def test_values(self):
# check system default flags
set_determinism(None)
self.assertTrue(not torch.backends.cudnn.deterministic)
self.assertTrue(get_seed() is None)
# set default seed
set_determinism()
self.assertTrue(get_seed() is not None)
self.assertTrue(torch.backends.cudnn.deterministic)
self.assertTrue(not torch.backends.cudnn.benchmark)
# resume default
set_determinism(None)
self.assertTrue(not torch.backends.cudnn.deterministic)
self.assertTrue(not torch.backends.cudnn.benchmark)
self.assertTrue(get_seed() is None)
# test seeds
seed = 255
set_determinism(seed=seed)
self.assertEqual(seed, get_seed())
a = np.random.randint(seed)
b = torch.randint(seed, (1,))
set_determinism(seed=seed)
c = np.random.randint(seed)
d = torch.randint(seed, (1,))
self.assertEqual(a, c)
self.assertEqual(b, d)
self.assertTrue(torch.backends.cudnn.deterministic)
self.assertTrue(not torch.backends.cudnn.benchmark)
set_determinism(seed=None)
def __init__(
self,
img: Sequence,
img_transform: Optional[Callable] = None,
seg: Optional[Sequence] = None,
seg_transform: Optional[Callable] = None,
labels: Optional[Sequence] = None,
label_transform: Optional[Callable] = None,
) -> None:
"""
Initializes the dataset with the filename lists. The transform `img_transform` is applied
to the images and `seg_transform` to the segmentations.
Args:
img: sequence of images.
img_transform: transform to apply to each element in `img`.
seg: sequence of segmentations.
seg_transform: transform to apply to each element in `seg`.
labels: sequence of labels.
label_transform: transform to apply to each element in `labels`.
"""
items = [(img, img_transform), (seg, seg_transform),
(labels, label_transform)]
self.set_random_state(seed=get_seed())
datasets = [Dataset(x[0], x[1]) for x in items if x[0] is not None]
self.dataset = datasets[0] if len(datasets) == 1 else ZipDataset(
datasets)
self._seed = 0 # transform synchronization seed
def __init__(
self,
img_files,
img_transform: Optional[Callable] = None,
seg_files=None,
seg_transform: Optional[Callable] = None,
labels=None,
label_transform: Optional[Callable] = None,
):
"""
Initializes the dataset with the filename lists. The transform `img_transform` is applied
to the images and `seg_transform` to the segmentations.
Args:
img_files (iterable, list of str): list of image filenames
img_transform (Callable, optional): transform to apply to image arrays
seg_files (iterable, list of str): if in segmentation task, list of segmentation filenames
seg_transform (Callable, optional): transform to apply to segmentation arrays
labels (iterable, list or array): if in classification task, list of classification labels
label_transform (Callable, optional): transform to apply to label arrays
"""
items = [(img_files, img_transform), (seg_files, seg_transform),
(labels, label_transform)]
self.set_random_state(seed=get_seed())
super().__init__(
[Dataset(x[0], x[1]) for x in items if x[0] is not None])
def test_inverse(self, _, data_name, acceptable_diff, *transforms):
name = _
data = self.all_data[data_name]
forwards = [data.copy()]
# Apply forwards
for t in transforms:
if isinstance(t, Randomizable):
t.set_random_state(seed=get_seed())
forwards.append(t(forwards[-1]))
