Add data caching, and new pad and crop features
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Yin Li
parent
d03bcb59a1
commit
843fe09a92
@ -28,12 +28,12 @@ def add_common_args(parser):
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parser.add_argument('--loader-workers', default=0, type=int,
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help='number of data loading workers, per GPU in training or '
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'in total in testing')
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parser.add_argument('--pad-or-crop', default=0, type=int_tuple,
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help='pad (>0) or crop (<0) the input data; '
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'can be a int or a 6-tuple (by a comma-sep. list); '
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'can be asymmetric to align the data with downsample '
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'and upsample convolutions; '
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'padding assumes periodic boundary condition')
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parser.add_argument('--cache', action='store_true',
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help='enable caching in field datasets')
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parser.add_argument('--crop', type=int,
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help='size to crop the input and target data')
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parser.add_argument('--pad', default=0, type=int,
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help='pad the input data assuming periodic boundary condition')
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def add_train_args(parser):
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@ -80,11 +80,11 @@ def str_list(s):
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return s.split(',')
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def int_tuple(t):
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t = t.split(',')
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t = tuple(int(i) for i in t)
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if len(t) == 1:
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t = t[0]
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elif len(t) != 6:
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raise ValueError('pad or crop size must be int or 6-tuple')
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return t
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#def int_tuple(t):
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# t = t.split(',')
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# t = tuple(int(i) for i in t)
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# if len(t) == 1:
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# t = t[0]
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# elif len(t) != 6:
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# raise ValueError('size must be int or 6-tuple')
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# return t
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@ -14,15 +14,15 @@ class FieldDataset(Dataset):
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Likewise `tgt_patterns` is for target fields.
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Input and target samples of all fields are matched by sorting the globbed files.
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Input fields can be padded (>0) or cropped (<0) with `pad_or_crop`.
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Padding assumes periodic boundary condition.
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Input and target fields can be cached, and they can be cropped.
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Input fields can be padded assuming periodic boundary condition.
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Data augmentations are supported for scalar and vector fields.
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`norms` can be a list of callables to normalize each field.
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"""
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def __init__(self, in_patterns, tgt_patterns, pad_or_crop=0, augment=False,
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norms=None):
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def __init__(self, in_patterns, tgt_patterns, cache=False, crop=None, pad=0,
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augment=False, norms=None):
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in_file_lists = [sorted(glob(p)) for p in in_patterns]
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self.in_files = list(zip(* in_file_lists))
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@ -35,47 +35,80 @@ class FieldDataset(Dataset):
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self.in_channels = sum(np.load(f).shape[0] for f in self.in_files[0])
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self.tgt_channels = sum(np.load(f).shape[0] for f in self.tgt_files[0])
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if isinstance(pad_or_crop, int):
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pad_or_crop = (pad_or_crop,) * 6
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assert isinstance(pad_or_crop, tuple) and len(pad_or_crop) == 6, \
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'pad or crop size must be int or 6-tuple'
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self.pad_or_crop = np.array((0,) * 2 + pad_or_crop).reshape(4, 2)
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self.size = np.load(self.in_files[0][0]).shape[-3:]
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self.size = np.asarray(self.size)
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self.ndim = len(self.size)
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self.cache = cache
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if self.cache:
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self.in_fields = []
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self.tgt_fields = []
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for idx in range(len(self.in_files)):
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self.in_fields.append([np.load(f) for f in self.in_files[idx]])
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self.tgt_fields.append([np.load(f) for f in self.tgt_files[idx]])
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if crop is None:
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self.crop = self.size
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self.reps = np.ones_like(self.size)
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else:
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self.crop = np.broadcast_to(crop, self.size.shape)
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self.reps = self.size // self.crop
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self.tot_reps = int(np.prod(self.reps))
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assert isinstance(pad, int), 'only support symmetric padding for now'
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self.pad = np.broadcast_to(pad, (self.ndim, 2))
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self.augment = augment
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if self.ndim == 1 and self.augment:
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raise ValueError('cannot augment 1D fields')
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if norms is not None:
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if norms is not None: # FIXME: in_norms, tgt_norms
