Package | Description |
---|---|
apps | |
data | |
data.compartments | |
fitters | |
imaging | |
inverters | |
mesd | |
models | |
models.compartments | |
optimizers | |
tools | |
tractography |
Modifier and Type | Method and Description |
---|---|
static DiffusionInversion |
ModelFit.getIndexedInversion(ModelIndex[] indices,
DW_Scheme imPars)
Creates and returns the indexed diffusion inversion.
|
Constructor and Description |
---|
BootstrapDataSynthFromInput(DataSynthFromInput input,
int repeats,
DW_Scheme scheme,
int samples,
double snr,
int seed) |
BootstrapDataSynthFromInput(DataSynthFromInput input,
int repeats,
DW_Scheme scheme,
int samples,
double snr,
java.util.Random ran) |
DataSynthesizer(ModelPDF pdf,
DW_Scheme ip,
double s)
Constructor requires the
DW_Scheme , the test function and the
signal to noise level. |
DataSynthesizer(ModelPDF pdf,
DW_Scheme ip,
double s,
int numVox)
Constructor includes the number of voxels in the synthetic data source.
|
DataSynthesizer(ModelPDF pdf,
DW_Scheme ip,
double s,
int numVox,
int seed)
Constructor includes the number of voxels in the synthetic data source.
|
DataSynthesizer(ModelPDF pdf,
DW_Scheme ip,
double s,
int numVox,
java.util.Random ran)
Constructor includes the number of voxels in the synthetic data
source and the actual
Random object to use. |
DataSynthFromBallStickInput(java.lang.String filename,
java.lang.String inputDataType,
DW_Scheme ip,
double s) |
DataSynthFromBallStickInput(java.lang.String filename,
java.lang.String inputDataType,
DW_Scheme ip,
double s,
int seed) |
DataSynthFromDT_Input(java.lang.String filename,
java.lang.String inputDataType,
DW_Scheme ip,
double s)
The constructor requires the name of the data file and the details of the
acquisition sequence to use for data synthesis.
|
DataSynthFromDT_Input(java.lang.String filename,
java.lang.String inputDataType,
DW_Scheme ip,
double s,
int seed)
The constructor requires the name of the data file and the details of the
acquisition sequence to use for data synthesis.
|
DataSynthFromInput(java.lang.String filename,
java.lang.String inputDataType,
DW_Scheme ip,
double s)
The constructor requires the name of the data file and the details of the
acquisition sequence to use for data synthesis.
|
DataSynthFromInput(java.lang.String filename,
java.lang.String inputDataType,
DW_Scheme ip,
double s,
int seed)
This constructor allows the random number generator seed to be specified.
|
DataSynthFromMultiTensorInput(java.lang.String filename,
java.lang.String inputDataType,
DW_Scheme ip,
int maxComps,
double s) |
DataSynthFromMultiTensorInput(java.lang.String filename,
java.lang.String inputDataType,
DW_Scheme ip,
int maxComps,
double s,
int seed) |
DataSynthFromThreeTensorInput(java.lang.String filename,
java.lang.String inputDataType,
DW_Scheme ip,
double s)
The constructor requires the name of the data file and the details of the
acquisition sequence to use for data synthesis.
|
DataSynthFromThreeTensorInput(java.lang.String filename,
java.lang.String inputDataType,
DW_Scheme ip,
double s,
int seed)
The constructor requires the name of the data file and the details of the
acquisition sequence to use for data synthesis.
|
DataSynthFromTwoTensorInput(java.lang.String filename,
java.lang.String inputDataType,
DW_Scheme ip,
double s)
The constructor requires the name of the data file and the details of the
acquisition sequence to use for data synthesis.
|
DataSynthFromTwoTensorInput(java.lang.String filename,
java.lang.String inputDataType,
DW_Scheme ip,
double s,
int seed)
The constructor requires the name of the data file and the details of the
acquisition sequence to use for data synthesis.
|
SyntheticBootstrapper(ModelPDF pdf,
DW_Scheme ip,
double s,
int samples,
int numVox)
Constructor includes the number of voxels in the synthetic data source.
|
SyntheticBootstrapper(ModelPDF pdf,
DW_Scheme ip,
double s,
int samples,
int numVox,
int seed)
Constructor includes the number of voxels in the synthetic data source.
|
SyntheticBootstrapper(ModelPDF pdf,
DW_Scheme ip,
double s,
int samples,
int numVox,
java.util.Random ran)
Constructor includes the number of voxels in the synthetic data source.
|
VoxelOrderDW_DataSource(java.lang.String filename,
java.lang.String type,
DW_Scheme imParams)
Constructor requires the filename, the number of values in each voxel and
the data type.
|
WildBootstrapDataSynth(DataSource input,
DW_Scheme scheme,
int samples) |
WildBootstrapDataSynth(DataSource input,
DW_Scheme scheme,
int samples,
int seed) |
WildBootstrapDataSynth(DataSource input,
DW_Scheme scheme,
int samples,
java.util.Random ran)
This is the constructor that actually does everything, so ensure that this eventually gets
called.
|
WildBS_DT_DataSynth(DataSource input,
DW_Scheme scheme,
int samples) |
WildBS_DT_DataSynth(DataSource input,
DW_Scheme scheme,
int samples,
int seed) |
WildBS_DT_DataSynth(DataSource input,
DW_Scheme scheme,
int samples,
java.util.Random ran) |
Modifier and Type | Method and Description |
---|---|
RealMatrix |
Zeppelin.getJacobian(double[] modParams,
DW_Scheme scheme) |
RealMatrix |
Tensor.getJacobian(double[] modParams,
DW_Scheme scheme) |
RealMatrix |
CylinderGPD.getJacobian(double[] modParams,
DW_Scheme scheme) |
RealMatrix |
CompartmentModel.getJacobian(double[] modParams,
DW_Scheme scheme)
Get Jacobian for each compartment separately.
|
double |
Zeppelin.getSignal(double[] params,
DW_Scheme rawScheme,
int i) |
double |
Tensor.getSignal(double[] params,
DW_Scheme rawScheme,
int i)
generates signals from this compartment for each line
in the scheme given.
