dwifslpreproc: Handle non-ascii data in eddy error outputs #2313
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The FSL eddy commands sometimes contain a small block of binary data at the end of their outputs. If, when attempting to write those data to a text file in the scratchh directory, an encoding operation occurs, such data may yield a UnicodeEncodeError. This commit changes the output text files to be opened in binary mode, so such an encoding should no longer be applied.
jdtournier
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- On EddyQC failure, write text file containing stdout / stderr contents in binary mode, just as is done for eddy (#2313). - For EddyQC exports, deal with prospect of whitespace in output directory path.
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The FSL
eddycommands sometimes contain a small block of binary data at the end of their outputs. If, when attempting to write those data to a text file in the scratch directory, an encoding operation occurs, such data may yield aUnicodeEncodeError. This commit changes the output text files to be opened in binary mode, so such an encoding should no longer be applied.(Note that
__str__()is defined forMRtrixCmdErroras a straight concatenation ofstdoutandstderrcontents, so there shouldn't be anyasciiconversion happening there)