X-Git-Url: http://gitweb.michael.orlitzky.com/?a=blobdiff_plain;f=src%2FMRI.hs;h=52be3f7b1cba92c96d9bb64142ed7b3dd4acb546;hb=97117af7a6b89e64b84ac0d1a74734dd6ee9fa6c;hp=9f97b08777058ac001ebc6705b5507631b1792de;hpb=2032a8190ba101305a0e10300dbb7ec37b7daea1;p=spline3.git

diff --git a/src/MRI.hs b/src/MRI.hs
index 9f97b08..52be3f7 100644
--- a/src/MRI.hs
+++ b/src/MRI.hs
@@ -1,5 +1,3 @@
-{-# LANGUAGE ScopedTypeVariables #-}
-
 module MRI
 where
 
@@ -9,6 +7,7 @@ import Data.Array.Repa                  as R
 import Data.Array.Repa.IO.Binary        as R
 import Data.Array.Repa.IO.ColorRamp     as R
 
+import Values
 
 mri_depth :: Int
 mri_depth = 109
@@ -20,14 +19,16 @@ 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)
 
 type RawData sh = Array sh Word16
 type RawData3D = RawData DIM3
@@ -39,52 +40,61 @@ 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 f arr
+  where
+    f = bracket
+
 
 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 =
@@ -125,3 +135,26 @@ blue_dbl_data =
     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)
+
+
+transpose_zx :: Elt a => Array DIM3 a -> Array DIM3 a
+transpose_zx arr =
+  traverse arr
+           (\(Z :. zdim :. ydim :. xdim) -> (Z :. xdim :. ydim :. zdim))
+           (\_ -> (\(Z :. z :. y :. x) -> arr ! (Z :. x :. y :. z)))
+
+
+z_slice3 :: Elt a => Int -> Array DIM3 a -> Array DIM3 a
+z_slice3 n arr
+  | n == 0 = transpose_zx $ current R.++ next
+  | n == zdim-1 = transpose_zx $ previous R.++ current
+  | otherwise = transpose_zx $ previous R.++ current R.++ next
+  where
+    (Z :. zdim :. _ :. _) = extent arr
+    previous = transpose_zx $ reshape mri_slice3d (z_slice (n-1) arr)
+    current = transpose_zx $ reshape mri_slice3d (z_slice n arr)
+    next = transpose_zx $ reshape mri_slice3d (z_slice (n+1) arr)