diff --git a/doc/Makefile b/doc/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..c2f31ab0bbebb10dfeace56fb5082f4d0cfdf3dd
--- /dev/null
+++ b/doc/Makefile
@@ -0,0 +1,177 @@
+# Makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+PAPER         =
+BUILDDIR      = build
+
+# User-friendly check for sphinx-build
+ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $$?), 1)
+$(error The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don't have Sphinx installed, grab it from http://sphinx-doc.org/)
+endif
+
+# Internal variables.
+PAPEROPT_a4     = -D latex_paper_size=a4
+PAPEROPT_letter = -D latex_paper_size=letter
+ALLSPHINXOPTS   = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source
+# the i18n builder cannot share the environment and doctrees with the others
+I18NSPHINXOPTS  = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source
+
+.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext
+
+help:
+	@echo "Please use \`make <target>' where <target> is one of"
+	@echo "  html       to make standalone HTML files"
+	@echo "  dirhtml    to make HTML files named index.html in directories"
+	@echo "  singlehtml to make a single large HTML file"
+	@echo "  pickle     to make pickle files"
+	@echo "  json       to make JSON files"
+	@echo "  htmlhelp   to make HTML files and a HTML help project"
+	@echo "  qthelp     to make HTML files and a qthelp project"
+	@echo "  devhelp    to make HTML files and a Devhelp project"
+	@echo "  epub       to make an epub"
+	@echo "  latex      to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
+	@echo "  latexpdf   to make LaTeX files and run them through pdflatex"
+	@echo "  latexpdfja to make LaTeX files and run them through platex/dvipdfmx"
+	@echo "  text       to make text files"
+	@echo "  man        to make manual pages"
+	@echo "  texinfo    to make Texinfo files"
+	@echo "  info       to make Texinfo files and run them through makeinfo"
+	@echo "  gettext    to make PO message catalogs"
+	@echo "  changes    to make an overview of all changed/added/deprecated items"
+	@echo "  xml        to make Docutils-native XML files"
+	@echo "  pseudoxml  to make pseudoxml-XML files for display purposes"
+	@echo "  linkcheck  to check all external links for integrity"
+	@echo "  doctest    to run all doctests embedded in the documentation (if enabled)"
+
+clean:
+	rm -rf $(BUILDDIR)/*
+
+html:
+	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
+
+dirhtml:
+	$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
+
+singlehtml:
+	$(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
+	@echo
+	@echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
+
+pickle:
+	$(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
+	@echo
+	@echo "Build finished; now you can process the pickle files."
+
+json:
+	$(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
+	@echo
+	@echo "Build finished; now you can process the JSON files."
+
+htmlhelp:
+	$(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp
+	@echo
+	@echo "Build finished; now you can run HTML Help Workshop with the" \
+	      ".hhp project file in $(BUILDDIR)/htmlhelp."
+
+qthelp:
+	$(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp
+	@echo
+	@echo "Build finished; now you can run "qcollectiongenerator" with the" \
+	      ".qhcp project file in $(BUILDDIR)/qthelp, like this:"
+	@echo "# qcollectiongenerator $(BUILDDIR)/qthelp/LSMTool.qhcp"
+	@echo "To view the help file:"
+	@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/LSMTool.qhc"
+
+devhelp:
+	$(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
+	@echo
+	@echo "Build finished."
+	@echo "To view the help file:"
+	@echo "# mkdir -p $$HOME/.local/share/devhelp/LSMTool"
+	@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/LSMTool"
+	@echo "# devhelp"
+
+epub:
+	$(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
+	@echo
+	@echo "Build finished. The epub file is in $(BUILDDIR)/epub."
+
+latex:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo
+	@echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
+	@echo "Run \`make' in that directory to run these through (pdf)latex" \
+	      "(use \`make latexpdf' here to do that automatically)."
+
+latexpdf:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo "Running LaTeX files through pdflatex..."
+	$(MAKE) -C $(BUILDDIR)/latex all-pdf
+	@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
+
+latexpdfja:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo "Running LaTeX files through platex and dvipdfmx..."
+	$(MAKE) -C $(BUILDDIR)/latex all-pdf-ja
+	@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
+
+text:
+	$(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text
+	@echo
+	@echo "Build finished. The text files are in $(BUILDDIR)/text."
+
+man:
+	$(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man
+	@echo
+	@echo "Build finished. The manual pages are in $(BUILDDIR)/man."
+
+texinfo:
+	$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
+	@echo
+	@echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo."
+	@echo "Run \`make' in that directory to run these through makeinfo" \
+	      "(use \`make info' here to do that automatically)."
+
+info:
+	$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
+	@echo "Running Texinfo files through makeinfo..."
+	make -C $(BUILDDIR)/texinfo info
+	@echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo."
+
+gettext:
+	$(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale
+	@echo
+	@echo "Build finished. The message catalogs are in $(BUILDDIR)/locale."
+
+changes:
+	$(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
+	@echo
+	@echo "The overview file is in $(BUILDDIR)/changes."
+
+linkcheck:
+	$(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck
+	@echo
+	@echo "Link check complete; look for any errors in the above output " \
+	      "or in $(BUILDDIR)/linkcheck/output.txt."
+
+doctest:
+	$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
+	@echo "Testing of doctests in the sources finished, look at the " \
+	      "results in $(BUILDDIR)/doctest/output.txt."
+
+xml:
+	$(SPHINXBUILD) -b xml $(ALLSPHINXOPTS) $(BUILDDIR)/xml
+	@echo
+	@echo "Build finished. The XML files are in $(BUILDDIR)/xml."
+
+pseudoxml:
+	$(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml
+	@echo
+	@echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml."
diff --git a/doc/build/doctrees/code.doctree b/doc/build/doctrees/code.doctree
new file mode 100644
index 0000000000000000000000000000000000000000..4473eeb73cbc2c4005cff1b63ae6f5aa184f3c8b
Binary files /dev/null and b/doc/build/doctrees/code.doctree differ
diff --git a/doc/build/doctrees/environment.pickle b/doc/build/doctrees/environment.pickle
new file mode 100644
index 0000000000000000000000000000000000000000..b0cd2ca5915e884eae852d9ac49b835995e10651
Binary files /dev/null and b/doc/build/doctrees/environment.pickle differ
diff --git a/doc/build/doctrees/index.doctree b/doc/build/doctrees/index.doctree
new file mode 100644
index 0000000000000000000000000000000000000000..9fb62513db848cacc5a7140f0cd781590c384958
Binary files /dev/null and b/doc/build/doctrees/index.doctree differ
diff --git a/doc/build/html/.buildinfo b/doc/build/html/.buildinfo
new file mode 100644
index 0000000000000000000000000000000000000000..da7689df25b0a3ffc6024e8e624a6c1df39f1c61
--- /dev/null
+++ b/doc/build/html/.buildinfo
@@ -0,0 +1,4 @@
+# Sphinx build info version 1
+# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: f29df357724c9e5ce1e609136e6f8a9c
+tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/doc/build/html/_sources/code.txt b/doc/build/html/_sources/code.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d184c03adb17c0c890f8333941539f66e6e55b10
--- /dev/null
+++ b/doc/build/html/_sources/code.txt
@@ -0,0 +1,7 @@
+LSMTool: the LOFAR Local Sky Model Tool
+***************************************
+
+.. automodule:: lsmtool
+    :members:
+.. autoclass:: SkyModel
+    :members:
diff --git a/doc/build/html/_sources/index.txt b/doc/build/html/_sources/index.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c6b45d5b81712dc74703c35c5d8ea486dfe15834
--- /dev/null
+++ b/doc/build/html/_sources/index.txt
@@ -0,0 +1,27 @@
+.. LSMTool documentation master file, created by
+   sphinx-quickstart on Thu Jun 19 17:05:13 2014.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to LSMTool's documentation!
+===================================
+
+LSMTool is a Python package which allow the manipulation of sky models in the ``makesourcedb`` format understood by BBS. Note that LSMTool is still in beta. Please report bugs to ``drafferty@hs.uni-hamburg.de``. To initialize your environment for LSMTool, users on CEP1 and CEP2 should run the following commands::
+
+    use LofIm
+    source ~rafferty/init_lsmtool
+
+Note that the Pythonlibs LOFAR package includes an older version of astropy that conflicts with LSMTool and cannot be used in conjunction with it.
+
+.. toctree::
+   :maxdepth: 2
+
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
+
diff --git a/doc/build/html/_static/ajax-loader.gif b/doc/build/html/_static/ajax-loader.gif
new file mode 100644
index 0000000000000000000000000000000000000000..61faf8cab23993bd3e1560bff0668bd628642330
Binary files /dev/null and b/doc/build/html/_static/ajax-loader.gif differ
diff --git a/doc/build/html/_static/basic.css b/doc/build/html/_static/basic.css
new file mode 100644
index 0000000000000000000000000000000000000000..c959cf0db10b0d30c9b059a9cd52fcba205119e9
--- /dev/null
+++ b/doc/build/html/_static/basic.css
@@ -0,0 +1,537 @@
+/*
+ * basic.css
+ * ~~~~~~~~~
+ *
+ * Sphinx stylesheet -- basic theme.
+ *
+ * :copyright: Copyright 2007-2013 by the Sphinx team, see AUTHORS.
+ * :license: BSD, see LICENSE for details.
+ *
+ */
+
+/* -- main layout ----------------------------------------------------------- */
+
+div.clearer {
+    clear: both;
+}
+
+/* -- relbar ---------------------------------------------------------------- */
+
+div.related {
+    width: 100%;
+    font-size: 90%;
+}
+
+div.related h3 {
+    display: none;
+}
+
+div.related ul {
+    margin: 0;
+    padding: 0 0 0 10px;
+    list-style: none;
+}
+
+div.related li {
+    display: inline;
+}
+
+div.related li.right {
+    float: right;
+    margin-right: 5px;
+}
+
+/* -- sidebar --------------------------------------------------------------- */
+
+div.sphinxsidebarwrapper {
+    padding: 10px 5px 0 10px;
+}
+
+div.sphinxsidebar {
+    float: left;
+    width: 230px;
+    margin-left: -100%;
+    font-size: 90%;
+}
+
+div.sphinxsidebar ul {
+    list-style: none;
+}
+
+div.sphinxsidebar ul ul,
+div.sphinxsidebar ul.want-points {
+    margin-left: 20px;
+    list-style: square;
+}
+
+div.sphinxsidebar ul ul {
+    margin-top: 0;
+    margin-bottom: 0;
+}
+
+div.sphinxsidebar form {
+    margin-top: 10px;
+}
+
+div.sphinxsidebar input {
+    border: 1px solid #98dbcc;
+    font-family: sans-serif;
+    font-size: 1em;
+}
+
+div.sphinxsidebar #searchbox input[type="text"] {
+    width: 170px;
+}
+
+div.sphinxsidebar #searchbox input[type="submit"] {
+    width: 30px;
+}
+
+img {
+    border: 0;
+    max-width: 100%;
+}
+
+/* -- search page ----------------------------------------------------------- */
+
+ul.search {
+    margin: 10px 0 0 20px;
+    padding: 0;
+}
+
+ul.search li {
+    padding: 5px 0 5px 20px;
+    background-image: url(file.png);
+    background-repeat: no-repeat;
+    background-position: 0 7px;
+}
+
+ul.search li a {
+    font-weight: bold;
+}
+
+ul.search li div.context {
+    color: #888;
+    margin: 2px 0 0 30px;
+    text-align: left;
+}
+
+ul.keywordmatches li.goodmatch a {
+    font-weight: bold;
+}
+
+/* -- index page ------------------------------------------------------------ */
+
+table.contentstable {
+    width: 90%;
+}
+
+table.contentstable p.biglink {
+    line-height: 150%;
+}
+
+a.biglink {
+    font-size: 1.3em;
+}
+
+span.linkdescr {
+    font-style: italic;
+    padding-top: 5px;
+    font-size: 90%;
+}
+
+/* -- general index --------------------------------------------------------- */
+
+table.indextable {
+    width: 100%;
+}
+
+table.indextable td {
+    text-align: left;
+    vertical-align: top;
+}
+
+table.indextable dl, table.indextable dd {
+    margin-top: 0;
+    margin-bottom: 0;
+}
+
+table.indextable tr.pcap {
+    height: 10px;
+}
+
+table.indextable tr.cap {
+    margin-top: 10px;
+    background-color: #f2f2f2;
+}
+
+img.toggler {
+    margin-right: 3px;
+    margin-top: 3px;
+    cursor: pointer;
+}
+
+div.modindex-jumpbox {
+    border-top: 1px solid #ddd;
+    border-bottom: 1px solid #ddd;
+    margin: 1em 0 1em 0;
+    padding: 0.4em;
+}
+
+div.genindex-jumpbox {
+    border-top: 1px solid #ddd;
+    border-bottom: 1px solid #ddd;
+    margin: 1em 0 1em 0;
+    padding: 0.4em;
+}
+
+/* -- general body styles --------------------------------------------------- */
+
+a.headerlink {
+    visibility: hidden;
+}
+
+h1:hover > a.headerlink,
+h2:hover > a.headerlink,
+h3:hover > a.headerlink,
+h4:hover > a.headerlink,
+h5:hover > a.headerlink,
+h6:hover > a.headerlink,
+dt:hover > a.headerlink {
+    visibility: visible;
+}
+
+div.body p.caption {
+    text-align: inherit;
+}
+
+div.body td {
+    text-align: left;
+}
+
+.field-list ul {
+    padding-left: 1em;
+}
+
+.first {
+    margin-top: 0 !important;
+}
+
+p.rubric {
+    margin-top: 30px;
+    font-weight: bold;
+}
+
+img.align-left, .figure.align-left, object.align-left {
+    clear: left;
+    float: left;
+    margin-right: 1em;
+}
+
+img.align-right, .figure.align-right, object.align-right {
+    clear: right;
+    float: right;
+    margin-left: 1em;
+}
+
+img.align-center, .figure.align-center, object.align-center {
+  display: block;
+  margin-left: auto;
+  margin-right: auto;
+}
+
+.align-left {
+    text-align: left;
+}
+
+.align-center {
+    text-align: center;
+}
+
+.align-right {
+    text-align: right;
+}
+
+/* -- sidebars -------------------------------------------------------------- */
+
+div.sidebar {
+    margin: 0 0 0.5em 1em;
+    border: 1px solid #ddb;
+    padding: 7px 7px 0 7px;
+    background-color: #ffe;
+    width: 40%;
+    float: right;
+}
+
+p.sidebar-title {
+    font-weight: bold;
+}
+
+/* -- topics ---------------------------------------------------------------- */
+
+div.topic {
+    border: 1px solid #ccc;
+    padding: 7px 7px 0 7px;
+    margin: 10px 0 10px 0;
+}
+
+p.topic-title {
+    font-size: 1.1em;
+    font-weight: bold;
+    margin-top: 10px;
+}
+
+/* -- admonitions ----------------------------------------------------------- */
+
+div.admonition {
+    margin-top: 10px;
+    margin-bottom: 10px;
+    padding: 7px;
+}
+
+div.admonition dt {
+    font-weight: bold;
+}
+
+div.admonition dl {
+    margin-bottom: 0;
+}
+
+p.admonition-title {
+    margin: 0px 10px 5px 0px;
+    font-weight: bold;
+}
+
+div.body p.centered {
+    text-align: center;
+    margin-top: 25px;
+}
+
+/* -- tables ---------------------------------------------------------------- */
+
+table.docutils {
+    border: 0;
+    border-collapse: collapse;
+}
+
+table.docutils td, table.docutils th {
+    padding: 1px 8px 1px 5px;
+    border-top: 0;
+    border-left: 0;
+    border-right: 0;
+    border-bottom: 1px solid #aaa;
+}
+
+table.field-list td, table.field-list th {
+    border: 0 !important;
+}
+
+table.footnote td, table.footnote th {
+    border: 0 !important;
+}
+
+th {
+    text-align: left;
+    padding-right: 5px;
+}
+
+table.citation {
+    border-left: solid 1px gray;
+    margin-left: 1px;
+}
+
+table.citation td {
+    border-bottom: none;
+}
+
+/* -- other body styles ----------------------------------------------------- */
+
+ol.arabic {
+    list-style: decimal;
+}
+
+ol.loweralpha {
+    list-style: lower-alpha;
+}
+
+ol.upperalpha {
+    list-style: upper-alpha;
+}
+
+ol.lowerroman {
+    list-style: lower-roman;
+}
+
+ol.upperroman {
+    list-style: upper-roman;
+}
+
+dl {
+    margin-bottom: 15px;
+}
+
+dd p {
+    margin-top: 0px;
+}
+
+dd ul, dd table {
+    margin-bottom: 10px;
+}
+
+dd {
+    margin-top: 3px;
+    margin-bottom: 10px;
+    margin-left: 30px;
+}
+
+dt:target, .highlighted {
+    background-color: #fbe54e;
+}
+
+dl.glossary dt {
+    font-weight: bold;
+    font-size: 1.1em;
+}
+
+.field-list ul {
+    margin: 0;
+    padding-left: 1em;
+}
+
+.field-list p {
+    margin: 0;
+}
+
+.optional {
+    font-size: 1.3em;
+}
+
+.versionmodified {
+    font-style: italic;
+}
+
+.system-message {
+    background-color: #fda;
+    padding: 5px;
+    border: 3px solid red;
+}
+
+.footnote:target  {
+    background-color: #ffa;
+}
+
+.line-block {
+    display: block;
+    margin-top: 1em;
+    margin-bottom: 1em;
+}
+
+.line-block .line-block {
+    margin-top: 0;
+    margin-bottom: 0;
+    margin-left: 1.5em;
+}
+
+.guilabel, .menuselection {
+    font-family: sans-serif;
+}
+
+.accelerator {
+    text-decoration: underline;
+}
+
+.classifier {
+    font-style: oblique;
+}
+
+abbr, acronym {
+    border-bottom: dotted 1px;
+    cursor: help;
+}
+
+/* -- code displays --------------------------------------------------------- */
+
+pre {
+    overflow: auto;
+    overflow-y: hidden;  /* fixes display issues on Chrome browsers */
+}
+
+td.linenos pre {
+    padding: 5px 0px;
+    border: 0;
+    background-color: transparent;
+    color: #aaa;
+}
+
+table.highlighttable {
+    margin-left: 0.5em;
+}
+
+table.highlighttable td {
+    padding: 0 0.5em 0 0.5em;
+}
+
+tt.descname {
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+    font-weight: bold;
+    font-size: 1.2em;
+}
+
+tt.descclassname {
+    background-color: transparent;
+}
+
+tt.xref, a tt {
+    background-color: transparent;
+    font-weight: bold;
+}
+
+h1 tt, h2 tt, h3 tt, h4 tt, h5 tt, h6 tt {
+    background-color: transparent;
+}
+
+.viewcode-link {
+    float: right;
+}
+
+.viewcode-back {
+    float: right;
+    font-family: sans-serif;
+}
+
+div.viewcode-block:target {
+    margin: -1px -10px;
+    padding: 0 10px;
+}
+
+/* -- math display ---------------------------------------------------------- */
+
+img.math {
+    vertical-align: middle;
+}
+
+div.body div.math p {
+    text-align: center;
+}
+
+span.eqno {
+    float: right;
+}
+
+/* -- printout stylesheet --------------------------------------------------- */
+
+@media print {
+    div.document,
+    div.documentwrapper,
+    div.bodywrapper {
+        margin: 0 !important;
+        width: 100%;
+    }
+
+    div.sphinxsidebar,
+    div.related,
+    div.footer,
+    #top-link {
+        display: none;
+    }
+}
\ No newline at end of file
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diff --git a/doc/build/html/_static/default.css b/doc/build/html/_static/default.css
new file mode 100644
index 0000000000000000000000000000000000000000..e534a07802b94d88019ee1b61e28541e6fc05856
--- /dev/null
+++ b/doc/build/html/_static/default.css
@@ -0,0 +1,256 @@
+/*
+ * default.css_t
+ * ~~~~~~~~~~~~~
+ *
+ * Sphinx stylesheet -- default theme.
+ *
+ * :copyright: Copyright 2007-2013 by the Sphinx team, see AUTHORS.
+ * :license: BSD, see LICENSE for details.
+ *
+ */
+
+@import url("basic.css");
+
+/* -- page layout ----------------------------------------------------------- */
+
+body {
+    font-family: sans-serif;
+    font-size: 100%;
+    background-color: #11303d;
+    color: #000;
+    margin: 0;
+    padding: 0;
+}
+
+div.document {
+    background-color: #1c4e63;
+}
+
+div.documentwrapper {
+    float: left;
+    width: 100%;
+}
+
+div.bodywrapper {
+    margin: 0 0 0 230px;
+}
+
+div.body {
+    background-color: #ffffff;
+    color: #000000;
+    padding: 0 20px 30px 20px;
+}
+
+div.footer {
+    color: #ffffff;
+    width: 100%;
+    padding: 9px 0 9px 0;
+    text-align: center;
+    font-size: 75%;
+}
+
+div.footer a {
+    color: #ffffff;
+    text-decoration: underline;
+}
+
+div.related {
+    background-color: #133f52;
+    line-height: 30px;
+    color: #ffffff;
+}
+
+div.related a {
+    color: #ffffff;
+}
+
+div.sphinxsidebar {
+}
+
+div.sphinxsidebar h3 {
+    font-family: 'Trebuchet MS', sans-serif;
+    color: #ffffff;
+    font-size: 1.4em;
+    font-weight: normal;
+    margin: 0;
+    padding: 0;
+}
+
+div.sphinxsidebar h3 a {
+    color: #ffffff;
+}
+
+div.sphinxsidebar h4 {
+    font-family: 'Trebuchet MS', sans-serif;
+    color: #ffffff;
+    font-size: 1.3em;
+    font-weight: normal;
+    margin: 5px 0 0 0;
+    padding: 0;
+}
+
+div.sphinxsidebar p {
+    color: #ffffff;
+}
+
+div.sphinxsidebar p.topless {
+    margin: 5px 10px 10px 10px;
+}
+
+div.sphinxsidebar ul {
+    margin: 10px;
+    padding: 0;
+    color: #ffffff;
+}
+
+div.sphinxsidebar a {
+    color: #98dbcc;
+}
+
+div.sphinxsidebar input {
+    border: 1px solid #98dbcc;
+    font-family: sans-serif;
+    font-size: 1em;
+}
+
+
+
+/* -- hyperlink styles ------------------------------------------------------ */
+
+a {
+    color: #355f7c;
+    text-decoration: none;
+}
+
+a:visited {
+    color: #355f7c;
+    text-decoration: none;
+}
+
+a:hover {
+    text-decoration: underline;
+}
+
+
+
+/* -- body styles ----------------------------------------------------------- */
+
+div.body h1,
+div.body h2,
+div.body h3,
+div.body h4,
+div.body h5,
+div.body h6 {
+    font-family: 'Trebuchet MS', sans-serif;
+    background-color: #f2f2f2;
+    font-weight: normal;
+    color: #20435c;
+    border-bottom: 1px solid #ccc;
+    margin: 20px -20px 10px -20px;
+    padding: 3px 0 3px 10px;
+}
+
+div.body h1 { margin-top: 0; font-size: 200%; }
+div.body h2 { font-size: 160%; }
+div.body h3 { font-size: 140%; }
+div.body h4 { font-size: 120%; }
+div.body h5 { font-size: 110%; }
+div.body h6 { font-size: 100%; }
+
+a.headerlink {
+    color: #c60f0f;
+    font-size: 0.8em;
+    padding: 0 4px 0 4px;
+    text-decoration: none;
+}
+
+a.headerlink:hover {
+    background-color: #c60f0f;
+    color: white;
+}
+
+div.body p, div.body dd, div.body li {
+    text-align: justify;
+    line-height: 130%;
+}
+
+div.admonition p.admonition-title + p {
+    display: inline;
+}
+
+div.admonition p {
+    margin-bottom: 5px;
+}
+
+div.admonition pre {
+    margin-bottom: 5px;
+}
+
+div.admonition ul, div.admonition ol {
+    margin-bottom: 5px;
+}
+
+div.note {
+    background-color: #eee;
+    border: 1px solid #ccc;
+}
+
+div.seealso {
+    background-color: #ffc;
+    border: 1px solid #ff6;
+}
+
+div.topic {
+    background-color: #eee;
+}
+
+div.warning {
+    background-color: #ffe4e4;
+    border: 1px solid #f66;
+}
+
+p.admonition-title {
+    display: inline;
+}
+
+p.admonition-title:after {
+    content: ":";
+}
+
+pre {
+    padding: 5px;
+    background-color: #eeffcc;
+    color: #333333;
+    line-height: 120%;
+    border: 1px solid #ac9;
+    border-left: none;
+    border-right: none;
+}
+
+tt {
+    background-color: #ecf0f3;
+    padding: 0 1px 0 1px;
+    font-size: 0.95em;
+}
+
+th {
+    background-color: #ede;
+}
+
+.warning tt {
+    background: #efc2c2;
+}
+
+.note tt {
+    background: #d6d6d6;
+}
+
+.viewcode-back {
+    font-family: sans-serif;
+}
+
+div.viewcode-block:target {
+    background-color: #f4debf;
+    border-top: 1px solid #ac9;
+    border-bottom: 1px solid #ac9;
+}
\ No newline at end of file
diff --git a/doc/build/html/_static/doctools.js b/doc/build/html/_static/doctools.js
new file mode 100644
index 0000000000000000000000000000000000000000..2036e5f5f812a93169ac1869f891e87da9658990
--- /dev/null
+++ b/doc/build/html/_static/doctools.js
@@ -0,0 +1,238 @@
+/*
+ * doctools.js
+ * ~~~~~~~~~~~
+ *
+ * Sphinx JavaScript utilities for all documentation.
+ *
+ * :copyright: Copyright 2007-2013 by the Sphinx team, see AUTHORS.
+ * :license: BSD, see LICENSE for details.
+ *
+ */
+
+/**
+ * select a different prefix for underscore
+ */
+$u = _.noConflict();
+
+/**
+ * make the code below compatible with browsers without
+ * an installed firebug like debugger
+if (!window.console || !console.firebug) {
+  var names = ["log", "debug", "info", "warn", "error", "assert", "dir",
+    "dirxml", "group", "groupEnd", "time", "timeEnd", "count", "trace",
+    "profile", "profileEnd"];
+  window.console = {};
+  for (var i = 0; i < names.length; ++i)
+    window.console[names[i]] = function() {};
+}
+ */
+
+/**
+ * small helper function to urldecode strings
+ */
+jQuery.urldecode = function(x) {
+  return decodeURIComponent(x).replace(/\+/g, ' ');
+};
+
+/**
+ * small helper function to urlencode strings
+ */
+jQuery.urlencode = encodeURIComponent;
+
+/**
+ * This function returns the parsed url parameters of the
+ * current request. Multiple values per key are supported,
+ * it will always return arrays of strings for the value parts.
+ */
+jQuery.getQueryParameters = function(s) {
+  if (typeof s == 'undefined')
+    s = document.location.search;
+  var parts = s.substr(s.indexOf('?') + 1).split('&');
+  var result = {};
+  for (var i = 0; i < parts.length; i++) {
+    var tmp = parts[i].split('=', 2);
+    var key = jQuery.urldecode(tmp[0]);
+    var value = jQuery.urldecode(tmp[1]);
+    if (key in result)
+      result[key].push(value);
+    else
+      result[key] = [value];
+  }
+  return result;
+};
+
+/**
+ * highlight a given string on a jquery object by wrapping it in
+ * span elements with the given class name.
+ */
+jQuery.fn.highlightText = function(text, className) {
+  function highlight(node) {
+    if (node.nodeType == 3) {
+      var val = node.nodeValue;
+      var pos = val.toLowerCase().indexOf(text);
+      if (pos >= 0 && !jQuery(node.parentNode).hasClass(className)) {
+        var span = document.createElement("span");
+        span.className = className;
+        span.appendChild(document.createTextNode(val.substr(pos, text.length)));
+        node.parentNode.insertBefore(span, node.parentNode.insertBefore(
+          document.createTextNode(val.substr(pos + text.length)),
+          node.nextSibling));
+        node.nodeValue = val.substr(0, pos);
+      }
+    }
+    else if (!jQuery(node).is("button, select, textarea")) {
+      jQuery.each(node.childNodes, function() {
+        highlight(this);
+      });
+    }
+  }
+  return this.each(function() {
+    highlight(this);
+  });
+};
+
+/**
+ * Small JavaScript module for the documentation.
+ */
+var Documentation = {
+
+  init : function() {
+    this.fixFirefoxAnchorBug();
+    this.highlightSearchWords();
+    this.initIndexTable();
+  },
+
+  /**
+   * i18n support
+   */
+  TRANSLATIONS : {},
+  PLURAL_EXPR : function(n) { return n == 1 ? 0 : 1; },
+  LOCALE : 'unknown',
+
+  // gettext and ngettext don't access this so that the functions
+  // can safely bound to a different name (_ = Documentation.gettext)
+  gettext : function(string) {
+    var translated = Documentation.TRANSLATIONS[string];
+    if (typeof translated == 'undefined')
+      return string;
+    return (typeof translated == 'string') ? translated : translated[0];
+  },
+
+  ngettext : function(singular, plural, n) {
+    var translated = Documentation.TRANSLATIONS[singular];
+    if (typeof translated == 'undefined')
+      return (n == 1) ? singular : plural;
+    return translated[Documentation.PLURALEXPR(n)];
+  },
+
+  addTranslations : function(catalog) {
+    for (var key in catalog.messages)
+      this.TRANSLATIONS[key] = catalog.messages[key];
+    this.PLURAL_EXPR = new Function('n', 'return +(' + catalog.plural_expr + ')');
+    this.LOCALE = catalog.locale;
+  },
+
+  /**
+   * add context elements like header anchor links
+   */
+  addContextElements : function() {
+    $('div[id] > :header:first').each(function() {
+      $('<a class="headerlink">\u00B6</a>').
+      attr('href', '#' + this.id).
+      attr('title', _('Permalink to this headline')).
+      appendTo(this);
+    });
+    $('dt[id]').each(function() {
+      $('<a class="headerlink">\u00B6</a>').
+      attr('href', '#' + this.id).
+      attr('title', _('Permalink to this definition')).
+      appendTo(this);
+    });
+  },
+
+  /**
+   * workaround a firefox stupidity
+   */
+  fixFirefoxAnchorBug : function() {
+    if (document.location.hash && $.browser.mozilla)
+      window.setTimeout(function() {
+        document.location.href += '';
+      }, 10);
+  },
+
+  /**
+   * highlight the search words provided in the url in the text
+   */
+  highlightSearchWords : function() {
+    var params = $.getQueryParameters();
+    var terms = (params.highlight) ? params.highlight[0].split(/\s+/) : [];
+    if (terms.length) {
+      var body = $('div.body');
+      if (!body.length) {
+        body = $('body');
+      }
+      window.setTimeout(function() {
+        $.each(terms, function() {
+          body.highlightText(this.toLowerCase(), 'highlighted');
+        });
+      }, 10);
+      $('<p class="highlight-link"><a href="javascript:Documentation.' +
+        'hideSearchWords()">' + _('Hide Search Matches') + '</a></p>')
+          .appendTo($('#searchbox'));
+    }
+  },
+
+  /**
+   * init the domain index toggle buttons
+   */
+  initIndexTable : function() {
+    var togglers = $('img.toggler').click(function() {
+      var src = $(this).attr('src');
+      var idnum = $(this).attr('id').substr(7);
+      $('tr.cg-' + idnum).toggle();
+      if (src.substr(-9) == 'minus.png')
+        $(this).attr('src', src.substr(0, src.length-9) + 'plus.png');
+      else
+        $(this).attr('src', src.substr(0, src.length-8) + 'minus.png');
+    }).css('display', '');
+    if (DOCUMENTATION_OPTIONS.COLLAPSE_INDEX) {
+        togglers.click();
+    }
+  },
+
+  /**
+   * helper function to hide the search marks again
+   */
+  hideSearchWords : function() {
+    $('#searchbox .highlight-link').fadeOut(300);
+    $('span.highlighted').removeClass('highlighted');
+  },
+
+  /**
+   * make the url absolute
+   */
+  makeURL : function(relativeURL) {
+    return DOCUMENTATION_OPTIONS.URL_ROOT + '/' + relativeURL;
+  },
+
+  /**
+   * get the current relative url
+   */
+  getCurrentURL : function() {
+    var path = document.location.pathname;
+    var parts = path.split(/\//);
+    $.each(DOCUMENTATION_OPTIONS.URL_ROOT.split(/\//), function() {
+      if (this == '..')
+        parts.pop();
+    });
+    var url = parts.join('/');
+    return path.substring(url.lastIndexOf('/') + 1, path.length - 1);
+  }
+};
+
+// quick alias for translations
+_ = Documentation.gettext;
+
+$(document).ready(function() {
+  Documentation.init();
+});
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diff --git a/doc/build/html/_static/jquery.js b/doc/build/html/_static/jquery.js
new file mode 100644
index 0000000000000000000000000000000000000000..83589daa707a25a1fb3e4112075d382e9a1611ab
--- /dev/null
+++ b/doc/build/html/_static/jquery.js
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+/*! jQuery v1.8.3 jquery.com | jquery.org/license */
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+.highlight .sh { color: #4070a0 } /* Literal.String.Heredoc */
+.highlight .si { color: #70a0d0; font-style: italic } /* Literal.String.Interpol */
+.highlight .sx { color: #c65d09 } /* Literal.String.Other */
+.highlight .sr { color: #235388 } /* Literal.String.Regex */
+.highlight .s1 { color: #4070a0 } /* Literal.String.Single */
+.highlight .ss { color: #517918 } /* Literal.String.Symbol */
+.highlight .bp { color: #007020 } /* Name.Builtin.Pseudo */
+.highlight .vc { color: #bb60d5 } /* Name.Variable.Class */
+.highlight .vg { color: #bb60d5 } /* Name.Variable.Global */
+.highlight .vi { color: #bb60d5 } /* Name.Variable.Instance */
+.highlight .il { color: #208050 } /* Literal.Number.Integer.Long */
\ No newline at end of file
diff --git a/doc/build/html/_static/searchtools.js b/doc/build/html/_static/searchtools.js
new file mode 100644
index 0000000000000000000000000000000000000000..f5c7e5fee71426595a839f84759f47681fd1a74d
--- /dev/null
+++ b/doc/build/html/_static/searchtools.js
@@ -0,0 +1,622 @@
+/*
+ * searchtools.js_t
+ * ~~~~~~~~~~~~~~~~
+ *
+ * Sphinx JavaScript utilties for the full-text search.
+ *
+ * :copyright: Copyright 2007-2013 by the Sphinx team, see AUTHORS.
+ * :license: BSD, see LICENSE for details.
+ *
+ */
+
+
+/**
+ * Porter Stemmer
+ */
+var Stemmer = function() {
+
+  var step2list = {
+    ational: 'ate',
+    tional: 'tion',
+    enci: 'ence',
+    anci: 'ance',
+    izer: 'ize',
+    bli: 'ble',
+    alli: 'al',
+    entli: 'ent',
+    eli: 'e',
+    ousli: 'ous',
+    ization: 'ize',
+    ation: 'ate',
+    ator: 'ate',
+    alism: 'al',
+    iveness: 'ive',
+    fulness: 'ful',
+    ousness: 'ous',
+    aliti: 'al',
+    iviti: 'ive',
+    biliti: 'ble',
+    logi: 'log'
+  };
+
+  var step3list = {
+    icate: 'ic',
+    ative: '',
+    alize: 'al',
+    iciti: 'ic',
+    ical: 'ic',
+    ful: '',
+    ness: ''
+  };
+
+  var c = "[^aeiou]";          // consonant
+  var v = "[aeiouy]";          // vowel
+  var C = c + "[^aeiouy]*";    // consonant sequence
+  var V = v + "[aeiou]*";      // vowel sequence
+
+  var mgr0 = "^(" + C + ")?" + V + C;                      // [C]VC... is m>0
+  var meq1 = "^(" + C + ")?" + V + C + "(" + V + ")?$";    // [C]VC[V] is m=1
+  var mgr1 = "^(" + C + ")?" + V + C + V + C;              // [C]VCVC... is m>1
+  var s_v   = "^(" + C + ")?" + v;                         // vowel in stem
+
+  this.stemWord = function (w) {
+    var stem;
+    var suffix;
+    var firstch;
+    var origword = w;
+
+    if (w.length < 3)
+      return w;
+
+    var re;
+    var re2;
+    var re3;
+    var re4;
+
+    firstch = w.substr(0,1);
+    if (firstch == "y")
+      w = firstch.toUpperCase() + w.substr(1);
+
+    // Step 1a
+    re = /^(.+?)(ss|i)es$/;
+    re2 = /^(.+?)([^s])s$/;
+
+    if (re.test(w))
+      w = w.replace(re,"$1$2");
+    else if (re2.test(w))
+      w = w.replace(re2,"$1$2");
+
+    // Step 1b
+    re = /^(.+?)eed$/;
+    re2 = /^(.+?)(ed|ing)$/;
+    if (re.test(w)) {
+      var fp = re.exec(w);
+      re = new RegExp(mgr0);
+      if (re.test(fp[1])) {
+        re = /.$/;
+        w = w.replace(re,"");
+      }
+    }
+    else if (re2.test(w)) {
+      var fp = re2.exec(w);
+      stem = fp[1];
+      re2 = new RegExp(s_v);
+      if (re2.test(stem)) {
+        w = stem;
+        re2 = /(at|bl|iz)$/;
+        re3 = new RegExp("([^aeiouylsz])\\1$");
+        re4 = new RegExp("^" + C + v + "[^aeiouwxy]$");
+        if (re2.test(w))
+          w = w + "e";
+        else if (re3.test(w)) {
+          re = /.$/;
+          w = w.replace(re,"");
+        }
+        else if (re4.test(w))
+          w = w + "e";
+      }
+    }
+
+    // Step 1c
+    re = /^(.+?)y$/;
+    if (re.test(w)) {
+      var fp = re.exec(w);
+      stem = fp[1];
+      re = new RegExp(s_v);
+      if (re.test(stem))
+        w = stem + "i";
+    }
+
+    // Step 2
+    re = /^(.+?)(ational|tional|enci|anci|izer|bli|alli|entli|eli|ousli|ization|ation|ator|alism|iveness|fulness|ousness|aliti|iviti|biliti|logi)$/;
+    if (re.test(w)) {
+      var fp = re.exec(w);
+      stem = fp[1];
+      suffix = fp[2];
+      re = new RegExp(mgr0);
+      if (re.test(stem))
+        w = stem + step2list[suffix];
+    }
+
+    // Step 3
+    re = /^(.+?)(icate|ative|alize|iciti|ical|ful|ness)$/;
+    if (re.test(w)) {
+      var fp = re.exec(w);
+      stem = fp[1];
+      suffix = fp[2];
+      re = new RegExp(mgr0);
+      if (re.test(stem))
+        w = stem + step3list[suffix];
+    }
+
+    // Step 4
+    re = /^(.+?)(al|ance|ence|er|ic|able|ible|ant|ement|ment|ent|ou|ism|ate|iti|ous|ive|ize)$/;
+    re2 = /^(.+?)(s|t)(ion)$/;
+    if (re.test(w)) {
+      var fp = re.exec(w);
+      stem = fp[1];
+      re = new RegExp(mgr1);
+      if (re.test(stem))
+        w = stem;
+    }
+    else if (re2.test(w)) {
+      var fp = re2.exec(w);
+      stem = fp[1] + fp[2];
+      re2 = new RegExp(mgr1);
+      if (re2.test(stem))
+        w = stem;
+    }
+
+    // Step 5
+    re = /^(.+?)e$/;
+    if (re.test(w)) {
+      var fp = re.exec(w);
+      stem = fp[1];
+      re = new RegExp(mgr1);
+      re2 = new RegExp(meq1);
+      re3 = new RegExp("^" + C + v + "[^aeiouwxy]$");
+      if (re.test(stem) || (re2.test(stem) && !(re3.test(stem))))
+        w = stem;
+    }
+    re = /ll$/;
+    re2 = new RegExp(mgr1);
+    if (re.test(w) && re2.test(w)) {
+      re = /.$/;
+      w = w.replace(re,"");
+    }
+
+    // and turn initial Y back to y
+    if (firstch == "y")
+      w = firstch.toLowerCase() + w.substr(1);
+    return w;
+  }
+}
+
+
+
+/**
+ * Simple result scoring code.
+ */
+var Scorer = {
+  // Implement the following function to further tweak the score for each result
+  // The function takes a result array [filename, title, anchor, descr, score]
+  // and returns the new score.
+  /*
+  score: function(result) {
+    return result[4];
+  },
+  */
+
+  // query matches the full name of an object
+  objNameMatch: 11,
+  // or matches in the last dotted part of the object name
+  objPartialMatch: 6,
+  // Additive scores depending on the priority of the object
+  objPrio: {0:  15,   // used to be importantResults
+            1:  5,   // used to be objectResults
+            2: -5},  // used to be unimportantResults
+  //  Used when the priority is not in the mapping.
+  objPrioDefault: 0,
+
+  // query found in title
+  title: 15,
+  // query found in terms
+  term: 5
+};
+
+
+/**
+ * Search Module
+ */
+var Search = {
+
+  _index : null,
+  _queued_query : null,
+  _pulse_status : -1,
+
+  init : function() {
+      var params = $.getQueryParameters();
+      if (params.q) {
+          var query = params.q[0];
+          $('input[name="q"]')[0].value = query;
+          this.performSearch(query);
+      }
+  },
+
+  loadIndex : function(url) {
+    $.ajax({type: "GET", url: url, data: null,
+            dataType: "script", cache: true,
+            complete: function(jqxhr, textstatus) {
+              if (textstatus != "success") {
+                document.getElementById("searchindexloader").src = url;
+              }
+            }});
+  },
+
+  setIndex : function(index) {
+    var q;
+    this._index = index;
+    if ((q = this._queued_query) !== null) {
+      this._queued_query = null;
+      Search.query(q);
+    }
+  },
+
+  hasIndex : function() {
+      return this._index !== null;
+  },
+
+  deferQuery : function(query) {
+      this._queued_query = query;
+  },
+
+  stopPulse : function() {
+      this._pulse_status = 0;
+  },
+
+  startPulse : function() {
+    if (this._pulse_status >= 0)
+        return;
+    function pulse() {
+      var i;
+      Search._pulse_status = (Search._pulse_status + 1) % 4;
+      var dotString = '';
+      for (i = 0; i < Search._pulse_status; i++)
+        dotString += '.';
+      Search.dots.text(dotString);
+      if (Search._pulse_status > -1)
+        window.setTimeout(pulse, 500);
+    }
+    pulse();
+  },
+
+  /**
+   * perform a search for something (or wait until index is loaded)
+   */
+  performSearch : function(query) {
+    // create the required interface elements
+    this.out = $('#search-results');
+    this.title = $('<h2>' + _('Searching') + '</h2>').appendTo(this.out);
+    this.dots = $('<span></span>').appendTo(this.title);
+    this.status = $('<p style="display: none"></p>').appendTo(this.out);
+    this.output = $('<ul class="search"/>').appendTo(this.out);
+
+    $('#search-progress').text(_('Preparing search...'));
+    this.startPulse();
+
+    // index already loaded, the browser was quick!
+    if (this.hasIndex())
+      this.query(query);
+    else
+      this.deferQuery(query);
+  },
+
+  /**
+   * execute search (requires search index to be loaded)
+   */
+  query : function(query) {
+    var i;
+    var stopwords = ["a","and","are","as","at","be","but","by","for","if","in","into","is","it","near","no","not","of","on","or","such","that","the","their","then","there","these","they","this","to","was","will","with"];
+
+    // stem the searchterms and add them to the correct list
+    var stemmer = new Stemmer();
+    var searchterms = [];
+    var excluded = [];
+    var hlterms = [];
+    var tmp = query.split(/\s+/);
+    var objectterms = [];
+    for (i = 0; i < tmp.length; i++) {
+      if (tmp[i] !== "") {
+          objectterms.push(tmp[i].toLowerCase());
+      }
+
+      if ($u.indexOf(stopwords, tmp[i].toLowerCase()) != -1 || tmp[i].match(/^\d+$/) ||
