risk-network 0.0.7b11__py3-none-any.whl → 0.0.8__py3-none-any.whl

risk/network/plot/utils/color.py

@@ -0,0 +1,424 @@
+"""
+risk/network/plot/utils/color
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+"""
+
+from typing import Any, Dict, List, Tuple, Union
+
+import matplotlib
+import matplotlib.colors as mcolors
+import numpy as np
+
+from risk.network.graph import NetworkGraph
+from risk.network.plot.utils.layout import calculate_centroids
+
+
+def get_annotated_domain_colors(
+    graph: NetworkGraph,
+    cmap: str = "gist_rainbow",
+    color: Union[str, List, Tuple, np.ndarray, None] = None,
+    blend_colors: bool = False,
+    blend_gamma: float = 2.2,
+    min_scale: float = 0.8,
+    max_scale: float = 1.0,
+    scale_factor: float = 1.0,
+    random_seed: int = 888,
+) -> np.ndarray:
+    """Get colors for the domains based on node annotations, or use a specified color.
+
+    Args:
+        graph (NetworkGraph): The network data and attributes to be visualized.
+        cmap (str, optional): Colormap to use for generating domain colors. Defaults to "gist_rainbow".
+        color (str, List, Tuple, np.ndarray, or None, optional): Color to use for the domains. Can be a single color or an array of colors.
+            If None, the colormap will be used. Defaults to None.
+        blend_colors (bool, optional): Whether to blend colors for nodes with multiple domains. Defaults to False.
+        blend_gamma (float, optional): Gamma correction factor for perceptual color blending. Defaults to 2.2.
+        min_scale (float, optional): Minimum scale for color intensity when generating domain colors. Defaults to 0.8.
+        max_scale (float, optional): Maximum scale for color intensity when generating domain colors. Defaults to 1.0.
+        scale_factor (float, optional): Factor for adjusting the contrast in the colors generated based on enrichment. Higher values
+            increase the contrast. Defaults to 1.0.
+        random_seed (int, optional): Seed for random number generation to ensure reproducibility. Defaults to 888.
+
+    Returns:
+        np.ndarray: Array of RGBA colors for each domain.
+    """
+    # Generate domain colors based on the enrichment data
+    node_colors = get_domain_colors(
+        graph=graph,
+        cmap=cmap,
+        color=color,
+        blend_colors=blend_colors,
+        blend_gamma=blend_gamma,
+        min_scale=min_scale,
+        max_scale=max_scale,
+        scale_factor=scale_factor,
+        random_seed=random_seed,
+    )
+    annotated_colors = []
+    for _, node_ids in graph.domain_id_to_node_ids_map.items():
+        if len(node_ids) > 1:
+            # For multi-node domains, choose the brightest color based on RGB sum
+            domain_colors = np.array([node_colors[node] for node in node_ids])
+            brightest_color = domain_colors[
+                np.argmax(domain_colors[:, :3].sum(axis=1))  # Sum the RGB values
+            ]
+            annotated_colors.append(brightest_color)
+        else:
+            # Single-node domains default to white (RGBA)
+            default_color = np.array([1.0, 1.0, 1.0, 1.0])
+            annotated_colors.append(default_color)
+
+    return np.array(annotated_colors)
+
+
+def get_domain_colors(
+    graph: NetworkGraph,
+    cmap: str = "gist_rainbow",
+    color: Union[str, List, Tuple, np.ndarray, None] = None,
+    blend_colors: bool = False,
+    blend_gamma: float = 2.2,
+    min_scale: float = 0.8,
+    max_scale: float = 1.0,
+    scale_factor: float = 1.0,
+    random_seed: int = 888,
+) -> np.ndarray:
+    """Generate composite colors for domains based on enrichment or specified colors.
+
+    Args:
+        graph (NetworkGraph): The network data and attributes to be visualized.
+        cmap (str, optional): Name of the colormap to use for generating domain colors. Defaults to "gist_rainbow".
