def test_purge_table(self):
r"""We use either of two criterion functions"""
with self.assertRaises(AssertionError) as exception_info:
purge_table('I am not here', 'table', [True, False])
assert 'Input workspace I am not here does not exists' in str(exception_info.exception)
with self.assertRaises(AssertionError) as exception_info:
purge_table(self.cases['123455_bank20'], 'I am not here', [True, False])
assert 'Input table I am not here does not exists' in str(exception_info.exception)
# control bank, it has no problems. Thus, no tubes to purge
fit_bank(self.cases['123455_bank20'], 'bank20')
tube_fit_success = criterion_peak_pixel_position('PeakTable', zscore_threshold=2.5, deviation_threshold=3)
unpurged_row_count = mtd['CalibTable'].rowCount()
purge_table(self.cases['123455_bank20'], 'CalibTable', tube_fit_success)
assert mtd['CalibTable'].rowCount() == unpurged_row_count
DeleteWorkspaces(['CalibTable', 'PeakTable', 'PeakYTable', 'ParametersTable']) # a bit of clean-up
# tube11 is not working at all. Thus, purge only one tube
fit_bank(self.cases['124018_bank45'], 'bank45')
tube_fit_success = criterion_peak_vertical_position('PeakYTable', zscore_threshold=2.5,
deviation_threshold=0.0035)
unpurged_row_count = mtd['CalibTable'].rowCount()
purge_table(self.cases['124018_bank45'], 'CalibTable', tube_fit_success)
assert mtd['CalibTable'].rowCount() == unpurged_row_count - 256
self.assert_missing_tube('CalibTable', 11)
DeleteWorkspaces(['CalibTable', 'PeakTable', 'PeakYTable', 'ParametersTable']) # a bit of clean-up
def test_collect_bank_fit_results(self):
def spectra_labels(workspace_name):
workspace = mtd[str(workspace_name)]
axis = workspace.getAxis(1)
return [axis.label(spectrum_index) for spectrum_index in range(workspace.getNumberHistograms())]
fit_bank(self.cases['123455_bank20'], 'bank20', parameters_table_group='parameters_tables')
criterion_peak_vertical_position('PeakTable', summary='summary',
zscore_threshold=2.5, deviation_threshold=0.0035)
with self.assertRaises(AssertionError) as exception_info:
collect_bank_fit_results('fit_results', acceptance_summary=None, parameters_table_group=None)
assert 'fit results should be different than None' in str(exception_info.exception)
# collect only the acceptance criteria results
collect_bank_fit_results('fit_results', acceptance_summary='summary', parameters_table_group=None)
assert spectra_labels('fit_results') == ['success', 'deviation', 'Z-score']
assert_allclose(mtd['fit_results'].readY(0), mtd['summary'].readY(0))
DeleteWorkspaces(['fit_results'])
# collect only the polynomial coefficients
collect_bank_fit_results('fit_results', acceptance_summary=None, parameters_table_group='parameters_tables')
assert spectra_labels('fit_results') == ['A0', 'A1', 'A2']
for coefficient_idx in range(3): # we have three polynomial coefficients
for tube_idx in range(TUBES_IN_BANK):
self.assertAlmostEqual(mtd['fit_results'].readY(coefficient_idx)[tube_idx],
mtd[f'parameters_tables_{tube_idx}'].row(coefficient_idx)['Value'], delta=1e-6)
self.assertAlmostEqual(mtd['fit_results'].readE(coefficient_idx)[tube_idx],
mtd[f'parameters_tables_{tube_idx}'].row(coefficient_idx)['Error'], delta=1e-6)
DeleteWorkspaces(['fit_results'])
# collect both acceptance criteria and polynomial coefficients
collect_bank_fit_results('fit_results', acceptance_summary='summary',
parameters_table_group='parameters_tables')
assert spectra_labels('fit_results') == ['success', 'deviation', 'Z-score', 'A0', 'A1', 'A2']
for spectrum_idx in [0, 1, 2]:
assert_allclose(mtd['fit_results'].readY(spectrum_idx), mtd['summary'].readY(spectrum_idx))
assert_allclose(mtd['fit_results'].readE(spectrum_idx), mtd['summary'].readE(spectrum_idx))
for coefficient_idx, spectrum_idx in [(0, 3), (1, 4), (2, 5)]: # we have three polynomial coefficients
for tube_idx in range(TUBES_IN_BANK):
self.assertAlmostEqual(mtd['fit_results'].readY(spectrum_idx)[tube_idx],
