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algotom · Sep 1, 2022 · 53d813a · 53d813a
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diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -41,8 +41,8 @@
 ]
 
 bibtex_bibfiles = [
-    'bibtex/ref.bib',
-    'bibtex/cite.bib'
+    'toc/bibtex/ref.bib',
+    'toc/bibtex/cite.bib'
 ]
 
 # Napoleon settings
@@ -72,9 +72,10 @@
 master_doc = 'index'
 
 # General information about the project.
-Affiliation = u'Diamond Light Source, UK'
-project = u'Algotom-Reference'
-copyright = u'2021, Nghia T. Vo ' + Affiliation
+Affiliation1 = u' Diamond Light Source, UK'
+Affiliation2 = u'; NSLS-II, Brookhaven National Lab, US'
+project = u'Algotom'
+copyright = u'2021, Nghia T. Vo ' + Affiliation1 + Affiliation2
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
@@ -242,7 +243,7 @@
     ('index',
      project + '.tex',
      project + u' Documentation',
-     Affiliation, 'manual'),
+     Affiliation1 + Affiliation2, 'manual'),
 ]
 
 # The name of an image file (relative to this directory) to place at the top of
@@ -273,7 +274,7 @@
 man_pages = [
     ('index', project,
      project + u' Documentation',
-     [Affiliation, ], 1)
+     [Affiliation1 + Affiliation2, ], 1)
 ]
 
 # If true, show URL addresses after external links.
@@ -289,7 +290,7 @@
     ('index',
      project,
      project + u' Documentation',
-     Affiliation,
+     Affiliation1 + Affiliation2,
      project,
      'Algotom'),
 ]
@@ -319,3 +320,7 @@
     'scipy'
 ]
 autodoc_member_order = 'bysource'
+
+
+numfig = True
+numfig_secnum_depth = 2
diff --git a/docs/source/credits.rst b/docs/source/credits.rst
diff --git a/docs/source/favicon.ico b/docs/source/favicon.ico
diff --git a/docs/source/features.rst b/docs/source/features.rst
diff --git a/docs/source/img/logo2.png b/docs/source/img/logo2.png
diff --git a/docs/source/img/thumbnail.png b/docs/source/img/thumbnail.png
diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -1,40 +1,31 @@
-.. image:: img/logo.png
-   :width: 30%
-   :align: right
+.. figure:: toc/figs/logo.jpg
+  :figwidth: 35 %
+  :align: right
 
-=======
-Algotom
-=======
+Data processing algorithms for tomography
+=========================================
 
-Data processing (**ALGO**)rithms for (**TOM**)ography
+Welcome to Algotom's documentation about data processing algorithms for tomography.
+This documentation is not only to explain functions available in the Algotom
+package but also to present tomography-related tutorials,
+technical notes, and applications.
 
-**Algotom** is a Python package implementing methods for processing tomographic
-data acquired by non-standard scanning techniques such as grid scans, helical 
-scans, half-acquisition scans, or their combinations. Certainly, Algotom can 
-also be used for standard scans. The software includes 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.
+**Source code:** https://github.com/algotom/algotom
 
-The software is made available for the paper in :cite:`Vo:21`.
-
-**Source Code:** https://github.com/algotom/algotom
-
-**Documentation main page:** https://algotom.github.io
-
-This page is for Algotom functions reference.
-
-Content
--------
+Table of Contents
+=================
 
 .. toctree::
-   :maxdepth: 1
+   :numbered:
+   :maxdepth: 4
+
+   toc/section1
+   toc/section2
+   toc/section3
+   toc/section4
+   toc/section5
+   toc/section6
+   toc/api
+   toc/credits
+   toc/highlights
 
-   api
-   install
-   usage
-   features
-   highlights
-   credits
diff --git a/docs/source/install.rst b/docs/source/install.rst
diff --git a/docs/source/api.rst → docs/source/toc/api.rst b/docs/source/api.rst → docs/source/toc/api.rst
@@ -1,16 +1,15 @@
-=============
-API reference
+API Reference
 =============
 
-1. Input-output
----------------
+Input-output
+------------
 
 .. toctree::
    api/algotom.io.converter
    api/algotom.io.loadersaver
 
-2. Pre-processing
------------------
+Pre-processing
+--------------
 
 .. toctree::
 
@@ -21,28 +20,28 @@ API reference
    api/algotom.prep.removal
    api/algotom.prep.phase
 
