Routines for identifying particles

Functions
void	IPGZ::localMaximum2D (PixelArray2D< float > *intensityData, PixelArray2D< bool > *isMaxData, ParticleArray< float > *positionData, int filterWidth, int filterHeight, float minimumThreshold)
	Identifies the local maximum in 2D.
void	IPGZ::localMaximum3D (PixelArray3D< float > *intensityData, PixelArray3D< bool > *isMaxData, ParticleArray< float > *positionData, int filterWidth, int filterHeight, int filterDepth, float minimumThreshold)
	Identifies the local maximum in 3D.
void	IPGZ::eliminateNeighbors3D (PixelArray3D< bool > *inIsMaxData, PixelArray3D< bool > *outIsMaxData, ParticleArray< float > *inPosition, ParticleArray< float > *outPosition, int filterWidth, int filterHeight, int filterDepth)
	Eliminates any local maximum points that are too close together in 3D.
void	IPGZ::eliminateNeighbors2D (PixelArray2D< bool > *inIsMaxData, PixelArray2D< bool > *outIsMaxData, ParticleArray< float > *inPosition, ParticleArray< float > *outPosition, int filterWidth, int filterHeight)
	Eliminates any local maximum points that are too close together in 2D.
void	IPGZ::findParticles3D (PixelArray3D< float > *intensityData, PixelArray3D< bool > *isMaxData, ParticleArray< float > *positionData, int filterWidth, int filterHeight, int filterDepth, float minimumThreshold)
	Routine to identify particles in 3D; first calls the localMaximum3D() routine followed by eliminateNeighbors3D() routine and calculateCentroid3D().
void	IPGZ::findParticles2D (PixelArray2D< float > *intensityData, PixelArray2D< bool > *isMaxData, ParticleArray< float > *positionData, int filterWidth, int filterHeight, float minimumThreshold)
	Routine to identify particles in 2D; first calls the localMaximum2D() routine followed by eliminateNeighbors2D() routine and calculateCentroid2D().

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Function Documentation

void IPGZ::eliminateNeighbors2D	(	PixelArray2D< bool > *	inIsMaxData,
		PixelArray2D< bool > *	outIsMaxData,
		ParticleArray< float > *	inPosition,
		ParticleArray< float > *	outPosition,
		int	filterWidth,
		int	filterHeight
	)

Eliminates any local maximum points that are too close together in 2D.

The total number of particles is returned in the filteredPosition array via the size() function.

Parameters:

	inIsMaxData	Class instance that contains local maximum data.
	outIsMaxData	Class instance where filtered data will be saved.
	inPosition	Class instance that contains particle positions.
	outPosition	Class instance where filtered particle positions will be saved.
	filterWidth	Radius of filter along the width dimension of the array. Filter processes from -filterWidth to +filterWidth for each pixel.
	filterHeight	Radius of filter along the height dimension of the array. Filter processes from -filterHeight to +filterHeight for each pixel.

void IPGZ::eliminateNeighbors3D	(	PixelArray3D< bool > *	inIsMaxData,
		PixelArray3D< bool > *	outIsMaxData,
		ParticleArray< float > *	inPosition,
		ParticleArray< float > *	outPosition,
		int	filterWidth,
		int	filterHeight,
		int	filterDepth
	)

Eliminates any local maximum points that are too close together in 3D.

The total number of particles is returned in the filteredPosition array via the size() function.

Parameters:

	inIsMaxData	Class instance that contains local maximum data.
	outIsMaxData	Class instance where filtered data will be saved.
	inPosition	Class instance that contains particle positions.
	outPosition	Class instance where filtered particle positions will be saved.
	filterWidth	Radius of filter along the width dimension of the array. Filter processes from -filterWidth to +filterWidth for each pixel.
	filterHeight	Radius of filter along the height dimension of the array. Filter processes from -filterHeight to +filterHeight for each pixel.
	filterDepth	Radius of filter along the depth dimension of the array. Filter processes from -filterDepth to +filterDepth for each pixel.

void IPGZ::findParticles2D	(	PixelArray2D< float > *	intensityData,
		PixelArray2D< bool > *	isMaxData,
		ParticleArray< float > *	positionData,
		int	filterWidth,
		int	filterHeight,
		float	minimumThreshold
	)

Routine to identify particles in 2D; first calls the localMaximum2D() routine followed by eliminateNeighbors2D() routine and calculateCentroid2D().

