FBP with ASTRA or Tigre do not accept 2D image geometry with 3D data

[lauramurgatroyd]

Description

Image geometry's get_slice method returns a 2D shape if slicing on 3D data
To be able to reconstruct with ASTRA or Tigre, plugins or CIL's reocn module we require a 3D Image Geometry

Either:

• update get_slice to return a 3D Image geometry with size 1 on the slicing axis

OR:

• update the astra and tigre FBP to sort out the sizing issue

Environment

import cil, sys
print(cil.version.version, cil.version.commit_hash, sys.version, sys.platform)

[lauramurgatroyd]

Example code:

Note - this is a basic example where we have a parallel beam dataset and a single slice on the acquisition data is the same as a single slice on the image data. However, in the case we had cone beam or a tilted centre of rotation offset, then these would not be identical, explaining the use case for wanting to slice on image geometry.

# Demonstrate the problem with get slice

#%% 1
from cil.utilities.dataexample import SIMULATED_PARALLEL_BEAM_DATA
from cil.processors import TransmissionAbsorptionConverter
from cil.utilities.display import show2D

data = SIMULATED_PARALLEL_BEAM_DATA.get()
data = TransmissionAbsorptionConverter()(data)


#%% 2
from cil.plugins.astra import FBP as FBP_ASTRA
data.reorder('astra')
ig = data.geometry.get_ImageGeometry()


# %% 3
recon = FBP_ASTRA(ig, data.geometry)
recon.set_input(data)
full_recon = recon.get_output()
show2D(full_recon.get_slice(vertical=5), title="Slice 5 from full reconstruction")

# %% 4
ig_slice = ig.get_slice(vertical=5)
recon = FBP_ASTRA(ig_slice, data.geometry)
recon.set_input(data)
slice_5_astra = recon.get_output()

show2D(slice_5_astra)

# %% 5
from cil.plugins.tigre import FBP as FBP_TIGRE

data.reorder('tigre')
#ig_slice.reorder('tigre') - can't do - should we have a reorder for ImageGeometry??
ig_slice = ig.get_slice(vertical=5)
recon = FBP_TIGRE(ig_slice, data.geometry)
recon.set_input(data)
slice_5_tigre = recon.get_output()
show2D(slice_5_tigre, title="Slice 5 from TIGRE reconstruction")

# %% 6
from cil.recon import FBP as FBP_CIL
data.reorder('cil')
ig_slice = ig.get_slice(vertical=5)
recon = FBP_CIL(data, ig_slice)
slice_5_cil = recon.run()
show2D(slice_5_cil, title="Slice 5 from CIL reconstruction ")

[lauramurgatroyd]

Cell 4- reconstruction with 2D image geom with astra, fails with error:

RuntimeError                              Traceback (most recent call last)
Cell In[6], [line 5](vscode-notebook-cell:?execution_count=6&line=5)
      3 recon = FBP_ASTRA(ig_slice, data.geometry)
      4 recon.set_input(data)
----> [5](vscode-notebook-cell:?execution_count=6&line=5) slice_5_astra = recon.get_output()
      7 show2D(slice_5_astra)

File ~/miniconda3/envs/cil_25/lib/python3.12/site-packages/cil/plugins/astra/processors/FBP.py:102, in FBP.get_output(self, out)
    101 def get_output(self, out=None):
--> [102](https://vscode-remote+ssh-002dremote-002b130-002e246-002e214-002e56.vscode-resource.vscode-cdn.net/home/lhe97136/CIL/~/miniconda3/envs/cil_25/lib/python3.12/site-packages/cil/plugins/astra/processors/FBP.py:102)     return self.processor.get_output(out=out)

File ~/miniconda3/envs/cil_25/lib/python3.12/site-packages/cil/framework/processors.py:120, in Processor.get_output(self, out)
    117     raise ValueError('Output data not compatible with processor')
    119 if self.output is None or self.shouldRun:
--> [120](https://vscode-remote+ssh-002dremote-002b130-002e246-002e214-002e56.vscode-resource.vscode-cdn.net/home/lhe97136/CIL/~/miniconda3/envs/cil_25/lib/python3.12/site-packages/cil/framework/processors.py:120)     out = self.process(out=out)
    121     if self.store_output:
    122         self.output = out.copy()

File ~/miniconda3/envs/cil_25/lib/python3.12/site-packages/cil/plugins/astra/processors/FDK_Flexible.py:98, in FDK_Flexible.process(self, out)
     94 else:
     95     data_temp = DATA.as_array()
---> [98](https://vscode-remote+ssh-002dremote-002b130-002e246-002e214-002e56.vscode-resource.vscode-cdn.net/home/lhe97136/CIL/~/miniconda3/envs/cil_25/lib/python3.12/site-packages/cil/plugins/astra/processors/FDK_Flexible.py:98) rec_id = astra.data3d.create('-vol', self.vol_geom_astra)
     99 sinogram_id = astra.data3d.create('-sino', self.proj_geom_astra, data_temp)
    100 cfg = astra.astra_dict('FDK_CUDA')
...
---> [43](https://vscode-remote+ssh-002dremote-002b130-002e246-002e214-002e56.vscode-resource.vscode-cdn.net/home/lhe97136/CIL/~/miniconda3/envs/cil_25/lib/python3.12/site-packages/astra/data3d.py:43)     return d.create(datatype,geometry,data)

File astra/data3d_c.pyx:96, in astra.data3d_c.create()

RuntimeError: Geometry class not initialized.

[lauramurgatroyd]

Cell 5 - recon with 2D image geom with tigre, fails with a crashed kernel, as does cell 6, tigre from recon module

[lauramurgatroyd]

One proposed solution is to get Image Geometry to return data which has shape 1 in the sliced dimensions. However, this opens a can of worms - see #2217 (comment)