Building graph temporal dataset

username: ZSheikhb
cooked: <p>I am trying to build dataset class for dataloader which I can use to train pytorch graph temporal model. Here is my class</p>
<pre><code class="lang-auto">import torch
import numpy as np
from networkx import from_numpy_array, from_numpy_matrix
from torch_geometric_temporal.signal import temporal_signal_split
from torch_geometric.utils import dense_to_sparse
from torch_geometric_temporal.signal import StaticHeteroGraphTemporalSignal
import networkx as nx
import pandas as pd
def adjacency_matrix_transition(node_state_type_size, node_action_type_size):
    ns = node_state_type_size
    na = node_action_type_size
    A  = np.zeros((ns+na,ns+na)).astype(np.float32)
    for i in range(A.shape[0]):
        for j in range(A.shape[1]):
            if i!=j:
                 if i &lt;j:
                    if i&lt;ns and j&lt;ns:
                        A[i,j]=A[j,i]=1 
                    elif i&lt;ns and j&gt;=ns:
                        A[i,j]=A[j,i]=0.6 
                    elif i&gt;=ns and j&gt;=ns:
                        A[i,j]=A[j,i]=0.9
    return A


class GraphDataset(object):
    def __init__(self,
                 input_name,
                 target_name,
                 observation_size,
                 action_size,
                 reward_size,
                 filepath=None,
                 max_length=90,
                 device=torch.device("cuda:0" if torch.cuda.is_available() else "cpu")
                 ):
        super(GraphDataset, self).__init__()
        self.action_size = action_size
        self.observation_size = observation_size
        self.reward_size = reward_size
        self.input_filename = input_name
        self.target_filename = target_name
        self.filepath = filepath
        self.max_length = max_length
        self.device = device
        self._read_data()

    def _read_data(self):
        #input shape(Batch, seq_length_input_size)
        #
        self.X = torch.load(os.path.join(self.filepath, self.input_filename))[:,:self.max_length,:]
        self.Y = torch.load(os.path.join(self.filepath, self.target_filename))[:,:self.max_length,:]
        self.X = self.X.permute(0,2,1).unsqueeze(-2)## (B, N, F, T)
        self.Y = self.Y.permute(0,2,1)
        print(f"input data {self.X.shape}")
        print(f"target data {self.Y.shape}")


    def _get_edges_and_weights(self):
        self.edge_index_dicts=dict()
        self.edge_weights_dicts=dict()
        self.input_graph = torch.from_numpy(adjacency_matrix_transition(self.observation_size,self.action_size))
        edge_indices, values = dense_to_sparse(self.input_graph)
        edge_indices = edge_indices.numpy()
        values = values.numpy()
        self.edge_index_dicts["features"] = edge_indices
        self.edge_weights_dicts["features"] = values
        graph = from_numpy_array(self.input_graph.numpy())
        edge_list = nx.to_pandas_edgelist(graph)
        adj = nx.from_pandas_edgelist(edge_list, edge_attr=['weight'])
        adj = pd.DataFrame(nx.adjacency_matrix(adj, weight='weight').todense())
        adjacency = adj.copy()

        D = np.diag(np.sum(adjacency,axis=1))
        I = np.identity(adjacency.shape[0])
        D_inv_sqrt = np.linalg.inv(np.sqrt(D))
        L = I - np.dot(D_inv_sqrt, adjacency).dot(D_inv_sqrt)

        self.normalized_laplacian_input = L.copy()
        ##
        self.target_graph= torch.from_numpy(adjacency_matrix_transition(self.observation_size,self.reward_size))
        edge_indices, values = dense_to_sparse(self.target_graph)
        edge_indices = edge_indices.numpy()
        values = values.numpy()
        self.edge_index_dicts["targets"] = edge_indices
        self.edge_weights_dicts["targets"] = values
        graph = from_numpy_array(self.target_graph.numpy())
        edge_list = nx.to_pandas_edgelist(graph)
        adj = nx.from_pandas_edgelist(edge_list, edge_attr=['weight'])#,source=['source'], target=['target'])
        adj = pd.DataFrame(nx.adjacency_matrix(adj, weight='weight').todense())
        adjacency = adj.copy()

