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 Values
mri_shape :: DIM3
mri_shape = (Z :. mri_depth :. mri_height :. mri_width)
-mri_lower_threshold :: Int
+mri_lower_threshold :: Double
mri_lower_threshold = 1400
-mri_upper_threshold :: Int
+mri_upper_threshold :: Double
mri_upper_threshold = 2500
mri_slice3d :: DIM3
{-# INLINE bracket #-}
-bracket :: Int -> Int -> Int -> Word16
-bracket low high x
- | x < low = 0
- | x > high = 255
- | otherwise = truncate (r * 255)
+bracket :: Double -> Word16
+bracket x
+ | x < mri_lower_threshold = 0
+ | x > mri_upper_threshold = 255
+ | otherwise = truncate (r * 255)
where
- numerator = fromIntegral (x - low) :: Double
- denominator = fromIntegral (high - low) :: Double
+ numerator = x - mri_lower_threshold
+ denominator = mri_upper_threshold - mri_lower_threshold
r = numerator/denominator
{-# INLINE flip16 #-}
flip16 :: Word16 -> Word16
-flip16 xx =
+flip16 xx =
shift xx 8 .|. (shift xx (-8) .&. 0x00ff)
-bracket_array :: (Shape sh) => (RawData sh) -> (RawData sh)
+swap_bytes :: (Shape sh) => (RawData sh) -> (RawData sh)
+swap_bytes arr =
+ R.force $ R.map flip16 arr
+
+bracket_array :: (Shape sh) => (Values sh) -> (RawData sh)
bracket_array arr =
- R.map (bracket mri_lower_threshold mri_upper_threshold . fromIntegral . flip16) arr
+ R.force $ R.map f arr
+ where
+ f = bracket
+
flip_y :: RawData3D -> RawData3D
flip_y arr =
- R.traverse arr id (\get (Z :. z :. y :. x) -> get (Z :. z :. (mri_height - 1) - y :. x))
+ R.force $ R.traverse arr id
+ (\get (Z :. z :. y :. x) ->
+ get (Z :. z :. (mri_height - 1) - y :. x))
flip_x :: RawData3D -> RawData3D
flip_x arr =
- R.traverse arr id (\get (Z :. z :. y :. x) -> get (Z :. z :. y :. (mri_width - 1) - x))
+ R.force $ 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 = R.writeArrayToStorableFile
z_slice :: Elt a => Int -> Array DIM3 a -> Array DIM2 a
z_slice n arr =
slice arr (Any :. n :. All :. All)
+
+
+transpose_zx :: Elt a => Array DIM3 a -> Array DIM3 a
+transpose_zx arr =
+ traverse arr
+ (\(Z :. zdim :. ydim :. xdim) -> (Z :. xdim :. ydim :. zdim))
+ (\_ -> (\(Z :. z :. y :. x) -> arr ! (Z :. x :. y :. z)))
+
+
+z_slice3 :: Elt a => Int -> Array DIM3 a -> Array DIM3 a
+z_slice3 n arr
+ | n == 0 = transpose_zx $ current R.++ next
+ | n == zdim-1 = transpose_zx $ previous R.++ current
+ | otherwise = transpose_zx $ previous R.++ current R.++ next
+ where
+ (Z :. zdim :. _ :. _) = extent arr
+ previous = transpose_zx $ reshape mri_slice3d (z_slice (n-1) arr)
+ current = transpose_zx $ reshape mri_slice3d (z_slice n arr)
+ next = transpose_zx $ reshape mri_slice3d (z_slice (n+1) arr)
+
+
+write_values_slice_to_bitmap :: Values2D -> FilePath -> IO ()
+write_values_slice_to_bitmap v3d path =
+ R.writeComponentsToBMP path routput goutput boutput
+ 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
+
+
+write_values_chunk_to_bitmap :: Values3D -> FilePath -> IO ()
+write_values_chunk_to_bitmap v3d path
+ | zdim /= 3 = error "not a 3xMxN chunk"
+ | otherwise = write_values_slice_to_bitmap target_slice path
+ where
+ (Z :. zdim :. _ :. _) = extent v3d
+ target_slice = z_slice 1 v3d
+