Visualization

Diagnostic plotting for synthetic image optimization.

Generates side-by-side comparisons of real and synthetic microscope images with intensity histograms and region-specific quality metrics (SSIM, PSNR, histogram distance).

extract_masked_region(image: ndarray, mask: ndarray, region: str) → ndarray

Extract foreground or background region from image using mask.

Parameters:

  • image (np.ndarray) – Input image (float [0,1]).

  • mask (np.ndarray) – Segmentation mask (2D or 3D).

  • region (str) – Region to extract: ‘foreground’ or ‘background’.

Returns:

Image with the non-selected region zeroed out.

Return type:

np.ndarray

generate_detailed_plots(image_pairs: List[Tuple[Path, Path]], params: Dict, per_image_metrics: List[Dict], output_dir: Path, n_vertices: int) → None

Generate detailed per-image plots with region-specific analysis.

Creates one plot per image pair showing full, background, and foreground histogram comparisons along with image and mask visualizations.

Parameters:

  • image_pairs (List[Tuple[Path, Path]]) – List of (image_path, mask_path) tuples.

  • params (Dict) – Optimized synthetic parameters (bg_base_brightness, etc.).

  • per_image_metrics (List[Dict]) – Per-image metrics from compute_final_metrics().

  • output_dir (Path) – Output directory for saving plots.

  • n_vertices (int) – Number of vertices for cell shape extraction.

generate_comparison_plot(image_pairs: List[Tuple[Path, Path]], params: Dict, output_dir: Path, n_vertices: int, num_examples: int = 3)

Generate comparison plot showing original vs synthetic for example images.

Creates a single figure with histogram comparisons and side-by-side image views for a sample of image pairs.

Parameters:

  • image_pairs (List[Tuple[Path, Path]]) – List of (image_path, mask_path) tuples.

  • params (Dict) – Optimized synthetic parameters (bg_base_brightness, etc.).

  • output_dir (Path) – Output directory for saving the plot.

  • n_vertices (int) – Number of vertices for cell shape extraction.

  • num_examples (int) – Number of example images to show.