Merge branch 'master' into mesh_distance_symmetric

.github/workflows/Dockerfile

@@ -1,17 +1,20 @@
 # Based on old ubuntu to create more compatible binaries
 
 # To build (e.g. for ShapeWorks 6.5):
-#    docker build --progress=plain -t akenmorris/ubuntu-build-box-sw65 .
+#    docker build --progress=plain -t akenmorris/ubuntu-build-box-focal-sw65 .
 # To publish:
-#    docker push akenmorris/ubuntu-build-box-sw65
+#    docker push akenmorris/ubuntu-build-box-focal-sw65
 
-FROM ubuntu:bionic-20230308 AS env
+FROM ubuntu:focal-20240123 AS env
 MAINTAINER akenmorris@gmail.com
 
 # Set environment variables
 ENV PATH=/opt/conda/bin:/opt/rh/devtoolset-9/root/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
 ENV LDFLAGS=-L/opt/conda/lib
 
+ARG DEBIAN_FRONTEND=noninteractive
+ENV TZ=Etc/UTC
+
 # Update
 RUN apt-get update -y && apt-get upgrade -y && apt-get dist-upgrade -y && apt-get install build-essential software-properties-common -y && add-apt-repository ppa:ubuntu-toolchain-r/test -y && apt-get update -y
 

.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 }}
@@ -41,7 +41,10 @@ jobs:
       run: df -h
 
     - name: Free some space 
-      run: cd /__t ; rm -rf CodeQL go
+      run: cd /__t ; rm -rf CodeQL go PyPy Python Ruby
+
+    - name: Check usage 
+      run: cd /__t ; du -sh *
 
     - name: Check space2
       run: df -h
@@ -61,35 +64,35 @@ jobs:
       shell: bash -l {0}
       run: .github/workflows/restore_caches.sh
 
-    - name: Check space2
+    - name: Check space3
       run: df -h
 
     - name: Conda Installs
       shell: bash -l {0}
       run: .github/workflows/gha_conda.sh
 
-    - name: Check space3
+    - name: Check space4
       run: df -h
 
     - name: Build Dependencies
       shell: bash -l {0}
       run: .github/workflows/gha_deps.sh
 
-    - name: Check space4
+    - name: Check space5
       run: df -h
 
     - name: cmake
       shell: bash -l {0}
       run: conda activate shapeworks && mkdir build && cd build && cmake -DCMAKE_CXX_FLAGS=-g -DITK_DIR=$HOME/install/lib/cmake/ITK-5.2 -DVTK_DIR=$HOME/install/lib/cmake/vtk-9.1 -DXLNT_DIR=$HOME/install -DLIBIGL_DIR=$HOME/install -DOpenVDB_DIR=$HOME/install/lib/cmake/OpenVDB -DGEOMETRYCENTRAL_DIR=$HOME/install -DCMAKE_BUILD_TYPE=$BUILD_TYPE -DBuild_Studio=ON -DJKQTCommonSharedLib_DIR=$HOME/install/lib/cmake/JKQTCommonSharedLib -DJKQTMathTextSharedLib_DIR=$HOME/install/lib/cmake/JKQTMathTextSharedLib -DJKQTPlotterSharedLib_DIR=$HOME/install/lib/cmake/JKQTPlotterSharedLib -DACVD_DIR=$HOME/install -DCMAKE_PREFIX_PATH=${CONDA_PREFIX} -DCMAKE_INSTALL_PREFIX=${GITHUB_WORKSPACE}/shapeworks-install -DUSE_ORIGIN_RPATH=ON ..
 
-    - name: Check space5
+    - name: Check space6
       run: df -h
 
     - name: make
       shell: bash -l {0}
       run: conda activate shapeworks && cd build && make -j2
 
-    - name: Check space6
+    - name: Check space7
       run: df -h
 
     - name: make install

.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 +14,18 @@ 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
+
+    tar -xzvf windows_rsync.tar.gz
+
+    mv usr/bin/* "C:\Program Files\Git\usr\bin\\"
     echo "rsync installed on windows runner"
 fi
 

Applications/shapeworks/Commands.cpp

@@ -41,31 +41,7 @@ bool Example::execute(const optparse::Values &options, SharedCommandData &shared
 }
 #endif
 
