Implementation Wrap ScalableFM

geomfum/_registry.py

@@ -245,6 +245,10 @@ class HierarchicalMeshRegistry(WhichRegistry):
     MAP = {}
 
 
+class PoissonSamplerRegistry(WhichRegistry):
+    MAP = {}
+
+
 def _create_register_funcs(module):
     # create `register_` functions automatically
     for name, method in inspect.getmembers(module):

geomfum/sample.py

@@ -0,0 +1,54 @@
+import abc
+
+import numpy as np
+from sklearn.neighbors import NearestNeighbors
+
+import geomfum.wrap as _wrap  # noqa (for register)
+from geomfum._registry import PoissonSamplerRegistry, WhichRegistryMixins
+
+
+class BaseSampler(abc.ABC):
+    @abc.abstractmethod
+    def sample(self, shape):
+        pass
+
+
+class PoissonSampler(WhichRegistryMixins):
+    _Registry = PoissonSamplerRegistry
+
+
+class NearestNeighborsIndexSampler(BaseSampler):
+    # uses nearest neighbor to get indices of sample coordinates
+    # resulting from another sampler
+
+    # TODO: find better naming as this is confusing
+
+    def __init__(self, n_samples=None, sampler=None, neighbor_finder=None):
+        # n_samples are ignored if sampler is not None
+        if sampler is None:
+            sampler = PoissonSampler.from_registry(n_samples=n_samples)
+
+        if neighbor_finder is None:
+            neighbor_finder = NearestNeighbors(
+                n_neighbors=1, leaf_size=40, algorithm="kd_tree", n_jobs=1
+            )
+        if neighbor_finder.n_neighbors > 1:
+            raise ValueError("Expects `n_neighors = 1`.")
+
+        self.neighbor_finder = neighbor_finder
+        self.sampler = sampler
+
+    @property
+    def n_samples(self):
+        # TODO: this assumption may be too restrictive (only for logging...)
+        # TODO: add logger instead in main code and remove here
+        return self.sampler.n_samples
+
+    def sample(self, shape):
+        # returns array[index]
+        sampled_points = self.sampler.sample(shape)
+
+        self.neighbor_finder.fit(shape.vertices)
+        _, neighbor_indices = self.neighbor_finder.kneighbors(sampled_points)
+
+        return np.unique(neighbor_indices)

geomfum/shape/point_cloud.py

@@ -15,3 +15,13 @@ class PointCloud(Shape):
     def __init__(self, vertices):
         super().__init__(is_mesh=False)
         self.vertices = vertices
+
+    @property
+    def n_points(self):
+        """Number of vertices.
+
+        Returns
+        -------
+        n_vertices : int
+        """
+        return self.vertices.shape[0]

geomfum/wrap/__init__.py

@@ -5,6 +5,7 @@
     register_heat_kernel_signature,
     register_hierarchical_mesh,
     register_laplacian_finder,
+    register_poisson_sampler,
     register_wave_kernel_signature,
 )
 from geomfum._utils import has_package
@@ -52,7 +53,14 @@
     "pyfm", "PyFmFaceOrientationOperator", requires="pyFM", as_default=True
 )
 
-
 register_hierarchical_mesh(
     "pyrmt", "PyrmtHierarchicalMesh", requires="PyRMT", as_default=True
 )
+
+register_hierarchical_mesh(
+    "scalablefm", "ScalableHierarchicalMesh", requires="pyFM", as_default=True
+)
+
+register_poisson_sampler(
+    "pymeshlab", "PymeshlabPoissonSampler", requires="pymeshlab", as_default=True
+)

geomfum/wrap/pymeshlab.py

@@ -0,0 +1,38 @@
+import pymeshlab
+
+from geomfum.sample import BaseSampler
+
+
+class PymeshlabPoissonSampler(BaseSampler):
+    """Poisson disk sampling.
+
+    Parameters
+    ----------
+    n_samples : int
+        Number of samples to target.
+    """
+
+    def __init__(self, n_samples):
+        self.n_samples = n_samples
+
+    def sample(self, shape):
+        """Sample using Poisson disk sampling.
+
+        Parameters
+        ----------
+        shape : TriangleMesh
+            Mesh.
+
+        Returns
+        -------
+        samples : array-like, shape=[n_samples, 3]
+            Coordinates of samples.
+        """
+        ms = pymeshlab.MeshSet()
+        ms.add_mesh(
+            pymeshlab.Mesh(vertex_matrix=shape.vertices, face_matrix=shape.faces)
+        )
+
+        ms.generate_sampling_poisson_disk(samplenum=self.n_samples)
+
+        return ms.current_mesh().vertex_matrix()

geomfum/wrap/pyrmt.py

@@ -8,6 +8,7 @@
 from geomfum.shape.mesh import TriangleMesh
 
 
+
 class PyrmtHierarchicalMesh(HierarchicalShape):
     """Hierarchical mesh from PyRMT.