cmdline

Functionality to be exposed in the command line

Module: cmdline.conform

Conform neuroimaging volume to arbitrary shape and voxel size.

main([args])

Main program function.

Module: cmdline.dicomfs

DICOMFS(*args, **kwargs)

Not much happens here apart from initializing the parser attribute.

FileHandle(fno)

dummy_fuse()

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

get_opt_parser()

main([args])

Module: cmdline.diff

Quick summary of the differences among a set of neuroimaging files

Notes:
  • difference in data types for header fields will be detected, but endianness difference will not be detected. It is done so to compare files with native endianness used in data files.

are_values_different(*values)

Generically compare values, return True if different

diff(files[, header_fields, …])

display_diff(files, diff)

Format header differences into a nice string

get_data_diff(files[, max_abs, max_rel, dtype])

Get difference between data

get_data_hash_diff(files[, dtype])

Get difference between md5 values of data

get_headers_diff(file_headers[, names])

Get difference between headers

get_opt_parser()

main([args, out])

Getting the show on the road

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.roi

lossless_slice(img, slicers)

main([args])

parse_slice(crop[, allow_step])

sanitize(args)

Module: cmdline.stats

Compute image statistics

main([args])

Main program function.

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

main

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

Main program function.

DICOMFS

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

Bases: fuse.Fuse

Not much happens here apart from initializing the parser attribute. Arguments are forwarded to the constructor of the parser class almost unchanged.

The parser class is FuseOptParse unless you specify one using the parser_class keyword. (See FuseOptParse documentation for available options.)

__init__(*args, **kwargs)

Not much happens here apart from initializing the parser attribute. Arguments are forwarded to the constructor of the parser class almost unchanged.

The parser class is FuseOptParse unless you specify one using the parser_class keyword. (See FuseOptParse documentation for available options.)

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)

Bases: object

__init__(fno)

Initialize self. See help(type(self)) for accurate signature.

dummy_fuse

class nibabel.cmdline.dicomfs.dummy_fuse

Bases: object

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

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

Fuse

alias of builtins.object

get_opt_parser

nibabel.cmdline.dicomfs.get_opt_parser()

main

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

are_values_different

nibabel.cmdline.diff.are_values_different(*values)

Generically compare values, return True if different

Note that comparison is targetting reporting of comparison of the headers so has following specifics: - even a difference in data types is considered a difference, i.e. 1 != 1.0 - nans are considered to be the “same”, although generally nan != nan

diff

nibabel.cmdline.diff.diff(files, header_fields='all', data_max_abs_diff=None, data_max_rel_diff=None, dtype=<class 'numpy.float64'>)

display_diff

nibabel.cmdline.diff.display_diff(files, diff)

Format header differences into a nice string

Parameters
files: list of files that were compared so we can print their names
diff: dict of different valued header fields
Returns
str

string-formatted table of differences

get_data_diff

nibabel.cmdline.diff.get_data_diff(files, max_abs=0, max_rel=0, dtype=<class 'numpy.float64'>)

Get difference between data

Parameters
files: list of (str or ndarray)

If list of strings is provided – they must be existing file names

max_abs: float, optional

Maximal absolute difference to tolerate.

max_rel: float, optional

Maximal relative (abs(diff)/mean(diff)) difference to tolerate. If max_abs is specified, then those data points with lesser than that absolute difference, are not considered for relative difference testing

dtype: np, optional

Datatype to be used when extracting data from files

Returns
diffs: OrderedDict

An ordered dict with a record per each file which has differences with other files subsequent detected. Each record is a list of difference records, one per each file pair. Each difference record is an Ordered Dict with possible keys ‘abs’ or ‘rel’ showing maximal absolute or relative differences in the file or the record (‘CMP’: ‘incompat’) if file shapes are incompatible.

get_data_hash_diff

nibabel.cmdline.diff.get_data_hash_diff(files, dtype=<class 'numpy.float64'>)

Get difference between md5 values of data

Parameters
files: list of actual files
Returns
list

np.array: md5 values of respective files

get_headers_diff

nibabel.cmdline.diff.get_headers_diff(file_headers, names=None)

Get difference between headers

Parameters
file_headers: list of actual headers (dicts) from files
names: list of header fields to test
Returns
dict

str: list for each header field which differs, return list of values per each file

get_opt_parser

nibabel.cmdline.diff.get_opt_parser()

main

nibabel.cmdline.diff.main(args=None, out=None)

Getting the show on the road

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)

lossless_slice

nibabel.cmdline.roi.lossless_slice(img, slicers)

main

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

parse_slice

nibabel.cmdline.roi.parse_slice(crop, allow_step=True)

sanitize

nibabel.cmdline.roi.sanitize(args)

main

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

Main program function.

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
tablelist of lists of strings

What is aimed to be printed

outNone 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