class TestTlogFluence(TestCase):
def setUp(self):
self.log = MachineLog()
self.log.load_demo_trajectorylog()
def test_fluence(self):
fluence = self.log.fluence
fluence.gamma.calc_map()
self.assertAlmostEqual(fluence.gamma.pass_prcnt, 100, delta=0.1)
self.assertAlmostEqual(fluence.gamma.avg_gamma, 0.001, delta=0.005)
self.assertAlmostEqual(fluence.gamma.histogram()[0][0], 240000, delta=100)
def test_plotting(self):
# raise error if map hasn't yet been calc'ed.
with self.assertRaises(AttributeError):
self.log.fluence.actual.plot_map()
self.log.fluence.actual.calc_map()
self.log.fluence.actual.plot_map()
def test_saving_plots(self):
self.log.fluence.gamma.calc_map()
save_file('test.png', self.log.fluence.gamma.save_map)
def test_subbeam_data(self):
"""Test accessing the subbeam data."""
expected_vals = [310, 180, 3.7, 3.4, 3.8, 3.9]
for item, expval in zip(('gantry_angle', 'collimator_angle', 'jaw_x1', 'jaw_x2', 'jaw_y1', 'jaw_y2'), expected_vals):
val = getattr(self.log.subbeams[0], item)
self.assertAlmostEqual(val.actual, expval, delta=0.1)
def test_trajectorylog(self):
tlog_file = osp.join(self.anon_folder, 'PatientID_4DC Treatment_JST90_TX_20140712094246.bin')
tlog = MachineLog(tlog_file)
tlog.anonymize()
files = tlog.anonymize(inplace=True, suffix='inplace')
self.assertIsInstance(files, list)
for file in files:
self.assertTrue('inplace' in file)
def test_mlc(self):
mlc = self.log.axis_data.mlc
self.assertTrue(mlc.hdmlc)
self.assertEqual(mlc.num_leaves, 120)
self.assertEqual(mlc.num_pairs, 60)
self.assertEqual(mlc.num_snapshots, 1021)
log_no_exclusion = MachineLog()
log_no_exclusion.load_demo_trajectorylog(exclude_beam_off=False)
self.assertEqual(log_no_exclusion.axis_data.mlc.num_snapshots, 5200)
def test_trajectorylog(self):
tlog_file = osp.join(
self.anon_folder,
'PatientID_4DC Treatment_JST90_TX_20140712094246.bin')
tlog = MachineLog(tlog_file)
tlog.anonymize()
files = tlog.anonymize(inplace=True, suffix='inplace')
self.assertIsInstance(files, list)
for file in files:
self.assertTrue('inplace' in file)
def test_dynalog(self):
# test making an anonymized copy
dlog_file = osp.join(self.anon_folder, 'A1234_patientid.dlg')
dlog = MachineLog(dlog_file)
dlog.anonymize()
# test doing inplace anonymization
files = dlog.anonymize(inplace=True, suffix='inplace')
self.assertIsInstance(files, list)
for file in files:
self.assertTrue('inplace' in file)
def test_dynalog(self):
# test making an anonymized copy
dlog_file = osp.join(self.anon_folder, 'A1234_patientid.dlg')
dlog = MachineLog(dlog_file)
dlog.anonymize()
# test doing inplace anonymization
files = dlog.anonymize(inplace=True, suffix='inplace')
self.assertIsInstance(files, list)
for file in files:
self.assertTrue('inplace' in file)
class Test_Tlog_Fluence(TestCase):
def setUp(self):
self.log = MachineLog()
self.log.load_demo_trajectorylog()
def test_fluence(self):
fluence = self.log.fluence
fluence.gamma.calc_map()
self.assertAlmostEqual(fluence.gamma.pass_prcnt, 100, delta=0.1)
self.assertAlmostEqual(fluence.gamma.avg_gamma, 0.001, delta=0.005)
self.assertAlmostEqual(fluence.gamma.histogram()[0][0], 240000, delta=100)
def test_dynalog_loading(self):
a_file = osp.join(TEST_DIR, 'dlogs', 'Adlog1.dlg')
MachineLog(a_file)
b_file = osp.join(TEST_DIR, 'dlogs', 'Bdlog1.dlg')
MachineLog(b_file)
a_but_not_b_dir = osp.join(TEST_DIR, 'a_no_b_dir', 'Adlog1.dlg')
self.assertRaises(FileNotFoundError, MachineLog, a_but_not_b_dir)
b_but_not_a_dir = osp.join(TEST_DIR, 'b_no_a_dir', 'Bdlog1.dlg')
self.assertRaises(FileNotFoundError, MachineLog, b_but_not_a_dir)
bad_name_dlg = osp.join(TEST_DIR, 'bad_names', 'bad_name_dlg.dlg')
self.assertRaises(ValueError, MachineLog, bad_name_dlg)
def test_loading(self):
"""Test that loading the badly-named dynalog still loads and identifies properly."""
