Added Molecular Glass Orientation Mapping

CSSFrancis commented 1 year ago

@SyHuang19 @TimothyLambdenCambridge Is there a chance you can look at this notebook for doing Orientation analysis on molecular glasses and make sure things look good?

I think that this is a good example of how to integrate some custom functions in with hyperspy/ pyxem so while these features might be added later I think a good first step is to show how this can be done. In order to add this completely into hyperspy/pyxem we would probably have to make some changes into hyperspy as to how the model fitting works when you want to use multiple cores.

As these datasets can get a little large it is important to have the ability to operate in parallel.

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CSSFrancis commented 1 year ago

You can look at the notebook here

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SyHuang19 commented on 2023-06-08T20:15:14Z ----------------------------------------------------------------

Line #3.                        label=["Chi^2","y_offset", "Orientation", "Peak1 Amplitude", "Peak2 Amplitude", "Sigma"],

It's probably better to change "y_offset" to "Background" since its more inline with other labels which have physical meanings to thems.

_CSSFrancis commented on 2023-06-08T20:23:45Z_ ----------------------------------------------------------------

Good idea!

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SyHuang19 commented on 2023-06-08T20:15:16Z ----------------------------------------------------------------

I'm not sure why this line is repeated again

CSSFrancis commented on 2023-06-08T20:24:06Z ----------------------------------------------------------------

Yea I think did that accidentally

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SyHuang19 commented on 2023-06-08T20:15:17Z ----------------------------------------------------------------

Line #3.    both.plot(navigator_kwds={"cmap":cmap,

Can you add a label to either the color bar or the image?

_CSSFrancis commented on 2023-06-08T20:29:38Z_ ----------------------------------------------------------------

I think that is one of the limitations to plotting interactively with hyperspy. I don't know if you can set a label or custom ticks for a color bar.

I was going to add that upstream to hyperspy eventually but never got around to it.

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SyHuang19 commented on 2023-06-08T20:15:19Z ----------------------------------------------------------------

Line #3.    im = axs.imshow(peaks.isig[2].data,

Same as above

_CSSFrancis commented on 2023-06-08T20:30:11Z_ ----------------------------------------------------------------

Here I can label the color bar! That is a good idea

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SyHuang19 commented on 2023-06-08T20:19:26Z ----------------------------------------------------------------

I wouldn't say these are helper functions. They are actual fitting functions.

CSSFrancis commented 1 year ago

Good idea!

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CSSFrancis commented 1 year ago

Yea I think did that accidentally

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CSSFrancis commented 1 year ago

I think that is one of the limitations to plotting interactively with hyperspy. I don't know if you can set a label or custom ticks for a color bar.

I was going to add that upstream to hyperspy eventually but never got around to it.

View entire conversation on ReviewNB

CSSFrancis commented 1 year ago

Here I can label the color bar! That is a good idea

View entire conversation on ReviewNB

pyxem / pyxem-demos

Added Molecular Glass Orientation Mapping #84