module MRI (
flip_x,
flip_y,
- mri_shape,
- mri_slice3d,
read_word16s,
round_array,
swap_bytes,
import Data.Word
import Data.Bits
-import Data.Array.Repa as R
-import Data.Array.Repa.Repr.Unboxed as R
-import Data.Array.Repa.IO.Binary as R
+import Data.Array.Repa as R
+import Data.Array.Repa.Eval as R (now)
+import Data.Array.Repa.Repr.Unboxed as R
+import Data.Array.Repa.IO.Binary as R
import Data.Array.Repa.Algorithms.ColorRamp as R
-import Data.Array.Repa.IO.BMP as R (writeImageToBMP)
+import Data.Array.Repa.Operators.Traversal as R (unsafeTraverse)
+import Data.Array.Repa.IO.BMP as R (writeImageToBMP)
import Values
-mri_depth :: Int
-mri_depth = 109
-
-mri_width :: Int
-mri_width = 256
-
-mri_height :: Int
-mri_height = 256
-
-mri_shape :: DIM3
-mri_shape = (Z :. mri_depth :. mri_height :. mri_width)
-
mri_lower_threshold :: Double
mri_lower_threshold = 1400
mri_upper_threshold :: Double
mri_upper_threshold = 2500
-mri_slice3d :: DIM3
-mri_slice3d = (Z :. 1 :. mri_height :. mri_width)
-
-- | RawData is an array of words (16 bits), as contained in the MRI
-- data files.
type RawData sh = Array U sh Word16
{-# INLINE read_word16s #-}
-read_word16s :: FilePath -> IO RawData3D
-read_word16s path = do
+read_word16s :: FilePath -> DIM3 -> IO RawData3D
+read_word16s path mri_shape = do
arr <- R.readArrayFromStorableFile path mri_shape
- now $ R.copy arr
+ c <- R.copyP arr
+ now $ c
{-# INLINE swap_bytes #-}
-swap_bytes :: (Shape sh, Repr r Word16) => Array r sh Word16
+swap_bytes :: (Shape sh, Source r Word16) => Array r sh Word16
-> Array D sh Word16
swap_bytes =
R.map flip16
R.map round
-flip_y :: Repr r Word16 => Array r DIM3 Word16 -> Array D DIM3 Word16
-flip_y arr =
+flip_y :: Source r Word16 => Int -> Array r DIM3 Word16 -> Array D DIM3 Word16
+flip_y height arr =
R.unsafeTraverse arr id
(\get (Z :. z :. y :. x) ->
- get (Z :. z :. (mri_height - 1) - y :. x))
+ get (Z :. z :. (height - 1) - y :. x))
-flip_x :: Repr r Word16 => Array r DIM3 Word16 -> Array D DIM3 Word16
-flip_x arr =
+flip_x :: Source r Word16 => Int -> Array r DIM3 Word16 -> Array D DIM3 Word16
+flip_x width arr =
R.unsafeTraverse arr id
(\get (Z :. z :. y :. x) ->
- get (Z :. z :. y :. (mri_width - 1) - x))
+ get (Z :. z :. y :. (width - 1) - x))
{-# INLINE write_word16s #-}
-values_to_colors :: (Shape sh) => (Values sh) -> (ColorData sh)
+--
+-- Instead of IO, we could get away with a generic monad 'm'
+-- here. However, /we/ only call this function from within IO.
+--
+values_to_colors :: (Shape sh) => (Values sh) -> IO (ColorData sh)
values_to_colors arr =
- R.compute $ R.map (truncate_rgb . ramp_it) arr
+ R.computeUnboxedP $ R.map (truncate_rgb . ramp_it) arr
where
ramp_it :: Double -> (Double, Double, Double)
ramp_it x =
b' = truncate (b * 255)
-z_slice :: (R.Unbox a, Repr r a) => Int -> Array r DIM3 a -> Array D DIM2 a
+z_slice :: (R.Unbox a, Source r a) => Int -> Array r DIM3 a -> Array D DIM2 a
z_slice n arr =
slice arr (Any :. n :. All :. All)
write_values_slice_to_bitmap :: Values2D -> FilePath -> IO ()
-write_values_slice_to_bitmap v3d path =
+write_values_slice_to_bitmap v3d path = do
+ values <- R.computeUnboxedP $ R.map fromIntegral arr_bracketed
+ colors <- values_to_colors $ values
R.writeImageToBMP path colors
where
arr_bracketed = bracket_array v3d
- colors = values_to_colors $ R.compute $ R.map fromIntegral arr_bracketed