Created
November 1, 2018 17:00
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Recursively convert rpy2 objects to nested Python data structures.
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| #!/usr/bin/env python3 | |
| """ | |
| Recursively convert rpy2 objects to nested Python data structures. | |
| """ | |
| import numpy as np | |
| from rpy2.robjects import default_converter, globalenv, \ | |
| NULL, numpy2ri, pandas2ri, ListVector, r | |
| def scalarize(x): | |
| if not np.isscalar(x) and len(x) == 1: | |
| return np.asscalar(x) | |
| else: | |
| return x | |
| converter = default_converter+numpy2ri.converter+pandas2ri.converter | |
| def convert(ri): | |
| """ | |
| Recursively convert rpy2 object to nested Python object. | |
| Objects containing R code (typeof(x) == 'language') are filtered out. | |
| Objects containing R lists with no string tags are converted to Python | |
| lists. | |
| """ | |
| if isinstance(ri, ListVector): | |
| if ri.names == NULL: | |
| result = [convert(tmp[1]) for tmp in ri.items()] | |
| else: | |
| result = {} | |
| for name in ri.names: | |
| globalenv['tmp'] = ri.rx2(name) | |
| if r('typeof(tmp)')[0] != 'language': | |
| result[name] = convert(ri.rx2(name)) | |
| return result | |
| else: | |
| return scalarize(converter.ri2py(ri)) |
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