pg-sui 0.2.0__py3-none-any.whl → 1.6.14.dev9__py3-none-any.whl

pgsui/utils/classification_viz.py

@@ -0,0 +1,608 @@
+# -*- coding: utf-8 -*-
+from __future__ import annotations
+
+from dataclasses import dataclass, field
+from typing import TYPE_CHECKING, Dict, List, Optional, Tuple, Union
+
+import matplotlib as mpl
+import matplotlib.pyplot as plt
+import numpy as np
+import pandas as pd
+import plotly.graph_objects as go
+import seaborn as sns
+from matplotlib.colors import LinearSegmentedColormap
+from mpl_toolkits.axes_grid1.inset_locator import inset_axes
+
+if TYPE_CHECKING:
+    from matplotlib.figure import Figure
+
+
+@dataclass
+class ClassificationReportVisualizer:
+    """Pretty plotting for scikit-learn classification reports (output_dict=True).
+
+    Adds neon cyberpunk aesthetics, a per-class support overlay, and optional bootstrap confidence intervals.
+
+    Attributes:
+        retro_palette: Hex colors for neon vibe.
+        background_hex: Matplotlib/Plotly dark background.
+        grid_hex: Gridline color for dark theme.
+        reset_kwargs: Keyword args for resetting Matplotlib rcParams.
+    """
+
+    retro_palette: List[str] = field(
+        default_factory=lambda: [
+            "#ff00ff",
+            "#9400ff",
+            "#00f0ff",
+            "#00ff9f",
+            "#ff6ec7",
+            "#7d00ff",
+            "#39ff14",
+            "#00bcd4",
+        ]
+    )
+    background_hex: str = "#0a0a15"
+    grid_hex: str = "#2a2a3a"
+    reset_kwargs: Dict[str, bool | str] | None = None
+
+    # ---------- Core data prep ----------
+    def to_dataframe(self, report: Dict[str, Dict[str, float]]) -> pd.DataFrame:
+        """Convert sklearn classification_report output_dict to a tidy DataFrame.
+
+        This method standardizes the output of scikit-learn's classification_report function.
+
+        Args:
+            report (Dict[str, Dict[str, float]]): Dictionary from `classification_report(..., output_dict=True)`.
+
+        Returns:
+            pd.DataFrame: Index are classes/avg rows (str). Columns include ["precision", "recall", "f1-score", "support"]. The "accuracy" scalar (if present) is stored in df.attrs["accuracy"], and the row is removed.
+        """
+        df = pd.DataFrame(report).T
+        for col in ["precision", "recall", "f1-score", "support"]:
+            if col not in df.columns:
+                df[col] = np.nan
+
+        if "accuracy" in df.index:
+            # sklearn puts accuracy scalar in "accuracy" row, usually in 'precision'
+            try:
+                acc_val = df.loc["accuracy", "precision"]
+                if pd.api.types.is_number(acc_val):
+                    df.attrs["accuracy"] = float(str(acc_val))
+            except Exception:
+                squeezed_val = df.loc["accuracy"].squeeze()
+                if pd.api.types.is_number(squeezed_val):
+                    df.attrs["accuracy"] = float(str(squeezed_val))
+            df = df.drop(index="accuracy", errors="ignore")
+
+        df.index = df.index.astype(str)
+
+        is_avg = df.index.str.contains("avg", case=False, regex=True)
+        class_df = df.loc[~is_avg].copy()
+        avg_df = df.loc[is_avg].copy()
+
+        num_cols = ["precision", "recall", "f1-score", "support"]
+        class_df[num_cols] = class_df[num_cols].apply(pd.to_numeric, errors="coerce")
+        avg_df[num_cols] = avg_df[num_cols].apply(pd.to_numeric, errors="coerce")
+
+        class_df = class_df.sort_index()
+        tidy = pd.concat([class_df, avg_df], axis=0)
+        return tidy
+
+    def compute_ci(
+        self,
+        boot_reports: List[Dict[str, Dict[str, float]]],
+        ci: float = 0.95,
+        metrics: Tuple[str, ...] = ("precision", "recall", "f1-score"),
+    ) -> pd.DataFrame:
+        """Compute per-class bootstrap CIs from multiple report dicts.
