Source code for monai.transforms.io.array

# 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.
"""
A collection of "vanilla" transforms for IO functions
https://github.com/Project-MONAI/MONAI/wiki/MONAI_Design
"""

import inspect
import logging
import sys
import traceback
import warnings
from pathlib import Path
from pydoc import locate
from typing import Dict, List, Optional, Sequence, Type, Union

import numpy as np
import torch

from monai.config import DtypeLike, NdarrayOrTensor, PathLike
from monai.data import image_writer
from monai.data.folder_layout import FolderLayout, default_name_formatter
from monai.data.image_reader import (
    ImageReader,
    ITKReader,
    NibabelReader,
    NrrdReader,
    NumpyReader,
    PILReader,
    PydicomReader,
)
from monai.data.meta_tensor import MetaTensor
from monai.transforms.transform import Transform
from monai.transforms.utility.array import EnsureChannelFirst
from monai.utils import GridSamplePadMode
from monai.utils import ImageMetaKey as Key
from monai.utils import OptionalImportError, convert_to_dst_type, ensure_tuple, look_up_option, optional_import

nib, _ = optional_import("nibabel")
Image, _ = optional_import("PIL.Image")
nrrd, _ = optional_import("nrrd")

__all__ = ["LoadImage", "SaveImage", "SUPPORTED_READERS"]

SUPPORTED_READERS = {
    "pydicomreader": PydicomReader,
    "itkreader": ITKReader,
    "nrrdreader": NrrdReader,
    "numpyreader": NumpyReader,
    "pilreader": PILReader,
    "nibabelreader": NibabelReader,
}


def switch_endianness(data, new="<"):
    """
    Convert the input `data` endianness to `new`.

    Args:
        data: input to be converted.
        new: the target endianness, currently support "<" or ">".
    """
    if isinstance(data, np.ndarray):
        # default to system endian
        sys_native = "<" if (sys.byteorder == "little") else ">"
        current_ = sys_native if data.dtype.byteorder not in ("<", ">") else data.dtype.byteorder
        if new not in ("<", ">"):
            raise NotImplementedError(f"Not implemented option new={new}.")
        if current_ != new:
            data = data.byteswap().newbyteorder(new)
    elif isinstance(data, tuple):
        data = tuple(switch_endianness(x, new) for x in data)
    elif isinstance(data, list):
        data = [switch_endianness(x, new) for x in data]
    elif isinstance(data, dict):
        data = {k: switch_endianness(v, new) for k, v in data.items()}
    elif not isinstance(data, (bool, str, float, int, type(None))):
        raise RuntimeError(f"Unknown type: {type(data).__name__}")
    return data


