def makeFiles(self):
simpleapi.CreateWorkspace(OutputWorkspace='data',
DataX='1,2,3,4,5',
DataY='1,0,1,4,4',
DataE='1,0,1,2,2')
simpleapi.CreateWorkspace(OutputWorkspace='sim',
DataX='1,2,3,4,5',
DataY='1,1,1,1,1',
DataE='0,0,0,0,0')
simpleapi.CreateWorkspace(OutputWorkspace='simwrong',
DataX='1,2,3,4',
DataY='1,1,1,1',
DataE='0,0,0,0')
self.datafile = os.path.join(config.getString('defaultsave.directory'),
'DakotaChiSquared_data.nxs')
self.simfile = os.path.join(config.getString('defaultsave.directory'),
'DakotaChiSquared_sim.nxs')
self.simwrongfile = os.path.join(
config.getString('defaultsave.directory'),
'DakotaChiSquared_simwrong.nxs')
self.chifile = os.path.join(config.getString('defaultsave.directory'),
'DakotaChiSquared_chi.txt')
simpleapi.SaveNexus('data', self.datafile)
simpleapi.SaveNexus('sim', self.simfile)
simpleapi.SaveNexus('simwrong', self.simwrongfile)
ads = AnalysisDataServiceImpl.Instance()
ads.remove("data")
ads.remove("sim")
ads.remove("simwrong")
def _focus_mode_groups(cycle_information, output_file_paths, save_range,
calibrated_spectra):
output_list = []
to_save = _sum_groups_of_three_ws(calibrated_spectra, output_file_paths)
workspaces_4_to_9_name = output_file_paths["output_name"] + "_mods4-9"
workspaces_4_to_9 = mantid.Plus(LHSWorkspace=to_save[1],
RHSWorkspace=to_save[2])
workspaces_4_to_9 = mantid.Scale(InputWorkspace=workspaces_4_to_9,
Factor=0.5,
OutputWorkspace=workspaces_4_to_9_name)
to_save.append(workspaces_4_to_9)
append = False
index = 1
for ws in to_save:
if cycle_information["instrument_version"] == "new":
mantid.SaveGSS(InputWorkspace=ws,
Filename=output_file_paths["gss_filename"],
Append=append,
Bank=index)
elif cycle_information["instrument_version"] == "new2":
mantid.SaveGSS(InputWorkspace=ws,
Filename=output_file_paths["gss_filename"],
Append=False,
Bank=index)
workspace_names = ws.name()
dspacing_ws = mantid.ConvertUnits(InputWorkspace=ws,
OutputWorkspace=workspace_names,
Target="dSpacing")
remove_intermediate_workspace(ws)
output_list.append(dspacing_ws)
mantid.SaveNexus(Filename=output_file_paths["nxs_filename"],
InputWorkspace=dspacing_ws,
Append=append)
append = True
index += 1
for i in range(0, save_range):
monitor_ws_name = output_file_paths["output_name"] + "_mod" + str(i +
10)
monitor_ws = calibrated_spectra[i + 9]
to_save = mantid.CloneWorkspace(InputWorkspace=monitor_ws,
OutputWorkspace=monitor_ws_name)
mantid.SaveGSS(InputWorkspace=to_save,
Filename=output_file_paths["gss_filename"],
Append=True,
Bank=i + 5)
to_save = mantid.ConvertUnits(InputWorkspace=to_save,
OutputWorkspace=monitor_ws_name,
Target="dSpacing")
mantid.SaveNexus(Filename=output_file_paths["nxs_filename"],
InputWorkspace=to_save,
Append=True)
output_list.append(to_save)
return output_list
def _focus_mode_trans(output_file_paths, atten, instrument,
calibrated_spectra):
summed_ws = mantid.CloneWorkspace(InputWorkspace=calibrated_spectra[0])
for i in range(1, 9): # Add workspaces 2-9 to workspace 1
summed_ws = mantid.Plus(LHSWorkspace=summed_ws,
RHSWorkspace=calibrated_spectra[i])
summed_ws = mantid.Scale(InputWorkspace=summed_ws,
Factor=0.111111111111111)
if atten:
# Clone a workspace which is not attenuated
no_att = output_file_paths["output_name"] + "_noatten"
mantid.CloneWorkspace(InputWorkspace=summed_ws, OutputWorkspace=no_att)
summed_ws = mantid.ConvertUnits(InputWorkspace=summed_ws,
Target="dSpacing")
summed_ws = instrument._attenuate_workspace(summed_ws)
summed_ws = mantid.ConvertUnits(InputWorkspace=summed_ws, Target="TOF")
mantid.SaveGSS(InputWorkspace=summed_ws,
Filename=output_file_paths["gss_filename"],
Append=False,
Bank=1)
mantid.SaveFocusedXYE(InputWorkspace=summed_ws,
Filename=output_file_paths["tof_xye_filename"],
Append=False,
IncludeHeader=False)
summed_ws = mantid.ConvertUnits(InputWorkspace=summed_ws,
Target="dSpacing")
# Rename to user friendly name:
summed_ws_name = output_file_paths["output_name"] + "_mods1-9"
summed_ws = mantid.RenameWorkspace(InputWorkspace=summed_ws,
OutputWorkspace=summed_ws_name)
mantid.SaveFocusedXYE(InputWorkspace=summed_ws,
Filename=output_file_paths["dspacing_xye_filename"],
