def __call__(self, file_name, workspace):
"""Write a PeaksWorkspace to an ASCII file using this formatter.
:param file_name: the file name to output data to.
:param workspace: the PeaksWorkspace to write to file.
"""
if has_modulated_indexing(workspace):
raise NotImplementedError("Cannot currently save modulated structures to GSAS or SHELX formats")
SaveHKL(Filename=file_name, InputWorkspace=workspace, OutputWorkspace=workspace.name())
def __call__(self, file_name, workspace, _):
"""Write a PeaksWorkspace to an ASCII file using this formatter.
:param file_name: the file name to output data to.
:param workspace: the PeaksWorkspace to write to file.
:param _: Ignored parameter for compatability with other savers
"""
if has_modulated_indexing(workspace):
raise RuntimeError(
"Cannot currently save modulated structures to GSAS or SHELX formats")
from mantid.simpleapi import SaveHKL
SaveHKL(Filename=file_name, InputWorkspace=workspace, OutputWorkspace=workspace.name())
def PyExec(self):
input_workspaces, peak_workspaces = self._expand_groups()
output_workspace_name = self.getPropertyValue("OutputWorkspace")
peak_radius = self.getProperty("PeakRadius").value
inner_radius = self.getProperty("BackgroundInnerRadius").value
outer_radius = self.getProperty("BackgroundOuterRadius").value
remove_0_intensity = self.getProperty("RemoveZeroIntensity").value
use_lorentz = self.getProperty("ApplyLorentz").value
multi_ws = len(input_workspaces) > 1
output_workspaces = []
for input_ws, peak_ws in zip(input_workspaces, peak_workspaces):
if multi_ws:
peaks_ws_name = input_ws + '_' + output_workspace_name
output_workspaces.append(peaks_ws_name)
else:
peaks_ws_name = output_workspace_name
IntegratePeaksMD(InputWorkspace=input_ws,
PeakRadius=peak_radius,
BackgroundInnerRadius=inner_radius,
BackgroundOuterRadius=outer_radius,
PeaksWorkspace=peak_ws,
OutputWorkspace=peaks_ws_name)
if multi_ws:
peaks_ws_name = output_workspace_name
CreatePeaksWorkspace(
InstrumentWorkspace=input_workspaces[0],
NumberOfPeaks=0,
OutputWorkspace=peaks_ws_name,
OutputType=mtd[peak_workspaces[0]].id().replace(
'sWorkspace', ''))
CopySample(InputWorkspace=output_workspaces[0],
OutputWorkspace=peaks_ws_name,
CopyName=False,
CopyMaterial=False,
CopyEnvironment=False,
CopyShape=False,
CopyLattice=True)
for peak_ws in output_workspaces:
CombinePeaksWorkspaces(peaks_ws_name,
peak_ws,
OutputWorkspace=peaks_ws_name)
DeleteWorkspace(peak_ws)
if use_lorentz:
# Apply Lorentz correction:
peaks = AnalysisDataService[peaks_ws_name]
for p in range(peaks.getNumberPeaks()):
peak = peaks.getPeak(p)
lorentz = abs(
np.sin(peak.getScattering() * np.cos(peak.getAzimuthal())))
peak.setIntensity(peak.getIntensity() * lorentz)
if remove_0_intensity:
FilterPeaks(InputWorkspace=peaks_ws_name,
OutputWorkspace=peaks_ws_name,
FilterVariable='Intensity',
FilterValue=0,
Operator='>')
# Write output only if a file path was provided
if not self.getProperty("OutputFile").isDefault:
out_format = self.getProperty("OutputFormat").value
filename = self.getProperty("OutputFile").value
if out_format == "SHELX":
SaveHKL(InputWorkspace=peaks_ws_name,
Filename=filename,
DirectionCosines=True,
OutputWorkspace="__tmp")
DeleteWorkspace("__tmp")
elif out_format == "Fullprof":
SaveReflections(InputWorkspace=peaks_ws_name,
Filename=filename,
Format="Fullprof")
else:
# This shouldn't happen
RuntimeError("Invalid output format given")
self.setProperty("OutputWorkspace", AnalysisDataService[peaks_ws_name])