garnet.utilities package

Submodules

garnet.utilities.autoreduce module

class AutoReduce(filename)

Bases: object

Methods

compress
elastic
plot_instrument
publish_plots

compress(ws)

elastic(time_offset=14000)

plot_instrument()

publish_plots()

garnet.utilities.calculate module

class CalculateUB(a, b, c, alpha, beta, gamma)

Bases: object

Optimizer of crystal orientation from peaks and known lattice parameters.

Attributes:

a, b, cfloat

Lattice constants in ansgroms.

alpha, beta, gammafloat

Lattice angles in degrees.

Methods

UB_matrix(U, B)	Calculate \(UB\)-matrix.
cost(param, B, kf_ki_dir, wavelength)	Cost function for indexing given a proposed orientation.
indexer(UB, kf_ki_dir, wavelength[, tol, alpha])	Laue indexer for a given \(UB\) matrix.
metric_G_star_tensor()	Calculate the reciprocal metric tensor \(G^*\).
metric_G_tensor()	Calculate the metric tensor \(G\).
minimize(kf_ki_dir, wavelength[, n_proc])	Fit the orientation and other parameters.
objective(x)	Objective function.
orientation_U(u0, u1, u2)	The sample orientation matrix \(U\).
reciprocal_lattice_B()	The reciprocal lattice \(B\)-matrix.
refine(kf_ki_dir, wavelength[, cell, error])	Refine the orientation and lattice parameters under constraints.
residual(x, kf_ki_dir, hkl, wavelength, fun)	Optimization residual function.

cartesian_matrix_metric_tensor
cubic
get_lattice_constants
get_orientation_parameters
hexagonal
index
monoclinic
orthorhombic
rhombohedral
set_lattice_constants
set_orientation_parameters
softplus
tetragonal
triclinic

UB_matrix(U, B)

Calculate \(UB\)-matrix.

Parameters:

U2d-array

3x3 orientation matrix.

B2d-array

3x3 reciprocal lattice vectors Cartesian matrix.

Returns:

UB2d-array

3x3 oriented reciprocal lattice.

cartesian_matrix_metric_tensor(a, b, c, alpha, beta, gamma)

cost(param, B, kf_ki_dir, wavelength)

Cost function for indexing given a proposed orientation.

Parameters:

paramtuple, float

Orientation parameters.

Barray, float

Reciprocal lattice B-matrix.

kf_ki_dirarray, float

wavelengthlist, float

Wavelength band (min, max).

Returns:

errorfloat

Total indexing cost.

cubic(x)

get_lattice_constants()

get_orientation_parameters()

hexagonal(x)

index(kf_ki_dir, wavelength)

indexer(UB, kf_ki_dir, wavelength, tol=0.1, alpha=0.1)

Laue indexer for a given \(UB\) matrix.

Parameters:

UB2d-array

3x3 sample oriented lattice matrix.

kf_ki_dirlist

Difference between scattering and incident beam directions.

wavelengthlist

Wavelength of each reflection.

tolfloat, optional

Indexing tolerance. Default is 0.15.

Returns:

errfloat

Indexing cost.

numint

Number of peaks index.

hkllist

Miller indices. Un-indexed are labeled [0,0,0].

lamdalist

Resolved wavelength. Unindexed are labeled inf.

metric_G_star_tensor()

Calculate the reciprocal metric tensor \(G^*\).

Returns:

Gstar2d-array

3x3 matrix of reciprocal lattice info for Cartesian transforms.

metric_G_tensor()

Calculate the metric tensor \(G\).

Returns:

G2d-array

3x3 matrix of lattice parameter info for Cartesian transforms.

minimize(kf_ki_dir, wavelength, n_proc=-1)

Fit the orientation and other parameters.

Parameters:

n_procint, optional

Number of processes to use. The default is -1.

Returns:

numint

Number of peaks index.

hkllist

Miller indices. Un-indexed are labeled [0,0,0].

lamdalist

Resolved wavelength. Un-indexed are labeled inf.

monoclinic(x)

objective(x)

Objective function.

