diff --git a/cfelpyutils/crystfel_utils.py b/cfelpyutils/crystfel_utils.py
index ac7b96b4a14a74db5b8dbe4ef74399aea5092866..ba3c8fe3316ccd8ff442707eaa73f2edc3d04fd4 100644
--- a/cfelpyutils/crystfel_utils.py
+++ b/cfelpyutils/crystfel_utils.py
@@ -361,7 +361,7 @@ def load_crystfel_geometry(filename):
This function is a reimplementation of the get_detector_geometry_2 function from
CrystFEL. It reads information from a CrystFEL geometry file.
-
+
For a full documentation of the CrystFEL geometry format, see the relevant `man
page <http://www.desy.de/~twhite/crystfel/manual-crystfel_geometry.html>`_.
@@ -375,7 +375,6 @@ def load_crystfel_geometry(filename):
* The code of this function is currently synchronized with the code of the function
'get_detector_geometry_2' in CrystFEL at commit 41a8fa9819010.
-
Arguments:
filename (str): the absolute or relative path to a CrystFEL geometry file.
diff --git a/cfelpyutils/geometry_utils.py b/cfelpyutils/geometry_utils.py
index 0efdb03c5886d87884c878ec85fba68ce77957ea..e2c4e558f5aab2bd9ac0dee2183306714bfe592b 100644
--- a/cfelpyutils/geometry_utils.py
+++ b/cfelpyutils/geometry_utils.py
@@ -134,7 +134,7 @@ def compute_visualization_pix_maps(geometry):
This function takes as input some geometry information read from a `CrystFEL
<http://www.desy.de/~twhite/crystfel/manual-crystfel_geometry.html>`_ file, and
returns a set of pre-computed pixel maps that can be used to display data in an
- ImageView widget from the `PyQtGraph <http://pyqtgraph.org/>`_ library.
+ ImageView widget (from the `PyQtGraph <http://pyqtgraph.org/>`_ library).
These pixel maps are different from the ones generated by the
:func:`~compute_pix_maps` function. The main differences are:
@@ -187,9 +187,9 @@ def apply_geometry_to_data(data, geometry):
the input data, and is symmetric around the center of the reference system
(i.e: the beam interaction point).
- This restrictions often cause the returned array to be bigger than the minimum size
- needed to store the physical layout of the pixels in the detector, particularly if
- the detector is not centered at the beam interaction point.
+ These restrictions often cause the returned array to be bigger than the minimum
+ size needed to store the physical layout of the pixels in the detector,
+ particularly if the detector is not centered at the beam interaction point.
Arguments:
@@ -202,7 +202,7 @@ def apply_geometry_to_data(data, geometry):
Returns:
numpy.ndarray: an array containing the data with the geometry information
- applied.
+ applied.
"""
pixel_maps = compute_pix_maps(geometry)
x_map, y_map = pixel_maps.x, pixel_maps.y
diff --git a/docs/_modules/cfelpyutils/crystfel_utils.html b/docs/_modules/cfelpyutils/crystfel_utils.html
index f114828d0b06f39b048819472b0a1d8f02aee83f..8d1f451c36483926812bdfdcc50feac418cf92c1 100644
--- a/docs/_modules/cfelpyutils/crystfel_utils.html
+++ b/docs/_modules/cfelpyutils/crystfel_utils.html
@@ -703,7 +703,6 @@
<h3>Navigation</h3>
<ul>
<li class="toctree-l1"><a class="reference internal" href="../../cfelpyutils.html">The cfelpyutils Package</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../../documentation_guidelines_for_contributors.html">Guidelines for Contributors</a></li>
</ul>
<div class="relations">
diff --git a/docs/_modules/cfelpyutils/geometry_utils.html b/docs/_modules/cfelpyutils/geometry_utils.html
index 61de150ac343caea069add2e37dfbec77a55e77a..32df1d9b1c427a5be4265fac572d92a0ecbf39e6 100644
--- a/docs/_modules/cfelpyutils/geometry_utils.html
+++ b/docs/_modules/cfelpyutils/geometry_utils.html
@@ -270,7 +270,6 @@
<h3>Navigation</h3>
<ul>
<li class="toctree-l1"><a class="reference internal" href="../../cfelpyutils.html">The cfelpyutils Package</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../../documentation_guidelines_for_contributors.html">Guidelines for Contributors</a></li>
</ul>
<div class="relations">
diff --git a/docs/_modules/cfelpyutils/named_tuples.html b/docs/_modules/cfelpyutils/named_tuples.html
index 5c11e47d12ac2cd84ecbfda54af3a339e330b363..f12c4e8928e8792ff64f2cff968c91d1f2d6265f 100644
--- a/docs/_modules/cfelpyutils/named_tuples.html
+++ b/docs/_modules/cfelpyutils/named_tuples.html
@@ -94,7 +94,6 @@
<h3>Navigation</h3>
<ul>
<li class="toctree-l1"><a class="reference internal" href="../../cfelpyutils.html">The cfelpyutils Package</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../../documentation_guidelines_for_contributors.html">Guidelines for Contributors</a></li>
