u8string for filesystem

SliceModel.cpp

@@ -214,7 +214,7 @@ bool CustomSliceModel::load_slices(const std::vector<std::string>& files,bool is
     name = QFileInfo(files[0].c_str()).completeBaseName().remove(".nii").toStdString();
     to_dif.identity();
     to_slice.identity();
-    tipl::progress prog("open ",std::filesystem::path(files[0]).filename().string().c_str());
+    tipl::progress prog("open ",std::filesystem::path(files[0]).filename().u8string().c_str());
     // picture as slice
     if(QFileInfo(files[0].c_str()).suffix() == "bmp" ||
        QFileInfo(files[0].c_str()).suffix() == "jpg" ||
@@ -360,7 +360,7 @@ bool CustomSliceModel::load_slices(const std::vector<std::string>& files,bool is
             {
                 if(QFileInfo(files[0].c_str()).fileName().toLower().contains("mni"))
                 {
-                    tipl::out() << std::filesystem::path(files[0]).filename().string() <<
+                    tipl::out() << std::filesystem::path(files[0]).filename().u8string() <<
                                  " has 'mni' in the file name and has a different image size from DWI. It will be spatially normalized from template space to native space." << std::endl;
                     is_mni = true;
                 }

auto_track.cpp

@@ -22,7 +22,7 @@ auto_track::auto_track(QWidget *parent) :
     // populate tractography atlas list
     ui->template_list->clear();
     for(const auto& each : fa_template_list)
-        ui->template_list->addItem(tipl::split(std::filesystem::path(each).filename().string(),'.').front().c_str());
+        ui->template_list->addItem(tipl::split(std::filesystem::path(each).filename().u8string(),'.').front().c_str());
     ui->template_list->setCurrentIndex(0);
     timer = std::make_shared<QTimer>(this);
     timer->stop();
@@ -206,7 +206,7 @@ std::string run_auto_track(tipl::program_option<tipl::out>& po,const std::vector
     {
         prog = int(i);
         std::string fib_file_name = file_list[i];
-        std::string cur_file_base_name = std::filesystem::path(fib_file_name).filename().string();
+        std::string cur_file_base_name = std::filesystem::path(fib_file_name).filename().u8string();
         scan_names.push_back(cur_file_base_name);
         tipl::out() << "processing " << cur_file_base_name << std::endl;
         std::shared_ptr<fib_data> handle;
@@ -470,7 +470,7 @@ std::string run_auto_track(tipl::program_option<tipl::out>& po,const std::vector
                 if(lines.size() < metrics_names.size())
                 {
                     std::string error("inconsistent stat file (remove it and rerun): ");
-                    error += std::filesystem::path(stat_files[t][s]).filename().string();
+                    error += std::filesystem::path(stat_files[t][s]).filename().u8string();
                     error += " metrics count: ";
                     error += std::to_string(lines.size());
                     error += " others: ";

cmd/ana.cpp

@@ -166,7 +166,7 @@ int ana_region(tipl::program_option<tipl::out>& po,std::shared_ptr<fib_data> han
     {
         std::string output = po.get("output");
         if(QFileInfo(output.c_str()).isDir())
-            file_name = output + std::string("/") + std::filesystem::path(file_name).filename().string();
+            file_name = output + std::string("/") + std::filesystem::path(file_name).filename().u8string();
         else
             file_name = output;
         if(file_name.find(".txt") == std::string::npos)
@@ -209,7 +209,7 @@ int ana_tract(tipl::program_option<tipl::out>& po,std::shared_ptr<fib_data> hand
         tracts.push_back(std::make_shared<TractModel>(handle));
         if(!load_tracts(tract_files[i].c_str(),handle,tracts.back(),roi_mgr))
             return 1;
-        tract_name.push_back(std::filesystem::path(tract_files[i]).filename().string());
+        tract_name.push_back(std::filesystem::path(tract_files[i]).filename().u8string());
     }
     tipl::out() << "a total of " << tract_files.size() << " tract file(s) loaded" << std::endl;
 

