src/MRI.hs

   1 -- | The MRI module contains functionsd and definitions relevant (and
   2 --   specific) to the MRI data files found at,
   3 --
   4 --   <http://graphics.stanford.edu/data/voldata/>
   5 --
   6 module MRI (
   7   flip_x,
   8   flip_y,
   9   mri_shape,
  10   mri_slice3d,
  11   read_word16s,
  12   round_array,
  13   swap_bytes,
  14   write_values_slice_to_bitmap,
  15   write_word16s,
  16   z_slice
  17   )
  18 where
  19
  20 import Data.Word
  21 import Data.Bits
  22 import Data.Array.Repa                  as R
  23 import Data.Array.Repa.IO.Binary        as R
  24 import Data.Array.Repa.IO.ColorRamp     as R
  25 import Data.Array.Repa.IO.BMP           as R (writeComponentsToBMP)
  26
  27 import Values
  28
  29 mri_depth :: Int
  30 mri_depth = 109
  31
  32 mri_width :: Int
  33 mri_width = 256
  34
  35 mri_height :: Int
  36 mri_height = 256
  37
  38 mri_shape :: DIM3
  39 mri_shape = (Z :. mri_depth :. mri_height :. mri_width)
  40
  41 mri_lower_threshold :: Double
  42 mri_lower_threshold = 1400
  43
  44 mri_upper_threshold :: Double
  45 mri_upper_threshold = 2500
  46
  47 mri_slice3d :: DIM3
  48 mri_slice3d = (Z :. 1 :. mri_height  :. mri_width)
  49
  50 -- | RawData is an array of words (16 bits), as contained in the MRI
  51 --   data files.
  52 type RawData sh = Array sh Word16
  53
  54 -- | A specialization of the 'RawData' type, to three dimensions.
  55 type RawData3D = RawData DIM3
  56
  57 type RGB = (Word8, Word8, Word8)
  58 type ColorData sh = Array sh RGB
  59
  60
  61 read_word16s :: FilePath -> IO RawData3D
  62 read_word16s path = do
  63   arr <- R.readArrayFromStorableFile path mri_shape
  64   arr `deepSeqArray` return ()
  65   return arr
  66
  67
  68 bracket :: Double -> Word16
  69 bracket x
  70         | x < mri_lower_threshold      = 0
  71         | x > mri_upper_threshold      = 255
  72         | otherwise                    = truncate (r * 255)
  73             where
  74               numerator = x - mri_lower_threshold
  75               denominator = mri_upper_threshold - mri_lower_threshold
  76               r = numerator/denominator
  77
  78
  79 flip16 :: Word16 -> Word16
  80 flip16 xx =
  81   shift xx 8 .|. (shift xx (-8) .&. 0x00ff)
  82
  83
  84 swap_bytes :: (Shape sh) => (RawData sh) -> (RawData sh)
  85 swap_bytes arr =
  86     R.force $ R.map flip16 arr
  87
  88
  89 bracket_array :: (Shape sh) => (Values sh) -> (RawData sh)
  90 bracket_array arr =
  91   R.force $ R.map bracket arr
  92
  93
  94 round_array :: (Shape sh) => (Values sh) -> (RawData sh)
  95 round_array arr =
  96   R.force $ R.map round arr
  97
  98
  99 flip_y :: RawData3D -> RawData3D
 100 flip_y arr =
 101   R.force $ R.traverse arr id
 102               (\get (Z :. z :. y :. x) ->
 103                    get (Z :. z :. (mri_height - 1) - y :. x))
 104
 105 flip_x :: RawData3D -> RawData3D
 106 flip_x arr =
 107   R.force $ R.traverse arr id
 108               (\get (Z :. z :. y :. x) ->
 109                    get (Z :. z :. y :. (mri_width - 1) - x))
 110
 111 write_word16s :: (Shape sh) => FilePath -> (RawData sh) -> IO ()
 112 write_word16s = R.writeArrayToStorableFile
 113
 114
 115 values_to_colors :: (Shape sh) => (Values sh) -> (ColorData sh)
 116 values_to_colors arr =
 117   R.force $ R.map (truncate_rgb . ramp_it) arr
 118   where
 119     ramp_it :: Double -> (Double, Double, Double)
 120     ramp_it x =
 121       if x == 0 then
 122         (0, 0, 0)
 123       else
 124         rampColorHotToCold 0 255 x
 125
 126     truncate_rgb :: (Double, Double, Double) -> (Word8, Word8, Word8)
 127     truncate_rgb (r, g, b) =
 128       (r', g', b')
 129       where
 130         r' = truncate (r * 255)
 131         g' = truncate (g * 255)
 132         b' = truncate (b * 255)
 133
 134
 135
 136 z_slice :: Elt a => Int -> Array DIM3 a -> Array DIM2 a
 137 z_slice n arr =
 138   slice arr (Any :. n :. All :. All)
 139
 140
 141
 142 write_values_slice_to_bitmap :: Values2D -> FilePath -> IO ()
 143 write_values_slice_to_bitmap v3d path =
 144   R.writeComponentsToBMP path routput goutput boutput
 145   where
 146     arr_bracketed = bracket_array v3d
 147     colors = values_to_colors $ R.map fromIntegral arr_bracketed
 148     routput = R.map (\(red, _,     _)    -> red)   colors
 149     goutput = R.map (\(_,   green, _)    -> green) colors
 150     boutput = R.map (\(_,   _,     blue) -> blue)  colors