Skip to content

Calculate Dewarp Parameters

Group (Subgroup)

Processing (Processing)

Description

This Filter uses a derivative of itk::AmoebaOptimizer to calculate the parameters required for dewarping a specified montage. It does this by performing an itk::FFTConvolutionImageFilter over the overlaps in a GridMontage for each set of parameters checked by the amoeba filter. The amoeba filter then tries to find the set of parameters that maximizes the sum of the max values from each overlap. These max values are used to determine how similar the overlapping region is. Maximizing the summation is done to find the set of dewarp parameters resulting in the best-matching overlaps.

Once the amoeba optimizer is completed, a new DataContainer, AttributeMatrix, and DataArray are generated to store the dewarp parameters. The actual application of dewarping is not performed in this filter.

The process for finding the parameters works centering the tile around (0,0) and warping around that location each tile using components from a 3rd degree polynomial as described below to find the location of the corresponding pixel in the original data for each set of parameters tested using an amoeba optimizer.

x'n = xnew - im_dim_x / 2

y'n = ynew - im_dim_y / 2

x'old = a0 * x'n + a1 * y'n + a2 * x'n2 + a3 * y'n2 + a4 * x'ny'n + a5 * x'n2y'n + a6 * x'ny'n2

y'old = b0 * x'n + b1 * y'n + b2 * x'n2 + b3 * y'n2 + b4 * x'ny'n + b5 * x'n2y'n + b6 * x'ny'n2

xold = x'old + im_dim_x / 2

yold = y'old + im_dim_y / 2

Parameters

Name Type Description
Parameter Name Parameter Type Description of parameter...
Montage Name GridMontage GridMontage to dewarp
Max Iterations Integer Maximum number of iterations to perform
Delta Integer Maximum offset in cells when calculating the initial step size
Fractional Convergence Tolerance Float Fractional difference between min/max values for convergence
Specify Initial Simplex LinkedBoolean Enables or disables X Factors and Y Factors
X Factors FloatVec7Type a parameters for calculating x'
Y Factors FloatVec7Type b parameters for calculating y'
Attribute Matrix Name Text AttributeMatrix name containing the IPFColors
IPF Colors Array Name Text IPFColors array name within the target AttributeMatrix

Required Geometry

Not Applicable

Required Objects

Not Applicable

Created Objects

Kind Default Name Type Component Dimensions Description
Data Container Dewarp Data N/A N/A DataContainer holding dewarp parameters
Attribute Matrix Transform Matrix Generic N/A AttributeMatrix holding dewarp parameters
Element Attribute Array Transform Double (14) DataArray holding dewarp parameters

Example Pipelines

None

Please see the description file distributed with this plugin.

DREAM3D Mailing Lists

If you need more help with a filter, please consider asking your question on the DREAM3D Users mailing list: DREAM.3D Users Google group!