</ul>
<div class="relations">
diff --git a/docs/_modules/index.html b/docs/_modules/index.html
index a28cdf28c4b7094fd60c51780af2e82370e397ca..0426bf54bd656d3c0d95f66c067ab2aa714127f7 100644
--- a/docs/_modules/index.html
+++ b/docs/_modules/index.html
@@ -56,7 +56,6 @@
<h3>Navigation</h3>
<ul>
<li class="toctree-l1"><a class="reference internal" href="../cfelpyutils.html">The cfelpyutils Package</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../documentation_guidelines_for_contributors.html">Guidelines for Contributors</a></li>
</ul>
<div class="relations">
diff --git a/docs/_sources/documentation_guidelines_for_contributors.rst.txt b/docs/_sources/documentation_guidelines_for_contributors.rst.txt
index bcdb3cbbd84cdc0dcbf1b78b56f85305a1c14b4d..60bcb635ac96faa65abaef5140dedad24a3c0546 100644
--- a/docs/_sources/documentation_guidelines_for_contributors.rst.txt
+++ b/docs/_sources/documentation_guidelines_for_contributors.rst.txt
@@ -1,3 +1,5 @@
+:orphan:
+
Guidelines for Contributors
===========================
diff --git a/docs/_sources/index.rst.txt b/docs/_sources/index.rst.txt
index a3b5c6edd53bf827b02c983c043da0e871a8aa0c..ef4ad25986e24009b703d68ae92c52c93c51a810 100644
--- a/docs/_sources/index.rst.txt
+++ b/docs/_sources/index.rst.txt
@@ -3,14 +3,13 @@
You can adapt this file completely to your liking, but it should at least
contain the root `toctree` directive.
-CFELPyUtils
-===========
+The CFELPyUtils Library
+=======================
.. toctree::
:hidden:
cfelpyutils
- documentation_guidelines_for_contributors
Introduction
diff --git a/docs/_sources/modules.rst.txt b/docs/_sources/modules.rst.txt
deleted file mode 100644
index 31f2701ff23895a94e820cf656c94b82a0c378ea..0000000000000000000000000000000000000000
--- a/docs/_sources/modules.rst.txt
+++ /dev/null
@@ -1,7 +0,0 @@
-cfelpyutils
-===========
-
-.. toctree::
- :maxdepth: 4
-
- cfelpyutils
diff --git a/docs/cfelpyutils.crystfel_utils.html b/docs/cfelpyutils.crystfel_utils.html
index 58736dfc28e6fb4e091027531de5df77b4d3e392..d162d9e98be24bde366a9733821c98c0cd7e59cd 100644
--- a/docs/cfelpyutils.crystfel_utils.html
+++ b/docs/cfelpyutils.crystfel_utils.html
@@ -95,7 +95,6 @@ file.</td>
<li class="toctree-l2"><a class="reference internal" href="cfelpyutils.named_tuples.html">named_tuples</a></li>
</ul>
</li>
-<li class="toctree-l1"><a class="reference internal" href="documentation_guidelines_for_contributors.html">Guidelines for Contributors</a></li>
</ul>
<div class="relations">
diff --git a/docs/cfelpyutils.geometry_utils.html b/docs/cfelpyutils.geometry_utils.html
index a4741023327231ca89d3d78a367ea041b0b119db..411b8e2af01527f3897b4d68aa81cc8476711ba9 100644
--- a/docs/cfelpyutils.geometry_utils.html
+++ b/docs/cfelpyutils.geometry_utils.html
@@ -161,7 +161,6 @@ applied.</p>
<li class="toctree-l2"><a class="reference internal" href="cfelpyutils.named_tuples.html">named_tuples</a></li>
</ul>
</li>
-<li class="toctree-l1"><a class="reference internal" href="documentation_guidelines_for_contributors.html">Guidelines for Contributors</a></li>
</ul>
<div class="relations">
diff --git a/docs/cfelpyutils.html b/docs/cfelpyutils.html
index e7a0d92a28538de55ba588e0bee27efbbd88546a..24ffb504ac80e7c995ad4ba015d5477f415493cf 100644
--- a/docs/cfelpyutils.html
+++ b/docs/cfelpyutils.html
@@ -70,7 +70,6 @@
<li class="toctree-l2"><a class="reference internal" href="cfelpyutils.named_tuples.html">named_tuples</a></li>
</ul>
</li>
-<li class="toctree-l1"><a class="reference internal" href="documentation_guidelines_for_contributors.html">Guidelines for Contributors</a></li>
</ul>
<div class="relations">
diff --git a/docs/cfelpyutils.named_tuples.html b/docs/cfelpyutils.named_tuples.html
index 377126c6fe5a5c92f10b80488c3c1ff069a04eeb..66a4c7cfefd6052804d7eff52417f1045f5c1fb9 100644
--- a/docs/cfelpyutils.named_tuples.html
+++ b/docs/cfelpyutils.named_tuples.html
@@ -16,7 +16,6 @@
<script type="text/javascript" src="_static/language_data.js"></script>
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
- <link rel="next" title="Guidelines for Contributors" href="documentation_guidelines_for_contributors.html" />
<link rel="prev" title="The geometry_utils Module" href="cfelpyutils.geometry_utils.html" />
<link rel="stylesheet" href="_static/custom.css" type="text/css" />
