get_camera3d_from_world() got an unexpected keyword argument 'phi'
lkccu opened this issue · 11 comments
Hi author @mathiasunberath ,I have encountered a bug when implementing func projector.project_over_carm_range().Here are the errors.Could you please give me a hand? thx.
TypeError Traceback (most recent call last)
Input In [21], in <cell line: 1>()
1 with deepdrr.Projector(
2 volume=volume,
3 carm=carm,
(...)
10
11 ) as projector:
---> 12 images = projector.project_over_carm_range(
13 (-40,40,40),
14 (-45,45,45))
15 for i,image in enumerate(images):
16 plt.imshow(image,cmap ='gray')
File ~/deepdrr/deepdrr/projector/projector.py:813, in Projector.project_over_carm_range(self, phi_range, theta_range, degrees)
811 phis, thetas = utils.generate_uniform_angles(phi_range, theta_range)
812 for phi, theta in zip(phis, thetas):
--> 813 extrinsic = self.device.get_camera3d_from_world(
814 self.device.isocenter,
815 phi=phi,
816 theta=theta,
817 degrees=degrees,
818 )
820 camera_projections.append(
821 geo.CameraProjection(self.camera_intrinsics, extrinsic)
822 )
824 return self.project(*camera_projections)
TypeError: get_camera3d_from_world() got an unexpected keyword argument 'phi'
Here are the codes.
volume = deepdrr.Volume.from_nifti(path,
materials ='Bone')
camera_intrinsics = deepdrr.geo.CameraIntrinsicTransform.from_sizes(
sensor_size = 512,
pixel_size = 0.5,
source_to_detector_distance = 1118.38
)
center = volume.world_from_ijk @ deepdrr.geo.point(160,160,160)
carm = deepdrr.MobileCArm(isocenter=center,
source_to_detector_distance = 689.1,
min_alpha = -40,
max_alpha = 40,
# note that this would collide with the patient. Suggested to limit to +/- 45
min_beta = -45,
max_beta = 45,
pixel_size =0.5,
sensor_height =320,
sensor_width =320,)
alphas,betas = utils.generate_uniform_angles(
(-40,40,40),
(-45,45,45)
)
output_dir = Path("/root/autodl-tmp/drr_result")
output_dir.mkdir(exist_ok = True)
with deepdrr.Projector(
volume=volume,
carm=carm,
step=0.1, # stepsize along projection ray, measured in voxels
spectrum="90KV_AL40", # energy spectrum
photon_count=100000, # number of photons to simulate
scatter_num=0, # number of scatter events to simulate
neglog=True, # apply negative log transform to image (convenient for visualization)
intensity_upper_bound=3, # Good default for windowing
) as projector:
images = projector.project_over_carm_range(
(-40,40,40),
(-45,45,45))
for i,image in enumerate(images):
plt.imshow(image,cmap ='gray')
plt.title(f'alpha,beta ={alphas[i],betas[i]}')
display(Image.fromarray((image * 255).astype(np.uint8)))
print("### finish ###")
And how can I make use of the arg materials,I searched that in issues and I found materials = dict["bone = seg_array"] ,but I am not sure how can I specify the seg_array variable or there is a solution? Thanks
Regards.
@benjamindkilleen you want to take a look at this?
@lkccu The first issue is because project_over_carm_range works with the CArm class and not the MobileCArm class. (This will raise an error in future releases.) I recommend to update the pose of the carm directly with the carm.move_to function, using the alphas,betas you have defined, and calling the projector for each image. (This is what project_over_carm_range does under the hood.
For the latter issue, it would be materials = dict(bone=seg_array), where seg_array is a 3D numpy binary array giving the segmentation of bone. This is syntactically equal to materials = {"bone": seg_array}, which may be more familiar. The materials argument should be the whole dictionary.
Thank you for that, I mistakes what arg material is doing. So does that mean 'material' is doing seg from an known segmentation nifti data?what should I do to generate a bone-styled DRR image from scratch?
Regards.
I specify in the volume that "segmentation = True", however I got an terrible result.I wonder whether it is because my data is not that good.Can you give me a hand?Here is the minimum example .
before seg.
Hi author @mathiasunberath, happy CNY!I have encountered the same trouble now.I wonder how can I make use of sample nifti image dataset6_CLINIC_0001_mask_4label_1.nii.gz.I inspected in Slicer and that seg mask looks so great.However,when I tried to load it as a 3-d array and specify arg materials in func Volume.from_nifti, it turned out a dark image.Could you please give me a hand?Thank you very much!The codes are as follows.
seg_array = nib.load('/root/autodl-tmp/datasets/DeepDRR_Data/CTPelvic1K_dataset6_CLINIC_0001/dataset6_CLINIC_0001_mask_4label_1.nii.gz')
print(seg_array.shape)
seg_array = seg_array.get_fdata()
volume = deepdrr.Volume.from_nifti(path,
materials=dict(bone=seg_array))
volume.supine()
carm = deepdrr.MobileCArm(isocenter=volume.center_in_world, alpha=0, beta=0, degrees=True)
with deepdrr.Projector(
volume=volume,
carm=carm,
step=0.2, # stepsize along projection ray, measured in voxels
spectrum="90KV_AL40", # energy spectrum
photon_count=10000, # number of photons to simulate
scatter_num=0, # number of catter events to simulate
collected_energy =False, # apply negative log transform to image (convenient for visualization)
intensity_upper_bound=2, # Good default for windowing
) as projector:
for z in range(-500, -100, 50):
carm.move_to(isocenter_in_world=volume.center_in_world + geo.v(0, 0, z))
print(f"Projecting at z={z}")
image = projector.project()
display(Image.fromarray((image * 255).astype(np.uint8)))
print("###### finish ######")
Hi author!
Hello,I am wondering what can I do in my func to ensure that the projector is initialized or set it initialized?
projector.initialize(), which is a no-op if already initialized.
projector.initialize(), which is a no-op if already initialized.
Thank you.I want to initialized the projector in the beginning of code and turn it into a parameter of functions like
drr(projector=projector, rtvec=X)where function drr is generating drr images of the very volume rotating and translating ,carm.What should I do?Please give me a hand.