Additional Synchronised Traces - Orthopaedic Ward - Hospital Efficiency Project

This is the orthopaedic surgery model developed as part of the hospital efficiency project.

original model author = Harper, Alison and Monks, Thomas

license = MIT

title = Hospital Efficiency Project Orthopaedic Planning Model Discrete-Event Simulation

url = https://github.com/AliHarp/HEP

It has been used as a test case here to allow the development and testing of several key features of the event log animations:

import time
import pandas as pd
import plotly.express as px
import plotly.graph_objects as go
from examples.example_13_additional_synchronised_traces_method_1.simulation_execution_functions import multiple_replications
from examples.example_13_additional_synchronised_traces_method_1.model_classes import Scenario, Schedule
from vidigi.prep import reshape_for_animations, generate_animation_df
from vidigi.animation import generate_animation
from plotly.subplots import make_subplots

import plotly.io as pio
pio.renderers.default = "notebook"

TRACE = True
debug_mode=True

schedule = Schedule()
/opt/conda/envs/vidigi_package_dev/lib/python3.11/site-packages/sim_tools/output_analysis.py:18: UserWarning:

A NumPy version >=1.26.4 and <2.7.0 is required for this version of SciPy (detected version 1.26.2)

4 theatres

5 day/week

Each theatre has three sessions per day:

Morning: 1 revision OR 2 primary

Afternoon: 1 revision OR 2 primary

Evening: 1 primary

40 ring-fenced beds for recovery from these operations

(pd.DataFrame.from_dict(schedule.sessions_per_weekday, orient="index")
        .rename(columns={0: "Sessions"}).merge(

        pd.DataFrame.from_dict(schedule.theatres_per_weekday, orient="index")
            .rename(columns={0: "Theatre Capacity"}),
            left_index=True, right_index=True

        ).merge(

        pd.DataFrame.from_dict(schedule.allocation, orient="index"),
        left_index=True, right_index=True

        ))
Sessions Theatre Capacity 0 1 2
Monday 3 4 2P_or_1R 2P_or_1R 1P
Tuesday 3 4 2P_or_1R 2P_or_1R 1P
Wednesday 3 4 2P_or_1R 2P_or_1R 1P
Thursday 3 4 2P_or_1R 2P_or_1R 1P
Friday 3 4 2P_or_1R 2P_or_1R 1P
Saturday 0 0 None None None
Sunday 0 0 None None None 
n_beds = 35

primary_hip_los = 4.4

primary_knee_los = 4.7

revision_hip_los = 6.9

revision_knee_los = 7.2

unicompart_knee_los = 2.9

los_delay = 16.5
los_delay_sd = 15.2

prop_delay = 0.076

replications = 30
runtime = 60
warmup=7

args = Scenario(schedule=schedule,
                primary_hip_mean_los=primary_hip_los,
                primary_knee_mean_los=primary_knee_los,
                revision_hip_mean_los=revision_hip_los,
                revision_knee_mean_los=revision_knee_los,
                unicompart_knee_mean_los=unicompart_knee_los,
                prob_ward_delay=prop_delay,
                n_beds=n_beds,
                delay_post_los_mean=los_delay,
                delay_post_los_sd=los_delay_sd
                )


results = multiple_replications(
                return_detailed_logs=True,
                scenario=args,
                n_reps=replications,
                results_collection=runtime
            )

# Join the event log with a list of patients to add a column that will determine
# the icon set used for a patient (in this case, we want to distinguish between the
# knee/hip patients)
event_log = results[4]
event_log = event_log[event_log['rep'] == 1].copy()
event_log['patient'] = event_log['patient'].astype('str') + event_log['pathway']

primary_patients = results[2]
primary_patients = primary_patients[primary_patients['rep'] == 1]
primary_patients['patient class'] = primary_patients['patient class'].str.title()
primary_patients['ID'] = primary_patients['ID'].astype('str') + primary_patients['patient class']

revision_patients = results[3]
revision_patients = revision_patients[revision_patients['rep'] == 1]
revision_patients['patient class'] = revision_patients['patient class'].str.title()
revision_patients['ID'] = revision_patients['ID'].astype('str') + revision_patients['patient class']

full_log_with_patient_details = event_log.merge(pd.concat([primary_patients, revision_patients]),
                                                    how="left",
                                                left_on=["patient", "pathway"],
                                                right_on=["ID", "patient class"]).reset_index(drop=True).drop(columns="ID")

pid_table = full_log_with_patient_details[['patient']].drop_duplicates().reset_index(drop=True).reset_index(drop=False).rename(columns={'index': 'pid'})

full_log_with_patient_details = full_log_with_patient_details.merge(pid_table, how='left', on='patient').drop(columns='patient').rename(columns={'pid':'patient'})
/tmp/ipykernel_881/3232257187.py:51: SettingWithCopyWarning:


A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy

/tmp/ipykernel_881/3232257187.py:52: SettingWithCopyWarning:


A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy

/tmp/ipykernel_881/3232257187.py:56: SettingWithCopyWarning:


A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy

/tmp/ipykernel_881/3232257187.py:57: SettingWithCopyWarning:


A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy


event_position_df = pd.DataFrame([
            # {'event': 'arrival', 'x':  10, 'y': 250, 'label': "Arrival" },

            # Triage - minor and trauma
            {'event': 'enter_queue_for_bed',
                'x':  300, 'y': 600, 'label': "Waiting for<br>Availability of<br>Bed to be Confirmed<br>Before Surgery" },

