module Main
where
-import Data.Maybe (fromJust)
-import Control.Monad (when)
+import Control.Monad ( when )
import qualified Data.Array.Repa as R
-import Data.Maybe (isJust)
-import GHC.Conc (getNumProcessors, setNumCapabilities)
-import System.IO (hPutStrLn, stderr)
-import System.Exit (exitSuccess, exitWith, ExitCode(..))
+import Data.Maybe ( fromJust )
+import GHC.Conc ( getNumProcessors, setNumCapabilities )
+import System.IO ( hPutStrLn, stderr )
+import System.Exit ( exitSuccess, exitWith, ExitCode(..) )
-import CommandLine (Args(..), apply_args)
+import CommandLine ( Args(..), apply_args )
import ExitCodes
-import Grid (zoom)
-import MRI (
+import Grid ( zoom )
+import Volumetric (
+ bracket_array,
flip_x,
flip_y,
read_word16s,
round_array,
swap_bytes,
- write_values_slice_to_bitmap,
+ write_values_to_bmp,
write_word16s,
- z_slice
- )
+ z_slice )
validate_args :: Args -> IO ()
num_procs <- getNumProcessors
setNumCapabilities num_procs
+ let shape = (R.Z R.:. depth R.:. height R.:. width) :: R.DIM3
+
-- Determine whether we're doing 2d or 3d. If we're given a slice,
-- assume 2d.
- let mri_shape = (R.Z R.:. depth R.:. height R.:. width) :: R.DIM3
-
- if (isJust slice) then
- main2d args mri_shape
- else
- main3d args mri_shape
+ let main_function = case slice of
+ Nothing -> main3d
+ Just _ -> main2d
+ main_function args shape
exitSuccess
- where
-
-
main3d :: Args -> R.DIM3 -> IO ()
-main3d Args{..} mri_shape = do
+main3d Args{..} shape = do
let zoom_factor = (scale, scale, scale)
- arr <- read_word16s input mri_shape
- let arr' = swap_bytes arr
- let arrMRI = R.reshape mri_shape arr'
- dbl_data <- R.computeUnboxedP $ R.map fromIntegral arrMRI
+ arr <- read_word16s input shape
+ let arr_swapped = swap_bytes arr
+ let arr_shaped = R.reshape shape arr_swapped
+ dbl_data <- R.computeUnboxedP $ R.map fromIntegral arr_shaped
raw_output <- zoom dbl_data zoom_factor
- word16_output <- R.computeUnboxedP $ round_array raw_output
- write_word16s output word16_output
+ let word16_output = round_array raw_output
+ -- Switch the bytes order back to what it was. This lets us use the
+ -- same program to view the input/output data.
+ swapped_output <- R.computeUnboxedP $ swap_bytes word16_output
+ write_word16s output swapped_output
main2d :: Args -> R.DIM3 -> IO ()
-main2d Args{..} mri_shape = do
+main2d Args{..} shape = do
let zoom_factor = (1, scale, scale)
- arr <- read_word16s input mri_shape
+ arr <- read_word16s input shape
arrSlice <- R.computeUnboxedP
$ z_slice (fromJust slice)
$ flip_x width
$ flip_y height
$ swap_bytes arr
- let arrSlice' = R.reshape mri_slice3d arrSlice
+ let arrSlice' = R.reshape slice3d arrSlice
-- If zoom isn't being inlined we need to extract the slice before hand,
-- and convert it to the require formed.
- dbl_data <- R.computeUnboxedP $ R.map fromIntegral arrSlice'
- raw_output <- zoom dbl_data zoom_factor
- arrSlice0 <- R.computeUnboxedP $ z_slice 0 raw_output
+ dbl_data <- R.computeUnboxedP $ R.map fromIntegral arrSlice'
+ raw_output <- zoom dbl_data zoom_factor
+ arrSlice0 <- R.computeUnboxedP $ z_slice 0 raw_output
+
+ -- Make doubles from the thresholds which are given as Ints.
+ let lt = fromIntegral lower_threshold
+ let ut = fromIntegral upper_threshold
+
+ let arr_bracketed = bracket_array lt ut arrSlice0
+ values <- R.computeUnboxedP $ R.map fromIntegral arr_bracketed
+ write_values_to_bmp output values
- write_values_slice_to_bitmap arrSlice0 output
where
- mri_slice3d :: R.DIM3
- mri_slice3d = (R.Z R.:. 1 R.:. height R.:. width)
+ slice3d :: R.DIM3
+ slice3d = (R.Z R.:. 1 R.:. height R.:. width)