|
double |
Stick.getSignal(double[] params,
DW_Scheme rawScheme,
int i) |
double |
SphereGPD.getSignal(double[] params,
DW_Scheme rawScheme,
int i) |
double |
ListDistributionCompartment.getSignal(double[] params,
DW_Scheme scheme,
int line) |
double |
GammaDistribRadiiCylinders.getSignal(double[] params,
DW_Scheme rawScheme,
int i) |
double |
Dot.getSignal(double[] params,
DW_Scheme scheme,
int i)
return a single signal from the scheme from the dot model
|
double |
CylinderGPD.getSignal(double[] params,
DW_Scheme rawScheme,
int i)
generates signals from this compartment for each line
in the scheme given.
|
double |
CompartmentModel.getSignal(double[] modParams,
DW_Scheme scheme,
int line)
sum up the signals from each compartment
|
double |
Ball.getSignal(double[] params,
DW_Scheme scheme,
int i)
generates signals from this compartment for each line
in the scheme given.
|
double |
Astrosticks.getSignal(double[] params,
DW_Scheme rawScheme,
int i)
generates signals from this compartment for each line
in the scheme given.
|
double |
Astrocylinders.getSignal(double[] params,
DW_Scheme rawScheme,
int i)
generates signals from this compartment for the given line
in the scheme given.
|
RealMatrix |
Zeppelin.getSignals(double[] params,
DW_Scheme rawScheme)
generates signals from this compartment for each line
in the scheme given.
|
RealMatrix |
Tensor.getSignals(double[] params,
DW_Scheme rawScheme)
generates signals from this compartment for each line
in the scheme given.
|
RealMatrix |
Stick.getSignals(double[] params,
DW_Scheme rawScheme)
generates signals from this compartment for each line
in the scheme given.
|
RealMatrix |
SphereGPD.getSignals(double[] params,
DW_Scheme rawScheme)
generates signals from this compartment for each line
in the scheme given.
|
RealMatrix |
ListDistributionCompartment.getSignals(double[] params,
DW_Scheme scheme) |
RealMatrix |
GammaDistribRadiiCylinders.getSignals(double[] params,
DW_Scheme rawScheme)
generates signals from this compartment for each line
in the scheme given.
|
RealMatrix |
Dot.getSignals(double[] params,
DW_Scheme rawScheme)
generates signals from this compartment for each line
in the scheme given.
|
RealMatrix |
CylinderGPD.getSignals(double[] params,
DW_Scheme rawScheme)
generates signals from this compartment for each line
in the scheme given.
|
RealMatrix |
CompartmentModel.getSignals(double[] modParams,
DW_Scheme scheme)
sum up the signals from each compartment
|
RealMatrix |
Ball.getSignals(double[] params,
DW_Scheme scheme)
generates signals from this compartment for each line
in the scheme given.
|
RealMatrix |
Astrosticks.getSignals(double[] params,
DW_Scheme rawScheme)
generates signals from this compartment for each line
in the scheme given.
|
RealMatrix |
Astrocylinders.getSignals(double[] params,
DW_Scheme rawScheme)
generates signals from this compartment for each line
in the scheme given.
|
Constructor and Description |
---|
CompartmentModel(java.lang.String[] comps,
double[] params,
DW_Scheme scheme)
constructor with scheme for use in data synthesis.
|
Constructor and Description |
---|
BallAndStickLM_GaussianFitter(DW_Scheme scheme)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
BallAndStickLM_OffGaussFitter(DW_Scheme scheme,
double sigma)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
BallAndStickLM_RicianFitter(DW_Scheme scheme,
double sigma)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
BallAndStickMultiRunLM_GaussianFitter(DW_Scheme scheme,
int repeats,
int seed)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
BallCylinderAstrocylindersLM_Fitter(DW_Scheme scheme)
Constructor implements the mapping between model and optimized parameters
in the Codec object.
|
BallCylinderAstrocylindersMultiRunLM_Fitter(DW_Scheme scheme,
int repeats,
int seed)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
BallCylinderAstrosticksLM_Fitter(DW_Scheme scheme)
Constructor implements the mapping between model and optimized parameters
in the Codec object.
|
BallCylinderAstrosticksMultiRunLM_Fitter(DW_Scheme scheme,
int repeats,
int seed)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
BallCylinderDotLM_Fitter(DW_Scheme scheme)
Constructor implements the mapping between model and optimized parameters
in the Codec object.
|
BallCylinderDotMultiRunLM_Fitter(DW_Scheme scheme,
int repeats,
int seed)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
BallCylinderLM_Fitter(DW_Scheme scheme)
Constructor implements the mapping between model and optimized parameters
in the Codec object.
|
BallCylinderMultiRunLM_Fitter(DW_Scheme scheme,
int repeats,
int seed)
Constructor implements the mapping between model and optimized parameters
in the Codec object.
|
BallCylinderSphereLM_Fitter(DW_Scheme scheme)
Constructor implements the mapping between model and optimized parameters
in the Codec object.
|
BallCylinderSphereMultiRunLM_Fitter(DW_Scheme scheme,
int repeats,
int seed)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
BallGDRCylindersAstrocylindersLM_Fitter(DW_Scheme scheme)
Constructor implements the mapping between model and optimized parameters
in the Codec object.
|
BallGDRCylindersAstrocylindersMultiRunLM_Fitter(DW_Scheme scheme,
int repeats,
int seed)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
BallGDRCylindersAstrosticksLM_Fitter(DW_Scheme scheme)
Constructor implements the mapping between model and optimized parameters
in the Codec object.
|
BallGDRCylindersAstrosticksMultiRunLM_Fitter(DW_Scheme scheme,
int repeats,
int seed)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
BallGDRCylindersDotLM_Fitter(DW_Scheme scheme)
Constructor implements the mapping between model and optimized parameters
in the Codec object.
|
BallGDRCylindersDotMultiRunLM_Fitter(DW_Scheme scheme,
int repeats,
int seed)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
BallGDRCylindersLM_Fitter(DW_Scheme scheme)
Constructor implements the mapping between model and optimized parameters
in the Codec object.