+          tmp[i] === "") {
+        // skip this "word"
+        continue;
+      }
+      // stem the word
+      var word = stemmer.stemWord(tmp[i].toLowerCase());
+      var toAppend;
+      // select the correct list
+      if (word[0] == '-') {
+        toAppend = excluded;
+        word = word.substr(1);
+      }
+      else {
+        toAppend = searchterms;
+        hlterms.push(tmp[i].toLowerCase());
+      }
+      // only add if not already in the list
+      if (!$u.contains(toAppend, word))
+        toAppend.push(word);
+    }
+    var highlightstring = '?highlight=' + $.urlencode(hlterms.join(" "));
+
+    // console.debug('SEARCH: searching for:');
+    // console.info('required: ', searchterms);
+    // console.info('excluded: ', excluded);
+
+    // prepare search
+    var terms = this._index.terms;
+    var titleterms = this._index.titleterms;
+
+    // array of [filename, title, anchor, descr, score]
+    var results = [];
+    $('#search-progress').empty();
+
+    // lookup as object
+    for (i = 0; i < objectterms.length; i++) {
+      var others = [].concat(objectterms.slice(0, i),
+                             objectterms.slice(i+1, objectterms.length));
+      results = results.concat(this.performObjectSearch(objectterms[i], others));
+    }
+
+    // lookup as search terms in fulltext
+    results = results.concat(this.performTermsSearch(searchterms, excluded, terms, Scorer.term))
+                     .concat(this.performTermsSearch(searchterms, excluded, titleterms, Scorer.title));
+
+    // let the scorer override scores with a custom scoring function
+    if (Scorer.score) {
+      for (i = 0; i < results.length; i++)
+        results[i][4] = Scorer.score(results[i]);
+    }
+
+    // now sort the results by score (in opposite order of appearance, since the
+    // display function below uses pop() to retrieve items) and then
+    // alphabetically
+    results.sort(function(a, b) {
+      var left = a[4];
+      var right = b[4];
+      if (left > right) {
+        return 1;
+      } else if (left < right) {
+        return -1;
+      } else {
+        // same score: sort alphabetically
+        left = a[1].toLowerCase();
+        right = b[1].toLowerCase();
+        return (left > right) ? -1 : ((left < right) ? 1 : 0);
+      }
+    });
+
+    // for debugging
+    //Search.lastresults = results.slice();  // a copy
+    //console.info('search results:', Search.lastresults);
+
+    // print the results
+    var resultCount = results.length;
+    function displayNextItem() {
+      // results left, load the summary and display it
+      if (results.length) {
+        var item = results.pop();
+        var listItem = $('<li style="display:none"></li>');
+        if (DOCUMENTATION_OPTIONS.FILE_SUFFIX === '') {
+          // dirhtml builder
+          var dirname = item[0] + '/';
+          if (dirname.match(/\/index\/$/)) {
+            dirname = dirname.substring(0, dirname.length-6);
+          } else if (dirname == 'index/') {
+            dirname = '';
+          }
+          listItem.append($('<a/>').attr('href',
+            DOCUMENTATION_OPTIONS.URL_ROOT + dirname +
+            highlightstring + item[2]).html(item[1]));
+        } else {
+          // normal html builders
+          listItem.append($('<a/>').attr('href',
+            item[0] + DOCUMENTATION_OPTIONS.FILE_SUFFIX +
+            highlightstring + item[2]).html(item[1]));
+        }
+        if (item[3]) {
+          listItem.append($('<span> (' + item[3] + ')</span>'));
+          Search.output.append(listItem);
+          listItem.slideDown(5, function() {
+            displayNextItem();
+          });
+        } else if (DOCUMENTATION_OPTIONS.HAS_SOURCE) {
+          $.ajax({url: DOCUMENTATION_OPTIONS.URL_ROOT + '_sources/' + item[0] + '.txt',
+                  dataType: "text",
+                  complete: function(jqxhr, textstatus) {
+                    var data = jqxhr.responseText;
+                    if (data !== '') {
+                      listItem.append(Search.makeSearchSummary(data, searchterms, hlterms));
+                    }
+                    Search.output.append(listItem);
+                    listItem.slideDown(5, function() {
+                      displayNextItem();
+                    });
+                  }});
+        } else {
+          // no source available, just display title
+          Search.output.append(listItem);
+          listItem.slideDown(5, function() {
+            displayNextItem();
+          });
+        }
+      }
+      // search finished, update title and status message
+      else {
+        Search.stopPulse();
+        Search.title.text(_('Search Results'));
+        if (!resultCount)
+          Search.status.text(_('Your search did not match any documents. Please make sure that all words are spelled correctly and that you\'ve selected enough categories.'));
+        else
+            Search.status.text(_('Search finished, found %s page(s) matching the search query.').replace('%s', resultCount));
+        Search.status.fadeIn(500);
+      }
+    }
+    displayNextItem();
+  },
+
+  /**
+   * search for object names
+   */
+  performObjectSearch : function(object, otherterms) {
+    var filenames = this._index.filenames;
+    var objects = this._index.objects;
+    var objnames = this._index.objnames;
+    var titles = this._index.titles;
+
+    var i;
+    var results = [];
+
+    for (var prefix in objects) {
+      for (var name in objects[prefix]) {
+        var fullname = (prefix ? prefix + '.' : '') + name;
+        if (fullname.toLowerCase().indexOf(object) > -1) {
+          var score = 0;
+          var parts = fullname.split('.');
+          // check for different match types: exact matches of full name or
+          // "last name" (i.e. last dotted part)
+          if (fullname == object || parts[parts.length - 1] == object) {
+            score += Scorer.objNameMatch;
+          // matches in last name
+          } else if (parts[parts.length - 1].indexOf(object) > -1) {
+            score += Scorer.objPartialMatch;
+          }
+          var match = objects[prefix][name];
+          var objname = objnames[match[1]][2];
+          var title = titles[match[0]];
+          // If more than one term searched for, we require other words to be
+          // found in the name/title/description
+          if (otherterms.length > 0) {
+            var haystack = (prefix + ' ' + name + ' ' +
+                            objname + ' ' + title).toLowerCase();
+            var allfound = true;
+            for (i = 0; i < otherterms.length; i++) {
+              if (haystack.indexOf(otherterms[i]) == -1) {
+                allfound = false;
+                break;
+              }
+            }
+            if (!allfound) {
+              continue;
+            }
+          }
+          var descr = objname + _(', in ') + title;
+
+          var anchor = match[3];
+          if (anchor === '')
+            anchor = fullname;
+          else if (anchor == '-')
+            anchor = objnames[match[1]][1] + '-' + fullname;
+          // add custom score for some objects according to scorer
+          if (Scorer.objPrio.hasOwnProperty(match[2])) {
+            score += Scorer.objPrio[match[2]];
+          } else {
+            score += Scorer.objPrioDefault;
+          }
+          results.push([filenames[match[0]], fullname, '#'+anchor, descr, score]);
+        }
+      }
+    }
+
+    return results;
+  },
+
+  /**
+   * search for full-text terms in the index
+   */
+  performTermsSearch : function(searchterms, excluded, terms, score) {
+    var filenames = this._index.filenames;
+    var titles = this._index.titles;
+
+    var i, j, file, files;
+    var fileMap = {};
+    var results = [];
+
+    // perform the search on the required terms
+    for (i = 0; i < searchterms.length; i++) {
+      var word = searchterms[i];
+      // no match but word was a required one
+      if ((files = terms[word]) === undefined)
+        break;
+      if (files.length === undefined) {
+        files = [files];
+      }
+      // create the mapping
+      for (j = 0; j < files.length; j++) {
+        file = files[j];
+        if (file in fileMap)
+          fileMap[file].push(word);
+        else
+          fileMap[file] = [word];
+      }
+    }
+
+    // now check if the files don't contain excluded terms
+    for (file in fileMap) {
+      var valid = true;
+
+      // check if all requirements are matched
+      if (fileMap[file].length != searchterms.length)
+          continue;
+
+      // ensure that none of the excluded terms is in the search result
+      for (i = 0; i < excluded.length; i++) {
+        if (terms[excluded[i]] == file ||
+          $u.contains(terms[excluded[i]] || [], file)) {
+          valid = false;
+          break;
+        }
+      }
+
+      // if we have still a valid result we can add it to the result list
+      if (valid) {
+        results.push([filenames[file], titles[file], '', null, score]);
+      }
+    }
+    return results;
+  },
+
+  /**
+   * helper function to return a node containing the
+   * search summary for a given text. keywords is a list
+   * of stemmed words, hlwords is the list of normal, unstemmed
+   * words. the first one is used to find the occurance, the
+   * latter for highlighting it.
+   */
+  makeSearchSummary : function(text, keywords, hlwords) {
+    var textLower = text.toLowerCase();
+    var start = 0;
+    $.each(keywords, function() {
+      var i = textLower.indexOf(this.toLowerCase());
+      if (i > -1)
+        start = i;
+    });
+    start = Math.max(start - 120, 0);
+    var excerpt = ((start > 0) ? '...' : '') +
+      $.trim(text.substr(start, 240)) +
+      ((start + 240 - text.length) ? '...' : '');
+    var rv = $('<div class="context"></div>').text(excerpt);
+    $.each(hlwords, function() {
+      rv = rv.highlightText(this, 'highlighted');
+    });
+    return rv;
+  }
+};
+
+$(document).ready(function() {
+  Search.init();
+});
\ No newline at end of file
diff --git a/doc/build/html/_static/sidebar.js b/doc/build/html/_static/sidebar.js
new file mode 100644
index 0000000000000000000000000000000000000000..874a890a3cd928992933188798a6ae30a1543668
--- /dev/null
+++ b/doc/build/html/_static/sidebar.js
@@ -0,0 +1,159 @@
+/*
+ * sidebar.js
+ * ~~~~~~~~~~
+ *
+ * This script makes the Sphinx sidebar collapsible.
+ *
+ * .sphinxsidebar contains .sphinxsidebarwrapper.  This script adds
+ * in .sphixsidebar, after .sphinxsidebarwrapper, the #sidebarbutton
+ * used to collapse and expand the sidebar.
+ *
+ * When the sidebar is collapsed the .sphinxsidebarwrapper is hidden
+ * and the width of the sidebar and the margin-left of the document
+ * are decreased. When the sidebar is expanded the opposite happens.
+ * This script saves a per-browser/per-session cookie used to
+ * remember the position of the sidebar among the pages.
+ * Once the browser is closed the cookie is deleted and the position
+ * reset to the default (expanded).
+ *
+ * :copyright: Copyright 2007-2013 by the Sphinx team, see AUTHORS.
+ * :license: BSD, see LICENSE for details.
+ *
+ */
+
+$(function() {
+  
+  
+  
+  
+  
+  
+  
+
+  // global elements used by the functions.
+  // the 'sidebarbutton' element is defined as global after its
+  // creation, in the add_sidebar_button function
+  var bodywrapper = $('.bodywrapper');
+  var sidebar = $('.sphinxsidebar');
+  var sidebarwrapper = $('.sphinxsidebarwrapper');
+
+  // for some reason, the document has no sidebar; do not run into errors
+  if (!sidebar.length) return;
+
+  // original margin-left of the bodywrapper and width of the sidebar
+  // with the sidebar expanded
+  var bw_margin_expanded = bodywrapper.css('margin-left');
+  var ssb_width_expanded = sidebar.width();
+
+  // margin-left of the bodywrapper and width of the sidebar
+  // with the sidebar collapsed
+  var bw_margin_collapsed = '.8em';
+  var ssb_width_collapsed = '.8em';
+
+  // colors used by the current theme
+  var dark_color = $('.related').css('background-color');
+  var light_color = $('.document').css('background-color');
+
+  function sidebar_is_collapsed() {
+    return sidebarwrapper.is(':not(:visible)');
+  }
+
+  function toggle_sidebar() {
+    if (sidebar_is_collapsed())
+      expand_sidebar();
+    else
+      collapse_sidebar();
+  }
+
+  function collapse_sidebar() {
+    sidebarwrapper.hide();
+    sidebar.css('width', ssb_width_collapsed);
+    bodywrapper.css('margin-left', bw_margin_collapsed);
+    sidebarbutton.css({
+        'margin-left': '0',
+        'height': bodywrapper.height()
+    });
+    sidebarbutton.find('span').text('»');
+    sidebarbutton.attr('title', _('Expand sidebar'));
+    document.cookie = 'sidebar=collapsed';
+  }
+
+  function expand_sidebar() {
+    bodywrapper.css('margin-left', bw_margin_expanded);
+    sidebar.css('width', ssb_width_expanded);
+    sidebarwrapper.show();
+    sidebarbutton.css({
+        'margin-left': ssb_width_expanded-12,
+        'height': bodywrapper.height()
+    });
+    sidebarbutton.find('span').text('«');
+    sidebarbutton.attr('title', _('Collapse sidebar'));
+    document.cookie = 'sidebar=expanded';
+  }
+
+  function add_sidebar_button() {
+    sidebarwrapper.css({
+        'float': 'left',
+        'margin-right': '0',
+        'width': ssb_width_expanded - 28
+    });
+    // create the button
+    sidebar.append(
+        '<div id="sidebarbutton"><span>&laquo;</span></div>'
+    );
+    var sidebarbutton = $('#sidebarbutton');
+    light_color = sidebarbutton.css('background-color');
+    // find the height of the viewport to center the '<<' in the page
+    var viewport_height;
+    if (window.innerHeight)
+ 	  viewport_height = window.innerHeight;
+    else
+	  viewport_height = $(window).height();
+    sidebarbutton.find('span').css({
+        'display': 'block',
+        'margin-top': (viewport_height - sidebar.position().top - 20) / 2
+    });
+
+    sidebarbutton.click(toggle_sidebar);
+    sidebarbutton.attr('title', _('Collapse sidebar'));
+    sidebarbutton.css({
+        'color': '#FFFFFF',
+        'border-left': '1px solid ' + dark_color,
+        'font-size': '1.2em',
+        'cursor': 'pointer',
+        'height': bodywrapper.height(),
+        'padding-top': '1px',
+        'margin-left': ssb_width_expanded - 12
+    });
+
+    sidebarbutton.hover(
+      function () {
+          $(this).css('background-color', dark_color);
+      },
+      function () {
+          $(this).css('background-color', light_color);
+      }
+    );
+  }
+
+  function set_position_from_cookie() {
+    if (!document.cookie)
+      return;
+    var items = document.cookie.split(';');
+    for(var k=0; k<items.length; k++) {
+      var key_val = items[k].split('=');
+      var key = key_val[0].replace(/ /, "");  // strip leading spaces
+      if (key == 'sidebar') {
+        var value = key_val[1];
+        if ((value == 'collapsed') && (!sidebar_is_collapsed()))
+          collapse_sidebar();
+        else if ((value == 'expanded') && (sidebar_is_collapsed()))
+          expand_sidebar();
+      }
+    }
+  }
+
+  add_sidebar_button();
+  var sidebarbutton = $('#sidebarbutton');
+  set_position_from_cookie();
+});
\ No newline at end of file
diff --git a/doc/build/html/_static/underscore.js b/doc/build/html/_static/underscore.js
new file mode 100644
index 0000000000000000000000000000000000000000..5b55f32beaca186f84cca115514f02cddbd1bbd5
--- /dev/null
+++ b/doc/build/html/_static/underscore.js
@@ -0,0 +1,31 @@
+// Underscore.js 1.3.1
+// (c) 2009-2012 Jeremy Ashkenas, DocumentCloud Inc.
+// Underscore is freely distributable under the MIT license.
+// Portions of Underscore are inspired or borrowed from Prototype,
+// Oliver Steele's Functional, and John Resig's Micro-Templating.
+// For all details and documentation:
+// http://documentcloud.github.com/underscore
+(function(){function q(a,c,d){if(a===c)return a!==0||1/a==1/c;if(a==null||c==null)return a===c;if(a._chain)a=a._wrapped;if(c._chain)c=c._wrapped;if(a.isEqual&&b.isFunction(a.isEqual))return a.isEqual(c);if(c.isEqual&&b.isFunction(c.isEqual))return c.isEqual(a);var e=l.call(a);if(e!=l.call(c))return false;switch(e){case "[object String]":return a==String(c);case "[object Number]":return a!=+a?c!=+c:a==0?1/a==1/c:a==+c;case "[object Date]":case "[object Boolean]":return+a==+c;case "[object RegExp]":return a.source==
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diff --git a/doc/build/html/_static/up-pressed.png b/doc/build/html/_static/up-pressed.png
new file mode 100644
index 0000000000000000000000000000000000000000..8bd587afee2fe38989383ff82010147ea56b93dd
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diff --git a/doc/build/html/_static/up.png b/doc/build/html/_static/up.png
new file mode 100644
index 0000000000000000000000000000000000000000..b94625680b4a4b9647c3a6f3f283776930696aa9
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diff --git a/doc/build/html/_static/websupport.js b/doc/build/html/_static/websupport.js
new file mode 100644
index 0000000000000000000000000000000000000000..19fcda5647b4c91f66bd99c653c15475ec86fcc2
--- /dev/null
+++ b/doc/build/html/_static/websupport.js
@@ -0,0 +1,808 @@
+/*
+ * websupport.js
+ * ~~~~~~~~~~~~~
+ *
+ * sphinx.websupport utilties for all documentation.
+ *
+ * :copyright: Copyright 2007-2013 by the Sphinx team, see AUTHORS.
+ * :license: BSD, see LICENSE for details.
+ *
+ */
+
+(function($) {
+  $.fn.autogrow = function() {
+    return this.each(function() {
+    var textarea = this;
+
+    $.fn.autogrow.resize(textarea);
+
+    $(textarea)
+      .focus(function() {
+        textarea.interval = setInterval(function() {
+          $.fn.autogrow.resize(textarea);
+        }, 500);
+      })
+      .blur(function() {
+        clearInterval(textarea.interval);
+      });
+    });
+  };
+
+  $.fn.autogrow.resize = function(textarea) {
+    var lineHeight = parseInt($(textarea).css('line-height'), 10);
+    var lines = textarea.value.split('\n');
+    var columns = textarea.cols;
+    var lineCount = 0;
+    $.each(lines, function() {
+      lineCount += Math.ceil(this.length / columns) || 1;
+    });
+    var height = lineHeight * (lineCount + 1);
+    $(textarea).css('height', height);
+  };
+})(jQuery);
+
+(function($) {
+  var comp, by;
+
+  function init() {
+    initEvents();
+    initComparator();
+  }
+
+  function initEvents() {
+    $('a.comment-close').live("click", function(event) {
+      event.preventDefault();
+      hide($(this).attr('id').substring(2));
+    });
+    $('a.vote').live("click", function(event) {
+      event.preventDefault();
+      handleVote($(this));
+    });
+    $('a.reply').live("click", function(event) {
+      event.preventDefault();
+      openReply($(this).attr('id').substring(2));
+    });
+    $('a.close-reply').live("click", function(event) {
+      event.preventDefault();
+      closeReply($(this).attr('id').substring(2));
+    });
+    $('a.sort-option').live("click", function(event) {
+      event.preventDefault();
+      handleReSort($(this));
+    });
+    $('a.show-proposal').live("click", function(event) {
+      event.preventDefault();
+      showProposal($(this).attr('id').substring(2));
+    });
+    $('a.hide-proposal').live("click", function(event) {
+      event.preventDefault();
+      hideProposal($(this).attr('id').substring(2));
+    });
+    $('a.show-propose-change').live("click", function(event) {
+      event.preventDefault();
+      showProposeChange($(this).attr('id').substring(2));
+    });
+    $('a.hide-propose-change').live("click", function(event) {
+      event.preventDefault();
+      hideProposeChange($(this).attr('id').substring(2));
+    });
+    $('a.accept-comment').live("click", function(event) {
+      event.preventDefault();
+      acceptComment($(this).attr('id').substring(2));
+    });
+    $('a.delete-comment').live("click", function(event) {
+      event.preventDefault();
+      deleteComment($(this).attr('id').substring(2));
+    });
+    $('a.comment-markup').live("click", function(event) {
+      event.preventDefault();
+      toggleCommentMarkupBox($(this).attr('id').substring(2));
+    });
+  }
+
+  /**
+   * Set comp, which is a comparator function used for sorting and
+   * inserting comments into the list.
+   */
+  function setComparator() {
+    // If the first three letters are "asc", sort in ascending order
+    // and remove the prefix.
+    if (by.substring(0,3) == 'asc') {
+      var i = by.substring(3);
+      comp = function(a, b) { return a[i] - b[i]; };
+    } else {
+      // Otherwise sort in descending order.
+      comp = function(a, b) { return b[by] - a[by]; };
+    }
+
+    // Reset link styles and format the selected sort option.
+    $('a.sel').attr('href', '#').removeClass('sel');
+    $('a.by' + by).removeAttr('href').addClass('sel');
+  }
+
+  /**
+   * Create a comp function. If the user has preferences stored in
+   * the sortBy cookie, use those, otherwise use the default.
+   */
+  function initComparator() {
+    by = 'rating'; // Default to sort by rating.
+    // If the sortBy cookie is set, use that instead.
+    if (document.cookie.length > 0) {
+      var start = document.cookie.indexOf('sortBy=');
+      if (start != -1) {
+        start = start + 7;
+        var end = document.cookie.indexOf(";", start);
+        if (end == -1) {
+          end = document.cookie.length;
+          by = unescape(document.cookie.substring(start, end));
+        }
+      }
+    }
+    setComparator();
+  }
+
+  /**
+   * Show a comment div.
+   */
+  function show(id) {
+    $('#ao' + id).hide();
+    $('#ah' + id).show();
+    var context = $.extend({id: id}, opts);
+    var popup = $(renderTemplate(popupTemplate, context)).hide();
+    popup.find('textarea[name="proposal"]').hide();
+    popup.find('a.by' + by).addClass('sel');
+    var form = popup.find('#cf' + id);
+    form.submit(function(event) {
+      event.preventDefault();
+      addComment(form);
+    });
+    $('#s' + id).after(popup);
+    popup.slideDown('fast', function() {
+      getComments(id);
+    });
+  }
+
+  /**
+   * Hide a comment div.
+   */
+  function hide(id) {
+    $('#ah' + id).hide();
+    $('#ao' + id).show();
+    var div = $('#sc' + id);
+    div.slideUp('fast', function() {
+      div.remove();
+    });
+  }
+
+  /**
+   * Perform an ajax request to get comments for a node
+   * and insert the comments into the comments tree.
+   */
+  function getComments(id) {
+    $.ajax({
+     type: 'GET',
+     url: opts.getCommentsURL,
+     data: {node: id},
+     success: function(data, textStatus, request) {
+       var ul = $('#cl' + id);
+       var speed = 100;
+       $('#cf' + id)
+         .find('textarea[name="proposal"]')
+         .data('source', data.source);
+
+       if (data.comments.length === 0) {
+         ul.html('<li>No comments yet.</li>');
+         ul.data('empty', true);
+       } else {
+         // If there are comments, sort them and put them in the list.
+         var comments = sortComments(data.comments);
+         speed = data.comments.length * 100;
+         appendComments(comments, ul);
+         ul.data('empty', false);
+       }
+       $('#cn' + id).slideUp(speed + 200);
+       ul.slideDown(speed);
+     },
+     error: function(request, textStatus, error) {
+       showError('Oops, there was a problem retrieving the comments.');
+     },
+     dataType: 'json'
+    });
+  }
+
+  /**
+   * Add a comment via ajax and insert the comment into the comment tree.
+   */
+  function addComment(form) {
+    var node_id = form.find('input[name="node"]').val();
+    var parent_id = form.find('input[name="parent"]').val();
+    var text = form.find('textarea[name="comment"]').val();
+    var proposal = form.find('textarea[name="proposal"]').val();
+
+    if (text == '') {
+      showError('Please enter a comment.');
+      return;
+    }
+
+    // Disable the form that is being submitted.
+    form.find('textarea,input').attr('disabled', 'disabled');
+
+    // Send the comment to the server.
+    $.ajax({
+      type: "POST",
+      url: opts.addCommentURL,
+      dataType: 'json',
+      data: {
+        node: node_id,
+        parent: parent_id,
+        text: text,
+        proposal: proposal
+      },
+      success: function(data, textStatus, error) {
+        // Reset the form.
+        if (node_id) {
+          hideProposeChange(node_id);
+        }
+        form.find('textarea')
+          .val('')
+          .add(form.find('input'))
+          .removeAttr('disabled');
+	var ul = $('#cl' + (node_id || parent_id));
+        if (ul.data('empty')) {
+          $(ul).empty();
+          ul.data('empty', false);
+        }
+        insertComment(data.comment);
+        var ao = $('#ao' + node_id);
+        ao.find('img').attr({'src': opts.commentBrightImage});
+        if (node_id) {
+          // if this was a "root" comment, remove the commenting box
+          // (the user can get it back by reopening the comment popup)
+          $('#ca' + node_id).slideUp();
+        }
+      },
+      error: function(request, textStatus, error) {
+        form.find('textarea,input').removeAttr('disabled');
+        showError('Oops, there was a problem adding the comment.');
+      }
+    });
+  }
+
+  /**
+   * Recursively append comments to the main comment list and children
+   * lists, creating the comment tree.
+   */
+  function appendComments(comments, ul) {
+    $.each(comments, function() {
+      var div = createCommentDiv(this);
+      ul.append($(document.createElement('li')).html(div));
+      appendComments(this.children, div.find('ul.comment-children'));
+      // To avoid stagnating data, don't store the comments children in data.
+      this.children = null;
+      div.data('comment', this);
+    });
+  }
+
+  /**
+   * After adding a new comment, it must be inserted in the correct
+   * location in the comment tree.
+   */
+  function insertComment(comment) {
+    var div = createCommentDiv(comment);
+
+    // To avoid stagnating data, don't store the comments children in data.
+    comment.children = null;
+    div.data('comment', comment);
+
+    var ul = $('#cl' + (comment.node || comment.parent));
+    var siblings = getChildren(ul);
+
+    var li = $(document.createElement('li'));
+    li.hide();
+
+    // Determine where in the parents children list to insert this comment.
+    for(i=0; i < siblings.length; i++) {
+      if (comp(comment, siblings[i]) <= 0) {
+        $('#cd' + siblings[i].id)
+          .parent()
+          .before(li.html(div));
+        li.slideDown('fast');
+        return;
+      }
+    }
+
+    // If we get here, this comment rates lower than all the others,
+    // or it is the only comment in the list.
+    ul.append(li.html(div));
+    li.slideDown('fast');
+  }
+
+  function acceptComment(id) {
+    $.ajax({
+      type: 'POST',
+      url: opts.acceptCommentURL,
+      data: {id: id},
+      success: function(data, textStatus, request) {
+        $('#cm' + id).fadeOut('fast');
+        $('#cd' + id).removeClass('moderate');
+      },
+      error: function(request, textStatus, error) {
+        showError('Oops, there was a problem accepting the comment.');
+      }
+    });
+  }
+
+  function deleteComment(id) {
+    $.ajax({
+      type: 'POST',
+      url: opts.deleteCommentURL,
+      data: {id: id},
+      success: function(data, textStatus, request) {
+        var div = $('#cd' + id);
+        if (data == 'delete') {
+          // Moderator mode: remove the comment and all children immediately
+          div.slideUp('fast', function() {
+            div.remove();
+          });
+          return;
+        }
+        // User mode: only mark the comment as deleted
+        div
+          .find('span.user-id:first')
+          .text('[deleted]').end()
+          .find('div.comment-text:first')
+          .text('[deleted]').end()
+          .find('#cm' + id + ', #dc' + id + ', #ac' + id + ', #rc' + id +
+                ', #sp' + id + ', #hp' + id + ', #cr' + id + ', #rl' + id)
+          .remove();
+        var comment = div.data('comment');
+        comment.username = '[deleted]';
+        comment.text = '[deleted]';
+        div.data('comment', comment);
+      },
+      error: function(request, textStatus, error) {
+        showError('Oops, there was a problem deleting the comment.');
+      }
+    });
+  }
+
+  function showProposal(id) {
+    $('#sp' + id).hide();
+    $('#hp' + id).show();
+    $('#pr' + id).slideDown('fast');
+  }
+
+  function hideProposal(id) {
+    $('#hp' + id).hide();
+    $('#sp' + id).show();
+    $('#pr' + id).slideUp('fast');
+  }
+
+  function showProposeChange(id) {
+    $('#pc' + id).hide();
+    $('#hc' + id).show();
+    var textarea = $('#pt' + id);
+    textarea.val(textarea.data('source'));
+    $.fn.autogrow.resize(textarea[0]);
+    textarea.slideDown('fast');
+  }
+
+  function hideProposeChange(id) {
+    $('#hc' + id).hide();
+    $('#pc' + id).show();
+    var textarea = $('#pt' + id);
+    textarea.val('').removeAttr('disabled');
+    textarea.slideUp('fast');
+  }
+
+  function toggleCommentMarkupBox(id) {
+    $('#mb' + id).toggle();
+  }
+
+  /** Handle when the user clicks on a sort by link. */
+  function handleReSort(link) {
+    var classes = link.attr('class').split(/\s+/);
+    for (var i=0; i<classes.length; i++) {
+      if (classes[i] != 'sort-option') {
+	by = classes[i].substring(2);
+      }
+    }
+    setComparator();
+    // Save/update the sortBy cookie.
+    var expiration = new Date();
+    expiration.setDate(expiration.getDate() + 365);
+    document.cookie= 'sortBy=' + escape(by) +
+                     ';expires=' + expiration.toUTCString();
+    $('ul.comment-ul').each(function(index, ul) {
+      var comments = getChildren($(ul), true);
+      comments = sortComments(comments);
+      appendComments(comments, $(ul).empty());
+    });
+  }
+
+  /**
+   * Function to process a vote when a user clicks an arrow.
+   */
+  function handleVote(link) {
+    if (!opts.voting) {
+      showError("You'll need to login to vote.");
+      return;
+    }
+
+    var id = link.attr('id');
+    if (!id) {
+      // Didn't click on one of the voting arrows.
+      return;
+    }
+    // If it is an unvote, the new vote value is 0,
+    // Otherwise it's 1 for an upvote, or -1 for a downvote.
+    var value = 0;
+    if (id.charAt(1) != 'u') {
+      value = id.charAt(0) == 'u' ? 1 : -1;
+    }
+    // The data to be sent to the server.
+    var d = {
+      comment_id: id.substring(2),
+      value: value
+    };
+
+    // Swap the vote and unvote links.
+    link.hide();
+    $('#' + id.charAt(0) + (id.charAt(1) == 'u' ? 'v' : 'u') + d.comment_id)
+      .show();
+
+    // The div the comment is displayed in.
+    var div = $('div#cd' + d.comment_id);
+    var data = div.data('comment');
+
+    // If this is not an unvote, and the other vote arrow has
+    // already been pressed, unpress it.
+    if ((d.value !== 0) && (data.vote === d.value * -1)) {
+      $('#' + (d.value == 1 ? 'd' : 'u') + 'u' + d.comment_id).hide();
+      $('#' + (d.value == 1 ? 'd' : 'u') + 'v' + d.comment_id).show();
+    }
+
+    // Update the comments rating in the local data.
+    data.rating += (data.vote === 0) ? d.value : (d.value - data.vote);
+    data.vote = d.value;
+    div.data('comment', data);
+
+    // Change the rating text.
+    div.find('.rating:first')
+      .text(data.rating + ' point' + (data.rating == 1 ? '' : 's'));
+
+    // Send the vote information to the server.
+    $.ajax({
+      type: "POST",
+      url: opts.processVoteURL,
+      data: d,
+      error: function(request, textStatus, error) {
+        showError('Oops, there was a problem casting that vote.');
+      }
+    });
+  }
+
+  /**
+   * Open a reply form used to reply to an existing comment.
+   */
+  function openReply(id) {
+    // Swap out the reply link for the hide link
+    $('#rl' + id).hide();
+    $('#cr' + id).show();
+
+    // Add the reply li to the children ul.
+    var div = $(renderTemplate(replyTemplate, {id: id})).hide();
+    $('#cl' + id)
+      .prepend(div)
+      // Setup the submit handler for the reply form.
+      .find('#rf' + id)
+      .submit(function(event) {
+        event.preventDefault();
+        addComment($('#rf' + id));
+        closeReply(id);
+      })
+      .find('input[type=button]')
+      .click(function() {
+        closeReply(id);
+      });
+    div.slideDown('fast', function() {
+      $('#rf' + id).find('textarea').focus();
+    });
+  }
+
+  /**
+   * Close the reply form opened with openReply.
+   */
+  function closeReply(id) {
+    // Remove the reply div from the DOM.
+    $('#rd' + id).slideUp('fast', function() {
+      $(this).remove();
+    });
+
+    // Swap out the hide link for the reply link
+    $('#cr' + id).hide();
+    $('#rl' + id).show();
+  }
+
+  /**
+   * Recursively sort a tree of comments using the comp comparator.
+   */
+  function sortComments(comments) {
+    comments.sort(comp);
+    $.each(comments, function() {
+      this.children = sortComments(this.children);
+    });
+    return comments;
+  }
+
+  /**
+   * Get the children comments from a ul. If recursive is true,
+   * recursively include childrens' children.
+   */
+  function getChildren(ul, recursive) {
+    var children = [];
+    ul.children().children("[id^='cd']")
+      .each(function() {
+        var comment = $(this).data('comment');
+        if (recursive)
+          comment.children = getChildren($(this).find('#cl' + comment.id), true);
+        children.push(comment);
+      });
+    return children;
+  }
+
+  /** Create a div to display a comment in. */
+  function createCommentDiv(comment) {
+    if (!comment.displayed && !opts.moderator) {
+      return $('<div class="moderate">Thank you!  Your comment will show up '
+               + 'once it is has been approved by a moderator.</div>');
+    }
+    // Prettify the comment rating.
+    comment.pretty_rating = comment.rating + ' point' +
+      (comment.rating == 1 ? '' : 's');
+    // Make a class (for displaying not yet moderated comments differently)
+    comment.css_class = comment.displayed ? '' : ' moderate';
+    // Create a div for this comment.
+    var context = $.extend({}, opts, comment);
+    var div = $(renderTemplate(commentTemplate, context));
+
+    // If the user has voted on this comment, highlight the correct arrow.
+    if (comment.vote) {
+      var direction = (comment.vote == 1) ? 'u' : 'd';
+      div.find('#' + direction + 'v' + comment.id).hide();
+      div.find('#' + direction + 'u' + comment.id).show();
+    }
+
+    if (opts.moderator || comment.text != '[deleted]') {
+      div.find('a.reply').show();
+      if (comment.proposal_diff)
+        div.find('#sp' + comment.id).show();
+      if (opts.moderator && !comment.displayed)
+        div.find('#cm' + comment.id).show();
+      if (opts.moderator || (opts.username == comment.username))
+        div.find('#dc' + comment.id).show();
+    }
+    return div;
+  }
+
+  /**
+   * A simple template renderer. Placeholders such as <%id%> are replaced
+   * by context['id'] with items being escaped. Placeholders such as <#id#>
+   * are not escaped.
+   */
+  function renderTemplate(template, context) {
+    var esc = $(document.createElement('div'));
+
+    function handle(ph, escape) {
+      var cur = context;
+      $.each(ph.split('.'), function() {
+        cur = cur[this];
+      });
+      return escape ? esc.text(cur || "").html() : cur;
+    }
+
+    return template.replace(/<([%#])([\w\.]*)\1>/g, function() {
+      return handle(arguments[2], arguments[1] == '%' ? true : false);
+    });
+  }
+
+  /** Flash an error message briefly. */
+  function showError(message) {
+    $(document.createElement('div')).attr({'class': 'popup-error'})
+      .append($(document.createElement('div'))
+               .attr({'class': 'error-message'}).text(message))
+      .appendTo('body')
+      .fadeIn("slow")
+      .delay(2000)
+      .fadeOut("slow");
+  }
+
+  /** Add a link the user uses to open the comments popup. */
+  $.fn.comment = function() {
+    return this.each(function() {
+      var id = $(this).attr('id').substring(1);
+      var count = COMMENT_METADATA[id];
+      var title = count + ' comment' + (count == 1 ? '' : 's');
+      var image = count > 0 ? opts.commentBrightImage : opts.commentImage;
+      var addcls = count == 0 ? ' nocomment' : '';
+      $(this)
+        .append(
+          $(document.createElement('a')).attr({
+            href: '#',
+            'class': 'sphinx-comment-open' + addcls,
+            id: 'ao' + id
+          })
+            .append($(document.createElement('img')).attr({
+              src: image,
+              alt: 'comment',
+              title: title
+            }))
+            .click(function(event) {
+              event.preventDefault();
+              show($(this).attr('id').substring(2));
+            })
+        )
+        .append(
+          $(document.createElement('a')).attr({
+            href: '#',
+            'class': 'sphinx-comment-close hidden',
+            id: 'ah' + id
+          })
+            .append($(document.createElement('img')).attr({
+              src: opts.closeCommentImage,
+              alt: 'close',
+              title: 'close'
+            }))
+            .click(function(event) {
+              event.preventDefault();
+              hide($(this).attr('id').substring(2));
+            })
+        );
+    });
+  };
+
+  var opts = {
+    processVoteURL: '/_process_vote',
+    addCommentURL: '/_add_comment',
+    getCommentsURL: '/_get_comments',
+    acceptCommentURL: '/_accept_comment',
+    deleteCommentURL: '/_delete_comment',
+    commentImage: '/static/_static/comment.png',
+    closeCommentImage: '/static/_static/comment-close.png',
+    loadingImage: '/static/_static/ajax-loader.gif',
+    commentBrightImage: '/static/_static/comment-bright.png',
+    upArrow: '/static/_static/up.png',
+    downArrow: '/static/_static/down.png',
+    upArrowPressed: '/static/_static/up-pressed.png',
+    downArrowPressed: '/static/_static/down-pressed.png',
+    voting: false,
+    moderator: false
+  };
+
+  if (typeof COMMENT_OPTIONS != "undefined") {
+    opts = jQuery.extend(opts, COMMENT_OPTIONS);
+  }
+
+  var popupTemplate = '\
+    <div class="sphinx-comments" id="sc<%id%>">\
+      <p class="sort-options">\
+        Sort by:\
+        <a href="#" class="sort-option byrating">best rated</a>\
+        <a href="#" class="sort-option byascage">newest</a>\
+        <a href="#" class="sort-option byage">oldest</a>\
+      </p>\
+      <div class="comment-header">Comments</div>\
+      <div class="comment-loading" id="cn<%id%>">\
+        loading comments... <img src="<%loadingImage%>" alt="" /></div>\
+      <ul id="cl<%id%>" class="comment-ul"></ul>\
+      <div id="ca<%id%>">\
+      <p class="add-a-comment">Add a comment\
+        (<a href="#" class="comment-markup" id="ab<%id%>">markup</a>):</p>\
+      <div class="comment-markup-box" id="mb<%id%>">\
+        reStructured text markup: <i>*emph*</i>, <b>**strong**</b>, \
+        <tt>``code``</tt>, \
+        code blocks: <tt>::</tt> and an indented block after blank line</div>\
+      <form method="post" id="cf<%id%>" class="comment-form" action="">\
+        <textarea name="comment" cols="80"></textarea>\
+        <p class="propose-button">\
+          <a href="#" id="pc<%id%>" class="show-propose-change">\
+            Propose a change &#9657;\
+          </a>\
+          <a href="#" id="hc<%id%>" class="hide-propose-change">\
+            Propose a change &#9663;\
+          </a>\
+        </p>\
+        <textarea name="proposal" id="pt<%id%>" cols="80"\
+                  spellcheck="false"></textarea>\
+        <input type="submit" value="Add comment" />\
+        <input type="hidden" name="node" value="<%id%>" />\
+        <input type="hidden" name="parent" value="" />\
+      </form>\
+      </div>\
+    </div>';
+
+  var commentTemplate = '\
+    <div id="cd<%id%>" class="sphinx-comment<%css_class%>">\
+      <div class="vote">\
+        <div class="arrow">\
+          <a href="#" id="uv<%id%>" class="vote" title="vote up">\
