ACR - Slice Ordering and Orientation Checks

[YassineAzma]

Add function to determine if the slice order needs to be inverted or the images need to be swapped left-right to restore the expected view of the ACR phantom

This resolves #345.

Note: this is based off work on the #343 PR. Once this has been merged, I'll rebase this PR to the active hazen branch.

[github-actions[bot]]

Coverage Report

File	Stmts	Miss	Cover	Missing
hazenlib
ACRObject.py	101	10	90%	59–61, 66–69, 107, 123–124
HazenTask.py	25	3	88%	32–34
__init__.py	54	17	69%	125–133, 145, 179–181, 184–186, 193–196, 207
exceptions.py	21	4	81%	17–21
relaxometry.py	285	86	70%	182–200, 377, 423–425, 492, 566–588, 606–621, 1037–1040, 1046–1052, 1085–1130
utils.py	189	43	77%	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.py	121	64	47%	41–73, 121–146, 160–194
acr_ghosting.py	109	43	61%	34–49, 75–77, 107–109, 145–186
acr_slice_position.py	135	47	65%	46–61, 187–233
acr_slice_thickness.py	134	58	57%	34–48, 157–216
acr_snr.py	135	63	53%	43–83, 93, 163–173, 207–222, 255–272
acr_spatial_resolution.py	209	71	66%	58–83, 128, 171, 184–193, 275–326
acr_uniformity.py	83	33	60%	35–51, 108–133
ghosting.py	152	53	65%	18–35, 50, 112–113, 117, 127–128, 154–156, 173–175, 221–259
relaxometry.py	7	7	0%	1–11
slice_position.py	117	23	80%	28, 37–38, 49, 103–104, 130, 210, 217–234
slice_width.py	357	53	85%	34–37, 41, 109, 168–188, 453, 458–459, 465, 470, 532–533, 782–823
snr.py	166	67	60%	51, 68–73, 167–185, 200–209, 227–237, 264–274, 279–289, 320–333, 338–346, 375–388
snr_map.py	104	1	99%	291
spatial_resolution.py	247	45	82%	36–39, 43, 64, 149, 208, 334–370
uniformity.py	79	20	75%	42–45, 51, 93–94, 101, 135–149
TOTAL	2855	811	72%

Tests	Skipped	Failures	Errors	Time
201	0 :zzz:	0 :x:	0 :fire:	3m 21s :stopwatch:

[tomaroberts]

I'll review this soon too Yassine. Thanks.

[tomaroberts]

@YassineAzma – I've had a quick look through the changes in this PR and it looks sensible to me. I'll revisit properly once we've merged #343.

I agree with Sophie about the naming convention, because the class is more than just a set of useful helper tools. Let's merge #343, then can you raise a new PR with the naming changes.

Can you change:

• acr_tools.py -> ACRObject.py
• ACRTools class -> ACRObject

[RebeccaThornley]

Hi, on a recent data set the slice order inversion did not seem to work for some tests: SNR, ghosting, uniformity.

Though inversion seem to be applied correctly for geometric accuracy, the measurements were not performed correctly/not displayed correctly on the report.

[RebeccaThornley]

In relation to comment above, report showing SNR measurement made on wrong slice due to no slice order inversion