Merge pull request #264 from daavoo/add-open3d-integration

Add open3d integration

README.rst

@@ -54,3 +54,59 @@ With the following concise code:
     new_cloud = cloud.get_sample("voxelgrid_nearest", voxelgrid_id=voxelgrid_id, as_PyntCloud=True)
 
     new_cloud.to_file("out_file.npz")
+
+Integration with other libraries
+================================
+
+pyntcloud offers seamless integration with other 3D processing libraries.
+
+You can create / convert PyntCloud instances from / to many 3D processing libraries using the `from_instance` / `to_instance` methods:
+
+- `Open3D <https://www.open3d.org>`_
+
+.. code-block:: python
+
+    import open3d as o3d
+    from pyntcloud import PyntCloud
+
+    # FROM Open3D
+    original_triangle_mesh = o3d.io.read_triangle_mesh("diamond.ply")
+    cloud = PyntCloud.from_instance("open3d", original_triangle_mesh)
+    assert cloud.mesh is not None
+    assert np.allclose(cloud.mesh.values, original_triangle_mesh.triangles)
+    assert np.allclose(cloud.xyz, original_triangle_mesh.vertices)
+    assert {'red', 'green', 'blue'}.issubset(cloud.points.columns)
+    assert np.allclose(cloud.points[['red', 'green', 'blue']].values / 255., original_triangle_mesh.vertex_colors)
+    assert {'nx', 'ny', 'nz'}.issubset(cloud.points.columns)
+    assert np.allclose(cloud.points[['nx', 'ny', 'nz']].values,  original_triangle_mesh.vertex_normals)
+
+    # TO Open3D
+    cloud = PyntCloud.from_file("diamond.ply")
+    converted_triangle_mesh = cloud.to_instance("open3d", mesh=True)  # mesh=True by default
+    assert isinstance(converted_triangle_mesh, o3d.geometry.TriangleMesh)
+    assert np.allclose(cloud.xyz, converted_triangle_mesh.vertices)
+    assert np.allclose(cloud.mesh.values, converted_triangle_mesh.triangles)
+
+- `PyVista <https://docs.pyvista.org>`_
+
+.. code-block:: python
+
+    import pyvista as pv
+    from pyntcloud import PyntCloud
+
+    # FROM PyVista
+    original_point_cloud = pv.read("diamond.ply")
+    cloud = PyntCloud.from_instance("pyvista", original_point_cloud)
+    assert np.allclose(cloud.xyz, original_point_cloud.points)
+    assert {'red', 'green', 'blue'}.issubset(cloud.points.columns)
+    assert np.allclose(cloud.points[['red', 'green', 'blue']].values, original_point_cloud.point_arrays["RGB"])
+    assert {'nx', 'ny', 'nz'}.issubset(cloud.points.columns)
+    assert np.allclose(cloud.points[['nx', 'ny', 'nz']].values,  original_point_cloud.point_arrays["Normals"])
+
+    # TO PyVista
+    cloud = PyntCloud.from_file("diamond.ply")
+    converted_triangle_mesh = cloud.to_instance("open3d", mesh=True)
+    assert isinstance(converted_triangle_mesh, pv.PolyData)
+    assert np.allclose(cloud.xyz, converted_triangle_mesh.points)
+    assert np.allclose(cloud.mesh.values, converted_triangle_mesh.faces[:, 1:])
+

docs/conf.py

@@ -67,9 +67,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = '0.0.1'
+version = '0.0.2'
 # The full version, including alpha/beta/rc tags.
-release = '0.0.1'
+release = '0.0.2'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

pyntcloud/core_class.py

@@ -131,7 +131,7 @@ def from_file(cls, filename, **kwargs):
 
     @classmethod
     def from_instance(cls, library, instance, **kwargs):
-        """Extract data from file and construct a PyntCloud with it.
+        """Convert library's instance to PyntCloud intstance.
 
         Parameters
         ----------
@@ -182,7 +182,7 @@ def to_file(self, filename, also_save=None, **kwargs):
         TO_FILE[ext](**kwargs)
 
     def to_instance(self, library, **kwargs):
-        """Save PyntCloud data to file.
+        """Convert PyntCloud's instance to library's instance.
 
