MR: Correction in corner plot + Readthedocs update

exoAtmospheres · Sep 19, 2024 · 202359e · 202359e
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diff --git a/ForMoSA/plotting/plotting_class.py b/ForMoSA/plotting/plotting_class.py
@@ -356,10 +356,10 @@ def plot_corner(self, levels_sig=[0.997, 0.95, 0.68], bins=100, quantiles=(0.16,
         self._get_posteriors()
 
 
-        fig = corner.corner(self.posterior_to_plot[burn_in:,:-1],
+        fig = corner.corner(self.posterior_to_plot[burn_in:],
                             weights=self.weights[burn_in:],
-                            labels=self.posteriors_names[:-1],
-                            range=[0.999999 for p in self.posteriors_names[:-1]],
+                            labels=self.posteriors_names,
+                            range=[0.999999 for p in self.posteriors_names],
                             levels=levels_sig,
                             bins=bins,
                             smooth=1,

diff --git a/docs/_build/doctrees/adapt.doctree b/docs/_build/doctrees/adapt.doctree
diff --git a/docs/_build/doctrees/api.doctree b/docs/_build/doctrees/api.doctree
diff --git a/docs/_build/doctrees/demo.doctree b/docs/_build/doctrees/demo.doctree
diff --git a/docs/_build/doctrees/environment.pickle b/docs/_build/doctrees/environment.pickle
diff --git a/docs/_build/doctrees/index.doctree b/docs/_build/doctrees/index.doctree
diff --git a/docs/_build/doctrees/installation.doctree b/docs/_build/doctrees/installation.doctree
diff --git a/docs/_build/doctrees/main_utilities.doctree b/docs/_build/doctrees/main_utilities.doctree
diff --git a/docs/_build/doctrees/nbsphinx/tutorials/config_file.ipynb b/docs/_build/doctrees/nbsphinx/tutorials/config_file.ipynb
diff --git a/docs/_build/doctrees/nbsphinx/tutorials/demoabpic.ipynb b/docs/_build/doctrees/nbsphinx/tutorials/demoabpic.ipynb
@@ -4,10 +4,10 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# demo AB Pic b\n",
+    "# Demo AB Pic b\n",
     "\n",
     "\n",
-    "This tutorial is intended as a quick start. \n",
+    "This tutorial is intended as a quick start when using a single observation. \n",
     "\n",
     "\n",
     "We will use medium resolution VLT/SINFONI K-band data of AB Pic b. These observations and example model were published in [P. Palma-Bifani et al (2023)](https://www.aanda.org/articles/aa/pdf/2023/02/aa44294-22.pdf).\n",
@@ -41,7 +41,7 @@
    "source": [
     "## 0. Setup\n",
     "\n",
-    "You need to create a config file with extension <.ini> and modify the parameters. Learn more about our config files in it's specific tutorial.\n",
+    "You need to create a config file with extension ``.ini`` and modify the parameters. Learn more about our config files in it's specific tutorial.\n",
     "\n",
     "To initialize ForMoSA we need to read the config.ini file and setup the outputs directory and global parameters as follows"
    ]

