rawtools 0.5.0

Utility library for consuming and manipulating x-ray data in RAW format

Utility library for consuming and manipulating x-ray volume data in .raw format.

Features

• Convert float32, uint16, and uint8 versions of .raw XRT volume data

• Extract image slices from .raw files

• Read, parse, and generate metadata files (.dat) for XRT data

• Convert proprietary .nsihdr files into .raw format (Windows only). Batch conversion supported as CLI and minimal GUI.

• Generate previews of XRT volumes for quality control (e.g., maximum density projections, midslice extraction, etc.)

Planned Features

• Generate dummy .raw files for testing downstream pipelines

• Batch conversion of .nsihdr on Linux systems

• Density adjustment (similar to automated adjustment MATLAB scripts for rootseg)

Related Projects

• xrcap: root crown image analysis pipeline

• DynamicRoots: tool for reconstructing and analyzing the growth of a plant root system

• TopoRoot: high-throughput computational method that computes fine-grained architectural traits from 3D CT images of excavated maize root crowns

• rootseg: ML-based segmentation for soil rich samples

• xrt-dmt: data management tool for tracking and archiving XRT (meta)data

Credits

This package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.

History

0.3.0 (2021-07-18)

Added

• License

• Basic tests on core functionality for scaling data

Changed

• Updated URL for any references to GitHub repo

• Updated docstring header for raw2img module

• Updated README to be more descriptive

0.2.0 (2021-01-04)

• Added efX-SDK library

• Added module to export/convert nsihdr files to uint raw files using the efX-SDK (Windows only)

• Tentatively implemented a GUI for the nsihdr2raw export tool

• Tweaked logging path for log files generated relative to input data for nsihdr2raw

0.1.4 (2020-10-27)

• Code clean up, remove unnecessary transposing of data, improved debug statements and logging

0.1.3 (2020-10-26)

• Fixed font file missing when installing via pip

0.1.2 (2020-09-25)

• Fix typo in log messages when checking expected file size to actual file size (.raw)

0.1.0 (2020-06-19)

• Initial version