+            <img src="<%upArrow%>" />\
+          </a>\
+          <a href="#" id="uu<%id%>" class="un vote" title="vote up">\
+            <img src="<%upArrowPressed%>" />\
+          </a>\
+        </div>\
+        <div class="arrow">\
+          <a href="#" id="dv<%id%>" class="vote" title="vote down">\
+            <img src="<%downArrow%>" id="da<%id%>" />\
+          </a>\
+          <a href="#" id="du<%id%>" class="un vote" title="vote down">\
+            <img src="<%downArrowPressed%>" />\
+          </a>\
+        </div>\
+      </div>\
+      <div class="comment-content">\
+        <p class="tagline comment">\
+          <span class="user-id"><%username%></span>\
+          <span class="rating"><%pretty_rating%></span>\
+          <span class="delta"><%time.delta%></span>\
+        </p>\
+        <div class="comment-text comment"><#text#></div>\
+        <p class="comment-opts comment">\
+          <a href="#" class="reply hidden" id="rl<%id%>">reply &#9657;</a>\
+          <a href="#" class="close-reply" id="cr<%id%>">reply &#9663;</a>\
+          <a href="#" id="sp<%id%>" class="show-proposal">proposal &#9657;</a>\
+          <a href="#" id="hp<%id%>" class="hide-proposal">proposal &#9663;</a>\
+          <a href="#" id="dc<%id%>" class="delete-comment hidden">delete</a>\
+          <span id="cm<%id%>" class="moderation hidden">\
+            <a href="#" id="ac<%id%>" class="accept-comment">accept</a>\
+          </span>\
+        </p>\
+        <pre class="proposal" id="pr<%id%>">\
+<#proposal_diff#>\
+        </pre>\
+          <ul class="comment-children" id="cl<%id%>"></ul>\
+        </div>\
+        <div class="clearleft"></div>\
+      </div>\
+    </div>';
+
+  var replyTemplate = '\
+    <li>\
+      <div class="reply-div" id="rd<%id%>">\
+        <form id="rf<%id%>">\
+          <textarea name="comment" cols="80"></textarea>\
+          <input type="submit" value="Add reply" />\
+          <input type="button" value="Cancel" />\
+          <input type="hidden" name="parent" value="<%id%>" />\
+          <input type="hidden" name="node" value="" />\
+        </form>\
+      </div>\
+    </li>';
+
+  $(document).ready(function() {
+    init();
+  });
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diff --git a/doc/build/html/code.html b/doc/build/html/code.html
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@@ -0,0 +1,893 @@
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+            
+  <div class="section" id="module-lsmtool">
+<span id="lsmtool-the-lofar-local-sky-model-tool"></span><h1>LSMTool: the LOFAR Local Sky Model Tool<a class="headerlink" href="#module-lsmtool" title="Permalink to this headline">¶</a></h1>
+<p>LSMTool: the LOFAR Local Sky Model Tool</p>
+<dl class="function">
+<dt id="lsmtool.load">
+<tt class="descclassname">lsmtool.</tt><tt class="descname">load</tt><big>(</big><em>fileName</em>, <em>beamMS=None</em><big>)</big><a class="headerlink" href="#lsmtool.load" title="Permalink to this definition">¶</a></dt>
+<dd><p>Loads a sky model from a file and returns a SkyModel object.</p>
+<dl class="docutils">
+<dt>fileName <span class="classifier-delimiter">:</span> <span class="classifier">str</span></dt>
+<dd>Input ASCII file from which the sky model is read. Must
+respect the makesourcedb format</dd>
+<dt>beamMS <span class="classifier-delimiter">:</span> <span class="classifier">str, optional</span></dt>
+<dd>Measurement set from which the primary beam will be estimated. A
+column of attenuated Stokes I fluxes will be added to the table.</dd>
+</dl>
+<p>Load a sky model into a SkyModel object:</p>
+<div class="highlight-python"><div class="highlight"><pre><span class="gp">&gt;&gt;&gt; </span><span class="kn">import</span> <span class="nn">lsmtool</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">s</span> <span class="o">=</span> <span class="n">lsmtool</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="s">&#39;sky.model&#39;</span><span class="p">)</span>
+</pre></div>
+</div>
+<p>Load a sky model with a beam MS so that apparent fluxes will
+be available (in addition to intrinsic fluxes)::</p>
+<div class="highlight-python"><div class="highlight"><pre><span class="gp">&gt;&gt;&gt; </span><span class="n">s</span> <span class="o">=</span> <span class="n">lsmtool</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="s">&#39;sky.model&#39;</span><span class="p">,</span> <span class="s">&#39;SB100.MS&#39;</span><span class="p">)</span>
+</pre></div>
+</div>
+</dd></dl>
+
+<dl class="class">
+<dt id="lsmtool.SkyModel">
+<em class="property">class </em><tt class="descclassname">lsmtool.</tt><tt class="descname">SkyModel</tt><big>(</big><em>fileName</em>, <em>beamMS=None</em>, <em>checkDup=False</em><big>)</big><a class="headerlink" href="#lsmtool.SkyModel" title="Permalink to this definition">¶</a></dt>
+<dd><p>Object that stores the sky model and provides methods for accessing it.</p>
+<dl class="method">
+<dt id="lsmtool.SkyModel.add">
+<tt class="descname">add</tt><big>(</big><em>colNamesVals</em><big>)</big><a class="headerlink" href="#lsmtool.SkyModel.add" title="Permalink to this definition">¶</a></dt>
+<dd><p>Add a source to the sky model.</p>
+<dl class="docutils">
+<dt>colNamesVals <span class="classifier-delimiter">:</span> <span class="classifier">dict</span></dt>
+<dd>A dictionary that specifies the row values for the source to be added.</dd>
+</dl>
+<p>Add a point source:</p>
+<div class="highlight-python"><div class="highlight"><pre><span class="gp">&gt;&gt;&gt; </span><span class="n">source</span> <span class="o">=</span> <span class="p">{</span><span class="s">&#39;Name&#39;</span><span class="p">:</span><span class="s">&#39;src1&#39;</span><span class="p">,</span> <span class="s">&#39;Type&#39;</span><span class="p">:</span><span class="s">&#39;POINT&#39;</span><span class="p">,</span> <span class="s">&#39;Ra&#39;</span><span class="p">:</span><span class="s">&#39;12:32:10.1&#39;</span><span class="p">,</span>
+<span class="go">    &#39;Dec&#39;:&#39;23.43.21.21&#39;, &#39;I&#39;:2.134}</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">s</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">source</span><span class="p">)</span>
+</pre></div>
+</div>
+</dd></dl>
+
+<dl class="method">
+<dt id="lsmtool.SkyModel.concatenate">
+<tt class="descname">concatenate</tt><big>(</big><em>LSM2</em>, <em>matchBy='name'</em>, <em>radius=0.1</em>, <em>keep='all'</em><big>)</big><a class="headerlink" href="#lsmtool.SkyModel.concatenate" title="Permalink to this definition">¶</a></dt>
+<dd><p>Concatenate two sky models</p>
+<dl class="docutils">
+<dt>LSM2 <span class="classifier-delimiter">:</span> <span class="classifier">SkyModel object</span></dt>
+<dd>Sky model to concatenate with the parent sky model</dd>
+<dt>matchBy <span class="classifier-delimiter">:</span> <span class="classifier">str, optional</span></dt>
+<dd><p class="first">Determines how duplicate sources are determined:
+- &#8216;name&#8217; =&gt; duplicates are identified by name
+- &#8216;position&#8217; =&gt; duplicates are identified by radius. Sources within the</p>
+<blockquote class="last">
+<div>radius specified by the radius parameter are considered duplicates</div></blockquote>
+</dd>
+<dt>radius <span class="classifier-delimiter">:</span> <span class="classifier">float, optional</span></dt>
+<dd>Radius in degrees for matching when matchBy=&#8217;position&#8217;</dd>
+<dt>keep <span class="classifier-delimiter">:</span> <span class="classifier">str, optional</span></dt>
+<dd><p class="first">Determines how duplicates are treated:
+- &#8216;all&#8217; =&gt; all duplicates are kept; those with identical names are re-</p>
+<blockquote>
+<div>named</div></blockquote>
+<ul class="last simple">
+<li>&#8216;from1&#8217; =&gt; duplicates kept are those from sky model 1 (the parent)</li>
+<li>&#8216;from2&#8217; =&gt; duplicates kept are those from sky model 2 (LSM2)</li>
+</ul>
+</dd>
+</dl>
+<p>Concatenate two sky models, identifying duplicates by matching to the source
+names. When duplicates are found, keep the source from the parent sky model
+and discard the duplicate from second sky model (this might be useful when
+merging two gsm.py sky models that have some overlap):</p>
+<div class="highlight-python"><div class="highlight"><pre><span class="gp">&gt;&gt;&gt; </span><span class="n">LSM2</span> <span class="o">=</span> <span class="n">lsmtool</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="s">&#39;gsm_sky2.model&#39;</span><span class="p">)</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">s</span><span class="o">.</span><span class="n">concatenate</span><span class="p">(</span><span class="n">LSM2</span><span class="p">,</span> <span class="n">matchBy</span><span class="o">=</span><span class="s">&#39;name&#39;</span><span class="p">,</span> <span class="n">keep</span><span class="o">=</span><span class="s">&#39;from1&#39;</span><span class="p">)</span>
+</pre></div>
+</div>
+<p>Concatenate two sky models, identifying duplicates by matching to the source
+positions within a radius of 10 arcsec. When duplicates are found, keep the
+source from the second sky model and discard the duplicate from the parent
+sky model (this might be useful when replacing parts of a low-resolution
+sky model with a high-resolution one):</p>
+<div class="highlight-python"><div class="highlight"><pre><span class="gp">&gt;&gt;&gt; </span><span class="n">LSM2</span> <span class="o">=</span> <span class="n">lsmtool</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="s">&#39;high_res_sky.model&#39;</span><span class="p">)</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">s</span><span class="o">.</span><span class="n">concatenate</span><span class="p">(</span><span class="n">LSM2</span><span class="p">,</span> <span class="n">matchBy</span><span class="o">=</span><span class="s">&#39;position&#39;</span><span class="p">,</span> <span class="n">radius</span><span class="o">=</span><span class="mf">10.0</span><span class="o">/</span><span class="mf">3600.0</span><span class="p">,</span>
+<span class="go">    keep=&#39;from2&#39;)</span>
+</pre></div>
+</div>
+</dd></dl>
+
+<dl class="method">
+<dt id="lsmtool.SkyModel.copy">
+<tt class="descname">copy</tt><big>(</big><big>)</big><a class="headerlink" href="#lsmtool.SkyModel.copy" title="Permalink to this definition">¶</a></dt>
+<dd><p>Returns a copy of the sky model</p>
+</dd></dl>
+
+<dl class="method">
+<dt id="lsmtool.SkyModel.getColNames">
+<tt class="descname">getColNames</tt><big>(</big><big>)</big><a class="headerlink" href="#lsmtool.SkyModel.getColNames" title="Permalink to this definition">¶</a></dt>
+<dd><p>Returns a list of all available column names.</p>
+<p>Get column names:</p>
+<div class="highlight-python"><div class="highlight"><pre><span class="gp">&gt;&gt;&gt; </span><span class="n">s</span><span class="o">.</span><span class="n">getColNames</span><span class="p">()</span>
+</pre></div>
+</div>
+</dd></dl>
+
+<dl class="method">
+<dt id="lsmtool.SkyModel.getColValues">
+<tt class="descname">getColValues</tt><big>(</big><em>colName</em>, <em>units=None</em>, <em>aggregate=None</em>, <em>weight=False</em>, <em>applyBeam=False</em><big>)</big><a class="headerlink" href="#lsmtool.SkyModel.getColValues" title="Permalink to this definition">¶</a></dt>
+<dd><p>Returns a numpy array of column values.</p>
+<dl class="docutils">
+<dt>colName <span class="classifier-delimiter">:</span> <span class="classifier">str</span></dt>
+<dd>Name of column</dd>
+<dt>units <span class="classifier-delimiter">:</span> <span class="classifier">str, optional</span></dt>
+<dd>Output units (the values are converted as needed). By default, the
+units are those used by makesourcedb, with the exception of Ra and
+Dec which have default units of degrees.</dd>
+<dt>aggregate <span class="classifier-delimiter">:</span> <span class="classifier">str, optional</span></dt>
+<dd><p class="first">If set, the array returned will be of values aggregated
+over the patch members. The following aggregation functions are
+available:</p>
+<blockquote>
+<div><ul class="simple">
+<li>&#8216;sum&#8217;: sum of patch values</li>
+<li>&#8216;mean&#8217;: mean of patch values</li>
+<li>&#8216;wmean&#8217;: Stokes I weighted mean of patch values</li>
+<li>&#8216;min&#8217;: minimum of patch values</li>
+<li>&#8216;max&#8217;: maximum of patch values</li>
+</ul>
+</div></blockquote>
+<p class="last">Note that, in certain cases, certain aggregation functions will not
+produce meaningful results. For example, asking for the sum of
+the MajorAxis values per patch will not give a good indication of
+the size of the patch (to get the sizes, use the getPatchSizes()
+method). Additionally, applying the &#8216;mean&#8217; or &#8216;wmean&#8217; functions to
+the RA or Dec columns may give strange results near the poles or
+near RA = 0h. For aggregated RA and Dec values, use the
+getPatchPositions() method instead which projects the sources onto
+the image plane before aggregation.</p>
+</dd>
+<dt>applyBeam <span class="classifier-delimiter">:</span> <span class="classifier">bool, optional</span></dt>
+<dd>If True, fluxes will be attenuated by the beam. This attenuation
+also applies to fluxes used in aggregation functions.</dd>
+</dl>
+<p>Get Stokes I fluxes in Jy:</p>
+<div class="highlight-python"><div class="highlight"><pre><span class="gp">&gt;&gt;&gt; </span><span class="n">s</span><span class="o">.</span><span class="n">getColValues</span><span class="p">(</span><span class="s">&#39;I&#39;</span><span class="p">)</span>
+<span class="go">array([ 60.4892,   1.2413,   1.216 , ...,   1.12  ,   1.25  ,   1.16  ])</span>
+</pre></div>
+</div>
+<p>Get Stokes I fluxes in mJy:</p>
+<div class="highlight-python"><div class="highlight"><pre><span class="gp">&gt;&gt;&gt; </span><span class="n">s</span><span class="o">.</span><span class="n">getColValues</span><span class="p">(</span><span class="s">&#39;I&#39;</span><span class="p">,</span> <span class="n">units</span><span class="o">=</span><span class="s">&#39;mJy&#39;</span><span class="p">)</span>
+<span class="go">array([ 60489.2,   1241.3,   1216. , ...,   1120. ,   1250. ,   1160. ])</span>
+</pre></div>
+</div>
+<p>Get total Stokes I flux for the patches:</p>
+<div class="highlight-python"><div class="highlight"><pre><span class="gp">&gt;&gt;&gt; </span><span class="n">s</span><span class="o">.</span><span class="n">getColValues</span><span class="p">(</span><span class="s">&#39;I&#39;</span><span class="p">,</span> <span class="n">aggregate</span><span class="o">=</span><span class="s">&#39;sum&#39;</span><span class="p">)</span>
+<span class="go">array([ 61.7305,   1.216 ,   3.9793, ...,   1.12  ,   1.25  ,   1.16  ])</span>
+</pre></div>
+</div>
+<p>Get flux-weighted average RA and Dec for the patches. As noted above, the
+getColValues() method is not appropriate for use with RA or Dec, so
+we must use getPatchPositions() instead:</p>
+<div class="highlight-python"><div class="highlight"><pre><span class="gp">&gt;&gt;&gt; </span><span class="n">RA</span><span class="p">,</span> <span class="n">Dec</span> <span class="o">=</span> <span class="n">s</span><span class="o">.</span><span class="n">getPatchPositions</span><span class="p">(</span><span class="n">method</span><span class="o">=</span><span class="s">&#39;wmean&#39;</span><span class="p">,</span> <span class="n">asArray</span><span class="o">=</span><span class="bp">True</span><span class="p">)</span>
+</pre></div>
+</div>
+</dd></dl>
+
+<dl class="method">
+<dt id="lsmtool.SkyModel.getDefaltValues">
+<tt class="descname">getDefaltValues</tt><big>(</big><big>)</big><a class="headerlink" href="#lsmtool.SkyModel.getDefaltValues" title="Permalink to this definition">¶</a></dt>
+<dd><p>Returns dict of {colName:default} values for all columns with defaults</p>
+</dd></dl>
+
+<dl class="method">
+<dt id="lsmtool.SkyModel.getPatchNames">
+<tt class="descname">getPatchNames</tt><big>(</big><big>)</big><a class="headerlink" href="#lsmtool.SkyModel.getPatchNames" title="Permalink to this definition">¶</a></dt>
+<dd><p>Returns array of patch names.</p>
+</dd></dl>
+
+<dl class="method">
+<dt id="lsmtool.SkyModel.getPatchPositions">
+<tt class="descname">getPatchPositions</tt><big>(</big><em>patchName=None</em>, <em>asArray=False</em>, <em>method=None</em>, <em>applyBeam=False</em>, <em>perPatchProjection=True</em><big>)</big><a class="headerlink" href="#lsmtool.SkyModel.getPatchPositions" title="Permalink to this definition">¶</a></dt>
+<dd><p>Returns arrays or a dict of patch positions (as {&#8216;patchName&#8217;:(RA, Dec)}).</p>
+<dl class="docutils">
+<dt>patchName <span class="classifier-delimiter">:</span> <span class="classifier">str or list, optional</span></dt>
+<dd>List of patch names for which the positions are desired</dd>
+<dt>asArray <span class="classifier-delimiter">:</span> <span class="classifier">bool, optional</span></dt>
+<dd>If True, returns arrays of RA, Dec instead of a dict</dd>
+<dt>method <span class="classifier-delimiter">:</span> <span class="classifier">None or str, optional</span></dt>
+<dd>This parameter specifies the method used to calculate the patch
+positions. If None, the current patch positions stored in the sky
+model, if any, will be returned.
+- &#8216;mid&#8217; =&gt; calculate the midpoint of the patch
+- &#8216;mean&#8217; =&gt; calculate the mean RA and Dec of the patch
+- &#8216;wmean&#8217; =&gt; calculate the flux-weighted mean RA and Dec of the patch
+- None =&gt; current patch positions are returned
+Note that the mid, mean, and wmean positions are calculated from TAN-
+projected values.</dd>
+<dt>applyBeam <span class="classifier-delimiter">:</span> <span class="classifier">bool, optional</span></dt>
+<dd>If True, fluxes used as weights will be attenuated by the beam.</dd>
+<dt>perPatchProjection <span class="classifier-delimiter">:</span> <span class="classifier">bool, optional</span></dt>
+<dd>If True, a different projection center is used per patch. If False,
+a single projection center is used for all patches.</dd>
+</dl>
+<p>Get the current patch positions:</p>
+<div class="highlight-python"><div class="highlight"><pre><span class="gp">&gt;&gt;&gt; </span><span class="n">s</span><span class="o">.</span><span class="n">getPatchPositions</span><span class="p">()</span>
+<span class="go">{&#39;bin0&#39;: [&lt;Angle 91.77565208333331 deg&gt;, &lt;Angle 41.57834805555555 deg&gt;],</span>
+<span class="go"> &#39;bin1&#39;: [&lt;Angle 91.59991874999997 deg&gt;, &lt;Angle 41.90387583333333 deg&gt;],</span>
+<span class="go"> &#39;bin2&#39;: [&lt;Angle 90.83773333333332 deg&gt;, &lt;Angle 42.189861944444445 deg&gt;],</span>
+</pre></div>
+</div>
+<p>Get them as RA and Dec arrays in degrees:</p>
+<div class="highlight-python"><div class="highlight"><pre><span class="gp">&gt;&gt;&gt; </span><span class="n">s</span><span class="o">.</span><span class="n">getPatchPositions</span><span class="p">(</span><span class="n">asArray</span><span class="o">=</span><span class="bp">True</span><span class="p">)</span>
+<span class="go">(array([ 91.77565208,  91.59991875,  90.83773333]),</span>
+<span class="go"> array([ 41.57834806,  41.90387583,  42.18986194]))</span>
+</pre></div>
+</div>
+<p>Calculate the flux-weighted mean positions of each patch:</p>
+<div class="highlight-python"><div class="highlight"><pre><span class="gp">&gt;&gt;&gt; </span><span class="n">s</span><span class="o">.</span><span class="n">getPatchPositions</span><span class="p">(</span><span class="n">method</span><span class="o">=</span><span class="s">&#39;wmean&#39;</span><span class="p">,</span> <span class="n">asArray</span><span class="o">=</span><span class="bp">True</span><span class="p">)</span>
+</pre></div>
+</div>
+</dd></dl>
+
+<dl class="method">
+<dt id="lsmtool.SkyModel.getPatchSizes">
+<tt class="descname">getPatchSizes</tt><big>(</big><em>units=None</em>, <em>weight=False</em>, <em>applyBeam=False</em><big>)</big><a class="headerlink" href="#lsmtool.SkyModel.getPatchSizes" title="Permalink to this definition">¶</a></dt>
+<dd><p>Returns array of patch sizes.</p>
+</dd></dl>
+
+<dl class="method">
+<dt id="lsmtool.SkyModel.getRowIndex">
+<tt class="descname">getRowIndex</tt><big>(</big><em>rowName</em><big>)</big><a class="headerlink" href="#lsmtool.SkyModel.getRowIndex" title="Permalink to this definition">¶</a></dt>
+<dd><p>Returns index or indices for specified source or patch as a list.</p>
+<dl class="docutils">
+<dt>rowName <span class="classifier-delimiter">:</span> <span class="classifier">str</span></dt>
+<dd>Name of the source or patch</dd>
+</dl>
+<p>Get row index for the source &#8216;src1&#8217;:</p>
+<div class="highlight-python"><div class="highlight"><pre><span class="gp">&gt;&gt;&gt; </span><span class="n">s</span><span class="o">.</span><span class="n">getRowIndex</span><span class="p">(</span><span class="s">&#39;src1&#39;</span><span class="p">)</span>
+<span class="go">[0]</span>
+</pre></div>
+</div>
+<p>Get row indices for the patch &#8216;bin1&#8217; and verify the patch name:</p>
+<div class="highlight-python"><div class="highlight"><pre><span class="gp">&gt;&gt;&gt; </span><span class="n">ind</span> <span class="o">=</span> <span class="n">s</span><span class="o">.</span><span class="n">getRowIndex</span><span class="p">(</span><span class="s">&#39;bin1&#39;</span><span class="p">)</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="k">print</span><span class="p">(</span><span class="n">s</span><span class="o">.</span><span class="n">getPatchNames</span><span class="p">()[</span><span class="n">ind</span><span class="p">])</span>
+<span class="go">[&#39;bin1&#39; &#39;bin1&#39;]</span>
+</pre></div>
+</div>
+</dd></dl>
+
+<dl class="method">
+<dt id="lsmtool.SkyModel.getRowValues">
+<tt class="descname">getRowValues</tt><big>(</big><em>rowName</em>, <em>colName=None</em><big>)</big><a class="headerlink" href="#lsmtool.SkyModel.getRowValues" title="Permalink to this definition">¶</a></dt>
+<dd><p>Returns an astropy table or table row for specified source or patch.</p>
+<dl class="docutils">
+<dt>rowName <span class="classifier-delimiter">:</span> <span class="classifier">str</span></dt>
+<dd>Name of the source or patch</dd>
+<dt>colName <span class="classifier-delimiter">:</span> <span class="classifier">str, optional</span></dt>
+<dd>Column name. If given, returns row values for specified
+column only.</dd>
+</dl>
+<p>Get row values for the source &#8216;src1&#8217;:</p>
+<div class="highlight-python"><div class="highlight"><pre><span class="gp">&gt;&gt;&gt; </span><span class="n">r</span> <span class="o">=</span> <span class="n">s</span><span class="o">.</span><span class="n">getRowValues</span><span class="p">(</span><span class="s">&#39;src1&#39;</span><span class="p">)</span>
+</pre></div>
+</div>
+<p>Sum over the fluxes of sources in the &#8216;bin1&#8217; patch:</p>
+<div class="highlight-python"><div class="highlight"><pre><span class="gp">&gt;&gt;&gt; </span><span class="n">rows</span> <span class="o">=</span> <span class="n">s</span><span class="o">.</span><span class="n">getRowValues</span><span class="p">(</span><span class="s">&#39;bin1&#39;</span><span class="p">)</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">tot</span> <span class="o">=</span> <span class="mf">0.0</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="n">rows</span><span class="p">:</span> <span class="n">tot</span> <span class="o">+=</span> <span class="n">r</span><span class="p">[</span><span class="s">&#39;I&#39;</span><span class="p">]</span>
+</pre></div>
+</div>
+</dd></dl>
+
+<dl class="method">
+<dt id="lsmtool.SkyModel.group">
+<tt class="descname">group</tt><big>(</big><em>algorithm</em>, <em>targetFlux=None</em>, <em>numClusters=100</em>, <em>applyBeam=False</em><big>)</big><a class="headerlink" href="#lsmtool.SkyModel.group" title="Permalink to this definition">¶</a></dt>
+<dd><p>Groups sources into patches</p>
+<dl class="docutils">
+<dt>LSM <span class="classifier-delimiter">:</span> <span class="classifier">SkyModel object</span></dt>
+<dd>Input sky model.</dd>
+<dt>algorithm <span class="classifier-delimiter">:</span> <span class="classifier">str</span></dt>
+<dd><p class="first">Algorithm to use for grouping:
+- &#8216;single&#8217; =&gt; all sources are grouped into a single patch
+- &#8216;every&#8217; =&gt; every source gets a separate patch
+- &#8216;cluster&#8217; =&gt; SAGECAL clustering algorithm that groups sources into</p>
+<blockquote>
+<div>specified number of clusters (specified by the numClusters parameter).</div></blockquote>
+<ul class="last">
+<li><dl class="first docutils">
+<dt>&#8216;tessellate&#8217; =&gt; group into tiles whose total flux approximates</dt>
+<dd><p class="first last">the target flux (specified by the targetFlux parameter).</p>
+</dd>
+</dl>
+</li>
+<li><dl class="first docutils">
+<dt>the filename of a mask image =&gt; group by masked regions (where mask =</dt>
+<dd><p class="first last">True). Source outside of masked regions are given patches of their
+own.</p>
+</dd>
+</dl>
+</li>
+</ul>
+</dd>
+<dt>targetFlux <span class="classifier-delimiter">:</span> <span class="classifier">str or float, optional</span></dt>
+<dd>Target flux for tessellation (the total flux of each tile will be close
+to this value). The target flux can be specified as either a float in Jy
+or as a string with units (e.g., &#8216;25.0 mJy&#8217;).</dd>
+<dt>numClusters <span class="classifier-delimiter">:</span> <span class="classifier">int, optional</span></dt>
+<dd>Number of clusters for clustering. Sources are grouped around the
+numClusters brightest sources.</dd>
+<dt>applyBeam <span class="classifier-delimiter">:</span> <span class="classifier">bool, optional</span></dt>
+<dd>If True, fluxes will be attenuated by the beam.</dd>
+</dl>
+<p>Tesselate the sky model into patches with approximately 30 Jy total
+flux:</p>
+<div class="highlight-python"><div class="highlight"><pre><span class="gp">&gt;&gt;&gt; </span><span class="n">s</span><span class="o">.</span><span class="n">group</span><span class="p">(</span><span class="s">&#39;tessellate&#39;</span><span class="p">,</span> <span class="n">targetFlux</span><span class="o">=</span><span class="mf">30.0</span><span class="p">)</span>
+</pre></div>
+</div>
+</dd></dl>
+
+<dl class="method">
+<dt id="lsmtool.SkyModel.info">
+<tt class="descname">info</tt><big>(</big><big>)</big><a class="headerlink" href="#lsmtool.SkyModel.info" title="Permalink to this definition">¶</a></dt>
+<dd><p>Prints information about the sky model.</p>
+</dd></dl>
+
+<dl class="method">
+<dt id="lsmtool.SkyModel.merge">
+<tt class="descname">merge</tt><big>(</big><em>patches</em>, <em>name=None</em><big>)</big><a class="headerlink" href="#lsmtool.SkyModel.merge" title="Permalink to this definition">¶</a></dt>
+<dd><p>Merge two or more patches together</p>
+<dl class="docutils">
+<dt>patches <span class="classifier-delimiter">:</span> <span class="classifier">list of str</span></dt>
+<dd>List of patches to merge</dd>
+<dt>name <span class="classifier-delimiter">:</span> <span class="classifier">str, optional</span></dt>
+<dd>Name of resulting merged patch</dd>
+</dl>
+<p>Merge three patches into one:</p>
+<div class="highlight-python"><div class="highlight"><pre><span class="gp">&gt;&gt;&gt; </span><span class="n">s</span><span class="o">.</span><span class="n">merge</span><span class="p">([</span><span class="s">&#39;bin0&#39;</span><span class="p">,</span> <span class="s">&#39;bin1&#39;</span><span class="p">,</span> <span class="s">&#39;bin2&#39;</span><span class="p">],</span> <span class="s">&#39;binmerged&#39;</span><span class="p">)</span>
+</pre></div>
+</div>
+</dd></dl>
+
+<dl class="method">
+<dt id="lsmtool.SkyModel.more">
+<tt class="descname">more</tt><big>(</big><em>colName=None</em>, <em>patchName=None</em>, <em>sourceName=None</em>, <em>sortBy=None</em>, <em>lowToHigh=False</em><big>)</big><a class="headerlink" href="#lsmtool.SkyModel.more" title="Permalink to this definition">¶</a></dt>
+<dd><p>Prints the sky model table to the screen with more-like commands</p>
+<dl class="docutils">
+<dt>colName <span class="classifier-delimiter">:</span> <span class="classifier">str, list of str, optional</span></dt>
+<dd>Name of column or columns to print. If None, all columns are printed</dd>
+<dt>patchName <span class="classifier-delimiter">:</span> <span class="classifier">str, list of str, optional</span></dt>
+<dd>If given, returns column values for specified patch or patches only</dd>
+<dt>sourceName <span class="classifier-delimiter">:</span> <span class="classifier">str, list of str, optional</span></dt>
+<dd>If given, returns column value for specified source or sources only</dd>
+<dt>sortBy <span class="classifier-delimiter">:</span> <span class="classifier">str or list of str, optional</span></dt>
+<dd>Name of columns to sort on. If None, no sorting is done. If
+a list is given, sorting is done on the columns in the order given</dd>
+<dt>lowToHigh <span class="classifier-delimiter">:</span> <span class="classifier">bool, optional</span></dt>
+<dd>If True, sort values from low to high instead of high to low</dd>
+</dl>
+<p>Print the entire model:</p>
+<div class="highlight-python"><div class="highlight"><pre><span class="gp">&gt;&gt;&gt; </span><span class="n">s</span><span class="o">.</span><span class="n">more</span><span class="p">()</span>
+</pre></div>
+</div>
+<p>Print only the &#8216;Name&#8217; and &#8216;I&#8217; columns for the &#8216;bin0&#8217; patch:</p>
+<div class="highlight-python"><div class="highlight"><pre><span class="gp">&gt;&gt;&gt; </span><span class="n">s</span><span class="o">.</span><span class="n">more</span><span class="p">([</span><span class="s">&#39;Name&#39;</span><span class="p">,</span> <span class="s">&#39;I&#39;</span><span class="p">],</span> <span class="s">&#39;bin0&#39;</span><span class="p">,</span> <span class="n">sortBy</span><span class="o">=</span><span class="p">[</span><span class="s">&#39;I&#39;</span><span class="p">])</span>
+</pre></div>
+</div>
+</dd></dl>
+
+<dl class="method">
+<dt id="lsmtool.SkyModel.move">
+<tt class="descname">move</tt><big>(</big><em>name</em>, <em>position=None</em>, <em>shift=None</em><big>)</big><a class="headerlink" href="#lsmtool.SkyModel.move" title="Permalink to this definition">¶</a></dt>
+<dd><p>Move or shift a source.</p>
+<p>If both a position and a shift are specified, the source is moved to the
+new position and then shifted.</p>
+<dl class="docutils">
+<dt>name <span class="classifier-delimiter">:</span> <span class="classifier">str</span></dt>
+<dd>Source name.</dd>
+<dt>position <span class="classifier-delimiter">:</span> <span class="classifier">list, optional</span></dt>
+<dd>A list specifying a new position as [RA, Dec] in either makesourcedb
+format (e.g., [&#8216;12:23:43.21&#8217;, &#8216;+22.34.21.2&#8217;]) or in degrees (e.g.,
+[123.2312, 23.3422]).</dd>
+<dt>shift <span class="classifier-delimiter">:</span> <span class="classifier">list, optional</span></dt>
+<dd>A list specifying the shift as [RAShift, DecShift] in
+in degrees (e.g., [0.02312, 0.00342]).</dd>
+</dl>
+<p>Move source &#8216;1609.6+6556&#8217; to a new position:</p>
+<div class="highlight-python"><div class="highlight"><pre><span class="gp">&gt;&gt;&gt; </span><span class="n">s</span><span class="o">.</span><span class="n">move</span><span class="p">(</span><span class="s">&#39;1609.6+6556&#39;</span><span class="p">,</span> <span class="n">position</span><span class="o">=</span><span class="p">[</span><span class="s">&#39;16:10:00&#39;</span><span class="p">,</span> <span class="s">&#39;+65.57.00&#39;</span><span class="p">])</span>
+</pre></div>
+</div>
+<p>Shift the source by 10 arcsec in Dec:</p>
+<div class="highlight-python"><div class="highlight"><pre><span class="gp">&gt;&gt;&gt; </span><span class="n">s</span><span class="o">.</span><span class="n">move</span><span class="p">(</span><span class="s">&#39;1609.6+6556&#39;</span><span class="p">,</span> <span class="n">shift</span><span class="o">=</span><span class="p">[</span><span class="mf">0.0</span><span class="p">,</span> <span class="mf">10.0</span><span class="o">/</span><span class="mf">3600.0</span><span class="p">])</span>
+</pre></div>
+</div>
+</dd></dl>
+
+<dl class="method">
+<dt id="lsmtool.SkyModel.plot">
+<tt class="descname">plot</tt><big>(</big><em>fileName=None</em><big>)</big><a class="headerlink" href="#lsmtool.SkyModel.plot" title="Permalink to this definition">¶</a></dt>
+<dd><p>Shows a simple plot of the sky model.</p>
+<p>The circles in the plot are scaled with flux. If the sky model is grouped
+into patches, sources are colored by patch and the patch positions are
+indicated with stars.</p>
+<dl class="docutils">
+<dt>fileName <span class="classifier-delimiter">:</span> <span class="classifier">str, optional</span></dt>
+<dd>If given, the plot is saved to a file instead of displayed.</dd>
+</dl>
+<p>Plot and display to the screen:</p>
+<div class="highlight-python"><div class="highlight"><pre><span class="gp">&gt;&gt;&gt; </span><span class="n">s</span><span class="o">.</span><span class="n">plot</span><span class="p">()</span>
+</pre></div>
+</div>
+<p>Plot and save to a PDF file:</p>
+<div class="highlight-python"><div class="highlight"><pre><span class="gp">&gt;&gt;&gt; </span><span class="n">s</span><span class="o">.</span><span class="n">plot</span><span class="p">(</span><span class="s">&#39;sky_plot.pdf&#39;</span><span class="p">)</span>
+</pre></div>
+</div>
+</dd></dl>
+
+<dl class="method">
+<dt id="lsmtool.SkyModel.remove">
+<tt class="descname">remove</tt><big>(</big><em>filterExpression</em>, <em>aggregate=None</em>, <em>applyBeam=None</em>, <em>useRegEx=False</em>, <em>force=False</em><big>)</big><a class="headerlink" href="#lsmtool.SkyModel.remove" title="Permalink to this definition">¶</a></dt>
+<dd><p>Filters the sky model, removing all sources that meet the given expression.</p>
+<p>After filtering, the sky model contains only those sources for which the
+given filter expression is false.</p>
+<dl class="docutils">
+<dt>filterExpression <span class="classifier-delimiter">:</span> <span class="classifier">str or dict</span></dt>
+<dd><dl class="first docutils">
+<dt>A string specifying the filter expression in the form:</dt>
+<dd>&#8216;&lt;property&gt; &lt;operator&gt; &lt;value&gt; [&lt;units&gt;]&#8217;</dd>
+</dl>
+<p>(e.g., &#8216;I &lt;= 10.5 Jy&#8217;). These elements can also be given as a
+dictionary in the form:</p>
+<blockquote>
+<div><dl class="docutils">
+<dt>{&#8216;filterProp&#8217;:property, &#8216;filterOper&#8217;:operator,</dt>
+<dd>&#8216;filterVal&#8217;:value, &#8216;filterUnits&#8217;:units}</dd>
+</dl>
+</div></blockquote>
+<dl class="docutils">
+<dt>or as a list:</dt>
+<dd>[property, operator, value, value]</dd>
+</dl>
+<p>The property to filter on must be a valid column name or the filename
+of a mask image.</p>
+<dl class="docutils">
+<dt>Supported operators are:</dt>
+<dd><ul class="first last simple">
+<li>!=</li>
+<li>&lt;=</li>
+<li>&gt;=</li>
+<li>&gt;</li>
+<li>&lt;</li>
+<li>= (or &#8216;==&#8217;)</li>
+</ul>
+</dd>
+</dl>
+<p class="last">Units are optional and must be specified as required by astropy.units.</p>
+</dd>
+<dt>aggregate <span class="classifier-delimiter">:</span> <span class="classifier">str, optional</span></dt>
+<dd><p class="first">If set, the array returned will be of values aggregated
+over the patch members. The following aggregation functions are
+available:</p>
+<blockquote class="last">
+<div><ul>
+<li><p class="first">&#8216;sum&#8217;: sum of patch values</p>
+</li>
+<li><p class="first">&#8216;mean&#8217;: mean of patch values</p>
+</li>
+<li><p class="first">&#8216;wmean&#8217;: Stokes I weighted mean of patch values</p>
+</li>
+<li><p class="first">&#8216;min&#8217;: minimum of patch values</p>
+</li>
+<li><p class="first">&#8216;max&#8217;: maximum of patch values</p>
+</li>
+<li><dl class="first docutils">
+<dt>True: only valid when the filter indices are specified directly as</dt>
+<dd><p class="first last">a numpy array. If True, filtering is done on patches instead of
+sources.</p>
+</dd>
+</dl>
+</li>
+</ul>
+</div></blockquote>
+</dd>
+<dt>applyBeam <span class="classifier-delimiter">:</span> <span class="classifier">bool, optional</span></dt>
+<dd>If True, apparent fluxes will be used.</dd>
+<dt>useRegEx <span class="classifier-delimiter">:</span> <span class="classifier">bool, optional</span></dt>
+<dd>If True, string matching will use regular expression matching. If
+False, string matching uses Unix filename matching.</dd>
+</dl>
+<p>Filter on column &#8216;I&#8217; (Stokes I flux). This filter will remove all sources
+with Stokes I flux greater than 1.5 Jy:</p>
+<div class="highlight-python"><div class="highlight"><pre><span class="gp">&gt;&gt;&gt; </span><span class="n">s</span><span class="o">.</span><span class="n">remove</span><span class="p">(</span><span class="s">&#39;I &gt; 1.5 Jy&#39;</span><span class="p">)</span>
+<span class="go">INFO: Removed 1102 sources.</span>
+</pre></div>
+</div>
+<p>If the sky model has patches and the filter is desired per patch, use
+<tt class="docutils literal"><span class="pre">aggregate</span> <span class="pre">=</span> <span class="pre">function</span></tt>. For example, to select on the sum of the patch
+fluxes:</p>
+<div class="highlight-python"><div class="highlight"><pre><span class="gp">&gt;&gt;&gt; </span><span class="n">s</span><span class="o">.</span><span class="n">remove</span><span class="p">(</span><span class="s">&#39;I &gt; 1.5 Jy&#39;</span><span class="p">,</span> <span class="n">aggregate</span><span class="o">=</span><span class="s">&#39;sum&#39;</span><span class="p">)</span>
+</pre></div>
+</div>
+<p>Filter on source names, removing those that match &#8220;src*_1?&#8221;:</p>
+<div class="highlight-python"><div class="highlight"><pre><span class="gp">&gt;&gt;&gt; </span><span class="n">s</span><span class="o">.</span><span class="n">remove</span><span class="p">(</span><span class="s">&#39;Name == src*_1?&#39;</span><span class="p">)</span>
+</pre></div>
+</div>
+<p>Use a CASA clean mask image to remove sources that lie in masked regions:</p>
+<div class="highlight-python"><div class="highlight"><pre><span class="gp">&gt;&gt;&gt; </span><span class="n">s</span><span class="o">.</span><span class="n">remove</span><span class="p">(</span><span class="s">&#39;clean_mask.mask == True&#39;</span><span class="p">)</span>
+</pre></div>
+</div>
+</dd></dl>
+
+<dl class="method">
+<dt id="lsmtool.SkyModel.select">
+<tt class="descname">select</tt><big>(</big><em>filterExpression</em>, <em>aggregate=None</em>, <em>applyBeam=False</em>, <em>useRegEx=False</em>, <em>force=False</em><big>)</big><a class="headerlink" href="#lsmtool.SkyModel.select" title="Permalink to this definition">¶</a></dt>
+<dd><p>Filters the sky model, keeping all sources that meet the given expression.</p>
+<p>After filtering, the sky model contains only those sources for which the
+given filter expression is true.</p>
+<dl class="docutils">
+<dt>filterExpression <span class="classifier-delimiter">:</span> <span class="classifier">str or dict</span></dt>
+<dd><dl class="first docutils">
+<dt>A string specifying the filter expression in the form:</dt>
+<dd>&#8216;&lt;property&gt; &lt;operator&gt; &lt;value&gt; [&lt;units&gt;]&#8217;</dd>
+</dl>
+<p>(e.g., &#8216;I &lt;= 10.5 Jy&#8217;). These elements can also be given as a
+dictionary in the form:</p>
+<blockquote>
+<div><dl class="docutils">
+<dt>{&#8216;filterProp&#8217;:property, &#8216;filterOper&#8217;:operator,</dt>
+<dd>&#8216;filterVal&#8217;:value, &#8216;filterUnits&#8217;:units}</dd>
+</dl>
+</div></blockquote>
+<dl class="docutils">
+<dt>or as a list:</dt>
+<dd>[property, operator, value, value]</dd>
+</dl>
+<p>The property to filter on must be a valid column name or the filename
+of a mask image.</p>
+<dl class="docutils">
+<dt>Supported operators are:</dt>
+<dd><ul class="first last simple">
+<li>!=</li>
+<li>&lt;=</li>
+<li>&gt;=</li>
+<li>&gt;</li>
+<li>&lt;</li>
+<li>= (or &#8216;==&#8217;)</li>