            {'event': 'no_bed_available',
                'x':  800, 'y': 600, 'label': "No Bed<br>Available:<br>Surgery Cancelled" },

            {'event': 'post_surgery_stay_begins',
                'x':  850, 'y': 220, 'resource':'n_beds', 'label': "In Bed:<br>Recovering from<br>Surgery" },

            {'event': 'discharged_after_stay',
                'x':  770, 'y': 50, 'label': "Discharged from Hospital<br>After Recovery"}
            # {'event': 'exit',
            #  'x':  670, 'y': 100, 'label': "Exit"}

            ])
full_patient_df = reshape_for_animations(full_log_with_patient_details,
                                         entity_col_name="patient",
                                            every_x_time_units=1,
                                            limit_duration=runtime,
                                            step_snapshot_max=50,
                                            debug_mode=debug_mode
                                            )

if debug_mode:
    print(f'Reshaped animation dataframe finished construction at {time.strftime("%H:%M:%S", time.localtime())}')
/workspace/vidigi/prep.py:281: FutureWarning:

DataFrameGroupBy.apply operated on the grouping columns. This behavior is deprecated, and in a future version of pandas the grouping columns will be excluded from the operation. Either pass `include_groups=False` to exclude the groupings or explicitly select the grouping columns after groupby to silence this warning.

/workspace/vidigi/prep.py:281: FutureWarning:

DataFrameGroupBy.apply operated on the grouping columns. This behavior is deprecated, and in a future version of pandas the grouping columns will be excluded from the operation. Either pass `include_groups=False` to exclude the groupings or explicitly select the grouping columns after groupby to silence this warning.

/workspace/vidigi/prep.py:281: FutureWarning:

DataFrameGroupBy.apply operated on the grouping columns. This behavior is deprecated, and in a future version of pandas the grouping columns will be excluded from the operation. Either pass `include_groups=False` to exclude the groupings or explicitly select the grouping columns after groupby to silence this warning.

/workspace/vidigi/prep.py:281: FutureWarning:

DataFrameGroupBy.apply operated on the grouping columns. This behavior is deprecated, and in a future version of pandas the grouping columns will be excluded from the operation. Either pass `include_groups=False` to exclude the groupings or explicitly select the grouping columns after groupby to silence this warning.

/workspace/vidigi/prep.py:281: FutureWarning:

DataFrameGroupBy.apply operated on the grouping columns. This behavior is deprecated, and in a future version of pandas the grouping columns will be excluded from the operation. Either pass `include_groups=False` to exclude the groupings or explicitly select the grouping columns after groupby to silence this warning.

/workspace/vidigi/prep.py:281: FutureWarning:

DataFrameGroupBy.apply operated on the grouping columns. This behavior is deprecated, and in a future version of pandas the grouping columns will be excluded from the operation. Either pass `include_groups=False` to exclude the groupings or explicitly select the grouping columns after groupby to silence this warning.

/workspace/vidigi/prep.py:281: FutureWarning:

DataFrameGroupBy.apply operated on the grouping columns. This behavior is deprecated, and in a future version of pandas the grouping columns will be excluded from the operation. Either pass `include_groups=False` to exclude the groupings or explicitly select the grouping columns after groupby to silence this warning.

/workspace/vidigi/prep.py:281: FutureWarning:

DataFrameGroupBy.apply operated on the grouping columns. This behavior is deprecated, and in a future version of pandas the grouping columns will be excluded from the operation. Either pass `include_groups=False` to exclude the groupings or explicitly select the grouping columns after groupby to silence this warning.

/workspace/vidigi/prep.py:281: FutureWarning:

DataFrameGroupBy.apply operated on the grouping columns. This behavior is deprecated, and in a future version of pandas the grouping columns will be excluded from the operation. Either pass `include_groups=False` to exclude the groupings or explicitly select the grouping columns after groupby to silence this warning.

/workspace/vidigi/prep.py:281: FutureWarning:

DataFrameGroupBy.apply operated on the grouping columns. This behavior is deprecated, and in a future version of pandas the grouping columns will be excluded from the operation. Either pass `include_groups=False` to exclude the groupings or explicitly select the grouping columns after groupby to silence this warning.

/workspace/vidigi/prep.py:281: FutureWarning:

DataFrameGroupBy.apply operated on the grouping columns. This behavior is deprecated, and in a future version of pandas the grouping columns will be excluded from the operation. Either pass `include_groups=False` to exclude the groupings or explicitly select the grouping columns after groupby to silence this warning.

/workspace/vidigi/prep.py:281: FutureWarning:

DataFrameGroupBy.apply operated on the grouping columns. This behavior is deprecated, and in a future version of pandas the grouping columns will be excluded from the operation. Either pass `include_groups=False` to exclude the groupings or explicitly select the grouping columns after groupby to silence this warning.

/workspace/vidigi/prep.py:281: FutureWarning:

DataFrameGroupBy.apply operated on the grouping columns. This behavior is deprecated, and in a future version of pandas the grouping columns will be excluded from the operation. Either pass `include_groups=False` to exclude the groupings or explicitly select the grouping columns after groupby to silence this warning.

/workspace/vidigi/prep.py:281: FutureWarning:

DataFrameGroupBy.apply operated on the grouping columns. This behavior is deprecated, and in a future version of pandas the grouping columns will be excluded from the operation. Either pass `include_groups=False` to exclude the groupings or explicitly select the grouping columns after groupby to silence this warning.

