def plot_flow_params(plotter: StreamlitPlotter, app: AppRegion):
# Assume a COVID model
model = app.build_model(app.params["default"])
flow_names = sorted(list({f.name for f in model._flows}))
flow_name = st.sidebar.selectbox("Select flow", flow_names)
flows = [f for f in model._flows if f.name == flow_name]
is_logscale = st.sidebar.checkbox("Log scale")
flow_funcs = [f.get_weight_value for f in flows]
plots.model.plots.plot_time_varying_input(
plotter, f"flow-weights-{flow_name}", flow_funcs, model.times, is_logscale
)
t = st.slider("Time", min_value=0, max_value=int(model.times[-1]))
init_dict = {}
for f in flows:
f_name = ""
src = getattr(f, "source", None)
dest = getattr(f, "dest", None)
if src:
f_name += f"from {src}"
if dest:
f_name += f" to {dest}"
f_name = f_name.strip()
init_dict[f_name] = f.get_weight_value(t)
st.write("Values at start time:")
st.write(init_dict)
def plot_dynamic_mixing_matrix(plotter: StreamlitPlotter, app: AppRegion):
model = app.build_model(app.params["default"])
t = st.slider("Time", min_value=0, max_value=int(model.times[-1]))
mixing_matrix = model._get_mixing_matrix(t)
fig, _, _, _, _, _ = plotter.get_figure()
pyplot.imshow(mixing_matrix, cmap="hot", interpolation="none", extent=[0, 80, 80, 0])
plotter.save_figure(fig, filename="mixing-matrix", title_text="Mixing matrix")
st.write(mixing_matrix)
def plot_dynamic_inputs(plotter: StreamlitPlotter, app: AppRegion):
# Assume a COVID model
model = app.build_model(app.params["default"])
tvs = model.time_variants
tv_options = sorted(list(tvs.keys()))
tv_key = st.sidebar.selectbox("Select function", tv_options)
is_logscale = st.sidebar.checkbox("Log scale")
tv_func = tvs[tv_key]
plots.model.plots.plot_time_varying_input(plotter, tv_key, tv_func, model.times, is_logscale)
from apps.tuberculosis_strains.model import build_model
from autumn.region import Region
from autumn.utils.model_register import AppRegion
from .calibrate import run_calibration_chain
philippines_region = AppRegion(
app_name="tuberculosis_strains",
region_name=Region.PHILIPPINES,
build_model=build_model,
calibrate_model=run_calibration_chain,
)
from apps.covid_19.model import build_model
from autumn.region import Region
from autumn.utils.model_register import AppRegion
from .calibrate import run_calibration_chain
manila_region = AppRegion(
app_name="covid_19",
region_name=Region.MANILA,
build_model=build_model,
calibrate_model=run_calibration_chain,
)
from apps.covid_19.model import build_model
from autumn.region import Region
from autumn.utils.model_register import AppRegion
from .calibrate import run_calibration_chain
sabah_region = AppRegion(
app_name="covid_19",
region_name=Region.SABAH,
build_model=build_model,
calibrate_model=run_calibration_chain,
)
from apps.covid_19.model import build_model
from autumn.region import Region
from autumn.utils.model_register import AppRegion
from .calibrate import run_calibration_chain
italy_region = AppRegion(
app_name="covid_19",
region_name=Region.ITALY,
build_model=build_model,
calibrate_model=run_calibration_chain,
)
from apps.covid_19.model import build_model
from autumn.region import Region
from autumn.utils.model_register import AppRegion
from .calibrate import run_calibration_chain
belgium_region = AppRegion(
app_name="covid_19",
region_name=Region.BELGIUM,
build_model=build_model,
calibrate_model=run_calibration_chain,
)
from apps.covid_19.model import build_model
from autumn.region import Region
from autumn.utils.model_register import AppRegion
from .calibrate import run_calibration_chain
penang_region = AppRegion(
app_name="covid_19",
region_name=Region.PENANG,
build_model=build_model,
calibrate_model=run_calibration_chain,
)
from apps.covid_19.model import build_model
from autumn.region import Region
