Refactor Graph class to support custom edge attribute logic
This commit is contained in:
FilippoOlivo
committed by
Nicola Demo
Nicola Demo
parent
78b276d995
commit
bbdd5d4bf1
173
pina/graph.py
173
pina/graph.py
@@ -5,6 +5,7 @@ import torch
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from . import LabelTensor
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from torch_geometric.data import Data
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from torch_geometric.utils import to_undirected
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import inspect
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class Graph:
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@@ -12,14 +13,17 @@ class Graph:
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Class for the graph construction.
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"""
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def __init__(self,
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x,
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pos,
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edge_index,
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edge_attr=None,
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build_edge_attr=False,
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undirected=False,
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additional_params=None):
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def __init__(
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self,
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x,
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pos,
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edge_index,
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edge_attr=None,
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build_edge_attr=False,
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undirected=False,
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custom_build_edge_attr=None,
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additional_params=None
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):
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"""
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Constructor for the Graph class.
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:param x: The node features.
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@@ -34,45 +38,23 @@ class Graph:
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:type build_edge_attr: bool
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:param undirected: Whether to build an undirected graph.
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:type undirected: bool
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:param custom_build_edge_attr: Custom function to build the edge
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attributes.
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:type custom_build_edge_attr: function
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:param additional_params: Additional parameters.
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:type additional_params: dict
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"""
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self.data = []
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x, pos, edge_index = Graph._check_input_consistency(x, pos, edge_index)
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x, pos, edge_index = self._check_input_consistency(x, pos, edge_index)
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# Check input dimension consistency and store the number of graphs
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data_len = self._check_len_consistency(x, pos)
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if inspect.isfunction(custom_build_edge_attr):
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self._build_edge_attr = custom_build_edge_attr
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# Initialize additional_parameters (if present)
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if additional_params is not None:
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if not isinstance(additional_params, dict):
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raise TypeError("additional_params must be a dictionary.")
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for param, val in additional_params.items():
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# Check if the values are tensors or lists of tensors
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if isinstance(val, torch.Tensor):
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# If the tensor is 3D, we split it into a list of 2D tensors
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# In this case there must be a additional parameter for each
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# node
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if val.ndim == 3:
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additional_params[param] = [val[i] for i in
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range(val.shape[0])]
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# If the tensor is 2D, we replicate it for each node
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elif val.ndim == 2:
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additional_params[param] = [val] * data_len
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# If the tensor is 1D, each graph has a scalar values as
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# additional parameter
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if val.ndim == 1:
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if len(val) == data_len:
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additional_params[param] = [val[i] for i in
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range(len(val))]
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else:
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additional_params[param] = [val for _ in
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range(data_len)]
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elif not isinstance(val, list):
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raise TypeError("additional_params values must be tensors "
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"or lists of tensors.")
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else:
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additional_params = {}
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# Check consistency and initialize additional_parameters (if present)
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additional_params = self._check_additional_params(additional_params,
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data_len)
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# Make the graphs undirected
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if undirected:
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@@ -81,27 +63,17 @@ class Graph:
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else:
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edge_index = to_undirected(edge_index)
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if build_edge_attr:
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if edge_attr is not None:
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warning("Edge attributes are provided, build_edge_attr is set "
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"to True. The provided edge attributes will be ignored.")
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edge_attr = self._build_edge_attr(pos, edge_index)
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# Prepare internal lists to create a graph list (same positions but
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# different node features)
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if isinstance(x, list) and isinstance(pos,
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(torch.Tensor, LabelTensor)):
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# Replicate the positions, edge_index and edge_attr
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pos, edge_index = [pos] * data_len, [edge_index] * data_len
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if edge_attr is not None:
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edge_attr = [edge_attr] * data_len
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# Prepare internal lists to create a list containing a single graph
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elif isinstance(x, (torch.Tensor, LabelTensor)) and isinstance(pos, (
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torch.Tensor, LabelTensor)):
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# Encapsulate the input tensors into lists
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x, pos, edge_index = [x], [pos], [edge_index]
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if isinstance(edge_attr, torch.Tensor):
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edge_attr = [edge_attr]
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# Prepare internal lists to create a list of graphs (same node features
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# but different positions)
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elif (isinstance(x, (torch.Tensor, LabelTensor))
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@@ -111,6 +83,10 @@ class Graph:
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elif not isinstance(x, list) and not isinstance(pos, list):
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raise TypeError("x and pos must be lists or tensors.")
