Merge remote-tracking branch 'origin/master'

# Conflicts:
#	docs/star_shine/api/run_first_use.html

Author: LucIJspeert

docs/search.js

@@ -52,9 +52,9 @@ <h1 class="modulename">
                         <div class="docstring"><p>STAR SHINE
 Satellite Time-series Analysis Routine using Sinusoids and Harmonics through Iterative Non-linear Extraction</p>
 
-<p>This Python script is meant to be run before first use, it ensures that the Just-In-Time compiler has done its job
-and cache the compiled functions. If your own use case involves time series longer than a few thousand data points,
-this is strongly recommended. If not, this is less important, but do keep in mind that the first run will be slower.</p>
+<p>This Python script is meant to be run before first use, it ensures that the Just-In-Time compiler has done its job.
+If your own use case involves time series longer than a few thousand data points, this is strongly recommended.
+If not, this is less important, but do keep in mind that the first run will be slower.</p>
 
 <p>Code written by: Luc IJspeert</p>
 </div>
@@ -66,9 +66,9 @@ <h1 class="modulename">
                         <div class="pdoc-code codehilite"><pre><span></span><span id="L-1"><a href="#L-1"><span class="linenos"> 1</span></a><span class="sd">&quot;&quot;&quot;STAR SHINE</span>
 </span><span id="L-2"><a href="#L-2"><span class="linenos"> 2</span></a><span class="sd">Satellite Time-series Analysis Routine using Sinusoids and Harmonics through Iterative Non-linear Extraction</span>
 </span><span id="L-3"><a href="#L-3"><span class="linenos"> 3</span></a>
-</span><span id="L-4"><a href="#L-4"><span class="linenos"> 4</span></a><span class="sd">This Python script is meant to be run before first use, it ensures that the Just-In-Time compiler has done its job</span>
-</span><span id="L-5"><a href="#L-5"><span class="linenos"> 5</span></a><span class="sd">and cache the compiled functions. If your own use case involves time series longer than a few thousand data points,</span>
-</span><span id="L-6"><a href="#L-6"><span class="linenos"> 6</span></a><span class="sd">this is strongly recommended. If not, this is less important, but do keep in mind that the first run will be slower.</span>
+</span><span id="L-4"><a href="#L-4"><span class="linenos"> 4</span></a><span class="sd">This Python script is meant to be run before first use, it ensures that the Just-In-Time compiler has done its job.</span>
+</span><span id="L-5"><a href="#L-5"><span class="linenos"> 5</span></a><span class="sd">If your own use case involves time series longer than a few thousand data points, this is strongly recommended.</span>
+</span><span id="L-6"><a href="#L-6"><span class="linenos"> 6</span></a><span class="sd">If not, this is less important, but do keep in mind that the first run will be slower.</span>
 </span><span id="L-7"><a href="#L-7"><span class="linenos"> 7</span></a>
 </span><span id="L-8"><a href="#L-8"><span class="linenos"> 8</span></a><span class="sd">Code written by: Luc IJspeert</span>
 </span><span id="L-9"><a href="#L-9"><span class="linenos"> 9</span></a><span class="sd">&quot;&quot;&quot;</span>
@@ -90,24 +90,17 @@ <h1 class="modulename">
 </span><span id="L-25"><a href="#L-25"><span class="linenos">25</span></a>    <span class="n">data</span> <span class="o">=</span> <span class="n">sts</span><span class="o">.</span><span class="n">Data</span><span class="o">.</span><span class="n">load_data</span><span class="p">(</span><span class="n">file_list</span><span class="p">,</span> <span class="n">data_dir</span><span class="o">=</span><span class="s1">&#39;&#39;</span><span class="p">,</span> <span class="n">target_id</span><span class="o">=</span><span class="n">target_id</span><span class="p">,</span> <span class="n">data_id</span><span class="o">=</span><span class="s1">&#39;&#39;</span><span class="p">,</span> <span class="n">logger</span><span class="o">=</span><span class="kc">None</span><span class="p">)</span>
 </span><span id="L-26"><a href="#L-26"><span class="linenos">26</span></a>    <span class="n">pipeline</span> <span class="o">=</span> <span class="n">sts</span><span class="o">.</span><span class="n">Pipeline</span><span class="p">(</span><span class="n">data</span><span class="p">,</span> <span class="n">save_dir</span><span class="o">=</span><span class="n">data_path</span><span class="p">,</span> <span class="n">logger</span><span class="o">=</span><span class="kc">None</span><span class="p">)</span>
 </span><span id="L-27"><a href="#L-27"><span class="linenos">27</span></a>
-</span><span id="L-28"><a href="#L-28"><span class="linenos">28</span></a>    <span class="c1"># first only extract 10 sinusoids</span>
-</span><span id="L-29"><a href="#L-29"><span class="linenos">29</span></a>    <span class="n">pipeline</span><span class="o">.</span><span class="n">iterative_prewhitening</span><span class="p">(</span><span class="n">n_extract</span><span class="o">=</span><span class="mi">10</span><span class="p">)</span>
-</span><span id="L-30"><a href="#L-30"><span class="linenos">30</span></a>    <span class="n">pipeline</span><span class="o">.</span><span class="n">optimise_sinusoid</span><span class="p">()</span>
