使用 SimpleITK 和 PyTorch 读取 dicom 文件的性能

Question

I want to directly load image from memory to python in pytorch tensor format. I modified GetArrayViewFromImage() function by replacing those lines:

image_memory_view = _GetMemoryViewFromImage(image)
array_view = numpy.asarray(image_memory_view).view(dtype = dtype)

by:

image_memory_view = _GetMemoryViewFromImage(image)
array_view = torch.as_tensor(image_memory_view, dtype = dtype)

in practise it is so slow I replaced it with:

image_memory_view = _GetMemoryViewFromImage(image)
array_view = numpy.asarray(image_memory_view).view(dtype = dtype)
array_view  = torch.as_tensor(array_view)

Now I have two questions:

1. it is much slower, and I don't really know why reading it with numpy and converting it is faster.
2. even though I add the dtype argument and it returns a tensor with a correct dtype it reads it wrong (ex. -1000 in numpy is read as 252 no matter what torch.dtype I choose) which is not a problem when reading with numpy and converting, why is that happening?

Answer 1

While this does not directly answer your question, I strongly recommend using the torchio package, instead of dealing with these IO issues yourself (torchio uses SimpleITK under the hood).