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<!DOCTYPE html>
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<title>Start guide for the devicely package — devicely 1.1.1 documentation</title>
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<li class="toctree-l1 current"><a class="current reference internal" href="#">Start guide for the devicely package</a></li>
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<li class="toctree-l2"><a class="reference internal" href="#Empatica-E4">Empatica E4</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#Read-the-data">Read the data</a></li>
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.nblast.container + .nbinput.container {
margin-top: -19px;
}
.admonition > p:before {
margin-right: 4px; /* make room for the exclamation icon */
}
/* Fix math alignment, see https://github.com/rtfd/sphinx_rtd_theme/pull/686 */
.math {
text-align: unset;
}
</style>
<div class="section" id="Start-guide-for-the-devicely-package">
<h1>Start guide for the devicely package<a class="headerlink" href="#Start-guide-for-the-devicely-package" title="Permalink to this headline">¶</a></h1>
<p>To install devicely locally just run <code class="docutils literal notranslate"><span class="pre">pip</span> <span class="pre">install</span> <span class="pre">devicely</span></code></p>
</div>
<div class="section" id="Use-devicely">
<h1>Use devicely<a class="headerlink" href="#Use-devicely" title="Permalink to this headline">¶</a></h1>
<div class="nbinput nblast docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[43]:
</pre></div>
</div>
<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
<span></span><span class="kn">import</span> <span class="nn">os</span>
<span class="kn">import</span> <span class="nn">devicely</span>
<span class="n">write_dir</span> <span class="o">=</span> <span class="s1">'New'</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">isdir</span><span class="p">(</span><span class="n">write_dir</span><span class="p">):</span>
<span class="n">os</span><span class="o">.</span><span class="n">makedirs</span><span class="p">(</span><span class="n">write_dir</span><span class="p">)</span>
</pre></div>
</div>
</div>
<div class="section" id="Empatica-E4">
<h2>Empatica E4<a class="headerlink" href="#Empatica-E4" title="Permalink to this headline">¶</a></h2>
<p>The Empatice E4 wristband can be used to obtain data from inter-beat intervals, electrodermal activity, heart rate, temperature and blood volume pulse. The wristband uses <a class="reference external" href="https://github.com/hpi-dhc/devicely-example/tree/main/Empatica">this directory structure</a> for its measurement data.</p>
<div class="section" id="Read-the-data">
<h3>Read the data<a class="headerlink" href="#Read-the-data" title="Permalink to this headline">¶</a></h3>
<p>Create an EmpaticaReader object:</p>
<div class="nbinput nblast docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[44]:
</pre></div>
</div>
<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
<span></span><span class="n">empatica_reader</span> <span class="o">=</span> <span class="n">devicely</span><span class="o">.</span><span class="n">EmpaticaReader</span><span class="p">(</span><span class="s1">'Empatica'</span><span class="p">)</span>
</pre></div>
</div>
</div>
<p>Access the sampling frequencies and starting times for all signals:</p>
<div class="nbinput docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[45]:
</pre></div>
</div>
<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
<span></span><span class="n">empatica_reader</span><span class="o">.</span><span class="n">start_times</span>
</pre></div>
</div>
</div>
<div class="nboutput nblast docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[45]:
</pre></div>
</div>
<div class="output_area docutils container">
<div class="highlight"><pre>
{'ACC': Timestamp('2020-10-16 17:04:29'),
'BVP': Timestamp('2020-10-16 17:04:29'),
'EDA': Timestamp('2020-10-16 17:04:29'),
'HR': Timestamp('2020-10-16 17:04:39'),
'TEMP': Timestamp('2020-10-16 17:04:29'),