+
+        Args:
+            boot_reports (List[Dict[str, Dict[str, float]]]): List of `output_dict=True` results over bootstrap repeats.
+            ci (float): Confidence level (e.g., 0.95 for 95%).
+            metrics (Tuple[str, ...]): Metrics to compute bounds for.
+
+        Returns:
+            pd.DataFrame: Multi-index columns with (metric, ["lower","upper","mean"]). Index contains any class/avg labels present in the bootstrap reports.
+        """
+        if not boot_reports:
+            raise ValueError("boot_reports is empty; provide at least one dict.")
+
+        # Gather frames; union of indices (classes/avg rows) across repeats
+        frames = []
+        for rep in boot_reports:
+            df = self.to_dataframe(rep)
+            frames.append(df)
+
+        # Align on index, stack into 3D array (repeat x class x metric)
+        common_index = sorted(set().union(*[f.index for f in frames]))
+        arrs = []
+        for f in frames:
+            sub = f.reindex(common_index)
+            arrs.append(sub[[m for m in metrics]].to_numpy(dtype=float))
+        arr = np.stack(arrs, axis=0)  # shape: (B, C, M)
+
+        alpha = (1 - ci) / 2
+        lower_q = 100 * alpha
+        upper_q = 100 * (1 - alpha)
+
+        lower = np.nanpercentile(arr, lower_q, axis=0)  # (C, M)
+        upper = np.nanpercentile(arr, upper_q, axis=0)  # (C, M)
+        mean = np.nanmean(arr, axis=0)  # (C, M)
+
+        out = pd.DataFrame(index=common_index)
+        column_tuples = []
+        for j, m in enumerate(metrics):
+            out[(m, "lower")] = lower[:, j]
+            out[(m, "upper")] = upper[:, j]
+            out[(m, "mean")] = mean[:, j]
+            column_tuples.extend([(m, "lower"), (m, "upper"), (m, "mean")])
+
+        out.columns = pd.MultiIndex.from_tuples(column_tuples)
+        return out
+
+    # ---------- Palettes & styles ----------
+    def _retro_cmap(self, n: int = 256) -> LinearSegmentedColormap:
+        """Create a neon gradient colormap.
+
+        This colormap transitions through a series of bright, neon colors.
+
+        Args:
+            n (int): Number of discrete colors in the colormap. Defaults to 256.
+
+        Returns:
+            LinearSegmentedColormap: The generated colormap.
+        """
+        anchors = ["#241937", "#7d00ff", "#ff00ff", "#ff6ec7", "#00f0ff", "#00ff9f"]
+        return LinearSegmentedColormap.from_list("retro_neon", anchors, N=n)
+
+    def _set_mpl_style(self) -> None:
+        """Apply a dark neon Matplotlib theme.
+
+        This method modifies global rcParams; call before plotting.
+        """
+        plt.rcParams.update(
+            {
+                "figure.facecolor": self.background_hex,
+                "axes.facecolor": self.background_hex,
+                "axes.edgecolor": self.grid_hex,
+                "axes.labelcolor": "#e8e8ff",
+                "xtick.color": "#d7d7ff",
+                "ytick.color": "#d7d7ff",
+                "grid.color": self.grid_hex,
+                "text.color": "#f7f7ff",
+                "axes.grid": True,
+                "grid.linestyle": "--",
+                "grid.linewidth": 0.5,
+                "legend.facecolor": "#121222",
+                "legend.edgecolor": self.grid_hex,
+            }
+        )
+
+    def _reset_mpl_style(self) -> None:
+        """Reset Matplotlib rcParams to default."""
