def __init__(
self,
keys: KeysCollection,
range_x: Union[Tuple[float, float], float] = 0.0,
range_y: Union[Tuple[float, float], float] = 0.0,
range_z: Union[Tuple[float, float], float] = 0.0,
prob: float = 0.1,
keep_size: bool = True,
mode: GridSampleModeSequence = GridSampleMode.BILINEAR,
padding_mode: GridSamplePadModeSequence = GridSamplePadMode.BORDER,
align_corners: Union[Sequence[bool], bool] = False,
):
super().__init__(keys)
self.range_x = ensure_tuple(range_x)
if len(self.range_x) == 1:
self.range_x = tuple(sorted([-self.range_x[0], self.range_x[0]]))
self.range_y = ensure_tuple(range_y)
if len(self.range_y) == 1:
self.range_y = tuple(sorted([-self.range_y[0], self.range_y[0]]))
self.range_z = ensure_tuple(range_z)
if len(self.range_z) == 1:
self.range_z = tuple(sorted([-self.range_z[0], self.range_z[0]]))
self.prob = prob
self.keep_size = keep_size
self.mode = ensure_tuple_rep(mode, len(self.keys))
self.padding_mode = ensure_tuple_rep(padding_mode, len(self.keys))
self.align_corners = ensure_tuple_rep(align_corners, len(self.keys))
self._do_transform = False
self.x = 0.0
self.y = 0.0
self.z = 0.0
def randomize(self) -> None: # type: ignore # see issue #495
self._do_transform = self.R.random_sample() < self.prob
if isinstance(self.min_zoom, Iterable):
_min_zoom = ensure_tuple(self.min_zoom)
_max_zoom = ensure_tuple(self.max_zoom)
self._zoom = [self.R.uniform(l, h) for l, h in zip(_min_zoom, _max_zoom)]
else:
# to keep the spatial shape ratio, use same random zoom factor for all dims
self._zoom = self.R.uniform(self.min_zoom, self.max_zoom)
def __init__(self, keys: KeysCollection):
self.keys: Tuple[Any, ...] = ensure_tuple(keys)
if not self.keys:
raise ValueError("keys unspecified")
for key in self.keys:
if not isinstance(key, Hashable):
raise ValueError(f"keys should be a hashable or a sequence of hashables, got {type(key)}")
def __init__(self, keys: KeysCollection, times: int,
names: KeysCollection):
"""
Args:
keys: keys of the corresponding items to be transformed.
See also: :py:class:`ponai.transforms.compose.MapTransform`
times: expected copy times, for example, if keys is "img", times is 3,
it will add 3 copies of "img" data to the dictionary.
names: the names coresponding to the newly copied data,
the length should match `len(keys) x times`. for example, if keys is ["img", "seg"]
and times is 2, names can be: ["img_1", "seg_1", "img_2", "seg_2"].
Raises:
ValueError: times must be greater than 0.
ValueError: length of names does not match `len(keys) x times`.
"""
super().__init__(keys)
if times < 1:
raise ValueError("times must be greater than 0.")
self.times = times
names = ensure_tuple(names)
if len(names) != (len(self.keys) * times):
raise ValueError(
"length of names does not match `len(keys) x times`.")
self.names = names
def generate_spatial_bounding_box(
img: np.ndarray,
select_fn: Callable = lambda x: x > 0,
channel_indexes: Optional[IndexSelection] = None,
margin: int = 0,
):
"""
generate the spatial bounding box of foreground in the image with start-end positions.
Users can define arbitrary function to select expected foreground from the whole image or specified channels.
And it can also add margin to every dim of the bounding box.
Args:
img (ndarrary): source image to generate bounding box from.
select_fn: function to select expected foreground, default is to select values > 0.
channel_indexes: if defined, select foreground only on the specified channels
of image. if None, select foreground on the whole image.
margin: add margin to all dims of the bounding box.
"""
assert isinstance(margin, int), "margin must be int type."
data = img[[*(ensure_tuple(channel_indexes))]] if channel_indexes is not None else img
data = np.any(select_fn(data), axis=0)
nonzero_idx = np.nonzero(data)
box_start = list()
box_end = list()
for i in range(data.ndim):
assert len(nonzero_idx[i]) > 0, f"did not find nonzero index at spatial dim {i}"
box_start.append(max(0, np.min(nonzero_idx[i]) - margin))
box_end.append(min(data.shape[i], np.max(nonzero_idx[i]) + margin + 1))
return box_start, box_end
def randomize(self, img_size):
self._size = fall_back_tuple(self.roi_size, img_size)
if self.random_size:
self._size = [self.R.randint(low=self._size[i], high=img_size[i] + 1) for i in range(len(img_size))]
if self.random_center:
valid_size = get_valid_patch_size(img_size, self._size)
self._slices = ensure_tuple(slice(None)) + get_random_patch(img_size, valid_size, self.R)
def __call__(self, img, mode: Optional[Union[NumpyPadMode, str]] = None):
"""
Args:
img: data to be transformed, assuming `img` is channel-first and
padding doesn't apply to the channel dim.
