def run(case_service="Cardiac Surgery", item_id="1686"):
analytics = ScmAnalytics.ScmAnalytics(lhs_config)
case_service_filter = [{
"dim": "case_service",
"op": "eq",
"val": case_service
}]
usage_df = analytics.usage_df
usage_df = usage_df[usage_df["start_date"].notna()]
usage_df = Analytics.process_filters(usage_df, filters=case_service_filter)
usage_events = set(usage_df["event_id"])
item_usage_df = usage_df[usage_df["item_id"] == item_id]
surgery_df = pre_process_columns(analytics.surgery_df)
surgery_df = surgery_df[surgery_df["start_date"].notna()]
surgery_df = surgery_df[
surgery_df["start_date"] > datetime.date(2016, 1, 1)]
surgery_df = Analytics.process_filters(surgery_df,
filters=case_service_filter)
surgery_df = surgery_df[surgery_df["event_id"].isin(usage_events)]
surgery_df = surgery_df.join(
item_usage_df.set_index("event_id")[["used_qty"]],
on="event_id",
how="left").fillna(0)
surgery_df["procedures"] = surgery_df["procedures"].apply(
lambda x: frozenset(x))
usage_dist = surgery_df.groupby(["procedures"]).agg({
"used_qty":
lambda x: list(x)
}).reset_index()
usage_dist["occurrences"] = usage_dist["used_qty"].apply(lambda x: len(x))
usage_dist = usage_dist[usage_dist["occurrences"] > 25]
usage_dist["mean"] = usage_dist["used_qty"].apply(lambda x: np.mean(x))
usage_dist["variance"] = usage_dist["used_qty"].apply(
lambda x: np.var(x, ddof=1))
usage_dist["var/mean"] = usage_dist["variance"] / usage_dist["mean"]
df = surgery_df[surgery_df["procedures"].isin(
usage_dist["procedures"])][["start_date", "used_qty"]]
rolling_df = df[["used_qty"]].rolling(100).mean()
plt.plot(list(rolling_df["used_qty"]))
rolling_df = df[["used_qty"]].rolling(50).mean()
plt.plot(list(rolling_df["used_qty"]))
plt.savefig("{}_rolling_usage.png".format(item_id), format="png")
traces = []
x_max = 0
for i in range(len(usage_dist)):
case = usage_dist.iloc[i]["procedures"]
data = usage_dist.iloc[i]["used_qty"]
label = ", ".join(case)
end = max(usage_dist.iloc[i]["used_qty"]) + 1
traces.append(
go.Histogram(x=data,
name=label,
xbins=dict(start=0, end=end, size=1),
histnorm='probability',
opacity=0.75))
x_max = int(end) if end > x_max else x_max
def boostrap_info_process(item_id="38242"):
case_service = "Cardiac Surgery"
#item_id = "3824ns_info_state_rvs2"
info_granularity = 1
eps_trunk = 1e-3
elective_outdir = "scm_implementation/ns_info_state_rvs/elective"
emergency_outdir = "scm_implementation/ns_info_state_rvs/emergency"
analytics = ScmAnalytics.ScmAnalytics(lhs_config)
filters = [{
"dim": "case_service",
"op": "eq",
"val": case_service
}, {
"dim": "urgent_elective",
"op": "eq",
"val": "Elective"
}]
elective_filter = [{
"dim": "urgent_elective",
"op": "eq",
"val": "Elective"
}]
emergency_filter = [{
"dim": "urgent_elective",
"op": "eq",
"val": "Urgent"
}]
case_service_filter = [{
"dim": "case_service",
"op": "eq",
"val": case_service
}]
surgery_df = pre_process_columns(analytics.surgery_df)
surgery_df = surgery_df[surgery_df["start_date"].notna()]
surgery_df = surgery_df[
surgery_df["start_date"] > datetime.date(2016, 1, 1)]
surgery_df = Analytics.process_filters(surgery_df,
filters=elective_filter +
case_service_filter)
dist_df = surgeries_per_day_distribution(surgery_df,
day_group_by="is_weekday",
filters=[])
data = dist_df.set_index("is_weekday").loc[True]["data"]
bins = range(1 + int(max(data)))
binom_x = [x + 0.5 for x in bins]
n = int(max(data))
p = np.mean(data) / n
surgery_df = pre_process_columns(analytics.surgery_df)
surgery_df = surgery_df[surgery_df["start_date"].notna()]
