Merge pull request #2206 from SCIInstitute/release_v6.5

Release v6.5

.github/workflows/build-linux-debug.yml

@@ -24,12 +24,12 @@ jobs:
   build:
 
     runs-on: ubuntu-latest
-    container: akenmorris/ubuntu-build-box-sw65
+    container: akenmorris/ubuntu-build-box-focal-sw65
 
     steps:
 
     - name: Install SSH Key
-      uses: shimataro/ssh-key-action@v2
+      uses: shimataro/ssh-key-action@v2.7.0
       with:
         key: ${{ secrets.SSH_PRIVATE_KEY }}
         known_hosts: ${{ secrets.KNOWN_HOSTS }}

.github/workflows/build-linux.yml

@@ -25,12 +25,12 @@ jobs:
   build:
 
     runs-on: ubuntu-latest
-    container: akenmorris/ubuntu-build-box-sw65
+    container: akenmorris/ubuntu-build-box-focal-sw65
 
     steps:
 
     - name: Install SSH Key
-      uses: shimataro/ssh-key-action@v2
+      uses: shimataro/ssh-key-action@v2.7.0
       with:
         key: ${{ secrets.SSH_PRIVATE_KEY }}
         known_hosts: ${{ secrets.KNOWN_HOSTS }}

.github/workflows/copy_artifact.sh

@@ -14,18 +14,16 @@ if [[ "$PLATFORM" == "windows" ]]; then
     # install rsync on for windows/msys2 (the one from chocolatey doesn't work)
     # (adapted from https://github.com/GuillaumeFalourd/setup-rsync)
     echo "Installing rsync for Windows/msys2"
-    curl.exe --output rsync-3.2.3-2-x86_64.pkg.tar.zst --url https://repo.msys2.org/msys/x86_64/rsync-3.2.3-1-x86_64.pkg.tar.zst
-    zstd -d rsync-3.2.3-2-x86_64.pkg.tar.zst
-    tar -xvf rsync-3.2.3-2-x86_64.pkg.tar
-    mv usr/bin/rsync.exe "C:\Program Files\Git\usr\bin\\"
-    curl.exe --output libzstd-1.5.2-1-x86_64.pkg.tar.zst https://repo.msys2.org/msys/x86_64/libzstd-1.5.2-1-x86_64.pkg.tar.zst
-    zstd -d libzstd-1.5.2-1-x86_64.pkg.tar.zst
-    tar -xvf libzstd-1.5.2-1-x86_64.pkg.tar
-    mv usr/bin/msys-zstd-1.dll "C:\Program Files\Git\usr\bin\\"
-    curl.exe --output libxxhash-0.8.0-1-x86_64.pkg.tar.zst https://repo.msys2.org/msys/x86_64/libxxhash-0.8.0-1-x86_64.pkg.tar.zst
-    zstd -d libxxhash-0.8.0-1-x86_64.pkg.tar.zst
-    tar -xvf libxxhash-0.8.0-1-x86_64.pkg.tar
-    mv usr/bin/msys-xxhash-0.8.0.dll "C:\Program Files\Git\usr\bin\\"
+
+    # These were the original URLs, but they keep changing and it's time consuming to keep up
+    # So I have just combined them in this windows_rsync.tar.gz that I'm hosting myself
+
+    # https://repo.msys2.org/msys/x86_64/rsync-3.2.3-1-x86_64.pkg.tar.zst
+    # https://repo.msys2.org/msys/x86_64/libzstd-1.5.2-1-x86_64.pkg.tar.zst
+    # https://repo.msys2.org/msys/x86_64/libxxhash-0.8.1-1-x86_64.pkg.tar.zst
+    curl.exe --output windows_rsync.tar.gz http://www.sci.utah.edu/~amorris/windows_rsync.tar.gz
+
+    mv usr/bin/* "C:\Program Files\Git\usr\bin\\"
     echo "rsync installed on windows runner"
 fi
 