'IBI': Timestamp('2020-10-16 17:04:29')}
</pre></div></div>
</div>
<div class="nbinput docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[46]:
</pre></div>
</div>
<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
<span></span><span class="n">empatica_reader</span><span class="o">.</span><span class="n">sample_freqs</span>
</pre></div>
</div>
</div>
<div class="nboutput nblast docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[46]:
</pre></div>
</div>
<div class="output_area docutils container">
<div class="highlight"><pre>
{'ACC': 32.0, 'BVP': 64.0, 'EDA': 4.0, 'HR': 1.0, 'TEMP': 4.0}
</pre></div></div>
</div>
<p>Access the individual dataframes via the attributes ACC, BVP, EDA, HR, TEMP, IBI and tags:</p>
<div class="nbinput docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[47]:
</pre></div>
</div>
<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
<span></span><span class="n">empatica_reader</span><span class="o">.</span><span class="n">HR</span><span class="o">.</span><span class="n">head</span><span class="p">()</span>
</pre></div>
</div>
</div>
<div class="nboutput nblast docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[47]:
</pre></div>
</div>
<div class="output_area docutils container">
<div class="highlight"><pre>
2020-10-16 17:04:39 51.00
2020-10-16 17:04:40 51.50
2020-10-16 17:04:41 51.00
2020-10-16 17:04:42 52.75
2020-10-16 17:04:43 64.00
Name: HR, dtype: float64
</pre></div></div>
</div>
<p>Access a joined dataframe of all signals:</p>
<div class="nbinput docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[48]:
</pre></div>
</div>
<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
<span></span><span class="n">empatica_reader</span><span class="o">.</span><span class="n">data</span><span class="o">.</span><span class="n">head</span><span class="p">()</span>
</pre></div>
</div>
</div>
<div class="nboutput nblast docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[48]:
</pre></div>
</div>
<div class="output_area rendered_html docutils container">
<div>
<style scoped>
.dataframe tbody tr th:only-of-type {
vertical-align: middle;
}
.dataframe tbody tr th {
vertical-align: top;
}
.dataframe thead th {
text-align: right;
}
</style>
<table border="1" class="dataframe">
<thead>
<tr style="text-align: right;">
<th></th>
<th>ACC_X</th>
<th>ACC_Y</th>
<th>ACC_Z</th>
<th>BVP</th>
<th>EDA</th>
<th>HR</th>
<th>TEMP</th>
</tr>
</thead>
<tbody>
<tr>
<th>2020-10-16 17:04:29.000000</th>
<td>-3.0</td>
<td>11.0</td>
<td>60.0</td>
<td>-0.0</td>
<td>0.0</td>
<td>NaN</td>
<td>31.13</td>
</tr>
<tr>
<th>2020-10-16 17:04:29.015625</th>
<td>NaN</td>
<td>NaN</td>
<td>NaN</td>
<td>-0.0</td>
<td>NaN</td>
<td>NaN</td>
<td>NaN</td>
</tr>
<tr>
<th>2020-10-16 17:04:29.031250</th>
<td>-3.0</td>
<td>11.0</td>
<td>60.0</td>
<td>-0.0</td>
<td>NaN</td>
<td>NaN</td>
<td>NaN</td>
</tr>
<tr>
<th>2020-10-16 17:04:29.046875</th>
<td>NaN</td>
<td>NaN</td>
<td>NaN</td>
<td>-0.0</td>
<td>NaN</td>
<td>NaN</td>
<td>NaN</td>
</tr>
<tr>
<th>2020-10-16 17:04:29.062500</th>
<td>-2.0</td>
<td>11.0</td>
<td>60.0</td>
<td>-0.0</td>
<td>NaN</td>
<td>NaN</td>
<td>NaN</td>
</tr>
</tbody>
</table>
</div></div>
</div>
<p>The dataframe contains nan values because the individual signals have different sampling frequencies.</p>
</div>
<div class="section" id="Timeshift-the-data">
<h3>Timeshift the data<a class="headerlink" href="#Timeshift-the-data" title="Permalink to this headline">¶</a></h3>
<p>Apply a timeshift:</p>
<div class="nbinput docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[49]:
</pre></div>
</div>
<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
<span></span><span class="n">empatica_reader</span><span class="o">.</span><span class="n">timeshift</span><span class="p">()</span>
<span class="n">empatica_reader</span><span class="o">.</span><span class="n">start_times</span>
</pre></div>
</div>
</div>
<div class="nboutput nblast docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[49]:
</pre></div>
</div>
<div class="output_area docutils container">
<div class="highlight"><pre>
