@brainpilot/skills 0.0.6 → 0.0.7

package/skills/16_Animal_Behavior/ethoclaw-multiparameter-violin-stats-generate/scripts/h5_inspect.py

@@ -0,0 +1,79 @@
+#!/usr/bin/env python3
+"""Inspect an HDF5 (.h5/.hdf5) file and print a tree of groups/datasets.
+
+Usage:
+  python h5_inspect.py path/to/file.h5
+
+Notes:
+- Requires: h5py
+- Prints dataset shapes/dtypes and a preview for small 1D datasets.
+"""
+
+from __future__ import annotations
+
+import sys
+from typing import Any
+
+
+def _fmt(obj: Any) -> str:
+    try:
+        return str(obj)
+    except Exception:
+        return repr(obj)
+
+
+def _walk(h5, path: str = "/", indent: int = 0) -> None:
+    import h5py  # local import for nicer dependency error
+
+    item = h5[path]
+    pad = "  " * indent
+
+    if isinstance(item, h5py.Dataset):
+        shape = item.shape
+        dtype = item.dtype
+        print(f"{pad}{path}  [Dataset] shape={shape} dtype={dtype}")
+        # small preview
+        try:
+            if shape is not None and len(shape) == 1 and shape[0] <= 10:
+                data = item[...]
+                print(f"{pad}  preview: {_fmt(data)}")
+        except Exception:
+            pass
+        return
+
+    print(f"{pad}{path}  [Group]")
+    for key in item.keys():
+        child_path = (path.rstrip("/") + "/" + key) if path != "/" else "/" + key
+        _walk(h5, child_path, indent + 1)
+
+
+def main(argv: list[str]) -> int:
+    if len(argv) != 2 or argv[1] in {"-h", "--help"}:
+        print(__doc__.strip())
+        return 0
+
+    h5_path = argv[1]
+
+    try:
+        import h5py  # noqa: F401
+    except Exception as e:
+        print(
+            "ERROR: missing dependency 'h5py'.\n"
+            "Install options:\n"
+            "  - Ubuntu/Debian: apt install python3-pip python3-venv && pip install h5py\n"
+            "  - Or use a dedicated venv/conda env.\n"
+            f"Details: {e}",
+            file=sys.stderr,
+        )
+        return 2
+
+    import h5py
+
+    with h5py.File(h5_path, "r") as h5:
+        _walk(h5, "/", 0)
+
+    return 0
+
+
+if __name__ == "__main__":
+    raise SystemExit(main(sys.argv))

package/skills/16_Animal_Behavior/ethoclaw-multiparameter-violin-stats-generate/scripts/h5_violin_batch.py

@@ -0,0 +1,624 @@
+#!/usr/bin/env python3
+"""Batch-generate violin plots for *all parameters* from a folder of .h5 files.
+
+Designed to match `h5-multiparameter-violin-stats` rules + config, but works in batch mode:
+- Reads every *.h5/*.hdf5 under --input-dir (non-recursive by default)
+- Infers group from filename: rec-<id>-<group>-<timestamp>.h5
+- Extracts:
+  - AdvancedParameters/*  (scalar per file)
+  - KinematicParameter/*  (per-file mean across frames)
+- Writes one violin plot per parameter to --out-dir.
+
+Config:
+- Default config: ../config.toml (in this skill folder)
+- Supports Python 3.11+ tomllib, and Python<3.11 via `toml` package.
+
+Usage:
+  python h5_violin_batch.py --input-dir /path/to/project/random_project
+
+Windows example (conda python):
+  D:\\Anaconda3\\python.exe h5_violin_batch.py \\
+    --input-dir C:\\Users\\ASUS\\Desktop\\2Dxy_test_project\\random_project
+"""
+
+from __future__ import annotations
+
+import argparse
+import math
+import os
+import re
+from dataclasses import dataclass
+from pathlib import Path
+from typing import Dict, List, Literal, Sequence, Tuple
+
+
+Method = Literal["auto", "ttest", "mannwhitney", "anova", "kruskal"]
+
+FNAME_RE = re.compile(r"rec-(?P<rec>\d+)-(?P<group>[A-Za-z]+)-(?P<ts>\d+)\.h5$", re.IGNORECASE)
+
+
+def _die(msg: str, code: int = 2) -> "NoReturn":
+    raise SystemExit(f"ERROR: {msg}")
+
+
+def _deep_get(d: dict, keys: list[str], default=None):
+    cur = d
+    for k in keys:
+        if not isinstance(cur, dict) or k not in cur:
+            return default
+        cur = cur[k]
+    return cur
+
+
+def _load_toml(path: str) -> dict:
+    # Prefer tomllib (py3.11+). For older Python, avoid extra deps by parsing with stdlib.
