ma-agents 3.6.2 → 3.9.0

package/lib/bmad-extension-plugin/skills/ml-eda/scripts/eda_analyzer.py

@@ -0,0 +1,654 @@
+#!/usr/bin/env python3
+"""
+eda_analyzer.py — BMAD DL Lifecycle  (inspired by K-Dense claude-scientific-skills)
+ML-focused Exploratory Data Analysis for common deep learning data formats.
+
+Supported formats:
+  - Image datasets  : directory of images (class-labeled subdirs or flat)
+  - CSV / TSV       : tabular feature/label datasets
+  - NumPy           : .npy / .npz arrays
+  - HDF5            : .h5 / .hdf5 files
+  - JSON annotations: COCO-style or flat label files
+
+Generates a structured markdown EDA report aligned with TSK-001 requirements:
+  class distributions, annotation quality, missing values, split verification.
+
+Usage:
+    python3 scripts/eda_analyzer.py <data_path> [--output report.md] [--splits train val test]
+    python3 scripts/eda_analyzer.py data/images/ --splits train val test
+    python3 scripts/eda_analyzer.py data/features.csv
+
+Exit codes:
+    0 — success, report written
+    1 — warnings (partial data)
+    2 — error
+"""
+
+from __future__ import annotations
+
+import argparse
+import json
+import sys
+from collections import Counter, defaultdict
+from dataclasses import dataclass, field
+from datetime import datetime
+from pathlib import Path
+from typing import Any
+
+
+# ── Optional imports ───────────────────────────────────────────────────────────
+
+try:
+    import numpy as np
+    HAS_NUMPY = True
+except ImportError:
+    HAS_NUMPY = False
+
+try:
+    import csv as _csv
+    HAS_CSV = True
+except ImportError:
+    HAS_CSV = False  # csv is stdlib, always available
+
+HAS_PIL = False
+try:
+    from PIL import Image
+    HAS_PIL = True
+except ImportError:
+    pass
+
+HAS_H5PY = False
+try:
+    import h5py
+    HAS_H5PY = True
+except ImportError:
+    pass
+
+
+# ── Data structures ────────────────────────────────────────────────────────────
+
+IMAGE_EXTENSIONS = {".jpg", ".jpeg", ".png", ".bmp", ".tiff", ".tif", ".webp"}
+
+@dataclass
+class ClassInfo:
+    name: str
+    count: int
+    sample_files: list[str] = field(default_factory=list)
+
+
+@dataclass
+class EDAReport:
+    data_path: Path
+    format_detected: str
+    warnings: list[str] = field(default_factory=list)
+    errors: list[str] = field(default_factory=list)
+
+    # Image dataset
+    total_images: int = 0
+    classes: list[ClassInfo] = field(default_factory=list)
+    image_sizes: list[tuple[int, int]] = field(default_factory=list)
+    corrupt_files: list[str] = field(default_factory=list)
+    splits_found: dict[str, int] = field(default_factory=dict)
+
+    # Tabular
+    num_rows: int = 0
+    num_cols: int = 0
+    columns: list[str] = field(default_factory=list)
+    missing_values: dict[str, int] = field(default_factory=dict)
+    label_distribution: dict[str, int] = field(default_factory=dict)
+    numeric_stats: dict[str, dict[str, float]] = field(default_factory=dict)
+
+    # NumPy
+    array_shapes: list[tuple] = field(default_factory=list)
+    array_dtypes: list[str] = field(default_factory=list)
+    array_stats: dict[str, Any] = field(default_factory=dict)
+
+    # HDF5
+    hdf5_keys: list[str] = field(default_factory=list)
+    hdf5_shapes: dict[str, tuple] = field(default_factory=dict)
+
+    # Annotation JSON
+    annotation_classes: dict[str, int] = field(default_factory=dict)
+    annotation_count: int = 0
+    images_without_annotations: int = 0
+
+
+# ── Format detection ───────────────────────────────────────────────────────────
+
+def detect_format(path: Path) -> str:
+    if path.is_dir():
+        # Check if it's an image dataset directory
+        image_files = list(path.rglob("*"))
+        if any(f.suffix.lower() in IMAGE_EXTENSIONS for f in image_files[:50]):
+            return "image_dir"
+        return "unknown_dir"
+    suffix = path.suffix.lower()
+    if suffix in (".csv", ".tsv"):
+        return "csv"
+    if suffix in (".npy", ".npz"):
+        return "numpy"
+    if suffix in (".h5", ".hdf5"):
+        return "hdf5"