@@ -119,7 +118,6 @@ pixel, the center of the reference system, and the x axis.</li>
<li class="toctree-l2 current"><a class="current reference internal" href="#">named_tuples</a></li>
</ul>
</li>
-<li class="toctree-l1"><a class="reference internal" href="documentation_guidelines_for_contributors.html">Guidelines for Contributors</a></li>
</ul>
<div class="relations">
@@ -128,7 +126,6 @@ pixel, the center of the reference system, and the x axis.</li>
<li><a href="index.html">Documentation overview</a><ul>
<li><a href="cfelpyutils.html">The cfelpyutils Package</a><ul>
<li>Previous: <a href="cfelpyutils.geometry_utils.html" title="previous chapter">The geometry_utils Module</a></li>
- <li>Next: <a href="documentation_guidelines_for_contributors.html" title="next chapter">Guidelines for Contributors</a></li>
</ul></li>
</ul></li>
</ul>
diff --git a/docs/documentation_guidelines_for_contributors.html b/docs/documentation_guidelines_for_contributors.html
index 81baa5aa32f8cd18d9321394afc3cde2a6a244e7..1791906cdaf51eb2c8d3eac66b5cb13cba2a751d 100644
--- a/docs/documentation_guidelines_for_contributors.html
+++ b/docs/documentation_guidelines_for_contributors.html
@@ -16,7 +16,6 @@
<script type="text/javascript" src="_static/language_data.js"></script>
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
- <link rel="prev" title="The named_tuples Module" href="cfelpyutils.named_tuples.html" />
<link rel="stylesheet" href="_static/custom.css" type="text/css" />
@@ -104,7 +103,7 @@ Python.</li>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
<div class="sphinxsidebarwrapper">
- <h3><a href="index.html">Table of Contents</a></h3>
+ <h3><a href="index.html">CFELPyUtils</a></h3>
<ul>
<li><a class="reference internal" href="#">Guidelines for Contributors</a><ul>
<li><a class="reference internal" href="#version-control">Version Control</a></li>
diff --git a/docs/genindex.html b/docs/genindex.html
index 19e0c10386752bfe9ebb701eeb41c28878b67ec6..c2a43c1d5a1ff45d2b4cede518565357864db04c 100644
--- a/docs/genindex.html
+++ b/docs/genindex.html
@@ -147,7 +147,6 @@
<h3>Navigation</h3>
<ul>
<li class="toctree-l1"><a class="reference internal" href="cfelpyutils.html">The cfelpyutils Package</a></li>
-<li class="toctree-l1"><a class="reference internal" href="documentation_guidelines_for_contributors.html">Guidelines for Contributors</a></li>
</ul>
<div class="relations">
diff --git a/docs/index.html b/docs/index.html
index 6e919023c8c32ddf9acffc5095b6620a77aa10d3..1b1aac8698de1699d3621fa1567b9e93af4bcafa 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="X-UA-Compatible" content="IE=Edge" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>CFELPyUtils — CFELPyUtils 1.0.0 documentation</title>
+ <title>The CFELPyUtils Library — CFELPyUtils 1.0.0 documentation</title>
<link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
<script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
@@ -33,8 +33,8 @@
<div class="body" role="main">
- <div class="section" id="cfelpyutils">
-<h1>CFELPyUtils<a class="headerlink" href="#cfelpyutils" title="Permalink to this headline">¶</a></h1>
+ <div class="section" id="the-cfelpyutils-library">
+<h1>The CFELPyUtils Library<a class="headerlink" href="#the-cfelpyutils-library" title="Permalink to this headline">¶</a></h1>
<div class="toctree-wrapper compound">
</div>
<div class="section" id="introduction">
@@ -97,9 +97,9 @@ to the project:</p>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
<div class="sphinxsidebarwrapper">
- <h3><a href="#">Table of Contents</a></h3>
+ <h3><a href="#">CFELPyUtils</a></h3>
<ul>
-<li><a class="reference internal" href="#">CFELPyUtils</a><ul>
+<li><a class="reference internal" href="#">The CFELPyUtils Library</a><ul>
<li><a class="reference internal" href="#introduction">Introduction</a></li>
<li><a class="reference internal" href="#installation">Installation</a></li>
<li><a class="reference internal" href="#authors">Authors</a></li>
diff --git a/docs/modules.html b/docs/modules.html
deleted file mode 100644
index c6b1e688e34bcb7f129db659fedfe545efd48e0f..0000000000000000000000000000000000000000
--- a/docs/modules.html
+++ /dev/null
@@ -1,114 +0,0 @@
-
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
- "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
-
-<html xmlns="http://www.w3.org/1999/xhtml" lang="en">
- <head>
