napari-tmidas 0.2.2__py3-none-any.whl → 0.2.5__py3-none-any.whl

napari_tmidas/processing_functions/grid_view_overlay.py

@@ -0,0 +1,703 @@
+# processing_functions/grid_view_overlay.py
+"""
+Processing function for displaying grid view of intensity images overlaid with labels.
+"""
+import concurrent.futures
+import inspect
+import os
+from pathlib import Path
+
+import numpy as np
+from tqdm import tqdm
+
+from napari_tmidas._registry import BatchProcessingRegistry
+
+# Lazy imports for optional dependencies
+try:
+    import tifffile
+
+    _HAS_TIFFFILE = True
+except ImportError:
+    tifffile = None
+    _HAS_TIFFFILE = False
+
+# Global flags to ensure grid is created and saved only once per batch
+_grid_created = False
+_cached_grid = None
+_grid_saved = False
+_grid_output_path = None
+
+
+def _get_intensity_filename(label_filename: str) -> str:
+    """
+    Get intensity filename from label filename by removing label suffix.
+
+    Parameters
+    ----------
+    label_filename : str
+        Label image filename
+
+    Returns
+    -------
+    str
+        Intensity image filename
+    """
+    # Remove common label suffixes (handle both with and without .tif extension)
+    suffixes_to_remove = [
+        "_convpaint_labels_filtered.tif",
+        "_labels_filtered.tif",
+        "_labels.tif",
+        "_intensity_filtered.tif",
+        "_convpaint_labels_filtered",
+        "_labels_filtered",
+        "_labels",
+        "_intensity_filtered",
+    ]
+
+    for suffix in suffixes_to_remove:
+        if label_filename.endswith(suffix):
+            base = label_filename.replace(suffix, "")
+            # Ensure .tif extension
+            if not base.endswith(".tif"):
+                base += ".tif"
+            return base
+
+    # If no known suffix found, just use the filename as-is (already has .tif)
+    return label_filename
+
+
+def _downsample_image(image: np.ndarray, target_size: int) -> np.ndarray:
+    """
+    Downsample image to target size while preserving aspect ratio.
+
+    Uses skimage which handles all dtypes including uint32.
+
+    Parameters
+    ----------
+    image : np.ndarray
+        Input image
+    target_size : int
+        Target size for the larger dimension
+
+    Returns
+    -------
+    np.ndarray
+        Downsampled image
+    """
+    from skimage.transform import resize
+
+    h, w = image.shape[:2]
+    max_dim = max(h, w)
+
+    if max_dim <= target_size:
+        return image  # No downsampling needed
+
+    scale = target_size / max_dim
+    new_h = int(h * scale)
+    new_w = int(w * scale)
+
+    # skimage handles all dtypes including uint32
+    if len(image.shape) == 2:
+        downsampled = resize(
+            image,
+            (new_h, new_w),
+            order=1,
+            preserve_range=True,
+            anti_aliasing=True,
+        )
+    else:
+        downsampled = resize(
+            image,
+            (new_h, new_w, image.shape[2]),
+            order=1,
+            preserve_range=True,
+            anti_aliasing=True,
+        )
+
+    return downsampled.astype(image.dtype)
+
+
+def _create_overlay(
+    intensity_image: np.ndarray,
+    label_image: np.ndarray,
+    target_size: int = None,
+    label_opacity: float = 0.6,
+    show_overlay: bool = True,
+) -> np.ndarray:
+    """
+    Create an overlay of intensity and label images with transparency.
+
+    Parameters
+    ----------
+    intensity_image : np.ndarray
+        Intensity image
+    label_image : np.ndarray
+        Label image
+    target_size : int, optional
+        Target size for downsampling (max dimension). If None, no downsampling.
+    label_opacity : float, optional
+        Opacity of label overlay (0-1). Default is 0.6 (60%).
+    show_overlay : bool, optional
+        If True, show colored label overlay on intensity (default).
+        If False, show only intensity in grayscale.