diff --git a/docs/_build/doctrees/nbsphinx/tutorials/demobetapic.ipynb b/docs/_build/doctrees/nbsphinx/tutorials/demobetapic.ipynb
diff --git a/docs/_build/doctrees/nbsphinx/tutorials/format_obs.ipynb b/docs/_build/doctrees/nbsphinx/tutorials/format_obs.ipynb
@@ -0,0 +1,142 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Observation format\n",
+    "\n",
+    "This section will help you convert your observationnal data into the ForMoSA format\n",
+    "\n",
+    "## Imports"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from astropy.io import fits\n",
+    "from astropy.table import Table"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Data ``.fits``\n",
+    "\n",
+    "Your observed data (spectroscopy and/or photometry) should be formated in a ``.fits`` file with the following extensions:\n",
+    "\n",
+    "- **'WAV'** : (array) wavelength grid\n",
+    "- **'FLX'** : (array) flux\n",
+    "- **'ERR'** or **'COV'** : (array or 2D-array) errors or covariance matrix. The covariance matrix should have ``diag(COV)=ERR²``\n",
+    "- **'RES'** : (array) resolution\n",
+    "- **'INS'** : (array) instrument name\n",
+    "\n",
+    "exemple :"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 34,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "ColDefs(\n",
+      "    name = 'WAV'; format = 'D'\n",
+      "    name = 'FLX'; format = 'D'\n",
+      "    name = 'ERR'; format = 'D'\n",
+      "    name = 'RES'; format = 'D'\n",
+      "    name = 'INS'; format = '3A'\n",
+      ")\n"
+     ]
+    }
+   ],
+   "source": [
+    "# CHECKUP FORMAT\n",
+    "hdul = fits.open('~/YOUR/PATH/formosa_desk/inversion_targetname/inputs/data.fits')\n",
+    "print(hdul[1].columns)\n",
+    "wav = hdul[1].data['WAV']\n",
+    "flx = hdul[1].data['FLX']\n",
+    "err = hdul[1].data['ERR']\n",
+    "res = hdul[1].data['RES']\n",
+    "ins = hdul[1].data['INS']"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "optional extensions can also be used when dealing with stellar-contaminated high-resolution spectroscopy:\n",
+    "- **'TRANSM'** : (array) transmission (atmospheric + instrumental)\n",
+    "- **'STAR_FLX'** or **'STAR_FLXi'** : (array or i arrays) star flux or shifted star flux (to account for LSF changes)\n",
+    "- **'SYSTEM'** or **'SYSTEMj'** : (array or j arrays) systematic model(s) (usually computed from PCA)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Format your data\n",
+    "\n",
+    "To format your data, you can use the simple Python routine below :"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 35,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "correction successful\n"
+     ]
+    }
+   ],
+   "source": [
+    "# FITS converter :\n",
+    "table = Table([wav, flx, res, res, ins], names=('WAV', 'FLX', 'ERR', 'RES', 'INS'))\n",
+    "hdul = fits.HDUList()\n",
+    "hdu = fits.BinTableHDU(table)\n",
+    "hdul.append(hdu)\n",
+    "hdul.writeto('~/YOUR/PATH/formosa_desk/inversion_targetname/inputs/data.fits')\n",
+    "print('correction successful')"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "If you have multiple observations, we recommand that you create separated ``.fits`` files (e.g ``data_1.fits``, ``data_2.fits``, ...)"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "pRT3_env",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.11.5"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}
diff --git a/docs/_build/doctrees/nbsphinx/tutorials_demobetapic_11_1.png b/docs/_build/doctrees/nbsphinx/tutorials_demobetapic_11_1.png
diff --git a/docs/_build/doctrees/nbsphinx/tutorials_demobetapic_13_2.png b/docs/_build/doctrees/nbsphinx/tutorials_demobetapic_13_2.png
diff --git a/docs/_build/doctrees/nbsphinx/tutorials_demobetapic_15_1.png b/docs/_build/doctrees/nbsphinx/tutorials_demobetapic_15_1.png
diff --git a/docs/_build/doctrees/nested_sampling.doctree b/docs/_build/doctrees/nested_sampling.doctree
diff --git a/docs/_build/doctrees/plotting.doctree b/docs/_build/doctrees/plotting.doctree
diff --git a/docs/_build/doctrees/tutorials/config_file.doctree b/docs/_build/doctrees/tutorials/config_file.doctree
diff --git a/docs/_build/doctrees/tutorials/demoabpic.doctree b/docs/_build/doctrees/tutorials/demoabpic.doctree
diff --git a/docs/_build/doctrees/tutorials/demobetapic.doctree b/docs/_build/doctrees/tutorials/demobetapic.doctree
diff --git a/docs/_build/doctrees/tutorials/exorem_info.doctree b/docs/_build/doctrees/tutorials/exorem_info.doctree
diff --git a/docs/_build/doctrees/tutorials/format_obs.doctree b/docs/_build/doctrees/tutorials/format_obs.doctree
diff --git a/docs/_build/doctrees/tutorials/inputs.doctree b/docs/_build/doctrees/tutorials/inputs.doctree
diff --git a/docs/_build/html/.buildinfo b/docs/_build/html/.buildinfo
@@ -1,4 +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: 3d69bd81622fe4392ef94600d12c6fdb
+config: d4763c4acadf04200e3866f19bc6a8cf
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/_build/html/_images/tutorials_demobetapic_11_1.png b/docs/_build/html/_images/tutorials_demobetapic_11_1.png
diff --git a/docs/_build/html/_images/tutorials_demobetapic_13_2.png b/docs/_build/html/_images/tutorials_demobetapic_13_2.png
diff --git a/docs/_build/html/_images/tutorials_demobetapic_15_1.png b/docs/_build/html/_images/tutorials_demobetapic_15_1.png
diff --git a/docs/_build/html/_modules/ForMoSA/adapt/adapt_obs_mod.html b/docs/_build/html/_modules/ForMoSA/adapt/adapt_obs_mod.html
@@ -167,11 +167,12 @@ <h1>Source code for ForMoSA.adapt.adapt_obs_mod</h1><div class="highlight"><pre>
                     <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">transm_obs_extract</span><span class="p">)</span> <span class="o">!=</span> <span class="mi">0</span><span class="p">:</span>
                         <span class="n">transm_obs_extract</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">concatenate</span><span class="p">((</span><span class="n">transm_obs_extract</span><span class="p">,</span> <span class="n">obs_opt</span><span class="p">[</span><span class="n">c</span><span class="p">][</span><span class="mi">1</span><span class="p">]))</span>
                     <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">star_flx_obs_extract</span><span class="p">)</span> <span class="o">!=</span> <span class="mi">0</span><span class="p">:</span>
-                        <span class="n">star_flx_obs_extract</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">concatenate</span><span class="p">((</span><span class="n">star_flx_obs_extract</span><span class="p">,</span> <span class="n">obs_opt</span><span class="p">[</span><span class="n">c</span><span class="p">][</span><span class="mi">2</span><span class="p">]))</span>
+                        <span class="n">star_flx_obs_extract</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">concatenate</span><span class="p">((</span><span class="n">star_flx_obs_extract</span><span class="p">,</span> <span class="n">obs_opt</span><span class="p">[</span><span class="n">c</span><span class="p">][</span><span class="mi">2</span><span class="p">]),</span> <span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
                     <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">system_obs_extract</span><span class="p">)</span> <span class="o">!=</span> <span class="mi">0</span><span class="p">:</span>
                         <span class="n">system_obs_extract</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">concatenate</span><span class="p">((</span><span class="n">system_obs_extract</span><span class="p">,</span> <span class="n">obs_opt</span><span class="p">[</span><span class="n">c</span><span class="p">][</span><span class="mi">3</span><span class="p">]),</span> <span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
                     <span class="c1"># Save the interpolated resolution of the grid</span>
                     <span class="n">res_mod_obs_merge</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">res_mod_cut</span><span class="p">)</span>
+
 