cmd/img.cpp

@@ -116,7 +116,7 @@ bool variant_image::load_from_file(const char* file_name,std::string& info)
     tipl::io::dicom dicom;
     is_mni = false;
     T.identity();
-    tipl::progress prog("open image file ",std::filesystem::path(file_name).filename().string().c_str());
+    tipl::progress prog("open image file ",std::filesystem::path(file_name).filename().u8string().c_str());
     if(QString(file_name).endsWith(".nhdr"))
     {
         tipl::io::nrrd<tipl::progress> nrrd;

cmd/rec.cpp

@@ -263,7 +263,7 @@ int rec(tipl::program_option<tipl::out>& po)
     {
         std::string output = po.get("output");
         if(QFileInfo(output.c_str()).isDir())
-            src.file_name = output + "/" + std::filesystem::path(src.file_name).filename().string();
+            src.file_name = output + "/" + std::filesystem::path(src.file_name).filename().u8string();
         else
             src.file_name = output;
     }

cmd/reg.cpp

@@ -32,7 +32,7 @@ bool dual_reg<3>::apply_warping(const char* from,const char* to) const
         }
         if(I[0].shape() != I_list[0].shape())
         {
-            error_msg = std::filesystem::path(from).filename().string();
+            error_msg = std::filesystem::path(from).filename().u8string();
             error_msg += " has an image size or srow matrix from that of the original --from image.";
             return false;
         }
@@ -66,7 +66,7 @@ bool dual_reg<3>::apply_warping(const char* from,const char* to) const
     if(I[0].shape() != I3.shape())
     {
         tipl::out() << "--from dim: " << I[0].shape();
-        error_msg = std::filesystem::path(from).filename().string();
+        error_msg = std::filesystem::path(from).filename().u8string();
         error_msg += " has an image size or srow matrix from that of the original --from image.";
         return false;
     }

cmd/ren.cpp

@@ -7,8 +7,8 @@ void dicom2src_and_nii(std::string dir_);
 int ren(tipl::program_option<tipl::out>& po)
 {
     tipl::progress prog("run ren");
-    auto source = std::filesystem::path(po.get("source")).string();
-    auto output = std::filesystem::path(po.get("output",po.get("source"))).string();
+    auto source = std::filesystem::path(po.get("source")).u8string();
+    auto output = std::filesystem::path(po.get("output",po.get("source"))).u8string();
     auto subject_dir = rename_dicom_at_dir(source.c_str(),output.c_str());
     if(po.get("to_src_nii",0))
     {

cmd/src.cpp

@@ -152,7 +152,7 @@ bool handle_bids_folder(const std::vector<std::string>& dwi_nii_files,
         phase_dir.push_back(phase_str);
 
         dwi_file.push_back(each);
-        tipl::out() << std::filesystem::path(dwi_file.back()).filename().string();
+        tipl::out() << std::filesystem::path(dwi_file.back()).filename().u8string();
         tipl::out() << "image size: " << image_size.back();
         tipl::out() << "dwi count: " << dwi_count.back();
         tipl::out() << "phase encoding: " << phase_dir.back();
@@ -180,8 +180,8 @@ bool handle_bids_folder(const std::vector<std::string>& dwi_nii_files,
             }
         image_size[i] = tipl::shape<3>();
         dwi_file[i].erase(dwi_file[i].length() - 7, 7); // remove .nii.gz
-        auto src_name = output_dir + "/" + std::filesystem::path(dwi_file[i]).filename().string() + ".src.gz";
-        auto rsrc_name = output_dir + "/" + std::filesystem::path(dwi_file[i]).filename().string() + ".rsrc.gz";
+        auto src_name = output_dir + "/" + std::filesystem::path(dwi_file[i]).filename().u8string() + ".src.gz";
+        auto rsrc_name = output_dir + "/" + std::filesystem::path(dwi_file[i]).filename().u8string() + ".rsrc.gz";
         if(!overwrite && std::filesystem::exists(src_name))
             tipl::out() << "skipping " << src_name << " already exists";
         else
@@ -227,7 +227,7 @@ bool nii2src(const std::vector<std::string>& dwi_nii_files,
         }
         else
         {
-            auto src_name = output_dir + "/" + std::filesystem::path(dwi_nii_files[i]).filename().string() + ".src.gz";
+            auto src_name = output_dir + "/" + std::filesystem::path(dwi_nii_files[i]).filename().u8string() + ".src.gz";
             if(!overwrite && std::filesystem::exists(src_name))
                 tipl::out() << "skipping " << src_name << " already exists";
             else
@@ -372,7 +372,7 @@ int src(tipl::program_option<tipl::out>& po)
     auto output = po.get("output",file_list.front() + ".src.gz");
 
