X-Git-Url: https://gitweb.michael.orlitzky.com/?a=blobdiff_plain;f=src%2FCommandLine.hs;h=f413e2fb214b98840795c8c5201b8d18df517104;hb=02df1d5763a5d2bfe750bbc30b5c001ee9b23b17;hp=6479145b2693f6a36e48f53c33db4eb9b836d687;hpb=35b9e3c87866d956c1ffd34ec5f4823947f51fc2;p=spline3.git

diff --git a/src/CommandLine.hs b/src/CommandLine.hs
index 6479145..f413e2f 100644
--- a/src/CommandLine.hs
+++ b/src/CommandLine.hs
@@ -45,9 +45,11 @@ data Args =
   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)
 
@@ -65,35 +67,75 @@ spline3_summary :: String
 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