Class defining a spatial grid, i.e. a matrix of double. The grid is padded, 3D grid. More...

Inheritance diagram for simulator.SpatialGrid:

Public Member Functions
	SpatialGrid ()
	Blank constructor. More...

	SpatialGrid (int nI, int nJ, int nK, double resolution)
	Default constructor for an empty spatial grid. More...

	SpatialGrid (int nI, int nJ, double resolution)
	Default constructor for an empty 2D spatial grid. More...

boolean	isValid (DiscreteVector dC)
	Determine if a given discrete position is valid or outside the grid (Padding excluded) More...

boolean	isValidOrPadded (DiscreteVector dC)
	Determine if a given discrete position is valid or outside the grid (Padding included) More...

boolean	isValidorPadded (int i, int j, int k)
	Determine if a given voxel coordinate is valid or outside the grid. More...

boolean	isValid (ContinuousVector cc)
	Determine if a given continuous location is valid or outside the grid. More...

boolean	isValidOrPadded (ContinuousVector cc)
	Test if a location is valid or is outside the grid. Note padding is included as valid. More...

DiscreteVector	getDiscreteCoordinates (ContinuousVector cC)
	Transform a location, expressed as a continuous vector into a discrete position on the basis of the resolution of the grid. More...

ContinuousVector	getContinuousCoordinates (DiscreteVector dC)
	Transform a position, expressed as a discrete vector into a continuous location on the basis of the resolution of the grid. More...

ContinuousVector	getContinuousCoordinates (int i, int j, int k)
	Convert a set of voxel coordinates into a continuous vector. More...

double	getMax ()
	Return the maximum value on this grid (padding included) More...

double	getAverage ()
	Return the average value on this grid (padding included) More...

double	getSum ()
	Return the sum of this grid. More...

double	getMin ()
	Return the minimum value on this grid (padding included) More...

double	diff2X (int i, int j, int k)
	For a given location, calculate the 2nd spatial derivative according to X. More...

double	diff2X (DiscreteVector dV)
	For a given location, expressed as a discrete vector, calculate the 2nd spatial derivative according to X. More...

double	diffX (int i, int j, int k)
	For a given location, calculate the 1st spatial derivative according to X. More...

double	diffX (DiscreteVector dV)
	For a given location, expressed as a discrete vector, calculate the 1st spatial derivative according to X. More...

double	diff2Y (int i, int j, int k)
	For a given location, calculate the 2nd spatial derivative according to Y. More...

double	diff2Y (DiscreteVector dV)
	For a given location, expressed as a discrete vector, calculate the 2nd spatial derivative according to Y. More...

double	diffY (int i, int j, int k)
	For a given location, calculate the 1st spatial derivative according to Y. More...

double	diffY (DiscreteVector dV)
	For a given location, expressed as a discrete vector, calculate the 1st spatial derivative according to Y. More...

double	diff2Z (int i, int j, int k)
	For a given location, calculate the 2nd spatial derivative according to Z. More...

double	diffZ (int i, int j, int k)
	For a given location, calculate the 1st spatial derivative according to Z. More...

double	diffZ (DiscreteVector dV)
	For a given location, expressed as a discrete vector, calculate the 1st spatial derivative according to Z. More...

double	getValueAround (ContinuousVector cC, double extReso)
	Computes the average concentration seen in a sphere (or cube) centered around a given point. More...

double	getValueAround (LocatedAgent aLocAgent)
	Returns the average grid value seen in a sphere (or cube) located around a given agent. More...

double	getValueAt (ContinuousVector cC)
	Return the value stored at the location given by the stated continuous vector. More...

ContinuousVector	getGradient (ContinuousVector cC)
	Returns a vector of the first spatial derivatives in x, y & z. More...

