voxelkit 0.1.2

Library-first toolkit for inspecting, previewing, and QA reporting imaging datasets.

VoxelKit

VoxelKit helps you inspect, preview, and QA-check multidimensional imaging files from one consistent CLI and Python API.

Quick CLI Demo

# Inspect structure/metadata
python -m voxelkit.cli inspect tests/fixtures/sample_nested.h5

# Generate a PNG preview slice
python -m voxelkit.cli preview tests/fixtures/sample_3d.nii.gz --plane axial --slice 4 --output nifti_preview.png

# Run per-file QA stats + warnings
python -m voxelkit.cli report tests/fixtures/sample_nested.h5 --dataset data/subject01/run1/bold

# Run directory-level QA summary
python -m voxelkit.cli report-batch tests/fixtures --output batch_report.json

Why VoxelKit?

Low-level libraries like nibabel, h5py, and tifffile are powerful and flexible. VoxelKit does not replace them.

Instead, VoxelKit provides a unified workflow on top for day-to-day dataset triage:

• inspect file structure and metadata quickly
• preview representative slices as PNGs
• generate QA stats and warnings for suspicious arrays
• summarize QA signals across whole directories with report-batch

This keeps common inspection and QA tasks fast, scriptable, and consistent across formats.

Supported Formats

• NIfTI (.nii, .nii.gz)
• HDF5 (.h5, .hdf5)
• NumPy arrays (.npy, .npz)
• TIFF (.tif, .tiff) in format routing (full inspect/preview/report coverage is in progress)

Installation

Editable install (recommended while iterating on the project):

cd VoxelKit
pip install -e .

Optional dependencies used by demos/tests:

pip install -r requirements.txt

When a PyPI release is available, installation will be:

pip install voxelkit

Python Usage

from voxelkit import inspect_file, preview_file, report_file, report_batch

# Inspect
info = inspect_file("tests/fixtures/sample_nested.h5")

# Preview (returns PNG bytes)
png = preview_file(
    "tests/fixtures/sample_3d.nii.gz",
    plane="axial",
    slice_index=4,
)
with open("nifti_preview.png", "wb") as f:
    f.write(png)

# Single-file QA report
single_report = report_file(
    "tests/fixtures/sample_nested.h5",
    dataset_path="data/subject01/run1/bold",
)

# Batch QA report
batch = report_batch("tests/fixtures", recursive=True)

Visual Demos

Add screenshots/snippets here so visitors can see value in under 30 seconds:

• Terminal screenshot: inspect and report output side by side
• Preview image: one generated PNG slice (nifti_preview.png or h5_preview.png)
• Batch report snippet: short JSON excerpt showing files_with_warnings and warning_counts

Run The API

py -m uvicorn app.main:app --reload

Open API docs:

• Swagger UI: http://127.0.0.1:8000/docs

Optional Local GUI

VoxelKit includes an optional Streamlit prototype for local/offline inspect, report, and preview workflows. The GUI runs entirely on your machine and does not upload files to external services.

Install optional GUI extras:

pip install -e .[gui]

Launch the GUI:

voxelkit gui

If Streamlit is not installed, the CLI prints:

Install GUI extras with: pip install voxelkit[gui]

API Endpoints

• POST /h5/inspect
• POST /h5/slice
• POST /nifti/metadata
• POST /nifti/preview
• GET /health

API Usage Examples

NIfTI Metadata

curl -X POST "http://127.0.0.1:8000/nifti/metadata" \
	-F "file=@tests/fixtures/sample_3d.nii.gz"

NIfTI Preview

curl -X POST "http://127.0.0.1:8000/nifti/preview?plane=axial&slice_index=4" \
	-F "file=@tests/fixtures/sample_3d.nii.gz" \
	--output nifti_preview.png

HDF5 Inspect

curl -X POST "http://127.0.0.1:8000/h5/inspect" \
	-F "file=@tests/fixtures/sample_nested.h5"

HDF5 Slice

curl -X POST "http://127.0.0.1:8000/h5/slice?dataset_path=data/subject01/run1/bold&axis=2&slice_index=3" \
	-F "file=@tests/fixtures/sample_nested.h5" \
	--output h5_preview.png

Project Layout

voxelkit/
  core/      # shared cross-format utilities (validation, types, errors, normalization)
  h5/        # HDF5 inspect/preview logic
  nifti/     # NIfTI metadata/preview logic

app/
  routers/   # thin FastAPI wrappers over voxelkit library functions

Test Fixtures

Generate tiny deterministic fixtures for local testing/demo:

py tests/create_fixtures.py

This creates:

• tests/fixtures/sample_3d.nii.gz: small 3D NIfTI volume
• tests/fixtures/sample_2d.h5: 2D HDF5 dataset at image
• tests/fixtures/sample_3d.h5: 3D HDF5 dataset at volume
• tests/fixtures/sample_nested.h5: nested HDF5 dataset at data/subject01/run1/bold

Running Tests

pytest -q

Extending CLI Formats

The CLI in voxelkit/cli.py is registry-based and intentionally thin.

To add a new image format later (for example, GeoTIFF):

1. Implement library functions in a format module (inspect + preview bytes).
2. Implement a format report function in the format module.
3. Add small CLI adapters in voxelkit/cli.py that map CLI args into preview/report functions.
4. Register the format in _register_builtin_formats() with register_format(FormatRoute(...)).
5. Add any new format-specific CLI flags in build_parser() only if needed.

Minimal registration pattern:

register_format(
	FormatRoute(
		name="geotiff",
		extensions=(".tif", ".tiff"),
		inspect_fn=inspect_geotiff,
		preview_fn=_preview_geotiff,
		report_fn=_report_geotiff,
	)
)

This keeps CLI routing simple while all format behavior remains in the library layer.

Roadmap

• multi-file request support
• CI for tests
• docs expansion for format-specific library usage
• pip packaging

Contributing

Please see CONTRIBUTING.md for contribution workflow, coding standards, and pull request guidance.

Disclaimer

VoxelKit is a developer/research utility tool. It is not a clinical decision system and must not be used for diagnosis or treatment decisions.