IPAnalysis: IPAnalysis/IPGZ.h File Reference

#include "pstream.h"
#include <iostream>
#include <fstream>
#include <tiffio.h>
#include <vector>
#include <math.h>
#include <pthread.h>
#include <stdio.h>
#include <stdlib.h>
#include "PixelArray.h"
#include "ParticleArray.h"


Namespaces
namespace	IPGZ
Defines
#define	IP_COMPRESS 0
	Library to proide routines for input/output of TIFF images of colloidal particles and determination/tracking of colloidal particles.
#define	IP_NONE 1
#define	IP_DOT 0
#define	IP_PLUS 1
#define	IP_RED 0
#define	IP_BLUE 1
#define	IP_GREEN 2
#define	IP_GRAY 3
Functions
void	IPGZ::readTiff2Float2D (char inFilename, PixelArray2D< float > data, int channel)
	Method to read a TIFF file into an instance of the PixelArray2D class.
void	IPGZ::readTiff2Float3D (char inFilenamePattern, int min, int max, PixelArray3D< float > data, int channel)
	Method to read a series of TIFF files into an instance of the PixelArray3D class.
void	IPGZ::readTiff2Uint32 (char inFilename, PixelArray2D< uint32 > data)
	General routine to read a TIFF image as RGBA data into unsigned integer PixelArray2D. This is primarily called by other functions (readTiff2Float3D(), readTiff2Float2D()) and will not typically be called directly.
void	IPGZ::readTiff2Uint32 (char inFilename, uint32 raster, uint32 width, uint32 height)
	General routine to read a TIFF image as RGBA data into unsigned integer array. This is primarily called by other functions and will not typically be called directly.
void	IPGZ::writeFloat2Tiff2D (char outFilename, PixelArray2D< float > data, int R, int G, int B, int compress)
	Routine to write floating point information stored in the PixelArray2D class to a TIFF file.
void	IPGZ::writeFloat2Tiff2D (char outFilename, PixelArray2D< float > data1, int R1, int G1, int B1, PixelArray2D< float > *data2, int R2, int G2, int B2, int compress)
	Routine to merge floating point information stored in two instances of the PixelArray2D class and write to a TIFF file.
void	IPGZ::writeOverlay2Tiff (char inFilename, char outFilename, PixelArray2D< bool > *data, int R, int G, int B, int compress, int outputStyle)
	Routine to read in a TIFF file and selectively overwrite certain information corresponding to particle positions and then write to a tiff file.
void	IPGZ::writeOverlay2Tiff3D (char inFilenamePattern, int min, int max, char outFilenamePattern, PixelArray3D< bool > *data, int R, int G, int B, int compress, int outputStyle)
	Routine to read in a series of TIFF images and selectively overwrite certain information corresponding to particle positions and then write out corresponding tiff file.
void	IPGZ::writeIntensity2Tiff (char outFilename, PixelArray2D< bool > data, int R, int G, int B, int compress, int outputStyle)
	Routine to write a TIFF file using intensity data to selectively overwrite certain pixels.
void	IPGZ::minimumFilter2D (PixelArray2D< float > inData, PixelArray2D< float > outData, float minimumThreshold)
	Routine to remove background noise in 2D.
void	IPGZ::minimumFilter3D (PixelArray3D< float > inData, PixelArray3D< float > outData, float minimumThreshold)
	Routine to remove background noise in 3D.
void	IPGZ::normalize2D (PixelArray2D< float > inData, PixelArray2D< float > outData)
	Routine to normalize intensity by maximum value in 2D.
void	IPGZ::normalize3D (PixelArray3D< float > inData, PixelArray3D< float > outData)
	Routine to normalize intensity by maximum value in 3D.
void	IPGZ::invert2D (PixelArray2D< float > inData, PixelArray2D< float > outData)
	Routine to invert intensity in 2D.
void	IPGZ::invert3D (PixelArray3D< float > inData, PixelArray3D< float > outData)
	Routine to invert intensity in 3D.
void	IPGZ::gaussianMask2D (PixelArray2D< float > rawData, PixelArray2D< float > filteredData, int filterWidth, int filterHeight)
	Routine to apply a gaussian mask in 2D.
void	IPGZ::gaussianMask2D (PixelArray2D< float > rawData, PixelArray2D< float > filteredData, int filterWidth, int filterHeight, float minimumThreshold)
	Routine to apply a gaussian mask in 2D with minimum threshold coarse-graining.
void	IPGZ::gaussianMask3D (PixelArray3D< float > rawData, PixelArray3D< float > filteredData, int filterWidth, int filterHeight, int filterDepth)
	Routine to apply a gaussian mask in 3D.
void	IPGZ::gaussianMask3D (PixelArray3D< float > rawData, PixelArray3D< float > filteredData, int filterWidth, int filterHeight, int filterDepth, float minimumThreshold)
	Routine to apply a gaussian mask in 3D with minimum threshold coarse-graining.
void	IPGZ::gaussianMask3Dparallel (PixelArray3D< float > rawData, PixelArray3D< float > filteredData, int filterWidth, int filterHeight, int filterDepth, int numThreads)
	Routine to apply a gaussian mask in 3D with support for multiple processors.
void	IPGZ::gaussianMask3Dparallel (PixelArray3D< float > rawData, PixelArray3D< float > filteredData, int filterWidth, int filterHeight, int filterDepth, float minimumThreshold, int numThreads)
	Routine to apply a gaussian mask in 3D with minimum threshold coarse-graining and support for multiple processors.
void	IPGZ::gaussianMask3DStartFinish (PixelArray3D< float > rawData, PixelArray3D< float > filteredData, int filterWidth, int filterHeight, int filterDepth, float minimumThreshold, int start, int finish)
	Routine to apply a gaussian mask in 3D with minimum threshold coarse-graining.
void	IPGZ::gaussianMask3DStartFinish (PixelArray3D< float > rawData, PixelArray3D< float > filteredData, int filterWidth, int filterHeight, int filterDepth, int start, int finish)
	Routine to apply a gaussian mask in 3D.
void *	IPGZ::launchThreadGaussianMaskMin3D (void *data)
	Method lauched when creating new threads for the gaussian mask calculation with minimum threshold coarse-graining.
void *	IPGZ::launchThreadGaussianMask3D (void *data)
	Method lauched when creating new threads for the gaussian mask calculation.
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().
void	IPGZ::calculateCentroid3D (PixelArray3D< float > intensityData, ParticleArray< float > positionData, int filterWidth, int filterHeight, int filterDepth)
	Routine to calculate the centroid of a particle in 3D.
void	IPGZ::calculateCentroid2D (PixelArray2D< float > intensityData, ParticleArray< float > positionData, int filterWidth, int filterHeight)
	Routine to calculate the centroid of a particle in 2D.
void	IPGZ::realPosition (ParticleArray< float > positionData, ParticleArray< float > realPositionData, float scaleWidth, float scaleHeight, float scaleDepth)
	Routine to calculate the real position of a particle based on the centroid data. This routine is indentical for 2D and 3D.

#define IP_COMPRESS 0

Library to proide routines for input/output of TIFF images of colloidal particles and determination/tracking of colloidal particles.

IPGZ library

IPGZ.h IPGZ

IPAnalysis/IPGZ.h File Reference

Namespaces

Defines

Functions

Define Documentation