def astensor(x, *, dtype=None, device=None, escape=None):
try:
if x is None or (escape is not None and isinstance(x, escape)):
return x
except TypeError:
raise TypeError(f"argument 'escape' must be a type or tuple of types.")
if dtype is None:
dtype = gf.infer_type(x)
if isinstance(dtype, (np.dtype, str)):
dtype = data_type_dict().get(str(dtype), dtype)
elif not isinstance(dtype, torch.dtype):
raise TypeError(
f"argument 'dtype' must be torch.dtype, np.dtype or str, but got {type(dtype)}."
)
if is_tensor(x):
tensor = x.to(dtype)
elif gf.is_tensor(x, backend='tensorflow'):
return astensor(gf.tensoras(x),
dtype=dtype,
device=device,
escape=escape)
elif sp.isspmatrix(x):
if gg.backend() == "dgl_torch":
import dgl
tensor = dgl.from_scipy(x, idtype=getattr(torch, gg.intx()))
elif gg.backend() == "pyg":
edge_index, edge_weight = gf.sparse_adj_to_edge(x)
return (astensor(edge_index,
dtype=gg.intx(),
device=device,
escape=escape),
astensor(edge_weight,
dtype=gg.floatx(),
device=device,
escape=escape))
else:
tensor = sparse_adj_to_sparse_tensor(x, dtype=dtype)
elif any((isinstance(x, (np.ndarray, np.matrix)), gg.is_listlike(x),
gg.is_scalar(x))):
tensor = torch.tensor(x, dtype=dtype, device=device)
else:
raise TypeError(
f"Invalid type of inputs. Allowed data type (Tensor, SparseTensor, Numpy array, Scipy sparse tensor, None), but got {type(x)}."
)
return tensor.to(device)
def astensor(x, dtype=None, device=None, kind=None):
"""Convert input matrices to Tensor or SparseTensor.
Parameters:
----------
x: tf.Tensor, tf.Variable, Scipy sparse matrix,
Numpy array-like, etc.
dtype: The type of Tensor `x`, if not specified,
it will automatically using appropriate data type.
See `graphgallery.infer_type`.
device (:class:`torch.device` or `tf.device`, optional): the desired device of returned tensor.
Default: if ``None``, uses the current device for the default tensor type
kind: str
"T" tf
"P" torch
Returns:
----------
Tensor or SparseTensor with dtype:
1. `graphgallery.floatx()` if `x` is floating
2. `graphgallery.intx() ` if `x` is integer
3. `Bool` if `x` is bool.
"""
if kind is None:
kind = backend().kind
else:
assert kind in {"T", "P"}
device = parse_device(device, kind)
if kind == "T":
return tf_tensor.astensor(x, dtype=dtype, device=device)
else:
return th_tensor.astensor(x, dtype=dtype, device=device)
def astensors(*xs, device=None, kind=None):
"""Convert input matrices to Tensor(s) or SparseTensor(s).
Parameters:
----------
xs: tf.Tensor, tf.Variable, Scipy sparse matrix,
Numpy array-like, or a list of them, etc.
device (:class:`torch.device`, optional): the desired device of returned tensor.
Default: if ``None``, uses the current device for the default tensor type
(see :func:`torch.set_default_tensor_type`). :attr:`device` will be the CPU
for CPU tensor types and the current CUDA device for CUDA tensor types.
NOTE:
----------
The argument `device` only work for `PyTorch backend`.
Returns:
----------
Tensor(s) or SparseTensor(s) with dtype:
1. `graphgallery.floatx()` if `x` in `xs` is floating
2. `graphgallery.intx() ` if `x` in `xs` is integer
3. `Bool` if `x` in `xs` is bool.
"""
if kind is None:
kind = backend().kind
else:
assert kind in {"T", "P"}
if kind == "T":
return tf_tensor.astensors(*xs, device=device)
else:
return th_tensor.astensors(*xs, device=device)
def is_sparse_tensor(x):
"""Check whether `x` is a sparse Tensor."""
if backend().kind == "T":
return is_tf_sparse_tensor(x)
else:
return is_th_sparse_tensor(x)
def astensors(*xs, dtype=None, device=None, backend=None, escape=None):
"""Convert input matrices to Tensor(s) or SparseTensor(s).
Parameters:
----------
xs: one or a list of python object(s)
dtype: The type of Tensor 'x', if not specified,
it will automatically use appropriate data type.
