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Adding ct loader #86

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Adding ct loader #86

wants to merge 199 commits into from

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NewtonSander
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@NewtonSander NewtonSander commented Jun 28, 2023 •
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This PR adds the functionality of loading the brain and skull masks of a CT scan.

NewtonSander and others added 30 commits May 2, 2023 16:52
@NewtonSander
Merge pull request #1 from agencyenterprise/removing_stride_dependency
e3d41f2 
Removing stride dependency
@NewtonSander @github-actions
Poetry version updated
1721927
@NewtonSander
Releasing to pypi main repo
f9582d4
@NewtonSander
Merge pull request #2 from agencyenterprise/release_to_pypi_main_repo
3a179ea 
Releasing to pypi main repo
@NewtonSander @github-actions
Poetry version updated
d76a41d
@NewtonSander
Updating installation instructions of the README.md
b5beb2c
@NewtonSander @github-actions
Poetry version updated
02c8127
@NewtonSander
Adding stride dependencies to pyproject.toml
8008da2
@NewtonSander
Updating docs and CI to install stride with no dependencies
6bc7c82
@NewtonSander
Merge pull request #3 from agencyenterprise/regenerating_poetry_lock_…
716882e 
…file

Regenerating poetry lock file
@NewtonSander @github-actions
Poetry version updated
715e1c7
@NewtonSander
Changing scipy dependency of ndk so that it doesn't conflict with str…
06c6078 
…ide's dependency
@NewtonSander
Merge pull request #5 from agencyenterprise/reverting_stride_dependen…
37162d7 
…cy_change

Changing scipy dependency of ndk so that it doesn't conflict with stride's dependency
@NewtonSander @github-actions
Poetry version updated
2c21b3c
@NewtonSander
Adding frozenset to main dependencies
a2c0a0b
@NewtonSander @github-actions
Poetry version updated
c5013e0
@rob-luke
Update README with text from docs landing page (#4)
39800cd
@d-lucena @github-actions
Poetry version updated
f2d073b
@NewtonSander
Downgrading mkdocs gallery
32dd0d4
@NewtonSander
Merge pull request #6 from agencyenterprise/downgrading_mkdocs_gallery
fd2ca4e 
Downgrading mkdocs gallery
@NewtonSander @github-actions
Poetry version updated
8d119ae
@NewtonSander
Adding bounds to operator. Fixing devito version
d5f7bd7
@NewtonSander
Merge pull request #7 from agencyenterprise/reverting_bounds_removal
955bbeb 
Adding bounds to operator. Fixing devito version
@NewtonSander @github-actions
Poetry version updated
9785838
@NewtonSander
Mentioning libomp in the installation instructions
1f212fd
@NewtonSander
Mentioning libomp CPATH environment variable
7b743f5
@NewtonSander
Merge pull request #9 from agencyenterprise/improving_docs
d5f805c 
Mentioning libomp in the installation instructions
@NewtonSander @github-actions
Poetry version updated
9f946ed
@florin-pop
Redirect README to docs/index
3a8deb5
@florin-pop
Add circle config
0263621
NewtonSander and others added 20 commits July 17, 2023 05:55
@NewtonSander @github-actions
Poetry version updated
5bd680e
@conditg
various documentation changes and corrections (#111)
6de043c
@charlesbmi @d-lucena
Update napari install instructions to Qt6 on Mac M1 (#121)
699d311 
* Update napari install instructions to Qt6 on Mac M1

* lint code

* improve error message

Co-authored-by: Diogo de Lucena <[email protected]>

---------

Co-authored-by: Diogo de Lucena <[email protected]>
@charlesincharge @github-actions
Poetry version updated
955c8d2
@NewtonSander
Fixing gallery example
8a9fe05
@NewtonSander
Add resource estimation for pulsed simulations (#81)
6303cd8 
* Adding resource estimation for pulsed simulations
@NewtonSander @github-actions
Poetry version updated
f3efe05
@vaiana
Add Dockerfile-gpu (#112) (#113)
1c4e912
@NewtonSander
Adding default labeler to PRs (#120)
191213d
@charlesbmi
fix typo: type-hint vs default-value (#125)
081e0a9
@NewtonSander @github-actions
Poetry version updated
02bc8ce
@NewtonSander
Compiling problem on render_layout if it was not compiled previously (#…
4b5e4a1 
…124)
@NewtonSander
Not adding default labels if PR is already labeled (#127)
e62c90b 
* Not adding default labels if PR is already labeled

* Triggering CI

* Fixing labeler condition

* Trigger CI

* Reverting changes
@NewtonSander
Adding ct loader
e0310aa
@NewtonSander
Removing opencv dependency, using PCA to calculate rotation angle
a968997
@NewtonSander
Adding new words to spellchecker's whitelist
593c98a
@NewtonSander
Replacing pydicom with nibabel
b5db7f4
@NewtonSander
Adding test for loading a ct scan on dicom
1705bd0
@NewtonSander
Adding test for ct loader
d7fa8a5
@NewtonSander
Improving gallery docs
c9db93c
@NewtonSander NewtonSander force-pushed the load_ct branch 2 times, most recently from dd88ef8 to 3a9c6cd Compare July 28, 2023 09:32
@NewtonSander NewtonSander marked this pull request as draft August 9, 2023 17:45
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@d-lucena d-lucena Awaiting requested review from d-lucena

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9 participants
@NewtonSander @codecov-commenter @rob-luke @d-lucena @florin-pop @charlesbmi @conditg @charlesincharge @vaiana