fsl.scripts.atlasq
¶
This module contains the FSL atlasq
program, the successor to
atlasquery
.
-
exception
fsl.scripts.atlasq.
IdentifyError
¶ Bases:
Exception
Exception raised by the
identifyAtlas
when an atlas cannot be identified.
-
class
fsl.scripts.atlasq.
HelpFormatter
(prog, indent_increment=2, max_help_position=24, width=None)¶ Bases:
argparse.RawDescriptionHelpFormatter
A custom
argparse.HelpFormatter
class which customises a few annoying things about defaultargparse
behaviour.
-
fsl.scripts.atlasq.
listAtlases
(namespace)¶ List all available atlases.
-
fsl.scripts.atlasq.
summariseAtlas
(namespace)¶ Print information about one atlas.
-
fsl.scripts.atlasq.
queryAtlas
(namespace)¶ Query an atlas with coordinates or masks.
-
fsl.scripts.atlasq.
queryShortOutput
(atlas, sources, types, allLabels, allProps)¶ Called by
queryAtlas
when short output is requested.
-
fsl.scripts.atlasq.
queryLongOutput
(atlas, sources, types, allLabels, allProps)¶ Called by
queryAtlas
when long output is requested.
-
fsl.scripts.atlasq.
ohi
(namespace)¶ Emulates the FSL
atlasquery
tool.
-
fsl.scripts.atlasq.
atlasOrDesc
(aord, *args, **kwargs)¶ 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)¶ Converts the given sequence of
labels
into region names.
-
fsl.scripts.atlasq.
maskQuery
(atlas, masks, *args, **kwargs)¶ Queries the
atlas
at the givenmasks
.
-
fsl.scripts.atlasq.
coordQuery
(atlas, coords, voxel, *args, **kwargs)¶ Queries the
atlas
at the givencoords
.
-
fsl.scripts.atlasq.
identifyAtlas
(idOrName)¶ 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)¶ 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)¶ Parses command line arguments, returning an
argparse.Namespace
object.
-
fsl.scripts.atlasq.
main
(args=None)¶ Entry point for
atlasq
. Parses arguments, and runs the requested command.
-
fsl.scripts.atlasq.
atlasquery_emulation
(args=None)¶ Entry point for
atlasquery
. Runs asatlasq
inohi
mode.