diff --git a/README.md b/README.md
index 53b0439ec42f7beef311774dcf2f38d3b17db0f3..c6dc89fa47c1cfb9856cc17f309c64749b93d369 100644
--- a/README.md
+++ b/README.md
@@ -28,6 +28,7 @@ The following operations are available:
* MERGE: Merge two or more patches into one
* CONCATENATE: Concatenate two sky models
* ADD: Add a source
+* SETPATCHPOSITIONS: Calculate and set patch positions
* PLOT: Plot the sky model
For details, please see the full documentation (doc/lsmtool.tex).
diff --git a/doc/build/doctrees/code.doctree b/doc/build/doctrees/code.doctree
index 4473eeb73cbc2c4005cff1b63ae6f5aa184f3c8b..733fdd15cf85ca374750e314b9b69fe4bcc0b93c 100644
Binary files a/doc/build/doctrees/code.doctree and b/doc/build/doctrees/code.doctree differ
diff --git a/doc/build/doctrees/environment.pickle b/doc/build/doctrees/environment.pickle
index b0cd2ca5915e884eae852d9ac49b835995e10651..4a79bd472d52bc7dc6e1a8ae46dc68135c309091 100644
Binary files a/doc/build/doctrees/environment.pickle and b/doc/build/doctrees/environment.pickle differ
diff --git a/doc/build/doctrees/index.doctree b/doc/build/doctrees/index.doctree
index 9fb62513db848cacc5a7140f0cd781590c384958..60515b93738f06130f2d82b359e64fb099a2f039 100644
Binary files a/doc/build/doctrees/index.doctree and b/doc/build/doctrees/index.doctree differ
diff --git a/doc/build/html/_sources/code.txt b/doc/build/html/_sources/code.txt
index d184c03adb17c0c890f8333941539f66e6e55b10..be389bb9029c5ae2813ef0b7d9b2da919ef6b008 100644
--- a/doc/build/html/_sources/code.txt
+++ b/doc/build/html/_sources/code.txt
@@ -1,6 +1,3 @@
-LSMTool: the LOFAR Local Sky Model Tool
-***************************************
-
.. automodule:: lsmtool
:members:
.. autoclass:: SkyModel
diff --git a/doc/build/html/_sources/index.txt b/doc/build/html/_sources/index.txt
index c6b45d5b81712dc74703c35c5d8ea486dfe15834..1caa8c0a70ec68e23cd58f05c93e0a90913c99f3 100644
--- a/doc/build/html/_sources/index.txt
+++ b/doc/build/html/_sources/index.txt
@@ -1,27 +1,20 @@
-.. 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
+LSMTool is a Python package which allows for the manipulation of LOFAR sky models in the ``makesourcedb`` format.
-Note that the Pythonlibs LOFAR package includes an older version of astropy that conflicts with LSMTool and cannot be used in conjunction with it.
+Contents
+========
.. toctree::
:maxdepth: 2
-
+ overview.rst
+ lsmtool.rst
Indices and tables
==================
* :ref:`genindex`
-* :ref:`modindex`
* :ref:`search`
diff --git a/doc/build/html/_static/basic.css b/doc/build/html/_static/basic.css
index c959cf0db10b0d30c9b059a9cd52fcba205119e9..967e36ce05f3933b61037c1ddbf5bffcf23d2176 100644
--- a/doc/build/html/_static/basic.css
+++ b/doc/build/html/_static/basic.css
@@ -4,7 +4,7 @@
*
* Sphinx stylesheet -- basic theme.
*
- * :copyright: Copyright 2007-2013 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2014 by the Sphinx team, see AUTHORS.
* :license: BSD, see LICENSE for details.
*
*/
diff --git a/doc/build/html/_static/default.css b/doc/build/html/_static/default.css
index e534a07802b94d88019ee1b61e28541e6fc05856..5f1399abd5d85bc2519ad8f3a0c266cfa51fd2a4 100644
--- a/doc/build/html/_static/default.css
+++ b/doc/build/html/_static/default.css
@@ -4,7 +4,7 @@
*
* Sphinx stylesheet -- default theme.
*
- * :copyright: Copyright 2007-2013 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2014 by the Sphinx team, see AUTHORS.
* :license: BSD, see LICENSE for details.
*
*/
diff --git a/doc/build/html/_static/doctools.js b/doc/build/html/_static/doctools.js
index 2036e5f5f812a93169ac1869f891e87da9658990..c5455c905dcf5323dc6bd0ac8b93c3851daeeecd 100644
--- a/doc/build/html/_static/doctools.js
+++ b/doc/build/html/_static/doctools.js
@@ -4,7 +4,7 @@
*
* Sphinx JavaScript utilities for all documentation.
*
- * :copyright: Copyright 2007-2013 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2014 by the Sphinx team, see AUTHORS.
* :license: BSD, see LICENSE for details.
*
*/
diff --git a/doc/build/html/_static/searchtools.js b/doc/build/html/_static/searchtools.js
index f5c7e5fee71426595a839f84759f47681fd1a74d..6e1f06bd1b9b1e3969cbd453a4ed16eb31f7977d 100644
--- a/doc/build/html/_static/searchtools.js
+++ b/doc/build/html/_static/searchtools.js
@@ -4,7 +4,7 @@
*
* Sphinx JavaScript utilties for the full-text search.
*
- * :copyright: Copyright 2007-2013 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2014 by the Sphinx team, see AUTHORS.
* :license: BSD, see LICENSE for details.
*
*/
diff --git a/doc/build/html/_static/sidebar.js b/doc/build/html/_static/sidebar.js
index 874a890a3cd928992933188798a6ae30a1543668..4f09a0df1f433af4e045a62871ebb12169557710 100644
--- a/doc/build/html/_static/sidebar.js
+++ b/doc/build/html/_static/sidebar.js
@@ -16,7 +16,7 @@
* 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.
+ * :copyright: Copyright 2007-2014 by the Sphinx team, see AUTHORS.
* :license: BSD, see LICENSE for details.
*
*/
diff --git a/doc/build/html/_static/websupport.js b/doc/build/html/_static/websupport.js
index 19fcda5647b4c91f66bd99c653c15475ec86fcc2..71c0a1364aa3074b12315515f53be3694fd632c4 100644
--- a/doc/build/html/_static/websupport.js
+++ b/doc/build/html/_static/websupport.js
@@ -4,7 +4,7 @@
*
* sphinx.websupport utilties for all documentation.
*
- * :copyright: Copyright 2007-2013 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2014 by the Sphinx team, see AUTHORS.
* :license: BSD, see LICENSE for details.