mode: {``"constant"``, ``"edge"``, ``"linear_ramp"``, ``"maximum"``, ``"mean"``,
``"median"``, ``"minimum"``, ``"reflect"``, ``"symmetric"``, ``"wrap"``, ``"empty"``}
One of the listed string values or a user supplied function. Defaults to ``self.mode``.
See also: https://numpy.org/doc/1.18/reference/generated/numpy.pad.html
Raises:
ValueError: spatial_border must be int number and can not be less than 0.
ValueError: unsupported length of spatial_border definition.
"""
spatial_shape = img.shape[1:]
spatial_border = ensure_tuple(self.spatial_border)
for b in spatial_border:
if b < 0 or not isinstance(b, int):
raise ValueError("spatial_border must be int number and can not be less than 0.")
if len(spatial_border) == 1:
data_pad_width = [(spatial_border[0], spatial_border[0]) for _ in range(len(spatial_shape))]
elif len(spatial_border) == len(spatial_shape):
data_pad_width = [(spatial_border[i], spatial_border[i]) for i in range(len(spatial_shape))]
elif len(spatial_border) == len(spatial_shape) * 2:
data_pad_width = [(spatial_border[2 * i], spatial_border[2 * i + 1]) for i in range(len(spatial_shape))]
else:
raise ValueError("unsupported length of spatial_border definition.")
return np.pad(
img, [(0, 0)] + data_pad_width, mode=self.mode.value if mode is None else NumpyPadMode(mode).value
)
def create_translate(spatial_dims: int, shift):
"""
create a translation matrix
Args:
spatial_dims: spatial rank
shift (floats): translate factors, defaults to 0.
"""
shift = ensure_tuple(shift)
affine = np.eye(spatial_dims + 1)
for i, a in enumerate(shift[:spatial_dims]):
affine[i, spatial_dims] = a
return affine
def __init__(
self, select_fn: Callable = lambda x: x > 0, channel_indexes: Optional[IndexSelection] = None, margin: int = 0
):
"""
Args:
select_fn: function to select expected foreground, default is to select values > 0.
channel_indexes: if defined, select foreground only on the specified channels
of image. if None, select foreground on the whole image.
margin: add margin to all dims of the bounding box.
"""
self.select_fn = select_fn
self.channel_indexes = ensure_tuple(channel_indexes) if channel_indexes is not None else None
self.margin = margin
def __init__(
self,
spatial_size=None,
normalized: bool = False,
mode: Union[GridSampleMode, str] = GridSampleMode.BILINEAR,
padding_mode: Union[GridSamplePadMode, str] = GridSamplePadMode.ZEROS,
align_corners: bool = False,
reverse_indexing: bool = True,
):
"""
Apply affine transformations with a batch of affine matrices.
When `normalized=False` and `reverse_indexing=True`,
it does the commonly used resampling in the 'pull' direction
following the ``scipy.ndimage.affine_transform`` convention.
In this case `theta` is equivalent to (ndim+1, ndim+1) input ``matrix`` of ``scipy.ndimage.affine_transform``,
operates on homogeneous coordinates.
See also: https://docs.scipy.org/doc/scipy/reference/generated/scipy.ndimage.affine_transform.html
When `normalized=True` and `reverse_indexing=False`,
it applies `theta` to the normalized coordinates (coords. in the range of [-1, 1]) directly.
This is often used with `align_corners=False` to achieve resolution-agnostic resampling,
thus useful as a part of trainable modules such as the spatial transformer networks.
See also: https://pytorch.org/tutorials/intermediate/spatial_transformer_tutorial.html
Args:
spatial_size (list or tuple of int): output spatial shape, the full output shape will be
`[N, C, *spatial_size]` where N and C are inferred from the `src` input of `self.forward`.
normalized: indicating whether the provided affine matrix `theta` is defined
for the normalized coordinates. If `normalized=False`, `theta` will be converted
to operate on normalized coordinates as pytorch affine_grid works with the normalized
coordinates.
mode: {``"bilinear"``, ``"nearest"``}
Interpolation mode to calculate output values. Defaults to ``"bilinear"``.
