Hello,
I have been trying to reuse the array of a UniformGrid (PyVista’s equivalent to vtkImageData) with ITK. The resulting data seems to be cropped by 1 voxel. How can I load the data as cells with ITK?
(Extra.) Ultimately, the point is to perform registration on this data, and to store the results in a VTK format (e.g. VTI, VTU, VTS). In the code below, the data is loaded from a VTI file, which could be achieved with ITK in some way, but in the actual case, a Gmsh file is loaded as PyVista data and processed before it arrives to ITK.
Thank you!
# License: GPLv3 (GNU Public License version 3.0)
import numpy as np
import pyvista as pv
import itk
ref_vti = pv.UniformGrid("tmp_gmsh.vti")
ref_vti.save("tmp_ref_vti.vti")
print("tmp_ref_vti.vti")
# * Convert grid into ITK images
image_type = itk.Image[itk.F, 3]
nx, ny, nz = [val - 1 for val in ref_vti.dimensions]
fixed_image_arr = np.reshape(
ref_vti.cell_data["material"], [nz, nx, ny])
fixed_image = itk.image_from_array(
fixed_image_arr.astype(np.float32), ttype=image_type)
# # Does not work:
#
# itk.image_from_vtk_image(ref_vti)
#
# # Result:
# # File "/home/edgar/.local/lib/python3.10/site-packages/itk/support/extras.py", line 746, in image_from_vtk_image
# # array = vtk_to_numpy(point_data.GetScalars())
# # File "/usr/lib/python3.10/site-packages/vtkmodules/util/numpy_support.py", line 215, in vtk_to_numpy
# # AttributeError: 'NoneType' object has no attribute 'GetDataType'
# Trying to set the right dimensions on the grid
fixed_image.SetSpacing(ref_vti.spacing)
fixed_image.SetOrigin(ref_vti.GetOrigin())
# * Save VTK
first_frame_vtk = "tmp_itk_reference.vtk"
itk.imwrite(fixed_image, first_frame_vtk)
print(first_frame_vtk)
np.savez(first_frame_vtk.replace(".vtk", ".npz"),
fixed_image_arr)
# | itk | 5.3.0 |
# | itk-core | 5.3.0 |
# | itk-elastix | 0.15.0 |
# | itk-filtering | 5.3.0 |
# | itk-io | 5.3.0 |
# | itk-meshtopolydata | 0.10.0 |
# | itk-minimalpathextraction | 1.2.4 |
# | itk-numerics | 5.3.0 |
# | itk-registration | 5.3.0 |
# | itk-segmentation | 5.3.0 |
# | itk-strain | 0.3.6 |
# | itk-tubetk | 1.3.4 |
# | itkwidgets | 0.32.5 |
# | numpy | 1.24.1 |
# | pyvista | 0.37.0 |
# | scipy | 1.10.0 |
# | python | 3.10.9 |
I also tried with this
itk.vtk_image_import("tmp_gmsh.vti", ttype=image_type)
Which results in this
Traceback (most recent call last):
File "/home/edgar/.local/lib/python3.10/site-packages/itk/support/extras.py", line 1526, in set_inputs
new_itk_object.SetInput(setInputNb, arg)
AttributeError: 'itkVTKImageImportIF3' object has no attribute 'SetInput'. Did you mean: 'GetInputs'?
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "<string>", line 19, in __PYTHON_EL_eval
File "/home/edgar/GlassFibre/Code/examples/feed_vti_into_dvc.py", line 1, in <module>
# License: GPLv3 (GNU Public License version 3.0)
File "/home/edgar/.local/lib/python3.10/site-packages/itk/support/helpers.py", line 176, in image_filter_wrapper
return image_filter(*args, **kwargs)
File "/home/edgar/.local/lib/python3.10/site-packages/itk/itkVTKImageImportPython.py", line 1576, in vtk_image_import
instance = itk.VTKImageImport.New(*args, **kwargs)
File "/home/edgar/.local/lib/python3.10/site-packages/itk/support/template_class.py", line 735, in New
return self[list(keys)[0]].New(*args, **kwargs)
File "/home/edgar/.local/lib/python3.10/site-packages/itk/itkVTKImageImportPython.py", line 616, in New
template_class.New(obj, *args, **kargs)
File "/home/edgar/.local/lib/python3.10/site-packages/itk/support/template_class.py", line 800, in New
itk.set_inputs(self, args, kargs)
File "/home/edgar/.local/lib/python3.10/site-packages/itk/support/extras.py", line 1554, in set_inputs
raise AttributeError("No method found to set the input.")
AttributeError: No method found to set the input.
tmp_size_mismatch.tar.gz (91.4 KB)
Here is a related question: Slack
[EDIT]
I hope that posting the raw code helps (it’s part of the tar.gz). Thanks!
# License: GPLv3 (GNU Public License version 3.0)
import numpy as np
import pyvista as pv
import itk
ref_vti = pv.UniformGrid("tmp_gmsh.vti")
ref_vti.save("tmp_ref_vti.vti")
print("tmp_ref_vti.vti")
# * Convert grid into ITK images
image_type = itk.Image[itk.F, 3]
nx, ny, nz = [val - 1 for val in ref_vti.dimensions]
fixed_image_arr = np.reshape(
ref_vti.cell_data["material"], [nz, nx, ny])
fixed_image = itk.image_from_array(
fixed_image_arr.astype(np.float32), ttype=image_type)
# # Does not work:
#
# itk.image_from_vtk_image(ref_vti)
#
# # Result:
# # File "/home/edgar/.local/lib/python3.10/site-packages/itk/support/extras.py", line 746, in image_from_vtk_image
# # array = vtk_to_numpy(point_data.GetScalars())
# # File "/usr/lib/python3.10/site-packages/vtkmodules/util/numpy_support.py", line 215, in vtk_to_numpy
# # AttributeError: 'NoneType' object has no attribute 'GetDataType'
# Trying to set the right dimensions on the grid
fixed_image.SetSpacing(ref_vti.spacing)
fixed_image.SetOrigin(ref_vti.GetOrigin())
# * Save VTK
first_frame_vtk = "tmp_itk_reference.vtk"
itk.imwrite(fixed_image, first_frame_vtk)
print(first_frame_vtk)
np.savez(first_frame_vtk.replace(".vtk", ".npz"),
fixed_image_arr)
# | itk | 5.3.0 |
# | itk-core | 5.3.0 |
# | itk-elastix | 0.15.0 |
# | itk-filtering | 5.3.0 |
# | itk-io | 5.3.0 |
# | itk-meshtopolydata | 0.10.0 |
# | itk-minimalpathextraction | 1.2.4 |
# | itk-numerics | 5.3.0 |
# | itk-registration | 5.3.0 |
# | itk-segmentation | 5.3.0 |
# | itk-strain | 0.3.6 |
# | itk-tubetk | 1.3.4 |
# | itkwidgets | 0.32.5 |
# | numpy | 1.24.1 |
# | pyvista | 0.37.0 |
# | scipy | 1.10.0 |
# feed_vti_into_dvc.py ends here
tmp_gmsh.vti (25.6 KB)
tmp_paraview.pvsm (407.0 KB)