Align Sections (Feature Centroid)

Group (Subgroup)

Reconstruction (Alignment)

Description

This Filter attempts to align 'sections' of the sample perpendicular to the Z-direction by determining the position that closest aligns the centroid(s) 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. Determine the centroid of all Cells that are flagged with a boolean value equal to true for each section
  2. Determine the shifts that place centroids of consecutive sections on top of one another
  3. Round the shifts determined in step 2 to the nearest multiple of the Cell resolution. (This forces the sections to be shifted by full Cell increments)

If the user elects to Use Reference Slice, then each section's centroid is shifted to lie on top of the reference slice's centroid position and not its neighboring section's centroid position.

Note that this is algorithm cannot 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.

Parameters

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
Use Refernece Slice bool Whether the centroids of each section should be compared to a reference slice instead of their neighboring section
Reference Slice int32_t Slice number to use as reference. Only needed if Use Reference Slice is checked

Required Geometry

Image

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

None

Example Pipelines

  • (10) SmallIN100 Full Reconstruction
  • (03) SmallIN100 Alignment

Please see the description file distributed with this Plugin

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