surgery_df = surgery_df[
surgery_df["start_date"] > datetime.date(2016, 1, 1)]
surgery_df = Analytics.process_filters(surgery_df,
filters=emergency_filter +
case_service_filter)
dist_df = surgeries_per_day_distribution(surgery_df, filters=[])
emergency_surgeries_mean = np.mean(dist_df)
surgery_df = Analytics.process_filters(analytics.surgery_df,
filters=case_service_filter)
surgery_df["procedure_count"] = surgery_df["procedures"].apply(
lambda x: len(x))
procedure_count_df = surgery_df.groupby("procedure_count").agg({
"event_id":
"count"
}).reset_index()
procedure_count_df = procedure_count_df[
procedure_count_df["procedure_count"] != 6]
procedure_count_df["p"] = procedure_count_df["procedure_count"] / sum(
procedure_count_df["procedure_count"])
procedure_count_rv = pacal.DiscreteDistr(
procedure_count_df["procedure_count"], procedure_count_df["p"])
"""
Procedure weights
"""
usage_events = set(analytics.usage_df["event_id"])
surgery_df = analytics.surgery_df[analytics.surgery_df["event_id"].isin(
usage_events)]
surgery_df = Analytics.process_filters(surgery_df,
filters=case_service_filter)
surgery_df["procedures"] = surgery_df["procedures"].apply(
lambda x: set(e.replace(" ", "_") for e in x))
procedures = surgery_df["procedures"].apply(lambda x: list(x)).to_list()
procedures = pd \
.DataFrame({"procedure": [val for sublist in procedures for val in sublist],
"count": [1 for sublist in procedures for val in sublist]}) \
.groupby("procedure") \
.agg({"count": "count"}) \
.reset_index()
procedures["p"] = procedures["count"] / sum(procedures["count"])
def procedure_pick_rv(size):
return np.random.choice(procedures["procedure"],
p=procedures["p"],
replace=False,
size=size)
synthetic_surgeries = pd.DataFrame({"event_id": list(range(1000))})
synthetic_surgeries["procedure_count"] = procedure_count_rv.rand(1000)
synthetic_surgeries["procedures"] = synthetic_surgeries[
"procedure_count"].apply(lambda x: procedure_pick_rv(x))
synthetic_procedure_df = pd.concat(
[pd.Series(row['event_id'], row['procedures']) for _, row in synthetic_surgeries.iterrows()]) \
.reset_index() \
.rename(columns={"index": "procedure",
0: "event_id"}
)
synthetic_procedure_df["flag"] = 1
synthetic_surgeries_df = synthetic_procedure_df \
.pivot(index="event_id", columns="procedure", values="flag") \
.fillna(0) \
.reset_index()
feature_df = pd.read_csv(os.path.join("regression_results", item_id))
features = feature_df["feature"]
featured_procedures = list(
filter(lambda x: "." not in x, feature_df["feature"]))
if "other" in featured_procedures:
featured_procedures.remove("other")
for fp in featured_procedures:
if fp not in synthetic_surgeries_df:
print(procedures.set_index("procedure").loc[fp])
synthetic_surgeries_df[fp] = 0
all_procedures = set.union(*surgery_df["procedures"])
interactions = list(filter(lambda x: "." in x, feature_df["feature"]))
interactions = list(Interaction(i.split(".")) for i in interactions)
data, _ = SURegressionModel.extract_features_data(synthetic_surgeries_df,
featured_procedures, [],
interactions,
other=True)
for f in feature_df["feature"]:
if f not in data:
print(f)
data[f] = 0
synthetic_surgeries_df["feature_vector"] = data[features].values.tolist()
coeff = np.array(feature_df["estimate"])
synthetic_surgeries_df["expected_usage"] = synthetic_surgeries_df["feature_vector"] \
.apply(lambda x: np.exp(np.dot(x, coeff)))
"""
Information rv for empirical surgeries
"""
surgery_df = surgery_df.drop_duplicates("event_id", keep="last")