*
*/
diff --git a/doc/build/html/code.html b/doc/build/html/code.html
index 0d2c0b25bf993f557e6f0e0d97b456aae3a30abe..d7f057a9776ed9ce4ca4276fe22bceafbaa84742 100644
--- a/doc/build/html/code.html
+++ b/doc/build/html/code.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>LSMTool: the LOFAR Local Sky Model Tool — LSMTool 1.0.0 documentation</title>
+ <title><no title> — 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" />
@@ -45,9 +45,8 @@
<div class="bodywrapper">
<div class="body">
- <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>
+ <span class="target" id="module-lsmtool"></span><p>The load() convenience function is used to load a sky model file into a
+SkyModel object.</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>
@@ -157,7 +156,7 @@ sky model with a high-resolution one):</p>
<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>
+<tt class="descname">getColValues</tt><big>(</big><em>colName</em>, <em>units=None</em>, <em>aggregate=None</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>
@@ -492,46 +491,27 @@ dictionary in the form:</p>
</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><=</li>
-<li>>=</li>
-<li>></li>
-<li><</li>
-<li>= (or ‘==’)</li>
-</ul>
-</dd>
-</dl>
+<p>Supported operators are:
+- !=
+- <=
+- >=
+- >
+- <
+- = (or ‘==’)</p>
<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
+<dd>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">‘sum’: sum of patch values</p>
-</li>
-<li><p class="first">‘mean’: mean of patch values</p>
-</li>
-<li><p class="first">‘wmean’: Stokes I weighted mean of patch values</p>
-</li>
-<li><p class="first">‘min’: minimum of patch values</p>
-</li>
-<li><p class="first">‘max’: 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>
+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.</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>
@@ -569,20 +549,12 @@ 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>‘<property> <operator> <value> [<units>]’</dd>
-</dl>
-<p>(e.g., ‘I <= 10.5 Jy’). These elements can also be given as a
-dictionary in the form:</p>
-<blockquote>
-<div><dl class="docutils">
-<dt>{‘filterProp’:property, ‘filterOper’:operator,</dt>
-<dd>‘filterVal’:value, ‘filterUnits’:units}</dd>
-</dl>
-</div></blockquote>
-<dl class="docutils">
-<dt>or as a list:</dt>
-<dd>[property, operator, value, value]</dd>
+<dt>The filter expression specified as:</dt>
+<dd><ul class="first last simple">
+<li>a string of <tt class="docutils literal"><span class="pre">'<property></span> <span class="pre"><operator></span> <span class="pre"><value></span> <span class="pre">[<units>]'</span></tt></li>
+<li>a list of <tt class="docutils literal"><span class="pre">[property,</span> <span class="pre">operator,</span> <span class="pre">value,</span> <span class="pre">value]</span></tt></li>
+</ul>
+</dd>
</dl>
<p>The property to filter on must be a valid column name or the filename
of a mask image.</p>
@@ -601,31 +573,17 @@ of a mask image.</p>
<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
+<dd>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">‘sum’: sum of patch values</p>
-</li>
-<li><p class="first">‘mean’: mean of patch values</p>
-</li>
-<li><p class="first">‘wmean’: Stokes I weighted mean of patch values</p>
-</li>
-<li><p class="first">‘min’: minimum of patch values</p>
-</li>
-<li><p class="first">‘max’: 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>
+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.</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>
@@ -710,12 +668,9 @@ where both RA and Dec are degrees J2000 or in makesourcedb format.</dd>
to set the patch positions:
- ‘mid’ => the position is set to the midpoint of the patch
- ‘mean’ => the positions is set to the mean RA and Dec of the patch
-- ‘wmean’ => the position is set to the flux-weighted mean RA and</p>
-<blockquote>
-<div>Dec of the patch</div></blockquote>
-<ul class="simple">
-<li>‘zero’ => set all positions to [0.0, 0.0]</li>
-</ul>
+- ‘wmean’ => the position is set to the flux-weighted mean RA and
+Dec of the patch
+- ‘zero’ => set all positions to [0.0, 0.0]</p>
<p class="last">Note that the mid, mean, and wmean positions are calculated from TAN-
projected values.</p>
</dd>
@@ -843,7 +798,6 @@ BBS:</p>
</dd></dl>
-</div>
</div>
@@ -887,7 +841,7 @@ BBS:</p>
</div>
<div class="footer">
© Copyright 2014, David Rafferty.
- Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.1.
+ Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.2.
</div>
</body>
</html>
\ No newline at end of file
diff --git a/doc/build/html/genindex.html b/doc/build/html/genindex.html
index c34cd1641a3bc43f704913b37997792a7e3b6169..52c2f36a0cf4210aa856d77157b5b7130871c10e 100644
--- a/doc/build/html/genindex.html
+++ b/doc/build/html/genindex.html
@@ -52,8 +52,11 @@
<div class="genindex-jumpbox">
<a href="#A"><strong>A</strong></a>
| <a href="#C"><strong>C</strong></a>
+ | <a href="#D"><strong>D</strong></a>
+ | <a href="#F"><strong>F</strong></a>
| <a href="#G"><strong>G</strong></a>
| <a href="#I"><strong>I</strong></a>
+ | <a href="#K"><strong>K</strong></a>
| <a href="#L"><strong>L</strong></a>
| <a href="#M"><strong>M</strong></a>
| <a href="#P"><strong>P</strong></a>
@@ -62,13 +65,34 @@
| <a href="#T"><strong>T</strong></a>
| <a href="#U"><strong>U</strong></a>
| <a href="#W"><strong>W</strong></a>
+ | <a href="#X"><strong>X</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><a href="lsmtool.operations.html#lsmtool.operations.add.add">add() (in module lsmtool.operations.add)</a>
+ </dt>
+
+ <dd><dl>
+
+ <dt><a href="lsmtool.html#lsmtool.skymodel.SkyModel.add">(lsmtool.skymodel.SkyModel method)</a>
+ </dt>
+
+ </dl></dd>
+
+ <dt><a href="lsmtool.operations.html#lsmtool.operations.group.addEvery">addEvery() (in module lsmtool.operations.group)</a>
+ </dt>
+
+ </dl></td>
+ <td style="width: 33%" valign="top"><dl>
+
+ <dt><a href="lsmtool.operations.html#lsmtool.operations.group.addSingle">addSingle() (in module lsmtool.operations.group)</a>
+ </dt>
+
+
+ <dt><a href="lsmtool.html#lsmtool.operations_lib.attenuate">attenuate() (in module lsmtool.operations_lib)</a>
</dt>
</dl></td>
@@ -78,13 +102,49 @@
<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><a href="lsmtool.operations.html#lsmtool.operations.concatenate.concatenate">concatenate() (in module lsmtool.operations.concatenate)</a>
</dt>
+ <dd><dl>
+
+ <dt><a href="lsmtool.html#lsmtool.skymodel.SkyModel.concatenate">(lsmtool.skymodel.SkyModel method)</a>
+ </dt>
+
+ </dl></dd>
</dl></td>
<td style="width: 33%" valign="top"><dl>
- <dt><a href="code.html#lsmtool.SkyModel.copy">copy() (lsmtool.SkyModel method)</a>
+ <dt><a href="lsmtool.html#lsmtool.skymodel.SkyModel.copy">copy() (lsmtool.skymodel.SkyModel method)</a>
+ </dt>
+
+ </dl></td>
+</tr></table>
+
+<h2 id="D">D</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+ <td style="width: 33%" valign="top"><dl>
+
+ <dt><a href="lsmtool.html#lsmtool.tableio.Dec2Angle">Dec2Angle() (in module lsmtool.tableio)</a>
+ </dt>
+
+
+ <dt><a href="lsmtool.operations.html#lsmtool.operations.plot.Dectickformatter">Dectickformatter() (in module lsmtool.operations.plot)</a>
+ </dt>
+
+ </dl></td>
+ <td style="width: 33%" valign="top"><dl>
+
+ <dt><a href="lsmtool.html#lsmtool.tableio.ds9RegionWriter">ds9RegionWriter() (in module lsmtool.tableio)</a>
+ </dt>
+
+ </dl></td>
+</tr></table>
+
+<h2 id="F">F</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+ <td style="width: 33%" valign="top"><dl>
+
+ <dt><a href="lsmtool.operations.html#lsmtool.operations.plot.formatCoord">formatCoord() (in module lsmtool.operations.plot)</a>
