Package bar :: Module barAllenApiAtlasPreprocessor

Module barAllenApiAtlasPreprocessor

Classes

barAllenApiAtlasPreprocessor
Class barAllenApiAtlasPreprocessor

Functions

str

cleanStructName(structName)
Provided acronyms are usually fine but sometimes they are not compatibile with 3dBar naming convention.

Variables

[hide private]

BAR_CONF_ALLEN_API_ATLASES_INDEX = 'http://www.brain-map.org/B...

BAR_CONF_ALLEN_API_ATLAS_INFO = 'Info.xml'

BAR_CONF_ALLEN_API_ATLAS_ANNOTATION = 'Annotation'

BAR_CONF_ALLEN_API_ATLAS_ONTOLOGY = 'ontology.csv'

BAR_CONF_ALLEN_API_HIERARCHY_FILANEME = 'parents.txt'

BAR_CONF_ALLEN_API_SPACES_DIRNAME = 'Spaces'

BAR_CONF_ALLEN_API_MAPPING_FILENAME = 'mappings.txt'

BAR_CONF_ALLEN_API_VOL_RES_MULTIPLIER = 0.001

__package__ = 'bar'

Function Details

[hide private]

cleanStructName(structName)

Provided acronyms are usually fine but sometimes they are not compatibile with 3dBar naming convention. Here we process them so they can pass 3dBAR name validataion.

Parameters:

structName (str) - initial sturcture name, potentially invalid

Returns: str

structure name transformed in the way that passes 3dBAR name validation

To Do: this function should be a part of the base.py module

Variables Details

[hide private]

BAR_CONF_ALLEN_API_ATLASES_INDEX

Value:

'http://www.brain-map.org/BrainExplorer2/atlases.xml'