com.xinapse.apps.perfusion
Class AbstractDynamicContrastModel

java.lang.Object
  com.xinapse.apps.perfusion.AbstractDynamicContrastModel

All Implemented Interfaces:

DynamicModel

Direct Known Subclasses:

DCEMRIModel

public abstract class AbstractDynamicContrastModel
extends java.lang.Object
implements DynamicModel

A Model that can be fitted to dynamic data where contrast agent is injected, and the tissue response to an input function is measured.

Nested Class Summary

Nested classes/interfaces inherited from interface com.xinapse.dynamic.DynamicModel

DynamicModel.SpecifierPanel

Field Summary

protected float[]

Cpa The blood plasma concentration in the feeding artery, Cpa(t).

Constructor Summary

protected

AbstractDynamicContrastModel(java.lang.String name, java.lang.String description, java.lang.String[] varNames, java.lang.String[] varUnits) Constructor used by sub-classes.

Method Summary

boolean	computesRMSDiff() Returns whether the dynamic contrast model computed the RMS difference between the model fit and the data.
abstract AbstractDynamicContrastResult	fit(float[] Ct, int col, int row, int slice, AutoCorrelationEstimate autoCorrelationEstimate) Calculate the model parameters that best fit the data.
boolean	getCorrectAutoCorrelation() Returns false, since the DynamicContrastModels do not do a correction for temporal autocorrelation.
boolean	getDoBonferroni() Returns false, since Bonferroni correction is not performed because significance value for the fitted parameters are not computed.
float	getDt() Returns the time between data samples.
java.lang.String	getModelDescription() Returns a String describing this dynamic contrast model.
java.lang.String	getModelName() Returns the model name.
ColourMapping[]	getVarColourMappings() Returns an array of ColourMappings, applicable for each of the output images.
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) Does nothing, since Bonferroni correction is not performed because significance value for the fitted parameters are not computed.
java.lang.String	toString() Returns the name of this DCEMRIModel.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

Cpa

protected float[] Cpa

The blood plasma concentration in the feeding artery, Cpa(t).

Constructor Detail

AbstractDynamicContrastModel

protected AbstractDynamicContrastModel(java.lang.String name,
                                       java.lang.String description,
                                       java.lang.String[] varNames,
                                       java.lang.String[] varUnits)

Constructor used by sub-classes. The varNames and varUnits must be in an order so that the variable names are matched to the correct units.

Parameters:

name - the model name.

description - a short description of the model.

varNames - the array of fitted variable names.

varUnits - the units of the fitted variables.

Method Detail

getModelName

public java.lang.String getModelName()

Returns the model name.

Specified by:

getModelName in interface DynamicModel

Returns:

the name of the dynamic contrast model.

getModelDescription

public java.lang.String getModelDescription()

Returns a String describing this dynamic contrast model.

Specified by:

getModelDescription in interface DynamicModel

Returns:

a String describing this dynamic contrast model.

getVarNames

public final 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().

Specified by:

getVarNames in interface DynamicModel

Returns:

the names of the fitted variables.

getVarUnits

public final 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().

Specified by:

getVarUnits in interface DynamicModel

Returns:

the fitted variable units.

getVarColourMappings

public ColourMapping[] getVarColourMappings()

Returns an array of ColourMappings, applicable for each of the output images. If any of the output images does not have a specific ColourMapping, the array entry should be null for the corresponding image.

Specified by:

getVarColourMappings in interface DynamicModel

Returns:

an array of ColourMappings, the length of which must be equal to the number of output parameters computed by the model. The default implementation returns an array of null values.

computesRMSDiff

public boolean computesRMSDiff()

Returns whether the dynamic contrast model computed the RMS difference between the model fit and the data.

Specified by:

computesRMSDiff in interface DynamicModel

Returns:

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

getDt

public float getDt()
            throws java.lang.IllegalStateException

Returns the time between data samples.

Specified by:

getDt in interface DynamicModel

Returns:

the time (in seconds) between data samples.

Throws:

java.lang.IllegalStateException

getDoBonferroni

public final boolean getDoBonferroni()

Returns false, since Bonferroni correction is not performed because significance value for the fitted parameters are not computed.

Specified by:

getDoBonferroni in interface DynamicModel

Returns:

true if this DynmicModel does Bonferroni correction; false otherwise.

setBonferroniN

public final void setBonferroniN(float nTests)

Does nothing, since Bonferroni correction is not performed because significance value for the fitted parameters are not computed.

Specified by:

setBonferroniN in interface DynamicModel

Parameters:

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

fit

public abstract AbstractDynamicContrastResult fit(float[] Ct,
                                                  int col,
                                                  int row,
                                                  int slice,
                                                  AutoCorrelationEstimate autoCorrelationEstimate)

Calculate the model parameters that best fit the data.

Specified by:

fit in interface DynamicModel

Parameters:

Ct - the tissue contrast agent concentration function, Ct(t), post-contrast.

col - the image column number that is being analysed - ignored.

row - the image column number that is being analysed - ignored.

slice - the slice number - ignored.

autoCorrelationEstimate - - ignored.

getCorrectAutoCorrelation

public boolean getCorrectAutoCorrelation()

Returns false, since the DynamicContrastModels do not do a correction for temporal autocorrelation.

Specified by:

getCorrectAutoCorrelation in interface DynamicModel

Returns:

false.

toString

public java.lang.String toString()

Returns the name of this DCEMRIModel.

Overrides:

toString in class java.lang.Object

Returns:

the name of this DCEMRIModel.