Merge pull request #2211 from SCIInstitute/release_v6.5

Release v6.5 changes

Author: akenmorris

.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 [email protected]
 
 # 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

@@ -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/copy_artifact.sh

@@ -22,6 +22,8 @@ if [[ "$PLATFORM" == "windows" ]]; then
     # 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"

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;

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-RC3")
+SET(SHAPEWORKS_VERSION_STRING "6.5.0-RC4")
 SET(SHAPEWORKS_VERSION "${SHAPEWORKS_MAJOR_VERSION}.${SHAPEWORKS_MINOR_VERSION}.${SHAPEWORKS_PATCH_VERSION}")
 
 # First, check that files were checked out properly using git-lfs

Libs/Common/Logging.h

@@ -4,6 +4,7 @@
 
 #include <QString>
 #include <functional>
+#include <iostream>
 
 template <>
 struct fmt::formatter<QString> {
@@ -15,6 +16,18 @@ struct fmt::formatter<QString> {
   }
 };
 
+template <typename... Args>
+std::string safe_format(const std::string& fmt_str, const Args&... args) {
+  std::string result;
+  try {
+    result = fmt::format(fmt_str, args...);
+  } catch (const std::exception& e) {
+    // Handle formatting errors here, example:
+    std::cerr << "Error formatting string: " << fmt_str << " : " << e.what() << std::endl;
+  }
+  return result;
+}
+
 namespace shapeworks {
 
 /**
@@ -105,7 +118,7 @@ class Logging {
   void show_progress(double value, const std::string& message);
 
   //! Log a debug message, use SW_DEBUG macro
-  void log_debug(const std::string& message, const int line, const char* file, const char *function) const;
+  void log_debug(const std::string& message, const int line, const char* file, const char* function) const;
 
   //! Log a warning message, use SW_WARN macro
   void log_warning(const std::string& message, const int line, const char* file) const;
@@ -156,44 +169,44 @@ class Logging {
 
 //! Log message macro
 #define SW_LOG(message, ...) \
-  shapeworks::Logging::Instance().log_message(fmt::format(message, ##__VA_ARGS__), __LINE__, __FILE__)
+  shapeworks::Logging::Instance().log_message(safe_format(message, ##__VA_ARGS__), __LINE__, __FILE__);
 
 //! Log warning macro
 #define SW_WARN(message, ...) \
-  shapeworks::Logging::Instance().log_warning(fmt::format(message, ##__VA_ARGS__), __LINE__, __FILE__)
+  shapeworks::Logging::Instance().log_warning(safe_format(message, ##__VA_ARGS__), __LINE__, __FILE__)
 
 //! Log error macro
 #define SW_ERROR(message, ...) \
-  shapeworks::Logging::Instance().log_error(fmt::format(message, ##__VA_ARGS__), __LINE__, __FILE__)
+  shapeworks::Logging::Instance().log_error(safe_format(message, ##__VA_ARGS__), __LINE__, __FILE__)
 
 //! Log debug macro
 #define SW_DEBUG(message, ...) \
-  shapeworks::Logging::Instance().log_debug(fmt::format(message, ##__VA_ARGS__), __LINE__, __FILE__, __FUNCTION__)
+  shapeworks::Logging::Instance().log_debug(safe_format(message, ##__VA_ARGS__), __LINE__, __FILE__, __FUNCTION__)
 
 //! Variable trace macro (e.g. output variable name = <variable value>)
 #define SW_TRACE(x) SW_DEBUG(#x " = {}", x);
 
 //! Log show message macro
 #define SW_MESSAGE(message, ...) \
-  shapeworks::Logging::Instance().show_message(fmt::format(message, ##__VA_ARGS__), __LINE__, __FILE__)
+  shapeworks::Logging::Instance().show_message(safe_format(message, ##__VA_ARGS__), __LINE__, __FILE__)
 