|
BallGDRCylindersMultiRunLM_Fitter(DW_Scheme scheme,
int repeats,
int seed)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
BallGDRCylindersSphereLM_Fitter(DW_Scheme scheme)
Constructor implements the mapping between model and optimized parameters
in the Codec object.
|
BallGDRCylindersSphereMultiRunLM_Fitter(DW_Scheme scheme,
int repeats,
int seed)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
BallStickAstrocylindersLM_Fitter(DW_Scheme scheme)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
BallStickAstrocylindersLM_Fitter(DW_Scheme scheme,
java.lang.String[] compNames,
double[] initialParams)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
BallStickAstrocylindersMultiRunLM_Fitter(DW_Scheme scheme,
int repeats,
int seed)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
BallStickAstrosticksLM_Fitter(DW_Scheme scheme)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
BallStickAstrosticksLM_Fitter(DW_Scheme scheme,
java.lang.String[] compNames,
double[] initialParams)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
BallStickAstrosticksMultiRunLM_Fitter(DW_Scheme scheme,
int repeats,
int seed)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
BallStickDotLM_Fitter(DW_Scheme scheme)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
BallStickDotLM_Fitter(DW_Scheme scheme,
java.lang.String[] compNames,
double[] initialParams)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
BallStickDotMultiRunLM_Fitter(DW_Scheme scheme,
int repeats,
int seed)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
BallStickLM_Fitter(DW_Scheme scheme)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
BallStickLM_Fitter(DW_Scheme scheme,
java.lang.String[] compNames,
double[] initialParams)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
BallStickLM_GaussianFitter(DW_Scheme scheme)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
BallStickLM_GaussianFitter(DW_Scheme scheme,
java.lang.String[] compNames,
double[] initialParams)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
BallStickMCMC_Fitter(DW_Scheme scheme)
Basic constructor extracts model particulars and calls
full constructor.
|
BallStickMCMC_Fitter(DW_Scheme scheme,
java.lang.String[] compNames,
double[] initialParams)
Constructor sets up various required objects for MCMC.
|
BallStickMultiRunLM_Fitter(DW_Scheme scheme,
int repeats,
int seed)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
BallStickMultiRunLM_GaussianFitter(DW_Scheme scheme,
int repeats,
int seed)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
BallStickSphereLM_Fitter(DW_Scheme scheme)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
BallStickSphereLM_Fitter(DW_Scheme scheme,
java.lang.String[] compNames,
double[] initialParams)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
BallStickSphereMultiRunLM_Fitter(DW_Scheme scheme,
int repeats,
int seed)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
BiexponLM_GaussianFitter(DW_Scheme scheme)
Constructor implements the mapping between model and optimized parameters
in the Codec object.
|
BiexponMultiRunLM_GaussianFitter(DW_Scheme scheme,
int repeats,
int seed)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
BiZeppelinLM_Fitter(DW_Scheme scheme)
Constructor implements the mapping between model and optimized parameters
in the Codec object.
|
BiZeppelinMultiRunLM_Fitter(DW_Scheme scheme,
int repeats,
int seed)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
MCMC_Fitter(DW_Scheme scheme,
java.lang.String[] compNames,
double[] initialParams)
Constructor sets up various required objects for MCMC.
|
MMWMD_BasicLM_DirectFitter(DW_Scheme scheme)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
MMWMD_BasicLM_DirectFitter(DW_Scheme scheme,
java.lang.String[] compNames,
double[] initialParams)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
MMWMD_BasicMCMC_Fitter(DW_Scheme scheme)
Basic constructor extracts model particulars and calls
full constructor.
|
MMWMD_BasicMCMC_Fitter(DW_Scheme scheme,
java.lang.String[] compNames,
double[] initialParams)
Constructor sets up various required objects for MCMC.
|
MMWMD_BasicMultiRunLM_DirectFitter(DW_Scheme scheme,
int repeats,
int seed)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
MMWMD_FixedLM_DirectFitter(DW_Scheme scheme)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
MMWMD_FixedLM_DirectFitter(DW_Scheme scheme,
java.lang.String[] compNames,
double[] initialParams)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
MMWMD_FixedMCMC_Fitter(DW_Scheme scheme)
Basic constructor extracts model particulars and calls
full constructor.
|
MMWMD_FixedMCMC_Fitter(DW_Scheme scheme,
java.lang.String[] compNames,
double[] initialParams)
Constructor sets up various required objects for MCMC.
|
MMWMD_FixedMultiRunLM_DirectFitter(DW_Scheme scheme,
int repeats,
int seed)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
MMWMD_InVivoLM_DirectFitter(DW_Scheme scheme)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
MMWMD_InVivoLM_DirectFitter(DW_Scheme scheme,
java.lang.String[] compNames,
double[] initialParams)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
MMWMD_InVivoLM_GaussianFitter(DW_Scheme scheme)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
MMWMD_InVivoLM_GaussianFitter(DW_Scheme scheme,
java.lang.String[] compNames,
double[] initialParams)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
MMWMD_InVivoMCMC_Fitter(DW_Scheme scheme)
Basic constructor extracts model particulars and calls
full constructor.
|
MMWMD_InVivoMCMC_Fitter(DW_Scheme scheme,
java.lang.String[] compNames,
double[] initialParams)
Constructor sets up various required objects for MCMC.
|
MMWMD_InVivoMultiRunLM_DirectFitter(DW_Scheme scheme,
int repeats,
int seed)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
TensorCylinderAstrocylindersLM_Fitter(DW_Scheme scheme)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
TensorCylinderAstrocylindersMultiRunLM_Fitter(DW_Scheme scheme,
int repeats,
int seed)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
TensorCylinderAstrosticksLM_Fitter(DW_Scheme scheme)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
TensorCylinderAstrosticksMultiRunLM_Fitter(DW_Scheme scheme,
int repeats,
int seed)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
TensorCylinderDotLM_Fitter(DW_Scheme scheme)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
TensorCylinderDotMultiRunLM_Fitter(DW_Scheme scheme,
int repeats,
int seed)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
TensorCylinderLM_Fitter(DW_Scheme scheme)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
TensorCylinderMultiRunLM_Fitter(DW_Scheme scheme,
int repeats,
int seed)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
TensorCylinderSphereLM_Fitter(DW_Scheme scheme)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
TensorCylinderSphereMultiRunLM_Fitter(DW_Scheme scheme,
int repeats,
int seed)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
TensorGDRCylindersAstrocylindersLM_Fitter(DW_Scheme scheme)
Constructor implements the mapping between model and optimized parameters
in the Codec object.
