`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.convert`¶

Convert neuroimaging file to new parameters

main([args])

Main program function.

Module: `cmdline.dicomfs`¶

`DICOMFS`(args, *kwargs)
`FileHandle`(fno)
`dummy_fuse`()	Dummy fuse "module" so that nose does not blow during doctests
`fuse`	alias of `dummy_fuse`
`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.

main¶

nibabel.cmdline.convert.main(args=None)¶: Main program function.

`DICOMFS`¶

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

Bases: object

__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)¶

Bases: object

__init__(fno)¶

`dummy_fuse`¶

class nibabel.cmdline.dicomfs.dummy_fuse¶

Bases: object

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

__init__(*args, **kwargs)¶

Fuse¶: alias of object

fuse_python_api = (0, 2)¶

`fuse`¶

nibabel.cmdline.dicomfs.fuse¶: alias of dummy_fuse

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 targeting 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

NiBabel

Access a cacophony of neuro-imaging file formats

cmdline¶

Module: cmdline.conform¶

Module: cmdline.convert¶

Module: cmdline.dicomfs¶

Module: cmdline.diff¶

Module: cmdline.ls¶

Module: cmdline.nifti_dx¶

Module: cmdline.parrec2nii¶

Module: cmdline.roi¶

Module: cmdline.stats¶

Module: cmdline.tck2trk¶

Module: cmdline.trk2tck¶

Module: cmdline.utils¶

main¶

main¶

DICOMFS¶

FileHandle¶

dummy_fuse¶

fuse¶

get_opt_parser¶

main¶

are_values_different¶

diff¶

display_diff¶

get_data_diff¶

get_data_hash_diff¶

get_headers_diff¶

get_opt_parser¶

main¶

get_opt_parser¶

main¶

proc_file¶

main¶

error¶

get_opt_parser¶

main¶

proc_file¶

verbose¶

lossless_slice¶

main¶

parse_slice¶

sanitize¶

main¶

main¶

parse_args¶

main¶

parse_args¶

ap¶

safe_get¶

table2string¶

verbose¶

`cmdline`¶

Module: `cmdline.conform`¶

Module: `cmdline.convert`¶

Module: `cmdline.dicomfs`¶

Module: `cmdline.diff`¶

Module: `cmdline.ls`¶

Module: `cmdline.nifti_dx`¶

Module: `cmdline.parrec2nii`¶

Module: `cmdline.roi`¶

Module: `cmdline.stats`¶

Module: `cmdline.tck2trk`¶

Module: `cmdline.trk2tck`¶

Module: `cmdline.utils`¶

`DICOMFS`¶

`FileHandle`¶

`dummy_fuse`¶

`fuse`¶