+    if suffix == ".json":
+        return "json_annotations"
+    return "unknown"
+
+
+# ── Image dataset analysis ─────────────────────────────────────────────────────
+
+def analyze_image_dir(path: Path, report: EDAReport, split_names: list[str]) -> None:
+    report.format_detected = "Image Dataset (directory)"
+
+    # Check for split subdirectories
+    subdirs = [d for d in path.iterdir() if d.is_dir()]
+    split_dirs = [d for d in subdirs if d.name.lower() in (s.lower() for s in split_names)]
+
+    if split_dirs:
+        # Split-structured dataset: path/train/class/img.jpg
+        for split_dir in split_dirs:
+            class_dirs = [d for d in split_dir.iterdir() if d.is_dir()]
+            split_count = sum(
+                len([f for f in cd.iterdir() if f.suffix.lower() in IMAGE_EXTENSIONS])
+                for cd in class_dirs
+            )
+            report.splits_found[split_dir.name] = split_count
+
+        # Analyze class distribution from train split (or first split)
+        ref_split = next((d for d in split_dirs if "train" in d.name.lower()), split_dirs[0])
+        _analyze_class_structure(ref_split, report)
+    else:
+        # Flat or class-labeled directory: path/class/img.jpg
+        _analyze_class_structure(path, report)
+
+    report.total_images = sum(c.count for c in report.classes)
+
+    # Sample image sizes
+    if HAS_PIL:
+        _sample_image_sizes(path, report)
+    else:
+        report.warnings.append(
+            "PIL not installed — skipping image size and corruption checks. "
+            "Install with: pip install Pillow"
+        )
+
+    # Class balance check
+    if report.classes:
+        counts = [c.count for c in report.classes]
+        max_c, min_c = max(counts), min(counts)
+        if min_c > 0 and max_c / min_c > 5:
+            report.warnings.append(
+                f"Severe class imbalance detected: ratio {max_c/min_c:.1f}:1 "
+                f"({report.classes[counts.index(max_c)].name} vs "
+                f"{report.classes[counts.index(min_c)].name}). "
+                f"Consider oversampling, undersampling, or weighted loss."
+            )
+        elif min_c > 0 and max_c / min_c > 2:
+            report.warnings.append(
+                f"Moderate class imbalance: ratio {max_c/min_c:.1f}:1. "
+                f"Monitor per-class metrics during training."
+            )
+
+
+def _analyze_class_structure(base_dir: Path, report: EDAReport) -> None:
+    class_dirs = [d for d in base_dir.iterdir() if d.is_dir()]
+    if class_dirs:
+        for class_dir in sorted(class_dirs):
+            images = [f for f in class_dir.iterdir() if f.suffix.lower() in IMAGE_EXTENSIONS]
+            report.classes.append(ClassInfo(
+                name=class_dir.name,
+                count=len(images),
+                sample_files=[f.name for f in images[:3]],
+            ))
+    else:
+        # Flat directory
+        images = [f for f in base_dir.iterdir() if f.suffix.lower() in IMAGE_EXTENSIONS]
+        if images:
+            report.classes.append(ClassInfo(name="(unlabeled)", count=len(images)))
+            report.warnings.append(
+                "No class subdirectories found — images appear unlabeled. "
+                "Organize into class subdirectories for supervised training."
+            )
+
+
+def _sample_image_sizes(base_dir: Path, report: EDAReport, max_samples: int = 100) -> None:
+    all_images = list(base_dir.rglob("*"))
+    image_files = [f for f in all_images if f.suffix.lower() in IMAGE_EXTENSIONS][:max_samples]
+    sizes: list[tuple[int, int]] = []
+
+    for img_path in image_files:
+        try:
+            with Image.open(img_path) as img:
+                sizes.append(img.size)  # (width, height)
+        except Exception:
+            report.corrupt_files.append(str(img_path.relative_to(base_dir)))
+
+    report.image_sizes = sizes
+    if report.corrupt_files:
+        report.warnings.append(
+            f"{len(report.corrupt_files)} corrupt or unreadable image(s) found."
