rpotter6298
616 lines
20 KiB
Python
616 lines
20 KiB
Python
"""
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Phase 5 explainability — confidence strips and head comparison.
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Works from saved prediction CSVs. If patient_id column is present (requires
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a re-run after the v3_hypertower.py update), points are colored by VFI
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severity group. Otherwise falls back to a single color per true class.
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VFI severity groups (VF_MD from clinical data):
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Early VF_MD > -6
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Moderate VF_MD -6 to -12
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Severe VF_MD < -12
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Produces (all in figures/explainability/):
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confidence_strips.png — vertical strip: P(glaucoma) by true class, VFI colored
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head_comparison.png — fused vs img vs md distributions side by side
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Usage:
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python -m v3.scripts.output_analysis.explainability.confidence_strips
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python -m v3.scripts.output_analysis.explainability.confidence_strips \
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--run phase5/logit_mlp_head --clinical-dir Papila/ClinicalData
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"""
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from __future__ import annotations
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import argparse
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from pathlib import Path
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import matplotlib
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matplotlib.use("Agg")
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import matplotlib.pyplot as plt
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import matplotlib.patches as mpatches
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import numpy as np
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import pandas as pd
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REPO_ROOT = Path(__file__).resolve().parents[4]
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RESULTS_ROOT = REPO_ROOT / "v3" / "results"
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FIGURES_ROOT = REPO_ROOT / "v3" / "figures"
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CLINICAL_DIR = REPO_ROOT / "Papila" / "ClinicalData"
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FONT = "DejaVu Sans"
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# Colour palette
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C_NORMAL = "#78909C" # blue-grey — healthy controls (no VFI staging)
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C_EARLY = "#29B6F6" # sky-blue — glaucoma, early VFI loss
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C_MODERATE = "#FFB300" # amber — glaucoma, moderate VFI loss
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C_SEVERE = "#E53935" # vivid red — glaucoma, severe VFI loss
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C_UNKNOWN = "#BDBDBD" # light grey — glaucoma, VFI not recorded
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SEV_LABELS = {
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"normal": "Normal",
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"early": "Glaucoma — early (VF_MD > −6)",
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"moderate": "Glaucoma — moderate (−12 to −6)",
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"severe": "Glaucoma — severe (VF_MD < −12)",
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"unknown": "Glaucoma — VF_MD not recorded",
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}
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SEV_COLORS = {
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"normal": C_NORMAL,
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"early": C_EARLY,
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"moderate": C_MODERATE,
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"severe": C_SEVERE,
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"unknown": C_UNKNOWN,
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}
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HEAD_COLORS = {"fused": "#d4a017", "img": "#4e8d3a", "md": "#4c72b0"}
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HEAD_LABELS = {
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"fused": "Fused head",
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"img": "Image-only head",
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"md": "Clinical-only head",
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}
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# ── VFI data ──────────────────────────────────────────────────────────────────
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def load_vfi(clinical_dir: Path) -> pd.DataFrame:
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"""Return DataFrame with columns [patient_id (int), vf_md (float), severity (str)].
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Only includes patients in the binary study (Diagnosis 0=Normal, 1=Glaucoma).
