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T2 Rician noise #204

Merged
merged 6 commits into from
Jul 17, 2023
Merged

T2 Rician noise #204

merged 6 commits into from
Jul 17, 2023

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pcw24601
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Fixes #104

@pcw24601 pcw24601 self-assigned this Jan 14, 2022
@pcw24601 pcw24601 changed the base branch from main to release/0.6.0 January 14, 2022 11:14
pcw24601 and others added 3 commits January 14, 2022 16:32
Estimates image ROI values based upon a Rician noise model rather
than Gaussian. No in-depth testing yet carried out, preliminary
observations:
 1. As expected, the model does fall to zero for long TEs.
 2. ROIs with long T2 reach a solution with a large sigma (e.g. ~100
     instead of ~10).

Tests not yet updated.
The revised algorithm produces slightly different T2 measurements.
These have been updated.
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github-actions bot commented Apr 1, 2022

Coverage

Coverage Report
FileStmtsMissCoverMissing
hazenlib
   HazenTask.py25388%32–34
   __init__.py1514173%141, 145, 155, 160, 197, 204–209, 220, 223–230, 250–252, 270–272, 291–293, 302, 307, 313, 363, 374, 380–386, 400–401, 405
   exceptions.py21481%17–21
   relaxometry.py3119071%248–266, 640, 699–701, 755, 803–825, 843–858, 1186–1189, 1198–1201, 1213–1226, 1229–1234, 1245–1274
   shapes.py20955%13, 16, 24–29, 32
   tools.py84890%43–50, 92, 101, 117
hazenlib/tasks
   acr_geometric_accuracy.py1455562%38–72, 176–192, 206–230
   acr_ghosting.py1164264%33–53, 91–93, 123–125, 161–194
   acr_slice_position.py1545366%53–74, 152, 213–258
   acr_slice_thickness.py1536359%40–60, 186–241
   acr_snr.py1375858%34–71, 96, 165–175, 208–221, 254–267
   acr_spatial_resolution.py2427270%66–86, 165, 208, 221–230, 319–374
   acr_uniformity.py893264%34–54, 121–138
   ghosting.py1505166%18–32, 47, 109–110, 114, 124–125, 151–153, 170–172, 218–256
   relaxometry.py7271%10–11
   slice_position.py1182281%31, 40–41, 103–104, 130, 210, 217–234
   slice_width.py3565285%34–37, 107, 166–186, 451, 456–457, 463, 468, 530–531, 780–821
   snr.py1636660%62–67, 161–179, 194–203, 221–231, 258–268, 273–283, 314–327, 332–340, 369–382
   snr_map.py106199%294
   spatial_resolution.py2464482%36–39, 62, 147, 206, 332–368
   uniformity.py781976%42–45, 91–92, 99, 133–147
TOTAL288878773% 

Tests Skipped Failures Errors Time
219 0 💤 0 ❌ 0 🔥 3m 0s ⏱️

@pcw24601 pcw24601 changed the title WIP-T2 Rician noise T2 Rician noise Apr 1, 2022
@pcw24601 pcw24601 requested a review from Lucrezia-Cester April 1, 2022 15:09
@pcw24601 pcw24601 changed the base branch from release/0.6.0 to release/0.7.0 April 7, 2022 08:33
@tomaroberts tomaroberts self-assigned this Jul 14, 2023
@tomaroberts tomaroberts requested review from tomaroberts and removed request for Lucrezia-Cester July 14, 2023 14:47
@tomaroberts tomaroberts changed the base branch from release/0.7.0 to main July 17, 2023 12:46
@tomaroberts tomaroberts changed the base branch from main to dev July 17, 2023 12:57
@tomaroberts tomaroberts changed the base branch from dev to main July 17, 2023 12:59
tomaroberts
tomaroberts previously approved these changes Jul 17, 2023
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May need additional updates after PR #351 merged into main due to fundamental updates to __init__.py and utils file.

@tomaroberts tomaroberts merged commit 8eeca28 into main Jul 17, 2023
@sophie22
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May need additional updates after PR #351 merged into main due to fundamental updates to __init__.py and utils file.

as long as the main function in the relaxometry script is not changed (which it isn't), then it does not cause merge or functionality issues to #351. relaxometry task does not rely/use any of the utility functions from utils.py

@pcw24601 pcw24601 deleted the t2-rician-noise branch August 6, 2023 18:46
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[HZN-105] Fit T2 relaxometry model with Rician PDF
3 participants