### Test Installation

Source: https://pymeshfix.pyvista.org/index.html

Verify the installation using the built-in examples module.

```python
from pymeshfix import examples

# Test of pymeshfix without VTK module
examples.native()

# Performs same mesh repair while leveraging VTK's plotting/mesh loading
examples.with_vtk()
```

--------------------------------

### Install PyMeshFix

Source: https://pymeshfix.pyvista.org/index.html

Installation commands for PyMeshFix via pip or from source.

```bash
pip install pymeshfix
```

```bash
git clone https://github.com/pyvista/pymeshfix
cd pymeshfix
pip install .
```

```bash
pip install pymeshfix[extras]
```

--------------------------------

### Load and Visualize Torso Mesh

Source: https://pymeshfix.pyvista.org/examples/torso.html

Loads the example torso mesh and prints its properties. Use this to inspect the mesh before repair.

```python
# sphinx_gallery_thumbnail_number = 2
import pyvista as pv
from pyvista import examples

import pymeshfix as mf

mesh = examples.download_torso()
print(mesh)
```

```python
PolyData (0x7f5d8912cee0)
  N Cells:    12448
  N Points:   12015
  N Strips:   0
  X Bounds:   -1.680e+02, 1.720e+02
  Y Bounds:   -1.624e+02, 1.320e+02
  Z Bounds:   -6.442e+02, 9.083e+01
  N Arrays:   0
```

```python
cpos = [(-1053.0, -1251.0, 83.0), (2.0, -15.0, -276.0), (0.12, 0.18, 1)]

mesh.plot(color=True, show_edges=True, cpos=cpos)
```

--------------------------------

### Load and Display Torso Mesh

Source: https://pymeshfix.pyvista.org/_downloads/8c2304a7db3bb5ef65786189c6b6749c/torso.ipynb

Loads the torso example mesh from PyVista and prints its information. This is the initial step before any mesh processing.

```python
# sphinx_gallery_thumbnail_number = 2
import pyvista as pv
from pyvista import examples

import pymeshfix as mf

mesh = examples.download_torso()
print(mesh)
```

--------------------------------

### Load and Visualize Bunny Mesh with Holes

Source: https://pymeshfix.pyvista.org/_downloads/87ff65eb9bf4b89622fc5038dfb7623a/bunny.ipynb

Load the bunny example mesh from PyVista and define a camera position to clearly show the holes. Visualize the mesh with eye-dome lighting and anti-aliasing.

```python
bunny = examples.download_bunny()

# Define a camera position that shows the holes in the mesh
cpos = [(-0.2, -0.13, 0.12), (-0.015, 0.10, -0.0), (0.28, 0.26, 0.9)]

# Show mesh
bunny.plot(cpos=cpos, eye_dome_lighting=True, anti_aliasing=True, smooth_shading=True)
```

--------------------------------

### Accessing Mesh Faces with MeshFix

Source: https://pymeshfix.pyvista.org/_autosummary/_autosummary/pymeshfix.MeshFix.faces.html

Demonstrates initializing a MeshFix object from a PyVista example mesh and retrieving its face indices.

```python
>>> from pyvista import examples
>>> from pymeshfix import MeshFix
>>> cow = examples.download_cow()
>>> mfix = MeshFix(cow)
>>> mfix.faces
array([[ 210,  252,  251],
       [ 250,  251,  252],
       [ 201,  253,  210],
       ...,
       [1965, 2193, 2194],
       [2391, 2398,  970],
       [ 966,  961,  970]])
```

--------------------------------

### Load and Prepare Cow Mesh

Source: https://pymeshfix.pyvista.org/_downloads/a765c73a2265f8a59b388228b14b1937/cow.ipynb

Load the cow example mesh, add random cell data, and create a version with holes by thresholding and extracting geometry. The mesh is then triangulated.

```python
cow = examples.download_cow()

# Add holes and cast to triangulated PolyData
cow["random"] = np.random.rand(cow.n_cells)
cow_w_holes = cow.threshold(0.9, invert=True).extract_geometry().triangulate()
print(cow_w_holes)
```

--------------------------------

### Retrieve mesh points using MeshFix

Source: https://pymeshfix.pyvista.org/_autosummary/_autosummary/pymeshfix.MeshFix.points.html

Demonstrates initializing a MeshFix object from a PyVista example mesh and accessing its points property.

```python
>>> from pyvista import examples
>>> from pymeshfix import MeshFix
>>> cow = examples.download_cow()
>>> mfix = MeshFix(cow)
>>> mfix.points
pyvista_ndarray([[3.71636 , 2.343387, 0.      ],
                 [4.126565, 0.642027, 0.      ],
                 [3.454971, 2.169877, 0.      ],
                 ...,
                 [4.12616 , 2.12093 , 1.17252 ],
                 [4.133175, 2.175231, 1.259323],
                 [4.232341, 1.903079, 0.534362]], dtype=float32)
```

--------------------------------

### Plot Mesh with Holes

Source: https://pymeshfix.pyvista.org/_autosummary/_autosummary/pymeshfix.MeshFix.plot.html

Load an example mesh and plot it, showing mesh boundaries. Requires pyvista and pymeshfix libraries.

```python
from pyvista import examples
from pymeshfix import MeshFix
mesh = examples.download_bunny()
mfix = MeshFix(mesh)
mfix.plot(show_holes=True)
```

--------------------------------

### Import Libraries and Download Cow Mesh

Source: https://pymeshfix.pyvista.org/_sources/examples/cow.rst.txt

Imports necessary libraries and downloads the cow mesh example. This sets up the environment for mesh manipulation and repair. The cow mesh is then processed to add holes and triangulated.

```Python
import numpy as np

# sphinx_gallery_thumbnail_number = 1
import pyvista as pv
from pyvista import examples

import pymeshfix as mf
```

```Python
cow = examples.download_cow()

# Add holes and cast to triangulated PolyData
cow["random"] = np.random.rand(cow.n_cells)
cow_w_holes = cow.threshold(0.9, invert=True).extract_geometry().triangulate()
print(cow_w_holes)
```

--------------------------------

### Accessing Mesh Points

Source: https://pymeshfix.pyvista.org/_autosummary/_autosummary/pymeshfix.MeshFix.points.html

