AtlasCreator::AtlasCreatorLogic::AtlasCreatorLogic Class Reference

Inheritance diagram for AtlasCreator::AtlasCreatorLogic::AtlasCreatorLogic:
object

List of all members.

Public Member Functions

def __init__
def CombineToAtlas
def ComputeMeanImage
def Destructor
def EnableDryrunMode
def Helper
def PerformPCAAnalysis
def Register
def Resample
def Start

Private Attributes

 __dryRun
 __parentClass
 _parentClass

Detailed Description

    The logic class for the Atlas Creator
    
    In this class, all files are passed as lists of filepaths to enable possible parallelized
    computation in a grid environment 
==========================================================================================

Member Function Documentation

def AtlasCreator::AtlasCreatorLogic::AtlasCreatorLogic::__init__ (   self,
  parentClass 
)
    Initialize this class
    
    parentClass
a pointer to the parentClass

    Returns
n/a
def AtlasCreator::AtlasCreatorLogic::AtlasCreatorLogic::CombineToAtlas (   self,
  schedulerCommand,
  filePathsList,
  labelsList,
  reCastString,
  normalizeTo,
  outputAtlasDirectory,
  outputScriptsDirectory,
  outputNotifyDirectory,
  sleepValue = 5 
)
    Combine segmentations to an Atlas based on labels. For each label an Atlas gets created. Additionally,
    a combined Atlas is generated. All output is saved.
    
    schedulerCommand
the schedulerCommand if used else ""            
    filePathsList
list of existing filepaths to segmentations
    labelsList
list of labels to analyze and build Atlases for
    reCastString
re-Cast the Atlases to a certain type defined as a String
"Char"
"Unsigned Char"
"Double"
"Float"
"Int"
"Unsigned Int"
"Long"
"Unsigned Long"
"Short"
"Unsigned Short"
other values will result in "Short"
    normalizeTo
flag to enable the normalization of Atlas values
-1: disable
any other: upper value for normalization
    outputAtlasDirectory
directory to save the Atlases
    outputScriptsDirectory
directory to use for generated scripts
    outputNotifyDirectory
directory to use for notification files                    
    sleepValue
seconds to wait between each check on completed jobs
                
    Returns
TRUE or FALSE depending on success
def AtlasCreator::AtlasCreatorLogic::AtlasCreatorLogic::ComputeMeanImage (   self,
  schedulerCommand,
  filePathsList,
  outputFilePath,
  outputScriptsDirectory,
  outputNotifyDirectory,
  sleepValue = 5 
)
    Get the mean image of a set of images and save it

    schedulerCommand
the schedulerCommand if used else ""            
    filePathsList
list of file paths to the images
    outputFilePath
the filePath where the meanImage gets stored
    outputScriptsDirectory
directory to use for generated scripts
    outputNotifyDirectory
directory to use for notification files
    sleepValue
seconds to wait between each check on completed jobs                           

    Returns
TRUE or FALSE depending on Success
def AtlasCreator::AtlasCreatorLogic::AtlasCreatorLogic::Destructor (   self  ) 
    Destruct this class
    
    Returns
n/a
def AtlasCreator::AtlasCreatorLogic::AtlasCreatorLogic::EnableDryrunMode (   self  ) 
    Enables the dryrun Mode
    
    Returns
n/a
def AtlasCreator::AtlasCreatorLogic::AtlasCreatorLogic::Helper (   self  ) 
    Return the helper
    
    Returns
the helper
def AtlasCreator::AtlasCreatorLogic::AtlasCreatorLogic::PerformPCAAnalysis (   self,
  labelsList,
  filePathsList,
  outputDirectory,
  maxEigenVectors,
  combine 
)
    Performs PCA Analysis on top of the Atlas Generation.
    
    labelsList
list of labels to perform PCA analysis for
    filePathsList
list of existing filepaths to segmentations
    outputDirectory
directory to write the PCA analysis, trailing slash is required
    maxEigenVectors
number of max EigenVectors to use for PCA as integer
    combine
TRUE if all structures should be combined or FALSE

    Returns
TRUE or FALSE depending on success
def AtlasCreator::AtlasCreatorLogic::AtlasCreatorLogic::Register (   self,
  schedulerCommand,
  filePathsList,
  templateFilePath,
  outputTransformsDirectory,
  outputAlignedDirectory,
  outputScriptsDirectory,
  outputNotifyDirectory,
  registrationType,
  multiThreading,
  useCMTK = False,
  sleepValue = 5 
)
    Register a set of images, get a transformation and save it
    
    schedulerCommand
the schedulerCommand if used else ""
    filePathsList
list of existing filepaths to images
    templateFilePath
file path to the template
    outputTransformsDirectory
directory to save the generated transformation
    outputAlignedDirectory
directory to save the aligned images
    outputScriptsDirectory
directory to use for generated scripts
    outputNotifyDirectory
directory to use for notification files
    registrationType
type of registration as String, could be "affine" and "non-rigid"
if the value is invalid, affine registration is assumed
    multiThreading
if TRUE, use multiThreading
    useCMTK
if TRUE, use CMTK instead of BRAINSFit
    sleepValue
seconds to wait between each check on completed jobs

    Returns
A list of filepaths to the aligned Images or None depending on success
def AtlasCreator::AtlasCreatorLogic::AtlasCreatorLogic::Resample (   self,
  schedulerCommand,
  filePathsList,
  templateFilePath,
  transformDirectory,
  outputSegmentationDirectory,
  outputScriptsDirectory,
  outputNotifyDirectory,
  useCMTK = False,
  sleepValue = 5 
)
    Resample a set of segmentations using exising transforms
    
    schedulerCommand
the schedulerCommand if used else ""
    filePathsList
list of existing filepaths to segmentations
    templateFilePath
file path to the template
    transformDirectory
directory to existing transformations
the transformation has to be named after the basename of the filepaths with a .mat extension      
(can be a directory as well)
    outputSegmentationDirectory
directory to save the resampled images
    outputScriptsDirectory
directory to use for generated scripts
    outputNotifyDirectory
directory to use for notification files                
    useCMTK
if TRUE, use CMTK instead of BRAINSFit
    sleepValue
seconds to wait between each check on completed jobs
                
    Returns
TRUE or FALSE depending on success
def AtlasCreator::AtlasCreatorLogic::AtlasCreatorLogic::Start (   self,
  node 
)
    Entry point for the Atlas Creation
    
    node
an AtlasCreator MRML Node (vtkMRMLAtlasCreatorNode) transporting a configuration

    Returns
TRUE or FALSE

Member Data Documentation


The documentation for this class was generated from the following file:

Generated on 6 Apr 2011 for Slicer3 by  doxygen 1.6.1