update docs

Author: tuoyl

docs/APIdocs/pulse.html

@@ -904,7 +904,7 @@ <h2>Pulse Analysis<a class="headerlink" href="#pulse-analysis" title="Permalink
 <span id="timing-analysis"></span><h3>Timing Analysis<a class="headerlink" href="#module-tatpulsar.pulse.residuals" title="Permalink to this headline"></a></h3>
 <dl class="py function">
 <dt class="sig sig-object py" id="tatpulsar.pulse.residuals.cal_residual">
-<span class="sig-prename descclassname"><span class="pre">tatpulsar.pulse.residuals.</span></span><span class="sig-name descname"><span class="pre">cal_residual</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">toas</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">toa_errs</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">f_set_all</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">PEPOCH_all</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start_time</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">stop_time</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">inperiod</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/tuoyl/tat-pulsar/blob/master/tatpulsar/pulse/residuals.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#tatpulsar.pulse.residuals.cal_residual" title="Permalink to this definition"></a></dt>
+<span class="sig-prename descclassname"><span class="pre">tatpulsar.pulse.residuals.</span></span><span class="sig-name descname"><span class="pre">cal_residual</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">toas</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">toa_errs</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">f_set_all</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">PEPOCH_all</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start_time</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">stop_time</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">inperiod</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">phi_shift</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/tuoyl/tat-pulsar/blob/master/tatpulsar/pulse/residuals.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#tatpulsar.pulse.residuals.cal_residual" title="Permalink to this definition"></a></dt>
 <dd><p>calculate the residuals for toas in each Ephemeride</p>
 <p>return the residuals as one</p>
 </dd></dl>
@@ -980,7 +980,7 @@ <h2>Pulse Analysis<a class="headerlink" href="#pulse-analysis" title="Permalink
 
   <div role="contentinfo">
     <p>&#169; Copyright 2022, Youli.
-      <span class="lastupdated">Last updated on 2023 Jun 06 at 12:09:33 UTC.
+      <span class="lastupdated">Last updated on 2023 Jun 07 at 15:30:44 UTC.
       </span></p>
   </div>
 

docs/_images/notebooks_PulsarTimingAnalysis_14_1.png

@@ -137,7 +137,7 @@ <h1>TAT-pulsar package API<a class="headerlink" href="#tat-pulsar-package-api" t
 
   <div role="contentinfo">
     <p>&#169; Copyright 2022, Youli.
-      <span class="lastupdated">Last updated on 2023 Jun 06 at 12:09:33 UTC.
+      <span class="lastupdated">Last updated on 2023 Jun 07 at 15:30:44 UTC.
       </span></p>
   </div>
 

docs/_images/notebooks_PulsarTimingAnalysis_16_1.png

@@ -342,7 +342,7 @@ <h2 id="T">T</h2>
 
   <div role="contentinfo">
     <p>&#169; Copyright 2022, Youli.
-      <span class="lastupdated">Last updated on 2023 Jun 06 at 12:20:23 UTC.
+      <span class="lastupdated">Last updated on 2023 Jun 07 at 15:30:44 UTC.
       </span></p>
   </div>
 

docs/_images/notebooks_PulsarTimingAnalysis_17_1.png

@@ -171,7 +171,7 @@ <h2>Contents<a class="headerlink" href="#contents" title="Permalink to this head
 
   <div role="contentinfo">
     <p>&#169; Copyright 2022, Youli.
-      <span class="lastupdated">Last updated on 2023 Jun 06 at 12:20:23 UTC.
+      <span class="lastupdated">Last updated on 2023 Jun 07 at 15:30:44 UTC.
       </span></p>
   </div>
 

docs/_sources/notebooks/PulsarTimingAnalysis.ipynb.txt

@@ -807,7 +807,7 @@ <h3>Solving Kepler equation<a class="headerlink" href="#Solving-Kepler-equation"
 
