Update some documentation.

[spline3.git] / src / MRI.hs

diff --git a/src/MRI.hs b/src/MRI.hs
index ce1bb7d9d078e567ebde68323d1b112e4e9166f3..c142dcd22b4d74e5b815841b894e212181131791 100644 (file)
--- a/src/MRI.hs
+++ b/src/MRI.hs
@@ -1,4 +1,20 @@
-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
@@ -6,6 +22,7 @@ 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
 
@@ -21,24 +38,25 @@ 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)
 
+-- | 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 :: FilePath -> IO RawData3D
 read_word16s path = do
@@ -47,19 +65,17 @@ read_word16s path = do
   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 =
   shift xx 8 .|. (shift xx (-8) .&. 0x00ff)
@@ -69,11 +85,15 @@ swap_bytes :: (Shape sh) => (RawData sh) -> (RawData sh)
 swap_bytes arr =
     R.force $ R.map flip16 arr
 
-bracket_array :: (Shape sh) => (RawData sh) -> (RawData sh)
+
+bracket_array :: (Shape sh) => (Values sh) -> (RawData sh)
 bracket_array arr =
-  R.force $ R.map f arr
-  where
-    f = (bracket mri_lower_threshold mri_upper_threshold) . fromIntegral
+  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
@@ -112,30 +132,19 @@ 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
-
-
-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
-
-
 
 z_slice :: Elt a => Int -> Array DIM3 a -> Array DIM2 a
 z_slice n arr =
   slice arr (Any :. n :. All :. All)
+
+
+
+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