{'ACC': Timestamp('2019-05-18 22:02:53.817793664'),
'BVP': Timestamp('2019-05-18 22:02:53.817793664'),
'EDA': Timestamp('2019-05-18 22:02:53.817793664'),
'HR': Timestamp('2019-05-18 22:03:03.817793664'),
'TEMP': Timestamp('2019-05-18 22:02:53.817793664'),
'IBI': Timestamp('2019-05-18 22:02:53.817793664')}
</pre></div></div>
</div>
<p>By providing no parameter to <code class="docutils literal notranslate"><span class="pre">timeshift</span></code> the data is shifted by a random time interval between one month and two years to the past. You can also provide a <code class="docutils literal notranslate"><span class="pre">pandas.Timedelta</span></code> object to shift the data by that timedelta or a <code class="docutils literal notranslate"><span class="pre">pandas.Timestamp</span></code> object to shift the data such that this timestamp is the earliest entry.</p>
</div>
<div class="section" id="Write-the-data">
<h3>Write the data<a class="headerlink" href="#Write-the-data" title="Permalink to this headline">¶</a></h3>
<div class="nbinput docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[50]:
</pre></div>
</div>
<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
<span></span><span class="n">empatica_write_path</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">write_dir</span><span class="p">,</span> <span class="s1">'Empatica'</span><span class="p">)</span>
<span class="n">empatica_reader</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">empatica_write_path</span><span class="p">)</span>
<span class="n">os</span><span class="o">.</span><span class="n">listdir</span><span class="p">(</span><span class="n">empatica_write_path</span><span class="p">)</span>
</pre></div>
</div>
</div>
<div class="nboutput nblast docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[50]:
</pre></div>
</div>
<div class="output_area docutils container">
<div class="highlight"><pre>
['EDA.csv', 'HR.csv', 'IBI.csv', 'TEMP.csv', 'tags.csv', 'BVP.csv', 'ACC.csv']
</pre></div></div>
</div>
</div>
</div>
<div class="section" id="Spacelabs-Blood-Pressure-Monitor">
<h2>Spacelabs Blood Pressure Monitor<a class="headerlink" href="#Spacelabs-Blood-Pressure-Monitor" title="Permalink to this headline">¶</a></h2>
<p>Spacelabs uses <a class="reference external" href="https://github.com/hpi-dhc/devicely-example/tree/main/Spacelabs">a single file</a> to output its metadata as well as the actual signals.</p>
<div class="section" id="id1">
<h3>Read the data<a class="headerlink" href="#id1" title="Permalink to this headline">¶</a></h3>
<p>Create a <code class="docutils literal notranslate"><span class="pre">SpacelabsReader</span></code> object:</p>
<div class="nbinput nblast docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[51]:
</pre></div>
</div>
<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
<span></span><span class="n">spacelabs_reader</span> <span class="o">=</span> <span class="n">devicely</span><span class="o">.</span><span class="n">SpacelabsReader</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="s1">'Spacelabs'</span><span class="p">,</span> <span class="s1">'spacelabs.abp'</span><span class="p">))</span>
</pre></div>
</div>
</div>
<p>Acess the metadata:</p>
<div class="nbinput docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[52]:
</pre></div>
</div>
<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
<span></span><span class="n">spacelabs_reader</span><span class="o">.</span><span class="n">subject</span>
</pre></div>
</div>
</div>
<div class="nboutput nblast docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[52]:
</pre></div>
</div>
<div class="output_area docutils container">
<div class="highlight"><pre>
'001V0'
</pre></div></div>
</div>
<div class="nbinput docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[53]:
</pre></div>
</div>
<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
<span></span><span class="n">spacelabs_reader</span><span class="o">.</span><span class="n">metadata</span>
</pre></div>
</div>
</div>
<div class="nboutput nblast docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[53]:
</pre></div>
</div>
<div class="output_area docutils container">
<div class="highlight"><pre>
{'PATIENTINFO': {'DOB': None, 'RACE': None},
'REPORTINFO': {'PHYSICIAN': None,
'NURSETECH': 'admin',
'STATUS': 'NOTCONFIRMED',
'CALIPERSUMMARY': {'COUNT': '0'}}}
</pre></div></div>
</div>
<p>Access the signal dataframe:</p>
<div class="nbinput docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[54]:
</pre></div>
</div>
<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
<span></span><span class="n">spacelabs_reader</span><span class="o">.</span><span class="n">data</span><span class="o">.</span><span class="n">head</span><span class="p">()</span>
</pre></div>
</div>
</div>
<div class="nboutput nblast docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[54]:
</pre></div>
</div>
<div class="output_area rendered_html docutils container">
<div>
<style scoped>
.dataframe tbody tr th:only-of-type {
vertical-align: middle;
}
.dataframe tbody tr th {
vertical-align: top;
}
.dataframe thead th {
text-align: right;
}
</style>
<table border="1" class="dataframe">
<thead>
<tr style="text-align: right;">
<th></th>
<th>date</th>
<th>time</th>
<th>SYS(mmHg)</th>
<th>DIA(mmHg)</th>
<th>UNKNOW_1</th>
<th>UNKNOW_2</th>
<th>UNKNOW_3</th>
<th>CODE</th>
</tr>
<tr>
<th>timestamp</th>
<th></th>
<th></th>
<th></th>
<th></th>
<th></th>
<th></th>
<th></th>
<th></th>
</tr>
</thead>
<tbody>
<tr>
<th>2019-03-01 16:18:00</th>
<td>2019-03-01</td>
<td>16:18:00</td>
<td>107</td>
<td>76</td>
<td>78.0</td>
<td>78.0</td>
<td>NaN</td>
<td>NaN</td>
</tr>
<tr>
<th>2019-03-01 16:19:00</th>
<td>2019-03-01</td>
<td>16:19:00</td>
<td>96</td>
<td>62</td>
<td>63.0</td>
<td>63.0</td>
<td>NaN</td>
<td>NaN</td>
</tr>
<tr>
<th>2019-03-01 16:22:00</th>
<td>2019-03-01</td>
<td>16:22:00</td>
<td>100</td>
<td>68</td>
<td>64.0</td>
<td>64.0</td>
<td>NaN</td>
<td>NaN</td>
</tr>
<tr>
<th>2019-03-01 16:23:00</th>
<td>2019-03-01</td>
<td>16:23:00</td>
<td>103</td>
<td>68</td>
<td>68.0</td>
<td>68.0</td>
<td>NaN</td>
<td>NaN</td>
</tr>
<tr>
<th>2019-03-01 16:25:00</th>
<td>2019-03-01</td>
<td>16:25:00</td>
<td>101</td>
<td>67</td>
<td>65.0</td>
<td>65.0</td>
<td>NaN</td>
<td>NaN</td>
</tr>
</tbody>
</table>
</div></div>
</div>
</div>
<div class="section" id="id2">
<h3>Timeshift the data<a class="headerlink" href="#id2" title="Permalink to this headline">¶</a></h3>
<p>Apply a timeshift:</p>
<div class="nbinput docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[55]:
</pre></div>
</div>
<div class="input_area highlight-ipython3 notranslate"><div class="highlight"><pre>
<span></span><span class="n">spacelabs_reader</span><span class="o">.</span><span class="n">timeshift</span><span class="p">()</span>
<span class="n">spacelabs_reader</span><span class="o">.</span><span class="n">data</span><span class="o">.</span><span class="n">head</span><span class="p">()</span>
</pre></div>
</div>
</div>
<div class="nboutput nblast docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[55]:
</pre></div>
</div>
<div class="output_area rendered_html docutils container">
<div>
<style scoped>
.dataframe tbody tr th:only-of-type {
vertical-align: middle;
}
.dataframe tbody tr th {
vertical-align: top;
}
.dataframe thead th {
text-align: right;
}
</style>
<table border="1" class="dataframe">
<thead>
<tr style="text-align: right;">
<th></th>
<th>date</th>
<th>time</th>
<th>SYS(mmHg)</th>
<th>DIA(mmHg)</th>
<th>UNKNOW_1</th>
<th>UNKNOW_2</th>
<th>UNKNOW_3</th>
<th>CODE</th>
</tr>
<tr>
<th>timestamp</th>
<th></th>
<th></th>
<th></th>
<th></th>
<th></th>
<th></th>
<th></th>
<th></th>
</tr>
</thead>
<tbody>
<tr>
<th>2018-02-28 18:14:00</th>
<td>2018-02-28</td>
<td>18:14:00</td>
<td>107</td>
<td>76</td>
<td>78.0</td>
<td>78.0</td>
<td>NaN</td>
<td>NaN</td>
</tr>
<tr>
<th>2018-02-28 18:15:00</th>
<td>2018-02-28</td>
<td>18:15:00</td>
<td>96</td>
<td>62</td>
<td>63.0</td>
<td>63.0</td>
<td>NaN</td>
<td>NaN</td>
</tr>
<tr>
<th>2018-02-28 18:18:00</th>
<td>2018-02-28</td>
<td>18:18:00</td>
<td>100</td>
<td>68</td>
<td>64.0</td>
<td>64.0</td>
<td>NaN</td>
<td>NaN</td>