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# Build the edge attributes
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edge_attr = self._check_and_build_edge_attr(edge_attr, build_edge_attr,
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data_len, edge_index, pos, x)
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# Perform the graph construction
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self._build_graph_list(x, pos, edge_index, edge_attr, additional_params)
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@@ -130,12 +106,8 @@ class Graph:
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**add_params_local))
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@staticmethod
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def _build_edge_attr(pos, edge_index):
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if isinstance(pos, torch.Tensor):
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pos = [pos]
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edge_index = [edge_index]
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distance = [pos_[edge_index_[0]] - pos_[edge_index_[1]] ** 2 for
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pos_, edge_index_ in zip(pos, edge_index)]
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def _build_edge_attr(x, pos, edge_index):
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distance = torch.abs(pos[edge_index[0]] - pos[edge_index[1]])
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return distance
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@staticmethod
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@@ -166,15 +138,65 @@ class Graph:
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edge_index = [edge_index[i] for i in range(edge_index.shape[0])]
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return x, pos, edge_index
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@staticmethod
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def _check_additional_params(additional_params, data_len):
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if additional_params is not None:
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if not isinstance(additional_params, dict):
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raise TypeError("additional_params must be a dictionary.")
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for param, val in additional_params.items():
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# Check if the values are tensors or lists of tensors
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if isinstance(val, torch.Tensor):
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# If the tensor is 3D, we split it into a list of 2D tensors
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# In this case there must be a additional parameter for each
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# node
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if val.ndim == 3:
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additional_params[param] = [val[i] for i in
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range(val.shape[0])]
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# If the tensor is 2D, we replicate it for each node
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elif val.ndim == 2:
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additional_params[param] = [val] * data_len
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# If the tensor is 1D, each graph has a scalar values as
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# additional parameter
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if val.ndim == 1:
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if len(val) == data_len:
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additional_params[param] = [val[i] for i in
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range(len(val))]
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else:
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additional_params[param] = [val for _ in
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range(data_len)]
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elif not isinstance(val, list):
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raise TypeError("additional_params values must be tensors "
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"or lists of tensors.")
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else:
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additional_params = {}
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return additional_params
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def _check_and_build_edge_attr(self, edge_attr, build_edge_attr, data_len,
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edge_index, pos, x):
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# Check if edge_attr is consistent with x and pos
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if edge_attr is not None:
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if build_edge_attr is True:
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warning("edge_attr is not None. build_edge_attr will not be "
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"considered.")
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if isinstance(edge_attr, list):
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if len(edge_attr) != data_len:
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raise ValueError("edge_attr must have the same length as x "
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"and pos.")
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return [edge_attr] * data_len
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if build_edge_attr:
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return [self._build_edge_attr(x,pos_, edge_index_) for
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pos_, edge_index_ in zip(pos, edge_index)]
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class RadiusGraph(Graph):
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def __init__(self,
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x,
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pos,
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r,
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build_edge_attr=False,
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undirected=False,
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additional_params=None, ):
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def __init__(
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self,
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x,
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pos,
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r,
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**kwargs
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):
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x, pos, edge_index = Graph._check_input_consistency(x, pos)
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if isinstance(pos, (torch.Tensor, LabelTensor)):
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@@ -183,9 +205,7 @@ class RadiusGraph(Graph):
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edge_index = [RadiusGraph._radius_graph(p, r) for p in pos]
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super().__init__(x=x, pos=pos, edge_index=edge_index,
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build_edge_attr=build_edge_attr,
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undirected=undirected,
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additional_params=additional_params)
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**kwargs)
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@staticmethod
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def _radius_graph(points, r):
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@@ -204,23 +224,20 @@ class RadiusGraph(Graph):
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class KNNGraph(Graph):
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def __init__(self,
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x,
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pos,
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k,
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build_edge_attr=False,
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undirected=False,
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additional_params=None,
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):
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def __init__(
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self,
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x,
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pos,
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k,
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**kwargs
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):
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x, pos, edge_index = Graph._check_input_consistency(x, pos)
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if isinstance(pos, (torch.Tensor, LabelTensor)):
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edge_index = KNNGraph._knn_graph(pos, k)
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else:
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edge_index = [KNNGraph._knn_graph(p, k) for p in pos]
