Merge branch 'master' into release_v6.4.0

Examples/Python/deep_ssm.py

@@ -249,7 +249,7 @@ def Run_Pipeline(args):
     project.save(spreadsheet_file)
 
     # Run optimization
-    optimizeCmd = ('shapeworks optimize --name ' + spreadsheet_file).split()
+    optimizeCmd = ('shapeworks optimize --progress --name ' + spreadsheet_file).split()
     subprocess.check_call(optimizeCmd)
 
     print("To analyze train shape model, call:")
@@ -533,7 +533,7 @@ def Run_Pipeline(args):
     project.save(spreadsheet_file)
 
     # Run optimization
-    optimize_cmd = ('shapeworks optimize --name ' + spreadsheet_file).split()
+    optimize_cmd = ('shapeworks optimize --progress --name ' + spreadsheet_file).split()
     subprocess.check_call(optimize_cmd)
 
     print("To analyze validation shape model, call:")
@@ -690,4 +690,4 @@ def check_results(args, mean_dist):
         print("Done with test, verification succeeded.")
         exit(0)
     else:
-        return
+        return

Examples/Python/ellipsoid.py

@@ -206,7 +206,7 @@ def Run_Pipeline(args):
     project.save(spreadsheet_file)
 
     # Run optimization
-    optimize_cmd = ('shapeworks optimize --name ' + spreadsheet_file).split()
+    optimize_cmd = ('shapeworks optimize --progress --name ' + spreadsheet_file).split()
     subprocess.check_call(optimize_cmd)
 
     # If tiny test or verify, check results and exit

Examples/Python/ellipsoid_cut.py

@@ -169,7 +169,7 @@ def Run_Pipeline(args):
     project.save(spreadsheet_file)
 
     # Run optimization
-    optimize_cmd = ('shapeworks optimize --name ' + spreadsheet_file).split()
+    optimize_cmd = ('shapeworks optimize --progress --name ' + spreadsheet_file).split()
     subprocess.check_call(optimize_cmd)
 
     # If tiny test or verify, check results and exit

Examples/Python/ellipsoid_fd.py

@@ -185,7 +185,7 @@ def Run_Pipeline(args):
     project.save(spreadsheet_file)
 
     # Run optimization
-    optimize_cmd = ('shapeworks optimize --name ' + spreadsheet_file).split()
+    optimize_cmd = ('shapeworks optimize --progress --name ' + spreadsheet_file).split()
     subprocess.check_call(optimize_cmd)
 
     # If tiny test or verify, check results and exit

Examples/Python/ellipsoid_mesh.py

@@ -173,7 +173,7 @@ def Run_Pipeline(args):
     project.save(spreadsheet_file)
 
     # Run optimization
-    optimize_cmd = ('shapeworks optimize --name ' + spreadsheet_file).split()
+    optimize_cmd = ('shapeworks optimize --progress --name ' + spreadsheet_file).split()
     subprocess.check_call(optimize_cmd)
 
     # If tiny test or verify, check results and exit

Examples/Python/ellipsoid_multiple_domain.py

@@ -271,7 +271,7 @@ def Run_Pipeline(args):
     project.save(spreadsheet_file)
 
     # Run optimization
-    optimize_cmd = ('shapeworks optimize --name ' + spreadsheet_file).split()
+    optimize_cmd = ('shapeworks optimize --progress --name ' + spreadsheet_file).split()
     subprocess.check_call(optimize_cmd)
 
     # If tiny test or verify, check results and exit

Examples/Python/ellipsoid_multiple_domain_mesh.py

@@ -204,7 +204,7 @@ def Run_Pipeline(args):
     project.save(spreadsheet_file)
 
     # Run optimization
-    optimize_cmd = ('shapeworks optimize --name ' + spreadsheet_file).split()
+    optimize_cmd = ('shapeworks optimize --progress --name ' + spreadsheet_file).split()
     subprocess.check_call(optimize_cmd)
 
     # If tiny test or verify, check results and exit

Examples/Python/femur_cut.py

@@ -225,7 +225,7 @@ def Run_Pipeline(args):
     project.save(spreadsheet_file)
 
     # Run optimization
-    optimizeCmd = ('shapeworks optimize --name ' + spreadsheet_file).split()
+    optimizeCmd = ('shapeworks optimize --progress --name ' + spreadsheet_file).split()
     subprocess.check_call(optimizeCmd)
 
     # If tiny test or verify, check results and exit

Examples/Python/hip_multiple_domain.py

@@ -248,7 +248,7 @@ def Run_Pipeline(args):
 
 
 	# Run optimization
-	optimize_cmd = ('shapeworks optimize --name ' + spreadsheet_file).split()
+	optimize_cmd = ('shapeworks optimize --progress --name ' + spreadsheet_file).split()
 	subprocess.check_call(optimize_cmd)
 