See 'graphgallery.infer_type'.
device: tf.device, optional. the desired device of returned tensor.
Default: if 'None', uses the CPU device for the default tensor type.
backend: String or BackendModule, optional.
'tensorflow', 'torch', TensorFlowBackend, PyTorchBackend, etc.
if not specified, return the current default backend module.
escape: a Class or a tuple of Classes, `astensor` will disabled if
`isinstance(x, escape)`.
Returns:
-------
Tensor(s) or SparseTensor(s) with dtype. If dtype is 'None',
dtype will be one of the following:
1. 'graphgallery.floatx()' if 'x' is floating.
2. 'graphgallery.intx()' if 'x' is integer.
3. 'graphgallery.boolx()' if 'x' is boolean.
"""
backend = gg.backend(backend)
device = gf.device(device, backend)
return _astensors_fn(*xs,
dtype=dtype,
device=device,
backend=backend,
escape=escape)
def is_tensor(x, kind=None):
"""Check whether `x` is
tf.Tensor,
tf.Variable,
tf.RaggedTensor,
tf.sparse.SparseTensor,
torch.Tensor,
torch.sparse.Tensor.
Parameters:
----------
x: A python object to check.
kind: str, optional.
"T" for TensorFlow
"P" for PyTorch
if not specified, using `backend().kind` instead.
Returns:
----------
`True` iff `x` is a (tf or torch) (sparse-)tensor.
"""
if kind is None:
kind = backend().kind
else:
assert_kind(kind)
if kind == "T":
return is_tf_tensor(x)
else:
return is_th_tensor(x)
def is_strided_tensor(x, kind=None):
"""Check whether `x` is a strided (dense) Tensor.
Parameters:
----------
x: A python object to check.
kind: str, optional.
"T" for TensorFlow
"P" for PyTorch
if not specified, using `backend().kind` instead.
Returns:
----------
`True` iff `x` is a (tf or torch) strided (dense) Tensor.
"""
if kind is None:
kind = backend().kind
else:
assert_kind(kind)
if kind == "T":
return is_tf_strided_tensor(x)
else:
return is_th_strided_tensor(x)
def load_models(backend_name=None):
_backend = backend(backend_name)
thismod = sys.modules[__name__]
mod = importlib.import_module(f".gallery_model.{_backend.abbr}", __name__)
global Gallery
Gallery = gf.Registry("GraphGalleryModels")
for model in _GALLERY_MODELS:
_model_class = mod.__dict__.get(model, None)
if _model_class is not None:
Gallery.register(_model_class)
setattr(thismod, model, _model_class)
else:
setattr(thismod, model, _gen_missing_model(model, _backend))
mod = importlib.import_module(f".sklearn_model", __name__)
for model in _SKLEARN_MODELS:
_model_class = mod.__dict__.get(model, None)
if _model_class is not None:
Gallery.register(_model_class)
setattr(thismod, model, _model_class)
else:
setattr(thismod, model, _gen_missing_model(model, _backend))
def get_module(backend: Optional[Backend] = None):
"""get the module of eigher
'graphgallery.functional.tensor.tensorflow'
or 'graphgallery.functional.tensor.pytorch'
by 'backend'.
Parameters
----------
backend: String or BackendModule, optional.
'tensorflow', 'torch', TensorFlowBackend,
PyTorchBackend, etc. if not specified,
return the current backend module.
Returns
-------
module:
- 'graphgallery.functional.tensor.tensorflow'
for tensorflow backend,
- 'graphgallery.functional.tensor.pytorch'
for pytorch backend
"""
backend = gg.backend(backend)
if backend == "tensorflow":
return tensorflow
else:
return pytorch
def asintarr(x, dtype: str = None):
"""Convert `x` to interger Numpy array.
Parameters:
----------
x: Tensor, Scipy sparse matrix,
Numpy array-like, etc.
Returns:
----------
Integer Numpy array with dtype or `graphgallery.intx()`
"""
if dtype is None:
dtype = intx()
if is_tensor(x):
if x.dtype != dtype:
kind = backend().kind
if kind == "T":
x = tf.cast(x, dtype=dtype)
else:
x = x.to(getattr(torch, dtype))
return x
if is_interger_scalar(x):
x = np.asarray([x], dtype=dtype)
elif is_list_like(x) or isinstance(x, (np.ndarray, np.matrix)):
x = np.asarray(x, dtype=dtype)
else:
raise ValueError(
f"Invalid input which should be either array-like or integer scalar, but got {type(x)}."