+        )
+
+    if sizes:
+        unique_sizes = set(sizes)
+        if len(unique_sizes) > 1:
+            report.warnings.append(
+                f"Inconsistent image sizes detected: {len(unique_sizes)} unique sizes in sample. "
+                f"Most common: {Counter(sizes).most_common(1)[0][0]}. "
+                f"Consider resizing to a fixed resolution."
+            )
+
+
+# ── CSV / tabular analysis ─────────────────────────────────────────────────────
+
+def analyze_csv(path: Path, report: EDAReport) -> None:
+    import csv
+    report.format_detected = "CSV/Tabular Dataset"
+
+    with path.open(newline="", encoding="utf-8", errors="replace") as f:
+        reader = csv.DictReader(f)
+        rows = list(reader)
+
+    if not rows:
+        report.errors.append("CSV file is empty.")
+        return
+
+    report.columns = list(rows[0].keys())
+    report.num_rows = len(rows)
+    report.num_cols = len(report.columns)
+
+    # Missing values per column
+    for col in report.columns:
+        missing = sum(1 for row in rows if not row.get(col, "").strip())
+        if missing:
+            report.missing_values[col] = missing
+
+    # Detect label column (common names)
+    label_col = next(
+        (c for c in report.columns if c.lower() in ("label", "class", "target", "y", "category")),
+        None,
+    )
+    if label_col:
+        label_counts = Counter(row[label_col].strip() for row in rows if row.get(label_col))
+        report.label_distribution = dict(label_counts.most_common())
+
+        counts = list(label_counts.values())
+        if counts and max(counts) / max(min(counts), 1) > 5:
+            report.warnings.append(
+                f"Class imbalance in '{label_col}': "
+                f"ratio {max(counts)/min(counts):.1f}:1"
+            )
+    else:
+        report.warnings.append(
+            "No standard label column found (tried: label, class, target, y, category). "
+            "Verify your column names."
+        )
+
+    # Numeric stats for up to 10 columns
+    if HAS_NUMPY:
+        numeric_cols = []
+        for col in report.columns[:20]:
+            try:
+                vals = [float(row[col]) for row in rows if row.get(col, "").strip()]
+                if vals:
+                    arr = np.array(vals)
+                    report.numeric_stats[col] = {
+                        "mean": float(arr.mean()),
+                        "std": float(arr.std()),
+                        "min": float(arr.min()),
+                        "max": float(arr.max()),
+                        "missing": report.missing_values.get(col, 0),
+                    }
+                    numeric_cols.append(col)
+                if len(numeric_cols) >= 10:
+                    break
+            except ValueError:
+                pass
+
+
+# ── NumPy analysis ─────────────────────────────────────────────────────────────
+
+def analyze_numpy(path: Path, report: EDAReport) -> None:
+    if not HAS_NUMPY:
+        report.errors.append("numpy not installed. Install with: pip install numpy")
+        return
+
+    report.format_detected = "NumPy Array"
+    if path.suffix == ".npz":
+        data = np.load(path, allow_pickle=True)
+        for key in data.files:
+            arr = data[key]
+            report.array_shapes.append((key, arr.shape))
+            report.array_dtypes.append(f"{key}: {arr.dtype}")
+            if arr.dtype.kind in ("f", "i", "u"):
+                report.array_stats[key] = {
+                    "shape": arr.shape,
+                    "dtype": str(arr.dtype),
+                    "min": float(arr.min()),
+                    "max": float(arr.max()),
+                    "mean": float(arr.mean()),
+                    "nan_count": int(np.isnan(arr).sum()) if arr.dtype.kind == "f" else 0,
+                }
+    else:
+        arr = np.load(path, allow_pickle=True)
+        report.array_shapes.append(("array", arr.shape))
+        report.array_dtypes.append(str(arr.dtype))
+        if arr.dtype.kind in ("f", "i", "u"):
+            report.array_stats["array"] = {
+                "shape": arr.shape,
+                "dtype": str(arr.dtype),
+                "min": float(arr.min()),
+                "max": float(arr.max()),
+                "mean": float(arr.mean()),
+                "nan_count": int(np.isnan(arr).sum()) if arr.dtype.kind == "f" else 0,
+            }
+
+
+# ── HDF5 analysis ──────────────────────────────────────────────────────────────
+
+def analyze_hdf5(path: Path, report: EDAReport) -> None:
+    if not HAS_H5PY:
+        report.errors.append("h5py not installed. Install with: pip install h5py")
+        return
+
+    report.format_detected = "HDF5 File"
+    with h5py.File(path, "r") as f:
+        def visitor(name, obj):
+            if isinstance(obj, h5py.Dataset):
+                report.hdf5_keys.append(name)
+                report.hdf5_shapes[name] = obj.shape
+
+        f.visititems(visitor)
+
+    if not report.hdf5_keys:
+        report.warnings.append("HDF5 file contains no datasets.")
