edu.rit.mri

Class PixelTissues

java.lang.Object

edu.rit.mri.PixelTissues

All Implemented Interfaces:

java.io.Externalizable, java.io.Serializable

public class PixelTissues
extends java.lang.Object
implements java.io.Externalizable

Class PixelTissues encapsulates the results of a spin relaxometry analysis on one pixel of a magnetic resonance image. This includes:

• File index.
• Pixel index.
• Pixel's computed spin density ρ for each tissue.
• Pixel's computed spin-lattice relaxation rate R1 for each tissue.

Each spin density and spin-lattice relaxation rate is stored as a value of type double.

Operations are provided to read a pixel tissues object from a DataInputStream and write a pixel tissues object to a DataOutputStream. The format is:

• Number of tissues, L (2-byte short).
• L spin density values, each an 8-byte double.
• L spin-lattice relaxation rate values, each an 8-byte double.

Operations are provided to read a pixel tissues object from an ObjectInputStream and write a pixel tissues object to an ObjectOutputStream. The format is:

• File index (4-byte int).
• Pixel index (4-byte int).
• Number of tissues, L (2-byte short).
• L spin density values, each an 8-byte double.
• L spin-lattice relaxation rate values, each an 8-byte double.

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
PixelTissues() Construct a new, uninitialized pixel tissues object.
PixelTissues(int fileIndex, int pixelIndex, java.util.List<java.lang.Double> rho_list, java.util.List<java.lang.Double> R1_list) Construct a new pixel tissues object.

Method Summary

Modifier and Type	Method and Description
int	fileIndex() Get the file index.
void	fileIndex(int index) Specify the file index.
int	numTissues() Get the number of tissues computed for this pixel.
int	pixelIndex() Get the pixel index.
void	pixelIndex(int index) Specify the pixel index.
double	R1(int i) Get the given tissue's spin-lattice relaxation rate.
void	read(java.io.DataInput in) Read this pixel tissues object from the given data input stream.
void	readExternal(java.io.ObjectInput in) Read this pixel tissues object from the given object input stream.
double	rho(int i) Get the given tissue's spin density.
Series	S_series(Series t_series) Get a series containing this pixel's computed spin signal for the given time series.
double	S(double t) Get this pixel's computed spin signal at the given time.
void	tissues(java.util.List<java.lang.Double> rho_list, java.util.List<java.lang.Double> R1_list) Specify the tissues for this pixel.
void	write(java.io.DataOutput out) Write this pixel tissues object to the given data output stream.
void	writeExternal(java.io.ObjectOutput out) Write this pixel tissues object to the given object output stream.

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

PixelTissues

public PixelTissues()

Construct a new, uninitialized pixel tissues object. This constructor is for use only by object deserialization.

PixelTissues

public PixelTissues(int fileIndex,
                    int pixelIndex,
                    java.util.List<java.lang.Double> rho_list,
                    java.util.List<java.lang.Double> R1_list)

Construct a new pixel tissues object. If a solution could not be computed for this pixel, rho and R1 are null.

Parameters:

fileIndex - File index.

pixelIndex - Pixel index.

rho_list - List containing computed spin densities, or null.

R1_list - List containing computed spin-lattice relaxation rates, or null.

Throws:

java.lang.IllegalArgumentException - (unchecked exception) Thrown if index < 0. Thrown if rho_list and R1_list are not the same length.

Method Detail

fileIndex

public int fileIndex()

Get the file index.

Returns:

File index.

fileIndex

public void fileIndex(int index)

Specify the file index.

Parameters:

index - File index.

pixelIndex

public int pixelIndex()

Get the pixel index.

Returns:

Pixel index.

pixelIndex

public void pixelIndex(int index)

Specify the pixel index.

Parameters:

index - Pixel index.

tissues

public void tissues(java.util.List<java.lang.Double> rho_list,
                    java.util.List<java.lang.Double> R1_list)

Specify the tissues for this pixel. If a solution could not be computed for this pixel, rho and R1 are null.

Parameters:

rho_list - List containing computed spin densities, or null.

R1_list - List containing computed spin-lattice relaxation rates, or null.

Throws:

java.lang.IllegalArgumentException - (unchecked exception) Thrown if rho_list and R1_list are not the same length.

numTissues

public int numTissues()

Get the number of tissues computed for this pixel. If the analysis could not find a solution for this pixel, 0 is returned.

Returns:

Number of tissues, L.

rho

public double rho(int i)

Get the given tissue's spin density.

Parameters:

i - Tissue index, 0 ≤ i ≤ L−1.

Returns:

Spin density, ρ_i.

Throws:

java.lang.IndexOutOfBoundsException - (unchecked exception) Thrown if i is out of bounds.

R1

public double R1(int i)

Get the given tissue's spin-lattice relaxation rate.

Parameters:

i - Tissue index, 0 ≤ i ≤ L−1.

Returns:

Spin-lattice relaxation rate, R1_i.

Throws:

java.lang.IndexOutOfBoundsException - (unchecked exception) Thrown if i is out of bounds.

S

public double S(double t)

Get this pixel's computed spin signal at the given time. The formula is: S(t) = Σ_i ρ_i [1 − 2 exp(−R1_i t)] If the analysis could not find a solution for this pixel, 0 is returned.

Parameters:

t - Time.

Returns:

Spin signal, S(t).

S_series

public Series S_series(Series t_series)

Get a series containing this pixel's computed spin signal for the given time series. If the analysis could not find a solution for this pixel, null is returned.

Parameters:

t_series - Series of times, t_j.

Returns:

Series of spin signals, S(t_j), or null.

write

public void write(java.io.DataOutput out)
           throws java.io.IOException

Write this pixel tissues object to the given data output stream.

Note: The file index and pixel index are not written.

Parameters:

out - Data output stream.

Throws:

java.io.IOException - Thrown if an I/O error occurred.

read

public void read(java.io.DataInput in)
          throws java.io.IOException

Read this pixel tissues object from the given data input stream.

Note: The file index and pixel index are not read.

Parameters:

in - Data input stream.

Throws:

java.io.IOException - Thrown if an I/O error occurred.

writeExternal

public void writeExternal(java.io.ObjectOutput out)
                   throws java.io.IOException

Write this pixel tissues object to the given object output stream.

Specified by:

writeExternal in interface java.io.Externalizable

Parameters:

out - Object output stream.

Throws:

java.io.IOException - Thrown if an I/O error occurred.

readExternal

public void readExternal(java.io.ObjectInput in)
                  throws java.io.IOException

Read this pixel tissues object from the given object input stream.

Specified by:

readExternal in interface java.io.Externalizable

Parameters:

in - Object input stream.

Throws:

java.io.IOException - Thrown if an I/O error occurred.