data_utils.py

import os
from collections import defaultdict
import random

import torch
import torch.nn.functional as F
import numpy as np
from scipy import sparse as sp
from torch_geometric.utils import degree, to_scipy_sparse_matrix


from torch_sparse import SparseTensor


def rand_train_test_idx_502525(label, train_prop=.5, valid_prop=.25, ignore_negative=True):
    """ randomly splits label into train/valid/test splits """
    if ignore_negative:
        labeled_nodes = torch.where(label != -1)[0]
    else:
        labeled_nodes = label

    n = labeled_nodes.shape[0]
    train_num = int(n * train_prop)
    valid_num = int(n * valid_prop)

    perm = torch.as_tensor(np.random.permutation(n))

    train_indices = perm[:train_num]
    val_indices = perm[train_num:train_num + valid_num]
    test_indices = perm[train_num + valid_num:]

    if not ignore_negative:
        return train_indices, val_indices, test_indices

    train_idx = labeled_nodes[train_indices]
    valid_idx = labeled_nodes[val_indices]
    test_idx = labeled_nodes[test_indices]

    return train_idx, valid_idx, test_idx


def rand_train_test_idx_602020(label, train_prop=.6, valid_prop=.2, ignore_negative=True):
    """ randomly splits label into train/valid/test splits """

    # random.seed(2022)

    if ignore_negative:
        labeled_nodes = torch.where(label != -1)[0]
    else:
        labeled_nodes = label

    n = labeled_nodes.shape[0]
    train_num = int(n * train_prop)
    valid_num = int(n * valid_prop)

    all_idx = np.arange(n)
    random.shuffle(all_idx)
    train_indices = all_idx[:train_num]
    val_indices = all_idx[train_num:train_num+valid_num]
    test_indices = all_idx[train_num+valid_num:]

    if not ignore_negative:
        return train_indices, val_indices, test_indices

    train_idx = labeled_nodes[train_indices]
    valid_idx = labeled_nodes[val_indices]
    test_idx = labeled_nodes[test_indices]

    return train_idx, valid_idx, test_idx


def load_fixed_splits(data_dir, dataset, name, protocol):
    splits_lst = []
    if name in ['cora', 'citeseer', 'pubmed'] and protocol == 'semi':
        splits = {}
        splits['train'] = torch.as_tensor(dataset.train_idx)
        splits['valid'] = torch.as_tensor(dataset.valid_idx)
        splits['test'] = torch.as_tensor(dataset.test_idx)
        splits_lst.append(splits)
    elif name in ['cora', 'citeseer', 'pubmed', 'chameleon', 'squirrel', 'film', 'cornell', 'texas', 'wisconsin']:
        for i in range(10):
            splits_file_path = '{}/geom-gcn/splits/{}'.format(data_dir, name) + '_split_0.6_0.2_' + str(i) + '.npz'
            splits = {}
            with np.load(splits_file_path) as splits_file:
                splits['train'] = torch.BoolTensor(splits_file['train_mask'])
                splits['valid'] = torch.BoolTensor(splits_file['val_mask'])
                splits['test'] = torch.BoolTensor(splits_file['test_mask'])
            splits_lst.append(splits)
    else:
        raise NotImplementedError

    return splits_lst


def class_rand_splits(label, label_num_per_class):
    train_idx, non_train_idx = [], []
    idx = torch.arange(label.shape[0])
    class_list = label.squeeze().unique()
    valid_num, test_num = 500, 1000
    for i in range(class_list.shape[0]):
        c_i = class_list[i]
        idx_i = idx[label.squeeze() == c_i]
        n_i = idx_i.shape[0]
        rand_idx = idx_i[torch.randperm(n_i)]
        train_idx += rand_idx[:label_num_per_class].tolist()
        non_train_idx += rand_idx[label_num_per_class:].tolist()
    train_idx = torch.as_tensor(train_idx)
    non_train_idx = torch.as_tensor(non_train_idx)
    non_train_idx = non_train_idx[torch.randperm(non_train_idx.shape[0])]
    valid_idx, test_idx = non_train_idx[:valid_num], non_train_idx[valid_num:valid_num + test_num]