# Check that error is thrown when inverse are used out of order.
t = SpatialPadd("image", [10, 5])
with self.assertRaises(RuntimeError):
t.inverse(forwards[-1])
# Apply inverses
fwd_bck = forwards[-1].copy()
for i, t in enumerate(reversed(transforms)):
if isinstance(t, InvertibleTransform):
fwd_bck = t.inverse(fwd_bck)
self.check_inverse(name, data.keys(), forwards[-i - 2],
fwd_bck, forwards[-1], acceptable_diff)
def test_inverse(self, _, data_name, acceptable_diff, is_meta,
*transforms):
name = _
data = self.all_data[data_name]
if is_meta:
data = ToMetaTensord(KEYS)(data)
forwards = [data.copy()]
# Apply forwards
for t in transforms:
if isinstance(t, Randomizable):
t.set_random_state(seed=get_seed())
forwards.append(t(forwards[-1]))
# Apply inverses
fwd_bck = forwards[-1].copy()
for i, t in enumerate(reversed(transforms)):
if isinstance(t, InvertibleTransform):
if isinstance(fwd_bck, list):
for j, _fwd_bck in enumerate(fwd_bck):
fwd_bck = t.inverse(_fwd_bck)
self.check_inverse(name, data.keys(), forwards[-i - 2],
fwd_bck, forwards[-1][j],
acceptable_diff)
else:
fwd_bck = t.inverse(fwd_bck)
self.check_inverse(name, data.keys(), forwards[-i - 2],
fwd_bck, forwards[-1], acceptable_diff)
def __init__(
self,
image_files: Sequence[str],
seg_files: Optional[Sequence[str]] = None,
labels: Optional[Sequence[float]] = None,
transform: Optional[Callable] = None,
seg_transform: Optional[Callable] = None,
label_transform: Optional[Callable] = None,
image_only: bool = True,
transform_with_metadata: bool = False,
dtype: DtypeLike = np.float32,
reader: Optional[Union[ImageReader, str]] = None,
*args,
**kwargs,
) -> None:
"""
Initializes the dataset with the image and segmentation filename lists. The transform `transform` is applied
to the images and `seg_transform` to the segmentations.
Args:
image_files: list of image filenames.
seg_files: if in segmentation task, list of segmentation filenames.
labels: if in classification task, list of classification labels.
transform: transform to apply to image arrays.
seg_transform: transform to apply to segmentation arrays.
label_transform: transform to apply to the label data.
image_only: if True return only the image volume, otherwise, return image volume and the metadata.
transform_with_metadata: if True, the metadata will be passed to the transforms whenever possible.
dtype: if not None convert the loaded image to this data type.
reader: register reader to load image file and meta data, if None, will use the default readers.
If a string of reader name provided, will construct a reader object with the `*args` and `**kwargs`
parameters, supported reader name: "NibabelReader", "PILReader", "ITKReader", "NumpyReader"
args: additional parameters for reader if providing a reader name.
kwargs: additional parameters for reader if providing a reader name.
Raises:
ValueError: When ``seg_files`` length differs from ``image_files``
"""
if seg_files is not None and len(image_files) != len(seg_files):
raise ValueError(
"Must have same the number of segmentation as image files: "
f"images={len(image_files)}, segmentations={len(seg_files)}.")
self.image_files = image_files
self.seg_files = seg_files
self.labels = labels
self.transform = transform
self.seg_transform = seg_transform
self.label_transform = label_transform
if image_only and transform_with_metadata:
raise ValueError(
"transform_with_metadata=True requires image_only=False.")
self.image_only = image_only
self.transform_with_metadata = transform_with_metadata
self.loader = LoadImage(reader, image_only, dtype, *args, **kwargs)
self.set_random_state(seed=get_seed())
self._seed = 0 # transform synchronization seed
def __init__(
self,
transforms: Optional[Union[Sequence[Callable],
Callable]] = None) -> None:
if transforms is None:
transforms = []
self.transforms = ensure_tuple(transforms)
self.set_random_state(seed=get_seed())
def __init__(
self,
inputZ01: Sequence,
inputZ02: Sequence,
inputZ03: Sequence,
inputZ04: Sequence,
inputZ05: Sequence,
inputZ06: Sequence,
inputZ07: Sequence,
targetC01: Sequence,
targetC02: Sequence,
targetC03: Sequence,
roi_size: int,
n_samples: int,
inputZ01_transform: Optional[Callable] = None,
inputZ02_transform: Optional[Callable] = None,
inputZ03_transform: Optional[Callable] = None,
inputZ04_transform: Optional[Callable] = None,
inputZ05_transform: Optional[Callable] = None,
inputZ06_transform: Optional[Callable] = None,
inputZ07_transform: Optional[Callable] = None,
targetC01_transform: Optional[Callable] = None,
targetC02_transform: Optional[Callable] = None,
targetC03_transform: Optional[Callable] = None,
) -> None:
"""
Initializes the dataset with the filename lists. The transform `img_transform` is applied
to the images and `seg_transform` to the segmentations.
