10.122. Regularize Z Spacing
Group (Subgroup)
Sampling (Resolution)
Description
This Filter resamples an Image Geometry that has irregular spacing along the Z axis onto a regular (uniform) Z spacing. This situation commonly arises from serial-sectioning data collection where the physical distance removed between successive sections is not constant.
The current physical Z position of every original slice boundary is read from a whitespace-delimited text file. The file must contain (ZPoints + 1) floating point values, where ZPoints is the number of cells (slices) along the Z axis of the selected Image Geometry. The first value is the position of the bottom boundary of the first slice, and the last value is the total Z extent of the volume.
The Filter computes a new number of Z slices as:
newZPoints = floor(totalZExtent / newZSpacing)
(with a minimum of 1). For each new, evenly spaced Z plane the Filter selects the original slice whose boundary interval contains that plane’s position and copies the entire XY slab of cell data from the original slice into the new slice. The X and Y dimensions, spacing, and the geometry origin are unchanged; only the Z dimension count and Z spacing are updated.
Input File Format
The input file is a simple text file with one floating point value per line (or whitespace-delimited). For an Image Geometry with 5 Z slices the file must contain 6 values, for example:
0.0
1.0
3.0
6.0
9.5
12.0
The values must be monotonically non-decreasing, and the final value (the total Z extent) must be greater than zero. The .txt extension is a file-dialog hint only; any readable text file is accepted.
Output Geometry
When Perform In Place is enabled the original Image Geometry is replaced by the resampled result. When it is disabled the resampled result is written to the Created Image Geometry path and the original geometry is left unchanged.
Input Parameter(s)
Parameter Name |
Parameter Type |
Parameter Notes |
Description |
|---|---|---|---|
Current Z Positions File |
FileSystemPath |
Path to a whitespace-delimited text file that contains the current Z position of each slice boundary (ZPoints + 1 float values). |
|
New Z Spacing |
Scalar Value |
Float32 |
The new, regular spacing to use along the Z axis. Must be greater than 0. |
Perform In Place |
Bool |
Removes the original Image Geometry after the filter is complete and renames the result to its name. |
Input Image Geometry
Parameter Name |
Parameter Type |
Parameter Notes |
Description |
|---|---|---|---|
Selected Image Geometry |
Geometry Selection |
Image |
The Image Geometry to resample along the Z axis. |
Output Image Geometry
Parameter Name |
Parameter Type |
Parameter Notes |
Description |
|---|---|---|---|
Created Image Geometry |
DataGroupCreation |
The path to the resampled Image Geometry. |
Example Pipelines
License & Copyright
Please see the description file distributed with this Plugin
DREAM3D-NX Help
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