ContinuousVector	getGradient2D (ContinuousVector cC)
	Returns a vector of the first spatial derivatives in x and y, for 2D simulations. More...

double	getValueAt (DiscreteVector dV)
	Return the value on the padded grid at a given position (the coordinates are NOT corrected) More...

double	getValueAt (int i, int j, int k)
	Return the value on the padded grid at a given position (the coordinates are NOT corrected) More...

void	setValueAt (double value, ContinuousVector cC)
	Set a grid location, expressed as a ContinuousVector, to a specified value. The coordinates are corrected. More...

void	setValueAt (double value, DiscreteVector dC)
	Set a grid location, expressed as a DiscreteVector, to a specified value. The coordinates are corrected. More...

void	setValueAt (double value, int i, int j, int k)
	Set a grid location to a specified value. Note the coordinates are NOT corrected. More...

void	addValueAt (double value, ContinuousVector cC)
	Add a value to that contained at the given discrete coordinates of this grid. Coordinates are corrected for padding. More...

void	addValueAt (double value, DiscreteVector dC)
	Add a value to that contained at the given discrete coordinates of this grid. Coordinates are corrected for padding. More...

void	addAllValues (double value)
	Add a value to all locations on this grid (including the padding) More...

void	truncateValueAt (int i, int j, int k)
	Checks a value at a given location and sets it to zero if the value is negative. More...

void	setAllValueAt (double value)
	Set all meshes of a grid with the same value (including the padding - if not a chemostat run) More...

int	getGridSizeI ()
	Return the number of voxels in the X direction. More...

int	getGridSizeJ ()
	Return the number of voxels in the Y direction. More...

int	getGridSizeK ()
	Return the number of voxels in the Z direction. More...

int	getGridTotalSize (int axeCode)
	Return the number of voxels along a given direction (axeCode) More...

double	getGridLength (int axeCode)
	Returns the length (in distance unit) along a given direction. More...

double	getVoxelVolume ()
	Return the volume of one voxel of the spatial grid. More...

double[][][]	getGrid ()
	Return the whole grid including the padding. More...

double[][][]	getCloneGrid ()
	Return a clone of this spatial grid. More...

double	getResolution ()
	Returns the resolution of this spatial grid. More...

boolean	is3D ()
	Determine if this spatial grid is 3D or 2D. More...

void	setGrid (double[][][] u)
	Set the values of this spatial grid to those contained in the supplied grid. More...

void	writeReport (ResultFile bufferState, ResultFile bufferSummary) throws Exception
	Write the contents of this grid to the XML results files. More...

Public Attributes
String	gridName

String	gridUnit = "g.L-1"

double[][][]	grid

Protected Member Functions
void	initGrids ()
	Creates the solute grid at the required size. More...

Protected Attributes
int	_nI

int	_nJ

int	_nK

double	_reso

boolean	_is3D

Detailed Description

Class defining a spatial grid, i.e. a matrix of double. The grid is padded, 3D grid.

Class defining a spatial grid, i.e. a matrix of double. The grid is padded, 3D grid

Author: Andreas Dötsch (andre.nosp@m.as.d.nosp@m.oetsc.nosp@m.h@he.nosp@m.lmhol.nosp@m.tz-h.nosp@m.zi.de), Helmholtz Centre for Infection Research (Germany); Laurent Lardon (lardo.nosp@m.nl@s.nosp@m.upagr.nosp@m.o.in.nosp@m.ra.fr), INRA, France; Sónia Martins (SCM80.nosp@m.8@bh.nosp@m.am.ac.nosp@m..uk), Centre for Systems Biology, University of Birmingham (UK)

Constructor & Destructor Documentation

simulator.SpatialGrid.SpatialGrid ( )

Blank constructor.

Blank constructor

simulator.SpatialGrid.SpatialGrid	(	int	nI,
		int	nJ,
		int	nK,
		double	resolution
	)

Default constructor for an empty spatial grid.

Default constructor for an empty spatial grid. Sets the grid resolution and dimensions as provided in the simulation protocol file

Parameters

nI	The number of grid locations in the I direction
nJ	The number of grid locations in the J direction
nK	The number of grid locations in the K direction
resolution	the grid resolution

simulator.SpatialGrid.SpatialGrid	(	int	nI,
		int	nJ,
		double	resolution
	)

Default constructor for an empty 2D spatial grid.

Default constructor for an empty 2D spatial grid. Sets the grid resolution and dimensions as provided in the simulation protocol file

Parameters

nI	The number of grid locations in the I direction
nJ	The number of grid locations in the J direction
resolution	the grid resolution

Member Function Documentation

void simulator.SpatialGrid.addAllValues ( double value )

Add a value to all locations on this grid (including the padding)

Parameters

value Value to be added to the contents of all grid voxels

void simulator.SpatialGrid.addValueAt	(	double	value,
		ContinuousVector	cC
	)

Add a value to that contained at the given discrete coordinates of this grid. Coordinates are corrected for padding.

