openreadout (Python)
Read raw lab-instrument files from Python without vendor software, Java or a C toolchain. The package wraps OpenReadout's Rust readers. It returns the same JSON as the openreadout command-line tool, and NumPy, dask or xarray arrays for pixels. The formats it reads are listed at https://openreadout.github.io/openreadout/formats.html.
pip install openreadout # needs only NumPy
pip install 'openreadout[xarray]' # adds dask and xarray for lazy, labelled arrays
One abi3 wheel per platform covers CPython 3.10 and newer on Linux (manylinux and musllinux, x86_64 and aarch64), macOS (x86_64 and arm64) and Windows (x64).
import openreadout
meta = openreadout.info("run42.czi") # header-only summary, a dict
meta["images"][0]["size_c"], meta["images"][0]["physical_size"]
with openreadout.File("run42.czi") as f:
plane = f.read_plane(image=0, c=1, z=4) # np.ndarray (Y, X), or (Y, X, 3) for RGB
stack = f.read_image(0) # np.ndarray (T, C, Z, Y, X[, S])
lazy = f.to_dask(0) # dask array, one chunk per plane, read on demand
xarr = f.to_xarray(0) # labelled: channel names, µm and s coordinates
f.check()["ok"] # integrity report
f.export("run42.ome.tiff") # verified OME-TIFF; the source is never modified
Tables, traces and spectra (flow cytometry, electrophysiology, chromatography, mass spectrometry) are read with File.read_table, File.read_trace and File.read_spectrum, and convert to Arrow or pandas with File.to_arrow and File.to_pandas.
Arrays use the dimension order TCZYX, with S added for interleaved RGB. File objects are thread-safe and picklable, so lazy arrays work with dask's threaded, multiprocessing and distributed schedulers.
Every error is an openreadout.OpenReadoutError and also the closest built-in exception (for example FileNotFoundError or ValueError). It carries the command-line tool's code, exit_code and a hint.
bioio-openreadout plugs these readers into bioio.BioImage, and napari-openreadout into napari.
Guide and full API: https://openreadout.github.io/openreadout/guides/python.html. Source: https://github.com/openreadout/openreadout. Licensed MIT OR Apache-2.0. OpenReadout is not affiliated with any instrument vendor.
1 maintainer
Metadata
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Release files for openreadout 0.2.0
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| openreadout-0.2.0.tar.gz | 3.2 MB | Details |
Built distributions (wheels)
| File | Reset | |||
|---|---|---|---|---|
| openreadout-0.2.0-cp310-abi3-win_amd64.whl | CPython 3.10 | abi3 | Windows x86-64 | Details |
| openreadout-0.2.0-cp310-abi3-musllinux_1_2_x86_64.whl | CPython 3.10 | abi3 | Linux musl 1.2+ x86-64 | Details |
| openreadout-0.2.0-cp310-abi3-musllinux_1_2_aarch64.whl | CPython 3.10 | abi3 | Linux musl 1.2+ ARM64 | Details |
| openreadout-0.2.0-cp310-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl | CPython 3.10 | abi3 | Linux glibc 2.17+ x86-64 | Details |
| openreadout-0.2.0-cp310-abi3-manylinux_2_17_aarch64.manylinux2014_aarch64.whl | CPython 3.10 | abi3 | Linux glibc 2.17+ ARM64 | Details |
| openreadout-0.2.0-cp310-abi3-macosx_11_0_arm64.whl | CPython 3.10 | abi3 | macOS 11.0+ ARM64 | Details |
| openreadout-0.2.0-cp310-abi3-macosx_10_12_x86_64.whl | CPython 3.10 | abi3 | macOS 10.12+ x86-64 | Details |
Total release size: 126.3 MB
Release files / openreadout-0.2.0.tar.gz
| Download URL | openreadout-0.2.0.tar.gz |
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| Size | 3.2 MB |
| Tags | Source |
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| Size | 19.1 MB |
| Tags | CPython 3.10 Windows x86-64 abi3 |
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| Size | 18.4 MB |
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