Demonstrates how to get the points (vertices) of a mesh using the `points` property of the `MeshFix` object.

```APIDOC
## GET MeshFix.points

### Description
Retrieves the points (vertices) of the mesh as a NumPy ndarray.

### Method
GET

### Endpoint
MeshFix.points

### Parameters
This is a property, not an endpoint with parameters.

### Request Example
```python
from pyvista import examples
from pymeshfix import MeshFix

cow = examples.download_cow()
mfix = MeshFix(cow)
mesh_points = mfix.points
print(mesh_points)
```

### Response
#### Success Response (200)
- **points** (numpy.ndarray) - An array containing the coordinates of the mesh vertices.

#### Response Example
```json
{
  "points": [[3.71636, 2.343387, 0.0], [4.126565, 0.642027, 0.0], ...]
}
```
```

--------------------------------

### Create MeshFix Object from PyVista Mesh

Source: https://pymeshfix.pyvista.org/_autosummary/pymeshfix.MeshFix.html

Initialize a MeshFix object using a PyVista PolyData mesh. Ensure PyVista examples are available.

```python
from pyvista import examples
from pymeshfix import MeshFix
cow = examples.download_cow()
mfix = MeshFix(cow)
```

--------------------------------

### GET PyTMesh.n_boundaries

Source: https://pymeshfix.pyvista.org/_autosummary/_autosummary/pymeshfix.PyTMesh.n_boundaries.html

Retrieves the count of boundary loops present in the mesh object.

```APIDOC
## GET PyTMesh.n_boundaries

### Description
Returns the number of boundary loops in the mesh.

### Endpoint
PyTMesh.n_boundaries

### Response
#### Success Response (200)
- **n_boundaries** (int) - The number of boundary loops in the mesh.
```

--------------------------------

### GET PyTMesh.n_faces

Source: https://pymeshfix.pyvista.org/_sources/_autosummary/_autosummary/pymeshfix.PyTMesh.n_faces.rst.txt

Retrieves the total number of faces currently defined in the PyTMesh object.

```APIDOC
## GET PyTMesh.n_faces

### Description
Returns the number of faces in the PyTMesh object.

### Method
GET

### Endpoint
PyTMesh.n_faces

### Response
#### Success Response (200)
- **n_faces** (int) - The total count of faces in the mesh.
```

--------------------------------

### Clean Mesh from Arrays

Source: https://pymeshfix.pyvista.org/_autosummary/pymeshfix.clean_from_arrays.html

Use this function to clean and repair a triangular surface mesh when you have vertex and face data as NumPy arrays. Ensure you have numpy and pymeshfix installed and the data loaded from files.

```python
import pymeshfix
import numpy as np
points = np.load('points.npy')
faces = np.load('faces.npy')
clean_points, clean_faces = pymeshfix.clean_from_arrays(points, faces)
```

--------------------------------

### Import Required Libraries

Source: https://pymeshfix.pyvista.org/_downloads/0a2188cdc9ab9d0a467401debbe3ab17/repair_planar.ipynb

Initializes the environment by importing NumPy, PyVista, and the PyMeshFix modules.

```python
# sphinx_gallery_thumbnail_number = 1
import numpy as np
import pyvista as pv
from pymeshfix import PyTMesh

from pymeshfix import MeshFix
from pymeshfix import examples
```

--------------------------------

### GET MeshFix.mesh

Source: https://pymeshfix.pyvista.org/_autosummary/_autosummary/pymeshfix.MeshFix.mesh.html

Retrieves the surface mesh from a MeshFix object as a PolyData object.

```APIDOC
## GET MeshFix.mesh

### Description
Returns the surface mesh associated with the MeshFix object.

### Response
- **mesh** (pyvista.PolyData) - The surface mesh object.
```

--------------------------------

### Repair a mesh using MeshFix

Source: https://pymeshfix.pyvista.org/_autosummary/_autosummary/pymeshfix.MeshFix.repair.html

Demonstrates initializing a MeshFix object with a sample mesh and executing the default repair process with verbose output enabled.

```python
>>> from pyvista import examples
>>> from pymeshfix import MeshFix
>>> mesh = examples.download_bunny()
>>> mfix = MeshFix(mesh, verbose=True)
>>> mfix.repair()
>>> mfix.plot(show_holes=True)
```

--------------------------------

### Load and Visualize Torso Mesh

Source: https://pymeshfix.pyvista.org/_sources/examples/torso.rst.txt

Initializes the PyVista environment and displays the raw torso mesh.

```Python
# sphinx_gallery_thumbnail_number = 2
import pyvista as pv
from pyvista import examples

import pymeshfix as mf

mesh = examples.download_torso()
print(mesh)
```

```Python
cpos = [(-1053.0, -1251.0, 83.0), (2.0, -15.0, -276.0), (0.12, 0.18, 1)]

mesh.plot(color=True, show_edges=True, cpos=cpos)
```

--------------------------------

### Initialize MeshFix and access mesh

Source: https://pymeshfix.pyvista.org/_autosummary/_autosummary/pymeshfix.MeshFix.mesh.html

Create a MeshFix object from a PyVista mesh and retrieve the underlying surface mesh.

```python
>>> from pyvista import examples
>>> from pymeshfix import MeshFix
>>> cow = examples.download_cow()
>>> mfix = MeshFix(cow)
>>> mfix.mesh
PolyData (0x7fa3c735f8e0)
  N Cells:    5804
  N Points:   2903
  N Strips:   0
  X Bounds:   -4.446e+00, 5.998e+00
  Y Bounds:   -3.637e+00, 2.760e+00
  Z Bounds:   -1.701e+00, 1.701e+00
  N Arrays:   0
```

--------------------------------

### Plot Initial Torso Mesh

Source: https://pymeshfix.pyvista.org/_downloads/8c2304a7db3bb5ef65786189c6b6749c/torso.ipynb

Visualizes the loaded torso mesh with specified camera position and edge highlighting. This helps in understanding the initial state of the mesh.

```python
cpos = [(-1053.0, -1251.0, 83.0), (2.0, -15.0, -276.0), (0.12, 0.18, 1)]

mesh.plot(color=True, show_edges=True, cpos=cpos)
```

--------------------------------

### PyTMesh.boundaries

Source: https://pymeshfix.pyvista.org/_sources/_autosummary/_autosummary/pymeshfix.PyTMesh.boundaries.rst.txt

Documentation for the PyTMesh.boundaries method.

```APIDOC
## PyTMesh.boundaries

### Description
Retrieves the boundaries of the PyTMesh object.

### Method
Method call

### Endpoint
pymeshfix.PyTMesh.boundaries
```