/workspace/vidigi/prep.py:281: FutureWarning:

DataFrameGroupBy.apply operated on the grouping columns. This behavior is deprecated, and in a future version of pandas the grouping columns will be excluded from the operation. Either pass `include_groups=False` to exclude the groupings or explicitly select the grouping columns after groupby to silence this warning.

/workspace/vidigi/prep.py:281: FutureWarning:

DataFrameGroupBy.apply operated on the grouping columns. This behavior is deprecated, and in a future version of pandas the grouping columns will be excluded from the operation. Either pass `include_groups=False` to exclude the groupings or explicitly select the grouping columns after groupby to silence this warning.

/workspace/vidigi/prep.py:281: FutureWarning:

DataFrameGroupBy.apply operated on the grouping columns. This behavior is deprecated, and in a future version of pandas the grouping columns will be excluded from the operation. Either pass `include_groups=False` to exclude the groupings or explicitly select the grouping columns after groupby to silence this warning.

/workspace/vidigi/prep.py:281: FutureWarning:

DataFrameGroupBy.apply operated on the grouping columns. This behavior is deprecated, and in a future version of pandas the grouping columns will be excluded from the operation. Either pass `include_groups=False` to exclude the groupings or explicitly select the grouping columns after groupby to silence this warning.

/workspace/vidigi/prep.py:281: FutureWarning:

DataFrameGroupBy.apply operated on the grouping columns. This behavior is deprecated, and in a future version of pandas the grouping columns will be excluded from the operation. Either pass `include_groups=False` to exclude the groupings or explicitly select the grouping columns after groupby to silence this warning.

/workspace/vidigi/prep.py:281: FutureWarning:

DataFrameGroupBy.apply operated on the grouping columns. This behavior is deprecated, and in a future version of pandas the grouping columns will be excluded from the operation. Either pass `include_groups=False` to exclude the groupings or explicitly select the grouping columns after groupby to silence this warning.

/workspace/vidigi/prep.py:281: FutureWarning:

DataFrameGroupBy.apply operated on the grouping columns. This behavior is deprecated, and in a future version of pandas the grouping columns will be excluded from the operation. Either pass `include_groups=False` to exclude the groupings or explicitly select the grouping columns after groupby to silence this warning.

/workspace/vidigi/prep.py:281: FutureWarning:

DataFrameGroupBy.apply operated on the grouping columns. This behavior is deprecated, and in a future version of pandas the grouping columns will be excluded from the operation. Either pass `include_groups=False` to exclude the groupings or explicitly select the grouping columns after groupby to silence this warning.

/workspace/vidigi/prep.py:281: FutureWarning:

DataFrameGroupBy.apply operated on the grouping columns. This behavior is deprecated, and in a future version of pandas the grouping columns will be excluded from the operation. Either pass `include_groups=False` to exclude the groupings or explicitly select the grouping columns after groupby to silence this warning.

/workspace/vidigi/prep.py:281: FutureWarning:

DataFrameGroupBy.apply operated on the grouping columns. This behavior is deprecated, and in a future version of pandas the grouping columns will be excluded from the operation. Either pass `include_groups=False` to exclude the groupings or explicitly select the grouping columns after groupby to silence this warning.

/workspace/vidigi/prep.py:281: FutureWarning:

DataFrameGroupBy.apply operated on the grouping columns. This behavior is deprecated, and in a future version of pandas the grouping columns will be excluded from the operation. Either pass `include_groups=False` to exclude the groupings or explicitly select the grouping columns after groupby to silence this warning.

/workspace/vidigi/prep.py:281: FutureWarning:

DataFrameGroupBy.apply operated on the grouping columns. This behavior is deprecated, and in a future version of pandas the grouping columns will be excluded from the operation. Either pass `include_groups=False` to exclude the groupings or explicitly select the grouping columns after groupby to silence this warning.

/workspace/vidigi/prep.py:281: FutureWarning:

DataFrameGroupBy.apply operated on the grouping columns. This behavior is deprecated, and in a future version of pandas the grouping columns will be excluded from the operation. Either pass `include_groups=False` to exclude the groupings or explicitly select the grouping columns after groupby to silence this warning.

/workspace/vidigi/prep.py:281: FutureWarning:

DataFrameGroupBy.apply operated on the grouping columns. This behavior is deprecated, and in a future version of pandas the grouping columns will be excluded from the operation. Either pass `include_groups=False` to exclude the groupings or explicitly select the grouping columns after groupby to silence this warning.

/workspace/vidigi/prep.py:281: FutureWarning:

DataFrameGroupBy.apply operated on the grouping columns. This behavior is deprecated, and in a future version of pandas the grouping columns will be excluded from the operation. Either pass `include_groups=False` to exclude the groupings or explicitly select the grouping columns after groupby to silence this warning.

/workspace/vidigi/prep.py:281: FutureWarning:

DataFrameGroupBy.apply operated on the grouping columns. This behavior is deprecated, and in a future version of pandas the grouping columns will be excluded from the operation. Either pass `include_groups=False` to exclude the groupings or explicitly select the grouping columns after groupby to silence this warning.

/workspace/vidigi/prep.py:281: FutureWarning:

DataFrameGroupBy.apply operated on the grouping columns. This behavior is deprecated, and in a future version of pandas the grouping columns will be excluded from the operation. Either pass `include_groups=False` to exclude the groupings or explicitly select the grouping columns after groupby to silence this warning.

/workspace/vidigi/prep.py:281: FutureWarning:

DataFrameGroupBy.apply operated on the grouping columns. This behavior is deprecated, and in a future version of pandas the grouping columns will be excluded from the operation. Either pass `include_groups=False` to exclude the groupings or explicitly select the grouping columns after groupby to silence this warning.