 //! Don't write to log, but set status (e.g. in the Studio statusbar)
 #define SW_STATUS(message, ...) \
-  shapeworks::Logging::Instance().show_status(fmt::format(message, ##__VA_ARGS__), __LINE__, __FILE__)
+  shapeworks::Logging::Instance().show_status(safe_format(message, ##__VA_ARGS__), __LINE__, __FILE__)
 
 #define SW_PROGRESS(value, message, ...) \
-  shapeworks::Logging::Instance().show_progress(value, fmt::format(message, ##__VA_ARGS__));
+  shapeworks::Logging::Instance().show_progress(value, safe_format(message, ##__VA_ARGS__));
 
 //! Close session macro
 #define SW_CLOSE_LOG() shapeworks::Logging::Instance().close_log();
 
 //! Log once macro, will only log the message once
-#define SW_LOG_ONCE(message, ...) \
-{ \
-    static bool logged = false; \
-    if (!logged) { \
+#define SW_LOG_ONCE(message, ...)     \
+  {                                   \
+    static bool logged = false;       \
+    if (!logged) {                    \
       SW_LOG(message, ##__VA_ARGS__); \
-      logged = true; \
-    } \
-}
+      logged = true;                  \
+    }                                 \
+  }
 }  // namespace shapeworks

Libs/Groom/Groom.cpp

@@ -727,13 +727,11 @@ std::string Groom::get_output_filename(std::string input, DomainType domain_type
   // check for and handle name clashes, e.g. a/foo.vtk, b/foo.vtk (see #1387)
   auto base_name = name;
   int count = 2;
-  while (used_names_.find(name) != used_names_.end()) {
-    name = base_name + std::to_string(count++);
+  while (used_names_.find(name + suffix) != used_names_.end()) {
+    name = base_name + "_" + std::to_string(count++);
   }
-  used_names_.insert(name);
-
   auto output = name + suffix;
-
+  used_names_.insert(output);
   return output;
 }
 

Libs/Mesh/MeshWarper.cpp

@@ -1,3 +1,4 @@
+#include <Logging.h>
 #include <Mesh/Mesh.h>
 #include <Mesh/MeshWarper.h>
 #include <igl/biharmonic_coordinates.h>
@@ -11,8 +12,6 @@
 #include <vtkPolyDataConnectivityFilter.h>
 #include <vtkTriangleFilter.h>
 
-#include <Logging.h>
-
 #include <set>
 
 namespace shapeworks {
@@ -113,7 +112,6 @@ void MeshWarper::add_particle_vertices(Eigen::MatrixXd& vertices) {
   // with each other.  If multiple particles (new vertices) land on the same triangle, the we will need
   // multiple passes since we will have to make the changes and rebuild the locator.
   while (not_all_done) {
-
     not_all_done = false;
 
     this->reference_mesh_->BuildLinks();
@@ -415,7 +413,7 @@ vtkSmartPointer<vtkPolyData> MeshWarper::recreate_mesh(vtkSmartPointer<vtkPolyDa
 
     if (cell->GetCellType() != VTK_EMPTY_CELL) {  // VTK_EMPTY_CELL means it was deleted
       // create an array of vtkIdType
-      vtkIdType *pts = new vtkIdType[cell->GetNumberOfPoints()];
+      vtkIdType* pts = new vtkIdType[cell->GetNumberOfPoints()];
       for (vtkIdType j = 0; j < cell->GetNumberOfPoints(); j++) {
         pts[j] = cell->GetPointId(j);
       }
@@ -556,14 +554,13 @@ Eigen::MatrixXd MeshWarper::extract_landmarks(vtkSmartPointer<vtkPolyData> warpe
 
   vtkSmartPointer<vtkDataArray> data_array = warped_mesh->GetPoints()->GetData();
 
-    for (auto ids : landmarks_map_)
-    {
-        auto id_landmark = ids.first;
-        auto id_vertice = ids.second;
+  for (auto ids : landmarks_map_) {
+    auto id_landmark = ids.first;
+    auto id_vertex = ids.second;
 
