Compress Seg 
Library for compressing and decompressing image segmentation (adapted from neuroglancer)
import compressed_segmentation as cseg
sx, sy, sz = (128,128,128)
dtype = np.uint64
order = 'C'
labels = np.arange(0, sx*sy*sz, dtype=dtype).reshape((sx,sy,sz), order=order)
compressed = cseg.compress(labels, order=order)
recovered = cseg.decompress(
compressed, (sx,sy,sz) dtype=dtype, order=order
)
arr = CompressedSegmentationArray(
compressed, shape=(sx,sy,sz), dtype=dtype
)
label = arr[54,32,103] # random access to single voxels w/o decompressing
uniq_labels = arr.labels() # get all distinct values w/o decompressing
binary2 = arr.remap({ 1: 2 }, preserve_missing_labels=False) # remap labels in segmentation w/o decompressing
recovered = arr.numpy() # decompress to a numpy array, same as decompress
124213 in arr # test if a value is in the array
cseg compress connectomics.npy
cseg decompress connectomics.npy.cseg --volume-size 512,512,512 --bytes 4
NOTE: This repository is the PyPI distribution repo but is based on work done by Jeremy Maitin-Shepard (Google), Stephen Plaza (Janelia Research Campus), and William Silversmith (Princeton) here: https://github.com/janelia-flyem/compressedseg
This library contains routined to decompress and compress segmentation and to manipulate compressed segmentation data defined by the neuroglancer project. compressed_segmentation essentially renumbers large bit width labels to smaller ones in chunks. This provides for large reductions in memory usage and higher compression.
Note that limitations in the compressed_segmentation format restrict the size of the chunk that can be compressed. As this limitation is data dependent, for example a random array with 1024 labels passes testing at 256x256x128, but 256x256x256 often does not.
Features
- Compression and decompression
- Random access to voxels without decompression
- Read out unique values without decompression
- Remap labels without decompression
- Command line interface for numpy files
- (TBD) Interface to relabel and manipulate segmentation from the compressed data
- C++, Python, and Go interface (see original repo for Golang)
C++ Compilation
Compiling as a shared library. Feel free to subsititute e.g. clang for the C++ compiler.
g++ -std=c++11 -O3 -fPIC -shared -I./include src/compress_segmentation.cc src/decompress_segmentation.cc -o compress_segmentation.so
Python Installation
pip Binary Installation
$ pip install compressed-segmentation
$ python
>>> import compressed_segmentation as cseg
>>> help(cseg)
If there are pre-built binaries available for your architecture this should just work.
pip Source Installation
If you need to build from source, you will need to have a C++ compiler installed:
$ sudo apt-get install g++ python3-dev
$ pip install numpy
$ pip install compressed-segmentation
$ python
>>> import compressed_segmentation as cseg
>>> help(cseg)
Direct Installation
Requires a C++ compiler such as g++ or clang.
Works with both Python 2 and 3. Encodes from / decodes to 3D or 4D numpy ndarrays.
$ sudo apt-get install g++ python3-dev
$ pip install -r requirements.txt
$ python setup.py install
$ python
>>> import compressed_segmentation as cseg
>>> help(cseg)
License
Please see the licenses in this repo.
Metadata
Release files for compressed-segmentation 2.3.3
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| compressed_segmentation-2.3.3.tar.gz | 26.8 kB | Details |
Built distributions (wheels)
Total release size: 37.4 MB
Release files / compressed_segmentation-2.3.3.tar.gz
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Release files / compressed_segmentation-2.3.3-cp312-cp312-macosx_10_13_x86_64.whl
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Release files / compressed_segmentation-2.3.3-cp311-cp311-win_amd64.whl
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Release files / compressed_segmentation-2.3.3-cp311-cp311-musllinux_1_2_x86_64.whl
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Release files / compressed_segmentation-2.3.3-cp311-cp311-manylinux_2_24_aarch64.manylinux_2_28_aarch64.whl
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Release files / compressed_segmentation-2.3.3-cp311-cp311-macosx_11_0_arm64.whl
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Release files / compressed_segmentation-2.3.3-cp311-cp311-macosx_10_9_x86_64.whl
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Release files / compressed_segmentation-2.3.3-cp310-cp310-win_amd64.whl
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Release files / compressed_segmentation-2.3.3-cp310-cp310-musllinux_1_2_x86_64.whl
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Release files / compressed_segmentation-2.3.3-cp310-cp310-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl
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Release files / compressed_segmentation-2.3.3-cp310-cp310-manylinux_2_24_aarch64.manylinux_2_28_aarch64.whl
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Release files / compressed_segmentation-2.3.3-cp310-cp310-macosx_11_0_arm64.whl
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Release files / compressed_segmentation-2.3.3-cp310-cp310-macosx_10_9_x86_64.whl
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Release files / compressed_segmentation-2.3.3-cp39-cp39-win_amd64.whl
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Release files / compressed_segmentation-2.3.3-cp39-cp39-musllinux_1_2_x86_64.whl
| Download URL | compressed_segmentation-2.3.3-cp39-cp39-musllinux_1_2_x86_64.whl |
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Release files / compressed_segmentation-2.3.3-cp39-cp39-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl
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Release files / compressed_segmentation-2.3.3-cp39-cp39-manylinux_2_24_aarch64.manylinux_2_28_aarch64.whl
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twine/6.1.0 CPython/3.11.3
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Release files / compressed_segmentation-2.3.3-cp39-cp39-macosx_11_0_arm64.whl
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Release files / compressed_segmentation-2.3.3-cp39-cp39-macosx_10_9_x86_64.whl
| Download URL | compressed_segmentation-2.3.3-cp39-cp39-macosx_10_9_x86_64.whl |
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No |
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twine/6.1.0 CPython/3.11.3
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Release files / compressed_segmentation-2.3.3-cp38-cp38-win_amd64.whl
| Download URL | compressed_segmentation-2.3.3-cp38-cp38-win_amd64.whl |
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twine/6.1.0 CPython/3.11.3
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Release files / compressed_segmentation-2.3.3-cp38-cp38-musllinux_1_2_x86_64.whl
| Download URL | compressed_segmentation-2.3.3-cp38-cp38-musllinux_1_2_x86_64.whl |
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No |
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Release files / compressed_segmentation-2.3.3-cp38-cp38-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl
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No |
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Release files / compressed_segmentation-2.3.3-cp38-cp38-manylinux_2_24_aarch64.manylinux_2_28_aarch64.whl
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Release files / compressed_segmentation-2.3.3-cp38-cp38-macosx_11_0_arm64.whl
| Download URL | compressed_segmentation-2.3.3-cp38-cp38-macosx_11_0_arm64.whl |
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No |
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Release files / compressed_segmentation-2.3.3-cp38-cp38-macosx_10_9_x86_64.whl
| Download URL | compressed_segmentation-2.3.3-cp38-cp38-macosx_10_9_x86_64.whl |
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