Modify Main/MRI to operate on the scalar values (as opposed to the individual RGB...

[spline3.git] / src / MRI.hs

diff --git a/src/MRI.hs b/src/MRI.hs
index 9f97b08777058ac001ebc6705b5507631b1792de..040dcc2a521ed9553974bca43e8fe23df9a63541 100644 (file)
--- 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
@@ -20,7 +19,7 @@ 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 = 1400
@@ -28,6 +27,8 @@ mri_lower_threshold = 1400
 mri_upper_threshold :: Int
 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
@@ -39,9 +40,9 @@ 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
 
@@ -77,14 +78,12 @@ flip_x arr =
   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 +124,7 @@ 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)