- <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>cfelpyutils — CFELPyUtils 1.0.0 documentation</title>
- <link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
- <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
- <script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
- <script type="text/javascript" src="_static/jquery.js"></script>
- <script type="text/javascript" src="_static/underscore.js"></script>
- <script type="text/javascript" src="_static/doctools.js"></script>
- <script type="text/javascript" src="_static/language_data.js"></script>
- <link rel="index" title="Index" href="genindex.html" />
- <link rel="search" title="Search" href="search.html" />
-
- <link rel="stylesheet" href="_static/custom.css" type="text/css" />
-
-
- <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
-
- </head><body>
-
-
- <div class="document">
- <div class="documentwrapper">
- <div class="bodywrapper">
-
-
- <div class="body" role="main">
-
- <div class="section" id="cfelpyutils">
-<h1>cfelpyutils<a class="headerlink" href="#cfelpyutils" title="Permalink to this headline">¶</a></h1>
-<div class="toctree-wrapper compound">
-<ul>
-<li class="toctree-l1"><a class="reference internal" href="cfelpyutils.html">The cfelpyutils Package</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="cfelpyutils.crystfel_utils.html">crystfel_utils</a></li>
-<li class="toctree-l2"><a class="reference internal" href="cfelpyutils.geometry_utils.html">geometry_utils</a></li>
-<li class="toctree-l2"><a class="reference internal" href="cfelpyutils.named_tuples.html">named_tuples</a></li>
-</ul>
-</li>
-</ul>
-</div>
-</div>
-
-
- </div>
-
- </div>
- </div>
- <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
- <div class="sphinxsidebarwrapper">
-<h1 class="logo"><a href="index.html">CFELPyUtils</a></h1>
-
-
-
-
-
-
-
-
-<h3>Navigation</h3>
-<ul>
-<li class="toctree-l1"><a class="reference internal" href="cfelpyutils.html">The cfelpyutils Package</a></li>
-</ul>
-
-<div class="relations">
-<h3>Related Topics</h3>
-<ul>
- <li><a href="index.html">Documentation overview</a><ul>
- </ul></li>
-</ul>
-</div>
-<div id="searchbox" style="display: none" role="search">
- <h3>Quick search</h3>
- <div class="searchformwrapper">
- <form class="search" action="search.html" method="get">
- <input type="text" name="q" />
- <input type="submit" value="Go" />
- <input type="hidden" name="check_keywords" value="yes" />
- <input type="hidden" name="area" value="default" />
- </form>
- </div>
-</div>
-<script type="text/javascript">$('#searchbox').show(0);</script>
-
-
-
-
-
-
-
-
- </div>
- </div>
- <div class="clearer"></div>
- </div>
- <div class="footer">
- ©2019, OnDA Team.
-
- |
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.5</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
-
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-
-
-
-
- </body>
-</html>
\ No newline at end of file
diff --git a/docs/objects.inv b/docs/objects.inv
index 4a820253d6ecab3d4028bc2d93308bcfad0ecf29..a7f57df54099dbcb716c8510407aa5ef15984664 100644
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diff --git a/docs/py-modindex.html b/docs/py-modindex.html
index b250e7947045705d5ded347fb794804d6ea35934..02294c3cdfa99d66eb51c404d1f3a85f35a11d58 100644
--- a/docs/py-modindex.html
+++ b/docs/py-modindex.html
@@ -88,7 +88,6 @@
<h3>Navigation</h3>
<ul>
<li class="toctree-l1"><a class="reference internal" href="cfelpyutils.html">The cfelpyutils Package</a></li>
-<li class="toctree-l1"><a class="reference internal" href="documentation_guidelines_for_contributors.html">Guidelines for Contributors</a></li>
</ul>
<div class="relations">
diff --git a/docs/search.html b/docs/search.html
index e7b25fce925230ba85e8f631a8f13acdcc233dde..a11796593e684e220d2c736d2087b4ebbc556ea1 100644
--- a/docs/search.html
+++ b/docs/search.html
@@ -83,7 +83,6 @@
<h3>Navigation</h3>
<ul>
<li class="toctree-l1"><a class="reference internal" href="cfelpyutils.html">The cfelpyutils Package</a></li>
-<li class="toctree-l1"><a class="reference internal" href="documentation_guidelines_for_contributors.html">Guidelines for Contributors</a></li>
</ul>
<div class="relations">
diff --git a/docs/searchindex.js b/docs/searchindex.js
index 2f17d5db1173fdf12014438b4c8a0fa0515a9907..ab1eb8a17176105aa3f67f506ce647f498b82724 100644
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+++ b/docs/searchindex.js
