pyspat 0.1.8

Spatial point pattern analysis in Python.

pySpat

pySpat is a small, native Python library for spatial point pattern analysis. It is also very much a work in progress.

What’s implemented

Windows (study regions)

• MaskWindow – binary raster window on a regular grid
  • area(), contains(xy), sample_uniform(n), erode(r), distance_to_boundary(), overlap_fraction(shift), rescale(factor)
• RectangleWindow – axis-aligned rectangle [xmin, xmax) × [ymin, ymax)
  • Analytic contains, area, sample_uniform, erode, overlap_fraction, distance_to_boundary (raster image), rescale
• PolyWindow – polygon/multipolygon (with holes) via Shapely
  • Exact area, contains, erode (buffer), overlap_fraction (intersection), dtb_at_points, raster distance_to_boundary, sample_uniform (rejection in bbox), rescale

Notes

• erode(r) is Minkowski erosion (negative buffer for polygons).
• distance_to_boundary() returns an Image with pixel-centre distances inside the window; useful for border corrections.
• overlap_fraction(shift) gives |W ∩ (W+shift)| / |W|.
  • Fast FFT path for MaskWindow (sub-pixel via bilinear interpolation).
  • Exact path for RectangleWindow (closed form) and PolyWindow (Shapely intersection).

Point patterns

• PPP – planar point pattern with:
  • Validation that all points lie inside the window
  • Optional marks
  • bbox(), intensity(), thin(p), rescale(factor), nndist(k)
  • Simple unit labelling (unit string carried through)

Summary statistics

• Ripley’s K: Kest(ppp, r, correction="translation"|"border")
• Besag’s L: Lest(ppp, r, correction=...)
• Pair correlation: pcf(ppp, r_edges, correction=...) (annular estimator)
• Nearest-neighbour distribution: Gest(ppp, r, method="border"|"raw")
• Empty-space function: Fest(ppp, r, method="border"|"raw", nsamp=..., rng=...)
• J-function: Jest(ppp, r, method_G=..., method_F=..., nsamp_F=..., rng=...)

Edge correction details

• Translation: weights are 1 / overlap_fraction(Δ).
  • MaskWindow: fast via FFT precomputation + bilinear interpolation.
  • RectangleWindow / PolyWindow: exact overlap per query (memoised).
• Border: anchors (or sample locations) require distance-to-boundary ≥ r; distances are sampled from the window’s distance_to_boundary() image.

Optional Plots

• Boolean showplot argument for each summary statistic, False by default. Setting True gives a basic matplotlib figure of the function against radius, with the function-specific CSR baseline also plotted.

Dependencies

• Required: numpy, scipy
• Optional: shapely (>=2.0 recommended)

Install

Not always up to date on PyPI. Install from source:

git clone https://github.com/j-peyton/pySpat
pip install ./pySpat
# or editable:
pip install -e ./pySpat

Quick start

import numpy as np
from pyspat.core import RectangleWindow, PPP
from pyspat.stats import Kest, Lest, pcf

# Window: 200 x 200 square
W = RectangleWindow(0.0, 0.0, 200.0, 200.0)

# CSR sample
rng = np.random.default_rng(7)
xy = W.sample_uniform(n=3000, rng=rng)
X = PPP(xy, W, unit="µm")

# K and L
r = np.linspace(2.0, 40.0, 25)
K = Kest(X, r, correction="translation")
L = Lest(X, r, correction="translation")

# Pair correlation
edges = np.linspace(2.0, 40.0, 60)
r_mid, g = pcf(X, edges, correction="translation")

Licence

MIT

Author

Jack Peyton, November 2025