+
+    Returns
+    -------
+    np.ndarray
+        RGB overlay image with intensity in grayscale and optional colored label regions
+    """
+    # Downsample if target size specified
+    if target_size is not None:
+        intensity_image = _downsample_image(intensity_image, target_size)
+        # Use nearest neighbor for labels to preserve label IDs
+        h, w = intensity_image.shape
+        if label_image.shape != (h, w):
+            from skimage.transform import resize
+
+            # skimage handles uint32 natively, use order=0 for nearest neighbor
+            label_image = resize(
+                label_image,
+                (h, w),
+                order=0,
+                preserve_range=True,
+                anti_aliasing=False,
+            ).astype(label_image.dtype)
+
+    # Normalize intensity image to 0-1 range
+    if (
+        intensity_image.dtype != np.float32
+        and intensity_image.dtype != np.float64
+    ):
+        intensity_norm = intensity_image.astype(np.float32)
+    else:
+        intensity_norm = intensity_image.copy()
+
+    if intensity_norm.max() > 0:
+        intensity_norm = (intensity_norm - intensity_norm.min()) / (
+            intensity_norm.max() - intensity_norm.min()
+        )
+
+    # Create RGB image with intensity in grayscale (all channels)
+    h, w = intensity_norm.shape
+    rgb = np.zeros((h, w, 3), dtype=np.float32)
+    rgb[:, :, 0] = intensity_norm  # Red
+    rgb[:, :, 1] = intensity_norm  # Green
+    rgb[:, :, 2] = intensity_norm  # Blue
+
+    # Create colored label overlay using simple colormap (only if show_overlay is True)
+    if show_overlay:
+        # Generate colors for each unique label (excluding background)
+        unique_labels = np.unique(label_image)
+        unique_labels = unique_labels[unique_labels > 0]  # Exclude background
+
+        if len(unique_labels) == 0:
+            # No labels found - image will be grayscale only
+            pass  # rgb already has intensity in all channels (grayscale)
+        elif len(unique_labels) > 0:
+            # Create a simple colormap using hue variation
+            # Use modulo to cycle through distinct colors even with many labels
+            for i, label_id in enumerate(unique_labels):
+                mask = label_image == label_id
+
+                # Generate color by cycling through hue values (0-360 degrees)
+                hue = (
+                    i * 137.5
+                ) % 360  # Golden angle for better color distribution
+
+                # Convert HSV to RGB (H=hue, S=1, V=1)
+                h_norm = hue / 60.0
+                h_int = int(h_norm) % 6
+                f = h_norm - int(h_norm)
+
+                if h_int == 0:
+                    r, g, b = 1.0, f, 0.0
+                elif h_int == 1:
+                    r, g, b = 1.0 - f, 1.0, 0.0
+                elif h_int == 2:
+                    r, g, b = 0.0, 1.0, f
+                elif h_int == 3:
+                    r, g, b = 0.0, 1.0 - f, 1.0
+                elif h_int == 4:
+                    r, g, b = f, 0.0, 1.0
+                else:
+                    r, g, b = 1.0, 0.0, 1.0 - f
+
+                # Blend with opacity
+                rgb[mask, 0] = (1 - label_opacity) * rgb[
+                    mask, 0
+                ] + label_opacity * r
+                rgb[mask, 1] = (1 - label_opacity) * rgb[
+                    mask, 1
+                ] + label_opacity * g
+                rgb[mask, 2] = (1 - label_opacity) * rgb[
+                    mask, 2
+                ] + label_opacity * b
+
+    # Convert to uint8
+    rgb_uint8 = (rgb * 255).astype(np.uint8)
+
+    return rgb_uint8
+
+
+def _create_grid(images: list, grid_cols: int = 4) -> np.ndarray:
+    """
+    Arrange images in a grid layout.
+
+    Parameters
+    ----------
+    images : list
+        List of images to arrange
+    grid_cols : int
+        Number of columns in grid
+
+    Returns
+    -------
+    np.ndarray
+        Grid image
+    """
+    if not images:
+        return None
+
+    # Calculate grid dimensions
+    n_images = len(images)
+    grid_rows = (n_images + grid_cols - 1) // grid_cols
+
+    # Get dimensions from first image
+    h, w = images[0].shape[:2]
+    has_channels = len(images[0].shape) == 3
+    n_channels = images[0].shape[2] if has_channels else 1
+
+    # Create grid
+    if has_channels:
+        grid = np.zeros(
+            (grid_rows * h, grid_cols * w, n_channels), dtype=images[0].dtype
+        )
+    else:
+        grid = np.zeros((grid_rows * h, grid_cols * w), dtype=images[0].dtype)
+
+    # Fill grid
+    for idx, img in enumerate(images):
+        row = idx // grid_cols
+        col = idx % grid_cols
+        y_start = row * h
+        y_end = (row + 1) * h
+        x_start = col * w
+        x_end = (col + 1) * w
+        grid[y_start:y_end, x_start:x_end] = img
+
+    return grid
+
+
+@BatchProcessingRegistry.register(
+    name="Grid View: Intensity + Labels Overlay",
+    suffix="_grid_overlay.tif",
+    description="Create grid view of intensity images with optional colored label overlay for selected files",
+    parameters={
+        "label_suffix": {
+            "type": str,
+            "default": "_labels.tif",
+            "description": "Example: _labels.tif. Leave empty for intensity-only grid.",
+        }
+    },
+)
+def create_grid_overlay(
+    image: np.ndarray, label_suffix: str = "_labels.tif"
+) -> np.ndarray:
+    """
+    Create a grid view showing intensity images with optional colored label overlay.