/workspace/vidigi/prep.py:281: FutureWarning:

DataFrameGroupBy.apply operated on the grouping columns. This behavior is deprecated, and in a future version of pandas the grouping columns will be excluded from the operation. Either pass `include_groups=False` to exclude the groupings or explicitly select the grouping columns after groupby to silence this warning.

/workspace/vidigi/prep.py:281: FutureWarning:

DataFrameGroupBy.apply operated on the grouping columns. This behavior is deprecated, and in a future version of pandas the grouping columns will be excluded from the operation. Either pass `include_groups=False` to exclude the groupings or explicitly select the grouping columns after groupby to silence this warning.

/workspace/vidigi/prep.py:281: FutureWarning:

DataFrameGroupBy.apply operated on the grouping columns. This behavior is deprecated, and in a future version of pandas the grouping columns will be excluded from the operation. Either pass `include_groups=False` to exclude the groupings or explicitly select the grouping columns after groupby to silence this warning.

/workspace/vidigi/prep.py:281: FutureWarning:

DataFrameGroupBy.apply operated on the grouping columns. This behavior is deprecated, and in a future version of pandas the grouping columns will be excluded from the operation. Either pass `include_groups=False` to exclude the groupings or explicitly select the grouping columns after groupby to silence this warning.

/workspace/vidigi/prep.py:281: FutureWarning:

DataFrameGroupBy.apply operated on the grouping columns. This behavior is deprecated, and in a future version of pandas the grouping columns will be excluded from the operation. Either pass `include_groups=False` to exclude the groupings or explicitly select the grouping columns after groupby to silence this warning.

/workspace/vidigi/prep.py:281: FutureWarning:

DataFrameGroupBy.apply operated on the grouping columns. This behavior is deprecated, and in a future version of pandas the grouping columns will be excluded from the operation. Either pass `include_groups=False` to exclude the groupings or explicitly select the grouping columns after groupby to silence this warning.

/workspace/vidigi/prep.py:281: FutureWarning:

DataFrameGroupBy.apply operated on the grouping columns. This behavior is deprecated, and in a future version of pandas the grouping columns will be excluded from the operation. Either pass `include_groups=False` to exclude the groupings or explicitly select the grouping columns after groupby to silence this warning.

/workspace/vidigi/prep.py:281: FutureWarning:

DataFrameGroupBy.apply operated on the grouping columns. This behavior is deprecated, and in a future version of pandas the grouping columns will be excluded from the operation. Either pass `include_groups=False` to exclude the groupings or explicitly select the grouping columns after groupby to silence this warning.

/workspace/vidigi/prep.py:281: FutureWarning:

DataFrameGroupBy.apply operated on the grouping columns. This behavior is deprecated, and in a future version of pandas the grouping columns will be excluded from the operation. Either pass `include_groups=False` to exclude the groupings or explicitly select the grouping columns after groupby to silence this warning.

/workspace/vidigi/prep.py:281: FutureWarning:

DataFrameGroupBy.apply operated on the grouping columns. This behavior is deprecated, and in a future version of pandas the grouping columns will be excluded from the operation. Either pass `include_groups=False` to exclude the groupings or explicitly select the grouping columns after groupby to silence this warning.

/workspace/vidigi/prep.py:281: FutureWarning:

DataFrameGroupBy.apply operated on the grouping columns. This behavior is deprecated, and in a future version of pandas the grouping columns will be excluded from the operation. Either pass `include_groups=False` to exclude the groupings or explicitly select the grouping columns after groupby to silence this warning.

/workspace/vidigi/prep.py:281: FutureWarning:

DataFrameGroupBy.apply operated on the grouping columns. This behavior is deprecated, and in a future version of pandas the grouping columns will be excluded from the operation. Either pass `include_groups=False` to exclude the groupings or explicitly select the grouping columns after groupby to silence this warning.

/workspace/vidigi/prep.py:281: FutureWarning:

DataFrameGroupBy.apply operated on the grouping columns. This behavior is deprecated, and in a future version of pandas the grouping columns will be excluded from the operation. Either pass `include_groups=False` to exclude the groupings or explicitly select the grouping columns after groupby to silence this warning.

/workspace/vidigi/prep.py:281: FutureWarning:

DataFrameGroupBy.apply operated on the grouping columns. This behavior is deprecated, and in a future version of pandas the grouping columns will be excluded from the operation. Either pass `include_groups=False` to exclude the groupings or explicitly select the grouping columns after groupby to silence this warning.

/workspace/vidigi/prep.py:281: FutureWarning:

DataFrameGroupBy.apply operated on the grouping columns. This behavior is deprecated, and in a future version of pandas the grouping columns will be excluded from the operation. Either pass `include_groups=False` to exclude the groupings or explicitly select the grouping columns after groupby to silence this warning.

/workspace/vidigi/prep.py:281: FutureWarning:

DataFrameGroupBy.apply operated on the grouping columns. This behavior is deprecated, and in a future version of pandas the grouping columns will be excluded from the operation. Either pass `include_groups=False` to exclude the groupings or explicitly select the grouping columns after groupby to silence this warning.

/workspace/vidigi/prep.py:281: FutureWarning:

DataFrameGroupBy.apply operated on the grouping columns. This behavior is deprecated, and in a future version of pandas the grouping columns will be excluded from the operation. Either pass `include_groups=False` to exclude the groupings or explicitly select the grouping columns after groupby to silence this warning.