</dt>
</dl></td>
@@ -94,43 +154,53 @@
<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><a href="lsmtool.html#lsmtool.skymodel.SkyModel.getColNames">getColNames() (lsmtool.skymodel.SkyModel method)</a>
</dt>
- <dt><a href="code.html#lsmtool.SkyModel.getColValues">getColValues() (lsmtool.SkyModel method)</a>
+ <dt><a href="lsmtool.html#lsmtool.skymodel.SkyModel.getColValues">getColValues() (lsmtool.skymodel.SkyModel method)</a>
</dt>
- <dt><a href="code.html#lsmtool.SkyModel.getDefaltValues">getDefaltValues() (lsmtool.SkyModel method)</a>
+ <dt><a href="lsmtool.html#lsmtool.skymodel.SkyModel.getDefaltValues">getDefaltValues() (lsmtool.skymodel.SkyModel method)</a>
</dt>
- <dt><a href="code.html#lsmtool.SkyModel.getPatchNames">getPatchNames() (lsmtool.SkyModel method)</a>
+ <dt><a href="lsmtool.html#lsmtool.skymodel.SkyModel.getPatchNames">getPatchNames() (lsmtool.skymodel.SkyModel method)</a>
</dt>
- <dt><a href="code.html#lsmtool.SkyModel.getPatchPositions">getPatchPositions() (lsmtool.SkyModel method)</a>
+ <dt><a href="lsmtool.operations.html#lsmtool.operations.group.getPatchNamesFromMask">getPatchNamesFromMask() (in module lsmtool.operations.group)</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><a href="lsmtool.html#lsmtool.skymodel.SkyModel.getPatchPositions">getPatchPositions() (lsmtool.skymodel.SkyModel method)</a>
+ </dt>
+
+
+ <dt><a href="lsmtool.html#lsmtool.skymodel.SkyModel.getPatchSizes">getPatchSizes() (lsmtool.skymodel.SkyModel method)</a>
</dt>
- <dt><a href="code.html#lsmtool.SkyModel.getRowIndex">getRowIndex() (lsmtool.SkyModel method)</a>
+ <dt><a href="lsmtool.html#lsmtool.skymodel.SkyModel.getRowIndex">getRowIndex() (lsmtool.skymodel.SkyModel method)</a>
</dt>
- <dt><a href="code.html#lsmtool.SkyModel.getRowValues">getRowValues() (lsmtool.SkyModel method)</a>
+ <dt><a href="lsmtool.html#lsmtool.skymodel.SkyModel.getRowValues">getRowValues() (lsmtool.skymodel.SkyModel method)</a>
</dt>
- <dt><a href="code.html#lsmtool.SkyModel.group">group() (lsmtool.SkyModel method)</a>
+ <dt><a href="lsmtool.operations.html#lsmtool.operations.group.group">group() (in module lsmtool.operations.group)</a>
+ </dt>
+
+ <dd><dl>
+
+ <dt><a href="lsmtool.html#lsmtool.skymodel.SkyModel.group">(lsmtool.skymodel.SkyModel method)</a>
</dt>
+ </dl></dd>
</dl></td>
</tr></table>
@@ -138,7 +208,17 @@
<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><a href="lsmtool.html#lsmtool.skymodel.SkyModel.info">info() (lsmtool.skymodel.SkyModel method)</a>
+ </dt>
+
+ </dl></td>
+</tr></table>
+
+<h2 id="K">K</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+ <td style="width: 33%" valign="top"><dl>
+
+ <dt><a href="lsmtool.html#lsmtool.tableio.kvisAnnWriter">kvisAnnWriter() (in module lsmtool.tableio)</a>
</dt>
</dl></td>
@@ -148,13 +228,73 @@
<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><a href="lsmtool.html#lsmtool.load">load() (in module lsmtool)</a>
+ </dt>
+
+
+ <dt><a href="lsmtool.html#module-lsmtool">lsmtool (module)</a>
+ </dt>
+
+
+ <dt><a href="lsmtool.operations.html#module-lsmtool.operations">lsmtool.operations (module)</a>
+ </dt>
+
+
+ <dt><a href="lsmtool.operations.html#module-lsmtool.operations.add">lsmtool.operations.add (module)</a>
+ </dt>
+
+
+ <dt><a href="lsmtool.operations.html#module-lsmtool.operations.concatenate">lsmtool.operations.concatenate (module)</a>
+ </dt>
+
+
+ <dt><a href="lsmtool.operations.html#module-lsmtool.operations.group">lsmtool.operations.group (module)</a>
+ </dt>
+
+
+ <dt><a href="lsmtool.operations.html#module-lsmtool.operations.merge">lsmtool.operations.merge (module)</a>
+ </dt>
+
+
+ <dt><a href="lsmtool.operations.html#module-lsmtool.operations.move">lsmtool.operations.move (module)</a>
+ </dt>
+
+
+ <dt><a href="lsmtool.operations.html#module-lsmtool.operations.plot">lsmtool.operations.plot (module)</a>
</dt>
</dl></td>
<td style="width: 33%" valign="top"><dl>
- <dt><a href="code.html#module-lsmtool">lsmtool (module)</a>
+ <dt><a href="lsmtool.operations.html#module-lsmtool.operations.remove">lsmtool.operations.remove (module)</a>
+ </dt>
+
+
+ <dt><a href="lsmtool.operations.html#module-lsmtool.operations.select">lsmtool.operations.select (module)</a>
+ </dt>
+
+
+ <dt><a href="lsmtool.operations.html#module-lsmtool.operations.setpatchpositions">lsmtool.operations.setpatchpositions (module)</a>
+ </dt>
+
+
+ <dt><a href="lsmtool.operations.html#module-lsmtool.operations.transfer">lsmtool.operations.transfer (module)</a>
+ </dt>
+
+
+ <dt><a href="lsmtool.operations.html#module-lsmtool.operations.ungroup">lsmtool.operations.ungroup (module)</a>
+ </dt>
+
+
+ <dt><a href="lsmtool.html#module-lsmtool.operations_lib">lsmtool.operations_lib (module)</a>
+ </dt>
+
+
+ <dt><a href="lsmtool.html#module-lsmtool.skymodel">lsmtool.skymodel (module)</a>
+ </dt>
+
+
+ <dt><a href="lsmtool.html#module-lsmtool.tableio">lsmtool.tableio (module)</a>
</dt>
</dl></td>
@@ -164,19 +304,31 @@
<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><a href="lsmtool.operations.html#lsmtool.operations.merge.merge">merge() (in module lsmtool.operations.merge)</a>
+ </dt>
+
+ <dd><dl>
+
+ <dt><a href="lsmtool.html#lsmtool.skymodel.SkyModel.merge">(lsmtool.skymodel.SkyModel method)</a>
</dt>
+ </dl></dd>
- <dt><a href="code.html#lsmtool.SkyModel.more">more() (lsmtool.SkyModel method)</a>
+ <dt><a href="lsmtool.html#lsmtool.skymodel.SkyModel.more">more() (lsmtool.skymodel.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><a href="lsmtool.operations.html#lsmtool.operations.move.move">move() (in module lsmtool.operations.move)</a>
+ </dt>
+
+ <dd><dl>
+
+ <dt><a href="lsmtool.html#lsmtool.skymodel.SkyModel.move">(lsmtool.skymodel.SkyModel method)</a>
</dt>
+ </dl></dd>
</dl></td>
</tr></table>
@@ -184,9 +336,15 @@
<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><a href="lsmtool.operations.html#lsmtool.operations.plot.plot">plot() (in module lsmtool.operations.plot)</a>
+ </dt>
+
+ <dd><dl>
+
+ <dt><a href="lsmtool.html#lsmtool.skymodel.SkyModel.plot">(lsmtool.skymodel.SkyModel method)</a>
</dt>
+ </dl></dd>
</dl></td>
</tr></table>
@@ -194,39 +352,127 @@
<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><a href="lsmtool.html#lsmtool.tableio.RA2Angle">RA2Angle() (in module lsmtool.tableio)</a>
+ </dt>
+
+
+ <dt><a href="lsmtool.html#lsmtool.operations_lib.radec2xy">radec2xy() (in module lsmtool.operations_lib)</a>
+ </dt>
+
+
+ <dt><a href="lsmtool.operations.html#lsmtool.operations.plot.RAtickformatter">RAtickformatter() (in module lsmtool.operations.plot)</a>
</dt>
</dl></td>
+ <td style="width: 33%" valign="top"><dl>
+
+ <dt><a href="lsmtool.operations.html#lsmtool.operations.remove.remove">remove() (in module lsmtool.operations.remove)</a>
+ </dt>
+
+ <dd><dl>
+
+ <dt><a href="lsmtool.html#lsmtool.skymodel.SkyModel.remove">(lsmtool.skymodel.SkyModel method)</a>
+ </dt>
+
+ </dl></dd>
+
+ <dt><a href="lsmtool.html#lsmtool.tableio.rowStr">rowStr() (in module lsmtool.tableio)</a>
+ </dt>
+
+
+ <dt><a href="lsmtool.operations.html#lsmtool.operations.add.run">run() (in module lsmtool.operations.add)</a>
+ </dt>
+
+ <dd><dl>
+
+ <dt><a href="lsmtool.operations.html#lsmtool.operations.concatenate.run">(in module lsmtool.operations.concatenate)</a>
+ </dt>
+
+
+ <dt><a href="lsmtool.operations.html#lsmtool.operations.group.run">(in module lsmtool.operations.group)</a>
+ </dt>
+
+
+ <dt><a href="lsmtool.operations.html#lsmtool.operations.merge.run">(in module lsmtool.operations.merge)</a>
+ </dt>
+
+
