cmdline

Functionality to be exposed in the command line

Module: cmdline.dicomfs

DICOMFS(*args, **kwargs)
FileHandle(fno)
dummy_fuse Dummy fuse “module” so that nose does not blow during doctests
get_opt_parser()
main([args])

Module: cmdline.ls

Output a summary table for neuroimaging files (resolution, dimensionality, etc.)

get_opt_parser()
main([args]) Show must go on
proc_file(f, opts)

Module: cmdline.nifti_dx

Print nifti diagnostics for header files

main([args]) Go go team

Module: cmdline.parrec2nii

Code for PAR/REC to NIfTI converter command

error(msg, exit_code)
get_opt_parser()
main()
proc_file(infile, opts)
verbose(msg[, indent])

Module: cmdline.tck2trk

Convert tractograms (TCK -> TRK).

main()
parse_args()

Module: cmdline.trk2tck

Convert tractograms (TRK -> TCK).

main()
parse_args()

Module: cmdline.utils

Helper utilities to be used in cmdline applications

ap(helplist, format_[, sep]) Little helper to enforce consistency
safe_get(obj, name) A getattr which would return ‘-‘ if getattr fails
table2string(table[, out]) Given list of lists figure out their common widths and print to out
verbose(thing, msg) Print s if thing is less than the verbose_level

DICOMFS

class nibabel.cmdline.dicomfs.DICOMFS(*args, **kwargs)

Bases: fuse.Fuse

__init__(*args, **kwargs)
get_paths()
getattr(path)
match_path(path)
open(path, flags)
read(path, size, offset, fh)
readdir(path, fh)
release(path, flags, fh)

FileHandle

class nibabel.cmdline.dicomfs.FileHandle(fno)
__init__(fno)

dummy_fuse

class nibabel.cmdline.dicomfs.dummy_fuse

Bases: object

Dummy fuse “module” so that nose does not blow during doctests

__init__()

x.__init__(...) initializes x; see help(type(x)) for signature

Fuse

alias of object

get_opt_parser

nibabel.cmdline.dicomfs.get_opt_parser()

main

nibabel.cmdline.dicomfs.main(args=None)

get_opt_parser

nibabel.cmdline.ls.get_opt_parser()

main

nibabel.cmdline.ls.main(args=None)

Show must go on

proc_file

nibabel.cmdline.ls.proc_file(f, opts)

main

nibabel.cmdline.nifti_dx.main(args=None)

Go go team

error

nibabel.cmdline.parrec2nii.error(msg, exit_code)

get_opt_parser

nibabel.cmdline.parrec2nii.get_opt_parser()

main

nibabel.cmdline.parrec2nii.main()

proc_file

nibabel.cmdline.parrec2nii.proc_file(infile, opts)

verbose

nibabel.cmdline.parrec2nii.verbose(msg, indent=0)

main

nibabel.cmdline.tck2trk.main()

parse_args

nibabel.cmdline.tck2trk.parse_args()

main

nibabel.cmdline.trk2tck.main()

parse_args

nibabel.cmdline.trk2tck.parse_args()

ap

nibabel.cmdline.utils.ap(helplist, format_, sep=', ')

Little helper to enforce consistency

safe_get

nibabel.cmdline.utils.safe_get(obj, name)

A getattr which would return ‘-‘ if getattr fails

table2string

nibabel.cmdline.utils.table2string(table, out=None)

Given list of lists figure out their common widths and print to out

Parameters:

table : list of lists of strings

What is aimed to be printed

out : None or stream

Where to print. If None – will print and return string

Returns:

string if out was None

verbose

nibabel.cmdline.utils.verbose(thing, msg)

Print s if thing is less than the verbose_level