fsl.scripts.atlasq
¶
This module contains the FSL atlasq
program, the successor to
atlasquery
.
-
exception
fsl.scripts.atlasq.
IdentifyError
[source]¶ Bases:
Exception
Exception raised by the
identifyAtlas
when an atlas cannot be identified.-
__module__
= 'fsl.scripts.atlasq'¶
-
__weakref__
¶ list of weak references to the object (if defined)
-
-
class
fsl.scripts.atlasq.
HelpFormatter
(prog, indent_increment=2, max_help_position=24, width=None)[source]¶ Bases:
argparse.RawDescriptionHelpFormatter
A custom
argparse.HelpFormatter
class which customises a few annoying things about defaultargparse
behaviour.-
__module__
= 'fsl.scripts.atlasq'¶
-
-
fsl.scripts.atlasq.
queryShortOutput
(atlas, sources, types, allLabels, allProps)[source]¶ Called by
queryAtlas
when short output is requested.
-
fsl.scripts.atlasq.
queryLongOutput
(atlas, sources, types, allLabels, allProps)[source]¶ Called by
queryAtlas
when long output is requested.
-
fsl.scripts.atlasq.
atlasOrDesc
(aord, *args, **kwargs)[source]¶ If
aord
is anAtlas
it is returned. Otherwise it is assumed to be anAtlasDescription
, in which case the correspondingAtlas
is loaded and returned.
-
fsl.scripts.atlasq.
labelNames
(atlas, labels)[source]¶ Converts the given sequence of
labels
into region names.
-
fsl.scripts.atlasq.
maskQuery
(atlas, masks, *args, **kwargs)[source]¶ Queries the
atlas
at the givenmasks
.
-
fsl.scripts.atlasq.
coordQuery
(atlas, coords, voxel, *args, **kwargs)[source]¶ Queries the
atlas
at the givencoords
.
-
fsl.scripts.atlasq.
identifyAtlas
(idOrName)[source]¶ Given a partial atlas ID or name, tries to find an atlas which uniquely matches it.
-
fsl.scripts.atlasq.
printColumns
(columns, titles=None, delim=' | ', sep=True, strip=False)[source]¶ Convenience function which pretty-prints a collection of columns in a tabular format.
Parameters: - columns – A sequence of columns, where each column is a list of strings.
- titles – A sequence of titles, one for each column.
-
fsl.scripts.atlasq.
parseArgs
(args)[source]¶ Parses command line arguments, returning an
argparse.Namespace
object.