+
+    This function processes all files selected in the batch processing queue.
+    If label_suffix is provided, it finds corresponding label files and creates
+    overlays. If label_suffix is empty, it creates a grid of intensity images only.
+
+    Parameters
+    ----------
+    image : np.ndarray
+        Input image (processed as part of the batch)
+    label_suffix : str, optional
+        Suffix pattern to identify label files (e.g., "_labels.tif", "_segmentation.tif").
+        If empty string, creates intensity-only grid without looking for labels.
+        Default is "_labels.tif".
+
+    Returns
+    -------
+    np.ndarray
+        Grid image with intensity images and optional overlays (RGB uint8)
+
+    Notes
+    -----
+    - Intensity is shown in grayscale
+    - When labels are used: each label gets a unique color with 60% opacity
+    - Images are automatically normalized for display
+    - Grid columns are automatically determined based on number of images
+    - Only processes files selected by user's suffix filter in batch processing
+    """
+    global _grid_created, _cached_grid
+
+    # Determine mode based on label_suffix
+    intensity_only_mode = label_suffix == "" or label_suffix is None
+    mode_str = (
+        "intensity only"
+        if intensity_only_mode
+        else f"intensity + labels (suffix: '{label_suffix}')"
+    )
+
+    # If grid has already been created in this batch, return None to skip saving
+    if _grid_created:
+        return None
+
+    if not _HAS_TIFFFILE:
+        print(
+            "⚠️  tifffile not available. Please install it: pip install tifffile"
+        )
+        return image
+
+    # Mark that we're creating the grid to prevent concurrent calls
+    _grid_created = True
+
+    # Suppress any stdout from this point to avoid verbose output
+    import io
+    import sys
+
+    old_stdout = sys.stdout
+    sys.stdout = io.StringIO()
+
+    try:
+        # Get the filepath, files list, and output folder from the call stack
+        current_filepath = None
+        file_list = None
+        output_folder = None
+
+        for frame_info in inspect.stack():
+            frame_locals = frame_info.frame.f_locals
+            if "filepath" in frame_locals:
+                current_filepath = Path(frame_locals["filepath"])
+            if "file_list" in frame_locals:
+                file_list = frame_locals["file_list"]
+            if "self" in frame_locals:
+                obj = frame_locals["self"]
+                if hasattr(obj, "output_folder"):
+                    output_folder = obj.output_folder
+            if (
+                current_filepath is not None
+                and file_list is not None
+                and output_folder is not None
+            ):
+                break
+    finally:
+        # Restore stdout
+        sys.stdout = old_stdout
+
+    if current_filepath is None:
+        print("⚠️  Could not determine current file path")
+        return image
+
+    label_folder = current_filepath.parent
+
+    # Use output folder from batch processing if available; default to parent folder
+    if output_folder is None:
+        output_folder = str(label_folder)
+
+    output_folder = Path(output_folder)
+
+    # When the batch UI output matches the input folder (blank value), save to parent
+    try:
+        same_as_input = output_folder.resolve() == label_folder.resolve()
+    except FileNotFoundError:
+        same_as_input = False
+
+    if same_as_input:
+        output_folder = label_folder.parent
+
+    output_folder.mkdir(parents=True, exist_ok=True)
+
+    # Use the file_list from batch processing if available
+    if file_list is not None:
+        label_files = [Path(f) for f in file_list]
+    else:
+        # Fallback: determine files based on mode
+        label_files = []
+
+        if intensity_only_mode:
+            # Intensity-only mode: use all TIFF files in folder
+            patterns = ["*.tif", "*.tiff"]
+        else:
+            # Label mode: honor user-provided suffix while keeping legacy patterns
+            patterns = []
+            if label_suffix:
+                suffixes = {label_suffix}
+                if label_suffix.lower().endswith(".tif"):
+                    suffixes.add(label_suffix[:-4] + ".tiff")
+                for suffix in suffixes:
+                    patterns.append(f"*{suffix}")
+
+            # Legacy fallback patterns
+            patterns.extend(["*_labels*.tif", "*_labels*.tiff"])
+
+        for pattern in patterns:
+            label_files.extend(label_folder.glob(pattern))
+
+        if not label_files:
+            msg = "intensity files" if intensity_only_mode else "label files"
+            print(f"⚠️  No {msg} found in folder")
