https://github.com/benmaier/cquadtree
Python API to a C++-implementation of a BarnesHutTree/QuadTree
https://github.com/benmaier/cquadtree
Last synced: 3 months ago
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Python API to a C++-implementation of a BarnesHutTree/QuadTree
- Host: GitHub
- URL: https://github.com/benmaier/cquadtree
- Owner: benmaier
- License: mit
- Created: 2022-12-05T10:38:37.000Z (over 2 years ago)
- Default Branch: main
- Last Pushed: 2022-12-07T12:47:28.000Z (over 2 years ago)
- Last Synced: 2024-10-11T11:06:58.324Z (8 months ago)
- Language: C++
- Size: 68.4 KB
- Stars: 1
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- Contributing: CONTRIBUTING.md
- License: LICENSE
- Code of conduct: CODE_OF_CONDUCT.md
Awesome Lists containing this project
README
# cQuadTree
Infinite jest with your favorite space-dividing trees. Fork from this C++-codebase: https://github.com/benmaier/BarnesHutTree/
* repository: https://github.com/benmaier/cQuadTree/
```python
>>> from cQuadTree import QuadTree
>>> points = [
... (1.0, 2.0),
... (0.1, 10.0),
... (0.5, 7.4),
... (6.0, 0.7),
... ]
>>> T = QuadTree(points)
>>> T
QuadTree(
geom=Extent(left=0.1,bottom=0.7,width=9.3,height=9.3),
current_data_quadrant=-1,
is_leaf=False,
number_of_contained_points=4,
center_of_mass=Point(x=1.9,y=5.025),
total_mass=4,
total_mass_position=Point(x=7.6,y=20.1),
number_of_occupied_subtrees=3
)
>>> print(T)
+- CM = 1.9, 5.025; M = 4; n = 4
| +- (nw) CM = 0.3, 8.7; M = 2; n = 2
| | +- (nw) 1 (0.1, 10)
| | +- (sw) 2 (0.5, 7.4)
| +- (se) 3 (6, 0.7)
| +- (sw) 0 (1, 2)
```
## Install
Your machine needs to have a C++11-compatible compiler installed.
pip install cQuadTree
So far, the package's functionality was tested on Mac OS X and CentOS only.
## Dependencies
`cQuadTree` directly depends on the following packages which will be installed by `pip` during the installation process
* `numpy>=1.20`
## Documentation
### Build the tree
```python
import numpy as np
from cQuadTree import QuadTree
points = np.random.rand(100,2).tolist()
T = QuadTree(points)
```
### Explore the tree recursively
As an example, here's a recursive function that collects all internal node boxes and leaf's points
```python
def get_points_and_boxes(quadtree):
points = []
boxes = []
if quadtree.is_leaf():
points.append(quadtree.this_pos)
boxes.append(quadtree.geom)
for tree in quadtree.get_subtrees():
_points, _boxes = get_points_and_boxes(tree)
points.extend(_points)
boxes.extend(_boxes)
return points, boxes
```
### Compute the force on a point
```python
>>> T.compute_force(point=(0.,0.001),theta=1.0) # default is theta=0.5
(0.117681690892212, 0.20856460584929215)
```
### Get all distances to a point
Note that per default, distances of value zero will be disregarded.
If you want to include those, set `ignore_zero_distance=False` in the
function call.
```python
>>> T.get_distances_to((0.,0),theta=1) # default is theta=0.2
[(8.705170877128145, 2), (6.040695324215583, 1), (2.23606797749979, 1)]
```
The first number is the distance to the query point, the second is the
number of points that lie at this approximate distance to the query point.
