X-Git-Url: http://gitweb.michael.orlitzky.com/?a=blobdiff_plain;f=src%2FMRI.hs;h=f63c729797cbdba81937736338506070de3c7bcc;hb=715be016934300f596a11e4fc5b8ca2ec42d6c34;hp=040dcc2a521ed9553974bca43e8fe23df9a63541;hpb=cb685a7b51ed0cce8898179cca4f6a5f26e59f41;p=spline3.git diff --git a/src/MRI.hs b/src/MRI.hs index 040dcc2..f63c729 100644 --- a/src/MRI.hs +++ b/src/MRI.hs @@ -1,11 +1,30 @@ -module MRI +{-# LANGUAGE FlexibleContexts #-} +-- | The MRI module contains functionsd and definitions relevant (and +-- specific) to the MRI data files found at, +-- +-- +-- +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 @@ -21,69 +40,90 @@ mri_height = 256 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 = +flip16 xx = shift xx 8 .|. (shift xx (-8) .&. 0x00ff) -bracket_array :: (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.map flip16 arr + + +bracket_array :: Shape sh => Values sh -> Array D sh Word16 bracket_array arr = - R.map (bracket mri_lower_threshold mri_upper_threshold . fromIntegral . flip16) arr + R.map bracket arr + -flip_y :: RawData3D -> RawData3D +{-# INLINE round_array #-} +round_array :: Shape sh => Values sh -> Array D sh Word16 +round_array arr = + R.map round arr + + +flip_y :: Repr r Word16 => Array r DIM3 Word16 -> Array D DIM3 Word16 flip_y arr = - R.traverse arr id (\get (Z :. z :. y :. x) -> get (Z :. z :. (mri_height - 1) - y :. x)) + 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.traverse arr id (\get (Z :. z :. y :. x) -> get (Z :. z :. y :. (mri_width - 1) - x)) + 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 = @@ -101,30 +141,14 @@ values_to_colors arr = 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