"""
items = [(inputZ01, inputZ01_transform), (inputZ02, inputZ02_transform), (inputZ03, inputZ03_transform),
(inputZ04, inputZ04_transform), (inputZ05, inputZ05_transform), (inputZ06, inputZ06_transform),
(inputZ07, inputZ07_transform),
(targetC01, targetC01_transform), (targetC02, targetC02_transform), (targetC03, targetC03_transform)]
self.roi_size = roi_size
self.n_samples = n_samples
self.set_random_state(seed=get_seed())
sampler = RandSpatialCropSamples(roi_size=(self.roi_size, self.roi_size),
num_samples=self.n_samples,
random_center=True,
random_size=False)
datasets = [PatchDataset(dataset=x[0],
patch_func=sampler,
samples_per_image=self.n_samples,
transform=x[1]) for x in items if x[0] is not None]
self.dataset = datasets[0] if len(datasets) == 1 else ZipDataset(datasets)
self._seed = 0 # transform synchronization seed
def __init__(
self,
transforms: Optional[Union[Sequence[Callable], Callable]] = None,
map_items: bool = True,
unpack_items: bool = False,
log_stats: bool = False,
) -> None:
if transforms is None:
transforms = []
self.transforms = ensure_tuple(transforms)
self.map_items = map_items
self.unpack_items = unpack_items
self.log_stats = log_stats
self.set_random_state(seed=get_seed())
def __init__(
self,
image_files: Sequence[str],
seg_files: Optional[Sequence[str]] = None,
labels: Optional[Sequence[float]] = None,
as_closest_canonical: bool = False,
transform: Optional[Callable] = None,
seg_transform: Optional[Callable] = None,
image_only: bool = True,
dtype: Optional[np.dtype] = np.float32,
) -> None:
"""
Initializes the dataset with the image and segmentation filename lists. The transform `transform` is applied
to the images and `seg_transform` to the segmentations.
Args:
image_files: list of image filenames
seg_files: if in segmentation task, list of segmentation filenames
labels: if in classification task, list of classification labels
as_closest_canonical: if True, load the image as closest to canonical orientation
transform: transform to apply to image arrays
seg_transform: transform to apply to segmentation arrays
image_only: if True return only the image volume, other return image volume and header dict
dtype: if not None convert the loaded image to this data type
Raises:
ValueError: When ``seg_files`` length differs from ``image_files``.
"""
if seg_files is not None and len(image_files) != len(seg_files):
raise ValueError(
"Must have same the number of segmentation as image files: "
f"images={len(image_files)}, segmentations={len(seg_files)}.")
self.image_files = image_files
self.seg_files = seg_files
self.labels = labels
self.as_closest_canonical = as_closest_canonical
self.transform = transform
self.seg_transform = seg_transform
self.image_only = image_only
self.dtype = dtype
self.set_random_state(seed=get_seed())
self._seed = 0 # transform synchronization seed
def __init__(self,
inputZ01: Sequence,
inputZ02: Sequence,
inputZ03: Sequence,
inputZ04: Sequence,
inputZ05: Sequence,
inputZ06: Sequence,
inputZ07: Sequence,
targetC01: Sequence,
targetC02: Sequence,
targetC03: Sequence,
inputZ01_transform: Optional[Callable] = None,
inputZ02_transform: Optional[Callable] = None,
inputZ03_transform: Optional[Callable] = None,
inputZ04_transform: Optional[Callable] = None,
inputZ05_transform: Optional[Callable] = None,
inputZ06_transform: Optional[Callable] = None,
inputZ07_transform: Optional[Callable] = None,
targetC01_transform: Optional[Callable] = None,
targetC02_transform: Optional[Callable] = None,
targetC03_transform: Optional[Callable] = None) -> None:
"""
Initializes the dataset with the filename lists. The transform `img_transform` is applied
to the images and `seg_transform` to the segmentations.
"""
items = [
(inputZ01, inputZ01_transform), (inputZ02, inputZ02_transform),
(inputZ03, inputZ03_transform), (inputZ04, inputZ04_transform),
(inputZ05, inputZ05_transform), (inputZ06, inputZ06_transform),
(inputZ07, inputZ07_transform), (targetC01, targetC01_transform),
(targetC02, targetC02_transform), (targetC03, targetC03_transform)
]
self.set_random_state(seed=get_seed())
datasets = [Dataset(x[0], x[1]) for x in items if x[0] is not None]
self.dataset = datasets[0] if len(datasets) == 1 else ZipDataset(
datasets)
self._seed = 0 # transform synchronization seed
def __init__(self, transforms=None) -> None:
if transforms is None:
transforms = []
self.transforms = ensure_tuple(transforms)
self.set_random_state(seed=get_seed())