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assert len(in_patterns) == len(norms), \
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'numbers of normalization callables and input fields do not match'
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norms = [import_norm(norm) for norm in norms if isinstance(norm, str)]
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self.norms = norms
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def __len__(self):
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return len(self.in_files) * self.tot_reps
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@property
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def channels(self):
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return self.in_channels, self.tgt_channels
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def __len__(self):
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return len(self.in_files)
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def __getitem__(self, idx):
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in_fields = [np.load(f) for f in self.in_files[idx]]
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tgt_fields = [np.load(f) for f in self.tgt_files[idx]]
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idx, sub_idx = idx // self.tot_reps, idx % self.tot_reps
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start = np.unravel_index(sub_idx, self.reps) * self.crop
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#print('==================================================')
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#print(f'idx = {idx}, sub_idx = {sub_idx}, start = {start}')
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#print(f'self.reps = {self.reps}, self.tot_reps = {self.tot_reps}')
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#print(f'self.crop = {self.crop}, self.size = {self.size}')
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#print(f'self.ndim = {self.ndim}, self.channels = {self.channels}')
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#print(f'self.pad = {self.pad}')
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padcrop(in_fields, self.pad_or_crop) # with numpy
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if self.cache:
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in_fields = self.in_fields[idx]
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tgt_fields = self.tgt_fields[idx]
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else:
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in_fields = [np.load(f) for f in self.in_files[idx]]
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tgt_fields = [np.load(f) for f in self.tgt_files[idx]]
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in_fields = crop(in_fields, start, self.crop, self.pad)
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tgt_fields = crop(tgt_fields, start, self.crop, np.zeros_like(self.pad))
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in_fields = [torch.from_numpy(f).to(torch.float32) for f in in_fields]
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tgt_fields = [torch.from_numpy(f).to(torch.float32) for f in tgt_fields]
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if self.augment:
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flip_axes = torch.randint(2, (3,), dtype=torch.bool)
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flip_axes = torch.arange(3)[flip_axes]
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flip_axes = torch.randint(2, (self.ndim,), dtype=torch.bool)
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flip_axes = torch.arange(self.ndim)[flip_axes]
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flip3d(in_fields, flip_axes)
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flip3d(tgt_fields, flip_axes)
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in_fields = flip(in_fields, flip_axes, self.ndim)
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tgt_fields = flip(tgt_fields, flip_axes, self.ndim)
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perm_axes = torch.randperm(3)
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perm_axes = torch.randperm(self.ndim)
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perm3d(in_fields, perm_axes)
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perm3d(tgt_fields, perm_axes)
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in_fields = perm(in_fields, perm_axes, self.ndim)
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tgt_fields = perm(tgt_fields, perm_axes, self.ndim)
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if self.norms is not None:
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for norm, ifield, tfield in zip(self.norms, in_fields, tgt_fields):
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@ -84,43 +117,49 @@ class FieldDataset(Dataset):
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in_fields = torch.cat(in_fields, dim=0)
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tgt_fields = torch.cat(tgt_fields, dim=0)
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#print(in_fields.shape, tgt_fields.shape)
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return in_fields, tgt_fields
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def padcrop(fields, width):
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for i, x in enumerate(fields):
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if (width >= 0).all():
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x = np.pad(x, width, mode='wrap')
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elif (width <= 0).all():
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x = x[...,
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-width[0, 0] : width[0, 1],
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-width[1, 0] : width[1, 1],
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-width[2, 0] : width[2, 1],
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]
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else:
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raise NotImplementedError('mixed pad-and-crop not supported')
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def crop(fields, start, crop, pad):
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new_fields = []
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for x in fields:
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for d, (i, N, (p0, p1)) in enumerate(zip(start, crop, pad)):
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x = x.take(range(i - p0, i + N + p1), axis=1 + d, mode='wrap')
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fields[i] = x
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new_fields.append(x)
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return new_fields
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def flip3d(fields, axes):
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for i, x in enumerate(fields):
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if x.size(0) == 3: # flip vector components
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def flip(fields, axes, ndim):
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assert ndim > 1, 'flipping is ambiguous for 1D vectors'
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new_fields = []
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for x in fields:
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if x.size(0) == ndim: # flip vector components
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x[axes] = - x[axes]
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axes = (1 + axes).tolist()
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x = torch.flip(x, axes)
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fields[i] = x