/workspace/vidigi/prep.py:281: FutureWarning:

DataFrameGroupBy.apply operated on the grouping columns. This behavior is deprecated, and in a future version of pandas the grouping columns will be excluded from the operation. Either pass `include_groups=False` to exclude the groupings or explicitly select the grouping columns after groupby to silence this warning.

/workspace/vidigi/prep.py:281: FutureWarning:

DataFrameGroupBy.apply operated on the grouping columns. This behavior is deprecated, and in a future version of pandas the grouping columns will be excluded from the operation. Either pass `include_groups=False` to exclude the groupings or explicitly select the grouping columns after groupby to silence this warning.

/workspace/vidigi/prep.py:281: FutureWarning:

DataFrameGroupBy.apply operated on the grouping columns. This behavior is deprecated, and in a future version of pandas the grouping columns will be excluded from the operation. Either pass `include_groups=False` to exclude the groupings or explicitly select the grouping columns after groupby to silence this warning.

/workspace/vidigi/prep.py:281: FutureWarning:

DataFrameGroupBy.apply operated on the grouping columns. This behavior is deprecated, and in a future version of pandas the grouping columns will be excluded from the operation. Either pass `include_groups=False` to exclude the groupings or explicitly select the grouping columns after groupby to silence this warning.

/workspace/vidigi/prep.py:281: FutureWarning:

DataFrameGroupBy.apply operated on the grouping columns. This behavior is deprecated, and in a future version of pandas the grouping columns will be excluded from the operation. Either pass `include_groups=False` to exclude the groupings or explicitly select the grouping columns after groupby to silence this warning.

/workspace/vidigi/prep.py:281: FutureWarning:

DataFrameGroupBy.apply operated on the grouping columns. This behavior is deprecated, and in a future version of pandas the grouping columns will be excluded from the operation. Either pass `include_groups=False` to exclude the groupings or explicitly select the grouping columns after groupby to silence this warning.

/workspace/vidigi/prep.py:281: FutureWarning:

DataFrameGroupBy.apply operated on the grouping columns. This behavior is deprecated, and in a future version of pandas the grouping columns will be excluded from the operation. Either pass `include_groups=False` to exclude the groupings or explicitly select the grouping columns after groupby to silence this warning.

/workspace/vidigi/prep.py:281: FutureWarning:

DataFrameGroupBy.apply operated on the grouping columns. This behavior is deprecated, and in a future version of pandas the grouping columns will be excluded from the operation. Either pass `include_groups=False` to exclude the groupings or explicitly select the grouping columns after groupby to silence this warning.

/workspace/vidigi/prep.py:281: FutureWarning:

DataFrameGroupBy.apply operated on the grouping columns. This behavior is deprecated, and in a future version of pandas the grouping columns will be excluded from the operation. Either pass `include_groups=False` to exclude the groupings or explicitly select the grouping columns after groupby to silence this warning.

/workspace/vidigi/prep.py:281: FutureWarning:

DataFrameGroupBy.apply operated on the grouping columns. This behavior is deprecated, and in a future version of pandas the grouping columns will be excluded from the operation. Either pass `include_groups=False` to exclude the groupings or explicitly select the grouping columns after groupby to silence this warning.

/workspace/vidigi/prep.py:281: FutureWarning:

DataFrameGroupBy.apply operated on the grouping columns. This behavior is deprecated, and in a future version of pandas the grouping columns will be excluded from the operation. Either pass `include_groups=False` to exclude the groupings or explicitly select the grouping columns after groupby to silence this warning.

/workspace/vidigi/prep.py:281: FutureWarning:

DataFrameGroupBy.apply operated on the grouping columns. This behavior is deprecated, and in a future version of pandas the grouping columns will be excluded from the operation. Either pass `include_groups=False` to exclude the groupings or explicitly select the grouping columns after groupby to silence this warning.

Iteration through time-unit-by-time-unit logs complete 10:29:01
Snapshot df concatenation complete at 10:29:01
Reshaped animation dataframe finished construction at 10:29:01
full_patient_df_plus_pos = generate_animation_df(
                            full_entity_df=full_patient_df,
                            entity_col_name="patient",
                            event_position_df=event_position_df,
                            wrap_queues_at=20,
                            wrap_resources_at=40,
                            step_snapshot_max=50,
                            gap_between_entities=20,
                            gap_between_resources=20,
                            gap_between_queue_rows=175,
                            gap_between_resource_rows=175,
                            debug_mode=debug_mode
                    )
Placement dataframe started construction at 10:29:01
Placement dataframe finished construction at 10:29:01
/tmp/ipykernel_881/4097784259.py:1: UserWarning:

`step_snapshot_max` is not a multiple of `wrap_queues_at`.The animation will display better if this is resolved.

def set_icon(row):
    if row["surgery type"] == "p_knee":
        return "🦵<br>1️⃣<br> "
    elif row["surgery type"] == "r_knee":
        return "🦵<br>♻️<br> "
    elif row["surgery type"] == "p_hip":
        return "🕺<br>1️⃣<br> "
    elif row["surgery type"] == "r_hip":
        return "🕺<br>♻️<br> "
    elif row["surgery type"] == "uni_knee":
        return "🦵<br>✳️<br> "
    else:
        return f"CHECK<br>{row['icon']}"

full_patient_df_plus_pos = full_patient_df_plus_pos.assign(icon=full_patient_df_plus_pos.apply(set_icon, axis=1))

