DREAM.3D v6 User Manual
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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:
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 |
Image
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 |
None
Please see the description file distributed with this Plugin
If you need more help with a Filter, please consider asking your question on the DREAM.3D Users Google group!