def fill_hetero_edges(self, encoded_edges, x, cell_x, start, end,
volume_id):
"""
Fill the heterogeneous edges with the corresponding encoders
"""
for encoder, combo in zip(self.edge_encoders, self.all_combos):
vol_ids_0, vol_ids_1 = torch.tensor(
self.hparams["model_ids"][combo[0]]["volume_ids"],
device=encoded_edges.device), torch.tensor(
self.hparams["model_ids"][combo[1]]["volume_ids"],
device=encoded_edges.device)
vol_edge_mask = torch.isin(volume_id[start],
vol_ids_0) & torch.isin(
volume_id[end], vol_ids_1)
encoded_edges[vol_edge_mask] = encoder(
torch.cat([
x[start[vol_edge_mask], :self.
hparams["model_ids"][combo[0]]["num_features"]],
cell_x[start[vol_edge_mask]],
x[end[vol_edge_mask], :self.
hparams["model_ids"][combo[1]]["num_features"]],
cell_x[end[vol_edge_mask]]
],
dim=-1))
return encoded_edges
def fill_hetero_edges(self, input_node_features, start, end, volume_id):
"""
Fill the heterogeneous edges with the corresponding encoders
"""
features_to_fill = torch.empty(
(start.shape[0], self.hparams["hidden"])).to(start.device)
for encoder, combo in zip(self.edge_encoders, self.all_combos):
vol_ids_0, vol_ids_1 = torch.tensor(
self.hparams["model_ids"][combo[0]]["volume_ids"],
device=features_to_fill.device), torch.tensor(
self.hparams["model_ids"][combo[1]]["volume_ids"],
device=features_to_fill.device)
vol_edge_mask = torch.isin(volume_id[start],
vol_ids_0) & torch.isin(
volume_id[end], vol_ids_1)
features_to_encode = torch.cat([
input_node_features[start[vol_edge_mask]],
input_node_features[end[vol_edge_mask]]
],
dim=-1)
features_to_fill[vol_edge_mask] = encoder(features_to_encode)
return features_to_fill
def test_isin_different_devices(self, device, dtype):
a = torch.arange(6, device=device, dtype=dtype).reshape([2, 3])
b = torch.arange(3, 30, device='cpu', dtype=dtype)
with self.assertRaises(RuntimeError):
torch.isin(a, b)
c = torch.arange(6, device='cpu', dtype=dtype).reshape([2, 3])
d = torch.arange(3, 30, device=device, dtype=dtype)
with self.assertRaises(RuntimeError):
torch.isin(c, d)
def assert_isin_equal(a, b):
# Compare to the numpy reference implementation.
x = torch.isin(a, b)
a = a.cpu().numpy() if torch.is_tensor(a) else np.array(a)
b = b.cpu().numpy() if torch.is_tensor(b) else np.array(b)
y = np.isin(a, b)
self.assertEqual(x, y)
def comparison_ops(self):
a = torch.randn(4)
b = torch.randn(4)
return (
torch.allclose(a, b),
torch.argsort(a),
torch.eq(a, b),
torch.equal(a, b),
torch.ge(a, b),
torch.greater_equal(a, b),
torch.gt(a, b),
torch.greater(a, b),
torch.isclose(a, b),
torch.isfinite(a),
torch.isin(a, b),
torch.isinf(a),
torch.isposinf(a),
torch.isneginf(a),
torch.isnan(a),
torch.isreal(a),
torch.kthvalue(a, 1),
torch.le(a, b),
torch.less_equal(a, b),
torch.lt(a, b),
torch.less(a, b),
torch.maximum(a, b),
torch.minimum(a, b),
torch.fmax(a, b),
torch.fmin(a, b),
torch.ne(a, b),
torch.not_equal(a, b),
torch.sort(a),
torch.topk(a, 1),
torch.msort(a),
)
def __call__(self, img: NdarrayOrTensor) -> NdarrayOrTensor:
"""
Filter the image on the `applied_labels`.
Args:
img: Pytorch tensor or numpy array of any shape.
Raises:
NotImplementedError: The provided image was not a Pytorch Tensor or numpy array.
Returns:
Pytorch tensor or numpy array of the same shape as the input.
