# Copyright (c) MONAI Consortium
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
from __future__ import annotations
import re
from collections.abc import Sequence
from typing import Any
import numpy as np
import torch
import monai
from monai.config.type_definitions import DtypeLike, NdarrayTensor
from monai.utils import optional_import
cp, has_cp = optional_import("cupy")
cp_ndarray, _ = optional_import("cupy", name="ndarray")
__all__ = [
"get_numpy_dtype_from_string",
"get_torch_dtype_from_string",
"dtype_torch_to_numpy",
"dtype_numpy_to_torch",
"get_equivalent_dtype",
"convert_data_type",
"get_dtype",
"convert_to_cupy",
"convert_to_numpy",
"convert_to_tensor",
"convert_to_dst_type",
]
# conversion map for types unsupported by torch.as_tensor
UNSUPPORTED_TYPES = {np.dtype("uint16"): np.int32, np.dtype("uint32"): np.int64, np.dtype("uint64"): np.int64}
[docs]
def get_numpy_dtype_from_string(dtype: str) -> np.dtype:
"""Get a numpy dtype (e.g., `np.float32`) from its string (e.g., `"float32"`)."""
return np.empty([], dtype=str(dtype).split(".")[-1]).dtype
[docs]
def get_torch_dtype_from_string(dtype: str) -> torch.dtype:
"""Get a torch dtype (e.g., `torch.float32`) from its string (e.g., `"float32"`)."""
return dtype_numpy_to_torch(get_numpy_dtype_from_string(dtype))
[docs]
def dtype_torch_to_numpy(dtype: torch.dtype) -> np.dtype:
"""Convert a torch dtype to its numpy equivalent."""
return torch.empty([], dtype=dtype).numpy().dtype # type: ignore
[docs]
def dtype_numpy_to_torch(dtype: np.dtype) -> torch.dtype:
"""Convert a numpy dtype to its torch equivalent."""
return torch.from_numpy(np.empty([], dtype=dtype)).dtype
[docs]
def get_equivalent_dtype(dtype, data_type):
"""Convert to the `dtype` that corresponds to `data_type`.
The input dtype can also be a string. e.g., `"float32"` becomes `torch.float32` or
`np.float32` as necessary.
Example::
im = torch.tensor(1)
dtype = get_equivalent_dtype(np.float32, type(im))
"""
if dtype is None:
return None
if data_type is torch.Tensor or data_type.__name__ == "MetaTensor":
if isinstance(dtype, torch.dtype):
# already a torch dtype and target `data_type` is torch.Tensor
return dtype
return dtype_numpy_to_torch(dtype)
if not isinstance(dtype, torch.dtype):
# assuming the dtype is ok if it is not a torch dtype and target `data_type` is not torch.Tensor
return dtype
return dtype_torch_to_numpy(dtype)
[docs]
def get_dtype(data: Any) -> DtypeLike | torch.dtype:
"""Get the dtype of an image, or if there is a sequence, recursively call the method on the 0th element.
This therefore assumes that in a `Sequence`, all types are the same.
"""
if hasattr(data, "dtype"):
return data.dtype # type: ignore
# need recursion
if isinstance(data, Sequence):
return get_dtype(data[0])
# objects like float don't have dtype, so return their type
return type(data)
[docs]
def convert_to_tensor(
data: Any,
dtype: DtypeLike | torch.dtype = None,
device: None | str | torch.device = None,
wrap_sequence: bool = False,
track_meta: bool = False,
safe: bool = False,
) -> Any:
"""
Utility to convert the input data to a PyTorch Tensor, if `track_meta` is True, the output will be a `MetaTensor`,
otherwise, the output will be a regular torch Tensor.
If passing a dictionary, list or tuple, recursively check every item and convert it to PyTorch Tensor.
Args:
data: input data can be PyTorch Tensor, numpy array, list, dictionary, int, float, bool, str, etc.
will convert Tensor, Numpy array, float, int, bool to Tensor, strings and objects keep the original.
for dictionary, list or tuple, convert every item to a Tensor if applicable.
dtype: target data type to when converting to Tensor.
device: target device to put the converted Tensor data.
wrap_sequence: if `False`, then lists will recursively call this function.
E.g., `[1, 2]` -> `[tensor(1), tensor(2)]`. If `True`, then `[1, 2]` -> `tensor([1, 2])`.
track_meta: whether to track the meta information, if `True`, will convert to `MetaTensor`.
default to `False`.
safe: if `True`, then do safe dtype convert when intensity overflow. default to `False`.
E.g., `[256, -12]` -> `[tensor(0), tensor(244)]`.
If `True`, then `[256, -12]` -> `[tensor(255), tensor(0)]`.
"""
def _convert_tensor(tensor: Any, **kwargs: Any) -> Any:
if not isinstance(tensor, torch.Tensor):
# certain numpy types are not supported as being directly convertible to Pytorch tensors
if isinstance(tensor, np.ndarray) and tensor.dtype in UNSUPPORTED_TYPES:
tensor = tensor.astype(UNSUPPORTED_TYPES[tensor.dtype])
# if input data is not Tensor, convert it to Tensor first
tensor = torch.as_tensor(tensor, **kwargs)
if track_meta and not isinstance(tensor, monai.data.MetaTensor):
return monai.data.MetaTensor(tensor)
if not track_meta and isinstance(tensor, monai.data.MetaTensor):
return tensor.as_tensor()
return tensor
if safe:
data = safe_dtype_range(data, dtype)
dtype = get_equivalent_dtype(dtype, torch.Tensor)
if isinstance(data, torch.Tensor):
return _convert_tensor(data).to(dtype=dtype, device=device, memory_format=torch.contiguous_format)
if isinstance(data, np.ndarray):
# skip array of string classes and object, refer to:
# https://github.com/pytorch/pytorch/blob/v1.9.0/torch/utils/data/_utils/collate.py#L13
if re.search(r"[SaUO]", data.dtype.str) is None:
# numpy array with 0 dims is also sequence iterable,
# `ascontiguousarray` will add 1 dim if img has no dim, so we only apply on data with dims
if data.ndim > 0:
data = np.ascontiguousarray(data)
return _convert_tensor(data, dtype=dtype, device=device)
elif (has_cp and isinstance(data, cp_ndarray)) or isinstance(data, (float, int, bool)):
return _convert_tensor(data, dtype=dtype, device=device)
elif isinstance(data, list):
list_ret = [convert_to_tensor(i, dtype=dtype, device=device, track_meta=track_meta) for i in data]
return _convert_tensor(list_ret, dtype=dtype, device=device) if wrap_sequence else list_ret
elif isinstance(data, tuple):
tuple_ret = tuple(convert_to_tensor(i, dtype=dtype, device=device, track_meta=track_meta) for i in data)
return _convert_tensor(tuple_ret, dtype=dtype, device=device) if wrap_sequence else tuple_ret
elif isinstance(data, dict):
return {k: convert_to_tensor(v, dtype=dtype, device=device, track_meta=track_meta) for k, v in data.items()}
return data
[docs]
def convert_to_numpy(data: Any, dtype: DtypeLike = None, wrap_sequence: bool = False, safe: bool = False) -> Any:
"""
Utility to convert the input data to a numpy array. If passing a dictionary, list or tuple,
recursively check every item and convert it to numpy array.
Args:
data: input data can be PyTorch Tensor, numpy array, list, dictionary, int, float, bool, str, etc.
will convert Tensor, Numpy array, float, int, bool to numpy arrays, strings and objects keep the original.
for dictionary, list or tuple, convert every item to a numpy array if applicable.
dtype: target data type when converting to numpy array.
wrap_sequence: if `False`, then lists will recursively call this function.
E.g., `[1, 2]` -> `[array(1), array(2)]`. If `True`, then `[1, 2]` -> `array([1, 2])`.
safe: if `True`, then do safe dtype convert when intensity overflow. default to `False`.
E.g., `[256, -12]` -> `[array(0), array(244)]`. If `True`, then `[256, -12]` -> `[array(255), array(0)]`.
"""
if safe:
data = safe_dtype_range(data, dtype)
if isinstance(data, torch.Tensor):
data = np.asarray(data.detach().to(device="cpu").numpy(), dtype=get_equivalent_dtype(dtype, np.ndarray))
elif has_cp and isinstance(data, cp_ndarray):
data = cp.asnumpy(data).astype(dtype, copy=False)
elif isinstance(data, (np.ndarray, float, int, bool)):
# Convert into a contiguous array first if the current dtype's size is smaller than the target dtype's size.
# This help improve the performance because (convert to contiguous array) -> (convert dtype) is faster
# than (convert dtype) -> (convert to contiguous array) when src dtype (e.g., uint8) is smaller than
# target dtype(e.g., float32) and we are going to convert it to contiguous array anyway later in this
# method.
if isinstance(data, np.ndarray) and data.ndim > 0 and data.dtype.itemsize < np.dtype(dtype).itemsize:
data = np.ascontiguousarray(data)
data = np.asarray(data, dtype=dtype)
elif isinstance(data, list):
list_ret = [convert_to_numpy(i, dtype=dtype) for i in data]
return np.asarray(list_ret) if wrap_sequence else list_ret
elif isinstance(data, tuple):
tuple_ret = tuple(convert_to_numpy(i, dtype=dtype) for i in data)
return np.asarray(tuple_ret) if wrap_sequence else tuple_ret
elif isinstance(data, dict):
return {k: convert_to_numpy(v, dtype=dtype) for k, v in data.items()}
if isinstance(data, np.ndarray) and data.ndim > 0:
data = np.ascontiguousarray(data)
return data
[docs]
def convert_to_cupy(data: Any, dtype: np.dtype | None = None, wrap_sequence: bool = False, safe: bool = False) -> Any:
"""
Utility to convert the input data to a cupy array. If passing a dictionary, list or tuple,
recursively check every item and convert it to cupy array.
Args:
data: input data can be PyTorch Tensor, numpy array, cupy array, list, dictionary, int, float, bool, str, etc.
Tensor, numpy array, cupy array, float, int, bool are converted to cupy arrays,
for dictionary, list or tuple, convert every item to a numpy array if applicable.
dtype: target data type when converting to Cupy array, tt must be an argument of `numpy.dtype`,
for more details: https://docs.cupy.dev/en/stable/reference/generated/cupy.array.html.
wrap_sequence: if `False`, then lists will recursively call this function.
E.g., `[1, 2]` -> `[array(1), array(2)]`. If `True`, then `[1, 2]` -> `array([1, 2])`.
safe: if `True`, then do safe dtype convert when intensity overflow. default to `False`.
E.g., `[256, -12]` -> `[array(0), array(244)]`. If `True`, then `[256, -12]` -> `[array(255), array(0)]`.
"""
if safe:
data = safe_dtype_range(data, dtype)
# direct calls
if isinstance(data, torch.Tensor) and data.device.type == "cuda":
# This is needed because of https://github.com/cupy/cupy/issues/7874#issuecomment-1727511030
if data.dtype == torch.bool:
data = data.detach().to(torch.uint8)
if dtype is None:
dtype = bool # type: ignore
data = cp.asarray(data, dtype)
elif isinstance(data, (cp_ndarray, np.ndarray, torch.Tensor, float, int, bool)):
data = cp.asarray(data, dtype)
elif isinstance(data, list):
list_ret = [convert_to_cupy(i, dtype) for i in data]
return cp.asarray(list_ret) if wrap_sequence else list_ret
elif isinstance(data, tuple):
tuple_ret = tuple(convert_to_cupy(i, dtype) for i in data)
return cp.asarray(tuple_ret) if wrap_sequence else tuple_ret
elif isinstance(data, dict):
return {k: convert_to_cupy(v, dtype) for k, v in data.items()}
# make it contiguous
if not isinstance(data, cp.ndarray):
raise ValueError(f"The input data type [{type(data)}] cannot be converted into cupy arrays!")
if data.ndim > 0:
data = cp.ascontiguousarray(data)
return data
[docs]
def convert_data_type(
data: Any,
output_type: type[NdarrayTensor] | None = None,
device: None | str | torch.device = None,
dtype: DtypeLike | torch.dtype = None,
wrap_sequence: bool = False,
safe: bool = False,
) -> tuple[NdarrayTensor, type, torch.device | None]:
"""
Convert to `MetaTensor`, `torch.Tensor` or `np.ndarray` from `MetaTensor`, `torch.Tensor`,
`np.ndarray`, `float`, `int`, etc.
