WIP: use std::filesystem for handling of file paths

cmd/5tt2gmwmi.cpp

@@ -25,6 +25,8 @@
 #include "dwi/tractography/ACT/act.h"
 #include "dwi/tractography/ACT/tissues.h"
 
+#include <filesystem>
+
 using namespace MR;
 using namespace App;
 
@@ -36,19 +38,19 @@ void usage() {
   SYNOPSIS = "Generate a mask image appropriate for seeding streamlines on the grey matter-white matter interface";
 
   REFERENCES
-    + "Smith, R. E.; Tournier, J.-D.; Calamante, F. & Connelly, A. " // Internal
-      "Anatomically-constrained tractography:"
-      " Improved diffusion MRI streamlines tractography through effective use of anatomical information. "
-      "NeuroImage, 2012, 62, 1924-1938";
+      + "Smith, R. E.; Tournier, J.-D.; Calamante, F. & Connelly, A. " // Internal
+        "Anatomically-constrained tractography:"
+        " Improved diffusion MRI streamlines tractography through effective use of anatomical information. "
+        "NeuroImage, 2012, 62, 1924-1938";
 
   ARGUMENTS
-    + Argument ("5tt_in", "the input 5TT segmented anatomical image").type_image_in()
-    + Argument ("mask_out", "the output mask image").type_image_out();
+      + Argument ("5tt_in", "the input 5TT segmented anatomical image").type_image_in()
+      + Argument ("mask_out", "the output mask image").type_image_out();
 
   OPTIONS
-    + Option("mask_in", "Filter an input mask image according to those voxels that lie upon the grey matter - white matter boundary. "
-                        "If no input mask is provided, "
-                        "the output will be a whole-brain mask image calculated using the anatomical image only.")
+      + Option("mask_in", "Filter an input mask image according to those voxels that lie upon the grey matter - white matter boundary. "
+                          "If no input mask is provided, "
+                          "the output will be a whole-brain mask image calculated using the anatomical image only.")
       + Argument ("image", "the input mask image").type_image_in();
 
 }
@@ -107,8 +109,11 @@ class Processor {
 };
 
 void run() {
+  const std::filesystem::path input_path{argument.front()};
+  const std::filesystem::path output_path{argument.begin()[1]};
+
+  auto input = Image<float>::open(input_path);
 
-  auto input = Image<float>::open(argument[0]);
   DWI::Tractography::ACT::verify_5TT_image(input);
   check_3D_nonunity(input);
 
@@ -132,7 +137,7 @@ void run() {
     H = input;
     H.ndim() = 3;
   }
-  auto output = Image<float>::create(argument[1], H);
+  auto output = Image<float>::create(output_path, H);
 
   ThreadedLoop("Generating GMWMI seed mask", input, 0, 3).run(Processor(mask), input, output);
 }

cmd/5tt2vis.cpp

@@ -22,6 +22,8 @@
 #include "dwi/tractography/ACT/act.h"
 #include "dwi/tractography/ACT/tissues.h"
 
+#include <filesystem>
+
 using namespace MR;
 using namespace App;
 
@@ -74,8 +76,10 @@ void usage() {
 // clang-format on
 
 void run() {
+  const std::filesystem::path input_path{argument.front()};
+  const std::filesystem::path output_path{argument.begin()[1]};
 
-  auto input = Image<float>::open(argument[0]);
+  auto input = Image<float>::open(input_path);
   DWI::Tractography::ACT::verify_5TT_image(input);
 
   Header H(input);
@@ -88,7 +92,7 @@ void run() {
   const float csf_multiplier = get_option_value("csf", VALUE_DEFAULT_CSF);
   const float path_multiplier = get_option_value("path", VALUE_DEFAULT_PATH);
 
-  auto output = Image<float>::create(argument[1], H);
+  auto output = Image<float>::create(output_path, H);
 
   auto f = [&](decltype(input) &in, decltype(output) &out) {
     const DWI::Tractography::ACT::Tissues t(in);

cmd/5ttcheck.cpp

@@ -26,6 +26,8 @@
 
 #include "dwi/tractography/ACT/act.h"
 
+#include <filesystem>
+
 using namespace MR;
 using namespace App;
 
@@ -54,15 +56,15 @@ void run() {
 
   size_t major_error_count = 0, minor_error_count = 0;
   for (size_t i = 0; i != argument.size(); ++i) {
-
-    auto in = Image<float>::open(argument[i]);
+    const std::filesystem::path inPath{argument[i]};
+    auto in = Image<float>::open(inPath);
 
     Image<bool> voxels;
     Header H_out(in);
     H_out.ndim() = 3;
     H_out.datatype() = DataType::Bit;
     if (!voxels_prefix.empty())
-      voxels = Image<bool>::scratch(H_out, "Scratch image for " + argument[i]);
+      voxels = Image<bool>::scratch(H_out, "Scratch image for " + inPath.string());
 
     try {
 
@@ -104,21 +106,21 @@ void run() {
       }
 
       if (voxel_error_sum == 1) {
-        INFO("Image \"" + argument[i] +
+        INFO("Image \"" + inPath.string() +
              "\" contains just one isolated voxel with non-unity sum of partial volume fractions");
       } else if (voxel_error_sum) {
-        WARN("Image \"" + argument[i] + "\" contains " + str(voxel_error_sum) +
+        WARN("Image \"" + inPath.string() + "\" contains " + str(voxel_error_sum) +
              " brain voxels with non-unity sum of partial volume fractions");
         if (!voxel_error_abs)
           ++minor_error_count;
       } else if (!voxel_error_abs) {
-        INFO("Image \"" + argument[i] + "\" conforms to 5TT format");
+        INFO("Image \"" + inPath.string() + "\" conforms to 5TT format");
       }
 
       if ((voxel_error_sum || voxel_error_abs) && voxels.valid()) {
         std::string path = voxels_prefix;
         if (argument.size() > 1) {
-          path += Path::basename(argument[i]);
+          path += inPath.filename();
         } else {
           bool has_extension = false;
           for (auto p = MR::Formats::known_extensions; *p; ++p) {

cmd/5ttedit.cpp

@@ -24,6 +24,8 @@
 
 #include "dwi/tractography/ACT/act.h"
 