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diff --git a/docs_src/_build/doctrees/documentation_guidelines_for_contributors.doctree b/docs_src/_build/doctrees/documentation_guidelines_for_contributors.doctree
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diff --git a/docs_src/_build/doctrees/index.doctree b/docs_src/_build/doctrees/index.doctree
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diff --git a/docs_src/_build/doctrees/modules.doctree b/docs_src/_build/doctrees/modules.doctree
deleted file mode 100644
index 4199b5bab20782ad04d80ffa107ac54a88f857bf..0000000000000000000000000000000000000000
Binary files a/docs_src/_build/doctrees/modules.doctree and /dev/null differ
diff --git a/docs_src/_build/html/_modules/cfelpyutils/crystfel_utils.html b/docs_src/_build/html/_modules/cfelpyutils/crystfel_utils.html
index f114828d0b06f39b048819472b0a1d8f02aee83f..8d1f451c36483926812bdfdcc50feac418cf92c1 100644
--- a/docs_src/_build/html/_modules/cfelpyutils/crystfel_utils.html
+++ b/docs_src/_build/html/_modules/cfelpyutils/crystfel_utils.html
@@ -703,7 +703,6 @@
<h3>Navigation</h3>
<ul>
<li class="toctree-l1"><a class="reference internal" href="../../cfelpyutils.html">The cfelpyutils Package</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../../documentation_guidelines_for_contributors.html">Guidelines for Contributors</a></li>
</ul>
<div class="relations">
diff --git a/docs_src/_build/html/_modules/cfelpyutils/geometry_utils.html b/docs_src/_build/html/_modules/cfelpyutils/geometry_utils.html
index 61de150ac343caea069add2e37dfbec77a55e77a..32df1d9b1c427a5be4265fac572d92a0ecbf39e6 100644
--- a/docs_src/_build/html/_modules/cfelpyutils/geometry_utils.html
+++ b/docs_src/_build/html/_modules/cfelpyutils/geometry_utils.html
@@ -270,7 +270,6 @@
<h3>Navigation</h3>
<ul>
<li class="toctree-l1"><a class="reference internal" href="../../cfelpyutils.html">The cfelpyutils Package</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../../documentation_guidelines_for_contributors.html">Guidelines for Contributors</a></li>
</ul>
<div class="relations">
diff --git a/docs_src/_build/html/_modules/cfelpyutils/named_tuples.html b/docs_src/_build/html/_modules/cfelpyutils/named_tuples.html
index 5c11e47d12ac2cd84ecbfda54af3a339e330b363..f12c4e8928e8792ff64f2cff968c91d1f2d6265f 100644
--- a/docs_src/_build/html/_modules/cfelpyutils/named_tuples.html
+++ b/docs_src/_build/html/_modules/cfelpyutils/named_tuples.html
@@ -94,7 +94,6 @@
<h3>Navigation</h3>
<ul>
<li class="toctree-l1"><a class="reference internal" href="../../cfelpyutils.html">The cfelpyutils Package</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../../documentation_guidelines_for_contributors.html">Guidelines for Contributors</a></li>
</ul>
<div class="relations">
diff --git a/docs_src/_build/html/_modules/index.html b/docs_src/_build/html/_modules/index.html
index a28cdf28c4b7094fd60c51780af2e82370e397ca..0426bf54bd656d3c0d95f66c067ab2aa714127f7 100644
--- a/docs_src/_build/html/_modules/index.html
+++ b/docs_src/_build/html/_modules/index.html
@@ -56,7 +56,6 @@
<h3>Navigation</h3>
<ul>
<li class="toctree-l1"><a class="reference internal" href="../cfelpyutils.html">The cfelpyutils Package</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../documentation_guidelines_for_contributors.html">Guidelines for Contributors</a></li>
</ul>
<div class="relations">
diff --git a/docs_src/_build/html/_sources/documentation_guidelines_for_contributors.rst.txt b/docs_src/_build/html/_sources/documentation_guidelines_for_contributors.rst.txt
index bcdb3cbbd84cdc0dcbf1b78b56f85305a1c14b4d..60bcb635ac96faa65abaef5140dedad24a3c0546 100644
--- a/docs_src/_build/html/_sources/documentation_guidelines_for_contributors.rst.txt
+++ b/docs_src/_build/html/_sources/documentation_guidelines_for_contributors.rst.txt
@@ -1,3 +1,5 @@
+:orphan:
+
Guidelines for Contributors
===========================
diff --git a/docs_src/_build/html/_sources/index.rst.txt b/docs_src/_build/html/_sources/index.rst.txt
index a3b5c6edd53bf827b02c983c043da0e871a8aa0c..ef4ad25986e24009b703d68ae92c52c93c51a810 100644
--- a/docs_src/_build/html/_sources/index.rst.txt
+++ b/docs_src/_build/html/_sources/index.rst.txt
@@ -3,14 +3,13 @@
You can adapt this file completely to your liking, but it should at least
contain the root `toctree` directive.
