Use cmdargs to parse command-line arguments.

[spline3.git] / src / MRI.hs

diff --git a/src/MRI.hs b/src/MRI.hs
index 5cca1aed9ffcd2ab9250cd5883326fd45a59f087..1c244c1c81c8b738b95bcf5385d52290e536082a 100644 (file)
--- a/src/MRI.hs
+++ b/src/MRI.hs
@@ -7,8 +7,6 @@
 module MRI (
   flip_x,
   flip_y,
-  mri_shape,
-  mri_slice3d,
   read_word16s,
   round_array,
   swap_bytes,
@@ -30,27 +28,12 @@ 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 U sh Word16
@@ -63,8 +46,8 @@ type ColorData sh = Array U sh RGB
 
 
 {-# INLINE read_word16s #-}
-read_word16s :: FilePath -> IO RawData3D
-read_word16s path = do
+read_word16s :: FilePath -> DIM3 -> IO RawData3D
+read_word16s path mri_shape = do
   arr <- R.readArrayFromStorableFile path mri_shape
   c   <- R.copyP arr
   now $ c
@@ -105,17 +88,17 @@ round_array =
   R.map round
 
 
-flip_y :: Source r Word16 => Array r DIM3 Word16 -> Array D DIM3 Word16
-flip_y arr =
+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 :: Source r Word16 => Array r DIM3 Word16 -> Array D DIM3 Word16
-flip_x arr =
+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 #-}