Rename MRI to Volumetric.
Args { depth :: Int,
height :: Int,
input :: FilePath,
+ lower_threshold :: Int,
+ output :: FilePath,
scale :: Int,
slice :: Maybe Int,
- output :: FilePath,
+ upper_threshold :: Int,
width :: Int }
deriving (Show, Data, Typeable)
spline3_summary =
program_name ++ "-" ++ (showVersion version)
+depth_default :: Int
+depth_default = 109
+
depth_help :: String
-depth_help = "The size of the z dimension (default: 109)"
+depth_help =
+ "The size of the z dimension (default: " ++ (show depth_default) ++ ")"
+
+height_default :: Int
+height_default = 256
height_help :: String
-height_help = "The size of the y dimension (default: 256)"
+height_help =
+ "The size of the y dimension (default: " ++ (show height_default) ++ ")"
+
+lower_threshold_default :: Int
+lower_threshold_default = 1400
+
+lower_threshold_help :: String
+lower_threshold_help =
+ "The lower limit for voxel values, only used in 2D (default: " ++
+ (show lower_threshold_default) ++ ")"
+
+scale_default :: Int
+scale_default = 2
scale_help :: String
scale_help =
"The magnification scale. A scale of 2 would result " ++
- "in an image twice as large as the original. (default: 2)"
+ "in an image twice as large as the original. (default: " ++
+ (show scale_default) ++ ")"
slice_help :: String
slice_help =
"The index of the two-dimensional slice to use if no depth is specified"
+upper_threshold_default :: Int
+upper_threshold_default = 2500
+
+upper_threshold_help :: String
+upper_threshold_help =
+ "The upper limit for voxel values, only used in 2D (default: " ++
+ (show upper_threshold_default) ++ ")"
+
+width_default :: Int
+width_default = 256
+
width_help :: String
-width_help = "The size of the x dimension (default: 256)"
+width_help =
+ "The size of the x dimension (default: " ++ (show width_default) ++ ")"
arg_spec :: Mode (CmdArgs Args)
arg_spec =
cmdArgsMode $
Args {
- depth = 109 &= groupname "Dimensions" &= help depth_help,
- height = 256 &= groupname "Dimensions" &= help height_help,
- input = def &= typ "INPUT" &= argPos 0,
- output = def &= typ "OUTPUT" &= argPos 1,
- scale = 2 &= help scale_help,
- slice = Nothing &= groupname "2D options" &= help slice_help,
- width = 256 &= groupname "Dimensions" &= help width_help
+ depth = depth_default &= groupname "Dimensions" &= help depth_help,
+ height = height_default &= groupname "Dimensions" &= help height_help,
+ input = def &= typ "INPUT" &= argPos 0,
+
+ lower_threshold = lower_threshold_default &= groupname "2D options"
+ &= help lower_threshold_help,
+
+ output = def &= typ "OUTPUT" &= argPos 1,
+ scale = scale_default &= help scale_help,
+ slice = Nothing &= groupname "2D options" &= help slice_help,
+
+ upper_threshold = upper_threshold_default &= groupname "2D options"
+ &= help upper_threshold_help,
+
+ width = width_default &= groupname "Dimensions" &= help width_help
}
&= program program_name
&= summary spline3_summary
import FunctionValues as X
import Grid as X
import Misc as X
-import MRI as X
import Point as X
import RealFunction as X
import Tetrahedron as X
import Values as X
+import Volumetric as X
\ No newline at end of file
import CommandLine (Args(..), apply_args)
import ExitCodes
import Grid (zoom)
-import MRI (
+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
)
-- 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
+ let shape = (R.Z R.:. depth R.:. height R.:. width) :: R.DIM3
if (isJust slice) then
- main2d args mri_shape
+ main2d args shape
else
- main3d args mri_shape
+ main3d args shape
exitSuccess
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
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)
{-# LANGUAGE FlexibleContexts #-}
--- | The MRI module contains functionsd and definitions relevant (and
--- specific) to the MRI data files found at,
+-- | The Volumetric module contains functions for manipulating the
+-- volumetric data files found at,
--
--- <http://graphics.stanford.edu/data/voldata/>
+-- <http://graphics.stanford.edu/data/voldata/>
--
-module MRI (
+module 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
)
import Values
-mri_lower_threshold :: Double
-mri_lower_threshold = 1400
-
-mri_upper_threshold :: Double
-mri_upper_threshold = 2500
-
--- | RawData is an array of words (16 bits), as contained in the MRI
--- data files.
+-- | RawData is an array of words (16 bits), as contained in the
+-- volumetric data files.
type RawData sh = Array U sh Word16
-- | A specialization of the 'RawData' type, to three dimensions.
{-# INLINE read_word16s #-}
read_word16s :: FilePath -> DIM3 -> IO RawData3D
-read_word16s path mri_shape = do
- arr <- R.readArrayFromStorableFile path mri_shape
+read_word16s path shape = do
+ arr <- R.readArrayFromStorableFile path shape
c <- R.copyP arr
now $ c
-bracket :: Double -> Word16
-bracket x
- | x < mri_lower_threshold = 0
- | x > mri_upper_threshold = 255
+bracket :: Double -> Double -> Double -> Word16
+bracket lower_threshold upper_threshold x
+ | x < lower_threshold = 0
+ | x > upper_threshold = 255
| otherwise = truncate (r * 255)
where
- numerator = x - mri_lower_threshold
- denominator = mri_upper_threshold - mri_lower_threshold
+ numerator = x - lower_threshold
+ denominator = upper_threshold - lower_threshold
r = numerator/denominator
R.map flip16
-bracket_array :: Shape sh => Values sh -> Array D sh Word16
-bracket_array =
- R.map bracket
+bracket_array :: Shape sh => Double -> Double -> Values sh -> Array D sh Word16
+bracket_array lt ut =
+ R.map (bracket lt ut)
{-# INLINE round_array #-}
b' = truncate (b * 255)
+write_values_to_bmp :: FilePath -> Values2D -> IO ()
+write_values_to_bmp path values = do
+ colors <- values_to_colors values
+ R.writeImageToBMP path colors
+
+
z_slice :: (R.Unbox a, Source r a) => Int -> Array r DIM3 a -> Array D DIM2 a
z_slice n arr =
slice arr (Any :. n :. All :. All)
-
-
-write_values_slice_to_bitmap :: Values2D -> FilePath -> IO ()
-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
projects / spline3.git / commitdiff