Append=False,
IncludeHeader=False)
mantid.SaveNexus(InputWorkspace=summed_ws,
Filename=output_file_paths["nxs_filename"],
Append=False)
output_list = [summed_ws]
for i in range(0, 9):
workspace_name = output_file_paths["output_name"] + "_mod" + str(i + 1)
to_save = mantid.ConvertUnits(InputWorkspace=calibrated_spectra[i],
Target="dSpacing",
OutputWorkspace=workspace_name)
output_list.append(to_save)
mantid.SaveNexus(Filename=output_file_paths["nxs_filename"],
InputWorkspace=to_save,
Append=True)
return output_list
def _focus_mode_trans(output_file_paths, attenuation_filepath,
calibrated_spectra):
summed_ws = mantid.MergeRuns(InputWorkspaces=calibrated_spectra[:9])
xList = summed_ws.readX(0)
summed_ws = mantid.CropWorkspace(InputWorkspace=summed_ws,
XMin=xList[1],
Xmax=xList[-2])
summed_ws = mantid.Scale(InputWorkspace=summed_ws,
Factor=0.111111111111111)
if attenuation_filepath:
summed_ws = _attenuate_workspace(
output_file_paths=output_file_paths,
attenuated_ws=summed_ws,
attenuation_filepath=attenuation_filepath)
summed_ws = mantid.ConvertUnits(InputWorkspace=summed_ws, Target="TOF")
mantid.SaveGSS(InputWorkspace=summed_ws,
Filename=output_file_paths["gss_filename"],
Append=False,
Bank=1)
mantid.SaveFocusedXYE(InputWorkspace=summed_ws,
Filename=output_file_paths["tof_xye_filename"],
Append=False,
IncludeHeader=False)
summed_ws = mantid.ConvertUnits(InputWorkspace=summed_ws,
Target="dSpacing")
# Rename to user friendly name:
summed_ws_name = output_file_paths["output_name"] + "_mods1-9"
summed_ws = mantid.RenameWorkspace(InputWorkspace=summed_ws,
OutputWorkspace=summed_ws_name)
mantid.SaveFocusedXYE(InputWorkspace=summed_ws,
Filename=output_file_paths["dspacing_xye_filename"],
Append=False,
IncludeHeader=False)
mantid.SaveNexus(InputWorkspace=summed_ws,
Filename=output_file_paths["nxs_filename"],
Append=False)
output_list = [summed_ws]
for i in range(0, 9):
workspace_name = output_file_paths["output_name"] + "_mod" + str(i + 1)
to_save = mantid.ConvertUnits(InputWorkspace=calibrated_spectra[i],
Target="dSpacing",
OutputWorkspace=workspace_name)
output_list.append(to_save)
mantid.SaveNexus(Filename=output_file_paths["nxs_filename"],
InputWorkspace=to_save,
Append=True)
return output_list
def _focus_mode_all(output_file_paths, processed_spectra,
attenuation_filepath):
summed_spectra_name = output_file_paths["output_name"] + "_mods1-9"
summed_spectra = mantid.MergeRuns(InputWorkspaces=processed_spectra[:9],
OutputWorkspace=summed_spectra_name)
summed_spectra = mantid.Scale(InputWorkspace=summed_spectra,
Factor=0.111111111111111,
OutputWorkspace=summed_spectra_name)
if attenuation_filepath:
summed_spectra = _attenuate_workspace(
output_file_paths=output_file_paths,
attenuated_ws=summed_spectra,
attenuation_filepath=attenuation_filepath)
summed_spectra = mantid.ConvertUnits(InputWorkspace=summed_spectra,
Target="TOF",
OutputWorkspace=summed_spectra_name)
mantid.SaveGSS(InputWorkspace=summed_spectra,
Filename=output_file_paths["gss_filename"],
Append=False,
Bank=1)
summed_spectra = mantid.ConvertUnits(InputWorkspace=summed_spectra,
Target="dSpacing",
OutputWorkspace=summed_spectra_name)
mantid.SaveNexus(Filename=output_file_paths["nxs_filename"],
InputWorkspace=summed_spectra,
Append=False)
output_list = [summed_spectra]
for i in range(0, 5):
spectra_index = (i + 9) # Compensate for 0 based index
ws_to_save = processed_spectra[
spectra_index] # Save out workspaces 10/11/12
output_name = output_file_paths["output_name"] + "_mod" + str(
spectra_index + 1)
ws_to_save = mantid.ConvertUnits(InputWorkspace=ws_to_save,
OutputWorkspace=ws_to_save,
Target="TOF")
mantid.SaveGSS(InputWorkspace=ws_to_save,
Filename=output_file_paths["gss_filename"],
Append=True,
Bank=i + 2)
ws_to_save = mantid.ConvertUnits(InputWorkspace=ws_to_save,
OutputWorkspace=output_name,
Target="dSpacing")
mantid.SaveNexus(Filename=output_file_paths["nxs_filename"],
InputWorkspace=ws_to_save,
Append=True)
output_list.append(ws_to_save)
return output_list
def filter_cross_sections(file_path, events=True, histo=False):
"""
Filter events according to polarization state.