+        plt.rcParams.update(mpl.rcParamsDefault)
+        mpl.rcParams.update(mpl.rcParamsDefault)
+
+        if self.reset_kwargs is not None:
+            plt.rcParams.update(self.reset_kwargs)
+            mpl.rcParams.update(self.reset_kwargs)
+
+    def plot_heatmap(
+        self,
+        df: pd.DataFrame,
+        title: str = "Classification Report — Per-Class Metrics",
+        classes_only: bool = True,
+        figsize: Tuple[int, int] = (12, 6),
+        annot_decimals: int = 3,
+        vmax: float = 1.0,
+        vmin: float = 0.0,
+        show_support_strip: bool = False,
+    ):
+        """Plot a per-class heatmap with an optional right-hand support strip.
+
+        This visualizes the classification metrics for each class.
+
+        Args:
+            df (pd.DataFrame): DataFrame from `to_dataframe()`.
+            title (str): Plot title.
+            classes_only (bool): If True, exclude avg rows.
+            figsize (Tuple[int, int]): Matplotlib figure size.
+            annot_decimals (int): Decimal places for annotations.
+            vmax (float): Max heatmap value.
+            vmin (float): Min heatmap value.
+            show_support_strip (bool): If True, draw normalized support strip at right.
+
+        Returns:
+            matplotlib.figure.Figure: The created figure.
+        """
+        self._set_mpl_style()
+
+        work = df.copy()
+        if classes_only:
+            work = work[~work.index.str.contains("avg", case=False, regex=True)]
+
+        metric_cols = ["precision", "recall", "f1-score"]
+        heat = work[metric_cols].astype(float)
+
+        fig, ax = plt.subplots(figsize=figsize)
+        cmap = self._retro_cmap()
+        sns.heatmap(
+            heat,
+            annot=True,
+            fmt=f".{annot_decimals}f",
+            cmap=cmap,
+            vmin=vmin,
+            vmax=vmax,
+            linewidths=0.5,
+            linecolor=self.grid_hex,
+            cbar_kws={"label": "Score"},
+            ax=ax,
+        )
+        ax.set_title(title, pad=12, fontweight="bold")
+        ax.set_xlabel("Metric")
+        ax.set_ylabel("Class")
+
+        # Optional support strip (normalized 0..1) as an inset axis
+        if show_support_strip and "support" in work.columns:
+            supports = work["support"].astype(float).fillna(0.0).to_numpy()
+            sup_norm = (supports - supports.min()) / (np.ptp(supports) + 1e-9)
+            ax_strip = inset_axes(
+                ax,
+                width="2%",
+                height="100%",
+                loc="right",
+                bbox_to_anchor=(0.03, 0.0, 1, 1),
+                bbox_transform=ax.transAxes,
+                borderpad=0,
+            )
+
+            strip_data = sup_norm[:, None]  # (n_classes, 1)
+
+            sns.heatmap(
+                strip_data,
+                cmap=self._retro_cmap(),
+                cbar=True,
+                cbar_kws={"label": "Support (normalized)"},
+                xticklabels=False,
+                yticklabels=False,
+                vmin=0.0,
+                vmax=1.0,
+                linewidths=0.0,
+                ax=ax_strip,
+            )
+
+            # Align strip y-limits to main heatmap
+            ax_strip.set_ylim(ax.get_ylim())
+
+        return fig
+
+    def plot_grouped_bars(
+        self,
+        df: pd.DataFrame,
+        title: str = "Per-Class Metrics (Grouped Bars)",
+        classes_only: bool = True,
+        figsize: Tuple[int, int] = (14, 7),
+        bar_alpha: float = 0.9,
+        ci_df: Optional[pd.DataFrame] = None,
+    ):
+        """Plot grouped bars for P/R/F1 with support markers and optional CI.
+
+        Args:
+            df (pd.DataFrame): DataFrame from `to_dataframe()`.
+            title (str): Plot title.
+            classes_only (bool): If True, exclude avg rows.
+            figsize (Tuple[int, int]): Figure size.
+            bar_alpha (float): Bar alpha.
