com.xinapse.dynamic
Interface DynamicModel

All Known Implementing Classes:

AbstractDynamicContrastModel, DCEMRIModel

public interface DynamicModel

An interface implemented by classes that can fit to dynamic signals that vary as a function of time.

Nested Class Summary

static class

DynamicModel.SpecifierPanel A JPanel that can be used to specify dynamic model parameters.

Method Summary

boolean	computesRMSDiff() Signals whether the model computes the root-mean-square (RMS) difference between the model and the data.
DynamicResult	fit(float[] S, int col, int row, int slice, AutoCorrelationEstimate autoCorrelationEstimate) Calculate the model parameters that best fit the data.
boolean	getCorrectAutoCorrelation() Signals whether the model requires the autocorrelation in the time-series to be estimated when computing significance levels.
boolean	getDoBonferroni() Returns true if this DynmicModel does Bonferroni correction; false otherwise.
float	getDt() Returns the time between data samples.
java.lang.String	getModelDescription() Returns a String describing this dynamic model.
java.lang.String	getModelName() Returns the model name.
ColourMapping[]	getVarColourMappings() Returns an array of the ColourMappings, in an order that matches the order of the variable names returned by getVarNames().
java.lang.String[]	getVarNames() Returns an array of the names of the fitted variables, in an order that matches the order of the variable units returned by getVarUnits().
java.lang.String[]	getVarUnits() Returns an array of the fitted variables units, in an order that matches the order of the variable names returned by getVarNames().
void	setBonferroniN(float nTests) Sets the number of independent fits that will be performed by the model.

Method Detail

getModelName

java.lang.String getModelName()

Returns the model name.

Returns:

the name of the dynamic model.

getModelDescription

java.lang.String getModelDescription()

Returns a String describing this dynamic model.

Returns:

a String describing this dynamic model.

getVarNames

java.lang.String[] getVarNames()

Returns an array of the names of the fitted variables, in an order that matches the order of the variable units returned by getVarUnits().

Returns:

the names of the fitted variables.

getVarUnits

java.lang.String[] getVarUnits()

Returns an array of the fitted variables units, in an order that matches the order of the variable names returned by getVarNames().

Returns:

the fitted variable units.

getVarColourMappings

ColourMapping[] getVarColourMappings()

Returns an array of the ColourMappings, in an order that matches the order of the variable names returned by getVarNames().

Returns:

the an array of ColourMappings for the calculated images. A null entry in the array indicates the corresponding variable image does not have a specific ColourMapping.

computesRMSDiff

boolean computesRMSDiff()

Signals whether the model computes the root-mean-square (RMS) difference between the model and the data.

Returns:

true if the model computes the (RMS) difference between the model and the data; false otherwise.

getCorrectAutoCorrelation

boolean getCorrectAutoCorrelation()

Signals whether the model requires the autocorrelation in the time-series to be estimated when computing significance levels. If autocorrelation is to be estimated, then the DynamicModelWorker uses a two-pass procedure, where the first pass is used only to estimate the residuals from which the autocorrelation is estimated. The second pass is used to calculate the model parameters.

Returns:

true if the model requires correction of autocorrelation; false otherwise.

getDt

float getDt()
            throws java.lang.IllegalStateException

Returns the time between data samples.

Returns:

the time between data samples.

Throws:

java.lang.IllegalStateException

getDoBonferroni

boolean getDoBonferroni()

Returns true if this DynmicModel does Bonferroni correction; false otherwise.

Returns:

true if this DynmicModel does Bonferroni correction; false otherwise.

setBonferroniN

void setBonferroniN(float nTests)
                    throws com.xinapse.util.InvalidArgumentException

Sets the number of independent fits that will be performed by the model. May be used for Bonferroni correction of calculated significance levels.

Parameters:

nTests - the number of independent fits that will be performed by the model.

Throws:

com.xinapse.util.InvalidArgumentException - if the significance level hasn't been set and Bonferroni correction has been turned on for this DynamicModel.

fit

DynamicResult fit(float[] S,
                  int col,
                  int row,
                  int slice,
                  AutoCorrelationEstimate autoCorrelationEstimate)

Calculate the model parameters that best fit the data.

Parameters:

S - the dynamic signal intensity S(t). S includes all the time points, including any data which is pre-steady-state.

col - the image column that is being analyzed.

row - the image row that is being analyzed.

slice - the image slice that is being analyzed.

autoCorrelationEstimate - an estimate of the temporal auto-correlation at each pixel.