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"""
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od = pd.read_excel(clinical_dir / "patient_data_od.xlsx", header=1)
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os_ = pd.read_excel(clinical_dir / "patient_data_os.xlsx", header=1)
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def _clean(df, eye):
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df = df.copy()
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if "Patient ID" not in df.columns and "ID" in df.columns:
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df.rename(columns={"ID": "Patient ID"}, inplace=True)
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df["Patient ID"] = (
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df["Patient ID"].astype(str).str.extract(r"(\d+)")[0].astype(int)
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)
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df["Diagnosis"] = pd.to_numeric(df["Diagnosis"], errors="coerce")
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df["VF_MD"] = pd.to_numeric(df["VF_MD"], errors="coerce")
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# PAPILA: 0=Normal, 1=Glaucoma, 2=Suspect — keep only binary patients
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df = df[df["Diagnosis"].isin([0, 1])].copy()
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df["eye"] = eye
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return df[["Patient ID", "Diagnosis", "VF_MD", "eye"]]
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combined = pd.concat([_clean(od, "OD"), _clean(os_, "OS")], ignore_index=True)
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# Per patient: modal diagnosis, worst (most negative) VF_MD across eyes
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diag = (
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combined.groupby("Patient ID")["Diagnosis"]
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.agg(lambda x: x.mode().iloc[0])
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.reset_index()
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)
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vf = combined.groupby("Patient ID")["VF_MD"].min().reset_index()
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worst = diag.merge(vf, on="Patient ID").rename(
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columns={"Patient ID": "patient_id", "VF_MD": "vf_md", "Diagnosis": "diagnosis"}
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)
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def _severity(row):
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if int(row["diagnosis"]) == 0:
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return "normal" # healthy control — no VFI staging
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v = row["vf_md"]
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if pd.isna(v):
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return "unknown" # glaucoma, no VFI recorded
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if v > -6:
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return "early"
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if v > -12:
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return "moderate"
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return "severe"
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worst["severity"] = worst.apply(_severity, axis=1)
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return worst
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# ── Prediction loading ────────────────────────────────────────────────────────
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def load_all_predictions(
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run_dir: Path, tower_path: str = "binary/ensemble"
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) -> pd.DataFrame:
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"""Pool predictions_test.csv across all reps and folds."""
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rows = []
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for rep_dir in sorted(run_dir.glob("rep*")):
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tm_dir = rep_dir / tower_path
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if not tm_dir.exists():
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continue
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for fold_dir in sorted(tm_dir.glob("fold[0-9]")):
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csv_path = fold_dir / "predictions_test.csv"
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if not csv_path.exists():
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continue
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df = pd.read_csv(csv_path)
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df["rep"] = rep_dir.name
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df["fold"] = fold_dir.name
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rows.append(df)
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if not rows:
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raise FileNotFoundError(f"No predictions_test.csv found under {run_dir}")
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return pd.concat(rows, ignore_index=True)
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# ── Figure 1: Confidence strips (vertical) ───────────────────────────────────
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def make_confidence_strips(
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df: pd.DataFrame, vfi: pd.DataFrame | None, out_path: Path
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) -> None:
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"""
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Vertical strip plot: x = true class, y = P(glaucoma).
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Points colored by VFI severity if patient_id column available, else uniform.
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"""
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rng = np.random.default_rng(42)
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has_vfi = (
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vfi is not None
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and "patient_id" in df.columns
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and df["patient_id"].notna().any()
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)
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if has_vfi:
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df = df.copy()
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df["patient_id"] = pd.to_numeric(df["patient_id"], errors="coerce").astype(
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"Int64"
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)
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vfi_merge = vfi.copy()
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vfi_merge["patient_id"] = vfi_merge["patient_id"].astype("Int64")
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df = df.merge(
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vfi_merge[["patient_id", "severity"]], on="patient_id", how="left"
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)
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df["severity"] = df["severity"].fillna("unknown")
