src/MRI.hs

   1 module MRI
   2 where
   3
   4 import Data.Word
   5 import Data.Bits
   6 import Data.Array.Repa                  as R
   7 import Data.Array.Repa.IO.Binary        as R
   8 import Data.Array.Repa.IO.ColorRamp     as R
   9
  10 import Values
  11
  12 mri_depth :: Int
  13 mri_depth = 109
  14
  15 mri_width :: Int
  16 mri_width = 256
  17
  18 mri_height :: Int
  19 mri_height = 256
  20
  21 mri_shape :: DIM3
  22 mri_shape = (Z :. mri_depth :. mri_height :. mri_width)
  23
  24 mri_lower_threshold :: Double
  25 mri_lower_threshold = 1400
  26
  27 mri_upper_threshold :: Double
  28 mri_upper_threshold = 2500
  29
  30 mri_slice3d :: DIM3
  31 mri_slice3d = (Z :. 1 :. mri_height  :. mri_width)
  32
  33 type RawData sh = Array sh Word16
  34 type RawData3D = RawData DIM3
  35
  36 type RGB = (Word8, Word8, Word8)
  37 type ColorData sh = Array sh RGB
  38
  39 rgb_to_dbl :: RGB -> (Double, Double, Double)
  40 rgb_to_dbl (x,y,z) = (fromIntegral x, fromIntegral y, fromIntegral z)
  41
  42
  43 read_word16s :: FilePath -> IO RawData3D
  44 read_word16s path = do
  45   arr <- R.readArrayFromStorableFile path mri_shape
  46   arr `deepSeqArray` return ()
  47   return arr
  48
  49
  50 {-# INLINE bracket #-}
  51 bracket :: Double -> Word16
  52 bracket x
  53         | x < mri_lower_threshold      = 0
  54         | x > mri_upper_threshold      = 255
  55         | otherwise                    = truncate (r * 255)
  56             where
  57               numerator = x - mri_lower_threshold
  58               denominator = mri_upper_threshold - mri_lower_threshold
  59               r = numerator/denominator
  60
  61
  62 {-# INLINE flip16 #-}
  63 flip16 :: Word16 -> Word16
  64 flip16 xx =
  65   shift xx 8 .|. (shift xx (-8) .&. 0x00ff)
  66
  67
  68 swap_bytes :: (Shape sh) => (RawData sh) -> (RawData sh)
  69 swap_bytes arr =
  70     R.force $ R.map flip16 arr
  71
  72 bracket_array :: (Shape sh) => (Values sh) -> (RawData sh)
  73 bracket_array arr =
  74   R.force $ R.map f arr
  75   where
  76     f = bracket
  77
  78
  79 flip_y :: RawData3D -> RawData3D
  80 flip_y arr =
  81   R.force $ R.traverse arr id
  82               (\get (Z :. z :. y :. x) ->
  83                    get (Z :. z :. (mri_height - 1) - y :. x))
  84
  85 flip_x :: RawData3D -> RawData3D
  86 flip_x arr =
  87   R.force $ R.traverse arr id
  88               (\get (Z :. z :. y :. x) ->
  89                    get (Z :. z :. y :. (mri_width - 1) - x))
  90
  91 write_word16s :: (Shape sh) => FilePath -> (RawData sh) -> IO ()
  92 write_word16s = R.writeArrayToStorableFile
  93
  94
  95 values_to_colors :: (Shape sh) => (Values sh) -> (ColorData sh)
  96 values_to_colors arr =
  97   R.force $ R.map (truncate_rgb . ramp_it) arr
  98   where
  99     ramp_it :: Double -> (Double, Double, Double)
 100     ramp_it x =
 101       if x == 0 then
 102         (0, 0, 0)
 103       else
 104         rampColorHotToCold 0 255 x
 105
 106     truncate_rgb :: (Double, Double, Double) -> (Word8, Word8, Word8)
 107     truncate_rgb (r, g, b) =
 108       (r', g', b')
 109       where
 110         r' = truncate (r * 255)
 111         g' = truncate (g * 255)
 112         b' = truncate (b * 255)
 113
 114
 115 red_dbl_data :: (Shape sh) => (ColorData sh) -> Array sh Double
 116 red_dbl_data =
 117   R.map (get_r . rgb_to_dbl)
 118   where
 119     get_r :: (Double, Double, Double) -> Double
 120     get_r (r, _, _) = r
 121
 122 green_dbl_data :: (Shape sh) => (ColorData sh) -> Array sh Double
 123 green_dbl_data =
 124   R.map (get_g . rgb_to_dbl)
 125   where
 126     get_g :: (Double, Double, Double) -> Double
 127     get_g (_, g, _) = g
 128
 129
 130 blue_dbl_data :: (Shape sh) => (ColorData sh) -> Array sh Double
 131 blue_dbl_data =
 132   R.map (get_b . rgb_to_dbl)
 133   where
 134     get_b :: (Double, Double, Double) -> Double
 135     get_b (_, _, b) = b
 136
 137
 138
 139 z_slice :: Elt a => Int -> Array DIM3 a -> Array DIM2 a
 140 z_slice n arr =
 141   slice arr (Any :. n :. All :. All)
 142
 143
 144 transpose_zx :: Elt a => Array DIM3 a -> Array DIM3 a
 145 transpose_zx arr =
 146   traverse arr
 147            (\(Z :. zdim :. ydim :. xdim) -> (Z :. xdim :. ydim :. zdim))
 148            (\_ -> (\(Z :. z :. y :. x) -> arr ! (Z :. x :. y :. z)))
 149
 150
 151 z_slice3 :: Elt a => Int -> Array DIM3 a -> Array DIM3 a
 152 z_slice3 n arr
 153   | n == 0 = transpose_zx $ current R.++ next
 154   | n == zdim-1 = transpose_zx $ previous R.++ current
 155   | otherwise = transpose_zx $ previous R.++ current R.++ next
 156   where
 157     (Z :. zdim :. _ :. _) = extent arr
 158     previous = transpose_zx $ reshape mri_slice3d (z_slice (n-1) arr)
 159     current = transpose_zx $ reshape mri_slice3d (z_slice n arr)
 160     next = transpose_zx $ reshape mri_slice3d (z_slice (n+1) arr)