1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 664 665 666 667 668 669 670 671 672 673 674 675 676 677 678 679 680 681 682 683 684 685 686 687 688 689 690 691 692 693 694 695 696 697 698 699 700 701 702 703 704 705 706 707 708 709 710 711 712 713 714 715 716 717 718 719 720 721 722 723 724 725 726 727 728 729 730 731 732 733 734 735 736 737 738 739 740 741 742 743 744 745 746 747 748 749 750 751 752 753 754 755 756 757 758 759 760 761 762 763 764 765 766 767 768 769 770 771 772 773 774 775
|
from textwrap import indent
from typing import Any, Dict, List, Optional, Tuple, Union
import numpy as np
import scipy.sparse
import torch
from torch_scatter import segment_csr
from torch_sparse.storage import SparseStorage, get_layout
@torch.jit.script
class SparseTensor(object):
storage: SparseStorage
def __init__(
self,
row: Optional[torch.Tensor] = None,
rowptr: Optional[torch.Tensor] = None,
col: Optional[torch.Tensor] = None,
value: Optional[torch.Tensor] = None,
sparse_sizes: Optional[Tuple[Optional[int], Optional[int]]] = None,
is_sorted: bool = False,
trust_data: bool = False,
):
self.storage = SparseStorage(
row=row,
rowptr=rowptr,
col=col,
value=value,
sparse_sizes=sparse_sizes,
rowcount=None,
colptr=None,
colcount=None,
csr2csc=None,
csc2csr=None,
is_sorted=is_sorted,
trust_data=trust_data,
)
@classmethod
def from_storage(self, storage: SparseStorage):
out = SparseTensor(
row=storage._row,
rowptr=storage._rowptr,
col=storage._col,
value=storage._value,
sparse_sizes=storage._sparse_sizes,
is_sorted=True,
trust_data=True,
)
out.storage._rowcount = storage._rowcount
out.storage._colptr = storage._colptr
out.storage._colcount = storage._colcount
out.storage._csr2csc = storage._csr2csc
out.storage._csc2csr = storage._csc2csr
return out
@classmethod
def from_edge_index(
self,
edge_index: torch.Tensor,
edge_attr: Optional[torch.Tensor] = None,
sparse_sizes: Optional[Tuple[Optional[int], Optional[int]]] = None,
is_sorted: bool = False,
trust_data: bool = False,
):
return SparseTensor(
row=edge_index[0],
rowptr=None,
col=edge_index[1],
value=edge_attr,
sparse_sizes=sparse_sizes,
is_sorted=is_sorted,
trust_data=trust_data,
)
@classmethod
def from_dense(self, mat: torch.Tensor, has_value: bool = True):
if mat.dim() > 2:
index = mat.abs().sum([i for i in range(2, mat.dim())]).nonzero()
else:
index = mat.nonzero()
index = index.t()
row = index[0]
col = index[1]
value: Optional[torch.Tensor] = None
if has_value:
value = mat[row, col]
return SparseTensor(
row=row,
rowptr=None,
col=col,
value=value,
sparse_sizes=(mat.size(0), mat.size(1)),
is_sorted=True,
trust_data=True,
)
@classmethod
def from_torch_sparse_coo_tensor(
self,
mat: torch.Tensor,
has_value: bool = True,
):
mat = mat.coalesce()
index = mat._indices()
row, col = index[0], index[1]
value: Optional[torch.Tensor] = None
if has_value:
value = mat.values()
return SparseTensor(
row=row,
rowptr=None,
col=col,
value=value,
sparse_sizes=(mat.size(0), mat.size(1)),
is_sorted=True,
trust_data=True,
)
@classmethod
def from_torch_sparse_csr_tensor(
self,
mat: torch.Tensor,
has_value: bool = True,
):
rowptr = mat.crow_indices()
col = mat.col_indices()
value: Optional[torch.Tensor] = None
if has_value:
value = mat.values()
return SparseTensor(
row=None,
rowptr=rowptr,
col=col,
value=value,
sparse_sizes=(mat.size(0), mat.size(1)),
is_sorted=True,
trust_data=True,
)
@classmethod
def eye(self,
M: int,
N: Optional[int] = None,
has_value: bool = True,
dtype: Optional[int] = None,
device: Optional[torch.device] = None,
fill_cache: bool = False):
N = M if N is None else N
row = torch.arange(min(M, N), device=device)
col = row
rowptr = torch.arange(M + 1, device=row.device)
if M > N:
rowptr[N + 1:] = N
value: Optional[torch.Tensor] = None
