Package | Description |
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apps | |
fitters | |
optimizers |
Class and Description |
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FitAlgorithm |
FitModel
list of models for fitting.
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Fitter
Purpose:
General base class for objects that fit a model to data.
|
NoiseModel |
Class and Description |
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BallAndStickLM_GaussianFitter
Purpose:
Fits the ball and stick model using one run of a Levenburg
Marquardt and assuming a Gaussian noise model.
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BallCylinderAstrocylindersLM_Fitter
Purpose:
Fits the ballcylinderastrocylinders model using one run of a Levenburg
Marquardt.
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BallCylinderAstrosticksLM_Fitter
Purpose:
Fits the ballcylinderastrosticks model using one run of a Levenburg
Marquardt and assuming a Gaussian noise model.
|
BallCylinderDotLM_Fitter
Purpose:
Fits the ballcylinder and dot model using one run of a Levenburg
Marquardt.
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BallCylinderLM_Fitter
Purpose:
Fits the ball and cylinder model using one run of a Levenburg Marquardt.
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BallCylinderSphereLM_Fitter
Purpose:
Fits the ballcylinderspherer model using one run of a Levenburg
Marquardt.
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BallGDRCylindersAstrocylindersLM_Fitter
Purpose:
Fits the ball and gamma distributed radii cylinders model using one run of a Levenburg Marquardt.
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BallGDRCylindersAstrosticksLM_Fitter
Purpose:
Fits the ball and gamma distributed radii cylinders model using one run of a Levenburg Marquardt.
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BallGDRCylindersDotLM_Fitter
Purpose:
Fits the ball and gamma distributed radii cylinders model using one run of a Levenburg Marquardt.
|
BallGDRCylindersLM_Fitter
Purpose:
Fits the ball and gamma distributed radii cylinders model using one run
of a Levenburg Marquardt.
|
BallGDRCylindersSphereLM_Fitter
Purpose:
Fits the ball and gamma distributed radii cylinders and sphere model using one run of a Levenburg Marquardt.
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BallStickAstrocylindersLM_Fitter
Purpose:
Fits the ballstick and astrocylinders model using one run of a Levenburg
Marquardt.
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BallStickAstrosticksLM_Fitter
Purpose:
Fits the ballstick and astrosticks model using one run of a Levenburg
Marquardt.
|
BallStickDotLM_Fitter
Purpose:
Fits the ballstickdot model using one run of a Levenburg
Marquardt.
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BallStickLM_Fitter
Purpose:
Fits the ball and stick model using one run of a Levenburg
Marquardt.
|
BallStickLM_GaussianFitter
Purpose:
Fits the ball and stick model using one run of a Levenburg
Marquardt and assuming a Gaussian noise model.
|
BallStickSphereLM_Fitter
Purpose:
Fits the ballstick and sphere model using one run of a Levenburg
Marquardt.
|
BiexponLM_GaussianFitter
Purpose:
Fits the biexponential model (two cylindrically symmetric tensors) using one run of a Levenburg
Marquardt and assuming a Gaussian noise model.
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BiZeppelinLM_Fitter
Purpose:
Fits the biexponential model (two cylindrically symmetric tensors) using one run of a Levenburg
Marquardt.
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CompartmentFitter
Fitter class specific to compartment models.
|
FitAlgorithm |
FitModel
list of models for fitting.
|
Fitter
Purpose:
General base class for objects that fit a model to data.
|
MCMC_Fitter
Purpose:
General purpose MCMC fitter with implementations of various
features of all fitters that use MCMC.
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MMWMD_BasicLM_DirectFitter
Purpose:
Fits the most basic minimal model of white matter diffusion, as
used for the simulations in Alexander et al NIMG 2010, using one run
of a Levenburg Marquardt with any specified noise model.
|
MMWMD_FixedLM_DirectFitter
Purpose:
Fits the minimal model of white matter diffusion, as described
in Alexander et al NIMG 2010, with fixed tissue settings using one
run of a Levenburg Marquardt with any specified noise model.
|
MMWMD_InVivoLM_DirectFitter
Purpose:
Fits the minimal model of white matter diffusion, as described
in Alexander et al NIMG 2010, with in-vivo settings using one run
of a Levenburg Marquardt with any specified noise model.
|
NoiseModel |
Perturbation
Purpose:
Base class for starting point perturbations (as in for example
MultiRunLM fitters) or proposal distributions required for Bayesian
fitting routines such as MCMC.
|
TensorCylinderAstrocylindersLM_Fitter
Purpose:
Fits the tensorcylinderastrocylinders model using one run of a Levenburg
Marquardt.