Args:
data: data to be converted
output_type: `monai.data.MetaTensor`, `torch.Tensor`, or `np.ndarray` (if `None`, unchanged)
device: if output is `MetaTensor` or `torch.Tensor`, select device (if `None`, unchanged)
dtype: dtype of output data. Converted to correct library type (e.g.,
`np.float32` is converted to `torch.float32` if output type is `torch.Tensor`).
If left blank, it remains unchanged.
wrap_sequence: if `False`, then lists will recursively call this function.
E.g., `[1, 2]` -> `[array(1), array(2)]`. If `True`, then `[1, 2]` -> `array([1, 2])`.
safe: if `True`, then do safe dtype convert when intensity overflow. default to `False`.
E.g., `[256, -12]` -> `[array(0), array(244)]`. If `True`, then `[256, -12]` -> `[array(255), array(0)]`.
Returns:
modified data, orig_type, orig_device
Note:
When both `output_type` and `dtype` are specified with different backend
(e.g., `torch.Tensor` and `np.float32`), the `output_type` will be used as the primary type,
for example::
>>> convert_data_type(1, torch.Tensor, dtype=np.float32)
(1.0, <class 'torch.Tensor'>, None)
"""
orig_type: type
if isinstance(data, monai.data.MetaTensor):
orig_type = monai.data.MetaTensor
elif isinstance(data, torch.Tensor):
orig_type = torch.Tensor
elif isinstance(data, np.ndarray):
orig_type = np.ndarray
elif has_cp and isinstance(data, cp.ndarray):
orig_type = cp.ndarray
else:
orig_type = type(data)
orig_device = data.device if isinstance(data, torch.Tensor) else None
output_type = output_type or orig_type
dtype_ = get_equivalent_dtype(dtype, output_type)
data_: NdarrayTensor
if issubclass(output_type, torch.Tensor):
track_meta = issubclass(output_type, monai.data.MetaTensor)
data_ = convert_to_tensor(
data, dtype=dtype_, device=device, wrap_sequence=wrap_sequence, track_meta=track_meta, safe=safe
)
return data_, orig_type, orig_device
if issubclass(output_type, np.ndarray):
data_ = convert_to_numpy(data, dtype=dtype_, wrap_sequence=wrap_sequence, safe=safe)
return data_, orig_type, orig_device
elif has_cp and issubclass(output_type, cp.ndarray):
data_ = convert_to_cupy(data, dtype=dtype_, wrap_sequence=wrap_sequence, safe=safe)
return data_, orig_type, orig_device
raise ValueError(f"Unsupported output type: {output_type}")
[docs]
def convert_to_dst_type(
src: Any,
dst: NdarrayTensor,
dtype: DtypeLike | torch.dtype | None = None,
wrap_sequence: bool = False,
device: None | str | torch.device = None,
safe: bool = False,
) -> tuple[NdarrayTensor, type, torch.device | None]:
"""
Convert source data to the same data type and device as the destination data.
If `dst` is an instance of `torch.Tensor` or its subclass, convert `src` to `torch.Tensor` with the same data type as `dst`,
if `dst` is an instance of `numpy.ndarray` or its subclass, convert to `numpy.ndarray` with the same data type as `dst`,
otherwise, convert to the type of `dst` directly.
Args:
src: source data to convert type.
dst: destination data that convert to the same data type as it.
dtype: an optional argument if the target `dtype` is different from the original `dst`'s data type.
wrap_sequence: if `False`, then lists will recursively call this function. E.g., `[1, 2]` -> `[array(1), array(2)]`.
If `True`, then `[1, 2]` -> `array([1, 2])`.
device: target device to put the converted Tensor data. If unspecified, `dst.device` will be used if possible.
safe: if `True`, then do safe dtype convert when intensity overflow. default to `False`.
E.g., `[256, -12]` -> `[array(0), array(244)]`. If `True`, then `[256, -12]` -> `[array(255), array(0)]`.
See Also:
:func:`convert_data_type`
"""
device = dst.device if device is None and isinstance(dst, torch.Tensor) else device
if dtype is None:
dtype = getattr(dst, "dtype", None) # sequence has no dtype
copy_meta = False
output_type: Any
if isinstance(dst, monai.data.MetaTensor):
output_type = monai.data.MetaTensor
if not isinstance(src, monai.data.MetaTensor):
copy_meta = True # converting a non-meta tensor to a meta tensor, probably take the metadata as well.
elif isinstance(dst, torch.Tensor):
output_type = torch.Tensor
elif isinstance(dst, np.ndarray):
output_type = np.ndarray
else:
output_type = type(dst)
output: NdarrayTensor
output, _type, _device = convert_data_type(
data=src, output_type=output_type, device=device, dtype=dtype, wrap_sequence=wrap_sequence, safe=safe
)
if copy_meta and isinstance(output, monai.data.MetaTensor):
output.copy_meta_from(dst)
return output, _type, _device
def convert_to_list(data: Sequence | torch.Tensor | np.ndarray) -> list:
"""
Convert to list from `torch.Tensor`/`np.ndarray`/`list`/`tuple` etc.
Args:
data: data to be converted
Returns:
a list
"""
return data.tolist() if isinstance(data, (torch.Tensor, np.ndarray)) else list(data)
def get_dtype_bound_value(dtype: DtypeLike | torch.dtype) -> tuple[float, float]:
"""
Get dtype bound value
Args:
dtype: dtype to get bound value
Returns:
(bound_min_value, bound_max_value)
"""
if dtype in UNSUPPORTED_TYPES:
is_floating_point = False
else:
is_floating_point = get_equivalent_dtype(dtype, torch.Tensor).is_floating_point
dtype = get_equivalent_dtype(dtype, np.array)
if is_floating_point:
return (np.finfo(dtype).min, np.finfo(dtype).max) # type: ignore
else:
return (np.iinfo(dtype).min, np.iinfo(dtype).max)
def safe_dtype_range(data: Any, dtype: DtypeLike | torch.dtype = None) -> Any:
"""
Utility to safely convert the input data to target dtype.
Args:
data: input data can be PyTorch Tensor, numpy array, list, dictionary, int, float, bool, str, etc.
will convert to target dtype and keep the original type.
for dictionary, list or tuple, convert every item.
dtype: target data type to convert.
"""
def _safe_dtype_range(data, dtype):
output_dtype = dtype if dtype is not None else data.dtype
dtype_bound_value = get_dtype_bound_value(output_dtype)
if data.ndim == 0:
data_bound = (data, data)
else:
if isinstance(data, torch.Tensor):
data_bound = (torch.min(data), torch.max(data))
else:
data_bound = (np.min(data), np.max(data))
if (data_bound[1] > dtype_bound_value[1]) or (data_bound[0] < dtype_bound_value[0]):
if isinstance(data, torch.Tensor):
return torch.clamp(data, dtype_bound_value[0], dtype_bound_value[1])
elif isinstance(data, np.ndarray):
return np.clip(data, dtype_bound_value[0], dtype_bound_value[1])
elif has_cp and isinstance(data, cp_ndarray):
return cp.clip(data, dtype_bound_value[0], dtype_bound_value[1])
else:
return data
if has_cp and isinstance(data, cp_ndarray):
return cp.asarray(_safe_dtype_range(data, dtype))
elif isinstance(data, np.ndarray):
return np.asarray(_safe_dtype_range(data, dtype))
elif isinstance(data, torch.Tensor):
return _safe_dtype_range(data, dtype)
elif isinstance(data, (float, int, bool)) and dtype is None:
return data
elif isinstance(data, (float, int, bool)) and dtype is not None:
output_dtype = dtype
dtype_bound_value = get_dtype_bound_value(output_dtype)
data = dtype_bound_value[1] if data > dtype_bound_value[1] else data
data = dtype_bound_value[0] if data < dtype_bound_value[0] else data
return data
elif isinstance(data, list):
return [safe_dtype_range(i, dtype=dtype) for i in data]
elif isinstance(data, tuple):
return tuple(safe_dtype_range(i, dtype=dtype) for i in data)
elif isinstance(data, dict):
return {k: safe_dtype_range(v, dtype=dtype) for k, v in data.items()}
return data