+            ci_df (Optional[pd.DataFrame]): Output of `compute_ci()`; adds error bars if provided.
+
+        Returns:
+            matplotlib.figure.Figure: The created figure.
+        """
+        self._set_mpl_style()
+        work = df.copy()
+        if classes_only:
+            work = work[~work.index.str.contains("avg", case=False, regex=True)]
+
+        metric_cols = ["precision", "recall", "f1-score"]
+
+        lng = (
+            work[metric_cols]
+            .reset_index(names="class")
+            .melt(id_vars="class", var_name="metric", value_name="score")
+            .dropna(subset=["score"])
+        )
+
+        homozygote_order = ["A", "C", "G", "T"]
+        classes = homozygote_order + [
+            c for c in lng["class"].unique().tolist() if c not in homozygote_order
+        ]
+
+        metrics = metric_cols
+        palette = self.retro_palette[: len(metrics)]
+
+        x = np.arange(len(classes))
+        width = 0.25
+        offsets = np.linspace(-width, width, num=len(metrics))
+
+        fig, ax = plt.subplots(figsize=figsize)
+
+        # Secondary axis for support markers
+        ax2 = ax.twinx()
+        supports = work.reindex(classes)["support"].astype(float).fillna(0.0).values
+
+        ax2.plot(
+            x,
+            np.asarray(supports),
+            linestyle="None",
+            marker="o",
+            markersize=6,
+            markerfacecolor="#39ff14",
+            markeredgecolor="#ffffff",
+            alpha=0.9,
+            label="Support",
+        )
+
+        # Plot bars with optional CI error bars
+        for i, m in enumerate(metrics):
+            vals = (
+                lng.loc[lng["metric"].eq(m)]
+                .set_index("class")
+                .reindex(classes)["score"]
+                .values
+            )
+
+            yerr = None
+            if ci_df is not None and (m, "lower") in ci_df.columns:
+                ci_reindexed = ci_df.reindex(classes)
+                lows = ci_reindexed[(m, "lower")].to_numpy(dtype=float)
+                ups = ci_reindexed[(m, "upper")].to_numpy(dtype=float)
+
+                # Convert to symmetric error around the point estimate
+                center = vals
+                yerr = np.vstack([center - lows, ups - center])
+
+            ax.bar(
+                x + offsets[i],
+                np.asarray(vals),
+                width=width * 0.95,
+                label=m.title(),
+                color=palette[i % len(palette)],
+                alpha=bar_alpha,
+                edgecolor="#ffffff",
+                linewidth=0.4,
+                yerr=yerr,
+                error_kw=dict(ecolor="#ffffff", elinewidth=0.9, capsize=3),
+            )
+
+        ax.set_xticks(x)
+        ax.set_xticklabels(classes, rotation=45, ha="right")
+        ax.set_ylim(0, 1.05)
+        ax.set_ylabel("Score")
+        ax.set_title(title, pad=12, fontweight="bold")
+        ax.legend(ncols=3, frameon=True, loc="upper left")
+
+        # Configure secondary (support) axis
+        ax2.set_ylabel("Support")
+        ax2.grid(False)
+        ax2.set_ylim(0, max(1.0, np.asarray(supports).max() * 1.15))
+        ax2.legend(loc="upper right", frameon=True)
+
+        ax.grid(axis="y", linestyle="--", alpha=0.6)
+        plt.tight_layout()
+        return fig
+
+    def plot_radar(
+        self,
+        df: pd.DataFrame,
+        title: str = "Macro/Weighted Averages & Top-K Class Radar",
+        top_k: int = 5,
+        include_micro: bool = True,
+        include_macro: bool = True,
+        include_weighted: bool = True,
+        ci_df: Optional[pd.DataFrame] = None,
+    ) -> go.Figure:
+        """Interactive radar chart of averages + top-k classes; optional CI bands.
+
+        This function creates a radar chart using Plotly, displaying the specified metrics for the top-k classes.
+
+        Args:
+            df (pd.DataFrame): DataFrame from `to_dataframe()`.
