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
- Access AIM and ISQ header metadata (
aim_info,isq_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_isq, write_aim
array, meta = read_aim("scan.AIM")
write_aim("copy.AIM", array, meta)
isq_array, isq_meta = read_isq("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)read_aim(path, density=False, hu=False) -> (array, meta)read_isq(path, unit="native") -> (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.
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.pyis adapted from Bonelab/Bonelab.py_aimio/header_log.pyis by Matthias Walle.
License
MIT
1 maintainer
Metadata
1 maintainer
Release files for aimio-py 0.1.4
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