Source code for monai.data.image_reader

# Copyright 2020 - 2021 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.

import os
from abc import ABC, abstractmethod
from typing import TYPE_CHECKING, Any, Callable, Dict, List, Optional, Sequence, Tuple, Union

import numpy as np
from torch.utils.data._utils.collate import np_str_obj_array_pattern

from monai.config import KeysCollection
from monai.data.utils import correct_nifti_header_if_necessary
from monai.utils import ensure_tuple, optional_import

from .utils import is_supported_format

if TYPE_CHECKING:
    import itk  # type: ignore
    import nibabel as nib
    from itk import Image  # type: ignore
    from nibabel.nifti1 import Nifti1Image
    from PIL import Image as PILImage

    has_itk = has_nib = has_pil = True
else:
    itk, has_itk = optional_import("itk", allow_namespace_pkg=True)
    Image, _ = optional_import("itk", allow_namespace_pkg=True, name="Image")
    nib, has_nib = optional_import("nibabel")
    Nifti1Image, _ = optional_import("nibabel.nifti1", name="Nifti1Image")
    PILImage, has_pil = optional_import("PIL.Image")

__all__ = ["ImageReader", "ITKReader", "NibabelReader", "NumpyReader", "PILReader"]


class ImageReader(ABC):
    """Abstract class to define interface APIs to load image files.
    users need to call `read` to load image and then use `get_data`
    to get the image data and properties from meta data.

    """

    @abstractmethod
    def verify_suffix(self, filename: Union[Sequence[str], str]) -> bool:
        """
        Verify whether the specified file or files format is supported by current reader.

        Args:
            filename: file name or a list of file names to read.
                if a list of files, verify all the suffixes.

        """
        raise NotImplementedError(f"Subclass {self.__class__.__name__} must implement this method.")

    @abstractmethod
    def read(self, data: Union[Sequence[str], str], **kwargs) -> Union[Sequence[Any], Any]:
        """
        Read image data from specified file or files.
        Note that it returns the raw data, so different readers return different image data type.

        Args:
            data: file name or a list of file names to read.
            kwargs: additional args for actual `read` API of 3rd party libs.

        """
        raise NotImplementedError(f"Subclass {self.__class__.__name__} must implement this method.")

    @abstractmethod
    def get_data(self, img) -> Tuple[np.ndarray, Dict]:
        """
        Extract data array and meta data from loaded image and return them.
        This function must return 2 objects, first is numpy array of image data, second is dict of meta data.

        Args:
            img: an image object loaded from a image file or a list of image objects.

        """
        raise NotImplementedError(f"Subclass {self.__class__.__name__} must implement this method.")


def _copy_compatible_dict(from_dict: Dict, to_dict: Dict):
    if not isinstance(to_dict, dict):
        raise ValueError(f"to_dict must be a Dict, got {type(to_dict)}.")
    if not to_dict:
        for key in from_dict:
            datum = from_dict[key]
            if isinstance(datum, np.ndarray) and np_str_obj_array_pattern.search(datum.dtype.str) is not None:
                continue
            to_dict[key] = datum
    else:
        affine_key, shape_key = "affine", "spatial_shape"
        if affine_key in from_dict and not np.allclose(from_dict[affine_key], to_dict[affine_key]):
            raise RuntimeError(
                "affine matrix of all images should be the same for channel-wise concatenation. "
                f"Got {from_dict[affine_key]} and {to_dict[affine_key]}."
            )
        if shape_key in from_dict and not np.allclose(from_dict[shape_key], to_dict[shape_key]):
            raise RuntimeError(
                "spatial_shape of all images should be the same for channel-wise concatenation. "
                f"Got {from_dict[shape_key]} and {to_dict[shape_key]}."
            )