)
return x
def __init__(self, *, device="cpu", seed=None, name=None, **cfg):
"""
Parameters:
----------
device: string. optional
The device where the model running on.
seed: interger scalar. optional
Used to create a reproducible sequence of tensors
across multiple calls.
name: string. optional
Specified name for the model. (default: :str: `class name`)
cfg: other custom keyword arguments.
"""
gg.set_seed(seed)
self.cfg = gf.BunchDict(cfg)
if self.cfg:
print(f"Receiving configs:\n{self.cfg}")
self.device = torch.device(device)
self.data_device = self.device
self.backend = gg.backend()
self.seed = seed
self.name = name or self.__class__.__name__
self._model = None
self._graph = None
self._cache = gf.BunchDict()
self.transform = gf.BunchDict()
def sparse_adj_to_sparse_tensor(x, kind=None):
"""Converts a Scipy sparse matrix to a TensorFlow/PyTorch SparseTensor.
Parameters
----------
x: Scipy sparse matrix
Matrix in Scipy sparse format.
kind: str, optional.
"T" for TensorFlow
"P" for PyTorch
if not specified, using `backend().kind` instead.
Returns
-------
S: SparseTensor
Matrix as a sparse tensor.
"""
if kind is None:
kind = backend().kind
else:
assert_kind(kind)
if kind == "T":
return T.tf_tensor.sparse_adj_to_sparse_tensor(x)
else:
return T.th_tensor.sparse_adj_to_sparse_tensor(x)
def normalize_edge_tensor(edge_index, edge_weight=None, n_nodes=None, fill_weight=1.0, rate=-0.5, kind=None):
if kind is None:
kind = backend().kind
else:
assert kind in {"T", "P"}
if kind == "T":
return tf_tensor.normalize_adj_tensor(edge_index, edge_weight=edge_weight, n_nodes=n_nodes, fill_weight=fill_weight, rate=rate)
else:
return th_tensor.normalize_adj_tensor(edge_index, edge_weight=edge_weight, n_nodes=n_nodes, fill_weight=fill_weight, rate=rate)
def random_seed(seed: int = None, backend: Optional[Backend] = None):
backend = gg.backend(backend)
np.random.seed(seed)
random.seed(seed)
if backend == "tensorflow":
tf.random.set_seed(seed)
else:
torch.manual_seed(seed)
torch.cuda.manual_seed(seed)
def add_selfloops_edge(edge_index, edge_weight, n_nodes=None, fill_weight=1.0, kind=None):
if kind is None:
kind = backend().kind
else:
assert kind in {"T", "P"}
if kind == "T":
return tf_tensor.normalize_adj_tensor(edge_index, edge_weight, n_nodes=n_nodes, fill_weight=fill_weight)
else:
return th_tensor.normalize_adj_tensor(edge_index, edge_weight, n_nodes=n_nodes, fill_weight=fill_weight)
def normalize_adj_tensor(adj, rate=-0.5, fill_weight=1.0, kind=None):
if kind is None:
kind = backend().kind
else:
assert kind in {"T", "P"}
if kind == "T":
return tf_tensor.normalize_adj_tensor(adj, rate=rate, fill_weight=fill_weight)
else:
return th_tensor.normalize_adj_tensor(adj, rate=rate, fill_weight=fill_weight)
def set_seed(seed: Optional[int] = None):
assert seed is None or isinstance(seed, Number), seed
np.random.seed(seed)
random.seed(seed)
if seed is not None:
torch.manual_seed(seed)
torch.cuda.manual_seed(seed)
if backend() == 'dgl':
import dgl
dgl.random.seed(seed)
def sparse_edges_to_sparse_tensor(edge_index: np.ndarray, edge_weight: np.ndarray = None, shape: tuple = None, kind=None):
if kind is None:
kind = backend().kind
else:
assert kind in {"T", "P"}
if kind == "T":
return tf_tensor.sparse_edges_to_sparse_tensor(edge_index, edge_weight, shape)
else:
return th_tensor.sparse_edges_to_sparse_tensor(edge_index, edge_weight, shape)
def sparse_tensor_to_sparse_adj(x, kind=None):
"""Converts a SparseTensor to a Scipy sparse matrix (CSR matrix)."""
if kind is None:
kind = backend().kind
else:
assert kind in {"T", "P"}
if kind == "T":
return tf_tensor.sparse_tensor_to_sparse_adj(x)
else:
return th_tensor.sparse_tensor_to_sparse_adj(x)
def get_model(model: str, backend_name=None):
backend = gg.backend(backend_name)
mod = importlib.import_module(f".{backend.abbr}", __name__)
_model_class = mod.__dict__.get(model, None)
if _model_class is not None:
return _model_class
else:
raise ImportError(f"model {model} is not supported by '{backend}'."
