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Added greedy and elastix registrators #119

Merged
merged 40 commits into from
Mar 24, 2025
Merged

Added greedy and elastix registrators #119

merged 40 commits into from
Mar 24, 2025

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sarthakpati
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@sarthakpati sarthakpati commented Mar 24, 2025 •
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Fixes #118

This PR includes #114 (since I wanted to base some of my work off of elastix). Happy to disentangle, if it helps.

@sarthakpati
added elastix
d9b6e6e
@sarthakpati
added init
cbe57bd
@sarthakpati
updated requirements for elastix to optional
06cb343
@sarthakpati
added a basic solution
7664922
@sarthakpati
added elastixRegistrator import to registration module
c063d60
@sarthakpati
added test case for elastixRegistrator in test_registrators.py
dcf143f
@sarthakpati
refactor elastixRegistrator constructor to remove unused configuratio…
dd955e0 
…n_file parameter
@sarthakpati
add elastix to poetry extras for improved dependency management
75e7f7e
@sarthakpati
update GitHub Actions workflow to use 'uv' for dependency installation
b3f1dbb
@sarthakpati
update GitHub Actions workflow to use --system flag for pip installat…
dc28b52 
…ions
@sarthakpati
rename elastix dependency to itk-elastix in pyproject.toml for clarity
6eb9d90
@sarthakpati
update poetry extras to replace elastix with itk-elastix for consistency
6b7dc8c
@sarthakpati
fix: update log file handling in elastixRegistrator to use base name …
21cb5eb 
…and set output directory
@sarthakpati
fix: update elastix registration to save multiple transform parameter…
bb56ee2 
… maps
@sarthakpati
fix: update elastix registration to use GetTransformParameterObject f…
e8fb4e9 
…or parameter maps
@sarthakpati
fix: update elastix registration to handle initial transform paramete…
3e6c7d2 
…rs more effectively
@sarthakpati
fix: refactor elastix registration to streamline parameter handling a…
69ab5da 
…nd improve logging
@sarthakpati
fix: enhance elastix registration logging to support console output w…
2fa0ad9 
…hen log file path is not provided
@sarthakpati
fix: add .txt suffix to matrix path for initial transform parameters
ee0ce53
@sarthakpati
fix: enhance elastix registration to support parameter object initial…
2bccf97 
…ization and streamline matrix path handling
@sarthakpati
fix: add output directory parameter to elastix registration for impro…
770fb92 
…ved log management
@sarthakpati
fix: correct log file handling in elastix registration to separate lo…
a5ec11c 
…g path and file name
@sarthakpati
```
97b2ded 
fix: no code changes made
```
@sarthakpati
Merge branch 'main' into elastix
229862b
@sarthakpati
feat: add utility function to check and add suffix to filenames
e766737
@sarthakpati
refactor: replace internal suffix function with utility function for …
47d6d61 
…matrix path handling
@sarthakpati
feat: add optional dependency for picsl_greedy in pyproject.toml
118f31e
@sarthakpati
feat: implement greedy registration class for image alignment
2cc0000
@sarthakpati
refactor: remove unnecessary blank lines in elastix.py and generic.py
f1558d1
@sarthakpati
feat: refactor greedy registration to use Greedy3D class and streamli…
6dc71ad 
…ne parameters
@sarthakpati sarthakpati changed the title Added greedy Added greedy registration as an option Mar 24, 2025
@neuronflow neuronflow requested a review from MarcelRosier March 24, 2025 07:42
@MarcelRosier MarcelRosier mentioned this pull request Mar 24, 2025
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Comments addressed.

@neuronflow neuronflow changed the title Added greedy registration as an option Added greedy and elastix registrators Mar 24, 2025
MarcelRosier
MarcelRosier approved these changes Mar 24, 2025
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lgtm

@MarcelRosier MarcelRosier merged commit 1baedcc into BrainLesion:main Mar 24, 2025
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@neuronflow neuronflow mentioned this pull request Mar 24, 2025
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@sarthakpati , can you please document the inclusion of the two registrators in the manuscript?
https://www.overleaf.com/project/641ae8bf9931214366a85eae

Just cite both registration tools in the Multi-modal image to atlas preprocessing paragraph.

@sarthakpati sarthakpati deleted the greedy branch March 24, 2025 17:10
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@MarcelRosier MarcelRosier MarcelRosier approved these changes

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[FEATURE] Add greedy as a registration option
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@sarthakpati @neuronflow @MarcelRosier