Delayed flows with new format

docs/_modules/index.html

@@ -143,7 +143,6 @@ <h1>All modules for which code is available</h1>
 <li><a href="teaspoon/MakeData/DynSysLib/DynSysLib.html">teaspoon.MakeData.DynSysLib.DynSysLib</a></li>
 <li><a href="teaspoon/MakeData/DynSysLib/autonomous_dissipative_flows.html">teaspoon.MakeData.DynSysLib.autonomous_dissipative_flows</a></li>
 <li><a href="teaspoon/MakeData/DynSysLib/conservative_flows.html">teaspoon.MakeData.DynSysLib.conservative_flows</a></li>
-<li><a href="teaspoon/MakeData/DynSysLib/delayed_flows.html">teaspoon.MakeData.DynSysLib.delayed_flows</a></li>
 <li><a href="teaspoon/MakeData/DynSysLib/driven_dissipative_flows.html">teaspoon.MakeData.DynSysLib.driven_dissipative_flows</a></li>
 <li><a href="teaspoon/MakeData/DynSysLib/maps.html">teaspoon.MakeData.DynSysLib.maps</a></li>
 <li><a href="teaspoon/MakeData/DynSysLib/medical_data.html">teaspoon.MakeData.DynSysLib.medical_data</a></li>

docs/genindex.html

@@ -367,8 +367,6 @@ <h2 id="L">L</h2>
 <h2 id="M">M</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="modules/MakeData/DynSysLib/delayed_flows.html#teaspoon.MakeData.DynSysLib.delayed_flows.mackey_glass">mackey_glass() (in module teaspoon.MakeData.DynSysLib.delayed_flows)</a>
-</li>
       <li><a href="modules/SP/network.html#teaspoon.SP.network_tools.make_network">make_network() (in module teaspoon.SP.network_tools)</a>
 </li>
       <li><a href="modules/TDA/persistence.html#teaspoon.TDA.Persistence.maxBirth">maxBirth() (in module teaspoon.TDA.Persistence)</a>
@@ -406,8 +404,6 @@ <h2 id="M">M</h2>
         <li><a href="modules/MakeData/DynSysLib/autonomous_dissipative_flows.html#module-teaspoon.MakeData.DynSysLib.autonomous_dissipative_flows">teaspoon.MakeData.DynSysLib.autonomous_dissipative_flows</a>
 </li>
         <li><a href="modules/MakeData/DynSysLib/conservative_flows.html#module-teaspoon.MakeData.DynSysLib.conservative_flows">teaspoon.MakeData.DynSysLib.conservative_flows</a>
-</li>
-        <li><a href="modules/MakeData/DynSysLib/delayed_flows.html#module-teaspoon.MakeData.DynSysLib.delayed_flows">teaspoon.MakeData.DynSysLib.delayed_flows</a>
 </li>
         <li><a href="modules/MakeData/DynSysLib/driven_dissipative_flows.html#module-teaspoon.MakeData.DynSysLib.driven_dissipative_flows">teaspoon.MakeData.DynSysLib.driven_dissipative_flows</a>
 </li>
@@ -580,13 +576,6 @@ <h2 id="T">T</h2>
 
       <ul>
         <li><a href="modules/MakeData/DynSysLib/conservative_flows.html#module-teaspoon.MakeData.DynSysLib.conservative_flows">module</a>
-</li>
-      </ul></li>
-      <li>
-    teaspoon.MakeData.DynSysLib.delayed_flows
-
-      <ul>
-        <li><a href="modules/MakeData/DynSysLib/delayed_flows.html#module-teaspoon.MakeData.DynSysLib.delayed_flows">module</a>
 </li>
       </ul></li>
       <li>
@@ -680,15 +669,15 @@ <h2 id="T">T</h2>
         <li><a href="modules/ParamSelection/MsPE.html#module-teaspoon.parameter_selection.MsPE">module</a>
 </li>
       </ul></li>
-  </ul></td>
-  <td style="width: 33%; vertical-align: top;"><ul>
       <li>
     teaspoon.parameter_selection.PAMI_delay
 
