Handled Virus custom choice and cleaned the code
This commit is contained in:
Luis Aleixo
parent
b64a221c75
commit
8ad3b41796
1 changed files with 55 additions and 97 deletions
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@ -6,11 +6,13 @@ import ipympl.backend_nbagg
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import ipywidgets as widgets
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import matplotlib
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import matplotlib.figure
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import numpy as np
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from matplotlib import pyplot as plt
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from cara import data, models, state
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import matplotlib.lines as mlines
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import matplotlib.patches as patches
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from matplotlib import pyplot as plt
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import numpy as np
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from cara import data, models, state
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def collapsible(widgets_to_collapse: typing.List, title: str, start_collapsed=False):
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collapsed = widgets.Accordion([widgets.VBox(widgets_to_collapse)])
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@ -110,8 +112,7 @@ class ExposureModelResult(View):
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self.figure = matplotlib.figure.Figure(figsize=(9, 6))
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ipympl_canvas(self.figure)
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self.html_output = widgets.HTML()
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self.ax = self.figure.add_subplot(1, 1, 1)
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self.ax2 = self.ax.twinx()
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self.ax, self.ax2 = self.initialize_axes()
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self.concentration_line = None
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self.concentration_area = None
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self.cumulative_line = None
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@ -128,9 +129,16 @@ class ExposureModelResult(View):
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ax.spines['right'].set_visible(False)
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ax.spines['top'].set_visible(False)
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ax.set_xlabel('Time (hours)')
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ax.set_ylabel('Concentration ($virions/m^{3}$)')
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ax.set_title('Concentration of virions')
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return ax
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ax.set_ylabel('Mean concentration ($virions/m^{3}$)')
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ax.set_title('Concentration of virions \nand Cumulative dose')
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ax2 = ax.twinx()
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ax2.spines['left'].set_visible(False)
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ax2.spines['top'].set_visible(False)
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ax2.set_ylabel('Mean cumulative dose (infectious virus)')
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ax2.spines['right'].set_linestyle((0,(1,4)))
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return ax, ax2
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def update(self, model: models.ExposureModel):
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self.update_plot(model)
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@ -148,57 +156,37 @@ class ExposureModelResult(View):
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])
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if self.concentration_line is None:
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[self.concentration_line] = self.ax.plot(ts, concentration, color='#3530fe', label='Concentration')
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ax = self.ax
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#ax.text(0.5, 0.9, 'Without masks & window open', transform=ax.transAxes, ha='center')
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ax.spines['right'].set_visible(False)
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ax.spines['top'].set_visible(False)
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ax.set_xlabel('Time (hours)')
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ax.set_ylabel('Mean concentration ($virions/m^{3}$)')
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ax.set_title('Concentration of virions \nand Cumulative dose')
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#cursor = SnaptoCursor(self.ax, ts, concentration)
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[self.concentration_line] = self.ax.plot(ts, concentration, color='#3530fe')
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else:
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self.ax.ignore_existing_data_limits = False
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self.concentration_line.set_data(ts, concentration)
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if self.concentration_area is None:
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self.concentration_area = self.ax.fill_between(x = ts, y1=0, y2=concentration, color="#96cbff", label="Exposed person presence",
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self.concentration_area = self.ax.fill_between(x = ts, y1=0, y2=concentration, color="#96cbff",
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where = ((model.exposed.presence.boundaries()[0][0] < ts) & (ts < model.exposed.presence.boundaries()[0][1]) |
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(model.exposed.presence.boundaries()[1][0] < ts) & (ts < model.exposed.presence.boundaries()[1][1])))
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else:
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self.concentration_area.remove()
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self.concentration_area = self.ax.fill_between(x = ts, y1=0, y2=concentration, color="#96cbff", label="Exposed person presence",
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self.concentration_area = self.ax.fill_between(x = ts, y1=0, y2=concentration, color="#96cbff",
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where = ((model.exposed.presence.boundaries()[0][0] < ts) & (ts < model.exposed.presence.boundaries()[0][1]) |
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(model.exposed.presence.boundaries()[1][0] < ts) & (ts < model.exposed.presence.boundaries()[1][1])))
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if self.cumulative_line is None:
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[self.cumulative_line] = self.ax2.plot(ts[:-1], cumulative_doses, color='#0000c8', label='Cumulative dose', linestyle='dotted')
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ax2 = self.ax2
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ax2.spines['left'].set_visible(False)
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ax2.spines['top'].set_visible(False)
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ax2.set_ylabel('Mean cumulative dose (infectious virus)')
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ax2.spines['right'].set_linestyle((0,(1,4)))
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[self.cumulative_line] = self.ax2.plot(ts[:-1], cumulative_doses, color='#0000c8', linestyle='dotted')
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else:
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self.ax2.ignore_existing_data_limits = False
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self.cumulative_line.set_data(ts[:-1], cumulative_doses)
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# Update the top limit based on the concentration if it exceeds 5
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# (rare but possible).