mtd[f'parameters_tables_{tube_idx}'].row(coefficient_idx)['Value'], delta=1e-6)
self.assertAlmostEqual(mtd['fit_results'].readE(spectrum_idx)[tube_idx],
mtd[f'parameters_tables_{tube_idx}'].row(coefficient_idx)['Error'], delta=1e-6)
DeleteWorkspaces(['CalibTable', 'fit_results', 'parameters_tables', 'PeakTable', 'PeakYTable', 'summary'])
def test_purge_table(self):
with self.assertRaises(AssertionError) as exception_info:
purge_table('I am not here', 'table', [True, False])
assert 'Input workspace I am not here does not exists' in str(exception_info.exception)
with self.assertRaises(AssertionError) as exception_info:
purge_table(self.cases['123455_bank20'], 'I am not here', [True, False])
assert 'Input table I am not here does not exists' in str(exception_info.exception)
# control bank, it has no problems. Thus, no tubes to purge
fit_bank(self.cases['123455_bank20'], 'bank20')
tube_fit_success = criterium_peak_pixel_position('PeakTable', zscore_threshold=2.5, deviation_threshold=3)
unpurged_row_count = mtd['CalibTable'].rowCount()
purge_table(self.cases['123455_bank20'], 'CalibTable', tube_fit_success)
assert mtd['CalibTable'].rowCount() == unpurged_row_count
# tube11 is not working at all. Thus, purge only one tube
fit_bank(self.cases['124018_bank45'], 'bank45')
tube_fit_success = criterium_peak_pixel_position('PeakTable', zscore_threshold=2.5, deviation_threshold=3)
unpurged_row_count = mtd['CalibTable'].rowCount()
purge_table(self.cases['124018_bank45'], 'CalibTable', tube_fit_success)
assert mtd['CalibTable'].rowCount() == unpurged_row_count - 256
self.assert_missing_tube('CalibTable', 11)
# tubes 3, 8, and 13 have very faint wire shadows. Thus, purge three tubes
fit_bank(self.cases['124023_bank14'], 'bank14')
tube_fit_success = criterium_peak_pixel_position('PeakTable', zscore_threshold=2.5, deviation_threshold=3)
unpurged_row_count = mtd['CalibTable'].rowCount()
purge_table(self.cases['124023_bank14'], 'CalibTable', tube_fit_success)
assert mtd['CalibTable'].rowCount() == unpurged_row_count - 256 * 3
for tube_number in (3, 8, 13):
self.assert_missing_tube('CalibTable', tube_number)
DeleteWorkspaces(['CalibTable', 'PeakTable']) # a bit of clean-up
def test_mask_bank(self):
# control bank, it has no problems. Thus, no mask to be created
fit_bank(self.cases['123455_bank20'], 'bank20')
tube_fit_success = criterium_peak_pixel_position('PeakTable', zscore_threshold=2.5, deviation_threshold=3)
assert mask_bank('bank20', tube_fit_success, 'masked_tubes') is None
# tube11 is not working at all. Thus, mask this tube
fit_bank(self.cases['124018_bank45'], 'bank45')
tube_fit_success = criterium_peak_pixel_position('PeakTable', zscore_threshold=2.5, deviation_threshold=3)
mask_bank('bank45', tube_fit_success, 'masked_tubes')
detector_ids = mtd['masked_tubes'].column(0)
assert detector_ids[0], detector_ids[-1] == [182784, 182784 + 256]
# tubes 3, 8, and 13 have very faint wire shadows. Thus, mask these tubes
fit_bank(self.cases['124023_bank14'], 'bank14')
tube_fit_success = criterium_peak_pixel_position('PeakTable', zscore_threshold=2.5, deviation_threshold=3)
mask_bank('bank14', tube_fit_success, 'masked_tubes')
detector_ids = mtd['masked_tubes'].column(0)
assert detector_ids[0], detector_ids[-1] == [182784, 182784 + 3 * 256]
DeleteWorkspaces(['CalibTable', 'PeakTable', 'masked_tubes']) # a bit of clean-up
def test_criterium_peak_pixel_position(self):
# control bank, it has no problems
fit_bank(self.cases['123455_bank20'], 'bank20')
expected = np.ones(16, dtype=bool)
assert_equal(criterium_peak_pixel_position('PeakTable', zscore_threshold=2.5, deviation_threshold=3), expected)
# beam center intensity spills over adjacent tubes, tube15 and tube16
fit_bank(self.cases['123454_bank58'], 'bank58')
expected = np.array([1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0], dtype=bool)