See also: https://pytorch.org/docs/stable/nn.functional.html#grid-sample
padding_mode: {``"zeros"``, ``"border"``, ``"reflection"``}
Padding mode for outside grid values. Defaults to ``"zeros"``.
See also: https://pytorch.org/docs/stable/nn.functional.html#grid-sample
align_corners: see also https://pytorch.org/docs/stable/nn.functional.html#grid-sample.
reverse_indexing: whether to reverse the spatial indexing of image and coordinates.
set to `False` if `theta` follows pytorch's default "D, H, W" convention.
set to `True` if `theta` follows `scipy.ndimage` default "i, j, k" convention.
"""
super().__init__()
self.spatial_size = ensure_tuple(spatial_size) if spatial_size is not None else None
self.normalized = normalized
self.mode: GridSampleMode = GridSampleMode(mode)
self.padding_mode: GridSamplePadMode = GridSamplePadMode(padding_mode)
self.align_corners = align_corners
self.reverse_indexing = reverse_indexing
def __call__(self, filename):
"""
Args:
filename (str, list, tuple, file): path file or file-like object or a list of files.
"""
filename = ensure_tuple(filename)
img_array = list()
compatible_meta = dict()
for name in filename:
img = nib.load(name)
img = correct_nifti_header_if_necessary(img)
header = dict(img.header)
header["filename_or_obj"] = name
header["affine"] = img.affine
header["original_affine"] = img.affine.copy()
header["as_closest_canonical"] = self.as_closest_canonical
ndim = img.header["dim"][0]
spatial_rank = min(ndim, 3)
header["spatial_shape"] = img.header["dim"][1:spatial_rank + 1]
if self.as_closest_canonical:
img = nib.as_closest_canonical(img)
header["affine"] = img.affine
img_array.append(np.array(img.get_fdata(dtype=self.dtype)))
img.uncache()
if self.image_only:
continue
if not compatible_meta:
for meta_key in header:
meta_datum = header[meta_key]
# pytype: disable=attribute-error
if (type(meta_datum).__name__ == "ndarray"
and np_str_obj_array_pattern.search(
meta_datum.dtype.str) is not None):
continue
# pytype: enable=attribute-error
compatible_meta[meta_key] = meta_datum
else:
assert np.allclose(
header["affine"], compatible_meta["affine"]
), "affine data of all images should be same."
img_array = np.stack(img_array,
axis=0) if len(img_array) > 1 else img_array[0]
if self.image_only:
return img_array
return img_array, compatible_meta
def __init__(self,
applied_labels,
independent: bool = True,
connectivity: Optional[int] = None):
"""
Args:
applied_labels (int, list or tuple of int): Labels for applying the connected component on.
If only one channel. The pixel whose value is not in this list will remain unchanged.
If the data is in one-hot format, this is used to determine what channels to apply.
independent (bool): consider several labels as a whole or independent, default is `True`.
Example use case would be segment label 1 is liver and label 2 is liver tumor, in that case
you want this "independent" to be specified as False.
connectivity: Maximum number of orthogonal hops to consider a pixel/voxel as a neighbor.
Accepted values are ranging from 1 to input.ndim. If ``None``, a full
connectivity of ``input.ndim`` is used.
"""
super().__init__()
self.applied_labels = ensure_tuple(applied_labels)
self.independent = independent
self.connectivity = connectivity
def create_rotate(spatial_dims: int, radians):
"""
create a 2D or 3D rotation matrix
Args:
spatial_dims: {``2``, ``3``} spatial rank
radians (float or a sequence of floats): rotation radians
when spatial_dims == 3, the `radians` sequence corresponds to
rotation in the 1st, 2nd, and 3rd dim respectively.
Raises:
ValueError: create_rotate got spatial_dims={spatial_dims}, radians={radians}.
"""
radians = ensure_tuple(radians)
if spatial_dims == 2:
if len(radians) >= 1:
sin_, cos_ = np.sin(radians[0]), np.cos(radians[0])
return np.array([[cos_, -sin_, 0.0], [sin_, cos_, 0.0], [0.0, 0.0, 1.0]])
if spatial_dims == 3:
affine = None
if len(radians) >= 1:
sin_, cos_ = np.sin(radians[0]), np.cos(radians[0])
affine = np.array(
[[1.0, 0.0, 0.0, 0.0], [0.0, cos_, -sin_, 0.0], [0.0, sin_, cos_, 0.0], [0.0, 0.0, 0.0, 1.0]]
)
if len(radians) >= 2:
sin_, cos_ = np.sin(radians[1]), np.cos(radians[1])
affine = affine @ np.array(
[[cos_, 0.0, sin_, 0.0], [0.0, 1.0, 0.0, 0.0], [-sin_, 0.0, cos_, 0.0], [0.0, 0.0, 0.0, 1.0]]
)
if len(radians) >= 3:
sin_, cos_ = np.sin(radians[2]), np.cos(radians[2])
affine = affine @ np.array(
[[cos_, -sin_, 0.0, 0.0], [sin_, cos_, 0.0, 0.0], [0.0, 0.0, 1.0, 0.0], [0.0, 0.0, 0.0, 1.0]]
)
return affine
raise ValueError(f"create_rotate got spatial_dims={spatial_dims}, radians={radians}.")