Add a value to that contained at the given discrete coordinates of this grid. Coordinates are corrected for padding

Parameters

value	Value to add to the specified grid location
cC	Continuous vector expressing the location of the grid to be increased

void simulator.SpatialGrid.addValueAt	(	double	value,
		DiscreteVector	dC
	)

Add a value to that contained at the given discrete coordinates of this grid. Coordinates are corrected for padding.

Add a value to that contained at the given discrete coordinates of this grid. Coordinates are corrected for padding

Parameters

value	Value to add to the specified grid location
dC	Discrete vector expressing the location of the grid to be increased

double simulator.SpatialGrid.diff2X	(	int	i,
		int	j,
		int	k
	)

For a given location, calculate the 2nd spatial derivative according to X.

For a given location, calculate the 2nd spatial derivative according to X

Parameters

i	I position on the spatial grid
j	J position on the spatial grid
k	K position on the spatial grid

Returns: 2nd spatial derivative according X

double simulator.SpatialGrid.diff2X ( DiscreteVector dV )

For a given location, expressed as a discrete vector, calculate the 2nd spatial derivative according to X.

For a given location, expressed as a discrete vector, calculate the 2nd spatial derivative according to X

Parameters

dV	DiscreteVector containing the position of a grid location

Returns: 2nd spatial derivative according X

double simulator.SpatialGrid.diff2Y	(	int	i,
		int	j,
		int	k
	)

For a given location, calculate the 2nd spatial derivative according to Y.

For a given location, calculate the 2nd spatial derivative according to Y

Parameters

i	I position on the spatial grid
j	J position on the spatial grid
k	K position on the spatial grid

Returns: 2nd spatial derivative according Y

double simulator.SpatialGrid.diff2Y ( DiscreteVector dV )

For a given location, expressed as a discrete vector, calculate the 2nd spatial derivative according to Y.

For a given location, expressed as a discrete vector, calculate the 2nd spatial derivative according to Y

Parameters

dV	DiscreteVector containing the position of a grid location

Returns: 2nd spatial derivative according Y

double simulator.SpatialGrid.diff2Z	(	int	i,
		int	j,
		int	k
	)

For a given location, calculate the 2nd spatial derivative according to Z.

For a given location, calculate the 2nd spatial derivative according to Z

Parameters

i	I position on the spatial grid
j	J position on the spatial grid
k	K position on the spatial grid

Returns: 2nd spatial derivative according Z

double simulator.SpatialGrid.diffX	(	int	i,
		int	j,
		int	k
	)

For a given location, calculate the 1st spatial derivative according to X.

For a given location, calculate the 1st spatial derivative according to X

Parameters

i	I position on the spatial grid
j	J position on the spatial grid
k	K position on the spatial grid

Returns: 1st spatial derivative according X

double simulator.SpatialGrid.diffX ( DiscreteVector dV )

For a given location, expressed as a discrete vector, calculate the 1st spatial derivative according to X.

For a given location, expressed as a discrete vector, calculate the 1st spatial derivative according to X

Parameters

dV	DiscreteVector containing the position of a grid location

Returns: 1st spatial derivative according X

double simulator.SpatialGrid.diffY	(	int	i,
		int	j,
		int	k
	)

For a given location, calculate the 1st spatial derivative according to Y.

For a given location, calculate the 1st spatial derivative according to Y

Parameters

i	I position on the spatial grid
j	J position on the spatial grid
k	K position on the spatial grid

Returns: 1st spatial derivative according Y

double simulator.SpatialGrid.diffY ( DiscreteVector dV )

For a given location, expressed as a discrete vector, calculate the 1st spatial derivative according to Y.

For a given location, expressed as a discrete vector, calculate the 1st spatial derivative according to Y

Parameters

dV	DiscreteVector containing the position of a grid location

Returns: 1st spatial derivative according Y

double simulator.SpatialGrid.diffZ	(	int	i,
		int	j,
		int	k
	)

For a given location, calculate the 1st spatial derivative according to Z.