Parameters:

xarray

Refineable parameters.

Returns:

neg_indint

Negative number of peaks indexed.

orientation_U(u0, u1, u2)

The sample orientation matrix \(U\).

Parameters:

u0, u1, u2float

Rotation paramters.

Returns:

U2d-array

3x3 sample orientation matrix.

orthorhombic(x)

reciprocal_lattice_B()

The reciprocal lattice \(B\)-matrix.

Returns:

B2d-array

3x3 matrix of reciprocal lattice in Cartesian coordinates.

refine(kf_ki_dir, wavelength, cell='Triclinic', error=0.15)

Refine the orientation and lattice parameters under constraints.

residual(x, kf_ki_dir, hkl, wavelength, fun)

Optimization residual function.

Parameters:

xlist

Parameters.

hkllist

Miller indices.

Qlist

Q-sample vectors.

funfunction

Lattice constraint function.

Returns:

residuallist

Least squares residuals.

rhombohedral(x)

set_lattice_constants(a, b, c, alpha, beta, gamma)

set_orientation_parameters(x)

softplus(z)

tetragonal(x)

triclinic(x)

garnet.utilities.calibration module

class Calibration(config)

Bases: object

Methods

calculate_goniometer_angles
calculate_goniometer_matrix
calculate_orientation_matrix
calculate_orientation_vector
calculate_tilt_matrices
calculate_tilt_matrix
calibrate_goniometer
calibrate_instrument
cell_symmetry_matrices
fix_offsets
generate_diagnostic
gravity_angle
initialize_peaks
load_instrument
load_peaks
optimize_goniometer
refine_goniometer
refine_offsets
reindex_peaks
residual
run

calculate_goniometer_angles(R)

calculate_goniometer_matrix(omega, chi, phi)

calculate_orientation_matrix(u0, u1, u2)

calculate_orientation_vector(U)

calculate_tilt_matrices(alpha, beta, gamma)

calculate_tilt_matrix(alpha, beta, gamma)

calibrate_goniometer(iteration)

calibrate_instrument(iteration)

cell_symmetry_matrices()

fix_offsets(x)

generate_diagnostic(iteration)

gravity_angle()

initialize_peaks()

load_instrument()

load_peaks()

optimize_goniometer()

refine_goniometer()

refine_offsets(x)

reindex_peaks()

residual(x, peak_dict, func, gamma)

run()

garnet.utilities.combine module

combine(filename)

find_partial_files(instance)

parse_args(argv=None)

garnet.utilities.confirm module

confirm_autoreduce(filename)

Confirm autoreduction status based on reduction logs.

Parameters:

filenamestr

Full data path containing facility, instrument, and IPTS fields.

Notes

Confirmation logic:

• Unknown → No .log files detected

• Yes → Logs exist and no failures detected

• Partially → Some runs failed

• No → All runs failed

garnet.utilities.crystal module

class CrystalStructure(filename)

Bases: object

Methods

add_material_info
get_chemical_formula_z_parameter
get_lattice_constants
get_scatterers
get_space_group
get_unit_cell_volume

add_material_info(filename)

get_chemical_formula_z_parameter()

get_lattice_constants()

get_scatterers()

get_space_group()

get_unit_cell_volume()

class SampleParameters(radii, u_vector=[0, 0, 1], v_vector=[1, 0, 0])

Bases: object

Methods

add_sample_info

add_sample_info(filename)

garnet.utilities.ipts module

garnet.utilities.macromolecular module

class Macromolecular(peaks='peaks')

Bases: object

Methods

write_mtz

write_mtz(filename, space_group='P 1')

garnet.utilities.peaks module

class Laue(ws)

Bases: object

Methods

find_UB(a, b, c, alpha, beta, gamma[, ...])	Fit the orientation and other parameters.
transform_lattice(peaks, transform[, tol])	Apply a cell transformation to the lattice.
uncertainty_line_segements()	The scattering vector scaled with the (unknown) wavelength.
wavelengths()	The Laue resolved wavelength.

calculate_transform
convert_conventional_to_primitive
refine_UB

calculate_transform(centering)

convert_conventional_to_primitive(a, b, c, alpha, beta, gamma, centering)

find_UB(a, b, c, alpha, beta, gamma, centering='P', n_proc=1)

Fit the orientation and other parameters.

