evaluate_code/ph_utils.py

import numpy as np
from scipy.sparse.csgraph import connected_components
import gudhi as gd
from persim import wasserstein
import bisect

def count_connected_components(edge_index, num_nodes):
    """Count the number of connected components in a graph"""
    # Create adjacency matrix
    adj_matrix = np.zeros((num_nodes, num_nodes))
    for i in range(edge_index.shape[1]):
        src, dst = edge_index[0, i], edge_index[1, i]
        adj_matrix[src, dst] = 1
        adj_matrix[dst, src] = 1
    
    # Calculate connected components using scipy
    n_components, _ = connected_components(adj_matrix)
    return n_components

def Filtration(edge_index, edge_attr,filt,filt_value):
    def filt_edge(edges,filt_value):
        upper_bounds = filt_value
        filted_edges = []
        for edge in edges:
            src, tgt, w = edge
            index = bisect.bisect_left(upper_bounds, w)
            if index < len(upper_bounds):
                assigned_upper = upper_bounds[index]
            else:
                assigned_upper = upper_bounds[-1]
            
            filted_edges.append((src, tgt, assigned_upper))
        
        return filted_edges
    edge_index = np.array(edge_index).reshape(2, -1)
    original_edges = []
    for i in range(edge_index.shape[1]):
        source = edge_index[0, i].item()
        target = edge_index[1, i].item()
        weight = edge_attr[i].item()
        original_edges.append((source, target, weight))
    if filt:
        original_edges = filt_edge(original_edges,filt_value)
    sorted_edges = sorted(original_edges, key=lambda x: x[2])    

    simplices = gd.SimplexTree()
    for u, v, weight in sorted_edges:
        simplices.insert([u, v], filtration=weight)
    simplices.expansion(2)
    filtration = simplices.get_filtration()
    simplex_list = []

    for simplex in filtration:
        simplex_list.append(simplex)

    simplices.persistence()
    barcode = []
    for i in range(2):
        intervals = simplices.persistence_intervals_in_dimension(i)
        barcode.append(intervals)

    vr_e_pd = {}
    for dim, intervals in enumerate(barcode):
        if intervals.size > 0 and dim<=2:
            intervals = intervals.tolist()
            intervals.sort(key=lambda x: x[0])
            vr_e_pd[f'{dim}dim'] = intervals
        else:
            vr_e_pd[f'{dim}dim'] = []

    return sorted_edges, simplex_list, vr_e_pd

def add_vr_ORI(dataset,filt,filt_value=None):
    for i in range(len(dataset)):
        edge_index = dataset[i]['edge_index']
        edge_attr = dataset[i]['edge_attr']
        

        sorted_edges,simplex_list, vr_e_pd = Filtration(edge_index, edge_attr,filt,filt_value)

        for dim in vr_e_pd:
            vr_e_pd[dim].sort(key=lambda interval: interval[0])
    
        # dataset[i].sorted_edges = sorted_edges  
        # dataset[i].simplex = simplex_list      
        # dataset[i].vr_e_pd = vr_e_pd
        
        if filt:
            dataset[i]['selected_vr_e_pd'] = vr_e_pd
        else:
            dataset[i]['vr_e_pd'] = vr_e_pd
            
def PD_to_diagram(PD):
    """
    Convert persistence diagram dictionary to numpy array format.
    """
    diagram = []
    for dim, intervals in PD.items():
        dim_int = int(dim[0]) 
        for interval in intervals:
            birth, death = interval
            diagram.append([birth, death, dim_int])
    return np.array(diagram)

def compute_wasserstein_distance(PD1, PD2):
    """
    Compute Wasserstein distance between two persistence diagrams.
    """
    diagram1 = PD_to_diagram(PD1)
    diagram2 = PD_to_diagram(PD2)

    # Handle infinite death times
    diagram1[~np.isfinite(diagram1[:, 1]), 1] = 1.1
    diagram2[~np.isfinite(diagram2[:, 1]), 1] = 1.1

    return wasserstein(diagram1, diagram2)


def check_graph_group(graphs, method='weight', pre_calculate=True, filt_value=None):
    """
    Check if four graphs satisfy the separation condition:
    1. Both distances within same class are smaller than all four distances between different classes
    2. Four graphs must be arranged in [1,1,-1,-1] order
    
    Args:
        graphs: List of 4 graphs arranged in [1,1,-1,-1] order
        method: Persistent homology calculation method
        pre_calculate: Whether persistence diagrams are pre-calculated
        filt_value: Filtration value for calculation
    
    Returns:
        tuple: (bool, list) - Whether separation condition is satisfied and list of distances
    """
    if len(graphs) != 4:
        raise ValueError("Must provide exactly 4 graphs")
    
    # Verify graph label order
    if not (graphs[0]['y'] == graphs[1]['y'] and graphs[2]['y'] == graphs[3]['y'] and graphs[0]['y'] != graphs[2]['y']):
        raise ValueError("Graphs must be ordered as [1,1,-1,-1]")
    
    if not pre_calculate:
        add_vr_ORI(graphs, filt=True, filt_value=filt_value)
        
    # Calculate distances between all graph pairs
    distances = []
    for i in range(4):
        for j in range(i+1, 4):
            if method == 'weight':
                if pre_calculate:
                    dist = compute_wasserstein_distance(graphs[i]['vr_e_pd'], graphs[j]['vr_e_pd'])
                else:
                    dist = compute_wasserstein_distance(graphs[i]['selected_vr_e_pd'], graphs[j]['selected_vr_e_pd'])
            else:
                dist = compute_wasserstein_distance(
                    getattr(graphs[i], f'vr_{method}_pd'),
                    getattr(graphs[j], f'vr_{method}_pd')
                )
            distances.append((i, j, dist))
    
    # Distances within same class
    same_class_distances = [dist for i, j, dist in distances 
                          if (i < 2 and j < 2) or (i >= 2 and j >= 2)]
    
    # Distances between different classes
    diff_class_distances = [dist for i, j, dist in distances 
                          if (i < 2 and j >= 2) or (i >= 2 and j < 2)]
    
    max_same = max(same_class_distances)
    min_diff = min(diff_class_distances)
    
    return max_same < min_diff, distances