test_tlog = osp.join(self.test_dir, 'tlogs', "qqq2106_4DC Treatment_JS0_TX_20140712095629.bin")
# should produce no errors
# load method 1
MachineLog(test_tlog)
# load method 2
log = MachineLog()
self.assertFalse(log.is_loaded)
log.load(test_tlog)
self.assertTrue(log.is_loaded)
# throw an error for files that aren't logs
not_a_file = test_tlog.replace(".bin", 'blahblah.bin')
self.assertRaises(FileExistsError, MachineLog, not_a_file)
not_a_log = osp.join(osp.dirname(__file__), 'test_files', 'VMAT', 'DRGSmlc-105-example.dcm')
self.assertRaises(IOError, MachineLog, not_a_log)
def test_txt_file_also_loads_if_around(self):
# has a .txt file
log_with_txt = osp.join(
TEST_DIR, 'mixed_types',
"Anonymous_4DC Treatment_JST90_TX_20140712094246.bin")
log = MachineLog(log_with_txt)
self.assertTrue(hasattr(log, 'txt'))
self.assertIsInstance(log.txt, dict)
self.assertEqual(log.txt['Patient ID'], 'Anonymous')
# DOESN'T have a txt file
log_no_txt = osp.join(
TEST_DIR, 'tlogs',
"Anonymous_4DC Treatment_JS0_TX_20140712095629.bin")
log = MachineLog(log_no_txt)
self.assertFalse(hasattr(log, 'txt'))
class TestLogPlottingSaving(TestCase):
"""Test the plotting methods and plot saving methods."""
tlog = MachineLog.from_demo_trajectorylog()
dlog = MachineLog.from_demo_dynalog()
def test_save_tlog_to_csv(self):
save_file(self.tlog.to_csv)
def test_plot_axes(self):
for methodname in ('plot_actual', 'plot_expected', 'plot_difference'):
method = getattr(self.tlog.axis_data.gantry, methodname)
method() # shouldn't raise
def test_save_axes(self):
for methodname in ('save_plot_actual', 'save_plot_expected',
'save_plot_difference'):
# save matplotlib figures
method = getattr(self.tlog.axis_data.gantry, methodname)
save_file(method)
# save MPLD3 HTML
save_file(method, interactive=True, as_file_object='str')
def test_fluence_plotting(self):
# raise error if map hasn't yet been calc'ed.
with self.assertRaises(AttributeError):
self.dlog.fluence.actual.plot_map()
self.dlog.fluence.actual.calc_map()
self.dlog.fluence.actual.plot_map()
self.dlog.fluence.gamma.calc_map()
self.dlog.fluence.gamma.histogram()
self.dlog.fluence.gamma.plot_histogram()
self.dlog.fluence.gamma.plot_passfail_map()
def test_saving_fluence_plots(self):
self.dlog.fluence.gamma.calc_map()
save_file(self.dlog.fluence.gamma.save_map)
save_file(self.dlog.fluence.gamma.save_histogram)
def test_save_summary(self):
self.tlog.fluence.gamma.calc_map()
save_file(self.tlog.save_summary)
class TestDlogFluence(TestCase):
def setUp(self):
self.log = MachineLog()
self.log.load_demo_dynalog()
def test_demo(self):
self.log.run_dlog_demo()
def test_fluence(self):
fluence = self.log.fluence
self.assertFalse(fluence.actual.map_calced)
self.assertFalse(fluence.expected.map_calced)
self.assertFalse(fluence.gamma.map_calced)
self.assertRaises(AttributeError, fluence.actual.plot_map)
# do repeating fluence calcs; ensure semi-lazy property
start = time.time()
fluence.actual.calc_map()
end = time.time()
first_calc_time = end - start
start = time.time()
fluence.actual.calc_map()
end = time.time()
second_calc_time = end - start
self.assertLess(second_calc_time, first_calc_time)
# same for gamma
start = time.time()
fluence.gamma.calc_map(resolution=0.15)
end = time.time()
first_calc_time = end - start
start = time.time()
fluence.gamma.calc_map(resolution=0.15)
end = time.time()
second_calc_time = end - start
self.assertLess(second_calc_time, first_calc_time)
self.assertAlmostEqual(fluence.gamma.pass_prcnt, 99.85, delta=0.1)
self.assertAlmostEqual(fluence.gamma.avg_gamma, 0.019, delta=0.005)
self.assertAlmostEqual(fluence.gamma.histogram()[0][0], 155804, delta=100)
def test_loading(self):
"""Test that loading the badly-named dynalog still loads and identifies properly."""