+</span><span id="L-28"><a href="#L-28"><span class="linenos">28</span></a>    <span class="c1"># do a first run without fitting every step and lower group size</span>
+</span><span id="L-29"><a href="#L-29"><span class="linenos">29</span></a>    <span class="n">sts</span><span class="o">.</span><span class="n">update_config</span><span class="p">(</span><span class="n">settings</span><span class="o">=</span><span class="p">{</span><span class="s1">&#39;optimise_step&#39;</span><span class="p">:</span> <span class="kc">False</span><span class="p">,</span> <span class="s1">&#39;min_group&#39;</span><span class="p">:</span> <span class="mi">15</span><span class="p">,</span> <span class="s1">&#39;max_group&#39;</span><span class="p">:</span> <span class="mi">20</span><span class="p">})</span>
+</span><span id="L-30"><a href="#L-30"><span class="linenos">30</span></a>    <span class="n">pipeline</span><span class="o">.</span><span class="n">run</span><span class="p">()</span>
 </span><span id="L-31"><a href="#L-31"><span class="linenos">31</span></a>
-</span><span id="L-32"><a href="#L-32"><span class="linenos">32</span></a>    <span class="c1"># start new pipeline for the second part</span>
-</span><span id="L-33"><a href="#L-33"><span class="linenos">33</span></a>    <span class="n">pipeline</span> <span class="o">=</span> <span class="n">sts</span><span class="o">.</span><span class="n">Pipeline</span><span class="p">(</span><span class="n">data</span><span class="p">,</span> <span class="n">save_dir</span><span class="o">=</span><span class="n">data_path</span><span class="p">,</span> <span class="n">logger</span><span class="o">=</span><span class="kc">None</span><span class="p">)</span>
-</span><span id="L-34"><a href="#L-34"><span class="linenos">34</span></a>
-</span><span id="L-35"><a href="#L-35"><span class="linenos">35</span></a>    <span class="c1"># do a first run without fitting every step and lower group size</span>
-</span><span id="L-36"><a href="#L-36"><span class="linenos">36</span></a>    <span class="n">sts</span><span class="o">.</span><span class="n">update_config</span><span class="p">(</span><span class="n">settings</span><span class="o">=</span><span class="p">{</span><span class="s1">&#39;optimise_step&#39;</span><span class="p">:</span> <span class="kc">False</span><span class="p">,</span> <span class="s1">&#39;min_group&#39;</span><span class="p">:</span> <span class="mi">15</span><span class="p">,</span> <span class="s1">&#39;max_group&#39;</span><span class="p">:</span> <span class="mi">20</span><span class="p">})</span>
-</span><span id="L-37"><a href="#L-37"><span class="linenos">37</span></a>    <span class="n">pipeline</span><span class="o">.</span><span class="n">run</span><span class="p">()</span>
-</span><span id="L-38"><a href="#L-38"><span class="linenos">38</span></a>
-</span><span id="L-39"><a href="#L-39"><span class="linenos">39</span></a>    <span class="c1"># do a second run with fitting every step</span>
-</span><span id="L-40"><a href="#L-40"><span class="linenos">40</span></a>    <span class="n">sts</span><span class="o">.</span><span class="n">update_config</span><span class="p">(</span><span class="n">settings</span><span class="o">=</span><span class="p">{</span><span class="s1">&#39;optimise_step&#39;</span><span class="p">:</span> <span class="kc">True</span><span class="p">})</span>
-</span><span id="L-41"><a href="#L-41"><span class="linenos">41</span></a>    <span class="n">pipeline</span><span class="o">.</span><span class="n">run</span><span class="p">()</span>
-</span><span id="L-42"><a href="#L-42"><span class="linenos">42</span></a>
-</span><span id="L-43"><a href="#L-43"><span class="linenos">43</span></a>
-</span><span id="L-44"><a href="#L-44"><span class="linenos">44</span></a><span class="k">if</span> <span class="vm">__name__</span> <span class="o">==</span> <span class="s1">&#39;__main__&#39;</span><span class="p">:</span>
-</span><span id="L-45"><a href="#L-45"><span class="linenos">45</span></a>    <span class="n">first_use_script</span><span class="p">()</span>
+</span><span id="L-32"><a href="#L-32"><span class="linenos">32</span></a>    <span class="c1"># do a second run with fitting every step</span>
+</span><span id="L-33"><a href="#L-33"><span class="linenos">33</span></a>    <span class="n">sts</span><span class="o">.</span><span class="n">update_config</span><span class="p">(</span><span class="n">settings</span><span class="o">=</span><span class="p">{</span><span class="s1">&#39;optimise_step&#39;</span><span class="p">:</span> <span class="kc">True</span><span class="p">})</span>
+</span><span id="L-34"><a href="#L-34"><span class="linenos">34</span></a>    <span class="n">pipeline</span><span class="o">.</span><span class="n">run</span><span class="p">()</span>
+</span><span id="L-35"><a href="#L-35"><span class="linenos">35</span></a>
+</span><span id="L-36"><a href="#L-36"><span class="linenos">36</span></a>
+</span><span id="L-37"><a href="#L-37"><span class="linenos">37</span></a><span class="k">if</span> <span class="vm">__name__</span> <span class="o">==</span> <span class="s1">&#39;__main__&#39;</span><span class="p">:</span>
+</span><span id="L-38"><a href="#L-38"><span class="linenos">38</span></a>    <span class="n">first_use_script</span><span class="p">()</span>
 </span></pre></div>
 
