API: Replace .type_various()

.github/workflows/checks.yml

@@ -57,9 +57,15 @@ jobs:
     - name: build
       run: cmake --build build
 
+    - name: interface tests
+      run: cd build && ctest -L cli --output-on-failure
+
     - name: unit tests
       run: cd build && ctest -L unittest --output-on-failure --parallel 4
 
+    - name: compatibility tests
+      run: cd build && ctest -L compatibility --output-on-failure
+
     - name: binary tests
       run: cd build && ctest -L binary --output-on-failure
 #
@@ -116,9 +122,15 @@ jobs:
     - name: build
       run: cmake --build build
 
+    - name: interface tests
+      run: cd build && ctest -L cli --output-on-failure
+
     - name: unit tests
       run: cd build && ctest -L unittest --output-on-failure --parallel 4
 
+    - name: compatibility tests
+      run: cd build && ctest -L compatibility --output-on-failure
+
     - name: binary tests
       run: cd build && ctest -L binary --output-on-failure
 #
@@ -171,9 +183,15 @@ jobs:
     - name: build
       run: cmake --build build
 
+    - name: interface tests
+      run: cd build && ctest -L cli --output-on-failure
+
     - name: unit tests
       run: cd build && ctest -L unittest --output-on-failure --parallel 4
 
+    - name: compatibility tests
+      run: cd build && ctest -L compatibility --output-on-failure
+
     - name: binary tests
       run: cd build && ctest -L binary --output-on-failure
 #
@@ -243,9 +261,15 @@ jobs:
       - name: build
         run: cmake --build build
 
+      - name: interface tests
+        run: cd build && ctest -L cli --output-on-failure
+
       - name: unit tests
         run: cd build && ctest -L unittest --output-on-failure --parallel 4
 
+      - name: compatibility tests
+        run: cd build && ctest -L compatibility --output-on-failure
+
       - name: binary tests
         run: cd build && ctest -L binary --output-on-failure
 #

cpp/cmd/connectomeedit.cpp

@@ -34,12 +34,12 @@ void usage() {
   SYNOPSIS = "Perform basic operations on a connectome";
 
   ARGUMENTS
-  + Argument ("input", "the input connectome.").type_text ()
+  + Argument ("input", "the input connectome.").type_file_in()
 
   + Argument ("operation", "the operation to apply,"
                            " one of: " + join(operations, ", ") + ".").type_choice (operations)
 
-  + Argument ("output", "the output connectome.").type_text();
+  + Argument ("output", "the output connectome.").type_file_out();
 
 }
 // clang-format on

cpp/cmd/dirstat.cpp

@@ -88,11 +88,12 @@ void usage() {
     + Argument ("dirs", "the text file or image containing the directions.").type_file_in();
 
   OPTIONS
+    // TODO This could be a different command-line argument type
     + Option ("output", "output selected metrics as a space-delimited list,"
                         "suitable for use in scripts."
                         " This will produce one line of values per selected shell."
                         " Valid metrics are as specified in the description above.")
-      + Argument ("list")
+      + Argument ("list").type_text()
     + DWI::ShellsOption
     + DWI::GradImportOptions();
 

cpp/cmd/dwi2fod.cpp

@@ -115,7 +115,7 @@ void usage() {
     + Argument ("algorithm", "the algorithm to use for FOD estimation. "
                              "(options are: " + join(algorithms, ",") + ")").type_choice (algorithms)
     + Argument ("dwi", "the input diffusion-weighted image").type_image_in()
-    + Argument ("response odf", "pairs of input tissue response and output ODF images").allow_multiple();
+    + Argument ("response odf", "pairs of input tissue response and output ODF images").type_file_in().type_image_out().allow_multiple();
 
   OPTIONS
     + DWI::GradImportOptions()

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

@@ -108,9 +108,7 @@ void usage() {
   + Argument ("contrast", "the contrast matrix,"
                           " specified as rows of weights").type_file_in ()
 
-  // .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()
 
   + Argument ("out_fixel_directory", "the output directory where results will be saved."
                                      " Will be created if it does not exist").type_text();
@@ -173,12 +171,6 @@ class SubjectFixelImport : public Math::Stats::SubjectDataImportBase {
 };
 
 void run() {
-  if (Path::has_suffix(argument[4], ".tck"))
-    throw Exception("This version of fixelcfestats requires as input not a track file, but a "
-                    "pre-calculated fixel-fixel connectivity matrix; in addition, input fixel "
-                    "data must be pre-smoothed. Please check command / pipeline documentation "
-                    "specific to this software version.");
-
   const value_type cfe_dh = get_option_value("cfe_dh", Fixel::Filter::cfe_default_dh);
   const value_type cfe_e = get_option_value("cfe_e", Fixel::Filter::cfe_default_e);
   const value_type cfe_h = get_option_value("cfe_h", Fixel::Filter::cfe_default_h);

cpp/cmd/fixelfilter.cpp

@@ -53,10 +53,10 @@ 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

@@ -406,7 +406,7 @@ 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/shconv.cpp

@@ -51,7 +51,7 @@ void usage() {
   + Math::SH::encoding_description;
 
   ARGUMENTS
-    + Argument ("odf response", "pairs of input ODF image and corresponding responses").allow_multiple()
+    + Argument ("odf response", "pairs of input ODF image and corresponding responses").type_image_in().type_file_in().allow_multiple()
     + Argument ("SH_out", "the output spherical harmonics coefficients image.").type_image_out();
 
   OPTIONS

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/transformcalc.cpp

@@ -47,7 +47,7 @@ void usage() {
   SYNOPSIS = "Perform calculations on linear transformation matrices";
 
   ARGUMENTS
-  + Argument ("inputs", "the input(s) for the specified operation").allow_multiple()
+  + Argument ("inputs", "the input(s) for the specified operation").type_image_in().type_file_in().allow_multiple()
   + Argument ("operation", "the operation to perform;"
                            " one of: " + join(operations, ", ") +
                            " (see description section for details).").type_choice (operations)

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")

cpp/cmd/transformconvert.cpp

@@ -56,7 +56,7 @@ void usage() {
              "");
 
   ARGUMENTS
-  + Argument ("input", "the input(s) for the specified operation").allow_multiple()
+  + Argument ("input", "the input(s) for the specified operation").type_file_in().type_image_in().allow_multiple()
   + Argument ("operation", "the operation to perform;"
                            " one of: " + join(operations, ", ")).type_choice (operations)
   + Argument ("output", "the output transformation matrix.").type_file_out ();