   <div role="contentinfo">
     <p>&#169; Copyright 2022, Youli.
-      <span class="lastupdated">Last updated on 2023 Jun 06 at 12:09:33 UTC.
+      <span class="lastupdated">Last updated on 2023 Jun 07 at 15:06:54 UTC.
       </span></p>
   </div>
 

docs/autodocs.html

@@ -53,6 +53,7 @@
 <li class="toctree-l2 current"><a class="current reference internal" href="#"> Crab Analysis</a><ul>
 <li class="toctree-l3"><a class="reference internal" href="#Search-the-best-frequency">Search the best frequency</a></li>
 <li class="toctree-l3"><a class="reference internal" href="#Bayrcentric-correction">Bayrcentric correction</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#Play-with-the-profile">Play with the profile</a></li>
 </ul>
 </li>
 <li class="toctree-l2"><a class="reference internal" href="BinaryAnalysis.html"> Binary System Analysis</a></li>
@@ -357,6 +358,8 @@
 </style>
 <div class="section" id="Pulsar-Timing-Analysis">
 <h1>Pulsar Timing Analysis<a class="headerlink" href="#Pulsar-Timing-Analysis" title="Permalink to this headline"></a></h1>
+<p>Welcome to our step-by-step Jupyter notebook tutorial on pulsar timing analysis using the TAT-Pulsar Python package.</p>
+<p>Throughout this guide, we’ll provide you with hands-on examples of how to use the key features of TAT-Pulsar.</p>
 <div class="section" id="Search-the-best-frequency">
 <h2>Search the best frequency<a class="headerlink" href="#Search-the-best-frequency" title="Permalink to this headline"></a></h2>
 <div class="nbinput nblast docutils container">
@@ -368,7 +371,7 @@ <h2>Search the best frequency<a class="headerlink" href="#Search-the-best-freque
 <span class="kn">import</span> <span class="nn">wget</span><span class="o">,</span> <span class="nn">os</span>
 <span class="kn">from</span> <span class="nn">astropy.io</span> <span class="kn">import</span> <span class="n">fits</span>
 
