DREAM3D User Manual
Align Sections (Feature)

Group (Subgroup)

Reconstruction Filters (Alignment)

Description

This filter attempts to align consecutive serial sections by determining the position that results in the most overlap of previously defined "regions". The "regions" are defined by a binary/boolean array where the Cells have been flagged by another filter. Typically, during reading of the data, each Cell is subject to a "Quality Metric" (or threshold) that defines if the Cell is "good". This threshold can be used to define areas of each slice that are bad, either due to actual features in the microstructure or external references inserted by the user/experimentalist. If these "regions" of "bad" Cells are believed to be consistent through sections, then this filter will preserve that by aligning those "regions" on top of one another on consecutive sections. The algorithm of this filter is as follows:

  1. Compare the value of the binary/boolean array for each Cell in a section with the value of the array for the Cell directly above it in the next section.
  2. Count the number of Cell pairs that do not have the same value and store that as the misalignment value for that position.
  3. Repeat steps 1 and 2 for each position when shifting the second slice (relative to the first) from three (3) Cells to the left to three (3) Cells to the right, as well as from three (3) Cells up to three (3) Cells down. Note that this creates a 7x7 grid
  4. Determine the position in the 7x7 grid that has the lowest misalignment value. (It will be the position with the fewest different Cell pairs).
  5. Repeat steps 1-4 with the center of each (new) 7x7 grid at the best position from the last 7x7 grid until the best position in the current/new 7x7 grid is the same as the last 7x7 grid. Note that this is similar to a downhill simplex and can get caught in a local minima

Parameters

None

Required DataContainers

Voxel

Required Arrays

Type Default Name Description Comment Filters Known to Create Data
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)

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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