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else:
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df["severity"] = "unknown"
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fig, ax = plt.subplots(figsize=(6, 7))
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fig.patch.set_facecolor("#e8e8e8")
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ax.set_facecolor("#e8e8e8")
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x_pos = {0: 0.0, 1: 1.0}
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jitter_scale = 0.18
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# Draw in severity order so severe is on top
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sev_order = ["normal", "unknown", "early", "moderate", "severe"]
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sev_alpha = {
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"normal": 0.40,
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"early": 0.55,
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"moderate": 0.70,
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"severe": 0.85,
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"unknown": 0.35,
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}
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sev_size = {"normal": 6, "early": 8, "moderate": 10, "severe": 12, "unknown": 6}
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for sev in sev_order:
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mask = df["severity"] == sev
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if not mask.any():
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continue
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sub = df[mask]
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jitter = rng.uniform(-jitter_scale, jitter_scale, len(sub))
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x = np.array([x_pos[int(v)] for v in sub["y_true"]]) + jitter
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ax.scatter(
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x,
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sub["prob_fused_c1"].values,
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c=SEV_COLORS[sev],
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s=sev_size[sev],
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alpha=sev_alpha[sev],
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linewidths=0,
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zorder=3,
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label=SEV_LABELS[sev],
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)
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# Median lines per class
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for cls, xc in x_pos.items():
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med = np.median(df.loc[df["y_true"] == cls, "prob_fused_c1"])
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ax.plot(
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[xc - jitter_scale - 0.04, xc + jitter_scale + 0.04],
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[med, med],
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color="#222",
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lw=2.0,
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zorder=5,
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)
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ax.axhline(0.5, color="#888", lw=1.2, ls="--", alpha=0.7, zorder=2)
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ax.set_xticks([0, 1])
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ax.set_xticklabels(["Normal", "Glaucoma"], fontsize=11)
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ax.set_ylabel("Predicted P(Glaucoma)", fontsize=11)
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ax.set_ylim(-0.04, 1.04)
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ax.set_xlim(-0.55, 1.55)
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ax.set_title(
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"Confidence Strips — Fused Head\n(Phase 5, all folds)",
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fontsize=12,
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fontweight="bold",
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)
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ax.grid(axis="y", alpha=0.3, zorder=1)
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# Legend — only show groups that appear
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handles, labels = ax.get_legend_handles_labels()
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if handles:
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ax.legend(
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handles=handles,
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labels=labels,
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fontsize=8.5,
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loc="upper center",
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framealpha=0.75,
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ncol=2,
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)
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if not has_vfi:
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ax.text(
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0.98,
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0.02,
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"Re-run with updated v3_hypertower.py\nto enable VFI severity coloring",
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transform=ax.transAxes,
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ha="right",
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va="bottom",
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fontsize=7.5,
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color="#888",
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style="italic",
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)
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fig.tight_layout()
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out_path.parent.mkdir(parents=True, exist_ok=True)
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fig.savefig(out_path, dpi=180, bbox_inches="tight")
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plt.close(fig)
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print(f" Saved: {out_path}")
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# ── Figure 2: Head comparison ─────────────────────────────────────────────────
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def make_head_comparison(df: pd.DataFrame, out_path: Path) -> None:
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"""Side-by-side violin + strip of P(glaucoma) by true class for each head."""
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heads = ["fused", "img", "md"]
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prob_cols = {"fused": "prob_fused_c1", "img": "prob_img_c1", "md": "prob_md_c1"}
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rng = np.random.default_rng(42)
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fig, axes = plt.subplots(1, 3, figsize=(11, 4.5), sharey=True)
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fig.patch.set_facecolor("#e8e8e8")
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fig.suptitle(
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"Head Comparison — P(Glaucoma) by True Class (Phase 5, all folds)",