       <ul>
         <li><a href="modules/ParamSelection/PAMI.html#module-teaspoon.parameter_selection.PAMI_delay">module</a>
 </li>
       </ul></li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
       <li>
     teaspoon.SP.adaptivePart
 

docs/modules/MakeData/DynSysLib/delayed_flows.html

@@ -19,8 +19,6 @@
         <script src="../../../_static/doctools.js"></script>
         <script src="../../../_static/sphinx_highlight.js"></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>window.MathJax = {"tex": {"inlineMath": [["$", "$"], ["\\(", "\\)"]], "processEscapes": true}, "options": {"ignoreHtmlClass": "tex2jax_ignore|mathjax_ignore|document", "processHtmlClass": "tex2jax_process|mathjax_process|math|output_area"}}</script>
-        <script defer="defer" src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.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" />
@@ -173,37 +171,8 @@
 </style>
 <section id="delayed-flows">
 <h1><span class="section-number">2.1.2.1.8. </span>Delayed Flows<a class="headerlink" href="#delayed-flows" title="Permalink to this heading"></a></h1>
-<section id="module-teaspoon.MakeData.DynSysLib.delayed_flows">
-<span id="main-functions"></span><h2><span class="section-number">2.1.2.1.8.1. </span>Main Functions<a class="headerlink" href="#module-teaspoon.MakeData.DynSysLib.delayed_flows" title="Permalink to this heading"></a></h2>
-<dl class="py function">
-<dt class="sig sig-object py" id="teaspoon.MakeData.DynSysLib.delayed_flows.mackey_glass">
-<span class="sig-prename descclassname"><span class="pre">teaspoon.MakeData.DynSysLib.delayed_flows.</span></span><span class="sig-name descname"><span class="pre">mackey_glass</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">parameters</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">fs</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">5</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">SampleSize</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1000</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">L</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">400</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">dynamic_state</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'periodic'</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../../_modules/teaspoon/MakeData/DynSysLib/delayed_flows.html#mackey_glass"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#teaspoon.MakeData.DynSysLib.delayed_flows.mackey_glass" title="Permalink to this definition"></a></dt>
-<dd><p>The Mackey-Glass Delayed Differential Equation is</p>
-<div class="math notranslate nohighlight">
-\[\dot{x}(t) = -\gamma*x(t) + \beta*\frac{x(t - \tau)}{1 + x(t - \tau)^n}\]</div>
-<p>where we chose the parameters <span class="math notranslate nohighlight">\(\tau = 2, \beta = 2, \gamma = 1,\)</span> and <span class="math notranslate nohighlight">\(n = 9.65\)</span>. We solve this system for 400 seconds with a sampling rate of 50 Hz. The solution was then downsampled to 5 Hz and the last 200 seconds were used for the figure.</p>
-<figure class="align-default">
-<img alt="../../../_images/Mackey_Glass_Delayed_Differential_Equation.png" src="../../../_images/Mackey_Glass_Delayed_Differential_Equation.png" />
-</figure>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters<span class="colon">:</span></dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>parameters</strong> (<em>Optional</em><em>[</em><em>floats</em><em>]</em>) – Array of four floats [gamma, tau, beta, n]</p></li>
-<li><p><strong>fs</strong> (<em>Optional</em><em>[</em><em>float</em><em>]</em>) – Sampling rate for simulation</p></li>
-<li><p><strong>SampleSize</strong> (<em>Optional</em><em>[</em><em>int</em><em>]</em>) – length of sample at end of entire time series</p></li>
-<li><p><strong>L</strong> (<em>Optional</em><em>[</em><em>int</em><em>]</em>) – Number of iterations</p></li>
-<li><p><strong>dynamic_state</strong> (<em>Optional</em><em>[</em><em>str</em><em>]</em>) – Set dynamic state as either ‘periodic’ or ‘chaotic’ is not supplying parameters.</p></li>
-</ul>
-</dd>
-<dt class="field-even">Returns<span class="colon">:</span></dt>
-<dd class="field-even"><p>Array of the time indices as <cite>t</cite> and the simulation time series <cite>ts</cite></p>
-</dd>
-<dt class="field-odd">Return type<span class="colon">:</span></dt>
-<dd class="field-odd"><p>array</p>
-</dd>
-</dl>
-</dd></dl>
-
+<section id="main-functions">
+<h2><span class="section-number">2.1.2.1.8.1. </span>Main Functions<a class="headerlink" href="#main-functions" title="Permalink to this heading"></a></h2>
 </section>
 <section id="meta-function">
 <h2><span class="section-number">2.1.2.1.8.2. </span>Meta Function<a class="headerlink" href="#meta-function" title="Permalink to this heading"></a></h2>

