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Package bar :: Module mbatParser :: Class barMBATParser
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Class barMBATParser

Generic parser for MBAT atlases (http://mbat.loni.ucla.edu/). Parser requires volumetric file and MBAT atlas file.

Change Log: Thu Mar 17 12:58:22 CET 2011. Initial version

Instance Methods [hide private]
None
__init__(self, inputAtlasFile, outputDirectory, **kwargs)
Returns: None
None
__loadAtlasFile(self)
Loads MBAT atlas file and extracts volumetric dataset and hierarchy filename.
None
_defineSlideRange(self)
Generates self.slideRange attribute.
None
__loadVolume(self, volumeFilename)
Loads volumetric dataset, store header and volume data
None
__extractHierarchy(self, hierarchyFilename)
Extracts fullname mapping, color mapping and hierarchy and stores them as instance attribuutes.
barTracedSlideRenderer
parse(self, slideNumber, generateLabels=True, useIndexer=False, writeSlide=True)
Returns: Traced slide with given slideNumber.
None
reindex(self)
Returns: None
None
parseAll(self)
Performs tracing of all slides enumerated in self.slideRange.
PIL image
_getSourceImage(self, slideNumber)
Returns: raw bitmap with slide slideNumber
PIL image
_createMask(self, image, colorValue)
Returns: Black and white image with structure mask.
(float, float, float, float)
_getIndexerRefMatrix(self)
Returns reference matrix stored in index file.
str
_getNewPathID(self, structName=None)
Returns: path id

Inherited from parsers.barBitmapParser (private): _getPath, _getSlide, _getSpatialTransfMatrix, _getUniqeColours, _getZCoord, _parseTracerOutput, _processStructure

Inherited from parsers.barGenericParser: RGBToHTMLColor, getProperty, parseRange, setProperty, writeIndex

Inherited from parsers.barGenericParser (private): _getIndexFilename, _getOutputFilename, _performTracing, _validateInternalData

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Class Variables [hide private]
list _requiredInternalData = ['outputDirectory', 'filenameTemplates...
Required instance attributtes.
Instance Variables [hide private]
int _pathNumber
internal path number iterator.
niftii volume _volume
Dataset containing labelled brain volume

Inherited from parsers.barBitmapParser: imageToStructure, structureColours

Inherited from parsers.barGenericParser: filenameTemplates, outputDirectory, renderingProperties, slideRange, tracingProperties

Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

__init__(self, inputAtlasFile, outputDirectory, **kwargs)
(Constructor)

 

x.__init__(...) initializes x; see x.__class__.__doc__ for signature

Parameters:
  • inputAtlasFile (str) - location of mbat atlas file (.atlas)
  • outputDirectory (str) - directory, where resulting caf will be stored
Returns: None
None
Overrides: object.__init__

__loadAtlasFile(self)

 

Loads MBAT atlas file and extracts volumetric dataset and hierarchy filename.

Returns: None
None

_defineSlideRange(self)

 

Generates self.slideRange attribute.

Returns: None
None

__loadVolume(self, volumeFilename)

 

Loads volumetric dataset, store header and volume data

Parameters:
  • volumeFilename (str) - full location of volumetric dataset
Returns: None
None

__extractHierarchy(self, hierarchyFilename)

 

Extracts fullname mapping, color mapping and hierarchy and stores them as instance attribuutes.

Parameters:
  • volumeFilename (str) - full location of volumetric dataset
Returns: None
None

parse(self, slideNumber, generateLabels=True, useIndexer=False, writeSlide=True)

 
Parameters:
  • slideNumber - Number of slide to parse
Returns: barTracedSlideRenderer
Traced slide with given slideNumber.

Performs all operation related to creating CAF slide from souce data. Should be customized in each parser.

Overrides: parsers.barGenericParser.parse
(inherited documentation)

reindex(self)

 
Returns: None
None

Reindexes all slides in self.slideRange. This option is useful when consecutive slides were not indexed during tracing procedure.

Overrides: parsers.barGenericParser.reindex
(inherited documentation)

parseAll(self)

 

Performs tracing of all slides enumerated in self.slideRange. Should be customized in each parser. Has the same effect as parseRange(slideRange[0],slideRange[-1]).

Returns: None
None
Overrides: parsers.barGenericParser.parseAll
(inherited documentation)

_getSourceImage(self, slideNumber)

 
Parameters:
  • slideNumber - number of slide to process.
Returns: PIL image
raw bitmap with slide slideNumber
Overrides: parsers.barBitmapParser._getSourceImage
(inherited documentation)

_createMask(self, image, colorValue)

 
Parameters:
  • image - Image basing on which mask will be created.
  • colorValue - Colour in '#%x%x%x' format
Returns: PIL image
Black and white image with structure mask.
Overrides: parsers.barBitmapParser._createMask
(inherited documentation)

_getIndexerRefMatrix(self)

 

Returns reference matrix stored in index file.

Returns: (float, float, float, float)
None

_getNewPathID(self, structName=None)

 
Parameters:
  • structName - Name of the structure that will be represented by given path.
Returns: str
path id
Overrides: parsers.barBitmapParser._getNewPathID
(inherited documentation)

Class Variable Details [hide private]

_requiredInternalData

Required instance attributtes. Without prividing them parsing cannot be invoked. Meaning of each attribute is explained below.
Type:
list
Value:
['outputDirectory',
 'filenameTemplates',
 'slideRange',
 'tracingProperties',
 'renderingProperties',
 'imageToStructure',
 'structureColours',
 'backgroundColor',
...

Instance Variable Details [hide private]

_pathNumber

internal path number iterator. Required for correct path parsing
Type:
int

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