+        color (str, List, Tuple, np.ndarray, or None, optional): A specific color or array of colors to use for all domains.
+            If None, the colormap will be used. Defaults to None.
+        blend_colors (bool, optional): Whether to blend colors for nodes with multiple domains. Defaults to False.
+        blend_gamma (float, optional): Gamma correction factor for perceptual color blending. Defaults to 2.2.
+        min_scale (float, optional): Minimum intensity scale for the colors generated by the colormap. Controls the dimmest colors.
+            Defaults to 0.8.
+        max_scale (float, optional): Maximum intensity scale for the colors generated by the colormap. Controls the brightest colors.
+            Defaults to 1.0.
+        scale_factor (float, optional): Exponent for adjusting the color scaling based on enrichment scores. Higher values increase
+            contrast by dimming lower scores more. Defaults to 1.0.
+        random_seed (int, optional): Seed for random number generation to ensure reproducibility of color assignments. Defaults to 888.
+
+    Returns:
+        np.ndarray: Array of RGBA colors generated for each domain, based on enrichment or the specified color.
+    """
+    # Get colors for each domain
+    domain_colors = _get_domain_colors(graph=graph, cmap=cmap, color=color, random_seed=random_seed)
+    # Generate composite colors for nodes
+    node_colors = _get_composite_node_colors(
+        graph=graph, domain_colors=domain_colors, blend_colors=blend_colors, blend_gamma=blend_gamma
+    )
+    # Transform colors to ensure proper alpha values and intensity
+    transformed_colors = _transform_colors(
+        node_colors,
+        graph.node_enrichment_sums,
+        min_scale=min_scale,
+        max_scale=max_scale,
+        scale_factor=scale_factor,
+    )
+    return transformed_colors
+
+
+def _get_domain_colors(
+    graph: NetworkGraph,
+    cmap: str = "gist_rainbow",
+    color: Union[str, List, Tuple, np.ndarray, None] = None,
+    random_seed: int = 888,
+) -> Dict[int, Any]:
+    """Get colors for each domain.
+
+    Args:
+        graph (NetworkGraph): The network data and attributes to be visualized.
+        cmap (str, optional): The name of the colormap to use. Defaults to "gist_rainbow".
+        color (str, List, Tuple, np.ndarray, or None, optional): A specific color or array of colors to use for the domains.
+            If None, the colormap will be used. Defaults to None.
+        random_seed (int, optional): Seed for random number generation. Defaults to 888.
+
+    Returns:
+        Dict[int, Any]: A dictionary mapping domain keys to their corresponding RGBA colors.
+    """
+    # Get colors for each domain based on node positions
+    domain_colors = _get_colors(
+        graph.network,
+        graph.domain_id_to_node_ids_map,
+        cmap=cmap,
+        color=color,
+        random_seed=random_seed,
+    )
+    return dict(zip(graph.domain_id_to_node_ids_map.keys(), domain_colors))
+
+
+def _get_composite_node_colors(
+    graph, domain_colors: np.ndarray, blend_colors: bool = False, blend_gamma: float = 2.2
+) -> np.ndarray:
+    """Generate composite colors for nodes based on domain colors and enrichment values, with optional color blending.
+
+    Args:
+        graph (NetworkGraph): The network data and attributes to be visualized.
+        domain_colors (np.ndarray): Array or list of RGBA colors corresponding to each domain.
+        blend_colors (bool): Whether to blend colors for nodes with multiple domains. Defaults to False.
+        blend_gamma (float, optional): Gamma correction factor to be used for perceptual color blending.
+            This parameter is only relevant if blend_colors is True. Defaults to 2.2.
+
+    Returns:
+        np.ndarray: Array of composite colors for each node.