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concentration_top = max([1e-5, max(concentration)])
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concentration_top = max(concentration)
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self.ax.set_ylim(bottom=0., top=concentration_top)
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cumulative_top = max([1e-5, max(cumulative_doses)])
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cumulative_top = max(cumulative_doses)
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self.ax2.set_ylim(bottom=0., top=cumulative_top)
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self.ax.set_xlim(left = min(min(model.concentration_model.infected.presence.boundaries()[0]), min(model.exposed.presence.boundaries()[0])), right = max(max(model.concentration_model.infected.presence.boundaries()[1]), max(model.exposed.presence.boundaries()[1])))
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self.ax.set_xlim(left = min(min(model.concentration_model.infected.presence.boundaries()[0]), min(model.exposed.presence.boundaries()[0])),
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right = max(max(model.concentration_model.infected.presence.boundaries()[1]), max(model.exposed.presence.boundaries()[1])))
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figure_legends = [mlines.Line2D([], [], color='#3530fe', markersize=15, label='Mean concentration'),
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mlines.Line2D([], [], color='#0000c8', markersize=15, ls="dotted", label='Cumulative dose'),
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@ -229,10 +217,7 @@ class ExposureComparissonResult(View):
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self.figure = matplotlib.figure.Figure(figsize=(9, 6))
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ipympl_canvas(self.figure)
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self.html_output = widgets.HTML()
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self.ax = self.figure.add_subplot(1, 1, 1)
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self.ax2 = self.ax.twinx()
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self.concentration_line = None
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self.cumulative_line = None
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self.ax, self.ax2 = self.initialize_axes()
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@property
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def widget(self):
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@ -240,6 +225,24 @@ class ExposureComparissonResult(View):
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# unless the widget is wrapped in a container (it is seen on all tabs otherwise!).
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return widgets.HBox([self.figure.canvas])
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def initialize_axes(self) -> matplotlib.figure.Axes:
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ax = self.figure.add_subplot(1, 1, 1)
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ax.spines['right'].set_visible(False)
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ax.spines['top'].set_visible(False)
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ax.set_xlabel('Time (hours)')
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ax.set_ylabel('Mean concentration ($virions/m^{3}$)')
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ax.set_title('Concentration of virions \nand Cumulative dose')
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ax2 = ax.twinx()
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ax2.spines['left'].set_visible(False)
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ax2.spines['top'].set_visible(False)
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ax2.spines['right'].set_linestyle((0,(1,4)))
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ax2.set_ylabel('Mean cumulative dose (infectious virus)')
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return ax, ax2
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def scenarios_updated(self, scenarios: typing.Sequence[ScenarioType], _):
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updated_labels, updated_models = zip(*scenarios)
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exp_models = tuple(
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@ -264,51 +267,13 @@ class ExposureComparissonResult(View):
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for label, cumulative_dose, color in zip(labels, cumulative_doses, colors):
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self.ax2.plot(ts[:-1], cumulative_dose, label=label, color=color, linestyle="dotted")
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if self.concentration_line is None:
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[self.concentration_line] = self.ax.plot(ts, concentration, '#3530fe', label='Concentration')
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ax = self.ax
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ax.spines['right'].set_visible(False)
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ax.spines['top'].set_visible(False)
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ax.set_xlabel('Time (hours)')
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ax.set_ylabel('Mean concentration ($virions/m^{3}$)')
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ax.set_title('Concentration of virions \nand Cumulative dose')
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else:
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self.ax.ignore_existing_data_limits = True
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self.concentration_line.set_data(ts, concentration)
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if self.cumulative_line is None:
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[self.cumulative_line] = self.ax2.plot(ts[:-1], cumulative_dose, '#1ffd01', label='Cumulative dose', linestyle='dotted')
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ax2 = self.ax2
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ax2.spines['left'].set_visible(False)
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ax2.spines['top'].set_visible(False)
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ax2.set_ylabel('Mean cumulative dose (infectious virus)')
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ax2.spines['right'].set_linestyle((0,(1,4)))
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self.cumulative_line.set_linestyle((0,(1,4)))
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else:
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self.ax2.ignore_existing_data_limits = True
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self.cumulative_line.set_data(ts[:-1], cumulative_dose)
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# Update the top limit based on the concentration if it exceeds 5
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# (rare but possible).
