From b6ce041d136d56fb3d0638c4abadbae64b94b2e5 Mon Sep 17 00:00:00 2001
From: Michael Orlitzky <michael@orlitzky.com>
Date: Tue, 17 Apr 2012 00:01:40 -0400
Subject: [PATCH] Fix all of the sequential operations with the caveat that it
 now segfaults.

---
 src/Grid.hs | 18 +++++++++++-------
 src/MRI.hs  | 16 +++++++++++-----
 src/Main.hs | 17 +++++++++--------
 3 files changed, 31 insertions(+), 20 deletions(-)

diff --git a/src/Grid.hs b/src/Grid.hs
index 192bbaf..953c6a3 100644
--- a/src/Grid.hs
+++ b/src/Grid.hs
@@ -118,15 +118,19 @@ zoom_result v3d (sfx, sfy, sfz) (R.Z R.:. m R.:. n R.:. o) =
     f = polynomial t
 
 
-zoom :: Values3D -> ScaleFactor -> Values3D
+--
+-- Instead of IO, we could get away with a generic monad 'm'
+-- here. However, /we/ only call this function from within IO.
+--
+zoom :: Values3D -> ScaleFactor -> IO Values3D
 zoom v3d scale_factor
-    | xsize == 0 || ysize == 0 || zsize == 0 = empty3d
+    | xsize == 0 || ysize == 0 || zsize == 0 = return empty3d
     | otherwise =
-        R.computeS $ R.unsafeTraverse v3d transExtent f
-          where
-            (xsize, ysize, zsize) = dims v3d
-            transExtent = zoom_shape scale_factor
-            f = zoom_lookup v3d scale_factor
+        R.computeUnboxedP $ R.unsafeTraverse v3d transExtent f
+        where
+          (xsize, ysize, zsize) = dims v3d
+          transExtent = zoom_shape scale_factor
+          f = zoom_lookup v3d scale_factor
 
 
 -- | Check all coefficients of tetrahedron0 belonging to the cube
diff --git a/src/MRI.hs b/src/MRI.hs
index 094991c..d741091 100644
--- a/src/MRI.hs
+++ b/src/MRI.hs
@@ -66,7 +66,8 @@ type ColorData sh = Array U sh RGB
 read_word16s :: FilePath -> IO RawData3D
 read_word16s path = do
   arr <- R.readArrayFromStorableFile path mri_shape
-  now $ R.copyS arr
+  c   <- R.copyP arr
+  now $ c
 
 
 
@@ -123,9 +124,13 @@ 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.computeS $ 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 =
@@ -149,8 +154,9 @@ z_slice n arr =
 
 
 write_values_slice_to_bitmap :: Values2D -> FilePath -> IO ()
-write_values_slice_to_bitmap v3d path =
+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.computeS $ R.map fromIntegral arr_bracketed
diff --git a/src/Main.hs b/src/Main.hs
index c1456f4..1a71683 100644
--- a/src/Main.hs
+++ b/src/Main.hs
@@ -34,10 +34,11 @@ main3d = do
   arr <- read_word16s in_file
   let arr'          = swap_bytes arr
   let arrMRI        = R.reshape mri_shape arr'
-  let dbl_data      = R.computeS $ R.map fromIntegral arrMRI
-  let output        = zoom dbl_data zoom_factor
-  let word16_output = R.computeS $ round_array output
+  dbl_data <- R.computeUnboxedP $ R.map fromIntegral arrMRI
+  output <- zoom dbl_data zoom_factor
+  word16_output <- R.computeUnboxedP $ round_array output
   write_word16s out_file word16_output
+  return ()
 
 
 main2d :: IO ()
@@ -46,14 +47,14 @@ main2d = do
   let scale = read s :: Int
   let zoom_factor = (1, scale, scale)
   let out_file = "output.bmp"
-  arr           <- read_word16s in_file
-  let arrSlice  = R.computeUnboxedS $ z_slice 50 $ flip_x $ flip_y $ swap_bytes arr
+  arr <- read_word16s in_file
+  arrSlice <- R.computeUnboxedP $ z_slice 50 $ flip_x $ flip_y $ swap_bytes arr
   let arrSlice' = R.reshape mri_slice3d arrSlice
 
   -- If zoom isn't being inlined we need to extract the slice before hand,
   -- and convert it to the require formed.
-  let dbl_data  = R.computeS $ R.map fromIntegral arrSlice'
-  let output    = zoom dbl_data zoom_factor
-  let arrSlice0 = R.computeUnboxedS $ z_slice 0 output
+  dbl_data      <- R.computeUnboxedP $ R.map fromIntegral arrSlice'
+  output        <- zoom dbl_data zoom_factor
+  arrSlice0     <- R.computeUnboxedP $ z_slice 0 output
   
   write_values_slice_to_bitmap arrSlice0 out_file
-- 
2.44.2