-CFELPyUtils
-===========
+The CFELPyUtils Library
+=======================
.. toctree::
:hidden:
cfelpyutils
- documentation_guidelines_for_contributors
Introduction
diff --git a/docs_src/_build/html/_sources/modules.rst.txt b/docs_src/_build/html/_sources/modules.rst.txt
deleted file mode 100644
index 31f2701ff23895a94e820cf656c94b82a0c378ea..0000000000000000000000000000000000000000
--- a/docs_src/_build/html/_sources/modules.rst.txt
+++ /dev/null
@@ -1,7 +0,0 @@
-cfelpyutils
-===========
-
-.. toctree::
- :maxdepth: 4
-
- cfelpyutils
diff --git a/docs_src/_build/html/cfelpyutils.crystfel_utils.html b/docs_src/_build/html/cfelpyutils.crystfel_utils.html
index 58736dfc28e6fb4e091027531de5df77b4d3e392..d162d9e98be24bde366a9733821c98c0cd7e59cd 100644
--- a/docs_src/_build/html/cfelpyutils.crystfel_utils.html
+++ b/docs_src/_build/html/cfelpyutils.crystfel_utils.html
@@ -95,7 +95,6 @@ file.</td>
<li class="toctree-l2"><a class="reference internal" href="cfelpyutils.named_tuples.html">named_tuples</a></li>
</ul>
</li>
-<li class="toctree-l1"><a class="reference internal" href="documentation_guidelines_for_contributors.html">Guidelines for Contributors</a></li>
</ul>
<div class="relations">
diff --git a/docs_src/_build/html/cfelpyutils.geometry_utils.html b/docs_src/_build/html/cfelpyutils.geometry_utils.html
index a4741023327231ca89d3d78a367ea041b0b119db..411b8e2af01527f3897b4d68aa81cc8476711ba9 100644
--- a/docs_src/_build/html/cfelpyutils.geometry_utils.html
+++ b/docs_src/_build/html/cfelpyutils.geometry_utils.html
@@ -161,7 +161,6 @@ applied.</p>
<li class="toctree-l2"><a class="reference internal" href="cfelpyutils.named_tuples.html">named_tuples</a></li>
</ul>
</li>
-<li class="toctree-l1"><a class="reference internal" href="documentation_guidelines_for_contributors.html">Guidelines for Contributors</a></li>
</ul>
<div class="relations">
diff --git a/docs_src/_build/html/cfelpyutils.html b/docs_src/_build/html/cfelpyutils.html
index e7a0d92a28538de55ba588e0bee27efbbd88546a..24ffb504ac80e7c995ad4ba015d5477f415493cf 100644
--- a/docs_src/_build/html/cfelpyutils.html
+++ b/docs_src/_build/html/cfelpyutils.html
@@ -70,7 +70,6 @@
<li class="toctree-l2"><a class="reference internal" href="cfelpyutils.named_tuples.html">named_tuples</a></li>
</ul>
</li>
-<li class="toctree-l1"><a class="reference internal" href="documentation_guidelines_for_contributors.html">Guidelines for Contributors</a></li>
</ul>
<div class="relations">
diff --git a/docs_src/_build/html/cfelpyutils.named_tuples.html b/docs_src/_build/html/cfelpyutils.named_tuples.html
index 377126c6fe5a5c92f10b80488c3c1ff069a04eeb..66a4c7cfefd6052804d7eff52417f1045f5c1fb9 100644
--- a/docs_src/_build/html/cfelpyutils.named_tuples.html
+++ b/docs_src/_build/html/cfelpyutils.named_tuples.html
@@ -16,7 +16,6 @@
<script type="text/javascript" src="_static/language_data.js"></script>
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
- <link rel="next" title="Guidelines for Contributors" href="documentation_guidelines_for_contributors.html" />
<link rel="prev" title="The geometry_utils Module" href="cfelpyutils.geometry_utils.html" />
<link rel="stylesheet" href="_static/custom.css" type="text/css" />
@@ -119,7 +118,6 @@ pixel, the center of the reference system, and the x axis.</li>
<li class="toctree-l2 current"><a class="current reference internal" href="#">named_tuples</a></li>
</ul>
</li>
-<li class="toctree-l1"><a class="reference internal" href="documentation_guidelines_for_contributors.html">Guidelines for Contributors</a></li>
</ul>
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@@ -128,7 +126,6 @@ pixel, the center of the reference system, and the x axis.</li>
<li><a href="index.html">Documentation overview</a><ul>
<li><a href="cfelpyutils.html">The cfelpyutils Package</a><ul>
<li>Previous: <a href="cfelpyutils.geometry_utils.html" title="previous chapter">The geometry_utils Module</a></li>
- <li>Next: <a href="documentation_guidelines_for_contributors.html" title="next chapter">Guidelines for Contributors</a></li>
</ul></li>
</ul></li>
</ul>
diff --git a/docs_src/_build/html/documentation_guidelines_for_contributors.html b/docs_src/_build/html/documentation_guidelines_for_contributors.html
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+++ b/docs_src/_build/html/documentation_guidelines_for_contributors.html
@@ -16,7 +16,6 @@
<script type="text/javascript" src="_static/language_data.js"></script>
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
