mcemtools 0.11.1

State of the art analysis tools for 4D STEM

mcemtools

Deep unsupervised analysis tools for Four-dimensional Scanning Transmission Electron Microscopy (4D-STEM)

In order to run the pyms simulations, you have to get it from:

https://github.com/Michael-MD/py_multislice

Then also there is a utils.py in the examples directory that helps.

• Free software: MIT license

• Documentation: https://mcemtools.readthedocs.io.

Features

• Denoising 4D-STEM data

• a few tools to help pre-process 4D-STEM data

Credits

This package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.

History

0.1.0 (2022-09-07)

• First release on PyPI.

0.2.0 (2023-07-11)

• Many functions used for 4D-STEM analysis have been added.

• OOP is avoided as much as possible.

0.3.0 (2023-07-11)

• Tests are increasing in number

• init includes import of mcemtools

0.4.0 (2023-07-11)

• Many small bugs are fixed

0.5.0 (2023-07-12)

• Added binning to transforms

0.6.0 (2023-07-14)

• More tests are added

• Names are consistant accross the package.

0.7.0 (2023-07-15)

• markimage bug is fixed

0.8.0 (2023-07-19)

• markimage bug is fixed really as US version of centre is center.

• napari based GUI is added to mcemtools.

• bianary files can be read too.

0.8.1 (2023-07-27)

• viewer_4D is a lot more concise and bug free.

0.8.2 (2023-07-27)

• by pressing i, you get shapes info, m shows the mask and F5 updates the mask.

0.8.3 (2023-07-28)

• critical bug was fixed in viewer_4D

0.8.4 (2023-07-28)

• critical bug was fixed in viewer_4D

0.8.5 (2023-08-03)

• bug fixed in image_by_windows

0.8.6 (2023-08-05)

• viewer_4D handles arrows to move the selected objects.

0.8.7 (2023-08-31)

• added load_raw and load_dm4.

• bug fixed in viewer_4D, moves a lot smoother than before.

• viewer_4D shows a single image when size of the mask is 1 pixel, rapidly.

• conv_4D added to analysis

0.8.8 (2023-09-04)

• critical bug fixed in bin_4D

0.8.9 (2023-09-20)

• bug removed from Normalize_4D

• bug removed from SymmetrySTEM

• tets added to locate atom and …

0.8.10 (2023-09-12)

• bug removed from SymmetrySTEM and mirror is added

• data_maker_4D can be updated

• remove_islands_by_size bug fixed

0.8.11 (2023-09-25)

• Bug fixed in viewer_4D

0.9.0 (2023-10-13)

• added denoise4net

• added clustering4net and feature_maker_4D

0.9.1 (2024-02-23)

• added denoise4_tsvd

• faster bin_4D

• torch handler does not update the model if the loss is inf or nan

0.9.2 (2024-03-23)

• annular mask can handle even sized image

0.9.2 (2024-05-02)

• viewer_4D takes second mask to subtract

0.9.3 (2024-05-24)

• viewer_4D takes second mask to subtract

0.9.4 (2024-06-01)

• minimal requirenments and test scripts for denoising is added

• first denoising example added

• many bugs fixed for the denoiser

• More concerete example is added for geometric flow based denoising for the paper

0.9.5 (2024-11-08)

• Annular mask fixed

• added supervised 2D denoiser

• renamed denoise4net to denoise4_unet

0.9.6 (2024-11-08)

• denoiser needed a fix

0.9.7 (2024-11-15)

• critical bug fixed in applying spatial incoherence

0.9.8 (2024-11-15)

• Maybe the installer should not install napari stuff

• removed autoconvolution from symmstem

0.9.9 (2024-12-19)

• CapsNet is complete

0.9.10 (2025-01-18)

• Denoising examples become consistant with current pyms version

0.9.11 (2025-01-18)

• Adding a link to Michael pyms in the ReadMe file.

• fixed markimage

0.9.11 (2025-05-30)

• fixed capsul network to handle any number of features in the output

0.9.13 (2025-09-01)

• Annular mask bug fixed for non-square inputs

0.9.14 (2025-10-16)

• Added Transformerregressir

0.9.15 (2025-11-07)

• more advanced confidence head

0.9.16 (2026-01-27)

• recycling and reconstruction error added to the regressor

0.10.0 (2026-01-27)

• reconstruction error of the regressor is weighted.

0.10.1 (2026-01-27)

• better show_detector_response

• segmented_detector_maker returns the ring ids

0.10.2 (2026-03-03)

• Fixed bugs in the denoiser

0.11.0 (2026-05-06)

• CoM corrections and leaving Monash University

0.11.1 (2026-05-24)

• Fixed the affine transform and registration function and added a test