--------------------------------

### Initialize MeshFix and Extract Holes

Source: https://pymeshfix.pyvista.org/_downloads/87ff65eb9bf4b89622fc5038dfb7623a/bunny.ipynb

Create an instance of pymeshfix.MeshFix using the PyVista PolyData object. Extract the holes from the mesh for visualization.

```python
mfix = MeshFix(bunny, verbose=True)
holes = mfix.extract_holes()
```

--------------------------------

### PyTMesh.clean Method

Source: https://pymeshfix.pyvista.org/_sources/_autosummary/_autosummary/pymeshfix.PyTMesh.clean.rst.txt

Documentation for the clean method of the PyTMesh class.

```APIDOC
## PyTMesh.clean

### Description
Cleans the mesh using the PyTMesh class functionality.

### Method
Method call

### Endpoint
pymeshfix.PyTMesh.clean
```

--------------------------------

### Constructor: pymeshfix.MeshFix

Source: https://pymeshfix.pyvista.org/_autosummary/pymeshfix.MeshFix.html

Initializes a new MeshFix object for processing surface meshes.

```APIDOC
## Constructor: pymeshfix.MeshFix

### Description
Initializes the MeshFix object with a surface mesh provided as a pyvista object, numpy arrays, or a file path.

### Parameters
#### Request Body
- **args** (pyvista.PolyData | (np.ndarray, np.ndarray) | pathlib.Path | str) - Required - Either a pyvista surface mesh, a tuple of vertex and face arrays, or a file path.
- **verbose** (bool) - Optional - Set to True to enable additional output from MeshFix. Defaults to False.
```

--------------------------------

### Convenience Methods

Source: https://pymeshfix.pyvista.org/_sources/api.rst.txt

Provides lower-level convenience methods for mesh fixing operations without direct use of `pyvista`.

```APIDOC
## pymeshfix.clean_from_file

### Description
A convenience method to clean mesh data directly from a file.

### Method
(Method type not specified, likely a function call)

### Endpoint
(Not applicable for a function)

### Parameters
(Specific parameters are not detailed in the provided text.)

### Request Example
(No request examples are provided in the source text.)

### Response
#### Success Response
(No specific success responses are detailed in the provided text.)

#### Response Example
(No response examples are provided in the source text.)
```

```APIDOC
## pymeshfix.clean_from_arrays

### Description
A convenience method to clean mesh data provided as arrays.

### Method
(Method type not specified, likely a function call)

### Endpoint
(Not applicable for a function)

### Parameters
(Specific parameters are not detailed in the provided text.)

### Request Example
(No request examples are provided in the source text.)

### Response
#### Success Response
(No specific success responses are detailed in the provided text.)

#### Response Example
(No response examples are provided in the source text.)
```

--------------------------------

### Fill Small Boundaries via PyTMesh

Source: https://pymeshfix.pyvista.org/_downloads/0a2188cdc9ab9d0a467401debbe3ab17/repair_planar.ipynb

Uses the low-level PyTMesh interface to fill holes based on boundary edge count constraints.

```python
mfix = PyTMesh()
mfix.set_quiet(True)
mfix.load_file(examples.planar_mesh)

# Fills all the holes having at at most 'nbe' boundary edges. If
# 'refine' is true, adds inner vertices to reproduce the sampling
# density of the surroundings. Returns number of holes patched. If
# 'nbe' is 0 (default), all the holes are patched.
mfix.fill_small_boundaries(nbe=100, refine=True)
```

--------------------------------

### Import Libraries for Mesh Repair

Source: https://pymeshfix.pyvista.org/_downloads/a765c73a2265f8a59b388228b14b1937/cow.ipynb

Import necessary libraries including numpy, pyvista, and pymeshfix. This is a prerequisite for all subsequent operations.

```python
import numpy as np

# sphinx_gallery_thumbnail_number = 1
import pyvista as pv
from pyvista import examples

import pymeshfix as mf
```

--------------------------------

### Repair and Verify Mesh

Source: https://pymeshfix.pyvista.org/_sources/examples/torso.rst.txt

Executes the repair process and displays the resulting watertight mesh.

```Python
meshfix.repair()
```

```Python
meshfix.mesh.plot(cpos=cpos, show_edges=True)
```

--------------------------------

### Import Libraries for Mesh Repair

Source: https://pymeshfix.pyvista.org/_downloads/87ff65eb9bf4b89622fc5038dfb7623a/bunny.ipynb

Import necessary libraries including PyVista for mesh handling and visualization, and MeshFix from pymeshfix for repair operations.

```python
# sphinx_gallery_thumbnail_number = 2
import pyvista as pv
from pyvista import examples

from pymeshfix import MeshFix
```

--------------------------------

### Advanced Mesh Cleaning with PyTMesh

Source: https://pymeshfix.pyvista.org/index.html

Use the PyTMesh object for granular control over the cleaning algorithm, including hole filling and component joining.

```python
import pymeshfix

# Create TMesh object
tin = pymeshfix.PyTMesh()

tin.LoadFile(infile)
# tin.load_array(v, f) # or read arrays from memory

# Attempt to join nearby components
# tin.join_closest_components()

# Fill holes
tin.fill_small_boundaries()
print(f'There are {tin.boundaries()} boundaries')

# Clean (removes self intersections)
tin.clean(max_iters=10, inner_loops=3)

# Check mesh for holes again
print(f'There are {tin.boundaries()} boundaries')

# Clean again if necessary...

# Output mesh
tin.save_file(outfile)

 # or return numpy arrays
vclean, fclean = tin.return_arrays()
```

--------------------------------

### Visualize Mesh with Holes and Extract Holes

Source: https://pymeshfix.pyvista.org/_downloads/a765c73a2265f8a59b388228b14b1937/cow.ipynb

Initialize a PyVista plotter, add the mesh with holes, and highlight the extracted holes in red. Configure camera position and lighting for better visualization. This step helps in understanding the mesh's state before repair.

```python
# A nice camera location to view the cow
cpos = [(6.56, 8.73, 22.03), (0.77, -0.44, 0.0), (-0.13, 0.93, -0.35)]

meshfix = mf.MeshFix(cow_w_holes, verbose=True)
holes = meshfix.extract_holes()

# Render the mesh and outline the holes
p = pv.Plotter()
p.add_mesh(cow_w_holes, color=True, smooth_shading=True, split_sharp_edges=True)
p.add_mesh(holes, color="r", line_width=8)
p.camera_position = cpos
p.camera.zoom(1.5)
p.enable_eye_dome_lighting()  # helps depth perception
p.enable_anti_aliasing("ssaa")
p.show()
```

