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qim3d/features/_common_features_methods.py
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import numpy as np
import qim3d.processing
from qim3d.utils._logger import log
import trimesh
import qim3d
from pygel3d import hmesh
def volume(obj: np.ndarray|trimesh.Trimesh,
**mesh_kwargs
) -> float:
"""
Compute the volume of a 3D volume or mesh.
Args:
obj (np.ndarray or trimesh.Trimesh): Either a np.ndarray volume or a mesh object of type trimesh.Trimesh.
**mesh_kwargs (Any): Additional arguments for mesh creation if the input is a volume.
Returns:
volume (float): The volume of the object.
Example:
Compute volume from a mesh:
```python
import qim3d
# Load a mesh from a file
mesh = qim3d.io.load_mesh('path/to/mesh.obj')
# Compute the volume of the mesh
vol = qim3d.features.volume(mesh)
print('Volume:', vol)
```
Compute volume from a np.ndarray:
```python
import qim3d
# Generate a 3D blob
synthetic_blob = qim3d.generate.noise_object(noise_scale = 0.015)
synthetic_blob = qim3d.generate.noise_object(noise_scale = 0.015)
# Compute the volume of the blob
volume = qim3d.features.volume(synthetic_blob, level=0.5)
volume = qim3d.features.volume(synthetic_blob, level=0.5)
print('Volume:', volume)
```
"""
if isinstance(obj, np.ndarray):
log.info("Converting volume to mesh.")
obj = qim3d.mesh.from_volume(obj, **mesh_kwargs)
return obj.volume
def area(obj: np.ndarray|trimesh.Trimesh,
**mesh_kwargs
) -> float:
"""
Compute the surface area of a 3D volume or mesh.
Args:
obj (np.ndarray or trimesh.Trimesh): Either a np.ndarray volume or a mesh object of type trimesh.Trimesh.
**mesh_kwargs (Any): Additional arguments for mesh creation if the input is a volume.
Returns:
area (float): The surface area of the object.
Example:
Compute area from a mesh:
```python
import qim3d
# Load a mesh from a file
mesh = qim3d.io.load_mesh('path/to/mesh.obj')
# Compute the surface area of the mesh
area = qim3d.features.area(mesh)
area = qim3d.features.area(mesh)
print(f"Area: {area}")
```
Compute area from a np.ndarray:
```python
import qim3d
# Generate a 3D blob
synthetic_blob = qim3d.generate.noise_object(noise_scale = 0.015)
synthetic_blob = qim3d.generate.noise_object(noise_scale = 0.015)
# Compute the surface area of the blob
area = qim3d.features.area(synthetic_blob, level=0.5)
area = qim3d.features.area(synthetic_blob, level=0.5)
print('Area:', area)
```
"""
if isinstance(obj, np.ndarray):
log.info("Converting volume to mesh.")
obj = qim3d.mesh.from_volume(obj, **mesh_kwargs)
return obj.area
def sphericity(obj: np.ndarray|trimesh.Trimesh,
**mesh_kwargs
) -> float:
"""
Compute the sphericity of a 3D volume or mesh.
Sphericity is a measure of how spherical an object is. It is defined as the ratio
of the surface area of a sphere with the same volume as the object to the object's
actual surface area.
Args:
obj (np.ndarray or trimesh.Trimesh): Either a np.ndarray volume or a mesh object of type trimesh.Trimesh.
**mesh_kwargs (Any): Additional arguments for mesh creation if the input is a volume.
Returns:
sphericity (float): A float value representing the sphericity of the object.
Example:
Compute sphericity from a mesh:
```python
import qim3d
# Load a mesh from a file
mesh = qim3d.io.load_mesh('path/to/mesh.obj')
# Compute the sphericity of the mesh
sphericity = qim3d.features.sphericity(mesh)
sphericity = qim3d.features.sphericity(mesh)
```
Compute sphericity from a np.ndarray:
```python
import qim3d
# Generate a 3D blob
synthetic_blob = qim3d.generate.noise_object(noise_scale = 0.015)
synthetic_blob = qim3d.generate.noise_object(noise_scale = 0.015)
# Compute the sphericity of the blob
sphericity = qim3d.features.sphericity(synthetic_blob, level=0.5)
sphericity = qim3d.features.sphericity(synthetic_blob, level=0.5)
```
!!! info "Limitations due to pixelation"
Sphericity is particularly sensitive to the resolution of the mesh, as it directly impacts the accuracy of surface area and volume calculations.
Since the mesh is generated from voxel-based 3D volume data, the discrete nature of the voxels leads to pixelation effects that reduce the precision of sphericity measurements.
Higher resolution meshes may mitigate these errors but often at the cost of increased computational demands.
"""
if isinstance(obj, np.ndarray):
log.info("Converting volume to mesh.")
obj = qim3d.mesh.from_volume(obj, **mesh_kwargs)
volume = qim3d.features.volume(obj)
area = qim3d.features.area(obj)
volume = qim3d.features.volume(obj)
area = qim3d.features.area(obj)
if area == 0:
log.warning("Surface area is zero, sphericity is undefined.")
return np.nan
sphericity = (np.pi ** (1 / 3) * (6 * volume) ** (2 / 3)) / area
log.info(f"Sphericity: {sphericity}")
return sphericity
def volume_pygel3d(obj: np.ndarray|hmesh.Manifold) -> float:
def volume(obj: np.ndarray|hmesh.Manifold) -> float:
"""
Compute the volume of a 3D mesh using the Pygel3D library.
@@ -180,11 +17,11 @@ def volume_pygel3d(obj: np.ndarray|hmesh.Manifold) -> float:
if isinstance(obj, np.ndarray):
log.info("Converting volume to mesh.")
obj = qim3d.mesh.from_volume_pygel3d(obj)
obj = qim3d.mesh.from_volume(obj)
return hmesh.volume(obj)
def area_pygel3d(obj: np.ndarray|hmesh.Manifold) -> float:
def area(obj: np.ndarray|hmesh.Manifold) -> float:
"""
Compute the surface area of a 3D mesh using the Pygel3D library.
@@ -197,7 +34,7 @@ def area_pygel3d(obj: np.ndarray|hmesh.Manifold) -> float:
if isinstance(obj, np.ndarray):
log.info("Converting volume to mesh.")
obj = qim3d.mesh.from_volume_pygel3d(obj)
obj = qim3d.mesh.from_volume(obj)
return hmesh.area(obj)
@@ -216,8 +53,8 @@ def sphericity_pygel3d(obj: np.ndarray|hmesh.Manifold) -> float:
log.info("Converting volume to mesh.")
obj = qim3d.mesh.from_volume_pygel3d(obj)
volume = volume_pygel3d(obj)
area = area_pygel3d(obj)
volume = volume(obj)
area = area(obj)
if area == 0:
log.warning("Surface area is zero, sphericity is undefined.")