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)
23 mri_shape = (Z :. mri_depth :. mri_height :. mri_width)
25 mri_lower_threshold :: Double
26 mri_lower_threshold = 1400
28 mri_upper_threshold :: Double
29 mri_upper_threshold = 2500
32 mri_slice3d = (Z :. 1 :. mri_height :. mri_width)
34 type RawData sh = Array sh Word16
35 type RawData3D = RawData DIM3
37 type RGB = (Word8, Word8, Word8)
38 type ColorData sh = Array sh RGB
40 rgb_to_dbl :: RGB -> (Double, Double, Double)
41 rgb_to_dbl (x,y,z) = (fromIntegral x, fromIntegral y, fromIntegral z)
44 read_word16s :: FilePath -> IO RawData3D
45 read_word16s path = do
46 arr <- R.readArrayFromStorableFile path mri_shape
47 arr `deepSeqArray` return ()
51 bracket :: Double -> Word16
53 | x < mri_lower_threshold = 0
54 | x > mri_upper_threshold = 255
55 | otherwise = truncate (r * 255)
57 numerator = x - mri_lower_threshold
58 denominator = mri_upper_threshold - mri_lower_threshold
59 r = numerator/denominator
62 flip16 :: Word16 -> Word16
64 shift xx 8 .|. (shift xx (-8) .&. 0x00ff)
67 swap_bytes :: (Shape sh) => (RawData sh) -> (RawData sh)
69 R.force $ R.map flip16 arr
72 bracket_array :: (Shape sh) => (Values sh) -> (RawData sh)
74 R.force $ R.map bracket arr
77 round_array :: (Shape sh) => (Values sh) -> (RawData sh)
79 R.force $ R.map round arr
82 flip_y :: RawData3D -> RawData3D
84 R.force $ R.traverse arr id
85 (\get (Z :. z :. y :. x) ->
86 get (Z :. z :. (mri_height - 1) - y :. x))
88 flip_x :: RawData3D -> RawData3D
90 R.force $ R.traverse arr id
91 (\get (Z :. z :. y :. x) ->
92 get (Z :. z :. y :. (mri_width - 1) - x))
94 write_word16s :: (Shape sh) => FilePath -> (RawData sh) -> IO ()
95 write_word16s = R.writeArrayToStorableFile
98 values_to_colors :: (Shape sh) => (Values sh) -> (ColorData sh)
99 values_to_colors arr =
100 R.force $ R.map (truncate_rgb . ramp_it) arr
102 ramp_it :: Double -> (Double, Double, Double)
107 rampColorHotToCold 0 255 x
109 truncate_rgb :: (Double, Double, Double) -> (Word8, Word8, Word8)
110 truncate_rgb (r, g, b) =
113 r' = truncate (r * 255)
114 g' = truncate (g * 255)
115 b' = truncate (b * 255)
118 red_dbl_data :: (Shape sh) => (ColorData sh) -> Array sh Double
120 R.map (get_r . rgb_to_dbl)
122 get_r :: (Double, Double, Double) -> Double
125 green_dbl_data :: (Shape sh) => (ColorData sh) -> Array sh Double
127 R.map (get_g . rgb_to_dbl)
129 get_g :: (Double, Double, Double) -> Double
133 blue_dbl_data :: (Shape sh) => (ColorData sh) -> Array sh Double
135 R.map (get_b . rgb_to_dbl)
137 get_b :: (Double, Double, Double) -> Double
142 z_slice :: Elt a => Int -> Array DIM3 a -> Array DIM2 a
144 slice arr (Any :. n :. All :. All)
147 transpose_zx :: Elt a => Array DIM3 a -> Array DIM3 a
150 (\(Z :. zdim :. ydim :. xdim) -> (Z :. xdim :. ydim :. zdim))
151 (\_ -> (\(Z :. z :. y :. x) -> arr ! (Z :. x :. y :. z)))
154 z_slice3 :: Elt a => Int -> Array DIM3 a -> Array DIM3 a
156 | n == 0 = transpose_zx $ current R.++ next
157 | n == zdim-1 = transpose_zx $ previous R.++ current
158 | otherwise = transpose_zx $ previous R.++ current R.++ next
160 (Z :. zdim :. _ :. _) = extent arr
161 previous = transpose_zx $ reshape mri_slice3d (z_slice (n-1) arr)
162 current = transpose_zx $ reshape mri_slice3d (z_slice n arr)
163 next = transpose_zx $ reshape mri_slice3d (z_slice (n+1) arr)
166 write_values_slice_to_bitmap :: Values2D -> FilePath -> IO ()
167 write_values_slice_to_bitmap v3d path =
168 R.writeComponentsToBMP path routput goutput boutput
170 arr_bracketed = bracket_array v3d
171 colors = values_to_colors $ R.map fromIntegral arr_bracketed
172 routput = R.map (\(red, _, _) -> red) colors
173 goutput = R.map (\(_, green, _) -> green) colors
174 boutput = R.map (\(_, _, blue) -> blue) colors