Merge pull request #1976 from gdevenyi/update-commandline-docs

DOC: Update all command-line help to correspond to code

Author: ntustison

Examples/ANTSIntegrateVelocityField.cxx

@@ -163,8 +163,11 @@ ANTSIntegrateVelocityField(std::vector<std::string> args, std::ostream * /*out_s
 
   if (argc < 4)
   {
-    std::cerr << "Usage:   " << argv[0] << " reference_image  VelocityIn.mhd DeformationOut.nii.gz  time0 time1 dT  "
+    std::cerr << "Usage:   " << argv[0] << " reference_image VelocityIn.mhd DeformationOut.nii.gz time0 time1 dT  "
               << std::endl;
+    std::cerr << "  time0: start time for integration (e.g. 0)" << std::endl;
+    std::cerr << "  time1: end time for integration (e.g. 1)" << std::endl;
+    std::cerr << "  dT: time step for integration (e.g. 0.1)" << std::endl;
     if (argc >= 2 && (std::string(argv[1]) == std::string("--help") || std::string(argv[1]) == std::string("-h")))
     {
       return EXIT_SUCCESS;

Examples/ANTSJacobian.cxx

@@ -597,7 +597,7 @@ ANTSJacobian(std::vector<std::string> args, std::ostream * /*out_stream = nullpt
 
   if (argc < 3)
   {
-    std::cout << "Usage: " << argv[0] << " ImageDim gWarp outfile uselog maskfn normbytotalbool projectionvector "
+    std::cout << "Usage: " << argv[0] << " ImageDim gWarp outfile {uselog=0} {maskfn} {normbytotalbool=0} {projectionvector}"
               << std::endl;
     std::cout << " for example " << std::endl
               << " ANTSJacobian 3  myWarp.nii   Output  1   templatebrainmask.nii   1 1x0 " << std::endl;

Examples/ANTSUseDeformationFieldToGetAffineTransform.cxx

@@ -469,8 +469,8 @@ ANTSUseDeformationFieldToGetAffineTransform(std::vector<std::string> args, std::
               << " zzzWarp.nii.gz load_ratio(ex: 0.01) [rigid | affine] OutAffine.txt [mask.nii.gz]" << std::endl;
     std::cout << " we expect the input deformation field in the same physical space as the images you want to "
               << std::endl;
-    std::cout << "load_ratio: ratio of points to be loaded from deformation field (to save memory) " << std::endl;
-    std::cout << " the mask gives the region from which points will be selected ... " << std::endl;
+    std::cout << "load_ratio: ratio of points to be loaded from deformation field (to save memory, e.g. 0.01)" << std::endl;
+    std::cout << " mask.nii.gz: optional mask to restrict point selection (default: no mask)" << std::endl;
     if (argc >= 2 && (std::string(argv[1]) == std::string("--help") || std::string(argv[1]) == std::string("-h")))
     {
       return EXIT_SUCCESS;

Examples/AverageTensorImages.cxx

@@ -136,8 +136,8 @@ AverageTensorImages(std::vector<std::string> args, std::ostream * /*out_stream =
   {
     if (argc - 4 < 1)
     {
-      std::cerr << "Basic useage ex: " << std::endl;
-      std::cerr << argv[0] << " ImageDimension  average.nii mathtype list-of-files-via-wildcard " << std::endl;
+      std::cerr << "Usage: " << std::endl;
+      std::cerr << argv[0] << " ImageDimension average.nii mathtype list-of-files-via-wildcard " << std::endl;
       std::cerr << " e.g. \n   AverageTensorImages 3  average.nii  1  *registered.nii " << std::endl;
       std::cerr << " mathtype=[0=log-euclidean, 1=euclidean] " << std::endl;
       if (argc >= 2 && (std::string(argv[1]) == std::string("--help") || std::string(argv[1]) == std::string("-h")))