+</ul>
+</dd>
+</dl>
+<p class="last">Units are optional and must be specified as required by astropy.units.</p>
+</dd>
+<dt>aggregate <span class="classifier-delimiter">:</span> <span class="classifier">str, optional</span></dt>
+<dd><p class="first">If set, the array returned will be of values aggregated
+over the patch members. The following aggregation functions are
+available:</p>
+<blockquote class="last">
+<div><ul>
+<li><p class="first">&#8216;sum&#8217;: sum of patch values</p>
+</li>
+<li><p class="first">&#8216;mean&#8217;: mean of patch values</p>
+</li>
+<li><p class="first">&#8216;wmean&#8217;: Stokes I weighted mean of patch values</p>
+</li>
+<li><p class="first">&#8216;min&#8217;: minimum of patch values</p>
+</li>
+<li><p class="first">&#8216;max&#8217;: maximum of patch values</p>
+</li>
+<li><dl class="first docutils">
+<dt>True: only valid when the filter indices are specify directly as</dt>
+<dd><p class="first last">a numpy array. If True, filtering is done on patches instead of
+sources.</p>
+</dd>
+</dl>
+</li>
+</ul>
+</div></blockquote>
+</dd>
+<dt>applyBeam <span class="classifier-delimiter">:</span> <span class="classifier">bool, optional</span></dt>
+<dd>If True, apparent fluxes will be used.</dd>
+<dt>useRegEx <span class="classifier-delimiter">:</span> <span class="classifier">bool, optional</span></dt>
+<dd>If True, string matching will use regular expression matching. If
+False, string matching uses Unix filename matching.</dd>
+</dl>
+<p>Filter on column &#8216;I&#8217; (Stokes I flux). This filter will select all sources
+with Stokes I flux greater than 1.5 Jy:</p>
+<div class="highlight-python"><div class="highlight"><pre><span class="gp">&gt;&gt;&gt; </span><span class="n">s</span><span class="o">.</span><span class="n">select</span><span class="p">(</span><span class="s">&#39;I &gt; 1.5 Jy&#39;</span><span class="p">)</span>
+<span class="go">INFO: Kept 1102 sources.</span>
+</pre></div>
+</div>
+<p>If the sky model has patches and the filter is desired per patch, use
+<tt class="docutils literal"><span class="pre">aggregate</span> <span class="pre">=</span> <span class="pre">function</span></tt>. For example, to select on the sum of the patch
+fluxes:</p>
+<div class="highlight-python"><div class="highlight"><pre><span class="gp">&gt;&gt;&gt; </span><span class="n">s</span><span class="o">.</span><span class="n">select</span><span class="p">(</span><span class="s">&#39;I &gt; 1.5 Jy&#39;</span><span class="p">,</span> <span class="n">aggregate</span><span class="o">=</span><span class="s">&#39;sum&#39;</span><span class="p">)</span>
+</pre></div>
+</div>
+<p>Filter on source names, keeping those that match &#8220;src*_1?&#8221;:</p>
+<div class="highlight-python"><div class="highlight"><pre><span class="gp">&gt;&gt;&gt; </span><span class="n">s</span><span class="o">.</span><span class="n">select</span><span class="p">(</span><span class="s">&#39;Name == src*_1?&#39;</span><span class="p">)</span>
+</pre></div>
+</div>
+<p>Use a CASA clean mask image to keep sources that lie in masked regions:</p>
+<div class="highlight-python"><div class="highlight"><pre><span class="gp">&gt;&gt;&gt; </span><span class="n">s</span><span class="o">.</span><span class="n">filter</span><span class="p">(</span><span class="s">&#39;clean_mask.mask == True&#39;</span><span class="p">)</span>
+</pre></div>
+</div>
+</dd></dl>
+
+<dl class="method">
+<dt id="lsmtool.SkyModel.setColValues">
+<tt class="descname">setColValues</tt><big>(</big><em>colName</em>, <em>values</em>, <em>mask=None</em>, <em>index=None</em><big>)</big><a class="headerlink" href="#lsmtool.SkyModel.setColValues" title="Permalink to this definition">¶</a></dt>
+<dd><p>Sets column values.</p>
+<dl class="docutils">
+<dt>colName <span class="classifier-delimiter">:</span> <span class="classifier">str</span></dt>
+<dd>Name of column. If not already present in the table, a new column
+will be created.</dd>
+<dt>values <span class="classifier-delimiter">:</span> <span class="classifier">list, numpy array, or dict</span></dt>
+<dd>Array of values or dict of {sourceName:value} pairs. If list or
+array, the length must match the number of rows in the table. If
+dict, missing values will be masked unless already present. Values
+are assumed to be in units required by makesourcedb.</dd>
+<dt>mask <span class="classifier-delimiter">:</span> <span class="classifier">list or array of bools, optional</span></dt>
+<dd>If values is a list or array, a mask can be specified (True means
+the value is masked).</dd>
+<dt>index <span class="classifier-delimiter">:</span> <span class="classifier">int, optional</span></dt>
+<dd>Index that specifies the column position in the table, if column is
+not already present in the table</dd>
+</dl>
+<p>Set Stokes I fluxes:</p>
+<div class="highlight-python"><div class="highlight"><pre><span class="gp">&gt;&gt;&gt; </span><span class="n">s</span><span class="o">.</span><span class="n">setColValues</span><span class="p">(</span><span class="s">&#39;I&#39;</span><span class="p">,</span> <span class="p">[</span><span class="mf">1.0</span><span class="p">,</span> <span class="mf">1.1</span><span class="p">,</span> <span class="mf">1.2</span><span class="p">,</span> <span class="mf">0.0</span><span class="p">,</span> <span class="mf">1.3</span><span class="p">],</span> <span class="n">mask</span><span class="o">=</span><span class="p">[</span><span class="bp">False</span><span class="p">,</span>
+<span class="go">        False, False, True, False])</span>
+</pre></div>
+</div>
+</dd></dl>
+
+<dl class="method">
+<dt id="lsmtool.SkyModel.setDefaltValues">
+<tt class="descname">setDefaltValues</tt><big>(</big><em>colDict</em><big>)</big><a class="headerlink" href="#lsmtool.SkyModel.setDefaltValues" title="Permalink to this definition">¶</a></dt>
+<dd><p>Sets default column values</p>
+<dl class="docutils">
+<dt>colDict <span class="classifier-delimiter">:</span> <span class="classifier">dict</span></dt>
+<dd>Dict specifying column names and default values as
+{&#8216;colName&#8217;:value} where the value is in the units accepted by
+makesourcedb (e.g., Hz for ReferenceFrequency).</dd>
+</dl>
+<p>Set new default value for ReferenceFrequency:</p>
+<div class="highlight-python"><div class="highlight"><pre><span class="gp">&gt;&gt;&gt; </span><span class="n">s</span><span class="o">.</span><span class="n">setDefaultValues</span><span class="p">({</span><span class="s">&#39;ReferenceFrequency&#39;</span><span class="p">:</span> <span class="mf">140e6</span><span class="p">})</span>
+</pre></div>
+</div>
+</dd></dl>
+
+<dl class="method">
+<dt id="lsmtool.SkyModel.setPatchPositions">
+<tt class="descname">setPatchPositions</tt><big>(</big><em>patchDict=None</em>, <em>method='mid'</em>, <em>applyBeam=False</em>, <em>perPatchProjection=True</em><big>)</big><a class="headerlink" href="#lsmtool.SkyModel.setPatchPositions" title="Permalink to this definition">¶</a></dt>
+<dd><p>Sets the patch positions.</p>
+<dl class="docutils">
+<dt>patchDict <span class="classifier-delimiter">:</span> <span class="classifier">dict</span></dt>
+<dd>Dict specifying patch names and positions as {&#8216;patchName&#8217;:[RA, Dec]}
+where both RA and Dec are degrees J2000 or in makesourcedb format.</dd>
+<dt>method <span class="classifier-delimiter">:</span> <span class="classifier">None or str, optional</span></dt>
+<dd><p class="first">If no patchDict is given, this parameter specifies the method used
+to set the patch positions:
+- &#8216;mid&#8217; =&gt; the position is set to the midpoint of the patch
+- &#8216;mean&#8217; =&gt; the positions is set to the mean RA and Dec of the patch
+- &#8216;wmean&#8217; =&gt; the position is set to the flux-weighted mean RA and</p>
+<blockquote>
+<div>Dec of the patch</div></blockquote>
+<ul class="simple">
+<li>&#8216;zero&#8217; =&gt; set all positions to [0.0, 0.0]</li>
+</ul>
+<p class="last">Note that the mid, mean, and wmean positions are calculated from TAN-
+projected values.</p>
+</dd>
+<dt>applyBeam <span class="classifier-delimiter">:</span> <span class="classifier">bool, optional</span></dt>
+<dd>If True, fluxes used as weights will be attenuated by the beam.</dd>
+<dt>perPatchProjection <span class="classifier-delimiter">:</span> <span class="classifier">bool, optional</span></dt>
+<dd>If True, a different projection center is used per patch. If False,
+a single projection center is used for all patches.</dd>
+</dl>
+<p>Set all patch positions to their (projected) midpoints:</p>
+<div class="highlight-python"><div class="highlight"><pre><span class="gp">&gt;&gt;&gt; </span><span class="n">s</span><span class="o">.</span><span class="n">setPatchPositions</span><span class="p">()</span>
+</pre></div>
+</div>
+<p>Set all patch positions to their (projected) flux-weighted mean
+positions:</p>
+<div class="highlight-python"><div class="highlight"><pre><span class="gp">&gt;&gt;&gt; </span><span class="n">s</span><span class="o">.</span><span class="n">setPatchPositions</span><span class="p">(</span><span class="n">method</span><span class="o">=</span><span class="s">&#39;wmean&#39;</span><span class="p">)</span>
+</pre></div>
+</div>
+<p>Set new position for the &#8216;bin0&#8217; patch only:</p>
+<div class="highlight-python"><div class="highlight"><pre><span class="gp">&gt;&gt;&gt; </span><span class="n">s</span><span class="o">.</span><span class="n">setPatchPositions</span><span class="p">({</span><span class="s">&#39;bin0&#39;</span><span class="p">:</span> <span class="p">[</span><span class="mf">123.231</span><span class="p">,</span> <span class="mf">23.4321</span><span class="p">]})</span>
+</pre></div>
+</div>
+</dd></dl>
+
+<dl class="method">
+<dt id="lsmtool.SkyModel.setRowValues">
+<tt class="descname">setRowValues</tt><big>(</big><em>values</em>, <em>mask=None</em><big>)</big><a class="headerlink" href="#lsmtool.SkyModel.setRowValues" title="Permalink to this definition">¶</a></dt>
+<dd><p>Sets values for a single row.</p>
+<dl class="docutils">
+<dt>values <span class="classifier-delimiter">:</span> <span class="classifier">list, numpy array, or dict</span></dt>
+<dd>Array of values or dict of {colName:value} pairs. If list or
+array, the length must match the number and order of the columns in
+the table. If dict, missing values will be masked unless already
+present.</dd>
+<dt>mask <span class="classifier-delimiter">:</span> <span class="classifier">list or array of bools, optional</span></dt>
+<dd>If values is a list or array, a mask can be specified (True means
+the value is masked).</dd>
+</dl>
+<p>Set row values for the source &#8216;src1&#8217;:</p>
+<div class="highlight-python"><div class="highlight"><pre><span class="gp">&gt;&gt;&gt; </span><span class="n">s</span><span class="o">.</span><span class="n">setRowValues</span><span class="p">({</span><span class="s">&#39;Name&#39;</span><span class="p">:</span><span class="s">&#39;src1&#39;</span><span class="p">,</span> <span class="s">&#39;Ra&#39;</span><span class="p">:</span><span class="mf">213.123</span><span class="p">,</span> <span class="s">&#39;Dec&#39;</span><span class="p">:</span><span class="mf">23.1232</span><span class="p">,</span>
+<span class="go">    &#39;I&#39;:23.2, &#39;Type&#39;:&#39;POINT&#39;}</span>
+</pre></div>
+</div>
+<p>The RA and Dec values can be in degrees (as above) or in makesourcedb
+format. E.g.:</p>
+<div class="highlight-python"><div class="highlight"><pre><span class="gp">&gt;&gt;&gt; </span><span class="n">s</span><span class="o">.</span><span class="n">setRowValues</span><span class="p">({</span><span class="s">&#39;Name&#39;</span><span class="p">:</span><span class="s">&#39;src1&#39;</span><span class="p">,</span> <span class="s">&#39;Ra&#39;</span><span class="p">:</span><span class="s">&#39;12:22:21.1&#39;</span><span class="p">,</span>
+<span class="go">    &#39;Dec&#39;:&#39;+14.46.31.5&#39;, &#39;I&#39;:23.2, &#39;Type&#39;:&#39;POINT&#39;}</span>
+</pre></div>
+</div>
+</dd></dl>
+
+<dl class="method">
+<dt id="lsmtool.SkyModel.transfer">
+<tt class="descname">transfer</tt><big>(</big><em>patchFile</em><big>)</big><a class="headerlink" href="#lsmtool.SkyModel.transfer" title="Permalink to this definition">¶</a></dt>
+<dd><p>Transfer patches from the input sky model.</p>
+<p>Sources with the same name as those in patchFile will be grouped into
+the patches defined in patchFile. Sources that do not appear in patchFile
+will be placed into separate patches (one per source). Patch positions are
+not transferred.</p>
+<dl class="docutils">
+<dt>patchFile <span class="classifier-delimiter">:</span> <span class="classifier">str</span></dt>
+<dd>Input sky model from which to transfer patches.</dd>
+</dl>
+<p>Transfer patches from one sky model to another and set their positions:</p>
+<div class="highlight-python"><div class="highlight"><pre><span class="gp">&gt;&gt;&gt; </span><span class="n">s</span><span class="o">.</span><span class="n">transfer</span><span class="p">(</span><span class="s">&#39;master_sky.model&#39;</span><span class="p">)</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">s</span><span class="o">.</span><span class="n">setPatchPositions</span><span class="p">(</span><span class="n">method</span><span class="o">=</span><span class="s">&#39;mid&#39;</span><span class="p">)</span>
+</pre></div>
+</div>
+</dd></dl>
+
+<dl class="method">
+<dt id="lsmtool.SkyModel.ungroup">
+<tt class="descname">ungroup</tt><big>(</big><big>)</big><a class="headerlink" href="#lsmtool.SkyModel.ungroup" title="Permalink to this definition">¶</a></dt>
+<dd><p>Removes all patches from the sky model.</p>
+<p>Remove all patches:</p>
+<div class="highlight-python"><div class="highlight"><pre><span class="gp">&gt;&gt;&gt; </span><span class="n">s</span><span class="o">.</span><span class="n">ungroup</span><span class="p">()</span>
+</pre></div>
+</div>
+</dd></dl>
+
+<dl class="method">
+<dt id="lsmtool.SkyModel.write">
+<tt class="descname">write</tt><big>(</big><em>fileName=None</em>, <em>format='makesourcedb'</em>, <em>clobber=False</em>, <em>sortBy=None</em>, <em>lowToHigh=False</em><big>)</big><a class="headerlink" href="#lsmtool.SkyModel.write" title="Permalink to this definition">¶</a></dt>
+<dd><p>Writes the sky model to a file.</p>
+<dl class="docutils">
+<dt>filename <span class="classifier-delimiter">:</span> <span class="classifier">str</span></dt>
+<dd>Name of output file.</dd>
+<dt>format: str, optional</dt>
+<dd><dl class="first last docutils">
+<dt>Format of the output file. Allowed formats are:</dt>
+<dd><ul class="first last simple">
+<li>&#8216;makesourcedb&#8217; (BBS format)</li>
+<li>&#8216;fits&#8217;</li>
+<li>&#8216;votable&#8217;</li>
+<li>&#8216;hdf5&#8217;</li>
+<li>&#8216;ds9&#8217;</li>
+<li>&#8216;kvis&#8217;</li>
+<li>plus all other formats supported by the astropy.table package</li>
+</ul>
+</dd>
+</dl>
+</dd>
+<dt>clobber <span class="classifier-delimiter">:</span> <span class="classifier">bool, optional</span></dt>
+<dd>If True, an existing file is overwritten.</dd>
+<dt>sortBy <span class="classifier-delimiter">:</span> <span class="classifier">str or list of str, optional</span></dt>
+<dd>Name of columns to sort on. If None, no sorting is done. If
+a list is given, sorting is done on the columns in the order given</dd>
+<dt>lowToHigh <span class="classifier-delimiter">:</span> <span class="classifier">bool, optional</span></dt>
+<dd>If True, sort values from low to high instead of high to low</dd>
+</dl>
+<p>Write the model to a makesourcedb sky model file suitable for use with
+BBS:</p>
+<div class="highlight-python"><div class="highlight"><pre><span class="gp">&gt;&gt;&gt; </span><span class="n">s</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">&#39;modsky.model&#39;</span><span class="p">)</span>
+</pre></div>
+</div>
+<p>Write to a fits catalog:</p>
+<div class="highlight-python"><div class="highlight"><pre><span class="gp">&gt;&gt;&gt; </span><span class="n">s</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">&#39;sky.fits&#39;</span><span class="p">,</span> <span class="n">format</span><span class="o">=</span><span class="s">&#39;fits&#39;</span><span class="p">)</span>
+</pre></div>
+</div>
+<p>Write to a ds9 region file:</p>
+<div class="highlight-python"><div class="highlight"><pre><span class="gp">&gt;&gt;&gt; </span><span class="n">s</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="s">&#39;sky.reg&#39;</span><span class="p">,</span> <span class="n">format</span><span class="o">=</span><span class="s">&#39;ds9&#39;</span><span class="p">)</span>
+</pre></div>
+</div>
+</dd></dl>
+
+</dd></dl>
+
+</div>
+
+
+          </div>
+        </div>
+      </div>
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diff --git a/doc/build/html/genindex.html b/doc/build/html/genindex.html
new file mode 100644
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--- /dev/null
+++ b/doc/build/html/genindex.html
@@ -0,0 +1,309 @@
+
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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+<html xmlns="http://www.w3.org/1999/xhtml">
+  <head>
+    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
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+             >modules</a> |</li>
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+    <div class="document">
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+        <div class="bodywrapper">
+          <div class="body">
+            
+
+<h1 id="index">Index</h1>
+
+<div class="genindex-jumpbox">
+ <a href="#A"><strong>A</strong></a>
+ | <a href="#C"><strong>C</strong></a>
+ | <a href="#G"><strong>G</strong></a>
+ | <a href="#I"><strong>I</strong></a>
+ | <a href="#L"><strong>L</strong></a>
+ | <a href="#M"><strong>M</strong></a>
+ | <a href="#P"><strong>P</strong></a>
+ | <a href="#R"><strong>R</strong></a>
+ | <a href="#S"><strong>S</strong></a>
+ | <a href="#T"><strong>T</strong></a>
+ | <a href="#U"><strong>U</strong></a>
+ | <a href="#W"><strong>W</strong></a>
+ 
+</div>
+<h2 id="A">A</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%" valign="top"><dl>
+      
+  <dt><a href="code.html#lsmtool.SkyModel.add">add() (lsmtool.SkyModel method)</a>
+  </dt>
+
+  </dl></td>
+</tr></table>
+
+<h2 id="C">C</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%" valign="top"><dl>
+      
+  <dt><a href="code.html#lsmtool.SkyModel.concatenate">concatenate() (lsmtool.SkyModel method)</a>
+  </dt>
+
+  </dl></td>
+  <td style="width: 33%" valign="top"><dl>
+      
+  <dt><a href="code.html#lsmtool.SkyModel.copy">copy() (lsmtool.SkyModel method)</a>
+  </dt>
+
+  </dl></td>
+</tr></table>
+
+<h2 id="G">G</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%" valign="top"><dl>
+      
+  <dt><a href="code.html#lsmtool.SkyModel.getColNames">getColNames() (lsmtool.SkyModel method)</a>
+  </dt>
+
+      
+  <dt><a href="code.html#lsmtool.SkyModel.getColValues">getColValues() (lsmtool.SkyModel method)</a>
+  </dt>
+
+      
+  <dt><a href="code.html#lsmtool.SkyModel.getDefaltValues">getDefaltValues() (lsmtool.SkyModel method)</a>
+  </dt>
+
+      
+  <dt><a href="code.html#lsmtool.SkyModel.getPatchNames">getPatchNames() (lsmtool.SkyModel method)</a>
+  </dt>
+
+      
+  <dt><a href="code.html#lsmtool.SkyModel.getPatchPositions">getPatchPositions() (lsmtool.SkyModel method)</a>
+  </dt>
+
+  </dl></td>
+  <td style="width: 33%" valign="top"><dl>
+      
+  <dt><a href="code.html#lsmtool.SkyModel.getPatchSizes">getPatchSizes() (lsmtool.SkyModel method)</a>
+  </dt>
+
+      
+  <dt><a href="code.html#lsmtool.SkyModel.getRowIndex">getRowIndex() (lsmtool.SkyModel method)</a>
+  </dt>
+
+      
+  <dt><a href="code.html#lsmtool.SkyModel.getRowValues">getRowValues() (lsmtool.SkyModel method)</a>
+  </dt>
+
+      
+  <dt><a href="code.html#lsmtool.SkyModel.group">group() (lsmtool.SkyModel method)</a>
+  </dt>
+
+  </dl></td>
+</tr></table>
+
+<h2 id="I">I</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%" valign="top"><dl>
+      
+  <dt><a href="code.html#lsmtool.SkyModel.info">info() (lsmtool.SkyModel method)</a>
+  </dt>
+
+  </dl></td>
+</tr></table>
+
+<h2 id="L">L</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%" valign="top"><dl>
+      
+  <dt><a href="code.html#lsmtool.load">load() (in module lsmtool)</a>
+  </dt>
+
+  </dl></td>
+  <td style="width: 33%" valign="top"><dl>
+      
+  <dt><a href="code.html#module-lsmtool">lsmtool (module)</a>
+  </dt>
+
+  </dl></td>
+</tr></table>
+
+<h2 id="M">M</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%" valign="top"><dl>
+      
+  <dt><a href="code.html#lsmtool.SkyModel.merge">merge() (lsmtool.SkyModel method)</a>
+  </dt>
+
+      
+  <dt><a href="code.html#lsmtool.SkyModel.more">more() (lsmtool.SkyModel method)</a>
+  </dt>
+
+  </dl></td>
+  <td style="width: 33%" valign="top"><dl>
+      
+  <dt><a href="code.html#lsmtool.SkyModel.move">move() (lsmtool.SkyModel method)</a>
+  </dt>
+
+  </dl></td>
+</tr></table>
+
+<h2 id="P">P</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%" valign="top"><dl>
+      
+  <dt><a href="code.html#lsmtool.SkyModel.plot">plot() (lsmtool.SkyModel method)</a>
+  </dt>
+
+  </dl></td>
+</tr></table>
+
+<h2 id="R">R</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%" valign="top"><dl>
+      
+  <dt><a href="code.html#lsmtool.SkyModel.remove">remove() (lsmtool.SkyModel method)</a>
+  </dt>
+
+  </dl></td>
+</tr></table>
+
+<h2 id="S">S</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%" valign="top"><dl>
+      
+  <dt><a href="code.html#lsmtool.SkyModel.select">select() (lsmtool.SkyModel method)</a>
+  </dt>
+
+      
+  <dt><a href="code.html#lsmtool.SkyModel.setColValues">setColValues() (lsmtool.SkyModel method)</a>
+  </dt>
+
+      
+  <dt><a href="code.html#lsmtool.SkyModel.setDefaltValues">setDefaltValues() (lsmtool.SkyModel method)</a>
+  </dt>
+
+  </dl></td>
+  <td style="width: 33%" valign="top"><dl>
+      
+  <dt><a href="code.html#lsmtool.SkyModel.setPatchPositions">setPatchPositions() (lsmtool.SkyModel method)</a>
+  </dt>
+
+      
+  <dt><a href="code.html#lsmtool.SkyModel.setRowValues">setRowValues() (lsmtool.SkyModel method)</a>
+  </dt>
+
+      
+  <dt><a href="code.html#lsmtool.SkyModel">SkyModel (class in lsmtool)</a>
+  </dt>
+
+  </dl></td>
+</tr></table>
+
+<h2 id="T">T</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%" valign="top"><dl>
+      
+  <dt><a href="code.html#lsmtool.SkyModel.transfer">transfer() (lsmtool.SkyModel method)</a>
+  </dt>
+
+  </dl></td>
+</tr></table>
+
+<h2 id="U">U</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%" valign="top"><dl>
+      
+  <dt><a href="code.html#lsmtool.SkyModel.ungroup">ungroup() (lsmtool.SkyModel method)</a>
+  </dt>
+
+  </dl></td>
+</tr></table>
+
+<h2 id="W">W</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%" valign="top"><dl>
+      
+  <dt><a href="code.html#lsmtool.SkyModel.write">write() (lsmtool.SkyModel method)</a>
+  </dt>
+
+  </dl></td>
+</tr></table>
+
+
+
+          </div>
+        </div>
+      </div>
+      <div class="sphinxsidebar">
+        <div class="sphinxsidebarwrapper">
+
+   
+
+<div id="searchbox" style="display: none">
+  <h3>Quick search</h3>
+    <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>
+    <p class="searchtip" style="font-size: 90%">
+    Enter search terms or a module, class or function name.
+    </p>
+</div>
+<script type="text/javascript">$('#searchbox').show(0);</script>
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+          <a href="py-modindex.html" title="Python Module Index"
+             >modules</a> |</li>
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+      </ul>
+    </div>
+    <div class="footer">
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+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.1.
+    </div>
+  </body>
+</html>
\ No newline at end of file
diff --git a/doc/build/html/index.html b/doc/build/html/index.html
new file mode 100644
index 0000000000000000000000000000000000000000..388d62c7ac2f62ef447e2550ff1854c96c91254e
--- /dev/null
+++ b/doc/build/html/index.html
@@ -0,0 +1,121 @@
+<!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">
+  <head>
+    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+    
+    <title>Welcome to LSMTool’s documentation! &mdash; LSMTool 1.0.0 documentation</title>
+    
+    <link rel="stylesheet" href="_static/default.css" type="text/css" />
+    <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
+    
+    <script type="text/javascript">
+      var DOCUMENTATION_OPTIONS = {
+        URL_ROOT:    './',
+        VERSION:     '1.0.0',
+        COLLAPSE_INDEX: false,
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+        HAS_SOURCE:  true
+      };
+    </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="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+    <link rel="top" title="LSMTool 1.0.0 documentation" href="#" /> 
+  </head>
+  <body>
+    <div class="related">
+      <h3>Navigation</h3>
+      <ul>
+        <li class="right" style="margin-right: 10px">
+          <a href="genindex.html" title="General Index"
+             accesskey="I">index</a></li>
+        <li class="right" >
+          <a href="py-modindex.html" title="Python Module Index"
+             >modules</a> |</li>
+        <li><a href="#">LSMTool 1.0.0 documentation</a> &raquo;</li> 
+      </ul>
+    </div>  
+
+    <div class="document">
+      <div class="documentwrapper">
+        <div class="bodywrapper">
+          <div class="body">
+            
+  <div class="section" id="welcome-to-lsmtool-s-documentation">
+<h1>Welcome to LSMTool&#8217;s documentation!<a class="headerlink" href="#welcome-to-lsmtool-s-documentation" title="Permalink to this headline">¶</a></h1>
+<p>LSMTool is a Python package which allow the manipulation of sky models in the <tt class="docutils literal"><span class="pre">makesourcedb</span></tt> format understood by BBS. Note that LSMTool is still in beta. Please report bugs to <tt class="docutils literal"><span class="pre">drafferty&#64;hs.uni-hamburg.de</span></tt>. To initialize your environment for LSMTool, users on CEP1 and CEP2 should run the following commands:</p>
+<div class="highlight-python"><div class="highlight"><pre>use LofIm
+source ~rafferty/init_lsmtool
+</pre></div>
+</div>
+<p>Note that the Pythonlibs LOFAR package includes an older version of astropy that conflicts with LSMTool and cannot be used in conjunction with it.</p>
+<div class="toctree-wrapper compound">
+<ul class="simple">
+</ul>
+</div>
+</div>
+<div class="section" id="indices-and-tables">
+<h1>Indices and tables<a class="headerlink" href="#indices-and-tables" title="Permalink to this headline">¶</a></h1>
+<ul class="simple">
+<li><a class="reference internal" href="genindex.html"><em>Index</em></a></li>
+<li><a class="reference internal" href="py-modindex.html"><em>Module Index</em></a></li>
+<li><a class="reference internal" href="search.html"><em>Search Page</em></a></li>
+</ul>
+</div>
+
+
+          </div>
+        </div>
+      </div>
+      <div class="sphinxsidebar">
+        <div class="sphinxsidebarwrapper">
+  <h3><a href="#">Table Of Contents</a></h3>
+  <ul>
+<li><a class="reference internal" href="#">Welcome to LSMTool&#8217;s documentation!</a></li>
+<li><a class="reference internal" href="#indices-and-tables">Indices and tables</a></li>
+</ul>
+
+  <h3>This Page</h3>
+  <ul class="this-page-menu">
+    <li><a href="_sources/index.txt"
+           rel="nofollow">Show Source</a></li>
+  </ul>
+<div id="searchbox" style="display: none">
+  <h3>Quick search</h3>
+    <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>
+    <p class="searchtip" style="font-size: 90%">
+    Enter search terms or a module, class or function name.
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+<script type="text/javascript">$('#searchbox').show(0);</script>
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+    </div>
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+      <h3>Navigation</h3>
+      <ul>
+        <li class="right" style="margin-right: 10px">
+          <a href="genindex.html" title="General Index"
+             >index</a></li>
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+          <a href="py-modindex.html" title="Python Module Index"
+             >modules</a> |</li>
+        <li><a href="#">LSMTool 1.0.0 documentation</a> &raquo;</li> 
+      </ul>
+    </div>
+    <div class="footer">
+        &copy; Copyright 2014, David Rafferty.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.1.
+    </div>
+  </body>
+</html>
\ No newline at end of file
diff --git a/doc/build/html/objects.inv b/doc/build/html/objects.inv
new file mode 100644
index 0000000000000000000000000000000000000000..d62ac62bc30952b92ac08587bfd7950735c42d52
Binary files /dev/null and b/doc/build/html/objects.inv differ
diff --git a/doc/build/html/py-modindex.html b/doc/build/html/py-modindex.html
new file mode 100644
index 0000000000000000000000000000000000000000..ca56c3e665858e43da511275189366b7c7a994e3
--- /dev/null
+++ b/doc/build/html/py-modindex.html
@@ -0,0 +1,113 @@
+<!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">
+  <head>
+    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+    
+    <title>Python Module Index &mdash; LSMTool 1.0.0 documentation</title>
+    
+    <link rel="stylesheet" href="_static/default.css" type="text/css" />
+    <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
+    
+    <script type="text/javascript">
+      var DOCUMENTATION_OPTIONS = {
+        URL_ROOT:    './',
+        VERSION:     '1.0.0',
+        COLLAPSE_INDEX: false,
+        FILE_SUFFIX: '.html',
+        HAS_SOURCE:  true
+      };
+    </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="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+    <link rel="top" title="LSMTool 1.0.0 documentation" href="index.html" />
+ 
+
+    <script type="text/javascript">
+      DOCUMENTATION_OPTIONS.COLLAPSE_INDEX = true;
+    </script>
+
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+  </head>
+  <body>
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+      <h3>Navigation</h3>
+      <ul>
+        <li class="right" style="margin-right: 10px">
+          <a href="genindex.html" title="General Index"
+             accesskey="I">index</a></li>
+        <li class="right" >
+          <a href="#" title="Python Module Index"
+             >modules</a> |</li>
+        <li><a href="index.html">LSMTool 1.0.0 documentation</a> &raquo;</li> 
+      </ul>
+    </div>  
+
+    <div class="document">
+      <div class="documentwrapper">
+        <div class="bodywrapper">
+          <div class="body">
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+
+   <h1>Python Module Index</h1>
+
+   <div class="modindex-jumpbox">
+   <a href="#cap-l"><strong>l</strong></a>
+   </div>
+
+   <table class="indextable modindextable" cellspacing="0" cellpadding="2">
+     <tr class="pcap"><td></td><td>&nbsp;</td><td></td></tr>
+     <tr class="cap" id="cap-l"><td></td><td>
+       <strong>l</strong></td><td></td></tr>
+     <tr>
+       <td></td>
+       <td>
+       <a href="code.html#module-lsmtool"><tt class="xref">lsmtool</tt></a></td><td>
+       <em></em></td></tr>
+   </table>
+
+
+          </div>
+        </div>
+      </div>
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+        <div class="sphinxsidebarwrapper">
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+  <h3>Quick search</h3>
+    <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" />
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+    </form>
+    <p class="searchtip" style="font-size: 90%">
+    Enter search terms or a module, class or function name.
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+        <li class="right" style="margin-right: 10px">
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+             >index</a></li>
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+          <a href="#" title="Python Module Index"
+             >modules</a> |</li>
+        <li><a href="index.html">LSMTool 1.0.0 documentation</a> &raquo;</li> 
+      </ul>
+    </div>
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+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.1.
+    </div>
+  </body>
+</html>
\ No newline at end of file
diff --git a/doc/build/html/search.html b/doc/build/html/search.html
new file mode 100644
index 0000000000000000000000000000000000000000..205dacb20f266e38784a4eee220c313e88af17dd
--- /dev/null
+++ b/doc/build/html/search.html
@@ -0,0 +1,106 @@
+<!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">
+  <head>
+    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+    
+    <title>Search &mdash; LSMTool 1.0.0 documentation</title>
+    
+    <link rel="stylesheet" href="_static/default.css" type="text/css" />
+    <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
+    
+    <script type="text/javascript">
+      var DOCUMENTATION_OPTIONS = {
+        URL_ROOT:    './',
+        VERSION:     '1.0.0',
+        COLLAPSE_INDEX: false,
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+      };
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+    <script type="text/javascript" src="_static/jquery.js"></script>
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+    <script type="text/javascript" src="_static/searchtools.js"></script>
+    <link rel="top" title="LSMTool 1.0.0 documentation" href="index.html" />
+  <script type="text/javascript">
+    jQuery(function() { Search.loadIndex("searchindex.js"); });
+  </script>
+  
+  <script type="text/javascript" id="searchindexloader"></script>
+   
+
+  </head>
+  <body>
+    <div class="related">
+      <h3>Navigation</h3>
+      <ul>
+        <li class="right" style="margin-right: 10px">
+          <a href="genindex.html" title="General Index"
+             accesskey="I">index</a></li>
+        <li class="right" >
+          <a href="py-modindex.html" title="Python Module Index"
+             >modules</a> |</li>
+        <li><a href="index.html">LSMTool 1.0.0 documentation</a> &raquo;</li> 
+      </ul>
+    </div>  
+
+    <div class="document">
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+        <div class="bodywrapper">
+          <div class="body">
+            
+  <h1 id="search-documentation">Search</h1>
+  <div id="fallback" class="admonition warning">
+  <script type="text/javascript">$('#fallback').hide();</script>
+  <p>
+    Please activate JavaScript to enable the search
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+  </div>
+  <p>
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+          <a href="py-modindex.html" title="Python Module Index"
+             >modules</a> |</li>
+        <li><a href="index.html">LSMTool 1.0.0 documentation</a> &raquo;</li> 
+      </ul>
+    </div>
+    <div class="footer">
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+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.1.
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\ No newline at end of file
diff --git a/doc/build/html/searchindex.js b/doc/build/html/searchindex.js
new file mode 100644
index 0000000000000000000000000000000000000000..f5238d145a4b7b7722306d52f3120709bafaf354
--- /dev/null
+++ b/doc/build/html/searchindex.js
@@ -0,0 +1 @@
+Search.setIndex({envversion:42,terms:{all:1,per:1,follow:[0,1],row:1,arcsec:1,lsm2:1,present:1,sourc:[0,1],everi:1,string:1,fals:1,print:1,appar:1,strang:1,list:1,pleas:0,second:1,aggreg:1,index:[0,1],appear:1,sum:1,access:1,version:0,"new":1,method:1,whose:1,valu:1,convert:1,hdf5:1,shift:1,within:1,clean_mask:1,appli:1,approxim:1,"140e6":1,filenam:1,unix:1,src1:1,total:1,select:1,plot:1,from:1,two:1,type:1,patchdict:1,sort:1,desir:1,must:1,none:1,can:1,meet:1,dec:1,deg:1,give:1,colnamesv:1,accept:1,high:1,minimum:1,tan:1,anoth:1,write:1,how:1,low:1,makesourcedb:[0,1],tile:1,verifi:1,simpl:1,bin0:1,bin2:1,lowtohigh:1,astropi:[0,1],max:1,getcolvalu:1,after:1,befor:1,catalog:1,plane:1,attenu:1,mai:1,coldict:1,averag:1,element:1,inform:1,environ:0,allow:[0,1],order:1,over:1,move:1,filterv:1,rashift:1,still:0,paramet:1,conjunct:0,group:1,fit:1,might:1,them:1,good:1,"return":1,greater:1,python:0,initi:0,instead:1,name:1,bin1:1,separ:1,each:1,found:1,mean:1,weight:1,replac:1,content:[],suitabl:1,high_res_ski:1,asarrai:1,numclust:1,reg:1,rownam:1,manipul:0,midpoint:1,given:1,brightest:1,dictionari:1,ask:1,ds9:1,angl:1,checkdup:1,keep:1,filter:1,length:1,place:1,filterop:1,outsid:1,onto:1,oper:1,directli:1,arrai:1,number:1,alreadi:1,setrowvalu:1,patchnam:1,miss:1,primari:1,size:1,differ:1,sb100:1,tot:1,skymodel:1,circl:1,colnam:1,store:1,includ:0,option:1,filterunit:1,copi:1,specifi:1,targetflux:1,part:1,from1:1,from2:1,than:1,center:1,target:1,provid:1,remov:1,zero:1,project:1,str:1,posit:1,ani:1,packag:[0,1],votabl:1,have:1,need:1,getdefaltvalu:1,lie:1,min:1,mid:1,note:[0,1],also:1,which:[0,1],singl:1,sky_plot:1,unless:1,cep1:0,cep2:0,object:1,setdefaltvalu:1,beta:0,regular:1,referencefrequ:1,pair:1,"class":1,useregex:1,mjy:1,determin:1,show:1,radiu:1,current:1,onli:1,should:0,dict:1,getcolnam:1,overwritten:1,lsm:1,get:1,express:1,beam:1,getpatchposit:1,cannot:0,beamm:1,report:0,requir:1,rafferti:0,intrins:1,patch:1,contain:1,where:1,set:1,maximum:1,result:1,close:1,"import":1,getpatchnam:1,parent:1,filterexpress:1,screen:1,entir:1,pythonlib:0,addit:1,both:1,region:1,getpatchs:1,pdf:1,load:1,point:1,color:1,pole:1,respect:1,assum:1,duplic:1,addition:1,numpi:1,three:1,treat:1,ungroup:1,imag:1,resolut:1,search:0,togeth:1,hamburg:0,those:1,"case":1,ident:1,casa:1,properti:1,defin:1,calcul:1,abov:1,cluster:1,setcolvalu:1,ascii:1,same:1,member:1,conflict:0,user:0,uni:0,appropri:1,kept:1,sortbi:1,older:0,clobber:1,exampl:1,command:[0,1],thi:1,getrowvalu:1,decshift:1,gsm:1,identifi:1,wmean:1,except:1,setdefaultvalu:1,add:1,valid:1,input:1,save:1,modul:0,match:1,drafferti:0,around:1,format:[0,1],read:1,filterprop:1,measur:1,like:1,flux:1,either:1,output:1,page:0,sagec:1,some:1,understood:0,binmerg:1,scale:1,getrowindex:1,overlap:1,estim:1,unit:1,plu:1,run:0,perpatchproject:1,src:1,about:1,column:1,degre:1,done:1,discard:1,produc:1,own:1,consid:1,"float":1,your:0,merg:1,transfer:1,support:1,avail:1,modski:1,"function":1,form:1,forc:1,majoraxi:1,"true":1,bug:0,info:1,concaten:1,j2000:1,"default":1,displai:1,init_lsmtool:0,more:1,lofim:0,creat:1,patchfil:1,"int":1,certain:1,exist:1,file:1,matchbi:1,ind:1,when:1,setpatchposit:1,other:1,bool:1,applybeam:1,star:1,clean:1,kvi:1,meaning:1,tessel:1,stoke:1,master_ski:1,sourcenam:1,algorithm:1,mask:1,gsm_sky2:1},objtypes:{"0":"py:module","1":"py:method","2":"py:function","3":"py:class"},objnames:{"0":["py","module","Python module"],"1":["py","method","Python method"],"2":["py","function","Python function"],"3":["py","class","Python class"]},filenames:["index","code"],titles:["Welcome to LSMTool&#8217;s documentation!","LSMTool: the LOFAR Local Sky Model Tool"],objects:{"":{lsmtool:[1,0,0,"-"]},lsmtool:{load:[1,2,1,""],SkyModel:[1,3,1,""]},"lsmtool.SkyModel":{setRowValues:[1,1,1,""],setPatchPositions:[1,1,1,""],getPatchNames:[1,1,1,""],select:[1,1,1,""],move:[1,1,1,""],plot:[1,1,1,""],group:[1,1,1,""],getColNames:[1,1,1,""],getRowValues:[1,1,1,""],getRowIndex:[1,1,1,""],transfer:[1,1,1,""],setDefaltValues:[1,1,1,""],write:[1,1,1,""],add:[1,1,1,""],ungroup:[1,1,1,""],more:[1,1,1,""],concatenate:[1,1,1,""],getDefaltValues:[1,1,1,""],getPatchPositions:[1,1,1,""],getPatchSizes:[1,1,1,""],getColValues:[1,1,1,""],copy:[1,1,1,""],info:[1,1,1,""],setColValues:[1,1,1,""],remove:[1,1,1,""],merge:[1,1,1,""]}},titleterms:{lsmtool:[0,1],welcom:0,tool:1,lofar:1,sky:1,indic:0,tabl:0,model:1,document:0,local:1}})
\ No newline at end of file
diff --git a/doc/lsmtool.pdf b/doc/lsmtool.pdf
index f917b2dd2fa7c77c46d60896382183125e2cf37d..f34b3350219b8a434fdbcc39c8505e8f3e8395c4 100644
Binary files a/doc/lsmtool.pdf and b/doc/lsmtool.pdf differ
diff --git a/doc/lsmtool.tex b/doc/lsmtool.tex
index dacb8bd65170dec8e6225cd0968d25ef7d3c5fda..62eee53732b3bf25bd88c6e4e3c4356d031aea8f 100644
--- a/doc/lsmtool.tex
+++ b/doc/lsmtool.tex
@@ -75,7 +75,7 @@ These are the operations that LSMTool can perform:
 