- <link rel="prev" title="The named_tuples Module" href="cfelpyutils.named_tuples.html" />
<link rel="stylesheet" href="_static/custom.css" type="text/css" />
@@ -104,7 +103,7 @@ Python.</li>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
<div class="sphinxsidebarwrapper">
- <h3><a href="index.html">Table of Contents</a></h3>
+ <h3><a href="index.html">CFELPyUtils</a></h3>
<ul>
<li><a class="reference internal" href="#">Guidelines for Contributors</a><ul>
<li><a class="reference internal" href="#version-control">Version Control</a></li>
diff --git a/docs_src/_build/html/genindex.html b/docs_src/_build/html/genindex.html
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+++ b/docs_src/_build/html/genindex.html
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+++ b/docs_src/_build/html/index.html
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<head>
<meta http-equiv="X-UA-Compatible" content="IE=Edge" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>CFELPyUtils — CFELPyUtils 1.0.0 documentation</title>
+ <title>The CFELPyUtils Library — CFELPyUtils 1.0.0 documentation</title>
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<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
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<div class="body" role="main">
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-<h1>CFELPyUtils<a class="headerlink" href="#cfelpyutils" title="Permalink to this headline">¶</a></h1>
+ <div class="section" id="the-cfelpyutils-library">
+<h1>The CFELPyUtils Library<a class="headerlink" href="#the-cfelpyutils-library" title="Permalink to this headline">¶</a></h1>
<div class="toctree-wrapper compound">
</div>
<div class="section" id="introduction">
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</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
<div class="sphinxsidebarwrapper">
- <h3><a href="#">Table of Contents</a></h3>
+ <h3><a href="#">CFELPyUtils</a></h3>
<ul>
-<li><a class="reference internal" href="#">CFELPyUtils</a><ul>
+<li><a class="reference internal" href="#">The CFELPyUtils Library</a><ul>
<li><a class="reference internal" href="#introduction">Introduction</a></li>
<li><a class="reference internal" href="#installation">Installation</a></li>
<li><a class="reference internal" href="#authors">Authors</a></li>
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- <div class="sphinxsidebarwrapper">
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-<li class="toctree-l1"><a class="reference internal" href="cfelpyutils.html">The cfelpyutils Package</a></li>
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-<div class="relations">
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- <li><a href="index.html">Documentation overview</a><ul>
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\ No newline at end of file
+Search.setIndex({docnames:["cfelpyutils","cfelpyutils.crystfel_utils","cfelpyutils.geometry_utils","cfelpyutils.named_tuples","documentation_guidelines_for_contributors","index"],envversion:{"sphinx.domains.c":1,"sphinx.domains.changeset":1,"sphinx.domains.cpp":1,"sphinx.domains.javascript":1,"sphinx.domains.math":2,"sphinx.domains.python":1,"sphinx.domains.rst":1,"sphinx.domains.std":1,"sphinx.ext.todo":1,"sphinx.ext.viewcode":1,sphinx:55},filenames:["cfelpyutils.rst","cfelpyutils.crystfel_utils.rst","cfelpyutils.geometry_utils.rst","cfelpyutils.named_tuples.rst","documentation_guidelines_for_contributors.rst","index.rst"],objects:{"":{cfelpyutils:[0,0,0,"-"]},"cfelpyutils.crystfel_utils":{load_crystfel_geometry:[1,1,1,""]},"cfelpyutils.geometry_utils":{apply_geometry_to_data:[2,1,1,""],compute_pix_maps:[2,1,1,""],compute_visualization_pix_maps:[2,1,1,""]},"cfelpyutils.named_tuples":{PixelMaps:[3,2,1,""]},"cfelpyutils.named_tuples.PixelMaps":{phi:[3,3,1,""],r:[3,3,1,""],x:[3,3,1,""],y:[3,3,1,""],z:[3,3,1,""]},cfelpyutils:{crystfel_utils:[1,0,0,"-"],geometry_utils:[2,0,0,"-"],named_tuples:[3,0,0,"-"]}},objnames:{"0":["py","module","Python module"],"1":["py","function","Python function"],"2":["py","class","Python class"],"3":["py","attribute","Python