Initial commit before Ralph loop

2026-02-04 13:04:29 +00:00
commit fdd33a67af
89 changed files with 20660 additions and 0 deletions
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+"""
+Visualization package for patient pathway charts.
+
+This package contains functions for generating interactive Plotly visualizations:
+- plotly_generator: Create icicle charts for patient pathway analysis
+"""
+
+from visualization.plotly_generator import (
+    create_icicle_figure,
+    save_figure_html,
+    open_figure_in_browser,
+)
+
+__all__ = [
+    "create_icicle_figure",
+    "save_figure_html",
+    "open_figure_in_browser",
+]
@@ -0,0 +1,231 @@
+"""
+Plotly chart generation for patient pathway analysis.
+
+This module contains functions for creating interactive icicle charts
+that visualize patient treatment pathways. The charts display hierarchical
+data: Trust → Directory → Drug → Pathway.
+"""
+
+import webbrowser
+from typing import Optional
+
+import numpy as np
+import pandas as pd
+import plotly.graph_objects as go
+
+from core.logging_config import get_logger
+
+logger = get_logger(__name__)
+
+
+def create_icicle_figure(ice_df: pd.DataFrame, title: str) -> go.Figure:
+    """
+    Create Plotly icicle figure from prepared DataFrame.
+
+    This function generates an interactive icicle chart showing patient pathway
+    hierarchies with custom data including costs, dates, and treatment durations.
+
+    Args:
+        ice_df: DataFrame with columns:
+            - parents: Parent node in hierarchy
+            - ids: Unique identifier for each node
+            - labels: Display label for each node
+            - value: Number of patients
+            - colour: Color value for visualization
+            - cost: Total cost
+            - costpp: Cost per patient
+            - cost_pp_pa: Cost per patient per annum
+            - First seen: First intervention date
+            - Last seen: Last intervention date
+            - First seen (Parent): Earliest date in parent group
+            - Last seen (Parent): Latest date in parent group
+            - average_spacing: Formatted string with dosing information
+            - avg_days: Average treatment duration
+        title: Chart title
+
+    Returns:
+        Plotly Figure object ready for display or export
+    """
+    ice_df = ice_df.copy()
+    ice_df.sort_values(by=["labels"], ascending=True, inplace=True, ignore_index=True)
+
+    first_seen = ice_df["First seen"].astype(str).replace("NaT", "N/A").to_list()
+    last_seen = ice_df["Last seen"].astype(str).replace("NaT", "N/A").to_list()
+    first_seen_parent = ice_df["First seen (Parent)"].astype(str).to_list()
+    last_seen_parent = ice_df["Last seen (Parent)"].astype(str).to_list()
+    average_spacing = ice_df.average_spacing.astype(str).to_list()
+
+    fig = go.Figure(
+        go.Icicle(
+            labels=ice_df.labels,
+            ids=ice_df.ids,
+            parents=ice_df.parents,
+            customdata=np.stack(
+                (
+                    ice_df.value,
+                    ice_df.colour,
+                    ice_df.cost,
+                    ice_df.costpp,
+                    first_seen,
+                    last_seen,
+                    first_seen_parent,
+                    last_seen_parent,
+                    average_spacing,
+                    ice_df.cost_pp_pa,
+                ),
+                axis=1,
+            ),
+            values=ice_df.value,
+            branchvalues="total",
+            marker=dict(colors=ice_df.colour, colorscale="Viridis"),
+            maxdepth=3,
+            texttemplate="<b>%{label}</b> "
+            "<br><b>Total patients:</b> %{customdata[0]} (including children/further treatments)"
+            "<br><b>First seen:</b> %{customdata[4]}"
+            "<br><b>Last seen (including further treatments):</b> %{customdata[7]}"
+            "<br><b>Average treatment duration:</b> %{customdata[8]}"
+            "<br><b>Total cost:</b> £%{customdata[2]:.3~s}"
+            "<br><b>Average cost per patient:</b> £%{customdata[3]:.3~s}"
+            "<br><b>Average cost per patient per annum:</b> £%{customdata[9]:.3~s}",
+            hovertemplate="<b>%{label}</b>"
+            "<br><b>Total patients:</b> %{customdata[0]} - %{customdata[1]:.3p} of patients in level"
+            "<br><b>Total cost:</b> £%{customdata[2]:.3~s}"
+            "<br><b>Average cost per patient:</b> £%{customdata[3]:.3~s}"
+            "<br><b>Average cost per patient per annum:</b> £%{customdata[9]:.3~s}"
+            "<br><b>First seen:</b> %{customdata[4]}"
+            "<br><b>Last seen (including further treatments):</b> %{customdata[7]}"
+            "<br><b>Average treatment duration:</b>"
+            "%{customdata[8]}"
+            "<extra></extra>",
+        )
+    )
+    fig.update_traces(sort=False)
+    fig.update_layout(
+        margin=dict(t=60, l=1, r=1, b=60),
+        title=f"Norfolk & Waveney ICS high-cost drug patient pathways - {title}",
+        title_x=0.5,
+        hoverlabel=dict(font_size=16),
+    )
+
+    return fig
+
+
+def save_figure_html(
+    fig: go.Figure, save_dir: str, title: str, open_browser: bool = False
+) -> str:
+    """
+    Save Plotly figure to HTML file.