+ <dt><a href="lsmtool.operations.html#lsmtool.operations.move.run">(in module lsmtool.operations.move)</a>
+ </dt>
+
+
+ <dt><a href="lsmtool.operations.html#lsmtool.operations.plot.run">(in module lsmtool.operations.plot)</a>
+ </dt>
+
+
+ <dt><a href="lsmtool.operations.html#lsmtool.operations.remove.run">(in module lsmtool.operations.remove)</a>
+ </dt>
+
+
+ <dt><a href="lsmtool.operations.html#lsmtool.operations.select.run">(in module lsmtool.operations.select)</a>
+ </dt>
+
+
+ <dt><a href="lsmtool.operations.html#lsmtool.operations.setpatchpositions.run">(in module lsmtool.operations.setpatchpositions)</a>
+ </dt>
+
+
+ <dt><a href="lsmtool.operations.html#lsmtool.operations.transfer.run">(in module lsmtool.operations.transfer)</a>
+ </dt>
+
+
+ <dt><a href="lsmtool.operations.html#lsmtool.operations.ungroup.run">(in module lsmtool.operations.ungroup)</a>
+ </dt>
+
+ </dl></dd>
+ </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><a href="lsmtool.operations.html#lsmtool.operations.select.select">select() (in module lsmtool.operations.select)</a>
+ </dt>
+
+ <dd><dl>
+
+ <dt><a href="lsmtool.html#lsmtool.skymodel.SkyModel.select">(lsmtool.skymodel.SkyModel method)</a>
+ </dt>
+
+ </dl></dd>
+
+ <dt><a href="lsmtool.html#lsmtool.skymodel.SkyModel.setColValues">setColValues() (lsmtool.skymodel.SkyModel method)</a>
+ </dt>
+
+
+ <dt><a href="lsmtool.html#lsmtool.skymodel.SkyModel.setDefaltValues">setDefaltValues() (lsmtool.skymodel.SkyModel method)</a>
</dt>
- <dt><a href="code.html#lsmtool.SkyModel.setColValues">setColValues() (lsmtool.SkyModel method)</a>
+ <dt><a href="lsmtool.html#lsmtool.skymodel.SkyModel.setPatchPositions">setPatchPositions() (lsmtool.skymodel.SkyModel method)</a>
</dt>
- <dt><a href="code.html#lsmtool.SkyModel.setDefaltValues">setDefaltValues() (lsmtool.SkyModel method)</a>
+ <dt><a href="lsmtool.html#lsmtool.skymodel.SkyModel.setRowValues">setRowValues() (lsmtool.skymodel.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><a href="lsmtool.html#lsmtool.skymodel.SkyModel">SkyModel (class in lsmtool.skymodel)</a>
+ </dt>
+
+
+ <dt><a href="lsmtool.html#lsmtool.tableio.skyModelIdentify">skyModelIdentify() (in module lsmtool.tableio)</a>
</dt>
- <dt><a href="code.html#lsmtool.SkyModel.setRowValues">setRowValues() (lsmtool.SkyModel method)</a>
+ <dt><a href="lsmtool.html#lsmtool.tableio.skyModelReader">skyModelReader() (in module lsmtool.tableio)</a>
</dt>
- <dt><a href="code.html#lsmtool.SkyModel">SkyModel (class in lsmtool)</a>
+ <dt><a href="lsmtool.html#lsmtool.tableio.skyModelWriter">skyModelWriter() (in module lsmtool.tableio)</a>
</dt>
</dl></td>
@@ -236,9 +482,15 @@
<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><a href="lsmtool.operations.html#lsmtool.operations.transfer.transfer">transfer() (in module lsmtool.operations.transfer)</a>
</dt>
+ <dd><dl>
+
+ <dt><a href="lsmtool.html#lsmtool.skymodel.SkyModel.transfer">(lsmtool.skymodel.SkyModel method)</a>
+ </dt>
+
+ </dl></dd>
</dl></td>
</tr></table>
@@ -246,7 +498,7 @@
<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><a href="lsmtool.html#lsmtool.skymodel.SkyModel.ungroup">ungroup() (lsmtool.skymodel.SkyModel method)</a>
</dt>
</dl></td>
@@ -256,7 +508,17 @@
<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><a href="lsmtool.html#lsmtool.skymodel.SkyModel.write">write() (lsmtool.skymodel.SkyModel method)</a>
+ </dt>
+
+ </dl></td>
+</tr></table>
+
+<h2 id="X">X</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+ <td style="width: 33%" valign="top"><dl>
+
+ <dt><a href="lsmtool.html#lsmtool.operations_lib.xy2radec">xy2radec() (in module lsmtool.operations_lib)</a>
</dt>
</dl></td>
@@ -303,7 +565,7 @@
</div>
<div class="footer">
© Copyright 2014, David Rafferty.
- Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.1.
+ Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.2.
</div>
</body>
</html>
\ No newline at end of file
diff --git a/doc/build/html/index.html b/doc/build/html/index.html
index 388d62c7ac2f62ef447e2550ff1854c96c91254e..723d9906984b068f1edd20e597baed3c5ecd7273 100644
--- a/doc/build/html/index.html
+++ b/doc/build/html/index.html
@@ -24,7 +24,8 @@
<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="#" />
+ <link rel="top" title="LSMTool 1.0.0 documentation" href="#" />
+ <link rel="next" title="LSMTool: the LOFAR Local Sky Model Tool" href="overview.html" />
</head>
<body>
<div class="related">
@@ -36,6 +37,9 @@
<li class="right" >
<a href="py-modindex.html" title="Python Module Index"
>modules</a> |</li>
+ <li class="right" >
+ <a href="overview.html" title="LSMTool: the LOFAR Local Sky Model Tool"
+ accesskey="N">next</a> |</li>
<li><a href="#">LSMTool 1.0.0 documentation</a> »</li>
</ul>
</div>
@@ -47,14 +51,26 @@
<div class="section" id="welcome-to-lsmtool-s-documentation">
<h1>Welcome to LSMTool’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@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>
+<p>LSMTool is a Python package which allows for the manipulation of LOFAR sky models in the <tt class="docutils literal"><span class="pre">makesourcedb</span></tt> format.</p>
</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="section" id="contents">
+<h1>Contents<a class="headerlink" href="#contents" title="Permalink to this headline">¶</a></h1>
<div class="toctree-wrapper compound">
-<ul class="simple">
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="overview.html">LSMTool: the LOFAR Local Sky Model Tool </a><ul>
+<li class="toctree-l2"><a class="reference internal" href="overview.html#usage">Usage</a></li>
+<li class="toctree-l2"><a class="reference internal" href="overview.html#operations">Operations</a></li>
+<li class="toctree-l2"><a class="reference internal" href="overview.html#example-parset">Example parset</a></li>
+<li class="toctree-l2"><a class="reference internal" href="overview.html#interactive-use-and-scripting">Interactive use and scripting</a></li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="lsmtool.html">LSMTool Module Documentation</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="lsmtool.html#module-lsmtool">lsmtool module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="lsmtool.html#module-lsmtool.operations_lib">lsmtool.operations_lib module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="lsmtool.html#module-lsmtool.skymodel">lsmtool.skymodel module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="lsmtool.html#module-lsmtool.tableio">lsmtool.tableio module</a></li>
+</ul>
+</li>
</ul>
</div>
</div>
@@ -62,7 +78,6 @@ source ~rafferty/init_lsmtool
<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>
@@ -76,9 +91,13 @@ source ~rafferty/init_lsmtool
<h3><a href="#">Table Of Contents</a></h3>
<ul>
<li><a class="reference internal" href="#">Welcome to LSMTool’s documentation!</a></li>
+<li><a class="reference internal" href="#contents">Contents</a></li>
<li><a class="reference internal" href="#indices-and-tables">Indices and tables</a></li>
</ul>
+ <h4>Next topic</h4>
+ <p class="topless"><a href="overview.html"
+ title="next chapter">LSMTool: the LOFAR Local Sky Model Tool </a></p>
<h3>This Page</h3>
<ul class="this-page-menu">
<li><a href="_sources/index.txt"
@@ -110,12 +129,15 @@ source ~rafferty/init_lsmtool
<li class="right" >
<a href="py-modindex.html" title="Python Module Index"
>modules</a> |</li>
+ <li class="right" >
+ <a href="overview.html" title="LSMTool: the LOFAR Local Sky Model Tool"
+ >next</a> |</li>
<li><a href="#">LSMTool 1.0.0 documentation</a> »</li>
</ul>
</div>
<div class="footer">
© Copyright 2014, David Rafferty.
- Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.1.
+ Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.2.
</div>
</body>
</html>
\ No newline at end of file
diff --git a/doc/build/html/objects.inv b/doc/build/html/objects.inv
index d62ac62bc30952b92ac08587bfd7950735c42d52..1ad4e57d44aeede78777686874d3cff4463ad167 100644
Binary files a/doc/build/html/objects.inv and b/doc/build/html/objects.inv differ
diff --git a/doc/build/html/py-modindex.html b/doc/build/html/py-modindex.html
index ca56c3e665858e43da511275189366b7c7a994e3..6e362de5e68da1f118fe01e9a5d0e34870503439 100644
--- a/doc/build/html/py-modindex.html
+++ b/doc/build/html/py-modindex.html
@@ -27,10 +27,6 @@
<link rel="top" title="LSMTool 1.0.0 documentation" href="index.html" />
- <script type="text/javascript">
- DOCUMENTATION_OPTIONS.COLLAPSE_INDEX = true;
- </script>
-
</head>
<body>
@@ -64,9 +60,85 @@
<tr class="cap" id="cap-l"><td></td><td>
<strong>l</strong></td><td></td></tr>
<tr>
- <td></td>
+ <td><img src="_static/minus.png" class="toggler"
+ id="toggle-1" style="display: none" alt="-" /></td>
<td>
- <a href="code.html#module-lsmtool"><tt class="xref">lsmtool</tt></a></td><td>
+ <a href="lsmtool.html#module-lsmtool"><tt class="xref">lsmtool</tt></a></td><td>
+ <em></em></td></tr>
+ <tr class="cg-1">
+ <td></td>
+ <td>
+ <a href="lsmtool.operations.html#module-lsmtool.operations"><tt class="xref">lsmtool.operations</tt></a></td><td>
+ <em></em></td></tr>
+ <tr class="cg-1">
+ <td></td>
+ <td>
+ <a href="lsmtool.operations.html#module-lsmtool.operations.add"><tt class="xref">lsmtool.operations.add</tt></a></td><td>
+ <em></em></td></tr>
+ <tr class="cg-1">
+ <td></td>
+ <td>
+ <a href="lsmtool.operations.html#module-lsmtool.operations.concatenate"><tt class="xref">lsmtool.operations.concatenate</tt></a></td><td>
+ <em></em></td></tr>
+ <tr class="cg-1">
+ <td></td>
+ <td>
+ <a href="lsmtool.operations.html#module-lsmtool.operations.group"><tt class="xref">lsmtool.operations.group</tt></a></td><td>
+ <em></em></td></tr>
+ <tr class="cg-1">
+ <td></td>
+ <td>
+ <a href="lsmtool.operations.html#module-lsmtool.operations.merge"><tt class="xref">lsmtool.operations.merge</tt></a></td><td>
+ <em></em></td></tr>
+ <tr class="cg-1">
+ <td></td>
+ <td>
+ <a href="lsmtool.operations.html#module-lsmtool.operations.move"><tt class="xref">lsmtool.operations.move</tt></a></td><td>
+ <em></em></td></tr>
+ <tr class="cg-1">
+ <td></td>
+ <td>
+ <a href="lsmtool.operations.html#module-lsmtool.operations.plot"><tt class="xref">lsmtool.operations.plot</tt></a></td><td>
+ <em></em></td></tr>
+ <tr class="cg-1">
+ <td></td>
+ <td>
+ <a href="lsmtool.operations.html#module-lsmtool.operations.remove"><tt class="xref">lsmtool.operations.remove</tt></a></td><td>
+ <em></em></td></tr>
+ <tr class="cg-1">
+ <td></td>
+ <td>
+ <a href="lsmtool.operations.html#module-lsmtool.operations.select"><tt class="xref">lsmtool.operations.select</tt></a></td><td>
+ <em></em></td></tr>
+ <tr class="cg-1">
+ <td></td>
+ <td>
+ <a href="lsmtool.operations.html#module-lsmtool.operations.setpatchpositions"><tt class="xref">lsmtool.operations.setpatchpositions</tt></a></td><td>
+ <em></em></td></tr>
+ <tr class="cg-1">
+ <td></td>
+ <td>
+ <a href="lsmtool.operations.html#module-lsmtool.operations.transfer"><tt class="xref">lsmtool.operations.transfer</tt></a></td><td>
+ <em></em></td></tr>
+ <tr class="cg-1">
+ <td></td>
+ <td>
+ <a href="lsmtool.operations.html#module-lsmtool.operations.ungroup"><tt class="xref">lsmtool.operations.ungroup</tt></a></td><td>
+ <em></em></td></tr>
+ <tr class="cg-1">
+ <td></td>
+ <td>
+ <a href="lsmtool.html#module-lsmtool.operations_lib"><tt class="xref">lsmtool.operations_lib</tt></a></td><td>
+ <em></em></td></tr>
+ <tr class="cg-1">
+ <td></td>
+ <td>
+ <a href="lsmtool.html#module-lsmtool.skymodel"><tt class="xref">lsmtool.skymodel</tt></a></td><td>
+ <em></em></td></tr>
+ <tr class="cg-1">
+ <td></td>
+ <td>
+ <a href="lsmtool.html#module-lsmtool.tableio"><tt class="xref">lsmtool.tableio</tt></a></td><td>
<em></em></td></tr>
</table>
@@ -107,7 +179,7 @@
</div>
<div class="footer">
© Copyright 2014, David Rafferty.
- Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.1.
+ Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.2.
</div>
</body>
</html>
\ No newline at end of file
diff --git a/doc/build/html/search.html b/doc/build/html/search.html
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--- a/doc/build/html/search.html
+++ b/doc/build/html/search.html
@@ -100,7 +100,7 @@
</div>
<div class="footer">
© Copyright 2014, David Rafferty.
- Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.1.
+ Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.2.