 This is an example parset that filters on the flux, adds a source, and then groups the sources into patches:
 \begin{verbatim}
-LSMTool.Steps = [selectbright, addsrc, grp]
+LSMTool.Steps = [selectbright, addsrc, grp, setpos]
 
 # Select only sources above 1 mJy
 LSMTool.Steps.selectbright.Operation = SELECT
@@ -89,16 +89,18 @@ LSMTool.Steps.addsrc.Dec = 48.3689
 LSMTool.Steps.addsrc.I = 0.69
 
 # Group using tessellation to a target flux of 50 Jy
-# and write final skymodel
 LSMTool.Steps.grp.Operation = GROUP
 LSMTool.Steps.grp.Algorithm = tessellate
 LSMTool.Steps.grp.TargetFlux = 50.0 Jy
 LSMTool.Steps.grp.Method = mid
-LSMTool.Steps.grp.Outfile = 'grouped.sky'
+
+# Set the patch positions to their midpoint and write final skymodel
+LSMTool.Steps.setpos.Method = mid
+LSMTool.Steps.setpos.Outfile = grouped.sky
 \end{verbatim}
 
 In the first line of this parset the step names are defined. In the next sections, the
-step parameters for every step are defined. A list of step-specific parameters is given in Table~\ref{lsmtool:tab:local_val}.
+step parameters for every step are defined. Steps are applied sequentially, in the same order defined in the list of steps. A list of step-specific parameters is given in Table~\ref{lsmtool:tab:local_val}.
 
