def _setup_sample_for_cylinder_absorb_corrections(ws_to_correct,
sample_details_obj):
geometry_json = common.generate_sample_geometry(sample_details_obj)
material_json = common.generate_sample_material(sample_details_obj)
mantid.SetSample(InputWorkspace=ws_to_correct,
Geometry=geometry_json,
Material=material_json)
def generate_ts_pdf(run_number, focus_file_path, merge_banks=False, q_lims=None, cal_file_name=None,
sample_details=None, delta_r=None, delta_q=None, pdf_type="G(r)", lorch_filter=None,
freq_params=None, debug=False):
focused_ws = _obtain_focused_run(run_number, focus_file_path)
focused_ws = mantid.ConvertUnits(InputWorkspace=focused_ws, Target="MomentumTransfer", EMode='Elastic')
raw_ws = mantid.Load(Filename='POLARIS'+str(run_number)+'.nxs')
sample_geometry = common.generate_sample_geometry(sample_details)
sample_material = common.generate_sample_material(sample_details)
self_scattering_correction = mantid.TotScatCalculateSelfScattering(
InputWorkspace=raw_ws,
CalFileName=cal_file_name,
SampleGeometry=sample_geometry,
SampleMaterial=sample_material,
CrystalDensity=sample_details.material_object.crystal_density)
ws_group_list = []
for i in range(self_scattering_correction.getNumberHistograms()):
ws_name = 'correction_' + str(i)
mantid.ExtractSpectra(InputWorkspace=self_scattering_correction, OutputWorkspace=ws_name,
WorkspaceIndexList=[i])
ws_group_list.append(ws_name)
self_scattering_correction = mantid.GroupWorkspaces(InputWorkspaces=ws_group_list)
self_scattering_correction = mantid.RebinToWorkspace(WorkspaceToRebin=self_scattering_correction,
WorkspaceToMatch=focused_ws)
focused_ws = mantid.Subtract(LHSWorkspace=focused_ws, RHSWorkspace=self_scattering_correction)
if delta_q:
focused_ws = mantid.Rebin(InputWorkspace=focused_ws, Params=delta_q)
if merge_banks:
q_min, q_max = _load_qlims(q_lims)
merged_ws = mantid.MatchAndMergeWorkspaces(InputWorkspaces=focused_ws, XMin=q_min, XMax=q_max,
CalculateScale=False)
fast_fourier_filter(merged_ws, freq_params=freq_params)
pdf_output = mantid.PDFFourierTransform(Inputworkspace="merged_ws", InputSofQType="S(Q)-1", PDFType=pdf_type,
Filter=lorch_filter, DeltaR=delta_r,
rho0=sample_details.material_object.crystal_density)
else:
for ws in focused_ws:
fast_fourier_filter(ws, freq_params=freq_params)
pdf_output = mantid.PDFFourierTransform(Inputworkspace='focused_ws', InputSofQType="S(Q)-1", PDFType=pdf_type,
Filter=lorch_filter, DeltaR=delta_r,
rho0=sample_details.material_object.crystal_density)
pdf_output = mantid.RebinToWorkspace(WorkspaceToRebin=pdf_output, WorkspaceToMatch=pdf_output[4],
PreserveEvents=True)
if not debug:
common.remove_intermediate_workspace('self_scattering_correction')
# Rename output ws
if 'merged_ws' in locals():
mantid.RenameWorkspace(InputWorkspace='merged_ws', OutputWorkspace=run_number + '_merged_Q')
mantid.RenameWorkspace(InputWorkspace='focused_ws', OutputWorkspace=run_number+'_focused_Q')
if isinstance(focused_ws, WorkspaceGroup):
for i in range(len(focused_ws)):
mantid.RenameWorkspace(InputWorkspace=focused_ws[i], OutputWorkspace=run_number+'_focused_Q_'+str(i+1))
mantid.RenameWorkspace(InputWorkspace='pdf_output', OutputWorkspace=run_number+'_pdf_R')
if isinstance(pdf_output, WorkspaceGroup):
for i in range(len(pdf_output)):
mantid.RenameWorkspace(InputWorkspace=pdf_output[i], OutputWorkspace=run_number+'_pdf_R_'+str(i+1))
return pdf_output
def test_generate_sample_geometry(self):
# Create mock SampleDetails
sample_details = SampleDetails(height=4.0, radius=3.0,
center=[0.5, 1.0, -3.2], shape='cylinder')
# Run test
result = common.generate_sample_geometry(sample_details)
# Validate result
expected = {'Shape': 'Cylinder',
'Height': 4.0,
'Radius': 3.0,
'Center': [0.5, 1.0, -3.2]}
self.assertEqual(result, expected)
def test_generate_sample_geometry(self):
# Create mock SampleDetails
sample_details = SampleDetails(height=4.0, radius=3.0,