Examples/ClusterImageStatistics.cxx

@@ -334,16 +334,17 @@ ClusterImageStatistics(std::vector<std::string> args, std::ostream * /*out_strea
     std::cout << " Given an ROI and Label Image, find the max and average value   \n in a value image  where the value "
                  "> some user-defined threshold \n and the cluster size  is larger than some min size. \n "
               << std::endl;
-    std::cout << "Usage: \n  " << std::endl;
+    std::cout << "Usage: " << std::endl;
     std::cout << argv[0]
-              << "  ImageDimension ROIMask.ext LabelImage.ext  OutPrefix   MinimumClusterSize  ValueImageThreshold  "
-                 "Image1WithValuesOfInterest.ext ...  ImageNWithValuesOfInterest.ext  \n \n "
+              << " ImageDimension ROIMask.ext LabelImage.ext OutPrefix {MinimumClusterSize=1} {ValueImageThreshold=0} "
+                 "Image1WithValuesOfInterest.ext ... ImageNWithValuesOfInterest.ext"
               << std::endl;
-    std::cout << " ROIMask.ext -- overall region of interest \n  \n LabelImage.ext -- labels for the sub-regions, e.g. "
-                 "Brodmann or just unique labels (see  LabelClustersUniquely ) \n \n  OutputPrefix -- all output  has "
-                 "this prefix  \n \n  MinimumClusterSize -- the minimum size of clusters of interest  \n  \n "
-                 "ValueImageThreshold -- minimum value of interest \n \n   Image*WithValuesOfInterest.ext  ---  "
-                 "image(s) that define the values you want to measure \n ";
+    std::cout << "  ROIMask.ext -- overall region of interest" << std::endl;
+    std::cout << "  LabelImage.ext -- labels for sub-regions (see LabelClustersUniquely)" << std::endl;
+    std::cout << "  OutPrefix -- prefix for all output files" << std::endl;
+    std::cout << "  MinimumClusterSize -- minimum cluster size in voxels (default: 1)" << std::endl;
+    std::cout << "  ValueImageThreshold -- minimum value of interest (default: 0)" << std::endl;
+    std::cout << "  Image*WithValuesOfInterest.ext -- image(s) that define the values to measure" << std::endl;
     if (argc >= 2 && (std::string(argv[1]) == std::string("--help") || std::string(argv[1]) == std::string("-h")))
     {
       return EXIT_SUCCESS;

Examples/ComposeMultiTransform.cxx

@@ -330,7 +330,7 @@ ComposeMultiTransform(std::vector<std::string> args, std::ostream * /*out_stream
   {
     std::cout << "ComposeMultiTransform ImageDimension output_field [-R reference_image] "
               << "{[deformation_field | [-i] affine_transform_txt ]}" << std::endl;
-    std::cout << "  Usage has the same form as WarpImageMultiTransform " << std::endl;
+    std::cout << "  Composes multiple transforms (warp fields and/or affine) into a single combined transform." << std::endl;
     std::cout << " For Example: " << std::endl;
     std::cout << std::endl;
     std::cout << argv[0] << " Dimension  outwarp.nii   -R template.nii   ExistingWarp.nii  ExistingAffine.nii "

Examples/ConvertImagePixelType.cxx

@@ -138,7 +138,7 @@ ConvertImagePixelType(std::vector<std::string> args, std::ostream * /*out_stream
 
   if (argc < 3)
   {
-    std::cout << "Usage:   " << argv[0] << " infile.nii out.ext TYPE-OPTION " << std::endl;
+    std::cout << "Usage:   " << argv[0] << " infile.nii out.ext TYPE-OPTION (default: 0 = char) " << std::endl;
     std::cout << " ext is the extension you want, e.g. tif.  " << std::endl;
     std::cout << " TYPE-OPTION  :  TYPE " << std::endl;
     std::cout << "  0  :  char   " << std::endl;

Examples/ConvertInputImagePixelTypeToFloat.cxx

@@ -122,7 +122,8 @@ ConvertInputImagePixelTypeToFloat(std::vector<std::string> args, std::ostream *
 
   if (argc < 3)
   {
-    std::cout << "Usage:   " << argv[0] << " infile.nii out.ext TYPE-OPTION " << std::endl;
+    std::cout << "Usage:   " << argv[0] << " infile.nii out.ext TYPE-OPTION (default: 0 = char) " << std::endl;
+    std::cout << " TYPE-OPTION specifies the input image pixel type for reading (output is always float). " << std::endl;
     std::cout << " ext is the extension you want, e.g. tif.  " << std::endl;
     std::cout << " TYPE-OPTION  :  TYPE " << std::endl;
     std::cout << "  0  :  char   " << std::endl;

Examples/CopyImageHeaderInformation.cxx

@@ -173,7 +173,7 @@ CopyImageHeaderInformation(std::vector<std::string> args, std::ostream * /*out_s
   {
     std::cout << "Usage:  " << argv[0]
               << " refimage.ext imagetocopyrefimageinfoto.ext imageout.ext   boolcopydirection  boolcopyorigin "
-                 "boolcopyspacing  {bool-Image2-IsTensor}"
+                 "boolcopyspacing  {bool-Image2-IsTensor=0}"
               << std::endl;
     if (argc >= 2 && (std::string(argv[1]) == std::string("--help") || std::string(argv[1]) == std::string("-h")))
     {

Examples/CreateDTICohort.cxx

@@ -907,7 +907,7 @@ InitializeCommandLineOptions(itk::ants::CommandLineParser * parser)
                               std::string("images.  Van Hecke uses the noise-estimation method of Sijbers et ") +
                               std::string("al. \"Automatic estimation of the noise variance from the ") +
                               std::string("histogram of a magnetic resonance image\", Phys. Med. Biol. ") +
-                              std::string("52:1335-1348, 2007.");
+                              std::string("52:1335-1348, 2007.  Default = 0 (no noise added).");
 
     OptionType::Pointer option = OptionType::New();
     option->SetLongName("noise-sigma");