edt · PyPI

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Python Instructions for MLAEDT-3D

Compute the Euclidean Distance Transform of a 1d, 2d, or 3d labeled image containing multiple labels in a single pass with support for anisotropic dimensions.

Python Installation

Requires a C++ compiler

The installation process depends on edt.cpp for the Python bindings derived from edt.pyx. edt.hpp contains the algorithm implementation.

pip install numpy
pip install edt

Recompiling `edt.pyx`

Requires Cython and a C++ compiler

cd python
cython -3 --cplus edt.pyx # generates edt.cpp
python setup.py develop # compiles edt.cpp and edt.hpp 
                        # together into a shared binary e.g. edt.cpython-36m-x86_64-linux-gnu.so

Python Usage

Consult help(edt) after importing. The edt module contains: edt and edtsq which compute the euclidean and squared euclidean distance respectively. Both functions select dimension based on the shape of the numpy array fed to them. 1D, 2D, and 3D volumes are supported. 1D processing is extremely fast. Numpy boolean arrays are handled specially for faster processing.

If for some reason you'd like to use a specific 'D' function, edt1d, edt1dsq, edt2d, edt2dsq, edt3d, and edt3dsq are available.

The three optional parameters are anisotropy, black_border, and order. Anisotropy is used to correct for distortions in voxel space, e.g. if X and Y were acquired with a microscope, but the Z axis was cut more corsely.

black_border allows you to specify that the edges of the image should be considered in computing pixel distances (it's also slightly faster).

order allows the programmer to determine how the underlying array should be interpreted. 'C' (C-order, XYZ, row-major) and 'F' (Fortran-order, ZYX, column major) are supported. 'C' order is the default.

parallel controls the number of threads. Set it <= 0 to automatically determine your CPU count.

import edt
import numpy as np

# e.g. 6nm x 6nm x 30nm for the S1 dataset by Kasthuri et al., 2014
labels = np.ones(shape=(512, 512, 512), dtype=np.uint32, order='F')
dt = edt.edt(labels, anisotropy=(6, 6, 30), black_border=True, order='F', parallel=1)

Metadata

Release files for edt 1.3.2

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Source distribution (sdist)

Source distribution for edt 1.3.2
File	Size	Uploaded
edt-1.3.2.tar.gz	172.2 kB	May 15, 2019	Details

Built distributions (wheels)

Table of built distributions (wheels) for edt 1.3.2
File	Interpreter	ABI	Platform	Reset
edt-1.3.2-cp38-cp38-manylinux1_x86_64.whl 1.1 MB Oct 23, 2019	CPython 3.8	CPython 3.8	Linux glibc 2.5+ x86-64	Details
edt-1.3.2-cp38-cp38-macosx_10_9_x86_64.whl 197.6 kB Oct 23, 2019	CPython 3.8	CPython 3.8	macOS 10.9+ x86-64	Details
edt-1.3.2-cp37-cp37m-win_amd64.whl 245.1 kB Jul 3, 2019	CPython 3.7	CPython 3.7 pymalloc	Windows x86-64	Details
edt-1.3.2-cp37-cp37m-manylinux1_x86_64.whl 1.1 MB May 15, 2019	CPython 3.7	CPython 3.7 pymalloc	Linux glibc 2.5+ x86-64	Details
edt-1.3.2-cp37-cp37m-macosx_10_9_x86_64.whl 196.1 kB May 15, 2019	CPython 3.7	CPython 3.7 pymalloc	macOS 10.9+ x86-64	Details
edt-1.3.2-cp36-cp36m-win_amd64.whl 235.2 kB Jul 3, 2019	CPython 3.6	CPython 3.6 pymalloc	Windows x86-64	Details
edt-1.3.2-cp36-cp36m-manylinux1_x86_64.whl 1.1 MB May 15, 2019	CPython 3.6	CPython 3.6 pymalloc	Linux glibc 2.5+ x86-64	Details
edt-1.3.2-cp36-cp36m-macosx_10_13_x86_64.whl 200.3 kB May 15, 2019	CPython 3.6	CPython 3.6 pymalloc	macOS 10.13+ x86-64	Details
edt-1.3.2-cp35-cp35m-manylinux1_x86_64.whl 1.1 MB May 15, 2019	CPython 3.5	CPython 3.5 pymalloc	Linux glibc 2.5+ x86-64	Details
edt-1.3.2-cp27-cp27m-manylinux1_x86_64.whl 1.1 MB May 15, 2019	CPython 2.7	CPython 2.7 pymalloc	Linux glibc 2.5+ x86-64	Details
edt-1.3.2-cp27-cp27m-macosx_10_14_intel.whl 193.7 kB May 15, 2019	CPython 2.7	CPython 2.7 pymalloc	macOS 10.14+ Intel (x86-64, i386)	Details

