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fsl, vbm and csv parsers

Project description

coinstacparsers

This package includes fsl_parser, vbm_parser and csv parser. fsl_parser parses the freesurfer files (specified in inputspec.json) as dependencies and returns the covariates (X) and dependent (y) matrices as dataframes. The format of inputspec.json should be as shown in the example inputspec.json here. Similarly vbm_parser parses NIfTI images as dependencies and returns the covariates (X) and dependent (y) matrices as dataframes. csv_parser reads the values specified in inputspec.json file and returns the covariates (X) and dependent (y) matrices as dataframes.

How to install

pip install coinstacparsers

How to run

for fsl parser:
     import coinstacparsers
     from coinstacparsers import parsers
     args = json.loads(sys.stdin.read())
     (X, y) = parsers.fsl_parser(args)
for vbm parser:
     import coinstacparsers
     from coinstacparsers import parsers
     args = json.loads(sys.stdin.read())
     mask = os.path.join('/computation', mask_directory, mask_file_name)
     (X, y) = parsers.vbm_parser(args, mask) for csv parser:
     import coinstacparsers
     from coinstacparsers import parsers
     args = json.loads(sys.stdin.read())
     (X, y) = parsers.csv_parser(args)

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