center=[0.5, 1.0, -3.2], shape='cylinder')
# Run test
result = common.generate_sample_geometry(sample_details)
# Validate result
expected = {'Shape': 'Cylinder',
'Height': 4.0,
'Radius': 3.0,
'Center': [0.5, 1.0, -3.2]}
self.assertEquals(result, expected)
def generate_ts_pdf(run_number, focus_file_path, merge_banks=False, q_lims=None, cal_file_name=None,
sample_details=None, output_binning=None, pdf_type="G(r)", freq_params=None):
focused_ws = _obtain_focused_run(run_number, focus_file_path)
focused_ws = mantid.ConvertUnits(InputWorkspace=focused_ws, Target="MomentumTransfer", EMode='Elastic')
raw_ws = mantid.Load(Filename='POLARIS'+str(run_number)+'.nxs')
sample_geometry = common.generate_sample_geometry(sample_details)
sample_material = common.generate_sample_material(sample_details)
self_scattering_correction = mantid.TotScatCalculateSelfScattering(InputWorkspace=raw_ws,
CalFileName=cal_file_name,
SampleGeometry=sample_geometry,
SampleMaterial=sample_material)
ws_group_list = []
for i in range(self_scattering_correction.getNumberHistograms()):
ws_name = 'correction_' + str(i)
mantid.ExtractSpectra(InputWorkspace=self_scattering_correction, OutputWorkspace=ws_name,
WorkspaceIndexList=[i])
ws_group_list.append(ws_name)
self_scattering_correction = mantid.GroupWorkspaces(InputWorkspaces=ws_group_list)
self_scattering_correction = mantid.RebinToWorkspace(WorkspaceToRebin=self_scattering_correction,
WorkspaceToMatch=focused_ws)
focused_ws = mantid.Subtract(LHSWorkspace=focused_ws, RHSWorkspace=self_scattering_correction)
if merge_banks:
q_min, q_max = _load_qlims(q_lims)
merged_ws = mantid.MatchAndMergeWorkspaces(InputWorkspaces=focused_ws, XMin=q_min, XMax=q_max,
CalculateScale=False)
fast_fourier_filter(merged_ws, freq_params)
pdf_output = mantid.PDFFourierTransform(Inputworkspace="merged_ws", InputSofQType="S(Q)-1", PDFType=pdf_type,
Filter=True)
else:
for ws in focused_ws:
fast_fourier_filter(ws, freq_params)
pdf_output = mantid.PDFFourierTransform(Inputworkspace='focused_ws', InputSofQType="S(Q)-1",
PDFType=pdf_type, Filter=True)
pdf_output = mantid.RebinToWorkspace(WorkspaceToRebin=pdf_output, WorkspaceToMatch=pdf_output[4],
PreserveEvents=True)
common.remove_intermediate_workspace('self_scattering_correction')
if output_binning is not None:
try:
pdf_output = mantid.Rebin(InputWorkspace=pdf_output, Params=output_binning)
except RuntimeError:
return pdf_output
return pdf_output
def _focus_one_ws(input_workspace, run_number, instrument,
perform_vanadium_norm, absorb, sample_details,
vanadium_path):
run_details = instrument._get_run_details(run_number_string=run_number)
if perform_vanadium_norm:
_test_splined_vanadium_exists(instrument, run_details)
# Subtract empty instrument runs, as long as this run isn't an empty and user hasn't turned empty subtraction off
if not common.runs_overlap(run_number, run_details.empty_runs
) and instrument.should_subtract_empty_inst():
input_workspace = common.subtract_summed_runs(
ws_to_correct=input_workspace,
instrument=instrument,
empty_sample_ws_string=run_details.empty_runs)
# Subtract a sample empty if specified
if run_details.sample_empty:
input_workspace = common.subtract_summed_runs(
ws_to_correct=input_workspace,
instrument=instrument,
empty_sample_ws_string=run_details.sample_empty,
scale_factor=instrument._inst_settings.sample_empty_scale)
# Crop to largest acceptable TOF range
input_workspace = instrument._crop_raw_to_expected_tof_range(
ws_to_crop=input_workspace)
# Correct for absorption / multiple scattering if required
if absorb:
input_workspace = instrument._apply_absorb_corrections(
run_details=run_details, ws_to_correct=input_workspace)
else:
# Set sample material if specified by the user
if sample_details is not None:
mantid.SetSample(
InputWorkspace=input_workspace,
Geometry=common.generate_sample_geometry(sample_details),
Material=common.generate_sample_material(sample_details))