[docs]class ITKReader(ImageReader): """ Load medical images based on ITK library. All the supported image formats can be found: https://github.com/InsightSoftwareConsortium/ITK/tree/master/Modules/IO The loaded data array will be in C order, for example, a 3D image NumPy array index order will be `CDWH`. Args: kwargs: additional args for `itk.imread` API. more details about available args: https://github.com/InsightSoftwareConsortium/ITK/blob/master/Wrapping/Generators/Python/itkExtras.py """ def __init__(self, **kwargs): super().__init__() self.kwargs = kwargs if has_itk and int(itk.Version.GetITKMajorVersion()) == 5 and int(itk.Version.GetITKMinorVersion()) < 2: # warning the ITK LazyLoading mechanism was not threadsafe until version 5.2.0, # requesting access to the itk.imread function triggers the lazy loading of the relevant itk modules # before the parallel use of the function. _ = itk.imread
[docs] def verify_suffix(self, filename: Union[Sequence[str], str]) -> bool: """ Verify whether the specified file or files format is supported by ITK reader. Args: filename: file name or a list of file names to read. if a list of files, verify all the suffixes. """ return has_itk
[docs] def read(self, data: Union[Sequence[str], str], **kwargs): """ Read image data from specified file or files. Note that the returned object is ITK image object or list of ITK image objects. Args: data: file name or a list of file names to read, kwargs: additional args for `itk.imread` API, will override `self.kwargs` for existing keys. More details about available args: https://github.com/InsightSoftwareConsortium/ITK/blob/master/Wrapping/Generators/Python/itkExtras.py """ img_: List[Image] = [] filenames: Sequence[str] = ensure_tuple(data) kwargs_ = self.kwargs.copy() kwargs_.update(kwargs) for name in filenames: if os.path.isdir(name): # read DICOM series of 1 image in a folder, refer to: https://github.com/RSIP-Vision/medio names_generator = itk.GDCMSeriesFileNames.New() names_generator.SetUseSeriesDetails(True) names_generator.AddSeriesRestriction("0008|0021") # Series Date names_generator.SetDirectory(name) series_uid = names_generator.GetSeriesUIDs() if len(series_uid) == 0: raise FileNotFoundError(f"no DICOMs in: {name}.") if len(series_uid) > 1: raise OSError(f"the directory: {name} contains more than one DICOM series.") series_identifier = series_uid[0] name = names_generator.GetFileNames(series_identifier) img_.append(itk.imread(name, **kwargs_)) return img_ if len(filenames) > 1 else img_[0]
[docs] def get_data(self, img): """ Extract data array and meta data from loaded image and return them. This function returns 2 objects, first is numpy array of image data, second is dict of meta data. It constructs `affine`, `original_affine`, and `spatial_shape` and stores in meta dict. If loading a list of files, stack them together and add a new dimension as first dimension, and use the meta data of the first image to represent the stacked result. Args: img: a ITK image object loaded from a image file or a list of ITK image objects. """ img_array: List[np.ndarray] = [] compatible_meta: Dict = {} for i in ensure_tuple(img): header = self._get_meta_dict(i) header["original_affine"] = self._get_affine(i) header["affine"] = header["original_affine"].copy() header["spatial_shape"] = self._get_spatial_shape(i) img_array.append(self._get_array_data(i)) _copy_compatible_dict(header, compatible_meta) img_array_ = np.stack(img_array, axis=0) if len(img_array) > 1 else img_array[0] return img_array_, compatible_meta