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new_fields.append(x)
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return new_fields
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def perm3d(fields, axes):
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for i, x in enumerate(fields):
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if x.size(0) == 3: # permutate vector components
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def perm(fields, axes, ndim):
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assert ndim > 1, 'permutation is not necessary for 1D fields'
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new_fields = []
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for x in fields:
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if x.size(0) == ndim: # permutate vector components
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x = x[axes]
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axes = [0] + (1 + axes).tolist()
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x = x.permute(axes)
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fields[i] = x
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new_fields.append(x)
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return new_fields
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@ -11,9 +11,11 @@ def test(args):
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test_dataset = FieldDataset(
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in_patterns=args.test_in_patterns,
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tgt_patterns=args.test_tgt_patterns,
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cache=args.cache,
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crop=args.crop,
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pad=args.pad,
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augment=False,
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norms=args.norms,
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pad_or_crop=args.pad_or_crop,
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)
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test_loader = DataLoader(
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test_dataset,
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@ -44,7 +46,7 @@ def test(args):
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with torch.no_grad():
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for i, (input, target) in enumerate(test_loader):
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output = model(input)
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if args.pad_or_crop > 0: # FIXME
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if args.pad > 0: # FIXME
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output = narrow_like(output, target)
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input = narrow_like(input, target)
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else:
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@ -48,9 +48,11 @@ def gpu_worker(local_rank, args):
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train_dataset = FieldDataset(
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in_patterns=args.train_in_patterns,
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tgt_patterns=args.train_tgt_patterns,
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cache=args.cache,
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crop=args.crop,
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pad=args.pad,
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augment=args.augment,
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norms=args.norms,
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pad_or_crop=args.pad_or_crop,
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)
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#train_sampler = DistributedSampler(train_dataset, shuffle=True)
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train_sampler = DistributedSampler(train_dataset)
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@ -66,9 +68,11 @@ def gpu_worker(local_rank, args):
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val_dataset = FieldDataset(
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in_patterns=args.val_in_patterns,
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tgt_patterns=args.val_tgt_patterns,
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cache=args.cache,
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crop=args.crop,
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pad=args.pad,
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augment=False,
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norms=args.norms,
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pad_or_crop=args.pad_or_crop,
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)
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#val_sampler = DistributedSampler(val_dataset, shuffle=False)
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val_sampler = DistributedSampler(val_dataset)
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@ -29,7 +29,7 @@ tgt_dir="nonlin"
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test_dirs="0" # FIXME
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files="dis/128x???.npy"
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files="dis/512x???.npy"
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in_files="$files"
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tgt_files="$files"
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@ -37,8 +37,8 @@ tgt_files="$files"
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m2m.py test \
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--test-in-patterns "$data_root_dir/$in_dir/$test_dirs/$in_files" \
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--test-tgt-patterns "$data_root_dir/$tgt_dir/$test_dirs/$tgt_files" \
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--norms cosmology.dis --model VNet \
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--batches 1 --loader-workers 0 --pad-or-crop 40 \
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--norms cosmology.dis --model VNet --cache --crop 128 --pad 50 \
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--batches 1 --loader-workers 0 \
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--load-state best_model.pth
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@ -29,7 +29,7 @@ tgt_dir="nonlin"
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test_dirs="0" # FIXME
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files="vel/128x???.npy"
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files="vel/512x???.npy"
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in_files="$files"
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tgt_files="$files"
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@ -37,8 +37,8 @@ tgt_files="$files"
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m2m.py test \
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--test-in-patterns "$data_root_dir/$in_dir/$test_dirs/$in_files" \
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--test-tgt-patterns "$data_root_dir/$tgt_dir/$test_dirs/$tgt_files" \
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--norms cosmology.vel --model VNet \
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--batches 1 --loader-workers 0 --pad-or-crop 40 \
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--norms cosmology.vel --model VNet --cache --crop 128 --pad 50 \
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--batches 1 --loader-workers 0 \
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--load-state best_model.pth
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