9.72. Crop Geometry (Image)

Description

This Filter allows the user to crop a region of interest (ROI) from an Image Geometry. The input parameters are in units of voxels or physical coordinates.

It is possible to also crop specific dimensions of the Image Geometry by toggling Crop X Dimension, Crop Y Dimension, and Crop Z Dimension ON and OFF.

WARNING: NeighborList Removal

If the option to “Renumber Features” is turn ON and the Cell Feature AttributeMatrix contains any NeighborList data arrays, those arrays will be REMOVED because those lists are now invalid. Re-run the Find Neighbors filter to re-create the lists.

Examples

In the following examples, the following image is being used.

• Origin: [0.0, 0.0, 0.0]

• Spacing: {0.5, 0.5, 1.0}

• Dimensions: {100, 100, 1}

So the bounds of the image is (0-50 micron, 0-50 micron, 0-1 micron)

Example 1

If the user wanted to crop the last 50 voxels in the X and Y axis then the user would use the following values:

Xmin = 50,
Xmax = 99,
Ymin = 50,
Ymax = 99,
Zmin = 0,
Zmax = 0 

Note: the units in the above image is in microns.

Note: The input parameters are inclusive and begin at 0, so in the above example 50-99 will include the last 50 voxels.

Example 2

If the user would like to crop out the middle 50 voxels from the image, these are the inputs:

Xmin = 25,
Xmax = 74,
Ymin = 25,
Ymax = 74,
Zmin = 0,
Zmax = 0

Example 3

In this example the user is going to define the crop using physical coordinates and also selecting an upper bound that exceeds the actual bounds of the image. In this case, the filter will instead use the maximum bounds from that axis.

Xmin = 30 microns,
Xmax = 65 microns,
Ymin = 30 microns,
Ymax = 65 microns,
Zmin = 0 microns,
Zmax = 65 microns

Note: This will work because at least some portion of the cropped image is within the original image. If ALL cropped values fall out side of the image bounds then the filter will error out in preflight.

User may note that the way the bounds are determined are affected by the origin and spacing, so be sure to take these into account when supplying coordinate bounds for the crop.

Renumber Features

It is possible with this Filter to fully remove Features from the volume, possibly resulting in consistency errors if more Filters process the data in the pipeline. If the user selects to Renumber Features then the Feature Ids array will be adjusted so that all Features are continuously numbered starting from 1. The user should decide if they would like their Features renumbered or left alone (in the case where the cropped output is being compared to some larger volume).

The user has the option to save the cropped volume as a new Data Container or overwrite the current volume.

Input Parameter(s)

Parameter Name	Parameter Type	Parameter Notes	Description
Use Physical Units For Bounds	Bool		If true define physical coordinates for bounds, If false define voxel indices for bounds
Crop X Dimension	Bool		Enable cropping in the X dimension.
Crop Y Dimension	Bool		Enable cropping in the Y dimension.
Crop Z Dimension	Bool		Enable cropping in the Z dimension.
Min Voxel	Vector of UInt64 Values	Order=X (Column),Y (Row),Z (Plane)	Lower bound of voxels of the volume to crop out
Max Voxel [Inclusive]	Vector of UInt64 Values	Order=X (Column),Y (Row),Z (Plane)	Upper bound in voxels of the volume to crop out
Min Coordinate (Physical Units)	Vector of Float64 Values	Order=X,Y,Z	Lower bound in real units of the volume to crop.
Max Coordinate (Physical Units) [Inclusive]	Vector of Float64 Values	Order=X,Y,Z	Upper bound in real units of the volume to crop.
Perform In Place	Bool		Removes the original Image Geometry after filter is completed

Input Image Geometry

Parameter Name	Parameter Type	Parameter Notes	Description
Selected Image Geometry	Geometry Selection	Image	DataPath to the source Image Geometry

Optional Renumber Features

Parameter Name	Parameter Type	Parameter Notes	Description
Renumber Features	Bool		Specifies if the feature IDs should be renumbered
Cell Feature Ids	Array Selection	Allowed Types: int32 Comp. Shape: 1	Specifies to which feature each cell belongs.
Feature Attribute Matrix	AttributeMatrixSelection		DataPath to the feature Attribute Matrix

Output Image Geometry

Parameter Name	Parameter Type	Parameter Notes	Description
Created Image Geometry	DataGroupCreation		The DataPath to store the created Image Geometry

Example Pipelines

License & Copyright

Please see the description file distributed with this Plugin

DREAM3D-NX Help

If you need help, need to file a bug report or want to request a new feature, please head over to the DREAM3DNX-Issues GitHub site where the community of DREAM3D-NX users can help answer your questions.