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Align Sections (Feature)

Group (Subgroup)

Reconstruction (Alignment)


This Filter attempts to align 'sections' of the sample perpendicular to the Z-direction by determining the position that results in the most overlap of previously defined "regions". The "regions" are defined by a boolean array where the Cells have been flagged by another Filter. Typically, during reading/processing 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 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.
  6. Repeat steps 1-5 for each pair of neighboring sections

Note that this is similar to a downhill simplex and can get caught in a local minimum!

The user can choose to write the determined shift to an output file by enabling Write Alignment Shifts File and providing a file path.

The user can also decide to remove a background shift present in the sample. The process for this is to fit a line to the X and Y shifts along the Z-direction of the sample. The individual shifts are then modified to make the slope of the fit line be 0. Effectively, this process is trying to keep the top and bottom section of the sample fixed. Some combinations of sample geometry and internal features can result in this algorithm introducing a 'shear' in the sample and the Linear Background Subtraction will attempt to correct for this.


Name Type Description
Write Alignment Shift File bool Whether to write the shifts applied to each section to a file
Alignment File File Path The output file path where the user would like the shifts applied to the section to be written. Only needed if Write Alignment Shifts File is checked
Linear Background Subtraction bool Whether to remove a background shift present in the alignment

Required Geometry


Required Objects

Kind Default Name Type Component Dimensions Description
Cell Attribute Array Mask bool (1) Specifies if the Cell is to be counted as part of the sample or not

Created Objects


Example Pipelines

Please see the description file distributed with this Plugin

DREAM.3D Mailing Lists

If you need more help with a Filter, please consider asking your question on the DREAM.3D Users Google group!