def test_loading(self):
"""Test various loading schemes."""
# load demo images
CBCT.from_demo_images()
# load from folder directly
folder = osp.join(varian_test_file_dir, 'Pelvis')
CBCT(folder)
# load from zip file
zfile = osp.join(varian_test_file_dir, 'Pelvis.zip')
CBCT.from_zip_file(zfile)
def test_loading(self):
"""Test various loading schemes."""
# load demo images
CBCT.from_demo_images()
# load from folder directly
folder = osp.join(varian_test_file_dir, 'Pelvis')
CBCT(folder)
# load from zip file
zfile = osp.join(varian_test_file_dir, 'Pelvis.zip')
CBCT.from_zip_file(zfile)
class Test_General(unittest.TestCase):
"""Test general things when using cbct module."""
def setUp(self):
self.cbct = CBCT()
def test_demo(self):
"""Run the demo to make sure it works."""
self.cbct.run_demo(show=False)
def test_images_not_loaded(self):
"""Raise error if trying to analyze when images aren't loaded yet."""
self.assertRaises(AttributeError, self.cbct.analyze)
def test_bad_files(self):
"""Test bad file inputs."""
not_a_folder = "notafolder"
self.assertRaises(NotADirectoryError, self.cbct.load_folder, not_a_folder)
not_a_zip = "notazip.zip"
self.assertRaises(FileExistsError, self.cbct.load_zip_file, not_a_zip)
not_image_folder = osp.join(osp.dirname(__file__), 'core')
self.assertRaises(FileNotFoundError, self.cbct.load_folder, not_image_folder)
def test_too_few_images_loaded(self):
"""Test when too few images are given to be loaded."""
pass
def test_phan_center(self):
"""Test locations of the phantom center."""
self.cbct.load_demo_images()
known_phan_center = Point(257, 255)
self.cbct._construct_HU()
self.assertAlmostEqual(self.cbct.HU.phan_center.x, known_phan_center.x, delta=0.7)
self.assertAlmostEqual(self.cbct.HU.phan_center.y, known_phan_center.y, delta=0.7)
# test a shifted image set
shifted_phan_center = Point(287, 255)
self.cbct.settings.images = np.roll(self.cbct.settings.images, 30, axis=1)
self.cbct._construct_HU()
self.assertAlmostEqual(self.cbct.HU.phan_center.x, shifted_phan_center.x, delta=0.7)
self.assertAlmostEqual(self.cbct.HU.phan_center.y, shifted_phan_center.y, delta=0.7)
def setUp(self):
self.cbct = CBCT()
def setUpClass(cls):
cls.cbct = CBCT.from_demo_images()
class Test_General(unittest.TestCase):
"""Test general things when using cbct module."""
def setUp(self):
self.cbct = CBCT()
def test_demo(self):
"""Run the demo to make sure it works."""
self.cbct.run_demo()
def test_loading(self):
"""Test various loading schemes."""
# load demo images
CBCT.from_demo_images()
# load from folder directly
folder = osp.join(varian_test_file_dir, 'Pelvis')
CBCT(folder)
# load from zip file
zfile = osp.join(varian_test_file_dir, 'Pelvis.zip')
CBCT.from_zip_file(zfile)
def test_images_not_loaded(self):
"""Raise error if trying to analyze when images aren't loaded yet."""
self.assertRaises(AttributeError, self.cbct.analyze)
def test_bad_files(self):
"""Test bad file inputs."""
not_a_folder = "notafolder"
self.assertRaises(NotADirectoryError, self.cbct.load_folder, not_a_folder)
not_a_zip = "notazip.zip"
self.assertRaises(FileExistsError, self.cbct.load_zip_file, not_a_zip)
not_image_folder = osp.join(osp.dirname(__file__), 'core')
self.assertRaises(FileNotFoundError, self.cbct.load_folder, not_image_folder)
no_CT_images_zip = osp.join(varian_test_file_dir, 'dummy.zip')
self.assertRaises(FileNotFoundError, self.cbct.load_zip_file, no_CT_images_zip)
def test_images_not_from_same_study(self):
"""Loading images from different studies should raise and error."""
mixed_zip = osp.join(varian_test_file_dir, 'mixed_studies.zip')
with self.assertRaises(InvalidDicomError):
self.cbct.load_zip_file(mixed_zip)
def test_phan_center(self):
"""Test locations of the phantom center."""