def __init__(
self,
keys: KeysCollection,
source_key: str,
select_fn: Callable = lambda x: x > 0,
channel_indexes: Optional[IndexSelection] = None,
margin: int = 0,
):
"""
Args:
keys: keys of the corresponding items to be transformed.
See also: :py:class:`ponai.transforms.compose.MapTransform`
source_key: data source to generate the bounding box of foreground, can be image or label, etc.
select_fn: function to select expected foreground, default is to select values > 0.
channel_indexes: if defined, select foreground only on the specified channels
of image. if None, select foreground on the whole image.
margin: add margin to all dims of the bounding box.
"""
super().__init__(keys)
self.source_key = source_key
self.select_fn = select_fn
self.channel_indexes = ensure_tuple(
channel_indexes) if channel_indexes is not None else None
self.margin = margin
def __call__(self, filename):
"""
Args:
filename (str, list, tuple, file): path file or file-like object or a list of files.
"""
filename = ensure_tuple(filename)
img_array = list()
compatible_meta = None
for name in filename:
img = Image.open(name)
data = np.asarray(img)
if self.dtype:
data = data.astype(self.dtype)
img_array.append(data)
meta = dict()
meta["filename_or_obj"] = name
meta["spatial_shape"] = data.shape[:2]
meta["format"] = img.format
meta["mode"] = img.mode
meta["width"] = img.width
meta["height"] = img.height
meta["info"] = img.info
if self.image_only:
continue
if not compatible_meta:
compatible_meta = meta
else:
assert np.allclose(
meta["spatial_shape"], compatible_meta["spatial_shape"]
), "all the images in the list should have same spatial shape."
img_array = np.stack(img_array,
axis=0) if len(img_array) > 1 else img_array[0]
return img_array if self.image_only else (img_array, compatible_meta)
def __init__(
self,
device,
max_epochs: int,
amp: bool,
data_loader,
prepare_batch: Callable = default_prepare_batch,
iteration_update: Optional[Callable] = None,
post_transform=None,
key_metric=None,
additional_metrics=None,
handlers=None,
):
# pytype: disable=invalid-directive
# pytype: disable=wrong-arg-count
super().__init__(iteration_update
if iteration_update is not None else self._iteration)
# pytype: enable=invalid-directive
# pytype: enable=wrong-arg-count
# FIXME:
if amp:
self.logger.info(
"Will add AMP support when PyTorch v1.6 released.")
if not isinstance(device, torch.device):
raise ValueError("device must be PyTorch device object.")
if not isinstance(data_loader,
torch.utils.data.DataLoader): # type: ignore
raise ValueError("data_loader must be PyTorch DataLoader.")
# set all sharable data for the workflow based on Ignite engine.state
self.state = State(
seed=0,
iteration=0,
epoch=0,
max_epochs=max_epochs,
epoch_length=-1,
output=None,
batch=None,
metrics={},
dataloader=None,
device=device,
amp=amp,
key_metric_name=
None, # we can set many metrics, only use key_metric to compare and save the best model
best_metric=-1,
best_metric_epoch=-1,
)
self.data_loader = data_loader
self.prepare_batch = prepare_batch
if post_transform is not None:
@self.on(Events.ITERATION_COMPLETED)
def run_post_transform(engine):
engine.state.output = apply_transform(post_transform,
engine.state.output)
if key_metric is not None:
if not isinstance(key_metric, dict):
raise ValueError("key_metric must be a dict object.")
self.state.key_metric_name = list(key_metric.keys())[0]
metrics = key_metric
if additional_metrics is not None and len(additional_metrics) > 0:
if not isinstance(additional_metrics, dict):
raise ValueError(
"additional_metrics must be a dict object.")
metrics.update(additional_metrics)
for name, metric in metrics.items():
metric.attach(self, name)
@self.on(Events.EPOCH_COMPLETED)
def _compare_metrics(engine):
if engine.state.key_metric_name is not None:
current_val_metric = engine.state.metrics[
engine.state.key_metric_name]
if current_val_metric > engine.state.best_metric:
self.logger.info(
f"Got new best metric of {engine.state.key_metric_name}: {current_val_metric}"
)
engine.state.best_metric = current_val_metric
engine.state.best_metric_epoch = engine.state.epoch
if handlers is not None:
handlers = ensure_tuple(handlers)
for handler in handlers:
handler.attach(self)
def forward(self, src, theta, spatial_size=None):
"""
``theta`` must be an affine transformation matrix with shape
3x3 or Nx3x3 or Nx2x3 or 2x3 for spatial 2D transforms,
4x4 or Nx4x4 or Nx3x4 or 3x4 for spatial 3D transforms,
where `N` is the batch size. `theta` will be converted into float Tensor for the computation.