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fontsize=12,
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fontweight="bold",
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)
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c_normal = "#4c72b0"
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c_glaucoma = "#c44e52"
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for ax, head in zip(axes, heads):
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ax.set_facecolor("#e8e8e8")
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col = prob_cols[head]
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data_by_class = [df.loc[df["y_true"] == cls, col].values for cls in [0, 1]]
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vp = ax.violinplot(
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data_by_class,
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positions=[0, 1],
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widths=0.6,
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showmedians=True,
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showextrema=False,
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)
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for body, color in zip(vp["bodies"], [c_normal, c_glaucoma]):
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body.set_facecolor(color)
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body.set_alpha(0.35)
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vp["cmedians"].set_color("#222")
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vp["cmedians"].set_linewidth(2)
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for cls, color in zip([0, 1], [c_normal, c_glaucoma]):
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vals = data_by_class[cls]
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jitter = rng.uniform(-0.12, 0.12, len(vals))
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ax.scatter(
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cls + jitter, vals, color=color, s=4, alpha=0.30, linewidths=0, zorder=3
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)
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ax.axhline(0.5, color="#888", lw=1.0, ls="--", alpha=0.6)
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ax.set_xticks([0, 1])
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ax.set_xticklabels(["Normal", "Glaucoma"], fontsize=9)
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ax.set_title(
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HEAD_LABELS[head], fontsize=10, fontweight="bold", color=HEAD_COLORS[head]
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)
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ax.set_ylim(-0.05, 1.05)
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ax.grid(axis="y", alpha=0.3)
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if head == "fused":
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ax.set_ylabel("Predicted P(Glaucoma)", fontsize=10)
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from sklearn.metrics import roc_auc_score
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try:
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auc = roc_auc_score(df["y_true"], df[col])
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ax.text(
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0.97,
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0.04,
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f"AUC = {auc:.3f}",
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transform=ax.transAxes,
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ha="right",
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va="bottom",
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fontsize=9,
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color="#333",
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bbox=dict(facecolor="white", alpha=0.65, edgecolor="none", pad=2),
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)
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except Exception:
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pass
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fig.tight_layout()
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out_path.parent.mkdir(parents=True, exist_ok=True)
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fig.savefig(out_path, dpi=180, bbox_inches="tight")
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plt.close(fig)
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print(f" Saved: {out_path}")
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# ── Multi-model comparison strip ──────────────────────────────────────────────
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def make_comparison_strips(
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run_configs: list[dict], vfi: pd.DataFrame, out_path: Path
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) -> None:
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"""
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Side-by-side confidence strips for multiple runs.
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Each config: {"label": str, "df": DataFrame}.
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"""
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from sklearn.metrics import roc_auc_score
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rng = np.random.default_rng(42)
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n = len(run_configs)
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fig, axes = plt.subplots(1, n, figsize=(4.5 * n, 7), sharey=True)
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if n == 1:
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axes = [axes]
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fig.patch.set_facecolor("#e8e8e8")
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fig.suptitle(
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"Confidence Strips by Model (Phase 5, all folds)",
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fontsize=13,
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fontweight="bold",
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)
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sev_order = ["normal", "unknown", "early", "moderate", "severe"]
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sev_alpha = {
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"normal": 0.40,
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"early": 0.55,
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"moderate": 0.70,
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"severe": 0.85,
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"unknown": 0.35,
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}
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sev_size = {"normal": 6, "early": 8, "moderate": 10, "severe": 12, "unknown": 6}
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x_pos = {0: 0.0, 1: 1.0}
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jitter_scale = 0.18
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for ax, cfg in zip(axes, run_configs):
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ax.set_facecolor("#e8e8e8")
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df = cfg["df"]
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# Attach VFI severity
