updates to TomoPhantom plugin to use v3.0

[paskino]

Description

Update to use TomoPhantom v3.0 from httomo channel.
Update: binaries for Tomophantom 3.0.3 provided by anaconda ccpi, and the tomo share.

We now have the python wrappers no-arch as:
https://anaconda.org/channels/ccpi/packages/tomophantom/files

And the c layer build for windows and linux:
https://anaconda.org/channels/ccpi/packages/libtomophantom/overview

This is now not linked to any specific version of Python and NumPy as it uses ctypes instead of Cython.

Depends on:

• Remove np py pin dkazanc/TomoPhantom#128
• setup conda correctly dkazanc/TomoPhantom#130

A followup will be to move to the httomo channel when

• a suitable version of TomoPhantom on httomo, probably v3.0.3

Example Usage

No change in the user interface.

Contribution Notes

• The content of this Pull Request (the Contribution) is intentionally submitted for inclusion in CIL (the Work) under the terms and conditions of the Apache-2.0 License
• I confirm that the contribution does not violate any intellectual property rights of third parties

Changes

Testing you performed

Please add any demo scripts to https://github.com/TomographicImaging/CIL-Demos/tree/main/misc

Unittests on local Linux installation. Tested the following and it works as expected and as in the CIL-Demos.

Unittests on local Windows installation.

from cil.plugins import TomoPhantom as cilTomoPhantom
from cil.framework import ImageGeometry

n = 256
ig = ImageGeometry(voxel_num_x=n, 
                   voxel_num_y=n, 
                   voxel_size_x=2/n, 
                   voxel_size_y=2/n)
print(ig)
#%%
phantom2D = cilTomoPhantom.get_ImageData(num_model=1, geometry=ig)


#%%
from cil.utilities.display import show2D

show2D(phantom2D)

Related issues/links

• closes CIL channel tomophantom - updating to latest version. #2085

Checklist

• I have performed a self-review of my code
• I have added docstrings in line with the guidance in the developer guide
• I have updated the relevant documentation
• I have implemented unit tests that cover any new or modified functionality
• CHANGELOG.md has been updated with any functionality change
• Request review from all relevant developers

[paskino]

Currently v3.0.2 of TomoPhantom has been released however, it seems to depend on Python 3.14 only.

[paskino]

Fixes in Tomophantom as:

• conda package for libtomophantom version 3.0.2 depends on python 3.14 dkazanc/TomoPhantom#129
• setup conda correctly dkazanc/TomoPhantom#130

[lauramurgatroyd]

We're working on uploading a release of tomophantom v3.0.3 to the ccpi channel. We will use this or the one from httomo, whatever is ready fastest. Then we can merge in before the numpy 2 PR

https://anaconda.org/channels/ccpi/packages/tomophantom/files
https://anaconda.org/channels/ccpi/packages/libtomophantom/overview

[gfardell]

I have built the binaries for windows and linux (currently available on ccpi/label/dev), to make this not pinned to a python version I removed this line:
https://github.com/dkazanc/TomoPhantom/blob/e5dede43cef35d4856ba36aee65174ad48524231/conda-recipe_library/meta.yaml#L19

For linux the binaries seem to work:

(tomo_test) tpc56154@reconvm3:~/GitHub/CIL$ conda list tomophantom
# packages in environment at /home/tpc56154/miniforge3/envs/tomo_test:
#
# Name                    Version                   Build  Channel
libtomophantom            3.0.3                         0    ccpi/label/dev
tomophantom               3.0.3              pyh2b07374_0    ccpi/label/dev
(tomo_test) tpc56154@reconvm3:~/GitHub/CIL$ python
Python 3.12.13 | packaged by conda-forge | (main, Mar  5 2026, 16:50:00) [GCC 14.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> from cil.plugins import TomoPhantom
>>>

but on windows the library isn't found, it might be as simple as making sure ctypes is looking in the right place, but I think requires a code change, not just a new build of 3.0.3.

(tomo_test) C:\Users\gemst>conda list tomophantom
# packages in environment at C:\Users\gemst\miniforge3\envs\tomo_test:
#
# Name                    Version                   Build  Channel
libtomophantom            3.0.3                         0    ccpi/label/dev
tomophantom               3.0.3              pyh2b07374_0    ccpi/label/dev

(tomo_test) C:\Users\gemst>python
Python 3.10.20 | packaged by conda-forge | (main, Mar  5 2026, 16:36:49) [MSC v.1944 64 bit (AMD64)] on win32
Type "help", "copyright", "credits" or "license" for more information.
>>> from cil.plugins import TomoPhantom
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "C:\Users\gemst\miniforge3\envs\tomo_test\lib\site-packages\cil\plugins\TomoPhantom.py", line 21, in <module>
    import tomophantom
  File "C:\Users\gemst\miniforge3\envs\tomo_test\lib\site-packages\tomophantom\__init__.py", line 3, in <module>
    from tomophantom.TomoP2D import *
  File "C:\Users\gemst\miniforge3\envs\tomo_test\lib\site-packages\tomophantom\TomoP2D.py", line 22, in <module>
    import tomophantom.ctypes.external as external
  File "C:\Users\gemst\miniforge3\envs\tomo_test\lib\site-packages\tomophantom\ctypes\external.py", line 36, in <module>
    LIB_TOMOPHANTOM = c_shared_lib("tomophantom")
  File "C:\Users\gemst\miniforge3\envs\tomo_test\lib\site-packages\tomophantom\ctypes\__init__.py", line 44, in c_shared_lib
    raise ModuleNotFoundError(
ModuleNotFoundError: TomoPhantom links to compiled components which are installed separately and loaded using ctypes.util.find_library(). A required library, tomophantom, was not found.
>>>

EDIT: I'd built the dll as 32bit, making sure it's built as 64bit fixed it.

[casperdcl]

note that dkazanc/TomoPhantom#124 could be split into 2 PRs:

• scikit-build-core (easy, quick)
• migrate ctypes to nanobind/pybind11 etc (hard, not required)

the former would allow a simple cross-platform approach like we use in Wrappers/Python/cil/framework/cilacc.py

[gfardell]

This is now passing tests on windows locally. So I think we can promote the binaries ccpi/label/dev -> main and merge this PR.

[gfardell]

I'm not sure if the changes to build.yml are needed. @casperdcl do you know? I suspect that was just as @paskino was testing.

[lauramurgatroyd]

Please open an issue about windows support when you merge

[gfardell]

Tests all pass on the duplicate local branch.

https://github.com/TomographicImaging/CIL/actions/runs/24558373845/workflow