-<span class="n">mpl</span><span class="o">.</span><span class="n">rcParams</span><span class="p">[</span><span class="s1">&#39;figure.dpi&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="mi">150</span>
+<span class="n">mpl</span><span class="o">.</span><span class="n">rcParams</span><span class="p">[</span><span class="s1">&#39;figure.dpi&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="mi">250</span>
 <span class="n">plt</span><span class="o">.</span><span class="n">style</span><span class="o">.</span><span class="n">use</span><span class="p">([</span><span class="s1">&#39;science&#39;</span><span class="p">,</span> <span class="s1">&#39;nature&#39;</span><span class="p">,</span> <span class="s1">&#39;no-latex&#39;</span><span class="p">])</span>
 </pre></div>
 </div>
@@ -444,24 +447,24 @@ <h2>Bayrcentric correction<a class="headerlink" href="#Bayrcentric-correction" t
 </div>
 <div class="output_area docutils container">
 <div class="highlight"><pre>
-PSR_B         0531+21
-RA_hh               5
-RA_mm              34
-RA_ss          31.972
-DEC_hh             22
-DEC_mm              0
-DEC_ss          52.07
-MJD1            57966
-MJD2            57997
-t0geo           57981
-f0            29.6394
-f1       -3.68701e-10
-f2           9.29e-21
-RMS               0.6
-O                   J
-B               DE200
-name          0531+21
-Notes             NaN
+PSR_B       0531+21
+RA_hh             5
+RA_mm            34
+RA_ss        31.972
+DEC_hh           22
+DEC_mm            0
+DEC_ss        52.07
+MJD1          57966
+MJD2          57997
+t0geo       57981.0
+f0        29.639378
+f1             -0.0
+f2              0.0
+RMS             0.6
+O                 J
+B             DE200
+name        0531+21
+Notes           NaN
 Name: 374, dtype: object
 </pre></div></div>
 </div>
@@ -556,6 +559,69 @@ <h2>Bayrcentric correction<a class="headerlink" href="#Bayrcentric-correction" t
 </div>
 </div>
 </div>
+<div class="section" id="Play-with-the-profile">
+<h2>Play with the profile<a class="headerlink" href="#Play-with-the-profile" title="Permalink to this headline"></a></h2>
+<div class="nbinput docutils container">
+<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[8]:
+</pre></div>
+</div>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="n">profile</span><span class="o">.</span><span class="n">cycles</span> <span class="o">=</span> <span class="mi">2</span> <span class="c1"># set the phase cycls of profile</span>
+<span class="n">plt</span><span class="o">.</span><span class="n">errorbar</span><span class="p">(</span><span class="n">profile</span><span class="o">.</span><span class="n">phase</span><span class="p">,</span>
+             <span class="n">profile</span><span class="o">.</span><span class="n">counts</span><span class="p">,</span>
+             <span class="n">yerr</span><span class="o">=</span><span class="n">profile</span><span class="o">.</span><span class="n">error</span><span class="p">,</span>
+             <span class="n">ds</span><span class="o">=</span><span class="s1">&#39;steps-mid&#39;</span><span class="p">)</span>
+<span class="n">plt</span><span class="o">.</span><span class="n">xlabel</span><span class="p">(</span><span class="s2">&quot;Phase&quot;</span><span class="p">)</span>
+<span class="n">plt</span><span class="o">.</span><span class="n">ylabel</span><span class="p">(</span><span class="s2">&quot;Counts&quot;</span><span class="p">)</span>
+</pre></div>
+</div>
+</div>
+<div class="nboutput docutils container">
+<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[8]:
+</pre></div>
+</div>
+<div class="output_area docutils container">
+<div class="highlight"><pre>
+Text(0, 0.5, &#39;Counts&#39;)
+</pre></div></div>
+</div>
+<div class="nboutput nblast docutils container">
+<div class="prompt empty docutils container">
+</div>
+<div class="output_area docutils container">
+<img alt="../_images/notebooks_PulsarTimingAnalysis_16_1.png" src="../_images/notebooks_PulsarTimingAnalysis_16_1.png" />
+</div>
+</div>
+<div class="nbinput docutils container">
+<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[20]:
+</pre></div>
+</div>
+<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="n">profile</span><span class="o">.</span><span class="n">norm</span><span class="p">(</span><span class="n">method</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span> <span class="c1"># Normalization</span>
+<span class="n">profile_new</span> <span class="o">=</span> <span class="n">profile</span><span class="o">.</span><span class="n">resample</span><span class="p">(</span><span class="n">sample_num</span><span class="o">=</span><span class="mi">1000</span><span class="p">)</span>
+
+<span class="n">plt</span><span class="o">.</span><span class="n">imshow</span><span class="p">(</span><span class="n">profile_new</span><span class="p">,</span> <span class="n">aspect</span><span class="o">=</span><span class="s1">&#39;auto&#39;</span><span class="p">,</span>
+           <span class="n">extent</span><span class="o">=</span><span class="p">[</span><span class="mi">0</span><span class="p">,</span><span class="mi">2</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span> <span class="mi">1000</span><span class="p">])</span>
+<span class="n">plt</span><span class="o">.</span><span class="n">xlabel</span><span class="p">(</span><span class="s2">&quot;phase&quot;</span><span class="p">)</span>
+<span class="n">plt</span><span class="o">.</span><span class="n">ylabel</span><span class="p">(</span><span class="s2">&quot;numbers of profiles&quot;</span><span class="p">)</span>
+</pre></div>
+</div>
+</div>
+<div class="nboutput docutils container">
+<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[20]:
+</pre></div>
+</div>
+<div class="output_area docutils container">
+<div class="highlight"><pre>
+Text(0, 0.5, &#39;numbers of profiles&#39;)
+</pre></div></div>
+</div>
+<div class="nboutput nblast docutils container">
+<div class="prompt empty docutils container">
+</div>
+<div class="output_area docutils container">
+<img alt="../_images/notebooks_PulsarTimingAnalysis_17_1.png" src="../_images/notebooks_PulsarTimingAnalysis_17_1.png" />
+</div>
+</div>
+</div>
 </div>
 
 
@@ -570,7 +636,7 @@ <h2>Bayrcentric correction<a class="headerlink" href="#Bayrcentric-correction" t
 
   <div role="contentinfo">
     <p>&#169; Copyright 2022, Youli.
-      <span class="lastupdated">Last updated on 2023 Jun 06 at 12:09:33 UTC.
+      <span class="lastupdated">Last updated on 2023 Jun 07 at 15:30:44 UTC.
       </span></p>
   </div>
 

docs/genindex.html

@@ -144,7 +144,7 @@ <h1>Python Module Index</h1>
 
   <div role="contentinfo">
     <p>&#169; Copyright 2022, Youli.
-      <span class="lastupdated">Last updated on 2023 Jun 06 at 12:20:23 UTC.
+      <span class="lastupdated">Last updated on 2023 Jun 07 at 15:30:44 UTC.
       </span></p>
   </div>
 

docs/index.html

@@ -97,7 +97,7 @@
 
   <div role="contentinfo">
     <p>&#169; Copyright 2022, Youli.
-      <span class="lastupdated">Last updated on 2023 Jun 06 at 12:20:23 UTC.
+      <span class="lastupdated">Last updated on 2023 Jun 07 at 15:30:44 UTC.
       </span></p>
   </div>