 \begin{table}[!ht]
 \centering
@@ -135,8 +137,8 @@ Shift & list of floats & [0.001, 0.0] & RA and Dec in degrees to shift by\\
 Patches & list of strings & [bin1, bin2, bin3] & Patch names to merge\\
 Name & string & merged\_patch & Name of new merged patch\\
 \hline
-\multicolumn{4}{l}{\textbf{SETPOSITIONS}}\\
-Method & string & mid & Set patch positions by mid, mean, or wmean\\
+\multicolumn{4}{l}{\textbf{SETPATCHPOSITIONS}}\\
+Method & string & mid & Set patch positions to mid, mean, or wmean positions\\
 \hline
 \multicolumn{4}{l}{\textbf{CONCATENATE}}\\
 Skymodel2 & string & in\_sky\_model2.sky & Name of second sky model to concatenate\\
@@ -175,11 +177,12 @@ All of the operations described in Section~\ref{lsmtool:operations} are availabl
 \begin{verbatim}
 >>> LSM.select('I > 1.0 mJy')
 >>> LSM.add({'Name':'new_source', 'Type':'POINT', 'Ra':277.4232, 'Dec':48.3689, 'I':0.69})
->>> LSM.group(algorithm='tesselate', targetFlux='10.0 Jy', method='mid')
+>>> LSM.group(algorithm='tesselate', targetFlux='10.0 Jy')
+>>> LSM.setPatchPositions(method='mid')
 \end{verbatim}
 In many cases, the methods accept parameters with the same names as those used in a parset (see the full documentation for details). The sky model can then written to a new file with:
 \begin{verbatim}
->>> LSM.write('outskymodel.sky')
+>>> LSM.write('grouped.sky')
 \end{verbatim}
 Additionally, sky models can be written out as ds9 region files and kvis annotation files (as well as all the formats supported by the astropy.table package, such at VOTable, HDF5, and FITS):
 \begin{verbatim}
@@ -190,8 +193,7 @@ Additionally, sky models can be written out as ds9 region files and kvis annotat
 >>> LSM.write('outskymodel.vo', format='votable')
 \end{verbatim}
 