+            return image
+
+    # Filter out any grid overlay files to prevent reprocessing
+    label_files = [f for f in label_files if "_grid_overlay" not in f.name]
+
+    # Deduplicate and sort for deterministic ordering
+    label_files = sorted(set(label_files))
+
+    if not label_files:
+        print("⚠️  No valid label files found after filtering")
+        return image
+
+    # Calculate square grid dimensions
+    import math
+
+    # For square grid: use sqrt to get equal rows and columns
+    grid_cols = max(1, math.ceil(math.sqrt(len(label_files))))
+    grid_rows = grid_cols  # Square grid
+
+    # Target final dimensions (aim for ~12000px max dimension for PNG compatibility)
+    # Square grid means we can use same calculation for both dimensions
+    max_grid_dimension = 12000
+    target_per_image = max_grid_dimension // grid_cols
+
+    # Clamp to reasonable range (not too small, not too large)
+    target_per_image = max(100, min(target_per_image, 500))
+
+    print(
+        f"\n📊 Processing {len(label_files)} images → {target_per_image}px per image, {grid_cols}×{grid_rows} grid (square), {mode_str}"
+    )
+
+    # Create overlays for each pair using parallel processing
+    def process_image_pair(file_path):
+        """Process a single image file (with or without labels)."""
+        filename = file_path.name
+
+        if intensity_only_mode:
+            # Intensity-only mode: use the file itself as intensity, no labels
+            intensity_path = file_path
+            label_path = None
+        else:
+            # Label mode: file is a label, find corresponding intensity
+            intensity_filename = _get_intensity_filename(filename)
+            intensity_path = label_folder / intensity_filename
+            label_path = file_path
+
+            if not intensity_path.exists():
+                return (
+                    None,
+                    f"⚠️  Skipping {filename}: no intensity image found",
+                )
+
+        try:
+            # Load intensity image
+            intensity_img = tifffile.imread(str(intensity_path))
+
+            # Load label image if in label mode
+            if label_path is not None:
+                label_img = tifffile.imread(str(label_path))
+            else:
+                label_img = None
+
+            # Handle 3D data by taking max projection
+            if len(intensity_img.shape) > 2:
+                intensity_img = np.max(intensity_img, axis=0)
+
+            if label_img is not None:
+                if len(label_img.shape) > 2:
+                    label_img = np.max(label_img, axis=0)
+
+                # Check for labels
+                unique_labels = np.unique(label_img)
+                n_labels = len(unique_labels[unique_labels > 0])
+
+                # Ensure matching dimensions
+                if intensity_img.shape != label_img.shape:
+                    return None, (
+                        f"⚠️  Skipping {filename}: dimension mismatch "
+                        f"(intensity: {intensity_img.shape}, labels: {label_img.shape})"
+                    )
+            else:
+                # Intensity-only mode: create dummy zero label image
+                label_img = np.zeros(intensity_img.shape, dtype=np.uint16)
+                n_labels = 0
+
+            # Create overlay with intelligent downsampling and 60% label opacity
+            # When label_img is all zeros (intensity_only_mode), this creates grayscale output
+            overlay = _create_overlay(
+                intensity_img,
+                label_img,
+                target_size=target_per_image,
+                label_opacity=0.6,
+                show_overlay=(not intensity_only_mode),
+            )
+
+            # Explicitly delete large arrays to free memory immediately
+            del intensity_img, label_img
+
+            return (overlay, n_labels), None
+
+        except (FileNotFoundError, OSError) as e:
+            return None, f"⚠️  Error processing {filename}: {e}"
+
+    # Process in parallel with ThreadPoolExecutor
+    # Use max 4 workers for better memory management with large datasets
+    max_workers = min(4, os.cpu_count() or 4)
+
+    # Process in batches to manage memory
+    batch_size = 100  # Process 100 images at a time
+    sorted_label_files = sorted(label_files)
+    all_overlays = []
+    valid_pairs = 0
+    errors = []
+    total_labels = 0
+    images_with_labels = 0
+
+    # Progress bar for overall processing
+    with tqdm(
+        total=len(sorted_label_files), desc="Creating overlays", unit="pair"
+    ) as pbar:
+        for batch_start in range(0, len(sorted_label_files), batch_size):
+            batch_end = min(batch_start + batch_size, len(sorted_label_files))