+#include <filesystem>
+
 using namespace MR;
 using namespace App;
 
@@ -128,10 +130,12 @@ class Modifier {
 };
 
 void run() {
+  const std::filesystem::path input_path{argument[0]};
+  const std::filesystem::path output_path{argument[1]};
 
-  auto in = Image<float>::open(argument[0]);
+  auto in = Image<float>::open(input_path);
   DWI::Tractography::ACT::verify_5TT_image(in);
-  auto out = Image<float>::create(argument[1], in);
+  auto out = Image<float>::create(output_path, in);
 
   Modifier modifier(in, out);
 

cmd/afdconnectivity.cpp

@@ -25,6 +25,8 @@
 #include "memory.h"
 #include "version.h"
 
+#include <filesystem>
+
 using namespace MR;
 using namespace MR::DWI;
 using namespace App;
@@ -287,18 +289,20 @@ void AFDConnectivity::save(const std::string &path) {
 }
 
 void run() {
-  const std::string wbft_path = get_option_value<std::string>("wbft", "");
+  const std::filesystem::path input_image_path{argument[0]};
+  const std::filesystem::path input_tracks_path{argument[1]};
+  const std::filesystem::path wbft_path{get_option_value<std::string>("wbft", "")};
 
   DWI::Directions::FastLookupSet dirs(1281);
-  auto fod = Image<value_type>::open(argument[0]);
+  auto fod = Image<value_type>::open(input_image_path);
   Math::SH::check(fod);
   check_3D_nonunity(fod);
-  AFDConnectivity model(fod, dirs, argument[1], wbft_path);
+  AFDConnectivity model(fod, dirs, input_tracks_path, wbft_path);
 
   auto opt = get_options("all_fixels");
   model.set_all_fixels(!opt.empty());
 
-  const value_type connectivity_value = model.get(argument[1]);
+  const value_type connectivity_value = model.get(input_tracks_path);
 
   // output the AFD sum using std::cout. This enables output to be redirected to a file without the console output.
   std::cout << connectivity_value << std::endl;

cmd/amp2response.cpp

@@ -30,6 +30,8 @@
 #include "math/sphere.h"
 #include "types.h"
 
+#include <filesystem>
+
 using namespace MR;
 using namespace App;
 
@@ -198,7 +200,12 @@ class Accumulator {
 void run() {
 
   // Get directions from either selecting a b-value shell, or the header, or external file
-  auto header = Header::open(argument[0]);
+  const std::filesystem::path amps_input_path{argument[0]};
+  const std::filesystem::path mask_input_path{argument[1]};
+  const std::filesystem::path directions_input_path{argument[2]};
+  const std::filesystem::path response_output_path{argument[3]};
+
+  auto header = Header::open(amps_input_path);
 
   // May be dealing with multiple shells
   std::vector<Eigen::MatrixXd> dirs_azel;
@@ -275,13 +282,14 @@ void run() {
   }
 
   auto image = header.get_image<float>();
-  auto mask = Image<bool>::open(argument[1]);
+  auto mask = Image<bool>::open(mask_input_path);
   check_dimensions(image, mask, 0, 3);
   if (!(mask.ndim() == 3 || (mask.ndim() == 4 && mask.size(3) == 1)))
     throw Exception("input mask must be a 3D image");
-  auto dir_image = Image<float>::open(argument[2]);
+  auto dir_image = Image<float>::open(directions_input_path);
   if (dir_image.ndim() < 4 || dir_image.size(3) < 3)
-    throw Exception("input direction image \"" + std::string(argument[2]) + "\" does not have expected dimensions");
+    throw Exception("input direction image \"" + directions_input_path.string() +
+                    "\" does not have expected dimensions");
   check_dimensions(image, dir_image, 0, 3);
 
   size_t num_voxels = 0;
@@ -365,5 +373,5 @@ void run() {
       line += "," + str<int>((*shells)[i].get_mean());
     keyvals["Shells"] = line;
   }
-  File::Matrix::save_matrix(responses, argument[3], keyvals);
+  File::Matrix::save_matrix(responses, response_output_path, keyvals);
 }

cmd/amp2sh.cpp

@@ -24,6 +24,8 @@
 #include "phase_encoding.h"
 #include "progressbar.h"
 
+#include <filesystem>
+
 using namespace MR;
 using namespace App;
 
@@ -183,7 +185,10 @@ class Amp2SH {
 };
 
 void run() {
-  auto amp = Image<value_type>::open(argument[0]).with_direct_io(3);
+  const std::filesystem::path input_path{argument[0]};
+  const std::filesystem::path output_path{argument[1]};
+
+  auto amp = Image<value_type>::open(input_path).with_direct_io(3);
   Header header(amp);
 
   std::vector<size_t> bzeros, dwis;
@@ -229,7 +234,7 @@ void run() {
 
   header.size(3) = sh2amp.cols();
   Stride::set_from_command_line(header);
-  auto SH = Image<value_type>::create(argument[1], header);
+  auto SH = Image<value_type>::create(output_path, header);
 
   Amp2SHCommon common(sh2amp, bzeros, dwis, normalise);