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Add sampling masks (MagicMask, VariableDensityPoissonMask) #216

Merged
merged 43 commits into from
Jul 22, 2022
Merged

Add sampling masks (MagicMask, VariableDensityPoissonMask) #216

merged 43 commits into from
Jul 22, 2022

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georgeyiasemis
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@georgeyiasemis georgeyiasemis commented Jun 19, 2022 •
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Adding:

  • Variable density Poisson masking function
    • cython implementation
    • setup.py changes
  • Fastmri's Magic masking function
  • Additional tests
    Update:
  • torch.where output needed to be made contiguous to be inputted to fft, due to new torch version

@georgeyiasemis georgeyiasemis self-assigned this Jun 19, 2022
This was linked to issues Jun 19, 2022
Create Variable Density Disk Poisson Sub-Sampling #185
Closed
Create MagicFastMRI sub-sampling pattern #213
Closed
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codecov bot commented Jun 19, 2022 •
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Codecov Report

Merging #216 (e7120e2) into main (88eacc6) will decrease coverage by 0.46%.
The diff coverage is 95.55%.

@@            Coverage Diff             @@
##             main     #216      +/-   ##
==========================================
- Coverage   81.97%   81.50%   -0.47%     
==========================================
  Files          72       72              
  Lines        5708     5418     -290     
==========================================
- Hits         4679     4416     -263     
+ Misses       1029     1002      -27
Impacted Files Coverage Δ
direct/nn/crossdomain/crossdomain.py 90.16% <ø> (ø)
direct/nn/kikinet/kikinet.py 91.66% <ø> (ø)
direct/nn/lpd/lpd.py 90.36% <ø> (ø)
direct/common/subsample.py 84.63% <95.55%> (+13.78%) ⬆️
direct/data/h5_data.py 64.82% <0.00%> (-4.33%) ⬇️
direct/data/transforms.py 94.47% <0.00%> (-2.05%) ⬇️
direct/data/datasets.py 88.45% <0.00%> (-1.83%) ⬇️
direct/data/mri_transforms.py 98.92% <0.00%> (-0.41%) ⬇️
direct/utils/dataset.py 94.73% <0.00%> (+2.42%) ⬆️
direct/cli/utils.py 60.00% <0.00%> (+3.47%) ⬆️
... and 1 more

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@github-actions github-actions bot added the ci label Jun 20, 2022
georgeyiasemis
georgeyiasemis commented Jun 26, 2022
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OK

@georgeyiasemis
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@jonasteuwen The issue was fixed, so you can now review.

georgeyiasemis
georgeyiasemis commented Jun 27, 2022
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OK

jonasteuwen
jonasteuwen reviewed Jul 14, 2022
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Small comments

.github/workflows/tox.yml Outdated Show resolved Hide resolved
direct/common/_poisson.pyx Show resolved Hide resolved
@github-actions github-actions bot added the documentation Improvements or additions to documentation label Jul 19, 2022
jonasteuwen
jonasteuwen approved these changes Jul 22, 2022
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LGTM

@georgeyiasemis georgeyiasemis merged commit de905b1 into main Jul 22, 2022
@jonasteuwen jonasteuwen deleted the add-sampling-masks branch July 22, 2022 14:49
georgeyiasemis added a commit that referenced this pull request Jul 31, 2022
@georgeyiasemis
Adding sampling masks (MagicMask, VariableDensityPoissonMask) (#216, C…
c4b1ca7 
…loses #185, #213)

Adding new sampling patterbs:

* Variable density Poisson masking function (cython implementation)
    * setup.py changes
* Fastmri's Magic masking function

Bug fix/update:
* `torch.where` output needed to be made contiguous to be inputted to fft, due to new torch version
georgeyiasemis added a commit that referenced this pull request Jul 31, 2022
@georgeyiasemis
Adding sampling masks (MagicMask, VariableDensityPoissonMask) (#216, C…
f8bb009 
…loses #185, #213)

Adding new sampling patterbs:

* Variable density Poisson masking function (cython implementation)
    * setup.py changes
* Fastmri's Magic masking function

Bug fix/update:
* `torch.where` output needed to be made contiguous to be inputted to fft, due to new torch version
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@jonasteuwen jonasteuwen jonasteuwen approved these changes

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Create MagicFastMRI sub-sampling pattern Create Variable Density Disk Poisson Sub-Sampling
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