if has_value:
value = torch.ones(row.numel(), dtype=dtype, device=row.device)
rowcount: Optional[torch.Tensor] = None
colptr: Optional[torch.Tensor] = None
colcount: Optional[torch.Tensor] = None
csr2csc: Optional[torch.Tensor] = None
csc2csr: Optional[torch.Tensor] = None
if fill_cache:
rowcount = torch.ones(M, dtype=torch.long, device=row.device)
if M > N:
rowcount[N:] = 0
colptr = torch.arange(N + 1, dtype=torch.long, device=row.device)
colcount = torch.ones(N, dtype=torch.long, device=row.device)
if N > M:
colptr[M + 1:] = M
colcount[M:] = 0
csr2csc = csc2csr = row
out = SparseTensor(
row=row,
rowptr=rowptr,
col=col,
value=value,
sparse_sizes=(M, N),
is_sorted=True,
trust_data=True,
)
out.storage._rowcount = rowcount
out.storage._colptr = colptr
out.storage._colcount = colcount
out.storage._csr2csc = csr2csc
out.storage._csc2csr = csc2csr
return out
def copy(self):
return self.from_storage(self.storage)
def clone(self):
return self.from_storage(self.storage.clone())
def type(self, dtype: torch.dtype, non_blocking: bool = False):
value = self.storage.value()
if value is None or dtype == value.dtype:
return self
return self.from_storage(
self.storage.type(dtype=dtype, non_blocking=non_blocking))
def type_as(self, tensor: torch.Tensor, non_blocking: bool = False):
return self.type(dtype=tensor.dtype, non_blocking=non_blocking)
def to_device(self, device: torch.device, non_blocking: bool = False):
if device == self.device():
return self
return self.from_storage(
self.storage.to_device(device=device, non_blocking=non_blocking))
def device_as(self, tensor: torch.Tensor, non_blocking: bool = False):
return self.to_device(device=tensor.device, non_blocking=non_blocking)
# Formats #################################################################
def coo(self) -> Tuple[torch.Tensor, torch.Tensor, Optional[torch.Tensor]]:
return self.storage.row(), self.storage.col(), self.storage.value()
def csr(self) -> Tuple[torch.Tensor, torch.Tensor, Optional[torch.Tensor]]:
return self.storage.rowptr(), self.storage.col(), self.storage.value()
def csc(self) -> Tuple[torch.Tensor, torch.Tensor, Optional[torch.Tensor]]:
perm = self.storage.csr2csc()
value = self.storage.value()
if value is not None:
value = value[perm]
return self.storage.colptr(), self.storage.row()[perm], value
# Storage inheritance #####################################################
def has_value(self) -> bool:
return self.storage.has_value()
def set_value_(
self,
value: Optional[torch.Tensor],
layout: Optional[str] = None,
):
self.storage.set_value_(value, layout)
return self
def set_value(
self,
value: Optional[torch.Tensor],
layout: Optional[str] = None,
):
return self.from_storage(self.storage.set_value(value, layout))
def sparse_sizes(self) -> Tuple[int, int]:
return self.storage.sparse_sizes()
def sparse_size(self, dim: int) -> int:
return self.storage.sparse_sizes()[dim]
def sparse_resize(self, sparse_sizes: Tuple[int, int]):
return self.from_storage(self.storage.sparse_resize(sparse_sizes))
def sparse_reshape(self, num_rows: int, num_cols: int):
return self.from_storage(
self.storage.sparse_reshape(num_rows, num_cols))
def is_coalesced(self) -> bool:
return self.storage.is_coalesced()
def coalesce(self, reduce: str = "sum"):
return self.from_storage(self.storage.coalesce(reduce))
def fill_cache_(self):
self.storage.fill_cache_()
return self
def clear_cache_(self):
self.storage.clear_cache_()
return self
def __eq__(self, other) -> bool:
if not isinstance(other, self.__class__):
return False
if self.sizes() != other.sizes():
return False
rowptrA, colA, valueA = self.csr()
rowptrB, colB, valueB = other.csr()
if valueA is None and valueB is not None:
return False
if valueA is not None and valueB is None:
return False
if not torch.equal(rowptrA, rowptrB):
return False
if not torch.equal(colA, colB):
return False
if valueA is None and valueB is None:
return True
return torch.equal(valueA, valueB)
# Utility functions #######################################################
def fill_value_(self, fill_value: float, dtype: Optional[int] = None):
value = torch.full(
(self.nnz(), ),
fill_value,
dtype=dtype,
device=self.device(),
)
return self.set_value_(value, layout='coo')
def fill_value(self, fill_value: float, dtype: Optional[int] = None):
value = torch.full(
(self.nnz(), ),
fill_value,
dtype=dtype,
device=self.device(),
)
return self.set_value(value, layout='coo')
def sizes(self) -> List[int]:
sparse_sizes = self.sparse_sizes()
value = self.storage.value()
if value is not None:
return list(sparse_sizes) + list(value.size())[1:]
else:
return list(sparse_sizes)
def size(self, dim: int) -> int:
return self.sizes()[dim]
def dim(self) -> int:
return len(self.sizes())
def nnz(self) -> int:
return self.storage.col().numel()
def numel(self) -> int:
value = self.storage.value()
if value is not None:
return value.numel()
else:
return self.nnz()
def density(self) -> float:
if self.sparse_size(0) == 0 or self.sparse_size(1) == 0:
return 0.0
return self.nnz() / (self.sparse_size(0) * self.sparse_size(1))
def sparsity(self) -> float:
return 1 - self.density()
def avg_row_length(self) -> float:
return self.nnz() / self.sparse_size(0)
def avg_col_length(self) -> float:
return self.nnz() / self.sparse_size(1)
def bandwidth(self) -> int:
row, col, _ = self.coo()
return int((row - col).abs_().max())
def avg_bandwidth(self) -> float:
row, col, _ = self.coo()
return float((row - col).abs_().to(torch.float).mean())
def bandwidth_proportion(self, bandwidth: int) -> float:
row, col, _ = self.coo()
tmp = (row - col).abs_()
return int((tmp <= bandwidth).sum()) / self.nnz()
def is_quadratic(self) -> bool:
return self.sparse_size(0) == self.sparse_size(1)
def is_symmetric(self) -> bool:
if not self.is_quadratic():
return False
rowptr, col, value1 = self.csr()
colptr, row, value2 = self.csc()
if (rowptr != colptr).any() or (col != row).any():
return False
if value1 is None or value2 is None:
return True
else:
return bool((value1 == value2).all())
def to_symmetric(self, reduce: str = "sum"):
N = max(self.size(0), self.size(1))
row, col, value = self.coo()
idx = col.new_full((2 * col.numel() + 1, ), -1)
idx[1:row.numel() + 1] = row
idx[row.numel() + 1:] = col
idx[1:] *= N
idx[1:row.numel() + 1] += col
idx[row.numel() + 1:] += row
idx, perm = idx.sort()
mask = idx[1:] > idx[:-1]
perm = perm[1:].sub_(1)
idx = perm[mask]
if value is not None:
ptr = mask.nonzero().flatten()
ptr = torch.cat([ptr, ptr.new_full((1, ), perm.size(0))])
value = torch.cat([value, value])[perm]
value = segment_csr(value, ptr, reduce=reduce)
new_row = torch.cat([row, col], dim=0)[idx]
new_col = torch.cat([col, row], dim=0)[idx]
out = SparseTensor(
row=new_row,
rowptr=None,
col=new_col,
value=value,
sparse_sizes=(N, N),
is_sorted=True,
trust_data=True,
)
return out
def detach_(self):
value = self.storage.value()
if value is not None:
value.detach_()
return self
def detach(self):
value = self.storage.value()
if value is not None:
value = value.detach()
return self.set_value(value, layout='coo')
def requires_grad(self) -> bool:
value = self.storage.value()
if value is not None:
return value.requires_grad
else:
return False
def requires_grad_(
self,
requires_grad: bool = True,
dtype: Optional[int] = None,
):
if requires_grad and not self.has_value():
self.fill_value_(1., dtype)
value = self.storage.value()
if value is not None:
value.requires_grad_(requires_grad)
return self
def pin_memory(self):
