aimio-py

Python bindings for the Numerics88 AimIO C++ library.

aimio-py provides a small Python API to read and write AIM files as NumPy arrays, read ISQ files, inspect metadata, and work with processing logs.

Features

Read AIM files into NumPy arrays
Write AIM files from NumPy arrays
Read ISQ files into NumPy arrays
Read SCV scout-view files into NumPy arrays
Read AIM, ISQ, or SCV files with a single read_image dispatcher
Access AIM, ISQ, and SCV header metadata (aim_info, isq_info, scv_info)
Convert processing logs between text and dictionary formats
Optional density/HU conversion helpers

Installation

From PyPI (recommended):

pip install aimio-py

From source:

git clone https://github.com/wallematthias/aimio-py.git
cd aimio-py
git submodule update --init --recursive
pip install -e .

Quickstart

from py_aimio import read_aim, read_image, read_isq, read_scv, write_aim

array, meta = read_aim("scan.AIM")
print(meta["origin"], meta["spacing"], meta["direction"])
write_aim("copy.AIM", array, meta)

isq_array, isq_meta = read_isq("scan.ISQ")
scout_array, scout_meta = read_scv("scout.SCV")

image, image_meta = read_image("scan.ISQ")

Reading ISQ files

from py_aimio import isq_info, read_isq

info = isq_info("scan.ISQ")
print("Dimensions:", info["dimensions"])
print("Voxel spacing:", info["spacing"])

array, meta = read_isq("scan.ISQ")
print(array.shape, array.dtype)  # (z, y, x), int16

hu_array, hu_meta = read_isq("scan.ISQ", unit="hu")
bmd_array, bmd_meta = read_isq("scan.ISQ", unit="density")

API

aim_info(path)
isq_info(path)
scv_info(path)
read_image(path, format="auto", **kwargs) -> (array, meta)
read_aim(path, density=False, hu=False) -> (array, meta)
read_isq(path, unit="native") -> (array, meta)
read_scv(path) -> (array, meta)
write_aim(path, array, meta=None, unit=None)
get_aim_density_equation(processing_log)
get_aim_hu_equation(processing_log)
log_to_dict(log)
dict_to_log(dct)

For ISQ files, unit="native" returns stored scanner values. unit="hu" and unit="density"/unit="bmd" use calibration metadata from the ISQ extended header when present.

Read metadata includes SimpleITK-style geometry keys for both AIM and ISQ: origin, spacing, and direction. For AIM, spacing is copied from element_size and origin follows the ITKIOScanco-compatible convention: (position + offset) * spacing. The older vtkbone-style half-voxel-shifted origin is also exposed as vtkbone_origin. For ISQ, spacing comes from the ISQ header and origin defaults to (0.0, 0.0, 0.0). direction currently defaults to the 3D identity direction, matching the practical behavior observed from ITKIOScanco for ISQ files without explicit orientation metadata.

Development

Run tests:

pytest -q

Run tests with coverage:

pytest -q --cov=py_aimio --cov-report=term-missing --cov-report=xml:coverage.xml

Build local artifacts:

python -m build --wheel --sdist

Build documentation from docstrings:

pip install sphinx
make -C docs html

Generated HTML will be in docs/build/html/index.html.

Important build note

This project depends on the external/AimIO and external/n88util git submodules. If they are missing, extension builds will fail.

Attribution

py_aimio/calibration.py is adapted from Bonelab/Bonelab.
py_aimio/header_log.py is by Matthias Walle.

License

MIT

Metadata

Release files for aimio-py 0.1.7

For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.

Source distribution (sdist)

Source distribution for aimio-py 0.1.7
File	Size	Uploaded
aimio_py-0.1.7.tar.gz	61.5 kB	Jul 10, 2026	Details

Built distributions (wheels)

Table of built distributions (wheels) for aimio-py 0.1.7
File	Interpreter	ABI	Platform	Reset
aimio_py-0.1.7-cp313-cp313-win_amd64.whl 317.3 kB Jul 10, 2026	CPython 3.13	CPython 3.13	Windows x86-64	Details
aimio_py-0.1.7-cp313-cp313-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl 1.7 MB Jul 10, 2026	CPython 3.13	CPython 3.13	Linux glibc 2.28+ x86-64, Linux glibc 2.24+ x86-64	Details
aimio_py-0.1.7-cp313-cp313-macosx_11_0_arm64.whl 127.5 kB Jul 10, 2026	CPython 3.13	CPython 3.13	macOS 11.0+ ARM64	Details
aimio_py-0.1.7-cp313-cp313-macosx_10_13_x86_64.whl 133.7 kB Jul 10, 2026	CPython 3.13	CPython 3.13	macOS 10.13+ x86-64	Details
aimio_py-0.1.7-cp312-cp312-win_amd64.whl 317.2 kB Jul 10, 2026	CPython 3.12	CPython 3.12	Windows x86-64	Details
aimio_py-0.1.7-cp312-cp312-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl 1.7 MB Jul 10, 2026	CPython 3.12	CPython 3.12	Linux glibc 2.28+ x86-64, Linux glibc 2.24+ x86-64	Details
aimio_py-0.1.7-cp312-cp312-macosx_11_0_arm64.whl 127.4 kB Jul 10, 2026	CPython 3.12	CPython 3.12	macOS 11.0+ ARM64	Details
aimio_py-0.1.7-cp312-cp312-macosx_10_13_x86_64.whl 133.6 kB Jul 10, 2026	CPython 3.12	CPython 3.12	macOS 10.13+ x86-64	Details
aimio_py-0.1.7-cp311-cp311-win_amd64.whl 314.6 kB Jul 10, 2026	CPython 3.11	CPython 3.11	Windows x86-64	Details
aimio_py-0.1.7-cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl 1.7 MB Jul 10, 2026	CPython 3.11	CPython 3.11	Linux glibc 2.24+ x86-64, Linux glibc 2.28+ x86-64	Details
aimio_py-0.1.7-cp311-cp311-macosx_11_0_arm64.whl 125.8 kB Jul 10, 2026	CPython 3.11	CPython 3.11	macOS 11.0+ ARM64	Details
aimio_py-0.1.7-cp311-cp311-macosx_10_9_x86_64.whl 131.4 kB Jul 10, 2026	CPython 3.11	CPython 3.11	macOS 10.9+ x86-64	Details
aimio_py-0.1.7-cp310-cp310-win_amd64.whl 313.9 kB Jul 10, 2026	CPython 3.10	CPython 3.10	Windows x86-64	Details
aimio_py-0.1.7-cp310-cp310-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl 1.6 MB Jul 10, 2026	CPython 3.10	CPython 3.10	Linux glibc 2.24+ x86-64, Linux glibc 2.28+ x86-64	Details
aimio_py-0.1.7-cp310-cp310-macosx_11_0_arm64.whl 124.4 kB Jul 10, 2026	CPython 3.10	CPython 3.10	macOS 11.0+ ARM64	Details
aimio_py-0.1.7-cp310-cp310-macosx_10_9_x86_64.whl 130.0 kB Jul 10, 2026	CPython 3.10	CPython 3.10	macOS 10.9+ x86-64	Details