|
TensorGDRCylindersAstrocylindersMultiRunLM_Fitter(DW_Scheme scheme,
int repeats,
int seed)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
TensorGDRCylindersAstrosticksLM_Fitter(DW_Scheme scheme)
Constructor implements the mapping between model and optimized parameters
in the Codec object.
|
TensorGDRCylindersAstrosticksMultiRunLM_Fitter(DW_Scheme scheme,
int repeats,
int seed)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
TensorGDRCylindersDotLM_Fitter(DW_Scheme scheme)
Constructor implements the mapping between model and optimized parameters
in the Codec object.
|
TensorGDRCylindersDotMultiRunLM_Fitter(DW_Scheme scheme,
int repeats,
int seed)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
TensorGDRCylindersLM_Fitter(DW_Scheme scheme)
Constructor implements the mapping between model and optimized parameters
in the Codec object.
|
TensorGDRCylindersMultiRunLM_Fitter(DW_Scheme scheme,
int repeats,
int seed)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
TensorGDRCylindersSphereLM_Fitter(DW_Scheme scheme)
Constructor implements the mapping between model and optimized parameters
in the Codec object.
|
TensorGDRCylindersSphereMultiRunLM_Fitter(DW_Scheme scheme,
int repeats,
int seed)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
TensorStickAstrocylindersLM_Fitter(DW_Scheme scheme)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
TensorStickAstrocylindersMultiRunLM_Fitter(DW_Scheme scheme,
int repeats,
int seed)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
TensorStickAstrosticksLM_Fitter(DW_Scheme scheme)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
TensorStickAstrosticksMultiRunLM_Fitter(DW_Scheme scheme,
int repeats,
int seed)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
TensorStickDotLM_Fitter(DW_Scheme scheme)
Constructor implements the mapping between model and optimized parameters
in the Codec object.
|
TensorStickDotMultiRunLM_Fitter(DW_Scheme scheme,
int repeats,
int seed)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
TensorStickLM_Fitter(DW_Scheme scheme)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
TensorStickMultiRunLM_Fitter(DW_Scheme scheme,
int repeats,
int seed)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
TensorStickSphereLM_Fitter(DW_Scheme scheme)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
TensorStickSphereMultiRunLM_Fitter(DW_Scheme scheme,
int repeats,
int seed)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
ZeppelinCylinderAstrocylindersLM_Fitter(DW_Scheme scheme)
Constructor implements the mapping between model and optimized parameters
in the Codec object.
|
ZeppelinCylinderAstrocylindersMultiRunLM_Fitter(DW_Scheme scheme,
int repeats,
int seed)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
ZeppelinCylinderAstrosticksLM_Fitter(DW_Scheme scheme)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
ZeppelinCylinderAstrosticksMultiRunLM_Fitter(DW_Scheme scheme,
int repeats,
int seed)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
ZeppelinCylinderDotCSF_LM_DirectFitter(DW_Scheme scheme)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
ZeppelinCylinderDotCSF_LM_DirectFitter(DW_Scheme scheme,
java.lang.String[] compNames,
double[] initialParams)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
ZeppelinCylinderDotCSF_MultiRunLM_DirectFitter(DW_Scheme scheme,
int repeats,
int seed)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
ZeppelinCylinderDotLM_DirectFitter(DW_Scheme scheme)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
ZeppelinCylinderDotLM_DirectFitter(DW_Scheme scheme,
java.lang.String[] compNames,
double[] initialParams)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
ZeppelinCylinderDotLM_Fitter(DW_Scheme scheme)
Constructor implements the mapping between model and optimized parameters
in the Codec object.
|
ZeppelinCylinderDotLM_GaussianFitter(DW_Scheme scheme)
Constructor implements the mapping between model and optimized parameters
in the Codec object.
|
ZeppelinCylinderDotMCMC_GaussianFitter(DW_Scheme scheme)
Basic constructor extracts model particulars and calls
full constructor.
|
ZeppelinCylinderDotMCMC_GaussianFitter(DW_Scheme scheme,
java.lang.String[] compNames,
double[] initialParams)
Constructor sets up various required objects for MCMC.
|
ZeppelinCylinderDotMultiRunLM_DirectFitter(DW_Scheme scheme,
int repeats,
int seed)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
ZeppelinCylinderDotMultiRunLM_Fitter(DW_Scheme scheme,
int repeats,
int seed)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
ZeppelinCylinderDotMultiRunLM_GaussianFitter(DW_Scheme scheme,
int repeats,
int seed)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
ZeppelinCylinderLM_DirectFitter(DW_Scheme scheme)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
ZeppelinCylinderLM_DirectFitter(DW_Scheme scheme,
java.lang.String[] compNames,
double[] initialParams)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
ZeppelinCylinderLM_Fitter(DW_Scheme scheme)
Constructor implements the mapping between model and optimized parameters
in the Codec object.
|
ZeppelinCylinderLM_GaussianFitter(DW_Scheme scheme)
Constructor implements the mapping between model and optimized parameters
in the Codec object.
|
ZeppelinCylinderMultiRunLM_DirectFitter(DW_Scheme scheme,
int repeats,
int seed)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
ZeppelinCylinderMultiRunLM_Fitter(DW_Scheme scheme,
int repeats,
int seed)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
ZeppelinCylinderMultiRunLM_GaussianFitter(DW_Scheme scheme,
int repeats,
int seed)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
ZeppelinCylinderSphereLM_Fitter(DW_Scheme scheme)
Constructor implements the mapping between model and optimized parameters
in the Codec object.
