Add artifact removal capability

[KedoKudo]

This PR introduces the following changes:

• update previous existing notebook to ensure that can run again (this resolves check all notebooks to make them run again #1)
• add new derivation for tof cylindrical geometry correction
• add new development notebook to showcase tof cylindrical geometry correction plus wavelet filter based denoising.

Testing instructions

• Checkout the branch and setup environment with pixi
• Run pixi run test to ensure unit test runs
• Check 00_development.ipynb in notebooks folder, change the data path to local tof neutron transmission radiograph data.
• Check derivation.md in the documentation folder.

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Summary [AI]

This pull request introduces several improvements and cleanups to the neutron geometry correction project. The main changes include significant updates to documentation (including a new derivation document and improved README), removal of obsolete or redundant code and files, and the addition of a .gitignore for notebook-generated data. There are also configuration tweaks to pre-commit hooks and code coverage. These updates improve the usability, maintainability, and clarity of the project for both users and developers.

Documentation improvements:

• Added a comprehensive derivation document (documentation/derivation.md) explaining the cylindrical geometry correction methodology, including the Beer-Lambert law and robust attenuation coefficient estimation methods.
• Major reorganization and enhancement of the README.md for clarity, including clearer installation, usage, and development instructions, and improved formatting. [1] [2] [3] [4]

Code and notebook cleanup:

• Removed unused or obsolete Python utility scripts: notebooks/file_handler.py and notebooks/geometry_correction.py. [1] [2]
• Removed the archived notebook documentation/source/archived_notebooks_backup/tutorial_inhomogeneous_tiff.ipynb and renamed/updated the homogeneous tutorial notebook for clarity and improved code structure. [1] [2] [3]

Repository and configuration updates:

• Added a .gitignore for notebook-generated data files to prevent accidental commits of large or unnecessary files.
• Increased the maximum allowed file size for the check-added-large-files pre-commit hook from 8 MB to 30 MB to accommodate larger data files. (.pre-commit-config.yaml)
• Removed the codecov token from codecov.yml for improved security.

[Copilot]

Pull Request Overview

This PR introduces comprehensive file I/O capabilities for neutron imaging data, supporting both FITS and TIFF formats. It also includes artifact removal by cleaning up outdated files and reorganizing the repository structure.

• Adds a new file_handler module with robust FITS and TIFF file operations
• Removes legacy notebook files and outdated artifacts from the repository
• Updates project dependencies and notebook structure for better organization

Reviewed Changes

Copilot reviewed 17 out of 41 changed files in this pull request and generated 3 comments.

Show a summary per file

File	Description
src/neutron_geomcorr/file_handler.py	New comprehensive file I/O module with FITS/TIFF support and validation
tests/test_file_handler.py	Extensive test suite covering all file operations and error conditions
src/neutron_geomcorr/init.py	Exports file handler functions for public API
src/neutron_geomcorr/geometry_correction.py	Minor import cleanup and comment removal
pyproject.toml	Adds multiple new dependencies for enhanced functionality
notebooks/*.ipynb	Updates tutorial notebooks with modern structure and removes obsolete ones
documentation/derivation.md	Adds mathematical derivation documentation

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[JeanBilheux]

I just added a few minor doc changed just for my understanding of some of the filters used.