--------------------------------

### Create MeshFix Object from NumPy Arrays

Source: https://pymeshfix.pyvista.org/_autosummary/_autosummary/pymeshfix.MeshFix.load_arrays.html

Use this method to initialize a `MeshFix` object when your mesh data is already in NumPy arrays. Ensure your vertex array has shape (n, 3) and your face array has shape (m, 3).

```python
from pymeshfix import MeshFix
import numpy as np
points = np.array(
    [
        [3.71636, 2.343387, 0.0],
        [4.126565, 0.642027, 0.0],
        [3.454971, 2.169877, 0.0],
        ...,
        [4.12616, 2.12093, 1.17252],
        [4.133175, 2.175231, 1.259323],
        [4.232341, 1.903079, 0.534362],
    ],
    dtype=float32,
)
faces = np.array(
    [
        [210, 252, 251],
        [250, 251, 252],
        [201, 253, 210],
        ...,
        [1965, 2193, 2194],
        [2391, 2398, 970],
        [966, 961, 970],
    ]
)
mfix = MeshFix(points, faces)
```

--------------------------------

### PyTMesh.boundaries()

Source: https://pymeshfix.pyvista.org/_autosummary/_autosummary/pymeshfix.PyTMesh.boundaries.html

The boundaries() method of the PyTMesh class is used to identify and work with the boundaries of a mesh. It does not take any arguments and returns None.

```APIDOC
## PyTMesh.boundaries()

### Description
Identifies and processes the boundaries of a mesh. This method does not return any value.

### Method
`None`

### Endpoint
`None`

### Parameters
This method does not accept any parameters.

### Request Example
```python
# Assuming 'mesh' is an instance of PyTMesh
mesh.boundaries()
```

### Response
This method returns `None`.
```

--------------------------------

### PyTMesh.remove_smallest_components

Source: https://pymeshfix.pyvista.org/_sources/_autosummary/_autosummary/pymeshfix.PyTMesh.remove_smallest_components.rst.txt

Documentation for the remove_smallest_components method within the PyTMesh class.

```APIDOC
## PyTMesh.remove_smallest_components

### Description
Removes the smallest components from the mesh structure.

### Method
Method call on PyTMesh object

### Endpoint
pymeshfix.PyTMesh.remove_smallest_components
```

--------------------------------

### Display Repaired Mesh

Source: https://pymeshfix.pyvista.org/_downloads/a765c73a2265f8a59b388228b14b1937/cow.ipynb

Access the repaired mesh from the `MeshFix` object and print its information. Then, visualize the repaired mesh using PyVista, applying similar camera settings as before for comparison.

```python
repaired = meshfix.mesh
print(repaired)
```

```python
repaired.plot(cpos=cpos, zoom=1.5, smooth_shading=True, split_sharp_edges=True)
```

--------------------------------

### PyTMesh.load_file

Source: https://pymeshfix.pyvista.org/_autosummary/_autosummary/pymeshfix.PyTMesh.load_file.html

Method to load a surface mesh from a file into the PyTMesh object.

```APIDOC
## PyTMesh.load_file

### Description
Load a surface mesh from a file.

### Parameters
#### Path Parameters
- **filename** (str) - Required - Path to the input mesh file.

### Response
- **None**
```

--------------------------------

### MeshFix.save Method

Source: https://pymeshfix.pyvista.org/_sources/_autosummary/_autosummary/pymeshfix.MeshFix.save.rst.txt

Documentation for the save method used to write mesh data to a file.

```APIDOC
## MeshFix.save

### Description
Saves the current mesh data to a specified file path.

### Method
Method call

### Endpoint
pymeshfix.MeshFix.save
```

--------------------------------

### MeshFix.save()

Source: https://pymeshfix.pyvista.org/_autosummary/_autosummary/pymeshfix.MeshFix.save.html

Writes the points and faces of a surface mesh to disk using PyVista.

```APIDOC
## MeshFix.save()

### Description
Writes the points and faces as a surface mesh to disk using PyVista. This is a simple wrapper for :pyvista:`pyvista.PolyData.save`.

### Method
POST

### Endpoint
/websites/pymeshfix_pyvista

### Parameters
#### Path Parameters
None

#### Query Parameters
None

#### Request Body
- **filename** (str) - Required - Filename of mesh to be written. Filetype is inferred from the extension of the filename unless overridden with ftype. Generally one of the following types: ".ply", ".stl", ".vtk"
- **binary** (bool) - Optional - Default: True - Write the file using a binary writer. Binary files read and write much faster than ASCII.

### Request Example
```json
{
  "filename": ".stl",
  "binary": true
}
```

### Response
#### Success Response (200)
- **message** (str) - Indicates successful saving of the mesh.

#### Response Example
```json
{
  "message": "Mesh successfully saved to file.stl"
}
```
```

--------------------------------

### pymeshfix.clean_from_file

Source: https://pymeshfix.pyvista.org/_autosummary/pymeshfix.clean_from_file.html

Clean and repair a triangular surface mesh from a file.

```APIDOC
## FUNCTION clean_from_file

### Description
Clean and repair a triangular surface mesh from a file.

### Parameters
- **infile** (str) - Required - Input mesh filename.
- **outfile** (str) - Required - Output mesh filename.
- **verbose** (bool) - Optional (default: False) - Enable verbose output.
- **joincomp** (bool) - Optional (default: False) - Attempt to join nearby open components.

### Request Example
```python
import pymeshfix
pymeshfix.clean_from_file('inmesh.ply', 'outmesh.ply')
```

### Response
- **Returns** (None) - The function performs the operation on the specified files.
```

