[SyneRBI/SIRF-Exercises] Minor fixes (PR #251)
Kris Thielemans
You can view, comment on, or merge this pull request online at:
https://github.com/SyneRBI/SIRF-Exercises/pull/251
Commit Summary
- edc5049 edit outdated comments for mMR normalisation file
- 814261b remove use of deprecated scipy.ndimage.filters
File Changes
(5 files)
- M environment.yml (2)
- M notebooks/PET/reconstruct_measured_data.ipynb (8)
- M notebooks/Synergistic/BrainWeb-single_slice_motion.ipynb (2)
- M notebooks/Synergistic/MAPEM_Bowsher.ipynb (2)
- M requirements.txt (2)
Patch Links:
- https://github.com/SyneRBI/SIRF-Exercises/pull/251.patch
- https://github.com/SyneRBI/SIRF-Exercises/pull/251.diff
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Kris Thielemans
KrisThielemans left a comment (SyneRBI/SIRF-Exercises#251)@ColomboMatte0 could you quickly test the edits?
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Casper da Costa-Luis
@casperdcl commented on this pull request.
In environment.yml:
> @@ -13,7 +13,7 @@ dependencies: - numpy - cil # make synergistic notebooks work - astra-toolbox # needed for ct examples - - scipy + - scipy>=1.16
We can't do this as it requires python>=3.11
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Kris Thielemans
KrisThielemans left a comment (SyneRBI/SIRF-Exercises#251)That's kind of weird. Maybe I saw those deprecation messages then on other systems, not our docker.
So, we will need to postpone this. (we could put in some workaround checking scipy version, but that seems overkill)
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Kris Thielemans
@KrisThielemans pushed 1 commit.
- 6f23b5f remove use of deprecated scipy.ndimage.filters
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Kris Thielemans
KrisThielemans left a comment (SyneRBI/SIRF-Exercises#251)I've rebased this after merging #254 to keep only 1 commit
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Kris Thielemans
@KrisThielemans commented on this pull request.
In environment.yml:
> @@ -13,7 +13,7 @@ dependencies: - numpy - cil # make synergistic notebooks work - astra-toolbox # needed for ct examples - - scipy + - scipy>=1.16
@casperdcl I took this version by attempting to see when scipy switched to the new structure. Maybe I have the wrong version? (seems unlikely we actually would need python 3.11, as some notebooks have the "new" import already I believe)
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Kris Thielemans
@KrisThielemans commented on this pull request.
In environment.yml:
> @@ -13,7 +13,7 @@ dependencies: - numpy - cil # make synergistic notebooks work - astra-toolbox # needed for ct examples - - scipy + - scipy>=1.16
we are using python 3.12 now in docker etc, so will go ahead with this.
⬇️ Suggested change- - scipy>=1.16 + - scipy>=1.16 + - python>=3.12
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Kris Thielemans
@KrisThielemans pushed 1 commit.
- e33e02f require python 3.12
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Kris Thielemans
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