assert_equal(criterium_peak_pixel_position('PeakTable', zscore_threshold=2.5, deviation_threshold=3), expected)
# tube11 is not working at all
fit_bank(self.cases['124018_bank45'], 'bank45')
expected = np.array([1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1], dtype=bool)
assert_equal(criterium_peak_pixel_position('PeakTable', zscore_threshold=2.5, deviation_threshold=3), expected)
# tube 13 has shadows at pixel numbers quite different from the rest
fit_bank(self.cases['124023_bank10'], 'bank10')
expected = np.array([1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1], dtype=bool)
assert_equal(criterium_peak_pixel_position('PeakTable', zscore_threshold=2.5, deviation_threshold=3), expected)
# tubes 3, 8, and 13 have very faint wire shadows
fit_bank(self.cases['124023_bank14'], 'bank14')
expected = np.array([1, 1, 0, 1, 1, 1, 1, 0, 1, 1, 1, 1, 0, 1, 1, 1], dtype=bool)
assert_equal(criterium_peak_pixel_position('PeakTable', zscore_threshold=2.5, deviation_threshold=3), expected)
# one spurious shadow in tube14, not enough to flag a discrepancy
fit_bank(self.cases['124023_bank15'], 'bank15')
expected = np.ones(16, dtype=bool)
assert_equal(criterium_peak_pixel_position('PeakTable', zscore_threshold=2.5, deviation_threshold=3), expected)
# check for the summary workspace
fit_bank(self.cases['123455_bank20'], 'bank20')
criterium_peak_pixel_position('PeakTable', summary='summary', zscore_threshold=2.5, deviation_threshold=3)
assert AnalysisDataService.doesExist('summary')
workspace = mtd['summary']
axis = workspace.getAxis(1)
assert [axis.label(workspace_index) for workspace_index in (0, 1, 2)] == ['success', 'deviation', 'Z-score']
self.assertEqual(min(workspace.readY(0)), 1.0)
self.assertAlmostEqual(max(workspace.readY(2)), 1.728, delta=0.001)
DeleteWorkspaces(['CalibTable', 'PeakTable', 'summary']) # a bit of clean-up
def test_fit_bank(self):
with self.assertRaises(AssertionError) as exception_info:
fit_bank('I_am_not_here', 'bank42')
assert 'Input workspace I_am_not_here does not exists' in str(exception_info.exception)
control = self.cases['123455_bank20'] # a bank with a reasonable wire scan
with self.assertRaises(AssertionError) as exception_info:
fit_bank(control, 'bank20', shadow_height=-1000)
assert 'shadow height must be positive' in str(exception_info.exception)
with self.assertRaises(AssertionError) as exception_info:
fit_bank(control, 'tree/bank51')
assert 'The bank name must be of the form' in str(exception_info.exception)
with self.assertRaises(AssertionError) as exception_info:
fit_bank(self.cases['123555_bank20'], 'bank20')
assert 'Insufficient counts per pixel in workspace CORELLI_123555_bank20' in str(exception_info.exception)
fit_bank(control, 'bank20')
# Expect default name for calibration table
assert AnalysisDataService.doesExist('CalibTable')
# Expect default name for peak pixel position table
assert AnalysisDataService.doesExist('PeakTable')
DeleteWorkspaces(['CalibTable', 'PeakTable'])
fit_bank(control, 'bank20', calibration_table='table_20', peak_pixel_positions_table='pixel_20')
assert AnalysisDataService.doesExist('table_20')
assert AnalysisDataService.doesExist('pixel_20')
DeleteWorkspaces(['CalibTable', 'PeakTable']) # a bit of clean-up
def test_fit_bank(self):
control = self.cases['123455_bank20'] # a bank with a reasonable wire scan
with self.assertRaises(AssertionError) as exception_info:
fit_bank('I_am_not_here', 'bank42')
with self.assertRaises(AssertionError) as exception_info:
fit_bank(control, 'bank20', shadow_height=-1000)
assert 'shadow height must be positive' in str(exception_info.exception)
with self.assertRaises(AssertionError) as exception_info:
fit_bank(control, 'tree/bank51')
assert 'The bank name must be of the form' in str(exception_info.exception)
with self.assertRaises(AssertionError) as exception_info:
fit_bank(self.cases['123555_bank20'], 'bank20')
