Variable List

Settings Structure

Variable	Comment
Settings.AccelVoltage
Settings.SampleTilt
Settings.SampleAzimuthal
Settings.CameraElevation
Settings.CameraAzimuthal
Settings.AngFilePath
Settings.GrainFilePath
Settings.CustomFilePath
Settings.FirstImagePath
Settings.OutputPath
Settings.DoUsePCFile	Switch to register if there is a file with pattern center info for each point
Settings.PCFilePath
Settings.DoParallel	Number of cores to use in parallel processing pool. 1 turns off parallel processing.
Settings.DoShowPlot	Switch for showing ROI shifts for each pattern. Only works for non-parallel processing.
Settings.Material
Settings.ScanType	Square or Hexagonal scan
Settings.ROISizePercent	Size of ROI relative to EBSP
Settings.NumROIs	Number of ROIs
Settings.ROIStyle	Method of selecting ROIs (grid, radial, or intensity base selection)
Settings.ROIFilter	1x4 numeric vector: [lower radius (pixels), upper radius, smooth lower radius filter switch, smooth upper radius filter switch]. Used in CalcF.m for error function filter. Filtered by custffx.m. If smooth switches are off, it cuts out high and low frequencies in FFT space; if switches are on it smooths the interface at the cut-offs.
Settings.ImageFilter	Same as ROIFilter, but for entire image. Called in GetDefGradientTensor.m to ReadEBSDImage.m to custimfilt.m.
Settings.HROIMMethod	Switch for real or simulated pattern method
Settings.IterationLimit	Number of iteration for simulated pattern convergence.
Settings.FCalcMethod	Uses either Wilkinson Ultramicroscopy 2006 paper method (in sample or crystal frame) or Landon, Kacher Ultramicroscopy 2009 paper method (in sample or crystal frame) for calculating deformation gradient from ROI shifts.
Settings.GrainRefImageType	Method for selecting reference image in each grain for real image method (e.g. IQ gets highest weight).
Settings.KernelAvgMisoPath	Path for KAM file if this is used to find best position for reference pattern in grain ***(check)
Settings.StandardDeviation	Standard deviation of ROI shifts beyond which ROIs with this size shift rejected
Settings.DoPCStrainMin	Switch to find pattern center using strain minimzation
Settings.largefftmeth	Not currently used***
Settings.PixelSize	Number of pixels in image (currently any image is cropped to be square)
Settings.ROISize	Number of pixels in ROI (square)
Settings.LImageNamesList	Image names list when L-grid is being used
Settings.Angles	Original Euler angles for each point from scan file (.ang or .ctf file)
Settings.XData	X position for each scan point from scan file
Settings.YData	Y position for each scan point from scan file
Settings.IQ	Image quality for each scan point point from scan file
Settings.CI	Confidence index for each scan point from scan file
Settings.Fit	Fit for each scan point from scan file
Settings.ImageNamesList	Cell with path/filename for the image associated with each scan point
Settings.RefImageNames	Cell with path/filename for the reference image associated with each scan point (e.g. this will be the same image for all points in a grain)
Settings.Phi1Ref	First euler angle for reference pattern associated with each scan point
Settings.PHIRef	Second euler angle for reference pattern associated with each scan point
Settings.Phi2Ref	Third euler angle for reference pattern associated with each scan point
Settings.grainID	Grain number for each scan point. Assigned by grain file or findgrains.m
Settings.XStar	Pattern center x-value for each point in the scan
Settings.YStar	Pattern center y-value for each point in the scan
Settings.ZStar	Pattern center z-value for each point in the scan
Settings.g	Adjusted rotation matrix for each scan point (for real patterns it is the orientation of the reference pattern for that grain adjusted by the relative rotation from the reference)
Settings.F	Deformation gradient tensor between reference and scan point for real pattern approach, or absolute deformation for simulated pattern approach (in crystal frame). (L-Scans only)
Settings.Fa	Deformation gradient tensor between scan point and selected neighbor in x-direction (in crystal frame) (L-Scans only)
Settings.Fc	Deformation gradient tensor between scan point and selected neighbor in y-direction (in crystal frame) (L-Scans only)
Settings.U	Strain tensor for each point (obtained from polar decomposition of F) - either relative to reference point (real pattern method) or absolute (simulated pattern). (L-Scans only)
Settings.Ua	Relative strain tensor between scan point and selected neighbor in x-direction (L-Scans only)
Settings.Uc	Relative strain tensor between scan point and selected neighbor in y-direction (L-Scans only)
Settings.SSE	'Sum-squared error' of ROI shifts between reference and scan pattern
Settings.SSEa	'Sum-squared error' of ROI shifts between neighboring reference pattern in x direction and scan pattern (L-Scans only)
Settings.SSEc	'Sum-squared error' of ROI shifts between neightboring reference pattern in y direction and scan pattern (L-Scans only)
Settings.NewAngles	Euler angles for Settings.g
Settings.AverageSSE	Average of all SSE values
Settings.data	See variables below
Settings.roixc	Center of ROIs in x direction
Settings.roiyc	Center of ROIs in y direction
Settings.data.cols	Number of points in the X direction
Settings.data.rows	Number of points in the Y direction
Settings.data.IQ	Same as Settings.IQ
Settings.data.SSE	Same as Settings.SSE
Settings.data.SSEa	Same as Settings.SSE (L-Scans only)
Settings.data.SSEc	Same as Settings.SEE(L-Scans only)
Settings.data.F	Deformation gradient tensor between reference and scan point for real pattern approach, or absolute deformation for simulated pattern approach
Settings.data.Fa	See Settings.Fa (L-Scans only)
Settings.data.Fc	See Settings.Fc (L-Scans only)
Settings.data.g	Same as Settings.NewAngles
Settings.data.phi1rn	Same as Settings.data.g but individual Euler angles
Settings.data.PHIrn	Same as Settings.data.g but individual Euler angles
Settings.data.phi2rn	Same as Settings.data.g but individual Euler angles
Settings.data.xpos	Same as Settings.XData
Settings.data.ypos	Same as Settings.YData

Alpha_data Structure

Variable	Comment
alpha_data.r	Number of points in the x direction
alpha_data.c	Number of points in the y direction
alpha_data.Fa	See Settings.Fa
alpha_data.Fc	See Settings.Fc
alpha_data.alpha_total3	GND density calculated from column 3 of Nye tensor
alpha_data.alpha_total5	GND density calculated from 5 Pantleon conditions
alpha_data.alpha_total9	GND density calculated from all available elements of Nye tensor
alpha_data.alpha	GND density using whichever is the preferred method (currently 3-term method**)
alpha_data.misang	Maximum misorientation between scan point and chosen neighbor points (x and y)
alpha_data.discount	Number of points not used in GND calc (due to high misorientation)
alpha_data.intensityr	Not currently used***
alpha_data.stepsize	Step size between neighbors used in GND calculation