+    """
+    # Determine the number of nodes
+    num_nodes = len(graph.node_coordinates)
+    # Initialize composite colors array with shape (number of nodes, 4) for RGBA
+    composite_colors = np.zeros((num_nodes, 4))
+
+    # If blending is not required, directly assign domain colors to nodes
+    if not blend_colors:
+        for domain_id, nodes in graph.domain_id_to_node_ids_map.items():
+            color = domain_colors[domain_id]
+            for node in nodes:
+                composite_colors[node] = color
+
+    # If blending is required
+    else:
+        for node, node_info in graph.node_id_to_domain_ids_and_enrichments_map.items():
+            domains = node_info["domains"]  # List of domain IDs
+            enrichments = node_info["enrichments"]  # List of enrichment values
+            # Filter domains and enrichments to keep only those with corresponding colors in domain_colors
+            filtered_domains_enrichments = [
+                (domain_id, enrichment)
+                for domain_id, enrichment in zip(domains, enrichments)
+                if domain_id in domain_colors
+            ]
+            # If no valid domains exist, skip this node
+            if not filtered_domains_enrichments:
+                continue
+
+            # Unpack filtered domains and enrichments
+            filtered_domains, filtered_enrichments = zip(*filtered_domains_enrichments)
+            # Get the colors corresponding to the valid filtered domains
+            colors = [domain_colors[domain_id] for domain_id in filtered_domains]
+            # Blend the colors using the given gamma (default is 2.2 if None)
+            gamma = blend_gamma if blend_gamma is not None else 2.2
+            composite_color = _blend_colors_perceptually(colors, filtered_enrichments, gamma)
+            # Assign the composite color to the node
+            composite_colors[node] = composite_color
+
+    return composite_colors
+
+
+def _get_colors(
+    network,
+    domain_id_to_node_ids_map,
+    cmap: str = "gist_rainbow",
+    color: Union[str, List, Tuple, np.ndarray, None] = None,
+    random_seed: int = 888,
+) -> List[Tuple]:
+    """Generate a list of RGBA colors based on domain centroids, ensuring that domains
+    close in space get maximally separated colors, while keeping some randomness.
+
+    Args:
+        network (NetworkX graph): The graph representing the network.
+        domain_id_to_node_ids_map (Dict[int, Any]): Mapping from domain IDs to lists of node IDs.
+        cmap (str, optional): The name of the colormap to use. Defaults to "gist_rainbow".
+        color (str, List, Tuple, np.ndarray, or None, optional): A specific color or array of colors to use for the domains.
+            If None, the colormap will be used. Defaults to None.
+        random_seed (int, optional): Seed for random number generation. Defaults to 888.
+
+    Returns:
+        List[Tuple]: List of RGBA colors.
+    """
+    # Set random seed for reproducibility
+    np.random.seed(random_seed)
+    # Determine the number of colors to generate based on the number of domains
+    num_colors_to_generate = len(domain_id_to_node_ids_map)
+    if color:
+        # Generate all colors as the same specified color
+        rgba = to_rgba(color, num_repeats=num_colors_to_generate)
+        return rgba
+
+    # Load colormap
+    colormap = matplotlib.colormaps.get_cmap(cmap)
+    # Step 1: Calculate centroids for each domain
+    centroids = calculate_centroids(network, domain_id_to_node_ids_map)
+    # Step 2: Calculate pairwise distances between centroids
+    centroid_array = np.array(centroids)
+    dist_matrix = np.linalg.norm(centroid_array[:, None] - centroid_array, axis=-1)
+    # Step 3: Assign distant colors to close centroids
+    color_positions = _assign_distant_colors(dist_matrix, num_colors_to_generate)
+    # Step 4: Randomly shift the entire color palette while maintaining relative distances
+    global_shift = np.random.uniform(-0.1, 0.1)  # Small global shift to change the overall palette
+    color_positions = (color_positions + global_shift) % 1  # Wrap around to keep within [0, 1]
+    # Step 5: Ensure that all positions remain between 0 and 1
+    color_positions = np.clip(color_positions, 0, 1)
+
+    # Step 6: Generate RGBA colors based on positions
+    return [colormap(pos) for pos in color_positions]
+
+
+def _assign_distant_colors(dist_matrix, num_colors_to_generate):
+    """Assign colors to centroids that are close in space, ensuring stark color differences.