Args:
src (array_like): image in spatial 2D or 3D (N, C, spatial_dims),
where N is the batch dim, C is the number of channels.
theta (array_like): Nx3x3, Nx2x3, 3x3, 2x3 for spatial 2D inputs,
Nx4x4, Nx3x4, 3x4, 4x4 for spatial 3D inputs. When the batch dimension is omitted,
`theta` will be repeated N times, N is the batch dim of `src`.
spatial_size (list or tuple of int): output spatial shape, the full output shape will be
`[N, C, *spatial_size]` where N and C are inferred from the `src`.
Raises:
TypeError: both src and theta must be torch Tensor, got {type(src).__name__}, {type(theta).__name__}.
ValueError: affine must be Nxdxd or dxd.
ValueError: affine must be Nx3x3 or Nx4x4, got: {theta.shape}.
ValueError: src must be spatially 2D or 3D.
ValueError: batch dimension of affine and image does not match, got affine: {} and image: {}.
"""
# validate `theta`
if not torch.is_tensor(theta) or not torch.is_tensor(src):
raise TypeError(
f"both src and theta must be torch Tensor, got {type(src).__name__}, {type(theta).__name__}."
)
if theta.ndim not in (2, 3):
raise ValueError("affine must be Nxdxd or dxd.")
if theta.ndim == 2:
theta = theta[None] # adds a batch dim.
theta = theta.clone() # no in-place change of theta
theta_shape = tuple(theta.shape[1:])
if theta_shape in ((2, 3), (3, 4)): # needs padding to dxd
pad_affine = torch.tensor([0, 0, 1] if theta_shape[0] == 2 else [0, 0, 0, 1])
pad_affine = pad_affine.repeat(theta.shape[0], 1, 1).to(theta)
pad_affine.requires_grad = False
theta = torch.cat([theta, pad_affine], dim=1)
if tuple(theta.shape[1:]) not in ((3, 3), (4, 4)):
raise ValueError(f"affine must be Nx3x3 or Nx4x4, got: {theta.shape}.")
# validate `src`
sr = src.ndim - 2 # input spatial rank
if sr not in (2, 3):
raise ValueError("src must be spatially 2D or 3D.")
# set output shape
src_size = tuple(src.shape)
dst_size = src_size # default to the src shape
if self.spatial_size is not None:
dst_size = src_size[:2] + self.spatial_size
if spatial_size is not None:
dst_size = src_size[:2] + ensure_tuple(spatial_size)
# reverse and normalise theta if needed
if not self.normalized:
theta = to_norm_affine(
affine=theta, src_size=src_size[2:], dst_size=dst_size[2:], align_corners=self.align_corners
)
if self.reverse_indexing:
rev_idx = torch.as_tensor(range(sr - 1, -1, -1), device=src.device)
theta[:, :sr] = theta[:, rev_idx]
theta[:, :, :sr] = theta[:, :, rev_idx]
if (theta.shape[0] == 1) and src_size[0] > 1:
# adds a batch dim to `theta` in order to match `src`
theta = theta.repeat(src_size[0], 1, 1)
if theta.shape[0] != src_size[0]:
raise ValueError(
"batch dimension of affine and image does not match, got affine: {} and image: {}.".format(
theta.shape[0], src_size[0]
)
)
grid = nn.functional.affine_grid(theta=theta[:, :sr], size=dst_size, align_corners=self.align_corners)
dst = nn.functional.grid_sample(
input=src.contiguous(),
grid=grid,
mode=self.mode.value,
padding_mode=self.padding_mode.value,
align_corners=self.align_corners,
)
return dst
def __init__(self, transforms=None) -> None:
if transforms is None:
transforms = []
self.transforms = ensure_tuple(transforms)
self.set_random_state(seed=get_seed())
def __call__(self, engine):
args = ensure_tuple(self.step_transform(engine))
self.lr_scheduler.step(*args)
if self.print_lr:
self.logger.info(
f"Current learning rate: {self.lr_scheduler._last_lr[0]}")