empirical_procedure_df = pd.concat(
[pd.Series(row['event_id'], row['procedures']) for _, row in surgery_df.iterrows()]) \
.reset_index() \
.rename(columns={"index": "procedure",
0: "event_id"}
)
empirical_procedure_df["flag"] = 1
empirical_surgeries_df = empirical_procedure_df \
.pivot(index="event_id", columns="procedure", values="flag") \
.fillna(0) \
.reset_index()
data, _ = SURegressionModel.extract_features_data(empirical_surgeries_df,
featured_procedures, [],
interactions,
other=True)
empirical_surgeries_df["feature_vector"] = data[features].values.tolist()
empirical_surgeries_df["expected_usage"] = empirical_surgeries_df["feature_vector"] \
.apply(lambda x: np.exp(np.dot(x, coeff)))
"""
Plotly histogram for per surgery info rv, empirical surgeries and synthetic using regression results
"""
s = 0
e = int(
max(max(empirical_surgeries_df["expected_usage"]),
max(synthetic_surgeries_df["expected_usage"])) + 1)
empirical_trace = go.Histogram(
x=empirical_surgeries_df["expected_usage"],
name='Empirical Surgery Info RV (mean={:0.2f})'.format(
np.mean(empirical_surgeries_df["expected_usage"])),
xbins=dict(start=s, end=e, size=info_granularity),
histnorm='probability density',
opacity=0.75)
synthetic_trace = go.Histogram(
x=synthetic_surgeries_df["expected_usage"],
name='Synthetic Surgery Info RV (mean={:0.2f})'.format(
np.mean(synthetic_surgeries_df["expected_usage"])),
xbins=dict(start=s, end=e, size=info_granularity),
histnorm='probability density',
opacity=0.75)
layout = go.Layout(title="Per Surgery Info R.V Item: {0}".format(item_id),
xaxis={'title': 'Info [Expected Usage]'},
yaxis={'title': 'Probability Density'})
figure = go.Figure(data=[empirical_trace, synthetic_trace], layout=layout)
plot(figure, filename="{0}_Per_Surgery_Info_Rv.html".format(item_id))
"""
Plotly histogram for per weekday elective surgery RV
"""
empirical_rv_df = empirical_surgeries_df.groupby(["expected_usage"]) \
.agg({"event_id": "count"}) \
.rename(columns={"event_id": "count"}) \
.reset_index()
empirical_rv_df["p"] = empirical_rv_df["count"] / sum(
empirical_rv_df["count"])
emp_surgery_rv = pacal.DiscreteDistr(empirical_rv_df["expected_usage"],
empirical_rv_df["p"])
surgery_demand_rv = pacal.BinomialDistr(n, p)
days = 100000
elective_samples = [
sum(emp_surgery_rv.rand(x)) for x in np.random.binomial(n, p, days)
]
elective_samples = [
round(sample / info_granularity) * info_granularity
for sample in elective_samples
]
weekday_elective_trace = go.Histogram(
x=elective_samples,
name='{} Elective Info RV (mean={:0.2f})'.format(
item_id, np.mean(elective_samples)),
xbins=dict(start=0, end=max(elective_samples), size=info_granularity),
histnorm='probability',
opacity=0.75)
"""
Plotly histogram for per day emergency surgery RV
"""
emergency_samples = [
sum(emp_surgery_rv.rand(x))
for x in np.random.poisson(emergency_surgeries_mean, days)
]
emergency_samples = [
round(sample / info_granularity) * info_granularity
for sample in emergency_samples
]
emergency_trace = go.Histogram(
x=emergency_samples,
name='{} Emergency Info RV (mean={:0.2f})'.format(
item_id, np.mean(emergency_samples)),
xbins=dict(start=0, end=max(emergency_samples), size=info_granularity),
histnorm='probability',
opacity=0.75)
layout = go.Layout(
title="Weekday Elective Info R.V Item: {0}".format(item_id),
xaxis={'title': 'Info State (Poisson Usage)]'},
yaxis={'title': 'Probability'})
figure = go.Figure(data=[weekday_elective_trace, emergency_trace],
layout=layout)
