Purpose of the script below is to prepare input data for the Allen
Brain Atlas 2011 volumetric dataset. Two partial datasets are processed.
The first one is the labelled volume containing volume element to
structure's name assignment. This volume is provided by Allen Institute
in form of raw binary file and one needs to figure out what are the voxel
dimensions and volume origin. Volume is processed by preprocessVolume
function.
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{str : barAllenApiAtlas, ... }
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_updateAvailableAtlases(self)
This method downloads and parses summary of atlases available trought
Allen Brain Institute API. |
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None
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_downloadAtlas(self)
Download source data for currently processed atlas. |
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None
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processAtlas(self,
atlasId,
spaceName,
fetchSourceData=True)
Returns:
None |
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_getSourceDatasetZipfileName(self) |
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_getZipOutputZipfilename(self) |
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_getAnnotationsFilename(self) |
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_getOntologyFilename(self) |
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str
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_getHierarchyFilename(self) |
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_getMappingsFilename(self) |
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processVolume(self,
applyPermutation=( 0, 1, 2) ,
reverseAxes=( False, False, False) ,
dataType=<type 'numpy.uint16'>,
reshapePermutation=( 0, 1, 2) ,
headerUpdate={ } ,
qfac=1)
@type applyPermutation: (int, int, int)
@param applyPermutation: Permutation of the axis' order. |
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numpy volume
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_loadRawAnnotationFile(self,
dataType=<type 'numpy.uint16'>,
reshapePermutation=( 0, 1, 2) )
Returns:
NumPy volume created ba parsing raw annotation file. |
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None
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_assignHeaderInformation(self,
niftiImage,
applyPermutation=( 0, 1, 2) ,
reshapePermutation=( 0, 1, 2) ,
headerDict={ } ,
qfac=1)
Returns:
None |
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_processOntology(self)
Extract and process structure ontology information from source dataset. |
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(str, str)
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cleanup(self)
Remove atals package and extracted files of currently processed
atlas. |
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