Merge pull request #2023 from SCIInstitute/minor_issues

Minor additions

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/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")

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)

docs/new/ssm-eval.md

@@ -37,6 +37,7 @@ shapeworks readparticlesystem --name *.particles -- specificity    --nmodes 1
 ```
 
 ## ShapeWorks Python tools
+
 ```python
 # Read the particle files from a pre-trained shape model
 particle_data = sw.ParticleSystem(<list of local point files>)
@@ -45,7 +46,7 @@ shapeworks.ShapeEvaluation.ComputeCompactness(particleSystem=particle_data, nMod
 shapeworks.ShapeEvaluation.ComputeGeneralization(particleSystem=particle_data, nModes=1, saveTo=save_dir)
 shapeworks.ShapeEvaluation.ComputeSpecificity(particleSystem=particle_data, nModes=1, saveTo=save_dir)
 ```
-
+Details about the evaluation functions can be found [in the API Reference](http://sciinstitute.github.io/ShapeWorks/latest/api/Classes/classshapeworks_1_1ShapeEvaluation.html#function-shapeevaluation)
 
 <p><video src="https://sci.utah.edu/~shapeworks/doc-resources/mp4s/eval_ShellDemo.mp4" autoplay muted loop controls style="width:100%"></p>
 

docs/use-cases/stats-based/ellipsoid-evaluate.md

@@ -48,6 +48,9 @@ allGeneralization = sw.ShapeEvaluation.ComputeFullGeneralization(particleSystem=
 #Get specificity values for all modes
 allSpecificity = sw.ShapeEvaluation.ComputeFullSpecificity(particleSystem=particle_data)
 ```
+
+Details about the evaluation functions can be found [in the API Reference](http://sciinstitute.github.io/ShapeWorks/latest/api/Classes/classshapeworks_1_1ShapeEvaluation.html#function-shapeevaluation)
+
 Generalization value of the 3rd mode -  0.09600121582319728
 
 Generalization Best Reconstruction![Generalization Best Reconstruction](https://sci.utah.edu/~shapeworks/doc-resources/pngs/generalization_best_recon.png)

docs/use-cases/stats-based/ellipsoid-pca.md

@@ -36,6 +36,7 @@ Using `shape_statistics` object, you can now extract the following entities:
 * Dimension of each shape: `numDims()`
 * Variance explained by each mode: `percentVarByMode()`
 
+Details about shape statistics functions can be found [in the API Reference](http://sciinstitute.github.io/ShapeWorks/latest/api/Classes/classshapeworks_1_1ParticleShapeStatistics.html#function-particleshapestatistics)
 
 When the use case is run, plots similar to those below will be generated.
 ![PCA Loading Violin Plot](https://sci.utah.edu/~shapeworks/doc-resources/pngs/pca_loadings_violin_plot.png)