return self.from_storage(self.storage.pin_memory())
def is_pinned(self) -> bool:
return self.storage.is_pinned()
def device(self):
return self.storage.col().device
def cpu(self):
return self.to_device(device=torch.device('cpu'), non_blocking=False)
def cuda(self):
return self.from_storage(self.storage.cuda())
def is_cuda(self) -> bool:
return self.storage.col().is_cuda
def dtype(self):
value = self.storage.value()
return value.dtype if value is not None else torch.float
def is_floating_point(self) -> bool:
value = self.storage.value()
return torch.is_floating_point(value) if value is not None else True
def bfloat16(self):
return self.type(dtype=torch.bfloat16, non_blocking=False)
def bool(self):
return self.type(dtype=torch.bool, non_blocking=False)
def byte(self):
return self.type(dtype=torch.uint8, non_blocking=False)
def char(self):
return self.type(dtype=torch.int8, non_blocking=False)
def half(self):
return self.type(dtype=torch.half, non_blocking=False)
def float(self):
return self.type(dtype=torch.float, non_blocking=False)
def double(self):
return self.type(dtype=torch.double, non_blocking=False)
def short(self):
return self.type(dtype=torch.short, non_blocking=False)
def int(self):
return self.type(dtype=torch.int, non_blocking=False)
def long(self):
return self.type(dtype=torch.long, non_blocking=False)
# Conversions #############################################################
def to_dense(self, dtype: Optional[int] = None) -> torch.Tensor:
row, col, value = self.coo()
if value is not None:
mat = torch.zeros(
self.sizes(),
dtype=value.dtype,
device=self.device(),
)
else:
mat = torch.zeros(self.sizes(), dtype=dtype, device=self.device())
if value is not None:
mat[row, col] = value
else:
mat[row, col] = torch.ones(
self.nnz(),
dtype=mat.dtype,
device=mat.device,
)
return mat
def to_torch_sparse_coo_tensor(
self,
dtype: Optional[int] = None,
) -> torch.Tensor:
row, col, value = self.coo()
index = torch.stack([row, col], dim=0)
if value is None:
value = torch.ones(self.nnz(), dtype=dtype, device=self.device())
return torch.sparse_coo_tensor(index, value, self.sizes())
def to_torch_sparse_csr_tensor(
self,
dtype: Optional[int] = None,
) -> torch.Tensor:
rowptr, col, value = self.csr()
if value is None:
value = torch.ones(self.nnz(), dtype=dtype, device=self.device())
return torch.sparse_csr_tensor(rowptr, col, value, self.sizes())
def to_torch_sparse_csc_tensor(
self,
dtype: Optional[int] = None,
) -> torch.Tensor:
colptr, row, value = self.csc()
if value is None:
value = torch.ones(self.nnz(), dtype=dtype, device=self.device())
return torch.sparse_csc_tensor(colptr, row, value, self.sizes())
# Python Bindings #############################################################
def share_memory_(self: SparseTensor) -> SparseTensor:
self.storage.share_memory_()
return self
def is_shared(self: SparseTensor) -> bool:
return self.storage.is_shared()
def to(self, *args: Optional[List[Any]],
**kwargs: Optional[Dict[str, Any]]) -> SparseTensor:
device, dtype, non_blocking = torch._C._nn._parse_to(*args, **kwargs)[:3]
if dtype is not None:
self = self.type(dtype=dtype, non_blocking=non_blocking)
if device is not None:
self = self.to_device(device=device, non_blocking=non_blocking)
return self
def cpu(self) -> SparseTensor:
return self.device_as(torch.tensor(0., device='cpu'))
def cuda(
self,
device: Optional[Union[int, str]] = None,
non_blocking: bool = False,
):
return self.device_as(torch.tensor(0., device=device or 'cuda'))
def __getitem__(self: SparseTensor, index: Any) -> SparseTensor:
index = list(index) if isinstance(index, tuple) else [index]
# More than one `Ellipsis` is not allowed...
if len([
i for i in index
if not isinstance(i, (torch.Tensor, np.ndarray)) and i == ...
