Use cmdargs to parse command-line arguments.

[spline3.git] / src / MRI.hs

diff --git a/src/MRI.hs b/src/MRI.hs
index c142dcd22b4d74e5b815841b894e212181131791..1c244c1c81c8b738b95bcf5385d52290e536082a 100644 (file)
--- a/src/MRI.hs
+++ b/src/MRI.hs
@@ -1,3 +1,4 @@
+{-# LANGUAGE FlexibleContexts #-}
 -- | The MRI module contains functionsd and definitions relevant (and
 --   specific) to the MRI data files found at,
 --
@@ -6,8 +7,6 @@
 module MRI (
   flip_x,
   flip_y,
-  mri_shape,
-  mri_slice3d,
   read_word16s,
   round_array,
   swap_bytes,
@@ -19,50 +18,40 @@ where
 
 import Data.Word
 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 Data.Array.Repa                          as R
+import Data.Array.Repa.Eval                     as R (now)
+import Data.Array.Repa.Repr.Unboxed             as R
+import Data.Array.Repa.IO.Binary                as R
+import Data.Array.Repa.Algorithms.ColorRamp     as R
+import Data.Array.Repa.Operators.Traversal      as R (unsafeTraverse)
+import Data.Array.Repa.IO.BMP                   as R (writeImageToBMP)
 
 import Values
 
-mri_depth :: Int
-mri_depth = 109
-
-mri_width :: Int
-mri_width = 256
-
-mri_height :: Int
-mri_height = 256
-
-mri_shape :: DIM3
-mri_shape = (Z :. mri_depth :. mri_height :. mri_width)
-
 mri_lower_threshold :: Double
 mri_lower_threshold = 1400
 
 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
+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
+type ColorData sh = Array U sh RGB
 
 
-read_word16s :: FilePath -> IO RawData3D
-read_word16s path = do
+{-# INLINE read_word16s #-}
+read_word16s :: FilePath -> DIM3 -> IO RawData3D
+read_word16s path mri_shape = do
   arr <- R.readArrayFromStorableFile path mri_shape
-  arr `deepSeqArray` return ()
-  return arr
+  c   <- R.copyP arr
+  now $ c
+
 
 
 bracket :: Double -> Word16
@@ -81,40 +70,50 @@ flip16 xx =
   shift xx 8 .|. (shift xx (-8) .&. 0x00ff)
 
 
-swap_bytes :: (Shape sh) => (RawData sh) -> (RawData sh)
-swap_bytes arr =
-    R.force $ R.map flip16 arr
+{-# INLINE swap_bytes #-}
+swap_bytes :: (Shape sh, Source r Word16) => Array r sh Word16
+             -> Array D sh Word16
+swap_bytes =
+  R.map flip16
 
 
-bracket_array :: (Shape sh) => (Values sh) -> (RawData sh)
-bracket_array arr =
-  R.force $ R.map bracket arr
+bracket_array :: Shape sh => Values sh -> Array D sh Word16
+bracket_array =
+  R.map bracket
 
 
-round_array :: (Shape sh) => (Values sh) -> (RawData sh)
-round_array arr =
-  R.force $ R.map round arr
+{-# INLINE round_array #-}
+round_array :: Shape sh => Values sh -> Array D sh Word16
+round_array =
+  R.map round
 
 
-flip_y :: RawData3D -> RawData3D
-flip_y arr =
-  R.force $ R.traverse arr id
+flip_y :: Source r Word16 => Int -> Array r DIM3 Word16 -> Array D DIM3 Word16
+flip_y height arr =
+  R.unsafeTraverse arr id
               (\get (Z :. z :. y :. x) ->
-                   get (Z :. z :. (mri_height - 1) - y :. x))
+                   get (Z :. z :. (height - 1) - y :. x))
 
-flip_x :: RawData3D -> RawData3D
-flip_x arr =
-  R.force $ R.traverse arr id
+flip_x :: Source r Word16 => Int -> Array r DIM3 Word16 -> Array D DIM3 Word16
+flip_x width arr =
+  R.unsafeTraverse arr id
               (\get (Z :. z :. y :. x) ->
-                   get (Z :. z :. y :. (mri_width - 1) - x))
+                   get (Z :. z :. y :. (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)
+
+--
+-- Instead of IO, we could get away with a generic monad 'm'
+-- here. However, /we/ only call this function from within IO.
+--
+values_to_colors :: (Shape sh) => (Values sh) -> IO (ColorData sh)
 values_to_colors arr =
-  R.force $ R.map (truncate_rgb . ramp_it) arr
+  R.computeUnboxedP $ R.map (truncate_rgb . ramp_it) arr
   where
     ramp_it :: Double -> (Double, Double, Double)
     ramp_it x =
@@ -132,19 +131,15 @@ values_to_colors arr =
         b' = truncate (b * 255)
 
 
-
-z_slice :: Elt a => Int -> Array DIM3 a -> Array DIM2 a
+z_slice :: (R.Unbox a, Source r a) => Int -> Array r DIM3 a -> Array D 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
+write_values_slice_to_bitmap v3d path = do
+  values <- R.computeUnboxedP $ R.map fromIntegral arr_bracketed
+  colors <- values_to_colors $ values
+  R.writeImageToBMP path colors
   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