+    try:
+        import tomllib  # type: ignore
+
+        with open(path, "rb") as f:
+            return tomllib.load(f)
+    except Exception:
+        pass
+
+    # Minimal TOML parser for this skill's simple config (sections + key = value).
+    # Supports: strings, ints, floats, booleans.
+    cfg: dict = {}
+    cur: dict = cfg
+    section: list[str] = []
+
+    def set_in(d: dict, keys: list[str], k: str, v):
+        node = d
+        for kk in keys:
+            node = node.setdefault(kk, {})
+        node[k] = v
+
+    def parse_value(s: str):
+        s = s.strip()
+        if not s:
+            return ""
+        if s.lower() in {"true", "false"}:
+            return s.lower() == "true"
+        if (s.startswith('"') and s.endswith('"')) or (s.startswith("'") and s.endswith("'")):
+            return s[1:-1]
+        # number
+        try:
+            if "." in s or "e" in s.lower():
+                return float(s)
+            return int(s)
+        except Exception:
+            return s
+
+    with open(path, "r", encoding="utf-8") as f:
+        for raw in f:
+            line = raw.strip()
+            if not line or line.startswith("#"):
+                continue
+            if line.startswith("[") and line.endswith("]"):
+                sec = line[1:-1].strip()
+                section = [x.strip() for x in sec.split(".") if x.strip()]
+                continue
+            if "=" not in line:
+                continue
+            k, v = line.split("=", 1)
+            k = k.strip()
+            # strip inline comment
+            v = v.split("#", 1)[0].strip()
+            set_in(cfg, section, k, parse_value(v))
+
+    return cfg
+
+
+def _default_config_path() -> str:
+    here = os.path.dirname(os.path.abspath(__file__))
+    return os.path.join(os.path.dirname(here), "config.toml")
+
+
+def _parse_group(p: Path) -> str:
+    m = FNAME_RE.search(p.name)
+    if not m:
+        return "unknown"
+    return m.group("group")
+
+
+@dataclass
+class TestResult:
+    test: str
+    p_value: float
+    statistic: float | None = None
+
+
+def _holm_bonferroni(p_values: Sequence[float]) -> list[float]:
+    m = len(p_values)
+    order = sorted(range(m), key=lambda i: p_values[i])
+    adj = [0.0] * m
+    prev = 0.0
+    for k, i in enumerate(order):
+        raw = p_values[i]
+        val = (m - k) * raw
+        val = max(val, prev)
+        prev = val
+        adj[i] = min(val, 1.0)
+    return adj
+
+
+def _choose_method(n_groups: int, method: Method, cfg: dict) -> str:
+    if method != "auto":
+        return method
+    m2 = _deep_get(cfg, ["stats", "default_2_groups"], "ttest")
+    m3 = _deep_get(cfg, ["stats", "default_3plus_groups"], "kruskal")
+    return str(m2) if n_groups == 2 else str(m3)
+
+
+def _run_overall(groups: List[str], values: List[float], method: str) -> TestResult:
+    import numpy as np
+    from scipy import stats
+
+    uniq = sorted(set(groups))
+    arrays = [np.asarray([v for g, v in zip(groups, values) if g == u], dtype=float) for u in uniq]
+
+    if len(uniq) == 2:
+        a, b = arrays
+        if method == "ttest":
