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RTK GPU transfer
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import numpy as np | |
import itk | |
from itk import RTK as rtk | |
GPU_IMG = rtk.CudaImage[itk.F, 3] | |
CPU_IMG = rtk.Image[itk.F, 3] | |
def cpu_to_gpu_image(cpu_img, gpu_img=None): | |
if gpu_img is None: | |
gpu_img = GPU_IMG.New() | |
gpu_img.SetPixelContainer(cpu_img.GetPixelContainer()) | |
gpu_img.CopyInformation(cpu_img) | |
gpu_img.SetBufferedRegion(cpu_img.GetBufferedRegion()) | |
gpu_img.SetRequestedRegion(cpu_img.GetRequestedRegion()) | |
return gpu_img | |
def forwardproject(vol, geometry, proj_shape, proj_origin, proj_spacing, img_spacing, img_origin): | |
"""\ | |
vol : 3d array | |
volume to be forward projected | |
geometry : rtk geometry object | |
proj_shape : 3 element tuple/list | |
proj_shape = (num_angles, proj_shape_x, proj_shape_y) | |
proj_origin : 2 element tuple/list | |
proj_origin = (proj_origin_x, proj_origin_y) | |
proj_spacing : 2 element tuple/list | |
proj_spacing = (proj_spacing_x, proj_spacing_y) | |
img_spacing : 3 element tuple/list | |
img_origin : 3 element tuple_list | |
All arguments in C order indexing. Will be converted to ITK indexing inside function. | |
""" | |
assert vol.dtype == np.float32 | |
assert vol.flags.c_contiguous | |
out = np.zeros(proj_shape, dtype=np.float32) | |
proj_img = itk.GetImageViewFromArray(out) | |
proj_img.SetOrigin(proj_origin[::-1] + [0]) # [::-1] for indexing of ITK; + [0] for RTK convention | |
proj_img.SetSpacing(proj_spacing[::-1] + [1]) # [::-1] for indexing of ITK; + [1] for RTK convention | |
vol_img = itk.GetImageViewFromArray(vol) | |
vol_img.SetOrigin(img_origin[::-1]) | |
vol_img.SetSpacing(img_spacing[::-1]) | |
# copy to gpu | |
proj_img_gpu = cpu_to_gpu_image(proj_img) | |
vol_img_gpu = cpu_to_gpu_image(vol_img) | |
man = proj_img_gpu.GetCudaDataManager() | |
fwd = rtk.CudaForwardProjectionImageFilter[GPU_IMG].New() | |
fwd.SetGeometry(geometry) | |
fwd.SetInput(0, proj_img_gpu) | |
fwd.SetInput(1, vol_img_gpu) | |
fwd.Update() | |
# copy data to cpu | |
man.SetCPUBufferPointer(proj_img.GetBufferPointer()) | |
man.UpdateCPUBuffer() | |
return out |
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