</div>
</body>
</html>
\ No newline at end of file
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diff --git a/doc/lsmtool.pdf b/doc/lsmtool.pdf
index f34b3350219b8a434fdbcc39c8505e8f3e8395c4..fcfc164ed97b2de4d618d472f3f6403b8ce726ff 100644
Binary files a/doc/lsmtool.pdf and b/doc/lsmtool.pdf differ
diff --git a/doc/lsmtool.tex b/doc/lsmtool.tex
index 62eee53732b3bf25bd88c6e4e3c4356d031aea8f..6a46b24815549954188e2d24aaa19596184d6ea7 100644
--- a/doc/lsmtool.tex
+++ b/doc/lsmtool.tex
@@ -29,7 +29,7 @@
\section[LSMTool: the LOFAR Local Sky Model Tool]{LSMTool: the LOFAR Local Sky Model Tool\footnote{This section is maintained by David Rafferty ({\tt drafferty@hs.uni-hamburg.de}).}}
\label{lsmtool}
-LSMTool is a Python package which allow the manipulation of sky models in the \texttt{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:
+LSMTool is a Python package which allows for the manipulation of sky models in the \texttt{makesourcedb} format (understood by BBS and NDPPP). 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:
\begin{verbatim}
use LofIm
source ~rafferty/init_lsmtool
@@ -40,7 +40,7 @@ Note that the Pythonlibs LOFAR package includes an older version of astropy that
\subsection{Usage}
\label{lsmtool:usage}
-LSMTool can be run as follows:
+The command-line version of LSMTool can be run as follows:
\begin{verbatim}
Usage: lsmtool.py <skymodel> <parset> [<beam MS>]
Options:
@@ -66,6 +66,7 @@ These are the operations that LSMTool can perform:
\item[MERGE]: Merge two or more patches into one
\item[CONCATENATE]: Concatenate two sky models
\item[ADD]: Add a source
+ \item[SETPATCHPOSITIONS]: Calculate and set patch positions
\item[PLOT]: Plot a simple representation of the sky model
\end{description}
@@ -122,9 +123,9 @@ PatchFile & string & sky\_model\_with\_patches.sky & File with patches that will
\hline
\multicolumn{4}{l}{\textbf{GROUP}}\\
Algorithm & string & tessellate & One of tessellate, cluster, single, every\\
-TargetFlux & string & 10.0 Jy & target total flux of patches (tessellate only)\\
+TargetFlux & string & 10.0 Jy & Target total flux of patches (tessellate only)\\
+NumClusters & int & 100 & Number of clusters (cluster only)\\
ApplyBeam & bool & True & If true, apparent fluxes will be used \\
-Method & string & mid & Set patch positions by mid, mean, or wmean\\
\hline
\multicolumn{4}{l}{\textbf{UNGROUP}}\\
\hline
diff --git a/doc/source/.DS_Store b/doc/source/.DS_Store
index 5008ddfcf53c02e82d7eee2e57c38e5672ef89f6..6a60f02d7148f197b444804ed2b729f5833465d3 100644
Binary files a/doc/source/.DS_Store and b/doc/source/.DS_Store differ
diff --git a/doc/source/code.rst b/doc/source/code.rst
deleted file mode 100644
index d184c03adb17c0c890f8333941539f66e6e55b10..0000000000000000000000000000000000000000
--- a/doc/source/code.rst
+++ /dev/null
@@ -1,7 +0,0 @@
-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
index 6553401d659cce99ea491a1812d48e81135d6732..3a2182ee76c2bb38fe5ab791c27e069bd7a1e8e5 100644
--- a/doc/source/conf.py
+++ b/doc/source/conf.py
@@ -30,9 +30,9 @@ import os
# ones.
extensions = [
'sphinx.ext.autodoc',
- 'sphinx.ext.doctest',
'sphinx.ext.intersphinx',
'sphinx.ext.mathjax',
+ 'numpydoc',
]
# Add any paths that contain templates here, relative to this directory.
diff --git a/doc/source/index.rst b/doc/source/index.rst
index c6b45d5b81712dc74703c35c5d8ea486dfe15834..1caa8c0a70ec68e23cd58f05c93e0a90913c99f3 100644
--- a/doc/source/index.rst
+++ b/doc/source/index.rst
@@ -1,27 +1,20 @@
-.. 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
+LSMTool is a Python package which allows for the manipulation of LOFAR sky models in the ``makesourcedb`` format.
-Note that the Pythonlibs LOFAR package includes an older version of astropy that conflicts with LSMTool and cannot be used in conjunction with it.
+Contents
+========
.. toctree::
:maxdepth: 2
-
+ overview.rst
+ lsmtool.rst
Indices and tables
==================
* :ref:`genindex`
-* :ref:`modindex`
* :ref:`search`
diff --git a/lsmtool/__init__.py b/lsmtool/__init__.py
index 7dc418a742bd53b3dae069f04cb16fcecb97697d..4bf7f9ea5684f2b6900683d7c3bec68eb9c0ebd0 100644
--- a/lsmtool/__init__.py
+++ b/lsmtool/__init__.py
@@ -16,7 +16,8 @@
# 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
+"""The load() convenience function is used to load a sky model file into a
+SkyModel object.
.. moduleauthor:: David Rafferty <drafferty@hs.uni-hamburg.de>
@@ -39,6 +40,12 @@ def load(fileName, beamMS=None):
Measurement set from which the primary beam will be estimated. A
column of attenuated Stokes I fluxes will be added to the table.
+ Returns
+ -------
+ SkyModel object
+ A SkyModel object that stores the sky model and provides methods for
+ accessing it.
+
Examples
--------
Load a sky model into a SkyModel object::
@@ -47,7 +54,7 @@ def load(fileName, beamMS=None):
>>> s = lsmtool.load('sky.model')
Load a sky model with a beam MS so that apparent fluxes will
- be available (in addition to intrinsic fluxes):::
+ be available (in addition to intrinsic fluxes)::
>>> s = lsmtool.load('sky.model', 'SB100.MS')
diff --git a/lsmtool/_version.py b/lsmtool/_version.py
index 28c169c1bfd88d434ec76102a02cc4b346e341b8..f8a0f3b9f7fd634a3c6c87f5ca99381f77e372e4 100644
--- a/lsmtool/_version.py
+++ b/lsmtool/_version.py
@@ -1,6 +1,6 @@
# -*- coding: utf-8 -*-
#
-#This module stores the version and changelog
+# This module stores the version and changelog
# Version number
__version__ = '1.0.0'
@@ -10,7 +10,7 @@ def changelog():
log = """
LSMTool Changelog.
-----------------------------------------------
- 2014/05/25 - Version 1.0.0 (initial release)
+ 2014/06/25 - Version 1.0.0 (initial release)
"""
print(log)
diff --git a/lsmtool/lsmtool.py b/lsmtool/lsmtool.py
index c1b7d573c27ddb081e9f70053c86df57d6942c0b..d3b4f0cd77477860c179412e4314cbbf549dec04 100755
--- a/lsmtool/lsmtool.py
+++ b/lsmtool/lsmtool.py
@@ -1,5 +1,21 @@
-#!/usr/bin/env python
# -*- coding: utf-8 -*-
+#
+# This is the command-line script that performs the operations defined in a
+# LSMTool parset.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
# Authors:
# David Raffery
diff --git a/lsmtool/operations/_filter.py b/lsmtool/operations/_filter.py
index 1fd23b6e508e9a341aa6ee883d73fe5295d453f0..18d9662d6b77a2acd0af4c985531e453d919862f 100644
--- a/lsmtool/operations/_filter.py
+++ b/lsmtool/operations/_filter.py
@@ -246,8 +246,8 @@ def filter(LSM, filterExpression, exclusive=False, aggregate=None,
def parseFilter(filterExpression):
"""
- Takes a filter expression and returns tuple of
- (property, operation, val, units), all as strings
+ Takes a filter expression and returns tuple of (property, operation, val,
+ units), all as strings.
"""
try:
from ..tableio import allowedColumnNames
@@ -352,7 +352,7 @@ def convertOperStr(operStr):
def getFilterIndices(colVals, filterOper, filterVal, useRegEx=False):
"""
- Returns the indices that correspond to the input filter expression
+ Returns the indices that correspond to the input filter expression.
"""
import operator as op
import fnmatch
@@ -388,7 +388,7 @@ def getFilterIndices(colVals, filterOper, filterVal, useRegEx=False):
def getMaskValues(mask, RARad, DecRad):
"""
- Returns an array of mask values for each (RA, Dec) pair in radians
+ Returns an array of mask values for each (RA, Dec) pair in radians.