    return train_idx, valid_idx, test_idx


def even_quantile_labels(vals, nclasses, verbose=True):
    """ partitions vals into nclasses by a quantile based split,
    where the first class is less than the 1/nclasses quantile,
    second class is less than the 2/nclasses quantile, and so on

    vals is np array
    returns an np array of int class labels
    """
    label = -1 * np.ones(vals.shape[0], dtype=np.int)
    interval_lst = []
    lower = -np.inf
    for k in range(nclasses - 1):
        upper = np.quantile(vals, (k + 1) / nclasses)
        interval_lst.append((lower, upper))
        inds = (vals >= lower) * (vals < upper)
        label[inds] = k
        lower = upper
    label[vals >= lower] = nclasses - 1
    interval_lst.append((lower, np.inf))
    if verbose:
        print('Class Label Intervals:')
        for class_idx, interval in enumerate(interval_lst):
            print(f'Class {class_idx}: [{interval[0]}, {interval[1]})]')
    return label

def to_planetoid(dataset):
    """
        Takes in a NCDataset and returns the dataset in H2GCN Planetoid form, as follows:
        x => the feature vectors of the training instances as scipy.sparse.csr.csr_matrix object;
        tx => the feature vectors of the test instances as scipy.sparse.csr.csr_matrix object;
        allx => the feature vectors of both labeled and unlabeled training instances
            (a superset of ind.dataset_str.x) as scipy.sparse.csr.csr_matrix object;
        y => the one-hot labels of the labeled training instances as numpy.ndarray object;
        ty => the one-hot labels of the test instances as numpy.ndarray object;
        ally => the labels for instances in ind.dataset_str.allx as numpy.ndarray object;
        graph => a dict in the format {index: [index_of_neighbor_nodes]} as collections.defaultdict
            object;
        split_idx => The ogb dictionary that contains the train, valid, test splits
    """
    split_idx = dataset.get_idx_split('random', 0.25)
    train_idx, valid_idx, test_idx = split_idx["train"], split_idx["valid"], split_idx["test"]

    graph, label = dataset[0]

    label = torch.squeeze(label)

    print("generate x")
    x = graph['node_feat'][train_idx].numpy()
    x = sp.csr_matrix(x)

    tx = graph['node_feat'][test_idx].numpy()
    tx = sp.csr_matrix(tx)

    allx = graph['node_feat'].numpy()
    allx = sp.csr_matrix(allx)

    y = F.one_hot(label[train_idx]).numpy()
    ty = F.one_hot(label[test_idx]).numpy()
    ally = F.one_hot(label).numpy()

    edge_index = graph['edge_index'].T

    graph = defaultdict(list)

    for i in range(0, label.shape[0]):
        graph[i].append(i)

    for start_edge, end_edge in edge_index:
        graph[start_edge.item()].append(end_edge.item())

    return x, tx, allx, y, ty, ally, graph, split_idx


def to_sparse_tensor(edge_index, edge_feat, num_nodes):
    """ converts the edge_index into SparseTensor
    """
    num_edges = edge_index.size(1)

    (row, col), N, E = edge_index, num_nodes, num_edges
    perm = (col * N + row).argsort()
    row, col = row[perm], col[perm]

    value = edge_feat[perm]
    adj_t = SparseTensor(row=col, col=row, value=value,
                         sparse_sizes=(N, N), is_sorted=True)

    # Pre-process some important attributes.
    adj_t.storage.rowptr()
    adj_t.storage.csr2csc()

    return adj_t


def normalize(edge_index):
    """ normalizes the edge_index
    """
    adj_t = edge_index.set_diag()
    deg = adj_t.sum(dim=1).to(torch.float)
    deg_inv_sqrt = deg.pow(-0.5)
    deg_inv_sqrt[deg_inv_sqrt == float('inf')] = 0
    adj_t = deg_inv_sqrt.view(-1, 1) * adj_t * deg_inv_sqrt.view(1, -1)
    return adj_t


def gen_normalized_adjs(dataset):
    """ returns the normalized adjacency matrix
    """
    row, col = dataset.graph['edge_index']
    N = dataset.graph['num_nodes']
    adj = SparseTensor(row=row, col=col, sparse_sizes=(N, N))
    deg = adj.sum(dim=1).to(torch.float)
    D_isqrt = deg.pow(-0.5)
    D_isqrt[D_isqrt == float('inf')] = 0