docs/py-modindex.html

@@ -168,11 +168,6 @@ <h1>Python Module Index</h1>
        <td>&#160;&#160;&#160;
        <a href="modules/MakeData/DynSysLib/conservative_flows.html#module-teaspoon.MakeData.DynSysLib.conservative_flows"><code class="xref">teaspoon.MakeData.DynSysLib.conservative_flows</code></a></td><td>
        <em></em></td></tr>
-     <tr class="cg-1">
-       <td></td>
-       <td>&#160;&#160;&#160;
-       <a href="modules/MakeData/DynSysLib/delayed_flows.html#module-teaspoon.MakeData.DynSysLib.delayed_flows"><code class="xref">teaspoon.MakeData.DynSysLib.delayed_flows</code></a></td><td>
-       <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&#160;&#160;&#160;

teaspoon/teaspoon/MakeData/DynSysLib/delayed_flows.py

@@ -1,4 +1,5 @@
 import numpy as np
+from ddeint import ddeint
 
 def delayed_flows(system, dynamic_state=None, L=None, fs=None,
                   SampleSize=None, parameters=None, InitialConditions=None):
@@ -8,7 +9,7 @@ def delayed_flows(system, dynamic_state=None, L=None, fs=None,
 
     return t, ts
 
-def mackey_glass(parameters=None, fs=5, SampleSize=1000, L=400, dynamic_state='periodic'):
+def mackey_glass(parameters=[1.0001, 2.0, 2.0, 7.75], fs=5, SampleSize=1000, L=400, dynamic_state=None):
     """
     The Mackey-Glass Delayed Differential Equation is
 
@@ -20,38 +21,37 @@ def mackey_glass(parameters=None, fs=5, SampleSize=1000, L=400, dynamic_state='p
     .. figure:: ../../../figures/Delayed_Flows/Mackey_Glass_Delayed_Differential_Equation.png
     
     Parameters:
-        parameters (Optional[floats]): Array of four floats [gamma, tau, beta, n]
+        parameters (Optional[floats]): Array of four floats [gamma, tau, beta, n] or None if using the dynamic_state variable
         fs (Optional[float]): Sampling rate for simulation
         SampleSize (Optional[int]): length of sample at end of entire time series
         L (Optional[int]): Number of iterations
-        dynamic_state (Optional[str]): Set dynamic state as either 'periodic' or 'chaotic' is not supplying parameters.
+        dynamic_state (Optional[str]): Set dynamic state as either 'periodic' or 'chaotic' if not supplying parameters.
         
     Returns:
         array: Array of the time indices as `t` and the simulation time series `ts`
     
     """
 
-    # This requires installation of ddeint (pip install ddeint)
-    from ddeint import ddeint
-
     t = np.linspace(0, L, int(L*fs))
 
-    # setting system parameters
-    if len(parameters) != 4:
-        print(
-            'Warning: needed 4 parameters. Defaulting to periodic solution parameters.')
-        parameters = None
-    else:
-        gamma, τ, B, n = parameters[0], parameters[1], parameters[2], parameters[3]
-
-    if parameters == None:
+    if len(parameters) != 3:
+        raise ValueError('Need 3 parameters as specified in documentation.')
+    elif dynamic_state != None:
         if dynamic_state == 'periodic':
             n = 7.75
-        if dynamic_state == 'chaotic':
+            τ = 2.0
+            B = 2.0
+            gamma = 1.0001
+        elif dynamic_state == 'chaotic':
             n = 9.65
-        τ = 2.0
-        B = 2.0
-        gamma = 1.0001
+            τ = 2.0
+            B = 2.0
+            gamma = 1.0001
+        else:
+            raise ValueError('dynamic_state needs to be either "periodic" or "chaotic" or provide an array of length 3 in parameters.')
+    else:
+        gamma, τ, B, n = parameters[0], parameters[1], parameters[2], parameters[3]
+
 
     def mackey_glass(X, t, d):
         x = X(t)
@@ -67,4 +67,4 @@ def g(t): return np.array([1, 1])
     ts = [((states[0])[::int(fsolve/fs)])[-SampleSize:]]
     t = tt[::int(fsolve/fs)][-SampleSize:]
 
-    return t, ts
+    return t, ts