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23 changes: 8 additions & 15 deletions source/Makefile
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# Makefile for Sphinx documentation
# Minimal makefile for Sphinx documentation
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# You can set these variables from the command line, and also
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SPHINXOPTS ?=
SPHINXBUILD ?= sphinx-build
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SPHINXOPTS =
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SOURCEDIR = .
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AUTODOCDIR = api

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$(error "The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don't have Sphinx installed, grab it from http://sphinx-doc.org/")
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.PHONY: help clean Makefile

# Put it first so that "make" without argument is like "make help".
help:
@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

clean:
rm -rf $(BUILDDIR)/* $(AUTODOCDIR)
.PHONY: help Makefile

# Catch-all target: route all unknown targets to Sphinx using the new
# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS).
%: Makefile
@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs:
echo "Hello world"
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# Sphinx build info version 1
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config: 1770db6057773924fd89da8a129c176a
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<p class="caption" role="heading"><span class="caption-text">PECG API REFERENCE:</span></p>
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<div class="section" id="physiozoo-ecg-documentation">
<h1>PhysioZoo ECG documentation<a class="headerlink" href="#physiozoo-ecg-documentation" title="Permalink to this heading"></a></h1>
<p>Digital electrocardiography biomarkers to assess cardiac conduction.</p>
<p>Based on the paper
S. Gendelman et al., “PhysioZoo ECG: Digital electrocardiography biomarkers to assess cardiac conduction,” 2021 Computing in Cardiology (CinC), 2021, pp. 1-4, doi: 10.23919/CinC53138.2021.9662857.</p>
<div class="section" id="introduction">
<h2>Introduction<a class="headerlink" href="#introduction" title="Permalink to this heading"></a></h2>
<p>The electrocardiogram (ECG) is a standard tool used in medical practice for identifying cardiac pathologies. Because the necessary expertise to interpret this tracing is not readily available in all medical institutions or at all in some large areas of developing countries, there is a need to create a data-driven approach that can automatically capture the information contained in this physiological time series. The primary objective of this package is to identify and implement clinically important digital ECG biomarkers for the purpose of creating a reference toolbox and software for ECG morphological analysis.</p>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this heading"></a></h2>
<p>Few steps are required to extract the morphological ECG biomarkers, thos steps are impelemented in the PEBM toolbox:</p>
<ol class="arabic simple">
<li><p>ECG Signal Preprocessing - Before computing the ECG morphological biomarkers, prefiltering of the raw ECG time series is performed to remove the baseline wander as well as remove high frequency noise. Specifically, the toolbox include a zero phase second-order infinite impulse response bandpass filter with the passband of 0.67Hz - 100Hz to remove baseline wander and high frequency noise. Also, the toolbox include an optional Notch filter that can be set to 50 or 60Hz to remove the power-line interference.</p></li>
<li><p>ECG Fiducial Points Detection - The toolbox include the epltd R-peaks algorithem, and the the well-known wavedet algorithm for ECG fiducial points detection.</p></li>
<li><p>Engineering of ECG Biomarkers - Using the fiducial points ECG biomarkers are engineered for individual ECG cycles. When a biomarker cannot be engineered because some fiducial points could not be detected by wavedet then the feature was marked as a NaN. For an ECG channel a total of 14 features are extracted from intervals duration and 8 from waves characteristics to describe the ECG morphology.</p></li>
</ol>
<a class="reference internal image-reference" href="_images/ecg_wth_bio.png"><img alt="_images/ecg_wth_bio.png" src="_images/ecg_wth_bio.png" style="width: 600px;" /></a>
<ol class="arabic simple" start="4">
<li><p>Summary Statistics - For a specified time window the five summary statistics (median, min, max, Ql and Q3) are computed for all ECG biomarkers.</p></li>
</ol>
</div>
<div class="section" id="installation">
<h2>Installation<a class="headerlink" href="#installation" title="Permalink to this heading"></a></h2>
<p>Available on pip, with the command:
pip install pebm</p>
<p>pip project: pip install -i <a class="reference external" href="https://test.pypi.org/simple/">https://test.pypi.org/simple/</a> pecg</p>
</div>
<div class="section" id="requirements">
<h2>Requirements<a class="headerlink" href="#requirements" title="Permalink to this heading"></a></h2>
<p>Python &gt;= 3.6</p>
<p>numpy == 1.19.4</p>
<p>mne == 0.23.4</p>
<p>scipy == 1.5.2</p>
<p>wfdb == 3.4.0</p>
<p>All the requirements are installed when the toolbox is installed, no need for additional commands.</p>
</div>
<div class="section" id="system-requirements">
<h2>System Requirements<a class="headerlink" href="#system-requirements" title="Permalink to this heading"></a></h2>
<p>To run the wavdet fiucial-points detector matlab runtime (MCR) 2021a is requierd. <a class="reference external" href="https://www.mathworks.com/products/compiler/matlab-runtime.html">https://www.mathworks.com/products/compiler/matlab-runtime.html</a></p>
<p>To run the epltd peak detector additional wfdb toolbox is requierd. <a class="reference external" href="https://archive.physionet.org/physiotools/wfdb-linux-quick-start.shtml">https://archive.physionet.org/physiotools/wfdb-linux-quick-start.shtml</a></p>
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<div class="section" id="documentation">
<h2>Documentation<a class="headerlink" href="#documentation" title="Permalink to this heading"></a></h2>
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