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seto77 / ReciPro

The software ReciPro makes various crystallographic calculations, visualizes a crystal structure, simulates a diffraction pattern and high-resolution TEM image, indexes diffraction spots, plots stereographic projection, and so on.
https://seto77.github.io/ReciPro/
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Real type image from HRTEM simulation #13

Open wangyuchenphy opened 2 years ago

wangyuchenphy commented 2 years ago

Thank you for the program. The functions are extremely amazing to me! I mainly use the HRTEM simultion function, the live simulation is really powerful. Now I am using the simulated peak intensity as a refer for quantitative analysis of experiment imge. It seems that the simulated HRTEM from ReciPro is normalized to 2^16, similar to integer data image maybe?. It is harder to compare intensity with each other. So is it possible to get a real data type image like QSTEM or mactempax, whose intensity from vacuum is normalized to 1? In that case, the peak intensity could be compared directly with experimental images Thank you very much.

seto77 commented 2 years ago

Thank you for your request. It is not difficult at all to normalize the maximum intensity to 1. I myself do not remember exactly why I normalize it at 2^16. In the next version, the maximum value will be normalized to 1. Is 32-bit tiff format the preferred saving format?

wangyuchenphy commented 2 years ago

Thank you so much! Actually my meaning is keep the vacuum area to be 1, and the intensity at each atom column will increase or decrease as the number of atoms increasing. Then intensity could be connected with the number of atoms in each columns. Is that easy to be realized? 32-bit tiff format is preferred because I could process them with other software like DM. Thanks again

seto77 commented 2 years ago

In HRTEM images, depending on the thickness and defocus value, the vacuum area may be brightened. Are you assuming a very thin thickness and a Scherzer defocus condition? In any case, in the next version, the maximum and minimum values should be able to be normalized manually. Please wait for a little.