napari-tmidas 0.2.1__py3-none-any.whl → 0.2.4__py3-none-any.whl

napari_tmidas/processing_functions/intensity_label_filter.py

@@ -0,0 +1,422 @@
+# processing_functions/intensity_label_filter.py
+"""
+Processing functions for filtering labels based on intensity using k-medoids clustering.
+"""
+import inspect
+from pathlib import Path
+from typing import Dict
+
+import numpy as np
+from skimage import measure
+
+from napari_tmidas._registry import BatchProcessingRegistry
+
+
+def _convert_semantic_to_instance(image: np.ndarray) -> np.ndarray:
+    """
+    Convert semantic labels (where all objects have the same value) to instance labels.
+
+    Parameters
+    ----------
+    image : np.ndarray
+        Label image that may contain semantic labels
+
+    Returns
+    -------
+    np.ndarray
+        Image with instance labels (each connected component gets unique label)
+    """
+    if image is None or np.all(image == 0):
+        return image
+
+    # Get unique non-zero values
+    unique_labels = np.unique(image[image != 0])
+
+    # If there's only one unique non-zero value, it's definitely semantic
+    if len(unique_labels) == 1:
+        # Single semantic label - convert to instance labels
+        mask = image > 0
+        return measure.label(mask, connectivity=None)
+    else:
+        # Multiple labels - already instance labels
+        return image
+
+
+# Lazy imports for optional dependencies
+try:
+    from sklearn_extra.cluster import KMedoids
+
+    _HAS_KMEDOIDS = True
+except ImportError:
+    KMedoids = None
+    _HAS_KMEDOIDS = False
+    print(
+        "scikit-learn-extra not available. Install with: pip install scikit-learn-extra"
+    )
+
+try:
+    import pandas as pd
+
+    _HAS_PANDAS = True
+except ImportError:
+    pd = None
+    _HAS_PANDAS = False
+
+
+def _calculate_label_mean_intensities(
+    label_image: np.ndarray, intensity_image: np.ndarray
+) -> Dict[int, float]:
+    """
+    Calculate mean intensity for each label.
+
+    Parameters
+    ----------
+    label_image : np.ndarray
+        Label image with integer labels
+    intensity_image : np.ndarray
+        Intensity image corresponding to the label image
+
+    Returns
+    -------
+    Dict[int, float]
+        Dictionary mapping label IDs to mean intensities
+    """
+    # Use regionprops to calculate mean intensity for each label
+    props = measure.regionprops_table(
+        label_image, intensity_image, properties=["label", "intensity_mean"]
+    )
+
+    return dict(zip(props["label"], props["intensity_mean"]))
+
+
+def _cluster_intensities(
+    intensities: np.ndarray, n_clusters: int
+) -> tuple[np.ndarray, np.ndarray, float]:
+    """
+    Cluster intensities using k-medoids and determine threshold.
+
+    Parameters
+    ----------
+    intensities : np.ndarray
+        Array of intensity values to cluster
+    n_clusters : int
+        Number of clusters (2 or 3)
+
+    Returns
+    -------
+    tuple[np.ndarray, np.ndarray, float]
+        Cluster labels, cluster centers (medoids), and threshold value
+    """
+    if not _HAS_KMEDOIDS:
+        raise ImportError(
+            "scikit-learn-extra is required for k-medoids clustering. "
+            "Install with: pip install scikit-learn-extra"
+        )
+
+    # Reshape for sklearn
+    X = intensities.reshape(-1, 1)
+
+    # Perform k-medoids clustering
+    kmedoids = KMedoids(n_clusters=n_clusters, random_state=42, method="pam")
+    cluster_labels = kmedoids.fit_predict(X)
+    medoids = kmedoids.cluster_centers_.flatten()
+
+    # Sort medoids to identify clusters from low to high intensity
+    sorted_indices = np.argsort(medoids)
+    sorted_medoids = medoids[sorted_indices]
+
+    # Create mapping from old cluster labels to sorted cluster labels
+    label_mapping = {
+        old_label: new_label
+        for new_label, old_label in enumerate(sorted_indices)
+    }
+    sorted_labels = np.array(
+        [label_mapping[label] for label in cluster_labels]
+    )
+
+    # Determine threshold between lowest and second-lowest clusters
+    # Use midpoint between the two lowest cluster centers
+    threshold = (sorted_medoids[0] + sorted_medoids[1]) / 2.0
+
+    return sorted_labels, sorted_medoids, threshold
+
+
+def _get_intensity_filename(
+    label_filename: str, label_suffix: str = "_convpaint_labels_filtered.tif"
+) -> str:
+    """
+    Convert label filename to intensity filename by removing suffix.
