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Additional Exercises – Programming with Python
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<h1 class="maintitle">Analyzing Data from Multiple Files - Exercises</h1>
<blockquote class="challenge">
<h2 id="plotting-differences">Plotting Differences</h2>
<p>Plot the difference between the average inflammations reported in the first and second datasets
(stored in <code class="language-plaintext highlighter-rouge">inflammation-01.csv</code> and <code class="language-plaintext highlighter-rouge">inflammation-02.csv</code>, correspondingly),
i.e., the difference between the leftmost plots of the first two figures.</p>
<blockquote class="solution">
<h2 id="solution">Solution</h2>
<div class="language-python highlighter-rouge"><div class="highlight"><pre class="highlight"><code><span class="kn">import</span> <span class="nn">glob</span>
<span class="kn">import</span> <span class="nn">numpy</span>
<span class="kn">import</span> <span class="nn">matplotlib.pyplot</span>
<span class="n">filenames</span> <span class="o">=</span> <span class="nb">sorted</span><span class="p">(</span><span class="n">glob</span><span class="p">.</span><span class="n">glob</span><span class="p">(</span><span class="s">'inflammation*.csv'</span><span class="p">))</span>
<span class="n">data0</span> <span class="o">=</span> <span class="n">numpy</span><span class="p">.</span><span class="n">loadtxt</span><span class="p">(</span><span class="n">fname</span><span class="o">=</span><span class="n">filenames</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">delimiter</span><span class="o">=</span><span class="s">','</span><span class="p">)</span>
<span class="n">data1</span> <span class="o">=</span> <span class="n">numpy</span><span class="p">.</span><span class="n">loadtxt</span><span class="p">(</span><span class="n">fname</span><span class="o">=</span><span class="n">filenames</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="n">delimiter</span><span class="o">=</span><span class="s">','</span><span class="p">)</span>
<span class="n">fig</span> <span class="o">=</span> <span class="n">matplotlib</span><span class="p">.</span><span class="n">pyplot</span><span class="p">.</span><span class="n">figure</span><span class="p">(</span><span class="n">figsize</span><span class="o">=</span><span class="p">(</span><span class="mf">10.0</span><span class="p">,</span> <span class="mf">3.0</span><span class="p">))</span>
<span class="n">matplotlib</span><span class="p">.</span><span class="n">pyplot</span><span class="p">.</span><span class="n">ylabel</span><span class="p">(</span><span class="s">'Difference in average'</span><span class="p">)</span>
<span class="n">matplotlib</span><span class="p">.</span><span class="n">pyplot</span><span class="p">.</span><span class="n">plot</span><span class="p">(</span><span class="n">numpy</span><span class="p">.</span><span class="n">mean</span><span class="p">(</span><span class="n">data0</span><span class="p">,</span> <span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span> <span class="o">-</span> <span class="n">numpy</span><span class="p">.</span><span class="n">mean</span><span class="p">(</span><span class="n">data1</span><span class="p">,</span> <span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">))</span>
<span class="n">fig</span><span class="p">.</span><span class="n">tight_layout</span><span class="p">()</span>
<span class="n">matplotlib</span><span class="p">.</span><span class="n">pyplot</span><span class="p">.</span><span class="n">show</span><span class="p">()</span>
</code></pre></div> </div>
</blockquote>
</blockquote>
<blockquote class="challenge">
<h2 id="generate-composite-statistics">Generate Composite Statistics</h2>
<p>Use each of the files once to generate a dataset containing values averaged over all patients:</p>
<div class="language-python highlighter-rouge"><div class="highlight"><pre class="highlight"><code><span class="n">filenames</span> <span class="o">=</span> <span class="n">glob</span><span class="p">.</span><span class="n">glob</span><span class="p">(</span><span class="s">'inflammation*.csv'</span><span class="p">)</span>
<span class="n">composite_data</span> <span class="o">=</span> <span class="n">numpy</span><span class="p">.</span><span class="n">zeros</span><span class="p">((</span><span class="mi">60</span><span class="p">,</span><span class="mi">40</span><span class="p">))</span>
<span class="k">for</span> <span class="n">filename</span> <span class="ow">in</span> <span class="n">filenames</span><span class="p">:</span>
<span class="c1"># sum each new file's data into composite_data as it's read
</span> <span class="c1">#
# and then divide the composite_data by number of samples
</span><span class="n">composite_data</span> <span class="o">=</span> <span class="n">composite_data</span> <span class="o">/</span> <span class="nb">len</span><span class="p">(</span><span class="n">filenames</span><span class="p">)</span>
