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BEP032tools-0.3.3.dev0
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مشاهده بیشترتوضیحات
Checks the validity of a directory with respect to the BEP032 specifications
| ویژگی | مقدار |
|---|---|
| سیستم عامل | - |
| نام فایل | BEP032tools-0.3.3.dev0 |
| نام | BEP032tools |
| نسخه کتابخانه | 0.3.3.dev0 |
| نگهدارنده | [] |
| ایمیل نگهدارنده | [] |
| نویسنده | Jeremy Garcia, Sylvain Takerkart , Julia Sprenger |
| ایمیل نویسنده | - |
| آدرس صفحه اصلی | - |
| آدرس اینترنتی | https://pypi.org/project/BEP032tools/ |
| مجوز | MIT |
# BEP032 tools
This repository collects tools supporting the [BEP032 proposal](https://bids.neuroimaging.io/bep032). It originally emerged under the name `AnDO` (Animal Data Organization) and gathers a set of tools facilitating the usage of the proposed structure. For the documentation of BIDS itself, see https://bids-specification.readthedocs.io. The proposal is open to any type of feedback from the community and we are welcoming all types of constructive comments.
The provided tools integrating with BEP032 are :
- BEP032Validator script to check if your dataset follows the current BEP032 rules
- BEP032Generator script to create a BEP032 compatible folder structure **without** metadata files for a given set of subjects and sessions. These files need to be listed in an input CSV file.
- BEP032Templater script to generate a BEP032 compatible folder structure **including** dummy files to be extended manually, e.g. using Excel or a text editor
- _BEP032Viewer script to display your dataset directory in a convenient way. (deprecated)_
[](https://pypi.python.org/pypi/ansicolortags/)[](https://www.python.org/)[](https://github.com/INT-NIT/BEP032tools/actions)[](https://coveralls.io/github/INT-NIT/BEP032tools?branch=master)
## Installation
### Dependencies
BEP032Validator requires:
- Python (>= 3.7)
- Pip3
### User installation
To include all packages required for the BEP032 tools download the repository from https://github.com/INT-NIT/BEP032tools and run the following in the unpacked version of the repository
```bash
> pip install BEP032tools[tools]
```
By installing BEP032Validator the following scripts will be installed:
### General usage for the BEP032Validator script
```term
usage: BEP032Validator.py [-h] [-v] path
positional arguments:
path Path to your folder
optional arguments: -h, --help show this help message and exit
-v, --verbose increase output verbosity
```
### Specific usage
The validator can be directly used from the command line interface (CLI)
```bash
> BEP032Validator -v tests/dataset001/Landing
```
or from within Python
```python
> from bep032tools.validator import BEP032Validator
> BEP032Validator.is_valid('tests/dataset001/Landing')
```
-----------
### General usage for the Generator script
The generator can be used to create a BEP032 compatible folder structure (**without metadata files**) based on a list of sessions and subject. This list of sessions and subject has to be provided in form of a CSV file:
```term
usage: BEP032Generator.py [-h] pathToCsv pathToDir
positional arguments:
pathToCsv Path to your folder
pathToDir Path to your csv file
optional arguments:
-h, --help show this help message and exit
```
The generator can be directly used from the command line interface (CLI)
```bash
> BEP032Generator data.csv data/
```
-----------
### General usage for the Templater script
```term
usage: BEP032Temlater.py [-h] pathToCsv pathToDir
positional arguments:
pathToCsv Path to your folder
pathToDir Path to your csv file
optional arguments:
-h, --help show this help message and exit
```
The templater can be directly used from the command line interface (CLI)
```bash
> BEP032Templater data.csv data/
```
## How to create a BEP032 structure **including** custom metadata
There are two options to add custom metadata (files) to a BEP032 structure
1) Generation of the structure including dummy metadata files using the `BEP032Templator` and manual entry of the metadata in those files.
2) Programmatic extension of the `BEP032Generator`. For this you need to create a Python class that inherits from `bep032tools.generator.BE032Generator` and implements the missing metadata methods:
- `generate_metadata_file_sessions`
- `generate_metadata_file_tasks`
- `generate_metadata_file_dataset_description`
- `generate_metadata_file_participants`
- `generate_metadata_file_probes`
- `generate_metadata_file_probes`
- `generate_metadata_file_channels`
- `generate_metadata_file_contacts`
- `generate_metadata_file_scans`
These methods should fetch the corresponding metadata information from your project specific location and create the corresponding CSV or JSON file using the `generator.utils.save_json` and `generator.utils.save_tsv` functions correspondingly. When all missing methods are implemented `generator.BEP032Generator.generate_struct()` will not only create the corresponding folder structure, but also all metadata files with the metadata provided.
### Installation issues
In some cases pandas might not be properly installed via pip. In this case we recommend installing pandas via conda.
# Development
We welcome new contributors of all experience levels.
Important links
---------------
- Official source code repo: https://github.com/INT-NIT/BEP032tools
- (In planning) Download releases: https://pypi.org/project/BEP032tools/
- Issue tracker:https://github.com/INT-NIT/BEP032tools/issues
Contributing
------------
To contribute to the development of BEP032tools, please open an [issue](https://github.com/INT-NIT/BEP032tools/issues) or [pull request](https://github.com/INT-NIT/BEP032tools/pulls) or directly comment in the [BEP032 proposal](https://bids.neuroimaging.io/bep032).
نیازمندی
| مقدار | نام |
|---|---|
| - | pytest |
| - | datalad |
| - | pandas |
| - | pynwb |
زبان مورد نیاز
| مقدار | نام |
|---|---|
| >=3.7 | Python |
نحوه نصب
نصب پکیج whl BEP032tools-0.3.3.dev0:
pip install BEP032tools-0.3.3.dev0.whl
نصب پکیج tar.gz BEP032tools-0.3.3.dev0:
pip install BEP032tools-0.3.3.dev0.tar.gz