Switch to 0.6.1

raphaelvallat · Mar 15, 2022 · 71c0a82 · 71c0a82
1 parent d1cb4aa
commit 71c0a82
Show file tree

Hide file tree

Showing 53 changed files with 650 additions and 475 deletions.
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: ef3c46c5d2e20009f4576c5641b7f714
+config: 7d440e1bf4ab7dd814452f500decfcbf
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/build/html/_modules/index.html b/docs/build/html/_modules/index.html
@@ -3,7 +3,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml">
   <head>
     <meta charset="utf-8" />
-    <title>Overview: module code &#8212; yasa 0.6.0 documentation</title>
+    <title>Overview: module code &#8212; yasa 0.6.1 documentation</title>
     <link rel="stylesheet" href="../_static/bootstrap-sphinx.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
     <link rel="stylesheet" type="text/css" href="../_static/plot_directive.css" />
@@ -41,7 +41,7 @@
         </button>
         <a class="navbar-brand" href="../index.html"><span><img src="../_static/yasa_128x128.png"></span>
           yasa</a>
-        <span class="navbar-text navbar-version pull-left"><b>0.6.0</b></span>
+        <span class="navbar-text navbar-version pull-left"><b>0.6.1</b></span>
       </div>
 
         <div class="collapse navbar-collapse nav-collapse">

diff --git a/docs/build/html/_modules/yasa/detection.html b/docs/build/html/_modules/yasa/detection.html
@@ -3,7 +3,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml">
   <head>
     <meta charset="utf-8" />
-    <title>yasa.detection &#8212; yasa 0.6.0 documentation</title>
+    <title>yasa.detection &#8212; yasa 0.6.1 documentation</title>
     <link rel="stylesheet" href="../../_static/bootstrap-sphinx.css" type="text/css" />
     <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
     <link rel="stylesheet" type="text/css" href="../../_static/plot_directive.css" />
@@ -41,7 +41,7 @@
         </button>
         <a class="navbar-brand" href="../../index.html"><span><img src="../../_static/yasa_128x128.png"></span>
           yasa</a>
-        <span class="navbar-text navbar-version pull-left"><b>0.6.0</b></span>
+        <span class="navbar-text navbar-version pull-left"><b>0.6.1</b></span>
       </div>
 
         <div class="collapse navbar-collapse nav-collapse">
@@ -674,6 +674,12 @@ <h1>Source code for yasa.detection</h1><div class="highlight"><pre>
 
 <span class="sd">    For better results, apply this detection only on artefact-free NREM sleep.</span>
 
+<span class="sd">    .. warning::</span>
+<span class="sd">        A critical bug was fixed in YASA 0.6.1, in which the number of detected spindles could</span>
+<span class="sd">        vary drastically depending on the sampling frequency of the data. Please make sure to check</span>
+<span class="sd">        any results obtained with this function prior to the 0.6.1 release.</span>
+
+
 <span class="sd">    References</span>
 <span class="sd">    ----------</span>
 <span class="sd">    The sleep spindles detection algorithm is based on:</span>
@@ -812,9 +818,12 @@ <h1>Source code for yasa.detection</h1><div class="highlight"><pre>
 
         <span class="c1"># The detection using the three thresholds tends to underestimate the</span>
         <span class="c1"># real duration of the spindle. To overcome this, we compute a soft</span>
-        <span class="c1"># threshold by smoothing the idx_sum vector with a 100 ms window.</span>
+        <span class="c1"># threshold by smoothing the idx_sum vector with a ~100 ms window.</span>
+        <span class="c1"># Sampling frequency = 100 Hz --&gt; w = 10 samples</span>
+        <span class="c1"># Sampling frequecy = 256 Hz --&gt; w = 25 samples = 97 ms</span>
         <span class="n">w</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="mf">0.1</span> <span class="o">*</span> <span class="n">sf</span><span class="p">)</span>
-        <span class="n">idx_sum</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">convolve</span><span class="p">(</span><span class="n">idx_sum</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">ones</span><span class="p">(</span><span class="n">w</span><span class="p">)</span> <span class="o">/</span> <span class="n">w</span><span class="p">,</span> <span class="n">mode</span><span class="o">=</span><span class="s1">&#39;same&#39;</span><span class="p">)</span>
+        <span class="c1"># Critical bugfix March 2022, see https://github.com/raphaelvallat/yasa/pull/55</span>
+        <span class="n">idx_sum</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">convolve</span><span class="p">(</span><span class="n">idx_sum</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">ones</span><span class="p">(</span><span class="n">w</span><span class="p">),</span> <span class="n">mode</span><span class="o">=</span><span class="s1">&#39;same&#39;</span><span class="p">)</span> <span class="o">/</span> <span class="n">w</span>
         <span class="c1"># And we then find indices that are strictly greater than 2, i.e. we</span>
         <span class="c1"># find the &#39;true&#39; beginning and &#39;true&#39; end of the events by finding</span>
         <span class="c1"># where at least two out of the three treshold were crossed.</span>

