ACR Slice Thickness Functionality

[YassineAzma]

Adds an ACR Slice Thickness script and associated unit tests that calculates the slice thickness of the ACR phantom for slice 1. 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 location of the ramps within the phantom.
    • Draw line profiles along the length of the ramps within the phantom using different offsets around the ramp locations found in the previous step.
    • The FWHM is determined for each line profile.
    • Calculates the slice thickness, dz, using the following formula for all line profile configurations: $$dz = 0.2 (L_{upper} L{lower})/(L{upper} + L_{lower}) $$
    • Select the closest dz to the true slice thickness, as defined in the DICOM metadata, as the final result.

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

[github-actions[bot]]

Coverage Report

File	Stmts	Miss	Cover	Missing
hazenlib
HazenTask.py	25	3	88%	32–34
__init__.py	151	41	73%	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.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
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_slice_position.py	154	53	66%	53–74, 152, 213–258
acr_slice_thickness.py	153	63	59%	40–60, 186–241
acr_snr.py	137	58	58%	34–71, 96, 165–175, 208–221, 254–267
acr_spatial_resolution.py	242	72	70%	66–86, 165, 208, 221–230, 319–374
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	106	1	99%	294
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	2894	787	73%

Tests	Skipped	Failures	Errors	Time
219	0 :zzz:	0 :x:	0 :fire:	2m 34s :stopwatch:

[YassineAzma]

Hi, @Lucrezia-Cester. This PR is ready for review whenever you're available.