-module MRI
+{-# LANGUAGE FlexibleContexts #-}
+-- | The MRI module contains functionsd and definitions relevant (and
+-- specific) to the MRI data files found at,
+--
+-- <http://graphics.stanford.edu/data/voldata/>
+--
+module MRI (
+ flip_x,
+ flip_y,
+ mri_shape,
+ mri_slice3d,
+ read_word16s,
+ round_array,
+ swap_bytes,
+ write_values_slice_to_bitmap,
+ write_word16s,
+ z_slice
+ )
where
import Data.Word
import Data.Bits
import Data.Array.Repa as R
+import Data.Array.Repa.Repr.Unboxed as R
import Data.Array.Repa.IO.Binary as R
-import Data.Array.Repa.IO.ColorRamp as R
+import Data.Array.Repa.Algorithms.ColorRamp as R
+import Data.Array.Repa.IO.BMP as R (writeImageToBMP)
import Values
mri_shape :: DIM3
mri_shape = (Z :. mri_depth :. mri_height :. mri_width)
-mri_lower_threshold :: Int
+mri_lower_threshold :: Double
mri_lower_threshold = 1400
-mri_upper_threshold :: Int
+mri_upper_threshold :: Double
mri_upper_threshold = 2500
mri_slice3d :: DIM3
mri_slice3d = (Z :. 1 :. mri_height :. mri_width)
-type RawData sh = Array sh Word16
+-- | RawData is an array of words (16 bits), as contained in the MRI
+-- data files.
+type RawData sh = Array U sh Word16
+
+-- | A specialization of the 'RawData' type, to three dimensions.
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)
+type ColorData sh = Array U sh RGB
+{-# INLINE read_word16s #-}
read_word16s :: FilePath -> IO RawData3D
read_word16s path = do
arr <- R.readArrayFromStorableFile path mri_shape
- arr `deepSeqArray` return ()
- return arr
+ arr' <- now $ R.copy arr
+ return arr'
-{-# INLINE bracket #-}
-bracket :: Int -> Int -> Int -> Word16
-bracket low high x
- | x < low = 0
- | x > high = 255
- | otherwise = truncate (r * 255)
+bracket :: Double -> Word16
+bracket x
+ | x < mri_lower_threshold = 0
+ | x > mri_upper_threshold = 255
+ | otherwise = truncate (r * 255)
where
- numerator = fromIntegral (x - low) :: Double
- denominator = fromIntegral (high - low) :: Double
+ numerator = x - mri_lower_threshold
+ denominator = mri_upper_threshold - mri_lower_threshold
r = numerator/denominator
-{-# INLINE flip16 #-}
flip16 :: Word16 -> Word16
flip16 xx =
shift xx 8 .|. (shift xx (-8) .&. 0x00ff)
-swap_bytes :: (Shape sh) => (RawData sh) -> (RawData sh)
+{-# INLINE swap_bytes #-}
+swap_bytes :: (Shape sh, Repr r Word16) => Array r sh Word16
+ -> Array D sh Word16
swap_bytes arr =
- R.force $ R.map flip16 arr
+ R.map flip16 arr
+
-bracket_array :: (Shape sh) => (RawData sh) -> (RawData sh)
+bracket_array :: Shape sh => Values sh -> Array D sh Word16
bracket_array arr =
- R.force $ R.map f arr
- where
- f = (bracket mri_lower_threshold mri_upper_threshold) . fromIntegral
+ R.map bracket arr
+
+{-# INLINE round_array #-}
+round_array :: Shape sh => Values sh -> Array D sh Word16
+round_array arr =
+ R.map round arr
-flip_y :: RawData3D -> RawData3D
+
+flip_y :: Repr r Word16 => Array r DIM3 Word16 -> Array D DIM3 Word16
flip_y arr =
- R.force $ R.traverse arr id
+ R.unsafeTraverse arr id
(\get (Z :. z :. y :. x) ->
get (Z :. z :. (mri_height - 1) - y :. x))
-flip_x :: RawData3D -> RawData3D
+flip_x :: Repr r Word16 => Array r DIM3 Word16 -> Array D DIM3 Word16
flip_x arr =
- R.force $ R.traverse arr id
+ R.unsafeTraverse arr id
(\get (Z :. z :. y :. x) ->
get (Z :. z :. y :. (mri_width - 1) - x))
+
+{-# INLINE write_word16s #-}
write_word16s :: (Shape sh) => FilePath -> (RawData sh) -> IO ()
write_word16s = R.writeArrayToStorableFile
+
values_to_colors :: (Shape sh) => (Values sh) -> (ColorData sh)
values_to_colors arr =
- R.force $ R.map (truncate_rgb . ramp_it) arr
+ R.compute $ R.map (truncate_rgb . ramp_it) arr
where
ramp_it :: Double -> (Double, Double, Double)
ramp_it x =
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
+z_slice :: (R.Unbox a, Repr r a) => Int -> Array r DIM3 a -> Array D DIM2 a
+z_slice n arr =
+ slice arr (Any :. n :. All :. All)
-blue_dbl_data :: (Shape sh) => (ColorData sh) -> Array sh Double
-blue_dbl_data =
- R.map (get_b . rgb_to_dbl)
+write_values_slice_to_bitmap :: Values2D -> FilePath -> IO ()
+write_values_slice_to_bitmap v3d path =
+ R.writeImageToBMP path colors
where
- get_b :: (Double, Double, Double) -> Double
- get_b (_, _, b) = b
-
-
-
-z_slice :: Elt a => Int -> Array DIM3 a -> Array DIM2 a
-z_slice n arr =
- slice arr (Any :. n :. All :. All)
+ arr_bracketed = bracket_array v3d
+ colors = values_to_colors $ R.compute $ R.map fromIntegral arr_bracketed