"""
import math
import pyrap
diff --git a/lsmtool/operations/concatenate.py b/lsmtool/operations/concatenate.py
index aec428d0a77a435a139578afc9e430a41283f8e9..284d5cea942a1a82325c04cef6700222e1bf7104 100644
--- a/lsmtool/operations/concatenate.py
+++ b/lsmtool/operations/concatenate.py
@@ -60,7 +60,7 @@ def concatenate(LSM1, LSM2, matchBy='name', radius=0.1, keep='all'):
Determines how duplicates are treated:
- 'all' => all duplicates are kept; those with identical names are re-
named
- - 'from1' => duplicates kept are those from sky model 1 (the parent)
+ - 'from1' => duplicates kept are those from sky model 1 (LSM1)
- 'from2' => duplicates kept are those from sky model 2 (LSM2)
Examples
diff --git a/lsmtool/operations_lib.py b/lsmtool/operations_lib.py
index 8da995d4287a5a349d57ee67a54c6d4c8890514a..f384bc19d2173d6ee52a5a2f391ef70dbf1ee228 100644
--- a/lsmtool/operations_lib.py
+++ b/lsmtool/operations_lib.py
@@ -24,6 +24,22 @@ import os
def attenuate(beamMS, fluxes, RADeg, DecDeg):
"""
Returns flux attenuated by primary beam.
+
+ Parameters
+ ----------
+ beamMS : str
+ Measurement set for which the beam model is made
+ fluxes : list
+ List of fluxes to attenuate
+ RADeg : list
+ List of RA values in degrees
+ DecDeg : list
+ List of Dec values in degrees
+
+ Returns
+ -------
+ attFluxes : numpy array
+
"""
import numpy as np
@@ -75,7 +91,29 @@ def attenuate(beamMS, fluxes, RADeg, DecDeg):
def radec2xy(RA, Dec, refRA=None, refDec=None):
- """Returns x, y for input ra, dec
+ """Returns x, y for input ra, dec.
+
+ Note that the reference RA and Dec must be the same in calls to both
+ radec2xy() and xy2radec() if matched pairs of (x, y) <=> (RA, Dec) are
+ desired.
+
+ Parameters
+ ----------
+ RA : list
+ List of RA values in degrees
+ Dec : list
+ List of Dec values in degrees
+ refRA : float, optional
+ Reference RA in degrees.
+ refDec : float, optional
+ Reference Dec in degrees
+
+ Returns
+ -------
+ x, y : list, list
+ Lists of x and y pixel values corresponding to the input RA and Dec
+ values
+
"""
from astropy.wcs import WCS
import numpy as np
@@ -104,8 +142,30 @@ def radec2xy(RA, Dec, refRA=None, refDec=None):
def xy2radec(x, y, refRA=0.0, refDec=0.0):
- """Returns x, y for input ra, dec
- """
+ """Returns x, y for input ra, dec.
+
+ Note that the reference RA and Dec must be the same in calls to both
+ radec2xy() and xy2radec() if matched pairs of (x, y) <=> (RA, Dec) are
+ desired.
+
+ Parameters
+ ----------
+ x : list
+ List of x values in pixels
+ y : list
+ List of y values in pixels
+ refRA : float, optional
+ Reference RA in degrees
+ refDec : float, optional
+ Reference Dec in degrees
+
+ Returns
+ -------
+ RA, Dec : list, list
+ Lists of RA and Dec values corresponding to the input x and y pixel
+ values
+
+ """
from astropy.wcs import WCS
import numpy as np
@@ -126,135 +186,3 @@ def xy2radec(x, y, refRA=0.0, refDec=0.0):
Dec.append(w.wcs_pix2world(x_y, 0)[0][1])
return RA, Dec
-
-
-class StatusBar():
- # class variables:
- # max: number of total items to be completed
- # pos: number of completed items
- # spin_pos: current position in array of busy_chars
- # inc: amount of items to increment completed 'pos' by
- # (shared resource)
- # comp: amount of '=' to display in the progress bar
- # started: whether or not the statusbar has been started
- # color: color of text
- def __init__(self, text, pos=0, max=100, color='\033[0m'):
- self.text = text
- self.pos = pos
- self.max = max
- self.busy_char = '|'
- self.spin_pos = 0
- self.inc = 0
- self.started = 0
- self.color = color
- self.__getsize()
- if max > 0:
- self.comp = int(float(self.pos) / self.max * self.columns)
- else:
- self.comp = 0
-
- # find number of columns in terminal
- def __getsize(self):
- try:
- rows, columns = getTerminalSize()
- except ValueError:
- rows = columns = 0
- if int(columns) > self.max + 2 + 44 + (len(str(self.max))*2 + 2):
- self.columns = self.max
- else:
- # note: -2 is for brackets, -44 for 'Fitting islands...' text, rest is for pos/max text
- self.columns = int(columns) - 2 - 44 - (len(str(self.max))*2 + 2)
- return
-
- # redraw progress bar
- def __print(self):
- self.__getsize()
-
- sys.stdout.write('\x1b[1G')
- if self.max == 0:
- sys.stdout.write(self.color + self.text + '[] 0/0\033[0m\n')
- else:
- sys.stdout.write(self.color + self.text + '[' + '=' * self.comp + self.busy_char + '-'*(self.columns - self.comp - 1) + '] ' + str(self.pos) + '/' + str(self.max) + '\033[0m')
- sys.stdout.write('\x1b[' + str(self.comp + 2 + 44) + 'G')
- sys.stdout.flush()
- return
-
- # spin the spinner by one increment
- def spin(self):
- busy_chars = ['|','/','-','\\']
- self.spin_pos += 1
- if self.spin_pos >= len(busy_chars):
- self.spin_pos = 0
- # display the busy spinning icon
- self.busy_char = busy_chars[self.spin_pos]
- sys.stdout.write(self.color + busy_chars[self.spin_pos] + '\x1b[1D' + '\033[0m')
- sys.stdout.flush()
-
- # increment number of completed items
- def increment(self):
- self.inc = 1
- if (self.pos + self.inc) >= self.max:
- self.pos = self.max
- self.comp = self.columns
- self.busy_char = ''
- self.__print()
- return 0
- else:
- self.pos += self.inc
- self.inc = 0
- self.spin()
- self.comp = int(float(self.pos) / self.max \
- * self.columns)
- self.__print()
- return 1
-
- def start(self):
- self.started = 1
- self.__print()
-
- def stop(self):
- if self.started:
- self.pos = self.max
- self.comp = self.columns
- self.busy_char = ''
- self.__print()
- sys.stdout.write('\n')
- self.started = 0
- return 0
-
-
-def getTerminalSize():
- """
- returns (lines:int, cols:int)
- """
- import os, struct
- def ioctl_GWINSZ(fd):
- import fcntl, termios
- return struct.unpack("hh", fcntl.ioctl(fd, termios.TIOCGWINSZ, "1234"))
- # try stdin, stdout, stderr
- for fd in (0, 1, 2):
- try:
- return ioctl_GWINSZ(fd)
- except:
- pass
- # try os.ctermid()
- try:
- fd = os.open(os.ctermid(), os.O_RDONLY)
- try:
- return ioctl_GWINSZ(fd)
- finally:
- os.close(fd)
- except:
- pass
- # try `stty size`
- try:
- return tuple(int(x) for x in os.popen("stty size", "r").read().split())
- except:
- pass
- # try environment variables
- try:
- return tuple(int(os.getenv(var)) for var in ("LINES", "COLUMNS"))
- except:
- pass
- # Give up. return 0.
- return (0, 0)
diff --git a/lsmtool/skymodel.py b/lsmtool/skymodel.py
index 210d077d62660ef780540f06d8dd61e1393a775b..ba39872bcd7bc7e9735b13e8c464a94f7b7ba2cd 100644
--- a/lsmtool/skymodel.py
+++ b/lsmtool/skymodel.py
@@ -141,7 +141,7 @@ class SkyModel(object):
def copy(self):
"""
- Returns a copy of the sky model
+ Returns a copy of the sky model.
