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,
+--
+--   <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
 
@@ -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