        D = np.diag(np.sum(adjacency,axis=1))
        I = np.identity(adjacency.shape[0])
        D_inv_sqrt = np.linalg.inv(np.sqrt(D))
        L = I - np.dot(D_inv_sqrt, adjacency).dot(D_inv_sqrt)

        self.normalized_laplacian_output = L.copy()

    def _get_targets_and_features(self, num_timesteps_in: int = 12, num_timesteps_out: int = 12):
        
        indices=[i
                 for i in range(self.X.shape[-1] - (num_timesteps_in + num_timesteps_out) + 1)]
        self.features,self.targets=[],[]
        for i in indices:
            self.features.append(self.X[:,:,:, i : i + num_timesteps_in].numpy())
            self.targets.append(self.Y[:,:,i : i + num_timesteps_in].numpy())
        
    def get_dataset(self, num_timesteps_in: int = 12, num_timesteps_out: int = 12) -&gt; StaticHeteroGraphTemporalSignal:
        """Returns data iterator as an instance of the static graph temporal signal class."""
        self._get_edges_and_weights()
        self._get_targets_and_features(num_timesteps_in, num_timesteps_out)
        dataset = StaticHeteroGraphTemporalSignal(
                                                  self.edge_index_dicts,
                                                  self.edge_weights_dicts,
                                                  self.features,
                                                  self.targets
                                                  )
        return dataset

def create_dataloader(train_dataset, DEVICE, bs, shuffle):
    train_input = np.array(train_dataset.features)
    train_target = np.array(train_dataset.targets)
    train_x_tensor = torch.from_numpy(train_input).type(torch.FloatTensor).to(DEVICE)  # (B, N, F, T)
    train_target_tensor = torch.from_numpy(train_target).type(torch.FloatTensor).to(DEVICE)  # (B, N, T)
    train_dataset_new = torch.utils.data.TensorDataset(train_x_tensor, train_target_tensor)
    train_loader = torch.utils.data.DataLoader(train_dataset_new, batch_size=bs, shuffle=shuffle, drop_last=True)
    return train_loader

DEVICE = torch.device("cuda:0" if torch.cuda.is_available() else "cpu")  # cuda
print(DEVICE)
shuffle = False
obs_size, act_size, r_size= 11, 3, 1
batch_size = 16
d_e=7*2
d_d=7
times = 20


# Read data

input_name = "inputs_features.pt"
target_name = "outputs_features.pt"
filepath ="/home/"
loader = GraphDataset(input_name, target_name, ob_size, act_size, r_size, filepath)
dataset = loader.get_dataset(num_timesteps_in=d_e, num_timesteps_out=d_d)
print(next(iter(dataset)))  # Show first sample
A_tilde = torch.from_numpy(loader.normalized_laplacian_input).to(DEVICE)
X_s = torch.from_numpy(loader.features).to(DEVICE)
</code></pre>
<p>I am getting this error running above code</p>
<pre><code class="lang-auto">input data torch.Size([4447, 14, 1, 90])
target data torch.Size([4447, 12, 90])

AttributeError                            Traceback (most recent call last)
/tmp/ipykernel_5880/605001366.py in &lt;module&gt;
    154 loader = GraphDataset(input_name, target_name, obs_size, act_size, r_size, filepath)
    155 dataset = loader.get_dataset(num_timesteps_in=d_e, num_timesteps_out=d_d)
--&gt; 156 print(next(iter(dataset)))  # Show first sample
    157 A_tilde = torch.from_numpy(loader.normalized_laplacian_input).to(DEVICE)
    158 X_s = torch.from_numpy(loader.features).to(DEVICE)

~/anaconda3/lib/python3.9/site-packages/torch_geometric_temporal/signal/static_hetero_graph_temporal_signal.py in __next__(self)
    201     def __next__(self):
    202         if self.t &lt; len(self.feature_dicts):
--&gt; 203             snapshot = self[self.t]
    204             self.t = self.t + 1
    205             return snapshot

~/anaconda3/lib/python3.9/site-packages/torch_geometric_temporal/signal/static_hetero_graph_temporal_signal.py in __getitem__(self, time_index)
    173             )
    174         else:
--&gt; 175             x_dict = self._get_features(time_index)
    176             edge_index_dict = self._get_edge_index()
    177             edge_weight_dict = self._get_edge_weight()

~/anaconda3/lib/python3.9/site-packages/torch_geometric_temporal/signal/static_hetero_graph_temporal_signal.py in _get_features(self, time_index)
    136             return self.feature_dicts[time_index]
    137         else:
--&gt; 138             return {key: torch.FloatTensor(value) for key, value in self.feature_dicts[time_index].items()
    139                     if value is not None}
    140 
AttributeError: 'numpy.ndarray' object has no attribute 'items'
</code></pre>
<p>any suggestion how I can fix this error?</p>
<p>I am also wondering whether my approach is correct for building tempporal graph where the input graph structure is different from the output graph ? Especially I am wondering whether <code>StaticHeteroGraphTemporalSignal</code> is a correct choice or not?</p>