AtlasCreator::AtlasCreatorLogic::AtlasCreatorLogic Class Reference
List of all members.
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
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Member Function Documentation
| def AtlasCreator::AtlasCreatorLogic::AtlasCreatorLogic::__init__ |
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parentClass | |
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Initialize this class
parentClass
a pointer to the parentClass
Returns
n/a
| def AtlasCreator::AtlasCreatorLogic::AtlasCreatorLogic::CombineToAtlas |
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self, |
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schedulerCommand, |
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filePathsList, |
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labelsList, |
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reCastString, |
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normalizeTo, |
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outputAtlasDirectory, |
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outputScriptsDirectory, |
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outputNotifyDirectory, |
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sleepValue = 5 | |
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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 |
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self, |
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schedulerCommand, |
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filePathsList, |
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outputFilePath, |
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outputScriptsDirectory, |
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outputNotifyDirectory, |
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sleepValue = 5 | |
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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 |
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Destruct this class
Returns
n/a
| def AtlasCreator::AtlasCreatorLogic::AtlasCreatorLogic::EnableDryrunMode |
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Enables the dryrun Mode
Returns
n/a
| def AtlasCreator::AtlasCreatorLogic::AtlasCreatorLogic::Helper |
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Return the helper
Returns
the helper
| def AtlasCreator::AtlasCreatorLogic::AtlasCreatorLogic::PerformPCAAnalysis |
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self, |
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labelsList, |
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filePathsList, |
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outputDirectory, |
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maxEigenVectors, |
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combine | |
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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 |
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self, |
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schedulerCommand, |
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filePathsList, |
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templateFilePath, |
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outputTransformsDirectory, |
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outputAlignedDirectory, |
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outputScriptsDirectory, |
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outputNotifyDirectory, |
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registrationType, |
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multiThreading, |
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useCMTK = False, |
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sleepValue = 5 | |
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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 |
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self, |
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schedulerCommand, |
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filePathsList, |
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templateFilePath, |
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transformDirectory, |
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outputSegmentationDirectory, |
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outputScriptsDirectory, |
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outputNotifyDirectory, |
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useCMTK = False, |
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sleepValue = 5 | |
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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 |
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self, |
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node | |
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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:
