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GSASIIRefineFitPeaks.py
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GSASIIRefineFitPeaks.py
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from __future__ import (absolute_import, division, print_function)
from contextlib import contextmanager
import numpy
import os
import sys
import tempfile
from mantid.kernel import *
from mantid.api import *
import mantid.simpleapi as mantid
class GSASIIRefineFitPeaks(PythonAlgorithm):
"""
Mantid algorithm to use the powder diffraction and related data
from the powder diffraction module of GSAS-II
(https://subversion.xray.aps.anl.gov/trac/pyGSAS)
"""
PROP_GROUP_PAWLEY_PARAMS = "Pawley Parameters"
PROP_GSAS_PROJ_PATH = "SaveGSASIIProjectFile"
PROP_INPUT_WORKSPACE = "InputWorkspace"
PROP_OUT_FITTED_PEAKS_WS = "OutputWorkspace"
PROP_OUT_GAMMA = "Gamma"
PROP_OUT_GROUP_RESULTS = "Results"
PROP_OUT_LATTICE_PARAMS = "LatticeParameters"
PROP_OUT_RWP = "Rwp"
PROP_OUT_SIGMA = "Sigma"
PROP_PATH_TO_GSASII = "PathToGSASII"
PROP_PATH_TO_INST_PARAMS = "InstrumentFile"
PROP_PATHS_TO_PHASE_FILES = "PhaseInfoFiles"
PROP_PAWLEY_DMIN = "PawleyDMin"
PROP_PAWLEY_NEGATIVE_WEIGHT = "PawleyNegativeWeight"
PROP_REFINE_GAMMA = "RefineGamma"
PROP_REFINE_SIGMA = "RefineSigma"
PROP_REFINEMENT_METHOD = "RefinementMethod"
PROP_SUPPRESS_GSAS_OUTPUT = "MuteGSASII"
PROP_WORKSPACE_INDEX = "WorkspaceIndex"
PROP_XMAX = "XMax"
PROP_XMIN = "XMin"
LATTICE_TABLE_PARAMS = ["length_a", "length_b", "length_c", "angle_alpha", "angle_beta", "angle_gamma", "volume"]
REFINEMENT_METHODS = ["Pawley refinement", "Rietveld refinement", "Peak fitting"]
def category(self):
return "Diffraction\\Engineering;Diffraction\\Fitting"
def name(self):
return "GSASIIRefineFitPeaks"
def summary(self):
return ("Perform Rietveld or Pawley refinement of lattice parameters on a diffraction spectrum "
"using GSAS-II scriptable API")
def validateInputs(self):
x_min = self.getProperty(self.PROP_XMIN)
x_max = self.getProperty(self.PROP_XMAX)
if not x_max.isDefault and x_max.value <= x_min.value:
return {self.PROP_XMAX: "{} must be greater than {}".format(self.PROP_XMAX, self.PROP_XMIN)}
return {}
def PyInit(self):
self.declareProperty(name=self.PROP_REFINEMENT_METHOD, defaultValue=self.REFINEMENT_METHODS[0],
validator=StringListValidator(self.REFINEMENT_METHODS), direction=Direction.Input,
doc="Refinement method (Rietvield or Pawley)")
self.declareProperty(WorkspaceProperty(name=self.PROP_INPUT_WORKSPACE, defaultValue="",
direction=Direction.Input), doc="Workspace with spectra to fit peaks")
self.declareProperty(name=self.PROP_WORKSPACE_INDEX, defaultValue=0, direction=Direction.Input,
doc="Index of the spectrum in InputWorkspace to fit. By default, the first spectrum "
"(ie the only one for a focused workspace) is used")
self.declareProperty(FileProperty(name=self.PROP_PATH_TO_INST_PARAMS, defaultValue="", action=FileAction.Load,
extensions=[".prm"]), doc="Location of the phase file")
self.declareProperty(MultipleFileProperty(name=self.PROP_PATHS_TO_PHASE_FILES, extensions=[".cif"]),
doc="Paths to each required phase file")
self.declareProperty(FileProperty(name=self.PROP_PATH_TO_GSASII, defaultValue="", action=FileAction.Directory),
doc="Path to the directory containing GSASII executable on the user's machine")
self.declareProperty(name=self.PROP_XMIN, defaultValue=0.0, direction=Direction.Input,
doc="Minimum x value to use for refinement, in the same units as the input workspace. " +
"Leave blank to refine in the range 0.0 to {}".format(self.PROP_XMAX))
self.declareProperty(name=self.PROP_XMAX, defaultValue=0.0, direction=Direction.Input,
doc="Maximum x value to use for refinement, in the same units as the input workspace. " +
"Leave blank to refine in the range {} to the end of the range".format(self.PROP_XMIN))
self.declareProperty(name=self.PROP_REFINE_SIGMA, defaultValue=False, direction=Direction.Input,
doc="Whether to refine the sigma-1 profile coefficient")
self.declareProperty(name=self.PROP_REFINE_GAMMA, defaultValue=False, direction=Direction.Input,
doc="Whether to refine the gamma-1 (called 'X' in GSAS-II) profile coefficient")
self.declareProperty(WorkspaceProperty(name=self.PROP_OUT_FITTED_PEAKS_WS, defaultValue="",
direction=Direction.Output), doc="Workspace with fitted peaks")
self.declareProperty(ITableWorkspaceProperty(name=self.PROP_OUT_LATTICE_PARAMS, direction=Direction.Output,
defaultValue=self.PROP_OUT_LATTICE_PARAMS),
doc="Table to output the lattice parameters (refined)")
self.declareProperty(name=self.PROP_OUT_RWP, direction=Direction.Output, defaultValue=0.0,
doc="Weighted profile R factor (as a percentage)")
self.declareProperty(name=self.PROP_OUT_SIGMA, direction=Direction.Output, defaultValue=0.0,
doc="Sigma-1 profile coefficient")
self.declareProperty(name=self.PROP_OUT_GAMMA, direction=Direction.Output, defaultValue=0.0,
doc="Gamma-1 profile coefficient (called X in GSAS-II)")
self.declareProperty(FileProperty(name=self.PROP_GSAS_PROJ_PATH, defaultValue="", action=FileAction.Save,
extensions=".gpx"), doc="GSASII Project to work on")
self.setPropertyGroup(self.PROP_OUT_FITTED_PEAKS_WS, self.PROP_OUT_GROUP_RESULTS)
self.setPropertyGroup(self.PROP_OUT_LATTICE_PARAMS, self.PROP_OUT_GROUP_RESULTS)
self.setPropertyGroup(self.PROP_OUT_RWP, self.PROP_OUT_GROUP_RESULTS)
self.setPropertyGroup(self.PROP_GSAS_PROJ_PATH, self.PROP_OUT_GROUP_RESULTS)
self.declareProperty(name=self.PROP_PAWLEY_DMIN, defaultValue=1.0, direction=Direction.Input,
doc="For Pawley refiment: as defined in GSAS-II, the minimum d-spacing to be used in a "
"Pawley refinement. Please refer to the GSAS-II documentation for full details.")
self.declareProperty(name=self.PROP_PAWLEY_NEGATIVE_WEIGHT, defaultValue=0.0, direction=Direction.Input,
doc="For Pawley refinement: as defined in GSAS-II, the weight for a penalty function "
"applied during a Pawley refinement on resulting negative intensities. "
"Please refer to the GSAS-II documentation for full details.")
self.setPropertyGroup(self.PROP_PAWLEY_DMIN, self.PROP_GROUP_PAWLEY_PARAMS)
self.setPropertyGroup(self.PROP_PAWLEY_NEGATIVE_WEIGHT, self.PROP_GROUP_PAWLEY_PARAMS)
self.declareProperty(name=self.PROP_SUPPRESS_GSAS_OUTPUT, defaultValue=False, direction=Direction.Input,
doc="Set to True to prevent GSAS run info from being "
"printed (not recommended, but can be useful for debugging)")
def PyExec(self):
refinement_method = self.getPropertyValue(self.PROP_REFINEMENT_METHOD)
if refinement_method == self.REFINEMENT_METHODS[2]: # Peak fitting
raise NotImplementedError("GSAS-II Peak fitting not yet implemented in Mantid")
with self._suppress_stdout():
gsas_proj = self._initialise_GSAS()
rwp, lattice_params = \
self._run_rietveld_pawley_refinement(gsas_proj=gsas_proj,
do_pawley=refinement_method == self.REFINEMENT_METHODS[0])
self._set_output_properties(lattice_params=lattice_params, rwp=rwp,
fitted_peaks_ws=self._generate_fitted_peaks_ws(gsas_proj),
gamma=gsas_proj.values()[5]["Instrument Parameters"][0]["X"][1],
sigma=gsas_proj.values()[5]["Instrument Parameters"][0]["sig-1"][1])
def _build_output_lattice_table(self, lattice_params):
table_name = self.getPropertyValue(self.PROP_OUT_LATTICE_PARAMS)
table = mantid.CreateEmptyTableWorkspace(OutputWorkspace=table_name, StoreInADS=False)
for param in self.LATTICE_TABLE_PARAMS:
table.addColumn("double", param.split("_")[-1])
table.addRow([float(lattice_params[param]) for param in self.LATTICE_TABLE_PARAMS])
return table
def _create_refinement_params_dict(self, num_phases):
basic_refinement = {"set": {"Background": {"no.coeffs": 3, "refine": True},
"Sample Parameters": ["Scale"]}}
x_max = self.getProperty(self.PROP_XMAX).value
if x_max:
x_min = self.getProperty(self.PROP_XMIN).value
basic_refinement["set"].update({"Limits": [x_min, x_max]})
scale_refinement = {"set": {"Scale": True},
"phases": range(1, num_phases)}
unit_cell_refinement = {"set": {"Cell": True}}
profile_coeffs_refinement = {"set": {"Instrument Parameters": []}}
refine_sigma = self.getProperty(self.PROP_REFINE_SIGMA).value
if refine_sigma:
profile_coeffs_refinement["set"]["Instrument Parameters"].append("sig-1")
refine_gamma = self.getProperty(self.PROP_REFINE_GAMMA).value
if refine_gamma:
profile_coeffs_refinement["set"]["Instrument Parameters"].append("X")
return [basic_refinement, scale_refinement, unit_cell_refinement, profile_coeffs_refinement, {}]
def _extract_spectrum_from_workspace(self):
"""
Extract a single spectrum from the input workspace. If the input workspace only has one spectrum then just
return the input workspace
:return: Single-spectrum workspace
"""
ws = self.getPropertyValue(self.PROP_INPUT_WORKSPACE)
if mtd[ws].getNumberHistograms > 1:
ws_index = self.getPropertyValue(self.PROP_WORKSPACE_INDEX)
spectrum = mantid.ExtractSpectra(InputWorkspace=ws, StartWorkspaceIndex=ws_index,
EndWorkspaceIndex=ws_index, StoreInADS=False)
else:
spectrum = mantid.CloneWorkspace(InputWorkspace=ws, StoreInADS=False)
return spectrum
def _generate_fitted_peaks_ws(self, gsas_proj):
input_ws = self.getPropertyValue(self.PROP_INPUT_WORKSPACE)
fitted_peaks_ws_name = self.getPropertyValue(self.PROP_OUT_FITTED_PEAKS_WS)
fitted_peaks_ws = mantid.CloneWorkspace(InputWorkspace=input_ws, OutputWorkspace=fitted_peaks_ws_name,
StoreInADS=False)
hist = gsas_proj.histogram(0)
fitted_peaks_y = hist.getdata(datatype="yCalc")
fitted_peaks_y_unmasked = self._replace_masked_elements_with_default(masked_array=fitted_peaks_y, default=0)
fitted_peaks_ws.setY(0, fitted_peaks_y_unmasked)
return fitted_peaks_ws
def _initialise_GSAS(self):
"""
Initialise a GSAS project object with a spectrum and an instrument parameter file
:return: GSAS project object
"""
gsas_path = self.getPropertyValue(self.PROP_PATH_TO_GSASII)
sys.path.append(gsas_path)
try:
import GSASIIscriptable as GSASII
except ImportError:
error_msg = "Could not import GSAS-II. Are you sure it's installed at {}?".format(gsas_path)
logger.error(error_msg)
raise ImportError(error_msg)
gsas_proj_path = self.getPropertyValue(self.PROP_GSAS_PROJ_PATH)
gsas_proj = GSASII.G2Project(filename=gsas_proj_path)