# Align
aligned_ws = mantid.AlignDetectors(
InputWorkspace=input_workspace,
CalibrationFile=run_details.offset_file_path)
# Focus the spectra into banks
focused_ws = mantid.DiffractionFocussing(
InputWorkspace=aligned_ws,
GroupingFileName=run_details.grouping_file_path)
calibrated_spectra = _apply_vanadium_corrections(
instrument=instrument,
input_workspace=focused_ws,
perform_vanadium_norm=perform_vanadium_norm,
vanadium_splines=vanadium_path)
output_spectra = instrument._crop_banks_to_user_tof(calibrated_spectra)
bin_widths = instrument._get_instrument_bin_widths()
if bin_widths:
# Reduce the bin width if required on this instrument
output_spectra = common.rebin_workspace_list(
workspace_list=output_spectra, bin_width_list=bin_widths)
# Output
d_spacing_group, tof_group = instrument._output_focused_ws(
output_spectra, run_details=run_details)
common.keep_single_ws_unit(d_spacing_group=d_spacing_group,
tof_group=tof_group,
unit_to_keep=instrument._get_unit_to_keep())
# Tidy workspaces from Mantid
common.remove_intermediate_workspace(input_workspace)
common.remove_intermediate_workspace(aligned_ws)
common.remove_intermediate_workspace(focused_ws)
common.remove_intermediate_workspace(output_spectra)
return d_spacing_group
def _setup_sample_for_cylinder_absorb_corrections(ws_to_correct, sample_details_obj):
geometry_json = common.generate_sample_geometry(sample_details_obj)
material_json = common.generate_sample_material(sample_details_obj)
mantid.SetSample(InputWorkspace=ws_to_correct, Geometry=geometry_json, Material=material_json)
def _focus_one_ws(input_workspace, run_number, instrument,
perform_vanadium_norm, absorb, sample_details,
vanadium_path):
run_details = instrument._get_run_details(run_number_string=run_number)
if perform_vanadium_norm:
_test_splined_vanadium_exists(instrument, run_details)
# Subtract empty instrument runs, as long as this run isn't an empty, user hasn't turned empty subtraction off, or
# The user has not supplied a sample empty
is_run_empty = common.runs_overlap(run_number, run_details.empty_inst_runs)
summed_empty = None
if not is_run_empty and instrument.should_subtract_empty_inst(
) and not run_details.sample_empty:
if os.path.isfile(run_details.summed_empty_inst_file_path):
logger.warning('Pre-summed empty instrument workspace found at ' +
run_details.summed_empty_inst_file_path)
summed_empty = mantid.LoadNexus(
Filename=run_details.summed_empty_inst_file_path)
else:
summed_empty = common.generate_summed_runs(
empty_sample_ws_string=run_details.empty_inst_runs,
instrument=instrument)
elif run_details.sample_empty:
# Subtract a sample empty if specified ie empty can
summed_empty = common.generate_summed_runs(
empty_sample_ws_string=run_details.sample_empty,
instrument=instrument,
scale_factor=instrument._inst_settings.sample_empty_scale)
if summed_empty is not None:
input_workspace = common.subtract_summed_runs(
ws_to_correct=input_workspace, empty_sample=summed_empty)
# Crop to largest acceptable TOF range
input_workspace = instrument._crop_raw_to_expected_tof_range(
ws_to_crop=input_workspace)
# Correct for absorption / multiple scattering if required
if absorb:
input_workspace = instrument._apply_absorb_corrections(
run_details=run_details, ws_to_correct=input_workspace)
else:
# Set sample material if specified by the user
if sample_details is not None:
mantid.SetSample(
InputWorkspace=input_workspace,
Geometry=common.generate_sample_geometry(sample_details),
Material=common.generate_sample_material(sample_details))
# Align
mantid.ApplyDiffCal(InstrumentWorkspace=input_workspace,
CalibrationFile=run_details.offset_file_path)
aligned_ws = mantid.ConvertUnits(InputWorkspace=input_workspace,
Target="dSpacing")
solid_angle = instrument.get_solid_angle_corrections(
run_details.vanadium_run_numbers, run_details)
if solid_angle:
aligned_ws = mantid.Divide(LHSWorkspace=aligned_ws,
RHSWorkspace=solid_angle)
mantid.DeleteWorkspace(solid_angle)