+            stat, p = stats.ttest_ind(a, b, equal_var=False, nan_policy="omit")
+            return TestResult("Welch t-test", float(p), None if stat is None else float(stat))
+        if method == "mannwhitney":
+            stat, p = stats.mannwhitneyu(a, b, alternative="two-sided")
+            return TestResult("Mann–Whitney U", float(p), float(stat))
+        _die(f"method '{method}' incompatible with 2 groups")
+
+    if method == "anova":
+        stat, p = stats.f_oneway(*arrays)
+        return TestResult("One-way ANOVA", float(p), float(stat))
+    if method == "kruskal":
+        stat, p = stats.kruskal(*arrays)
+        return TestResult("Kruskal–Wallis", float(p), float(stat))
+
+    _die(f"method '{method}' incompatible with {len(uniq)} groups")
+
+
+def _run_pairwise(groups: List[str], values: List[float], base_method: str, correction: str) -> List[dict]:
+    import numpy as np
+    from scipy import stats
+
+    uniq = sorted(set(groups))
+    by = {u: np.asarray([v for g, v in zip(groups, values) if g == u], dtype=float) for u in uniq}
+
+    rows = []
+    pvals = []
+    for i in range(len(uniq)):
+        for j in range(i + 1, len(uniq)):
+            a_name, b_name = uniq[i], uniq[j]
+            a, b = by[a_name], by[b_name]
+            if base_method in {"anova", "ttest"}:
+                stat, p = stats.ttest_ind(a, b, equal_var=False, nan_policy="omit")
+                test = "Welch t-test (pairwise)"
+                statv = None if stat is None else float(stat)
+            else:
+                stat, p = stats.mannwhitneyu(a, b, alternative="two-sided")
+                test = "Mann–Whitney U (pairwise)"
+                statv = float(stat)
+            pvals.append(float(p))
+            rows.append({"a": a_name, "b": b_name, "test": test, "p": float(p), "stat": statv})
+
+    corr = (correction or "holm").lower()
+    if corr == "holm":
+        adj = _holm_bonferroni(pvals)
+        for row, ap in zip(rows, adj):
+            row["p_adj"] = float(ap)
+            row["p_adj_method"] = "holm"
+    elif corr == "bonferroni":
+        m = len(pvals)
+        for row in rows:
+            row["p_adj"] = min(float(row["p"]) * m, 1.0)
+            row["p_adj_method"] = "bonferroni"
+    else:
+        _die(f"unsupported pairwise_correction: {correction}")
+
+    return rows
+
+
+def _mean_sem(arr) -> Tuple[float, float]:
+    import numpy as np
+
+    x = np.asarray(arr, dtype=float)
+    x = x[np.isfinite(x)]
+    if x.size == 0:
+        return (math.nan, math.nan)
+    mean = float(np.mean(x))
+    sem = float(np.std(x, ddof=1) / math.sqrt(x.size)) if x.size > 1 else 0.0
+    return mean, sem
+
+
+def _p_to_stars(p: float) -> str:
+    if p <= 1e-4:
+        return "****"
+    if p <= 1e-3:
+        return "***"
+    if p <= 1e-2:
+        return "**"
+    if p <= 5e-2:
+        return "*"
+    return "ns"
+
+
+def _add_sig_brackets(
+    ax,
+    order: list[str],
+    d,
+    y_col: str,
+    comparisons: list[dict],
+    cfg: dict,
+    alpha: float,
+) -> None:
+    """Add pairwise significance brackets to an existing Axes.
+
+    comparisons: list of dicts with keys: a, b, p (and optional p_adj).
