mcemtools 0.10.0
State of the art analysis tools for 4D STEM
License: MIT license
Requires Python: >=3.8
Keywords: mcemtools

=========
mcemtools
=========


.. image:: https://img.shields.io/pypi/v/mcemtools.svg
        :target: https://pypi.python.org/pypi/mcemtools

.. image:: https://img.shields.io/travis/arsadri/mcemtools.svg
        :target: https://travis-ci.com/arsadri/mcemtools

.. image:: https://readthedocs.org/projects/mcemtools/badge/?version=latest
        :target: https://mcemtools.readthedocs.io/en/latest/?version=latest
        :alt: Documentation Status

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.

.. _Cookiecutter: https://github.com/audreyr/cookiecutter
.. _`audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage


=======
History
=======

0.1.0 (2022-09-07)
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* First release on PyPI.

0.2.0 (2023-07-11)
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* Many functions used for 4D-STEM analysis have been added.
* OOP is avoided as much as possible.

0.3.0 (2023-07-11)
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* Tests are increasing in number
* init includes import of mcemtools

0.4.0 (2023-07-11)
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* Many small bugs are fixed

0.5.0 (2023-07-12)
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* Added binning to transforms

0.6.0 (2023-07-14)
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* More tests are added
* Names are consistant accross the package.

0.7.0 (2023-07-15)
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* markimage bug is fixed

0.8.0 (2023-07-19)
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* 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)
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* viewer_4D is a lot more concise and bug free.

0.8.2 (2023-07-27)
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* by pressing i, you get shapes info, m shows the mask and F5 updates the mask.

0.8.3 (2023-07-28)
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* critical bug was fixed in viewer_4D

0.8.4 (2023-07-28)
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* critical bug was fixed in viewer_4D

0.8.5 (2023-08-03)
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* bug fixed in image_by_windows

0.8.6 (2023-08-05)
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* viewer_4D handles arrows to move the selected objects.

0.8.7 (2023-08-31)
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* 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)
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* critical bug fixed in bin_4D

0.8.9 (2023-09-20)
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* bug removed from Normalize_4D
* bug removed from SymmetrySTEM
* tets added to locate atom and ...

0.8.10 (2023-09-12)
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* 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)
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* Bug fixed in viewer_4D

0.9.0 (2023-10-13)
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* added denoise4net
* added clustering4net and feature_maker_4D

0.9.1 (2024-02-23)
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* 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)
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* annular mask can handle even sized image

0.9.2 (2024-05-02)
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* viewer_4D takes second mask to subtract

0.9.3 (2024-05-24)
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* viewer_4D takes second mask to subtract

0.9.4 (2024-06-01)
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* 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)
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* Annular mask fixed
* added supervised 2D denoiser
* renamed denoise4net to denoise4_unet

0.9.6 (2024-11-08)
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* denoiser needed a fix

0.9.7 (2024-11-15)
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* critical bug fixed in applying spatial incoherence

0.9.8 (2024-11-15)
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* Maybe the installer should not install napari stuff
* removed autoconvolution from symmstem

0.9.9 (2024-12-19)
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* CapsNet is complete

0.9.10 (2025-01-18)
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* Denoising examples become consistant with current pyms version

0.9.11 (2025-01-18)
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* Adding a link to Michael pyms in the ReadMe file.
* fixed markimage

0.9.11 (2025-05-30)
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* fixed capsul network to handle any number of features in the output

0.9.13 (2025-09-01)
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* Annular mask bug fixed for non-square inputs

0.9.14 (2025-10-16)
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* Added Transformerregressir

0.9.15 (2025-11-07)
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* more advanced confidence head

0.9.16 (2026-01-27)
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* recycling and reconstruction error added to the regressor 

0.10.0 (2026-01-27)
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* reconstruction error of the regressor is weighted.