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Introduce_ereg #49

Merged
merged 34 commits into from
Apr 16, 2024
Merged

Introduce_ereg #49

merged 34 commits into from
Apr 16, 2024

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neuronflow
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@neuronflow
clean niftyr todo
01e696c 
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@neuronflow
foundation for ereg
acabda8 
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TODO
7984a3f 
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add todo
495c7a9 
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resample
b009597 
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format
d57c0bd 
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ereg
5707d13 
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@neuronflow neuronflow marked this pull request as draft December 14, 2023 14:54
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logs
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clean
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@neuronflow neuronflow added the enhancement New feature or request label Dec 14, 2023
This was linked to issues Dec 14, 2023
The pipeline doesn't run on MacOs #3
Closed
[feature request] simple reg #25
Closed
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clean
6f37639 
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clean
952ecde 
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@neuronflow
import ereg
aa58a70 
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add ereg to requirements
6931391 
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typing
91a37c0 
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@neuronflow neuronflow marked this pull request as ready for review February 15, 2024 11:07
@neuronflow neuronflow marked this pull request as draft February 15, 2024 11:07
@neuronflow neuronflow marked this pull request as ready for review March 30, 2024 12:43
neuronflow and others added 6 commits March 30, 2024 13:51
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ants
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merge
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Merge branch 'main' into introduce_ereg
c248cea
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specify version
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eReg
c4fd63c 
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configuration file
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import
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example
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@neuronflow neuronflow marked this pull request as draft March 30, 2024 13:27
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@sarthakpati hmm currently this crashes using eregs default parameters:

*** start ***
  0%|                                                                 | 0/2 [00:00<?, ?it/s]
Traceback (most recent call last):
  File "/home/florian/flow/BrainLesion/preprocessing/example/example_modality_centric_preprocessor.py", line 132, in <module>
    preprocess(exam)
  File "/home/florian/flow/BrainLesion/preprocessing/example/example_modality_centric_preprocessor.py", line 116, in preprocess
    preprocessor.run(
  File "/home/florian/flow/BrainLesion/preprocessing/brainles_preprocessing/preprocessor.py", line 132, in run
    moving_modality.register(
  File "/home/florian/flow/BrainLesion/preprocessing/brainles_preprocessing/modality.py", line 178, in register
    registrator.register(
  File "/home/florian/flow/BrainLesion/preprocessing/brainles_preprocessing/registration/eReg/eReg.py", line 41, in register
    registrator.register(
  File "/home/florian/miniconda3/envs/brainles2/lib/python3.10/site-packages/ereg/registration.py", line 153, in register
    if self.parameters["bias_correct"]:
KeyError: 'bias_correct'

@neuronflow neuronflow mentioned this pull request Mar 30, 2024
Closed
neuronflow added 11 commits March 30, 2024 18:56
@neuronflow
bump version
92fbf0e 
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bump version
0fbca21 
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handle missing suffixes
5c26c87 
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ereg test
837bed5 
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switch to mat
a5b8647 
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mat
6da9ae8 
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name
5c4ce46 
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nicer unit test
4ec1221 
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better tests
dcb1ab1 
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@neuronflow
bump version
b13906b 
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fix: tests
48ae7f8 
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@neuronflow neuronflow marked this pull request as ready for review April 16, 2024 21:23
@neuronflow neuronflow removed the request for review from sarthakpati April 16, 2024 21:23
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TODO we could fine-tune ereg parameters

@neuronflow neuronflow marked this pull request as draft April 16, 2024 21:42
@neuronflow neuronflow marked this pull request as ready for review April 16, 2024 21:43
@neuronflow neuronflow merged commit 5ad167b into main Apr 16, 2024
3 checks passed
@neuronflow neuronflow deleted the introduce_ereg branch April 16, 2024 21:44
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[feature request] simple reg The pipeline doesn't run on MacOs
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@neuronflow @sarthakpati