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

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)

diff --git a/src/Main.hs b/src/Main.hs
index c9165d3e3dc71287cdcee00590a5e35142a6e40b..f21856f41e0879189c10ebe84aeb550ee4688bb5 100644 (file)
--- a/src/Main.hs
+++ b/src/Main.hs
@@ -1,73 +1,35 @@
 module Main
 where
 
-import Data.Array.Repa (
-  DIM2,
-  DIM3,
-  Z(..),
-  (:.)(..),
-  slice,
-  reshape,
-  Any(..),
-  All(..)
-  )
-import qualified Data.Array.Repa as R (map)
-
-import Data.Array.Repa.IO.BMP (writeComponentsToBMP)
-import Data.Word
+import qualified Data.Array.Repa as R (map, reshape)
+import qualified Data.Array.Repa.IO.BMP as R (writeComponentsToBMP)
 import System.Environment (getArgs)
 
 import Grid (make_grid, zoom)
 import MRI
-import Values (read_values_3d, write_values_1d)
+import Values (drop_z, zoom_shape)
 
-mri_shape2d :: DIM2
-mri_shape2d = (Z :. 256*2 :. 256*2)
+zoom_factor :: (Int, Int, Int)
+zoom_factor = (1,2,2)
 
-mri_shape3d :: DIM3
-mri_shape3d = (Z :. 256 :. 256 :. 1)
 
 main :: IO ()
 main = do
 --  args <- getArgs
 --  let color = head args
---  let in_file  = "./data/MRbrain.40." ++ color
-  let out_file = "MRbrain.50.red.out"
-  arr <- read_word16s
+  let in_file = "./data/mri.bin"
+  let out_file = "output.bmp"
+  arr <- read_word16s in_file
   let arrBrack = bracket_array arr
   let arrInv   = flip_x $ flip_y arrBrack
-  let arrSlice = slice arrInv (Any :. (50 :: Int) :. All :. All)
-  let arrColor = raw_data_to_color arrSlice
-
-  let arrColor' = reshape mri_shape3d arrColor
-  let rdata = red_dbl_data arrColor'
-  let gdata = green_dbl_data arrColor'
-  let bdata = blue_dbl_data arrColor'
-
---  mridata <- read_values_3d mri_shape in_file
-
-  let gr = make_grid 1 rdata
-  let routput = zoom gr (2,2,1)
-
-  let gg = make_grid 1 gdata
-  let goutput = zoom gg (2,2,1)
-
-  let gb = make_grid 1 bdata
-  let boutput = zoom gb (2,2,1)
-
-  let routput' = R.map double_to_word8 (reshape mri_shape2d routput)
-  let goutput' = R.map double_to_word8 (reshape mri_shape2d goutput)
-  let boutput' = R.map double_to_word8 (reshape mri_shape2d boutput)
-
---  write_values_1d output out_file
-  writeComponentsToBMP out_file routput' goutput' boutput'
-  where
-    double_to_word8 :: Double -> Word8
-    double_to_word8 x =
-      if x > 255 then
-        255 :: Word8
-      else
-        if x < 0 then
-          0 :: Word8
-        else
-          fromIntegral $ truncate x
+  let arrSlice = z_slice 50 arrInv
+  let arrSlice' = R.reshape mri_slice3d arrSlice
+  let dbl_data = R.map fromIntegral arrSlice'
+  let g = make_grid 1 dbl_data
+  let output = zoom g zoom_factor
+  let mri_slice2d = drop_z $ zoom_shape zoom_factor mri_slice3d
+  let colors = values_to_colors $ R.reshape mri_slice2d output
+  let routput = R.map (\(red, _,     _)    -> red)   colors
+  let goutput = R.map (\(_,   green, _)    -> green) colors
+  let boutput = R.map (\(_,   _,     blue) -> blue)  colors
+  R.writeComponentsToBMP out_file routput goutput boutput