=========
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)
------------------
* 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
Raw data
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"description": "=========\nmcemtools\n=========\n\n\n.. image:: https://img.shields.io/pypi/v/mcemtools.svg\n :target: https://pypi.python.org/pypi/mcemtools\n\n.. image:: https://img.shields.io/travis/arsadri/mcemtools.svg\n :target: https://travis-ci.com/arsadri/mcemtools\n\n.. image:: https://readthedocs.org/projects/mcemtools/badge/?version=latest\n :target: https://mcemtools.readthedocs.io/en/latest/?version=latest\n :alt: Documentation Status\n\nDeep unsupervised analysis tools for Four-dimensional Scanning Transmission Electron Microscopy (4D-STEM) \n\nIn order to run the pyms simulations, you have to get it from:\n\nhttps://github.com/Michael-MD/py_multislice\n\nThen also there is a utils.py in the examples directory that helps.\n\n\n* Free software: MIT license\n* Documentation: https://mcemtools.readthedocs.io.\n\n\nFeatures\n--------\n\n* Denoising 4D-STEM data\n* a few tools to help pre-process 4D-STEM data\n\nCredits\n-------\n\nThis package was created with Cookiecutter_ 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