aimio-py

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, SCV, GOBJ, RAD, and RSQ 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 native RAD radiographs with header-derived mm spacing
• Read GOBJ contour masks into binary NumPy volumes
• Read AIM, ISQ, SCV, GOBJ, RAD, or RSQ files with single read_image and image_info dispatchers
• Read RSQ raw detector projections with optional read-only memory mapping
• Access format-specific header metadata (aim_info, isq_info, scv_info, gobj_info, rad_info, rsq_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 image_info, read_image, write_aim

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

header = image_info("scan.AIM")
write_aim("copy.AIM", array, meta)

The matching metadata CLI uses the same format resolution:

aimio-info scan.AIM
aimio-info mask.GOBJ --format gobj
aimio-info projections.RSQ --format rsq
aimio-info scout.RAD --format rad

Reading Options

read_image() detects AIM, ISQ, SCV, GOBJ, RAD, and RSQ files from the extension and forwards any extra keyword arguments to the format-specific reader.

aim, aim_meta = read_image("scan.AIM", density=True)
isq, isq_meta = read_image("scan.ISQ", unit="density")
scout, scout_meta = read_image("scout.SCV")
radiograph, rad_meta = read_image("scout.RAD")
mask, mask_meta = read_image("mask.GOBJ", value=1, crop="tight")
counts, rsq_meta = read_image("projections.RSQ", mmap=True)

The format-specific readers are also available directly:

• AIM: read_aim(path, density=False, hu=False)
• ISQ: read_isq(path, unit="native"), where unit can be "native", "hu", "density", or "bmd"
• SCV: read_scv(path)
• RAD: read_rad(path)
• GOBJ: read_gobj(path, value=127, crop="tight"), where crop can be "tight" or "header"
• RSQ: read_rsq(path, *, mmap=False)

At the moment, AIM and ISQ default to native stored values. For calibrated bone workflows, request density/BMD explicitly with density=True for AIM or unit="density"/unit="bmd" for ISQ.

API

• read_image(path, format="auto", **kwargs) -> (array, meta)
• image_info(path, format="auto") -> meta

Format-specific readers and metadata helpers are also available:

• read_aim(path, density=False, hu=False) -> (array, meta)
• read_isq(path, unit="native") -> (array, meta)
• read_scv(path) -> (array, meta)
• read_rad(path) -> (array, meta)
• read_gobj(path, value=127, crop="tight") -> (array, meta)
• read_rsq(path, *, mmap=False) -> (counts, meta)
• aim_info(path), isq_info(path), scv_info(path), gobj_info(path), rad_info(path), rsq_info(path)
• 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)

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.

GOBJ files are read as contour masks. Additive contours are rasterized as filled contours including their boundary. Subtractive contours, such as inner cortical boundaries, remove only the strict contour interior so the contour boundary remains part of the mask. crop="tight" returns the contour bounding box, while crop="header" returns the full CTDATA header grid.

SCV scout readers accept both stream exports and binary extracts that retain VMS variable-length record wrappers. RMS length words and odd-record alignment bytes are skipped in memory; the source file is never rewritten. Outer record lengths must match the enclosed SCV profiles. Metadata reports storage_format (stream or vms_variable_records), and record/payload offsets refer to the original file, including any wrappers.

SCV profile records contain a two-byte marker, a VMS F-floating row coordinate, a compressed-byte count, and the complete run-length-encoded pixel row. The first two compressed bytes are pixels, not a separate horizontal offset. Each decoded row must match the declared width; truncated runs and excess records are rejected. The aux and phase fields remain raw compatibility metadata, not geometry parameters.

The historical SCV spacing/origin convention matches IPL's scv_to_aim output for the paired reference scout. This does not establish calibrated physical geometry for every scanner variant: scouts with repeated/nonuniform row coordinates or invalid extents load with unit spacing and zero origin in pixel space, with a warning. geometry_unit, geometry_source, and geometry_warning identify this fallback; row_positions_mm and header_spacing retain the original information. Do not use pixel-space scouts for physical measurements or registration. Stripping VMS wrappers alone does not repair such geometry.

RAD radiographs

read_rad(path) returns a native signed-int16 2D array in (row, column) order; rad_info(path) inspects the header and validates storage without loading pixels. The pure-Python reader supports CTDATA-HEADER_V1, type-9 radiographs, including extra header blocks and optional zero padding to the next 512-byte boundary. The source file is never rewritten.

RAD physical dimensions are nanometres, unlike ISQ's micrometres. Metadata converts them to mm in physical_dimensions_mm, spacing, and element_size; dimensions is (width, height, 1), and the placeholder third-axis spacing is 1 mm, not a measured slice thickness. origin=(0,0,0) and identity direction describe a standalone display plane, not co-registration with CT. z_position_mm, reference_line_mm, and scan start/end positions are retained separately. No HU/density conversion is supported for this projection image.

Header interpretation follows the RAD branch of David Gobbi's vtk-dicom Scanco reader.

RSQ raw projections

from py_aimio import read_rsq, rsq_info

counts, meta = read_rsq("projections.RSQ;1", mmap=True)
print(counts.shape, meta["axis_order"])
header = rsq_info("projections.RSQ;1")

The supported RSQ storage interpretation uses the 16-byte CTDATA-HEADER_V1 magic and 128 little-endian unsigned header words. Arrays have shape (header_words[13], header_words[12], header_words[11]) and axes ("detector_row", "frame", "detector_column"). Values are decoded as little-endian unsigned 16-bit detector counts (<u2), preserving values up to 65535. Signedness has not been independently confirmed for every proprietary Scanco RSQ variant. mmap=True returns a read-only NumPy memory map.

Every stored frame is retained. Object views and any reference frames are not classified or discarded, and raw reading does not require a minimum number of frames. RSQ projections do not carry reconstructed volume origin, spacing, or direction keys. Spatial volume, HU, and density conversion requests through read_image() raise ValueError.

Metadata includes header_words, shape, axis_order, dtype, data_offset_bytes, and a geometry dictionary with explicit provenance and header positions. Geometry hints include requested output pitch and axial start in micrometers, native detector dimensions, detector size, source distances, binning, object view count, and angular interval in millidegrees. These are partially inferred header meanings, not independently validated reconstruction geometry. Words 21 and 22 are exposed as count_range; they do not define attenuation scaling. Patient-name fields are not decoded, although raw header words can still contain identifying data.

Both readers validate positive dimensions and require a detector payload length of 2 * product(shape) bytes after offset 512 * (header_words[127] + 1). An optional zero-filled tail extending exactly to the next 512-byte boundary is accepted for VMS block-aligned extracts and reported as padding_size_bytes. Unsupported magic, truncated data, nonzero padding, and other trailing bytes are rejected. rsq_info() checks file size and reads only the base header, final 512-byte header block, and any padding, not detector counts. When that block contains a recognized Beamhard.Corr. title, three float64 coefficients at bytes 476:500 are checked against the printed Corr at 2 3 6: anchors using delta(p) = a1*p + a2*p**2 + a3*p**3 with absolute tolerance 1e-6. Corrupt recognized calibration raises ValueError; absent or unrecognized calibration has beam_hardening["available"] = False. The reader exposes validated coefficients without applying them to counts.

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.
• py_aimio/scv.py and py_aimio/gobj.py are by Matthias Walle and Andrew Burghardt.

License

MIT