py4dstem / py4dstem/py4DSTEM

Crystalline Phase Mapping

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Dominant language
Python
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Forks
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Description

Thanks for this amazing piece of software!

Is your feature request related to a problem? Please describe.
The original py4DSTEM paper shows a very nice crystal phase map, but the execution is not well described there.

Describe the solution you'd like
I would like the code necessary to generate such phase map given a sample which has single crystalline and powder regions combined.

Describe alternatives you've considered
I am right now considering to use the classification method for the twinned crystal using voronoi tesellation, but I am not sure how to chose Qx and Qy for the voronoi in this case (with powder rings included).

I have developed a circular voronoi tesellation, but then I realize that in order to initialize th BraggVectorClassification class, the data has to be given as PointListArray instead of PointList. The only PointListArray I can extract from my braggpeaks PointList is braggpeaks._v_uncal, but of course this is uncalibrated...

Additional context
I attach my calibrated BraggVectorMap to show the combination of powder and crystal regions.

image

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  3. Fork the repository and make your change on a branch.
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Research direction

Start by reviewing BraggVectorClassification and the PointListArray versus PointList inputs, including the calibrated BraggVectorMap and braggpeaks._v_uncal mentioned in the issue. Done should provide a documented way to generate a crystal phase map from combined single-crystal and powder regions while preserving calibrated data.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
data, data-visualization
Issue type
Feature
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

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