Total release size: 9.0 MB

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Subject: aimio_py-0.1.7-cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl
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Release files / aimio_py-0.1.7-cp311-cp311-macosx_11_0_arm64.whl

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Uploaded via	`twine/6.1.0 CPython/3.13.12`

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Publishing platform: GitHub Actions
Publishing repository: github.com/wallematthias/aimio-py
Publishing commit: github.com/wallematthias/aimio-py/tree/cd0a6e2f407e2fc37a4b5561c18d5087c6a45fd9

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Release files / aimio_py-0.1.7-cp311-cp311-macosx_10_9_x86_64.whl

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Uploaded via	`twine/6.1.0 CPython/3.13.12`

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Publishing repository: github.com/wallematthias/aimio-py
Publishing commit: github.com/wallematthias/aimio-py/tree/cd0a6e2f407e2fc37a4b5561c18d5087c6a45fd9

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Release files / aimio_py-0.1.7-cp310-cp310-win_amd64.whl

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Publishing platform: GitHub Actions
Publishing repository: github.com/wallematthias/aimio-py
Publishing commit: github.com/wallematthias/aimio-py/tree/cd0a6e2f407e2fc37a4b5561c18d5087c6a45fd9

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Subject: aimio_py-0.1.7-cp310-cp310-win_amd64.whl
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Release files / aimio_py-0.1.7-cp310-cp310-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl

Download URL	aimio_py-0.1.7-cp310-cp310-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl
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Uploaded via	`twine/6.1.0 CPython/3.13.12`

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Publishing platform: GitHub Actions
Publishing repository: github.com/wallematthias/aimio-py
Publishing commit: github.com/wallematthias/aimio-py/tree/cd0a6e2f407e2fc37a4b5561c18d5087c6a45fd9

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Publishing configuration: github.com/wallematthias/aimio-py/blob/cd0a6e2f407e2fc37a4b5561c18d5087c6a45fd9/.github/workflows/build-wheels.yml
Publishing logs: github.com/wallematthias/aimio-py/actions/runs/29102176586/attempts/1

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Subject: aimio_py-0.1.7-cp310-cp310-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl
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Release files / aimio_py-0.1.7-cp310-cp310-macosx_11_0_arm64.whl

Download URL	aimio_py-0.1.7-cp310-cp310-macosx_11_0_arm64.whl
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Publishing repository: github.com/wallematthias/aimio-py
Publishing commit: github.com/wallematthias/aimio-py/tree/cd0a6e2f407e2fc37a4b5561c18d5087c6a45fd9

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Publishing configuration: github.com/wallematthias/aimio-py/blob/cd0a6e2f407e2fc37a4b5561c18d5087c6a45fd9/.github/workflows/build-wheels.yml
Publishing logs: github.com/wallematthias/aimio-py/actions/runs/29102176586/attempts/1

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Subject: aimio_py-0.1.7-cp310-cp310-macosx_11_0_arm64.whl
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Release files / aimio_py-0.1.7-cp310-cp310-macosx_10_9_x86_64.whl

Download URL	aimio_py-0.1.7-cp310-cp310-macosx_10_9_x86_64.whl
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Uploaded via	`twine/6.1.0 CPython/3.13.12`

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Publishing platform: GitHub Actions
Publishing repository: github.com/wallematthias/aimio-py
Publishing commit: github.com/wallematthias/aimio-py/tree/cd0a6e2f407e2fc37a4b5561c18d5087c6a45fd9

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Publishing configuration: github.com/wallematthias/aimio-py/blob/cd0a6e2f407e2fc37a4b5561c18d5087c6a45fd9/.github/workflows/build-wheels.yml
Publishing logs: github.com/wallematthias/aimio-py/actions/runs/29102176586/attempts/1

Artifact

Subject: aimio_py-0.1.7-cp310-cp310-macosx_10_9_x86_64.whl
SHA-256 checksum: 43890f7ddf8a31c777686d606b9e913897fa8458a7dbf7d4c9ceca5030a5ea50 Verifying attestations