+    """
+
+    import numpy as np
+
+    if not comparisons:
+        return
+
+    show = bool(_deep_get(cfg, ["annotate", "show"], True))
+    if not show:
+        return
+
+    use_adj = bool(_deep_get(cfg, ["annotate", "use_p_adj"], True))
+    show_ns = bool(_deep_get(cfg, ["annotate", "show_ns"], False))
+    only_sig = bool(_deep_get(cfg, ["annotate", "only_sig"], True))
+    max_pairs = int(_deep_get(cfg, ["annotate", "max_pairs"], 10))
+    fmt = str(_deep_get(cfg, ["annotate", "label_format"], "stars+p")).lower()
+
+    # choose which p to display
+    def pick_p(row: dict) -> float:
+        if use_adj and ("p_adj" in row) and (row["p_adj"] is not None):
+            return float(row["p_adj"])
+        return float(row["p"])
+
+    rows = []
+    for r in comparisons:
+        p = pick_p(r)
+        if only_sig and p > alpha:
+            continue
+        if (not show_ns) and _p_to_stars(p) == "ns":
+            continue
+        rows.append((r["a"], r["b"], p))
+
+    if not rows:
+        return
+
+    rows = rows[:max_pairs]
+
+    # map group -> x position
+    x_of = {g: i for i, g in enumerate(order)}
+
+    # compute baseline height
+    y = d[y_col].astype(float).to_numpy()
+    y = y[np.isfinite(y)]
+    if y.size == 0:
+        return
+    y_min = float(np.min(y))
+    y_max = float(np.max(y))
+    yr = y_max - y_min
+    if yr <= 0:
+        yr = 1.0
+
+    base = y_max + 0.05 * yr
+    step = float(_deep_get(cfg, ["annotate", "step"], 0.08)) * yr
+    h = float(_deep_get(cfg, ["annotate", "bracket_height"], 0.02)) * yr
+
+    for k, (a, b, p) in enumerate(rows):
+        if a not in x_of or b not in x_of:
+            continue
+        x1, x2 = x_of[a], x_of[b]
+        if x1 == x2:
+            continue
+        if x1 > x2:
+            x1, x2 = x2, x1
+
+        yk = base + k * step
+
+        # bracket
+        ax.plot([x1, x1, x2, x2], [yk, yk + h, yk + h, yk], lw=1.2, c="black")
+
+        stars = _p_to_stars(p)
+        ptxt = f"p={p:.3g}"
+        if fmt == "stars":
+            label = stars
+        elif fmt == "p":
+            label = ptxt
+        else:
+            label = f"{stars}\n{ptxt}" if stars != "ns" else ptxt
+
+        ax.text(
+            (x1 + x2) / 2,
+            yk + h,
+            label,
+            ha="center",
+            va="bottom",
+            fontsize=float(_deep_get(cfg, ["annotate", "fontsize"], 9)),
+        )
+
+    # make room on top
+    ax.set_ylim(top=base + (len(rows) + 1) * step)
+
+
+def _make_violin(
+    df,
+    param: str,
+    out_path: Path,
+    cfg: dict,
+    title: str,
+    comparisons: list[dict] | None = None,
+    alpha: float = 0.05,
+) -> None:
+    import numpy as np
+    import matplotlib
+
+    matplotlib.use("Agg")
+    import matplotlib.pyplot as plt
+    import seaborn as sns
+
+    style = _deep_get(cfg, ["plot", "style"], "whitegrid")
+    context = _deep_get(cfg, ["plot", "context"], "notebook")
+    sns.set_theme(style=style, context=context)
+
+    palette = _deep_get(cfg, ["plot", "palette"], "Set2")
+
+    fig_w = float(_deep_get(cfg, ["plot", "fig_width"], 10))
+    fig_h = float(_deep_get(cfg, ["plot", "fig_height"], 5))
+    cut = float(_deep_get(cfg, ["plot", "cut"], 0))
+
+    summary = str(_deep_get(cfg, ["plot", "summary"], "mean_sem")).lower()
+    inner = None
+    if summary in {"box", "quartile"}:
+        inner = "box" if summary == "box" else "quartile"
+
+    d = df[["group", param]].dropna().copy()
+    d = d[np.isfinite(d[param].astype(float))]
+
+    # keep a stable group order (alphabetical) for consistent bracket placement
+    order = sorted(d["group"].astype(str).unique().tolist())
+
+    plt.figure(figsize=(fig_w, fig_h))
+    ax = sns.violinplot(
+        data=d,
+        x="group",
+        y=param,
+        inner=inner,
+        cut=cut,
+        palette=palette,
+        order=order,
+    )
+
+    if bool(_deep_get(cfg, ["plot", "show_points"], True)):
+        sns.stripplot(