spectrum = self._extract_spectrum_from_workspace()
spectrum_path = self._save_temporary_fxye(spectrum=spectrum)
inst_param_path = self.getPropertyValue(self.PROP_PATH_TO_INST_PARAMS)
gsas_proj.add_powder_histogram(datafile=spectrum_path, iparams=inst_param_path, fmthint="xye")
self._remove_temporary_fxye(spectrum_path=spectrum_path)
return gsas_proj
def _replace_masked_elements_with_default(self, masked_array, default):
return numpy.array([val if not masked else default for val, masked in zip(masked_array, masked_array.mask)])
def _remove_temporary_fxye(self, spectrum_path):
try:
os.remove(spectrum_path)
except Exception as e:
raise Warning("Couldn't remove temporary spectrum file at location \"{}\":\n{}".format(spectrum_path, e))
def _run_rietveld_pawley_refinement(self, gsas_proj, do_pawley):
"""
Run a Rietveld or Pawley refinement
:param gsas_proj: The project to work on
:param do_pawley: True if doing a Pawley refinement (the default), False if doing a Rietveld refinement
:return: (R weighted profile, goodness-of-fit coefficient, table containing refined lattice parameters)
"""
phase_paths = self.getPropertyValue(self.PROP_PATHS_TO_PHASE_FILES).split(",")
refinements = self._create_refinement_params_dict(num_phases=len(phase_paths))
prog = Progress(self, start=0, end=1, nreports=len(refinements) + 1)
prog.report("Reading phase files")
for phase_path in phase_paths:
phase = gsas_proj.add_phase(phasefile=phase_path, histograms=[gsas_proj.histograms()[0]])
if do_pawley:
self._set_pawley_phase_parameters(phase)
for i, refinement in enumerate(refinements):
prog.report("Step {} of refinement recipe".format(i + 1))
gsas_proj.do_refinements([refinement])
gsas_proj.save()
rwp = gsas_proj.histogram(0).get_wR()
lattice_params = gsas_proj.phases()[0].get_cell()
lattice_params_table = self._build_output_lattice_table(lattice_params)
return rwp, lattice_params_table
def _save_temporary_fxye(self, spectrum):
"""
Create a temporary fxye file for GSAS to read the spectrum from. This is required as we cannot pass a workspace
straight to GSASIIscriptable, but rather it must be read from a file
:param spectrum: The spectrum to save
:return: Fully qualified path to the new file
"""
workspace_index = self.getPropertyValue(self.PROP_WORKSPACE_INDEX)
temp_dir = tempfile.gettempdir()
# Output file MUST end with "-n.fxye" where n is a number
# If you see "Runtime error: Rvals" from GSASIIscriptable.py, it may be because this name is badly formatted
file_path = os.path.join(temp_dir, "{}_focused_spectrum-{}.fxye".format(self.name(), workspace_index))
mantid.SaveFocusedXYE(Filename=file_path, InputWorkspace=spectrum, SplitFiles=False, IncludeHeader=False)
return file_path
def _set_output_properties(self, fitted_peaks_ws, rwp, lattice_params, sigma, gamma):
self.setProperty(self.PROP_OUT_FITTED_PEAKS_WS, fitted_peaks_ws)
self.setProperty(self.PROP_OUT_RWP, rwp)
self.setProperty(self.PROP_OUT_LATTICE_PARAMS, lattice_params)
self.setProperty(self.PROP_OUT_GAMMA, gamma)
self.setProperty(self.PROP_OUT_SIGMA, sigma)
def _set_pawley_phase_parameters(self, phase):
# Note from GSAS-II doc: "you probably should clear the Histogram scale factor refinement
# flag (found in Sample parameters for the powder data set) as it cannot be refined
# simultaneously with the Pawley reflection intensities"
phase.values()[2].values()[0]["Scale"] = [1.0, False]
phase_params = phase.values()[4]
phase_params["doPawley"] = True
pawley_dmin = self.getPropertyValue(self.PROP_PAWLEY_DMIN)
phase_params["Pawley dmin"] = pawley_dmin
pawley_neg_wt = self.getPropertyValue(self.PROP_PAWLEY_NEGATIVE_WEIGHT)
phase_params["Pawley neg wt"] = pawley_neg_wt
@contextmanager
def _suppress_stdout(self):
"""
Suppress output from print statements. This is mainly useful for debugging, as GSAS does a lot of printing.
"""
if self.getProperty(self.PROP_SUPPRESS_GSAS_OUTPUT).value:
self.log().information("Suppressing stdout")
with open(os.devnull, "w") as devnull:
old_stdout = sys.stdout
sys.stdout = devnull
try:
yield
finally:
sys.stdout = old_stdout
else:
yield
AlgorithmFactory.subscribe(GSASIIRefineFitPeaks)