Update documentation

.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: a803d0fe3dadd85f014b84bd8b4da315
+config: 3628f54a32356cfe1650941b9e5c1d37
 tags: 645f666f9bcd5a90fca523b33c5a78b7

README.html

@@ -174,6 +174,7 @@
 <li class="toctree-l1"><a class="reference internal" href="notebooks/3_velocity_corner.html">3. Velocity Joint Probability Distributions</a></li>
 <li class="toctree-l1"><a class="reference internal" href="notebooks/4_radio_maps.html">4. Radio Source Maps</a></li>
 <li class="toctree-l1"><a class="reference internal" href="notebooks/5_velocity_comparison.html">5. Velocity Comparison</a></li>
+<li class="toctree-l1"><a class="reference internal" href="notebooks/6_tropospheric_correction.html">6. Tropospheric Correction</a></li>
 </ul>
 
     </div>
@@ -385,7 +386,7 @@ <h2> Contents </h2>
 
   <section class="tex2jax_ignore mathjax_ignore" id="hr-1099-timelapse-vlbi">
 <h1>HR 1099 Timelapse VLBI<a class="headerlink" href="#hr-1099-timelapse-vlbi" title="Permalink to this heading">#</a></h1>
-<p><a class="reference external" href="https://arxiv.org/abs/2401.03045"><img alt="paper" src="https://img.shields.io/badge/read-the%20paper-B31B1B" /></a>
+<p><a class="reference external" href="https://ui.adsabs.harvard.edu/abs/2024arXiv240103045G/abstract"><img alt="paper" src="https://img.shields.io/badge/read-the%20paper-B31B1B" /></a>
 <a class="reference external" href="https://doi.org/10.5281/zenodo.10395762"><img alt="DOI" src="https://zenodo.org/badge/DOI/10.5281/zenodo.10395762.svg" /></a>
 <a class="reference external" href="https://wwgolay.github.io/HR1099-timelapse-vlbi"><img alt="Jupyter Book Badge" src="https://jupyterbook.org/badge.svg" /></a>
 <a class="reference external" href="https://opensource.org/licenses/MIT"><img alt="License: MIT" src="https://img.shields.io/badge/License-MIT-yellow.svg" /></a>
@@ -401,7 +402,7 @@ <h2>Issues<a class="headerlink" href="#issues" title="Permalink to this heading"
 </section>
 <section id="acknowledgements">
 <h2>Acknowledgements<a class="headerlink" href="#acknowledgements" title="Permalink to this heading">#</a></h2>
-<p>Logo designed by <a class="reference external" href="https://www.flaticon.com/free-icon/binary-star_5570363?term=binary+star&amp;related_id=5570363">Freepik</a>.</p>
+<p>Logo from <a class="reference external" href="https://www.flaticon.com/free-icon/binary-star_5570363?term=binary+star&amp;related_id=5570363">Freepik</a>.</p>
 </section>
 <div class="toctree-wrapper compound">
 </div>
@@ -488,7 +489,7 @@ <h2>Acknowledgements<a class="headerlink" href="#acknowledgements" title="Permal
 
   <p class="copyright">
 
-      © Copyright 2023.
+      © Copyright 2024.
       <br/>
 
   </p>

_sources/README.md

@@ -1,6 +1,6 @@
 # HR 1099 Timelapse VLBI
 
-[![paper](https://img.shields.io/badge/read-the%20paper-B31B1B)](https://arxiv.org/abs/2401.03045)
+[![paper](https://img.shields.io/badge/read-the%20paper-B31B1B)](https://ui.adsabs.harvard.edu/abs/2024arXiv240103045G/abstract)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.10395762.svg)](https://doi.org/10.5281/zenodo.10395762)
 [![Jupyter Book Badge](https://jupyterbook.org/badge.svg)](https://wwgolay.github.io/HR1099-timelapse-vlbi)
 [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
@@ -17,4 +17,4 @@ If you find any bugs or have any suggestions, please submit an issue [here](http
 
 ## Acknowledgements
 
-Logo designed by [Freepik](https://www.flaticon.com/free-icon/binary-star_5570363?term=binary+star&related_id=5570363).
+Logo from [Freepik](https://www.flaticon.com/free-icon/binary-star_5570363?term=binary+star&related_id=5570363).

