def test_save_file_check_contents(self):
save_file(self.wksp, self.out_ascii)
out_wksp = LoadAscii(self.out_ascii, Separator='Space')
out_wksp = ConvertToHistogram(out_wksp)
self.assertEqual(out_wksp.blocksize(),
self.wksp.blocksize())
self.assertEqual(out_wksp.getNumberHistograms(),
self.wksp.getNumberHistograms())
self.assertTrue(np.allclose(out_wksp.getAxis(0).extractValues(),
self.wksp.getAxis(0).extractValues())
)
def setUp(self):
'''
This file is the back-calculated spectrum of polyethylene moderator (ambient 300K)
prior to the efficiency correction described in Eq (3) of:
Mildner et al. "A cooled polyethylene moderator on a pulsed neutron source",
Nucl. Instr. Meth. 152, 1978, doi:/10.1016/0029-554X(78)90043-5
After the correction is applied, the workspace will replicated (b) in Fig. 2 of this article.
Similar results are shown in Fig 1.a for "ambient (300K)" in:
S. Howells, "On the choice of moderator for a liquids diffractometer on a pulsed neutron source",
Nucl. Instr. Meth. Phys. Res. 223, 1984, doi:10.1016/0167-5087(84)90256-4
'''
LoadAscii(
OutputWorkspace=self._input_wksp,
Filename=
"CalculateEfficiencyCorrection_milder_moderator_polyethlyene_300K.txt",
Unit="Wavelength")
ConvertToPointData(InputWorkspace=self._input_wksp,
OutputWorkspace=self._input_wksp)
def runTest(self):
prefix = 'mU6g7vP92_' # pseudo-random string to prefix workspace names
LoadAscii(Filename='SNAP_51984_peakcenters_tof.dat',
Separator='Tab',
Unit='Dimensionless', OutputWorkspace=prefix + 'peak_centers')
LoadEmptyInstrument(InstrumentName='SNAP', OutputWorkspace=prefix + 'snap')
with capture_logs(level='debug') as logs:
AlignComponents(PeakCentersTofTable=prefix + 'peak_centers',
PeakPositions='1.3143, 1.3854,1.6967, 1.8587, 2.0781',
AdjustmentsTable=prefix + 'adjustments',
DisplacementsTable=prefix + 'displacements',
InputWorkspace=prefix + 'snap',
OutputWorkspace=prefix + 'snap_modified',
FitSourcePosition=False, FitSamplePosition=False,
ComponentList='Column1',
XPosition=False, YPosition=False, ZPosition=True,
AlphaRotation=False, BetaRotation=False, GammaRotation=False)
assert 'First and last detectorID for Column1 are 0, 196607' in logs.getvalue()
# Clean up workspaces
temporary = ['peak_centers', 'snap', 'adjustments', 'displacements', 'snap_modified']
DeleteWorkspaces([prefix + suffix for suffix in temporary])
def load_gudrun_file(self, input_file, output_workspace, number_of_columns,
first_data_line):
"""
Loads the gudrun file using the mantid LoadAscii algorithm
:param input_file: The file to load
:param output_workspace: The workspace to be the result of the load
:param number_of_columns: The number of columns in the file being loaded
:param first_data_line: The first line to expect data on
:return: The outputWorkspace of the Load Algorithm
"""
if number_of_columns % 2 == 0:
print(number_of_columns)
raise ValueError(
'Incorrect data format: The input file {} must have an odd number '
'of columns in the format X , Y , E, Y1, E1, Y2, E2, ...'.
format(input_file))
elif number_of_columns == 3:
LoadAscii(Filename=input_file,
OutputWorkspace=output_workspace,
CommentIndicator='#')
else:
self.load_multi_column_file(input_file, output_workspace,
first_data_line)
def focus_run(self, sample_paths, banks, plot_output, instrument, rb_num,
spectrum_numbers):
"""
Focus some data using the current calibration.
:param sample_paths: The paths to the data to be focused.
:param banks: The banks that should be focused.
:param plot_output: True if the output should be plotted.
:param instrument: The instrument that the data came from.
:param rb_num: The experiment number, used to create directories. Can be None
:param spectrum_numbers: The specific spectra that should be focused. Used instead of banks.