For a given location, calculate the 1st spatial derivative according to Z

Parameters

i	I position on the spatial grid
j	J position on the spatial grid
k	K position on the spatial grid

Returns: 1st spatial derivative according Z

double simulator.SpatialGrid.diffZ ( DiscreteVector dV )

For a given location, expressed as a discrete vector, calculate the 1st spatial derivative according to Z.

For a given location, expressed as a discrete vector, calculate the 1st spatial derivative according to Z

Parameters

dV	DiscreteVector containing the position of a grid location

Returns: 1st spatial derivative according Z

double simulator.SpatialGrid.getAverage ( )

Return the average value on this grid (padding included)

Returns: Average value of the grid

double [][][] simulator.SpatialGrid.getCloneGrid ( )

Return a clone of this spatial grid.

Return a clone of this spatial grid

Returns: A clone of this spatial grid

ContinuousVector simulator.SpatialGrid.getContinuousCoordinates ( DiscreteVector dC )

Transform a position, expressed as a discrete vector into a continuous location on the basis of the resolution of the grid.

Transform a position, expressed as a discrete vector into a continuous location on the basis of the resolution of the grid

Parameters

dC	DiscreteVector to be transformed

Returns: ContinuousVector created from this discrete position

ContinuousVector simulator.SpatialGrid.getContinuousCoordinates	(	int	i,
		int	j,
		int	k
	)

Convert a set of voxel coordinates into a continuous vector.

Convert a set of voxel coordinates into a continuous vector

Parameters

i	I Coordinate of the grid location
j	J Coordinate of the grid location
k	K Coordinate of the grid location

Returns: ContinuousVector created from these voxel coordinates

DiscreteVector simulator.SpatialGrid.getDiscreteCoordinates ( ContinuousVector cC )

Transform a location, expressed as a continuous vector into a discrete position on the basis of the resolution of the grid.

Transform a location, expressed as a continuous vector into a discrete position on the basis of the resolution of the grid

Parameters

cC	ContinuousVector to be transformed

Returns: DiscreteVector created from this continuous location

ContinuousVector simulator.SpatialGrid.getGradient ( ContinuousVector cC )

Returns a vector of the first spatial derivatives in x, y & z.

Returns a vector of the first spatial derivatives in x, y & z (nabla cC - see http://en.wikipedia.org/wiki/Del). Does this by first converting the ContinuousVector to a DiscreteVector and then estimating then gradient using the Mean Value Theorem (http://en.wikipedia.org/wiki/Mean_value_theorem).

Parameters

cC	ContinuousVector position used to calculate the gradient

Returns: Vector of spatial derivatives in X,Y,Z

ContinuousVector simulator.SpatialGrid.getGradient2D ( ContinuousVector cC )

Returns a vector of the first spatial derivatives in x and y, for 2D simulations.

Returns a vector of the first spatial derivatives in x and y (nabla cC - see http://en.wikipedia.org/wiki/Del). Does this by first converting the ContinuousVector to a DiscreteVector and then estimating then gradient using the Mean Value Theorem (http://en.wikipedia.org/wiki/Mean_value_theorem).

Parameters

cC	ContinuousVector position used to calculate the gradient

Returns: Vector of spatial derivatives in X and Y

double [][][] simulator.SpatialGrid.getGrid ( )

Return the whole grid including the padding.

Return the whole grid including the padding

Returns: the spatial grid

double simulator.SpatialGrid.getGridLength ( int axeCode )

Returns the length (in distance unit) along a given direction.

Returns the length (in distance unit) along a given direction. The direction is stated as an integer: 1 for X, 2 for Y, 3 for Z

Parameters

axeCode The direction of which the length is required: 1-X, 2-Y, 3-Z

Returns: Double value stating the length (in distance unit) along a direction ignoring padding bands

int simulator.SpatialGrid.getGridSizeI ( )

Return the number of voxels in the X direction.

Return the number of voxels in the X direction (ignoring the padding)

Returns: Number of real voxels along X

int simulator.SpatialGrid.getGridSizeJ ( )

Return the number of voxels in the Y direction.

Return the number of voxels in the Y direction (ignoring the padding)

Returns: Number of real voxels along Y

int simulator.SpatialGrid.getGridSizeK ( )

Return the number of voxels in the Z direction.

