Commit e9377654 authored by Pierre Paleo's avatar Pierre Paleo
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Merge branch 'doc' into 'master'

Bootstrap documentation

See merge request paleo/nabu!7
parents 6e3a6813 abcd5223
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nabu.cuda package
=================
Subpackages
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.. toctree::
nabu.cuda.tests
Submodules
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nabu.cuda.convolution module
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nabu.cuda.kernel module
-----------------------
.. automodule:: nabu.cuda.kernel
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nabu.cuda.medfilt module
------------------------
.. automodule:: nabu.cuda.medfilt
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nabu.cuda.processing module
---------------------------
.. automodule:: nabu.cuda.processing
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nabu.cuda.utils module
----------------------
.. automodule:: nabu.cuda.utils
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Module contents
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.. automodule:: nabu.cuda
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nabu.cuda.tests package
=======================
Submodules
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nabu.cuda.tests.test\_medfilt module
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nabu.cuda.tests.test\_padding module
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Module contents
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nabu.distributed package
========================
Module contents
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.. automodule:: nabu.distributed
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nabu.io package
===============
Submodules
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nabu.io.config module
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nabu.io.reader module
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.. automodule:: nabu.io.reader
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Module contents
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.. automodule:: nabu.io
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nabu.misc package
=================
Subpackages
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.. toctree::
nabu.misc.tests
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nabu.misc.unsharp module
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.. automodule:: nabu.misc.unsharp
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nabu.misc.unsharp\_cuda module
------------------------------
.. automodule:: nabu.misc.unsharp_cuda
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nabu.misc.unsharp\_opencl module
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.. automodule:: nabu.misc.unsharp_opencl
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.. automodule:: nabu.misc
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nabu.misc.tests package
=======================
Submodules
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nabu.misc.tests.test\_unsharp module
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nabu.opencl package
===================
Module contents
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nabu.preproc package
====================
Subpackages
-----------
.. toctree::
nabu.preproc.tests
Submodules
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nabu.preproc.ccd module
-----------------------
.. automodule:: nabu.preproc.ccd
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nabu.preproc.ccd\_cuda module
-----------------------------
.. automodule:: nabu.preproc.ccd_cuda
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nabu.preproc.phase module
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.. automodule:: nabu.preproc.phase
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nabu.preproc.phase\_cuda module
-------------------------------
.. automodule:: nabu.preproc.phase_cuda
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nabu.preproc.sinogram module
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.. automodule:: nabu.preproc.sinogram
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nabu.preproc.sinogram\_cuda module
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nabu.preproc.tests package
==========================
Submodules
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nabu.preproc.tests.test\_ccd\_corr module
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nabu.preproc.tests.test\_flatfield module
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nabu.preproc.tests.test\_paganin module
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nabu.reconstruction package
===========================
Subpackages
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.. toctree::
nabu.reconstruction.tests
Submodules
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nabu.reconstruction.fbp module
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nabu.reconstruction.filtering module
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nabu.reconstruction.tests package
=================================
Submodules
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nabu.reconstruction.tests.test\_fbp module
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.. automodule:: nabu.reconstruction.tests.test_fbp
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nabu.resources.cli package
==========================
Submodules
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nabu.resources.cli.bootstrap module
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nabu.resources.cli.conf\_bootstrap module
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nabu.resources.cli.utils module
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nabu.resources package
======================
Subpackages
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.. toctree::
nabu.resources.cli
Submodules
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nabu.resources.dataset\_analyzer module
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nabu.resources.dataset\_validator module
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nabu.resources.nabu\_config module
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nabu.resources.utils module
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nabu.resources.validators module
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nabu API reference
==================
Subpackages
-----------
.. toctree::
nabu.cuda
nabu.distributed
nabu.io
nabu.misc
nabu.opencl
nabu.preproc
nabu.reconstruction
nabu.resources
nabu.thirdparty
Submodules
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nabu.tests module
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.. automodule:: nabu.tests
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nabu.testutils module
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nabu.utils module
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Module contents
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.. automodule:: nabu
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nabu.thirdparty package
=======================
Submodules
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nabu.thirdparty.tomopy\_phase module
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# CCD Processing
This section explains the various processing taking place in the "radios" domain.
## Introduction
Once a radios chunk is loaded into memory (see [radios chunk processing](definitions.md#radios-chunks)), various processing can be applied to each individual (sub)radio. The most common are:
- CCD hotspots removal
- Flat-Field normalization
- Phase retrieval
## The `CCDProcessing` class
The base class for handling these processing is `CCDProcessing` found in `nabu.preproc.ccd`. To instantiate a `CCDProcessing` class, only a stack of radios is required.
![CCD processing classes](images/ccd_processing_class.png)
......@@ -77,7 +77,11 @@ def setup(app):
app.add_config_value('recommonmark_config', {
'url_resolver': lambda url: github_doc_root + url,
'auto_toc_tree_section': 'Contents',
'enable_math': True,
'enable_inline_math': True,
}, True)
app.add_transform(AutoStructify)
# Document __init__
autoclass_content = 'both'
......@@ -12,14 +12,11 @@ Welcome to Nabu's documentation!
definitions.md
ccdprocessing.md
phase.md
nabu_config_file.md
validators.md
modules/index.rst
..
apidoc/nabu.rst
..
apidoc/nabu.rst
Indices and tables
......
# Phase Retrieval
Phase Retrieval is the process of extracting the phase shift, induced by the sample on the beam, acquired on the detector. This phase shift is then used to reconstruct a map of the (deviation from unity of the real part of) refractive index through tomographic reconstruction.
Nabu implements the following non-iterative phase retrieval methods.
## Paganin phase retrieval
This phase retrieval method was first described in [[1]](#references).
The implementation [PaganinPhaseRetrieval](apidoc/nabu.preproc.html#nabu.preproc.phase.PaganinPhaseRetrieval) follows the normalization of [[2]](#references) and is compatible with the implementation of [tomopy](https://github.com/tomopy/tomopy).
## Single-Distance CTF phase retrieval
This method, although based on Contrast Transfer Function (CTF) rather than Transport of Intensity (TIE), can also be expressed as a single step "filtering" processing. See for example [[2]](#references).
## References
[1] D. Paganin Et Al, "Simultaneous phase and amplitude extraction from a single defocused image of a homogeneous object", Journal of Microscopy, Vol 206, Part 1, 2002
[2] Boliang Yu Et Al, "Evaluation of phase retrieval approaches in magnified X-ray phase nano computerized tomography applied to bone tissue," Opt. Express 26, 11110-11124 (2018)
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