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
  74 bracket_array :: (Shape sh) => (Values sh) -> (RawData sh)
  75 bracket_array arr =
  76   R.force $ R.map bracket arr
  77
  78
  79 round_array :: (Shape sh) => (Values sh) -> (RawData sh)
  80 round_array arr =
  81   R.force $ R.map round arr
  82
  83
  84 flip_y :: RawData3D -> RawData3D
  85 flip_y arr =
  86   R.force $ R.traverse arr id
  87               (\get (Z :. z :. y :. x) ->
  88                    get (Z :. z :. (mri_height - 1) - y :. x))
  89
  90 flip_x :: RawData3D -> RawData3D
  91 flip_x arr =
  92   R.force $ R.traverse arr id
  93               (\get (Z :. z :. y :. x) ->
  94                    get (Z :. z :. y :. (mri_width - 1) - x))
  95
  96 write_word16s :: (Shape sh) => FilePath -> (RawData sh) -> IO ()
  97 write_word16s = R.writeArrayToStorableFile
  98
  99
 100 values_to_colors :: (Shape sh) => (Values sh) -> (ColorData sh)
 101 values_to_colors arr =
 102   R.force $ R.map (truncate_rgb . ramp_it) arr
 103   where
 104     ramp_it :: Double -> (Double, Double, Double)
 105     ramp_it x =
 106       if x == 0 then
 107         (0, 0, 0)
 108       else
 109         rampColorHotToCold 0 255 x
 110
 111     truncate_rgb :: (Double, Double, Double) -> (Word8, Word8, Word8)
 112     truncate_rgb (r, g, b) =
 113       (r', g', b')
 114       where
 115         r' = truncate (r * 255)
 116         g' = truncate (g * 255)
 117         b' = truncate (b * 255)
 118
 119
 120 red_dbl_data :: (Shape sh) => (ColorData sh) -> Array sh Double
 121 red_dbl_data =
 122   R.map (get_r . rgb_to_dbl)
 123   where
 124     get_r :: (Double, Double, Double) -> Double
 125     get_r (r, _, _) = r
 126
 127 green_dbl_data :: (Shape sh) => (ColorData sh) -> Array sh Double
 128 green_dbl_data =
 129   R.map (get_g . rgb_to_dbl)
 130   where
 131     get_g :: (Double, Double, Double) -> Double
 132     get_g (_, g, _) = g
 133
 134
 135 blue_dbl_data :: (Shape sh) => (ColorData sh) -> Array sh Double
 136 blue_dbl_data =
 137   R.map (get_b . rgb_to_dbl)
 138   where
 139     get_b :: (Double, Double, Double) -> Double
 140     get_b (_, _, b) = b
 141
 142
 143
 144 z_slice :: Elt a => Int -> Array DIM3 a -> Array DIM2 a
 145 z_slice n arr =
 146   slice arr (Any :. n :. All :. All)
 147
 148
 149 transpose_zx :: Elt a => Array DIM3 a -> Array DIM3 a
 150 transpose_zx arr =
 151   traverse arr
 152            (\(Z :. zdim :. ydim :. xdim) -> (Z :. xdim :. ydim :. zdim))
 153            (\_ -> (\(Z :. z :. y :. x) -> arr ! (Z :. x :. y :. z)))
 154
 155
 156 z_slice3 :: Elt a => Int -> Array DIM3 a -> Array DIM3 a
 157 z_slice3 n arr
 158   | n == 0 = transpose_zx $ current R.++ next
 159   | n == zdim-1 = transpose_zx $ previous R.++ current
 160   | otherwise = transpose_zx $ previous R.++ current R.++ next
 161   where
 162     (Z :. zdim :. _ :. _) = extent arr
 163     previous = transpose_zx $ reshape mri_slice3d (z_slice (n-1) arr)
 164     current = transpose_zx $ reshape mri_slice3d (z_slice n arr)
 165     next = transpose_zx $ reshape mri_slice3d (z_slice (n+1) arr)
 166
 167
 168 write_values_slice_to_bitmap :: Values2D -> FilePath -> IO ()
 169 write_values_slice_to_bitmap v3d path =
 170   R.writeComponentsToBMP path routput goutput boutput
 171   where
 172     arr_bracketed = bracket_array v3d
 173     colors = values_to_colors $ R.map fromIntegral arr_bracketed
 174     routput = R.map (\(red, _,     _)    -> red)   colors
 175     goutput = R.map (\(_,   green, _)    -> green) colors
 176     boutput = R.map (\(_,   _,     blue) -> blue)  colors