+
+
+# ── JSON annotation analysis ───────────────────────────────────────────────────
+
+def analyze_json_annotations(path: Path, report: EDAReport) -> None:
+    report.format_detected = "JSON Annotations"
+    data = json.loads(path.read_text(encoding="utf-8"))
+
+    # COCO format detection
+    if isinstance(data, dict) and "annotations" in data and "categories" in data:
+        categories = {c["id"]: c["name"] for c in data.get("categories", [])}
+        ann_counts: Counter = Counter()
+        for ann in data.get("annotations", []):
+            cat_id = ann.get("category_id")
+            ann_counts[categories.get(cat_id, f"id_{cat_id}")] += 1
+
+        report.annotation_count = len(data["annotations"])
+        report.annotation_classes = dict(ann_counts)
+
+        # Images without annotations
+        annotated_images = {ann["image_id"] for ann in data["annotations"]}
+        total_images = len(data.get("images", []))
+        report.images_without_annotations = total_images - len(annotated_images)
+        if report.images_without_annotations > 0:
+            pct = report.images_without_annotations / max(total_images, 1) * 100
+            report.warnings.append(
+                f"{report.images_without_annotations} images ({pct:.1f}%) have no annotations."
+            )
+        return
+
+    # Flat label dict format: {"image.jpg": "class_name", ...}
+    if isinstance(data, dict):
+        counter: Counter = Counter(str(v) for v in data.values())
+        report.annotation_classes = dict(counter)
+        report.annotation_count = len(data)
+        return
+
+    # List of dicts: [{"image": "...", "label": "..."}, ...]
+    if isinstance(data, list) and data and isinstance(data[0], dict):
+        label_key = next(
+            (k for k in data[0] if k.lower() in ("label", "class", "category", "target")),
+            None,
+        )
+        if label_key:
+            counter = Counter(str(item.get(label_key, "unknown")) for item in data)
+            report.annotation_classes = dict(counter)
+        report.annotation_count = len(data)
+
+
+# ── Report generation ──────────────────────────────────────────────────────────
+
+def generate_markdown_report(report: EDAReport) -> str:
+    lines: list[str] = []
+    now = datetime.now().strftime("%Y-%m-%d %H:%M")
+
+    lines += [
+        f"# EDA Report: {report.data_path.name}",
+        f"*Generated: {now} | Format: {report.format_detected}*",
+        "",
+        "---",
+        "",
+        "## A. Dataset Overview",
+        "",
+        f"| Property | Value |",
+        f"| :--- | :--- |",
+        f"| Path | `{report.data_path}` |",
+        f"| Format | {report.format_detected} |",
+    ]
+
+    # Format-specific overview
+    if report.classes:
+        lines += [
+            f"| Total Images | {report.total_images:,} |",
+            f"| Number of Classes | {len(report.classes)} |",
+        ]
+        if report.splits_found:
+            for split, count in report.splits_found.items():
+                lines.append(f"| Split: {split} | {count:,} images |")
+    if report.num_rows:
+        lines += [
+            f"| Rows | {report.num_rows:,} |",
+            f"| Columns | {report.num_cols} |",
+        ]
+
+    lines += ["", "---", "", "## B. Class Distribution", ""]
+
+    if report.classes:
+        total = sum(c.count for c in report.classes) or 1
+        lines += [
+            "| Class | Count | % of Total |",
+            "| :--- | ---: | ---: |",
+        ]
+        for c in sorted(report.classes, key=lambda x: -x.count):
+            pct = c.count / total * 100
+            bar = "█" * int(pct / 5)
+            lines.append(f"| {c.name} | {c.count:,} | {pct:.1f}% {bar} |")
+
+    elif report.label_distribution:
+        total = sum(report.label_distribution.values()) or 1
+        lines += [