Total release size: 7.0 MB

Release files / edt-1.3.2.tar.gz

Download URL	edt-1.3.2.tar.gz
Size	172.2 kB
Tags	Source
SHA-256 checksum How to use checksums	`accf53fab874c714398ba851e4886e41be98316adaa8b9af6963d4b6ea86b7f0`
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Uploaded via	`twine/1.12.1 pkginfo/1.4.2 requests/2.20.1 setuptools/40.6.2 requests-toolbelt/0.8.0 tqdm/4.28.1 CPython/3.6.6`

Release files / edt-1.3.2-cp38-cp38-manylinux1_x86_64.whl

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Download URL	edt-1.3.2-cp38-cp38-manylinux1_x86_64.whl
Size	1.1 MB
Tags	CPython 3.8 Linux glibc 2.5+ x86-64
SHA-256 checksum How to use checksums	`24fc87545c89007ed9c89bdfec8e9ca69613b927720228fec0ce049cc199242c`
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Size	197.6 kB
Tags	CPython 3.8 macOS 10.9+ x86-64
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Download URL	edt-1.3.2-cp37-cp37m-win_amd64.whl
Size	245.1 kB
Tags	CPython 3.7 CPython 3.7 pymalloc Windows x86-64
SHA-256 checksum How to use checksums	`0731d28e54194049417447a8b88f6a03cb903fbcbfd60652fd03d06efbf9a429`
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Release files / edt-1.3.2-cp37-cp37m-manylinux1_x86_64.whl

Download URL	edt-1.3.2-cp37-cp37m-manylinux1_x86_64.whl
Size	1.1 MB
Tags	CPython 3.7 CPython 3.7 pymalloc Linux glibc 2.5+ x86-64
SHA-256 checksum How to use checksums	`556c72dab835b020c502617f0c7aa32e79c36bd32d9928afcc7959a4b82bcb3d`
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Release files / edt-1.3.2-cp37-cp37m-macosx_10_9_x86_64.whl

Download URL	edt-1.3.2-cp37-cp37m-macosx_10_9_x86_64.whl
Size	196.1 kB
Tags	CPython 3.7 CPython 3.7 pymalloc macOS 10.9+ x86-64
SHA-256 checksum How to use checksums	`093881fb7aa9d3bf1cc421bb3e0ac104c4a428e7c419d28dc5a755a5cac8fcc7`
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Release files / edt-1.3.2-cp36-cp36m-win_amd64.whl

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Download URL	edt-1.3.2-cp36-cp36m-win_amd64.whl
Size	235.2 kB
Tags	CPython 3.6 CPython 3.6 pymalloc Windows x86-64
SHA-256 checksum How to use checksums	`f839a956a7de1f7fb87a16688b898489ee969058363a69daf556cbb4a8f4a539`
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Download URL	edt-1.3.2-cp36-cp36m-manylinux1_x86_64.whl
Size	1.1 MB
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Release files / edt-1.3.2-cp36-cp36m-macosx_10_13_x86_64.whl

Download URL	edt-1.3.2-cp36-cp36m-macosx_10_13_x86_64.whl
Size	200.3 kB
Tags	CPython 3.6 CPython 3.6 pymalloc macOS 10.13+ x86-64
SHA-256 checksum How to use checksums	`3d23f148cb156314ed092148fff6984f9c63e77f158dbe344adf3942d16bf39b`
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Release files / edt-1.3.2-cp35-cp35m-manylinux1_x86_64.whl

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Size	1.1 MB
Tags	CPython 3.5 CPython 3.5 pymalloc Linux glibc 2.5+ x86-64
SHA-256 checksum How to use checksums	`f2321626c628fb015a70a939f1dac6b883444eae0997f11c2eccb70165653e84`
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Release files / edt-1.3.2-cp27-cp27m-manylinux1_x86_64.whl

Download URL	edt-1.3.2-cp27-cp27m-manylinux1_x86_64.whl
Size	1.1 MB
Tags	CPython 2.7 CPython 2.7 pymalloc Linux glibc 2.5+ x86-64
SHA-256 checksum How to use checksums	`648f0db69c93fbd1d75d99dc750ecfd0b8a44b84bcbde125bc93fb4fcb02e560`
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Release files / edt-1.3.2-cp27-cp27m-macosx_10_14_intel.whl

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Size	193.7 kB
Tags	CPython 2.7 CPython 2.7 pymalloc macOS 10.14+ Intel (x86-64, i386)
SHA-256 checksum How to use checksums	`71f7b25a2fbd2036ff31280507075cc56185b50d7a9fc518350fd9819fa08928`
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edt 1.3.2

Python Instructions for MLAEDT-3D

Python Installation

Recompiling `edt.pyx`

Python Usage

Project links

Key dates

1 maintainer

Credits

License

Classifiers

Metadata

Project links

Key dates

1 maintainer

Credits

License

Classifiers

Release files for edt 1.3.2

Files added late

Source distribution (sdist)

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edt 1.3.2

Python Instructions for MLAEDT-3D

Python Installation

Recompiling edt.pyx

Python Usage

Project links

Key dates

1 maintainer

Credits

License

Classifiers

Metadata

Project links

Key dates

1 maintainer

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Release files for edt 1.3.2

Files added late

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Recompiling `edt.pyx`