:param str file_path: file to read
:param bool events: if True, an event nexus file will be written
:param bool histo: if True, a histo nexus file will be written
"""
cross_sections = {}
cross_sections_histo = {}
xs_list = api.MRFilterCrossSections(file_path,
PolState=POL_STATE,
AnaState=ANA_STATE,
PolVeto=POL_VETO,
AnaVeto=ANA_VETO)
if len(xs_list) > 0:
tof_min, tof_max = get_tof_range(xs_list[0])
for workspace in xs_list:
if "cross_section_id" in workspace.getRun():
entry = workspace.getRun().getProperty("cross_section_id").value
else:
entry = 'Off_Off'
api.AddSampleLog(Workspace=workspace,
LogName='cross_section_id',
LogText=entry)
if workspace.getNumberEvents() < 5:
logging.warn("No events in %s", entry)
continue
run_number = workspace.getRunNumber()
if events:
events_file = "/tmp/filtered_%s_%s_%s.nxs" % (run_number, entry,
"events")
api.SaveNexus(InputWorkspace=workspace,
Filename=events_file,
Title='entry_%s' % entry)
cross_sections['entry-%s' % entry] = events_file
if histo:
#tof_min = workspace.getTofMin()
#tof_max = workspace.getTofMax()
ws_binned = api.Rebin(InputWorkspace=workspace,
Params="%s, %s, %s" %
(tof_min, TOF_BIN, tof_max),
PreserveEvents=False)
histo_file = "/tmp/filtered_%s_%s_%s.nxs" % (run_number, entry,
"histo")
api.SaveNexus(InputWorkspace=ws_binned,
Filename=histo_file,
Title='entry_%s' % entry)
cross_sections_histo['entry-%s' % entry] = histo_file
return cross_sections, cross_sections_histo
def _save_out(run_number, focus_directory, focus_general, output, enginx_file_name_format, bank_id):
"""
save out the files required for the focus
@param run_number :: the run number of the focused run
@param focus_directory :: the user directory to save to
@param focus_general :: the general folder to copy the saved out files to
@param output :: the workspace to save
@param enginx_file_name_format :: the naming scheme of the files
@param bank_id :: the bank being saved
"""
# work out where to save the files
dat_name, genie_filename, gss_name, hdf5_name, nxs_name = _find_focus_file_location(bank_id, focus_directory,
enginx_file_name_format,
run_number)
if not str(bank_id).isnumeric():
bank_id = 0
# save the files out to the user directory
simple.SaveFocusedXYE(InputWorkspace=output, Filename=dat_name, SplitFiles=False,
StartAtBankNumber=bank_id)
simple.SaveGSS(InputWorkspace=output, Filename=gss_name, SplitFiles=False, Bank=bank_id)
simple.SaveOpenGenieAscii(InputWorkspace=output, Filename=genie_filename, OpenGenieFormat="ENGIN-X Format")
simple.SaveNexus(InputWorkspace=output, Filename=nxs_name)
simple.ExportSampleLogsToHDF5(InputWorkspace=output, Filename=hdf5_name, Blacklist="bankid")
if not focus_general == focus_directory:
if not os.path.exists(focus_general):
os.makedirs(focus_general)
# copy the files to the general directory
copy2(dat_name, focus_general)
copy2(gss_name, focus_general)
copy2(genie_filename, focus_general)
copy2(nxs_name, focus_general)
copy2(hdf5_name, focus_general)
def populate_Ei_data(sim_out, nxs):
import shutil
nxs_withmons = nxsfilename_with_monitors(nxs)
shutil.copyfile(nxs, nxs_withmons)
populate_monitor_data(sim_out, nxs_withmons)
print((" * Created ARCS NeXus file with monitor data: %s" % nxs_withmons))
#
import ast
props = ast.literal_eval(open(os.path.join(sim_out, 'props.json')).read())
Ei, unit = props['average energy'].split()
assert unit == 'meV'
t0, unit = props['emission time'].split()
assert unit == 'microsecond'
from mantid import simpleapi as msa
if sys.version_info < (3, 0) and isinstance(nxs, unicode):
nxs = nxs.encode('utf-8')
ws = msa.Load(nxs_withmons)
msa.AddSampleLog(ws,
LogName='mcvine-Ei',
LogText=str(Ei),
LogType='Number')
msa.AddSampleLog(ws,
LogName='mcvine-t0',
LogText=str(t0),
LogType='Number')
(fd, filename) = tempfile.mkstemp()
os.close(fd)
msa.SaveNexus(ws, filename)
mv(filename, nxs)
return
def _focus_mode_mods(output_file_paths, calibrated_spectra):
append = False
output_list = []
for index, ws in enumerate(calibrated_spectra):
output_name = output_file_paths["output_name"] + "_mod" + str(index +
1)
tof_ws = mantid.ConvertUnits(InputWorkspace=ws,
OutputWorkspace=output_name,
Target=WORKSPACE_UNITS.tof)
mantid.SaveFocusedXYE(InputWorkspace=tof_ws,
Filename=output_file_paths["tof_xye_filename"],