+            "| Label | Count | % of Total |",
+            "| :--- | ---: | ---: |",
+        ]
+        for label, count in report.label_distribution.items():
+            pct = count / total * 100
+            lines.append(f"| {label} | {count:,} | {pct:.1f}% |")
+
+    elif report.annotation_classes:
+        lines += [
+            f"Total annotations: {report.annotation_count:,}",
+            "",
+            "| Class | Count |",
+            "| :--- | ---: |",
+        ]
+        for cls, count in sorted(report.annotation_classes.items(), key=lambda x: -x[1]):
+            lines.append(f"| {cls} | {count:,} |")
+
+    else:
+        lines.append("*No class/label information available.*")
+
+    lines += ["", "---", "", "## C. Data Quality Assessment", ""]
+
+    # Image sizes
+    if report.image_sizes:
+        from collections import Counter as C
+        size_counts = C(report.image_sizes)
+        most_common_size, count = size_counts.most_common(1)[0]
+        pct = count / len(report.image_sizes) * 100
+        lines += [
+            f"| Property | Value |",
+            f"| :--- | :--- |",
+            f"| Most common image size | {most_common_size[0]}×{most_common_size[1]}px ({pct:.0f}% of sample) |",
+            f"| Unique sizes in sample | {len(size_counts)} |",
+            f"| Corrupt/unreadable files | {len(report.corrupt_files)} |",
+            "",
+        ]
+
+    # Missing values
+    if report.missing_values:
+        total = report.num_rows or 1
+        lines += [
+            "**Missing Values:**",
+            "",
+            "| Column | Missing | % |",
+            "| :--- | ---: | ---: |",
+        ]
+        for col, count in sorted(report.missing_values.items(), key=lambda x: -x[1]):
+            lines.append(f"| {col} | {count} | {count/total*100:.1f}% |")
+        lines.append("")
+    elif report.num_rows:
+        lines.append("✓ No missing values detected.")
+        lines.append("")
+
+    # NumPy stats
+    if report.array_stats:
+        lines += ["**Array Statistics:**", ""]
+        for key, stats in report.array_stats.items():
+            lines += [
+                f"*{key}*: shape={stats['shape']}, dtype={stats['dtype']}  ",
+                f"min={stats['min']:.4f}, max={stats['max']:.4f}, mean={stats['mean']:.4f}",
+                f"NaN count: {stats.get('nan_count', 0)}",
+                "",
+            ]
+
+    # HDF5
+    if report.hdf5_keys:
+        lines += [
+            "**HDF5 Datasets:**", "",
+            "| Dataset | Shape |",
+            "| :--- | :--- |",
+        ]
+        for key in report.hdf5_keys:
+            lines.append(f"| {key} | {report.hdf5_shapes[key]} |")
+        lines.append("")
+
+    # Split verification
+    lines += ["---", "", "## D. Split Verification", ""]
+    if report.splits_found:
+        total_split = sum(report.splits_found.values()) or 1
+        lines += [
+            "| Split | Count | % |",
+            "| :--- | ---: | ---: |",
+        ]
+        for split, count in report.splits_found.items():
+            pct = count / total_split * 100
+            lines.append(f"| {split} | {count:,} | {pct:.1f}% |")
+
+        # Check for reasonable split ratios
+        counts = list(report.splits_found.values())
+        if len(counts) >= 2:
+            train_count = report.splits_found.get("train", counts[0])
+            if train_count / total_split < 0.5:
+                report.warnings.append(
+                    f"Training split is only {train_count/total_split*100:.0f}% of total data. "
+                    f"Typical splits: 70-80% train, 10-15% val, 10-15% test."
+                )
+    else:
+        lines.append("⚠ No explicit split directories found.")
+        lines.append(
+            "Ensure you implement train/val/test splits in your DataLoader. "
+            "Recommended: 70/15/15 or 80/10/10."