 
@@ -135,20 +128,13 @@ <h1 class="modulename">
 </span><span id="first_use_script-26"><a href="#first_use_script-26"><span class="linenos">26</span></a>    <span class="n">data</span> <span class="o">=</span> <span class="n">sts</span><span class="o">.</span><span class="n">Data</span><span class="o">.</span><span class="n">load_data</span><span class="p">(</span><span class="n">file_list</span><span class="p">,</span> <span class="n">data_dir</span><span class="o">=</span><span class="s1">&#39;&#39;</span><span class="p">,</span> <span class="n">target_id</span><span class="o">=</span><span class="n">target_id</span><span class="p">,</span> <span class="n">data_id</span><span class="o">=</span><span class="s1">&#39;&#39;</span><span class="p">,</span> <span class="n">logger</span><span class="o">=</span><span class="kc">None</span><span class="p">)</span>
 </span><span id="first_use_script-27"><a href="#first_use_script-27"><span class="linenos">27</span></a>    <span class="n">pipeline</span> <span class="o">=</span> <span class="n">sts</span><span class="o">.</span><span class="n">Pipeline</span><span class="p">(</span><span class="n">data</span><span class="p">,</span> <span class="n">save_dir</span><span class="o">=</span><span class="n">data_path</span><span class="p">,</span> <span class="n">logger</span><span class="o">=</span><span class="kc">None</span><span class="p">)</span>
 </span><span id="first_use_script-28"><a href="#first_use_script-28"><span class="linenos">28</span></a>
-</span><span id="first_use_script-29"><a href="#first_use_script-29"><span class="linenos">29</span></a>    <span class="c1"># first only extract 10 sinusoids</span>
-</span><span id="first_use_script-30"><a href="#first_use_script-30"><span class="linenos">30</span></a>    <span class="n">pipeline</span><span class="o">.</span><span class="n">iterative_prewhitening</span><span class="p">(</span><span class="n">n_extract</span><span class="o">=</span><span class="mi">10</span><span class="p">)</span>
-</span><span id="first_use_script-31"><a href="#first_use_script-31"><span class="linenos">31</span></a>    <span class="n">pipeline</span><span class="o">.</span><span class="n">optimise_sinusoid</span><span class="p">()</span>
+</span><span id="first_use_script-29"><a href="#first_use_script-29"><span class="linenos">29</span></a>    <span class="c1"># do a first run without fitting every step and lower group size</span>
+</span><span id="first_use_script-30"><a href="#first_use_script-30"><span class="linenos">30</span></a>    <span class="n">sts</span><span class="o">.</span><span class="n">update_config</span><span class="p">(</span><span class="n">settings</span><span class="o">=</span><span class="p">{</span><span class="s1">&#39;optimise_step&#39;</span><span class="p">:</span> <span class="kc">False</span><span class="p">,</span> <span class="s1">&#39;min_group&#39;</span><span class="p">:</span> <span class="mi">15</span><span class="p">,</span> <span class="s1">&#39;max_group&#39;</span><span class="p">:</span> <span class="mi">20</span><span class="p">})</span>
+</span><span id="first_use_script-31"><a href="#first_use_script-31"><span class="linenos">31</span></a>    <span class="n">pipeline</span><span class="o">.</span><span class="n">run</span><span class="p">()</span>
 </span><span id="first_use_script-32"><a href="#first_use_script-32"><span class="linenos">32</span></a>
-</span><span id="first_use_script-33"><a href="#first_use_script-33"><span class="linenos">33</span></a>    <span class="c1"># start new pipeline for the second part</span>