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TensorCylinderAstrosticksLM_Fitter
Purpose:
Fits the tensorcylinderastrosticks model using one run of a Levenburg
Marquardt.
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TensorCylinderDotLM_Fitter
Purpose:
Fits the tensorcylinderdot model using one run of a Levenburg
Marquardt.
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TensorCylinderLM_Fitter
Purpose:
Fits the tensor and cylinder model using one run of a Levenburg
Marquardt.
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TensorCylinderSphereLM_Fitter
Purpose:
Fits the tensorcylindersphere model using one run of a Levenburg
Marquardt.
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TensorGDRCylindersAstrocylindersLM_Fitter
Purpose:
Fits the tensor and gamma distributed radii cylinders model using one run of a Levenburg Marquardt.
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TensorGDRCylindersAstrosticksLM_Fitter
Purpose:
Fits the tensor and gamma distributed radii cylinders model using one run of a Levenburg Marquardt.
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TensorGDRCylindersDotLM_Fitter
Purpose:
Fits the tensor and gamma distributed radii cylinders model using one run of a Levenburg Marquardt.
|
TensorGDRCylindersLM_Fitter
Purpose:
Fits the tensor and gamma distributed radii cylinders model using one run
of a Levenburg Marquardt.
|
TensorGDRCylindersSphereLM_Fitter
Purpose:
Fits the tensor and gamma distributed radii cylinders and sphere model using one run of a Levenburg Marquardt.
|
TensorStickAstrocylindersLM_Fitter
Purpose:
Fits the tensorstick and astrocylinders model using one run of a Levenburg
Marquard.
|
TensorStickAstrosticksLM_Fitter
Purpose:
Fits the tensorstick and astrosticks model using one run of a Levenburg
Marquardt.
|
TensorStickDotLM_Fitter
Purpose:
Fits the tensorstick and dot model using one run of a Levenburg
Marquardt.
|
TensorStickLM_Fitter
Purpose:
Fits the tensor and stick model using one run of a Levenburg
Marquardt.
|
TensorStickSphereLM_Fitter
Purpose:
Fits the tensorstick and sphere model using one run of a Levenburg
Marquardt.
|
ZeppelinCylinderAstrocylindersLM_Fitter
Purpose:
Fits the zeppelincylinderastrocylinders model using one run of a
Levenburg Marquardt.
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ZeppelinCylinderAstrosticksLM_Fitter
Purpose:
Fits the zeppelincylinderastrosticks model using one run of a Levenburg
Marquardt.
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ZeppelinCylinderDotCSF_LM_DirectFitter
Purpose:
Fits the zeppelin-cylinder-dot model, with additional
compartment for CSF contamination, using one run of a Levenburg
Marquardt.
|
ZeppelinCylinderDotLM_DirectFitter
Purpose:
Fits the zeppelin-cylinder-dot model using one run of a Levenburg
Marquardt.
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ZeppelinCylinderDotLM_Fitter
Purpose:
Fits the zeppelincylinderdot model using one run of a Levenburg
Marquardt.
|
ZeppelinCylinderDotLM_GaussianFitter
Purpose:
Fits the zeppelincylinderdot model using one run of a Levenburg
Marquardt and assuming a Gaussian noise model.
|
ZeppelinCylinderLM_DirectFitter
Purpose:
Fits the zeppelin and cylinder model using one run of a Levenburg
Marquardt.
|
ZeppelinCylinderLM_Fitter
Purpose:
Fits the zeppelin and cylinder model using one run of a Levenburg
Marquardt.
|
ZeppelinCylinderLM_GaussianFitter
Purpose:
Fits the zeppelin and cylinder model using one run of a Levenburg
Marquardt and assuming a Gaussian noise model.
|
ZeppelinCylinderSphereLM_Fitter
Purpose:
Fits the zeppelincylindersphere model using one run of a Levenburg
Marquardt.
|
ZeppelinCylinderTortLM_Fitter
Purpose:
Fits the zeppelin and cylinder model with tortuosity
approximation using one run of a Levenburg
Marquardt.
|
ZeppelinGDRCylindersAstrocylindersLM_Fitter
Purpose:
Fits the zeppelin and gamma distributed radii cylinders model using one run of a Levenburg Marquardt.