-
-In addition, a number of other methods are available:
+In addition to the operations described above, a number of other methods are available:
 \begin{description}
  \item[LSM.copy()]: Return a copy of the sky model object
  \item[LSM.info()]: Print information about the sky model
@@ -203,7 +205,6 @@ In addition, a number of other methods are available:
  \item[LSM.getPatchPositions()]: Returns patch RA and Dec values
  \item[LSM.getDefaltValues()]: Returns column default values
  \item[LSM.getPatchSizes()]: Returns an array of patch sizes
- \item[LSM.setPatchPositions()]: Set patch positions
  \item[LSM.setColValues()]: Sets column values
  \item[LSM.setRowValues()]: Sets row values
  \item[LSM.setDefaultValues()]: Sets default column values
diff --git a/doc/source/.DS_Store b/doc/source/.DS_Store
new file mode 100644
index 0000000000000000000000000000000000000000..5008ddfcf53c02e82d7eee2e57c38e5672ef89f6
Binary files /dev/null and b/doc/source/.DS_Store differ
diff --git a/doc/source/code.rst b/doc/source/code.rst
new file mode 100644
index 0000000000000000000000000000000000000000..d184c03adb17c0c890f8333941539f66e6e55b10
--- /dev/null
+++ b/doc/source/code.rst
@@ -0,0 +1,7 @@
+LSMTool: the LOFAR Local Sky Model Tool
+***************************************
+
+.. automodule:: lsmtool
+    :members:
+.. autoclass:: SkyModel
+    :members:
diff --git a/doc/source/conf.py b/doc/source/conf.py
new file mode 100644
index 0000000000000000000000000000000000000000..6553401d659cce99ea491a1812d48e81135d6732
--- /dev/null
+++ b/doc/source/conf.py
@@ -0,0 +1,267 @@
+# -*- coding: utf-8 -*-
+#
+# LSMTool documentation build configuration file, created by
+# sphinx-quickstart on Thu Jun 19 17:05:13 2014.
+#
+# This file is execfile()d with the current directory set to its
+# containing dir.
+#
+# Note that not all possible configuration values are present in this
+# autogenerated file.
+#
+# All configuration values have a default; values that are commented out
+# serve to show the default.
+
+import sys
+import os
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#sys.path.insert(0, os.path.abspath('.'))
+
+# -- General configuration ------------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+#needs_sphinx = '1.0'
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+    'sphinx.ext.autodoc',
+    'sphinx.ext.doctest',
+    'sphinx.ext.intersphinx',
+    'sphinx.ext.mathjax',
+]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# The suffix of source filenames.
+source_suffix = '.rst'
+
+# The encoding of source files.
+#source_encoding = 'utf-8-sig'
+
+# The master toctree document.
+master_doc = 'index'
+
+# General information about the project.
+project = u'LSMTool'
+copyright = u'2014, David Rafferty'
+
+# The version info for the project you're documenting, acts as replacement for
+# |version| and |release|, also used in various other places throughout the
+# built documents.
+#
+# The short X.Y version.
+version = '1.0.0'
+# The full version, including alpha/beta/rc tags.
+release = '1.0.0'
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#language = None
+
+# There are two options for replacing |today|: either, you set today to some
+# non-false value, then it is used:
+#today = ''
+# Else, today_fmt is used as the format for a strftime call.
+#today_fmt = '%B %d, %Y'
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+exclude_patterns = []
+
+# The reST default role (used for this markup: `text`) to use for all
+# documents.
+#default_role = None
+
+# If true, '()' will be appended to :func: etc. cross-reference text.
+#add_function_parentheses = True
+
+# If true, the current module name will be prepended to all description
+# unit titles (such as .. function::).
+#add_module_names = True
+
+# If true, sectionauthor and moduleauthor directives will be shown in the
+# output. They are ignored by default.
+#show_authors = False
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
+# A list of ignored prefixes for module index sorting.
+#modindex_common_prefix = []
+
+# If true, keep warnings as "system message" paragraphs in the built documents.
+#keep_warnings = False
+
+
+# -- Options for HTML output ----------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+html_theme = 'default'
+
+# Theme options are theme-specific and customize the look and feel of a theme
+# further.  For a list of options available for each theme, see the
+# documentation.
+#html_theme_options = {}
+
+# Add any paths that contain custom themes here, relative to this directory.
+#html_theme_path = []
+
+# The name for this set of Sphinx documents.  If None, it defaults to
+# "<project> v<release> documentation".
+#html_title = None
+
+# A shorter title for the navigation bar.  Default is the same as html_title.
+#html_short_title = None
+
+# The name of an image file (relative to this directory) to place at the top
+# of the sidebar.
+#html_logo = None
+
+# The name of an image file (within the static path) to use as favicon of the
+# docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
+# pixels large.
+#html_favicon = None
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']
+
+# Add any extra paths that contain custom files (such as robots.txt or
+# .htaccess) here, relative to this directory. These files are copied
+# directly to the root of the documentation.
+#html_extra_path = []
+
+# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
+# using the given strftime format.
+#html_last_updated_fmt = '%b %d, %Y'
+
+# If true, SmartyPants will be used to convert quotes and dashes to
+# typographically correct entities.
+#html_use_smartypants = True
+
+# Custom sidebar templates, maps document names to template names.
+#html_sidebars = {}
+
+# Additional templates that should be rendered to pages, maps page names to
+# template names.
+#html_additional_pages = {}
+
+# If false, no module index is generated.
+#html_domain_indices = True
+
+# If false, no index is generated.
+#html_use_index = True
+
+# If true, the index is split into individual pages for each letter.
+#html_split_index = False
+
+# If true, links to the reST sources are added to the pages.
+#html_show_sourcelink = True
+
+# If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
+#html_show_sphinx = True
+
+# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
+#html_show_copyright = True
+
+# If true, an OpenSearch description file will be output, and all pages will
+# contain a <link> tag referring to it.  The value of this option must be the
+# base URL from which the finished HTML is served.
+#html_use_opensearch = ''
+
+# This is the file name suffix for HTML files (e.g. ".xhtml").
+#html_file_suffix = None
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'LSMTooldoc'
+
+
+# -- Options for LaTeX output ---------------------------------------------
+
+latex_elements = {
+# The paper size ('letterpaper' or 'a4paper').
+#'papersize': 'letterpaper',
+
+# The font size ('10pt', '11pt' or '12pt').
+#'pointsize': '10pt',
+
+# Additional stuff for the LaTeX preamble.
+#'preamble': '',
+}
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title,
+#  author, documentclass [howto, manual, or own class]).
+latex_documents = [
+  ('index', 'LSMTool.tex', u'LSMTool Documentation',
+   u'David Rafferty', 'manual'),
+]
+
+# The name of an image file (relative to this directory) to place at the top of
+# the title page.
+#latex_logo = None
+
+# For "manual" documents, if this is true, then toplevel headings are parts,
+# not chapters.
+#latex_use_parts = False
+
+# If true, show page references after internal links.
+#latex_show_pagerefs = False
+
+# If true, show URL addresses after external links.
+#latex_show_urls = False
+
+# Documents to append as an appendix to all manuals.
+#latex_appendices = []
+
+# If false, no module index is generated.
+#latex_domain_indices = True
+
+
+# -- Options for manual page output ---------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [
+    ('index', 'lsmtool', u'LSMTool Documentation',
+     [u'David Rafferty'], 1)
+]
+
+# If true, show URL addresses after external links.
+#man_show_urls = False
+
+
+# -- Options for Texinfo output -------------------------------------------
+
+# Grouping the document tree into Texinfo files. List of tuples
+# (source start file, target name, title, author,
+#  dir menu entry, description, category)
+texinfo_documents = [
+  ('index', 'LSMTool', u'LSMTool Documentation',
+   u'David Rafferty', 'LSMTool', 'One line description of project.',
+   'Miscellaneous'),
+]
+
+# Documents to append as an appendix to all manuals.
+#texinfo_appendices = []
+
+# If false, no module index is generated.
+#texinfo_domain_indices = True
+
+# How to display URL addresses: 'footnote', 'no', or 'inline'.
+#texinfo_show_urls = 'footnote'
+
+# If true, do not generate a @detailmenu in the "Top" node's menu.
+#texinfo_no_detailmenu = False
+
+
+# Example configuration for intersphinx: refer to the Python standard library.
+intersphinx_mapping = {'http://docs.python.org/': None}
diff --git a/doc/source/index.rst b/doc/source/index.rst
new file mode 100644
index 0000000000000000000000000000000000000000..c6b45d5b81712dc74703c35c5d8ea486dfe15834
--- /dev/null
+++ b/doc/source/index.rst
@@ -0,0 +1,27 @@
+.. LSMTool documentation master file, created by
+   sphinx-quickstart on Thu Jun 19 17:05:13 2014.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to LSMTool's documentation!
+===================================
+
+LSMTool is a Python package which allow the manipulation of sky models in the ``makesourcedb`` format understood by BBS. Note that LSMTool is still in beta. Please report bugs to ``drafferty@hs.uni-hamburg.de``. To initialize your environment for LSMTool, users on CEP1 and CEP2 should run the following commands::
+
+    use LofIm
+    source ~rafferty/init_lsmtool
+
+Note that the Pythonlibs LOFAR package includes an older version of astropy that conflicts with LSMTool and cannot be used in conjunction with it.
+
+.. toctree::
+   :maxdepth: 2
+
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
+
diff --git a/lsmtool/__init__.py b/lsmtool/__init__.py
index c7c2561896628ef65bdadef62389049184acb655..7dc418a742bd53b3dae069f04cb16fcecb97697d 100644
--- a/lsmtool/__init__.py
+++ b/lsmtool/__init__.py
@@ -16,7 +16,15 @@
 # along with this program; if not, write to the Free Software
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
 
+"""LSMTool: the LOFAR Local Sky Model Tool
+
+.. moduleauthor:: David Rafferty <drafferty@hs.uni-hamburg.de>
+
+"""
+
 from ._version import changelog
+from .skymodel import SkyModel
+
 
 def load(fileName, beamMS=None):
     """
@@ -44,7 +52,5 @@ def load(fileName, beamMS=None):
         >>> s = lsmtool.load('sky.model', 'SB100.MS')
 
     """
-    from .skymodel import SkyModel
-
     return SkyModel(fileName, beamMS)
 
diff --git a/lsmtool/operations/_filter.py b/lsmtool/operations/_filter.py
index bdcee299b0e23ac5b6e6815fb1be19e7c5ae6bde..1fd23b6e508e9a341aa6ee883d73fe5295d453f0 100644
--- a/lsmtool/operations/_filter.py
+++ b/lsmtool/operations/_filter.py
@@ -66,7 +66,7 @@ def filter(LSM, filterExpression, exclusive=False, aggregate=None,
             - 'wmean': Stokes I weighted mean of patch values
             - 'min': minimum of patch values
             - 'max': maximum of patch values
-            - True: only valid when the filter indices are specify directly as
+            - True: only valid when the filter indices are specified directly as
                 a numpy array. If True, filtering is done on patches instead of
                 sources.
     applyBeam : bool, optional
@@ -82,28 +82,28 @@ def filter(LSM, filterExpression, exclusive=False, aggregate=None,
     Filter on column 'I' (Stokes I flux). This filter will select all sources
     with Stokes I flux greater than 1.5 Jy::
 
-        >>> s = SkyModel('sky.model')
-        >>> s.filter('I > 1.5 Jy')
+        >>> LSM = lsmtool.load('sky.model')
+        >>> filter(LSM, 'I > 1.5 Jy')
         INFO: Filtered out 1102 sources.
 
