Just memspace) (Just dataspace) Nothing data_out
freeze data_out
get_ub :: Dataset -> IO (Matrix Double)
get_ub dataset = do
v <- readDataset dataset Nothing Nothing
return $ reshape 3 v
-- | File
withH5File :: FilePath -> (File -> IO r) -> IO r
withH5File fp = bracket acquire release
where
acquire = openFile (pack fp) [ReadOnly] Nothing
release = closeFile
openH5 ∷ FilePath → IO File
openH5 f = openFile (pack f) [ReadOnly] Nothing
-- | Dataspace
-- check how to merge both methods
withDataspace' :: (Dataspace -> IO r) -> IO r
withDataspace' = bracket acquire release
where
acquire = createSimpleDataspace [HSize 1]
release = closeDataspace
withDataspace :: Dataset -> (Dataspace -> IO r) -> IO r
withDataspace d = bracket acquire release
where
acquire = getDatasetSpace d
release = closeDataspace
lenH5Dataspace :: Dataset -> IO (Maybe Int)
lenH5Dataspace = withDataspace'' len
where
withDataspace'' f d = withDataspace d f
len space_id = do
(HSize n) <- getSimpleDataspaceExtentNPoints space_id
return $ if n < 0 then Nothing else Just (fromIntegral n)
-- | WIP until I have decided what is the right way to go
type H5Iterate a = HId_t -> CString -> In H5L_info_t -> InOut a -> IO HErr_t
foreign import ccall "wrapper" mkOp :: H5Iterate a -> IO (FunPtr (H5Iterate a))
nxEntries ∷ FilePath → IO [String]
nxEntries f = withH5File f $ \h → do
state <- newIORef []
statePtr <- newStablePtr state
let opData = InOut $ castStablePtrToPtr statePtr
let startIndex = Nothing
let indexType = ByName
let order = Native
iop <- mkOp callback
_ <- withInOut_ (maybe 0 hSize startIndex) $ \ioStartIndex ->
h5l_iterate (hid h) (indexTypeCode indexType) (iterOrderCode order) ioStartIndex iop opData
freeHaskellFunPtr iop
freeStablePtr statePtr
-- retrieve the final state
readIORef state
where
callback ∷ H5Iterate a
callback _g n _i (InOut dataptr) =
do
let opData = castWrappedPtr dataptr
-- get the state
stRef <- deRefStablePtr (castPtrToStablePtr opData)
st <- readIORef stRef
-- compute the new state
name <- peekCString n
let newSt = st ++ [name]
-- store the new state
writeIORef stRef newSt
return $ HErr_t 0
|
