X-Git-Url: http://gitweb.michael.orlitzky.com/?a=blobdiff_plain;f=src%2FMRI.hs;h=f63c729797cbdba81937736338506070de3c7bcc;hb=715be016934300f596a11e4fc5b8ca2ec42d6c34;hp=2dd6f6592e6e3bb7ac8d1eefbe73a4764e3cf787;hpb=65eed42ae2b9ca947bd7c08c2a102c1cf5dce8cc;p=spline3.git diff --git a/src/MRI.hs b/src/MRI.hs index 2dd6f65..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 @@ -30,24 +49,25 @@ 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 :: Double -> Word16 bracket x | x < mri_lower_threshold = 0 @@ -59,42 +79,51 @@ bracket x 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) => (Values 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 + 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 = @@ -112,30 +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