" You can switch to other backends by setting"
" the 'graphgallery.backend' environment.")
def normalize_adj_tensor(adj, rate=-0.5, fill_weight=1.0, kind=None):
if kind is None:
kind = backend().kind
else:
assert_kind(kind)
if kind == "T":
return T.tf_tensor.normalize_adj_tensor(adj,
rate=rate,
fill_weight=fill_weight)
else:
# TODO
return T.th_tensor.normalize_adj_tensor(adj,
rate=rate,
fill_weight=fill_weight)
def is_tensor_or_variable(x):
"""Check whether `x` is tf.Tensor or tf.Variable or tf.RaggedTensor.
Parameters:
x: A python object to check.
Returns:
`True` iff `x` is a `tf.Tensor` or `tf.Variable` or `tf.RaggedTensor`.
"""
if backend().kind == "T":
return any((tf.is_tensor(x), isinstance(x, tf.Variable),
isinstance(x, tf.RaggedTensor), is_tf_sparse_tensor(x)))
else:
# TODO: is it really work for all torch tensors??
return torch.is_tensor(x)
def __init__(self, *, device="cpu", seed=None, name=None, **kwargs):
"""
Parameters:
----------
device: string. optional
The device where the model running on.
seed: interger scalar. optional
Used to create a reproducible sequence of tensors
across multiple calls.
name: string. optional
Specified name for the model. (default: :str: `class name`)
kwargs: other custom keyword arguments.
"""
# if graph is not None and not isinstance(graph, gg.data.BaseGraph):
# raise ValueError(f"Unrecognized graph: {graph}.")
kwargs.pop("self", None)
kwargs.pop("__class__", None)
cfg = gg.CfgNode()
cfg.merge_from_dict(kwargs)
cfg.intx = self.intx = gg.intx()
cfg.floatx = self.floatx = gg.floatx()
cfg.boolx = self.boolx = gg.boolx()
cfg.seed = self.seed = seed
cfg.name = self.name = name or self.__class__.__name__
cfg.device = device
_backend = gg.backend()
cfg.backend = getattr(_backend, "name", None)
if seed:
gf.random_seed(seed, _backend)
self.device = gf.device(device, _backend)
self.data_device = self.device
self.backend = _backend
# data types, default: `float32`,`int32` and `bool`
self._cache = gf.BunchDict()
self.transform = gf.BunchDict()
self._model = None
self._graph = None
self.cfg = cfg
self.setup_cfg()
self.custom_setup()
def __init__(self, *graph, device="cpu:0", seed=None, name=None, **kwargs):
"""
Parameters:
----------
graph: Graph or MultiGraph.
device: string. optional
The device where the model running on.
seed: interger scalar. optional
Used in combination with `tf.random.set_seed` & `np.random.seed`
& `random.seed` to create a reproducible sequence of tensors
across multiple calls.
name: string. optional
Specified name for the model. (default: :str: `class.__name__`)
kwargs: other custom keyword parameters.
"""
graph = parse_graph_inputs(*graph)
_backend = backend()
self.backend = _backend
self.kind = _backend.kind
raise_if_kwargs(kwargs)
if seed is not None:
np.random.seed(seed)
random.seed(seed)
if self.kind == "P":
torch.manual_seed(seed)
torch.cuda.manual_seed(seed)
# torch.cuda.manual_seed_all(seed)
else:
tf.random.set_seed(seed)
if name is None:
name = self.__class__.__name__
self.seed = seed
self.name = name
self.graph = graph.copy()
self.device = parse_device(device, self.kind)
# data types, default: `float32` and `int32`
self.floatx = floatx()
self.intx = intx()
def is_tensor(x):
"""Check whether `x` is
tf.Tensor,
tf.Variable,
tf.RaggedTensor,
tf.sparse.SparseTensor,
torch.Tensor,
torch.sparse.Tensor.
Parameters:
x: A python object to check.
Returns:
`True` iff `x` is a (tf or torch) (sparse-)tensor.
