Grid Indexing Widget Icon

Grid Indexing Widget#

The Grid Indexing widget is the spatial search engine of the 3DXRD pipeline. Grid Indexing performs a positional search across a 3D volume to locate grains and calculate their UBI matrices.

Functionality#

This widget allows you to:

  • Map Sample Space: Define a 3D search grid (X,Y,Z) corresponding to your sample’s physical dimensions.

  • Real-Time Monitoring: Observe grain generation dynamically in a 3D scene while tracking numerical progress in the logs.

User Interface#

Image showing the initial state of the grid indexing widget

Configuration#

  1. Sample and Beam Info: (Search Volume) These parameters define the 3D grid where the algorithm will search for grain origins:

    • Dimensions (X, Y, Z Limits): These should roughly match the illuminated volume of your sample (Sample Width × Sample Depth × Beam Height).

    • Grid Step: The spacing between search points. A smaller step increases resolution but significantly increases computation time.

  2. Grid Index Settings

    • Number of Peaks: The minimum number of reflections required to “confirm” a grain’s existence.

    • Ring 1 & Ring 2: The algorithm pairs peaks from these rings to generate trial orientations.

      Attention

      Ring 2 must be a subset of Ring 1. If Ring 1 is 0, 1 and Ring 2 is 0, the algorithm tries pairs from (0, 0) and (1, 0).

    • Tolerance Tuning: A sequence of tolerances (e.g., \((0.02, 0.015, 0.01)\)) used to iteratively refine the grain’s fit.

Execution and Monitoring#

Click Run Grid Indexing to start the execution.

  1. Grid Index Logs: A log manager captures real-time output from the background process, showing grain statistics and tolerance levels.

  2. Visual Feedback:

    • Incoming Peaks Tab: Shows the \(ds\)​ vs \(\eta\) (or intensity) distribution of peaks before indexing.

    • Generated Grains Tab: A 3D scene where grains appear as spheres.

      • Size: Represents the mean intensity of associated peaks.

      • Color: Represents the number of peaks assigned to that grain.

Image showing the generated grains plot of the grid indexing widget

Evaluating Results#

Manual validation is critical. A “good” indexing result typically shows:

  • Logical Distribution: Grains should be contained within the physical sample boundaries.

  • Low Overlap: While some overlap is expected (as spheres are only approximations of real grain shapes), excessive overlap suggests geometry errors or poor ring selection.

  • Consistent Count: The number of grains should align with the expected crystallinity of your sample.

Troubleshooting#

  • Empty Grain List: Try decreasing the Number of Peaks requirement or broadening the Tolerance Sequence.

  • High Grain Count/Noise: Revisit the Intensity Filter to remove weak signal or ensure no peaks were detected outside the diffraction spots during Segmentation.

  • Grains Outside Sample: Check your Geometry Transformation parameters; the instrument center or detector distance might be slightly off.