+        )
+
+    # Warnings and errors
+    if report.warnings or report.errors:
+        lines += ["", "---", "", "## E. Issues & Recommendations", ""]
+        for w in report.warnings:
+            lines.append(f"⚠ **Warning:** {w}")
+        for e in report.errors:
+            lines.append(f"✗ **Error:** {e}")
+        lines.append("")
+
+    lines += [
+        "---",
+        "",
+        "## F. EDA Summary for TSK-001",
+        "",
+        "| Check | Status |",
+        "| :--- | :--- |",
+        f"| Class distribution analyzed | {'✓' if report.classes or report.label_distribution or report.annotation_classes else '✗'} |",
+        f"| Missing/corrupt data checked | {'✓' if not report.errors else '⚠'} |",
+        f"| Class imbalance assessed | {'✓' if report.classes or report.label_distribution else 'N/A'} |",
+        f"| Split structure verified | {'✓' if report.splits_found else '⚠ manual check needed'} |",
+        f"| Issues found | {len(report.warnings)} warning(s), {len(report.errors)} error(s) |",
+        "",
+        "*Complete this EDA before proceeding to TSK-002 (DataLoader implementation).*",
+    ]
+
+    return "\n".join(lines)
+
+
+# ── Main ───────────────────────────────────────────────────────────────────────
+
+def analyze(data_path: Path, split_names: list[str] | None = None) -> EDAReport:
+    split_names = split_names or ["train", "val", "test", "validation"]
+    report = EDAReport(data_path=data_path, format_detected="unknown")
+    fmt = detect_format(data_path)
+
+    if fmt == "image_dir":
+        analyze_image_dir(data_path, report, split_names)
+    elif fmt == "csv":
+        analyze_csv(data_path, report)
+    elif fmt == "numpy":
+        analyze_numpy(data_path, report)
+    elif fmt == "hdf5":
+        analyze_hdf5(data_path, report)
+    elif fmt == "json_annotations":
+        analyze_json_annotations(data_path, report)
+    else:
+        report.errors.append(
+            f"Unrecognized format for '{data_path}'. "
+            f"Supported: image directory, CSV, .npy/.npz, .h5/.hdf5, .json (annotations)"
+        )
+
+    return report
+
+
+def main() -> int:
+    parser = argparse.ArgumentParser(description="ML EDA Analyzer for BMAD DL Lifecycle")
+    parser.add_argument("data_path", type=Path, help="Path to dataset file or directory")
+    parser.add_argument("--output", type=Path, default=None,
+                        help="Output markdown report path (default: <data_path>_eda_report.md)")
+    parser.add_argument("--splits", nargs="+", default=["train", "val", "test"],
+                        help="Expected split directory names")
+    args = parser.parse_args()
+
+    if not args.data_path.exists():
+        print(f"Error: Path not found: {args.data_path}", file=sys.stderr)
+        return 2
+
+    report = analyze(args.data_path, args.splits)
+    markdown = generate_markdown_report(report)
+
+    output_path = args.output or args.data_path.parent / f"{args.data_path.stem}_eda_report.md"
+    output_path.write_text(markdown, encoding="utf-8")
+
+    print(f"\n✓ EDA report written to: {output_path}")
+    print(f"  Format: {report.format_detected}")
+    if report.classes:
+        print(f"  Classes: {len(report.classes)}, Total samples: {report.total_images:,}")
+    if report.warnings:
+        print(f"  ⚠ {len(report.warnings)} warning(s) — review report for details")
+    if report.errors:
+        print(f"  ✗ {len(report.errors)} error(s)")
+        return 1
+
+    return 0
+
+
+if __name__ == "__main__":
+    sys.exit(main())

package/lib/bmad-extension-plugin/skills/ml-eda/skill.json

@@ -0,0 +1,7 @@
+{
+  "name": "ML Exploratory Data Analysis (EDA)",
+  "description": "Performs statistical analysis, establishes performance baselines, and interprets results with the Scientist Demerzel.",
+  "version": "1.0.0",
+  "author": "Demerzel (ML Scientist)",
+  "tags": ["Machine Learning", "Exploratory Data Analysis", "EDA", "Baselines"]
+}