assert 'Insufficient counts per pixel in workspace CORELLI_123555_bank20' in str(exception_info.exception)
fit_bank(control, 'bank20', parameters_table_group='parameters_table')
# Expect default name for calibration table
assert AnalysisDataService.doesExist('CalibTable')
# Expect default name for peak pixel position table
assert AnalysisDataService.doesExist('PeakTable')
# Expect default name for peak pixel position table
assert AnalysisDataService.doesExist('PeakYTable')
# assert the parameters tables are created
assert AnalysisDataService.doesExist('parameters_table')
for tube_number in range(TUBES_IN_BANK):
assert AnalysisDataService.doesExist(f'parameters_table_{tube_number}')
DeleteWorkspaces(['CalibTable', 'PeakTable', 'PeakYTable', 'parameters_table'])
fit_bank(control, 'bank20', calibration_table='table_20', peak_pixel_positions_table='pixel_20')
assert AnalysisDataService.doesExist('table_20')
assert AnalysisDataService.doesExist('pixel_20')
DeleteWorkspaces(['table_20', 'pixel_20', 'PeakYTable', 'ParametersTable']) # a bit of clean-up
def test_criterion_peak_vertical_position(self):
# control bank, it has no problems
fit_bank(self.cases['123455_bank20'], 'bank20')
expected = np.ones(16, dtype=bool)
actual = criterion_peak_vertical_position('PeakYTable', zscore_threshold=2.5, deviation_threshold=0.0035)
assert_equal(actual, expected)
DeleteWorkspaces(['CalibTable', 'ParametersTable', 'PeakTable', 'PeakYTable']) # a bit of clean-up
# beam center intensity spills over adjacent tubes, tube15 and tube16
fit_bank(self.cases['123454_bank58'], 'bank58')
expected = np.array([1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0], dtype=bool)
actual = criterion_peak_vertical_position('PeakYTable', zscore_threshold=2.5, deviation_threshold=0.0035)
assert_equal(actual, expected)
DeleteWorkspaces(['CalibTable', 'ParametersTable', 'PeakTable', 'PeakYTable']) # a bit of clean-up
# tube11 is not working at all
fit_bank(self.cases['124018_bank45'], 'bank45')
expected = np.array([1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1], dtype=bool)
actual = criterion_peak_vertical_position('PeakYTable', zscore_threshold=2.5, deviation_threshold=0.0035)
assert_equal(actual, expected)
DeleteWorkspaces(['CalibTable', 'ParametersTable', 'PeakTable', 'PeakYTable']) # a bit of clean-up
# tube 13 has shadows at pixel numbers quite different from the rest, but similar vertical positions
fit_bank(self.cases['124023_bank10'], 'bank10')
expected = np.array([1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1], dtype=bool)
actual = criterion_peak_vertical_position('PeakYTable', zscore_threshold=2.5, deviation_threshold=0.0035)
assert_equal(actual, expected)
DeleteWorkspaces(['CalibTable', 'ParametersTable', 'PeakTable', 'PeakYTable']) # a bit of clean-up
# one spurious shadow in tube14 throws away the fit
fit_bank(self.cases['124023_bank15'], 'bank15')
expected = np.array([1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1], dtype=bool)
actual = criterion_peak_vertical_position('PeakYTable', zscore_threshold=2.5, deviation_threshold=0.0035)
assert_equal(actual, expected)
DeleteWorkspaces(['CalibTable', 'ParametersTable', 'PeakTable', 'PeakYTable']) # a bit of clean-up
# check for the summary workspace
fit_bank(self.cases['123455_bank20'], 'bank20')
criterion_peak_vertical_position('PeakYTable', summary='summary',
zscore_threshold=2.5, deviation_threshold=0.0035)
assert AnalysisDataService.doesExist('summary')
workspace = mtd['summary']
axis = workspace.getAxis(1)
assert [axis.label(workspace_index) for workspace_index in (0, 1, 2)] == ['success', 'deviation', 'Z-score']
self.assertEqual(min(workspace.readY(0)), 1.0) # check success of first tube
self.assertAlmostEqual(max(workspace.readY(2)), 2.73, delta=0.01) # check maximum Z-score
DeleteWorkspaces(['CalibTable', 'ParametersTable', 'PeakTable', 'PeakYTable', 'summary']) # a bit of clean-up