     if(std::filesystem::is_directory(output))
-        output += std::string("/") + std::filesystem::path(file_list[0]).filename().string() + ".src.gz";
+        output += std::string("/") + std::filesystem::path(file_list[0]).filename().u8string() + ".src.gz";
     if(!tipl::ends_with(output,".src.gz"))
         output += ".src.gz";
 

cmd/trk.cpp

@@ -718,7 +718,7 @@ void set_template(std::shared_ptr<fib_data> handle,tipl::program_option<tipl::ou
     if(po.has("template"))
     {
         for(size_t id = 0;id < fa_template_list.size();++id)
-            tipl::out() << "template " << id << ": " << tipl::split(std::filesystem::path(fa_template_list[id]).filename().string(),'.').front() << std::endl;
+            tipl::out() << "template " << id << ": " << tipl::split(std::filesystem::path(fa_template_list[id]).filename().u8string(),'.').front() << std::endl;
         handle->set_template_id(po.get("template",size_t(0)));
     }
 }

connectometry/db_window.cpp

@@ -252,7 +252,7 @@ void db_window::on_actionSave_DB_as_triggered()
                            "Database files (*db?fib.gz *fib.gz);;All files (*)");
     if (filename.isEmpty())
         return;
-    tipl::progress prog_("saving ",std::filesystem::path(filename.toStdString()).filename().string().c_str());
+    tipl::progress prog_("saving ",std::filesystem::path(filename.toStdString()).filename().u8string().c_str());
     if(!vbc->handle->db.demo.empty() && !vbc->handle->db.parse_demo())
         QMessageBox::information(this,QApplication::applicationName(),
         QString("demographics not saved due to mismatch: ") + vbc->handle->db.error_msg.c_str());

connectometry/group_connectometry_analysis.cpp

@@ -635,9 +635,9 @@ void group_connectometry_analysis::generate_report(std::string& output)
     {
         if(fdr.empty())
             return;
-        html_report << "<p></p><img src = \""<< std::filesystem::path(output_file_name+"."+name+"_map.jpg").filename().string() << "\" width=\"600\"/>" << std::endl;
-        html_report << "<p></p><img src = \""<< std::filesystem::path(output_file_name+"."+name+"_map2.jpg").filename().string() << "\" width=\"600\"/>" << std::endl;
-        html_report << "<p></p><img src = \""<< std::filesystem::path(output_file_name+"."+name+".jpg").filename().string() << "\" width=\"1200\"/>" << std::endl;
+        html_report << "<p></p><img src = \""<< std::filesystem::path(output_file_name+"."+name+"_map.jpg").filename().u8string() << "\" width=\"600\"/>" << std::endl;
+        html_report << "<p></p><img src = \""<< std::filesystem::path(output_file_name+"."+name+"_map2.jpg").filename().u8string() << "\" width=\"600\"/>" << std::endl;
+        html_report << "<p></p><img src = \""<< std::filesystem::path(output_file_name+"."+name+".jpg").filename().u8string() << "\" width=\"1200\"/>" << std::endl;
         html_report << "<p><b>Fig.</b> Tracks with " << hypo << " " << fdr << "</p>" << std::endl;
     };
     auto report_fdr = [&](bool sig,std::string hypo,std::string result){
@@ -687,7 +687,7 @@ void group_connectometry_analysis::generate_report(std::string& output)
     {
         if(fdr_inc[length_threshold_voxels] < 0.2f || fdr_dec[length_threshold_voxels] < 0.2f)
         {
-            html_report << "<p></p><img src = \""<< std::filesystem::path(output_file_name+".pos_neg.jpg").filename().string() << "\" width=\"1200\"/>" << std::endl;
+            html_report << "<p></p><img src = \""<< std::filesystem::path(output_file_name+".pos_neg.jpg").filename().u8string() << "\" width=\"1200\"/>" << std::endl;
             html_report << "<p><b>Fig.</b> Correlational tractography showing " << hypothesis_inc << " (red)" << fdr_result_pos
                     << " and " << hypothesis_dec << " (blue)" << fdr_result_neg << ".</p>" << std::endl;
         }
@@ -701,15 +701,15 @@ void group_connectometry_analysis::generate_report(std::string& output)
 
