enable gpu load nifti

Signed-off-by: Yiheng Wang <[email protected]>

monai/data/image_reader.py

@@ -14,12 +14,15 @@
 import glob
 import os
 import re
+import gzip
+import io
 import warnings
 from abc import ABC, abstractmethod
 from collections.abc import Callable, Iterable, Iterator, Sequence
 from dataclasses import dataclass
 from pathlib import Path
 from typing import TYPE_CHECKING, Any
+import torch
 
 import numpy as np
 from torch.utils.data._utils.collate import np_str_obj_array_pattern
@@ -41,17 +44,21 @@
     import pydicom
     from nibabel.nifti1 import Nifti1Image
     from PIL import Image as PILImage
+    import cupy as cp
+    import kvikio
 
-    has_nrrd = has_itk = has_nib = has_pil = has_pydicom = True
+    has_nrrd = has_itk = has_nib = has_pil = has_pydicom = has_cp = has_kvikio = True
 else:
     itk, has_itk = optional_import("itk", allow_namespace_pkg=True)
     nib, has_nib = optional_import("nibabel")
     Nifti1Image, _ = optional_import("nibabel.nifti1", name="Nifti1Image")
     PILImage, has_pil = optional_import("PIL.Image")
     pydicom, has_pydicom = optional_import("pydicom")
     nrrd, has_nrrd = optional_import("nrrd", allow_namespace_pkg=True)
+    cp, has_cp = optional_import("cupy")
+    kvikio, has_kvikio = optional_import("kvikio")
 
-__all__ = ["ImageReader", "ITKReader", "NibabelReader", "NumpyReader", "PILReader", "PydicomReader", "NrrdReader"]
+__all__ = ["ImageReader", "ITKReader", "NibabelReader", "NibabelGPUReader", "NumpyReader", "PILReader", "PydicomReader", "NrrdReader"]
 
 
 class ImageReader(ABC):
@@ -1024,6 +1031,122 @@ def _get_array_data(self, img):
 
         """
         return np.asanyarray(img.dataobj, order="C")
+
+
+@require_pkg(pkg_name="nibabel")
+@require_pkg(pkg_name="cupy")
+@require_pkg(pkg_name="kvikio")
+class NibabelGPUReader(NibabelReader):
+
+    def _gds_load(self, file_path):
+        file_size = os.path.getsize(file_path)
+        image = cp.empty(file_size, dtype=cp.uint8)
+        with kvikio.CuFile(file_path, "r") as f:
+            f.read(image)
+
+        if file_path.endswith(".gz"):
+            # for compressed data, have to tansfer to CPU to decompress
+            # and then transfer back to GPU. It is not efficient compared to .nii file
+            # but it's still faster than Nibabel's default reader.
+            # TODO: can benchmark more, it may no need to do this since we don't have to use .gz
+            # since it's waste times especially in training
+            compressed_data = cp.asnumpy(image)
+            with gzip.GzipFile(fileobj=io.BytesIO(compressed_data)) as gz_file:
+                decompressed_data = gz_file.read()
+
+            file_size = len(decompressed_data)
+            image = cp.asarray(np.frombuffer(decompressed_data, dtype=np.uint8))
+
+        return image
+
+    def read(self, data: Sequence[PathLike] | PathLike, **kwargs):
+        """
+        Read image data from specified file or files, it can read a list of images
+        and stack them together as multi-channel data in `get_data()`.
+        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.
+
+        """
+        img_: list[Nifti1Image] = []
+
+        filenames: Sequence[PathLike] = ensure_tuple(data)
+        kwargs_ = self.kwargs.copy()
+        kwargs_.update(kwargs)
+        for name in filenames:
+            img = self._gds_load(name)
+            img_.append(img)  # type: ignore
+        return img_ if len(filenames) > 1 else img_[0]
+
+    def get_data(self, img):
+        """
+        Extract data array and metadata from loaded image and return them.
+        This function returns two objects, first is numpy array of image data, second is dict of metadata.
+        It constructs `affine`, `original_affine`, and `spatial_shape` and stores them in meta dict.
+        When loading a list of files, they are stacked together at a new dimension as the first dimension,
+        and the metadata of the first image is used to present the output metadata.
+
+        Args:
+            img: a Nibabel image object loaded from an image file or a list of Nibabel image objects.
+
+        """
+        compatible_meta: dict = {}
+        img_array = []
+        for i in ensure_tuple(img):
+            header = self._get_header(i)
+            data_offset = header.get_data_offset()
+            data_shape = header.get_data_shape()
+            data_dtype = header.get_data_dtype()
+            affine = header.get_best_affine()
+            meta = dict(header)
+            meta[MetaKeys.AFFINE] = affine
+            meta[MetaKeys.ORIGINAL_AFFINE] = affine
+            # TODO: as_closest_canonical
+            # TODO: correct_nifti_header_if_necessary
+            meta[MetaKeys.SPATIAL_SHAPE] = data_shape
+            # TODO: figure out why always RAS for NibabelReader ?
+            # meta[MetaKeys.SPACE] = SpaceKeys.RAS
+
+            data = i[data_offset:].view(data_dtype).reshape(data_shape, order="F")
+            # TODO: check channel
+            # if self.squeeze_non_spatial_dims:
+            img_array.append(data)
+            if self.channel_dim is None:  # default to "no_channel" or -1
+                header[MetaKeys.ORIGINAL_CHANNEL_DIM] = (
+                    float("nan") if len(data.shape) == len(header[MetaKeys.SPATIAL_SHAPE]) else -1
+                )
+            else:
+                header[MetaKeys.ORIGINAL_CHANNEL_DIM] = self.channel_dim
+            _copy_compatible_dict(header, compatible_meta)
+
+        return self._stack_images(img_array, compatible_meta), compatible_meta
+
+    def _get_header(self, img):
+        """
+        Get the all the metadata of the image and convert to dict type.
+
+        Args:
+            img: a Nibabel image object loaded from an image file.
+
+        """
+        header_bytes = cp.asnumpy(img[:348])
+        header = nib.Nifti1Header.from_fileobj(io.BytesIO(header_bytes))
+        # swap to little endian as PyTorch doesn't support big endian
+        try:
+            header = header.as_byteswapped("<")
+        except ValueError:
+            pass
+        return header
+
+    def _stack_images(self, image_list: list, meta_dict: dict):
+        if len(image_list) <= 1:
+            return image_list[0]
+        if not is_no_channel(meta_dict.get(MetaKeys.ORIGINAL_CHANNEL_DIM, None)):
+            channel_dim = int(meta_dict[MetaKeys.ORIGINAL_CHANNEL_DIM])
+            return torch.cat(image_list, axis=channel_dim)
+        meta_dict[MetaKeys.ORIGINAL_CHANNEL_DIM] = 0
+        return torch.stack(image_list, dim=0)
 
 
 class NumpyReader(ImageReader):

monai/transforms/io/array.py

@@ -35,6 +35,7 @@
     ImageReader,
     ITKReader,
     NibabelReader,
+    NibabelGPUReader,
     NrrdReader,
     NumpyReader,
     PILReader,
@@ -69,6 +70,7 @@
     "numpyreader": NumpyReader,
     "pilreader": PILReader,
     "nibabelreader": NibabelReader,
+    "nibabelgpureader": NibabelGPUReader,
 }