10.75. Crop Geometry (Image)

Group (Subgroup)

Core (Spatial)

Description

This Filter extracts a region of interest (ROI) from an Image Geometry, producing a new geometry that contains only the selected cells. Bounds can be specified either in cell indices (voxels) or in physical coordinates. Individual dimensions (X, Y, Z) can be cropped independently.

This is the inverse of Pad Image Geometry. Common uses are isolating a sample from its overscan border, focusing analysis on a single feature, or reducing data size for testing.

Bounds Mode

The Use Physical Bounds parameter selects how the crop bounds are interpreted:

Use Physical Bounds = false: bounds are integer cell indices (0-based, inclusive on both ends). Xmin=50, Xmax=99 keeps cells 50 through 99 (the last 50 cells of a 100-cell volume).
Use Physical Bounds = true: bounds are physical coordinates in the geometry’s units. The filter computes which cells fall inside the box defined by those coordinates, taking the geometry’s origin and spacing into account.

If any bound exceeds the geometry’s extent on that axis, the filter clamps to the geometry’s actual extent. The filter fails in preflight only when all of the requested bounds fall outside the geometry.

Per-Axis Cropping

The Crop X Dimension, Crop Y Dimension, and Crop Z Dimension booleans toggle whether each axis is cropped at all. An axis with its flag OFF retains all of its cells regardless of the bounds setting.

Examples

In the following examples, the source image has:

Origin: (0.0, 0.0, 0.0)
Spacing: (0.5, 0.5, 1.0)
Dimensions: (100, 100, 1)

So the physical bounds are (0-50 microns, 0-50 microns, 0-1 micron).

Base image for examples

Example 1 – Crop to the last 50 cells in X and Y

Xmin = 50, Xmax = 99
Ymin = 50, Ymax = 99
Zmin = 0,  Zmax = 0
Use Physical Bounds = false

Result:

Cropped image using voxels as the bounds

Example 2 – Crop to the middle 50 cells

Xmin = 25, Xmax = 74
Ymin = 25, Ymax = 74
Zmin = 0,  Zmax = 0
Use Physical Bounds = false

Result:

Cropped image using voxels as the bounds

Example 3 – Crop using physical coordinates, with one bound exceeding the volume

Xmin = 30 microns, Xmax = 65 microns
Ymin = 30 microns, Ymax = 65 microns
Zmin = 0 microns,  Zmax = 65 microns
Use Physical Bounds = true

The Zmax of 65 microns exceeds the geometry’s 1-micron Z extent and is silently clamped. The crop still succeeds because at least part of the requested box lies inside the geometry.

Cropped image using voxels as the bounds

Renumber Features

Cropping can fully remove some Features from the volume, which leaves their Feature IDs unused and produces gaps. If Renumber Features is enabled, the Cell Feature Attribute Matrix is resized to drop empty features and remaining Features are renumbered to be contiguous starting from 1. Leave this off if you intend to compare the cropped output against the original larger volume by Feature ID.

The user can save the cropped volume as a new Data Container or overwrite the current volume in place.

WARNING: NeighborList Removal

When Renumber Features is enabled and the Cell Feature Attribute Matrix contains any NeighborList arrays, those arrays are removed because they refer to the old Feature IDs. Re-run Compute Feature Neighbors afterward to rebuild them.

Required Input Sources

Input Image Geometry – the geometry to crop. Typically produced by Create Image Geometry, ITK Import Image Stack, or an EBSD reader.

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.