Append=False,
IncludeHeader=False)
mantid.SaveGSS(InputWorkspace=tof_ws,
Filename=output_file_paths["gss_filename"],
Append=append,
Bank=index + 1)
dspacing_ws = mantid.ConvertUnits(InputWorkspace=ws,
OutputWorkspace=output_name,
Target=WORKSPACE_UNITS.d_spacing)
output_list.append(dspacing_ws)
mantid.SaveNexus(Filename=output_file_paths["nxs_filename"],
InputWorkspace=dspacing_ws,
Append=append)
append = True
return output_list
def populate_metadata(sim_out, nxs, sample, detector):
if sys.version_info < (3, 0) and isinstance(nxs, unicode):
nxs = nxs.encode('utf-8')
import h5py
f = h5py.File(nxs, 'a')
entry = f['entry']
from mcvine.instruments.HYSPEC.nxs.raw import populateMetadata
populateMetadata(entry, sim_out, sample, detector)
f.close()
# add log entries
import ast, os
props = ast.literal_eval(open(os.path.join(sim_out, 'props.json')).read())
Ei, unit = props['average energy'].split()
assert unit == 'meV'
t0, unit = props['emission time'].split()
assert unit == 'microsecond'
from mantid import simpleapi as msa
ws = msa.Load(nxs)
msa.AddSampleLog(ws,
LogName='mcvine-Ei',
LogText=str(Ei),
LogType='Number')
msa.AddSampleLog(ws,
LogName='mcvine-t0',
LogText=str(t0),
LogType='Number')
msa.SaveNexus(ws, nxs)
return
def create_solid_angle_corrections(self, vanadium, run_details):
"""
Creates the solid angle corrections from a vanadium run, only applicable on HRPD otherwise return None
:param vanadium: The vanadium used to create this
:param run_details: the run details of to use
"""
if not self._inst_settings.do_solid_angle:
return
solid_angle = mantid.SolidAngle(InputWorkspace=vanadium)
scale = mantid.CreateSingleValuedWorkspace(DataValue='100')
correction = mantid.Multiply(LHSWorkspace=solid_angle,
RHSWorkspace=scale)
eff = mantid.Divide(LHSWorkspace=vanadium, RHSWorkspace=correction)
eff = mantid.ConvertUnits(InputWorkspace=eff, Target='Wavelength')
eff = mantid.Integration(InputWorkspace=eff,
RangeLower='1.3999999999999999',
RangeUpper='3')
correction = mantid.Multiply(LHSWorkspace=correction, RHSWorkspace=eff)
scale = mantid.CreateSingleValuedWorkspace(DataValue='100000')
correction = mantid.Divide(LHSWorkspace=correction, RHSWorkspace=scale)
name = "sac" + common.generate_splined_name(run_details.run_number, [])
path = run_details.van_paths
mantid.SaveNexus(InputWorkspace=correction,
Filename=os.path.join(path, name))
common.remove_intermediate_workspace(solid_angle)
common.remove_intermediate_workspace(scale)
common.remove_intermediate_workspace(eff)
common.remove_intermediate_workspace(correction)
def create_solid_angle_corrections(self, vanadium, run_details):
"""
Creates the solid angle corrections from a vanadium run, only applicable on HRPD otherwise return None
:param vanadium: The vanadium used to create this
:param run_details: the run details of to use
"""
settings = self._inst_settings
if not settings.do_solid_angle:
return
solid_angle = mantid.SolidAngle(InputWorkspace=vanadium)
solid_angle = mantid.Scale(InputWorkspace=solid_angle, Factor=100, Operation='Multiply')
eff = mantid.Divide(LHSWorkspace=vanadium, RHSWorkspace=solid_angle)
eff = mantid.ConvertUnits(InputWorkspace=eff, Target='Wavelength')
integration_range = settings.eff_integration_range
# use full range if no range is supplied
integration_range = integration_range if integration_range is not None else (None, None)
eff = mantid.Integration(InputWorkspace=eff,
RangeLower=integration_range[0],
RangeUpper=integration_range[1])
correction = mantid.Multiply(LHSWorkspace=solid_angle, RHSWorkspace=eff)
correction = mantid.Scale(InputWorkspace=correction, Factor=1e-5,
Operation='Multiply')
name = "sac" + common.generate_splined_name(run_details.run_number, [])
path = run_details.van_paths
mantid.SaveNexus(InputWorkspace=correction, Filename=os.path.join(path, name))
common.remove_intermediate_workspace(eff)
common.remove_intermediate_workspace(correction)
def _focus_mode_all(output_file_paths, calibrated_spectra):
first_spectrum = calibrated_spectra[0]
summed_spectra = mantid.CloneWorkspace(InputWorkspace=first_spectrum)
for i in range(1, 9): # TODO why is this 1-8
summed_spectra = mantid.Plus(LHSWorkspace=summed_spectra,
RHSWorkspace=calibrated_spectra[i])
summed_spectra_name = output_file_paths["output_name"] + "_mods1-9"
summed_spectra = mantid.Scale(InputWorkspace=summed_spectra,
Factor=0.111111111111111,
OutputWorkspace=summed_spectra_name)
mantid.SaveGSS(InputWorkspace=summed_spectra,
Filename=output_file_paths["gss_filename"],
Append=False,
Bank=1)
summed_spectra = mantid.ConvertUnits(InputWorkspace=summed_spectra,
Target="dSpacing",
OutputWorkspace=summed_spectra_name)
mantid.SaveNexus(Filename=output_file_paths["nxs_filename"],
InputWorkspace=summed_spectra,
Append=False)
output_list = [summed_spectra]
for i in range(0, 3):
spectra_index = (
i + 9
) # We want workspaces 10/11/12 so compensate for 0 based index
ws_to_save = calibrated_spectra[
spectra_index] # Save out workspaces 10/11/12
output_name = output_file_paths["output_name"] + "_mod" + str(
spectra_index + 1)
mantid.SaveGSS(InputWorkspace=ws_to_save,
Filename=output_file_paths["gss_filename"],
Append=True,
Bank=i + 2)
ws_to_save = mantid.ConvertUnits(InputWorkspace=ws_to_save,
OutputWorkspace=output_name,
Target="dSpacing")
output_list.append(ws_to_save)
mantid.SaveNexus(Filename=output_file_paths["nxs_filename"],
InputWorkspace=ws_to_save,
Append=True)
return output_list
def handle_van_curves(van_curves, van_path):
if len(van_curves) == 2:
curves_ws = simple.AppendSpectra(InputWorkspace1=van_curves[0], InputWorkspace2=van_curves[1])
simple.DeleteWorkspace(van_curves[1])
else:
curves_ws = van_curves[0]
simple.SaveNexus(curves_ws, van_path)
simple.DeleteWorkspace(van_curves[0])
simple.DeleteWorkspace(curves_ws)
def _save_output_files(focus_dirs,
sample_ws_foc,
calibration,
van_run,
rb_num=None):
# set bankid for use in fit tab
foc_suffix = calibration.get_foc_ws_suffix()
xunit = sample_ws_foc.getDimension(0).name
xunit_suffix = XUNIT_SUFFIXES[xunit]
sample_run_no = sample_ws_foc.run().get('run_number').value
# save all spectra to single ASCII files
ascii_fname = _generate_output_file_name(calibration.get_instrument(),
sample_run_no,
van_run,
calibration.get_group_suffix(),
xunit_suffix,
ext='')
for focus_dir in focus_dirs:
if not path.exists(focus_dir):
makedirs(focus_dir)
mantid.SaveGSS(InputWorkspace=sample_ws_foc,
Filename=path.join(focus_dir, ascii_fname + '.gss'),
SplitFiles=False,
UseSpectrumNumberAsBankID=True)
mantid.SaveFocusedXYE(InputWorkspace=sample_ws_foc,
Filename=path.join(focus_dir,
ascii_fname + ".abc"),
SplitFiles=False,
Format="TOPAS")
# Save nxs per spectrum
nxs_paths = []
mantid.AddSampleLog(Workspace=sample_ws_foc,
LogName="Vanadium Run",
LogText=van_run)
for ispec in range(sample_ws_foc.getNumberHistograms()):
# add a bankid and vanadium to log that is read by fitting model
bankid = foc_suffix if sample_ws_foc.getNumberHistograms(
) == 1 else f'{foc_suffix}_{ispec + 1}'
mantid.AddSampleLog(Workspace=sample_ws_foc,
LogName="bankid",
LogText=bankid.replace('_', ' ')) # overwrites
# save spectrum as nexus
filename = _generate_output_file_name(calibration.get_instrument(),
sample_run_no,
van_run,
bankid,
xunit_suffix,
ext=".nxs")
nxs_path = path.join(focus_dir, filename)
mantid.SaveNexus(InputWorkspace=sample_ws_foc,
Filename=nxs_path,
WorkspaceIndexList=[ispec])
nxs_paths.append(nxs_path)
return nxs_paths # from last focus_dir only
def create_vanadium(van_run, calibration_directory):
"""
create the vanadium run for the run number set of the object
@param van_run :: the run number for the vanadium
@param calibration_directory :: the directory to save the output to
"""
# find and load the vanadium
van_file = _gen_filename(van_run)
van_curves_file, van_int_file = _get_van_names(van_run, calibration_directory)
van_name = "eng_vanadium_ws"
simple.Load(van_file, OutputWorkspace=van_name)
# make the vanadium corrections
simple.EnggVanadiumCorrections(VanadiumWorkspace=van_name,
OutIntegrationWorkspace="eng_vanadium_integration",
OutCurvesWorkspace="eng_vanadium_curves")
# save out the vanadium and delete the original workspace
simple.SaveNexus("eng_vanadium_integration", van_int_file)
simple.SaveNexus("eng_vanadium_curves", van_curves_file)
simple.DeleteWorkspace(van_name)
def generate_vanadium_absorb_corrections(van_ws, output_filename):
shape_ws = mantid.CloneWorkspace(InputWorkspace=van_ws)
shape_ws = mantid.ConvertUnits(InputWorkspace=shape_ws, OutputWorkspace=shape_ws, Target="Wavelength")
mantid.CreateSampleShape(InputWorkspace=shape_ws, ShapeXML='<sphere id="sphere_1"> <centre x="0" y="0" z= "0" />\
<radius val="0.005" /> </sphere>')
absorb_ws = \
mantid.AbsorptionCorrection(InputWorkspace=shape_ws, AttenuationXSection="5.08",
ScatteringXSection="5.1", SampleNumberDensity="0.072",
NumberOfWavelengthPoints="25", ElementSize="0.05")
mantid.SaveNexus(Filename=output_filename,
InputWorkspace=absorb_ws, Append=False)
common.remove_intermediate_workspace(shape_ws)
return absorb_ws
def _create_vanadium_splines(focused_spectra, instrument, run_details):
splined_ws_list = instrument._spline_vanadium_ws(focused_spectra)
out_spline_van_file_path = run_details.splined_vanadium_file_path
append = False
for ws in splined_ws_list:
mantid.SaveNexus(Filename=out_spline_van_file_path, InputWorkspace=ws, Append=append)
append = True
# Group for user convenience
group_name = "Van_spline_data"
tt_mode = instrument._get_current_tt_mode()
if tt_mode:
group_name = group_name + '_' + tt_mode
mantid.GroupWorkspaces(InputWorkspaces=splined_ws_list, OutputWorkspace=group_name)
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 checkWorkspacesMatch(self, ws1, ws2):
checker = ms.AlgorithmManager.create("CompareWorkspaces")
checker.setLogging(True)
checker.setPropertyValue("Workspace1", ws1)
checker.setPropertyValue("Workspace2", ws2)
checker.setPropertyValue("Tolerance", str(self.tolerance))
checker.setPropertyValue("CheckInstrument","0")
checker.execute()
if not checker.getProperty("Result"):
print self.__class__.__name__
ms.SaveNexus(InputWorkspace=ws2,Filename=self.__class__.__name__+'-mismatch.nxs')
return False
return True
def generate_vanadium_absorb_corrections(van_ws):
raise NotImplementedError("Generating absorption corrections needs to be implemented correctly")
# TODO are these values applicable to all instruments
shape_ws = mantid.CloneWorkspace(InputWorkspace=van_ws)
mantid.CreateSampleShape(InputWorkspace=shape_ws, ShapeXML='<sphere id="sphere_1"> <centre x="0" y="0" z= "0" />\
<radius val="0.005" /> </sphere>')
calibration_full_paths = None
absorb_ws = \
mantid.AbsorptionCorrection(InputWorkspace=shape_ws, AttenuationXSection="5.08",
ScatteringXSection="5.1", SampleNumberDensity="0.072",
NumberOfWavelengthPoints="25", ElementSize="0.05")
mantid.SaveNexus(Filename=calibration_full_paths["vanadium_absorption"],
InputWorkspace=absorb_ws, Append=False)
common.remove_intermediate_workspace(shape_ws)
return absorb_ws
def save_calibration(ceria_run, calibration_directory, calibration_general, name, bank_names, zeros, difcs,
difas, bk2bk_params):
"""
save the calibration data
@param ceria_run :: the run number of the ceria
@param calibration_directory :: the user specific calibration directory to save to
@param calibration_general :: the general calibration directory to save to
@param name :: the name of the banks being saved
@param bank_names :: the list of banks to save
@param difas :: the list of difa values to save
@param difcs :: the list of difc values to save
@param zeros :: the list of tzero values to save
"""
file_save_prefix = os.path.join(calibration_directory, "ENGINX_" + ceria_run + "_")
gsas_iparm_fname = file_save_prefix + name + ".prm"
pdcals_to_save = dict() # fname: workspace
# work out what template to use, and which PDCalibration files to save
if name == "all_banks":
template_file = None
pdcals_to_save[file_save_prefix + "bank_North.nxs"] = 'engg_calibration_bank_1'
pdcals_to_save[file_save_prefix + "bank_South.nxs"] = 'engg_calibration_bank_2'
elif name == "bank_2":
template_file = "template_ENGINX_241391_South_bank.prm"
pdcals_to_save[file_save_prefix + "bank_South.nxs"] = 'engg_calibration_bank_2'
elif name == "bank_1":
template_file = "template_ENGINX_241391_North_bank.prm"
pdcals_to_save[file_save_prefix + "bank_North.nxs"] = 'engg_calibration_bank_1'
else: # cropped uses North bank template
template_file = "template_ENGINX_241391_North_bank.prm"
pdcals_to_save[file_save_prefix + "cropped.nxs"] = 'engg_calibration_cropped'
# write out the param file to the users directory
Utils.write_ENGINX_GSAS_iparam_file(output_file=gsas_iparm_fname, bank_names=bank_names, difa=difas, difc=difcs,