The total number of particles is returned in the filteredPosition array via the size() function.

Parameters:

	intensityData	Class instance that contains the intensity data.
	isMaxData	Class instance to store whether a pixel is a local maximum or not.
	positionData	Class instance to store particle positions.
	filterWidth	Radius of filter along the width dimension of the array. Filter processes from -filterWidth to +filterWidth for each pixel.
	filterHeight	Radius of filter along the height dimension of the array. Filter processes from -filterHeight to +filterHeight for each pixel.

void IPGZ::findParticles3D	(	PixelArray3D< float > *	intensityData,
		PixelArray3D< bool > *	isMaxData,
		ParticleArray< float > *	positionData,
		int	filterWidth,
		int	filterHeight,
		int	filterDepth,
		float	minimumThreshold
	)

Routine to identify particles in 3D; first calls the localMaximum3D() routine followed by eliminateNeighbors3D() routine and calculateCentroid3D().

The total number of particles is returned in the filteredPosition array via the size() function.

Parameters:

	intensityData	Class instance that contains the intensity data.
	isMaxData	Class instance to store whether a pixel is a local maximum or not.
	positionData	Class instance to store particle positions.
	filterWidth	Radius of filter along the width dimension of the array. Filter processes from -filterWidth to +filterWidth for each pixel.
	filterHeight	Radius of filter along the height dimension of the array. Filter processes from -filterHeight to +filterHeight for each pixel.
	filterDepth	Radius of filter along the depth dimension of the array. Filter processes from -filterDepth to +filterDepth for each pixel.

void IPGZ::localMaximum2D	(	PixelArray2D< float > *	intensityData,
		PixelArray2D< bool > *	isMaxData,
		ParticleArray< float > *	positionData,
		int	filterWidth,
		int	filterHeight,
		float	minimumThreshold
	)

Identifies the local maximum in 2D.

The total number of particles is returned in the positionData array via the size() function.

Parameters:

	intensityData	Original data to calculate local maximum from.
	isMaxData	Class to store local maximum locations.
	positionData	Class to store location of apparent particle centers.
	filterWidth	Radius of filter along the width dimension of the array. Filter processes from -filterWidth to +filterWidth for each pixel.
	filterHeight	Radius of filter along the height dimension of the array. Filter processes from -filterHeight to +filterHeight for each pixel.
	minimumThreshold	Values less than the minimum threshold are automatically excluded from comparison of local maximum calculation.

void IPGZ::localMaximum3D	(	PixelArray3D< float > *	intensityData,
		PixelArray3D< bool > *	isMaxData,
		ParticleArray< float > *	positionData,
		int	filterWidth,
		int	filterHeight,
		int	filterDepth,
		float	minimumThreshold
	)

Identifies the local maximum in 3D.

The total number of particles is returned in the positionData array via the size() function.

Parameters:

	intensityData	Original data to calculate local maximum from.
	isMaxData	Class to store local maximum locations.
	positionData	Class to store location of apparent particle centers.
	filterWidth	Radius of filter along the width dimension of the array. Filter processes from -filterWidth to +filterWidth for each pixel.
	filterHeight	Radius of filter along the height dimension of the array. Filter processes from -filterHeight to +filterHeight for each pixel.
	filterDepth	Radius of filter along the depth dimension of the array. Filter processes from -filterDepth to +filterDepth for each pixel.
	minimumThreshold	Values less than the minimum threshold are automatically excluded from comparison of local maximum calculation.
	candidateParticles	Pointer that will have its value set to the total number of identified particles.

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