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WIP: adding Philips XML/REC support #683

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WIP: adding Philips XML/REC support #683

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Commits on Oct 18, 2018

  1. add Philips XML/REC reader. 

    Philips now encourages the XML-style headers over the older PAR
format. This initial implementation reads the XML file, converting
each field to its PAR file equivalent and then inherits from the
PARRECHeader and PARRECImage to avoid excessive code duplication.
    @grlee77
    grlee77 committed Oct 18, 2018
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  2. add XMLRECImage support to imageclasses.py

    @grlee77
    grlee77 committed Oct 18, 2018
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Commits on Oct 19, 2018

  1. Assign an enumerated value of -1 in the PAR image_defs header for unr… 

    …ecognized enum strings.

add an error message with a hint regarding truncated XML files
    @grlee77
    grlee77 committed Oct 19, 2018
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  2. expand enums_dict using empirically determined values

    @grlee77
    grlee77 committed Oct 19, 2018
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  3. Fix reading strings into image_defs when dtype_format='xml'

    @grlee77
    grlee77 committed Oct 19, 2018
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  4. XMLRECImage: file extensions should be specified in lower case

    @grlee77
    grlee77 committed Oct 19, 2018
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  5. loading from .REC: special case to find .xml when .PAR not present

    @grlee77
    grlee77 committed Oct 19, 2018
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  6. remove explicit mention of PAR from warning/errors that could also oc… 

    …cur for XML/REC
    @grlee77
    grlee77 committed Oct 19, 2018
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  7. Add XML/REC support to parrec2nii.py 

    Add an xmlrec2nii command line script. This currently is identical to parrec2nii because the underlying
function now supports both formats.
    @grlee77
    grlee77 committed Oct 19, 2018
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  8. refactor/simplify. Do not convert to PAR/REC style names

    @grlee77
    grlee77 committed Oct 19, 2018
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  9. remove permit_truncated restriction

    @grlee77
    grlee77 committed Oct 19, 2018
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  10. minor cleanup

    @grlee77
    grlee77 committed Oct 19, 2018
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Commits on Oct 22, 2018

  1. XMLRECImage: fix for .REC expected case mismatch

    @grlee77
    grlee77 committed Oct 22, 2018
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  2. fix misnamed key within strict_sort

    @grlee77
    grlee77 committed Oct 22, 2018
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  3. fix for conversion of DWI scans where only the trace was retained

    @grlee77
    grlee77 committed Oct 22, 2018
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  4. fix bug in conversion of Boolean entries from string such as 'N' and 'Y' 

    prior to this commit, both would get stored as true because bool('N') == True
    @grlee77
    grlee77 committed Oct 22, 2018
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