def _get_meta_dict(self, img) -> Dict: """ Get all the meta data of the image and convert to dict type. Args: img: a ITK image object loaded from a image file. """ img_meta_dict = img.GetMetaDataDictionary() meta_dict = {} for key in img_meta_dict.GetKeys(): # ignore deprecated, legacy members that cause issues if key.startswith("ITK_original_"): continue meta_dict[key] = img_meta_dict[key] meta_dict["origin"] = np.asarray(img.GetOrigin()) meta_dict["spacing"] = np.asarray(img.GetSpacing()) meta_dict["direction"] = itk.array_from_matrix(img.GetDirection()) return meta_dict def _get_affine(self, img) -> np.ndarray: """ Get or construct the affine matrix of the image, it can be used to correct spacing, orientation or execute spatial transforms. Construct Affine matrix based on direction, spacing, origin information. Refer to: https://github.com/RSIP-Vision/medio Args: img: a ITK image object loaded from a image file. """ direction = itk.array_from_matrix(img.GetDirection()) spacing = np.asarray(img.GetSpacing()) origin = np.asarray(img.GetOrigin()) direction = np.asarray(direction) affine = np.eye(direction.shape[0] + 1) affine[(slice(-1), slice(-1))] = direction @ np.diag(spacing) affine[(slice(-1), -1)] = origin return affine def _get_spatial_shape(self, img) -> np.ndarray: """ Get the spatial shape of image data, it doesn't contain the channel dim. Args: img: a ITK image object loaded from a image file. """ shape = list(itk.size(img)) shape.reverse() return np.asarray(shape) def _get_array_data(self, img) -> np.ndarray: """ Get the raw array data of the image, converted to Numpy array. Following PyTorch conventions, the returned array data has contiguous channels, e.g. for an RGB image, all red channel image pixels are contiguous in memory. The first axis of the returned array is the channel axis. Args: img: a ITK image object loaded from a image file. """ channels = img.GetNumberOfComponentsPerPixel() if channels == 1: return itk.array_view_from_image(img, keep_axes=False) # The memory layout of itk.Image has all pixel's channels adjacent # in memory, i.e. R1G1B1R2G2B2R3G3B3. For PyTorch/MONAI, we need # channels to be contiguous, i.e. R1R2R3G1G2G3B1B2B3. arr = itk.array_view_from_image(img, keep_axes=False) dest = list(range(img.ndim)) source = dest.copy() end = source.pop() source.insert(0, end) return np.moveaxis(arr, source, dest)
[docs]class NibabelReader(ImageReader): """ Load NIfTI format images based on Nibabel library. Args: as_closest_canonical: if True, load the image as closest to canonical axis format. kwargs: additional args for `nibabel.load` API. more details about available args: https://github.com/nipy/nibabel/blob/master/nibabel/loadsave.py """ def __init__(self, as_closest_canonical: bool = False, dtype: Optional[np.dtype] = np.float32, **kwargs): super().__init__() self.as_closest_canonical = as_closest_canonical self.dtype = dtype self.kwargs = kwargs
[docs] def verify_suffix(self, filename: Union[Sequence[str], str]) -> bool: """ Verify whether the specified file or files format is supported by Nibabel reader. Args: filename: file name or a list of file names to read. if a list of files, verify all the suffixes. """ suffixes: Sequence[str] = ["nii", "nii.gz"] return has_nib and is_supported_format(filename, suffixes)
[docs] def read(self, data: Union[Sequence[str], str], **kwargs): """ Read image data from specified file or files. Note that the returned object is Nibabel image object or list of Nibabel image objects. Args: data: file name or a list of file names to read. kwargs: additional args for `nibabel.load` API, will override `self.kwargs` for existing keys. More details about available args: https://github.com/nipy/nibabel/blob/master/nibabel/loadsave.py """ img_: List[Nifti1Image] = [] filenames: Sequence[str] = ensure_tuple(data) kwargs_ = self.kwargs.copy() kwargs_.update(kwargs) for name in filenames: img = nib.load(name, **kwargs_) img = correct_nifti_header_if_necessary(img) img_.append(img) return img_ if len(filenames) > 1 else img_[0]
