# Mantid Repository : https://github.com/mantidproject/mantid
#
# Copyright © 2018 ISIS Rutherford Appleton Laboratory UKRI,
# NScD Oak Ridge National Laboratory, European Spallation Source
# & Institut Laue - Langevin
# SPDX - License - Identifier: GPL - 3.0 +
from __future__ import (absolute_import, division, print_function)
import mantid.simpleapi as mantid
from isis_powder.routines import absorb_corrections, common
from isis_powder.routines.common_enums import WORKSPACE_UNITS
from isis_powder.routines.run_details import create_run_details_object, get_cal_mapping_dict
from isis_powder.polaris_routines import polaris_advanced_config
from six import PY3
def calculate_van_absorb_corrections(ws_to_correct, multiple_scattering, is_vanadium):
mantid.MaskDetectors(ws_to_correct, SpectraList=list(range(1, 55)))
absorb_dict = polaris_advanced_config.absorption_correction_params
sample_details_obj = absorb_corrections.create_vanadium_sample_details_obj(config_dict=absorb_dict)
ws_to_correct = absorb_corrections.run_cylinder_absorb_corrections(
ws_to_correct=ws_to_correct, multiple_scattering=multiple_scattering, sample_details_obj=sample_details_obj,
is_vanadium=is_vanadium)
return ws_to_correct
def _get_run_numbers_for_key(current_mode_run_numbers, key):
err_message = "this must be under the relevant Rietveld or PDF mode."
return common.cal_map_dictionary_key_helper(current_mode_run_numbers, key=key,
append_to_error_message=err_message)
def _get_current_mode_dictionary(run_number_string, inst_settings):
mapping_dict = get_cal_mapping_dict(run_number_string, inst_settings.cal_mapping_path)
if inst_settings.mode is None:
ws = mantid.Load('POLARIS'+run_number_string+'.nxs')
mode, cropping_vals = _determine_chopper_mode(ws)
inst_settings.mode = mode
inst_settings.focused_cropping_values = cropping_vals
mantid.DeleteWorkspace(ws)
# Get the current mode "Rietveld" or "PDF" run numbers
return common.cal_map_dictionary_key_helper(mapping_dict, inst_settings.mode)
def get_run_details(run_number_string, inst_settings, is_vanadium_run):
mode_run_numbers = _get_current_mode_dictionary(run_number_string, inst_settings)
# Get empty and vanadium
err_message = "this must be under the relevant Rietveld or PDF mode."
empty_runs = common.cal_map_dictionary_key_helper(mode_run_numbers,
key="empty_run_numbers", append_to_error_message=err_message)
vanadium_runs = common.cal_map_dictionary_key_helper(mode_run_numbers, key="vanadium_run_numbers",
append_to_error_message=err_message)
grouping_file_name = inst_settings.grouping_file_name
return create_run_details_object(run_number_string=run_number_string, inst_settings=inst_settings,
is_vanadium_run=is_vanadium_run, empty_run_number=empty_runs,
vanadium_string=vanadium_runs, grouping_file_name=grouping_file_name)
def process_vanadium_for_focusing(bank_spectra, mask_path, spline_number):
bragg_masking_list = _read_masking_file(mask_path)
masked_workspace_list = _apply_bragg_peaks_masking(bank_spectra, mask_list=bragg_masking_list)
output = common.spline_workspaces(focused_vanadium_spectra=masked_workspace_list,
num_splines=spline_number)
common.remove_intermediate_workspace(masked_workspace_list)
return output
def save_unsplined_vanadium(vanadium_ws, output_path):
converted_workspaces = []
for ws_index in range(vanadium_ws.getNumberOfEntries()):
ws = vanadium_ws.getItem(ws_index)
previous_units = ws.getAxis(0).getUnit().unitID()
if previous_units != WORKSPACE_UNITS.tof:
ws = mantid.ConvertUnits(InputWorkspace=ws, Target=WORKSPACE_UNITS.tof)
ws = mantid.RenameWorkspace(InputWorkspace=ws, OutputWorkspace="van_bank_{}".format(ws_index + 1))
converted_workspaces.append(ws)
converted_group = mantid.GroupWorkspaces(",".join(ws.name() for ws in converted_workspaces))
mantid.SaveNexus(InputWorkspace=converted_group, Filename=output_path, Append=False)
mantid.DeleteWorkspace(converted_group)
def generate_ts_pdf(run_number, focus_file_path, merge_banks=False):
focused_ws = _obtain_focused_run(run_number, focus_file_path)
pdf_output = mantid.ConvertUnits(InputWorkspace=focused_ws.name(), Target="MomentumTransfer")
if merge_banks:
raise RuntimeError("Merging banks is currently not supported")
pdf_output = mantid.PDFFourierTransform(Inputworkspace=pdf_output, InputSofQType="S(Q)", PDFType="G(r)",
Filter=True)
pdf_output = mantid.RebinToWorkspace(WorkspaceToRebin=pdf_output, WorkspaceToMatch=pdf_output[4],
PreserveEvents=True)
return pdf_output
def _obtain_focused_run(run_number, focus_file_path):
"""
Searches for the focused workspace to use (based on user specified run number) in the ADS and then the output
directory.