### Get all distances between pairs of points in a list and points in the tree
```python
>>> T.get_distances_to_points(points,theta=1)
[(6.7364679172397155, 2), (5.166236541235796, 1), (2.630589287593181, 1), (11.013627921806693, 1), (8.050465825031493, 1), (2.630589287593181, 1), (8.668333173107735, 1), (5.4230987451825, 1), (9.822932352408825, 2), (5.166236541235796, 1)]
```
### Get all pairwise distances between points in the tree
```python
>>> T.get_pairwise_distances(theta=1.0)
[(2.630589287593181, 1), (11.013627921806693, 1), (8.050465825031493, 1), (2.630589287593181, 1), (8.668333173107735, 1), (5.4230987451825, 1), (9.822932352408825, 2), (5.166236541235796, 1), (6.7364679172397155, 2), (5.166236541235796, 1)]
```
### Build a distance histogram from distance counts
```python
from cQuadTree import histogram
dists, counts = zip(*T.get_pairwise_distances(theta=1.0))
bin_edges = np.logspace(-4,1/2,101,base=2)
pdf, _ = histogram(dists, counts, bin_edges)
```
### Plot tree as boxes and points
```python
from cQuadTree import get_points_and_boxes
from cQuadTree.plot import plot_box_tree
plot_box_tree(*get_points_and_boxes(T))
```
### Docstrings
#### QuadTree
```python
Help on class QuadTree in module _cQuadTree:
class QuadTree(pybind11_builtins.pybind11_object)
| A QuadTree.
|
| Method resolution order:
| QuadTree
| pybind11_builtins.pybind11_object
| builtins.object
|
| Methods defined here:
|
| __init__(...)
| __init__(*args, **kwargs)
| Overloaded function.
|
| 1. __init__(self: _cQuadTree.QuadTree) -> None
|
| Initialize an empty tree.
|
| 2. __init__(self: _cQuadTree.QuadTree, position_pairs: List[Tuple[float, float]], force_square: bool = True) -> None
|
| Initialize a tree given a list of positions.
|
| 3. __init__(self: _cQuadTree.QuadTree, position_pairs: List[Tuple[float, float]], masses: List[float], force_square: bool = True) -> None
|
| Initialize a tree given a list of positions and a list of corresponding masses.
|
| __repr__(...)
| __repr__(self: _cQuadTree.QuadTree) -> str
|
| Get string representation of object
|
| __str__(...)
| __str__(self: _cQuadTree.QuadTree) -> str
|
| Get a string representation of the full tree
|
| compute_force(...)
| compute_force(self: _cQuadTree.QuadTree, point: Tuple[float, float], theta: float = 0.5) -> Tuple[float, float]
|
|
| Compute the force on a single point using the Barnes-Hut-Algorithm
| with cutoff parameter :math:`\theta`.
|
| Parameters
| ----------
| point : 2-tuple of float
| Point in plane on which to compute the total force
| theta : float, default = 0.5
| If the distance between the point and the current internal node's
| center of mass is smaller than :math:`\theta` times the diameter
| of the internal node's extent (box), the algorithm will treat
| all children of this node as a giant point mass located at the
| center of mass of this internal node.
|
| Returns
| -------
| force : 2-tuple of float
| Evaluated force vector
|
| get_distances_to(...)
| get_distances_to(self: _cQuadTree.QuadTree, point: Tuple[float, float], theta: float = 0.2, ignore_zero_distance: bool = True, tree: _cQuadTree.QuadTree = None) -> List[Tuple[float, int]]
|
|
| Compute distances of point masses and mass clusters to a single point
| using the Barnes-Hut-Algorithm with cutoff parameter :math:`\theta`.
|
| Parameters
| ----------
| point : 2-tuple of float
| Points in the plane to which to measure the distances
| theta : float, default = 0.2
| If the distance between the point and the current internal node's
| center of mass is smaller than :math:`\theta` times the diameter
| of the internal node's extent (box), the algorithm will treat
| all children of this node as a giant point mass located at the
| center of mass of this internal node.
| ignore_zero_distance : bool, default = True
| If the distance is zero, do or do not include this result in
| the ``distance_counts``-list.
|
| Returns
| -------
| distance_counts : list of 2-tuple of double, int
| An item of this list is a distance-count pair,
| the first entry of the tuple containing a distance
| to the query point and the second entry being the
| number of points that lie at that approximate distance
| to the query point, such that it will look like this
|
| .. code:: python
|
| [
| (0.2, 1),
| (0.1, 1),
| (1.5, 32),
| ...
| ]
|
| get_distances_to_points(...)
| get_distances_to_points(self: _cQuadTree.QuadTree, points: List[Tuple[float, float]], theta: float = 0.2, ignore_zero_distance: bool = True, tree: _cQuadTree.QuadTree = None) -> List[Tuple[float, int]]
|
|
| Compute distances of point masses and mass clusters to a list of points
| using the Barnes-Hut-Algorithm with cutoff parameter :math:`\theta`.