Return the number of voxels in the Z direction (ignoring the padding)

Returns: Number of real voxels along Z

int simulator.SpatialGrid.getGridTotalSize ( int axeCode )

Return the number of voxels along a given direction (axeCode)

Return the number of voxels along a given direction (axeCode): 1-X, 2-Y,3-Z

Parameters

axeCode Integer noting the direction to query

Returns: : the number of voxels along a direction including padding bands

double simulator.SpatialGrid.getMax ( )

Return the maximum value on this grid (padding included)

Returns: Maximum value of the grid

double simulator.SpatialGrid.getMin ( )

Return the minimum value on this grid (padding included)

Returns: Minimum value of the grid

double simulator.SpatialGrid.getResolution ( )

Returns the resolution of this spatial grid.

Returns the resolution of this spatial grid

Returns: Double value stating the resolution (in micrometers) of this grid

double simulator.SpatialGrid.getSum ( )

Return the sum of this grid.

Return the sum of this grid

Returns: The sum of the values in this spatial grid

double simulator.SpatialGrid.getValueAround	(	ContinuousVector	cC,
		double	extReso
	)

Computes the average concentration seen in a sphere (or cube) centered around a given point.

Computes the average concentration seen in a sphere (or cube) centered around a given point

Parameters

cC	ContinuousVector containing the point to use as the centre of this search
extReso	Resolution to use in this search

Returns: Average grid value seen around this point

double simulator.SpatialGrid.getValueAround ( LocatedAgent aLocAgent )

Returns the average grid value seen in a sphere (or cube) located around a given agent.

Returns the average grid value seen in a sphere (or cube) located around a given agent

Parameters

aLocAgent The agent to use as the centre of the search

Returns: Average grid value seen around this point

double simulator.SpatialGrid.getValueAt ( ContinuousVector cC )

Return the value stored at the location given by the stated continuous vector.

Return the value stored at the location given by the stated continuous vector

Parameters

cC	ContinuousVector containing the grid location to return

Returns: Double value stored at that grid location

double simulator.SpatialGrid.getValueAt ( DiscreteVector dV )

Return the value on the padded grid at a given position (the coordinates are NOT corrected)

Parameters

dV	DiscreteVector containing the location of the grid whos value should be returned

Returns: The double value at that location

double simulator.SpatialGrid.getValueAt	(	int	i,
		int	j,
		int	k
	)

Return the value on the padded grid at a given position (the coordinates are NOT corrected)

Parameters

i	I Coordinate of the grid location to set
j	J Coordinate of the grid location to set
k	K Coordinate of the grid location to set

Returns: The double value at that location

double simulator.SpatialGrid.getVoxelVolume ( )

Return the volume of one voxel of the spatial grid.

Return the volume of one voxel of the spatial grid

Returns: Double value stating the volume of one voxel of the spatial grid

void simulator.SpatialGrid.initGrids ( )

protected

Creates the solute grid at the required size.

Creates the solute grid at the required size. If this is a chemostat, this will simple be a 1x1x1, if not there are further checks to determine whether we are simulating 3D or not

boolean simulator.SpatialGrid.is3D ( )

Determine if this spatial grid is 3D or 2D.

Determine if this spatial grid is 3D or 2D

Returns: Boolean noting whether this grid is 3D (true) or 2D (false)

boolean simulator.SpatialGrid.isValid ( DiscreteVector dC )

Determine if a given discrete position is valid or outside the grid (Padding excluded)

Parameters

dC	DiscreteVector to validate

Returns: Boolean stating whether this location is valid (true) or outside the grid

boolean simulator.SpatialGrid.isValid ( ContinuousVector cc )

Determine if a given continuous location is valid or outside the grid.

Determine if a given continuous location is valid or outside the grid

Parameters

cc	ContinuousVector to validate

Returns: Boolean stating whether this location is valid (true) or outside the grid

boolean simulator.SpatialGrid.isValidOrPadded ( DiscreteVector dC )

Determine if a given discrete position is valid or outside the grid (Padding included)

Determine if a given discrete position is valid or outside the grid

Parameters

dC	DiscreteVector to validate

Returns: Boolean stating whether this location is valid (true) or outside the grid

boolean simulator.SpatialGrid.isValidorPadded	(	int	i,
		int	j,
		int	k
	)

Determine if a given voxel coordinate is valid or outside the grid.