|
ZeppelinGDRCylindersAstrosticksLM_Fitter
Purpose:
Fits the zeppelin and gamma distributed radii cylinders model using one run of a Levenburg Marquardt.
|
ZeppelinGDRCylindersAstrosticksLM_GaussianFitter
Purpose:
Fits the zeppelin and gamma distributed radii cylinders model using one run of a Levenburg Marquardt
and assuming a Gaussian noise model.
|
ZeppelinGDRCylindersDotLM_Fitter
Purpose:
Fits the zeppelin and gamma distributed radii cylinders model using one run of a Levenburg Marquardt.
|
ZeppelinGDRCylindersDotLM_GaussianFitter
Purpose:
Fits the zeppelin and gamma distributed radii cylinders model using one run of a Levenburg Marquardt
and assuming a Gaussian noise model.
|
ZeppelinGDRCylindersLM_Fitter
Purpose:
Fits the zeppelin and gamma distributed radii cylinders model
using one run of a Levenburg Marquardt and assuming a Gaussian noise model.
|
ZeppelinGDRCylindersLM_GaussianFitter
Purpose:
Fits the zeppelin and gamma distributed radii cylinders model
using one run of a Levenburg Marquardt and assuming a Gaussian noise model.
|
ZeppelinGDRCylindersSphereLM_Fitter
Purpose:
Fits the zeppelin and gamma distributed radii cylinders and sphere model using one run of a Levenburg Marquardt
and assuming a Gaussian noise model.
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ZeppelinGDRCylindersSphereLM_GaussianFitter
Purpose:
Fits the zeppelin and gamma distributed radii cylinders and sphere model using one run of a Levenburg Marquardt
and assuming a Gaussian noise model.
|
ZeppelinStickAstrocylindersLM_Fitter
Purpose:
Fits the zeppelinstick and astrocylinders model using one run of a
Levenburg Marquardt and assuming a Gaussian noise model.
|
ZeppelinStickAstrocylindersLM_GaussianFitter
Purpose:
Fits the zeppelinstick and astrocylinders model using one run of a
Levenburg Marquardt and assuming a Gaussian noise model.
|
ZeppelinStickAstrosticksLM_Fitter
Purpose:
Fits the zeppelinstick and astrosticks model using one run of a Levenburg
Marquardt and assuming a Gaussian noise model.
|
ZeppelinStickAstrosticksLM_GaussianFitter
Purpose:
Fits the zeppelinstick and astrosticks model using one run of a Levenburg
Marquardt and assuming a Gaussian noise model.
|
ZeppelinStickDotLM_Fitter
Purpose:
Fits the zeppelinstick and dot model using one run of a Levenburg
Marquardt.
|
ZeppelinStickDotLM_GaussianFitter
Purpose:
Fits the zeppelinstick and dot model using one run of a Levenburg
Marquardt and assuming a Gaussian noise model.
|
ZeppelinStickLM_DirectFitter
Purpose:
Fits the zeppelin and stick model using one run of a Levenburg
Marquardt.
|
ZeppelinStickLM_Fitter
Purpose:
Fits the zeppelin and stick model using one run of a Levenburg Marquardt.
|
ZeppelinStickLM_GaussianFitter
Purpose:
Fits the zeppelin and stick model using one run of a Levenburg Marquardt
and assuming a Gaussian noise model.
|
ZeppelinStickSphereLM_Fitter
Purpose:
Fits the zeppelinstick and sphere model using one run of a
Levenburg Marquardt.
|
ZeppelinStickSphereLM_GaussianFitter
Purpose:
Fits the zeppelinstick and sphere model using one run of a
Levenburg Marquardt and assuming a Gaussian noise model.
|
ZeppelinStickTortLM_Fitter
Purpose:
Fits the zeppelin and stick model predicting zeppelin
perpendicular diffusivity from the volume fraction and
using one run of a Levenburg
Marquardt.
|
Class and Description |
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Codec
Purpose:
Base class for codec that maps model parameters to optimization
parameters during model fitting in order to enforce constraints on
parameter values.
|
Perturbation
Purpose:
Base class for starting point perturbations (as in for example
MultiRunLM fitters) or proposal distributions required for Bayesian
fitting routines such as MCMC.
|
Prior
Purpose:
Base class for prior probability distributions required for
Bayesian fitting routines such as MCMC.
|