"""
if not isinstance(img, (np.ndarray, torch.Tensor)):
raise NotImplementedError(
f"{self.__class__} can not handle data of type {type(img)}.")
if isinstance(img, torch.Tensor):
img = convert_to_tensor(img, track_meta=get_track_meta())
img_ = convert_to_tensor(img, track_meta=False)
if hasattr(torch, "isin"): # `isin` is new in torch 1.10.0
appl_lbls = torch.as_tensor(self.applied_labels,
device=img_.device)
out = torch.where(torch.isin(img_, appl_lbls), img_,
torch.tensor(0.0).to(img_))
return convert_to_dst_type(out, dst=img)[0]
out: NdarrayOrTensor = self(
img_.detach().cpu().numpy()) # type: ignore
out = convert_to_dst_type(out, img)[0] # type: ignore
return out
return np.asarray(np.where(np.isin(img, self.applied_labels), img, 0))
def __call__(self, img: NdarrayOrTensor) -> NdarrayOrTensor:
"""
Filter the image on the `applied_labels`.
Args:
img: Pytorch tensor or numpy array of any shape.
Raises:
NotImplementedError: The provided image was not a Pytorch Tensor or numpy array.
Returns:
Pytorch tensor or numpy array of the same shape as the input.
"""
if not isinstance(img, (np.ndarray, torch.Tensor)):
raise NotImplementedError(f"{self.__class__} can not handle data of type {type(img)}.")
if isinstance(img, torch.Tensor):
if hasattr(torch, "isin"):
appl_lbls = torch.as_tensor(self.applied_labels, device=img.device)
return torch.where(torch.isin(img, appl_lbls), img, 0)
else:
out = self(img.detach().cpu().numpy())
out, *_ = convert_to_dst_type(out, img)
return out
return np.asarray(np.where(np.isin(img, self.applied_labels), img, 0))
def save_scores(detector: NoveltyDetector,
output_folder,
patch=False,
quad_full_image=False):
(_, valid_loader, test_loader), class_to_idx = polycraft_dataloaders(
patch=patch,
include_novel=True,
ret_class_to_idx=True,
shuffle=False,
quad_full_image=quad_full_image)
normal_targets = torch.Tensor(
[class_to_idx[c] for c in data_const.NORMAL_CLASSES])
idx_to_class = {v: k for k, v in class_to_idx.items()}
for split in ["valid", "test"]:
loader = valid_loader if split == "valid" else test_loader
# collect scores, novelty labels with 1 as novel, and targets
novel_score = torch.Tensor([])
novel_true = torch.Tensor([])
targets = torch.Tensor([])
for data, target in loader:
novel_score = torch.hstack(
[novel_score, detector.novelty_score(data).cpu()])
novel_true = torch.hstack(
[novel_true, (~torch.isin(target, normal_targets)).long()])
targets = torch.hstack([targets, target])
# convert targets to names
classes = np.array([idx_to_class[target.item()] for target in targets])
# output data
folder_path = Path(output_folder)
folder_path.mkdir(exist_ok=True, parents=True)
torch.save(novel_score, folder_path / f"{split}_novel_score.pt")
torch.save(novel_true, folder_path / f"{split}_novel_true.pt")
np.save(folder_path / f"{split}_classes.npy", classes)
def sliceSparseCOO(t, idx):
row, col = t._indices()[:,
torch.where(torch.isin(t._indices()[1], idx))[0]]
col_index_map = {int(j): i for i, j in enumerate(idx)}
col = torch.LongTensor([col_index_map[int(i)] for i in col])
return torch.sparse_coo_tensor(torch.vstack([row, col]),
torch.ones(len(col), dtype=torch.float32),
size=[t.shape[0], len(idx)])
def test_isin_different_dtypes(self, device):
supported_types = all_types() if device == 'cpu' else all_types_and(torch.half)
for mult in [1, 10]:
for assume_unique in [False, True]:
for dtype1, dtype2 in product(supported_types, supported_types):
a = torch.tensor([1, 2, 3], device=device, dtype=dtype1)
b = torch.tensor([3, 4, 5] * mult, device=device, dtype=dtype2)
ec = torch.tensor([False, False, True], device=device)
c = torch.isin(a, b, assume_unique=assume_unique)
self.assertEqual(c, ec)
def fill_hetero_nodes(self, input_node_features, volume_id):
"""
Fill the heterogeneous nodes with the corresponding encoders
"""
features_to_fill = torch.empty((input_node_features.shape[0], self.hparams["hidden"])).to(input_node_features.device)