|
ZeppelinCylinderSphereMultiRunLM_Fitter(DW_Scheme scheme,
int repeats,
int seed)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
ZeppelinCylinderSphereMultiRunLM_GaussianFitter(DW_Scheme scheme,
int repeats,
int seed)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
ZeppelinCylinderTortLM_Fitter(DW_Scheme scheme)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
ZeppelinCylinderTortLM_Fitter(DW_Scheme scheme,
java.lang.String[] compNames,
double[] initialParams)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
ZeppelinCylinderTortMultiRunLM_Fitter(DW_Scheme scheme,
int repeats,
int seed)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
ZeppelinGDRCylindersAstrocylindersLM_Fitter(DW_Scheme scheme)
Constructor implements the mapping between model and optimized parameters
in the Codec object.
|
ZeppelinGDRCylindersAstrocylindersMultiRunLM_Fitter(DW_Scheme scheme,
int repeats,
int seed)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
ZeppelinGDRCylindersAstrosticksLM_Fitter(DW_Scheme scheme)
Constructor implements the mapping between model and optimized parameters
in the Codec object.
|
ZeppelinGDRCylindersAstrosticksLM_GaussianFitter(DW_Scheme scheme)
Constructor implements the mapping between model and optimized parameters
in the Codec object.
|
ZeppelinGDRCylindersAstrosticksMultiRunLM_Fitter(DW_Scheme scheme,
int repeats,
int seed)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
ZeppelinGDRCylindersAstrosticksMultiRunLM_GaussianFitter(DW_Scheme scheme,
int repeats,
int seed)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
ZeppelinGDRCylindersDotLM_Fitter(DW_Scheme scheme)
Constructor implements the mapping between model and optimized parameters
in the Codec object.
|
ZeppelinGDRCylindersDotLM_GaussianFitter(DW_Scheme scheme)
Constructor implements the mapping between model and optimized parameters
in the Codec object.
|
ZeppelinGDRCylindersDotMultiRunLM_Fitter(DW_Scheme scheme,
int repeats,
int seed)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
ZeppelinGDRCylindersDotMultiRunLM_GaussianFitter(DW_Scheme scheme,
int repeats,
int seed)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
ZeppelinGDRCylindersLM_Fitter(DW_Scheme scheme)
Constructor implements the mapping between model and optimized parameters
in the Codec object.
|
ZeppelinGDRCylindersLM_GaussianFitter(DW_Scheme scheme)
Constructor implements the mapping between model and optimized parameters
in the Codec object.
|
ZeppelinGDRCylindersMultiRunLM_Fitter(DW_Scheme scheme,
int repeats,
int seed)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
ZeppelinGDRCylindersMultiRunLM_GaussianFitter(DW_Scheme scheme,
int repeats,
int seed)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
ZeppelinGDRCylindersSphereLM_Fitter(DW_Scheme scheme)
Constructor implements the mapping between model and optimized parameters
in the Codec object.
|
ZeppelinGDRCylindersSphereLM_GaussianFitter(DW_Scheme scheme)
Constructor implements the mapping between model and optimized parameters
in the Codec object.
|
ZeppelinGDRCylindersSphereMultiRunLM_Fitter(DW_Scheme scheme,
int repeats,
int seed)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
ZeppelinGDRCylindersSphereMultiRunLM_GaussianFitter(DW_Scheme scheme,
int repeats,
int seed)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
ZeppelinStickAstrocylindersLM_Fitter(DW_Scheme scheme)
Constructor implements the mapping between model and optimized parameters
in the Codec object.
|
ZeppelinStickAstrocylindersLM_GaussianFitter(DW_Scheme scheme)
Constructor implements the mapping between model and optimized parameters
in the Codec object.
|
ZeppelinStickAstrocylindersMultiRunLM_Fitter(DW_Scheme scheme,
int repeats,
int seed)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
ZeppelinStickAstrocylindersMultiRunLM_GaussianFitter(DW_Scheme scheme,
int repeats,
int seed)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
ZeppelinStickAstrosticksLM_Fitter(DW_Scheme scheme)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
ZeppelinStickAstrosticksLM_GaussianFitter(DW_Scheme scheme)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
ZeppelinStickAstrosticksMultiRunLM_Fitter(DW_Scheme scheme,
int repeats,
int seed)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
ZeppelinStickAstrosticksMultiRunLM_GaussianFitter(DW_Scheme scheme,
int repeats,
int seed)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
ZeppelinStickDotLM_Fitter(DW_Scheme scheme)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
ZeppelinStickDotLM_GaussianFitter(DW_Scheme scheme)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
ZeppelinStickDotMultiRunLM_Fitter(DW_Scheme scheme,
int repeats,
int seed)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
ZeppelinStickDotMultiRunLM_GaussianFitter(DW_Scheme scheme,
int repeats,
int seed)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
ZeppelinStickLM_DirectFitter(DW_Scheme scheme)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
ZeppelinStickLM_DirectFitter(DW_Scheme scheme,
java.lang.String[] compNames,
double[] initialParams)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
ZeppelinStickLM_Fitter(DW_Scheme scheme)
Constructor implements the mapping between model and optimized parameters
in the Codec object.
|
ZeppelinStickLM_GaussianFitter(DW_Scheme scheme)
Constructor implements the mapping between model and optimized parameters
in the Codec object.
|
ZeppelinStickMultiRunLM_DirectFitter(DW_Scheme scheme,
int repeats,
int seed)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
ZeppelinStickMultiRunLM_Fitter(DW_Scheme scheme,
int repeats,
int seed)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
ZeppelinStickMultiRunLM_GaussianFitter(DW_Scheme scheme,
int repeats,
int seed)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
ZeppelinStickSphereLM_Fitter(DW_Scheme scheme)
Constructor implements the mapping between model and optimized parameters
in the Codec object.
|
ZeppelinStickSphereLM_GaussianFitter(DW_Scheme scheme)
Constructor implements the mapping between model and optimized parameters
in the Codec object.