</code></pre></div> </div>
<p>Then use pyplot to generate average, max, and min for all patients.</p>
<blockquote class="solution">
<h2 id="solution-1">Solution</h2>
<div class="language-python highlighter-rouge"><div class="highlight"><pre class="highlight"><code><span class="kn">import</span> <span class="nn">glob</span>
<span class="kn">import</span> <span class="nn">numpy</span>
<span class="kn">import</span> <span class="nn">matplotlib.pyplot</span>
<span class="n">filenames</span> <span class="o">=</span> <span class="n">glob</span><span class="p">.</span><span class="n">glob</span><span class="p">(</span><span class="s">'inflammation*.csv'</span><span class="p">)</span>
<span class="n">composite_data</span> <span class="o">=</span> <span class="n">numpy</span><span class="p">.</span><span class="n">zeros</span><span class="p">((</span><span class="mi">60</span><span class="p">,</span><span class="mi">40</span><span class="p">))</span>
<span class="k">for</span> <span class="n">filename</span> <span class="ow">in</span> <span class="n">filenames</span><span class="p">:</span>
<span class="n">data</span> <span class="o">=</span> <span class="n">numpy</span><span class="p">.</span><span class="n">loadtxt</span><span class="p">(</span><span class="n">fname</span> <span class="o">=</span> <span class="n">filename</span><span class="p">,</span> <span class="n">delimiter</span><span class="o">=</span><span class="s">','</span><span class="p">)</span>
<span class="n">composite_data</span> <span class="o">=</span> <span class="n">composite_data</span> <span class="o">+</span> <span class="n">data</span>
<span class="n">composite_data</span> <span class="o">=</span> <span class="n">composite_data</span> <span class="o">/</span> <span class="nb">len</span><span class="p">(</span><span class="n">filenames</span><span class="p">)</span>
<span class="n">fig</span> <span class="o">=</span> <span class="n">matplotlib</span><span class="p">.</span><span class="n">pyplot</span><span class="p">.</span><span class="n">figure</span><span class="p">(</span><span class="n">figsize</span><span class="o">=</span><span class="p">(</span><span class="mf">10.0</span><span class="p">,</span> <span class="mf">3.0</span><span class="p">))</span>
<span class="n">axes1</span> <span class="o">=</span> <span class="n">fig</span><span class="p">.</span><span class="n">add_subplot</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="mi">3</span><span class="p">,</span> <span class="mi">1</span><span class="p">)</span>
<span class="n">axes2</span> <span class="o">=</span> <span class="n">fig</span><span class="p">.</span><span class="n">add_subplot</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="mi">3</span><span class="p">,</span> <span class="mi">2</span><span class="p">)</span>
<span class="n">axes3</span> <span class="o">=</span> <span class="n">fig</span><span class="p">.</span><span class="n">add_subplot</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="mi">3</span><span class="p">,</span> <span class="mi">3</span><span class="p">)</span>
<span class="n">axes1</span><span class="p">.</span><span class="n">set_ylabel</span><span class="p">(</span><span class="s">'average'</span><span class="p">)</span>
<span class="n">axes1</span><span class="p">.</span><span class="n">plot</span><span class="p">(</span><span class="n">numpy</span><span class="p">.</span><span class="n">mean</span><span class="p">(</span><span class="n">composite_data</span><span class="p">,</span> <span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">))</span>
<span class="n">axes2</span><span class="p">.</span><span class="n">set_ylabel</span><span class="p">(</span><span class="s">'max'</span><span class="p">)</span>
<span class="n">axes2</span><span class="p">.</span><span class="n">plot</span><span class="p">(</span><span class="n">numpy</span><span class="p">.</span><span class="nb">max</span><span class="p">(</span><span class="n">composite_data</span><span class="p">,</span> <span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">))</span>
<span class="n">axes3</span><span class="p">.</span><span class="n">set_ylabel</span><span class="p">(</span><span class="s">'min'</span><span class="p">)</span>
<span class="n">axes3</span><span class="p">.</span><span class="n">plot</span><span class="p">(</span><span class="n">numpy</span><span class="p">.</span><span class="nb">min</span><span class="p">(</span><span class="n">composite_data</span><span class="p">,</span> <span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">))</span>
<span class="n">fig</span><span class="p">.</span><span class="n">tight_layout</span><span class="p">()</span>
<span class="n">matplotlib</span><span class="p">.</span><span class="n">pyplot</span><span class="p">.</span><span class="n">show</span><span class="p">()</span>
</code></pre></div> </div>
</blockquote>
</blockquote>
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