[docs]class LoadImage(Transform): """ Load image file or files from provided path based on reader. If reader is not specified, this class automatically chooses readers based on the supported suffixes and in the following order: - User-specified reader at runtime when calling this loader. - User-specified reader in the constructor of `LoadImage`. - Readers from the last to the first in the registered list. - Current default readers: (nii, nii.gz -> NibabelReader), (png, jpg, bmp -> PILReader), (npz, npy -> NumpyReader), (nrrd -> NrrdReader), (DICOM file -> ITKReader). Please note that for png, jpg, bmp, and other 2D formats, readers often swap axis 0 and 1 after loading the array because the `HW` definition for non-medical specific file formats is different from other common medical packages. See also: - tutorial: https://github.com/Project-MONAI/tutorials/blob/master/modules/load_medical_images.ipynb """
[docs] def __init__( self, reader=None, image_only: bool = False, dtype: Optional[DtypeLike] = np.float32, ensure_channel_first: bool = False, simple_keys: bool = False, prune_meta_pattern: Optional[str] = None, prune_meta_sep: str = ".", *args, **kwargs, ) -> None: """ Args: reader: reader to load image file and metadata - if `reader` is None, a default set of `SUPPORTED_READERS` will be used. - if `reader` is a string, it's treated as a class name or dotted path (such as ``"monai.data.ITKReader"``), the supported built-in reader classes are ``"ITKReader"``, ``"NibabelReader"``, ``"NumpyReader"``, ``"PydicomReader"``. a reader instance will be constructed with the `*args` and `**kwargs` parameters. - if `reader` is a reader class/instance, it will be registered to this loader accordingly. image_only: if True return only the image MetaTensor, otherwise return image and header dict. dtype: if not None convert the loaded image to this data type. ensure_channel_first: if `True` and loaded both image array and metadata, automatically convert the image array shape to `channel first`. default to `False`. simple_keys: whether to remove redundant metadata keys, default to False for backward compatibility. prune_meta_pattern: combined with `prune_meta_sep`, a regular expression used to match and prune keys in the metadata (nested dictionary), default to None, no key deletion. prune_meta_sep: combined with `prune_meta_pattern`, used to match and prune keys in the metadata (nested dictionary). default is ".", see also :py:class:`monai.transforms.DeleteItemsd`. e.g. ``prune_meta_pattern=".*_code$", prune_meta_sep=" "`` removes meta keys that ends with ``"_code"``. args: additional parameters for reader if providing a reader name. kwargs: additional parameters for reader if providing a reader name. Note: - The transform returns a MetaTensor, unless `set_track_meta(False)` has been used, in which case, a `torch.Tensor` will be returned. - If `reader` is specified, the loader will attempt to use the specified readers and the default supported readers. This might introduce overheads when handling the exceptions of trying the incompatible loaders. In this case, it is therefore recommended setting the most appropriate reader as the last item of the `reader` parameter. """ self.auto_select = reader is None self.image_only = image_only self.dtype = dtype self.ensure_channel_first = ensure_channel_first self.simple_keys = simple_keys self.pattern = prune_meta_pattern self.sep = prune_meta_sep self.readers: List[ImageReader] = [] for r in SUPPORTED_READERS: # set predefined readers as default try: self.register(SUPPORTED_READERS[r](*args, **kwargs)) except OptionalImportError: logging.getLogger(self.__class__.__name__).debug( f"required package for reader {r} is not installed, or the version doesn't match requirement." ) except TypeError: # the reader doesn't have the corresponding args/kwargs logging.getLogger(self.__class__.__name__).debug( f"{r} is not supported with the given parameters {args} {kwargs}." ) self.register(SUPPORTED_READERS[r]()) if reader is None: return # no user-specified reader, no need to register for _r in ensure_tuple(reader): if isinstance(_r, str): the_reader, has_built_in = optional_import("monai.data", name=f"{_r}") # search built-in if not has_built_in: the_reader = locate(f"{_r}") # search dotted path if the_reader is None: the_reader = look_up_option(_r.lower(), SUPPORTED_READERS) try: self.register(the_reader(*args, **kwargs)) except OptionalImportError: warnings.warn( f"required package for reader {_r} is not installed, or the version doesn't match requirement." ) except TypeError: # the reader doesn't have the corresponding args/kwargs warnings.warn(f"{_r} is not supported with the given parameters {args} {kwargs}.") self.register(the_reader()) elif inspect.isclass(_r): self.register(_r(*args, **kwargs)) else: self.register(_r) # reader instance, ignoring the constructor args/kwargs return
[docs] def register(self, reader: ImageReader): """ Register image reader to load image file and metadata. Args: reader: reader instance to be registered with this loader. """ if not isinstance(reader, ImageReader): warnings.warn(f"Preferably the reader should inherit ImageReader, but got {type(reader)}.") self.readers.append(reader)