plot(figure, filename="{0}_Weekday_Elective_Info_Rv.html".format(item_id))
elective_info_df = pd.DataFrame({"info": elective_samples, "count": [1] * len(elective_samples)}) \
.groupby(["info"]) \
.agg({"count": "count"}) \
.reset_index()
elective_info_df["p"] = elective_info_df["count"] / sum(
elective_info_df["count"])
elective_info_rv = pacal.DiscreteDistr(elective_info_df["info"],
elective_info_df["p"])
emergency_info_df = pd.DataFrame({"info": emergency_samples, "count": [1] * len(emergency_samples)}) \
.groupby(["info"]) \
.agg({"count": "count"}) \
.reset_index()
emergency_info_df["p"] = emergency_info_df["count"] / sum(
emergency_info_df["count"])
emergency_info_rv = pacal.DiscreteDistr(emergency_info_df["info"],
emergency_info_df["p"])
max_v = 999
for d in elective_info_rv.get_piecewise_pdf().getDiracs():
if 1 - elective_info_rv.cdf(d.a) < eps_trunk:
max_v = d.a
break
diracs = (pacal.CondLtDistr(elective_info_rv, max_v)) \
.get_piecewise_pdf().getDiracs()
diracs = list(filter(lambda d: d.f > 0, diracs))
elective_info_rv = pacal.DiscreteDistr([d.a for d in diracs],
[d.f for d in diracs])
max_v = 999
for d in emergency_info_rv.get_piecewise_pdf().getDiracs():
if 1 - emergency_info_rv.cdf(d.a) < eps_trunk:
max_v = d.a
break
diracs = (pacal.CondLtDistr(emergency_info_rv, max_v)) \
.get_piecewise_pdf().getDiracs()
diracs = list(filter(lambda d: d.f > 0, diracs))
emergency_info_rv = pacal.DiscreteDistr([d.a for d in diracs],
[d.f for d in diracs])
with open(os.path.join(elective_outdir, "{0}.pickle".format(item_id)),
"wb") as f:
pickle.dump(elective_info_rv, f)
with open(os.path.join(emergency_outdir, "{0}.pickle".format(item_id)),
"wb") as f:
pickle.dump(emergency_info_rv, f)
return emergency_trace, weekday_elective_trace
def elective_surgery_demand_graph(case_service=None):
# case_service = "Cardiac Surgery"
print(case_service)
surgery_df = pre_process_columns(analytics.surgery_df)
surgery_df = surgery_df[surgery_df["start_date"].notna()]
filters = [{
"dim": "case_service",
"op": "eq",
"val": case_service
}, {
"dim": "urgent_elective",
"op": "eq",
"val": "Elective"
}]
dist_df = surgeries_per_day_distribution(surgery_df,
day_group_by="is_weekday",
filters=filters)
data = dist_df.set_index("is_weekday").loc[True]["data"]
empirical = pd.DataFrame()
empirical["count"] = data
empirical["frequency"] = True
empirical = empirical.groupby(["count"]).agg({
"frequency": "count"
}).reset_index()
empirical["probability"] = empirical["frequency"] / sum(
empirical["frequency"])
bins = range(1 + int(max(data)))
binom_x = [x for x in bins]
n = int(max(data))
p = np.mean(data) / n
empirical_trace = go.Bar(x=empirical["count"],
y=empirical["probability"],
width=0.8,
opacity=0.75,
name="Empirical")
binom_trace = go.Bar(x=binom_x,
y=st.binom.pmf(bins, n, p),
width=0.2,
opacity=0.75,
name="Binomial")
layout = go.Layout(
title_text='Elective Surgeries Per Weekday',
xaxis_title_text='Surgeries Per Day',
yaxis_title_text='Probability',
barmode='overlay',
)
# fig = go.Figure(data=[empirical_trace,
# binom_trace],
# layout=layout)
# plot(fig)
# return {"data": [empirical_trace,
# binom_trace],
# "layout": layout}
empirical_x_json = json.dumps(list(empirical["count"]))
empirical_y_json = json.dumps(list(empirical["probability"]))
binom_n_json = json.dumps(n)
binom_p_json = json.dumps(p)
return empirical_x_json, empirical_y_json, binom_n_json, binom_p_json
import pandas as pd
import matplotlib.pyplot as plt
import numpy as np
import scipy.stats as st