If unsuccessful, a ValueError exception is thrown.
:param run_number: The run number to search for.
:param focus_file_path: The expected file path for the focused file.
:return: The focused workspace.
"""
# Try the ADS first to avoid undesired loading
if mantid.mtd.doesExist('%s-Results-TOF-Grp' % run_number):
focused_ws = mantid.mtd['%s-Results-TOF-Grp' % run_number]
elif mantid.mtd.doesExist('%s-Results-D-Grp' % run_number):
focused_ws = mantid.mtd['%s-Results-D-Grp' % run_number]
else:
# Check output directory
print('No loaded focused files found. Searching in output directory...')
try:
focused_ws = mantid.LoadNexus(Filename=focus_file_path, OutputWorkspace='focused_ws').OutputWorkspace
except ValueError:
raise ValueError("Could not find focused file for run number:%s\n"
"Please ensure a focused file has been produced and is located in the output directory."
% run_number)
return focused_ws
def _apply_bragg_peaks_masking(workspaces_to_mask, mask_list):
output_workspaces = list(workspaces_to_mask)
for ws_index, (bank_mask_list, workspace) in enumerate(zip(mask_list, output_workspaces)):
output_name = "masked_vanadium-" + str(ws_index + 1)
for mask_params in bank_mask_list:
output_workspaces[ws_index] = mantid.MaskBins(InputWorkspace=output_workspaces[ws_index],
OutputWorkspace=output_name,
XMin=mask_params[0], XMax=mask_params[1])
return output_workspaces
def _read_masking_file(masking_file_path):
all_banks_masking_list = []
bank_masking_list = []
ignore_line_prefixes = (' ', '\n', '\t', '#') # Matches whitespace or # symbol
# Python 3 requires the encoding to be included so an Angstrom
# symbol can be read, I'm assuming all file read here are
# `latin-1` which may not be true in the future. Python 2 `open`
# doesn't have an encoding option
if PY3:
encoding = {"encoding": "latin-1"}
else:
encoding = {}
with open(masking_file_path, **encoding) as mask_file:
for line in mask_file:
if line.startswith(ignore_line_prefixes):
# Push back onto new bank
if bank_masking_list:
all_banks_masking_list.append(bank_masking_list)
bank_masking_list = []
else:
# Parse and store in current list
line.rstrip()
bank_masking_list.append(line.split())
if bank_masking_list:
all_banks_masking_list.append(bank_masking_list)
return all_banks_masking_list
def _determine_chopper_mode(ws):
if ws.getRun().hasProperty('Frequency'):
frequency = ws.getRun()['Frequency'].lastValue()
print("No chopper mode provided")
if frequency == 50:
print("automatically chose Rietveld")
return 'Rietveld', polaris_advanced_config.rietveld_focused_cropping_values
if frequency == 0:
print("automatically chose PDF")
return 'PDF', polaris_advanced_config.pdf_focused_cropping_values
else:
raise ValueError("Chopper frequency not in log data. Please specify a chopper mode")