+            data=d,
+            x="group",
+            y=param,
+            color=_deep_get(cfg, ["plot", "point_color"], "black"),
+            size=float(_deep_get(cfg, ["plot", "point_size"], 3)),
+            alpha=float(_deep_get(cfg, ["plot", "point_alpha"], 0.4)),
+            jitter=float(_deep_get(cfg, ["plot", "point_jitter"], 0.2)),
+            order=order,
+        )
+
+    if summary == "mean_sem":
+        uniq = order
+        xs = np.arange(len(uniq))
+        col = _deep_get(cfg, ["plot", "summary_color"], "black")
+        cap = float(_deep_get(cfg, ["plot", "summary_capsize"], 4))
+        lw = float(_deep_get(cfg, ["plot", "summary_linewidth"], 1.5))
+
+        centers = []
+        errs = []
+        for u in uniq:
+            arr = d.loc[d["group"].astype(str) == u, param].astype(float).to_numpy()
+            m, sem = _mean_sem(arr)
+            centers.append(m)
+            errs.append(sem)
+
+        ax.errorbar(xs, centers, yerr=errs, fmt="o", color=col, capsize=cap, lw=lw, ms=4, zorder=10)
+
+    # significance brackets (pairwise) — default uses adjusted p if available
+    if comparisons:
+        _add_sig_brackets(ax, order=order, d=d, y_col=param, comparisons=comparisons, cfg=cfg, alpha=alpha)
+
+    ax.set_xlabel("Group")
+    ax.set_ylabel(param)
+    ax.set_title(title)
+
+    out_path.parent.mkdir(parents=True, exist_ok=True)
+    dpi = int(_deep_get(cfg, ["dump", "png_dpi"], 200))
+    save_pdf = bool(_deep_get(cfg, ["dump", "save_pdf"], False))
+
+    plt.tight_layout()
+
+    # Always save PNG
+    png_path = out_path
+    if png_path.suffix.lower() != ".png":
+        png_path = png_path.with_suffix(".png")
+    plt.savefig(str(png_path), dpi=dpi)
+
+    # Optionally save PDF alongside
+    if save_pdf:
+        pdf_path = png_path.with_suffix(".pdf")
+        plt.savefig(str(pdf_path))
+
+    plt.close()
+
+
+def _read_one_file(p: Path) -> Dict[str, float]:
+    import numpy as np
+    import h5py
+
+    row: Dict[str, float] = {}
+    with h5py.File(str(p), "r") as f:
+        # AdvancedParameters
+        if "AdvancedParameters" in f and "ParameterName" in f["AdvancedParameters"]:
+            names = [x.decode() if isinstance(x, (bytes, np.bytes_)) else str(x) for x in f["AdvancedParameters/ParameterName"][()]]
+            vals = np.asarray(f["AdvancedParameters/ParameterData"][()], dtype=float)
+            for n, v in zip(names, vals):
+                row[str(n)] = float(v)
+
+        # KinematicParameter means
+        if "KinematicParameter" in f and "ParameterName" in f["KinematicParameter"]:
+            names = [x.decode() if isinstance(x, (bytes, np.bytes_)) else str(x) for x in f["KinematicParameter/ParameterName"][()]]
+            data = np.asarray(f["KinematicParameter/ParameterData"], dtype=float)  # (frames, params)
+            means = np.nanmean(data, axis=0)
+            for n, v in zip(names, means):
+                row[f"mean_{str(n)}"] = float(v)
+
+    return row
+
+
+def build_parser() -> argparse.ArgumentParser:
+    p = argparse.ArgumentParser()
+    p.add_argument("--input-dir", required=True, help="Folder containing .h5 files")
+    p.add_argument(
+        "--out-dir",
+        default="",
+        help="Output folder (default: <input-dir>/results/violin_chart)",
+    )
+    p.add_argument(
+        "--config",
+        default="",
+        help="Path to config.toml (default: ../config.toml relative to this script)",
+    )
+    p.add_argument(
+        "--method",
+        default="auto",
+        choices=["auto", "ttest", "mannwhitney", "anova", "kruskal"],
+        help="Override stat method; auto uses config defaults",
+    )
+    p.add_argument("--alpha", type=float, default=0.05)
+    p.add_argument("--glob", default="*.h5", help="Glob pattern for input files")
+    return p
+
+
+def main(argv: Sequence[str]) -> int:
+    args = build_parser().parse_args(list(argv))
+
+    cfg_path = args.config.strip() or _default_config_path()
