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Description:

compiledcm2bidsconfig 1.4.3

compile-dcm2bids-config
Combine dcm2bids and d2b config files into a single config file while preserving the integrity of each separate config file's various IntendedFor fields.

Installation
For the basic functionality:
pip install compile-dcm2bids-config

If you have config files written in YAML you can install the yaml extra, for example:
pip install 'compile-dcm2bids-config[yaml]'

Usage
$ compile-dcm2bids-config --help
usage: compile-dcm2bids-config [-h] [-o OUT_FILE] [-v] in_file [in_file ...]

Combine multiple dcm2bids config files into a single config file.

positional arguments:
in_file The JSON config files to combine

optional arguments:
-h, --help show this help message and exit
-o OUT_FILE, --out-file OUT_FILE
The file to write the combined config file to. If not specified
outputs are written to stdout.
-v, --version show program's version number and exit

Getting Started
Suppose you have two config files:
example/config1.json:
{
"descriptions": [
{
"dataType": "anat",
"modalityLabel": "SWI",
"criteria": {
"SeriesDescription": "*SWI*"
}
},
{
"dataType": "fmap",
"modalityLabel": "fmap",
"criteria": {
"SidecarFilename": "*echo-4*"
},
"IntendedFor": 0
}
]
}

example/config2.json:
{
"descriptions": [
{
"dataType": "dwi",
"modalityLabel": "dwi",
"criteria": {
"SeriesDescription": "*DWI*"
}
},
{
"dataType": "anat",
"modalityLabel": "SWI",
"criteria": {
"SeriesDescription": "*SWI*"
}
},
{
"id": "my-func",
"dataType": "func",
"modalityLabel": "bold",
"customLabels": "task-rest",
"criteria": {
"SeriesDescription": "rs_fMRI"
},
"sidecarChanges": {
"SeriesDescription": "rsfMRI"
}
},
{
"dataType": "fmap",
"modalityLabel": "fmap",
"criteria": {
"SidecarFilename": "*echo-3*"
},
"IntendedFor": [0, "my-func"]
}
]
}

Then we can combine the two using the following command (outputs are written to stdout by default):
$ compile-dcm2bids-config example/config1.json example/config2.json
{
"descriptions": [
{
"dataType": "anat",
"modalityLabel": "SWI",
"criteria": {
"SeriesDescription": "*SWI*"
}
},
{
"dataType": "fmap",
"modalityLabel": "fmap",
"criteria": {
"SidecarFilename": "*echo-4*"
},
"IntendedFor": 0
},
{
"dataType": "dwi",
"modalityLabel": "dwi",
"criteria": {
"SeriesDescription": "*DWI*"
}
},
{
"dataType": "anat",
"modalityLabel": "SWI",
"criteria": {
"SeriesDescription": "*SWI*"
}
},
{
"id": "my-func",
"dataType": "func",
"modalityLabel": "bold",
"customLabels": "task-rest",
"criteria": {
"SeriesDescription": "rs_fMRI"
},
"sidecarChanges": {
"SeriesDescription": "rsfMRI"
}
},
{
"dataType": "fmap",
"modalityLabel": "fmap",
"criteria": {
"SidecarFilename": "*echo-3*"
},
"IntendedFor": [
2,
"my-func"
]
}
]
}

Notice that the IntendedFor fields have been updated appropriately.
Python API
You can also use this tool from within python:
import json
from pathlib import Path
from pprint import pp

from compile_dcm2bids_config import combine_config

config1 = json.loads(Path("example/config1.json").read_text())
config2 = json.loads(Path("example/config2.json").read_text())

all_together = combine_config([config1, config2])

pp(all_together)

The result being:
{'descriptions': [{'dataType': 'anat',
'modalityLabel': 'SWI',
'criteria': {'SeriesDescription': '*SWI*'}},
{'dataType': 'fmap',
'modalityLabel': 'fmap',
'criteria': {'SidecarFilename': '*echo-4*'},
'IntendedFor': 0},
{'dataType': 'dwi',
'modalityLabel': 'dwi',
'criteria': {'SeriesDescription': '*DWI*'}},
{'dataType': 'anat',
'modalityLabel': 'SWI',
'criteria': {'SeriesDescription': '*SWI*'}},
{'id': 'my-func',
'dataType': 'func',
'modalityLabel': 'bold',
'customLabels': 'task-rest',
'criteria': {'SeriesDescription': 'rs_fMRI'},
'sidecarChanges': {'SeriesDescription': 'rsfMRI'}},
{'dataType': 'fmap',
'modalityLabel': 'fmap',
'criteria': {'SidecarFilename': '*echo-3*'},
'IntendedFor': [2, 'my-func']}]}

YAML Configuration Files
This package can handle dcm2bids (or d2b) configuration files written in YAML, the user just has to install the PyYAML package, either separately:
pip install pyyaml

or all at once via the installation "extra":
pip install 'compile-dcm2bids-config[yaml]'

If PyYAML is available, then configuration files ending with .yml or .yaml can be passed as input files:
compile-dcm2bids-config config1.json config2.yaml > combined.json

The combined configuration file can also be formatted as YAML by adding the --to-yaml flag:
compile-dcm2bids-config --to-yaml config1.json config2.yaml > combined.yaml

Contributing

Have or install a recent version of poetry (version >= 1.1)
Fork the repo
Setup a virtual environment (however you prefer)
Run poetry install
Run pre-commit install
Add your changes (adding/updating tests is always nice too)
Commit your changes + push to your fork
Open a PR