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 import Data.Array.Repa.IO.BMP           as R (writeComponentsToBMP)
  10
  11 import Values
  12
  13 mri_depth :: Int
  14 mri_depth = 109
  15
  16 mri_width :: Int
  17 mri_width = 256
  18
  19 mri_height :: Int
  20 mri_height = 256
  21
  22 mri_shape :: DIM3
  23 mri_shape = (Z :. mri_depth :. mri_height :. mri_width)
  24
  25 mri_lower_threshold :: Double
  26 mri_lower_threshold = 1400
  27
  28 mri_upper_threshold :: Double
  29 mri_upper_threshold = 2500
  30
  31 mri_slice3d :: DIM3
  32 mri_slice3d = (Z :. 1 :. mri_height  :. mri_width)
  33
  34 type RawData sh = Array sh Word16
  35 type RawData3D = RawData DIM3
  36
  37 type RGB = (Word8, Word8, Word8)
  38 type ColorData sh = Array sh RGB
  39
  40 rgb_to_dbl :: RGB -> (Double, Double, Double)
  41 rgb_to_dbl (x,y,z) = (fromIntegral x, fromIntegral y, fromIntegral z)
  42
  43
  44 read_word16s :: FilePath -> IO RawData3D
  45 read_word16s path = do
  46   arr <- R.readArrayFromStorableFile path mri_shape
  47   arr `deepSeqArray` return ()
  48   return arr
  49
  50
  51 {-# INLINE bracket #-}
  52 bracket :: Double -> Word16
  53 bracket x
  54         | x < mri_lower_threshold      = 0
  55         | x > mri_upper_threshold      = 255
  56         | otherwise                    = truncate (r * 255)
  57             where
  58               numerator = x - mri_lower_threshold
  59               denominator = mri_upper_threshold - mri_lower_threshold
  60               r = numerator/denominator
  61
  62
  63 {-# INLINE flip16 #-}
  64 flip16 :: Word16 -> Word16
  65 flip16 xx =
  66   shift xx 8 .|. (shift xx (-8) .&. 0x00ff)
  67
  68
  69 swap_bytes :: (Shape sh) => (RawData sh) -> (RawData sh)
  70 swap_bytes arr =
  71     R.force $ R.map flip16 arr
  72
  73 bracket_array :: (Shape sh) => (Values sh) -> (RawData sh)
  74 bracket_array arr =
  75   R.force $ R.map f arr
  76   where
  77     f = bracket
  78
  79
  80 flip_y :: RawData3D -> RawData3D
  81 flip_y arr =
  82   R.force $ R.traverse arr id
  83               (\get (Z :. z :. y :. x) ->
  84                    get (Z :. z :. (mri_height - 1) - y :. x))
  85
  86 flip_x :: RawData3D -> RawData3D
  87 flip_x arr =
  88   R.force $ R.traverse arr id
  89               (\get (Z :. z :. y :. x) ->
  90                    get (Z :. z :. y :. (mri_width - 1) - x))
  91
  92 write_word16s :: (Shape sh) => FilePath -> (RawData sh) -> IO ()
  93 write_word16s = R.writeArrayToStorableFile
  94
  95
  96 values_to_colors :: (Shape sh) => (Values sh) -> (ColorData sh)
  97 values_to_colors arr =
  98   R.force $ R.map (truncate_rgb . ramp_it) arr
  99   where
 100     ramp_it :: Double -> (Double, Double, Double)
 101     ramp_it x =
 102       if x == 0 then
 103         (0, 0, 0)
 104       else
 105         rampColorHotToCold 0 255 x
 106
 107     truncate_rgb :: (Double, Double, Double) -> (Word8, Word8, Word8)
 108     truncate_rgb (r, g, b) =
 109       (r', g', b')
 110       where
 111         r' = truncate (r * 255)
 112         g' = truncate (g * 255)
 113         b' = truncate (b * 255)
 114
 115
 116 red_dbl_data :: (Shape sh) => (ColorData sh) -> Array sh Double
 117 red_dbl_data =
 118   R.map (get_r . rgb_to_dbl)
 119   where
 120     get_r :: (Double, Double, Double) -> Double
 121     get_r (r, _, _) = r
 122
 123 green_dbl_data :: (Shape sh) => (ColorData sh) -> Array sh Double
 124 green_dbl_data =
 125   R.map (get_g . rgb_to_dbl)
 126   where
 127     get_g :: (Double, Double, Double) -> Double
 128     get_g (_, g, _) = g
 129
 130
 131 blue_dbl_data :: (Shape sh) => (ColorData sh) -> Array sh Double
 132 blue_dbl_data =
 133   R.map (get_b . rgb_to_dbl)
 134   where
 135     get_b :: (Double, Double, Double) -> Double
 136     get_b (_, _, b) = b
 137
 138
 139
 140 z_slice :: Elt a => Int -> Array DIM3 a -> Array DIM2 a
 141 z_slice n arr =
 142   slice arr (Any :. n :. All :. All)
 143
 144
 145 transpose_zx :: Elt a => Array DIM3 a -> Array DIM3 a
 146 transpose_zx arr =
 147   traverse arr
 148            (\(Z :. zdim :. ydim :. xdim) -> (Z :. xdim :. ydim :. zdim))
 149            (\_ -> (\(Z :. z :. y :. x) -> arr ! (Z :. x :. y :. z)))
 150
 151
 152 z_slice3 :: Elt a => Int -> Array DIM3 a -> Array DIM3 a
 153 z_slice3 n arr
 154   | n == 0 = transpose_zx $ current R.++ next
 155   | n == zdim-1 = transpose_zx $ previous R.++ current
 156   | otherwise = transpose_zx $ previous R.++ current R.++ next
 157   where
 158     (Z :. zdim :. _ :. _) = extent arr
 159     previous = transpose_zx $ reshape mri_slice3d (z_slice (n-1) arr)
 160     current = transpose_zx $ reshape mri_slice3d (z_slice n arr)
 161     next = transpose_zx $ reshape mri_slice3d (z_slice (n+1) arr)
 162
 163
 164 write_values_slice_to_bitmap :: Values2D -> FilePath -> IO ()
 165 write_values_slice_to_bitmap v3d path =
 166   R.writeComponentsToBMP path routput goutput boutput
 167   where
 168     arr_bracketed = bracket_array v3d
 169     colors = values_to_colors $ R.map fromIntegral arr_bracketed
 170     routput = R.map (\(red, _,     _)    -> red)   colors
 171     goutput = R.map (\(_,   green, _)    -> green) colors
 172     boutput = R.map (\(_,   _,     blue) -> blue)  colors