from autumn.utils.model_register import AppRegion
from .calibrate import run_calibration_chain
united_kingdom_region = AppRegion(
app_name="covid_19",
region_name=Region.UNITED_KINGDOM,
build_model=build_model,
calibrate_model=run_calibration_chain,
)
from apps.covid_19.model import build_model
from autumn.region import Region
from autumn.utils.model_register import AppRegion
from .calibrate import run_calibration_chain
malaysia_region = AppRegion(
app_name="covid_19",
region_name=Region.MALAYSIA,
build_model=build_model,
calibrate_model=run_calibration_chain,
)
from apps.covid_19.model import build_model
from autumn.region import Region
from autumn.utils.model_register import AppRegion
from .calibrate import run_calibration_chain
johor_region = AppRegion(
app_name="covid_19",
region_name=Region.JOHOR,
build_model=build_model,
calibrate_model=run_calibration_chain,
)
from apps.covid_19.model import build_model
from autumn.region import Region
from autumn.utils.model_register import AppRegion
from .calibrate import run_calibration_chain
sweden_region = AppRegion(
app_name="covid_19",
region_name=Region.SWEDEN,
build_model=build_model,
calibrate_model=run_calibration_chain,
)
from apps.sir_example.model import build_model
from autumn.region import Region
from autumn.utils.model_register import AppRegion
from .calibrate import run_calibration_chain
victoria_region = AppRegion(
app_name="sir_example",
region_name=Region.VICTORIA,
build_model=build_model,
calibrate_model=run_calibration_chain,
)
from apps.covid_19.model import build_model
from autumn.region import Region
from autumn.utils.model_register import AppRegion
from .calibrate import run_calibration_chain
victoria_region = AppRegion(
app_name="covid_19",
region_name=Region.VICTORIA,
build_model=build_model,
calibrate_model=run_calibration_chain,
)
from apps.covid_19.model import build_model
from autumn.region import Region
from autumn.utils.model_register import AppRegion
from .calibrate import run_calibration_chain
davao_city_region = AppRegion(
app_name="covid_19",
region_name=Region.DAVAO_CITY,
build_model=build_model,
calibrate_model=run_calibration_chain,
)
from apps.covid_19.model import build_model
from autumn.region import Region
from autumn.utils.model_register import AppRegion
from .calibrate import run_calibration_chain
france_region = AppRegion(
app_name="covid_19",
region_name=Region.FRANCE,
build_model=build_model,
calibrate_model=run_calibration_chain,
)
def plot_flow_graph(plotter: StreamlitPlotter, app: AppRegion):
"""
Plot a graph of the model's compartments and flows
See NetworkX documentation: https://networkx.org/documentation/stable/index.html
"""
model = app.build_model(app.params["default"])
flow_types = st.multiselect("Flow types", ["Transition", "Entry", "Exit"],
default=["Transition"])
layout_lookup = {
"Spring": nx.spring_layout,
"Spectral": nx.spectral_layout,
"Kamada Kawai": nx.kamada_kawai_layout,
"Random": nx.random_layout,
}
layout_key = st.selectbox("Layout", list(layout_lookup.keys()))
layout_func = layout_lookup[layout_key]
is_node_labels_visible = st.checkbox("Show node labels")
include_connected_nodes = st.checkbox("Include connected nodes")
# ADD compartment selector
original_compartment_names = model._original_compartment_names
stratifications = model._stratifications
compartment_names = model.compartments
orig_comps = ["All"] + original_compartment_names
chosen_comp_names = st.multiselect("Compartments",
orig_comps,
default="All")
if "All" in chosen_comp_names:
chosen_comp_names = original_compartment_names
chosen_strata = {}
for strat in stratifications:
options = ["All"] + strat.strata
choices = st.multiselect(strat.name, options, default=["All"])
if "All" not in choices:
