-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,
+ 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.IO.Binary as R
-import Data.Array.Repa.IO.ColorRamp as R
-import Data.Array.Repa.IO.BMP as R (writeComponentsToBMP)
+import Data.Array.Repa as R
+import Data.Array.Repa.Eval as R (now)
+import Data.Array.Repa.Repr.Unboxed as R
+import Data.Array.Repa.IO.Binary as R
+import Data.Array.Repa.Algorithms.ColorRamp as R
+import Data.Array.Repa.Operators.Traversal as R (unsafeTraverse)
+import Data.Array.Repa.IO.BMP as R (writeImageToBMP)
import Values
-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_height :. mri_width)
-
mri_lower_threshold :: Double
mri_lower_threshold = 1400
mri_upper_threshold :: Double
mri_upper_threshold = 2500
-mri_slice3d :: DIM3
-mri_slice3d = (Z :. 1 :. mri_height :. mri_width)
+-- | RawData is an array of words (16 bits), as contained in the MRI
+-- data files.
+type RawData sh = Array U sh Word16
-type RawData sh = Array 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
-read_word16s :: FilePath -> IO RawData3D
-read_word16s path = do
+{-# INLINE read_word16s #-}
+read_word16s :: FilePath -> DIM3 -> IO RawData3D
+read_word16s path mri_shape = do
arr <- R.readArrayFromStorableFile path mri_shape
- arr `deepSeqArray` return ()
- return arr
+ c <- R.copyP arr
+ now $ c
+
bracket :: Double -> Word16
shift xx 8 .|. (shift xx (-8) .&. 0x00ff)
-swap_bytes :: (Shape sh) => (RawData sh) -> (RawData sh)
-swap_bytes arr =
- R.force $ R.map flip16 arr
+{-# INLINE swap_bytes #-}
+swap_bytes :: (Shape sh, Source r Word16) => Array r sh Word16
+ -> Array D sh Word16
+swap_bytes =
+ R.map flip16
-bracket_array :: (Shape sh) => (Values sh) -> (RawData sh)
-bracket_array arr =
- R.force $ R.map bracket arr
+bracket_array :: Shape sh => Values sh -> Array D sh Word16
+bracket_array =
+ R.map bracket
-round_array :: (Shape sh) => (Values sh) -> (RawData sh)
-round_array arr =
- R.force $ R.map round arr
+{-# INLINE round_array #-}
+round_array :: Shape sh => Values sh -> Array D sh Word16
+round_array =
+ R.map round
-flip_y :: RawData3D -> RawData3D
-flip_y arr =
- R.force $ R.traverse arr id
+flip_y :: Source r Word16 => Int -> Array r DIM3 Word16 -> Array D DIM3 Word16
+flip_y height arr =
+ R.unsafeTraverse arr id
(\get (Z :. z :. y :. x) ->
- get (Z :. z :. (mri_height - 1) - y :. x))
+ get (Z :. z :. (height - 1) - y :. x))
-flip_x :: RawData3D -> RawData3D
-flip_x arr =
- R.force $ R.traverse arr id
+flip_x :: Source r Word16 => Int -> Array r DIM3 Word16 -> Array D DIM3 Word16
+flip_x width arr =
+ R.unsafeTraverse arr id
(\get (Z :. z :. y :. x) ->
- get (Z :. z :. y :. (mri_width - 1) - x))
+ get (Z :. z :. y :. (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)
+
+--
+-- Instead of IO, we could get away with a generic monad 'm'
+-- here. However, /we/ only call this function from within IO.
+--
+values_to_colors :: (Shape sh) => (Values sh) -> IO (ColorData sh)
values_to_colors arr =
- R.force $ R.map (truncate_rgb . ramp_it) arr
+ R.computeUnboxedP $ 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
-
-
-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
-
-
-
-z_slice :: Elt a => Int -> Array DIM3 a -> Array DIM2 a
+z_slice :: (R.Unbox a, Source r a) => Int -> Array r DIM3 a -> Array D DIM2 a
z_slice n arr =
slice arr (Any :. n :. All :. All)
-transpose_zx :: Elt a => Array DIM3 a -> Array DIM3 a
-transpose_zx arr =
- traverse arr
- (\(Z :. zdim :. ydim :. xdim) -> (Z :. xdim :. ydim :. zdim))
- (\_ -> (\(Z :. z :. y :. x) -> arr ! (Z :. x :. y :. z)))
-
-
-z_slice3 :: Elt a => Int -> Array DIM3 a -> Array DIM3 a
-z_slice3 n arr
- | n == 0 = transpose_zx $ current R.++ next
- | n == zdim-1 = transpose_zx $ previous R.++ current
- | otherwise = transpose_zx $ previous R.++ current R.++ next
- where
- (Z :. zdim :. _ :. _) = extent arr
- previous = transpose_zx $ reshape mri_slice3d (z_slice (n-1) arr)
- current = transpose_zx $ reshape mri_slice3d (z_slice n arr)
- next = transpose_zx $ reshape mri_slice3d (z_slice (n+1) arr)
-
-
write_values_slice_to_bitmap :: Values2D -> FilePath -> IO ()
-write_values_slice_to_bitmap v3d path =
- R.writeComponentsToBMP path routput goutput boutput
+write_values_slice_to_bitmap v3d path = do
+ values <- R.computeUnboxedP $ R.map fromIntegral arr_bracketed
+ colors <- values_to_colors $ values
+ R.writeImageToBMP path colors
where
arr_bracketed = bracket_array v3d
- colors = values_to_colors $ R.map fromIntegral arr_bracketed
- routput = R.map (\(red, _, _) -> red) colors
- goutput = R.map (\(_, green, _) -> green) colors
- boutput = R.map (\(_, _, blue) -> blue) colors
projects / spline3.git / blobdiff