landmarkdiff 0.2.3__py3-none-any.whl

landmarkdiff/data_version.py

@@ -0,0 +1,301 @@
+"""Dataset versioning and provenance tracking.
+
+Tracks dataset composition, checksums, and lineage for reproducible training.
+Creates manifest files that record exactly which data was used for each
+training run.
+
+Usage:
+    from landmarkdiff.data_version import DataManifest
+
+    manifest = DataManifest.from_directory("data/training")
+    manifest.save("data/training/manifest.json")
+
+    # Later, verify data hasn't changed
+    manifest2 = DataManifest.from_directory("data/training")
+    assert manifest.checksum == manifest2.checksum
+"""
+
+from __future__ import annotations
+
+import hashlib
+import json
+from dataclasses import dataclass, field
+from datetime import datetime, timezone
+from pathlib import Path
+from typing import Any
+
+
+@dataclass
+class FileEntry:
+    """Metadata for a single dataset file."""
+
+    path: str
+    size_bytes: int
+    checksum: str  # md5 of first 64KB (fast approximate)
+    procedure: str = ""
+
+    @staticmethod
+    def from_path(filepath: Path, base_dir: Path | None = None) -> FileEntry:
+        """Create entry from a file path."""
+        rel = str(filepath.relative_to(base_dir)) if base_dir else str(filepath)
+        size = filepath.stat().st_size
+
+        # Fast checksum: first 64KB
+        h = hashlib.md5()
+        with open(filepath, "rb") as f:
+            h.update(f.read(65536))
+
+        # Infer procedure from filename
+        proc = ""
+        for p in [
+            "rhinoplasty",
+            "blepharoplasty",
+            "rhytidectomy",
+            "orthognathic",
+            "brow_lift",
+            "mentoplasty",
+        ]:
+            if p in filepath.name or p in str(filepath.parent):
+                proc = p
+                break
+
+        return FileEntry(path=rel, size_bytes=size, checksum=h.hexdigest(), procedure=proc)
+
+
+@dataclass
+class DataManifest:
+    """Dataset manifest for versioning and reproducibility.
+
+    Attributes:
+        version: Manifest format version.
+        created_at: Creation timestamp.
+        root_dir: Root directory of the dataset.
+        files: List of file entries.
+        metadata: Additional dataset metadata.
+    """
+
+    version: str = "1.0"
+    created_at: str = field(default_factory=lambda: datetime.now(timezone.utc).isoformat())
+    root_dir: str = ""
+    files: list[FileEntry] = field(default_factory=list)
+    metadata: dict[str, Any] = field(default_factory=dict)
+
+    @property
+    def total_files(self) -> int:
+        return len(self.files)
+
+    @property
+    def total_size_bytes(self) -> int:
+        return sum(f.size_bytes for f in self.files)
+
+    @property
+    def total_size_mb(self) -> float:
+        return self.total_size_bytes / (1024 * 1024)
+
+    @property
+    def checksum(self) -> str:
+        """Compute aggregate checksum from all file checksums."""
+        h = hashlib.md5()
+        for f in sorted(self.files, key=lambda x: x.path):
+            h.update(f"{f.path}:{f.checksum}:{f.size_bytes}".encode())
+        return h.hexdigest()
+
+    @property
+    def by_procedure(self) -> dict[str, int]:
+        """Count files by procedure."""
+        counts: dict[str, int] = {}
+        for f in self.files:
+            key = f.procedure or "unknown"
+            counts[key] = counts.get(key, 0) + 1
+        return counts
+
+    @staticmethod
+    def from_directory(
+        directory: str | Path,
+        extensions: set[str] | None = None,
+        include_patterns: list[str] | None = None,
+    ) -> DataManifest:
+        """Create manifest from a directory of dataset files.
+
+        Args:
+            directory: Path to dataset directory.
+            extensions: File extensions to include (default: image types).
+            include_patterns: Glob patterns to include.
+
+        Returns:
+            DataManifest with entries for all matching files.
+        """
+        directory = Path(directory)
+        if not directory.exists():
+            raise FileNotFoundError(f"Directory not found: {directory}")
+
+        if extensions is None:
+            extensions = {".png", ".jpg", ".jpeg", ".webp", ".npy", ".npz"}
+
+        files: list[FileEntry] = []
+        if include_patterns:
+            for pattern in include_patterns:
+                for fp in sorted(directory.glob(pattern)):
+                    if fp.is_file():
+                        files.append(FileEntry.from_path(fp, base_dir=directory))
+        else:
+            for fp in sorted(directory.rglob("*")):
+                if fp.is_file() and fp.suffix.lower() in extensions:
+                    files.append(FileEntry.from_path(fp, base_dir=directory))
+
+        manifest = DataManifest(
+            root_dir=str(directory),
+            files=files,
+            metadata={
+                "extensions": sorted(extensions),
+                "host": _get_hostname(),
+            },
+        )
+        return manifest
+
+    def save(self, path: str | Path) -> Path:
+        """Save manifest to JSON.