diff --git a/docs/build/html/_modules/yasa/hypno.html b/docs/build/html/_modules/yasa/hypno.html
@@ -3,7 +3,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml">
   <head>
     <meta charset="utf-8" />
-    <title>yasa.hypno &#8212; yasa 0.6.0 documentation</title>
+    <title>yasa.hypno &#8212; yasa 0.6.1 documentation</title>
     <link rel="stylesheet" href="../../_static/bootstrap-sphinx.css" type="text/css" />
     <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
     <link rel="stylesheet" type="text/css" href="../../_static/plot_directive.css" />
@@ -41,7 +41,7 @@
         </button>
         <a class="navbar-brand" href="../../index.html"><span><img src="../../_static/yasa_128x128.png"></span>
           yasa</a>
-        <span class="navbar-text navbar-version pull-left"><b>0.6.0</b></span>
+        <span class="navbar-text navbar-version pull-left"><b>0.6.1</b></span>
       </div>
 
         <div class="collapse navbar-collapse nav-collapse">

diff --git a/docs/build/html/_modules/yasa/others.html b/docs/build/html/_modules/yasa/others.html
@@ -3,7 +3,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml">
   <head>
     <meta charset="utf-8" />
-    <title>yasa.others &#8212; yasa 0.6.0 documentation</title>
+    <title>yasa.others &#8212; yasa 0.6.1 documentation</title>
     <link rel="stylesheet" href="../../_static/bootstrap-sphinx.css" type="text/css" />
     <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
     <link rel="stylesheet" type="text/css" href="../../_static/plot_directive.css" />
@@ -41,7 +41,7 @@
         </button>
         <a class="navbar-brand" href="../../index.html"><span><img src="../../_static/yasa_128x128.png"></span>
           yasa</a>
-        <span class="navbar-text navbar-version pull-left"><b>0.6.0</b></span>
+        <span class="navbar-text navbar-version pull-left"><b>0.6.1</b></span>
       </div>
 
         <div class="collapse navbar-collapse nav-collapse">

diff --git a/docs/build/html/_modules/yasa/plotting.html b/docs/build/html/_modules/yasa/plotting.html
@@ -3,7 +3,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml">
   <head>
     <meta charset="utf-8" />
-    <title>yasa.plotting &#8212; yasa 0.6.0 documentation</title>
+    <title>yasa.plotting &#8212; yasa 0.6.1 documentation</title>
     <link rel="stylesheet" href="../../_static/bootstrap-sphinx.css" type="text/css" />
     <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
     <link rel="stylesheet" type="text/css" href="../../_static/plot_directive.css" />
@@ -41,7 +41,7 @@
         </button>
         <a class="navbar-brand" href="../../index.html"><span><img src="../../_static/yasa_128x128.png"></span>
           yasa</a>
-        <span class="navbar-text navbar-version pull-left"><b>0.6.0</b></span>
+        <span class="navbar-text navbar-version pull-left"><b>0.6.1</b></span>
       </div>
 
