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386 Verbose option for slice position #387

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merged 12 commits into from
Oct 9, 2023
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sophie22
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@sophie22 sophie22 commented Oct 5, 2023

General improvement to the way of passing key word arguments from the CLI to the relevant HazenTask class (rather than to its .run() function.
Add CLI option to slice position task to display the rounded positions for all 40 slices with --verbose

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github-actions bot commented Oct 5, 2023

Coverage

Coverage Report
FileStmtsMissCoverMissing
hazenlib
   ACRObject.py1071190%74, 77–79, 84–87, 125, 168–169
   HazenTask.py29390%41–43
   __init__.py571574%166, 197–200, 202–206, 208–210, 225–230, 234
   exceptions.py21576%17–21, 38
   utils.py1894377%61, 65, 75, 80, 117, 124–129, 140, 143–150, 170–172, 190–192, 211–213, 222, 227, 233, 284, 287, 295–300, 303, 346, 355, 371
hazenlib/tasks
   acr_geometric_accuracy.py1196248%42–86, 96–121, 134–168
   acr_ghosting.py1074261%35–51, 77–79, 109–111, 145–187
   acr_slice_position.py1364865%47–68, 194–241
   acr_slice_thickness.py1366056%34–53, 162–224
   acr_snr.py1365857%46, 51–92, 102, 172–182, 216–231, 264–281
   acr_spatial_resolution.py2066867%59–86, 131, 174, 187–196, 278–330
   acr_uniformity.py813260%38–56, 112–138
   ghosting.py1515166%19–36, 51, 113–114, 118, 128–129, 155–157, 174–176, 222–259
   relaxometry.py2918969%207–208, 210, 221–224, 230–236, 268–312, 353, 387–405, 580, 626–628, 695, 769–791, 809–824
   slice_position.py1244068%26, 31–62, 114–115, 141, 221, 229–247
   slice_width.py3525285%36–38, 42, 107, 166–187, 441, 446–447, 453, 458, 516–517, 767–809
   snr.py1686760%61, 78–83, 179–197, 212–221, 239–249, 276–286, 291–301, 332–346, 351–359, 388–402
   snr_map.py108199%152
   spatial_resolution.py2494482%41–43, 47, 68, 153, 212, 338–375
   uniformity.py791976%47–49, 53, 95–96, 103, 137–152
TOTAL287181072% 

Tests Skipped Failures Errors Time
201 0 💤 0 ❌ 0 🔥 4m 0s ⏱️

@sophie22 sophie22 requested a review from tomaroberts October 5, 2023 12:01
@sophie22
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sophie22 commented Oct 5, 2023

@tomaroberts ready for review
small PR grew into a slim medium: changing the way CLI options are being passed to Task objects, primarily to enable adding the --verbose option to the slice position task as physicists requested, consequently updated the way SNR and ACR SNR tasks take their CLI args - relevant for @mollybuckley too! (happy to explain in detail)

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@sophie22 – this is ready to merge, however, there are a couple of merge conflicts which have popped up since I merged #381. Can you resolve and then we'll proceed.

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sophie22 commented Oct 9, 2023

merge conflicts resolved, ready for final review @tomaroberts

@tomaroberts tomaroberts merged commit 64010cb into main Oct 9, 2023
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@tomaroberts tomaroberts deleted the 386_slice-pos-verbose branch October 9, 2023 13:38
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2 participants