# Statistics via Python API **URL:** \ **Category:** Uncategorized\ **Created:** [April 10, 2024, 5:28pm UTC](https://shapeworks.discourse.group/t/statistics-via-python-api/222 "2024-04-10T17:28:35Z")\ **Posts on this page:** 8\ **Page:** 1
**Author:** ![joshcates](https://avatars.discourse-cdn.com/v4/letter/j/d2c977/32.png) [@joshcates](https://shapeworks.discourse.group/u/joshcates)\ **Post date:** [April 10, 2024, 5:28pm UTC](https://shapeworks.discourse.group/t/statistics-via-python-api/222/1 "2024-04-10T17:28:35Z")
Hello ShapeWorks! Is it possible to use the Python API to compute a mean shape, median shape, and other statistics? For example, something like the follow would be extremely useful: ```auto model = shapeworks.load_model("myssm.xlsx") mean_particles = sw.stats.mean(model) median_particles = sw.stats.median(model) ``` (A related question: Is the Python API fully documented somewhere?) thanks! ---
**Author:** ![amorris](https://avatars.discourse-cdn.com/v4/letter/a/73ab20/32.png) [@amorris](https://shapeworks.discourse.group/u/amorris)\ **Post date:** [April 10, 2024, 6:32pm UTC](https://shapeworks.discourse.group/t/statistics-via-python-api/222/2 "2024-04-10T18:32:01Z")
The python documentation is here: > **[Python API Reference - ShapeWorks](http://sciinstitute.github.io/ShapeWorks/latest/python/python-api.html)** > > The official documentation of ShapeWorks There is an `Analyze` module available that accomplishes some of this: ```auto import shapeworks as sw project = sw.Project() project.load("d2_pre_only.xlsx") analyze = sw.Analyze(project) mean_particles = analyze.get_mean_shape_points() ``` But it looks like there isn’t yet a method to return the median shape particles. It should be pretty easy to add if desired. ---
**Author:** ![joshcates](https://avatars.discourse-cdn.com/v4/letter/j/d2c977/32.png) [@joshcates](https://shapeworks.discourse.group/u/joshcates)\ **Post date:** [April 11, 2024, 1:17am UTC](https://shapeworks.discourse.group/t/statistics-via-python-api/222/3 "2024-04-11T01:17:32Z")
Thanks Alan! I’m not sure how I didn’t find the documentation, but now it is clear. ---
**Author:** ![Apoorva](https://avatars.discourse-cdn.com/v4/letter/a/d6d6ee/32.png) [@Apoorva](https://shapeworks.discourse.group/u/Apoorva)\ **Post date:** [July 18, 2024, 9:04am UTC](https://shapeworks.discourse.group/t/statistics-via-python-api/222/4 "2024-07-18T09:04:19Z")
Hey, Can you please tell how to get the shape meshes from these particles using python? ---
**Author:** ![amorris](https://avatars.discourse-cdn.com/v4/letter/a/73ab20/32.png) [@amorris](https://shapeworks.discourse.group/u/amorris)\ **Post date:** [July 18, 2024, 8:45pm UTC](https://shapeworks.discourse.group/t/statistics-via-python-api/222/5 "2024-07-18T20:45:12Z")
Mesh reconstruction from particles in ShapeWorks is typically done using mesh warping. A reference template mesh is used to warp based on the particles. For example: ```python from shapeworks import * reference_mesh = Mesh("template.vtk") particles = ParticleSystem("template_particles.particles"]).ShapeAsPointSet(0) warper = MeshWarper() warper.generateWarp(reference_mesh, particles) target_particles = ParticleSystem("target_particles.particles"]).ShapeAsPointSet(0) warped_mesh = warper.buildMesh(target_particles) ``` ---
**Author:** ![Apoorva](https://avatars.discourse-cdn.com/v4/letter/a/d6d6ee/32.png) [@Apoorva](https://shapeworks.discourse.group/u/Apoorva)\ **Post date:** [July 22, 2024, 9:29am UTC](https://shapeworks.discourse.group/t/statistics-via-python-api/222/6 "2024-07-22T09:29:36Z")
Thank you. But with the below code, from shapeworks import \* shape\_path = ‘_/mean\_geo/par\_512.stl’ shapeMesh = sw.Mesh(shape\_path) shapeMesh\_vtk = sw.sw2vtkMesh(shapeMesh) mean\_particles = '_/particles/mean\_particles.particles’ reference\_mesh =shapeMesh\_vtk # Mesh(shapeMesh\_vtk) particles = ParticleSystem([mean\_particles]).ShapeAsPointSet(0) warper = MeshWarper() warper.generateWarp(reference\_mesh, particles) it is showing me error as ’ generateWarp(): incompatible function arguments. The following argument types are supported: 1. (self: shapeworks\_py.MeshWarper, reference\_mesh: shapeworks\_py.Mesh, reference\_particles: numpy.ndarray[numpy.float64[m, n]]) → bool 2. (self: shapeworks\_py.MeshWarper, reference\_mesh: shapeworks\_py.Mesh, reference\_particles: numpy.ndarray[numpy.float64[m, n]], landmarks: numpy.ndarray[numpy.float64[m, n]]) → bool Invoked with: \, PolyData (0x2132f485040) N Cells: 17996 N Points: 9000 X Bounds: -5.189e+01, 3.424e+01 Y Bounds: -3.262e+01, 3.035e+01 Z Bounds: -1.396e+02, 9.510e+01 N Arrays: 0 , array([[-2.94732, 5.13163, -75.2647], [-5.07009, -23.7317 , 26.3011], [21.2718 , -5.59686, -30.3606], …, [9.99318, -25.7292 , 76.1548], [-29.259 , 13.1121 , 92.0959], [21.045 , 15.0181 , -136.303]])’ Please let me know how to move forward with this. It difficult to debug it. Thanks in advance I ---
**Author:** ![amorris](https://avatars.discourse-cdn.com/v4/letter/a/73ab20/32.png) [@amorris](https://shapeworks.discourse.group/u/amorris)\ **Post date:** [July 22, 2024, 3:39pm UTC](https://shapeworks.discourse.group/t/statistics-via-python-api/222/7 "2024-07-22T15:39:19Z")
> [@Apoorva](#): > > ```python > from shapeworks import * > > shape_path = '/mean_geo/par_512.stl' > shapeMesh = sw.Mesh(shape_path) > shapeMesh_vtk = sw.sw2vtkMesh(shapeMesh) > mean_particles = '/particles/mean_particles.particles' > > reference_mesh =shapeMesh_vtk # Mesh(shapeMesh_vtk) > particles = ParticleSystem([mean_particles]).ShapeAsPointSet(0) > > warper = MeshWarper() > warper.generateWarp(reference_mesh, particles) > > ``` The `generateWarp` call takes a ShapeWorks `Mesh` class, instead of a `vtkPolyData`. No need to use `sw.sw2vtkMesh` Try: ```python from shapeworks import * shape_path = '/mean_geo/par_512.stl' refrence_mesh = sw.Mesh(shape_path) mean_particles = '/particles/mean_particles.particles' particles = ParticleSystem([mean_particles]).ShapeAsPointSet(0) warper = MeshWarper() warper.generateWarp(reference_mesh, particles) ``` ---
**Author:** ![Apoorva](https://avatars.discourse-cdn.com/v4/letter/a/d6d6ee/32.png) [@Apoorva](https://shapeworks.discourse.group/u/Apoorva)\ **Post date:** [July 23, 2024, 9:19am UTC](https://shapeworks.discourse.group/t/statistics-via-python-api/222/8 "2024-07-23T09:19:08Z")
Thank you this was helpful.