         Parameters
         ----------

pyntcloud/io/__init__.py

@@ -1,3 +1,4 @@
+from pyntcloud.io.open3d import from_open3d, to_open3d
 from pyntcloud.io.pyvista import from_pyvista, to_pyvista
 from .ascii import read_ascii, write_ascii
 from .bin import read_bin, write_bin
@@ -23,7 +24,8 @@
     "XYZ": read_ascii,
 }
 FROM_INSTANCE = {
-    "PYVISTA": from_pyvista
+    "PYVISTA": from_pyvista,
+    "OPEN3D": from_open3d
 }
 
 TO_FILE = {
@@ -38,5 +40,6 @@
     "XYZ": write_ascii,
 }
 TO_INSTANCE = {
-    "PYVISTA": to_pyvista
+    "PYVISTA": to_pyvista,
+    "OPEN3D": to_open3d
 }

pyntcloud/io/open3d.py

@@ -0,0 +1,85 @@
+import numpy as np
+import pandas as pd
+
+
+def from_open3d(o3d_data, **kwargs):
+    """Create a PyntCloud instance from Open3D's PointCloud/TriangleMesh instance"""
+    try:
+        import open3d as o3d
+    except ImportError:
+        raise ImportError("Open3D must be installed. Try `pip install open3d`")
+
+    if not isinstance(o3d_data, (o3d.geometry.PointCloud, o3d.geometry.TriangleMesh)):
+        raise TypeError(f"Type {type(o3d_data)} not supported for conversion."
+                        f"Expected {o3d.geometry.PointCloud} or {o3d.geometry.TriangleMesh}")
+
+    mesh = None
+    if isinstance(o3d_data, o3d.geometry.TriangleMesh):
+        mesh = pd.DataFrame(data=np.asarray(o3d_data.triangles),
+                            columns=['v1', 'v2', 'v3'])
+
+        points = pd.DataFrame(data=np.asarray(o3d_data.vertices),
+                              columns=["x", "y", "z"])
+
+        if o3d_data.vertex_colors:
+            colors = (np.asarray(o3d_data.vertex_colors) * 255).astype(np.uint8)
+            points["red"] = colors[:, 0]
+            points["green"] = colors[:, 1]
+            points["blue"] = colors[:, 2]
+
+        if o3d_data.vertex_normals:
+            normals = np.asarray(o3d_data.vertex_normals)
+            points["nx"] = normals[:, 0]
+            points["ny"] = normals[:, 1]
+            points["nz"] = normals[:, 2]
+
+    elif isinstance(o3d_data, o3d.geometry.PointCloud):
+        points = pd.DataFrame(data=np.asarray(o3d_data.points),
+                              columns=["x", "y", "z"])
+
+        if o3d_data.colors:
+            colors = (np.asarray(o3d_data.colors) * 255).astype(np.uint8)
+            points["red"] = colors[:, 0]
+            points["green"] = colors[:, 1]
+            points["blue"] = colors[:, 2]
+
+        if o3d_data.normals:
+            normals = np.asarray(o3d_data.normals)
+            points["nx"] = normals[:, 0]
+            points["ny"] = normals[:, 1]
+            points["nz"] = normals[:, 2]
+
+    return {
+        "points": points,
+        "mesh": mesh
+    }
+
+
+def to_open3d(cloud,
+              mesh=True,
+              colors=True,
+              normals=True,
+              **kwargs):
+    """Convert PyntCloud's instance `cloud` to Open3D's PointCloud/TriangleMesh instance"""
+    try:
+        import open3d as o3d
+    except ImportError:
+        raise ImportError("Open3D must be installed. Try `pip install open3d`")
+
+    if mesh and cloud.mesh is not None:
+        triangle_mesh = o3d.geometry.TriangleMesh()
+        triangle_mesh.triangles = o3d.utility.Vector3iVector(cloud.mesh[["v1", "v2", "v3"]].values)
+        triangle_mesh.vertices = o3d.utility.Vector3dVector(cloud.xyz)
+        if colors and {'red', 'green', 'blue'}.issubset(cloud.points.columns):
+            triangle_mesh.vertex_colors = o3d.utility.Vector3dVector(cloud.points[['red', 'green', 'blue']].values)
+        if normals and {'nx', 'ny', 'nz'}.issubset(cloud.points.columns):
+            triangle_mesh.vertex_normals = o3d.utility.Vector3dVector(cloud.points[['nx', 'ny', 'nz']].values)
+        return triangle_mesh
+    else:
+        point_cloud = o3d.geometry.PointCloud()
+        point_cloud.points = o3d.utility.Vector3dVector(cloud.xyz)
+        if colors and {'red', 'green', 'blue'}.issubset(cloud.points.columns):
+            point_cloud.colors = o3d.utility.Vector3dVector(cloud.points[['red', 'green', 'blue']].values)
+        if normals and {'nx', 'ny', 'nz'}.issubset(cloud.points.columns):
+            point_cloud.normals = o3d.utility.Vector3dVector(cloud.points[['nx', 'ny', 'nz']].values)
+        return point_cloud