+
+    Args:
+        dist_matrix (ndarray): Matrix of pairwise centroid distances.
+        num_colors_to_generate (int): Number of colors to generate.
+
+    Returns:
+        np.array: Array of color positions in the range [0, 1].
+    """
+    color_positions = np.zeros(num_colors_to_generate)
+    # Step 1: Sort indices by centroid proximity (based on sum of distances to others)
+    proximity_order = sorted(
+        range(num_colors_to_generate), key=lambda idx: np.sum(dist_matrix[idx])
+    )
+    # Step 2: Assign colors starting with the most distant points in proximity order
+    for i, idx in enumerate(proximity_order):
+        color_positions[idx] = i / num_colors_to_generate
+
+    # Step 3: Adjust colors so that centroids close to one another are maximally distant on the color spectrum
+    half_spectrum = int(num_colors_to_generate / 2)
+    for i in range(half_spectrum):
+        # Split the spectrum so that close centroids are assigned distant colors
+        color_positions[proximity_order[i]] = (i * 2) / num_colors_to_generate
+        color_positions[proximity_order[-(i + 1)]] = ((i * 2) + 1) / num_colors_to_generate
+
+    return color_positions
+
+
+def _blend_colors_perceptually(
+    colors: Union[List, Tuple, np.ndarray], enrichments: List[float], gamma: float = 2.2
+) -> Tuple[float, float, float, float]:
+    """Blends a list of RGBA colors using gamma correction for perceptually uniform color mixing.
+
+    Args:
+        colors (List, Tuple, np.ndarray): List of RGBA colors. Can be a list, tuple, or NumPy array of RGBA values.
+        enrichments (List[float]): Corresponding list of enrichment values.
+        gamma (float, optional): Gamma correction factor, default is 2.2 (typical for perceptual blending).
+
+    Returns:
+        Tuple[float, float, float, float]: The blended RGBA color.
+    """
+    # Normalize enrichments so they sum up to 1 (proportions)
+    total_enrichment = sum(enrichments)
+    proportions = [enrichment / total_enrichment for enrichment in enrichments]
+    # Convert colors to gamma-corrected space (apply gamma correction to RGB channels)
+    gamma_corrected_colors = [[channel**gamma for channel in color[:3]] for color in colors]
+    # Blend the colors in gamma-corrected space
+    blended_color = np.dot(proportions, gamma_corrected_colors)
+    # Convert back from gamma-corrected space to linear space (by applying inverse gamma correction)
+    blended_color = [channel ** (1 / gamma) for channel in blended_color]
+    # Average the alpha channel separately (no gamma correction on alpha)
+    alpha = np.dot(proportions, [color[3] for color in colors])
+    return tuple(blended_color + [alpha])
+
+
+def _transform_colors(
+    colors: np.ndarray,
+    enrichment_sums: np.ndarray,
+    min_scale: float = 0.8,
+    max_scale: float = 1.0,
+    scale_factor: float = 1.0,
+) -> np.ndarray:
+    """Transform colors using power scaling to emphasize high enrichment sums more. Black colors are replaced with
+    very dark grey to avoid issues with color scaling (rgb(0.1, 0.1, 0.1)).
+
+    Args:
+        colors (np.ndarray): An array of RGBA colors.
+        enrichment_sums (np.ndarray): An array of enrichment sums corresponding to the colors.
+        min_scale (float, optional): Minimum scale for color intensity. Defaults to 0.8.
+        max_scale (float, optional): Maximum scale for color intensity. Defaults to 1.0.
+        scale_factor (float, optional): Exponent for scaling, where values > 1 increase contrast by dimming small
+            values more. Defaults to 1.0.
+
+    Returns:
+        np.ndarray: The transformed array of RGBA colors with adjusted intensities.