+
+        Args:
+            path: Output file path.
+
+        Returns:
+            Path to saved manifest.
+        """
+        path = Path(path)
+        path.parent.mkdir(parents=True, exist_ok=True)
+
+        data = {
+            "version": self.version,
+            "created_at": self.created_at,
+            "root_dir": self.root_dir,
+            "checksum": self.checksum,
+            "total_files": self.total_files,
+            "total_size_mb": round(self.total_size_mb, 2),
+            "by_procedure": self.by_procedure,
+            "metadata": self.metadata,
+            "files": [
+                {
+                    "path": f.path,
+                    "size_bytes": f.size_bytes,
+                    "checksum": f.checksum,
+                    "procedure": f.procedure,
+                }
+                for f in self.files
+            ],
+        }
+
+        with open(path, "w") as f:
+            json.dump(data, f, indent=2)
+
+        return path
+
+    @staticmethod
+    def load(path: str | Path) -> DataManifest:
+        """Load manifest from JSON.
+
+        Args:
+            path: Path to manifest file.
+
+        Returns:
+            DataManifest instance.
+        """
+        with open(path) as f:
+            data = json.load(f)
+
+        files = [
+            FileEntry(
+                path=fe["path"],
+                size_bytes=fe["size_bytes"],
+                checksum=fe["checksum"],
+                procedure=fe.get("procedure", ""),
+            )
+            for fe in data.get("files", [])
+        ]
+
+        return DataManifest(
+            version=data.get("version", "1.0"),
+            created_at=data.get("created_at", ""),
+            root_dir=data.get("root_dir", ""),
+            files=files,
+            metadata=data.get("metadata", {}),
+        )
+
+    def verify(self, directory: str | Path | None = None) -> tuple[bool, list[str]]:
+        """Verify dataset matches this manifest.
+
+        Args:
+            directory: Directory to verify (default: original root_dir).
+
+        Returns:
+            (all_match, list_of_issues)
+        """
+        directory = Path(directory or self.root_dir)
+        issues: list[str] = []
+
+        for entry in self.files:
+            fp = directory / entry.path
+            if not fp.exists():
+                issues.append(f"Missing: {entry.path}")
+                continue
+
+            actual_size = fp.stat().st_size
+            if actual_size != entry.size_bytes:
+                issues.append(
+                    f"Size mismatch: {entry.path} (expected {entry.size_bytes}, got {actual_size})"
+                )
+
+            # Check checksum
+            h = hashlib.md5()
+            with open(fp, "rb") as f:
+                h.update(f.read(65536))
+            if h.hexdigest() != entry.checksum:
+                issues.append(f"Checksum mismatch: {entry.path}")
+
+        return len(issues) == 0, issues
+
+    def diff(self, other: DataManifest) -> dict[str, list[str]]:
+        """Compare two manifests.
+
+        Returns:
+            Dict with 'added', 'removed', 'modified' file lists.
+        """
+        self_files = {f.path: f for f in self.files}
+        other_files = {f.path: f for f in other.files}
+
+        self_paths = set(self_files.keys())
+        other_paths = set(other_files.keys())
+
+        added = sorted(other_paths - self_paths)
+        removed = sorted(self_paths - other_paths)
+        modified = sorted(
+            p for p in self_paths & other_paths if self_files[p].checksum != other_files[p].checksum
+        )
+
+        return {"added": added, "removed": removed, "modified": modified}
+
+    def summary(self) -> str:
+        """Human-readable summary."""
+        lines = [
+            f"Dataset Manifest v{self.version}",
+            f"  Root: {self.root_dir}",
+            f"  Files: {self.total_files}",
+            f"  Size: {self.total_size_mb:.1f} MB",
+            f"  Checksum: {self.checksum}",
+        ]
+        procs = self.by_procedure
+        if procs:
+            lines.append("  By procedure:")
+            for proc, count in sorted(procs.items()):
+                lines.append(f"    {proc}: {count}")
+        return "\n".join(lines)
+
+
+def _get_hostname() -> str:
+    """Get hostname safely."""
+    try:
+        import socket
+
+        return socket.gethostname()
+    except Exception:
+        return "unknown"