+    cfg = _load_toml(cfg_path)
+
+    alpha = float(_deep_get(cfg, ["stats", "alpha"], args.alpha))
+    args.alpha = alpha
+
+    in_dir = Path(args.input_dir)
+    if not in_dir.exists():
+        _die(f"input-dir not found: {in_dir}")
+
+    out_dir = Path(args.out_dir) if args.out_dir.strip() else (in_dir / "results" / "violin_chart")
+    out_dir.mkdir(parents=True, exist_ok=True)
+
+    h5_paths = sorted(in_dir.glob(args.glob))
+    if not h5_paths:
+        _die(f"no files matched: {in_dir / args.glob}")
+
+    import pandas as pd
+
+    rows = []
+    for p in h5_paths:
+        group = _parse_group(p)
+        base = {"file": str(p), "record": p.stem, "group": group}
+        try:
+            base.update(_read_one_file(p))
+        except Exception as e:
+            # keep going; some files may be header-only
+            base["_error"] = str(e)
+        rows.append(base)
+
+    df = pd.DataFrame(rows)
+
+    # determine parameter columns
+    meta_cols = {"file", "record", "group", "_error"}
+    params = [c for c in df.columns if c not in meta_cols]
+    params = [c for c in params if df[c].dropna().shape[0] > 0]
+
+    if not params:
+        _die("no parameters found in H5 files (AdvancedParameters/KinematicParameter missing?)")
+
+    stats_rows = []
+    pair_rows = []
+
+    for param in params:
+        d = df[["group", param]].dropna().copy()
+        try:
+            d[param] = d[param].astype(float)
+        except Exception:
+            continue
+        d = d[~d[param].isna()]
+        if d.shape[0] < 2:
+            continue
+        groups = d["group"].astype(str).tolist()
+        vals = d[param].astype(float).tolist()
+        uniq = sorted(set(groups))
+        if len(uniq) < 2:
+            continue
+
+        method = _choose_method(len(uniq), args.method, cfg)
+        overall = _run_overall(groups, vals, method)
+
+        correction = str(_deep_get(cfg, ["stats", "pairwise_correction"], "holm"))
+        pairwise_only_if_sig = bool(_deep_get(cfg, ["stats", "pairwise_only_if_overall_sig"], True))
+
+        pairwise = []
+        if len(uniq) >= 3:
+            if (not pairwise_only_if_sig) or (overall.p_value <= args.alpha):
+                pairwise = _run_pairwise(groups, vals, method, correction=correction)
+
+        stats_rows.append(
+            {
+                "param": param,
+                "n": int(len(vals)),
+                "groups": ",".join(uniq),
+                "method": method,
+                "overall_test": overall.test,
+                "overall_p": overall.p_value,
+                "overall_stat": overall.statistic,
+            }
+        )
+        for r in pairwise:
+            r2 = dict(r)
+            r2["param"] = param
+            pair_rows.append(r2)
+
+        title = f"{param} | {overall.test} p={overall.p_value:.3g}"
+        out_path = out_dir / f"violin_{param}.png"
+
+        # choose comparisons to annotate on plot
+        # - if 2 groups: annotate the single overall test p
+        # - if 3+ groups: annotate pairwise results (adjusted p by default)
+        comparisons_for_plot: list[dict] = []
+        if len(uniq) == 2:
+            a, b = uniq[0], uniq[1]
+            comparisons_for_plot = [{"a": a, "b": b, "p": float(overall.p_value)}]
+        else:
+            comparisons_for_plot = list(pairwise)
+
+        _make_violin(
+            df,
+            param,
+            out_path,
+            cfg,
+            title,
+            comparisons=comparisons_for_plot,
+            alpha=args.alpha,
+        )
+
+    # dump stats
+    if stats_rows:
+        pd.DataFrame(stats_rows).to_csv(out_dir / "stats_overall.csv", index=False, encoding="utf-8-sig")
+    if pair_rows:
+        pd.DataFrame(pair_rows).to_csv(out_dir / "stats_pairwise.csv", index=False, encoding="utf-8-sig")
+
+    print(f"Done. Plots saved to: {out_dir}")
+    return 0
+
+
+if __name__ == "__main__":
+    import sys
+
+    raise SystemExit(main(sys.argv[1:]))