 
                 <span class="c1"># Compute the inverse of the merged covariance matrix (note: inv(C1, C2) = (in(C1), in(C2)) if C1 and C2 are block matrix on the diagonal)</span>

diff --git a/docs/_build/html/_modules/ForMoSA/adapt/extraction_functions.html b/docs/_build/html/_modules/ForMoSA/adapt/extraction_functions.html
@@ -18,6 +18,7 @@
         <script src="../../../_static/documentation_options.js?v=51b770b3"></script>
         <script src="../../../_static/doctools.js?v=9a2dae69"></script>
         <script src="../../../_static/sphinx_highlight.js?v=dc90522c"></script>
+        <script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
     <script src="../../../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../../../genindex.html" />
     <link rel="search" title="Search" href="../../../search.html" /> 
@@ -42,10 +43,10 @@
   </form>
 </div>
         </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
-              <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
+              <p class="caption" role="heading"><span class="caption-text">Contents</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="../../../installation.html">Installation</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../../../demo.html">DEMO</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../../demo.html">Tutorials</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../api.html">ForMoSA API</a></li>
 </ul>
 
@@ -231,7 +232,7 @@ <h1>Source code for ForMoSA.adapt.extraction_functions</h1><div class="highlight
             <span class="n">star_flx</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">asarray</span><span class="p">([])</span>   
             <span class="n">is_star</span> <span class="o">=</span> <span class="kc">False</span>
         <span class="k">try</span><span class="p">:</span>
-            <span class="n">star_flx</span> <span class="o">=</span> <span class="n">hdul</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="s1">&#39;STAR FLX&#39;</span><span class="p">][:,</span><span class="n">np</span><span class="o">.</span><span class="n">newaxis</span><span class="p">]</span>
+            <span class="n">star_flx</span> <span class="o">=</span> <span class="n">hdul</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">data</span><span class="p">[</span><span class="s1">&#39;STAR_FLX&#39;</span><span class="p">][:,</span><span class="n">np</span><span class="o">.</span><span class="n">newaxis</span><span class="p">]</span>
         <span class="k">except</span><span class="p">:</span>
             <span class="k">pass</span>
         <span class="k">try</span><span class="p">:</span>
@@ -258,6 +259,7 @@ <h1>Source code for ForMoSA.adapt.extraction_functions</h1><div class="highlight
                     <span class="n">i</span> <span class="o">+=</span> <span class="mi">1</span>
                 <span class="k">except</span><span class="p">:</span>
                     <span class="k">break</span>
+
         <span class="c1"># Only take the covariance if you use the chi2_covariance likelihood function (will need to be change when new likelihood functions using the</span>
         <span class="c1"># covariance matrix will come)</span>
         <span class="k">if</span> <span class="n">global_params</span><span class="o">.</span><span class="n">logL_type</span><span class="p">[</span><span class="n">indobs</span><span class="p">]</span> <span class="o">!=</span> <span class="s1">&#39;chi2_covariance&#39;</span><span class="p">:</span>
@@ -295,7 +297,6 @@ <h1>Source code for ForMoSA.adapt.extraction_functions</h1><div class="highlight
         <span class="k">else</span><span class="p">:</span>
             <span class="n">wav_for_adapt_tab</span> <span class="o">=</span> <span class="n">global_params</span><span class="o">.</span><span class="n">wav_for_adapt</span><span class="p">[</span><span class="n">indobs</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;/&#39;</span><span class="p">)</span>
 