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df = df.copy()
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df["patient_id"] = pd.to_numeric(df["patient_id"], errors="coerce").astype(
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"Int64"
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)
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vfi_m = vfi.copy()
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vfi_m["patient_id"] = vfi_m["patient_id"].astype("Int64")
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df = df.merge(vfi_m[["patient_id", "severity"]], on="patient_id", how="left")
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df["severity"] = df["severity"].fillna("unknown")
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for sev in sev_order:
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mask = df["severity"] == sev
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if not mask.any():
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continue
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sub = df[mask]
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jitter = rng.uniform(-jitter_scale, jitter_scale, len(sub))
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x = np.array([x_pos[int(v)] for v in sub["y_true"]]) + jitter
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ax.scatter(
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x,
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sub["prob_fused_c1"].values,
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c=SEV_COLORS[sev],
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s=sev_size[sev],
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alpha=sev_alpha[sev],
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linewidths=0,
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zorder=3,
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)
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# IQR box + median line per class
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iqr_w = 0.06
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xticklabels = []
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for cls, xc in x_pos.items():
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vals = df.loc[df["y_true"] == cls, "prob_fused_c1"]
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med = np.median(vals)
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q25 = np.percentile(vals, 25)
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q75 = np.percentile(vals, 75)
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# Subtle translucent IQR box
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ax.add_patch(
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plt.Rectangle(
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(xc - iqr_w, q25),
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2 * iqr_w,
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q75 - q25,
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facecolor="#555",
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alpha=0.18,
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linewidth=0,
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zorder=4,
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)
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)
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# Median line
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ax.plot(
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[xc - jitter_scale - 0.04, xc + jitter_scale + 0.04],
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[med, med],
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color="#222",
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lw=2.0,
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zorder=5,
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label="Median" if cls == 0 else None,
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)
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# TP / TN rate below x-label
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if cls == 1:
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rate = (vals > 0.5).mean() * 100
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xticklabels.append(f"Glaucoma\nTP {rate:.0f}%")
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else:
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rate = (vals <= 0.5).mean() * 100
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xticklabels.append(f"Normal\nTN {rate:.0f}%")
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ax.axhline(0.5, color="#888", lw=1.2, ls="--", alpha=0.7, zorder=2)
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ax.set_xticks([0, 1])
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ax.set_xticklabels(xticklabels, fontsize=10)
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ax.set_title(cfg["label"], fontsize=11, fontweight="bold")
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ax.set_ylim(-0.04, 1.04)
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ax.set_xlim(-0.55, 1.55)
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ax.grid(axis="y", alpha=0.3, zorder=1)
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try:
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fold_aucs = [
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roc_auc_score(g["y_true"], g["prob_fused_c1"])
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for _, g in df.groupby(["rep", "fold"])
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if g["y_true"].nunique() > 1
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]
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mean_auc = np.mean(fold_aucs)
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std_auc = np.std(fold_aucs)
|
||
ax.text(
|
||
0.65,
|
||
0.0,
|
||
f"AUC = {mean_auc:.3f} ± {std_auc:.3f}",
|
||
transform=ax.transAxes,
|
||
ha="right",
|
||
va="bottom",
|
||
fontsize=9,
|
||
color="#333",
|
||
bbox=dict(facecolor="white", alpha=0.65, edgecolor="none", pad=2),
|
||
)
|
||
except Exception:
|
||
pass
|
||
|
||
axes[0].set_ylabel("Predicted P(Glaucoma)", fontsize=11)
|
||
|
||
# Shared legend
|
||
legend_patches = [
|
||
mpatches.Patch(color=SEV_COLORS[s], label=SEV_LABELS[s])
|
||
for s in ["normal", "early", "moderate", "severe", "unknown"]
|
||
]
|
||
fig.legend(
|
||
handles=legend_patches,
|
||
fontsize=9,
|
||
loc="lower center",
|
||
ncol=len(legend_patches),
|
||
framealpha=0.75,
|
||
bbox_to_anchor=(0.5, -0.02),
|
||
)
|
||
|
||
fig.tight_layout(rect=[0, 0.06, 1, 1])
|
||
out_path.parent.mkdir(parents=True, exist_ok=True)
|
||
fig.savefig(out_path, dpi=180, bbox_inches="tight")
|
||
plt.close(fig)
|
||
print(f" Saved: {out_path}")
|
||
|
||
|
||
# ── Main ──────────────────────────────────────────────────────────────────────
|
||
|
||
# Default runs shown in the comparison
|
||
DEFAULT_RUNS = [
|
||
{
|
||
"run": "phase4/single",
|
||
"tower_path": "binary/single",
|
||
"label": "Single HyperTower",
|
||
},
|
||
{
|
||
"run": "phase5/ensemble_fused",
|
||
"tower_path": "binary/ensemble",
|
||
"label": "Bilateral Ensemble",
|
||
},
|
||
{
|
||
"run": "phase5/logit_mlp_head",
|
||
"tower_path": "binary/ensemble",
|
||
"label": "Fused Head",
|
||
},
|
||
]
|
||
|
||
|
||
def _aggregate_eye_to_patient(df: pd.DataFrame) -> pd.DataFrame:
|
||
"""
|
||
Single-mode predictions are eye-level (2 rows per patient per fold).