|
| Parameters
| ----------
| points : 2-tuple of float
| List of points in the plane to which to measure the distances
| theta : float, default = 0.2
| If the distance between the point and the current internal node's
| center of mass is smaller than :math:`\theta` times the diameter
| of the internal node's extent (box), the algorithm will treat
| all children of this node as a giant point mass located at the
| center of mass of this internal node.
| ignore_zero_distance : bool, default = True
| If the distance is zero, do or do not include this result in
| the ``distance_counts``-list.
|
| Returns
| -------
| distance_counts : list of 2-tuple of double, int
| An item of this list is a distance-count pair,
| the first entry of the tuple containing a distance
| to the query point and the second entry being the
| number of points that lie at that approximate distance
| to the query point, such that it will look like this
|
| .. code:: python
|
| [
| (0.2, 1),
| (0.1, 1),
| (1.5, 32),
| ...
| ]
|
| get_pairwise_distances(...)
| get_pairwise_distances(self: _cQuadTree.QuadTree, theta: float = 0.2, ignore_zero_distance: bool = True) ->
List[Tuple[float, int]]
|
|
| Compute distances between pairs of points and point clusters
| of a tree using the Barnes-Hut-Algorithm with cutoff parameter
| :math:`\theta`.
|
| Iterates over points by querying the tree recursively, which
| might take longer than simply externally iterating over a list of points
| if they're known.
|
| Parameters
| ----------
| theta : float, default = 0.2
| If the distance between the point and the current internal node's
| center of mass is smaller than :math:`\theta` times the diameter
| of the internal node's extent (box), the algorithm will treat
| all children of this node as a giant point mass located at the
| center of mass of this internal node.
| ignore_zero_distance : bool, default = True
| If the distance is zero, do or do not include this result in
| the ``distance_counts``-list.
|
| Returns
| -------
| distance_counts : list of 2-tuple of double, int
| An item of this list is a distance-count pair,
| the first entry of the tuple containing a distance
| to the query point and the second entry being the
| number of points that lie at that approximate distance
| to the query point, such that it will look like this
|
| .. code:: python
|
| [
| (0.2, 1),
| (0.1, 1),
| (1.5, 32),
| ...
| ]
|
| get_subtree(...)
| get_subtree(self: _cQuadTree.QuadTree, arg0: int) -> _cQuadTree.QuadTree
|
| Get subtree 0<=i<=3.
|
| get_subtrees(...)
| get_subtrees(self: _cQuadTree.QuadTree) -> List[_cQuadTree.QuadTree]
|
| Get a list of all of this node's children that contain data.
|
| is_leaf(...)
| is_leaf(self: _cQuadTree.QuadTree) -> bool
|
| Whether or not this node is a leaf.
|
| ----------------------------------------------------------------------
| Data descriptors defined here:
|
| center_of_mass
| Mass-weighted mean position of all points contained in this internal node.
|
| current_data_quadrant
| Quadrant of the parent geometry the data of this tree resides in.
|
| geom
| Extent of box this tree represents.
|
| number_of_contained_points
| Number of points contained in this internal node.
|
| parent
| The parent of this internal node.
|
| this_id
| Data index of the point contained in this leaf.
|
| this_mass
| Mass the point contained in this leaf.
|
| this_pos
| Position of the point contained in this leaf.
|
| total_mass
| Total mass of all points contained in this internal node.
|
| total_mass_position
| Sum of product of mass and position of all points contained in this internal node.
|
```
#### Extent
```python
class Extent(pybind11_builtins.pybind11_object)
| A rectangular geometry.
|
| Method resolution order:
| Extent
| pybind11_builtins.pybind11_object
| builtins.object
|
| Methods defined here:
|
| __init__(...)
| __init__(*args, **kwargs)
| Overloaded function.
|
| 1. __init__(self: _cQuadTree.Extent) -> None
|
| Initializes a zero-dimensional box.
|
| 2. __init__(self: _cQuadTree.Extent, left: float, bottom: float, width: float, height: float) -> None
|
| Initialize with position of bottom left corner, as well as width and height.
|
| __repr__(...)
| __repr__(self: _cQuadTree.Extent) -> str
|
| Get string representation of object
|
| b(...)
| b(self: _cQuadTree.Extent) -> float
|
| bottom(...)
| bottom(self: _cQuadTree.Extent) -> float
|
| h(...)
