9.36. Compute Feature Sizes
Group (Subgroup)
Statistics (Morphological)
Description
Note: Regarding using an Image Geometry as input, if you have a 1 in any of the dimensions it will be turned into a 2D calculation instead. See Image Geometry Additional Considerations section for more details.
This Filter calculates the sizes, volumes/areas, and equivalent diameters of all Features in an Image Geometry or Rectilinear Grid Geometry.
To do so, the Filter simply iterates through all Elements querying for the Feature that owns them and keeping a tally for each Feature. The tally is then stored as NumElements and the Volume and EquivalentDiameter are also calculated (and stored) by knowing the volume of each Element.
Note here that Image Geometry will always be faster than its equivalent Rectilinear Grid Geometry because we leverage the uniformity of voxel sizes to perform volume/area calculations at the feature level rather than the cell level.
During the computation of the Feature sizes, the size of each individual Element is computed and stored in the corresponding Geometry. By default, these sizes are deleted after executing the Filter to save memory. If you wish to store the Element sizes, select the Generate Missing Element Sizes option. The sizes will be stored within the Geometry definition itself, not as a separate Attribute Array.
Image Geometry Additional Considerations
A typical Image Stack (an Image Geometry that contains 3 dimensions greater than 1) conceptually consists of a series of 2D images stacked on top of one another to create a 3D object, thus it functions in 3D space as expected. This means it produces Volumes and Equivalent Spherical Diameters.
Due to the way Image Geometry is stored, if you have a 1 in any of the dimensions
it will be turned into a 2D calculation instead. This means Areas instead of Volumes and Equivalent Circular Diameters instead of Equivalent Spherical Diameters. Furthermore, you must have two dimensions greater than 1 to pass preflight. The reason for this being orientation becomes ambiguous once a second dimension is “empty”.
To illustrate why this is think about an image geometry with the dimensions of 1x1x5 (XYZ). There is no way to tell whether a Z * X or Z * Y scaling would be appropriate for the area calculation, given the current information accessible in the algorithm.
Input Parameter(s)
Parameter Name |
Parameter Type |
Parameter Notes |
Description |
|---|---|---|---|
Generate Missing Element Sizes |
Bool |
If checked this will generate and store the element sizes ONLY if the geometry does not already contain them. |
Input Cell Data
Parameter Name |
Parameter Type |
Parameter Notes |
Description |
|---|---|---|---|
Input Grid Geometry |
Geometry Selection |
Image, Rectilinear Grid |
DataPath to input Image or Rectilinear Grid Geometry |
Cell Feature Ids |
Array Selection |
Allowed Types: int32 Comp. Shape: 1 |
Specifies to which feature each cell belongs. |
Input Feature Data
Parameter Name |
Parameter Type |
Parameter Notes |
Description |
|---|---|---|---|
Feature Attribute Matrix |
AttributeMatrixSelection |
Feature Attribute Matrix of the selected Feature Ids |
Output Feature Data
Parameter Name |
Parameter Type |
Parameter Notes |
Description |
|---|---|---|---|
Feature Equivalent Diameters Name |
DataObjectName |
Name of the array that will store the equivalent spherical/circular diameters of each feature |
|
Feature Voxel Counts Name |
DataObjectName |
Name of the array that will store the number of voxels per feature |
|
Volumes/Area Name |
DataObjectName |
Name of the array that will store the volumes/area of each feature |
Example Pipelines
(03) Small IN100 Morphological Statistics
(02) Small IN100 Full Reconstruction
InsertTransformationPhase
(06) SmallIN100 Synthetic
(09) Image Segmentation
License & Copyright
Please see the description file distributed with this Plugin
DREAM3D-NX Help
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