Tomographic Reconstruction in Python
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KedoKudo and dgursoy speedup detector drift detection with multiprocessing and enhance rot…
…ation center finder (#373)

* useful math functions based on numpy [and pandas]

* add the slit corner detection function for aps_1id tomography data

* add functions related to detector drift analysis for aps_1id

* follow suggestion from numpy warning

* improved documentation on affine transformation

* switch back to old string formatting for backward compatibility

* switch to os.path.join for windows compatibility

* decouple from pandas

* remove plotting related function and options

* condense import

* remove comment as suggested

* move note from comment to function doc string

* add error messages

* fix typo

* add description of corners order to function doc string

* more detailed documentation on slit clipping

* hard rim clipping->median filting for better performance with noisy img

* add control of the kernel size to the top level function

some sampels might requiers larger kernel size, which could significanly incase the runtime

* add parallel support

* use intermedia caller functoin

* try submit this time

* add missing index

* remove outdated code

* implement adaptive kernel size

* add more debug print

* fix logic error

* use reference slit corner as a rough guide

* fix one syntax error

* better debug output

* adjust debug output

* relax checking criterion

* adjust debug output

* use smaller steps size when adjusting kernel size

* add fail safe if using too much steps

* allow larger kernel

* tighted the threshold slightly

* tweating params

* adjust 1d as well

* use numpy logic array

* gauss() -> gauss1d()

* update docstring for gauss1d

* remove explicit naming

* fix typo

* pass through "autopep8 --in-place --aggressive --aggressive"

* remove unsed import

* calc_cumu* -> discrete_cdf

* update doctring

* update docstring

* update docstring

* refactoring calc_affine_transform

* np.linalg.lstsq -> scipy.linalg.lstsq

* fix formatting with autopep8

* update docstring

* remove a blank line

* following naming convention

* add secondary description for CDF calculation

* add more explanation on the auto slit detection code

* scipy.linalg.lstsq has different API from numpy

* add image enhance method for APS 1ID

* leave one core for master process

* add documentation to doc string

* add enhancer to function name list

* remove trailing coma

* add function to identify empty slice in tomo data

* add new function to list

* adjust whether to use additional smoothing or not

* extend the phase registration method with initial guess

* calculate the init shift based on guessed value

* fix logic error

* remove debug output

* update docstring

* fix bug in image shift caller

* add more explanation about the image enhancer

* imgstacks -> imgstack, one stack of images at a time

* pep8 fix on corr.py

* pep8 fix on npmath.py

* pep8 fix for alignment

* follow name convention
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README.rst

TomoPy

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TomoPy is an open-source Python package for tomographic data processing and image reconstruction.

Features

  • Image reconstruction algorithms for tomography.
  • Various filters, ring removal algorithms, phase retrieval algorithms.
  • Forward projection operator for absorption and wave propagation.

Installation

Have Conda installed first, then open a terminal or a command prompt window and run:

conda install -c conda-forge tomopy

Try Now

You can try notebooks now using mybinder.org

Contribute

License

The project is licensed under the BSD-3 license.