CMakeLists.txt

@@ -6,7 +6,7 @@ cmake_minimum_required(VERSION 3.20)
 SET(SHAPEWORKS_MAJOR_VERSION 6 CACHE INTERNAL "Major version number" FORCE)
 SET(SHAPEWORKS_MINOR_VERSION 5 CACHE INTERNAL "Minor version number" FORCE)
 SET(SHAPEWORKS_PATCH_VERSION 0 CACHE INTERNAL "Patch version number" FORCE)
-SET(SHAPEWORKS_VERSION_STRING "6.5.0-dev")
+SET(SHAPEWORKS_VERSION_STRING "6.5.0-RC3")
 SET(SHAPEWORKS_VERSION "${SHAPEWORKS_MAJOR_VERSION}.${SHAPEWORKS_MINOR_VERSION}.${SHAPEWORKS_PATCH_VERSION}")
 
 # First, check that files were checked out properly using git-lfs

Libs/Analyze/Shape.cpp

@@ -148,12 +148,15 @@ bool Shape::import_global_point_files(std::vector<std::string> filenames) {
   global_point_filenames_.clear();
   for (int i = 0; i < filenames.size(); i++) {
     Eigen::VectorXd points;
-    if (filenames[i] != "") {
-      if (!Shape::import_point_file(filenames[i], points)) {
+    auto filename = filenames[i];
+    // replace \ with /
+    filename = StringUtils::replace_string(filename, "\\", "/");
+    if (filename != "") {
+      if (!Shape::import_point_file(filename, points)) {
         throw std::invalid_argument("Unable to import point file: " + filenames[i]);
       }
     }
-    global_point_filenames_.push_back(filenames[i]);
+    global_point_filenames_.push_back(filename);
     particles_.set_world_particles(i, points);
   }
   subject_->set_world_particle_filenames(global_point_filenames_);
@@ -165,12 +168,15 @@ bool Shape::import_local_point_files(std::vector<std::string> filenames) {
   local_point_filenames_.clear();
   for (int i = 0; i < filenames.size(); i++) {
     Eigen::VectorXd points;
-    if (filenames[i] != "") {
-      if (!Shape::import_point_file(filenames[i], points)) {
+    auto filename = filenames[i];
+    // replace \ with /
+    filename = StringUtils::replace_string(filename, "\\", "/");
+    if (filename != "") {
+      if (!Shape::import_point_file(filename, points)) {
         throw std::invalid_argument("Unable to import point file: " + filenames[i]);
       }
     }
-    local_point_filenames_.push_back(filenames[i]);
+    local_point_filenames_.push_back(filename);
     particles_.set_local_particles(i, points);
   }
   subject_->set_local_particle_filenames(local_point_filenames_);

Libs/Mesh/Mesh.cpp

@@ -488,7 +488,7 @@ Mesh& Mesh::fixElement() {
   FEMesh* meshFE = import.Load(this->poly_data_);
 
   if (meshFE == nullptr) {
-    throw std::invalid_argument("Unable to read file");
+    throw std::runtime_error("Unable to read mesh file");
   }
 
   FEFixMesh fix;

Libs/Mesh/MeshWarper.cpp

@@ -441,6 +441,13 @@ bool MeshWarper::generate_warp() {
   // prep points
   this->vertices_ = this->reference_particles_;
 
+  if (reference_mesh_->GetNumberOfPoints() == 0) {
+    SW_ERROR("Unable to warp mesh, no points in surface mesh");
+    update_progress(1.0);
+    warp_available_ = false;
+    return false;
+  }
+
   this->add_particle_vertices(this->vertices_);
 
   if (this->landmarks_points_.size() > 0) {

Libs/Particles/ParticleFile.cpp

@@ -63,7 +63,7 @@ Eigen::VectorXd read_particles(std::string filename) {
 
   std::ifstream in(filename);
   if (!in.good()) {
-    throw std::runtime_error("Unable to read file: " + filename);
+    throw std::runtime_error("Unable to read particle file: " + filename);
   }
   Eigen::VectorXd points;
 

Libs/Project/Project.cpp

@@ -94,8 +94,10 @@ void Project::set_project_path(const std::string& new_pathname) {
 
   auto fixup = [&](StringList paths) {
     StringList new_paths;
-    for (const auto& path : paths) {
+    for (auto path : paths) {
       if (fs::exists(path)) {
+        // replace \ with / in path
+        path = StringUtils::replace_string(path, "\\", "/");
         auto canonical = fs::canonical(path, old_path);
         new_paths.push_back(fs::relative(canonical, new_path).string());
       } else {
@@ -116,7 +118,10 @@ void Project::set_project_path(const std::string& new_pathname) {
     auto features = subject->get_feature_filenames();
     project::types::StringMap new_features;
     for (auto const& x : features) {
-      auto canonical = fs::canonical(x.second, old_path);
+      auto path = x.second;
+      // replace \ with / in path
+      path = StringUtils::replace_string(path, "\\", "/");
+      auto canonical = fs::canonical(path, old_path);
       new_features[x.first] = fs::relative(canonical, new_path).string();
     }
     subject->set_feature_filenames(new_features);