for encoder, model in zip(self.node_encoders, self.hparams["model_ids"]):
node_id_mask = torch.isin(volume_id, torch.tensor(model["volume_ids"]).to(input_node_features.device))
features_to_fill[node_id_mask] = encoder(input_node_features[node_id_mask])
return features_to_fill
def fill_hetero_nodes(self, encoded_nodes, x, volume_id):
"""
Fill the heterogeneous nodes with the corresponding encoders
"""
for encoder, model in zip(self.node_encoders,
self.hparams["model_ids"]):
node_id_mask = torch.isin(
volume_id,
torch.tensor(model["volume_ids"]).to(x.device))
encoded_nodes[node_id_mask] = checkpoint(
encoder, x[node_id_mask, :model["num_features"]])
return encoded_nodes
def get_unique_signal_segments(labels, pids, signal_pids):
labels_unique, labels_inverse, labels_counts = labels.unique(
return_counts=True, return_inverse=True)
segments_pids = torch.stack([labels, pids])
is_signal = torch.isin(
pids, pids[signal_pids]) & (labels_counts[labels_inverse] >= 3)
signal_segments_pids = segments_pids[:, is_signal]
unique_signal_segments_pids = signal_segments_pids.unique(dim=1)
return signal_segments_pids, unique_signal_segments_pids
def _compute_variance_term_scatter(cluster_means,
embeddings,
target,
norm,
delta_var,
instance_sizes,
ignore_labels=None):
assert cluster_means.shape[1] == embeddings.shape[1]
ndim = embeddings.ndim - 2
assert ndim in (2, 3), f"{ndim}"
n_instances = cluster_means.shape[0]
# compute the spatial mean and instance fields by scattering with the target tensor
cluster_means_spatial = cluster_means[target]
instance_sizes_spatial = instance_sizes[target]
# permute the embedding dimension to axis 1
if ndim == 2:
cluster_means_spatial = cluster_means_spatial.permute(0, 3, 1, 2)
dim_arg = (1, 2)
else:
cluster_means_spatial = cluster_means_spatial.permute(0, 4, 1, 2, 3)
dim_arg = (1, 2, 3)
assert embeddings.shape == cluster_means_spatial.shape
# compute the variance
variance = torch.norm(embeddings - cluster_means_spatial, norm, dim=1)
# apply the ignore labels (if given)
if ignore_labels is not None:
assert isinstance(ignore_labels, list)
# mask out the ignore labels
mask = torch.ones_like(variance)
mask[torch.isin(mask, torch.tensor(ignore_labels).to(mask.device))]
variance *= mask
# decrease number of instances
n_instances -= len(ignore_labels)
# if there are only ignore labels in the target return 0
if n_instances == 0:
return 0.0
# hinge the variance
variance = torch.clamp(variance - delta_var, min=0)**2
assert variance.shape == instance_sizes_spatial.shape
# normalize the variance by instance sizes and number of instances and sum it up
variance = torch.sum(variance / instance_sizes_spatial,
dim=dim_arg) / n_instances
return variance
def forward(self):
a = torch.tensor(0)
b = torch.tensor(1)
return len(
torch.allclose(a, b),
torch.argsort(a),
torch.eq(a, b),
torch.eq(a, 1),
torch.equal(a, b),
torch.ge(a, b),
torch.ge(a, 1),
torch.greater_equal(a, b),
torch.greater_equal(a, 1),
torch.gt(a, b),
torch.gt(a, 1),
torch.greater(a, b),
torch.isclose(a, b),
torch.isfinite(a),
torch.isin(a, b),
torch.isinf(a),
torch.isposinf(a),
torch.isneginf(a),
torch.isnan(a),
torch.isreal(a),
torch.kthvalue(a, 1),
torch.le(a, b),
torch.le(a, 1),
torch.less_equal(a, b),
torch.lt(a, b),
torch.lt(a, 1),
torch.less(a, b),
torch.maximum(a, b),
torch.minimum(a, b),
torch.fmax(a, b),
torch.fmin(a, b),
torch.ne(a, b),
torch.ne(a, 1),
torch.not_equal(a, b),
torch.sort(a),
torch.topk(a, 1),
torch.msort(a),
)
def _get_triple_mask(
ids: Collection[int],
triples: MappedTriples,
columns: Union[int, Collection[int]],
invert: bool = False,
max_id: Optional[int] = None,
) -> torch.BoolTensor:
# normalize input
triples = triples[:, columns]
if isinstance(columns, int):
columns = [columns]
mask = torch.isin(
elements=triples,
test_elements=torch.as_tensor(list(ids), dtype=torch.long),
assume_unique=False,
invert=invert,
)
if len(columns) > 1:
mask = mask.all(dim=-1)
return mask
def test_isin(self, device, dtype):
def assert_isin_equal(a, b):
