rtCommon.openNeuro
An interface to access OpenNeuro data and metadata. It can download and cache OpenNeuro data for playback.
Module Contents
Classes
- class rtCommon.openNeuro.OpenNeuroCache(cachePath='/tmp/openneuro/')
- getCachePath()
- getS3Client()
Returns an s3 client in order to reuse the same s3 client without always creating a new one. Not thread safe currently.
- getDatasetList(refresh=False)
Returns a list of all datasets available in OpenNeuro S3 storage. See https://openneuro.org/public/datasets for datasets info. Alternate method to access from a command line call: [aws s3 –no-sign-request ls s3://openneuro.org/]
- isValidAccessionNumber(dsAccessionNum)
- getSubjectList(dsAccessionNum)
Returns a list of all the subjects in a dataset
- Parameters:
dsAccessionNum – accession number of dataset to lookup
- Returns:
list of subjects in that dataset
- getDescription(dsAccessionNum)
Returns the dataset description file as a python dictionary
- getReadme(dsAccessionNum)
Return the contents of the dataset README file. Downloads toplevel dataset files if needed.
- getArchivePath(dsAccessionNum)
Returns the directory path to the cached dataset files
- downloadData(dsAccessionNum, downloadWholeDataset=False, **entities)
This command will sync the specified portion of the dataset to the cache directory. Note: if only the accessionNum is supplied then it will just sync the top-level files. Sync doesn’t re-download files that are already present in the directory. Consider using –delete which removes local cache files no longer on the remote.
- Parameters:
dsAccessionNum – accession number of the dataset to download data for.
downloadWholeDataset – boolean, if true all files in the dataset will be downloaded.
entities – BIDS entities (subject, session, task, run, suffix) that define the particular subject/run of the data to download.
- Returns:
Path to the directory containing the downloaded dataset data.