ACR Geometric Accuracy Functionality

[YassineAzma]

Adds an ACR Geometric Accuracy script and associated unit tests that calculates the vertical and horizontal length of the ACR phantom for slice 1, and the vertical, horizontal and diagonal lengths for slice 5. This is done within the new HazenTask framework. The methodology is as follows:

• Calculates the centroid of the object following morphological operations and a centre-of-mass calculation.
  • This step also produces a binary mask.
    • Uses line profiles to find the horizontal and vertical extent of the mask.
    • For diagonal line profiles:
    • The mask is first rotated by 45 degrees.
    • Vertical and horizontal line profiles are used to find the horizontal and vertical extent.
    • The start and end points of these profiles are then rotated back into the original coordinate system.
    • The distance is then calculated using these start and end points and an effective pixel spacing to reflect that the distance is no longer horizontal or vertical.

Resolves #189

The results are visualised in the report. Examples are shown below:

Distortion metrics, such as the average distance measurement error, maximum distance measurement error and coefficient of variation of all distance measurements, are reported in the terminal.

[github-actions[bot]]

Coverage Report

File	Stmts	Miss	Cover	Missing
hazenlib
HazenTask.py	25	4	84%	18, 32–34
__init__.py	155	44	72%	141, 145, 155, 160, 197, 204–209, 220, 223–230, 250–252, 270–272, 291–293, 302, 307, 313, 363, 374, 380–386, 396–398, 406–407, 411
exceptions.py	21	4	81%	17–21
relaxometry.py	317	90	72%	238–256, 631, 690–692, 746, 794–816, 834–849, 1174–1177, 1186–1189, 1201–1214, 1217–1222, 1233–1263
shapes.py	20	9	55%	13, 16, 24–29, 32
snr_map.py	111	5	95%	408, 413–415, 444
tools.py	84	8	90%	43–50, 92, 101, 117
hazenlib/tasks
acr_geometric_accuracy.py	145	55	62%	38–72, 176–192, 206–230
acr_ghosting.py	116	42	64%	33–53, 91–93, 123–125, 161–194
acr_snr.py	137	58	58%	34–71, 96, 165–175, 208–221, 254–267
acr_uniformity.py	89	32	64%	34–54, 121–138
ghosting.py	150	51	66%	18–32, 47, 109–110, 114, 124–125, 151–153, 170–172, 218–256
relaxometry.py	7	2	71%	10–11
slice_position.py	118	22	81%	31, 40–41, 103–104, 130, 210, 217–234
slice_width.py	356	52	85%	34–37, 107, 166–186, 451, 456–457, 463, 468, 530–531, 780–821
snr.py	163	66	60%	62–67, 161–179, 194–203, 221–231, 258–268, 273–283, 314–327, 332–340, 369–382
snr_map.py	7	7	0%	1–11
spatial_resolution.py	246	44	82%	36–39, 62, 147, 206, 332–368
uniformity.py	78	19	76%	42–45, 91–92, 99, 133–147
TOTAL	2361	614	74%

Tests	Skipped	Failures	Errors	Time
194	0 :zzz:	0 :x:	0 :fire:	2m 50s :stopwatch:

[Lucrezia-Cester]

Hi @YassineRMH, could you please re-base this PR to release 1.1.1 branch? Then I am happy to merge

[Lucrezia-Cester]

Hi @YassineRMH, could you merge the latest changes from release/1.1.1 into this branch please?