Python/DeepSSMUtilsPackage/DeepSSMUtils/eval_utils.py

@@ -49,7 +49,6 @@ def get_mesh_from_DT(DT_list, mesh_dir):
     if not os.path.exists(mesh_dir):
         os.makedirs(mesh_dir)
     mesh_files = []
-    xml_filename = mesh_dir + "temp.xml"
     for input_file in DT_list:
         print('	' + get_prefix(input_file))
         output_vtk = mesh_dir + "original_" + get_prefix(input_file) + ".vtk"
@@ -59,12 +58,22 @@ def get_mesh_from_DT(DT_list, mesh_dir):
     return sorted(mesh_files)
 
 
+def get_mesh(filename, iso_value=0):
+    if filename.endswith('.nrrd'):
+        image = sw.Image(filename)
+        return image.toMesh(iso_value)
+    else:
+        return sw.Mesh(filename)
+
+
 def get_mesh_from_particles(particle_list, mesh_dir, template_particles, template_mesh, planes=None):
     if not os.path.exists(mesh_dir):
         os.makedirs(mesh_dir)
 
     warp = sw.MeshWarper()
-    sw_mesh = sw.Mesh(template_mesh)
+
+    # Create mesh from file (mesh or segmentation)
+    sw_mesh = get_mesh(template_mesh)
     sw_particles = np.loadtxt(template_particles)
     warp.generateWarp(sw_mesh, sw_particles)
 
@@ -135,7 +144,7 @@ def get_mesh_distances(pred_particle_files, mesh_list, template_particles, templ
             mean_distances.append(-1)
             continue
         print(f"Computing distance between {mesh_list[index]} and {pred_mesh_list[index]}")
-        orig_mesh = sw.Mesh(mesh_list[index])
+        orig_mesh = get_mesh(mesh_list[index], iso_value=0.5)
         if planes is not None:
             orig_mesh.clip(planes[index][0], planes[index][1], planes[index][2])
         pred_mesh = sw.Mesh(pred_mesh_list[index])

Python/DeepSSMUtilsPackage/DeepSSMUtils/run_utils.py

@@ -282,7 +282,7 @@ def run_data_augmentation(project, num_samples, num_dim, percent_variability, sa
     train_image_filenames = []
     train_world_particle_filenames = []
     for i in get_training_indices(project):
-        train_image_filenames.append(deepssm_dir + f"/train_images/{i}.nrrd")
+        train_image_filenames.append(f"deepssm/train_images/{i}.nrrd")
         particle_file = subjects[i].get_world_particle_filenames()[0]
         train_world_particle_filenames.append(particle_file)
 

Studio/Data/Session.cpp

@@ -1102,14 +1102,14 @@ bool Session::get_image_3d_mode() { return params_.get("image_3d_mode", false);
 
 //---------------------------------------------------------------------------
 void Session::set_image_share_window_and_level(bool enabled) {
-  if (enabled == get_image_share_window_and_level() || is_loading()) {
+  if (enabled == get_image_share_brightness_contrast() || is_loading()) {
     return;
   }
   params_.set("image_share_window_and_level", enabled);
 }
 
 //---------------------------------------------------------------------------
-bool Session::get_image_share_window_and_level() { return params_.get("image_share_window_and_level", true); }
+bool Session::get_image_share_brightness_contrast() { return params_.get("image_share_window_and_level", true); }
 
 //---------------------------------------------------------------------------
 void Session::set_image_sync_slice(bool enabled) {

Studio/Data/Session.h

@@ -198,7 +198,7 @@ class Session : public QObject, public QEnableSharedFromThis<Session> {
 
   // image sync/share window width and level
   void set_image_share_window_and_level(bool enabled);
-  bool get_image_share_window_and_level();
+  bool get_image_share_brightness_contrast();
 
   // image sync slice
   void set_image_sync_slice(bool enabled);