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d2b-1.4.2rc0
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Organize data in the BIDS format
| ویژگی | مقدار |
|---|---|
| سیستم عامل | - |
| نام فایل | d2b-1.4.2rc0 |
| نام | d2b |
| نسخه کتابخانه | 1.4.2rc0 |
| نگهدارنده | [] |
| ایمیل نگهدارنده | [] |
| نویسنده | Andrew Ross |
| ایمیل نویسنده | andrew.ross.mail@gmail.com |
| آدرس صفحه اصلی | https://github.com/d2b-dev/d2b |
| آدرس اینترنتی | https://pypi.org/project/d2b/ |
| مجوز | - |
# d2b
Organize data in the BIDS format.
[](https://pypi.org/project/d2b/) [](https://codecov.io/gh/d2b-dev/d2b) [](https://github.com/d2b-dev/d2b/actions/workflows/test.yaml) [](https://github.com/d2b-dev/d2b/actions/workflows/lint.yaml) [](https://github.com/d2b-dev/d2b/actions/workflows/type-check.yaml)
Compatible with `dcm2bids` config files.
## Installation
```bash
pip install d2b
```
## Usage
The singular CLI entrypoint:
```bash
$ d2b --help
usage: d2b [-h] [-v] {run,scaffold} ...
d2b - Organize data in the BIDS format
positional arguments:
{run,scaffold}
optional arguments:
-h, --help show this help message and exit
-v, --version show program's version number and exit
```
Scaffold a BIDS dataset:
```bash
$ d2b scaffold --help
usage: d2b scaffold [-h] out_dir
Scaffold a BIDS dataset directory structure
positional arguments:
out_dir Output BIDS directory
optional arguments:
-h, --help show this help message and exit
```
Organize nifti data (sidecars required) into a BIDS-compliant structure:
```bash
$ d2b run --help
usage: d2b run [-h] -c CONFIG_FILE -p PARTICIPANT -o OUT_DIR [-s SESSION] [-l {DEBUG,INFO,WARNING,ERROR,CRITICAL}] in_dir [in_dir ...]
Organize data in the BIDS format
positional arguments:
in_dir Directory(ies) containing files to organize
required arguments:
-c CONFIG_FILE, --config CONFIG_FILE
JSON configuration file (see example/config.json)
-p PARTICIPANT, --participant PARTICIPANT
Participant ID
-o OUT_DIR, --out-dir OUT_DIR
Output BIDS directory
optional arguments:
-s SESSION, --session SESSION
Session ID
-l {DEBUG,INFO,WARNING,ERROR,CRITICAL}, --log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL}
Set logging level
```
## Motivation
This package offers a pluggable BIDS-ification workflow which attempts to mirror parts of the [`dcm2bids`](https://github.com/UNFmontreal/Dcm2Bids) CLI.
**One of the most important goals of this package is to support existing `dcm2bids` config files.**
A notable difference between `d2b` and `dcm2bids` is that the default assumption made by `d2b` is that you're **_NOT_** giving it DICOM data as input (although, if this is your use-case, there's a plugin to enable going straight from DICOM -> BIDS).
Out of the box, `d2b` assumes that you're working with NIfTI + NIfTI sidecar data.
The general premise of the `dcm2bids` workflow is very nice: _describe the files your interested in (in config) and the software will take the descriptions, find matching files, and organize those files accordingly_.
`d2b` (together with plugins powered by [`pluggy`](https://github.com/pytest-dev/pluggy)) tries to offer all functionality that `dcm2bids` offers, with an aim toward being _extensible_.
We wanted `dcm2bids` to do things that it was [never intended to do](https://github.com/UNFmontreal/Dcm2Bids/issues/100#issuecomment-733033859), hence `d2b` was born.
## `d2b` and `dcm2bids`
Similarities:
- **Config files used with `dcm2bids` are compatible with `d2b`**
- The `d2b run` command corresponds to `dcm2bids`
- The `d2b scaffold` command corresponds to `dcm2bids_scaffold`
Differences:
- `d2b` has a plugin system so that users can extend the core functionality to fit the needs of their specific use-case.
- The `d2b` code architecture is meant to make the BIDS dataset generation process less error prone.
- Out of the box, `d2b` doesn't try to convert DICOM files and in fact `dcm2niix` doesn't even need to be installed. To do DICOM -> BIDS conversions install the [`d2b-dcm2niix`](https://github.com/d2b-dev/d2b-dcm2niix) plugin
- Out of the box `defaceTpl` is no longer supported.