 	# # If tiny test or verify, check results and exit

Examples/Python/incremental_supershapes.py

@@ -198,7 +198,7 @@ def Run_Pipeline(args):
     project.save(spreadsheet_file)
 
     # Run optimization
-    optimize_cmd = ('shapeworks optimize --name ' + spreadsheet_file).split()
+    optimize_cmd = ('shapeworks optimize --progress --name ' + spreadsheet_file).split()
     print(optimize_cmd)
     subprocess.check_call(optimize_cmd)
 
@@ -284,7 +284,7 @@ def Run_Pipeline(args):
         project.save(spreadsheet_file)
 
         # Run optimization
-        optimize_cmd = ('shapeworks optimize --name ' +
+        optimize_cmd = ('shapeworks optimize --progress --name ' +
                         spreadsheet_file).split()
         subprocess.check_call(optimize_cmd)
 

Examples/Python/left_atrium.py

@@ -208,7 +208,7 @@ def Run_Pipeline(args):
         parameter_dictionary["multiscale"] = 1
         parameter_dictionary["multiscale_particles"] = 128
 
-    print('Generating project sheet')
+    print('Generating project file')
     # Add param dictionary to spreadsheet
     for key in parameter_dictionary:
         parameters.set(key, sw.Variant([parameter_dictionary[key]]))
@@ -217,7 +217,8 @@ def Run_Pipeline(args):
     project.save(spreadsheet_file)
 
     # Run optimization
-    optimize_cmd = ('shapeworks optimize --name ' + spreadsheet_file).split()
+    print('Running optimization')
+    optimize_cmd = ('shapeworks optimize --progress --name ' + spreadsheet_file).split()
     subprocess.check_call(optimize_cmd)
 
     # If tiny test or verify, check results and exit

Examples/Python/lumps.py

@@ -127,7 +127,7 @@ def Run_Pipeline(args):
     project.save(spreadsheet_file)
 
     # Run optimization
-    optimize_cmd = ('shapeworks optimize --name ' + spreadsheet_file).split()
+    optimize_cmd = ('shapeworks optimize --progress --name ' + spreadsheet_file).split()
     subprocess.check_call(optimize_cmd)
 
     # If tiny test or verify, check results and exit

Examples/Python/peanut_shared_boundary.py

@@ -218,7 +218,7 @@ def Run_Pipeline(args):
     project.save(spreadsheet_file)
 
     # Run optimization
-    optimize_cmd = ('shapeworks optimize --name ' + spreadsheet_file).split()
+    optimize_cmd = ('shapeworks optimize --progress --name ' + spreadsheet_file).split()
     subprocess.check_call(optimize_cmd)
 
     # If tiny test or verify, check results and exit

Examples/Python/supershapes_1mode_contour.py

@@ -99,7 +99,7 @@ def Run_Pipeline(args):
     project.save(spreadsheet_file)
 
     # Run optimization
-    optimize_cmd = ('shapeworks optimize --name ' + spreadsheet_file).split()
+    optimize_cmd = ('shapeworks optimize --progress --name ' + spreadsheet_file).split()
     subprocess.check_call(optimize_cmd)
 
     # If tiny test or verify, check results and exit

Examples/Python/thin_cavity_bean.py

@@ -123,7 +123,7 @@ def Run_Pipeline(args):
     project.save(spreadsheet_file)
 
     # Run optimization
-    optimize_cmd = ('shapeworks optimize --name ' + spreadsheet_file).split()
+    optimize_cmd = ('shapeworks optimize --progress --name ' + spreadsheet_file).split()
     subprocess.check_call(optimize_cmd)
 
     # If tiny test or verify, check results and exit

Installation/install_python_module.bat

@@ -2,7 +2,7 @@ REM Installs the shapeworks python module.
 REM  NOTE: assumes all library dependencies are in this directory\bin
 
 REM install pip module
-call pip install Python\shapeworks
+call pip install Python\shapeworks.tar.gz
 
 set CONDA_INSTALL_DIR=%CONDA_PREFIX%\lib\site-packages\shapeworks
 

Libs/Analyze/Particles.h

@@ -69,7 +69,7 @@ class Particles {
 
   vtkSmartPointer<vtkTransform> transform_;
   std::vector<vtkSmartPointer<vtkTransform>> procrustes_transforms_;
-  int alignment_type_;
+  int alignment_type_ = -1;
 
 };
 }  // namespace shapeworks

Libs/Mesh/Mesh.cpp

@@ -388,6 +388,19 @@ Mesh& Mesh::applyTransform(const MeshTransform transform) {
   return *this;
 }
 