test_tlog = osp.join(
TEST_DIR, 'tlogs',
"Anonymous_4DC Treatment_JS0_TX_20140712095629.bin")
# should produce no errors
MachineLog(test_tlog)
# throw an error for files that aren't logs
not_a_file = test_tlog.replace(".bin", 'blahblah.bin')
self.assertRaises(IOError, MachineLog, not_a_file)
not_a_log = osp.join(osp.dirname(__file__), 'test_files', 'VMAT',
'DRGSmlc-105-example.dcm')
self.assertRaises(IOError, MachineLog, not_a_log)
def test_append(self):
# append a directory
logs = MachineLogs(self.logs_altdir)
logs.append(self.logs_altdir)
self.assertEqual(logs.num_logs, 8)
# append a file string
single_file = osp.join(
self.logs_altdir,
'Anonymous_4DC Treatment_JST90_TX_20140712094246.bin')
logs.append(single_file)
# append a MachineLog
single_log = MachineLog(single_file)
logs.append(single_log)
# try to append something that's not a Log
log = None
with self.assertRaises(TypeError):
logs.append(log)
def test_bad_name(self):
"""Test that a log with a bad name (no underscore) fails gracefully."""
dlog_file = osp.join(self.anon_folder, 'A1234patientid.dlg')
dlog = MachineLog(dlog_file)
with self.assertRaises(NameError):
dlog.anonymize()
def setUpClass(cls):
cls.log = MachineLog(cls.get_filename())
cls.log.fluence.gamma.calc_map()
def test_demo(self):
"""Test the run demo method."""
# shouldn't raise
MachineLog.run_tlog_demo()
def setUpClass(cls):
cls.log = MachineLog.from_demo_trajectorylog()
cls.log.fluence.gamma.calc_map()
def test_from_url(self):
url = 'https://s3.amazonaws.com/assuranceqa-staging/uploads/imgs/Tlog2.bin'
log = MachineLog.from_url(url)
def setUp(self):
self.log = MachineLog()
self.log.load_demo_trajectorylog()
def setUpClass(cls):
cls.log = MachineLog.from_demo_trajectorylog()
cls.log.fluence.gamma.calc_map()
def test_demo(self):
"""Test the run demo method."""
# shouldn't raise
MachineLog.run_tlog_demo()
def setUp(self):
self.log = MachineLog()
self.log.load_demo_dynalog()
def test_destination(self):
tlog_file = osp.join(
self.anon_folder,
'PatientID_4DC Treatment_JST90_TX_20140712094246.bin')
tlog = MachineLog(tlog_file)
tlog.anonymize(destination=self.anon_folder) # shouldn't raise
def test_destination(self):
tlog_file = osp.join(self.anon_folder, 'PatientID_4DC Treatment_JST90_TX_20140712094246.bin')
tlog = MachineLog(tlog_file)
tlog.anonymize(destination=self.anon_folder) # shouldn't raise
def test_bad_name(self):
"""Test that a log with a bad name (no underscore) fails gracefully."""
dlog_file = osp.join(self.anon_folder, 'A1234patientid.dlg')
dlog = MachineLog(dlog_file)
with self.assertRaises(NameError):
dlog.anonymize()
def test_from_stream(self):
"""Anonymizing a log that was loaded from a stream should fail (no filename to replace)."""
url = 'https://s3.amazonaws.com/assuranceqa-staging/uploads/imgs/Tlog2.bin'
tlog = MachineLog.from_url(url)
with self.assertRaises(IOError):
tlog.anonymize()