semvec/pypi-packages huggingface dataset:
brimfile 1.4.2
A package to read and write to the brim file format, containing spectral data and metadata from Brillouin microscopy
Requires Python: >=3.11
Keywords: Brillouin microscopy

<div align="center">
    <img src="https://raw.githubusercontent.com/prevedel-lab/brimfile/refs/heads/main//brimfile_logo.png"/>
</div>

# brimfile package

[![Documentation](https://img.shields.io/badge/docs-GitHub%20Pages-blue)](https://prevedel-lab.github.io/brimfile/brimfile.html)

## What is it?

*brimfile* is a package to read and write to brim (**Br**illouin **im**aging) files, containing spectral data and metadata from Brillouin microscopy.

The detailed specs of the brim file format can be found [here](https://github.com/prevedel-lab/Brillouin-standard-file/blob/main/docs/brim_file_specs.md).

## How to install it

We recommend installing *brimfile* in a [virtual environment](https://docs.python.org/3/library/venv.html).

After activating the environment, *brimfile* can be installed from PyPI using `pip`:
```bash
pip install brimfile
```

## How to use it

The full documentation of the package can be found [here](https://prevedel-lab.github.io/brimfile/).

To quickly start reading an existing .brim file, the following code shows how to:
- open a .brim file 
- get an image for the Brillouin shift 
- get the spectrum at a specific pixel
- get the metadata.

```Python
from brimfile import File, Data, Metadata, AnalysisResults
Quantity = AnalysisResults.Quantity
PeakType = AnalysisResults.PeakType

filename = 'path/to/your/file.brim.zarr' 
f = File(filename)

# get the first data group in the file
d = f.get_data()

# get the first analysis results in the data group
ar = d.get_analysis_results()

# get the image for the shift
img, px_size = ar.get_image(Quantity.Shift, PeakType.average)

# get the spectrum at the pixel (pz,py,px)
(pz,py,px) = (0,0,0)
PSD, frequency, PSD_units, frequency_units = d.get_spectrum_in_image((pz,py,px))

# get the metadata 
md = d.get_metadata()
all_metadata = md.all_to_dict()

# close the file
f.close()
```
More examples could be found in the [examples folder](examples)

## Matlab support

You can download the [Matlab toolbox](https://github.com/prevedel-lab/brimfile/releases/tag/matlab_toolbox_main), which is basically a wrapper around the Python brimfile package, so you can refer to the [same documentation](https://prevedel-lab.github.io/brimfile/). We only support Matlab >= R2023b, as brimfile needs Python 3.11.

Note that the current version of the Matlab toolbox is not supporting all the functions defined in brimfile and it has not been tested extensively yet.
skst-safe-build 1.0.0
A safe builder for falling back to setuptools when scikit_build_core fails due to a missing c compiler.
Requires Python: >=3.10

# Skst Safe Build
[![PyPI version](https://badge.fury.io/py/skst_safe_build.svg)](https://badge.fury.io/py/skst_safe_build)
[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)

# skst_safe_build
A Python package for safely building and packaging CPP based Python projects. It provides tools and utilities to ensure that your build process works even if a C compiler is not available.
wcp-library 1.8.7
Common utilites for internal development at WCP
Requires Python: >=3.12.0

# WCP-Library

## Description
Commonly used functions for the D&A team.

## Installation
`pip install WCP-Library`

## Usage
See [Wiki](https://github.com/Whitecap-DNA/WCP-Library/wiki/) for more information.

## Authors and acknowledgment
Mitch Petersen

## Stakeholders
D&A Developers

## Project status
In Development
google-genai-haystack 3.5.0
Use models like Gemini via Google Gen AI SDK
Requires Python: >=3.10

# Google Gen AI Haystack Integration

[![PyPI - Version](https://img.shields.io/pypi/v/google-genai-haystack.svg)](https://pypi.org/project/google-genai-haystack)
[![PyPI - Python Version](https://img.shields.io/pypi/pyversions/google-genai-haystack.svg)](https://pypi.org/project/google-genai-haystack)

- [Integration page](https://haystack.deepset.ai/integrations/google-genai)
- [Changelog](https://github.com/deepset-ai/haystack-core-integrations/blob/main/integrations/google_genai/CHANGELOG.md)

---

## Contributing

Refer to the general [Contribution Guidelines](https://github.com/deepset-ai/haystack-core-integrations/blob/main/CONTRIBUTING.md).

To run integration tests locally, you need to export the `GOOGLE_API_KEY` environment variable.