"""
import copy
@@ -151,7 +151,7 @@ class SkyModel(object):
def more(self, colName=None, patchName=None, sourceName=None, sortBy=None,
lowToHigh=False):
"""
- Prints the sky model table to the screen with more-like commands
+ Prints the sky model table to the screen with more-like commands.
Parameters
----------
@@ -191,7 +191,6 @@ class SkyModel(object):
colName = [colName] # needed in order to get a table instead of a column
table = table[colName]
-
# Get patches
if patchName is not None:
pindx = self._getNameIndx(patchName, patch=True)
@@ -425,7 +424,7 @@ class SkyModel(object):
def setPatchPositions(self, patchDict=None, method='mid', applyBeam=False,
- perPatchProjection=True):
+ perPatchProjection=True):
"""
Sets the patch positions.
@@ -440,8 +439,9 @@ class SkyModel(object):
- 'mid' => the position is set to the midpoint of the patch
- 'mean' => the positions is set to the mean RA and Dec of the patch
- 'wmean' => the position is set to the flux-weighted mean RA and
- Dec of the patch
+ Dec of the patch
- 'zero' => set all positions to [0.0, 0.0]
+
Note that the mid, mean, and wmean positions are calculated from TAN-
projected values.
applyBeam : bool, optional
@@ -499,7 +499,7 @@ class SkyModel(object):
def _getXY(self, patchName=None):
"""
- Returns lists of projected x and y values for all sources
+ Returns lists of projected x and y values for all sources.
Parameters
----------
@@ -538,7 +538,7 @@ class SkyModel(object):
def getDefaltValues(self):
"""
- Returns dict of {colName:default} values for all columns with defaults
+ Returns dict of {colName:default} values for all columns with defaults.
"""
colNames = self.getColNames()
defaultDict = {}
@@ -550,7 +550,7 @@ class SkyModel(object):
def setDefaltValues(self, colDict):
"""
- Sets default column values
+ Sets default column values.
Parameters
----------
@@ -604,7 +604,7 @@ class SkyModel(object):
return self.table.keys()
- def getColValues(self, colName, units=None, aggregate=None, weight=False,
+ def getColValues(self, colName, units=None, aggregate=None,
applyBeam=False):
"""
Returns a numpy array of column values.
@@ -617,7 +617,7 @@ class SkyModel(object):
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.
- aggregate : str, optional
+ aggregate : {'sum', 'mean', 'wmean', 'min', max'}, optional
If set, the array returned will be of values aggregated
over the patch members. The following aggregation functions are
available:
@@ -944,6 +944,17 @@ class SkyModel(object):
def getPatchSizes(self, units=None, weight=False, applyBeam=False):
"""
Returns array of patch sizes.
+
+ Parameters
+ ----------
+ units : str, optional
+ Units for returned sizes (e.g., 'arcsec', 'degree')
+ weight : bool, optional
+ If True, weight the source positions inside the patch by flux
+ applyBeam : bool, optional
+ If True and weight is True, attenuate the fluxes used for weighting
+ by the beam
+
"""
if self.hasPatches:
col = self._getSizeColumn(weight=weight, applyBeam=applyBeam)
@@ -956,7 +967,7 @@ class SkyModel(object):
def getPatchNames(self):
"""
- Returns array of patch names.
+ Returns array of all patch names in the sky model.
"""
if self.hasPatches:
return self.table.groups.keys['Patch'].data
@@ -1086,7 +1097,7 @@ class SkyModel(object):
def _applyBeamToCol(self, col, patch=False):
"""
- Applies beam attenuation to the column values
+ Applies beam attenuation to the column values.
"""
from operations_lib import attenuate
@@ -1420,14 +1431,10 @@ class SkyModel(object):
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 filter expression specified as:
+ - a string of ``'<property> <operator> <value> [<units>]'``
+ - a list of ``[property, operator, value, unit]``
+
The property to filter on must be a valid column name or the filename
of a mask image.
@@ -1438,6 +1445,7 @@ class SkyModel(object):
- >
- <
- = (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
@@ -1448,9 +1456,7 @@ class SkyModel(object):
- '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.
+ - 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
@@ -1497,35 +1503,39 @@ class SkyModel(object):
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 '==')
+ - !=
+ - <=
+ - >=
+ - >
+ - <
+ - = (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.
+ - '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
@@ -1561,7 +1571,7 @@ class SkyModel(object):
def group(self, algorithm, targetFlux=None, numClusters=100, applyBeam=False):
"""
- Groups sources into patches
+ Groups sources into patches.
Parameters
----------
@@ -1681,7 +1691,7 @@ class SkyModel(object):
def merge(self, patches, name=None):
"""
- Merge two or more patches together
+ Merge two or more patches together.
Parameters
----------
@@ -1702,7 +1712,7 @@ class SkyModel(object):
def concatenate(self, LSM2, matchBy='name', radius=0.1, keep='all'):
"""
- Concatenate two sky models
+ Concatenate two sky models.
Parameters
----------
diff --git a/lsmtool/tableio.py b/lsmtool/tableio.py
index 3c38b534b400112dd337ed8f9ee866835d90240d..f1ac3ff1d6bdc98121add3b0164ff5fc6d79c0f0 100644
--- a/lsmtool/tableio.py
+++ b/lsmtool/tableio.py
@@ -47,7 +47,7 @@ allowedColumnDefaults = {'name':'N/A', 'type':'N/A', 'patch':'N/A', 'ra':'N/A',
def skyModelReader(fileName):
"""
- Reads a makesourcedb sky model file into an astropy table
+ Reads a makesourcedb sky model file into an astropy table.
Parameters
----------
@@ -58,6 +58,7 @@ def skyModelReader(fileName):
Returns
-------
table : astropy.table.Table object
+
"""
# Open the input file
try:
@@ -225,6 +226,17 @@ def skyModelReader(fileName):
def RA2Angle(RA):
"""
Returns Angle objects for input RA values.
+
+ Parameters
+ ----------
+ RA : str, float or list of str, float
+ Values of RA to convert. Can be strings in makesourcedb format or floats
+ in degrees.
+
+ Returns
+ -------
+ RAAngle : astropy.coordinates.Angle object
+
"""
if type(RA) is str or type(RA) is float:
RA = [RA]
@@ -244,6 +256,17 @@ def RA2Angle(RA):
def Dec2Angle(Dec):
"""
Returns Angle objects for input Dec values.
+
+ Parameters
+ ----------
+ Dec : str, float or list of str, float
+ Values of Dec to convert. Can be strings in makesourcedb format or floats
+ in degrees.
+
+ Returns
+ -------
+ DecAngle : astropy.coordinates.Angle object
+
"""
if type(Dec) is str or type(Dec) is float:
Dec = [Dec]
@@ -349,11 +372,16 @@ def skyModelWriter(table, fileName):
def rowStr(row):
"""
- Returns makesourcedb representation of a row
+ Returns makesourcedb representation of a row.
Parameters
----------
row : astropy.table.Row object
+
+ Returns
+ -------
+ line : str
+ Sting representing a row in a makesourcedb sky model file
"""
line = []
for colKey in row.columns:
diff --git a/setup.py b/setup.py
index fbbd16ebc3a82defd4f54385f59bcd7c0515b504..e469d5bc86f0f631690f6f4be25c19828fda4c84 100644
--- a/setup.py
+++ b/setup.py
@@ -45,7 +45,7 @@ setup(
'Topic :: Software Development :: Libraries :: Python Modules',
],
tests_require=['pytest'],
- install_requires=['numpy','cython','astropy'],
+ install_requires=['numpy','astropy'],
#scripts = ['say_hello.py'],
packages=['lsmtool','lsmtool.operations'],
test_suite='test',