+
+    Args:
+        fig: Plotly Figure object
+        save_dir: Directory to save the HTML file
+        title: Title used for filename
+        open_browser: If True, open the file in the default browser
+
+    Returns:
+        Path to the saved HTML file
+    """
+    filepath = f"{save_dir}/{title}.html"
+    fig.write_html(filepath)
+    logger.info(f"Success! File saved to {filepath}")
+
+    if open_browser:
+        open_figure_in_browser(filepath)
+
+    return filepath
+
+
+def open_figure_in_browser(filepath: str) -> None:
+    """
+    Open an HTML file in the default browser.
+
+    Args:
+        filepath: Path to the HTML file
+    """
+    webbrowser.open_new_tab("file:///" + filepath)
+
+
+def figure_legacy(ice_df: pd.DataFrame, dir_string: str, save_dir: str) -> None:
+    """
+    Create and display icicle figure (legacy interface).
+
+    This function maintains backward compatibility with the original figure()
+    function signature. It creates the figure, saves it to HTML, and opens
+    it in the browser.
+
+    Args:
+        ice_df: DataFrame with chart data
+        dir_string: Title string (used for filename and chart title)
+        save_dir: Directory to save the HTML file
+
+    Note:
+        This function is provided for backward compatibility.
+        New code should use create_icicle_figure() + save_figure_html() instead.
+    """
+    # Handle avg_days column for display
+    ice_df = ice_df.copy()
+    ice_df.sort_values(by=["labels"], ascending=True, inplace=True, ignore_index=True)
+
+    first_seen = ice_df["First seen"].astype(str).replace("NaT", "N/A").to_list()
+    last_seen = ice_df["Last seen"].astype(str).replace("NaT", "N/A").to_list()
+    first_seen_parent = ice_df["First seen (Parent)"].astype(str).to_list()
+    last_seen_parent = ice_df["Last seen (Parent)"].astype(str).to_list()
+    average_spacing = ice_df.average_spacing.astype(str).to_list()
+    avg_seen = ice_df["avg_days"].dt.round("D").astype(str).replace("0 days", "N/A").to_list()
+
+    fig = go.Figure(
+        go.Icicle(
+            labels=ice_df.labels,
+            ids=ice_df.ids,
+            parents=ice_df.parents,
+            customdata=np.stack(
+                (
+                    ice_df.value,
+                    ice_df.colour,
+                    ice_df.cost,
+                    ice_df.costpp,
+                    first_seen,
+                    last_seen,
+                    first_seen_parent,
+                    last_seen_parent,
+                    average_spacing,
+                    ice_df.cost_pp_pa,
+                ),
+                axis=1,
+            ),
+            values=ice_df.value,
+            branchvalues="total",
+            marker=dict(colors=ice_df.colour, colorscale="Viridis"),
+            maxdepth=3,
+            texttemplate="<b>%{label}</b> "
+            "<br><b>Total patients:</b> %{customdata[0]} (including children/further treatments)"
+            "<br><b>First seen:</b> %{customdata[4]}"
+            "<br><b>Last seen (including further treatments):</b> %{customdata[7]}"
+            "<br><b>Average treatment duration:</b> %{customdata[8]}"
+            "<br><b>Total cost:</b> £%{customdata[2]:.3~s}"
+            "<br><b>Average cost per patient:</b> £%{customdata[3]:.3~s}"
+            "<br><b>Average cost per patient per annum:</b> £%{customdata[9]:.3~s}",
+            hovertemplate="<b>%{label}</b>"
+            "<br><b>Total patients:</b> %{customdata[0]} - %{customdata[1]:.3p} of patients in level"
+            "<br><b>Total cost:</b> £%{customdata[2]:.3~s}"
+            "<br><b>Average cost per patient:</b> £%{customdata[3]:.3~s}"
+            "<br><b>Average cost per patient per annum:</b> £%{customdata[9]:.3~s}"
+            "<br><b>First seen:</b> %{customdata[4]}"
+            "<br><b>Last seen (including further treatments):</b> %{customdata[7]}"
+            "<br><b>Average treatment duration:</b>"
+            "%{customdata[8]}"
+            "<extra></extra>",
+        )
+    )
+    fig.update_traces(sort=False)
+    fig.update_layout(
+        margin=dict(t=60, l=1, r=1, b=60),
+        title=f"Norfolk & Waveney ICS high-cost drug patient pathways - {dir_string}",
+        title_x=0.5,
+        hoverlabel=dict(font_size=16),
+    )
+
+    filepath = f"{save_dir}/{dir_string}.html"
+    fig.write_html(filepath)
+    logger.info(f"Success! File saved to {filepath}")
+    webbrowser.open_new_tab("file:///" + filepath)