-
         <span class="c1"># Photometry part of the data (OUT OF THE WINDOW LOOP)</span>
         <span class="n">ind_photometry</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">where</span><span class="p">(</span><span class="n">res</span> <span class="o">==</span> <span class="mf">0.0</span><span class="p">)</span>
         <span class="n">obs_photo</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">asarray</span><span class="p">([</span><span class="n">wav</span><span class="p">[</span><span class="n">ind_photometry</span><span class="p">],</span> <span class="n">flx</span><span class="p">[</span><span class="n">ind_photometry</span><span class="p">],</span> <span class="n">err</span><span class="p">[</span><span class="n">ind_photometry</span><span class="p">],</span>
@@ -306,6 +307,7 @@ <h1>Source code for ForMoSA.adapt.extraction_functions</h1><div class="highlight
         <span class="n">obs_spectro</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">empty</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">wav_for_adapt_tab</span><span class="p">),</span> <span class="n">dtype</span><span class="o">=</span><span class="nb">object</span><span class="p">)</span>
         <span class="n">obs_opt</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">empty</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">wav_for_adapt_tab</span><span class="p">),</span> <span class="n">dtype</span><span class="o">=</span><span class="nb">object</span><span class="p">)</span>
         <span class="n">obs_spectro_ins</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">empty</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">wav_for_adapt_tab</span><span class="p">),</span> <span class="n">dtype</span><span class="o">=</span><span class="nb">object</span><span class="p">)</span>
+
 
         <span class="k">for</span> <span class="n">range_ind</span><span class="p">,</span> <span class="n">rangee</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">wav_for_adapt_tab</span><span class="p">):</span>
             <span class="n">rangee</span> <span class="o">=</span> <span class="n">rangee</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">&#39;,&#39;</span><span class="p">)</span>
@@ -331,14 +333,15 @@ <h1>Source code for ForMoSA.adapt.extraction_functions</h1><div class="highlight
                 <span class="n">transm_spectro</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">asarray</span><span class="p">([])</span>
 
             <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">star_flx</span><span class="p">)</span> <span class="o">!=</span> <span class="mi">0</span><span class="p">:</span>
-                <span class="n">star_flx_spectro</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">delete</span><span class="p">(</span><span class="n">star_flx</span><span class="p">[</span><span class="n">ind</span><span class="p">,:],</span> <span class="n">ind_photometry</span><span class="p">,</span> <span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
+                <span class="n">star_flx_spectro</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">delete</span><span class="p">(</span><span class="n">star_flx</span><span class="p">[</span><span class="n">ind</span><span class="p">,:],</span> <span class="n">ind_photometry</span><span class="p">,</span> <span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
             <span class="k">else</span><span class="p">:</span>
                 <span class="n">star_flx_spectro</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">asarray</span><span class="p">([])</span>
 
             <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">system</span><span class="p">)</span> <span class="o">!=</span> <span class="mi">0</span><span class="p">:</span>
-                <span class="n">system_spectro</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">delete</span><span class="p">(</span><span class="n">system</span><span class="p">[</span><span class="n">ind</span><span class="p">,:],</span> <span class="n">ind_photometry</span><span class="p">,</span> <span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
+                <span class="n">system_spectro</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">delete</span><span class="p">(</span><span class="n">system</span><span class="p">[</span><span class="n">ind</span><span class="p">,:],</span> <span class="n">ind_photometry</span><span class="p">,</span> <span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
             <span class="k">else</span><span class="p">:</span>
                 <span class="n">system_spectro</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">asarray</span><span class="p">([])</span>
+
 
             <span class="c1"># Merge spectroscopic data</span>
             <span class="n">obs_spectro</span><span class="p">[</span><span class="n">range_ind</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="n">wav_spectro</span><span class="p">,</span> <span class="n">flx_spectro</span><span class="p">,</span> <span class="n">err_spectro</span><span class="p">,</span> <span class="n">res_spectro</span><span class="p">]</span>