| h(self: _cQuadTree.Extent) -> float
|
| height(...)
| height(self: _cQuadTree.Extent) -> float
|
| l(...)
| l(self: _cQuadTree.Extent) -> float
|
| left(...)
| left(self: _cQuadTree.Extent) -> float
|
| w(...)
| w(self: _cQuadTree.Extent) -> float
|
| width(...)
| width(self: _cQuadTree.Extent) -> float
```
#### Point
```python
class Point(pybind11_builtins.pybind11_object)
| Minimal 2D-vector implementation based on code by openFrameworks
|
| Method resolution order:
| Point
| pybind11_builtins.pybind11_object
| builtins.object
|
| Methods defined here:
|
| __init__(...)
| __init__(*args, **kwargs)
| Overloaded function.
|
| 1. __init__(self: _cQuadTree.Point) -> None
|
| 2. __init__(self: _cQuadTree.Point, x: float, y: float) -> None
|
| Initialize with coordinates
|
| __repr__(...)
| __repr__(self: _cQuadTree.Point) -> str
|
| Get string representation of object
|
| length(...)
| length(self: _cQuadTree.Point) -> float
|
| Get the length of the vector
|
| ----------------------------------------------------------------------
| Data descriptors defined here:
|
| x
|
| y
```
#### Histogram
```python
>>> from cQuadTree import histogram
>>> help(histogram)
histogram(data, counts, bin_edges, density=True)
Returns a histogram from distance count data
received from a tree.
Parameters
==========
data : numpy.ndarray of float
Distances
counts : numpy.ndarray of int
Corresponding counts of distances in ``data``.
bin_edges : numpy.ndarray
Edges of bins for which the histogram should be computed
density : boolean, default = True
Whether or not to make the histogram a probability density
Returns
=======
hist : numpy.ndarray
Either count of data in bins, or pdf, will have length
``len(bin_edges)-1``.
bin_edges : numpy.ndarray
The used bin edges
```
#### Get points and boxes
```python
>>> from cQuadTree.utils import get_points_and_boxes
>>> help(get_points_and_boxes)
get_points_and_boxes(quadtree)
Returns two lists, one filled with "Extent" objects
representing the boxes of the tree that are occupied,
the other one contains the points that are located at
the leaf nodes
Parameters
==========
quadtree : :class:`_cQuadTree.QuadTree`
Self-explanatory, no?
Returns
=======
points : list of :class:`_cQuadTree.Point`
Points located at the leaves ot the tree
boxes : list of :class:`_cQuadTree.Extent`
The boxes that internal tree nodes represent
```
### Plot boxes
```python
>>> from cQuadTree.plot import plot_box_tree
>>> help(plot_box_tree)
plot_box_tree(list_of_points, list_of_boxes, ax=None, box_kwargs={}, point_kwargs={})
Plot a graphical representation of the tree as boxes and points on a matplotlib.Axes.
Use with data obtained from :func:`cQuadTree.utils.get_points_and_boxes`.
```
## Changelog
Changes are logged in a [separate file](https://github.com/benmaier/cQuadTree/blob/main/CHANGELOG.md).
## License
This project is licensed under the [MIT License](https://github.com/benmaier/cQuadTree/blob/main/LICENSE).
Note that this excludes any images/pictures/figures shown here or in the documentation.
## Contributing
If you want to contribute to this project, please make sure to read the [code of conduct](https://github.com/benmaier/cQuadTree/blob/main/CODE_OF_CONDUCT.md) and the [contributing guidelines](https://github.com/benmaier/cQuadTree/blob/main/CONTRIBUTING.md). In case you're wondering about what to contribute, we're always collecting ideas of what we want to implement next in the [outlook notes](https://github.com/benmaier/cQuadTree/blob/main/OUTLOOK.md).
[](code-of-conduct.md)
## Dev notes
Fork this repository, clone it, and install it in dev mode.
```bash
git clone [email protected]:YOURUSERNAME/cQuadTree.git
make
```
If you want to upload to PyPI, first convert the new `README.md` to `README.rst`
```bash
make readme
```
It will give you warnings about bad `.rst`-syntax. Fix those errors in `README.rst`. Then wrap the whole thing
```bash
make pypi
```
It will probably give you more warnings about `.rst`-syntax. Fix those until the warnings disappear. Then do
```bash
make upload
```