]) > 1:
raise SyntaxError
dim = 0
out = self
while len(index) > 0:
item = index.pop(0)
if isinstance(item, (list, tuple)):
item = torch.tensor(item, device=self.device())
if isinstance(item, np.ndarray):
item = torch.from_numpy(item).to(self.device())
if isinstance(item, int):
out = out.select(dim, item)
dim += 1
elif isinstance(item, slice):
if item.step is not None:
raise ValueError('Step parameter not yet supported.')
start = 0 if item.start is None else item.start
start = self.size(dim) + start if start < 0 else start
stop = self.size(dim) if item.stop is None else item.stop
stop = self.size(dim) + stop if stop < 0 else stop
out = out.narrow(dim, start, max(stop - start, 0))
dim += 1
elif torch.is_tensor(item):
if item.dtype == torch.bool:
out = out.masked_select(dim, item)
dim += 1
elif item.dtype == torch.long:
out = out.index_select(dim, item)
dim += 1
elif item == Ellipsis:
if self.dim() - len(index) < dim:
raise SyntaxError
dim = self.dim() - len(index)
else:
raise SyntaxError
return out
def __repr__(self: SparseTensor) -> str:
i = ' ' * 6
row, col, value = self.coo()
infos = []
infos += [f'row={indent(row.__repr__(), i)[len(i):]}']
infos += [f'col={indent(col.__repr__(), i)[len(i):]}']
if value is not None:
infos += [f'val={indent(value.__repr__(), i)[len(i):]}']
infos += [
f'size={tuple(self.sizes())}, nnz={self.nnz()}, '
f'density={100 * self.density():.02f}%'
]
infos = ',\n'.join(infos)
i = ' ' * (len(self.__class__.__name__) + 1)
return f'{self.__class__.__name__}({indent(infos, i)[len(i):]})'
SparseTensor.share_memory_ = share_memory_
SparseTensor.is_shared = is_shared
SparseTensor.to = to
SparseTensor.cpu = cpu
SparseTensor.cuda = cuda
SparseTensor.__getitem__ = __getitem__
SparseTensor.__repr__ = __repr__
# Scipy Conversions ###########################################################
ScipySparseMatrix = Union[scipy.sparse.coo_matrix, scipy.sparse.csr_matrix,
scipy.sparse.csc_matrix]
@torch.jit.ignore
def from_scipy(mat: ScipySparseMatrix, has_value: bool = True) -> SparseTensor:
colptr = None
if isinstance(mat, scipy.sparse.csc_matrix):
colptr = torch.from_numpy(mat.indptr).to(torch.long)
mat = mat.tocsr()
rowptr = torch.from_numpy(mat.indptr).to(torch.long)
mat = mat.tocoo()
row = torch.from_numpy(mat.row).to(torch.long)
col = torch.from_numpy(mat.col).to(torch.long)
value = None
if has_value:
value = torch.from_numpy(mat.data)
sparse_sizes = mat.shape[:2]
storage = SparseStorage(
row=row,
rowptr=rowptr,
col=col,
value=value,
sparse_sizes=sparse_sizes,
rowcount=None,
colptr=colptr,
colcount=None,
csr2csc=None,
csc2csr=None,
is_sorted=True,
)
return SparseTensor.from_storage(storage)
@torch.jit.ignore
def to_scipy(
self: SparseTensor,
layout: Optional[str] = None,
dtype: Optional[torch.dtype] = None,
) -> ScipySparseMatrix:
assert self.dim() == 2
layout = get_layout(layout)
if not self.has_value():
ones = torch.ones(self.nnz(), dtype=dtype).numpy()
if layout == 'coo':
row, col, value = self.coo()
row = row.detach().cpu().numpy()
col = col.detach().cpu().numpy()
value = value.detach().cpu().numpy() if self.has_value() else ones
return scipy.sparse.coo_matrix((value, (row, col)), self.sizes())
elif layout == 'csr':
rowptr, col, value = self.csr()
rowptr = rowptr.detach().cpu().numpy()
col = col.detach().cpu().numpy()
value = value.detach().cpu().numpy() if self.has_value() else ones
return scipy.sparse.csr_matrix((value, col, rowptr), self.sizes())
elif layout == 'csc':
colptr, row, value = self.csc()
colptr = colptr.detach().cpu().numpy()
row = row.detach().cpu().numpy()
value = value.detach().cpu().numpy() if self.has_value() else ones
return scipy.sparse.csc_matrix((value, row, colptr), self.sizes())
SparseTensor.from_scipy = from_scipy
SparseTensor.to_scipy = to_scipy
|