-static void setup_callbacks(bool show_progress, bool xml_status) {
-  if (show_progress) {
-    auto progress_callback = [](double progress, std::string message) {
-      // show status message and percentage complete
-      std::cout << fmt::format("{} ({:.1f}%)        \r", message, progress);
-      std::cout.flush();
-    };
-    Logging::Instance().set_progress_callback(progress_callback);
-  }
 
-  if (xml_status) {
-    auto progress_callback = [](double progress, std::string message) {
-      // print status message and percentage complete
-      std::cout << fmt::format("<xml><status>{}</status><progress>{:.1f}</progress></xml>\n", message, progress);
-      std::cout.flush();
-    };
-    Logging::Instance().set_progress_callback(progress_callback);
-
-    auto error_callback = [](std::string message) {
-      std::cout << fmt::format("<xml><error>{}</error></xml>\n", message);
-      std::cout.flush();
-    };
-    Logging::Instance().set_error_callback(error_callback);
-  }
-}
 
 ///////////////////////////////////////////////////////////////////////////////
 // Seed
@@ -87,7 +63,7 @@ void Seed::buildParser() {
 bool Seed::execute(const optparse::Values& options, SharedCommandData& sharedData) {
   int value = static_cast<int>(options.get("value"));
 
-  ShapeworksUtils::setRngSeed(value);
+  ShapeWorksUtils::set_rng_seed(value);
 
   return true;
 }
@@ -102,7 +78,10 @@ void OptimizeCommand::buildParser() {
 
   parser.add_option("--name").action("store").type("string").set_default("").help("Path to project file.");
   parser.add_option("--progress").action("store_true").set_default(false).help("Show progress [default: false].");
-  parser.add_option("--xmlconsole").action("store_true").set_default(false).help("XML console output [default: false].");
+  parser.add_option("--xmlconsole")
+      .action("store_true")
+      .set_default(false)
+      .help("XML console output [default: false].");
 
   Command::buildParser();
 }
@@ -120,13 +99,18 @@ bool OptimizeCommand::execute(const optparse::Values& options, SharedCommandData
   bool isProject = StringUtils::hasSuffix(projectFile, "xlsx") || StringUtils::hasSuffix(projectFile, "swproj");
 
   Optimize app;
-  setup_callbacks(show_progress, xml_status);
+  ShapeWorksUtils::setup_console_logging(show_progress, xml_status);
 
   if (isProject) {
     try {
       // load spreadsheet project
       ProjectHandle project = std::make_shared<Project>();
-      project->load(projectFile);
+      try {
+        project->load(projectFile);
+      } catch (std::exception& e) {
+        SW_ERROR("Project failed to load: {}", e.what());
+        return false;
+      }
 
       const auto oldBasePath = boost::filesystem::current_path();
       auto base = StringUtils::getPath(projectFile);
@@ -153,7 +137,7 @@ bool OptimizeCommand::execute(const optparse::Values& options, SharedCommandData
 
       return success;
     } catch (std::exception& e) {
-      SW_ERROR(e.what());
+      SW_ERROR("{}", e.what());
       return false;
     }
   } else {
@@ -173,7 +157,10 @@ void GroomCommand::buildParser() {
 
   parser.add_option("--name").action("store").type("string").set_default("").help("Path to project file.");
   parser.add_option("--progress").action("store_true").set_default(false).help("Show progress [default: false].");
-  parser.add_option("--xmlconsole").action("store_true").set_default(false).help("XML console output [default: false].");
+  parser.add_option("--xmlconsole")
+      .action("store_true")
+      .set_default(false)
+      .help("XML console output [default: false].");
 
   Command::buildParser();
 }
@@ -188,7 +175,7 @@ bool GroomCommand::execute(const optparse::Values& options, SharedCommandData& s
     return false;
   }
 