chosen_strata[strat.name] = choices
# Build the graph.
comps_to_graph = []
if "Entry" in flow_types:
comps_to_graph.append("ENTRY")
if "Exit" in flow_types:
comps_to_graph.append("EXIT")
for comp in compartment_names:
is_selected = True
if not comp.name in chosen_comp_names:
is_selected = False
for strat_name, strata in chosen_strata.items():
has_strat = strat_name in comp._strat_names
has_strata = any(comp.has_stratum(strat_name, s) for s in strata)
if has_strat and not has_strata:
is_selected = False
continue
if not is_selected:
continue
comps_to_graph.append(comp)
if not comps_to_graph:
st.write("Nothing to plot")
return
graph = nx.DiGraph()
for comp in comps_to_graph:
graph.add_node(comp)
flow_lookup = {}
for flow in model._flows:
if "Entry" in flow_types and is_flow_type(flow, BaseEntryFlow):
edge = ("ENTRY", flow.dest)
elif "Exit" in flow_types and is_flow_type(flow, BaseExitFlow):
edge = (flow.source, "EXIT")
elif "Transition" in flow_types and is_flow_type(
flow, BaseTransitionFlow):
edge = (flow.source, flow.dest)
else:
continue
if include_connected_nodes:
src_is_valid = edge[0] in comps_to_graph and edge[0] != "ENTRY"
dst_is_valid = edge[1] in comps_to_graph and edge[1] != "EXIT"
should_add_edge = src_is_valid or dst_is_valid
else:
src_is_valid = edge[0] in comps_to_graph
dst_is_valid = edge[1] in comps_to_graph
should_add_edge = src_is_valid and dst_is_valid
if should_add_edge:
graph.add_edge(*edge)
flow_lookup[edge_to_str(edge)] = flow
# Draw the graph.
pyplot.style.use("ggplot")
fig = pyplot.figure(figsize=[14 / 1.5, 9 / 1.5], dpi=300)
axis = fig.add_axes([0, 0, 1, 1])
# Specify a layout technique.
pos = layout_func(graph)
# Draw the nodes.
node_size = 12
for node in graph.nodes:
nx.draw_networkx_nodes(
graph,
pos,
nodelist=[node],
ax=axis,
node_size=node_size,
node_color="#333",
alpha=1,
)
if is_node_labels_visible:
labels = {}
for node in graph.nodes:
labels[node] = get_label(node)
nx.draw_networkx_labels(graph,
pos,
labels,
font_size=8,
verticalalignment="top",
alpha=0.8)
# Draw the edges between nodes.
for edge in graph.edges:
flow = flow_lookup[edge_to_str(edge)]
color = "#666"
style = "solid"
alpha = 0.8
for flow_style in FLOW_STYLES:
if is_flow_type(flow, flow_style["class"]):
color = flow_style["color"]
style = flow_style["style"]
alpha = flow_style["alpha"]
nx.draw_networkx_edges(
graph,
pos,
edgelist=[edge],
width=1,
node_size=node_size,
alpha=alpha,
edge_color=color,
style=style,
arrowsize=6,
)
st.pyplot(fig)
from apps.covid_19.model import build_model
from autumn.region import Region
from autumn.utils.model_register import AppRegion
from .calibrate import run_calibration_chain
central_visayas_region = AppRegion(
app_name="covid_19",
region_name=Region.CENTRAL_VISAYAS,
build_model=build_model,
calibrate_model=run_calibration_chain,
)
from apps.tuberculosis.model import build_model
from autumn.region import Region
from autumn.utils.model_register import AppRegion
from .calibrate import run_calibration_chain
marshall_islands_region = AppRegion(
app_name="tuberculosis",
region_name=Region.MARSHALL_ISLANDS,
build_model=build_model,
calibrate_model=run_calibration_chain,
)
from apps.covid_19.model import build_model
from autumn.region import Region
from autumn.utils.model_register import AppRegion
from .calibrate import run_calibration_chain
kuala_lumpur_region = AppRegion(
app_name="covid_19",
region_name=Region.KUALA_LUMPUR,
build_model=build_model,
calibrate_model=run_calibration_chain,
)
from apps.covid_19.model import build_model
from autumn.region import Region
from autumn.utils.model_register import AppRegion
from .calibrate import run_calibration_chain
selangor_region = AppRegion(
app_name="covid_19",
region_name=Region.SELANGOR,
build_model=build_model,
calibrate_model=run_calibration_chain,
)
from apps.covid_19.model import build_model
from autumn.region import Region
from autumn.utils.model_register import AppRegion
from .calibrate import run_calibration_chain
philippines_region = AppRegion(
app_name="covid_19",
region_name=Region.PHILIPPINES,
build_model=build_model,
calibrate_model=run_calibration_chain,
)
from apps.covid_19.model import build_model
from autumn.region import Region
from autumn.utils.model_register import AppRegion
from .calibrate import run_calibration_chain
calabarzon_region = AppRegion(
app_name="covid_19",
region_name=Region.CALABARZON,
build_model=build_model,
calibrate_model=run_calibration_chain,
)