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Merged
wyli merged 3 commits into from
Jan 18, 2022
Merged

DictPostFixes #3671

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a6be628
DictPostFixes
rijobro Jan 17, 2022
d923ef5
use fn
rijobro Jan 17, 2022
e1a0687
fix
rijobro Jan 18, 2022
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3 changes: 2 additions & 1 deletion monai/apps/deepedit/transforms.py
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Expand Up @@ -18,6 +18,7 @@
from monai.config import KeysCollection
from monai.transforms.transform import MapTransform, Randomizable, Transform
from monai.utils import optional_import
from monai.utils.enums import PostFix

logger = logging.getLogger(__name__)

Expand Down Expand Up @@ -68,7 +69,7 @@ def __call__(self, data):
d = dict(data)
current_shape = d[self.ref_image].shape[1:]

factor = np.divide(current_shape, d["image_meta_dict"]["dim"][1:4])
factor = np.divide(current_shape, d[PostFix.meta("image")]["dim"][1:4])
pos_clicks, neg_clicks = d["foreground"], d["background"]

pos = np.multiply(pos_clicks, factor).astype(int, copy=False).tolist() if len(pos_clicks) else []
Expand Down
15 changes: 9 additions & 6 deletions monai/apps/deepgrow/transforms.py
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Expand Up @@ -20,10 +20,13 @@
from monai.transforms.transform import MapTransform, Randomizable, Transform
from monai.transforms.utils import generate_spatial_bounding_box, is_positive
from monai.utils import InterpolateMode, deprecated_arg, ensure_tuple, ensure_tuple_rep, min_version, optional_import
from monai.utils.enums import PostFix

measure, _ = optional_import("skimage.measure", "0.14.2", min_version)
distance_transform_cdt, _ = optional_import("scipy.ndimage.morphology", name="distance_transform_cdt")

DEFAULT_POST_FIX = PostFix.meta()


# Transforms to support Training for Deepgrow models
class FindAllValidSlicesd(Transform):
Expand Down Expand Up @@ -391,7 +394,7 @@ def __init__(
channel_indices: Optional[IndexSelection] = None,
margin: int = 0,
meta_keys: Optional[KeysCollection] = None,
meta_key_postfix="meta_dict",
meta_key_postfix=DEFAULT_POST_FIX,
start_coord_key: str = "foreground_start_coord",
end_coord_key: str = "foreground_end_coord",
original_shape_key: str = "foreground_original_shape",
Expand Down Expand Up @@ -493,7 +496,7 @@ def __init__(
spatial_dims: int = 2,
slice_key: str = "slice",
meta_keys: Optional[str] = None,
meta_key_postfix: str = "meta_dict",
meta_key_postfix: str = DEFAULT_POST_FIX,
dimensions: Optional[int] = None,
):
self.ref_image = ref_image
Expand Down Expand Up @@ -604,7 +607,7 @@ def __init__(
spatial_size,
margin=20,
meta_keys: Optional[KeysCollection] = None,
meta_key_postfix="meta_dict",
meta_key_postfix=DEFAULT_POST_FIX,
start_coord_key: str = "foreground_start_coord",
end_coord_key: str = "foreground_end_coord",
original_shape_key: str = "foreground_original_shape",
Expand Down Expand Up @@ -720,7 +723,7 @@ def __init__(
guidance: str,
ref_image: str,
meta_keys: Optional[str] = None,
meta_key_postfix: str = "meta_dict",
meta_key_postfix: str = DEFAULT_POST_FIX,
cropped_shape_key: str = "foreground_cropped_shape",
) -> None:
self.guidance = guidance
Expand Down Expand Up @@ -803,7 +806,7 @@ def __init__(
mode: Union[Sequence[Union[InterpolateMode, str]], InterpolateMode, str] = InterpolateMode.NEAREST,
align_corners: Union[Sequence[Optional[bool]], Optional[bool]] = None,
meta_keys: Optional[str] = None,
meta_key_postfix: str = "meta_dict",
meta_key_postfix: str = DEFAULT_POST_FIX,
start_coord_key: str = "foreground_start_coord",
end_coord_key: str = "foreground_end_coord",
original_shape_key: str = "foreground_original_shape",
Expand Down Expand Up @@ -907,7 +910,7 @@ def __init__(
guidance="guidance",
axis: int = 0,
meta_keys: Optional[KeysCollection] = None,
meta_key_postfix: str = "meta_dict",
meta_key_postfix: str = DEFAULT_POST_FIX,
allow_missing_keys: bool = False,
):
super().__init__(keys, allow_missing_keys)
Expand Down
5 changes: 4 additions & 1 deletion monai/data/dataset_summary.py
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Expand Up @@ -20,6 +20,9 @@
from monai.data.dataset import Dataset
from monai.transforms import concatenate
from monai.utils import convert_data_type
from monai.utils.enums import PostFix

DEFAULT_POST_FIX = PostFix.meta()


class DatasetSummary:
Expand All @@ -42,7 +45,7 @@ def __init__(
image_key: Optional[str] = "image",
label_key: Optional[str] = "label",
meta_key: Optional[KeysCollection] = None,
meta_key_postfix: str = "meta_dict",
meta_key_postfix: str = DEFAULT_POST_FIX,
num_workers: int = 0,
**kwargs,
):
Expand Down
6 changes: 4 additions & 2 deletions monai/data/test_time_augmentation.py
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Expand Up @@ -24,7 +24,7 @@
from monai.transforms.inverse_batch_transform import BatchInverseTransform
from monai.transforms.transform import Randomizable
from monai.transforms.utils import allow_missing_keys_mode, convert_inverse_interp_mode
from monai.utils.enums import CommonKeys, TraceKeys
from monai.utils.enums import CommonKeys, PostFix, TraceKeys
from monai.utils.module import optional_import
from monai.utils.type_conversion import convert_data_type

Expand All @@ -37,6 +37,8 @@

__all__ = ["TestTimeAugmentation"]

DEFAULT_POST_FIX = PostFix.meta()


def _identity(x):
return x
Expand Down Expand Up @@ -106,7 +108,7 @@ def __init__(
orig_key=CommonKeys.LABEL,
nearest_interp: bool = True,
orig_meta_keys: Optional[str] = None,
meta_key_postfix="meta_dict",
meta_key_postfix=DEFAULT_POST_FIX,
return_full_data: bool = False,
progress: bool = True,
) -> None:
Expand Down
4 changes: 2 additions & 2 deletions monai/data/utils.py
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Expand Up @@ -344,14 +344,14 @@ def decollate_batch(batch, detach: bool = True, pad=True, fill_value=None):

batch_data = {
"image": torch.rand((2,1,10,10)),
"image_meta_dict": {"scl_slope": torch.Tensor([0.0, 0.0])}
DictPostFix.meta("image"): {"scl_slope": torch.Tensor([0.0, 0.0])}
}
out = decollate_batch(batch_data)
print(len(out))
>>> 2

print(out[0])
>>> {'image': tensor([[[4.3549e-01...43e-01]]]), 'image_meta_dict': {'scl_slope': 0.0}}
>>> {'image': tensor([[[4.3549e-01...43e-01]]]), DictPostFix.meta("image"): {'scl_slope': 0.0}}

batch_data = [torch.rand((2,1,10,10)), torch.rand((2,3,5,5))]
out = decollate_batch(batch_data)
Expand Down
11 changes: 6 additions & 5 deletions monai/transforms/croppad/dictionary.py
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Expand Up @@ -52,7 +52,7 @@
)
from monai.utils import ImageMetaKey as Key
from monai.utils import Method, NumpyPadMode, PytorchPadMode, ensure_tuple, ensure_tuple_rep, fall_back_tuple
from monai.utils.enums import TraceKeys
from monai.utils.enums import PostFix, TraceKeys

__all__ = [
"PadModeSequence",
Expand Down Expand Up @@ -105,6 +105,7 @@

NumpyPadModeSequence = Union[Sequence[Union[NumpyPadMode, str]], NumpyPadMode, str]
PadModeSequence = Union[Sequence[Union[NumpyPadMode, PytorchPadMode, str]], NumpyPadMode, PytorchPadMode, str]
DEFAULT_POST_FIX = PostFix.meta()


