formatting issues and introduction of pelt algorithm to display suggested transition times
This commit is contained in:
Luis Aleixo
parent
1c8775c807
commit
b0d94f2318
3 changed files with 81 additions and 13 deletions
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@ -20,6 +20,7 @@ import uuid
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import zlib
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import matplotlib.pyplot as plt
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import numpy as np
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import ruptures as rpt
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import jinja2
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import loky
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@ -352,14 +353,46 @@ class CO2Data(BaseRequestHandler):
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"""
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pass
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def generate_ventilation_plot(self, CO2Data, transition_times = None, ventilation_values = None):
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def find_change_points_with_pelt(self, CO2_data: dict):
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"""
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Perform change point detection using Pelt algorithm from ruptures library with pen=15.
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Returns a list of tuples containing (index, X-axis value) for the detected significant changes.
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"""
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times = CO2_data['times']
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CO2_values = CO2_data['CO2']
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if len(times) != len(CO2_values):
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raise ValueError("times and CO2 values must have the same length.")
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# Convert the input lists to numpy arrays for use with the ruptures library
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times_np = np.array(times)
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CO2_np = np.array(CO2_values)
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# Define the model for change point detection (Radial Basis Function kernel)
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model = "rbf"
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# Fit the Pelt algorithm to the data with the specified model
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algo = rpt.Pelt(model=model).fit(CO2_np)
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# Predict change points using the Pelt algorithm with a penalty value of 15
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result = algo.predict(pen=15)
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return [times_np[idx] for idx in result[:-1]]
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def generate_ventilation_plot(self, CO2_data: dict, transition_times: typing.Optional[list] = None, ventilation_values: typing.Optional[list] = None):
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times = CO2_data['times']
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CO2_data = CO2_data['CO2']
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fig = plt.figure(figsize=(7, 4), dpi=110)
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plt.plot(CO2Data['times'], CO2Data['CO2'])
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if (transition_times and ventilation_values):
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for index, time in enumerate(transition_times[:-1]):
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plt.plot(times, CO2_data)
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if (transition_times):
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for index, time in enumerate(transition_times):
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plt.axvline(x = time, color = 'grey', linewidth=0.5, linestyle='--')
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y_location = (CO2Data['CO2'][min(range(len(CO2Data['times'])), key=lambda i: abs(CO2Data['times'][i]-time))])
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plt.text(x = time + 0.04, y = y_location, s=round(ventilation_values[index], 2))
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if ventilation_values:
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y_location = (CO2_data[min(range(len(times)), key=lambda i: abs(times[i]-time))])
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plt.text(x = time + 0.04, y = y_location, s="{:.2g}".format(ventilation_values[index]))
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plt.xlabel('Time of day')
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plt.ylabel('Concentration (ppm)')
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return img2base64(_figure2bytes(fig))
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@ -377,8 +410,8 @@ class CO2Data(BaseRequestHandler):
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self.finish(json.dumps(response_json))
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return
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if endpoint == 'plot':
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self.finish({'CO2_plot': self.generate_ventilation_plot(form.CO2_data)})
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if endpoint.rstrip('/') == 'plot':
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self.finish({'CO2_plot': self.generate_ventilation_plot(form.CO2_data, self.find_change_points_with_pelt(form.CO2_data))})
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else:
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executor = loky.get_reusable_executor(
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max_workers=self.settings['handler_worker_pool_size'],
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@ -392,7 +425,7 @@ class CO2Data(BaseRequestHandler):
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result = dict(report.CO2_fit_params())
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result['fitting_ventilation_type'] = form.fitting_ventilation_type
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result['transition_times'] = report.ventilation_transition_times
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result['CO2_plot'] = self.generate_ventilation_plot(form.CO2_data, report.ventilation_transition_times, result['ventilation_values'])
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result['CO2_plot'] = self.generate_ventilation_plot(form.CO2_data, report.ventilation_transition_times[:-1], result['ventilation_values'])
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self.finish(result)
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@ -194,7 +194,37 @@ function validateCO2Form() {
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// validate input format
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try {
