Merge branch 'doc' into 'master'

Bootstrap documentation

See merge request paleo/nabu!7

doc/apidoc/nabu.cuda.rst

+nabu.cuda package
+=================
+
+Subpackages
+-----------
+
+.. toctree::
+
+   nabu.cuda.tests
+
+Submodules
+----------
+
+nabu.cuda.convolution module
+----------------------------
+
+.. automodule:: nabu.cuda.convolution
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+nabu.cuda.kernel module
+-----------------------
+
+.. automodule:: nabu.cuda.kernel
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+nabu.cuda.medfilt module
+------------------------
+
+.. automodule:: nabu.cuda.medfilt
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+nabu.cuda.processing module
+---------------------------
+
+.. automodule:: nabu.cuda.processing
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+nabu.cuda.utils module
+----------------------
+
+.. automodule:: nabu.cuda.utils
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: nabu.cuda
+   :members:
+   :undoc-members:
+   :show-inheritance:

doc/apidoc/nabu.cuda.tests.rst

+nabu.cuda.tests package
+=======================
+
+Submodules
+----------
+
+nabu.cuda.tests.test\_medfilt module
+------------------------------------
+
+.. automodule:: nabu.cuda.tests.test_medfilt
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+nabu.cuda.tests.test\_padding module
+------------------------------------
+
+.. automodule:: nabu.cuda.tests.test_padding
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: nabu.cuda.tests
+   :members:
+   :undoc-members:
+   :show-inheritance:

doc/apidoc/nabu.distributed.rst

+nabu.distributed package
+========================
+
+Module contents
+---------------
+
+.. automodule:: nabu.distributed
+   :members:
+   :undoc-members:
+   :show-inheritance:

doc/apidoc/nabu.io.rst

+nabu.io package
+===============
+
+Submodules
+----------
+
+nabu.io.config module
+---------------------
+
+.. automodule:: nabu.io.config
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+nabu.io.reader module
+---------------------
+
+.. automodule:: nabu.io.reader
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: nabu.io
+   :members:
+   :undoc-members:
+   :show-inheritance:

doc/apidoc/nabu.misc.rst

+nabu.misc package
+=================
+
+Subpackages
+-----------
+
+.. toctree::
+
+   nabu.misc.tests
+
+Submodules
+----------
+
+nabu.misc.unsharp module
+------------------------
+
+.. automodule:: nabu.misc.unsharp
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+nabu.misc.unsharp\_cuda module
+------------------------------
+
+.. automodule:: nabu.misc.unsharp_cuda
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+nabu.misc.unsharp\_opencl module
+--------------------------------
+
+.. automodule:: nabu.misc.unsharp_opencl
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: nabu.misc
+   :members:
+   :undoc-members:
+   :show-inheritance:

doc/apidoc/nabu.misc.tests.rst

+nabu.misc.tests package
+=======================
+
+Submodules
+----------
+
+nabu.misc.tests.test\_unsharp module
+------------------------------------
+
+.. automodule:: nabu.misc.tests.test_unsharp
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: nabu.misc.tests
+   :members:
+   :undoc-members:
+   :show-inheritance:

doc/apidoc/nabu.opencl.rst

+nabu.opencl package
+===================
+
+Module contents
+---------------
+
+.. automodule:: nabu.opencl
+   :members:
+   :undoc-members:
+   :show-inheritance:

doc/apidoc/nabu.preproc.rst

+nabu.preproc package
+====================
+
+Subpackages
+-----------
+
+.. toctree::
+
+   nabu.preproc.tests
+
+Submodules
+----------
+
+nabu.preproc.ccd module
+-----------------------
+
+.. automodule:: nabu.preproc.ccd
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+nabu.preproc.ccd\_cuda module
+-----------------------------
+
+.. automodule:: nabu.preproc.ccd_cuda
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+nabu.preproc.phase module
+-------------------------
+
+.. automodule:: nabu.preproc.phase
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+nabu.preproc.phase\_cuda module
+-------------------------------
+
+.. automodule:: nabu.preproc.phase_cuda
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+nabu.preproc.sinogram module
+----------------------------
+
+.. automodule:: nabu.preproc.sinogram
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+nabu.preproc.sinogram\_cuda module
+----------------------------------
+
+.. automodule:: nabu.preproc.sinogram_cuda
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: nabu.preproc
+   :members:
+   :undoc-members:
+   :show-inheritance:

doc/apidoc/nabu.preproc.tests.rst

+nabu.preproc.tests package
+==========================
+
+Submodules
+----------
+
+nabu.preproc.tests.test\_ccd\_corr module
+-----------------------------------------
+
+.. automodule:: nabu.preproc.tests.test_ccd_corr
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+nabu.preproc.tests.test\_flatfield module
+-----------------------------------------
+
+.. automodule:: nabu.preproc.tests.test_flatfield
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+nabu.preproc.tests.test\_paganin module
+---------------------------------------
+
+.. automodule:: nabu.preproc.tests.test_paganin
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: nabu.preproc.tests
+   :members:
+   :undoc-members:
+   :show-inheritance:

doc/apidoc/nabu.reconstruction.rst

+nabu.reconstruction package
+===========================
+
+Subpackages
+-----------
+
+.. toctree::
+
+   nabu.reconstruction.tests
+
+Submodules
+----------
+
+nabu.reconstruction.fbp module
+------------------------------
+
+.. automodule:: nabu.reconstruction.fbp
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+nabu.reconstruction.filtering module
+------------------------------------
+
+.. automodule:: nabu.reconstruction.filtering
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: nabu.reconstruction
+   :members:
+   :undoc-members:
+   :show-inheritance:

doc/apidoc/nabu.reconstruction.tests.rst

+nabu.reconstruction.tests package
+=================================
+
+Submodules
+----------
+
+nabu.reconstruction.tests.test\_fbp module
+------------------------------------------
+
+.. automodule:: nabu.reconstruction.tests.test_fbp
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: nabu.reconstruction.tests
+   :members:
+   :undoc-members:
+   :show-inheritance:

doc/apidoc/nabu.resources.cli.rst

+nabu.resources.cli package
+==========================
+
+Submodules
+----------
+
+nabu.resources.cli.bootstrap module
+-----------------------------------
+
+.. automodule:: nabu.resources.cli.bootstrap
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+nabu.resources.cli.conf\_bootstrap module
+-----------------------------------------
+
+.. automodule:: nabu.resources.cli.conf_bootstrap
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+nabu.resources.cli.utils module
+-------------------------------
+
+.. automodule:: nabu.resources.cli.utils
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: nabu.resources.cli
+   :members:
+   :undoc-members:
+   :show-inheritance:

doc/apidoc/nabu.resources.rst

+nabu.resources package
+======================
+
+Subpackages
+-----------
+
+.. toctree::
+
+   nabu.resources.cli
+
+Submodules
+----------
+
+nabu.resources.dataset\_analyzer module
+---------------------------------------
+
+.. automodule:: nabu.resources.dataset_analyzer
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+nabu.resources.dataset\_validator module
+----------------------------------------
+
+.. automodule:: nabu.resources.dataset_validator
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+nabu.resources.nabu\_config module
+----------------------------------
+
+.. automodule:: nabu.resources.nabu_config
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+nabu.resources.utils module
+---------------------------
+
+.. automodule:: nabu.resources.utils
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+nabu.resources.validators module
+--------------------------------
+
+.. automodule:: nabu.resources.validators
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: nabu.resources
+   :members:
+   :undoc-members:
+   :show-inheritance:

doc/apidoc/nabu.rst

+nabu API reference
+==================
+
+Subpackages
+-----------
+
+.. toctree::
+
+   nabu.cuda
+   nabu.distributed
+   nabu.io
+   nabu.misc
+   nabu.opencl
+   nabu.preproc
+   nabu.reconstruction
+   nabu.resources
+   nabu.thirdparty
+
+Submodules
+----------
+
+nabu.tests module
+-----------------
+
+.. automodule:: nabu.tests
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+nabu.testutils module
+---------------------
+
+.. automodule:: nabu.testutils
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+nabu.utils module
+-----------------
+
+.. automodule:: nabu.utils
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: nabu
+   :members:
+   :undoc-members:
+   :show-inheritance:

doc/apidoc/nabu.thirdparty.rst

+nabu.thirdparty package
+=======================
+
+Submodules
+----------
+
+nabu.thirdparty.tomopy\_phase module
+------------------------------------
+
+.. automodule:: nabu.thirdparty.tomopy_phase
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: nabu.thirdparty
+   :members:
+   :undoc-members:
+   :show-inheritance:

doc/ccdprocessing.md

+# 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)
+
+
+

doc/conf.py

@@ -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'

doc/index.rst

@@ -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

doc/phase.md

+# 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)
\ No newline at end of file