attribute"]},objtypes:{"0":"py:module","1":"py:function","2":"py:class","3":"py:attribute"},terms:{"41a8fa9819010":1,"class":[3,5],"function":[1,2,5],"return":[1,2],For:[1,5],The:4,These:2,absolut:1,accord:2,activ:4,alia:3,all:[2,4],along:2,also:5,amplitud:3,anaconda:5,andrew:5,angl:3,ani:[1,2],anton:5,appli:[2,4,5],apply_geometry_to_data:2,around:2,arrai:2,avail:[2,5],awai:2,axi:3,barti:5,base:3,beam:2,befor:4,between:3,big:2,bigger:2,binari:4,black:4,both:4,branch:4,c99:4,can:[2,4,5],caus:2,ceil:2,center:[2,3,5],centos7:4,cfel:5,cfelpyutil:[3,4],chapman:5,check:5,code:[1,4],collect:3,come:4,command:5,commit:1,commonli:4,compat:4,compil:4,complet:2,comput:2,compute_pix_map:2,compute_visualization_pix_map:2,conda:5,contain:[0,1,2,3,5],contribut:[4,5],convent:2,coordin:[2,3],corner:2,correspond:[1,5],creat:4,crystfel:[1,2],crystfel_util:0,current:[1,4,5],cython:4,data:[2,5],desi:5,detector:[2,5],develop:[4,5],dict:[1,2],dictionari:[1,2],differ:[2,5],direct:2,displai:2,distanc:3,distribut:5,docstr:4,document:1,driessen:4,each:3,electron:5,enough:2,ensur:4,entri:2,exampl:4,except:4,extens:4,facil:4,feel:4,field:3,file:[1,2,4],filenam:1,find:4,flow:4,folder:4,follow:4,format:1,formatt:4,found:5,free:[4,5],from:[1,2,3,5],full:1,futur:4,gcc:4,gener:2,geometri:[1,2,3,5],geometry_util:0,get_detector_geometry_2:1,git:4,gitflow:4,github:4,googl:4,guid:4,hamburg:5,hand:2,henri:5,here:[4,5],how:4,howev:4,imag:5,imageview:2,index:5,inform:[1,2,3,5],input:2,institut:5,interact:2,interfac:4,intern:5,iso:4,kei:1,known:4,lab:5,languag:[1,4],laser:5,layout:2,lcsl:4,left:2,librari:[0,2,3,4],like:2,lint:4,linux:4,load:1,load_crystfel_geometri:[1,2],main:[0,2],mainli:4,man:1,mani:5,manipul:2,manual:5,map:[2,3],mariani:5,match:1,matplotlib:2,minimum:2,morgan:5,most:4,mostli:5,must:4,name:[2,3],named_tupl:0,ndarrai:[2,3],need:2,none:2,number:3,numpi:[2,3],object:2,often:2,onda:4,ondateam:5,one:4,ones:2,onli:2,ontribut:[],order:4,orient:2,origin:2,other:2,out:5,packag:[1,5],page:1,paramet:[1,2,3],part:4,particularli:2,path:1,peopl:5,perform:[4,5],phi:[2,3],physic:2,pip:5,pixel:[2,3],pixelmap:[2,3],platform:4,pleas:[4,5],point:2,possibl:4,pre:2,process:5,program:4,project:[4,5],propos:4,pull:4,pylint:4,pylintrc:4,pypi:5,pyqtgraph:2,python2:5,python3:5,python:[1,5],rai:5,read:[1,2,5],reason:4,refer:[2,3],reimplement:1,rel:1,relat:5,releas:5,relev:1,repositori:[4,5],request:4,requir:4,restrict:2,rhel7:4,right:2,root:4,run:[4,5],same:2,scienc:5,see:[1,4,5],set:[2,4],setup:5,sever:5,shape:2,should:[2,4],size:2,softwar:[1,5],some:[1,2,4],sourc:[1,2],specif:4,stack:4,standard:4,state:4,store:[1,2,3],str:[1,2],strategi:4,style:4,submiss:4,submit:4,support:[4,5],symmetr:2,synchron:1,system:[2,3,4],take:2,task:5,test:5,than:2,thi:[1,2,3],thoma:5,throughout:3,top:2,toward:2,tupl:[2,3],two:4,type:[1,2],use:4,used:[2,3,4,5],uses:[1,4],using:[2,4,5],util:[1,2,5],valerio:5,valu:[1,2],variou:5,vincent:4,visual:2,welcom:[4,5],wheel:4,when:4,which:[0,2],white:5,whole:0,widget:2,worlwid:5,write:4,written:[4,5],zenith:2},titles:["The cfelpyutils Package","The crystfel_utils Module","The geometry_utils Module","The named_tuples Module","Guidelines for Contributors","The CFELPyUtils Library"],titleterms:{The:[0,1,2,3,5],author:5,cfelpyutil:[0,5],code:5,contributor:[4,5],control:4,crystfel_util:1,document:5,geometry_util:2,guidelin:[4,5],instal:5,introduct:5,librari:5,modul:[1,2,3],named_tupl:3,packag:0,python:4,version:4}})
\ No newline at end of file
diff --git a/docs_src/_templates/localtoc.html b/docs_src/_templates/localtoc.html
new file mode 100644
index 0000000000000000000000000000000000000000..24d564294d9f7d1038a64014bce794c0c7a32d6e
--- /dev/null
+++ b/docs_src/_templates/localtoc.html
@@ -0,0 +1,13 @@
+{#
+ basic/localtoc.html
+ ~~~~~~~~~~~~~~~~~~~
+
+ Sphinx sidebar template: local table of contents.
+
+ :copyright: Copyright 2007-2019 by the Sphinx team, see AUTHORS.
+ :license: BSD, see LICENSE for details.
+#}
+{%- if display_toc %}
+ <h3><a href="{{ pathto(master_doc) }}">{{ _('CFELPyUtils') }}</a></h3>
+ {{ toc }}
+{%- endif %}
diff --git a/docs_src/documentation_guidelines_for_contributors.rst b/docs_src/documentation_guidelines_for_contributors.rst
index bcdb3cbbd84cdc0dcbf1b78b56f85305a1c14b4d..60bcb635ac96faa65abaef5140dedad24a3c0546 100644
--- a/docs_src/documentation_guidelines_for_contributors.rst
+++ b/docs_src/documentation_guidelines_for_contributors.rst
@@ -1,3 +1,5 @@
+:orphan:
+
Guidelines for Contributors
===========================
diff --git a/docs_src/index.rst b/docs_src/index.rst
index a3b5c6edd53bf827b02c983c043da0e871a8aa0c..ef4ad25986e24009b703d68ae92c52c93c51a810 100644
--- a/docs_src/index.rst
+++ b/docs_src/index.rst
@@ -3,14 +3,13 @@
You can adapt this file completely to your liking, but it should at least
contain the root `toctree` directive.
-CFELPyUtils
-===========
+The CFELPyUtils Library
+=======================
.. toctree::
:hidden:
cfelpyutils
- documentation_guidelines_for_contributors
Introduction