# TODO: Check why this doesn't seem to be working quite right for the 'discharged after stay'
# step. e.g. 194Primary is discharged on 28th July showing a LOS of 1 but prior to this shows a LOS of 9.
def add_los_to_icon(row):
    if row["event"] == "post_surgery_stay_begins":
        return f'{row["icon"]}<br><br>{row["snapshot_time"]-row["time"]:.0f}'
    elif row["event"] == "discharged_after_stay":
        return f'{row["icon"]}<br>{row["los"]:.0f}'
    else:
        return row["icon"]

full_patient_df_plus_pos = full_patient_df_plus_pos.assign(icon=full_patient_df_plus_pos.apply(add_los_to_icon, axis=1))


def indicate_delay_via_icon(row):
    if row["delayed discharge"] is True:
        return f'{row["icon"]}<br>*'
    else:
        return f'{row["icon"]}<br> '

full_patient_df_plus_pos = full_patient_df_plus_pos.assign(icon=full_patient_df_plus_pos.apply(indicate_delay_via_icon, axis=1))

cancelled_due_to_no_bed_available = len(full_log_with_patient_details[full_log_with_patient_details['event'] == "no_bed_available"]["patient"].unique())
total_patients = len(full_log_with_patient_details["patient"].unique())

cancelled_perc = cancelled_due_to_no_bed_available/total_patients

# st.markdown(f"Surgeries cancelled due to no bed being available in time: {cancelled_perc:.2%} ({cancelled_due_to_no_bed_available} of {total_patients})")

# st.markdown(
#     """
#     **Key**:

#     🦵1️⃣: Primary Knee

#     🦵♻️: Revision Knee

#     🕺1️⃣: Primary Hip

#     🕺♻️: Revision Hip

#     🦵✳️: Primary Unicompartment Knee

#     An asterisk (*) indicates that the patient has a delayed discharge from the ward.

#     The numbers below patients indicate their length of stay.

#     Note that the "No Bed Available: Surgery Cancelled" and "Discharged from Hospital after Recovery" stages in the animation are lagged by one day.
#     For example, on the 2nd of July, this will show the patients who had their surgery cancelled on 1st July or were discharged on 1st July.
#     These steps are included to make it easier to understand the destinations of different clients, but due to the size of the simulation step shown (1 day) it is difficult to demonstrate this differently.
#     """
# )
counts_not_avail = full_patient_df_plus_pos[full_patient_df_plus_pos['event']=='no_bed_available'][['snapshot_time','patient']].groupby('snapshot_time').agg('count')
counts_not_avail = counts_not_avail.reset_index().merge(full_patient_df_plus_pos[['snapshot_time']].drop_duplicates(), how='right').sort_values('snapshot_time')
counts_not_avail['patient'] = counts_not_avail['patient'].fillna(0)
counts_not_avail['running_total'] = counts_not_avail['patient'].cumsum()

counts_not_avail = counts_not_avail.reset_index(drop=True)

counts_not_avail
snapshot_time patient running_total
0 0 0.0 0.0
1 1 0.0 0.0
2 2 0.0 0.0
3 3 6.0 6.0
4 4 15.0 21.0
... ... ... ...
56 56 0.0 308.0
57 57 0.0 308.0
58 58 8.0 316.0
59 59 8.0 324.0
60 60 8.0 332.0

61 rows × 3 columns


counts_ops_completed = full_patient_df_plus_pos[full_patient_df_plus_pos['event']=='post_surgery_stay_begins'][['snapshot_time','patient']].drop_duplicates('patient').groupby('snapshot_time').agg('count')
counts_ops_completed = counts_ops_completed.reset_index().merge(full_patient_df_plus_pos[['snapshot_time']].drop_duplicates(), how='right').sort_values('snapshot_time')
counts_ops_completed['patient'] = counts_ops_completed['patient'].fillna(0)
counts_ops_completed['running_total'] = counts_ops_completed['patient'].cumsum()

counts_ops_completed = counts_ops_completed.reset_index(drop=True)

counts_ops_completed
snapshot_time patient running_total
0 0 13.0 13.0
1 1 16.0 29.0
2 2 9.0 38.0
3 3 3.0 41.0
4 4 2.0 43.0
... ... ... ...
56 56 12.0 348.0
57 57 5.0 353.0
58 58 4.0 357.0
59 59 8.0 365.0
60 60 6.0 371.0

61 rows × 3 columns

counts_not_avail = counts_not_avail.merge(counts_ops_completed.rename(columns={'running_total':'completed'}), how="left", on="snapshot_time")
counts_not_avail['perc_slots_lost'] = counts_not_avail['running_total'] / (counts_not_avail['running_total'] + counts_not_avail['completed'])

counts_not_avail = counts_not_avail.reset_index(drop=True)

counts_not_avail
snapshot_time patient_x running_total patient_y completed perc_slots_lost
0 0 0.0 0.0 13.0 13.0 0.000000
1 1 0.0 0.0 16.0 29.0 0.000000
2 2 0.0 0.0 9.0 38.0 0.000000
3 3 6.0 6.0 3.0 41.0 0.127660
4 4 15.0 21.0 2.0 43.0 0.328125
... ... ... ... ... ... ...
56 56 0.0 308.0 12.0 348.0 0.469512
57 57 0.0 308.0 5.0 353.0 0.465961
58 58 8.0 316.0 4.0 357.0 0.469539
59 59 8.0 324.0 8.0 365.0 0.470247
60 60 8.0 332.0 6.0 371.0 0.472262

