| Name | bdpy JSON |
| Version |
0.25.1
JSON |
| download |
| home_page | None |
| Summary | Brain decoder toolbox for Python |
| upload_time | 2024-10-09 06:09:25 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | <3.12,>=3.6 |
| license | MIT License Copyright (c) 2017-2024 Kamitani Lab Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. |
| keywords |
brain decoding
fmri
machine learning
neuroimaging
neuroscience
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
# BdPy
[](https://badge.fury.io/py/bdpy)
[](https://github.com/KamitaniLab/bdpy/blob/master/LICENSE)
[](https://github.com/KamitaniLab/bdpy/actions/workflows/ci.yml)
Python package for brain decoding analysis
## Requirements
- Python 3.8 or later
- numpy
- scipy
- scikit-learn
- pandas
- h5py
- hdf5storage
- pyyaml
### Optional requirements
- `dataform` module
- pandas
- `dl.caffe` module
- Caffe
- Pillow
- tqdm
- `dl.torch` module
- PyTorch
- Pillow
- `fig` module
- matplotlib
- Pillow
- `bdpy.ml` module
- tqdm
- `mri` module
- nipy
- nibabel
- pandas
- `recon.torch` module
- PyTorch
- Pillow
### Optional requirements for testing
- fastl2lir
## Installation
Latest stable release:
``` shell
$ pip install bdpy
```
To install the latest development version ("master" branch of the repository), please run the following command.
```shell
$ pip install git+https://github.com/KamitaniLab/bdpy.git
```
## Packages
- bdata: BdPy data format (BData) core package
- dataform: Utilities for various data format
- distcomp: Distributed computation utilities
- dl: Deep learning utilities
- feature: Utilities for DNN features
- fig: Utilities for figure creation
- ml: Machine learning utilities
- mri: MRI utilities
- opendata: Open data utilities
- preproc: Utilities for preprocessing
- recon: Reconstruction methods
- stats: Utilities for statistics
- util: Miscellaneous utilities
## BdPy data format
BdPy data format (or BrainDecoderToolbox2 data format; BData) consists of two variables: dataset and metadata. **dataset** stores brain activity data (e.g., voxel signal value for fMRI data), target variables (e.g., ID of stimuli for vision experiments), and additional information specifying experimental design (e.g., run and block numbers for fMRI experiments). Each row corresponds to a single 'sample', and each column representes either single feature (voxel), target, or experiment design information. **metadata** contains data describing meta-information for each column in dataset.
See [BData API examples](https://github.com/KamitaniLab/bdpy/blob/main/docs/bdata_api_examples.md) for useage of BData.
## Developers
- Shuntaro C. Aoki (Kyoto Univ)
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