[docs] def get_data(self, img): """ Extract data array and meta data from loaded image and return them. This function returns 2 objects, first is numpy array of image data, second is dict of meta data. It constructs `affine`, `original_affine`, and `spatial_shape` and stores in meta dict. If loading a list of files, stack them together and add a new dimension as first dimension, and use the meta data of the first image to represent the stacked result. Args: img: a Nibabel image object loaded from a image file or a list of Nibabel image objects. """ img_array: List[np.ndarray] = [] compatible_meta: Dict = {} for i in ensure_tuple(img): header = self._get_meta_dict(i) header["affine"] = self._get_affine(i) header["original_affine"] = self._get_affine(i) header["as_closest_canonical"] = self.as_closest_canonical if self.as_closest_canonical: i = nib.as_closest_canonical(i) header["affine"] = self._get_affine(i) header["spatial_shape"] = self._get_spatial_shape(i) img_array.append(self._get_array_data(i)) _copy_compatible_dict(header, compatible_meta) img_array_ = np.stack(img_array, axis=0) if len(img_array) > 1 else img_array[0] return img_array_, compatible_meta
def _get_meta_dict(self, img) -> Dict: """ Get the all the meta data of the image and convert to dict type. Args: img: a Nibabel image object loaded from a image file. """ return dict(img.header) def _get_affine(self, img) -> np.ndarray: """ Get the affine matrix of the image, it can be used to correct spacing, orientation or execute spatial transforms. Args: img: a Nibabel image object loaded from a image file. """ return img.affine.copy() def _get_spatial_shape(self, img) -> np.ndarray: """ Get the spatial shape of image data, it doesn't contain the channel dim. Args: img: a Nibabel image object loaded from a image file. """ ndim = img.header["dim"][0] spatial_rank = min(ndim, 3) return np.asarray(img.header["dim"][1 : spatial_rank + 1]) def _get_array_data(self, img) -> np.ndarray: """ Get the raw array data of the image, converted to Numpy array. Args: img: a Nibabel image object loaded from a image file. """ _array = np.array(img.get_fdata(dtype=self.dtype)) img.uncache() return _array
[docs]class NumpyReader(ImageReader): """ Load NPY or NPZ format data based on Numpy library, they can be arrays or pickled objects. A typical usage is to load the `mask` data for classification task. It can load part of the npz file with specified `npz_keys`. Args: npz_keys: if loading npz file, only load the specified keys, if None, load all the items. stack the loaded items together to construct a new first dimension. kwargs: additional args for `numpy.load` API except `allow_pickle`. more details about available args: https://numpy.org/doc/stable/reference/generated/numpy.load.html """ def __init__(self, npz_keys: Optional[KeysCollection] = None, **kwargs): super().__init__() if npz_keys is not None: npz_keys = ensure_tuple(npz_keys) self.npz_keys = npz_keys self.kwargs = kwargs
[docs] def verify_suffix(self, filename: Union[Sequence[str], str]) -> bool: """ Verify whether the specified file or files format is supported by Numpy reader. Args: filename: file name or a list of file names to read. if a list of files, verify all the suffixes. """ suffixes: Sequence[str] = ["npz", "npy"] return is_supported_format(filename, suffixes)
[docs] def read(self, data: Union[Sequence[str], str], **kwargs): """ Read image data from specified file or files. Note that the returned object is Numpy array or list of Numpy arrays. Args: data: file name or a list of file names to read. kwargs: additional args for `numpy.load` API except `allow_pickle`, will override `self.kwargs` for existing keys. More details about available args: https://numpy.org/doc/stable/reference/generated/numpy.load.html """ img_: List[Nifti1Image] = [] filenames: Sequence[str] = ensure_tuple(data) kwargs_ = self.kwargs.copy() kwargs_.update(kwargs) for name in filenames: img = np.load(name, allow_pickle=True, **kwargs_) if name.endswith(".npz"): # load expected items from NPZ file npz_keys = [f"arr_{i}" for i in range(len(img))] if self.npz_keys is None else self.npz_keys for k in npz_keys: img_.append(img[k]) else: img_.append(img) return img_ if len(img_) > 1 else img_[0]