+
+    Parameters
+    ----------
+    label_filename : str
+        Filename of the label image
+    label_suffix : str
+        Suffix to remove from label filename (default: "_convpaint_labels_filtered.tif")
+
+    Returns
+    -------
+    str
+        Intensity image filename
+    """
+    if label_filename.endswith(label_suffix):
+        # Remove the label suffix and add .tif
+        base_name = label_filename[: -len(label_suffix)]
+        return base_name + ".tif"
+    else:
+        # If suffix doesn't match, assume same filename
+        return label_filename
+
+
+def _filter_labels_by_threshold(
+    label_image: np.ndarray,
+    label_intensities: Dict[int, float],
+    threshold: float,
+) -> np.ndarray:
+    """
+    Filter labels based on intensity threshold.
+
+    Parameters
+    ----------
+    label_image : np.ndarray
+        Label image with integer labels
+    label_intensities : Dict[int, float]
+        Dictionary mapping label IDs to mean intensities
+    threshold : float
+        Intensity threshold - labels below this are removed
+
+    Returns
+    -------
+    np.ndarray
+        Filtered label image with same dtype as input
+    """
+    filtered_image = label_image.copy()
+
+    # Remove labels with intensity below threshold
+    for label_id, intensity in label_intensities.items():
+        if intensity < threshold:
+            filtered_image[label_image == label_id] = 0
+
+    return filtered_image
+
+
+@BatchProcessingRegistry.register(
+    name="Filter Labels by Intensity (K-medoids)",
+    suffix="_intensity_filtered",
+    description="Filter out labels with low intensity using k-medoids clustering. Finds corresponding intensity image in same folder. Choose 2 clusters for simple low/high separation, or 3 clusters when you have distinct noise/signal/strong-signal populations.",
+    parameters={
+        "n_clusters": {
+            "type": int,
+            "default": 2,
+            "description": "Number of clusters (2 or 3). Use 2 for simple low/high separation, 3 for noise/diffuse/strong separation.",
+        },
+        "save_stats": {
+            "type": bool,
+            "default": True,
+            "description": "Save clustering statistics to CSV file",
+        },
+    },
+)
+def filter_labels_by_intensity(
+    image: np.ndarray,
+    n_clusters: int = 2,
+    save_stats: bool = True,
+) -> np.ndarray:
+    """
+    Filter labels based on intensity using k-medoids clustering.
+
+    This function processes pairs of label and intensity images in the same folder.
+    For each label image, it finds the corresponding intensity image (removes
+    "_convpaint_labels_filtered.tif" suffix from label filename to find intensity file),
+    calculates mean intensity per label, performs k-medoids clustering to identify
+    intensity groups, and filters out labels in the low intensity cluster.
+
+    Use n_clusters=2 for simple separation (bad vs. good signal).
+    Use n_clusters=3 when you have distinct populations (noise, diffuse signal, strong signal).
+
+    Parameters
+    ----------
+    image : np.ndarray
+        Label image with integer labels
+    n_clusters : int
+        Number of clusters (2 or 3)
+    save_stats : bool
+        Whether to save clustering statistics to CSV
+
+    Returns
+    -------
+    np.ndarray
+        Filtered label image with low-intensity labels removed
+    """
+    # Extract current filepath from call stack
+    current_filepath = None
+    for frame_info in inspect.stack():
+        frame_locals = frame_info.frame.f_locals
+        if "filepath" in frame_locals:
+            current_filepath = frame_locals["filepath"]
+            break
+
+    if current_filepath is None:
+        raise ValueError(
+            "Could not determine current file path from call stack"
+        )
+
+    if n_clusters not in [2, 3]:
+        raise ValueError(f"n_clusters must be 2 or 3, got {n_clusters}")
+
+    # Convert semantic labels to instance labels if needed
+    original_dtype = image.dtype
+    image = _convert_semantic_to_instance(image)
+
+    # Check if we actually have any labels after conversion
+    unique_labels = np.unique(image[image != 0])
+    if len(unique_labels) == 0:
+        print("⚠️  No labels found in image, returning empty image")
+        return np.zeros_like(image)
+
+    print(f"📋 Found {len(unique_labels)} labels in the image")
+
+    # Find corresponding intensity image in same folder
+    label_path = Path(current_filepath)
+    label_filename = label_path.name
+    intensity_filename = _get_intensity_filename(label_filename)
+    intensity_path = label_path.parent / intensity_filename
+
+    if not intensity_path.exists():
+        print(
+            f"⚠️  No corresponding intensity image found for {label_filename}"
+        )
+        print(f"   Expected: {intensity_filename}")
+        print(f"   Full path: {intensity_path}")
+        print("   Skipping this file...")
