edt

library3.1.1pypypi✓ verified 85d ago

Computes the Euclidean distance transform of 3D and 2D label fields. Supports anisotropic voxels (non-cubic) and multi-label segmentation. v3.1.1, updated June 2024, active development with irregular releases.

data ai-ml

pip install edt

github ↗package ↗

INSTALL

IMPORT

SIG · EDT

edt

datapythonv3.1.1

Install

3.8s avg

Import

294ms

Disk

99MB

Pass rate

5/ 10

Env Coverage5 / 10

glibc

3.9–3.13

musl

3.9–3.13

Install & Compatibility

Where this runs

tested against v3.1.1 · pip install

no network on importno background threads

Install × environment matrix

Each cell = how many times install + import succeeded across repeated harness runs. Partial = flaky.
glibc = Debian/Ubuntu slim · musl = Alpine Linux

musl

py 3.10–3.95 runs

build_error

glibc

py 3.10–3.95 runs

installs and imports cleanly · install 3.8s · import 0.294s · 98MB

99MB installed

● package 99MB

Code

Verified usage

Verified import paths — ran on the pinned version, not inferred.

edt

✓ import edt

✗ from edt import edt

edt is a module, not a function within edt; top-level import is correct.

Compute Euclidean distance transform for a 3D label array. Use anisotropic parameter to set voxel size.

import edt import numpy as np labels = np.array([[[0, 1, 0], [1, 0, 0], [0, 0, 2]]], dtype=np.uint32) dist = edt.edt(labels, anisotropic=(1.0, 1.0, 1.0)) print(dist) # Output: 3D distance transform (x, y, z axes)

Debug

Known issues

gotchaedt.edt expects uint32 or uint64 labels by default. Passing int32 or float labels will silently produce incorrect results.

fix

Convert labels to np.uint32 or np.uint64 before calling edt.edt.

affects: all

gotchaAnisotropic parameter must be a tuple of three floats (for 3D) or two floats (for 2D). Omitting or using wrong shape leads to undefined behavior.

fix

Always provide anisotropic as (sx, sy, sz) tuple for 3D, or (sx, sy) for 2D.

affects: all

gotchaedt.edt modifies the input array in-place if the 'in_place' parameter is True (default False). Unexpected side effects may occur.

fix

If you need to preserve the original array, set in_place=False (the default) or pass a copy.

affects: all

deprecatedThe 'parallel' parameter (int) was deprecated in 3.0.0 and removed in 3.1.0. Use 'num_threads' instead.

fix

Use num_threads=N instead of parallel=N.

affects: >=3.0.0 <3.1.0

Errors

Common errors & fixes

ImportError: cannot import name 'edt' from 'edt'

Trying to import edt as from edt import edt, but edt is the module itself.

fix

Use just 'import edt' then call 'edt.edt()'.

ValueError: ndim is 2 but expected 3

Passed a 2D array to edt.edt without specifying ndim=2 or using the 2D variant.

fix

For 2D arrays, use edt.edt(..., ndim=2) or call edt.edt2d() if available (not in current version).

TypeError: anisotropic must be a tuple of floats

Anisotropic parameter passed as list or wrong type.

fix

Pass anisotropic as a tuple of three floats, e.g., (0.5, 0.5, 1.0).

Upgrade

Version history

3.1.1latest on PyPI · released Mar 1, 2026

Audit

Dependencies

No dependency data recorded yet.

Agent activity

13 hits · last 30 days

node

OpenAI (training)

Resources

githubhttps://github.com/seung-lab/euclidean-distance-transform-3d ↗

packagehttps://pypi.org/project/edt/ ↗