+Mesh& Mesh::rotate(const double angle, const Axis axis){
+
+  Vector rotation(makeVector({0, 0, 0}));
+  rotation[axis] = 1;
+  auto com = center();
+
+  MeshTransform transform = MeshTransform::New();
+  transform->Translate(com[0], com[1], com[2]);
+  transform->RotateWXYZ(angle,rotation[0], rotation[1], rotation[2]);
+  transform->Translate(-com[0], -com[1], -com[2]);
+  return applyTransform(transform);
+}
+
 Mesh& Mesh::fillHoles() {
   auto filter = vtkSmartPointer<vtkFillHolesFilter>::New();
   filter->SetInputData(this->poly_data_);

Libs/Mesh/Mesh.h

@@ -93,6 +93,9 @@ class Mesh {
   /// applies the given transformation to the mesh
   Mesh& applyTransform(const MeshTransform transform);
 
+  /// applies the given rotation to the given axis 
+  Mesh& rotate(const double angle, const Axis axis);
+
   /// finds holes in a mesh and closes them
   Mesh& fillHoles();
 

Libs/Optimize/Optimize.cpp

@@ -2204,7 +2204,9 @@ void Optimize::ComputeTotalIterations() {
 void Optimize::UpdateProgress() {
   auto now = std::chrono::system_clock::now();
 
-  if ((now - m_last_update_time) > std::chrono::milliseconds(100)) {
+  bool final = current_particle_iterations_ == total_particle_iterations_;
+
+  if (final || (now - m_last_update_time) > std::chrono::milliseconds(100)) {
     m_last_update_time = now;
     std::chrono::duration<double> elapsed_seconds =
         std::chrono::duration_cast<std::chrono::seconds>(now - m_start_time);

Libs/Python/ShapeworksPython.cpp

@@ -1001,6 +1001,14 @@ PYBIND11_MODULE(shapeworks_py, m)
        "applies the given transformation to the mesh",
        "transform"_a, "imageTransform"_a=false)
 
+
+  .def("rotate",
+       [](Mesh& mesh, const double angle, const Axis axis) -> decltype(auto){
+          return mesh.rotate(angle, axis);
+       },
+       "rotate using axis by angle (in degrees)",
+       "angle"_a, "axis"_a)
+
   .def("fillHoles",
        &Mesh::fillHoles,
        "finds holes in a mesh and closes them")

Python/shapeworks/shapeworks/portal.py

@@ -101,15 +101,20 @@ def generate_download_flag(outputDirectory, folder):
     #if output/dataset + subfolders exits 
 
     dataset = Dataset.from_name(folder)
+    if dataset == None:
+        print(f"Error: Unable to locate dataset {folder} on data portal")
+        raise Exception(f"Dataset {folder} not found on data portal")
     if os.path.exists(outputDirectory):
         # if the folder is empty or has less than 3 files then download
         file_count = count_existing_files(outputDirectory)
+        print(f"file_count = {file_count}")
+        print(f"dataset = {dataset}")
         if file_count < 6 and dataset:
             download_flag = True
         elif file_count == 6 and dataset and not("tiny_test" in folder):
             download_flag = True
         else:
-            print("Data available in " + outputDirectory + "  is sufficient, no new data will be downloaded")
+            print("Data available in " + outputDirectory + " is sufficient, no new data will be downloaded")
     #if the subfolder folder does not exists then download
     else:
         download_flag = True        

Support/package_windows.sh

@@ -43,13 +43,12 @@ cp -r $BUILD/bin/Release bin
 rm bin/*Tests.pdb bin/Recon*.pdb bin/Mesh*.pdb
 rm -rf Post
 
-# Run auto-documentation
-cd $ROOT
-PATH=$BUILD/bin/Release/bin:$PATH
-
-# add $PATH to $PYTHONPATH
-PYTHONPATH=$PYTHONPATH:$PATH
-
+# Build python packages
+for package in DataAugmentationUtilsPackage DatasetUtilsPackage DeepSSMUtilsPackage DocumentationUtilsPackage ShapeCohortGenPackage shapeworks ; do
+    cd Python
+    tar czvf ${package}.tar.gz $package
+    cd ..
+done
 
 # Remove tests, they won't work for users anyway
 rm bin/*Tests.exe

Testing/PythonTests/rotate.py

@@ -4,14 +4,25 @@
 
 success = True
 
-def rotateTest():
+def rotateTest1():
   img = Image(os.environ["DATA"] + "/la-bin-centered.nrrd")
   img.rotate(0.7854, [1.0, 1.0, 1.0])
 
   compareImg = Image(os.environ["DATA"] + "/rotate2.nrrd")
 
   return img.compare(compareImg)
 
-success &= utils.test(rotateTest)
+success &= utils.test(rotateTest1)
+
+def rotateTest2():
+  mesh = Mesh(os.environ["DATA"] + "/femur.ply")
+  mesh.rotate(90, Axis.Y)
+
+  compareMesh = Mesh(os.environ["DATA"] + "/rotated_mesh.ply")
+
+  return mesh == compareMesh
+
+success &= utils.test(rotateTest2)
+
 
 sys.exit(not success)