Determine if a given voxel coordinate is valid or outside the grid

Parameters

i	I Coordinate of the grid location
j	J Coordinate of the grid location
k	K Coordinate of the grid location

Returns: Boolean stating whether this location is valid (true) or outside the grid

boolean simulator.SpatialGrid.isValidOrPadded ( ContinuousVector cc )

Test if a location is valid or is outside the grid. Note padding is included as valid.

Test if a location is valid or is outside the grid. Note padding is included as valid

Parameters

cc	ContinuousVector containing the location to be tested

Returns: Boolean stating whether this location is valid (true) or outside the grid

void simulator.SpatialGrid.setAllValueAt ( double value )

Set all meshes of a grid with the same value (including the padding - if not a chemostat run)

Set all meshes of a grid with the same value (including the padding if not a chemostat simulation)

Parameters

value Value at which to set all the elements of the grid

void simulator.SpatialGrid.setGrid ( double u[][][] )

Set the values of this spatial grid to those contained in the supplied grid.

Parameters

u	Matrix of values which to set the spatial grid to

void simulator.SpatialGrid.setValueAt	(	double	value,
		ContinuousVector	cC
	)

Set a grid location, expressed as a ContinuousVector, to a specified value. The coordinates are corrected.

Set a grid location, expressed as a ContinuousVector, to a specified value. The coordinates are corrected

Parameters

value	Value to set the specified location to
cC	Continuous vector stating the location of the grid to be set to the given value

void simulator.SpatialGrid.setValueAt	(	double	value,
		DiscreteVector	dC
	)

Set a grid location, expressed as a DiscreteVector, to a specified value. The coordinates are corrected.

Set a grid location, expressed as a DiscreteVector, to a specified value. The coordinates are corrected

Parameters

value	Value to set the specified location to
dC	Discrete vector stating the location of the grid to be set to the given value

void simulator.SpatialGrid.setValueAt	(	double	value,
		int	i,
		int	j,
		int	k
	)

Set a grid location to a specified value. Note the coordinates are NOT corrected.

Set a grid location to a specified value. Note the coordinates are NOT corrected

Parameters

value	Value to set the grid location to
i	I Coordinate of the grid location to set
j	J Coordinate of the grid location to set
k	K Coordinate of the grid location to set

void simulator.SpatialGrid.truncateValueAt	(	int	i,
		int	j,
		int	k
	)

Checks a value at a given location and sets it to zero if the value is negative.

Checks a value at a given location and sets it to zero if the value is negative

Parameters

i	Voxel coordinate in I direction
j	Voxel coordinate in J direction
k	Voxel coordinate in K direction

void simulator.SpatialGrid.writeReport	(	ResultFile	bufferState,
		ResultFile	bufferSummary
	)		throws Exception

Write the contents of this grid to the XML results files.

Write the contents of this grid to the XML results files. This shows the level of solute in each of the grid spaces

Parameters

bufferState	The output buffer writing the env_state file for this iteration
bufferSummary	The output buffer writing the env_sum file for this iteration

Exceptions

Exception Exception thrown if these buffers cannot be opened for writing to

Member Data Documentation

boolean simulator.SpatialGrid._is3D

protected

Boolean noting whether this grid is 3D (true) or 2D (false)

int simulator.SpatialGrid._nI

protected

Number of grid voxels in I direction

int simulator.SpatialGrid._nJ

protected

Number of grid voxels in J direction

int simulator.SpatialGrid._nK

protected

Number of grid voxels in K direction

double simulator.SpatialGrid._reso

protected

Grid resolution = side length of a voxel

double [][][] simulator.SpatialGrid.grid

The solute grid - a three dimesional array of double values

String simulator.SpatialGrid.gridName

Name assigned to this spacial grid. Taken from an XML tag in the protocol file

String simulator.SpatialGrid.gridUnit = "g.L-1"

The unit for all values stored on this grid

The documentation for this class was generated from the following file:

/home/kieran/Dropbox/workspace/iDynoMiCS/src/simulator/SpatialGrid.java

Public Member Functions

Public Attributes

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation