Merge pull request #308 from GSTT-CSC/306-refactor-relaxometry-to-use…

…-hazentask 306 refactor relaxometry to use hazentask
GSTT-CSC · Feb 2, 2023 · 0dc7620 · 0dc7620 · github-actions · Feb 2, 2023
2 parents ba10d0a + 2fce2be
commit 0dc7620
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Showing 11 changed files with 1,423 additions and 1,453 deletions.
diff --git a/.github/workflows/test_cli.yml b/.github/workflows/test_cli.yml
@@ -101,4 +101,3 @@ jobs:
         if: always()  # will always run regardless of whether previous step fails - useful to ensure all CLI functions tested
         run: |
           hazen relaxometry tests/data/relaxometry/T1/site1_20200218/plate5 --calc_t1 --plate_number=5 --report
-
diff --git a/.gitignore b/.gitignore
@@ -30,7 +30,6 @@ report
 # TODO: Remove the following if no longer needed
 tests/data/slicepos/results
 tests/data/uniformity/results
-hazenlib/data
 
 # docs
 docs/_build

diff --git a/hazenlib/__init__.py b/hazenlib/__init__.py
@@ -315,24 +315,6 @@ def get_field_of_view(dcm: pydicom.Dataset):
     return fov
 
 
-def parse_relaxometry_data(task, arguments, dicom_objects,
-                           report):  # def parse_relaxometry_data(arguments, dicom_objects, report):   #
-
-    # Relaxometry arguments
-    relaxometry_cli_args = {'--calc_t1', '--calc_t2', '--plate_number',
-                            '--show_template_fit', '--show_relax_fits',
-                            '--show_rois', '--verbose'}
-
-    # Pass arguments with dictionary, stripping initial double dash ('--')
-    relaxometry_args = {}
-
-    for key in relaxometry_cli_args:
-        relaxometry_args[key[2:]] = arguments[key]
-
-    return task.main(dicom_objects, report_path=report,
-                     **relaxometry_args)
-
-
 def main():
     arguments = docopt(__doc__, version=__version__)
     task_module = importlib.import_module(f"hazenlib.tasks.{arguments['<task>']}")
@@ -387,9 +369,19 @@ def main():
     # TODO: Refactor Relaxometry task into HazenTask object Relaxometry not currently converted to HazenTask object -
     #  this task accessible in the CLI using the old syntax until it can be refactored
     elif arguments['<task>'] == 'relaxometry':
-        task = importlib.import_module(f"hazenlib.{arguments['<task>']}")
-        dicom_objects = [pydicom.read_file(x, force=True) for x in files if is_dicom_file(x)]
-        result = parse_relaxometry_data(task, arguments, dicom_objects, report=True)
+
+        # Relaxometry arguments
+        relaxometry_cli_args = {'--calc_t1', '--calc_t2', '--plate_number',
+                                '--show_template_fit', '--show_relax_fits',
+                                '--show_rois', '--verbose'}
+
+        # Pass arguments with dictionary, stripping initial double dash ('--')
+        relaxometry_args = {}
+        for key in relaxometry_cli_args:
+            relaxometry_args[key[2:]] = arguments[key]
+
+        result = task.run(**relaxometry_args)
+
     else:
         result = task.run()
Original file line number	Diff line number	Diff line change
Expand Up		@@ -101,4 +101,3 @@ jobs:
		if: always() # will always run regardless of whether previous step fails - useful to ensure all CLI functions tested
		run: \|
		hazen relaxometry tests/data/relaxometry/T1/site1_20200218/plate5 --calc_t1 --plate_number=5 --report
File	Stmts	Miss	Cover	Missing
hazenlib
HazenTask.py	25	3	88%	32–34
__init__.py	147	41	72%	141, 145, 155, 160, 197, 204–209, 220, 223–230, 250–252, 270–272, 291–293, 302, 307, 313, 345, 356, 362–368, 392–393, 397
exceptions.py	21	4	81%	17–21
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	157	53	66%	53–74, 152, 215–260
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	326	90	72%	414, 467–469, 523, 571–593, 611–626, 656–674, 1174–1177, 1186–1189, 1203–1216, 1219–1224, 1235–1265
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	2500	650	74%