self.cbct.load_demo_images()
known_phan_center = Point(257, 255)
self.cbct._construct_HU()
self.assertAlmostEqual(self.cbct.HU.phan_center.x, known_phan_center.x, delta=0.7)
self.assertAlmostEqual(self.cbct.HU.phan_center.y, known_phan_center.y, delta=0.7)
# test a shifted image set
shifted_phan_center = Point(287, 255)
self.cbct.settings.images = np.roll(self.cbct.settings.images, 30, axis=1)
self.cbct._construct_HU()
self.assertAlmostEqual(self.cbct.HU.phan_center.x, shifted_phan_center.x, delta=0.7)
self.assertAlmostEqual(self.cbct.HU.phan_center.y, shifted_phan_center.y, delta=0.7)
@unittest.skip
def test_finding_HU_slice(self):
"""Test the robustness of the algorithm to find the HU linearity slice."""
self.cbct.load_demo_images()
self.assertEqual(self.cbct.settings.hu_slice_num, 32)
# roll the phantom data by 4 slices
np.roll(self.cbct.settings.images, 4, axis=2)
def test_save_image(self):
"""Test that saving an image does something."""
filename = 'saved_img.jpg'
self.cbct.load_demo_images()
self.cbct.analyze(hu_tolerance=10, scaling_tolerance=0.01)
for method in ['save_analyzed_image', 'save_analyzed_subimage']:
methodcall = getattr(self.cbct, method)
methodcall(filename)
time.sleep(0.1) # sleep just to let OS work
self.assertTrue(osp.isfile(filename), "Save file did not successfully save the image")
# cleanup
os.remove(filename)
self.assertFalse(osp.isfile(filename), "Save file test did not clean up saved image")
def test_plot_images(self):
"""Test the various plotting functions."""
self.cbct.load_demo_images()
self.cbct.analyze()
self.cbct.plot_analyzed_image()
for item in ['hu', 'unif', 'mtf', 'sr']:
self.cbct.plot_analyzed_subimage(item)
with self.assertRaises(ValueError):
self.cbct.plot_analyzed_subimage('srunif')
def setUpClass(cls):
if cls.zip:
cls.cbct = CBCT.from_zip_file(cls.location)
else:
cls.cbct = CBCT(cls.location)
class GeneralTests(unittest.TestCase):
"""Test general things when using cbct module."""
def setUp(self):
self.cbct = CBCT()
def test_demo(self):
"""Run the demo to make sure it works."""
self.cbct.run_demo()
def test_helpers(self):
"""Test the various helper methods."""
self.cbct.load_demo_images()
self.cbct.analyze()
self.cbct._return_results()
def test_loading(self):
"""Test various loading schemes."""
# load demo images
CBCT.from_demo_images()
# load from folder directly
folder = osp.join(varian_test_file_dir, 'Pelvis')
CBCT(folder)
# load from zip file
zfile = osp.join(varian_test_file_dir, 'Pelvis.zip')
CBCT.from_zip_file(zfile)
def test_images_not_loaded(self):
"""Raise error if trying to analyze when images aren't loaded yet."""
self.assertRaises(AttributeError, self.cbct.analyze)
def test_bad_files(self):
"""Test bad file inputs."""
not_a_folder = "notafolder"
self.assertRaises(NotADirectoryError, self.cbct.load_folder, not_a_folder)
not_a_zip = "notazip.zip"
self.assertRaises(FileExistsError, self.cbct.load_zip_file, not_a_zip)
not_image_folder = osp.join(osp.dirname(__file__), 'core')
self.assertRaises(FileNotFoundError, self.cbct.load_folder, not_image_folder)
no_CT_images_zip = osp.join(varian_test_file_dir, 'dummy.zip')
self.assertRaises(FileNotFoundError, self.cbct.load_zip_file, no_CT_images_zip)
@unittest.expectedFailure
def test_images_not_from_same_study(self):
"""Loading images from different studies should raise and error."""
mixed_zip = osp.join(varian_test_file_dir, 'mixed_studies.zip')
with self.assertRaises(ValueError):
self.cbct.load_zip_file(mixed_zip)
def test_phan_center(self):
"""Test locations of the phantom center."""
self.cbct.load_demo_images()
known_phan_center = Point(257, 255)
self.cbct.analyze()
self.assertAlmostEqual(self.cbct.hu.phan_center.x, known_phan_center.x, delta=0.7)
self.assertAlmostEqual(self.cbct.hu.phan_center.y, known_phan_center.y, delta=0.7)
@unittest.skip
def test_finding_HU_slice(self):
"""Test the robustness of the algorithm to find the HU linearity slice."""
self.cbct.load_demo_images()
self.assertEqual(self.cbct.settings.hu_slice_num, 32)
# roll the phantom data by 4 slices
np.roll(self.cbct.settings.images, 4, axis=2)
def test_save_image(self):
"""Test that saving an image does something."""
self.cbct.load_demo_images()
self.cbct.analyze(hu_tolerance=10, scaling_tolerance=0.01)
for method in ['save_analyzed_image', 'save_analyzed_subimage']:
methodcall = getattr(self.cbct, method)
save_file(methodcall)
def test_plot_images(self):
"""Test the various plotting functions."""
