updated documentation

WilfriedMercier · Mar 17, 2022 · 6c6c420 · 6c6c420
1 parent d208887
commit 6c6c420
Show file tree

Hide file tree

Showing 25 changed files with 861 additions and 391 deletions.
diff --git a/docs/API/catalogues.html b/docs/API/catalogues.html
diff --git a/docs/API/filters.html b/docs/API/filters.html
diff --git a/docs/API/index.html b/docs/API/index.html
@@ -13,7 +13,7 @@
 <link href="../search.html" rel="search" title="Search"/>
 <link href="../genindex.html" rel="index" title="Index"/>
 <link href="catalogues.html" rel="next" title="Catalogue classes"/>
-<link href="../examples/example2.html" rel="prev" title="Example 2: Resolved SFR map with LePhare from an output file"/>
+<link href="../examples/example3.html" rel="prev" title="Example 3: Generating a resolved stellar mass map with Cigale"/>
 </head>
 <body class="antialiased text-gray">
 <div class="h-screen xl:grid xl:grid-layout" data-action="keydown@window-&gt;search#focus" data-controller="sidebar search" id="page">
@@ -71,6 +71,7 @@
 <ul>
 <li class="toctree-l1"><div class="nav-link"><a class="reference internal" data-action="click-&gt;sidebar#close" href="../examples/example1.html">1. Resolved stellar mass map with LePhare</a></div></li>
 <li class="toctree-l1"><div class="nav-link"><a class="reference internal" data-action="click-&gt;sidebar#close" href="../examples/example2.html">2. Resolved SFR map from an already existing LePhare output file</a></div></li>
+<li class="toctree-l1"><div class="nav-link"><a class="reference internal" data-action="click-&gt;sidebar#close" href="../examples/example3.html">3. Resolved stellar mass map with Cigale</a></div></li>
 </ul>
 <p class="caption" role="heading"><span class="caption-text">―――――――――――――――</span></p>
 <ul class="current">
@@ -84,6 +85,7 @@
 </ul>
 </li>
 <li class="toctree-l2"><div class="nav-link"><a class="reference internal" data-action="click-&gt;sidebar#close" href="outputs.html">SED fitting code output classes</a></div></li>
+<li class="toctree-l2"><div class="nav-link"><a class="reference internal" data-action="click-&gt;sidebar#close" href="photometry.html">Photometry related fonctions</a></div></li>
 <li class="toctree-l2"><div class="nav-link"><a class="reference internal" data-action="click-&gt;sidebar#close" href="sed.html">SED classes</a></div></li>
 </ul>
 </li>
@@ -101,7 +103,7 @@
 </nav>
 <article class="flex-1" role="main">
 <section id="api">
-<h1>API<a aria-label="Click to copy this link" class="headerlink tooltipped tooltipped-ne tooltipped tooltipped-ne tooltipped tooltipped-ne" data-action="click-&gt;clipboard#copyHeaderLink" data-controller="clipboard" href="#api">¶</a></h1>
+<h1>API<a aria-label="Click to copy this link" class="headerlink tooltipped tooltipped-ne" data-action="click-&gt;clipboard#copyHeaderLink" data-controller="clipboard" href="#api">¶</a></h1>
 <div class="toctree-wrapper compound">
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="catalogues.html">Catalogue classes</a></li>
@@ -113,6 +115,7 @@ <h1>API<a aria-label="Click to copy this link" class="headerlink tooltipped tool
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="outputs.html">SED fitting code output classes</a></li>
+<li class="toctree-l1"><a class="reference internal" href="photometry.html">Photometry related fonctions</a></li>
 <li class="toctree-l1"><a class="reference internal" href="sed.html">SED classes</a></li>
 </ul>
 </div>