61 rows × 6 columns

fig = generate_animation(
        full_entity_df_plus_pos=full_patient_df_plus_pos,
        entity_col_name="patient",
        event_position_df=event_position_df,
        scenario=args,
        plotly_height=750,
        plotly_width=1000,
        override_x_max=1000,
        override_y_max=700,
        entity_icon_size=11,
        resource_icon_size=13,
        text_size=14,
        wrap_resources_at=40,
        gap_between_resources=20,
        include_play_button=True,
        add_background_image=None,
        # we want the stage labels, but due to a bug
        # when we add in additional animated traces later,
        # they will disappear - so better to leave them out here
        # and then re-add them manually
        display_stage_labels=True,
        custom_resource_icon="🛏️",
        time_display_units="d",
        simulation_time_unit="days",
        start_date="2022-06-27",
        setup_mode=False,
        frame_duration=1500, #milliseconds
        frame_transition_duration=1000, #milliseconds
        debug_mode=False
    )

fig
/workspace/vidigi/animation.py:314: FutureWarning:

The 'unit' keyword in TimedeltaIndex construction is deprecated and will be removed in a future version. Use pd.to_timedelta instead.

# Set up the desired subplot layout
ROWS = 4

sp = make_subplots(
    rows=ROWS,
    cols=1,
    row_heights=[0.75, 0.05, 0.05, 0.15],
    vertical_spacing=0.05,
    subplot_titles=(
        "", # Original Animation
        "", # Completed Operations
        "", # Lost Slot Cumulative Counts
        "" # Daily Lost Slots Plot
        )
    )

# Overwrite the domain of our original x and y axis with domain from the new axis
fig.layout['xaxis']['domain'] = sp.layout['xaxis']['domain']
fig.layout['yaxis']['domain'] = sp.layout['yaxis']['domain']

for i in range(2, ROWS+1):

    # Add in the attributes for the secondary axis from our subplot
    fig.layout[f'xaxis{i}'] = sp.layout[f'xaxis{i}']
    fig.layout[f'yaxis{i}'] = sp.layout[f'yaxis{i}']

# Final key step - copy over the _grid_ref attribute
# This isn't meant to be something we modify but it's an essential
# part of the subplot code because otherwise plotly doesn't truly know
# how the different subplots are arranged and referenced
fig._grid_ref = sp._grid_ref

fig.update_layout(
    xaxis2=dict(
        showgrid=False,
        zeroline=False,
        showline=False,
        showticklabels=False,
    ),
    yaxis2=dict(
        showgrid=False,
        zeroline=False,
        showline=False,
        showticklabels=False,
    ),
    xaxis3=dict(
        showgrid=False,
        zeroline=False,
        showline=False,
        showticklabels=False,
    ),
    yaxis3=dict(
        showgrid=False,
        zeroline=False,
        showline=False,
        showticklabels=False,
    ),
    xaxis4=dict(
        showticklabels=False
    )
)
print(len(fig.data))
3
#####################################################
# Adding additional animation traces
#####################################################

#####################################################
# Initialize static and animated traces
#####################################################

## First, add each trace so it will show up initially

# Plotly requires that all traces that will appear in animation frames are first
# defined in `fig.data`. Otherwise, they appear to "fly in" from undefined positions,
# or exhibit flickering due to missing interpolation references.

# We add each trace in order, with placeholder data and correct styling,
# so the animation engine has full knowledge of the traces from the outset.

# Due to issues detailed in the following SO threads, it's essential to initialize the traces
# outside of the frames argument else they will not show up at all (or show up intermittently)
# https://stackoverflow.com/questions/69867334/multiple-traces-per-animation-frame-in-plotly
# https://stackoverflow.com/questions/69367344/plotly-animating-a-variable-number-of-traces-in-each-frame-in-r
# TODO: More explanation and investigation needed of why sometimes traces do and don't show up after being added in
# via this method. Behaviour seems very inconsistent and not always logical (e.g. order you put traces in to the later
# loop sometimes seems to make a difference but sometimes doesn't; making initial trace transparent sometimes seems to
# stop it showing up when added in the frames but not always; sometimes the initial trace doesn't disappear).

# First, extract the trace containing the resource icons
position_label_trace = fig.data[1]
icon_trace = fig.data[2]

# Now keep our figure data as just the initial trace.
fig.data = (fig.data[0],)

# 1. BED ICONS TRACE
# Readd the bed icons trace in a consistent manner
# Confusingly, when we start messing with the naimation frames, we lose the bed/resource icon trace
# even though it appeared fine until this point - so we have to handle it here
fig.add_trace(icon_trace)

print(f"Length after adding bed trace: {len(fig.data)}")

# 2. EVENT LABELS (static position text, but added dynamically per frame to avoid disappearing)
# This is a similar thing to the fig labels - except we never added them in the first place!
# Add trace for the event labels (as these get lost from the animation once we start trying to add other things in,
# so need manually re-adding)
# fig.add_trace(go.Scatter(
#         x=[pos+10 for pos in event_position_df['x'].to_list()],
#         y=event_position_df['y'].to_list(),
#         mode="text",
#         name="",
#         text=event_position_df['label'].to_list(),
#         textposition="middle right",
#         hoverinfo='none'
#     ))

fig.add_trace(position_label_trace)

# Finally, match the font size for the position labels
fig.data[-1].textfont.size

print(f"Length after adding 'position labels:' trace: {len(fig.data)}")