self.cbct.load_demo_images()
self.cbct.analyze()
self.cbct.plot_analyzed_image()
for item in ['hu', 'un', 'mtf', 'sp', 'prof', 'lin', 'lc']:
self.cbct.plot_analyzed_subimage(item)
self.cbct.plot_analyzed_subimage('lin', delta=False)
with self.assertRaises(ValueError):
self.cbct.plot_analyzed_subimage('sr')
def setUpClass(cls):
if cls.zip:
cls.cbct = CBCT.from_zip_file(cls.location)
else:
cls.cbct = CBCT(cls.location)
cls.cbct.analyze(cls.hu_tolerance, cls.scaling_tolerance)
def setUpClass(cls):
cls.cbct = CBCT.from_demo_images()
cls.cbct.analyze()
def setUp(self):
self.cbct = CBCT()
class GeneralTests(unittest.TestCase):
"""Test general things when using cbct module."""
def setUp(self):
self.cbct = CBCT()
def test_demo(self):
"""Run the demo to make sure it works."""
self.cbct.run_demo()
def test_helpers(self):
"""Test the various helper methods."""
self.cbct.load_demo_images()
self.cbct.analyze()
self.cbct._return_results()
def test_loading(self):
"""Test various loading schemes."""
# load demo images
CBCT.from_demo_images()
# load from folder directly
folder = osp.join(varian_test_file_dir, 'Pelvis')
CBCT(folder)
# load from zip file
zfile = osp.join(varian_test_file_dir, 'Pelvis.zip')
CBCT.from_zip_file(zfile)
def test_images_not_loaded(self):
"""Raise error if trying to analyze when images aren't loaded yet."""
self.assertRaises(AttributeError, self.cbct.analyze)
def test_bad_files(self):
"""Test bad file inputs."""
not_a_folder = "notafolder"
self.assertRaises(NotADirectoryError, self.cbct.load_folder,
not_a_folder)
not_a_zip = "notazip.zip"
self.assertRaises(FileExistsError, self.cbct.load_zip_file, not_a_zip)
not_image_folder = osp.join(osp.dirname(__file__), 'core')
self.assertRaises(FileNotFoundError, self.cbct.load_folder,
not_image_folder)
no_CT_images_zip = osp.join(varian_test_file_dir, 'dummy.zip')
self.assertRaises(FileNotFoundError, self.cbct.load_zip_file,
no_CT_images_zip)
@unittest.expectedFailure
def test_images_not_from_same_study(self):
"""Loading images from different studies should raise and error."""
mixed_zip = osp.join(varian_test_file_dir, 'mixed_studies.zip')
with self.assertRaises(ValueError):
self.cbct.load_zip_file(mixed_zip)
def test_phan_center(self):
"""Test locations of the phantom center."""
self.cbct.load_demo_images()
known_phan_center = Point(257, 255)
self.cbct.analyze()
self.assertAlmostEqual(self.cbct.hu.phan_center.x,
known_phan_center.x,
delta=0.7)
self.assertAlmostEqual(self.cbct.hu.phan_center.y,
known_phan_center.y,
delta=0.7)
@unittest.skip
def test_finding_HU_slice(self):
"""Test the robustness of the algorithm to find the HU linearity slice."""
self.cbct.load_demo_images()
self.assertEqual(self.cbct.settings.hu_slice_num, 32)
# roll the phantom data by 4 slices
np.roll(self.cbct.settings.images, 4, axis=2)
def test_save_image(self):
"""Test that saving an image does something."""
self.cbct.load_demo_images()
self.cbct.analyze(hu_tolerance=10, scaling_tolerance=0.01)
for method in ['save_analyzed_image', 'save_analyzed_subimage']:
methodcall = getattr(self.cbct, method)
save_file(methodcall)
def test_plot_images(self):
"""Test the various plotting functions."""
self.cbct.load_demo_images()
self.cbct.analyze()
self.cbct.plot_analyzed_image()
for item in ['hu', 'un', 'mtf', 'sp', 'prof', 'lin', 'lc']:
self.cbct.plot_analyzed_subimage(item)
self.cbct.plot_analyzed_subimage('lin', delta=False)
with self.assertRaises(ValueError):
self.cbct.plot_analyzed_subimage('sr')
def setUpClass(cls):
if cls.zip:
cls.cbct = CBCT.from_zip_file(cls.location)
else:
cls.cbct = CBCT(cls.location)
cls.cbct.analyze(cls.hu_tolerance, cls.scaling_tolerance)
def setUpClass(cls):
cls.cbct = CBCT.from_zip_file(cls.thorax_zip)
def setUpClass(cls):
cls.cbct = CBCT.from_zip_file(cls.pelvis_zip)