[docs] def get_data(self, img): """ Extract data array and meta data from loaded data and return them. This function returns 2 objects, first is numpy array of image data, second is dict of meta data. It constructs `spatial_shape=data.shape` and stores in meta dict if the data is numpy array. If loading a list of files, stack them together and add a new dimension as first dimension, and use the meta data of the first image to represent the stacked result. Args: img: a Numpy array loaded from a file or a list of Numpy arrays. """ img_array: List[np.ndarray] = [] compatible_meta: Dict = {} if isinstance(img, np.ndarray): img = (img,) for i in ensure_tuple(img): header = {} if isinstance(i, np.ndarray): header["spatial_shape"] = i.shape img_array.append(i) _copy_compatible_dict(header, compatible_meta) img_array_ = np.stack(img_array, axis=0) if len(img_array) > 1 else img_array[0] return img_array_, compatible_meta
[docs]class PILReader(ImageReader): """ Load common 2D image format (supports PNG, JPG, BMP) file or files from provided path. Args: converter: additional function to convert the image data after `read()`. for example, use `converter=lambda image: image.convert("LA")` to convert image format. kwargs: additional args for `Image.open` API in `read()`, mode details about available args: https://pillow.readthedocs.io/en/stable/reference/Image.html#PIL.Image.open """ def __init__(self, converter: Optional[Callable] = None, **kwargs): super().__init__() self.converter = converter self.kwargs = kwargs
[docs] def verify_suffix(self, filename: Union[Sequence[str], str]) -> bool: """ Verify whether the specified file or files format is supported by PIL reader. Args: filename: file name or a list of file names to read. if a list of files, verify all the suffixes. """ suffixes: Sequence[str] = ["png", "jpg", "jpeg", "bmp"] return has_pil and is_supported_format(filename, suffixes)
[docs] def read(self, data: Union[Sequence[str], str, np.ndarray], **kwargs): """ Read image data from specified file or files. Note that the returned object is PIL image or list of PIL image. Args: data: file name or a list of file names to read. kwargs: additional args for `Image.open` API in `read()`, will override `self.kwargs` for existing keys. Mode details about available args: https://pillow.readthedocs.io/en/stable/reference/Image.html#PIL.Image.open """ img_: List[PILImage.Image] = [] filenames: Sequence[str] = ensure_tuple(data) kwargs_ = self.kwargs.copy() kwargs_.update(kwargs) for name in filenames: img = PILImage.open(name, **kwargs_) if callable(self.converter): img = self.converter(img) img_.append(img) return img_ if len(filenames) > 1 else img_[0]
[docs] def get_data(self, img): """ Extract data array and meta data from loaded data and return them. This function returns 2 objects, first is numpy array of image data, second is dict of meta data. It constructs `spatial_shape` and stores in meta dict. If loading a list of files, stack them together and add a new dimension as first dimension, and use the meta data of the first image to represent the stacked result. Args: img: a PIL Image object loaded from a file or a list of PIL Image objects. """ img_array: List[np.ndarray] = [] compatible_meta: Dict = {} for i in ensure_tuple(img): header = self._get_meta_dict(i) header["spatial_shape"] = self._get_spatial_shape(i) img_array.append(np.asarray(i)) _copy_compatible_dict(header, compatible_meta) img_array_ = np.stack(img_array, axis=0) if len(img_array) > 1 else img_array[0] return img_array_, compatible_meta
def _get_meta_dict(self, img) -> Dict: """ Get the all the meta data of the image and convert to dict type. Args: img: a PIL Image object loaded from a image file. """ return { "format": img.format, "mode": img.mode, "width": img.width, "height": img.height, } def _get_spatial_shape(self, img) -> np.ndarray: """ Get the spatial shape of image data, it doesn't contain the channel dim. Args: img: a PIL Image object loaded from a image file. """ return np.asarray((img.width, img.height))