--------------------------------

### PyTMesh Class Overview

Source: https://pymeshfix.pyvista.org/_autosummary/pymeshfix.PyTMesh.html

The PyTMesh class is designed for mesh repair and cleaning, wrapping the MeshFix Basic_TMesh functionality. It allows users to load, manipulate, and save mesh data, as well as perform various repair operations.

```APIDOC
## PyTMesh Class

### Description
Mesh repair and cleaning class. Wraps the MeshFix Basic_TMesh functionality and exposes it to Python. Provides methods to inspect, repair, and extract mesh data.

### Attributes
- **n_boundaries** (int) - Number of boundary loops in the mesh.
- **n_faces** (int) - Number of faces in the mesh.
- **n_points** (int) - Number of points in the mesh.

### Methods
- **boundaries()**: Returns None. Likely used for internal boundary processing.
- **clean(max_iters=None, inner_loops=None)**: Perform iterative mesh cleaning and repair.
- **fill_small_boundaries(nbe=None, ...)**: Fill small boundary loops (holes) in the mesh.
- **fix_connectivity()**: Repair mesh connectivity issues.
- **join_closest_components()**: Join the closest disconnected mesh components.
- **load_array(points_arr, faces_arr, ...)**: Load a surface mesh from vertex and face arrays.
- **load_file(filename)**: Load a surface mesh from a file.
- **remove_smallest_components()**: Remove all but the largest connected mesh component.
- **return_arrays()**: Return mesh data as vertex and face arrays.
- **return_faces()**: Return the face array.
- **return_points()**: Return the vertex array.
- **save_file(filename, back_approx=False)**: Save the mesh to a file.
- **select_intersecting_triangles(...)**: Select intersecting triangles in the mesh.
- **set_quiet(arg)**: Enable or disable console output.
- **strong_degeneracy_removal(arg)**: Iteratively removes degenerate triangles and closes holes.
- **strong_intersection_removal(arg)**: Iteratively removes self-intersecting triangles.
```

--------------------------------

### Repair Mesh with MeshFix Object

Source: https://pymeshfix.pyvista.org/index.html

Use the MeshFix class to repair meshes in memory, with optional PyVista visualization.

```python
import pymeshfix

# Create object from vertex and face arrays
meshfix = pymeshfix.MeshFix(v, f)

# Plot input
meshfix.plot()

# Repair input mesh
meshfix.repair()

# Access the repaired mesh with vtk
mesh = meshfix.mesh

# Or, access the resulting arrays directly from the object
meshfix.points # numpy np.float64 array
meshfix.faces # numpy np.int32 array

# View the repaired mesh (requires pyvista)
meshfix.plot()

# Save the mesh
meshfix.write('out.ply')
```

--------------------------------

### Visualize the repaired result

Source: https://pymeshfix.pyvista.org/examples/cow.html

Renders the final repaired mesh using PyVista.

```python
repaired.plot(cpos=cpos, zoom=1.5, smooth_shading=True, split_sharp_edges=True)
```

--------------------------------

### PyTMesh.load_array

Source: https://pymeshfix.pyvista.org/_autosummary/_autosummary/pymeshfix.PyTMesh.load_array.html

Loads a surface mesh from vertex and face arrays.

```APIDOC
## PyTMesh.load_array

### Description
Load a surface mesh from vertex and face arrays.

### Method
This is a method of the PyTMesh class.

### Parameters
#### Path Parameters
None

#### Query Parameters
None

#### Request Body
None

### Request Example
```python
# Assuming you have PyTMesh and numpy imported
# and an instance of PyTMesh called 'mesh'

points = np.array([[0,0,0], [1,0,0], [0,1,0]])
faces = np.array([[0,1,2]])

mesh.load_array(points_arr=points, faces_arr=faces)
```

### Response
#### Success Response (None)
This method does not return any value.

#### Response Example
None
```

--------------------------------

### Identify and Visualize Mesh Holes

Source: https://pymeshfix.pyvista.org/_downloads/0a2188cdc9ab9d0a467401debbe3ab17/repair_planar.ipynb

Reads a planar mesh and uses MeshFix to extract and visualize existing holes.

```python
orig_mesh = pv.read(examples.planar_mesh)
# orig_mesh.plot_boundaries()

meshfix = MeshFix(orig_mesh, verbose=True)
holes = meshfix.extract_holes()

# Render the mesh and outline the holes
pl = pv.Plotter()
pl.add_mesh(orig_mesh, color=True, smooth_shading=True)
pl.add_mesh(holes, color="r", line_width=8, render_lines_as_tubes=True, lighting=False)
pl.enable_eye_dome_lighting()  # helps depth perception
_ = pl.show()
```

--------------------------------

### Prepare Mesh for Repair

Source: https://pymeshfix.pyvista.org/_downloads/8c2304a7db3bb5ef65786189c6b6749c/torso.ipynb

Ensures the mesh consists only of triangles and extracts any holes present. This step is crucial for Pymeshfix to accurately identify and repair mesh defects.

```python
meshfix = mf.MeshFix(mesh.triangulate(), verbose=True)
holes = meshfix.extract_holes()
```

--------------------------------

### PyTMesh.return_points

Source: https://pymeshfix.pyvista.org/_sources/_autosummary/_autosummary/pymeshfix.PyTMesh.return_points.rst.txt

Retrieves the points associated with the PyTMesh object.

```APIDOC
## PyTMesh.return_points

### Description
Returns the points currently stored in the PyTMesh object.

### Method
METHOD_NOT_SPECIFIED

### Endpoint
PyTMesh.return_points
```

--------------------------------

### MeshFix.plot Method

Source: https://pymeshfix.pyvista.org/_sources/_autosummary/_autosummary/pymeshfix.MeshFix.plot.rst.txt

Documentation for the plot method used to visualize the mesh object.

```APIDOC
## MeshFix.plot

### Description
Visualizes the current mesh object using the underlying plotting capabilities of the library.

### Method
Method call on MeshFix object

### Endpoint
pymeshfix.MeshFix.plot
```

--------------------------------

### MeshFix.repair Method

Source: https://pymeshfix.pyvista.org/_sources/_autosummary/_autosummary/pymeshfix.MeshFix.repair.rst.txt

The `repair` method is part of the `MeshFix` class and is used to repair issues within a mesh. This is an automethod, meaning it's automatically generated and documented.

```APIDOC
## MeshFix.repair

### Description
Repairs issues within a mesh.

### Method
This is an automethod, typically called on an instance of the MeshFix class.

### Endpoint
N/A (This is a method within a Python class, not a REST API endpoint)

### Parameters
This method does not explicitly define parameters in the provided documentation. Refer to the PyVista MeshFix documentation for specific parameter details.

### Request Example
```python
# Assuming 'mesh' is a PyVista mesh object and 'mf' is an instance of MeshFix
# mf = pymeshfix.MeshFix(mesh)
# repaired_mesh = mf.repair()
```

### Response
#### Success Response
Returns a repaired mesh object.

#### Response Example
```json
{
  "repaired_mesh": "<PyVista Mesh Object>"
}
```
```