+    """
+    # Ensure that min_scale is less than max_scale
+    if min_scale == max_scale:
+        min_scale = max_scale - 10e-6  # Avoid division by zero
+
+    # Replace black colors (#000000) with very dark grey (#1A1A1A)
+    black_color = np.array([0.0, 0.0, 0.0])  # Pure black RGB
+    dark_grey = np.array([0.1, 0.1, 0.1])  # Very dark grey RGB (#1A1A1A)
+    # Check where colors are black (very close to [0, 0, 0]) and replace with dark grey
+    is_black = np.all(colors[:, :3] == black_color, axis=1)
+    colors[is_black, :3] = dark_grey
+
+    # Normalize the enrichment sums to the range [0, 1]
+    normalized_sums = enrichment_sums / np.max(enrichment_sums)
+    # Apply power scaling to dim lower values and emphasize higher values
+    scaled_sums = normalized_sums**scale_factor
+    # Linearly scale the normalized sums to the range [min_scale, max_scale]
+    scaled_sums = min_scale + (max_scale - min_scale) * scaled_sums
+    # Adjust RGB values based on scaled sums
+    for i in range(3):  # Only adjust RGB values
+        colors[:, i] = scaled_sums * colors[:, i]
+
+    return colors
+
+
+def to_rgba(
+    color: Union[str, List, Tuple, np.ndarray],
+    alpha: Union[float, None] = None,
+    num_repeats: Union[int, None] = None,
+) -> np.ndarray:
+    """Convert color(s) to RGBA format, applying alpha and repeating as needed.
+
+    Args:
+        color (str, List, Tuple, np.ndarray): The color(s) to convert. Can be a string (e.g., 'red'), a list or tuple of RGB/RGBA values,
+            or an `np.ndarray` of colors.
+        alpha (float, None, optional): Alpha value (transparency) to apply. If provided, it overrides any existing alpha values found
+            in color.
+        num_repeats (int, None, optional): If provided, the color(s) will be repeated this many times. Defaults to None.
+
+    Returns:
+        np.ndarray: Array of RGBA colors repeated `num_repeats` times, if applicable.
+    """
+
+    def convert_to_rgba(c: Union[str, List, Tuple, np.ndarray]) -> np.ndarray:
+        """Convert a single color to RGBA format, handling strings, hex, and RGB/RGBA lists."""
+        # Note: if no alpha is provided, the default alpha value is 1.0 by mcolors.to_rgba
+        if isinstance(c, str):
+            # Convert color names or hex values (e.g., 'red', '#FF5733') to RGBA
+            rgba = np.array(mcolors.to_rgba(c))
+        elif isinstance(c, (list, tuple, np.ndarray)) and len(c) in [3, 4]:
+            # Convert RGB (3) or RGBA (4) values to RGBA format
+            rgba = np.array(mcolors.to_rgba(c))
+        else:
+            raise ValueError(
+                f"Invalid color format: {c}. Must be a valid string or RGB/RGBA sequence."
+            )
+
+        if alpha is not None:  # Override alpha if provided
+            rgba[3] = alpha
+        return rgba
+
+    # If color is a 2D array of RGBA values, convert it to a list of lists
+    if isinstance(color, np.ndarray) and color.ndim == 2 and color.shape[1] == 4:
+        color = [list(c) for c in color]
+
+    # Handle a single color (string or RGB/RGBA list/tuple)
+    if (
+        isinstance(color, str)
+        or isinstance(color, (list, tuple, np.ndarray))
+        and not any(isinstance(c, (str, list, tuple, np.ndarray)) for c in color)
+    ):
+        rgba_color = convert_to_rgba(color)
+        if num_repeats:
+            return np.tile(
+                rgba_color, (num_repeats, 1)
+            )  # Repeat the color if num_repeats is provided
+        return np.array([rgba_color])  # Return a single color wrapped in a numpy array
+
+    # Handle a list/array of colors
+    elif isinstance(color, (list, tuple, np.ndarray)):
+        rgba_colors = np.array(
+            [convert_to_rgba(c) for c in color]
+        )  # Convert each color in the list to RGBA
+        # Handle repetition if num_repeats is provided
+        if num_repeats:
+            repeated_colors = np.array(
+                [rgba_colors[i % len(rgba_colors)] for i in range(num_repeats)]
+            )
+            return repeated_colors
+
+        return rgba_colors
+
+    else:
+        raise ValueError("Color must be a valid RGB/RGBA or array of RGB/RGBA colors.")