class SpatialPadd(MapTransform, InvertibleTransform):
Expand Down Expand Up @@ -755,7 +756,7 @@ def __init__(
random_center: bool = True,
random_size: bool = True,
meta_keys: Optional[KeysCollection] = None,
meta_key_postfix: str = "meta_dict",
meta_key_postfix: str = DEFAULT_POST_FIX,
allow_missing_keys: bool = False,
) -> None:
MapTransform.__init__(self, keys, allow_missing_keys)
Expand Down Expand Up @@ -951,7 +952,7 @@ def __init__(
num_samples: int = 1,
center_coord_key: Optional[str] = None,
meta_keys: Optional[KeysCollection] = None,
meta_key_postfix: str = "meta_dict",
meta_key_postfix: str = DEFAULT_POST_FIX,
allow_missing_keys: bool = False,
):
MapTransform.__init__(self, keys, allow_missing_keys)
Expand Down Expand Up @@ -1103,7 +1104,7 @@ def __init__(
fg_indices_key: Optional[str] = None,
bg_indices_key: Optional[str] = None,
meta_keys: Optional[KeysCollection] = None,
meta_key_postfix: str = "meta_dict",
meta_key_postfix: str = DEFAULT_POST_FIX,
allow_smaller: bool = False,
allow_missing_keys: bool = False,
) -> None:
Expand Down Expand Up @@ -1302,7 +1303,7 @@ def __init__(
image_threshold: float = 0.0,
indices_key: Optional[str] = None,
meta_keys: Optional[KeysCollection] = None,
meta_key_postfix: str = "meta_dict",
meta_key_postfix: str = DEFAULT_POST_FIX,
allow_smaller: bool = False,
allow_missing_keys: bool = False,
) -> None:
Expand Down
7 changes: 5 additions & 2 deletions monai/transforms/intensity/dictionary.py
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Expand Up @@ -56,6 +56,7 @@
from monai.transforms.utils import is_positive
from monai.utils import ensure_tuple, ensure_tuple_rep
from monai.utils.deprecate_utils import deprecated_arg
from monai.utils.enums import PostFix

__all__ = [
"RandGaussianNoised",
Expand Down Expand Up @@ -147,6 +148,8 @@
"RandKSpaceSpikeNoiseDict",
]

DEFAULT_POST_FIX = PostFix.meta()


class RandGaussianNoised(RandomizableTransform, MapTransform):
"""
Expand Down Expand Up @@ -285,7 +288,7 @@ def __init__(
offset: float,
factor_key: Optional[str] = None,
meta_keys: Optional[KeysCollection] = None,
meta_key_postfix: str = "meta_dict",
meta_key_postfix: str = DEFAULT_POST_FIX,
allow_missing_keys: bool = False,
) -> None:
"""
Expand Down Expand Up @@ -342,7 +345,7 @@ def __init__(
offsets: Union[Tuple[float, float], float],
factor_key: Optional[str] = None,
meta_keys: Optional[KeysCollection] = None,
meta_key_postfix: str = "meta_dict",
meta_key_postfix: str = DEFAULT_POST_FIX,
prob: float = 0.1,
allow_missing_keys: bool = False,
) -> None:
Expand Down
7 changes: 5 additions & 2 deletions monai/transforms/io/dictionary.py
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Expand Up @@ -25,9 +25,12 @@
from monai.transforms.io.array import LoadImage, SaveImage
from monai.transforms.transform import MapTransform
from monai.utils import GridSampleMode, GridSamplePadMode, InterpolateMode, ensure_tuple, ensure_tuple_rep
from monai.utils.enums import PostFix

__all__ = ["LoadImaged", "LoadImageD", "LoadImageDict", "SaveImaged", "SaveImageD", "SaveImageDict"]

DEFAULT_POST_FIX = PostFix.meta()


class LoadImaged(MapTransform):
"""
Expand Down Expand Up @@ -66,7 +69,7 @@ def __init__(
reader: Optional[Union[ImageReader, str]] = None,
dtype: DtypeLike = np.float32,
meta_keys: Optional[KeysCollection] = None,
meta_key_postfix: str = "meta_dict",
meta_key_postfix: str = DEFAULT_POST_FIX,
overwriting: bool = False,
image_only: bool = False,
allow_missing_keys: bool = False,
Expand Down Expand Up @@ -216,7 +219,7 @@ def __init__(
self,
keys: KeysCollection,
meta_keys: Optional[KeysCollection] = None,
meta_key_postfix: str = "meta_dict",
meta_key_postfix: str = DEFAULT_POST_FIX,
output_dir: Union[Path, str] = "./",
output_postfix: str = "trans",
output_ext: str = ".nii.gz",
Expand Down
7 changes: 5 additions & 2 deletions monai/transforms/post/dictionary.py
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Expand Up @@ -39,6 +39,7 @@
from monai.transforms.utility.array import ToTensor
from monai.transforms.utils import allow_missing_keys_mode, convert_inverse_interp_mode
from monai.utils import deprecated_arg, ensure_tuple, ensure_tuple_rep
from monai.utils.enums import PostFix

