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EnggSaveGSASIIFitResultsToHDF5 v1

Summary

Save input parameters and fit results from GSASIIRefineFitPeaks to an HDF5 file, indexed by bank ID

Properties

Name	Direction	Type	Default	Description
LatticeParamWorkspaces	Input	str list		Table workspace containing lattice parameters
RunNumbers	Input	int list		The run number of each fitted run
BankIDs	Input	int list		Bank IDs of the workspaces a fit was run on (1 for each workspace, in order. 1 for North, 2 for South)
RefinementMethod	Input	string	Pawley refinement	Which refinement method was used. Allowed values: [‘Pawley refinement’, ‘Rietveld refinement’]
XMin	Input	number	0	Minimum TOF value used for refinement
XMax	Input	number	0	Maximum TOF value used for refinement
PawleyDMin	Input	number	0	Minimum d spacing used for Pawley refinement
PawleyNegativeWeight	Input	number	0	Negative weight penalty used in Pawley refinement
RefineSigma	Input	boolean	False	Whether to sigma profile coefficient was refined
RefineGamma	Input	boolean	False	Whether gamma profile coefficient was refined
Sigma	Input	dbl list		GSAS-II profile coefficient sigma, one for each run (or none if sigma wasn’t refined)
Gamma	Input	dbl list		GSAS-II profile coefficient gamma, one for each run (or none if gamma wasn’t refined)
Rwp	Input	dbl list		Weighted profile R-factor, ‘goodness-of-fit’ measure. One for each run
Filename	Input	string	Mandatory	HDF5 file to save to. Allowed extensions: [‘.hdf5’, ‘.h5’, ‘.hdf’]

Description

Exports the results of a GSASIIRefineFitPeaks refinement, as well as the refinement parameters used, to an HDF5 file indexed by bank ID. If multiple sets of fit results are provided, then the file is divided into sub-groups for each run number, with the Run Number groups indexed further by bank ID.The results go in a sub-group of the Bank group called GSAS-II Fitting. The subgroups of this are the following:

Refinement Parameters

Settings passed to GSASIIRefineFitPeaks to generate this refinement.

• RefinementMethod - either Pawley or Rietveld refinement

• RefineSigma - whether sigma (Gaussian broadening term) was refined

• RefineGamma - whether gamma (Lorentzian broadening term) was refined

• XMin - the minimum TOF value used for refinement. Note this may not be the same as the XMin that you passed to GSASIIRefineFitPeaks, as XMin in GSASIIRefineFitPeaks will be overridden by PawleyDMin if the latter corresponds to a greater TOF value

• XMax - the maximum TOF value used for refinement

Additionally, if RefinementMethod is Pawley refinement, the two Pawley parameters will be saved:

• PawleyDMin - the minimum D spacing to use for refinement

• PawleyNegativeWeight - a weight penalty used in Pawley refinement

Lattice Parameters

The lattice parameters of the refined structure: alpha, beta, gamma, a, b, c and volume.

Profile Coefficients

Only saved if either RefineSigma or RefineGamma were turned on.

• Gamma - Lorentzian broadening term of the GSAS-II peak profile. Only saved if it was refined

• Sigma - Gaussian broadening term of the GSAS-II peak profile. Only saved if it was refined

Rwp (weighted-profile R-factor)

A measure of ‘goodness of fit’, as a percentage

File Structure

Obtaining fit results for banks 1 and 2 of run 123456 and then saving them with algorithm would yield the following file structure:

Obtaining fit results for banks 1 and 2 of run 123456 and bank 1 of 123457 and then saving them with the algorithm would yield the following file structure:

Usage

Warning

Due to a reliance on GSAS-II, the first example is not run on the build servers, so may not be correct. Please inform Mantid developers if you spot something awry

Example - Export refinement results to a new HDF5 file following GSAS-II refinement:

import os

path_to_gsas = r"C:\g2conda\GSASII"

gsas_proj_file = r"C:\mantid-data\280625.gpx"

data_dir = r"C:\mantid-data"
input_file = lambda file: os.path.join(data_dir, file)

phase_file = input_file("Fe-alpha.cif")
iparams_file = input_file("template_ENGINX_241391_236516_North_bank.prm")
input_ws = Load(Filename=input_file("ENGINX_280625_focused_bank_1.nxs"))

fitted_peaks, lattice_params, rwp, sigma, gamma = \
    GSASIIRefineFitPeaks(InputWorkspace=input_ws,
                         PhaseInfoFiles=phase_file,
                         InstrumentFile=iparams_file,
                         RefinementMethod="Rietveld refinement",
                         SaveGSASIIProjectFile=gsas_proj_file,
                         PathToGSASII=path_to_gsas,
                         RefineSigma=True,
                         RefineGamma=False)

EnggSaveGSASIIFitResultsToHDF5(LatticeParamWorkspaces=[lattice_params],
                               Filename=r"D:\doctest.hdf5",
                               BankIDs=[input_ws.run()["bankid"].value],
                               RefinementMethod="Rietveld refinement",
                               XMin=min(fitted_peaks.readX(0)),
                               XMax=max(fitted_peaks.readX(0)),
                               RefineSigma=True,
                               RefineGamma=False,
                               Sigma=sigma,
                               Rwp=rwp)

Example - Mock up fit results and then read them back in:

Below is an example of how to read the results back in using the Python h5py library.

import h5py
import os

# lattice_params table workspace is an output property of GSASIIRefineFitPeaks
lattice_params = CreateEmptyTableWorkspace()
lattice_param_headers = ["a", "b", "c", "alpha", "beta", "gamma", "volume"]
[lattice_params.addColumn("double", header) for header in lattice_param_headers]
lattice_params.addRow([2.8, 2.8, 2.8, 90, 90, 90, 25])

# Input properties of GSASIIRefineFitPeaks
refinement_method = "Pawley refinement"
x_min = 10000
x_max = 40000
refine_sigma = True
refine_gamma = False

# Output properties of GSASIIRefineFitPeaks
sigma = 81
rwp = 75

# Either read from the focused workspace sample logs or work it out from the title
bank_id = 1

filename = os.path.join(config["defaultsave.directory"],
                        "EnggSaveGSASIIFitResultsToHDF5DocTest.hdf5")

EnggSaveGSASIIFitResultsToHDF5(LatticeParamWorkspaces=[lattice_params],
                               Filename=filename,
                               BankIDs=[bank_id],
                               RefinementMethod=refinement_method,
                               XMin=x_min,
                               XMax=x_max,
                               RefineSigma=refine_sigma,
                               RefineGamma=refine_gamma,
                               Sigma=sigma,
                               Rwp=rwp)

with h5py.File(filename, "r") as f:
    fit_results_group = f["Bank 1"]["GSAS-II Fitting"]

    print("Lattice parameter a: {}".format(fit_results_group["Lattice Parameters"]["a"][()]))
    print("XMin: {}".format(fit_results_group["Refinement Parameters"]["XMin"][()]))
    print("RefineSigma: {}".format(bool(fit_results_group["Refinement Parameters"]["RefineSigma"])))
    print("Sigma: {}".format(fit_results_group["Profile Coefficients"]["Sigma"][()]))

Output:

Lattice parameter a: 2.8
XMin: 10000.0
RefineSigma: True
Sigma: 81.0

Categories: AlgorithmIndex | DataHandling

Source

Python: EnggSaveGSASIIFitResultsToHDF5.py