tzero=zeros, ceria_run=ceria_run,
template_file=template_file, bk2bk_params=bk2bk_params)
for fname, ws in pdcals_to_save.items():
simple.SaveNexus(InputWorkspace=ws, Filename=fname)
if not calibration_general == calibration_directory:
# copy the param file to the general directory
if not os.path.exists(calibration_general):
os.makedirs(calibration_general)
copy2(gsas_iparm_fname, calibration_general)
for fname in pdcals_to_save.keys():
copy2(fname, calibration_general)
def populate_Ei_data(sim_out, nxs):
import ast, os
props = ast.literal_eval(open(os.path.join(sim_out, 'props.json')).read())
Ei, unit = props['average energy'].split(); assert unit=='meV'
t0, unit = props['emission time'].split(); assert unit=='microsecond'
setEnergyRequest(nxs, float(Ei))
from mantid import simpleapi as msa
if sys.version_info<(3,0) and isinstance(nxs, unicode):
nxs = nxs.encode('utf-8')
ws = msa.Load(nxs)
msa.AddSampleLog(ws, LogName='mcvine-Ei', LogText=str(Ei), LogType='Number')
msa.AddSampleLog(ws, LogName='mcvine-t0', LogText=str(t0), LogType='Number')
(fd, filename) = tempfile.mkstemp(); os.close(fd)
msa.SaveNexus(ws, filename)
from ...ARCS.applications.nxs import mv
mv(filename, nxs)
return
def _generate_vanadium_absorb_corrections(calibration_full_paths, ws_to_match):
# TODO are these values applicable to all instruments
shape_ws = mantid.CloneWorkspace(InputWorkspace=ws_to_match)
mantid.CreateSampleShape(
InputWorkspace=shape_ws,
ShapeXML='<sphere id="sphere_1"> <centre x="0" y="0" z= "0" />\
<radius val="0.005" /> </sphere>'
)
absorb_ws = \
mantid.AbsorptionCorrection(InputWorkspace=shape_ws, AttenuationXSection="5.08",
ScatteringXSection="5.1", SampleNumberDensity="0.072",
NumberOfWavelengthPoints="25", ElementSize="0.05")
mantid.SaveNexus(Filename=calibration_full_paths["vanadium_absorption"],
InputWorkspace=absorb_ws,
Append=False)
remove_intermediate_workspace(shape_ws)
return absorb_ws
def _save_out(run_number, focus_directory, focus_general, output, join_string,
bank_id):
"""
save out the files required for the focus
@param run_number :: the run number of the focused run
@param focus_directory :: the user directory to save to
@param focus_general :: the general folder to copy the saved out files to
@param output :: the workspace to save
@param join_string :: the nameing scheme of the files
@param bank_id :: the bank being saved
"""
# work out where to save the files
filename = os.path.join(focus_directory,
join_string.format(run_number, bank_id))
hdf5_name = os.path.join(focus_directory, run_number + ".hdf5")
if not unicode(bank_id).isnumeric():
bank_id = 0
# save the files out to the user directory
simple.SaveFocusedXYE(InputWorkspace=output,
Filename=filename + ".dat",
SplitFiles=False,
StartAtBankNumber=bank_id)
simple.SaveGSS(InputWorkspace=output,
Filename=filename + ".gss",
SplitFiles=False,
Bank=bank_id)
simple.SaveOpenGenieAscii(InputWorkspace=output,
Filename=filename + ".his",
OpenGenieFormat="ENGIN-X Format")
simple.SaveNexus(InputWorkspace=output, Filename=filename + ".nxs")
simple.ExportSampleLogsToHDF5(InputWorkspace=output,
Filename=hdf5_name,
Blacklist="bankid")
if not focus_general == focus_directory:
if not os.path.exists(focus_general):
os.makedirs(focus_general)
# copy the files to the general directory
copy2(filename + ".dat", focus_general)
copy2(filename + ".gss", focus_general)
copy2(filename + ".his", focus_general)
copy2(filename + ".nxs", focus_general)
copy2(hdf5_name, focus_general)
def populate_Ei_data(sim_out, nxs):
import ast, os
props = ast.literal_eval(open(os.path.join(sim_out, 'props.json')).read())
Ei, unit = props['average energy'].split()
assert unit == 'meV'
t0, unit = props['emission time'].split()
assert unit == 'microsecond'
from mantid import simpleapi as msa
ws = msa.Load(nxs)
msa.AddSampleLog(ws,
LogName='mcvine-Ei',
LogText=str(Ei),
LogType='Number')
msa.AddSampleLog(ws,
LogName='mcvine-t0',
LogText=str(t0),
LogType='Number')
msa.SaveNexus(ws, nxs)
return
def create_output_files(calibration_dir, calibration, ws_foc):
"""
Create output files (.prm for GSAS and .nxs of calibration table) from the algorithms in the specified directory
:param calibration_dir: The directory to save the files into.