from scm_analytics.model.SurgeryModel import surgeries_per_day_distribution, pre_process_columns
from scm_analytics import ScmAnalytics
from scm_analytics.config import lhs_config
import datetime
case_service = "Cardiac Surgery"
analytics = ScmAnalytics.ScmAnalytics(lhs_config)
surgery_df = pre_process_columns(analytics.surgery_df)
surgery_df = surgery_df[surgery_df["start_date"].notna()]
surgery_df = surgery_df[surgery_df["start_date"] > datetime.date(2016, 1, 1)]
filters = [{
"dim": "case_service",
"op": "eq",
"val": case_service
}, {
"dim": "urgent_elective",
"op": "eq",
"val": "Elective"
}]
dist_df = surgeries_per_day_distribution(surgery_df,
day_group_by="is_weekday",
filters=filters)
data = dist_df.set_index("is_weekday").loc[True]["data"]
print(data)
def run(case_service="Cardiac Surgery", item_id="1686", procedure_set=None):
analytics = ScmAnalytics.ScmAnalytics(lhs_config)
case_service_filter = [{
"dim": "case_service",
"op": "eq",
"val": case_service
}]
usage_df = analytics.usage_df
usage_df = usage_df[usage_df["start_date"].notna()]
usage_df = Analytics.process_filters(usage_df, filters=case_service_filter)
usage_events = set(usage_df["event_id"])
item_usage_df = usage_df[usage_df["item_id"] == item_id]
surgery_df = pre_process_columns(analytics.surgery_df)
surgery_df = surgery_df[surgery_df["start_date"].notna()]
surgery_df = surgery_df[
surgery_df["start_date"] > datetime.date(2016, 1, 1)]
surgery_df = Analytics.process_filters(surgery_df,
filters=case_service_filter)
surgery_df = surgery_df[surgery_df["event_id"].isin(usage_events)]
surgery_df = surgery_df.join(
item_usage_df.set_index("event_id")[["used_qty"]],
on="event_id",
how="left").fillna(0)
surgery_df["procedures"] = surgery_df["procedures"].apply(
lambda x: frozenset(x))
surgery_df = surgery_df[surgery_df["procedures"] == procedure_set]
traces = []
x_max = int(max(surgery_df["used_qty"])) + 1
data = surgery_df["used_qty"]
label = ", ".join(procedure_set)
fn = "__".join(procedure_set)
fn = "Usage_Dist_item_" + item_id + "_" + fn.replace(" ", "_")
#
# traces.append(go.Histogram(
# x=data,
# name=label,
# xbins=dict(
# start=0,
# end=x_max,
# size=1
# ),
# histnorm='probability',
# opacity=1,
#
# ))
#
# tickvals = list(x + 0.5 for x in range(x_max))
# ticktext = list(str(x) for x in range(x_max))
# layout = go.Layout( # title="Item: {} Empirical Usage Distribution for common cases".format(item_id),
# xaxis={'title': 'Used Qty',
# 'tickvals': tickvals,
# 'ticktext': ticktext},
# yaxis={'title': 'Probability'},
# font={"size": 16},
# plot_bgcolor="white",
# bargap=0.2)
# figure = go.Figure(
# data=traces,
# layout=layout,
# )
# # figure.update_xaxes(showgrid=True, gridwidth=1, gridcolor='lightgrey')
# figure.update_yaxes(showgrid=True, gridwidth=1, gridcolor='lightgrey')
# # plot(figure, filename="{}_empircal_usage_distribution.html".format(item_id))
# figure.write_image(fn, width=900, height=600)
import matplotlib
import matplotlib.ticker as plticker
matplotlib.rcParams.update({'font.size': 12})
plt.figure(figsize=(4, 3.5))
plt.tight_layout()
plt.gcf().subplots_adjust(bottom=0.15, left=0.15)
n, bins, patches = plt.hist(data,
range(x_max + 1),
density=True,
facecolor='#08306b',
rwidth=0.95)
spacing = np.round((max(n) + 0.1) / 4, decimals=1)
plt.yticks(np.arange(0, max(n) + 0.1, spacing))
#matplotlib.pyplot.grid(b=True, which='major', axis='y')
plt.ylabel("Probability")
plt.xlabel("Used Quantity")
plt.xticks(range(x_max + 1))
plt.savefig(fn + ".svg", format='svg')
plt.savefig(fn + ".eps", format='eps')