|
ZeppelinStickSphereMultiRunLM_Fitter(DW_Scheme scheme,
int repeats,
int seed)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
ZeppelinStickSphereMultiRunLM_GaussianFitter(DW_Scheme scheme,
int repeats,
int seed)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
ZeppelinStickTortLM_Fitter(DW_Scheme scheme)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
ZeppelinStickTortLM_Fitter(DW_Scheme scheme,
java.lang.String[] compNames,
double[] initialParams)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
ZeppelinStickTortMultiRunLM_Fitter(DW_Scheme scheme,
int repeats,
int seed)
Constructor implements the mapping between model and optimized
parameters in the Codec object.
|
Modifier and Type | Class and Description |
---|---|
class |
B_VectorScheme
This class stores a list of b-values.
|
class |
GradientWaveform_Scheme
scheme object for general gradient waveforms.
|
class |
RectGradSteTanScheme
Stejskal-Tanner scheme with rectangular gradient blocks.
|
class |
RectGradTRSE_Scheme
Twice-refocused scheme with rectangular gradient pulses.
|
class |
StejskalTannerScheme
Superclass for Stejskal-Tanner imaging schemes.
|
class |
TRSE_Scheme
Scheme file for twice-refocused pulse sequences, which use four diffusion-weighting
pulses, which begin at time t_delN and last for delN seconds.
|
Modifier and Type | Method and Description |
---|---|
DW_Scheme |
RectGradTRSE_Scheme.flipX()
Negates the X component of the gradient directions.
|
DW_Scheme |
RectGradSteTanScheme.flipX()
Negates the X component of the gradient directions.
|
DW_Scheme |
GradientWaveform_Scheme.flipX()
returns a new copy of the current scheme
with gradients flipped in the x-direction
|
abstract DW_Scheme |
DW_Scheme.flipX()
Negates the X component of the gradient directions.
|
DW_Scheme |
B_VectorScheme.flipX()
Negates the X component of the gradient directions.
|
DW_Scheme |
RectGradTRSE_Scheme.flipY()
Negates the Y component of the gradient directions.
|
DW_Scheme |
RectGradSteTanScheme.flipY()
Negates the Y component of the gradient directions.
|
DW_Scheme |
GradientWaveform_Scheme.flipY()
returns a new copy of the current scheme
with gradients flipped in the y-direction
|
abstract DW_Scheme |
DW_Scheme.flipY()
Negates the Y component of the gradient directions.
|
DW_Scheme |
B_VectorScheme.flipY()
Negates the Y component of the gradient directions.
|
DW_Scheme |
RectGradTRSE_Scheme.flipZ()
Negates the Z component of the gradient directions.
|
DW_Scheme |
RectGradSteTanScheme.flipZ()
Negates the Z component of the gradient directions.
|
DW_Scheme |
GradientWaveform_Scheme.flipZ()
returns a new copy of the current scheme
with gradients flipped in the z-direction
|
abstract DW_Scheme |
DW_Scheme.flipZ()
Negates the Z component of the gradient directions.
|
DW_Scheme |
B_VectorScheme.flipZ()
Negates the Z component of the gradient directions.
|
DW_Scheme |
RectGradTRSE_Scheme.getSubsetScheme(int[] indices) |
DW_Scheme |
RectGradSteTanScheme.getSubsetScheme(int[] indices) |
DW_Scheme |
GradientWaveform_Scheme.getSubsetScheme(int[] indices)
generates a new scheme from a specified subset of the acquisitions
in the current scheme.
|
abstract DW_Scheme |
DW_Scheme.getSubsetScheme(int[] indices)
Gets a scheme composed of a subset of the measurements in this scheme.
|
DW_Scheme |
B_VectorScheme.getSubsetScheme(int[] indices)
Gets a scheme composed of a subset of the measurements.
|
DW_Scheme |
RectGradTRSE_Scheme.gradOrder(int[] order) |
DW_Scheme |
RectGradSteTanScheme.gradOrder(int[] order) |
DW_Scheme |
GradientWaveform_Scheme.gradOrder(int[] order)
constructs a new set of waveforms in an order specified by
the given array of indices.
|
abstract DW_Scheme |
DW_Scheme.gradOrder(int[] order)
Reorders the gradient directions.
|
DW_Scheme |
B_VectorScheme.gradOrder(int[] order)
Re-orders the components of the gradient vectors.
|
static DW_Scheme |
DW_Scheme.nullScheme()
This static method simply returns a default scheme for
various applications that require a scheme object without
actually using it.
|
static DW_Scheme |
DW_Scheme.readScheme(java.lang.String filename)
Reads a scheme from a scheme file.
|
Modifier and Type | Method and Description |
---|---|
static DT_Inversion |
DT_Inversion.getIndexedDT_Inversion(ModelIndex index,
DW_Scheme imPars)
Returns an indexed DT_Inversion.
|
Constructor and Description |
---|
BallStickFitter(DW_Scheme ip) |
BallStickInversion(DW_Scheme ip) |
EvenSphHarmFitter(DW_Scheme imParams,
int order)
The constructor computes the inversion matrix from the imaging parameters
for the sequence used in the data acquisition.
|
EvenSphHarmSignalFitter(DW_Scheme imParams,
int order)
The constructor computes the inversion matrix from the imaging parameters
for the sequence used in the data acquisition.
|
LinearADC_Inversion(DW_Scheme imParams)
The constructor requires the details of the sequence used to generate the
data that will be processed.
|
LinearDT_Inversion(DW_Scheme imParams)
The constructor requires the details of the sequence used to generate the
data that will be processed.
|
LinearInversion(DW_Scheme imParams,
java.lang.String matrixFile,
boolean norm,
boolean log)
The constructor requires the details of the sequence used to generate the
data that will be processed and the name of the file containing the
linear transformation matrix.
|
MultiTensorInversion(DW_Scheme imParams,
java.lang.String voxClassFile,
ModelIndex[][] modelIndices,
int maxComponents)
This constructor requires the details of the sequence, the name
of the file containing the voxel classification and the list of
indices of the inverters.
|
NonLinearDT_Inversion(DW_Scheme imParams)
This constructor takes only the imaging sequence parameters and creates a
fitter that does not use the Hessian of the objective function.
|
NonLinearDT_Inversion(DW_Scheme imParams,
ModelIndex index)
This constructor takes the imaging sequence parameters and an index
specifying the type of fitting to use.