<!-- ## Config File Schema -->
## Writing config files
To make writing `d2b` config files easier, we've included a [JSON schema](https://json-schema.org/) specification file ([schema.json](https://github.com/d2b-dev/d2b/blob/master/json-schemas/schema.json)). You can use this file in editors that support JSON Schema definitions to provide autocompletion:
<!-- markdownlint-disable MD033 -->
<div style="display: flex; align-items: center; justify-content: space-between;">
<img src="https://raw.githubusercontent.com/d2b-dev/d2b/master/assets/autocomplete1.png" width="40%"/>
<img src="https://raw.githubusercontent.com/d2b-dev/d2b/master/assets/autocomplete2.png" width="40%"/>
</div>
<!-- markdownlint-enable MD033 -->
as well as validation while you edit your config files:
<!-- markdownlint-disable MD033 -->
<div style="display: flex; align-items: center; justify-content: space-between;">
<img src="https://raw.githubusercontent.com/d2b-dev/d2b/master/assets/validation.png" width="40%"/>
</div>
<!-- markdownlint-enable MD033 -->
For example, with vscode you might create/add to your `.vscode/settings.json` file in the workspace to include:
```text
{
// ... other settings ...
"json.schemas": [
{
"fileMatch": ["*d2b-config*.json"],
"url": "https://raw.githubusercontent.com/d2b-dev/d2b/master/json-schemas/schema.json"
}
]
}
```
Having this setting enabled would mean that any file matching `*d2b-config*.json` would be validated against the latest JSON schema in the [`d2b` repo](https://github.com/d2b-dev/d2b/blob/master/json-schemas/schema.json)
## The plugin system
`d2b` uses [`pluggy`](https://github.com/pytest-dev/pluggy) to faciliate the discorvery and integration of plugins, as such familiarity with the [pluggy documentation](https://pluggy.readthedocs.io/en/latest/) is helpful.
That said, here's a small example:
Let's write a plugin that adds the command `d2b hello <name>` to `d2b`.
The convention is to name the package implementing the plugin `d2b-[plugin-name]`, so we'll name our package `d2b-hello`.
Let's add the plugin implementation
`d2b-hello/d2b_hello.py`:
```python
from __future__ import annotations
import argparse
from d2b.hookspecs import hookimpl
@hookimpl
def register_commands(subparsers: argparse._SubParsersAction):
parser = subparsers.add_parser("hello")
parser.add_argument("name", help="Greet this person")
parser.add_argument("--shout", action="store_true", help="Shout it!")
parser.set_defaults(handler=handler)
def handler(args: argparse.Namespace):
name: str = args.name
shout: bool | None = args.shout
greeting = f"Hello, {name}!"
print(greeting.upper() if shout else greeting)
```
The script above is tapping into one of the various pluggable locations (hookspecs in pluggy speak) by providing and implementation (hookimpl) of one of the desired hookspecs (`register_commands`) exposed by `d2b`.
There are many spots in `d2b` which allow for a user to extend or change the core functionality. Check out the module [`hookspecs.py`](https://github.com/d2b-dev/d2b/blob/master/src/d2b/hookspecs.py) to see which hooks are available.
In the case above `register_commands` is one of the hookspecs defined by `d2b` enabling for plugins to add subcommands to the `d2b` CLI.
How do we tell `d2b` about our plugin?
To discover the plugin `d2b` (via `pluggy`) uses [entrypoints](https://pluggy.readthedocs.io/en/latest/#loading-setuptools-entry-points). So we'll add a basic `setup.py` module:
`d2b-hello/setup.py`:
```python
from setuptools import find_packages
from setuptools import setup
setup(
name="d2b-hello",
install_requires="d2b>=0.2.3,<1.0",
entry_points={"d2b": ["d2b-hello=d2b_hello"]},
packages=find_packages(),
)
```
And now we can install our plugin:
```bash
pip install -e ./d2b-hello/
```
After which we have:
```bash
$ d2b --help
usage: d2b [-h] [-v] {run,scaffold,hello} ...
d2b - Organize data in the BIDS format
positional arguments:
{run,scaffold,hello}
optional arguments:
-h, --help show this help message and exit
-v, --version show program's version number and exit
```
Our `d2b hello` subcommand is there!
```bash
$ d2b hello --help
usage: d2b hello [-h] [--shout] name
positional arguments:
name Greet this person
optional arguments:
-h, --help show this help message and exit
--shout Shout it!
```
And, trying it out:
```bash
$ d2b hello Andrew --shout
HELLO, ANDREW!
```
Success! 🏆
## Contributing
1. Have or install a recent version of `poetry` (version >= 1.1)
1. Fork the repo
1. Setup a virtual environment (however you prefer)
1. Run `poetry install`
1. Run `pre-commit install`
1. Add your changes (adding/updating tests is always nice too)
1. Commit your changes + push to your fork
1. Open a PR
نیازمندی
| مقدار | نام |
|---|---|
| >=0.12,<1.0.0a1 | pluggy |
زبان مورد نیاز
| مقدار | نام |
|---|---|
| >=3.8.0,<4.0 | Python |
نحوه نصب
نصب پکیج whl d2b-1.4.2rc0:
pip install d2b-1.4.2rc0.whl
نصب پکیج tar.gz d2b-1.4.2rc0:
pip install d2b-1.4.2rc0.tar.gz