--------------------------------

### Render Mesh with Highlighted Holes

Source: https://pymeshfix.pyvista.org/_downloads/87ff65eb9bf4b89622fc5038dfb7623a/bunny.ipynb

Use a PyVista Plotter to display the original mesh and the extracted holes. The holes are rendered in red with thick lines to make them prominent. Enable advanced rendering features for better depth perception.

```python
pl = pv.Plotter()
pl.add_mesh(bunny, color=True, smooth_shading=True)
pl.add_mesh(holes, color="r", line_width=12, render_lines_as_tubes=True, lighting=False)
pl.camera_position = cpos
pl.enable_eye_dome_lighting()  # helps depth perception
pl.enable_anti_aliasing("ssaa")
pl.show()
```

--------------------------------

### Clean Mesh from File with pymeshfix

Source: https://pymeshfix.pyvista.org/_autosummary/pymeshfix.clean_from_file.html

Use this function to clean and repair a triangular surface mesh from a specified input file and save the result to an output file. It does not require pyvista or vtk.

```python
import pymeshfix
pymeshfix.clean_from_file('inmesh.ply', 'outmesh.ply')
```

--------------------------------

### PyTMesh.save_file

Source: https://pymeshfix.pyvista.org/_sources/_autosummary/_autosummary/pymeshfix.PyTMesh.save_file.rst.txt

Saves the current PyTMesh object to a file. The file format is determined by the file extension.

```APIDOC
## PyTMesh.save_file

### Description
Saves the current PyTMesh object to a file. The file format is determined by the file extension.

### Method
This is a method of the PyTMesh class.

### Endpoint
N/A (This is a method within a Python class, not a REST endpoint)

### Parameters
#### Path Parameters
None

#### Query Parameters
None

#### Request Body
None

### Request Example
```python
# Assuming 'mesh' is an instance of PyTMesh
mesh.save_file('output.stl')
mesh.save_file('output.ply')
```

### Response
#### Success Response (200)
This method does not return a value upon successful execution. It performs a file operation.

#### Response Example
N/A
```

--------------------------------

### Plot the underlying mesh

Source: https://pymeshfix.pyvista.org/_autosummary/_autosummary/pymeshfix.MeshFix.mesh.html

Visualize the surface mesh using the plot method.

```python
>>> mfix.mesh.plot()
```

--------------------------------

### pymeshfix.MeshFix Class

Source: https://pymeshfix.pyvista.org/api.html

The `MeshFix` class provides a high-level interface for cleaning and tetrahedralizing surface meshes. It requires the `pyvista` library for some of its functionalities.

```APIDOC
## `pymeshfix.MeshFix`

### Description
Clean and tetrahedralize surface meshes using MeshFix.

### Parameters
- `*args`: Variable length argument list.
- `verbose` (bool) - Optional - Controls the verbosity of the cleaning process.
```

--------------------------------

### PyTMesh.return_points

Source: https://pymeshfix.pyvista.org/_autosummary/_autosummary/pymeshfix.PyTMesh.return_points.html

Retrieves the vertex array from the PyTMesh instance.

```APIDOC
## GET PyTMesh.return_points

### Description
Returns the vertex array associated with the PyTMesh object.

### Method
GET

### Endpoint
PyTMesh.return_points()

### Response
#### Success Response (200)
- **vertex_array** (numpy.ndarray) - Vertex array of shape (N, 3) with dtype float64.
```

--------------------------------

### PyTMesh.fill_small_boundaries

Source: https://pymeshfix.pyvista.org/_autosummary/_autosummary/pymeshfix.PyTMesh.fill_small_boundaries.html

Method to fill small boundary loops (holes) in a mesh.

```APIDOC
## PyTMesh.fill_small_boundaries

### Description
Fill small boundary loops (holes) in the mesh.

### Parameters
#### Parameters
- **nbe** (int) - Optional (default: 0) - Maximum number of boundary edges to fill. If 0, fill all.
- **refine** (bool) - Optional (default: True) - Refine filled regions.

### Response
- **int** - Returns an integer representing the operation status or count.
```

--------------------------------

### MeshFix.join_closest_components()

Source: https://pymeshfix.pyvista.org/_autosummary/_autosummary/pymeshfix.MeshFix.join_closest_components.html

Attempts to join nearby open components of a mesh. This method modifies the mesh in place and does not return any value.

```APIDOC
## MeshFix.join_closest_components()

### Description
Attempt to join nearby open components.

### Method
None (This is a method of a class, not a standalone API endpoint)

### Endpoint
N/A

### Parameters
This method does not accept any parameters.

### Request Example
```python
mesh_fix_instance.join_closest_components()
```

### Response
#### Success Response (None)
This method returns `None` upon successful execution.

#### Response Example
```
None
```
```

--------------------------------

### Show Repaired Mesh

Source: https://pymeshfix.pyvista.org/_downloads/87ff65eb9bf4b89622fc5038dfb7623a/bunny.ipynb

Visualize the mesh after the repair process has been completed. The holes should now be filled.

```python
mfix.mesh.plot(cpos=cpos, eye_dome_lighting=True, anti_aliasing=True, smooth_shading=True)
```

--------------------------------

### Visualize Repaired Mesh

Source: https://pymeshfix.pyvista.org/_downloads/0a2188cdc9ab9d0a467401debbe3ab17/repair_planar.ipynb

Displays the final repaired mesh alongside the original hole boundaries.

```python
pl = pv.Plotter()
pl.add_mesh(mesh, color=True, smooth_shading=True)
pl.add_mesh(holes, color="r", line_width=8, render_lines_as_tubes=True, lighting=False)
pl.enable_eye_dome_lighting()  # helps depth perception
_ = pl.show()
```

--------------------------------

### Convert and Plot Repaired Mesh

Source: https://pymeshfix.pyvista.org/_sources/examples/repair_planar.rst.txt

Converts the repaired mesh from PyTMesh back to a pyvista mesh format and visualizes it with the original holes highlighted. Note that single-point boundary holes may not be filled.

```Python
vert, faces = mfix.return_arrays()
mesh = pv.make_tri_mesh(vert, faces)





pl = pv.Plotter()
pl.add_mesh(mesh, color=True, smooth_shading=True)
pl.add_mesh(holes, color="r", line_width=8, render_lines_as_tubes=True, lighting=False)
pl.enable_eye_dome_lighting()  # helps depth perception
_ = pl.show()
```