# 3. OPERATIONS COMPLETED TEXT (animated text annotation)
# Add animated text trace that gives running total of operations completed
fig.add_trace(go.Scatter(
                x=[5],
                y=[10],
                # text="",
                text=f"Operations Completed: {int(counts_ops_completed['running_total'][0])}",
                mode='text',
                textposition="middle left",
                textfont=dict(size=20),
                # opacity=0,
                showlegend=False,
                xaxis="x2",
                yaxis="y2"
        ), row=2, col=1)

print(f"Length after adding 'operations completed:' trace: {len(fig.data)}")

# 4. SLOTS LOST TEXT (animated text annotation)
# Add animated trace giving running total of slots lost and percentage of total slots this represents
fig.add_trace(go.Scatter(
    x=[5],
    y=[10],
    # text="",
    text=f"Total slots lost: {int(counts_not_avail['running_total'][0])} ({counts_not_avail['perc_slots_lost'][0]:.1%})",
    mode='text',
    textfont=dict(size=20),
    # opacity=0,
    showlegend=False,
    textposition="middle left",
    xaxis="x3",
    yaxis="y3"
), row=3, col=1)

print(f"Length after adding 'slots lost:' trace: {len(fig.data)}")


# # 5. LINE PLOT ON SECONDARY AXIS (animated line in subplot)
# Initialize with a single point and assign it to subplot axes (x2/y2)
fig.add_trace(go.Scatter(
    x=[counts_not_avail['snapshot_time'].iloc[0]],
    y=[counts_not_avail['patient_x'].iloc[0]],
    mode="lines",
    line=dict(color="rgba(255,0,0,1)"),  # semi-transparent initial
    showlegend=False,
    name="slots_lost_line",
    xaxis="x4",
    yaxis="y4"
    # We place it in our new subplot using the following line
), row=4, col=1)


# Add an initial trace to our secondary line chart
fig.add_trace(go.Scatter(
    x=counts_not_avail['snapshot_time'],
    y=counts_not_avail['patient_x'],
    mode='lines',
    showlegend=False,
    # name='line',
    opacity=0.2,
    xaxis="x4",
    yaxis="y4"
    # We place it in our new subplot using the following line
), row=4, col=1)

print(f"Length after adding additional line plot trace: {len(fig.data)}")
Length after adding bed trace: 2
Length after adding 'position labels:' trace: 3
Length after adding 'operations completed:' trace: 4
Length after adding 'slots lost:' trace: 5
Length after adding additional line plot trace: 7

##########################################################
# Define animation frames: one per simulation time step
##########################################################

##########################################################
# Now we need to add our traces to each individual frame
##########################################################
# IMPORTANT: To work correctly, these need to be provided in the same order as the traces above

# This includes:
# 0: bed icons
# 1: event labels
# 2: operations completed text
# 3: slots lost text
# 4: time series line in subplot

# # Now ensure we tell it which traces we are animating
# # (as per https://chart-studio.plotly.com/~empet/15243/animating-traces-in-subplotsbr/#/)
for i, frame in enumerate(fig.frames):
    # Your original frame.data
    # This will be a tuple
    # We'll ensure we only take the first entry
    # original_data = (frame.data[0], )

    original_data = frame.data

    # if i == 5:
    #     print(original_data)

    # The new data you want to add for this specific frame
    new_data = (
        # 0: bed icons
        icon_trace,

        # 1: Position labels
        go.Scatter(
            x=[pos+10 for pos in event_position_df['x'].to_list()],
            y=event_position_df['y'].to_list(),
            mode="text",
            text=event_position_df['label'].to_list(),
            textposition="middle right",
            hoverinfo='none',
            showlegend=False,
        ),

        # 2: Slots used/operations occurred
        go.Scatter(
            x=[5],
            y=[10],
            text=f"Operations Completed: {int(counts_ops_completed.sort_values('snapshot_time')['running_total'][i])}",
            mode='text',
            textposition="middle left",
            textfont=dict(size=20),
            showlegend=False,
            xaxis='x2',
            yaxis='y2'
        ),

        # 3: Slots lost
        go.Scatter(
            x=[5],
            y=[10],
            text=f"Total slots lost: {int(counts_not_avail.sort_values('snapshot_time')['running_total'][i])} ({counts_not_avail.sort_values('snapshot_time')['perc_slots_lost'][i]:.1%})",
            mode='text',
            textfont=dict(size=20),
            textposition="middle left",
            showlegend=False,
            xaxis='x3',
            yaxis='y3'
        ),

        # 4: Line subplot
        go.Scatter(
            x=counts_not_avail.sort_values('snapshot_time')['snapshot_time'][0: i+1].values,
            y=counts_not_avail.sort_values('snapshot_time')['patient_x'][0: i+1].values,
            mode="lines",
            showlegend=False,
            name="line_subplot",
            line=dict(color="rgba(255,0,0,1)"),  # semi-transparent initial
            xaxis='x4',
            yaxis='y4'
        ),
    )

    # print(f"Type of new data: {type(new_data)}")

    # Combine the original frame data with your new data
    frame.data = original_data + new_data

    # if i == 5:
    #     print(frame.data)

    # print(f"Type of final frame data: {type(frame.data)}")

# Finally, match the font size for the position labels
fig.data[2].textfont.size

fig
# After modifying the data in all frames, now correctly set the 'traces' property.

# Get the total number of animated traces from the first (now updated) frame.
num_total_traces = len(fig.frames[0].data)

# Create the list of indices that all traces will be mapped to.
# This should be [0, 1, 2, ..., n-1] where n is the total number of animated traces.
trace_indices = list(range(num_total_traces))

# Apply this correct list of indices to every frame.
for frame in fig.frames:
    frame.traces = trace_indices
fig
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