378 geom accuracy wrong slices

[mollybuckley]

The ACR geometric accuracy test was measuring from slice 7 rather than slices 1 and 5 as per the ACR guidance. I have:

• fixed this, so that the measurements were coming from the correct slices
• combined the separate functions for ACR geometric accuracy slice 1 and 5 (the previous difference was that the slice 5 function was taking diagonal measurements too but the slice 1 function was not). The function now has slice index as an input and if the slice index is 4 then the diagonal measurements are made.

I then realised that the mask was being created incorrectly on slice 1 of the GE data (this was not previously an issue as the slice was being created from slice 7). This was because one of the pixel values outside the phantom was above the masking threshold value. I have changed the threshold value so that it is no longer picking up background noise pixels and including these in the mask. The images on the report look acceptable but some future work could be to test this with more GE data. I then changed three of the unit tests accordingly, as there were very minor variations in the results following this change.

[sophie22]

resolves #378

[github-actions]

Coverage Report

File	Stmts	Miss	Cover	Missing
hazenlib
ACRObject.py	107	11	90%	92, 95–97, 102–105, 143, 197–200
HazenTask.py	29	3	90%	43–47
__init__.py	57	15	74%	173, 205–214, 216–225, 227–229, 246–250, 254
exceptions.py	21	5	76%	19–23, 42
utils.py	189	43	77%	72, 76, 86, 91, 130, 137–150, 161, 168–175, 195–197, 215–219, 238–242, 251, 256, 267, 319, 322, 330–335, 338, 385, 394, 409
hazenlib/tasks
acr_geometric_accuracy.py	112	58	48%	57–97, 119–180
acr_ghosting.py	107	42	61%	46–62, 105–107, 159–161, 211–293
acr_slice_position.py	136	48	65%	59–83, 286–353
acr_slice_thickness.py	136	60	56%	48–67, 238–322
acr_snr.py	134	58	57%	47, 62–113, 132, 227–242, 283–301, 348–373
acr_spatial_resolution.py	207	68	67%	69–100, 188, 286, 303–314, 460–539
acr_uniformity.py	81	32	60%	47–64, 148–200
ghosting.py	149	51	66%	28–47, 67, 171–172, 179, 196–197, 252–256, 271–275, 346–387
relaxometry.py	291	89	69%	210–211, 213, 226–231, 238–246, 277–326, 375, 409–431, 609, 655–659, 726, 811–833, 851–866
slice_position.py	124	40	68%	30, 43–71, 129–130, 157, 273, 283–306
slice_width.py	352	52	85%	44–48, 52, 123, 188–213, 555, 560–561, 567, 572, 648–649, 1021–1085
snr.py	173	69	60%	45–48, 87, 103–113, 206–225, 237–247, 287–302, 330–340, 345–361, 399–415, 428–434, 477–495
snr_map.py	108	1	99%	157
spatial_resolution.py	246	44	82%	50–54, 58, 90, 213, 294, 460–503
uniformity.py	80	19	76%	59–63, 67, 118–119, 126, 175–205
TOTAL	2864	808	72%

Tests	Skipped	Failures	Errors	Time
198	0 💤	0 ❌	0 🔥	2m 20s ⏱️

[sophie22]

Thank you! All comments have been satisfactorily addressed.
Happy to merge :)