--------------------------------

### Clean Mesh from Files or Arrays

Source: https://pymeshfix.pyvista.org/index.html

Perform basic mesh cleaning operations using file paths or existing vertex and face arrays.

```python
import pymeshfix

# Read mesh from infile and output cleaned mesh to outfile
pymeshfix.clean_from_file(infile, outfile)
```

```python
import pymeshfix

# Generate vertex and face arrays of cleaned mesh
# where v and f are numpy arrays
vclean, fclean = pymeshfix.clean_from_arrays(v, f)
```

--------------------------------

### pymeshfix.clean_from_arrays

Source: https://pymeshfix.pyvista.org/_sources/_autosummary/pymeshfix.clean_from_arrays.rst.txt

Documentation for the clean_from_arrays function used to process and clean mesh data from arrays.

```APIDOC
## clean_from_arrays

### Description
Cleans mesh data provided as arrays using the pymeshfix library.

### Endpoint
pymeshfix.clean_from_arrays
```

--------------------------------

### MeshFix.load_arrays

Source: https://pymeshfix.pyvista.org/_autosummary/_autosummary/pymeshfix.MeshFix.load_arrays.html

Loads a triangular mesh into the MeshFix object from provided vertex and face numpy arrays.

```APIDOC
## MeshFix.load_arrays

### Description
Load a triangular mesh from vertex and face numpy arrays. Both arrays should be 2D, with vertices containing XYZ data and faces containing three points.

### Parameters
#### Path Parameters
- **v** (np.ndarray[np.float64]) - Required - (n, 3) vertex array.
- **f** (np.ndarray[np.int32]) - Required - (m, 3) face array.

### Request Example
```python
from pymeshfix import MeshFix
import numpy as np

points = np.array([[3.71636, 2.343387, 0.0], ...], dtype=float32)
faces = np.array([[210, 252, 251], ...])
mfix = MeshFix(points, faces)
```
```

--------------------------------

### MeshFix Methods

Source: https://pymeshfix.pyvista.org/_autosummary/pymeshfix.MeshFix.html

Common methods available on the MeshFix object for mesh repair and manipulation.

```APIDOC
## MeshFix Methods

### clean(max_iters, inner_loops)
Remove degenerate triangles and self-intersections.

### degeneracy_removal(max_iter)
Remove degenerate triangles.

### extract_holes()
Extract the boundaries of the holes in this mesh to a new PyVista mesh of lines.

### fill_holes(n_edges, refine)
Fill small boundary loops (holes) in the mesh.

### intersection_removal(max_iter)
Remove self-intersecting triangles.

### join_closest_components()
Attempt to join nearby open components.

### load_arrays(v, f)
Load triangular mesh from vertex and face numpy arrays.

### plot(show_holes)
Plot the mesh.

### remove_smallest_components()
Remove all but the largest connected component.

### repair(joincomp, ...)
Perform mesh repair using MeshFix's default repair process.

### save(filename, binary)
Write the points and faces as a surface mesh to disk using PyVista.
```

--------------------------------

### MeshFix.plot

Source: https://pymeshfix.pyvista.org/_autosummary/_autosummary/pymeshfix.MeshFix.plot.html

Visualizes the mesh using the pyvista plotting backend.

```APIDOC
## MeshFix.plot

### Description
Plot the mesh using the pyvista plotting backend.

### Parameters
- **show_holes** (bool) - Optional (default: True) - If True, shows boundaries of the mesh.
- **kwargs** (Any) - Optional - Additional keyword arguments passed to pyvista.plot().

### Request Example
```python
from pyvista import examples
from pymeshfix import MeshFix
mesh = examples.download_bunny()
mfix = MeshFix(mesh)
mfix.plot(show_holes=True)
```
```

--------------------------------

### PyTMesh.return_arrays

Source: https://pymeshfix.pyvista.org/_autosummary/_autosummary/pymeshfix.PyTMesh.return_arrays.html

Retrieves the vertex and face arrays from the PyTMesh instance.

```APIDOC
## GET PyTMesh.return_arrays

### Description
Return mesh data as vertex and face arrays from the PyTMesh object.

### Method
Method call on PyTMesh instance

### Response
- **vertices** (numpy.ndarray) - Vertex array of shape (N, 3).
- **faces** (numpy.ndarray) - Face array of shape (M, 3).
```

--------------------------------

### Save the underlying mesh

Source: https://pymeshfix.pyvista.org/_autosummary/_autosummary/pymeshfix.MeshFix.mesh.html

Export the surface mesh to a file using the save method.

```python
>>> mfix.mesh.save("my_mesh.ply")
```

--------------------------------

### MeshFix.repair()

Source: https://pymeshfix.pyvista.org/_autosummary/_autosummary/pymeshfix.MeshFix.repair.html

Performs mesh repair using MeshFix's default repair process. This method can be called directly or individual repair functions can be invoked separately.

```APIDOC
## MeshFix.repair()

### Description
Perform mesh repair using MeshFix’s default repair process.

### Method
This is a method of the `MeshFix` class.

### Parameters
#### Path Parameters
None

#### Query Parameters
None

#### Request Body
None

### Parameters
- **joincomp** (_bool_, default: `False`) – Attempts to join nearby open components.
- **remove_smallest_components** (_bool_, default: `True`) – Remove all but the largest isolated component from the mesh before beginning the repair process.

### Notes
Vertex and face arrays can be accessed from:
  * `Meshfix.points`
  * `Meshfix.faces`

You can alternatively call individual repair functions if you desire specific fixes. For example `MeshFix.fill_holes()`.

### Request Example
```python
>>> from pyvista import examples
>>> from pymeshfix import MeshFix
>>> mesh = examples.download_bunny()
>>> mfix = MeshFix(mesh, verbose=True)
>>> mfix.repair()
>>> mfix.plot(show_holes=True)
```

### Response
#### Success Response (200)
This method does not return a value; it modifies the mesh in place.

#### Response Example
None
```