"""
if not Ads.doesExist(vanadium_corrections.INTEGRATED_WORKSPACE_NAME
) and not Ads.doesExist(
vanadium_corrections.CURVES_WORKSPACE_NAME):
return
integration_workspace = Ads.retrieve(
vanadium_corrections.INTEGRATED_WORKSPACE_NAME)
curves_workspace = Ads.retrieve(
vanadium_corrections.CURVES_WORKSPACE_NAME)
output_workspaces = [] # List of collated workspaces to plot.
full_calib_path = get_setting(path_handling.INTERFACES_SETTINGS_GROUP,
path_handling.ENGINEERING_PREFIX,
"full_calibration")
if full_calib_path is not None and path.exists(full_calib_path):
full_calib_workspace = LoadAscii(full_calib_path,
OutputWorkspace="det_pos",
Separator="Tab")
else:
full_calib_workspace = None
if spectrum_numbers is None:
for sample_path in sample_paths:
sample_workspace = path_handling.load_workspace(sample_path)
run_no = path_handling.get_run_number_from_path(
sample_path, instrument)
workspaces_for_run = []
for name in banks:
output_workspace_name = str(
run_no) + "_" + FOCUSED_OUTPUT_WORKSPACE_NAME + str(
name)
self._run_focus(sample_workspace, output_workspace_name,
integration_workspace, curves_workspace,
name, full_calib_workspace)
workspaces_for_run.append(output_workspace_name)
# Save the output to the file system.
self._save_output(instrument, sample_path, name,
output_workspace_name, rb_num)
output_workspaces.append(workspaces_for_run)
else:
for sample_path in sample_paths:
sample_workspace = path_handling.load_workspace(sample_path)
run_no = path_handling.get_run_number_from_path(
sample_path, instrument)
output_workspace_name = str(
run_no) + "_" + FOCUSED_OUTPUT_WORKSPACE_NAME + "cropped"
self._run_focus(sample_workspace, output_workspace_name,
integration_workspace, curves_workspace, None,
full_calib_workspace, spectrum_numbers)
output_workspaces.append([output_workspace_name])
self._save_output(instrument, sample_path, "cropped",
output_workspace_name, rb_num)
# Plot the output
if plot_output:
for ws_names in output_workspaces:
self._plot_focused_workspaces(ws_names)
def format_workspace(self, inputs):
""" inputs is a dict mapping filepaths to output names """
for path, output in inputs.items():
workspace = LoadAscii(path, OutputWorkspace=output)
workspace.getAxis(0).setUnit("Label").setLabel("Energy", "keV")
def create_new_calibration(self,
vanadium_path,
sample_path,
plot_output,
instrument,
rb_num=None,
bank=None,
spectrum_numbers=None):
"""
Create a new calibration from a vanadium run and sample run
:param vanadium_path: Path to vanadium data file.
:param sample_path: Path to sample (CeO2) data file
:param plot_output: Whether the output should be plotted.
:param instrument: The instrument the data relates to.
:param rb_num: The RB number for file creation.
:param bank: Optional parameter to crop by bank
:param spectrum_numbers: Optional parameter to crop using spectrum numbers.
"""
van_integration, van_curves = vanadium_corrections.fetch_correction_workspaces(
vanadium_path, instrument, rb_num=rb_num)
sample_workspace = path_handling.load_workspace(sample_path)
full_calib_path = get_setting(path_handling.INTERFACES_SETTINGS_GROUP,
path_handling.ENGINEERING_PREFIX, "full_calibration")
if full_calib_path is not None and path.exists(full_calib_path):
full_calib = LoadAscii(full_calib_path, OutputWorkspace="det_pos", Separator="Tab")
output = self.run_calibration(sample_workspace,
van_integration,
van_curves,
bank,
spectrum_numbers,
full_calib_ws=full_calib)
else:
output = self.run_calibration(sample_workspace, van_integration, van_curves, bank,
spectrum_numbers)
if plot_output:
self._plot_vanadium_curves()
for i in range(len(output)):
if spectrum_numbers:
bank_name = "cropped"
elif bank is None:
bank_name = str(i + 1)
else:
bank_name = bank
difa = output[i].DIFA
difc = output[i].DIFC
tzero = output[i].TZERO
self._generate_tof_fit_workspace(difa, difc, tzero, bank_name)
if bank is None and spectrum_numbers is None:
self._plot_tof_fit()
elif spectrum_numbers is None:
self._plot_tof_fit_single_bank_or_custom(bank)
else:
self._plot_tof_fit_single_bank_or_custom("cropped")
difa = [i.DIFC for i in output]
difc = [i.DIFC for i in output]
tzero = [i.TZERO for i in output]
params_table = []
for i in range(len(difc)):
params_table.append([i, difc[i], difa[i], tzero[i]])
self.update_calibration_params_table(params_table)
calib_dir = path.join(path_handling.get_output_path(), "Calibration", "")
self.create_output_files(calib_dir, difa, difc, tzero, sample_path, vanadium_path, instrument,
bank, spectrum_numbers)
if rb_num:
user_calib_dir = path.join(path_handling.get_output_path(), "User", rb_num,
"Calibration", "")
self.create_output_files(user_calib_dir, difa, difc, tzero, sample_path, vanadium_path,
instrument, bank, spectrum_numbers)