[docs] def __call__(self, filename: Union[Sequence[PathLike], PathLike], reader: Optional[ImageReader] = None): """ Load image file and metadata from the given filename(s). If `reader` is not specified, this class automatically chooses readers based on the reversed order of registered readers `self.readers`. Args: filename: path file or file-like object or a list of files. will save the filename to meta_data with key `filename_or_obj`. if provided a list of files, use the filename of first file to save, and will stack them together as multi-channels data. if provided directory path instead of file path, will treat it as DICOM images series and read. reader: runtime reader to load image file and metadata. """ filename = tuple(f"{Path(s).expanduser()}" for s in ensure_tuple(filename)) # allow Path objects img, err = None, [] if reader is not None: img = reader.read(filename) # runtime specified reader else: for reader in self.readers[::-1]: if self.auto_select: # rely on the filename extension to choose the reader if reader.verify_suffix(filename): img = reader.read(filename) break else: # try the user designated readers try: img = reader.read(filename) except Exception as e: err.append(traceback.format_exc()) logging.getLogger(self.__class__.__name__).debug(e, exc_info=True) logging.getLogger(self.__class__.__name__).info( f"{reader.__class__.__name__}: unable to load {filename}.\n" ) else: err = [] break if img is None or reader is None: if isinstance(filename, tuple) and len(filename) == 1: filename = filename[0] msg = "\n".join([f"{e}" for e in err]) raise RuntimeError( f"{self.__class__.__name__} cannot find a suitable reader for file: {filename}.\n" " Please install the reader libraries, see also the installation instructions:\n" " https://docs.monai.io/en/latest/installation.html#installing-the-recommended-dependencies.\n" f" The current registered: {self.readers}.\n{msg}" ) img_array: NdarrayOrTensor img_array, meta_data = reader.get_data(img) img_array = convert_to_dst_type(img_array, dst=img_array, dtype=self.dtype)[0] if not isinstance(meta_data, dict): raise ValueError("`meta_data` must be a dict.") # make sure all elements in metadata are little endian meta_data = switch_endianness(meta_data, "<") meta_data[Key.FILENAME_OR_OBJ] = f"{ensure_tuple(filename)[0]}" # Path obj should be strings for data loader img = MetaTensor.ensure_torch_and_prune_meta( img_array, meta_data, self.simple_keys, pattern=self.pattern, sep=self.sep ) if self.ensure_channel_first: img = EnsureChannelFirst()(img) if self.image_only: return img return img, img.meta if isinstance(img, MetaTensor) else meta_data
[docs]class SaveImage(Transform): """ Save the image (in the form of torch tensor or numpy ndarray) and metadata dictionary into files. The name of saved file will be `{input_image_name}_{output_postfix}{output_ext}`, where the `input_image_name` is extracted from the provided metadata dictionary. If no metadata provided, a running index starting from 0 will be used as the filename prefix. Args: output_dir: output image directory. output_postfix: a string appended to all output file names, default to `trans`. output_ext: output file extension name. output_dtype: data type (if not None) for saving data. Defaults to ``np.float32``. resample: whether to resample image (if needed) before saving the data array, based on the `spatial_shape` (and `original_affine`) from metadata. mode: This option is used when ``resample=True``. Defaults to ``"nearest"``. Depending on the writers, the possible options are - {``"bilinear"``, ``"nearest"``, ``"bicubic"``}. See also: https://pytorch.org/docs/stable/nn.functional.html#grid-sample - {``"nearest"``, ``"linear"``, ``"bilinear"``, ``"bicubic"``, ``"trilinear"``, ``"area"``}. See also: https://pytorch.org/docs/stable/nn.functional.html#interpolate padding_mode: This option is used when ``resample = True``. Defaults to ``"border"``. Possible options are {``"zeros"``, ``"border"``, ``"reflection"``} See also: https://pytorch.org/docs/stable/nn.functional.html#grid-sample scale: {``255``, ``65535``} postprocess data by clipping to [0, 1] and scaling [0, 255] (uint8) or [0, 65535] (uint16). Default is `None` (no scaling). dtype: data type during resampling computation. Defaults to ``np.float64`` for best precision. if None, use the data type of input data. To set the output data type, use `output_dtype`. squeeze_end_dims: if True, any trailing singleton dimensions will be removed (after the channel has been moved to the end). So if input is (C,H,W,D), this will be altered to (H,W,D,C), and then if C==1, it will be saved as (H,W,D). If D is also 1, it will be saved as (H,W). If `false`, image will always be saved as (H,W,D,C). data_root_dir: if not empty, it specifies the beginning parts of the input file's absolute path. It's used to compute `input_file_rel_path`, the relative path to the file from `data_root_dir` to preserve folder structure when saving in case there are files in different folders with the same file names. For example, with the following inputs: - input_file_name: `/foo/bar/test1/image.nii` - output_postfix: `seg` - output_ext: `.nii.gz` - output_dir: `/output` - data_root_dir: `/foo/bar` The output will be: /output/test1/image/image_seg.nii.gz