From 1ddbf64de37316205372bdaa12acaca7c4928997 Mon Sep 17 00:00:00 2001 From: lrdossan Date: Wed, 12 Jun 2024 14:51:17 +0200 Subject: [PATCH 1/7] fixed bug in plot for conditional probability of infection --- caimira/apps/calculator/report_generator.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/caimira/apps/calculator/report_generator.py b/caimira/apps/calculator/report_generator.py index 587c3b64..00ea8a68 100644 --- a/caimira/apps/calculator/report_generator.py +++ b/caimira/apps/calculator/report_generator.py @@ -293,8 +293,8 @@ def uncertainties_plot(infection_probability: models._VectorisedFloat, axs[0, 1].set_visible(False) - axs[0, 0].plot(viral_loads, np.array(pi_means)/100, label='Predictive total probability') - axs[0, 0].fill_between(viral_loads, np.array(lower_percentiles)/100, np.array(upper_percentiles)/100, alpha=0.1, label='5ᵗʰ and 95ᵗʰ percentile') + axs[0, 0].plot(viral_loads, np.array(pi_means), label='Predictive total probability') + axs[0, 0].fill_between(viral_loads, np.array(lower_percentiles), np.array(upper_percentiles), alpha=0.1, label='5ᵗʰ and 95ᵗʰ percentile') axs[0, 2].hist(infection_probability, bins=30, orientation='horizontal') axs[0, 2].set_xticks([]) @@ -304,8 +304,8 @@ def uncertainties_plot(infection_probability: models._VectorisedFloat, highest_bar = axs[0, 2].get_xlim()[1] axs[0, 2].set_xlim(0, highest_bar) - axs[0, 2].text(highest_bar * 0.5, 0.5, - rf"$\bf{np.round(np.mean(infection_probability), 1)}$%", ha='center', va='center') + axs[0, 2].text(highest_bar * 0.5, 50, + "$P(I)=$\n" + rf"$\bf{np.round(np.mean(infection_probability), 1)}$%", ha='center', va='center') axs[1, 0].hist(np.log10(viral_load_in_sputum), bins=150, range=(2, 10), color='grey') axs[1, 0].set_facecolor("lightgrey") From eb0f5cc8815b0524990f86b6470b73207b708738 Mon Sep 17 00:00:00 2001 From: lrdossan Date: Wed, 12 Jun 2024 15:51:05 +0200 Subject: [PATCH 2/7] modified methods to get conditional probability data --- caimira/apps/calculator/report_generator.py | 70 +++++++++---------- caimira/tests/test_conditional_probability.py | 2 +- 2 files changed, 34 insertions(+), 38 deletions(-) diff --git a/caimira/apps/calculator/report_generator.py b/caimira/apps/calculator/report_generator.py index 00ea8a68..59c1a539 100644 --- a/caimira/apps/calculator/report_generator.py +++ b/caimira/apps/calculator/report_generator.py @@ -171,26 +171,15 @@ def calculate_report_data(form: VirusFormData, model: models.ExposureModel, exec expected_new_cases = np.array(model.expected_new_cases()).mean() exposed_presence_intervals = [list(interval) for interval in model.exposed.presence_interval().boundaries()] - if (model.data_registry.virological_data['virus_distributions'][form.virus_type]['viral_load_in_sputum'] == ViralLoads.COVID_OVERALL.value # type: ignore - and form.conditional_probability_plot): # Only generate this data if covid_overall_vl_data is selected. - - viral_load_in_sputum: models._VectorisedFloat = model.concentration_model.infected.virus.viral_load_in_sputum - viral_loads, pi_means, lower_percentiles, upper_percentiles = manufacture_conditional_probability_data(model, prob) - - uncertainties_plot_src = img2base64(_figure2bytes(uncertainties_plot(prob, viral_load_in_sputum, viral_loads, - pi_means, lower_percentiles, upper_percentiles))) - conditional_probability_data = {key: value for key, value in - zip(('viral_loads', 'pi_means', 'lower_percentiles', 'upper_percentiles'), - (viral_loads, pi_means, lower_percentiles, upper_percentiles))} - vl_dist = list(np.log10(viral_load_in_sputum)) - - else: - uncertainties_plot_src = None - conditional_probability_data = None - vl = model.concentration_model.virus.viral_load_in_sputum - if isinstance(vl, np.ndarray): vl_dist = list(np.log10(model.concentration_model.virus.viral_load_in_sputum)) - else: vl_dist = np.log10(model.concentration_model.virus.viral_load_in_sputum) - + conditional_probability_data = None + uncertainties_plot_src = None + if (form.conditional_probability_viral_loads and + model.data_registry.virological_data['virus_distributions'][form.virus_type]['viral_load_in_sputum'] == ViralLoads.COVID_OVERALL.value): # type: ignore + # Generate all the required data for the conditional probability plot + conditional_prob_data = manufacture_conditional_probability_data(model, prob) + # Generate the matplotlib image based on the received data + uncertainties_plot_src = img2base64(_figure2bytes(uncertainties_plot(prob, conditional_prob_data))) + return { "model_repr": repr(model), "times": list(times), @@ -208,10 +197,9 @@ def calculate_report_data(form: VirusFormData, model: models.ExposureModel, exec "prob_hist_bins": list(prob_dist_bins), "prob_probabilistic_exposure": prob_probabilistic_exposure, "expected_new_cases": expected_new_cases, - "uncertainties_plot_src": uncertainties_plot_src, "CO2_concentrations": CO2_concentrations, - "vl_dist": vl_dist, "conditional_probability_data": conditional_probability_data, + "uncertainties_plot_src": uncertainties_plot_src, } @@ -235,7 +223,6 @@ def generate_permalink(base_url, get_root_url, get_root_calculator_url, form: V def conditional_prob_inf_given_vl_dist( - data_registry: DataRegistry, infection_probability: models._VectorisedFloat, viral_loads: np.ndarray, specific_vl: float, @@ -247,39 +234,48 @@ def conditional_prob_inf_given_vl_dist( upper_percentiles = [] for vl_log in viral_loads: + # Viral load corresponding to a certain viral load value in the distribution specific_prob = infection_probability[np.where((vl_log-step/2-specific_vl)*(vl_log+step/2-specific_vl)<0)[0]] #type: ignore + pi_means.append(specific_prob.mean()) lower_percentiles.append(np.quantile(specific_prob, 0.05)) upper_percentiles.append(np.quantile(specific_prob, 0.95)) - return pi_means, lower_percentiles, upper_percentiles + return np.array(pi_means), np.array(lower_percentiles), np.array(upper_percentiles) def manufacture_conditional_probability_data( exposure_model: models.ExposureModel, - infection_probability: models._VectorisedFloat + infection_probability: models._VectorisedFloat, ): - data_registry: DataRegistry = exposure_model.data_registry - min_vl = 2 max_vl = 10 step = (max_vl - min_vl)/100 viral_loads = np.arange(min_vl, max_vl, step) specific_vl = np.log10(exposure_model.concentration_model.virus.viral_load_in_sputum) - pi_means, lower_percentiles, upper_percentiles = conditional_prob_inf_given_vl_dist(data_registry, infection_probability, viral_loads, + pi_means, lower_percentiles, upper_percentiles = conditional_prob_inf_given_vl_dist(infection_probability, viral_loads, specific_vl, step) - - return list(viral_loads), list(pi_means), list(lower_percentiles), list(upper_percentiles) + log10_vl_in_sputum : models._VectorisedFloat = np.log10(exposure_model.concentration_model.infected.virus.viral_load_in_sputum) + + return { + 'viral_loads': viral_loads, + 'pi_means': pi_means, + 'lower_percentiles': lower_percentiles, + 'upper_percentiles': upper_percentiles, + 'log10_vl_in_sputum': log10_vl_in_sputum, + } def uncertainties_plot(infection_probability: models._VectorisedFloat, - viral_load_in_sputum: models._VectorisedFloat, - viral_loads: models._VectorisedFloat, - pi_means: models._VectorisedFloat, - lower_percentiles: models._VectorisedFloat, - upper_percentiles: models._VectorisedFloat): + conditional_prob_data: dict): - fig, axes = plt.subplots(2, 3, + viral_loads: models._VectorisedFloat = conditional_prob_data['viral_loads'] + pi_means: models._VectorisedFloat = conditional_prob_data['pi_means'] + lower_percentiles: models._VectorisedFloat = conditional_prob_data['lower_percentiles'] + upper_percentiles: models._VectorisedFloat = conditional_prob_data['upper_percentiles'] + log10_vl_in_sputum: models._VectorisedFloat = conditional_prob_data['log10_vl_in_sputum'] + + fig, axes = plt.subplots(2, 3, gridspec_kw={'width_ratios': [5, 0.5] + [1], 'height_ratios': [3, 1], 'wspace': 0}, sharey='row', @@ -306,7 +302,7 @@ def uncertainties_plot(infection_probability: models._VectorisedFloat, axs[0, 2].text(highest_bar * 0.5, 50, "$P(I)=$\n" + rf"$\bf{np.round(np.mean(infection_probability), 1)}$%", ha='center', va='center') - axs[1, 0].hist(np.log10(viral_load_in_sputum), + axs[1, 0].hist(log10_vl_in_sputum, bins=150, range=(2, 10), color='grey') axs[1, 0].set_facecolor("lightgrey") axs[1, 0].set_yticks([]) diff --git a/caimira/tests/test_conditional_probability.py b/caimira/tests/test_conditional_probability.py index 0e616ae7..9cb1a88d 100644 --- a/caimira/tests/test_conditional_probability.py +++ b/caimira/tests/test_conditional_probability.py @@ -72,7 +72,7 @@ def test_conditional_prob_inf_given_vl_dist(data_registry, baseline_exposure_mod specific_vl = np.log10(mc_model.concentration_model.infected.virus.viral_load_in_sputum) step = 8/100 actual_pi_means, actual_lower_percentiles, actual_upper_percentiles = ( - report_generator.conditional_prob_inf_given_vl_dist(data_registry, infection_probability, viral_loads, specific_vl, step) + report_generator.conditional_prob_inf_given_vl_dist(infection_probability, viral_loads, specific_vl, step) ) assert np.allclose(actual_pi_means, expected_pi_means, atol=0.002) From a11a559710cc7961e662038d193bd3991709762d Mon Sep 17 00:00:00 2001 From: lrdossan Date: Wed, 12 Jun 2024 15:51:21 +0200 Subject: [PATCH 3/7] handled display of data --- caimira/apps/calculator/__init__.py | 2 +- caimira/apps/calculator/defaults.py | 1 - caimira/apps/calculator/model_generator.py | 2 -- caimira/apps/calculator/report_generator.py | 4 ++-- caimira/apps/calculator/static/js/report.js | 10 +++++----- caimira/apps/templates/base/calculator.form.html.j2 | 2 +- caimira/apps/templates/base/calculator.report.html.j2 | 8 ++++---- 7 files changed, 13 insertions(+), 16 deletions(-) diff --git a/caimira/apps/calculator/__init__.py b/caimira/apps/calculator/__init__.py index 98f75762..98df93a5 100644 --- a/caimira/apps/calculator/__init__.py +++ b/caimira/apps/calculator/__init__.py @@ -193,7 +193,7 @@ class ConcentrationModel(BaseRequestHandler): ) # Re-generate the report with the conditional probability of infection plot if self.get_cookie('conditional_plot'): - form.conditional_probability_plot = True if self.get_cookie('conditional_plot') == '1' else False + form.conditional_probability_viral_loads = True if self.get_cookie('conditional_plot') == '1' else False self.clear_cookie('conditional_plot') # Clears cookie after changing the form value. report_task = executor.submit( diff --git a/caimira/apps/calculator/defaults.py b/caimira/apps/calculator/defaults.py index e12664eb..30cb928f 100644 --- a/caimira/apps/calculator/defaults.py +++ b/caimira/apps/calculator/defaults.py @@ -15,7 +15,6 @@ DEFAULTS = { 'precise_activity': '{}', 'calculator_version': NO_DEFAULT, 'ceiling_height': 0., - 'conditional_probability_plot': False, 'conditional_probability_viral_loads': False, 'CO2_fitting_result': '{}', 'exposed_coffee_break_option': 'coffee_break_0', diff --git a/caimira/apps/calculator/model_generator.py b/caimira/apps/calculator/model_generator.py index aa35ba1e..d1895848 100644 --- a/caimira/apps/calculator/model_generator.py +++ b/caimira/apps/calculator/model_generator.py @@ -31,7 +31,6 @@ class VirusFormData(FormData): arve_sensors_option: bool precise_activity: dict ceiling_height: float - conditional_probability_plot: bool conditional_probability_viral_loads: bool CO2_fitting_result: dict floor_area: float @@ -497,7 +496,6 @@ def baseline_raw_form_data() -> typing.Dict[str, typing.Union[str, float]]: 'air_changes': '', 'air_supply': '', 'ceiling_height': '', - 'conditional_probability_plot': '0', 'conditional_probability_viral_loads': '0', 'exposed_coffee_break_option': 'coffee_break_4', 'exposed_coffee_duration': '10', diff --git a/caimira/apps/calculator/report_generator.py b/caimira/apps/calculator/report_generator.py index 59c1a539..75a5c85c 100644 --- a/caimira/apps/calculator/report_generator.py +++ b/caimira/apps/calculator/report_generator.py @@ -234,7 +234,7 @@ def conditional_prob_inf_given_vl_dist( upper_percentiles = [] for vl_log in viral_loads: - # Viral load corresponding to a certain viral load value in the distribution + # Probability of infection corresponding to a certain viral load value in the distribution specific_prob = infection_probability[np.where((vl_log-step/2-specific_vl)*(vl_log+step/2-specific_vl)<0)[0]] #type: ignore pi_means.append(specific_prob.mean()) @@ -246,7 +246,7 @@ def conditional_prob_inf_given_vl_dist( def manufacture_conditional_probability_data( exposure_model: models.ExposureModel, - infection_probability: models._VectorisedFloat, + infection_probability: models._VectorisedFloat ): min_vl = 2 max_vl = 10 diff --git a/caimira/apps/calculator/static/js/report.js b/caimira/apps/calculator/static/js/report.js index b1c8b3fe..7c804dd9 100644 --- a/caimira/apps/calculator/static/js/report.js +++ b/caimira/apps/calculator/static/js/report.js @@ -1,6 +1,6 @@ -function on_report_load(conditional_probability_plot) { +function on_report_load(conditional_probability_viral_loads) { // Check/uncheck uncertainties image generation - document.getElementById('conditional_probability_plot').checked = conditional_probability_plot + document.getElementById('conditional_probability_viral_loads').checked = conditional_probability_viral_loads } /* Generate the concentration plot using d3 library. */ @@ -1164,14 +1164,14 @@ function display_rename_column(bool, id) { else document.getElementById(id).style.display = 'none'; } -function conditional_probability_plot(value, is_generated) { +function conditional_probability_viral_loads(value, is_generated) { // If the image was previously generated, there is no need to reload the page. if (value && is_generated == 1) { document.getElementById('conditional_probability_div').style.display = 'block' } else if (value && is_generated == 0) { - document.getElementById('label_conditional_probability_plot').innerHTML = `Loading...`; - document.getElementById('conditional_probability_plot').setAttribute('disabled', true); + document.getElementById('label_conditional_probability_viral_loads').innerHTML = `Loading...`; + document.getElementById('conditional_probability_viral_loads').setAttribute('disabled', true); document.cookie = `conditional_plot= 1; path=/`; window.location.reload(); } diff --git a/caimira/apps/templates/base/calculator.form.html.j2 b/caimira/apps/templates/base/calculator.form.html.j2 index 745612e6..aa6271bf 100644 --- a/caimira/apps/templates/base/calculator.form.html.j2 +++ b/caimira/apps/templates/base/calculator.form.html.j2 @@ -495,7 +495,7 @@
- +
diff --git a/caimira/apps/templates/base/calculator.report.html.j2 b/caimira/apps/templates/base/calculator.report.html.j2 index 041cf3ef..0709fb34 100644 --- a/caimira/apps/templates/base/calculator.report.html.j2 +++ b/caimira/apps/templates/base/calculator.report.html.j2 @@ -15,7 +15,7 @@ - +