diff --git a/docs/API/misc/enum.html b/docs/API/misc/enum.html
diff --git a/docs/API/misc/index.html b/docs/API/misc/index.html
@@ -102,7 +102,7 @@
 </nav>
 <article class="flex-1" role="main">
 <section id="miscellaneous">
-<h1>Miscellaneous<a aria-label="Click to copy this link" class="headerlink tooltipped tooltipped-ne tooltipped tooltipped-ne tooltipped tooltipped-ne tooltipped tooltipped-ne tooltipped tooltipped-ne tooltipped tooltipped-ne tooltipped tooltipped-ne tooltipped tooltipped-ne tooltipped tooltipped-ne tooltipped tooltipped-ne" data-action="click-&gt;clipboard#copyHeaderLink" data-controller="clipboard" href="#miscellaneous">¶</a></h1>
+<h1>Miscellaneous<a aria-label="Click to copy this link" class="headerlink tooltipped tooltipped-ne tooltipped tooltipped-ne tooltipped tooltipped-ne tooltipped tooltipped-ne tooltipped tooltipped-ne tooltipped tooltipped-ne tooltipped tooltipped-ne tooltipped tooltipped-ne tooltipped tooltipped-ne tooltipped tooltipped-ne tooltipped tooltipped-ne tooltipped tooltipped-ne tooltipped tooltipped-ne tooltipped tooltipped-ne" data-action="click-&gt;clipboard#copyHeaderLink" data-controller="clipboard" href="#miscellaneous">¶</a></h1>
 <div class="toctree-wrapper compound">
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="enum.html">Enumeration classes</a></li>

diff --git a/docs/API/misc/misc.html b/docs/API/misc/misc.html
diff --git a/docs/API/misc/properties.html b/docs/API/misc/properties.html
diff --git a/docs/API/outputs.html b/docs/API/outputs.html
diff --git a/docs/API/photometry.html b/docs/API/photometry.html
diff --git a/docs/API/sed.html b/docs/API/sed.html
diff --git a/docs/_modules/SED/photometry.html b/docs/_modules/SED/photometry.html
diff --git a/docs/_modules/index.html b/docs/_modules/index.html
@@ -82,6 +82,7 @@
 </ul>
 </li>
 <li class="toctree-l2"><div class="nav-link"><a class="reference internal" data-action="click-&gt;sidebar#close" href="../API/outputs.html">SED fitting code output classes</a></div></li>
+<li class="toctree-l2"><div class="nav-link"><a class="reference internal" data-action="click-&gt;sidebar#close" href="../API/photometry.html">Photometry related fonctions</a></div></li>
 <li class="toctree-l2"><div class="nav-link"><a class="reference internal" data-action="click-&gt;sidebar#close" href="../API/sed.html">SED classes</a></div></li>
 </ul>
 </li>
@@ -105,6 +106,7 @@ <h1>All modules for which code is available</h1>
 <li><a href="SED/misc/misc.html">SED.misc.misc</a></li>
 <li><a href="SED/misc/properties.html">SED.misc.properties</a></li>
 <li><a href="SED/outputs.html">SED.outputs</a></li>
+<li><a href="SED/photometry.html">SED.photometry</a></li>
 <li><a href="SED/sed.html">SED.sed</a></li>
 </ul>
 </article>