"""
if backend().kind == "T":
return is_tf_tensor(x)
else:
return is_th_tensor(x)
def astensor(x, *, dtype=None, device=None, escape=None):
try:
if x is None or (escape is not None and isinstance(x, escape)):
return x
except TypeError:
raise TypeError(f"argument 'escape' must be a type or tuple of types.")
if dtype is None:
dtype = gf.infer_type(x)
elif isinstance(dtype, tf.dtypes.DType):
dtype = dtype.name
elif isinstance(dtype, (np.dtype, str)):
dtype = str(dtype)
else:
raise TypeError(
f"argument 'dtype' must be tf.dtypes.DType, np.dtype or str, but got {type(dtype)}."
)
with tf.device(device):
if is_tensor(x):
if x.dtype != dtype:
return tf.cast(x, dtype=dtype)
return tf.identity(x)
elif gf.is_tensor(x, backend='torch'):
return astensor(gf.tensoras(x),
dtype=dtype,
device=device,
escape=escape)
elif sp.isspmatrix(x):
if gg.backend() == "dgl_tf":
import dgl
return dgl.from_scipy(x, idtype=getattr(tf,
gg.intx())).to(device)
else:
return sparse_adj_to_sparse_tensor(x, dtype=dtype)
elif any((isinstance(x, (np.ndarray, np.matrix)), gg.is_listlike(x),
gg.is_scalar(x))):
return tf.convert_to_tensor(x, dtype=dtype)
else:
raise TypeError(
f"Invalid type of inputs. Allowed data type(Tensor, SparseTensor, Numpy array, Scipy sparse matrix, None), but got {type(x)}."
)
def sparse_adj_to_sparse_tensor(x, kind=None):
"""Converts a Scipy sparse matrix to a TensorFlow/PyTorch SparseTensor.
Parameters
----------
x: scipy.sparse.sparse
Matrix in Scipy sparse format.
Returns
-------
S: SparseTensor
Matrix as a sparse tensor.
"""
if kind is None:
kind = backend().kind
else:
assert kind in {"T", "P"}
if kind == "T":
return tf_tensor.sparse_adj_to_sparse_tensor(x)
else:
return th_tensor.sparse_adj_to_sparse_tensor(x)
def __init__(self, graph, device="cpu", seed=None, name=None, **kwargs):
"""
Parameters:
----------
graph: Graph or MultiGraph.
device: string. optional
The device where the model running on.
seed: interger scalar. optional
Used in combination with `tf.random.set_seed` & `np.random.seed`
& `random.seed` to create a reproducible sequence of tensors
across multiple calls.
name: string. optional
Specified name for the model. (default: :str: `class.__name__`)
kwargs: other custom keyword arguments.
"""
if not isinstance(graph, gg.data.BaseGraph):
raise ValueError(f"Unrecognized graph: {graph}.")
_backend = gg.backend()
# It currently takes no keyword arguments
gg.utils.raise_error.raise_if_kwargs(kwargs)
if seed:
gf.random_seed(seed, _backend)
if name is None:
name = self.__class__.__name__
self.seed = seed
self.name = name
self.graph = graph.copy()
self.device = gf.device(device, _backend)
self.backend = _backend
# data types, default: `float32`,`int32` and `bool`
self.floatx = gg.floatx()
self.intx = gg.intx()
self.boolx = gg.boolx()
self._cache = gf.BunchDict()
def load_models(backend_name=None):
_backend = backend(backend_name)
thismod = sys.modules[__name__]
mod = importlib.import_module(f".gallery_model.{_backend.abbr}", __name__)
for model in _GALLERY_MODELS:
_model_class = mod.__dict__.get(model, None)
if _model_class is not None:
_enabled_models.add(model)
setattr(thismod, model, _model_class)
else:
setattr(thismod, model, _gen_missing_model(model, _backend))
mod = importlib.import_module(f".sklearn_model", __name__)
for model in _SKLEARN_MODELS:
_model_class = mod.__dict__.get(model, None)
if _model_class is not None:
_enabled_models.add(model)
setattr(thismod, model, _model_class)
else:
setattr(thismod, model, _gen_missing_model(model, _backend))
def __init__(self, dataset, device='cpu', escape=None, **kwargs):
super().__init__(dataset, **kwargs)
self.astensor = partial(gf.astensor, device=device, escape=escape)
self.astensors = partial(gf.astensors, device=device, escape=escape)
self.device = device
self.backend = gg.backend()