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shufflesnap

shufflesnap assigns large 2D point clouds to regular grids: every point gets its own grid cell, and the solver seeks a small total squared movement using multiscale local descent. It is a Python package with a native C++ core and nanobind bindings. The main use case is turning embeddings (UMAP, t-SNE, Isomap) into image atlases.

Instead of building an n x n cost matrix, shufflesnap refines a trivial legal assignment by solving exact linear assignment problems inside small grid windows at multiple scales — coarse-to-fine strided windows repair global structure in a handful of rounds, then stride-1 windows polish. The assignment is legal after every round, the cost never increases, memory is linear in the number of points plus grid cells, and random initialization works well on the tested distributions. Final accuracy and the number of polishing rounds have no worst-case guarantee.

The public API has three functions:

  1. snap_to_grid(points, width=None, height=None, cleanup_seconds=None, ...)
  2. window_cleanup(points, initial_assignment, rows, cols, budget_seconds=None, ...)
  3. linear_sum_assignment(cost_matrix)

Install

python -m pip install shufflesnap

To run the matplotlib example from the source tree:

python -m pip install -e '.[examples]'
python examples/basic_usage.py

API

snap_to_grid(points, width=None, height=None, cleanup_seconds=None, ...)

High-level wrapper for snapping a 2D point cloud onto a destination grid. Inputs must use the same coordinate system as the target grid (default range [0.03, 0.97] per axis); the API does not normalize inputs.

Behavior:

  • chooses a destination grid automatically when width and height are omitted: an exact factorization of n with aspect ratio in [1:1, 2:1] when one exists, otherwise a slightly larger near-square grid
  • supports any n <= width * height directly: the occupied cell subset is selected before cleanup and remains fixed
  • by default cleanup runs until none of the four scheduled half-offset tilings can improve the assignment; cleanup_seconds caps the time instead, and 0.0 returns the raw seed (a deterministic random permutation, with a fixed random cell subset when the grid has more cells than points)
  • polish_all_offsets=True adds one stride-1 sweep over every complete window placement after normal cleanup, reducing the remaining local error at additional cost
  • pass mask (a (height, width) bool array) to restrict which cells may be used — shaped atlases (circles, cut corners, a half-empty last row) work out of the box

Returns:

  • grid_points: (n, 2) float64 NumPy array of assigned destination points in original point order
  • assignment: (n,) int64 NumPy array of destination-grid cell ids in original point order
  • (width, height): destination-grid size tuple

window_cleanup(points, initial_assignment, rows, cols, budget_seconds=None, ...)

Improve any legal assignment with the native multiscale window cleanup kernel.

Key options:

  • budget_seconds=None runs until converged (a full stride-1 round changes nothing)
  • strides=None uses the automatic coarse-to-fine schedule; pass a list to override
  • window_size=6
  • all_offsets=True uses all window_size ** 2 tiling offsets instead of the default four and is substantially slower
  • num_threads=None to use std::thread::hardware_concurrency()
  • fixed_suffix_count to keep a suffix of target cells fixed; cell_mask to mark which cells may be used at all
  • trace_rounds=True to record per-round cost, elapsed time, and stride

Returns a dict with assignment, rounds_completed, elapsed_s, final_cost, and converged.

linear_sum_assignment(cost_matrix)

Solve a dense square linear assignment problem exactly with the native C++ Jonker-Volgenant implementation.

Returns:

  • row_ind: int64 NumPy array of shape (n,)
  • col_ind: int64 NumPy array of shape (n,)
  • total_cost: Python float

More

Metadata

Release files for shufflesnap 0.3.0

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Source distribution (sdist)