         html_report << "<h3>False discovery rate analysis</h3>" << std::endl;
 
-        html_report << "<p></p><img src = \""<< std::filesystem::path(output_file_name+".inc.dist.jpg").filename().string() << "\" width=\"320\"/>" << std::endl;
+        html_report << "<p></p><img src = \""<< std::filesystem::path(output_file_name+".inc.dist.jpg").filename().u8string() << "\" width=\"320\"/>" << std::endl;
         html_report << "<p><b>Fig.</b> Permutation test showing the histograms of track counts with "<< hypothesis_inc << ".</p>";
 
 
-        html_report << "<p></p><img src = \""<< std::filesystem::path(output_file_name+".dec.dist.jpg").filename().string() << "\" width=\"320\"/>" << std::endl;
+        html_report << "<p></p><img src = \""<< std::filesystem::path(output_file_name+".dec.dist.jpg").filename().u8string() << "\" width=\"320\"/>" << std::endl;
         html_report << "<p><b>Fig.</b> Permutation test showing the histograms of track counts with "<< hypothesis_dec << ".</p>";
 
         html_report << permutation_explained << std::endl;
-        html_report << "<p></p><img src = \""<< std::filesystem::path(output_file_name+".fdr.jpg").filename().string() << "\" width=\"320\"/>" << std::endl;
+        html_report << "<p></p><img src = \""<< std::filesystem::path(output_file_name+".fdr.jpg").filename().u8string() << "\" width=\"320\"/>" << std::endl;
         html_report << "<p><b>Fig.</b> The False discovery rate (FDR) at different track length </p>";
     }
 

dicom/dicom_parser.cpp

@@ -953,7 +953,7 @@ std::vector<QStringList> split_by_path(const QStringList &files)
 bool parse_dwi(QStringList file_list,
                     std::vector<std::shared_ptr<DwiHeader> >& dwi_files)
 {
-    tipl::progress prog("opening ",std::filesystem::path(file_list[0].toStdString()).stem().string().c_str());
+    tipl::progress prog("opening ",std::filesystem::path(file_list[0].toStdString()).stem().u8string().c_str());
     if(QFileInfo(file_list.front()).absolutePath() != QFileInfo(file_list.back()).absolutePath())
     {
         auto dwi_groups = split_by_path(file_list);

libs/dsi/image_model.cpp

@@ -554,7 +554,7 @@ bool src_data::command(std::string cmd,std::string param)
             error_msg = " please assign file name ";
             return false;
         }
-        tipl::progress prog_("saving ",std::filesystem::path(param).filename().string().c_str());
+        tipl::progress prog_("saving ",std::filesystem::path(param).filename().u8string().c_str());
         return save_to_file(param.c_str());
     }
     if(cmd == "[Step T2a][Open]")
@@ -1989,13 +1989,13 @@ bool src_data::run_eddy(std::string exec)
     }
 