    DAD = D_isqrt.view(-1,1) * adj * D_isqrt.view(1,-1)
    DA = D_isqrt.view(-1,1) * D_isqrt.view(-1,1) * adj
    AD = adj * D_isqrt.view(1,-1) * D_isqrt.view(1,-1)
    return DAD, DA, AD

def convert_to_adj(edge_index,n_node):
    '''convert from pyg format edge_index to n by n adj matrix'''
    adj=torch.zeros((n_node,n_node))
    row,col=edge_index
    adj[row,col]=1
    return adj

def adj_mul(adj_i, adj, N):
    adj_i_sp = torch.sparse_coo_tensor(adj_i, torch.ones(adj_i.shape[1], dtype=torch.float).to(adj.device), (N, N))
    adj_sp = torch.sparse_coo_tensor(adj, torch.ones(adj.shape[1], dtype=torch.float).to(adj.device), (N, N))
    adj_j = torch.sparse.mm(adj_i_sp, adj_sp)
    adj_j = adj_j.coalesce().indices()
    return adj_j

import subprocess

def get_gpu_memory_map():
    """Get the current gpu usage.
    Returns
    -------
    usage: dict
        Keys are device ids as integers.
        Values are memory usage as integers in MB.
    """
    result = subprocess.check_output(
        [
            'nvidia-smi', '--query-gpu=memory.used',
            '--format=csv,nounits,noheader'
        ], encoding='utf-8')
    # Convert lines into a dictionary
    gpu_memory = np.array([int(x) for x in result.strip().split('\n')])
    # gpu_memory_map = dict(zip(range(len(gpu_memory)), gpu_memory))
    return gpu_memory

def laplacian_positional_encoding(g, pos_enc_dim):
    """
        Graph positional encoding v/ Laplacian eigenvectors
    """

    # Laplacian
    # Calculate the adjacency matrix A using PyG's to_scipy_sparse_matrix function
    A = to_scipy_sparse_matrix(g.graph['edge_index'], num_nodes = g.graph['num_nodes']).tocsr()

    # Calculate the degree matrix N using PyG's degree function
    N = sp.diags((torch.clamp(degree(g.graph['edge_index'][1],num_nodes = g.graph['num_nodes'],dtype=torch.int), min=1).numpy())** -0.5, dtype=float)

    # Calculate the Laplacian matrix L
    L = sp.eye(g.graph['num_nodes']) - N * A * N

    # Eigenvectors with scipy
    #EigVal, EigVec = sp.linalg.eigs(L, k=pos_enc_dim+1, which='SR')
    EigVal, EigVec = sp.linalg.eigs(L, k=pos_enc_dim+1, which='SR', tol=1e-2) # for 40 PEs
    EigVec = EigVec[:, EigVal.argsort()] # increasing order
    lap_pos_enc = torch.from_numpy(EigVec[:,1:pos_enc_dim+1]).float() 

    return lap_pos_enc

dataset_drive_url = {
    'snap-patents' : '1ldh23TSY1PwXia6dU0MYcpyEgX-w3Hia', 
    'pokec' : '1dNs5E7BrWJbgcHeQ_zuy5Ozp2tRCWG0y', 
    'yelp-chi': '1fAXtTVQS4CfEk4asqrFw9EPmlUPGbGtJ', 
}

splits_drive_url = {
    'snap-patents' : '12xbBRqd8mtG_XkNLH8dRRNZJvVM4Pw-N', 
    'pokec' : '1ZhpAiyTNc0cE_hhgyiqxnkKREHK7MK-_',
}