risk-network 0.0.8b18__py3-none-any.whl → 0.0.9b26__py3-none-any.whl

risk/network/plot/utils/color.py

@@ -1,353 +0,0 @@
-"""
-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,
-    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.
-        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,
-        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,
-    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.
-        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)
-    # 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[str, 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: 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: NetworkGraph, domain_colors: np.ndarray) -> np.ndarray:
-    """Generate composite colors for nodes based on domain colors and counts.
-
-    Args:
-        graph (NetworkGraph): The network data and attributes to be visualized.
-        domain_colors (np.ndarray): Array of colors corresponding to each domain.
-
-    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))
-    # Assign colors to nodes based on domain_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
-
-    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): 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 _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

@@ -1,53 +0,0 @@
-"""
-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 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): 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

risk_network-0.0.8b18.dist-info/RECORD

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