DREAM3D User Manual
Align Sections (Mutual Information)

Group (Subgroup)

Reconstruction Filters (Alignment)

Description

This Filter segments 2D slices, creates GrainIds that are used to determine the mutual information and then aligns the slices. These GrainIds are temporary, and they apply to this filter only. So they are not related to the GrainIds generated in other Filters.

The user choses the level of misorientation tolerance by which to align Cells, where here the tolerance means the misorientation cannot exceed a given value. If the rotation angle is below the tolerance, then the Cell is grouped with other Cells that satisfy the criterion.

The approach used in this filter is to group neighboring Cells on a slice that have a misorientation below the tolerance the user entered. Misorientation here means the minimum rotation angle of one Cell's crystal axis needed to coincide with another Cell's crystal axis. When the Fields in the slices are defined, they are moved until _'disks'_ in neighboring slices align with each other.

Mutual information is one of many quantities that measures how much one random variable tells us about another. It is a dimensionless quantity with (generally) units of bits, and can be thought of as the reduction in uncertainty about one random variable given knowledge of another. High mutual information indicates a large reduction in uncertainty; low mutual information indicates a small reduction; and zero mutual information between two random variables means the variables are independent.

Source:www.scholarpedia.org/article/Mutual_information. A more detailed discussion is presented on this site. Journal articles on Mutual Information that are useful: Cover, T.M. and Thomas, J.A. (1991).

Elements of information theory. John Wiley & Sons, New York, NY.Gray, R.M. (1990).

Entropy and Information Theory. Springer-Verlag, New York, NY. Nirenberg, S. and Latham, P.E. (2003).

Decoding neuronal spike trains: how important are correlations? Proc. Natl. Acad. Sci. 100:7348-7353. Shannon, C.E. and Weaver, W. (1949).

The mathematical theory of communication. University of Illinois Press, Urbana, Illinois. Mézard, M. and Monatanari, A. (2009).

Information, Physics, and Computation. Oxford University Press, Oxford.

Parameters

Name Type
Misorientation Tolerance Double

Required DataContainers

Voxel

Required Arrays

Type Default Name Description Comment Filters Known to Create Data
Cell CellPhases Phase Id (int) specifying the phase of the Cell Values should be present from experimental data or synthetic generation and cannot be determined by this filter. Not having these values will result in the filter to fail/not execute. Read H5Ebsd File (IO), Pack Primary Phases (SyntheticBuilding), Insert Precipitate Phases (SyntheticBuilding), Establish Matrix Phase (SyntheticBuilding)
Cell GoodVoxels Boolean values used to define "regions" to be aligned Values are not required to be based on "good" or "bad" data, rather must only correspond to some identified "regions" Single Threshold (Cell Data) (Processing), Multi Threshold (Cell Data) (Processing)
Cell Quats Five (5) values (floats) that specify the orientation of the Cell in quaternion representation Filter will calculate the quaternion for each Cell if it is not already calculated. Find Cell Quaternions (Generic)
Ensemble CrystalStructures Enumeration (int) specifying the crystal structure of each Ensemble/phase (Hexagonal=0, Cubic=1, Orthorhombic=2) Values should be present from experimental data or synthetic generation and cannot be determined by this filter. Not having these values will result in the filter to fail/not execute. Read H5Ebsd File (IO), Read Ensemble Info File (IO), Initialize Synthetic Volume (SyntheticBuilding)

Created Arrays

None

Authors

Copyright: 2012 Michael A. Groeber (AFRL),2012 Michael A. Jackson (BlueQuartz Software)

Contact Info: dream.nosp@m.3d@b.nosp@m.luequ.nosp@m.artz.nosp@m..net

Version: 1.0.0

License: See the License.txt file that came with DREAM3D.

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