+            batch_files = sorted_label_files[batch_start:batch_end]
+
+            batch_overlays = []
+
+            with concurrent.futures.ThreadPoolExecutor(
+                max_workers=max_workers
+            ) as executor:
+                # Submit batch tasks
+                future_to_path = {
+                    executor.submit(process_image_pair, label_path): label_path
+                    for label_path in batch_files
+                }
+
+                # Collect batch results as they complete
+                for future in concurrent.futures.as_completed(future_to_path):
+                    result, error_msg = future.result()
+
+                    if error_msg:
+                        errors.append(error_msg)
+                    elif result is not None:
+                        overlay, n_labels = result
+                        batch_overlays.append(overlay)
+                        valid_pairs += 1
+                        total_labels += n_labels
+                        if n_labels > 0:
+                            images_with_labels += 1
+
+                    pbar.update(1)
+
+            # Add batch results to main list
+            all_overlays.extend(batch_overlays)
+
+            # Clear batch to free memory
+            del batch_overlays
+
+    # Print diagnostics after progress bar completes
+    print(f"\n✓ Processed {valid_pairs} images")
+    if not intensity_only_mode:
+        print(
+            f"  Labels found: {images_with_labels}/{valid_pairs} images ({total_labels} total labels)"
+        )
+
+        if total_labels == 0:
+            print("  ⚠️  WARNING: No labels detected in any image!")
+            print(
+                "      Output will be grayscale intensity only (no colored regions)"
+            )
+    else:
+        print("  Mode: Intensity only (no labels)")
+
+    if errors:
+        print(f"\n⚠️  {len(errors)} files skipped:")
+        for error in errors[:10]:  # Show first 10 errors
+            print(f"   {error}")
+        if len(errors) > 10:
+            print(f"   ... and {len(errors) - 10} more")
+
+    if not all_overlays:
+        print("⚠️  No valid image pairs found")
+        return image
+
+    overlays = all_overlays
+
+    mode_desc = (
+        "intensity only"
+        if intensity_only_mode
+        else "intensity + colored labels at 60% opacity"
+    )
+    print(
+        f"\n✨ Creating final grid: {valid_pairs} images, {grid_cols}×{grid_cols} square grid ({mode_desc})"
+    )
+
+    # Create grid
+    grid = _create_grid(overlays, grid_cols=grid_cols)
+
+    if grid is None:
+        print("⚠️  ERROR: Grid creation returned None!")
+        return image
+
+    print(f"✅ Complete! Grid shape: {grid.shape}")
+
+    # Cache the result for subsequent calls in the same batch
+    _cached_grid = grid
+
+    # Save the grid to file (only once)
+    global _grid_saved, _grid_output_path
+    if not _grid_saved:
+        # Save as compressed TIF for napari viewing
+        output_filename = f"{sorted_label_files[0].stem}_grid_overlay.tif"
+        output_path = output_folder / output_filename
+
+        try:
+            # Ensure output directory exists
+            output_folder.mkdir(parents=True, exist_ok=True)
+
+            # Save as compressed TIFF
+            tifffile.imwrite(
+                str(output_path),
+                grid,
+                compression="zlib",
+                compressionargs={"level": 6},
+            )
+            _grid_output_path = str(output_path)
+            _grid_saved = True
+
+            # Verify file was actually saved
+            if output_path.exists():
+                file_size = output_path.stat().st_size
+                print("\n" + "=" * 80)
+                print("💾 SAVED GRID IMAGE TO:")
+                print(f"   {output_path}")
+                print(f"   File size: {file_size / 1024 / 1024:.2f} MB")
+                print("   (Compressed TIF format)")
+                print("=" * 80 + "\n")
+            else:
+                print(
+                    f"⚠️  WARNING: File save appeared to succeed but file not found at {output_path}"
+                )
+        except (
+            OSError,
+            RuntimeError,
+            ValueError,
+            tifffile.TiffFileError,
+        ) as e:
+            print(f"⚠️  Error saving grid: {type(e).__name__}: {e}")
+            import traceback
+
+            traceback.print_exc()
+
+    return grid
+
+
+def reset_grid_cache():
+    """Reset the grid creation cache for a new batch run."""
+    global _grid_created, _cached_grid, _grid_saved, _grid_output_path
+    _grid_created = False
+    _cached_grid = None
+    _grid_saved = False
+    _grid_output_path = None