requirements.txt

@@ -7,3 +7,4 @@ matplotlib
 numba
 pytest
 pyvista
+open3d

tests/integration/io/test_from_instance.py

@@ -0,0 +1,82 @@
+import pytest
+import numpy as np
+from pyntcloud import PyntCloud
+
+try:
+    import pyvista as pv
+    SKIP_PYVISTA = False
+except:
+    pv = None
+    SKIP_PYVISTA = True
+
+try:
+    import open3d as o3d
+    SKIP_OPEN3D = False
+except:
+    o3d = None
+    SKIP_OPEN3D = True
+
+
+@pytest.mark.skipif(SKIP_PYVISTA, reason="Requires PyVista")
+def test_pyvista_conversion(data_path):
+    original_point_cloud = pv.read(str(data_path / "diamond.ply"))
+    cloud = PyntCloud.from_instance("pyvista", original_point_cloud)
+    assert np.allclose(cloud.xyz, original_point_cloud.points)
+    assert {'red', 'green', 'blue'}.issubset(cloud.points.columns)
+    assert np.allclose(cloud.points[['red', 'green', 'blue']].values, original_point_cloud.point_arrays["RGB"])
+    assert {'nx', 'ny', 'nz'}.issubset(cloud.points.columns)
+    assert np.allclose(cloud.points[['nx', 'ny', 'nz']].values,  original_point_cloud.point_arrays["Normals"])
+
+
+@pytest.mark.skipif(SKIP_PYVISTA, reason="Requires PyVista")
+def test_pyvista_normals_are_handled():
+    poly = pv.Sphere()
+    pc = PyntCloud.from_instance("pyvista", poly)
+    assert all(x in pc.points.columns for x in ["nx", "ny", "nz"])
+
+
+@pytest.mark.skipif(SKIP_PYVISTA, reason="Requires PyVista")
+def test_pyvista_multicomponent_scalars_are_splitted():
+    poly = pv.Sphere()
+    poly.point_arrays["foo"] = np.zeros_like(poly.points)
+    pc = PyntCloud.from_instance("pyvista", poly)
+    assert all(x in pc.points.columns for x in ["foo_0", "foo_1", "foo_2"])
+
+
+@pytest.mark.skipif(SKIP_PYVISTA, reason="Requires PyVista")
+def test_pyvista_rgb_is_handled():
+    """ Serves as regression test for old `in` behaviour that could cause a subtle bug
+    if poin_arrays contain a field with `name in "RGB"`
+    """
+    poly = pv.Sphere()
+    poly.point_arrays["RG"] = np.zeros_like(poly.points)[:, :2]
+    pc = PyntCloud.from_instance("pyvista", poly)
+    assert all(x in pc.points.columns for x in ["RG_0", "RG_1"])
+
+
+@pytest.mark.skipif(SKIP_OPEN3D, reason="Requires Open3D")
+def test_open3d_point_cloud(data_path):
+    point_cloud = o3d.io.read_point_cloud(str(data_path.joinpath("diamond.ply")))
+    cloud = PyntCloud.from_instance("open3d", point_cloud)
+    assert np.allclose(cloud.xyz, np.asarray(point_cloud.points))
+    assert {'red', 'green', 'blue'}.issubset(cloud.points.columns)
+    assert np.allclose(cloud.points[['red', 'green', 'blue']].values / 255., np.asarray(point_cloud.colors))
+
+    assert {'nx', 'ny', 'nz'}.issubset(cloud.points.columns)
+    assert np.allclose(cloud.points[['nx', 'ny', 'nz']].values,  np.asarray(point_cloud.normals))
+
+
+@pytest.mark.skipif(SKIP_OPEN3D, reason="Requires Open3D")
+def test_open3d_triangle_mesh(data_path):
+    triangle_mesh = o3d.io.read_triangle_mesh(str(data_path.joinpath("diamond.ply")))
+    cloud = PyntCloud.from_instance("open3d", triangle_mesh)
+    assert cloud.mesh is not None
+    assert np.allclose(cloud.mesh.values, triangle_mesh.triangles)
+
+    assert np.allclose(cloud.xyz, triangle_mesh.vertices)
+
+    assert {'red', 'green', 'blue'}.issubset(cloud.points.columns)
+    assert np.allclose(cloud.points[['red', 'green', 'blue']].values / 255., triangle_mesh.vertex_colors)
+
+    assert {'nx', 'ny', 'nz'}.issubset(cloud.points.columns)
+    assert np.allclose(cloud.points[['nx', 'ny', 'nz']].values,  triangle_mesh.vertex_normals)

