From Benoit P, use clitkDicomRTStruct2Image with image with direction cosine

[clitk.git] / tools / clitkDicomRTStruct2Image.ggo

diff --git a/tools/clitkDicomRTStruct2Image.ggo b/tools/clitkDicomRTStruct2Image.ggo
index 33fb3b75c4931a70c1625c4aaa1e984f70381575..861f31346b257bebf51d005a8871ca62ab2b5d70 100644 (file)
--- a/tools/clitkDicomRTStruct2Image.ggo
+++ b/tools/clitkDicomRTStruct2Image.ggo
@@ -1,22 +1,24 @@
 # file clitkDicomRTStruct2BinaryImage.ggo
 package "clitk"
-version "Convert DICOM RT Structure Set (contours) to binary image"
+version "1.0"
+description "Convert DICOM RT Structure Set (contours) to binary image"
 
-option "config"                 - "Config file"                     string     no
-option "verbose"         v "Verbose"                        flag       off
-option "verboseFile"     - "Verbose file content"            flag      off
-option "input"          i "Input Dicom file"                string     yes
-option "image"          j "Used to read image info (spacing, origin)"    string        yes
-option "output"                 o "Output image filename"       string yes
+option "config"       - "Config file"                                                           string  no
+option "verbose"      v "Verbose"                                                               flag    off
+option "verboseFile"  - "Verbose file content"                                                  flag    off
+option "input"        i "Input Dicom file"                                                      string  yes
+option "image"        j "Used to read image info (spacing, origin)"                             string  yes
+option "output"       o "Output image base filename (roi number and extension will be append)"  string  yes
+option "tolerance"    t "Tolerance for slice position"                                          double  no  default="0"
 
-defgroup "ROIoption" groupdesc="an option of this group is required" 
-groupoption "roi"     r "ROI to binarize (if -1 = all roi)"            int    no default="-1" group="ROIoption"
-groupoption "roiName"     n "ROI name to binarize (be wary of spaces in ROI names; if blank, use given 'roi' value)"            string    no default="" group="ROIoption"
-groupoption "roiNameSubstr"     s "Substring of ROI name to binarize (reuturns all matches; if blank, use given 'roiName' value)"            string    no default="" group="ROIoption"
-
-option "crop"           c "Crop binary mask"            flag off
-
-#option "roi"           r "ROI to print (ID)"           int            no
-#option "contour"       c "contour to print (ID)"       int            no
-#option "offset"                o "to display points as image offsets" flag    off
+text "\nOutput options - the default output format is mhd"
+option "crop"         c "Crop binary mask"                                                      flag off
+option "mha"          - "Write the RTStruct as a mha image to avoid special character problems" flag off
+option "nii"          - "Write the RTStruct as a nii image"                                     flag off
+option "niigz"        - "Write the RTStruct as a gzipped nii image"                             flag off
+option "vtk"          - "Write the vtk Mesh as a vtk file"                                      flag off
 
+defgroup "ROI option" groupdesc="an option of this group is required"
+groupoption "roi"           r "ROI number to binarize (if -1 = all roi)"                                                      int     no default="-1" group="ROI option"
+groupoption "roiName"       n "ROI name to binarize (be wary of spaces in ROI names; if blank, use given 'roi' value)"        string  no default=""   group="ROI option"
+groupoption "roiNameSubstr" s "Substring of ROI name to binarize (returns all matches; if blank, use given 'roiName' value)"  string  no default=""   group="ROI option"