_sources/notebooks/4_radio_maps.ipynb

@@ -78,23 +78,35 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "epochs, mean_x, mean_y, mean_jd, mean_x_err, mean_y_err = np.genfromtxt(\n",
+    "epochs, mean_jd = np.genfromtxt(\n",
     "    data_path + target + \"_I_positions.txt\",\n",
     "    skip_header=2,\n",
     "    dtype=\"U1,f8,f8,f8,f8,f8,f8,f8\",\n",
-    "    usecols=(0, 2, 3, 5, 6, 7),\n",
+    "    usecols=(0, 5),\n",
     "    unpack=True,\n",
     ")\n",
     "mean_mjd = np.round(mean_jd - 2400000.5, 1)\n",
     "\n",
     "models = {}\n",
+    "mean_x = np.array([])\n",
+    "mean_y = np.array([])\n",
     "for epoch in epochs:\n",
     "    beam = utils.get_beam(os.path.join(data_path, f\"{epoch}_{target}_sc.log\"))\n",
     "    models[epoch] = utils.vlb_model(\n",
     "        os.path.join(data_path, f\"{epoch}_{target}_sc.mod\"), beam\n",
     "    )\n",
     "    models[epoch].excise_components(200)\n",
     "\n",
+    "    x, y, jd, x_err, y_err = np.genfromtxt(\n",
+    "        data_path + epoch + \"_\" + target + \"_I_sub-epoch_positions.txt\",\n",
+    "        skip_header=2,\n",
+    "        dtype=\"U5,f8,f8,f8,f8,f8,f8,f8\",\n",
+    "        usecols=(2, 3, 5, 6, 7),\n",
+    "        unpack=True,\n",
+    "    )\n",
+    "    mean_x = np.append(mean_x, np.mean(x))\n",
+    "    mean_y = np.append(mean_y, np.mean(y))\n",
+    "\n",
     "sampler = emcee.backends.HDFBackend(data_path + target + \"_orbital_chain.h5\")\n",
     "flat_samples = sampler.get_chain(flat=True)\n",
     "flat_samples = np.divide(flat_samples, np.array([1, 1, deg, deg]))\n",
@@ -145,7 +157,7 @@
     "        corotate=False,\n",
     "        centroid=[mean_x[i] + med_val[0], mean_y[i] + med_val[1], 0, 0],\n",
     "        label=mean_mjd[i],\n",
-    "        cmap=cmc.lajolla,\n",
+    "        cmap=\"viridis\",\n",
     "        model=models[epoch],\n",
     "        mapsize=4,\n",
     "        cells=256,\n",
@@ -188,7 +200,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -264,7 +276,7 @@
     "            cells=256,\n",
     "            levs=[4, 8, 16, 32, 64],\n",
     "            beam=models[epochs[idx]].restoring_beam,\n",
-    "            cmap=cmc.lajolla,\n",
+    "            cmap=\"viridis\",\n",
     "            d=d,\n",
     "            fontsize=14,\n",
     "            bar_pos=\"lower left\",\n",

genindex.html

@@ -172,6 +172,7 @@
 <li class="toctree-l1"><a class="reference internal" href="notebooks/3_velocity_corner.html">3. Velocity Joint Probability Distributions</a></li>
 <li class="toctree-l1"><a class="reference internal" href="notebooks/4_radio_maps.html">4. Radio Source Maps</a></li>
 <li class="toctree-l1"><a class="reference internal" href="notebooks/5_velocity_comparison.html">5. Velocity Comparison</a></li>
+<li class="toctree-l1"><a class="reference internal" href="notebooks/6_tropospheric_correction.html">6. Tropospheric Correction</a></li>
 </ul>
 
     </div>
@@ -365,7 +366,7 @@ <h1 id="index">Index</h1>
 
   <p class="copyright">
 
-      © Copyright 2023.
+      © Copyright 2024.
       <br/>
 
   </p>

notebooks/1_calibrators.html

@@ -175,6 +175,7 @@
 <li class="toctree-l1"><a class="reference internal" href="3_velocity_corner.html">3. Velocity Joint Probability Distributions</a></li>
 <li class="toctree-l1"><a class="reference internal" href="4_radio_maps.html">4. Radio Source Maps</a></li>
 <li class="toctree-l1"><a class="reference internal" href="5_velocity_comparison.html">5. Velocity Comparison</a></li>
+<li class="toctree-l1"><a class="reference internal" href="6_tropospheric_correction.html">6. Tropospheric Correction</a></li>
 </ul>
 
     </div>
@@ -690,7 +691,7 @@ <h2>1.3. Plot<a class="headerlink" href="#plot" title="Permalink to this heading
 
   <p class="copyright">
 
-      © Copyright 2023.
+      © Copyright 2024.
       <br/>
 
   </p>

notebooks/2_HR1099_positions.html

@@ -175,6 +175,7 @@
 <li class="toctree-l1"><a class="reference internal" href="3_velocity_corner.html">3. Velocity Joint Probability Distributions</a></li>
 <li class="toctree-l1"><a class="reference internal" href="4_radio_maps.html">4. Radio Source Maps</a></li>
 <li class="toctree-l1"><a class="reference internal" href="5_velocity_comparison.html">5. Velocity Comparison</a></li>
+<li class="toctree-l1"><a class="reference internal" href="6_tropospheric_correction.html">6. Tropospheric Correction</a></li>
 </ul>
 
     </div>
@@ -763,7 +764,7 @@ <h2>2.3. Plot<a class="headerlink" href="#plot" title="Permalink to this heading
 
   <p class="copyright">
 
-      © Copyright 2023.
+      © Copyright 2024.
       <br/>
 
   </p>

notebooks/3_velocity_corner.html

@@ -175,6 +175,7 @@
 <li class="toctree-l1 current active"><a class="current reference internal" href="#">3. Velocity Joint Probability Distributions</a></li>
 <li class="toctree-l1"><a class="reference internal" href="4_radio_maps.html">4. Radio Source Maps</a></li>
 <li class="toctree-l1"><a class="reference internal" href="5_velocity_comparison.html">5. Velocity Comparison</a></li>
+<li class="toctree-l1"><a class="reference internal" href="6_tropospheric_correction.html">6. Tropospheric Correction</a></li>
 </ul>
 
     </div>
@@ -645,7 +646,7 @@ <h2>3.3. Plot<a class="headerlink" href="#plot" title="Permalink to this heading
 
   <p class="copyright">
 
-      © Copyright 2023.
+      © Copyright 2024.
       <br/>
 
   </p>