     If the sky model has patches and the filter is desired per patch, use
     ``aggregate = True``::
 
-        >>> s.filter('I > 1.5 Jy', aggregate=True)
+        >>> filter(LSM, 'I > 1.5 Jy', aggregate=True)
 
     Filter on source names, keeping those that match "src*_1?"::
 
-        >>> s.filter('Name == src*_1?')
+        >>> filter(LSM, 'Name == src*_1?')
 
     Use a CASA clean mask image to keep sources that lie in masked regions::
 
-        >>> s.filter('clean_mask.mask == True')
+        >>> filter(LSM, 'clean_mask.mask == True')
 
     Filter on patch size::
 
-        >>> sizes = s.getPatchSizes(units='arcsec', weight=True)
-        >>> indices = numpy.where(sizes <= maj_cut_arcsec)[0]
-        >>> s.select(indices)
+        >>> sizes = LSM.getPatchSizes(units='arcsec', weight=True)
+        >>> indices = numpy.where(sizes <= maj_cut_arcsec)
+        >>> filter(LSM, indices, aggregate=True)
 
     """
     import numpy as np
diff --git a/lsmtool/operations/concatenate.py b/lsmtool/operations/concatenate.py
index d8f764288c8cb8b2ab17c6bcd3c554e864e62114..aec428d0a77a435a139578afc9e430a41283f8e9 100644
--- a/lsmtool/operations/concatenate.py
+++ b/lsmtool/operations/concatenate.py
@@ -68,10 +68,10 @@ def concatenate(LSM1, LSM2, matchBy='name', radius=0.1, keep='all'):
     Concatenate two sky models, identifying duplicates by matching to the source
     names. When duplicates are found, keep the source from the parent sky model
     and discard the duplicate from second sky model (this might be useful when
-    merging two gsm.py sky models that have some overlap)::
+    merging two sky models that have some overlap)::
 
-        >>> LSM1 = lsmtool.load('gsm_sky1.model')
-        >>> LSM2 = lsmtool.load('gsm_sky2.model')
+        >>> LSM1 = lsmtool.load('sky1.model')
+        >>> LSM2 = lsmtool.load('sky2.model')
         >>> concatenate(LSM1, LSM2, matchBy='name', keep='from1')
 
     Concatenate two sky models, identifying duplicates by matching to the source
diff --git a/lsmtool/operations/merge.py b/lsmtool/operations/merge.py
index 2a47e3abc777b99589bb7f027c8ada91db8c8aea..26374d2d1f43975dc5e8cfaafe7a76d4439c98f3 100644
--- a/lsmtool/operations/merge.py
+++ b/lsmtool/operations/merge.py
@@ -47,14 +47,13 @@ def merge(LSM, patches, name=None):
         List of patches to merge
     name : str, optional
         Name of resulting merged patch
-    method : str, optional
-        Method to use in setting patch positons: 'mid', 'mean', or 'wmean'
 
     Examples
     --------
-    Merge three patches into one:
+    Merge three patches into one::
 
-        >>> s.merge(['bin0', 'bin1', 'bin2'], 'binmerged')
+        >>> LSM = lsmtool.load('sky.model')
+        >>> merge(LSM, ['bin0', 'bin1', 'bin2'], 'binmerged')
     """
     if name is None:
         name = patches[0]
diff --git a/lsmtool/operations/move.py b/lsmtool/operations/move.py
index eefd242a10c9a0683427b5c658d14c9219249eea..ed541efed87eebe9395e55934cfeea2c945c260e 100644
--- a/lsmtool/operations/move.py
+++ b/lsmtool/operations/move.py
@@ -65,11 +65,12 @@ def move(LSM, name, position=None, shift=None):
     --------
     Move source '1609.6+6556' to a new position::
 
-        >>> s.move('1609.6+6556', position=['16:10:00', '+65.57.00'])
+        >>> LSM = lsmtool.load('sky.model')
+        >>> move(LSM, '1609.6+6556', position=['16:10:00', '+65.57.00'])
 
     Shift the source by 10 arcsec in Dec::
 
-        >>> s.move('1609.6+6556', shift=[0.0, 10.0/3600.0])
+        >>> move(LSM, '1609.6+6556', shift=[0.0, 10.0/3600.0])
 
     """
     try:
diff --git a/lsmtool/operations/plot.py b/lsmtool/operations/plot.py
index 804cd5698e47d4703fea531e692c0c6041665bfa..453747eef34b750670aefb36c9df6faabd45b6f3 100644
--- a/lsmtool/operations/plot.py
+++ b/lsmtool/operations/plot.py
@@ -50,11 +50,12 @@ def plot(LSM, fileName=None):
     ---------
     Plot and display to the screen::
 
-        >>> s.plot()
+        >>> LSM = lsmtool.load('sky.model')
+        >>> plot(LSM)
 
     Plot and save to a PDF file::
 
-        >>>s.plot('sky_plot.pdf')
+        >>> plot(LSM, 'sky_plot.pdf')
 
     """
     import matplotlib.pyplot as plt
diff --git a/lsmtool/operations/remove.py b/lsmtool/operations/remove.py
index 9d2ab1630edf77b7f302131b9447be93db83a614..b5d6935ce55a646f709b3c7ef2692c9e1ce25773 100644
--- a/lsmtool/operations/remove.py
+++ b/lsmtool/operations/remove.py
@@ -81,6 +81,9 @@ def remove(LSM, filterExpression, aggregate=None, applyBeam=None,
             - 'wmean': Stokes I weighted mean of patch values
             - 'min': minimum of patch values
             - 'max': maximum of patch values
+            - True: only valid when the filter indices are specified directly as
+                a numpy array. If True, filtering is done on patches instead of
+                sources.
     applyBeam : bool, optional
         If True, apparent fluxes will be used.
     useRegEx : bool, optional
@@ -92,21 +95,23 @@ def remove(LSM, filterExpression, aggregate=None, applyBeam=None,
     Filter on column 'I' (Stokes I flux). This filter will remove all sources
     with Stokes I flux greater than 1.5 Jy::
 
-        >>> s.remove('I > 1.5 Jy')
-        INFO: Filtered out 1102 sources.
+        >>> LSM = lsmtool.load('sky.model')
+        >>> remove(LSM, 'I > 1.5 Jy')
+        INFO: Removed 1102 sources.
 
     If the sky model has patches and the filter is desired per patch, use
-    ``aggregate = True``::
+    ``aggregate = function``. For example, to select on the sum of the patch
+    fluxes::
 
-        >>> s.remove('I > 1.5 Jy', aggregate=True)
+        >>> remove(LSM, 'I > 1.5 Jy', aggregate='sum')
 
     Filter on source names, removing those that match "src*_1?"::
 
-        >>> s.remove('Name == src*_1?')
+        >>> remove(LSM, 'Name == src*_1?')
 
     Use a CASA clean mask image to remove sources that lie in masked regions::
 
-        >>> s.remove('clean_mask.mask == True')
+        >>> remove(LSM, 'clean_mask.mask == True')
 
     """
     from . import _filter
diff --git a/lsmtool/operations/select.py b/lsmtool/operations/select.py
index e60e18467ca4e51b9a4d53c0cb654d252643df36..e55a80a2f384515670fa163958815f1531d5691f 100644
--- a/lsmtool/operations/select.py
+++ b/lsmtool/operations/select.py
@@ -81,6 +81,9 @@ def select(LSM, filterExpression, aggregate=None, applyBeam=False,
             - 'wmean': Stokes I weighted mean of patch values
             - 'min': minimum of patch values
             - 'max': maximum of patch values
+            - True: only valid when the filter indices are specified directly as
+                a numpy array. If True, filtering is done on patches instead of
+                sources.
     applyBeam : bool, optional
         If True, apparent fluxes will be used.
     useRegEx : bool, optional
@@ -92,21 +95,23 @@ def select(LSM, filterExpression, aggregate=None, applyBeam=False,
     Filter on column 'I' (Stokes I flux). This filter will select all sources
     with Stokes I flux greater than 1.5 Jy::
 
-        >>> s.select('I > 1.5 Jy')
-        INFO: Filtered out 1102 sources.
+        >>> LSM = lsmtool.load('sky.model')
+        >>> select(LSM, 'I > 1.5 Jy')
+        INFO: Kept 1102 sources.
 
     If the sky model has patches and the filter is desired per patch, use
-    ``aggregate = True``::
+    ``aggregate = function``. For example, to select on the sum of the patch
+    fluxes::
 
-        >>> s.select('I > 1.5 Jy', aggregate=True)
+        >>> select(LSM, 'I > 1.5 Jy', aggregate='sum')
 
     Filter on source names, keeping those that match "src*_1?"::
 
-        >>> s.select('Name == src*_1?')
+        >>> select(LSM, 'Name == src*_1?')
 
     Use a CASA clean mask image to keep sources that lie in masked regions::
 
-        >>> s.filter('clean_mask.mask == True')
+        >>> filter(LSM, 'clean_mask.mask == True')
 
     """
     from . import _filter
diff --git a/lsmtool/operations/transfer.py b/lsmtool/operations/transfer.py
index 3a01d0aaaed9617c7671ed2f195378f37c8a6e4c..9930a3ee2a81903c66365d40f62bebbf16eb5e78 100644
--- a/lsmtool/operations/transfer.py
+++ b/lsmtool/operations/transfer.py
@@ -42,14 +42,21 @@ def transfer(LSM, patchFile):
 
     Sources with the same name as those in patchFile will be grouped into
     the patches defined in patchFile. Sources that do not appear in patchFile
-    will be placed into separate patches (one per source).
+    will be placed into separate patches (one per source). Patch positions are
+    not transferred.
 
     Parameters
     ----------
     patchFile : str
         Input sky model from which to transfer patches.
-    method : str, optional
-        Method to use in setting patch positons: 'mid', 'mean', or 'wmean'
+
+    Examples
+    --------
+    Transfer patches from one sky model to another and set their positions::
+
+        >>> LSM = lsmtool.load('sky.model')
+        >>> transfer(LSM, 'master_sky.model')
+        >>> setPatchPositions(LSM, method='mid')
 
     """
     try:
diff --git a/lsmtool/skymodel.py b/lsmtool/skymodel.py
index 96e7d36977aaa9ba86436dbd36b23cb721d85b5c..1a362b996d625d28287af374c1bfb64a6dead159 100644
--- a/lsmtool/skymodel.py
+++ b/lsmtool/skymodel.py
@@ -49,9 +49,9 @@ class SkyModel(object):
             >>> s = SkyModel('sky.model')
 
         Create a SkyModel object with a beam MS so that apparent fluxes will
-        be available as well as intrinsic fluxes:::
+        be available::
 
-            >>> s = SkyModel('sky.model', 'SB100.MS')
+            >>> s = SkyModel('sky.model', beamMS='SB100.MS')
 
         """
         from astropy.table import Table, Column
@@ -1409,22 +1409,154 @@ class SkyModel(object):
             logging.info('Removed {0} duplicate sources.'.format(nRowsOrig-nRowsNew))
 
 
-    def select(self, *args, **kwargs):
+    def select(self, filterExpression, aggregate=None, applyBeam=False,
+        useRegEx=False, force=False):
         """
-        Selects table rows on column values with the given expression.
+        Filters the sky model, keeping all sources that meet the given expression.
+
+        After filtering, the sky model contains only those sources for which the
+        given filter expression is true.
+
+        Parameters
+        ----------
+        filterExpression : str or dict
+            A string specifying the filter expression in the form:
+                '<property> <operator> <value> [<units>]'
+            (e.g., 'I <= 10.5 Jy'). These elements can also be given as a
+            dictionary in the form:
+                {'filterProp':property, 'filterOper':operator,
+                    'filterVal':value, 'filterUnits':units}
+            or as a list:
+                [property, operator, value, value]
+            The property to filter on must be a valid column name or the filename
+            of a mask image.
+
+            Supported operators are:
+                - !=
+                - <=
+                - >=
+                - >
+                - <
+                - = (or '==')
+            Units are optional and must be specified as required by astropy.units.
+        aggregate : str, optional
+            If set, the array returned will be of values aggregated
+            over the patch members. The following aggregation functions are
+            available:
+                - 'sum': sum of patch values
+                - 'mean': mean of patch values
+                - 'wmean': Stokes I weighted mean of patch values
+                - 'min': minimum of patch values
+                - 'max': maximum of patch values
+                - True: only valid when the filter indices are specify directly as
+                    a numpy array. If True, filtering is done on patches instead of
+                    sources.
+        applyBeam : bool, optional
+            If True, apparent fluxes will be used.
+        useRegEx : bool, optional
+            If True, string matching will use regular expression matching. If
+            False, string matching uses Unix filename matching.
+
+        Examples
+        --------
+        Filter on column 'I' (Stokes I flux). This filter will select all sources
+        with Stokes I flux greater than 1.5 Jy::
+
+            >>> s.select('I > 1.5 Jy')
+            INFO: Kept 1102 sources.
+
+        If the sky model has patches and the filter is desired per patch, use
+        ``aggregate = function``. For example, to select on the sum of the patch
+        fluxes::
+
+            >>> s.select('I > 1.5 Jy', aggregate='sum')
+
+        Filter on source names, keeping those that match "src*_1?"::
+
+            >>> s.select('Name == src*_1?')
+
+        Use a CASA clean mask image to keep sources that lie in masked regions::
+
+            >>> s.filter('clean_mask.mask == True')
 
-        See operations.select.select() for details.
         """
-        operations.select.select(self, *args, **kwargs)
+        operations.select.select(self, filterExpression, aggregate=aggregate,
+            applyBeam=applyBeam, useRegEx=useRegEx, force=force)
 
 
-    def remove(self, *args, **kwargs):
+    def remove(self, filterExpression, aggregate=None, applyBeam=None,
+        useRegEx=False, force=False):
         """
-        Removes table rows on column values with the given expression.
+        Filters the sky model, removing all sources that meet the given expression.
+
+        After filtering, the sky model contains only those sources for which the
+        given filter expression is false.
+
+        Parameters
+        ----------
+        filterExpression : str or dict
+            A string specifying the filter expression in the form:
+                '<property> <operator> <value> [<units>]'
+            (e.g., 'I <= 10.5 Jy'). These elements can also be given as a
+            dictionary in the form:
+                {'filterProp':property, 'filterOper':operator,
+                    'filterVal':value, 'filterUnits':units}
+            or as a list:
+                [property, operator, value, value]
+            The property to filter on must be a valid column name or the filename
+            of a mask image.
+
+            Supported operators are:
+                - !=
+                - <=
+                - >=
+                - >
+                - <
+                - = (or '==')
+            Units are optional and must be specified as required by astropy.units.
+        aggregate : str, optional
+            If set, the array returned will be of values aggregated
+            over the patch members. The following aggregation functions are
+            available:
+                - 'sum': sum of patch values
+                - 'mean': mean of patch values
+                - 'wmean': Stokes I weighted mean of patch values
+                - 'min': minimum of patch values
+                - 'max': maximum of patch values
+                - True: only valid when the filter indices are specified directly as
+                    a numpy array. If True, filtering is done on patches instead of
+                    sources.
+        applyBeam : bool, optional
+            If True, apparent fluxes will be used.
+        useRegEx : bool, optional
+            If True, string matching will use regular expression matching. If
+            False, string matching uses Unix filename matching.
+
+        Examples
+        --------
+        Filter on column 'I' (Stokes I flux). This filter will remove all sources
+        with Stokes I flux greater than 1.5 Jy::
+
+            >>> s.remove('I > 1.5 Jy')
+            INFO: Removed 1102 sources.
+
+        If the sky model has patches and the filter is desired per patch, use
+        ``aggregate = function``. For example, to select on the sum of the patch
+        fluxes::
+
+            >>> s.remove('I > 1.5 Jy', aggregate='sum')
+
+        Filter on source names, removing those that match "src*_1?"::
+
+            >>> s.remove('Name == src*_1?')
+
+        Use a CASA clean mask image to remove sources that lie in masked regions::
+
+            >>> s.remove('clean_mask.mask == True')
 
-        See operations.remove.remove() for details.
         """
-        operations.remove.remove(self, *args, **kwargs)
+        operations.remove.remove(self, filterExpression, aggregate=aggregate,
+            applyBeam=applyBeam, useRegEx=useRegEx, force=force)
 
 
     def group(self, algorithm, targetFlux=None, numClusters=100, applyBeam=False):
@@ -1433,6 +1565,8 @@ class SkyModel(object):
 
         Parameters
         ----------
+        LSM : SkyModel object
+            Input sky model.
         algorithm : str
             Algorithm to use for grouping:
             - 'single' => all sources are grouped into a single patch
@@ -1441,14 +1575,16 @@ class SkyModel(object):
                 specified number of clusters (specified by the numClusters parameter).
             - 'tessellate' => group into tiles whose total flux approximates
                 the target flux (specified by the targetFlux parameter).
+            - the filename of a mask image => group by masked regions (where mask =
+                True). Source outside of masked regions are given patches of their
+                own.
         targetFlux : str or float, optional
             Target flux for tessellation (the total flux of each tile will be close
             to this value). The target flux can be specified as either a float in Jy
-            or as a string with units (e.g., '25.0 mJy'). Valid for algorithm =
-            'tessellate' only.
+            or as a string with units (e.g., '25.0 mJy').
         numClusters : int, optional
             Number of clusters for clustering. Sources are grouped around the
-            numClusters brightest sources. Valid for algorithm = 'cluster' only.
+            numClusters brightest sources.
         applyBeam : bool, optional
             If True, fluxes will be attenuated by the beam.
 
@@ -1460,25 +1596,66 @@ class SkyModel(object):
             >>> s.group('tessellate', targetFlux=30.0)
 
         """
-        operations.group.group(self, algorithm, targetFlux, numClusters, applyBeam)
+        operations.group.group(self, algorithm, targetFlux=targetFlux,
+            numClusters=numClusters, applyBeam=applyBeam)
 
 
-    def transfer(self, *args, **kwargs):
+    def transfer(self, patchFile):
         """
-        Transfers the patch scheme from the input sky model.
+        Transfer patches from the input sky model.
+
+        Sources with the same name as those in patchFile will be grouped into
+        the patches defined in patchFile. Sources that do not appear in patchFile
+        will be placed into separate patches (one per source). Patch positions are
+        not transferred.
+
+        Parameters
+        ----------
+        patchFile : str
+            Input sky model from which to transfer patches.
+
+        Examples
+        --------
+        Transfer patches from one sky model to another and set their positions::
+
+            >>> s.transfer('master_sky.model')
+            >>> s.setPatchPositions(method='mid')
 
-        See operations.transfer.transfer() for details.
         """
-        operations.transfer.transfer(self, *args, **kwargs)
+        operations.transfer.transfer(self, patchFile)
 
 
-    def move(self, *args, **kwargs):
+    def move(self, name, position=None, shift=None):
         """
-        Moves a source or patch.
+        Move or shift a source.
+
+        If both a position and a shift are specified, the source is moved to the
+        new position and then shifted.
+
+        Parameters
+        ----------
+        name : str
+            Source name.
+        position : list, optional
+            A list specifying a new position as [RA, Dec] in either makesourcedb
+            format (e.g., ['12:23:43.21', '+22.34.21.2']) or in degrees (e.g.,
+            [123.2312, 23.3422]).
+        shift : list, optional
+            A list specifying the shift as [RAShift, DecShift] in
+            in degrees (e.g., [0.02312, 0.00342]).
+
+        Examples
+        --------
+        Move source '1609.6+6556' to a new position::
+
+            >>> s.move('1609.6+6556', position=['16:10:00', '+65.57.00'])
+
+        Shift the source by 10 arcsec in Dec::
+
+            >>> s.move('1609.6+6556', shift=[0.0, 10.0/3600.0])
 
-        See operations.move.move() for details.
         """
-        operations.move.move(self, *args, **kwargs)
+        operations.move.move(self, name, position=postition, shift=shift)
 
 
     def add(self, colNamesVals):
@@ -1502,13 +1679,25 @@ class SkyModel(object):
         operations.add.add(self, colNamesVals)
 
 
-    def merge(self, *args, **kwargs):
+    def merge(self, patches, name=None):
         """
-        Merges two or more patches.
+        Merge two or more patches together
 
-        See operations.merge.merge() for details.
-        """
-        operations.merge.merge(self, *args, **kwargs)
+        Parameters
+        ----------
+        patches : list of str
+            List of patches to merge
+        name : str, optional
+            Name of resulting merged patch
+
+        Examples
+        --------
+        Merge three patches into one::
+
+            >>> s.merge(['bin0', 'bin1', 'bin2'], 'binmerged')
+
+         """
+        operations.merge.merge(self, patches, name=name)
 
 
     def concatenate(self, LSM2, matchBy='name', radius=0.1, keep='all'):
@@ -1554,24 +1743,32 @@ class SkyModel(object):
                 keep='from2')
 
         """
-        operations.concatenate.concatenate(self, LSM2, matchBy, radius, keep)
+        operations.concatenate.concatenate(self, LSM2, matchBy=matchBy,
+            radius=radius, keep=keep)
 
 
-    def plot(self, *args, **kwargs):
+    def plot(self, fileName=None):
         """
-        Plot the sky model.
+        Shows a simple plot of the sky model.
 
-        See operations.plot.plot() for details.
-        """
-        operations.plot.plot(self, *args, **kwargs)
+        The circles in the plot are scaled with flux. If the sky model is grouped
+        into patches, sources are colored by patch and the patch positions are
+        indicated with stars.
+
+        Parameters
+        ----------
+        fileName : str, optional
+            If given, the plot is saved to a file instead of displayed.
 
+        Examples:
+        ---------
+        Plot and display to the screen::
+
+            >>> s.plot()
 
-# Forward the operation doc strings to the appropriate methods of the SkyModel
-# object.
-SkyModel.remove.__func__.__doc__ = operations.remove.remove.__doc__
-SkyModel.select.__func__.__doc__ = operations.select.select.__doc__
-SkyModel.transfer.__func__.__doc__ = operations.transfer.transfer.__doc__
-SkyModel.move.__func__.__doc__ = operations.move.move.__doc__
-SkyModel.plot.__func__.__doc__ = operations.plot.plot.__doc__
-SkyModel.merge.__func__.__doc__ = operations.merge.merge.__doc__
+        Plot and save to a PDF file::
 
+            >>> s.plot('sky_plot.pdf')
+
+        """
+        operations.plot.plot(self, fileName=fileName)