__all__ = [
"ActivationsD",
Expand Down Expand Up @@ -77,6 +78,8 @@
"VoteEnsembled",
]

DEFAULT_POST_FIX = PostFix.meta()


class Activationsd(MapTransform):
"""
Expand Down Expand Up @@ -544,7 +547,7 @@ def __init__(
orig_keys: KeysCollection,
meta_keys: Optional[KeysCollection] = None,
orig_meta_keys: Optional[KeysCollection] = None,
meta_key_postfix: str = "meta_dict",
meta_key_postfix: str = DEFAULT_POST_FIX,
nearest_interp: Union[bool, Sequence[bool]] = True,
to_tensor: Union[bool, Sequence[bool]] = True,
device: Union[Union[str, torch.device], Sequence[Union[str, torch.device]]] = "cpu",
Expand Down Expand Up @@ -669,7 +672,7 @@ def __init__(
self,
keys: KeysCollection,
meta_keys: Optional[KeysCollection] = None,
meta_key_postfix: str = "meta_dict",
meta_key_postfix: str = DEFAULT_POST_FIX,
saver: Optional[CSVSaver] = None,
output_dir: PathLike = "./",
filename: str = "predictions.csv",
Expand Down
7 changes: 4 additions & 3 deletions monai/transforms/spatial/dictionary.py
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Expand Up @@ -61,7 +61,7 @@
fall_back_tuple,
)
from monai.utils.deprecate_utils import deprecated_arg
from monai.utils.enums import TraceKeys
from monai.utils.enums import PostFix, TraceKeys
from monai.utils.module import optional_import
from monai.utils.type_conversion import convert_data_type, convert_to_dst_type

Expand Down Expand Up @@ -128,6 +128,7 @@
GridSamplePadModeSequence = Union[Sequence[Union[GridSamplePadMode, str]], GridSamplePadMode, str]
InterpolateModeSequence = Union[Sequence[Union[InterpolateMode, str]], InterpolateMode, str]
PadModeSequence = Union[Sequence[Union[NumpyPadMode, PytorchPadMode, str]], NumpyPadMode, PytorchPadMode, str]
DEFAULT_POST_FIX = PostFix.meta()


class Spacingd(MapTransform, InvertibleTransform):
Expand Down Expand Up @@ -156,7 +157,7 @@ def __init__(
align_corners: Union[Sequence[bool], bool] = False,
dtype: Optional[Union[Sequence[DtypeLike], DtypeLike]] = np.float64,
meta_keys: Optional[KeysCollection] = None,
meta_key_postfix: str = "meta_dict",
meta_key_postfix: str = DEFAULT_POST_FIX,
allow_missing_keys: bool = False,
) -> None:
"""
Expand Down Expand Up @@ -315,7 +316,7 @@ def __init__(
as_closest_canonical: bool = False,
labels: Optional[Sequence[Tuple[str, str]]] = tuple(zip("LPI", "RAS")),
meta_keys: Optional[KeysCollection] = None,
meta_key_postfix: str = "meta_dict",
meta_key_postfix: str = DEFAULT_POST_FIX,
allow_missing_keys: bool = False,
) -> None:
"""
Expand Down
8 changes: 5 additions & 3 deletions monai/transforms/utility/dictionary.py
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Expand Up @@ -63,7 +63,7 @@
from monai.transforms.utils import extreme_points_to_image, get_extreme_points
from monai.transforms.utils_pytorch_numpy_unification import concatenate
from monai.utils import convert_to_numpy, deprecated_arg, ensure_tuple, ensure_tuple_rep
from monai.utils.enums import TraceKeys, TransformBackends
from monai.utils.enums import PostFix, TraceKeys, TransformBackends
from monai.utils.type_conversion import convert_to_dst_type

__all__ = [
Expand Down Expand Up @@ -180,6 +180,8 @@
"ClassesToIndicesDict",
]

DEFAULT_POST_FIX = PostFix.meta()


class Identityd(MapTransform):
"""
Expand Down Expand Up @@ -291,7 +293,7 @@ def __init__(
self,
keys: KeysCollection,
meta_keys: Optional[KeysCollection] = None,
meta_key_postfix: str = "meta_dict",
meta_key_postfix: str = DEFAULT_POST_FIX,
strict_check: bool = True,
) -> None:
"""
Expand Down Expand Up @@ -1464,7 +1466,7 @@ def __init__(
mask_keys: Optional[KeysCollection] = None,
channel_wise: bool = False,
meta_keys: Optional[KeysCollection] = None,
meta_key_postfix: str = "meta_dict",
meta_key_postfix: str = DEFAULT_POST_FIX,
allow_missing_keys: bool = False,
) -> None:
super().__init__(keys, allow_missing_keys)
Expand Down
1 change: 1 addition & 0 deletions monai/utils/__init__.py
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Expand Up @@ -29,6 +29,7 @@
Method,
MetricReduction,
NumpyPadMode,
PostFix,
PytorchPadMode,
SkipMode,
TraceKeys,
Expand Down
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