         <div class="collapse navbar-collapse nav-collapse">

diff --git a/docs/build/html/_modules/yasa/sleepstats.html b/docs/build/html/_modules/yasa/sleepstats.html
@@ -3,7 +3,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml">
   <head>
     <meta charset="utf-8" />
-    <title>yasa.sleepstats &#8212; yasa 0.6.0 documentation</title>
+    <title>yasa.sleepstats &#8212; yasa 0.6.1 documentation</title>
     <link rel="stylesheet" href="../../_static/bootstrap-sphinx.css" type="text/css" />
     <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
     <link rel="stylesheet" type="text/css" href="../../_static/plot_directive.css" />
@@ -41,7 +41,7 @@
         </button>
         <a class="navbar-brand" href="../../index.html"><span><img src="../../_static/yasa_128x128.png"></span>
           yasa</a>
-        <span class="navbar-text navbar-version pull-left"><b>0.6.0</b></span>
+        <span class="navbar-text navbar-version pull-left"><b>0.6.1</b></span>
       </div>
 
         <div class="collapse navbar-collapse nav-collapse">

diff --git a/docs/build/html/_modules/yasa/spectral.html b/docs/build/html/_modules/yasa/spectral.html
@@ -3,7 +3,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml">
   <head>
     <meta charset="utf-8" />
-    <title>yasa.spectral &#8212; yasa 0.6.0 documentation</title>
+    <title>yasa.spectral &#8212; yasa 0.6.1 documentation</title>
     <link rel="stylesheet" href="../../_static/bootstrap-sphinx.css" type="text/css" />
     <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
     <link rel="stylesheet" type="text/css" href="../../_static/plot_directive.css" />
@@ -41,7 +41,7 @@
         </button>
         <a class="navbar-brand" href="../../index.html"><span><img src="../../_static/yasa_128x128.png"></span>
           yasa</a>
-        <span class="navbar-text navbar-version pull-left"><b>0.6.0</b></span>
+        <span class="navbar-text navbar-version pull-left"><b>0.6.1</b></span>
       </div>
 
         <div class="collapse navbar-collapse nav-collapse">

diff --git a/docs/build/html/_modules/yasa/staging.html b/docs/build/html/_modules/yasa/staging.html
@@ -3,7 +3,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml">
   <head>
     <meta charset="utf-8" />
-    <title>yasa.staging &#8212; yasa 0.6.0 documentation</title>
+    <title>yasa.staging &#8212; yasa 0.6.1 documentation</title>
     <link rel="stylesheet" href="../../_static/bootstrap-sphinx.css" type="text/css" />
     <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
     <link rel="stylesheet" type="text/css" href="../../_static/plot_directive.css" />
@@ -41,7 +41,7 @@
         </button>
         <a class="navbar-brand" href="../../index.html"><span><img src="../../_static/yasa_128x128.png"></span>
           yasa</a>
-        <span class="navbar-text navbar-version pull-left"><b>0.6.0</b></span>
+        <span class="navbar-text navbar-version pull-left"><b>0.6.1</b></span>
       </div>
 
         <div class="collapse navbar-collapse nav-collapse">

diff --git a/docs/build/html/_static/documentation_options.js b/docs/build/html/_static/documentation_options.js
@@ -1,6 +1,6 @@
 var DOCUMENTATION_OPTIONS = {
     URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
-    VERSION: '0.6.0',
+    VERSION: '0.6.1',
     LANGUAGE: 'None',
     COLLAPSE_INDEX: false,
     BUILDER: 'html',

diff --git a/docs/build/html/api.html b/docs/build/html/api.html
@@ -3,7 +3,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml">
   <head>
     <meta charset="utf-8" />
-    <title>API reference &#8212; yasa 0.6.0 documentation</title>
+    <title>API reference &#8212; yasa 0.6.1 documentation</title>
     <link rel="stylesheet" href="_static/bootstrap-sphinx.css" type="text/css" />
     <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
     <link rel="stylesheet" type="text/css" href="_static/plot_directive.css" />
@@ -41,7 +41,7 @@
         </button>
         <a class="navbar-brand" href="index.html"><span><img src="_static/yasa_128x128.png"></span>
           yasa</a>
-        <span class="navbar-text navbar-version pull-left"><b>0.6.0</b></span>
+        <span class="navbar-text navbar-version pull-left"><b>0.6.1</b></span>
       </div>
 
         <div class="collapse navbar-collapse nav-collapse">