API: Replace .type_various()

cpp/cmd/fixel2peaks.cpp

@@ -47,8 +47,8 @@ void usage() {
   + Fixel::format_description;
 
   ARGUMENTS
-  + Argument ("in",  "the input fixel information").type_various ()
-  + Argument ("out", "the output peaks image").type_image_out ();
+  + Argument ("in",  "the input fixel information").type_directory_in().type_image_in()
+  + Argument ("out", "the output peaks image").type_image_out();
 
   OPTIONS
   + Option ("number", "maximum number of fixels in each voxel"

cpp/cmd/fixelcfestats.cpp

@@ -119,7 +119,7 @@ void usage() {
 
   // .type_various() rather than .type_directory_in() to catch people trying to
   //   pass a track file, and give a more informative error message
-  + Argument ("connectivity", "the fixel-fixel connectivity matrix").type_various ()
+  + Argument ("connectivity", "the fixel-fixel connectivity matrix").type_directory_in().type_tracks_in()
 
   + Argument ("out_fixel_directory", "the output directory where results will be saved."
                                      " Will be created if it does not exist").type_text();

cpp/cmd/fixelconvert.cpp

@@ -78,8 +78,8 @@ void usage() {
              " to indicate which fixel data files should be used as the source(s) of this information.");
 
   ARGUMENTS
-  + Argument ("fixel_in",  "the input fixel file / directory.").type_various()
-  + Argument ("fixel_out", "the output fixel file / directory.").type_various();
+  + Argument ("fixel_in",  "the input fixel file / directory.").type_directory_in().type_image_in()
+  + Argument ("fixel_out", "the output fixel file / directory.").type_directory_out().type_image_out();
 
   OPTIONS
   + OptionGroup ("Options for converting from old to new format")

cpp/cmd/fixelfilter.cpp

@@ -52,10 +52,10 @@ void usage() {
   + Fixel::format_description;
 
   ARGUMENTS
-  + Argument ("input", "the input: either a fixel data file, or a fixel directory (see Description)").type_various()
+  + Argument ("input", "the input: either a fixel data file, or a fixel directory (see Description)").type_image_in().type_directory_in()
   + Argument ("filter", "the filtering operation to perform;"
                         " options are: " + join (filters, ", ")).type_choice (filters)
-  + Argument ("output", "the output: either a fixel data file, or a fixel directory (see Description)").type_various();
+  + Argument ("output", "the output: either a fixel data file, or a fixel directory (see Description)").type_image_out().type_directory_out();
 
   OPTIONS
   + Option ("matrix", "provide a fixel-fixel connectivity matrix"

cpp/cmd/mrcalc.cpp

@@ -403,7 +403,7 @@ ARGUMENTS
   + Argument ("operand", "an input image,"
                          " intensity value,"
                          " or special keyword"
-                         " (see Description)").type_various().allow_multiple();
+                         " (see Description)").type_image_in().type_image_out().type_float().type_text().allow_multiple();
 
 OPTIONS
 

cpp/cmd/mrconvert.cpp

@@ -234,7 +234,7 @@ void usage() {
   + Option ("copy_properties",
             "clear all generic properties"
             " and replace with the properties from the image / file specified.")
-  + Argument ("source").type_various()
+  + Argument ("source").type_image_in().type_file_in()
 
   + Stride::Options
 

cpp/cmd/mtnormalise.cpp

@@ -72,7 +72,7 @@ void usage() {
 
   ARGUMENTS
   + Argument("input output", "list of all input and output tissue compartment files"
-                             " (see example usage).").type_various().allow_multiple();
+                             " (see example usage).").type_image_in().type_image_out().allow_multiple();
 
   OPTIONS
   + Option("mask", "the mask defines the data used to compute the intensity normalisation."

cpp/cmd/tckconvert.cpp

@@ -60,8 +60,8 @@ void usage() {
               " output-0000.txt, output-0001.txt, output-0002.txt, ...");
 
   ARGUMENTS
-    + Argument ("input", "the input track file.").type_various()
-    + Argument ("output", "the output track file.").type_file_out();
+    + Argument ("input", "the input track file.").type_tracks_in().type_file_in().type_text()
+    + Argument ("output", "the output track file.").type_tracks_out().type_file_out();
 
   OPTIONS
     + Option ("scanner2voxel",

cpp/cmd/tckmap.cpp

@@ -64,7 +64,7 @@ const OptionGroup OutputDimOption = OptionGroup ("Options for the dimensionality
       "(references an internal direction set),"
       " or a path to a text file containing a set of directions"
       " stored as azimuth/elevation pairs")
-    + Argument ("path").type_various()
+    + Argument ("path").type_file_in().type_integer()
   + Option ("tod",
       "generate a Track Orientation Distribution (TOD) in each voxel;"
       " need to specify the maximum spherical harmonic degree lmax to use"

cpp/cmd/transformcompose.cpp

@@ -92,7 +92,7 @@ void usage() {
   + Argument ("output", "the output file"
                         " (may be a linear transformation text file,"
                         " or a deformation warp field image,"
-                        " depending on usage)").type_various();
+                        " depending on usage)").type_file_out().type_image_out();
 
   OPTIONS
   + Option ("template", "define the output grid defined by a template image")