-  setup_callbacks(show_progress, xml_status);
+  ShapeWorksUtils::setup_console_logging(show_progress, xml_status);
 
   try {
     ProjectHandle project = std::make_shared<Project>();
@@ -215,7 +202,7 @@ bool GroomCommand::execute(const optparse::Values& options, SharedCommandData& s
 
     return success;
   } catch (std::exception& e) {
-    SW_ERROR(e.what());
+    SW_ERROR("{}", e.what());
     return false;
   }
 }
@@ -230,8 +217,10 @@ void AnalyzeCommand::buildParser() {
 
   parser.add_option("--name").action("store").type("string").set_default("").help("Path to project file.");
   parser.add_option("--output").action("store").type("string").set_default("").help("Path to output file.");
-  parser.add_option("--range").action("store").type("float").set_default(3.0f).help("Standard deviation range for PCA [default: 3.0].");
-  parser.add_option("--steps").action("store").type("int").set_default(21).help("Number of steps to use for PCA [default: 21].");
+  parser.add_option("--range").action("store").type("float").set_default(3.0f).help(
+      "Standard deviation range for PCA [default: 3.0].");
+  parser.add_option("--steps").action("store").type("int").set_default(21).help(
+      "Number of steps to use for PCA [default: 21].");
 
   Command::buildParser();
 }

Applications/shapeworks/MeshCommands.cpp

@@ -1432,6 +1432,7 @@ bool WarpMesh::execute(const optparse::Values &options, SharedCommandData &share
   try {
     MeshWarper warper;
     Mesh inputMesh(inputMeshFilename);
+    inputMesh.clean();
     targetPointsFilenames.push_back(inputPointsFilename);
     ParticleSystemEvaluation particlesystem(targetPointsFilenames);
     Eigen::MatrixXd landmarks;
@@ -1469,6 +1470,7 @@ bool WarpMesh::execute(const optparse::Values &options, SharedCommandData &share
       movingPoints.resize(3, numParticles);
       movingPoints.transposeInPlace();
       Mesh output = warper.build_mesh(movingPoints);
+      SW_DEBUG("Writing mesh {} with {} points", filenm, output.numPoints());
       output.write(filenm);
       if (warp_along_with_landmarks) {
         std::string warped_landmarks_filename = targetPointsFilenames[i];
@@ -1541,6 +1543,11 @@ void ComputeThickness::buildParser() {
       .type("double")
       .set_default(100000.0)
       .help("Maximum distance to determine thickness");
+  parser.add_option("--median_radius")
+      .action("store")
+      .type("double")
+      .set_default(5.0)
+      .help("Median radius for smoothing, multiplier of average edge length");
   parser.add_option("--distance_mesh")
       .action("store")
       .type("string")
@@ -1565,15 +1572,17 @@ bool ComputeThickness::execute(const optparse::Values &options, SharedCommandDat
 
   double max_dist = static_cast<double>(options.get("max_dist"));
 
+  double median_radius = static_cast<double>(options.get("median_radius"));
+
   std::string dt_filename = static_cast<std::string>(options.get("distance_transform"));
 
   std::string distance_mesh_filename = static_cast<std::string>(options.get("distance_mesh"));
 
   if (dt_filename == "") {
-    sharedData.mesh->computeThickness(img, nullptr, max_dist, distance_mesh_filename);
+    sharedData.mesh->computeThickness(img, nullptr, max_dist, median_radius, distance_mesh_filename);
   } else {
     Image dt(dt_filename);
-    sharedData.mesh->computeThickness(img, &dt, max_dist, distance_mesh_filename);
+    sharedData.mesh->computeThickness(img, &dt, max_dist, median_radius, distance_mesh_filename);
   }
 
   return sharedData.validMesh();

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")
 SET(SHAPEWORKS_VERSION "${SHAPEWORKS_MAJOR_VERSION}.${SHAPEWORKS_MINOR_VERSION}.${SHAPEWORKS_PATCH_VERSION}")
 
 # First, check that files were checked out properly using git-lfs
@@ -80,9 +80,12 @@ SET(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin)
 SET(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin)
 SET(CMAKE_BUNDLE_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin)
 
-# make it easier to see more important compiler warnings and errors (# TODO: fix the actual cause of the warnings)
 if (APPLE)
+  # make it easier to see more important compiler warnings and errors (# TODO: fix the actual cause of the warnings)
   SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wno-inconsistent-missing-override")
+
+  # workaround for version of boost in use
+  add_definitions(-D_LIBCPP_ENABLE_CXX17_REMOVED_UNARY_BINARY_FUNCTION)
 endif()
 
 if(MSVC)