risk/network/plot/utils/layout.py

@@ -0,0 +1,91 @@
+"""
+risk/network/plot/utils/layout
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+"""
+
+from typing import Tuple
+
+import numpy as np
+
+
+def calculate_bounding_box(
+    node_coordinates: np.ndarray, radius_margin: float = 1.05
+) -> Tuple[np.ndarray, float]:
+    """Calculate the bounding box of the network based on node coordinates.
+
+    Args:
+        node_coordinates (np.ndarray): Array of node coordinates (x, y).
+        radius_margin (float, optional): Margin factor to apply to the bounding box radius. Defaults to 1.05.
+
+    Returns:
+        tuple: Center of the bounding box and the radius (adjusted by the radius margin).
+    """
+    # Find minimum and maximum x, y coordinates
+    x_min, y_min = np.min(node_coordinates, axis=0)
+    x_max, y_max = np.max(node_coordinates, axis=0)
+    # Calculate the center of the bounding box
+    center = np.array([(x_min + x_max) / 2, (y_min + y_max) / 2])
+    # Calculate the radius of the bounding box, adjusted by the margin
+    radius = max(x_max - x_min, y_max - y_min) / 2 * radius_margin
+    return center, radius
+
+
+def refine_center_iteratively(
+    node_coordinates: np.ndarray,
+    radius_margin: float = 1.05,
+    max_iterations: int = 10,
+    tolerance: float = 1e-2,
+) -> Tuple[np.ndarray, float]:
+    """Refine the center of the graph iteratively to minimize skew in node distribution.
+
+    Args:
+        node_coordinates (np.ndarray): Array of node coordinates (x, y).
+        radius_margin (float, optional): Margin factor to apply to the bounding box radius. Defaults to 1.05.
+        max_iterations (int, optional): Maximum number of iterations for refining the center. Defaults to 10.
+        tolerance (float, optional): Stopping tolerance for center adjustment. Defaults to 1e-2.
+
+    Returns:
+        tuple: Refined center and the final radius.
+    """
+    # Initial center and radius based on the bounding box
+    center, radius = calculate_bounding_box(node_coordinates, radius_margin)
+    for _ in range(max_iterations):
+        # Shift the coordinates based on the current center
+        shifted_coordinates = node_coordinates - center
+        # Calculate skew (difference in distance from the center)
+        skew = np.mean(shifted_coordinates, axis=0)
+        # If skew is below tolerance, stop
+        if np.linalg.norm(skew) < tolerance:
+            break
+
+        # Adjust the center by moving it in the direction opposite to the skew
+        center += skew
+
+    # After refinement, recalculate the bounding radius
+    shifted_coordinates = node_coordinates - center
+    new_radius = np.max(np.linalg.norm(shifted_coordinates, axis=1)) * radius_margin
+
+    return center, new_radius
+
+
+def calculate_centroids(network, domain_id_to_node_ids_map):
+    """Calculate the centroid for each domain based on node x and y coordinates in the network.
+
+    Args:
+        network (NetworkX graph): The graph representing the network.
+        domain_id_to_node_ids_map (Dict[int, Any]): Mapping from domain IDs to lists of node IDs.
+
+    Returns:
+        List[Tuple[float, float]]: List of centroids (x, y) for each domain.
+    """
+    centroids = []
+    for domain_id, node_ids in domain_id_to_node_ids_map.items():
+        # Extract x and y coordinates from the network nodes
+        node_positions = np.array(
+            [[network.nodes[node_id]["x"], network.nodes[node_id]["y"]] for node_id in node_ids]
+        )
+        # Compute the centroid as the mean of the x and y coordinates
+        centroid = np.mean(node_positions, axis=0)
+        centroids.append(tuple(centroid))
+
+    return centroids