|
||
In the test loader, OD rows come first (sorted patient ID order) then OS.
|
||
Average the two eyes to get one patient-level row per fold.
|
||
"""
|
||
rows = []
|
||
prob_cols = [c for c in df.columns if c.startswith("prob_")]
|
||
pred_cols = [c for c in df.columns if c.startswith("pred_")]
|
||
|
||
for (rep, fold), grp in df.groupby(["rep", "fold"]):
|
||
n = len(grp)
|
||
half = n // 2
|
||
od = grp.iloc[:half].reset_index(drop=True)
|
||
os_ = grp.iloc[half:].reset_index(drop=True)
|
||
pat = od.copy()
|
||
for col in prob_cols:
|
||
pat[col] = (od[col].values + os_[col].values) / 2
|
||
for col in pred_cols:
|
||
pat[col] = (pat[col.replace("pred_", "prob_") + "_c1"] >= 0.5).astype(int)
|
||
rows.append(pat)
|
||
|
||
return pd.concat(rows, ignore_index=True)
|
||
|
||
|
||
def _load_run(run: str, tower_path: str, clinical_dir: Path) -> pd.DataFrame:
|
||
run_dir = RESULTS_ROOT / run
|
||
print(f" Loading {run} ...")
|
||
df = load_all_predictions(run_dir, tower_path=tower_path)
|
||
if tower_path.endswith("/single"):
|
||
from v3.scripts.output_analysis.explainability.fold_patient_ids import (
|
||
attach_patient_ids_single,
|
||
)
|
||
|
||
df = attach_patient_ids_single(df, clinical_dir=clinical_dir, batch_size=8)
|
||
else:
|
||
from v3.scripts.output_analysis.explainability.fold_patient_ids import (
|
||
attach_patient_ids,
|
||
)
|
||
|
||
df = attach_patient_ids(df, clinical_dir=clinical_dir)
|
||
return df
|
||
|
||
|
||
def main():
|
||
ap = argparse.ArgumentParser(
|
||
description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter
|
||
)
|
||
ap.add_argument(
|
||
"--run", default="phase5/logit_mlp_head", help="Single run for standalone plots"
|
||
)
|
||
ap.add_argument("--tower-path", default="binary/ensemble")
|
||
ap.add_argument("--clinical-dir", type=Path, default=CLINICAL_DIR)
|
||
ap.add_argument("--out", type=Path, default=FIGURES_ROOT / "explainability")
|
||
args = ap.parse_args()
|
||
|
||
print("Loading VFI data ...")
|
||
vfi = load_vfi(args.clinical_dir)
|
||
|
||
# ── Single-run plots (strips + head comparison) ──────────────────────────
|
||
df = _load_run(args.run, args.tower_path, args.clinical_dir)
|
||
make_confidence_strips(df, vfi, args.out / "confidence_strips.png")
|
||
make_head_comparison(df, args.out / "head_comparison.png")
|
||
|
||
# ── Multi-model comparison ───────────────────────────────────────────────
|
||
print("Building comparison strips ...")
|
||
run_configs = []
|
||
for cfg in DEFAULT_RUNS:
|
||
try:
|
||
df_r = _load_run(cfg["run"], cfg["tower_path"], args.clinical_dir)
|
||
run_configs.append({"label": cfg["label"], "df": df_r})
|
||
except FileNotFoundError as e:
|
||
print(f" Skipping {cfg['run']}: {e}")
|
||
if run_configs:
|
||
make_comparison_strips(
|
||
run_configs, vfi, args.out / "confidence_strips_comparison.png"
|
||
)
|
||
|
||
|
||
if __name__ == "__main__":
|
||
main()
|