-3. Reconstruction
------------------
+Reconstruction
+--------------
 
 .. toctree::
    api/algotom.rec.reconstruction
 
-4. Post-processing
-------------------
+Post-processing
+---------------
 
 .. toctree::
    api/algotom.post.postprocessing
 
-5. Utility
-----------
+Utility
+-------
 
 .. toctree::
    api/algotom.util.calibration
    api/algotom.util.simulation
    api/algotom.util.utility
    api/algotom.util.correlation
-   
+
 .. automodule:: algotom
    :members:
    :undoc-members:
-   :show-inheritance: 
+   :show-inheritance:
diff --git a/docs/source/api/algotom.io.converter.rst → docs/source/toc/api/algotom.io.converter.rst b/docs/source/api/algotom.io.converter.rst → docs/source/toc/api/algotom.io.converter.rst
diff --git a/docs/source/api/algotom.io.loadersaver.rst → ...source/toc/api/algotom.io.loadersaver.rst b/docs/source/api/algotom.io.loadersaver.rst → ...source/toc/api/algotom.io.loadersaver.rst
diff --git a/...ource/api/algotom.post.postprocessing.rst → ...e/toc/api/algotom.post.postprocessing.rst b/...ource/api/algotom.post.postprocessing.rst → ...e/toc/api/algotom.post.postprocessing.rst
diff --git a/docs/source/api/algotom.prep.calculation.rst → ...urce/toc/api/algotom.prep.calculation.rst b/docs/source/api/algotom.prep.calculation.rst → ...urce/toc/api/algotom.prep.calculation.rst
diff --git a/docs/source/api/algotom.prep.conversion.rst → ...ource/toc/api/algotom.prep.conversion.rst b/docs/source/api/algotom.prep.conversion.rst → ...ource/toc/api/algotom.prep.conversion.rst
diff --git a/docs/source/api/algotom.prep.correction.rst → ...ource/toc/api/algotom.prep.correction.rst b/docs/source/api/algotom.prep.correction.rst → ...ource/toc/api/algotom.prep.correction.rst
diff --git a/docs/source/api/algotom.prep.filtering.rst → ...source/toc/api/algotom.prep.filtering.rst b/docs/source/api/algotom.prep.filtering.rst → ...source/toc/api/algotom.prep.filtering.rst
diff --git a/docs/source/api/algotom.prep.phase.rst → docs/source/toc/api/algotom.prep.phase.rst b/docs/source/api/algotom.prep.phase.rst → docs/source/toc/api/algotom.prep.phase.rst
diff --git a/docs/source/api/algotom.prep.removal.rst → docs/source/toc/api/algotom.prep.removal.rst b/docs/source/api/algotom.prep.removal.rst → docs/source/toc/api/algotom.prep.removal.rst
diff --git a/...source/api/algotom.rec.reconstruction.rst → ...ce/toc/api/algotom.rec.reconstruction.rst b/...source/api/algotom.rec.reconstruction.rst → ...ce/toc/api/algotom.rec.reconstruction.rst
diff --git a/docs/source/api/algotom.util.calibration.rst → ...urce/toc/api/algotom.util.calibration.rst b/docs/source/api/algotom.util.calibration.rst → ...urce/toc/api/algotom.util.calibration.rst
diff --git a/docs/source/api/algotom.util.correlation.rst → ...urce/toc/api/algotom.util.correlation.rst b/docs/source/api/algotom.util.correlation.rst → ...urce/toc/api/algotom.util.correlation.rst
@@ -1,5 +1,5 @@
 :mod:`algotom.util.correlation`
-==============================
+===============================
 
 .. automodule:: algotom.util.correlation
    :members:
@@ -11,8 +11,8 @@
    .. autosummary::
 
     normalize_image
-	generate_correlation_map
-	locate_peak
-	find_shift_based_correlation_map
-	find_local_shifts
-	find_global_shift_based_local_shifts
+    generate_correlation_map
+    locate_peak
+    find_shift_based_correlation_map
+    find_local_shifts
+    find_global_shift_based_local_shifts
diff --git a/docs/source/api/algotom.util.simulation.rst → ...ource/toc/api/algotom.util.simulation.rst b/docs/source/api/algotom.util.simulation.rst → ...ource/toc/api/algotom.util.simulation.rst
diff --git a/docs/source/api/algotom.util.utility.rst → docs/source/toc/api/algotom.util.utility.rst b/docs/source/api/algotom.util.utility.rst → docs/source/toc/api/algotom.util.utility.rst
diff --git a/docs/source/bibtex/cite.bib → docs/source/toc/bibtex/cite.bib b/docs/source/bibtex/cite.bib → docs/source/toc/bibtex/cite.bib
diff --git a/docs/source/bibtex/ref.bib → docs/source/toc/bibtex/ref.bib b/docs/source/bibtex/ref.bib → docs/source/toc/bibtex/ref.bib
diff --git a/docs/source/toc/credits.rst b/docs/source/toc/credits.rst
@@ -0,0 +1,25 @@
+Credits
+=======
+
+Citations
+---------
+
+If Algotom is useful for your project, citing the following article :cite:`Vo:21` is very much
+appreciated.
+
+.. bibliography:: bibtex/cite.bib
+   :style: plain
+   :labelprefix: R
+
+Algorithms, methods, or techniques implemented in a scientific software package
+are crucial for its success. This is the same for Algotom. Acknowledging
+algorithms you use through Algotom is also very much appreciated.
+
+
+References
+----------
+
+.. bibliography:: bibtex/ref.bib
+   :style: unsrt
+   :labelprefix: M
+   :all:
diff --git a/docs/source/toc/figs/logo.jpg b/docs/source/toc/figs/logo.jpg
diff --git a/docs/source/img/logo.png → docs/source/toc/figs/logo.png b/docs/source/img/logo.png → docs/source/toc/figs/logo.png
diff --git a/docs/source/highlights.rst → docs/source/toc/highlights.rst b/docs/source/highlights.rst → docs/source/toc/highlights.rst
diff --git a/docs/source/toc/section1.rst b/docs/source/toc/section1.rst
@@ -0,0 +1,8 @@
+Basic tutorials
+===============
+
+..  toctree::
+    section1/section1_1.rst
+    section1/section1_2.rst
+    section1/section1_3.rst
+    section1/section1_4.rst