# Compare to the numpy reference implementation.
x = torch.isin(a, b)
a = a.cpu().numpy() if torch.is_tensor(a) else np.array(a)
b = b.cpu().numpy() if torch.is_tensor(b) else np.array(b)
y = np.isin(a, b)
self.assertEqual(x, y)
# multi-dim tensor, multi-dim tensor
a = torch.arange(24, device=device, dtype=dtype).reshape([2, 3, 4])
b = torch.tensor([[10, 20, 30], [0, 1, 3], [11, 22, 33]], device=device, dtype=dtype)
assert_isin_equal(a, b)
# zero-dim tensor
zero_d = torch.tensor(3, device=device, dtype=dtype)
assert_isin_equal(zero_d, b)
assert_isin_equal(a, zero_d)
assert_isin_equal(zero_d, zero_d)
# empty tensor
empty = torch.tensor([], device=device, dtype=dtype)
assert_isin_equal(empty, b)
assert_isin_equal(a, empty)
assert_isin_equal(empty, empty)
# scalar
assert_isin_equal(a, 6)
assert_isin_equal(5, b)
def define_expected(lst, invert=False):
expected = torch.tensor(lst, device=device)
if invert:
expected = expected.logical_not()
return expected
# Adapted from numpy's in1d tests
for mult in [1, 10]:
for invert in [False, True]:
a = torch.tensor([5, 7, 1, 2], device=device, dtype=dtype)
b = torch.tensor([2, 4, 3, 1, 5] * mult, device=device, dtype=dtype)
ec = define_expected([True, False, True, True], invert=invert)
c = torch.isin(a, b, assume_unique=True, invert=invert)
self.assertEqual(c, ec)
a[0] = 8
ec = define_expected([False, False, True, True], invert=invert)
c = torch.isin(a, b, assume_unique=True, invert=invert)
self.assertEqual(c, ec)
a[0], a[3] = 4, 8
ec = define_expected([True, False, True, False], invert=invert)
c = torch.isin(a, b, assume_unique=True, invert=invert)
self.assertEqual(c, ec)
a = torch.tensor([5, 4, 5, 3, 4, 4, 3, 4, 3, 5, 2, 1, 5, 5], device=device, dtype=dtype)
b = torch.tensor([2, 3, 4] * mult, device=device, dtype=dtype)
ec = define_expected([False, True, False, True, True, True, True, True, True,
False, True, False, False, False], invert=invert)
c = torch.isin(a, b, invert=invert)
self.assertEqual(c, ec)
b = torch.tensor([2, 3, 4] * mult + [5, 5, 4] * mult, device=device, dtype=dtype)
ec = define_expected([True, True, True, True, True, True, True, True, True, True,
True, False, True, True], invert=invert)
c = torch.isin(a, b, invert=invert)
self.assertEqual(c, ec)
a = torch.tensor([5, 7, 1, 2], device=device, dtype=dtype)
b = torch.tensor([2, 4, 3, 1, 5] * mult, device=device, dtype=dtype)
ec = define_expected([True, False, True, True], invert=invert)
c = torch.isin(a, b, invert=invert)
self.assertEqual(c, ec)
a = torch.tensor([5, 7, 1, 1, 2], device=device, dtype=dtype)
b = torch.tensor([2, 4, 3, 3, 1, 5] * mult, device=device, dtype=dtype)
ec = define_expected([True, False, True, True, True], invert=invert)
c = torch.isin(a, b, invert=invert)
self.assertEqual(c, ec)
a = torch.tensor([5, 5], device=device, dtype=dtype)
b = torch.tensor([2, 2] * mult, device=device, dtype=dtype)
ec = define_expected([False, False], invert=invert)
c = torch.isin(a, b, invert=invert)
self.assertEqual(c, ec)
# multi-dimensional input case using sort-based algo
for assume_unique in [False, True]:
a = torch.arange(6, device=device, dtype=dtype).reshape([2, 3])
b = torch.arange(3, 30, device=device, dtype=dtype)
ec = define_expected([[False, False, False], [True, True, True]], invert=invert)
c = torch.isin(a, b, invert=invert, assume_unique=assume_unique)
self.assertEqual(c, ec)