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const parsedValue = JSON.parse(element.value);
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if (!Array.isArray(parsedValue)) {
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if (Array.isArray(parsedValue)) {
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if (parsedValue.length <= 1) {
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insertErrorFor(
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$("#DIVCO2_fitting_result"),
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`'${element.name}' must have more than one element.<br />`
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);
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submit = false;
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}
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else {
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const infected_finish = $(`[name=infected_finish]`)[0].value;
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const exposed_finish = $(`[name=exposed_finish]`)[0].value;
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const [hours_infected, minutes_infected] = infected_finish.split(":").map(Number);
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const elapsed_time_infected = hours_infected * 60 + minutes_infected;
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const [hours_exposed, minutes_exposed] = exposed_finish.split(":").map(Number);
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const elapsed_time_exposed = hours_exposed * 60 + minutes_exposed;
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const max_presence_time = Math.max(elapsed_time_infected, elapsed_time_exposed);
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const max_transition_time = parsedValue[parsedValue.length - 1] * 60;
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if (max_transition_time < max_presence_time) {
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insertErrorFor(
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$("#DIVCO2_fitting_result"),
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`The last transition time (${parsedValue[parsedValue.length - 1]}) should be after the last presence time (${max_presence_time / 60}).<br />`
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);
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submit = false;
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}
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}
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}
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else {
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insertErrorFor(
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$("#DIVCO2_fitting_result"),
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`'${element.name}' must be a list.</br>`
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@ -325,11 +355,15 @@ function submitFittingAlgorithm(url) {
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.then((response) => response.json())
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.then((json_response) => {
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displayFittingData(json_response);
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// Hide the suggestion transition lines warning
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$("#suggestion_lines_txt").hide();
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});
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}
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}
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function clearFittingResultComponent() {
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// Add the warning suggestion line
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$("#suggestion_lines_txt").show();
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// Remove all the previously generated fitting elements
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$("#generate_fitting_data").prop("disabled", true);
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$("#CO2_fitting_result").val("");
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@ -200,13 +200,13 @@
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<div>
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<input type="radio" id="no_ventilation" name="ventilation_type" value="no_ventilation" checked>
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<label for="no_ventilation">No ventilation</label>
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<input class="ml-2" type="radio" id="mechanical_ventilation" name="ventilation_type" value="mechanical_ventilation" data-enables="#DIVmechanical_ventilation">
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<input class="ml-3" type="radio" id="mechanical_ventilation" name="ventilation_type" value="mechanical_ventilation" data-enables="#DIVmechanical_ventilation">
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<label for="mechanical_ventilation">Mechanical</label>
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</div>
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<div>
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<div class="ml-0">
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<input type="radio" id="natural_ventilation" name="ventilation_type" value="natural_ventilation" data-enables="#DIVnatural_ventilation" data-toggle="modal" data-target="#warning_modal">
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<label for="natural_ventilation">Natural</label>
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<input class="ml-2" type="radio" id="from_fitting" name="ventilation_type" value="from_fitting" data-enables="#DIVfrom_fitting">
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<input class="ml-3" type="radio" id="from_fitting" name="ventilation_type" value="from_fitting" data-enables="#DIVfrom_fitting">
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<label for="from_fitting">Fitting</label>
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</div>
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</div>
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@ -339,6 +339,7 @@
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<div id="DIVCO2_fitting_to_submit" style="display: none">
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<img id="CO2_data_plot"/><br>
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<p id="suggestion_lines_txt" class="text-danger mb-3 text-center">The dashed lines are suggestions for the ventilation transition times (Pelt algorithm).</p>
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<strong>Ventilation scheme:</strong>
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<div>
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<input class="ml-2" type="radio" id="fitting_natural_ventilation" name="fitting_ventilation_type" value='fitting_natural_ventilation' checked="checked" data-enables="#DIVfitting_natural_ventilation" form="not-submitted" >
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