# Focus the spectra into banks
focused_ws = mantid.DiffractionFocussing(
InputWorkspace=aligned_ws,
GroupingFileName=run_details.grouping_file_path)
instrument.apply_calibration_to_focused_data(focused_ws)
calibrated_spectra = _apply_vanadium_corrections(
instrument=instrument,
input_workspace=focused_ws,
perform_vanadium_norm=perform_vanadium_norm,
vanadium_splines=vanadium_path)
output_spectra = instrument._crop_banks_to_user_tof(calibrated_spectra)
bin_widths = instrument._get_instrument_bin_widths()
if bin_widths:
# Reduce the bin width if required on this instrument
output_spectra = common.rebin_workspace_list(
workspace_list=output_spectra, bin_width_list=bin_widths)
# Output
d_spacing_group, tof_group = instrument._output_focused_ws(
output_spectra, run_details=run_details)
common.keep_single_ws_unit(d_spacing_group=d_spacing_group,
tof_group=tof_group,
unit_to_keep=instrument._get_unit_to_keep())
# Tidy workspaces from Mantid
common.remove_intermediate_workspace(input_workspace)
common.remove_intermediate_workspace(aligned_ws)
common.remove_intermediate_workspace(focused_ws)
common.remove_intermediate_workspace(output_spectra)
return d_spacing_group
def _focus_one_ws(input_workspace, run_number, instrument, perform_vanadium_norm, absorb, sample_details,
vanadium_path):
run_details = instrument._get_run_details(run_number_string=run_number)
if perform_vanadium_norm:
_test_splined_vanadium_exists(instrument, run_details)
# Subtract empty instrument runs, as long as this run isn't an empty and user hasn't turned empty subtraction off
if not common.runs_overlap(run_number, run_details.empty_runs) and instrument.should_subtract_empty_inst():
input_workspace = common.subtract_summed_runs(ws_to_correct=input_workspace, instrument=instrument,
empty_sample_ws_string=run_details.empty_runs)
# Subtract a sample empty if specified
if run_details.sample_empty:
input_workspace = common.subtract_summed_runs(ws_to_correct=input_workspace, instrument=instrument,
empty_sample_ws_string=run_details.sample_empty,
scale_factor=instrument._inst_settings.sample_empty_scale)
# Crop to largest acceptable TOF range
input_workspace = instrument._crop_raw_to_expected_tof_range(ws_to_crop=input_workspace)
# Correct for absorption / multiple scattering if required
if absorb:
input_workspace = instrument._apply_absorb_corrections(run_details=run_details, ws_to_correct=input_workspace)
else:
# Set sample material if specified by the user
if sample_details is not None:
mantid.SetSample(InputWorkspace=input_workspace,
Geometry=common.generate_sample_geometry(sample_details),
Material=common.generate_sample_material(sample_details))
# Align
aligned_ws = mantid.AlignDetectors(InputWorkspace=input_workspace,
CalibrationFile=run_details.offset_file_path)
# Focus the spectra into banks
focused_ws = mantid.DiffractionFocussing(InputWorkspace=aligned_ws,
GroupingFileName=run_details.grouping_file_path)
calibrated_spectra = _apply_vanadium_corrections(instrument=instrument,
input_workspace=focused_ws,
perform_vanadium_norm=perform_vanadium_norm,
vanadium_splines=vanadium_path)
output_spectra = instrument._crop_banks_to_user_tof(calibrated_spectra)
bin_widths = instrument._get_instrument_bin_widths()
if bin_widths:
# Reduce the bin width if required on this instrument
output_spectra = common.rebin_workspace_list(workspace_list=output_spectra,
bin_width_list=bin_widths)
# Output
d_spacing_group, tof_group = instrument._output_focused_ws(output_spectra, run_details=run_details)
common.keep_single_ws_unit(d_spacing_group=d_spacing_group, tof_group=tof_group,
unit_to_keep=instrument._get_unit_to_keep())
# Tidy workspaces from Mantid
common.remove_intermediate_workspace(input_workspace)
common.remove_intermediate_workspace(aligned_ws)
common.remove_intermediate_workspace(focused_ws)
common.remove_intermediate_workspace(output_spectra)
return d_spacing_group