-</span><span id="first_use_script-34"><a href="#first_use_script-34"><span class="linenos">34</span></a>    <span class="n">pipeline</span> <span class="o">=</span> <span class="n">sts</span><span class="o">.</span><span class="n">Pipeline</span><span class="p">(</span><span class="n">data</span><span class="p">,</span> <span class="n">save_dir</span><span class="o">=</span><span class="n">data_path</span><span class="p">,</span> <span class="n">logger</span><span class="o">=</span><span class="kc">None</span><span class="p">)</span>
-</span><span id="first_use_script-35"><a href="#first_use_script-35"><span class="linenos">35</span></a>
-</span><span id="first_use_script-36"><a href="#first_use_script-36"><span class="linenos">36</span></a>    <span class="c1"># do a first run without fitting every step and lower group size</span>
-</span><span id="first_use_script-37"><a href="#first_use_script-37"><span class="linenos">37</span></a>    <span class="n">sts</span><span class="o">.</span><span class="n">update_config</span><span class="p">(</span><span class="n">settings</span><span class="o">=</span><span class="p">{</span><span class="s1">&#39;optimise_step&#39;</span><span class="p">:</span> <span class="kc">False</span><span class="p">,</span> <span class="s1">&#39;min_group&#39;</span><span class="p">:</span> <span class="mi">15</span><span class="p">,</span> <span class="s1">&#39;max_group&#39;</span><span class="p">:</span> <span class="mi">20</span><span class="p">})</span>
-</span><span id="first_use_script-38"><a href="#first_use_script-38"><span class="linenos">38</span></a>    <span class="n">pipeline</span><span class="o">.</span><span class="n">run</span><span class="p">()</span>
-</span><span id="first_use_script-39"><a href="#first_use_script-39"><span class="linenos">39</span></a>
-</span><span id="first_use_script-40"><a href="#first_use_script-40"><span class="linenos">40</span></a>    <span class="c1"># do a second run with fitting every step</span>
-</span><span id="first_use_script-41"><a href="#first_use_script-41"><span class="linenos">41</span></a>    <span class="n">sts</span><span class="o">.</span><span class="n">update_config</span><span class="p">(</span><span class="n">settings</span><span class="o">=</span><span class="p">{</span><span class="s1">&#39;optimise_step&#39;</span><span class="p">:</span> <span class="kc">True</span><span class="p">})</span>
-</span><span id="first_use_script-42"><a href="#first_use_script-42"><span class="linenos">42</span></a>    <span class="n">pipeline</span><span class="o">.</span><span class="n">run</span><span class="p">()</span>
+</span><span id="first_use_script-33"><a href="#first_use_script-33"><span class="linenos">33</span></a>    <span class="c1"># do a second run with fitting every step</span>
+</span><span id="first_use_script-34"><a href="#first_use_script-34"><span class="linenos">34</span></a>    <span class="n">sts</span><span class="o">.</span><span class="n">update_config</span><span class="p">(</span><span class="n">settings</span><span class="o">=</span><span class="p">{</span><span class="s1">&#39;optimise_step&#39;</span><span class="p">:</span> <span class="kc">True</span><span class="p">})</span>
+</span><span id="first_use_script-35"><a href="#first_use_script-35"><span class="linenos">35</span></a>    <span class="n">pipeline</span><span class="o">.</span><span class="n">run</span><span class="p">()</span>
 </span></pre></div>