diff --git a/docs/_sources/API/index.rst.txt b/docs/_sources/API/index.rst.txt
@@ -7,4 +7,5 @@ API
     filters
     misc/index
     outputs
+    photometry
     sed
diff --git a/docs/_sources/API/photometry.rst.txt b/docs/_sources/API/photometry.rst.txt
@@ -0,0 +1,7 @@
+Photometry related fonctions
+============================
+
+.. automodule:: SED.photometry
+    :members:
+    :private-members:
+    :show-inheritance:
diff --git a/docs/examples/example1.html b/docs/examples/example1.html
@@ -101,7 +101,7 @@
 </nav>
 <article class="flex-1" role="main">
 <section id="example-1-generating-a-resolved-stellar-mass-map-with-lephare">
-<h1>Example 1: Generating a resolved stellar mass map with LePhare<a aria-label="Click to copy this link" class="headerlink tooltipped tooltipped-ne tooltipped tooltipped-ne tooltipped tooltipped-ne" data-action="click-&gt;clipboard#copyHeaderLink" data-controller="clipboard" href="#example-1-generating-a-resolved-stellar-mass-map-with-lephare">¶</a></h1>
+<h1>Example 1: Generating a resolved stellar mass map with LePhare<a aria-label="Click to copy this link" class="headerlink tooltipped tooltipped-ne tooltipped tooltipped-ne tooltipped tooltipped-ne tooltipped tooltipped-ne tooltipped tooltipped-ne tooltipped tooltipped-ne tooltipped tooltipped-ne" data-action="click-&gt;clipboard#copyHeaderLink" data-controller="clipboard" href="#example-1-generating-a-resolved-stellar-mass-map-with-lephare">¶</a></h1>
 <p>We start by importing <a class="reference external" href="https://docs.python.org/fr/3/library/os.path.html" rel="nofollow noopener">os.path<svg aria-hidden="true" class="external-link-icon" viewbox="0 0 24 24" xmlns="http://www.w3.org/2000/svg"><path d="M19 19H5V5h7V3H5a2 2 0 00-2 2v14a2 2 0 002 2h14c1.1 0 2-.9 2-2v-7h-2v7zM14 3v2h3.59l-9.83 9.83 1.41 1.41L19 6.41V10h2V3h-7z"></path></svg></a> module (useful to deal with paths between different OS), this library (<a class="reference external" href="https://github.com/WilfriedMercier/SED" rel="nofollow noopener">SED<svg aria-hidden="true" class="external-link-icon" viewbox="0 0 24 24" xmlns="http://www.w3.org/2000/svg"><path d="M19 19H5V5h7V3H5a2 2 0 00-2 2v14a2 2 0 002 2h14c1.1 0 2-.9 2-2v-7h-2v7zM14 3v2h3.59l-9.83 9.83 1.41 1.41L19 6.41V10h2V3h-7z"></path></svg></a>) and <a class="reference external" href="https://docs.astropy.org/en/stable/io/fits/index.html" rel="nofollow noopener">astropy.io.fits<svg aria-hidden="true" class="external-link-icon" viewbox="0 0 24 24" xmlns="http://www.w3.org/2000/svg"><path d="M19 19H5V5h7V3H5a2 2 0 00-2 2v14a2 2 0 002 2h14c1.1 0 2-.9 2-2v-7h-2v7zM14 3v2h3.59l-9.83 9.83 1.41 1.41L19 6.41V10h2V3h-7z"></path></svg></a> to open the mask file.</p>
 <p>We define the galaxy name, the bands used, their zeropoints and the absolute path of the flux and variance maps. Note that in this case our variance maps do not include Poisson noise so we need to add it. To do so, we also provide the flux maps convolved with the square of the PSF.</p>
 <div class="code-wrapper" data-controller="code">

diff --git a/docs/examples/example2.html b/docs/examples/example2.html
@@ -101,7 +101,7 @@
 </nav>
 <article class="flex-1" role="main">
 <section id="example-2-resolved-sfr-map-with-lephare-from-an-output-file">
-<h1>Example 2: Resolved SFR map with LePhare from an output file<a aria-label="Click to copy this link" class="headerlink tooltipped tooltipped-ne tooltipped tooltipped-ne tooltipped tooltipped-ne tooltipped tooltipped-ne tooltipped tooltipped-ne tooltipped tooltipped-ne tooltipped tooltipped-ne tooltipped tooltipped-ne tooltipped tooltipped-ne tooltipped tooltipped-ne" data-action="click-&gt;clipboard#copyHeaderLink" data-controller="clipboard" href="#example-2-resolved-sfr-map-with-lephare-from-an-output-file">¶</a></h1>
+<h1>Example 2: Resolved SFR map with LePhare from an output file<a aria-label="Click to copy this link" class="headerlink tooltipped tooltipped-ne tooltipped tooltipped-ne tooltipped tooltipped-ne tooltipped tooltipped-ne tooltipped tooltipped-ne tooltipped tooltipped-ne tooltipped tooltipped-ne tooltipped tooltipped-ne tooltipped tooltipped-ne tooltipped tooltipped-ne tooltipped tooltipped-ne tooltipped tooltipped-ne tooltipped tooltipped-ne tooltipped tooltipped-ne" data-action="click-&gt;clipboard#copyHeaderLink" data-controller="clipboard" href="#example-2-resolved-sfr-map-with-lephare-from-an-output-file">¶</a></h1>
 <p>We assume the SED fitting has already been performed and there is an output file named <code class="file docutils literal notranslate">example/1/<var>1.out</var></code>.</p>
 <p>Since we need the mean map, scale factor and exposure time to scale back the output properties, we start by building the FilterList oject as in <a class="reference internal" href="example1.html"><span class="doc">example 1</span></a></p>
 <div class="code-wrapper" data-controller="code">

