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algotom-1.2.0
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مشاهده بیشترتوضیحات
Data processing algorithms for tomography
| ویژگی | مقدار |
|---|---|
| سیستم عامل | - |
| نام فایل | algotom-1.2.0 |
| نام | algotom |
| نسخه کتابخانه | 1.2.0 |
| نگهدارنده | [] |
| ایمیل نگهدارنده | [] |
| نویسنده | Nghia Vo |
| ایمیل نویسنده | nvo@bnl.gov |
| آدرس صفحه اصلی | https://github.com/algotom/algotom |
| آدرس اینترنتی | https://pypi.org/project/algotom/ |
| مجوز | Apache 2.0 |
# Algotom
### Data processing (**ALGO**)rithms for (**TOM**)ography.
**Algotom** is a Python package implementing data processing methods for
tomography. It has methods in a full pipeline of data processing: reading-writing data,
pre-processing, tomographic reconstruction, post-processing, and data simulation.
Many utility methods are provided to help users quickly develop prototype-methods
or build a pipeline for processing their own data. From version 1.1, methods for
speckle-based phase-contrast tomography were added to the package.
The software was published for the paper; *"Data processing methods and data
acquisition for samples larger than the field of view in parallel-beam tomography,"*
Nghia T. Vo, Robert C. Atwood, Michael Drakopoulos, and Thomas Connolley, Opt.
Express 29, 17849-17874 (2021); https://doi.org/10.1364/OE.418448.
Features
--------
Algotom is a lightweight package. The software is built on top of a few core
Python libraries to ensure its ease-of-installation. Methods distributed in
Algotom have been developed and tested at synchrotron beamlines where massive
datasets are produced. This factor drives the methods developed to be easy-to-use,
robust, and practical. Some featuring methods in Algotom are as follows:
- Methods in a full data processing pipeline: reading-writing data,
pre-processing, tomographic reconstruction, and post-processing.
- Methods for processing grid scans (or tiled scans) with the offset rotation-axis
to multiply double the field-of-view (FOV) of a parallel-beam tomography system.
- Methods for processing helical scans (with/without the offset rotation-axis).
- Methods for determining the center-of-rotation (COR) and auto-stitching images
in half-acquisition scans (360-degree acquisition with the offset COR).
- Some practical methods developed and implemented for the package:
zinger removal, tilted sinogram generation, sinogram distortion correction,
beam hardening correction, DFI (direct Fourier inversion) reconstruction, FBP reconstruction,
and double-wedge filter for removing sample parts larger than the FOV in
a sinogram.
- Utility methods for [customizing ring/stripe artifact removal methods](https://sarepy.readthedocs.io/toc/section5.html)
and parallelizing computational work.
- Calibration methods for determining pixel-size in helical scans.
- Methods for generating simulation data: phantom creation, sinogram calculation
based on the Fourier slice theorem, and artifact generation.
- Methods for speckle-based phase-contrast tomography, image correlation, and image alignment.
Update notes
------------
- 13/05/2021: Publish codes.
- 26/01/2022:
+ Add phase.py module.
+ Add phase-unwrapping methods.
- 20/06/2022:
+ Add correlation.py module.
+ Add methods for speckle-based phase-contrast tomography.
+ Add methods for image alignment.
+ Release version 1.1.
- 27/06/2022: Publish https://algotom.github.io
- 20/10/2022: Publish implementation of the UMPA method.
- 20/10/2022: Release version 1.2.
Author
------
- Nghia T. Vo - *NSLS-II, Brookhaven National Lab, USA*; *Diamond Light Source, UK.*
How to install
--------------
- https://algotom.readthedocs.io/en/latest/toc/section3.html
- If users install Algotom to an existing environment and Numba fails to install due to the latest Numpy:
+ Downgrade Numpy and install Algotom/Numba again.
+ Create a new environment and install Algotom first, then other packages.
+ Use conda instead of pip.
- Avoid using the latest version of Python or Numpy as the Python ecosystem taking time to keep up with these twos.
How to use
----------
- https://algotom.readthedocs.io/en/latest/toc/section4.html
- https://algotom.readthedocs.io/en/latest/toc/section1/section1_4.html
- https://github.com/algotom/algotom/tree/master/examples
Highlights
----------
Algotom was used for some experiments featured on media:
- Scanning [Moon rocks and Martian meteorites](https://www.diamond.ac.uk/Home/News/LatestNews/2019/17-07-2019.html)
using helical scans with offset rotation-axis. Featured on [Reuters](https://www.reuters.com/article/idUKKCN1UC16V?edition-redirect=uk).
- Scanning [Herculaneum Scrolls](https://www.diamond.ac.uk/Home/News/LatestNews/2019/03-10-2019.html)
using grid scans with offset rotation-axis respect to the grid's FOV. Featured on [BBC](https://www.bbc.co.uk/news/av/uk-england-oxfordshire-49926789).
- Scanning ['Little Foot' fossil](https://www.diamond.ac.uk/Home/News/LatestNews/2021/02-03-21.html)
using two-camera detector with offset rotation-axis. Featured on [BBC](https://www.bbc.co.uk/news/science-environment-56241509).
نیازمندی
| مقدار | نام |
|---|---|
| >=1.18 | numpy |
| - | scipy |
| - | numba |
| - | pywavelets |
| - | pillow |
| - | h5py |
| - | joblib |
زبان مورد نیاز
| مقدار | نام |
|---|---|
| >=3.7 | Python |
نحوه نصب
نصب پکیج whl algotom-1.2.0:
pip install algotom-1.2.0.whl
نصب پکیج tar.gz algotom-1.2.0:
pip install algotom-1.2.0.tar.gz