X-Git-Url: http://gitweb.michael.orlitzky.com/?a=blobdiff_plain;f=src%2FMRI.hs;h=c142dcd22b4d74e5b815841b894e212181131791;hb=bebe7214d77fd80ae2d0cc376846165e06eace93;hp=9f97b08777058ac001ebc6705b5507631b1792de;hpb=2032a8190ba101305a0e10300dbb7ec37b7daea1;p=spline3.git

diff --git a/src/MRI.hs b/src/MRI.hs
index 9f97b08..c142dcd 100644
--- a/src/MRI.hs
+++ b/src/MRI.hs
@@ -1,6 +1,20 @@
-{-# LANGUAGE ScopedTypeVariables #-}
-
-module MRI
+-- | 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
@@ -8,7 +22,9 @@ 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 Values
 
 mri_depth :: Int
 mri_depth = 109
@@ -20,71 +36,85 @@ mri_height :: Int
 mri_height = 256
 
 mri_shape :: DIM3
-mri_shape = (Z :. mri_depth :. mri_width  :. mri_height)
+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)
 
+-- | RawData is an array of words (16 bits), as contained in the MRI
+--   data files.
 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)
 
-
-read_word16s :: IO RawData3D
-read_word16s = do
-  arr <- R.readArrayFromStorableFile "../data/mri.bin" mri_shape
+read_word16s :: FilePath -> IO RawData3D
+read_word16s path = do
+  arr <- R.readArrayFromStorableFile path 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)
+swap_bytes :: (Shape sh) => (RawData sh) -> (RawData sh)
+swap_bytes arr =
+    R.force $ R.map flip16 arr
+
+
+bracket_array :: (Shape sh) => (Values sh) -> (RawData sh)
 bracket_array arr =
-  R.map (bracket mri_lower_threshold mri_upper_threshold . fromIntegral . flip16) arr
+  R.force $ R.map bracket arr
+
+
+round_array :: (Shape sh) => (Values sh) -> (RawData sh)
+round_array arr =
+  R.force $ R.map round arr
+
 
 flip_y :: RawData3D -> RawData3D
 flip_y arr =
-  R.traverse arr id (\get (Z :. z :. y :. x) -> get (Z :. z :. (mri_height - 1) - y :. x))
+  R.force $ 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))
+  R.force $ R.traverse arr id
+              (\get (Z :. z :. y :. x) ->
+                   get (Z :. z :. y :. (mri_width - 1) - x))
 
 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
+values_to_colors :: (Shape sh) => (Values sh) -> (ColorData sh)
+values_to_colors arr =
+  R.force $ R.map (truncate_rgb . ramp_it) arr
   where
     ramp_it :: Double -> (Double, Double, Double)
     ramp_it x =
@@ -102,26 +132,19 @@ raw_data_to_color 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 :: Elt a => Int -> Array DIM3 a -> Array 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)
-  where
-    get_b :: (Double, Double, Double) -> Double
-    get_b (_, _, b) = b
 
 
+write_values_slice_to_bitmap :: Values2D -> FilePath -> IO ()
+write_values_slice_to_bitmap v3d path =
+  R.writeComponentsToBMP path routput goutput boutput
+  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