|
RestoreDT_Inversion(DW_Scheme imParams,
double noiseLevel)
Default constructor.
|
RestoreDT_Inversion(DW_Scheme imParams,
double noiseLevel,
int index)
This constructor takes the imaging sequence parameters and an index
specifying the type of non-linear fitting to use.
|
ThreeTensorInversion(DW_Scheme imParams)
This constructor requires the details of the sequence used to generate
the data that will be processed.
|
ThreeTensorInversion(DW_Scheme imParams,
ModelIndex threeTensorIndex,
ModelIndex dtInverterIndex)
This constructor requires the details of the sequence and the indexes of
the choices of ThreeTensorFitter and DT_Inverter.
|
TwoTensorInversion(DW_Scheme imParams)
This constructor requires the details of the sequence used to generate
the data that will be processed.
|
TwoTensorInversion(DW_Scheme imParams,
ModelIndex twoTensorIndex,
ModelIndex dtInverterIndex)
This constructor requires the details of the sequence and the indexes of
the choices of TwoTensorFitter and DT_Inverter.
|
WeightedLinearDT_Inversion(DW_Scheme imParams)
The constructor requires the details of the sequence used to generate the
data that will be processed.
|
Constructor and Description |
---|
MESD_Inversion(DW_Scheme imPars,
double[] params,
int numParams)
This constructor sets up the default fitter.
|
Modifier and Type | Method and Description |
---|---|
RealMatrix |
ParametricModel.getJacobian_old(double[] modParams,
DW_Scheme scheme)
Computes the Jacobian of the model numerically.
|
RealMatrix |
ParametricModel.getJacobian(double[] modParams,
DW_Scheme scheme) |
RealMatrix |
ParametricModel.getJacobian(double[] modParams,
DW_Scheme scheme,
int index)
Computes the Jacobian of the model numerically.
|
abstract double |
ParametricModel.getSignal(double[] modParams,
DW_Scheme scheme,
int i)
Returns the signals for the i-th measurement of specified
scheme from the model using the specified model parameters.
|
double |
BallAndStickModel.getSignal(double[] modParams,
DW_Scheme scheme,
int i) |
abstract RealMatrix |
ParametricModel.getSignals(double[] modParams,
DW_Scheme scheme)
Returns a list of signals for the specified scheme from the
model using the specified model parameters.
|
RealMatrix |
BallAndStickModel.getSignals(double[] modParams,
DW_Scheme scheme) |
Modifier and Type | Method and Description |
---|---|
RealMatrix |
Zeppelin.getJacobian(double[] modParams,
DW_Scheme scheme) |
RealMatrix |
Tensor.getJacobian(double[] modParams,
DW_Scheme scheme) |
RealMatrix |
Stick.getJacobian(double[] modParams,
DW_Scheme scheme) |
RealMatrix |
CompartmentModel.getJacobian(double[] modParams,
DW_Scheme scheme)
Get Jacobian for each compartment separately.
|
RealMatrix |
Ball.getJacobian(double[] modParams,
DW_Scheme scheme)
Compute the jacobian of the signal.
|
double |
Zeppelin.getSignal(double[] params,
DW_Scheme scheme,
int i) |
double |
Tensor.getSignal(double[] params,
DW_Scheme rawScheme,
int i)
generates signals from this compartment for each line
in the scheme given.
|
double |
Stick.getSignal(double[] params,
DW_Scheme scheme,
int i) |
double |
SphereGPD.getSignal(double[] params,
DW_Scheme rawScheme,
int i)
generates signals from this compartment for one particular line
in the scheme given.
|
double |
ListDistributionCompartment.getSignal(double[] params,
DW_Scheme scheme,
int line) |
double |
GDRCylinders.getSignal(double[] params,
DW_Scheme rawScheme,
int i) |
double |
Dot.getSignal(double[] params,
DW_Scheme scheme,
int i)
return a single signal from the scheme from the dot model
|
double |
CylinderGPD.getSignal(double[] params,
DW_Scheme rawScheme,
int i)
generates signals from this compartment for one particular line
in the scheme given.
|
double |
CompartmentModel.getSignal(double[] modParams,
DW_Scheme scheme,
int line)
sum up the signals from each compartment
|
double |
Ball.getSignal(double[] params,
DW_Scheme scheme,
int i)
generates signals from this compartment for each line
in the scheme given.
|
double |
Astrosticks.getSignal(double[] params,
DW_Scheme rawScheme,
int i)
generates signals from this compartment for each line
in the scheme given.
|
double |
Astrocylinders.getSignal(double[] params,
DW_Scheme rawScheme,
int i)
generates signals from this compartment for the given line in the scheme
given.
|
RealMatrix |
Zeppelin.getSignals(double[] params,
DW_Scheme scheme)
generates signals from this compartment for each line
in the scheme given.
|
RealMatrix |
Tensor.getSignals(double[] params,
DW_Scheme rawScheme)
generates signals from this compartment for each line
in the scheme given.
|
RealMatrix |
Stick.getSignals(double[] params,
DW_Scheme scheme)
generates signals from this compartment for each line
in the scheme given.
|
RealMatrix |
SphereGPD.getSignals(double[] params,
DW_Scheme rawScheme)
generates signals from this compartment for each line
in the scheme given.
|
RealMatrix |
ListDistributionCompartment.getSignals(double[] params,
DW_Scheme scheme) |
RealMatrix |
GDRCylinders.getSignals(double[] params,
DW_Scheme rawScheme)
generates signals from this compartment for each line
in the scheme given.
|
RealMatrix |
Dot.getSignals(double[] params,
DW_Scheme scheme)
generates signals from this compartment for each line
in the scheme given.
|
RealMatrix |
CylinderGPD.getSignals(double[] params,
DW_Scheme rawScheme)
generates signals from this compartment for each line
in the scheme given.
|
RealMatrix |
CompartmentModel.getSignals(double[] modParams,
DW_Scheme scheme)
sum up the signals from each compartment
|
RealMatrix |
Ball.getSignals(double[] params,
DW_Scheme scheme)
generates signals from this compartment for each line
in the scheme given.