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concentration_top = max([max(concentration) for concentration in concentrations])
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self.ax.set_ylim(bottom=0., top=concentration_top)
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cumulative_top = max([max(cumulative_dose) for cumulative_dose in cumulative_doses])
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self.ax2.set_ylim(bottom=0., top=cumulative_top)
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figure_legends = [mlines.Line2D([], [], color='#3530fe', markersize=15, label='Mean concentration'),
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mlines.Line2D([], [], color='#0000c8', markersize=15, ls="dotted", label='Cumulative dose')]
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self.figure.legend(handles=figure_legends)
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self.ax.legend()
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self.figure.canvas.draw()
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@ -724,7 +689,6 @@ class ModelWidgets(View):
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def _build_viral_load(self, node):
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viral_load_in_sputum = widgets.Text(continuous_update=False, value=("{:.2e}".format(node.viral_load_in_sputum)))
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def on_viral_load_change(change):
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viral_load_in_sputum.value = "{:.2e}".format(float(change['new']))
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node.viral_load_in_sputum = float(viral_load_in_sputum.value)
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@ -737,7 +701,7 @@ class ModelWidgets(View):
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presence_start = widgets.FloatRangeSlider(value = node.present_times[0], min = 8., max=13., step=0.1)
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presence_finish = widgets.FloatRangeSlider(value = node.present_times[1], min = 13., max=18., step=0.1)
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#node.present_times = ((presence_start), (presence_stop))
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def on_presence_start_change(change):
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node.present_times = (change['new'], presence_finish.value)
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@ -808,15 +772,14 @@ class ModelWidgets(View):
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return widgets.HBox([widgets.Label('HEPA Filtration (m³/h) '),HEPA_w], layout=widgets.Layout(justify_content='space-between'))
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def _build_infectivity(self,node):
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def _build_infectivity(self, node):
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return collapsible([widgets.VBox([
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self._build_virus(node.virus),
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])], title="Virus data")
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def _build_virus(self, node):
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virus = node.dcs_instance()
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for name, virus_ in models.Virus.types.items():
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if virus == virus_:
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if node.dcs_instance() == virus_:
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break
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virus_choice = widgets.Dropdown(options=list(models.Virus.types.keys()), value=name)
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transmissibility_factor = widgets.FloatSlider(value=node.transmissibility_factor, min=0, max=1, step=0.1)
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@ -829,17 +792,19 @@ class ModelWidgets(View):
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infectious_dose.value = virus.infectious_dose
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def on_transmissibility_change(change):
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virus = models.SARSCoV2(viral_load_in_sputum=ModelWidgets._build_viral_load(self, node).children[1].value, infectious_dose=infectious_dose.value, viable_to_RNA_ratio=0.5, transmissibility_factor=change['new'])
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virus = models.SARSCoV2(viral_load_in_sputum=node.dcs_instance().viral_load_in_sputum, infectious_dose=infectious_dose.value,
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viable_to_RNA_ratio=0.5, transmissibility_factor=change['new'])
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node.dcs_update_from(virus)
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if (transmissibility_factor.value != models.Virus.types[virus_choice.value].transmissibility_factor):
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virus_choice.options = list(models.Virus.types.keys()) + ["Custom"]
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virus_choice.value = "Custom"
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def on_infectious_dose_change(change):
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virus = models.SARSCoV2(viral_load_in_sputum=ModelWidgets._build_viral_load(self, node).children[1].value, infectious_dose=change['new'], viable_to_RNA_ratio=0.5, transmissibility_factor=transmissibility_factor.value)
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virus = models.SARSCoV2(viral_load_in_sputum=node.dcs_instance().viral_load_in_sputum, infectious_dose=change['new'],
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viable_to_RNA_ratio=0.5, transmissibility_factor=transmissibility_factor.value)
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node.dcs_update_from(virus)
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if (infectious_dose.value != models.Virus.types[virus_choice.value].infectious_dose):
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virus_choice.options = list(models.Virus.types.keys()) + ["Custom"]
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virus_choice.options.append("Custom")
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virus_choice.value = "Custom"
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virus_choice.observe(on_virus_change, names=['value'])
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@ -896,12 +861,6 @@ class CARAStateBuilder(state.StateBuilder):
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choices=models.Mask.types,
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)
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def build_type_Virus(self, _: dataclasses.Field):
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return state.DataclassStatePredefined(
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models.Virus,
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choices=models.Virus.types,
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)
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def build_type__VentilationBase(self, _: dataclasses.Field):
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s: state.DataclassStateNamed = state.DataclassStateNamed(
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states={
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@ -918,11 +877,10 @@ class CARAStateBuilder(state.StateBuilder):
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#Initialise the "Hinged window" state
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s._states['Hinged window'].dcs_update_from(
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models.HingedWindow(active=models.PeriodicInterval(period=120, duration=15),
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outside_temp=models.PiecewiseConstant((0,24.), (283.15,)),
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window_height=1.6, opening_length=0.6,
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window_width=10.
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outside_temp=models.PiecewiseConstant((0,24.), (283.15,)),
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window_height=1.6, opening_length=0.6,
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window_width=10.
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),
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)
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# Initialise the "HVAC" state
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s._states['HVACMechanical'].dcs_update_from(
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