Source distribution for shufflesnap 0.3.0
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shufflesnap-0.3.0-cp314-cp314-win_amd64.whl CPython 3.14 CPython 3.14 Windows x86-64 Details for shufflesnap-0.3.0-cp314-cp314-win_amd64.whl
shufflesnap-0.3.0-cp314-cp314-musllinux_1_2_x86_64.whl CPython 3.14 CPython 3.14 Linux musl 1.2+ x86-64 Details for shufflesnap-0.3.0-cp314-cp314-musllinux_1_2_x86_64.whl
shufflesnap-0.3.0-cp314-cp314-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl CPython 3.14 CPython 3.14 Linux glibc 2.28+ x86-64, Linux glibc 2.27+ x86-64 Details for shufflesnap-0.3.0-cp314-cp314-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl
shufflesnap-0.3.0-cp314-cp314-macosx_11_0_x86_64.whl CPython 3.14 CPython 3.14 macOS 11.0+ x86-64 Details for shufflesnap-0.3.0-cp314-cp314-macosx_11_0_x86_64.whl
shufflesnap-0.3.0-cp314-cp314-macosx_11_0_arm64.whl CPython 3.14 CPython 3.14 macOS 11.0+ ARM64 Details for shufflesnap-0.3.0-cp314-cp314-macosx_11_0_arm64.whl
shufflesnap-0.3.0-cp313-cp313-win_amd64.whl CPython 3.13 CPython 3.13 Windows x86-64 Details for shufflesnap-0.3.0-cp313-cp313-win_amd64.whl
shufflesnap-0.3.0-cp313-cp313-musllinux_1_2_x86_64.whl CPython 3.13 CPython 3.13 Linux musl 1.2+ x86-64 Details for shufflesnap-0.3.0-cp313-cp313-musllinux_1_2_x86_64.whl
shufflesnap-0.3.0-cp313-cp313-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl CPython 3.13 CPython 3.13 Linux glibc 2.27+ x86-64, Linux glibc 2.28+ x86-64 Details for shufflesnap-0.3.0-cp313-cp313-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl
shufflesnap-0.3.0-cp313-cp313-macosx_11_0_x86_64.whl CPython 3.13 CPython 3.13 macOS 11.0+ x86-64 Details for shufflesnap-0.3.0-cp313-cp313-macosx_11_0_x86_64.whl
shufflesnap-0.3.0-cp313-cp313-macosx_11_0_arm64.whl CPython 3.13 CPython 3.13 macOS 11.0+ ARM64 Details for shufflesnap-0.3.0-cp313-cp313-macosx_11_0_arm64.whl
shufflesnap-0.3.0-cp312-cp312-win_amd64.whl CPython 3.12 CPython 3.12 Windows x86-64 Details for shufflesnap-0.3.0-cp312-cp312-win_amd64.whl
shufflesnap-0.3.0-cp312-cp312-musllinux_1_2_x86_64.whl CPython 3.12 CPython 3.12 Linux musl 1.2+ x86-64 Details for shufflesnap-0.3.0-cp312-cp312-musllinux_1_2_x86_64.whl
shufflesnap-0.3.0-cp312-cp312-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl CPython 3.12 CPython 3.12 Linux glibc 2.28+ x86-64, Linux glibc 2.27+ x86-64 Details for shufflesnap-0.3.0-cp312-cp312-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl
shufflesnap-0.3.0-cp312-cp312-macosx_11_0_x86_64.whl CPython 3.12 CPython 3.12 macOS 11.0+ x86-64 Details for shufflesnap-0.3.0-cp312-cp312-macosx_11_0_x86_64.whl
shufflesnap-0.3.0-cp312-cp312-macosx_11_0_arm64.whl CPython 3.12 CPython 3.12 macOS 11.0+ ARM64 Details for shufflesnap-0.3.0-cp312-cp312-macosx_11_0_arm64.whl
shufflesnap-0.3.0-cp311-cp311-win_amd64.whl CPython 3.11 CPython 3.11 Windows x86-64 Details for shufflesnap-0.3.0-cp311-cp311-win_amd64.whl
shufflesnap-0.3.0-cp311-cp311-musllinux_1_2_x86_64.whl CPython 3.11 CPython 3.11 Linux musl 1.2+ x86-64 Details for shufflesnap-0.3.0-cp311-cp311-musllinux_1_2_x86_64.whl
shufflesnap-0.3.0-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl CPython 3.11 CPython 3.11 Linux glibc 2.27+ x86-64, Linux glibc 2.28+ x86-64 Details for shufflesnap-0.3.0-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl
shufflesnap-0.3.0-cp311-cp311-macosx_11_0_x86_64.whl CPython 3.11 CPython 3.11 macOS 11.0+ x86-64 Details for shufflesnap-0.3.0-cp311-cp311-macosx_11_0_x86_64.whl
shufflesnap-0.3.0-cp311-cp311-macosx_11_0_arm64.whl CPython 3.11 CPython 3.11 macOS 11.0+ ARM64 Details for shufflesnap-0.3.0-cp311-cp311-macosx_11_0_arm64.whl
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shufflesnap-0.3.0-cp310-cp310-musllinux_1_2_x86_64.whl CPython 3.10 CPython 3.10 Linux musl 1.2+ x86-64 Details for shufflesnap-0.3.0-cp310-cp310-musllinux_1_2_x86_64.whl
shufflesnap-0.3.0-cp310-cp310-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl CPython 3.10 CPython 3.10 Linux glibc 2.28+ x86-64, Linux glibc 2.27+ x86-64 Details for shufflesnap-0.3.0-cp310-cp310-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl
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