:param calibration: CalibrationInfo object with details of calibration and grouping
:param ws_foc: focused ceria workspace
"""
# create calibration dir of not exist
if not path.exists(calibration_dir):
makedirs(calibration_dir)
# save grouping ws if custom or cropped
if not calibration.group.banks:
calibration.save_grouping_workspace(calibration_dir)
# save prm file(s)
prm_filepath = path.join(calibration_dir,
calibration.generate_output_file_name())
write_prm_file(ws_foc, prm_filepath)
calibration.set_prm_filepath(prm_filepath)
# save pdcal output as nexus
filepath, ext = path.splitext(prm_filepath)
nxs_filepath = filepath + '.nxs'
mantid.SaveNexus(InputWorkspace=calibration.get_calibration_table(),
Filename=nxs_filepath)
# if both banks calibrated save individual banks separately as well
if calibration.group == GROUP.BOTH:
# output a separate prm for North and South when both banks included
for ibank, bank in enumerate(calibration.group.banks):
# get prm filename for individual banks by passing group enum as argument to generate_output_file_name
prm_filepath_bank = path.join(
calibration_dir,
calibration.generate_output_file_name(GROUP(str(ibank + 1))))
write_prm_file(ws_foc, prm_filepath_bank, spec_nums=[ibank])
# copy pdcal output nxs for both banks
filepath, ext = path.splitext(prm_filepath_bank)
nxs_filepath_bank = filepath + '.nxs'
copy2(nxs_filepath, nxs_filepath_bank)
logger.notice(f"\n\nCalibration files saved to: \"{calibration_dir}\"\n\n")
def checkWorkspacesMatch(self, ws1, ws2):
"""
Function to check two workspaces match
Used when the result of a test produces more than a single workspace
"""
checker = ms.AlgorithmManager.create("CompareWorkspaces")
checker.setLogging(True)
checker.setPropertyValue("Workspace1", ws1)
checker.setPropertyValue("Workspace2", ws2)
checker.setPropertyValue("Tolerance", str(self.tolerance))
checker.setPropertyValue("CheckInstrument", "0")
checker.execute()
if not checker.getProperty("Result"):
print(self.__class__.__name__)
ms.SaveNexus(InputWorkspace=ws2,
Filename=self.__class__.__name__ + '-mismatch.nxs')
return False
return True
def _focus_mode_mods(output_file_paths, calibrated_spectra):
index = 1
append = False
output_list = []
for ws in calibrated_spectra:
mantid.SaveGSS(InputWorkspace=ws,
Filename=output_file_paths["gss_filename"],
Append=append,
Bank=index)
output_name = output_file_paths["output_name"] + "_mod" + str(index)
dspacing_ws = mantid.ConvertUnits(InputWorkspace=ws,
OutputWorkspace=output_name,
Target="dSpacing")
output_list.append(dspacing_ws)
mantid.SaveNexus(Filename=output_file_paths["nxs_filename"],
InputWorkspace=dspacing_ws,
Append=append)
append = True
index += 1
return output_list
def create_vanadium_integration(van_run, calibration_directory):
"""
create the vanadium integration for the run number set of the object
@param van_run :: the run number for the vanadium
@param calibration_directory :: the directory to save the output to
"""
# find and load the vanadium
van_file = _gen_filename(van_run)
_, van_int_file = _get_van_names(van_run, calibration_directory)
van_name = "eng_vanadium_ws"
van_ws = simple.Load(van_file, OutputWorkspace=van_name)
# make the integration workspace
simple.NormaliseByCurrent(InputWorkspace=van_ws, OutputWorkspace=van_ws)
# sensitivity correction for van
ws_van_int = simple.Integration(InputWorkspace=van_ws)
ws_van_int /= van_ws.blocksize()
# save out the vanadium and delete the original workspace
simple.SaveNexus(ws_van_int, van_int_file)
simple.DeleteWorkspace(van_name)
simple.DeleteWorkspace(ws_van_int)