+            title (str): Figure title.
+            top_k (int): Include up to top_k classes by support (descending).
+            include_micro (bool): Include micro avg trace if available.
+            include_macro (bool): Include macro avg trace.
+            include_weighted (bool): Include weighted avg trace.
+            ci_df (Optional[pd.DataFrame]): Output of `compute_ci()`; draws semi-transparent CI bands.
+
+        Returns:
+            plotly.graph_objects.Figure: The interactive radar chart.
+        """
+        work = df.copy()
+
+        is_avg = work.index.str.contains("avg", case=False, regex=True)
+        classes = work.loc[~is_avg].copy().sort_values("support", ascending=False)
+        if top_k is not None and top_k > 0:
+            classes = classes.head(top_k)
+
+        avgs = []
+        if include_macro and "macro avg" in work.index:
+            avgs.append(("macro avg", work.loc["macro avg"]))
+        if include_weighted and "weighted avg" in work.index:
+            avgs.append(("weighted avg", work.loc["weighted avg"]))
+        if include_micro and "micro avg" in work.index:
+            avgs.append(("micro avg", work.loc["micro avg"]))
+
+        metrics = ["precision", "recall", "f1-score"]
+        theta = metrics + [metrics[0]]
+
+        fig = go.Figure()
+
+        def _add_ci_band(name: str, color: str):
+            if ci_df is None:
+                return
+            if not all([(m, "lower") in ci_df.columns for m in metrics]):
+                return
+            if name not in ci_df.index:
+                return
+            lows = [
+                float(pd.to_numeric(ci_df.loc[name, (m, "lower")], errors="coerce"))
+                for m in metrics
+            ]
+            ups = [
+                float(pd.to_numeric(ci_df.loc[name, (m, "upper")], errors="coerce"))
+                for m in metrics
+            ]
+            lows.append(lows[0])
+            ups.append(ups[0])
+
+            # Plotly polar CI band: plot upper path, then lower reversed with fill
+            fig.add_trace(
+                go.Scatterpolar(
+                    r=ups,
+                    theta=theta,
+                    mode="lines",
+                    line=dict(width=0),
+                    hoverinfo="skip",
+                    showlegend=False,
+                )
+            )
+            fig.add_trace(
+                go.Scatterpolar(
+                    r=lows[::-1],
+                    theta=theta[::-1],
+                    mode="lines",
+                    line=dict(width=0),
+                    fill="toself",
+                    fillcolor=(
+                        color.replace("#", "rgba(") if False else None
+                    ),  # placeholder
+                    hoverinfo="skip",
+                    name=f"{name} CI",
+                    showlegend=False,
+                    opacity=0.20,
+                )
+            )
+            # Workaround: directly set fillcolor via marker color on last trace
+            fig.data[-1].fillcolor = f"{color}33"  # add ~20% alpha
+
+        # Add average traces with CI first
+        for i, (name, row) in enumerate(avgs):
+            r = [float(row.get(m, np.nan)) for m in metrics]
+            r.append(r[0])
+            color = self.retro_palette[i % len(self.retro_palette)]
+            _add_ci_band(name, color)
+            fig.add_trace(
+                go.Scatterpolar(
+                    r=r,
+                    theta=theta,
+                    name=name.title(),
+                    mode="lines+markers",
+                    line=dict(width=3, color=color),
+                    marker=dict(size=7, color=color),
+                    opacity=0.95,
+                )
+            )
+
+        # Add class traces (top-k) with optional CI
+        base_idx = len(avgs)
+        for i, (cls, row) in enumerate(classes[metrics].iterrows()):
+            r = [float(row.get(m, np.nan)) for m in metrics]
+            r.append(r[0])
+            color = self.retro_palette[(base_idx + i) % len(self.retro_palette)]