separate_folder: whether to save every file in a separate folder. For example: for the input filename `image.nii`, postfix `seg` and folder_path `output`, if `separate_folder=True`, it will be saved as: `output/image/image_seg.nii`, if `False`, saving as `output/image_seg.nii`. Default to `True`. print_log: whether to print logs when saving. Default to `True`. output_format: an optional string of filename extension to specify the output image writer. see also: `monai.data.image_writer.SUPPORTED_WRITERS`. writer: a customised `monai.data.ImageWriter` subclass to save data arrays. if `None`, use the default writer from `monai.data.image_writer` according to `output_ext`. if it's a string, it's treated as a class name or dotted path (such as ``"monai.data.ITKWriter"``); the supported built-in writer classes are ``"NibabelWriter"``, ``"ITKWriter"``, ``"PILWriter"``. channel_dim: the index of the channel dimension. Default to `0`. `None` to indicate no channel dimension. output_name_formatter: a callable function (returning a kwargs dict) to format the output file name. see also: :py:func:`monai.data.folder_layout.default_name_formatter`. """ def __init__( self, output_dir: PathLike = "./", output_postfix: str = "trans", output_ext: str = ".nii.gz", output_dtype: Optional[DtypeLike] = np.float32, resample: bool = True, mode: str = "nearest", padding_mode: str = GridSamplePadMode.BORDER, scale: Optional[int] = None, dtype: DtypeLike = np.float64, squeeze_end_dims: bool = True, data_root_dir: PathLike = "", separate_folder: bool = True, print_log: bool = True, output_format: str = "", writer: Union[Type[image_writer.ImageWriter], str, None] = None, channel_dim: Optional[int] = 0, output_name_formatter=None, ) -> None: self.folder_layout = FolderLayout( output_dir=output_dir, postfix=output_postfix, extension=output_ext, parent=separate_folder, makedirs=True, data_root_dir=data_root_dir, ) self.output_ext = output_ext.lower() or output_format.lower() if isinstance(writer, str): writer_, has_built_in = optional_import("monai.data", name=f"{writer}") # search built-in if not has_built_in: writer_ = locate(f"{writer}") # search dotted path if writer_ is None: raise ValueError(f"writer {writer} not found") writer = writer_ self.writers = image_writer.resolve_writer(self.output_ext) if writer is None else (writer,) self.writer_obj = None _output_dtype = output_dtype if self.output_ext == ".png" and _output_dtype not in (np.uint8, np.uint16, None): _output_dtype = np.uint8 if self.output_ext == ".dcm" and _output_dtype not in (np.uint8, np.uint16, None): _output_dtype = np.uint8 self.init_kwargs = {"output_dtype": _output_dtype, "scale": scale} self.data_kwargs = {"squeeze_end_dims": squeeze_end_dims, "channel_dim": channel_dim} self.meta_kwargs = {"resample": resample, "mode": mode, "padding_mode": padding_mode, "dtype": dtype} self.write_kwargs = {"verbose": print_log} self.fname_formatter = default_name_formatter if output_name_formatter is None else output_name_formatter self._data_index = 0
[docs] def set_options(self, init_kwargs=None, data_kwargs=None, meta_kwargs=None, write_kwargs=None): """ Set the options for the underlying writer by updating the `self.*_kwargs` dictionaries. The arguments correspond to the following usage: - `writer = ImageWriter(**init_kwargs)` - `writer.set_data_array(array, **data_kwargs)` - `writer.set_metadata(meta_data, **meta_kwargs)` - `writer.write(filename, **write_kwargs)` """ if init_kwargs is not None: self.init_kwargs.update(init_kwargs) if data_kwargs is not None: self.data_kwargs.update(data_kwargs) if meta_kwargs is not None: self.meta_kwargs.update(meta_kwargs) if write_kwargs is not None: self.write_kwargs.update(write_kwargs)
[docs] def __call__(self, img: Union[torch.Tensor, np.ndarray], meta_data: Optional[Dict] = None): """ Args: img: target data content that save into file. The image should be channel-first, shape: `[C,H,W,[D]]`. meta_data: key-value pairs of metadata corresponding to the data. """ meta_data = img.meta if isinstance(img, MetaTensor) else meta_data kw = self.fname_formatter(meta_data, self) filename = self.folder_layout.filename(**kw) if meta_data and len(ensure_tuple(meta_data.get("spatial_shape", ()))) == len(img.shape): self.data_kwargs["channel_dim"] = None err = [] for writer_cls in self.writers: try: writer_obj = writer_cls(**self.init_kwargs) writer_obj.set_data_array(data_array=img, **self.data_kwargs) writer_obj.set_metadata(meta_dict=meta_data, **self.meta_kwargs) writer_obj.write(filename, **self.write_kwargs) self.writer_obj = writer_obj except Exception as e: err.append(traceback.format_exc()) logging.getLogger(self.__class__.__name__).debug(e, exc_info=True) logging.getLogger(self.__class__.__name__).info( f"{writer_cls.__class__.__name__}: unable to write {filename}.\n" ) else: self._data_index += 1 return img msg = "\n".join([f"{e}" for e in err]) raise RuntimeError( f"{self.__class__.__name__} cannot find a suitable writer for {filename}.\n" " Please install the writer libraries, see also the installation instructions:\n" " https://docs.monai.io/en/latest/installation.html#installing-the-recommended-dependencies.\n" f" The current registered writers for {self.output_ext}: {self.writers}.\n{msg}" )