     std::vector<std::string> param = {
-            std::string("--imain=") + std::filesystem::path(temp_nifti).filename().string(),
-            std::string("--mask=") + std::filesystem::path(mask_nifti).filename().string(),
+            std::string("--imain=") + std::filesystem::path(temp_nifti).filename().u8string(),
+            std::string("--mask=") + std::filesystem::path(mask_nifti).filename().u8string(),
             std::string("--acqp=") + acqparam_file,
-            std::string("--index=") + std::filesystem::path(index_file.c_str()).filename().string(),
-            std::string("--bvecs=") + std::filesystem::path(bvec_file.c_str()).filename().string(),
-            std::string("--bvals=") + std::filesystem::path(bval_file.c_str()).filename().string(),
-            std::string("--out=") + std::filesystem::path(corrected_file.c_str()).filename().string(),
+            std::string("--index=") + std::filesystem::path(index_file.c_str()).filename().u8string(),
+            std::string("--bvecs=") + std::filesystem::path(bvec_file.c_str()).filename().u8string(),
+            std::string("--bvals=") + std::filesystem::path(bval_file.c_str()).filename().u8string(),
+            std::string("--out=") + std::filesystem::path(corrected_file.c_str()).filename().u8string(),
             "--verbose=1"
             };
     if(has_topup)
@@ -2244,7 +2244,7 @@ void src_data::get_report(std::string& report)
 }
 bool src_data::save_to_file(const char* dwi_file_name)
 {
-    tipl::progress prog_("saving ",std::filesystem::path(dwi_file_name).filename().string().c_str());
+    tipl::progress prog_("saving ",std::filesystem::path(dwi_file_name).filename().u8string().c_str());
     std::string filename(dwi_file_name);
     if(!tipl::ends_with(filename,".gz"))
         filename += ".gz";
@@ -2347,19 +2347,19 @@ void save_idx(const char* file_name,std::shared_ptr<tipl::io::gz_istream> in)
     idx_name += ".idx";
     if(in->has_access_points() && in->sample_access_point && !std::filesystem::exists(idx_name))
     {
-        tipl::out() << "saving index file for accelerated loading: " << std::filesystem::path(idx_name).filename().string() << std::endl;
+        tipl::out() << "saving index file for accelerated loading: " << std::filesystem::path(idx_name).filename().u8string() << std::endl;
         in->save_index(idx_name.c_str());
     }
 }
 size_t match_volume(float volume);
 QImage read_qimage(QString filename,std::string& error);
 bool src_data::load_from_file(const char* dwi_file_name)
 {
-    tipl::progress prog("open SRC file ",std::filesystem::path(dwi_file_name).filename().string().c_str());
+    tipl::progress prog("open SRC file ",std::filesystem::path(dwi_file_name).filename().u8string().c_str());
     if(voxel.steps.empty())
     {
         voxel.steps = "[Step T2][Reconstruction] open ";
-        voxel.steps += std::filesystem::path(dwi_file_name).filename().string();
+        voxel.steps += std::filesystem::path(dwi_file_name).filename().u8string();
         voxel.steps += "\n";
     }
 

libs/tracking/fib_data.cpp

@@ -398,7 +398,7 @@ void prepare_idx(const char* file_name,std::shared_ptr<tipl::io::gz_istream> in)
 void save_idx(const char* file_name,std::shared_ptr<tipl::io::gz_istream> in);
 bool fib_data::load_from_file(const char* file_name)
 {
-    tipl::progress prog("opening ",std::filesystem::path(file_name).filename().string().c_str());
+    tipl::progress prog("opening ",std::filesystem::path(file_name).filename().u8string().c_str());
     tipl::image<3> I;
     tipl::io::gz_nifti header;
     fib_file_name = file_name;
@@ -994,7 +994,7 @@ void fib_data::match_template(void)
         tipl::out() << "image volume smaller than human young adult. try matching a template...";
         set_template_id(match_volume(std::count_if(dir.fa[0],dir.fa[0]+dim.size(),[](float v){return v > 0.0f;})*2.0f*vs[0]*vs[1]*vs[2]));
     }
-    tipl::out() << "matched template: " << tipl::split(std::filesystem::path(fa_template_list[template_id]).filename().string(),'.').front();
+    tipl::out() << "matched template: " << tipl::split(std::filesystem::path(fa_template_list[template_id]).filename().u8string(),'.').front();
 }
 
 const tipl::image<3,tipl::vector<3,float> >& fib_data::get_native_position(void) const