+            _add_ci_band(str(cls), color)
+            fig.add_trace(
+                go.Scatterpolar(
+                    r=r,
+                    theta=theta,
+                    name=str(cls),
+                    mode="lines+markers",
+                    line=dict(width=2, color=color),
+                    marker=dict(size=6, color=color),
+                    opacity=0.85,
+                )
+            )
+
+        fig.update_layout(
+            title=title,
+            template="plotly_dark",
+            paper_bgcolor=self.background_hex,
+            plot_bgcolor=self.background_hex,
+            polar=dict(
+                bgcolor="#111122",
+                radialaxis=dict(range=[0, 1.05], showline=True, gridcolor="#33334d"),
+                angularaxis=dict(gridcolor="#33334d"),
+            ),
+            legend=dict(
+                bgcolor="#121222",
+                bordercolor="#2a2a3a",
+                borderwidth=1,
+                orientation="h",
+                yanchor="bottom",
+                y=-0.15,
+                x=0.5,
+                xanchor="center",
+            ),
+        )
+
+        return fig
+
+    def plot_all(
+        self,
+        report: Dict[str, Dict[str, float]],
+        title_prefix: str = "Classification Report",
+        heatmap_classes_only: bool = True,
+        radar_top_k: int = 10,
+        boot_reports: Optional[List[Dict[str, Dict[str, float]]]] = None,
+        ci: float = 0.95,
+        show: bool = True,
+    ) -> Dict[str, Union["Figure", go.Figure]]:
+        """Generate all visuals, with optional CI from bootstrap reports.
+
+        Args:
+            report (Dict[str, Dict[str, float]]): The `output_dict=True` classification report (single run).
+            title_prefix (str): Common prefix for titles.
+            heatmap_classes_only (bool): Exclude averages in heatmap if True.
+            radar_top_k (int): Number of top classes (by support) on radar.
+            boot_reports (Optional[List[Dict[str, Dict[str, float]]]]): Optional list of bootstrap report dicts for CI.
+            ci (float): Confidence level (e.g., 0.95).
+            show (bool): If True, call plt.show() for Matplotlib figures.
+
+        Returns:
+            Dict[str, Union[matplotlib.figure.Figure, plotly.graph_objects.Figure]]: Keys: {"heatmap_fig", "bars_fig", "radar_fig"}.
+        """
+        df = self.to_dataframe(report)
+        acc = df.attrs.get("accuracy", None)
+        acc_str = f" (Accuracy: {acc:.3f})" if isinstance(acc, float) else ""
+
+        ci_df = None
+        if boot_reports:
+            ci_df = self.compute_ci(boot_reports, ci=ci)
+
+        heatmap_fig = self.plot_heatmap(
+            df,
+            title=f"{title_prefix} — Heatmap{acc_str}",
+            classes_only=heatmap_classes_only,
+            show_support_strip=False,
+        )
+        bars_fig = self.plot_grouped_bars(
+            df,
+            title=f"{title_prefix} — Grouped Bars{acc_str}",
+            classes_only=True,
+            ci_df=ci_df,
+        )
+        radar_fig = self.plot_radar(
+            df,
+            title=f"{title_prefix} — Averages & Top-{radar_top_k} Classes",
+            top_k=radar_top_k,
+            ci_df=ci_df,
+        )
+
+        if show:
+            plt.show()
+
+        return {
+            "heatmap_fig": heatmap_fig,
+            "bars_fig": bars_fig,
+            "radar_fig": radar_fig,
+        }

pgsui/utils/logging_utils.py

@@ -0,0 +1,22 @@
+import logging
+
+
+def configure_logger(
+    logger: logging.Logger,
+    *,
+    verbose: bool = False,
+    debug: bool = False,
+    quiet_level: int = logging.ERROR,
+) -> logging.Logger:
+    """Force a logger and its handlers to respect verbose/debug controls."""
+    if debug:
+        level = logging.DEBUG
+    elif verbose:
+        level = logging.INFO
+    else:
+        level = quiet_level
+
+    logger.setLevel(level)
+    for handler in getattr(logger, "handlers", ()):
+        handler.setLevel(level)
+    return logger