Metadata-Version: 2.4
Name: brighteyes-mcs-file
Version: 0.1.2
Summary: Utilities for reading and calibrating BrightEyes MCS HDF5 files.
Author-email: Mattia Donato <mattia.donato@iit.it>
License-Expression: GPL-3.0-or-later
Project-URL: Homepage, https://github.com/VicidominiLab/BrightEyes-MCS-File
Project-URL: Repository, https://github.com/VicidominiLab/BrightEyes-MCS-File
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Topic :: Scientific/Engineering :: Image Processing
Requires-Python: >=3.9
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: h5py
Requires-Dist: matplotlib
Requires-Dist: numpy
Requires-Dist: scipy
Requires-Dist: tqdm
Provides-Extra: fit
Requires-Dist: joblib; extra == "fit"
Requires-Dist: torch; extra == "fit"
Provides-Extra: dev
Requires-Dist: build; extra == "dev"
Requires-Dist: pytest; extra == "dev"
Requires-Dist: twine; extra == "dev"
Provides-Extra: notebook
Requires-Dist: jupyter; extra == "notebook"
Requires-Dist: pandas; extra == "notebook"
Dynamic: license-file

# BrightEyes MCS File

Python utilities for reading and calibrating BrightEyes MCS HDF5 files.

This package is structured with a `src/` layout so it can be published on PyPI
as `brighteyes-mcs-file` and imported as `brighteyes_mcs_file`.

## Install for Development

```bash
pip install -e .[fit]
```

## Basic Usage

```python
from brighteyes_mcs_file import (
    Alignment,
    calibrate_h5_file,
    metadata_load,
    plot_calibration_lifetime_summary,
    show_h5_structure_html,
    sum_channel_applying_shifts,
)

metadata = metadata_load("data.h5")
output_path = calibrate_h5_file("data.h5", "reference.h5")
show_h5_structure_html(output_path)
```

The package includes a local `mcs` module, so calibration no longer imports
`brighteyes_ism.dataio.mcs`.

The HDF5 calibration workflow notebook is in
`examples/Calibrate_h5_file_Workflow.ipynb`. Install notebook-only helpers with
`pip install -e .[notebook]`.