tests/integration/io/test_to_instance.py

@@ -0,0 +1,43 @@
+import pytest
+import numpy as np
+from pyntcloud import PyntCloud
+
+try:
+    import pyvista as pv
+    SKIP_PYVISTA = False
+except:
+    pv = None
+    SKIP_PYVISTA = True
+
+try:
+    import open3d as o3d
+    SKIP_OPEN3D = False
+except:
+    o3d = None
+    SKIP_OPEN3D = True
+
+
+@pytest.mark.skipif(SKIP_PYVISTA, reason="Requires PyVista")
+def test_pyvista_conversion(data_path):
+    cloud = PyntCloud.from_file(str(data_path.joinpath("diamond.ply")))
+    poly = cloud.to_instance("pyvista", mesh=True)
+    assert np.allclose(cloud.xyz, poly.points)
+    assert np.allclose(cloud.mesh.values, poly.faces[:, 1:])
+
+
+@pytest.mark.skipif(SKIP_OPEN3D, reason="Requires Open3D")
+def test_open3d_point_cloud_conversion(data_path):
+    cloud = PyntCloud.from_file(str(data_path.joinpath("diamond.ply")))
+    point_cloud = cloud.to_instance("open3d", mesh=False)
+    assert isinstance(point_cloud, o3d.geometry.PointCloud)
+    assert np.allclose(cloud.xyz, point_cloud.points)
+
+
+@pytest.mark.skipif(SKIP_OPEN3D, reason="Requires Open3D")
+def test_open3d_triangle_mesh_conversion(data_path):
+    cloud = PyntCloud.from_file(str(data_path.joinpath("diamond.ply")))
+    # mesh=True by default
+    triangle_mesh = cloud.to_instance("open3d")
+    assert isinstance(triangle_mesh, o3d.geometry.TriangleMesh)
+    assert np.allclose(cloud.xyz, triangle_mesh.vertices)
+    assert np.allclose(cloud.mesh.values, triangle_mesh.triangles)

tests/integration/test_core_class.py

@@ -1,17 +1,9 @@
-import os
 import pytest
 import numpy as np
 import pandas as pd
 from shutil import rmtree
 from pyntcloud import PyntCloud
 
-try:
-    import pyvista as pv
-    SKIP_PYVISTA = False
-except:
-    pv = None
-    SKIP_PYVISTA = True
-
 
 def test_points():
     """PyntCloud.points.
@@ -99,43 +91,3 @@ def test_split_on(data_path):
     assert len(output) == 8
 
     rmtree("tmp_out")
-
-
-@pytest.mark.skipif(SKIP_PYVISTA, reason="Requires PyVista")
-def test_pyvista_conversion(data_path):
-    print(data_path)
-    print(data_path.joinpath("diamond.ply"))
-    cloud = PyntCloud.from_file(str(data_path.joinpath("diamond.ply")))
-    poly = cloud.to_instance("pyvista", mesh=True)
-    pc = PyntCloud.from_instance("pyvista", poly)
-    assert np.allclose(cloud.points[['x', 'y', 'z']].values, poly.points)
-    assert np.allclose(cloud.mesh.values, pc.mesh.values)
-    poly = pv.read(str(data_path.joinpath("diamond.ply")))
-    pc = PyntCloud.from_instance("pyvista", poly)
-    assert np.allclose(pc.points[['x', 'y', 'z']].values, poly.points)
-
-
-@pytest.mark.skipif(SKIP_PYVISTA, reason="Requires PyVista")
-def test_pyvista_normals_are_handled():
-    poly = pv.Sphere()
-    pc = PyntCloud.from_instance("pyvista", poly)
-    assert all(x in pc.points.columns for x in ["nx", "ny", "nz"])
-
-
-@pytest.mark.skipif(SKIP_PYVISTA, reason="Requires PyVista")
-def test_pyvista_multicomponent_scalars_are_splitted():
-    poly = pv.Sphere()
-    poly.point_arrays["foo"] = np.zeros_like(poly.points)
-    pc = PyntCloud.from_instance("pyvista", poly)
-    assert all(x in pc.points.columns for x in ["foo_0", "foo_1", "foo_2"])
-
-
-@pytest.mark.skipif(SKIP_PYVISTA, reason="Requires PyVista")
-def test_pyvista_RGB_is_handled():
-    """ Serves as regression test for old `in` behaviour that could cause a subtle bug
-    if poin_arrays contain a field with `name in "RGB"`
-    """
-    poly = pv.Sphere()
-    poly.point_arrays["RG"] = np.zeros_like(poly.points)[:, :2]
-    pc = PyntCloud.from_instance("pyvista", poly)
-    assert all(x in pc.points.columns for x in ["RG_0", "RG_1"])