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super().__init__(x=x, pos=pos, edge_index=edge_index,
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build_edge_attr=build_edge_attr,
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undirected=undirected,
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additional_params=additional_params)
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**kwargs)
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@staticmethod
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def _knn_graph(points, k):
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@@ -240,6 +257,7 @@ class KNNGraph(Graph):
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edge_index = torch.stack([row, col], dim=0)
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return edge_index
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class TemporalGraph(Graph):
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def __init__(
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self,
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@@ -259,7 +277,8 @@ class TemporalGraph(Graph):
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edge_index = [RadiusGraph._radius_graph(p, r) for p in pos]
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additional_params = {'t': t}
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self._check_time_consistency(pos, t)
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super().__init__(x=x, pos=pos, edge_index=edge_index, edge_attr=edge_attr,
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super().__init__(x=x, pos=pos, edge_index=edge_index,
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edge_attr=edge_attr,
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build_edge_attr=build_edge_attr,
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undirected=undirected,
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additional_params=additional_params)
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@@ -7,10 +7,12 @@ from pina.graph import RadiusGraph, KNNGraph, TemporalGraph
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@pytest.mark.parametrize(
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"x, pos",
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[
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([torch.rand(10, 2) for _ in range(3)], [torch.rand(10, 3) for _ in range(3)]),
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([torch.rand(10, 2) for _ in range(3)], [torch.rand(10, 3) for _ in range(3)]),
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(torch.rand(3,10,2), torch.rand(3,10,3)),
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(torch.rand(3,10,2), torch.rand(3,10,3)),
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([torch.rand(10, 2) for _ in range(3)],
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[torch.rand(10, 3) for _ in range(3)]),
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([torch.rand(10, 2) for _ in range(3)],
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[torch.rand(10, 3) for _ in range(3)]),
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(torch.rand(3, 10, 2), torch.rand(3, 10, 3)),
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(torch.rand(3, 10, 2), torch.rand(3, 10, 3)),
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]
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)
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def test_build_multiple_graph_multiple_val(x, pos):
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@@ -28,7 +30,7 @@ def test_build_multiple_graph_multiple_val(x, pos):
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assert all(d.edge_attr is not None for d in data)
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assert all([d.edge_index.shape[1] == d.edge_attr.shape[0]] for d in data)
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graph = KNNGraph(x=x, pos=pos, build_edge_attr=True, k = 3)
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graph = KNNGraph(x=x, pos=pos, build_edge_attr=True, k=3)
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data = graph.data
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assert all(torch.isclose(d_.x, x_).all() for (d_, x_) in zip(data, x))
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assert all(torch.isclose(d_.pos, pos_).all() for d_, pos_ in zip(data, pos))
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@@ -112,36 +114,39 @@ def test_build_single_graph_single_val(pos):
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assert all(d.edge_attr is not None for d in data)
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assert all([d.edge_index.shape[1] == d.edge_attr.shape[0]] for d in data)
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def test_additional_parameters_1():
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x = torch.rand(3, 10, 2)
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pos = torch.rand(3, 10, 2)
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additional_parameters = {'y': torch.ones(3)}
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graph = RadiusGraph(x=x, pos=pos, build_edge_attr=True, r=.3,
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additional_params=additional_parameters)
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additional_params=additional_parameters)
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assert len(graph.data) == 3
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data = graph.data
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assert all(torch.isclose(d_.x, x_).all() for (d_, x_) in zip(data, x))
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assert all(hasattr(d, 'y') for d in data)
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assert all(d_.y == 1 for d_ in data)
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@pytest.mark.parametrize(
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"additional_parameters",
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[
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({'y': torch.rand(3,10,1)}),
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({'y': [torch.rand(10,1) for _ in range(3)]}),
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({'y': torch.rand(3, 10, 1)}),
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({'y': [torch.rand(10, 1) for _ in range(3)]}),
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]
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)
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def test_additional_parameters_2(additional_parameters):
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x = torch.rand(3, 10, 2)
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pos = torch.rand(3, 10, 2)
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graph = RadiusGraph(x=x, pos=pos, build_edge_attr=True, r=.3,
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additional_params=additional_parameters)
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additional_params=additional_parameters)
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assert len(graph.data) == 3
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data = graph.data
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assert all(torch.isclose(d_.x, x_).all() for (d_, x_) in zip(data, x))
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assert all(hasattr(d, 'y') for d in data)
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assert all(torch.isclose(d_.x, x_).all() for (d_, x_) in zip(data, x))
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def test_temporal_graph():
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x = torch.rand(3, 10, 2)
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pos = torch.rand(3, 10, 2)
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@@ -152,3 +157,21 @@ def test_temporal_graph():
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assert all(torch.isclose(d_.x, x_).all() for (d_, x_) in zip(data, x))
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assert all(hasattr(d, 't') for d in data)
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assert all(d_.t == t_ for (d_, t_) in zip(data, t))
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def test_custom_build_edge_attr_func():
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x = torch.rand(3, 10, 2)
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pos = torch.rand(3, 10, 2)
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def build_edge_attr(x, pos, edge_index):
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return torch.cat([pos[edge_index[0]], pos[edge_index[1]]], dim=-1)
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graph = RadiusGraph(x=x, pos=pos, build_edge_attr=True, r=.3,
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custom_build_edge_attr=build_edge_attr)
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assert len(graph.data) == 3
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data = graph.data
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assert all(hasattr(d, 'edge_attr') for d in data)
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assert all(d.edge_attr.shape[1] == 4 for d in data)
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assert all(torch.isclose(d.edge_attr,
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build_edge_attr(d.x, d.pos, d.edge_index)).all()
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for d in data)
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