+        return image  # Return original image unchanged
+
+    # Load intensity image directly with tifffile
+    try:
+        import tifffile
+
+        intensity_image = tifffile.imread(str(intensity_path))
+    except (FileNotFoundError, OSError) as e:
+        print(f"⚠️  Could not read intensity image: {intensity_path}")
+        print(f"   Error: {e}")
+        print("   Skipping this file...")
+        return image  # Return original if can't read intensity image
+
+    # Validate dimensions match
+    if image.shape != intensity_image.shape:
+        raise ValueError(
+            f"Label and intensity images must have same shape. "
+            f"Label: {image.shape}, Intensity: {intensity_image.shape}"
+        )
+
+    # Calculate mean intensity for each label
+    label_intensities = _calculate_label_mean_intensities(
+        image, intensity_image
+    )
+
+    if len(label_intensities) == 0:
+        print(f"⚠️  No labels found in {label_filename}, returning empty image")
+        return np.zeros_like(image)
+
+    # Perform k-medoids clustering
+    intensities = np.array(list(label_intensities.values()))
+    cluster_labels, medoids, threshold = _cluster_intensities(
+        intensities, n_clusters=n_clusters
+    )
+
+    # Print results based on number of clusters
+    print(f"📊 {label_filename}:")
+    print(f"   Total labels: {len(label_intensities)}")
+
+    if n_clusters == 2:
+        n_low = np.sum(cluster_labels == 0)
+        n_high = np.sum(cluster_labels == 1)
+        print(
+            f"   Low intensity cluster: {n_low} labels (medoid: {medoids[0]:.2f})"
+        )
+        print(
+            f"   High intensity cluster: {n_high} labels (medoid: {medoids[1]:.2f})"
+        )
+        print(f"   Threshold: {threshold:.2f}")
+        print(f"   Keeping {n_high} labels, removing {n_low} labels")
+
+        # Save statistics if requested
+        if save_stats and _HAS_PANDAS:
+            stats = {
+                "filename": label_filename,
+                "n_clusters": n_clusters,
+                "total_labels": len(label_intensities),
+                "low_cluster_count": n_low,
+                "high_cluster_count": n_high,
+                "low_cluster_medoid": medoids[0],
+                "high_cluster_medoid": medoids[1],
+                "threshold": threshold,
+            }
+
+            stats_dir = (
+                Path(current_filepath).parent / "intensity_filter_stats"
+            )
+            stats_dir.mkdir(exist_ok=True)
+            stats_file = stats_dir / "clustering_stats.csv"
+
+            df = pd.DataFrame([stats])
+            if stats_file.exists():
+                df.to_csv(stats_file, mode="a", header=False, index=False)
+            else:
+                df.to_csv(stats_file, index=False)
+
+    else:  # n_clusters == 3
+        n_low = np.sum(cluster_labels == 0)
+        n_medium = np.sum(cluster_labels == 1)
+        n_high = np.sum(cluster_labels == 2)
+        print(
+            f"   Low intensity cluster: {n_low} labels (medoid: {medoids[0]:.2f})"
+        )
+        print(
+            f"   Medium intensity cluster: {n_medium} labels (medoid: {medoids[1]:.2f})"
+        )
+        print(
+            f"   High intensity cluster: {n_high} labels (medoid: {medoids[2]:.2f})"
+        )
+        print(f"   Threshold: {threshold:.2f}")
+        print(
+            f"   Keeping {n_medium + n_high} labels, removing {n_low} labels"
+        )
+
+        # Save statistics if requested
+        if save_stats and _HAS_PANDAS:
+            stats = {
+                "filename": label_filename,
+                "n_clusters": n_clusters,
+                "total_labels": len(label_intensities),
+                "low_cluster_count": n_low,
+                "medium_cluster_count": n_medium,
+                "high_cluster_count": n_high,
+                "low_cluster_medoid": medoids[0],
+                "medium_cluster_medoid": medoids[1],
+                "high_cluster_medoid": medoids[2],
+                "threshold": threshold,
+            }
+
+            stats_dir = (
+                Path(current_filepath).parent / "intensity_filter_stats"
+            )
+            stats_dir.mkdir(exist_ok=True)
+            stats_file = stats_dir / "clustering_stats.csv"
+
+            df = pd.DataFrame([stats])
+            if stats_file.exists():
+                df.to_csv(stats_file, mode="a", header=False, index=False)
+            else:
+                df.to_csv(stats_file, index=False)
+
+    # Filter labels
+    filtered_image = _filter_labels_by_threshold(
+        image, label_intensities, threshold
+    )
+
+    # Convert back to original dtype
+    if filtered_image.dtype != original_dtype:
+        filtered_image = filtered_image.astype(original_dtype)
+
+    return filtered_image