-    landmarks(id_landmark, 0) = data_array->GetComponent(id_vertice, 0);
-    landmarks(id_landmark, 1) = data_array->GetComponent(id_vertice, 1);
-    landmarks(id_landmark, 2) = data_array->GetComponent(id_vertice, 2);
+    landmarks(id_landmark, 0) = data_array->GetComponent(id_vertex, 0);
+    landmarks(id_landmark, 1) = data_array->GetComponent(id_vertex, 1);
+    landmarks(id_landmark, 2) = data_array->GetComponent(id_vertex, 2);
   }
 
   return landmarks;

Studio/Analysis/AnalysisTool.cpp

@@ -186,7 +186,7 @@ std::string AnalysisTool::get_analysis_mode() {
 }
 
 //---------------------------------------------------------------------------
-bool AnalysisTool::get_group_difference_mode() { return ui_->difference_button->isChecked(); }
+bool AnalysisTool::get_group_difference_mode() { return groups_active() && ui_->difference_button->isChecked(); }
 
 //---------------------------------------------------------------------------
 std::vector<Shape::Point> AnalysisTool::get_group_difference_vectors() {
@@ -357,6 +357,8 @@ void AnalysisTool::handle_analysis_options() {
     pca_animate_timer_.stop();
   }
 
+  update_difference_particles();
+
   Q_EMIT update_view();
 }
 
@@ -1463,6 +1465,11 @@ void AnalysisTool::group_changed() {
 
 //---------------------------------------------------------------------------
 bool AnalysisTool::groups_active() {
+  // check that the group tab is active
+  if (ui_->tabWidget->currentWidget() != ui_->mean_tab) {
+    return false;
+  }
+
   std::string group_set = ui_->group_box->currentText().toStdString();
   bool groups_enabled = group_set != "" && group_set != "-None-";
   return groups_enabled;

Studio/Analysis/AnalysisTool.ui

@@ -1387,7 +1387,7 @@ QWidget#particles_panel {
                       <item row="2" column="0">
                        <widget class="QRadioButton" name="pca_scalar_only">
                         <property name="toolTip">
-                         <string>Multi-Level Component Analysis - Modes of variation highlighting only morphological changes in shape subspace.</string>
+                         <string>PCA analysis on scalars only</string>
                         </property>
                         <property name="text">
                          <string>Scalar Only</string>
@@ -1412,7 +1412,7 @@ QWidget#particles_panel {
                       <item row="1" column="0">
                        <widget class="QRadioButton" name="pca_scalar_shape_only">
                         <property name="toolTip">
-                         <string>Multi-Level Component Analysis - Modes of variation highlighting only morphological changes in shape subspace.</string>
+                         <string>PCA analysis on shape only</string>
                         </property>
                         <property name="text">
                          <string>Shape Only</string>
@@ -1428,7 +1428,7 @@ QWidget#particles_panel {
                       <item row="3" column="0">
                        <widget class="QRadioButton" name="pca_shape_and_scalar">
                         <property name="toolTip">
-                         <string>Multi-Level Component Analysis - Modes of variation highlighting only morphological changes in shape subspace.</string>
+                         <string>PCA analysis on shape+scalars combined</string>
                         </property>
                         <property name="text">
                          <string>Shape and Scalar</string>
@@ -1450,13 +1450,19 @@ QWidget#particles_panel {
                       </item>
                       <item row="1" column="1">
                        <widget class="QCheckBox" name="pca_predict_scalar">
+                        <property name="toolTip">
+                         <string>Predict scalars from shape using 2 block PLS fit</string>
+                        </property>
                         <property name="text">
                          <string>Predict Scalar</string>
                         </property>
                        </widget>
                       </item>
                       <item row="2" column="1">
                        <widget class="QCheckBox" name="pca_predict_shape">
+                        <property name="toolTip">
+                         <string>Predict shape from scalars using 2 block PLS fit</string>
+                        </property>
                         <property name="text">
                          <string>Predict Shape</string>
                         </property>