|
RealMatrix |
Astrosticks.getSignals(double[] params,
DW_Scheme rawScheme)
generates signals from this compartment for each line
in the scheme given.
|
RealMatrix |
Astrocylinders.getSignals(double[] params,
DW_Scheme rawScheme)
generates signals from this compartment for each line in the scheme
given.
|
Constructor and Description |
---|
CompartmentModel(java.lang.String[] comps,
double[] params,
DW_Scheme scheme)
constructor with scheme for use in data synthesis.
|
Constructor and Description |
---|
LM_GaussianMinimizer(DW_Scheme scheme,
ParametricModel pm,
Codec cod)
Constructor needs all the following:
|
LM_OffGaussMinimizer(DW_Scheme scheme,
ParametricModel pm,
Codec cod,
double sigma)
Constructor needs all the following:
|
LM_RicianMinimizer(DW_Scheme scheme,
ParametricModel pm,
Codec cod,
double sigma)
Constructor needs all the following:
|
MCMC_GaussianMinimizer(DW_Scheme scheme,
ParametricModel pm,
Codec cod,
Prior p,
Perturbation pb,
double sigma)
Constructor needs all the following:
|
MCMC_OffGaussMinimizer(DW_Scheme scheme,
ParametricModel pm,
Codec cod,
Prior p,
Perturbation pb,
double sigma)
Constructor needs all the following:
|
MCMC_RicianMinimizer(DW_Scheme scheme,
ParametricModel pm,
Codec cod,
Prior p,
Perturbation pb,
double sigma)
Constructor needs all the following:
|
MultiRunLM_GaussianMinimizer(DW_Scheme scheme,
ParametricModel pm,
Codec cod,
Perturbation p,
int repeats,
int seed) |
MultiRunLM_Minimizer(DW_Scheme scheme,
ParametricModel pm,
Codec cod,
Perturbation p,
int repeats,
int seed) |
MultiRunLM_OffGaussMinimizer(DW_Scheme scheme,
ParametricModel pm,
Codec cod,
Perturbation p,
int repeats,
int seed,
double sigma) |
MultiRunLM_RicianMinimizer(DW_Scheme scheme,
ParametricModel pm,
Codec cod,
Perturbation p,
int repeats,
int seed,
double sigma) |
MultiRunMinimizer(DW_Scheme scheme,
ParametricModel pm,
Codec cod,
Perturbation p,
int repeats,
int seed)
Constructor needs all the following:
|
Modifier and Type | Field and Description |
---|---|
static DW_Scheme |
CL_Initializer.imPars
The parameters of the imaging sequence corresponding to the input data.
|
Modifier and Type | Method and Description |
---|---|
static DataSource |
CL_Initializer.getDataSynthesizer(ModelPDF p,
DW_Scheme imPars,
double SNR,
int numVoxels,
int seed,
int bootstrap)
Creates the source of data from options specified on the command line.
|
Modifier and Type | Method and Description |
---|---|
static BayesDiracTractographyImage |
BayesDiracTractographyImage.getBayesDiracTractographyImage(java.lang.String inputFile,
java.lang.String dataType,
DW_Scheme scheme,
DataModel dataModel,
int[][][] numPDs,
double[][][] anisMap,
double anisThresh,
int[] dataDims,
double[] voxelDims,
int pointSetInd,
java.util.Random ran)
Gets an image from the data file.
|
static RepBS_DT_TractographyImage |
RepBS_DT_TractographyImage.getBS_TractographyImage(java.lang.String[] inputFiles,
java.lang.String dataType,
DW_Scheme imPars,
ModelIndex[] indices,
int[][][] vc,
double[][][] anisMap,
double anisThresh,
int[] dataDims,
double[] voxelDims,
java.util.Random ran)
Gets an image from the data file.
|
static WildBS_DT_TractographyImage |
WildBS_DT_TractographyImage.getBS_TractographyImage(java.lang.String inputFile,
java.lang.String dataType,
DW_Scheme imPars,
int[][][] vc,
double[][][] anisMap,
double anisThresh,
int[] dataDims,
double[] voxelDims,
java.util.Random ran)
Gets an image from the data file.
|
Constructor and Description |
---|
BayesDiracBallStickRandomizer(float[][][][] data,
DW_Scheme scheme,
int pointSetInd,
java.util.Random ran) |
BayesDiracBallStickRandomizer(float[][][][] data,
DW_Scheme scheme,
java.util.Random ran) |
BayesDiracCylSymmTensorRandomizer(float[][][][] data,
DW_Scheme scheme,
int pointSetInd,
java.util.Random ran) |
BayesDiracCylSymmTensorRandomizer(float[][][][] data,
DW_Scheme scheme,
java.util.Random ran) |
BayesDiracRandomizer(float[][][][] data,
DW_Scheme scheme,
int pointSetIndex,
java.util.Random ran) |
BayesDiracRandomizer(float[][][][] data,
DW_Scheme scheme,
java.util.Random ran) |
BayesDiracTractographyImage(float[][][][] data,
double[] voxelDims,
int[][][] numPDs,
DW_Scheme scheme,
DataModel model,
int pointSetInd,
java.util.Random ran)
Matlab constructor.
|
BootstrapTractographyImage(int[] dataDims,
double[] voxelDims,
int vectorsPerPD,
int[][][] vc,
DW_Scheme imPars,
java.util.Random r) |
BS_DT_TractographyImage(int[] dataDims,
double[] voxelDims,
int[][][] vc,
ModelIndex[] indices,
DW_Scheme imPars,
java.util.Random r)
Construct an image.
|
OneTensorLUTGenerator(DW_Scheme ip,
double snr,
double trace,
java.util.Random r) |
RepBS_DT_TractographyImage(float[][][][][] data,
double[] voxelDims,
int[][][] vc,
ModelIndex[] indices,
DW_Scheme imPars,
java.util.Random r) |
TwoTensorLUTGenerator(DW_Scheme ip,
double snr,
double trace,
double prop,
double cross,
java.util.Random r) |
WildBS_DT_TractographyImage(float[][][][] data,
double[] voxelDims,
int[][][] vc,
DW_Scheme imPars,
java.util.Random r) |