+{-# LANGUAGE ScopedTypeVariables #-}
+
+module MRI
+where
+
+import Data.Word
+import Data.Bits
+import Data.Array.Repa as R
+import Data.Array.Repa.IO.Binary as R
+import Data.Array.Repa.IO.ColorRamp as R
+
+
+mri_depth :: Int
+mri_depth = 109
+
+mri_width :: Int
+mri_width = 256
+
+mri_height :: Int
+mri_height = 256
+
+mri_shape :: DIM3
+mri_shape = (Z :. mri_depth :. mri_width :. mri_height)
+
+mri_lower_threshold :: Int
+mri_lower_threshold = 1400
+
+mri_upper_threshold :: Int
+mri_upper_threshold = 2500
+
+
+type RawData sh = Array sh Word16
+type RawData3D = RawData DIM3
+
+type RGB = (Word8, Word8, Word8)
+type ColorData sh = Array sh RGB
+
+rgb_to_dbl :: RGB -> (Double, Double, Double)
+rgb_to_dbl (x,y,z) = (fromIntegral x, fromIntegral y, fromIntegral z)
+
+
+read_word16s :: IO RawData3D
+read_word16s = do
+ arr <- R.readArrayFromStorableFile "../data/mri.bin" mri_shape
+ arr `deepSeqArray` return ()
+ return arr
+
+
+{-# INLINE bracket #-}
+bracket :: Int -> Int -> Int -> Word16
+bracket low high x
+ | x < low = 0
+ | x > high = 255
+ | otherwise = truncate (r * 255)
+ where
+ numerator = fromIntegral (x - low) :: Double
+ denominator = fromIntegral (high - low) :: Double
+ r = numerator/denominator
+
+
+{-# INLINE flip16 #-}
+flip16 :: Word16 -> Word16
+flip16 xx =
+ shift xx 8 .|. (shift xx (-8) .&. 0x00ff)
+
+
+bracket_array :: (Shape sh) => (RawData sh) -> (RawData sh)
+bracket_array arr =
+ R.map (bracket mri_lower_threshold mri_upper_threshold . fromIntegral . flip16) arr
+
+flip_y :: RawData3D -> RawData3D
+flip_y arr =
+ R.traverse arr id (\get (Z :. z :. y :. x) -> get (Z :. z :. (mri_height - 1) - y :. x))
+
+flip_x :: RawData3D -> RawData3D
+flip_x arr =
+ R.traverse arr id (\get (Z :. z :. y :. x) -> get (Z :. z :. y :. (mri_width - 1) - x))
+
+write_word16s :: (Shape sh) => FilePath -> (RawData sh) -> IO ()
+write_word16s =
+ -- dump the slice back as word16
+ R.writeArrayToStorableFile
+
+
+raw_data_to_color :: (Shape sh) => (RawData sh) -> (ColorData sh)
+raw_data_to_color arr =
+ R.force $ R.map (truncate_rgb . ramp_it . fromIntegral) arr
+ where
+ ramp_it :: Double -> (Double, Double, Double)
+ ramp_it x =
+ if x == 0 then
+ (0, 0, 0)
+ else
+ rampColorHotToCold 0 255 x
+
+ truncate_rgb :: (Double, Double, Double) -> (Word8, Word8, Word8)
+ truncate_rgb (r, g, b) =
+ (r', g', b')
+ where
+ r' = truncate (r * 255)
+ g' = truncate (g * 255)
+ b' = truncate (b * 255)
+
+
+red_dbl_data :: (Shape sh) => (ColorData sh) -> Array sh Double
+red_dbl_data =
+ R.map (get_r . rgb_to_dbl)
+ where
+ get_r :: (Double, Double, Double) -> Double
+ get_r (r, _, _) = r
+
+green_dbl_data :: (Shape sh) => (ColorData sh) -> Array sh Double
+green_dbl_data =
+ R.map (get_g . rgb_to_dbl)
+ where
+ get_g :: (Double, Double, Double) -> Double
+ get_g (_, g, _) = g
+
+
+blue_dbl_data :: (Shape sh) => (ColorData sh) -> Array sh Double
+blue_dbl_data =
+ R.map (get_b . rgb_to_dbl)
+ where
+ get_b :: (Double, Double, Double) -> Double
+ get_b (_, _, b) = b
+
+