--------------------------------

### pymeshfix.PyTMesh Class

Source: https://pymeshfix.pyvista.org/api.html

The `PyTMesh` class is a lower-level Cython extension for mesh repair and cleaning. It offers core mesh manipulation functionalities without requiring `pyvista`.

```APIDOC
## `pymeshfix.PyTMesh`

### Description
Mesh repair and cleaning class. Lower level convenience methods that expose the lower level functionality of meshfix without using pyvista.

### Parameters
- `*args`: Variable length argument list.
- `**kwargs`: Arbitrary keyword arguments.
```

--------------------------------

### Display repaired mesh information

Source: https://pymeshfix.pyvista.org/examples/cow.html

Retrieves the repaired mesh and prints its updated properties.

```python
repaired = meshfix.mesh
print(repaired)
```

--------------------------------

### PyTMesh.save_file

Source: https://pymeshfix.pyvista.org/_autosummary/_autosummary/pymeshfix.PyTMesh.save_file.html

Saves the current mesh to a specified file. This method allows for optional backward approximation during the saving process.

```APIDOC
## PyTMesh.save_file

### Description
Save the mesh to a file.

### Method
`save_file`

### Parameters
#### Path Parameters
- **filename** (str) - Required - Output filename.
- **back_approx** (bool) - Optional - Default: False - Use backward approximation when writing.

### Request Example
```python
mesh.save_file("output.stl")
mesh.save_file("output_approx.stl", back_approx=True)
```

### Response
#### Success Response (None)
This method does not return any value.

#### Response Example
None
```

--------------------------------

### PyTMesh.join_closest_components

Source: https://pymeshfix.pyvista.org/_autosummary/_autosummary/pymeshfix.PyTMesh.join_closest_components.html

Joins the closest disconnected mesh components of a PyTMesh object.

```APIDOC
## PyTMesh.join_closest_components()

### Description
Joins the closest disconnected mesh components.

### Method
None (This is a method of the PyTMesh class)

### Endpoint
N/A (This is a method call on an object instance)

### Parameters
#### Path Parameters
None

#### Query Parameters
None

#### Request Body
None

### Request Example
```python
# Assuming 'mesh' is an instance of PyTMesh
mesh.join_closest_components()
```

### Response
#### Success Response (None)
This method does not return any value.

#### Response Example
None
```

--------------------------------

### MeshFix Class Overview

Source: https://pymeshfix.pyvista.org/_sources/_autosummary/pymeshfix.MeshFix.rst.txt

The MeshFix class provides a comprehensive set of tools for mesh repair and manipulation. It allows users to clean meshes, remove degeneracies, fill holes, and more.

```APIDOC
## MeshFix Class

### Description
Provides tools for mesh repair and manipulation.

### Methods
- **clean()**: Cleans the mesh.
- **degeneracy_removal()**: Removes degenerate elements from the mesh.
- **extract_holes()**: Extracts holes from the mesh.
- **fill_holes()**: Fills holes in the mesh.
- **intersection_removal()**: Removes intersecting elements.
- **join_closest_components()**: Joins the closest components of the mesh.
- **load_arrays()**: Loads mesh data from arrays.
- **plot()**: Plots the mesh.
- **remove_smallest_components()**: Removes the smallest components of the mesh.
- **repair()**: Repairs the mesh.
- **save()**: Saves the mesh.

### Attributes
- **faces** (array): The faces of the mesh.
- **mesh** (object): The underlying mesh object.
- **n_boundaries** (int): The number of boundary components.
- **points** (array): The points (vertices) of the mesh.
```

--------------------------------

### Return hole count

Source: https://pymeshfix.pyvista.org/examples/repair_planar.html

The number of holes patched by the algorithm.

```text
16
```

--------------------------------

### MeshFix.load_arrays

Source: https://pymeshfix.pyvista.org/_sources/_autosummary/_autosummary/pymeshfix.MeshFix.load_arrays.rst.txt

The load_arrays method is part of the MeshFix class in the pymeshfix library. It is used to load mesh data from arrays.

```APIDOC
## MeshFix.load_arrays

### Description
Loads mesh data from arrays into a MeshFix object.

### Method
This is a method of the `MeshFix` class.

### Endpoint
N/A (This is a Python method, not a REST API endpoint)

### Parameters
This method likely accepts arrays representing vertices, faces, and potentially other mesh attributes. Specific parameter names and types would be detailed in the full library documentation.

### Request Example
```python
import pymeshfix

# Assuming you have vertex and face arrays
vertices = [...] # numpy array of shape (n_vertices, 3)
faces = [...]    # numpy array of shape (n_faces, 3) or similar

meshfix_object = pymeshfix.MeshFix()
meshfix_object.load_arrays(vertices, faces)
```

### Response
Upon successful execution, the `MeshFix` object will be populated with the mesh data from the provided arrays. Specific return values or side effects would be detailed in the full library documentation.
```

--------------------------------

### PyTMesh.set_quiet

Source: https://pymeshfix.pyvista.org/_autosummary/_autosummary/pymeshfix.PyTMesh.set_quiet.html

This method allows you to control whether PyTMesh outputs messages to the console. Set `quiet` to `True` to suppress output, or `False` to enable it.

```APIDOC
## PyTMesh.set_quiet

### Description
Enable or disable console output.

### Method
`set_quiet`

### Parameters
#### Path Parameters
None

#### Query Parameters
None

#### Request Body
- **quiet** (bool) - Required - If True, suppress output.

### Request Example
```json
{
  "quiet": true
}
```

### Response
#### Success Response (200)
None

#### Response Example
None
```

--------------------------------

### PyTMesh.return_arrays

Source: https://pymeshfix.pyvista.org/_sources/_autosummary/_autosummary/pymeshfix.PyTMesh.return_arrays.rst.txt

The return_arrays method of the PyTMesh class is used to retrieve arrays associated with the mesh.

```APIDOC
## PyTMesh.return_arrays

### Description
Retrieves arrays associated with the mesh.

### Method
This is a method of the PyTMesh class, typically called on an instance of PyTMesh.

### Endpoint
N/A (This is a Python method, not a REST API endpoint)

### Parameters
This method does not appear to take any explicit parameters.

### Request Example
```python
# Assuming 'mesh' is an instance of PyTMesh
arrays = mesh.return_arrays()
```

### Response
#### Success Response
- **arrays** (list or dict) - A collection of arrays related to the mesh data (e.g., vertices, faces, normals). The exact structure depends on the internal implementation of PyTMesh.

#### Response Example
```json
{
  "example": "[numpy.ndarray, numpy.ndarray, ...]"
}
```
```