diff --git a/docs/examples/example3.html b/docs/examples/example3.html
@@ -99,7 +99,7 @@
 </nav>
 <article class="flex-1" role="main">
 <section id="example-3-generating-a-resolved-stellar-mass-map-with-cigale">
-<h1>Example 3: Generating a resolved stellar mass map with Cigale<a aria-label="Click to copy this link" class="headerlink tooltipped tooltipped-ne tooltipped tooltipped-ne" data-action="click-&gt;clipboard#copyHeaderLink" data-controller="clipboard" href="#example-3-generating-a-resolved-stellar-mass-map-with-cigale">¶</a></h1>
+<h1>Example 3: Generating a resolved stellar mass map with Cigale<a aria-label="Click to copy this link" class="headerlink tooltipped tooltipped-ne tooltipped tooltipped-ne tooltipped tooltipped-ne tooltipped tooltipped-ne tooltipped tooltipped-ne tooltipped tooltipped-ne" data-action="click-&gt;clipboard#copyHeaderLink" data-controller="clipboard" href="#example-3-generating-a-resolved-stellar-mass-map-with-cigale">¶</a></h1>
 <p>We start by importing <a class="reference external" href="https://docs.python.org/fr/3/library/os.path.html" rel="nofollow noopener">os.path<svg aria-hidden="true" class="external-link-icon" viewbox="0 0 24 24" xmlns="http://www.w3.org/2000/svg"><path d="M19 19H5V5h7V3H5a2 2 0 00-2 2v14a2 2 0 002 2h14c1.1 0 2-.9 2-2v-7h-2v7zM14 3v2h3.59l-9.83 9.83 1.41 1.41L19 6.41V10h2V3h-7z"></path></svg></a> module (useful to deal with paths between different OS), this library (<a class="reference external" href="https://github.com/WilfriedMercier/SED" rel="nofollow noopener">SED<svg aria-hidden="true" class="external-link-icon" viewbox="0 0 24 24" xmlns="http://www.w3.org/2000/svg"><path d="M19 19H5V5h7V3H5a2 2 0 00-2 2v14a2 2 0 002 2h14c1.1 0 2-.9 2-2v-7h-2v7zM14 3v2h3.59l-9.83 9.83 1.41 1.41L19 6.41V10h2V3h-7z"></path></svg></a>) and <a class="reference external" href="https://docs.astropy.org/en/stable/io/fits/index.html" rel="nofollow noopener">astropy.io.fits<svg aria-hidden="true" class="external-link-icon" viewbox="0 0 24 24" xmlns="http://www.w3.org/2000/svg"><path d="M19 19H5V5h7V3H5a2 2 0 00-2 2v14a2 2 0 002 2h14c1.1 0 2-.9 2-2v-7h-2v7zM14 3v2h3.59l-9.83 9.83 1.41 1.41L19 6.41V10h2V3h-7z"></path></svg></a> to open the mask file.</p>
 <p>We define the galaxy name, the bands used, their zeropoints and the absolute path of the flux and variance maps. Note that in this case our variance maps do not include Poisson noise so we need to add it. To do so, we also provide the flux maps convolved with the square of the PSF.</p>
 <div class="code-wrapper" data-controller="code">

diff --git a/docs/index.html b/docs/index.html
@@ -84,6 +84,7 @@
 </ul>
 </li>
 <li class="toctree-l2"><div class="nav-link"><a class="reference internal" data-action="click-&gt;sidebar#close" href="API/outputs.html">SED fitting code output classes</a></div></li>
+<li class="toctree-l2"><div class="nav-link"><a class="reference internal" data-action="click-&gt;sidebar#close" href="API/photometry.html">Photometry related fonctions</a></div></li>
 <li class="toctree-l2"><div class="nav-link"><a class="reference internal" data-action="click-&gt;sidebar#close" href="API/sed.html">SED classes</a></div></li>
 </ul>
 </li>

diff --git a/docs/objects.inv b/docs/objects.inv
diff --git a/docs/search.html b/docs/search.html
@@ -82,6 +82,7 @@
 </ul>
 </li>
 <li class="toctree-l2"><div class="nav-link"><a class="reference internal" data-action="click-&gt;sidebar#close" href="API/outputs.html">SED fitting code output classes</a></div></li>
+<li class="toctree-l2"><div class="nav-link"><a class="reference internal" data-action="click-&gt;sidebar#close" href="API/photometry.html">Photometry related fonctions</a></div></li>
 <li class="toctree-l2"><div class="nav-link"><a class="reference internal" data-action="click-&gt;sidebar#close" href="API/sed.html">SED classes</a></div></li>
 </ul>
 </li>

diff --git a/docs/searchindex.js b/docs/searchindex.js
-Original file line number
+Diff line change
@@ Expand Up / @@ -7,4 +7,5 @@ API @@
         filters
         misc/index
         outputs
+        photometry
         sed