-{-# LANGUAGE ScopedTypeVariables #-}
-
-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
-
-
-mri_depth :: Int
-mri_depth = 109
-
-mri_width :: Int
-mri_width = 256
-
-mri_height :: Int
-mri_height = 256
+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)
-mri_shape :: DIM3
-mri_shape = (Z :. mri_depth :. mri_width :. mri_height)
+import Values
-mri_lower_threshold :: Int
+mri_lower_threshold :: Double
mri_lower_threshold = 1400
-mri_upper_threshold :: Int
+mri_upper_threshold :: Double
mri_upper_threshold = 2500
+-- | 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
+type ColorData sh = Array U sh RGB
-rgb_to_dbl :: RGB -> (Double, Double, Double)
-rgb_to_dbl (x,y,z) = (fromIntegral x, fromIntegral y, fromIntegral z)
+{-# INLINE read_word16s #-}
+read_word16s :: FilePath -> DIM3 -> IO RawData3D
+read_word16s path mri_shape = do
+ arr <- R.readArrayFromStorableFile path mri_shape
+ c <- R.copyP arr
+ now $ c
-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)
+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 =
+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
+{-# 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 -> Array D sh Word16
+bracket_array =
+ R.map bracket
+
+
+{-# 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.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))
+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 :. (height - 1) - y :. x))
+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 :. (width - 1) - x))
+
+
+{-# INLINE write_word16s #-}
write_word16s :: (Shape sh) => FilePath -> (RawData sh) -> IO ()
-write_word16s =
- -- dump the slice back as word16
- R.writeArrayToStorableFile
+write_word16s = 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
+
+--
+-- 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.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
+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)
-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 = do
+ values <- R.computeUnboxedP $ R.map fromIntegral arr_bracketed
+ colors <- values_to_colors $ values
+ R.writeImageToBMP path colors
where
- get_b :: (Double, Double, Double) -> Double
- get_b (_, _, b) = b
-
-
+ arr_bracketed = bracket_array v3d
projects / spline3.git / blobdiff