Parameters:

a, b, cfloat

Lattice lengths.

alpha, beta, gammafloat

Lattice angles.

centeringstr

Lattice centering.

n_procint, optional

Number of processes to use. The default is -1.

refine_UB(cell, wavelength)

transform_lattice(peaks, transform, tol=0.2)

Apply a cell transformation to the lattice.

Parameters:

transform3x3 array-like

Transform to apply to hkl values.

tolfloat, optional

Indexing tolerance. The default is 0.1.

uncertainty_line_segements()

The scattering vector scaled with the (unknown) wavelength.

Returns:

kf_ki_dirlist

Difference between scattering and incident beam directions.

wavelengths()

The Laue resolved wavelength.

Returns:

Wavelengthlist

Peak wavelength.

class Peaks(config)

Bases: object

Methods

calculate_limits
finalize_and_save
load_convert_runs
load_instrument
run

calculate_limits()

finalize_and_save(tol=0.2)

load_convert_runs(ipts, run_nos, tol=0.2, n_proc=10)

load_instrument()

run()

garnet.utilities.peakview module

garnet.utilities.refinement module

class NuclearStructureRefinement(cell, space_group, sites, filename, parameters=None)

Bases: object

Methods

beam_weights(sample_points, G, ds, bx, by, sigma)	Calculate Gaussian beam weights for sample points.
calculate_structure_amplitudes(params)	Compute complex structure amplitudes Fs (per unique hkl) for given params.
extinction_correction(param, F2)	Calculate structure factor-dependent extinction correction.
objective_correction(params)	Objective for absorption/extinction refinement.
objective_structure(params)	Objective for structure + scale refinement.
plot_hkl_families([filename])	Create multi-page PDF with one page per hkl family.
plot_sample_shape()	Plot the refined ellipsoidal sample shape with beam directions.
plot_wobble_correction(off[, filename])	Plot wobble correction scale factors vs rotation angle.
refine([report, cutoff, n_iter, abs_corr, ...])	Iterative refinement protocol: 7 stages per iteration.
save_corrected_peaks()	Apply absorption corrections to all peaks and save to new file.
wobble_correction(off)	Scale model for off-centering/wobble correction.

absorption_correction
add_absorption_extinction_parameters
add_beam_parameters
add_detector_run_scale_parameters
calculate_ellipsoid_surface
calculate_scale_factor
calculate_statistics
calculate_structure_factors
chemical_formula_z_parameter
cost
detector_bank_scale_factors
ellipsoid_parameters
extinction_xp
extinction_xs
extinction_xx
extract_info
extract_parameters
generate_parameters
generate_symmetry_transforms
initialize_correction
initialize_crystal_structure
initialize_material
initialize_unit_cell_atoms
load_hkls
normalization_correction
plot_absorption_correction
plot_result
prepare_absorption_table
report
run_angle_scale_factors
save_detector_scales
spherical_absorption
spherical_absorption_correction
spherical_extinction
update_sample

absorption_correction(coeffs)

add_absorption_extinction_parameters(params)

add_beam_parameters(params)

add_detector_run_scale_parameters(params)

beam_weights(sample_points, G, ds, bx, by, sigma)

Calculate Gaussian beam weights for sample points.

Parameters:

sample_pointsndarray, shape (N, 3)

Monte Carlo sample points in sample frame

Gndarray, shape (P, 3, 3)

Goniometer matrices for each peak

dsndarray, shape (P, 3)

Sample center offset in sample frame for each peak

bx, byfloat

Beam center position in lab frame

sigmafloat

Gaussian beam width

Returns:

bwndarray, shape (N, P)

Beam weights for each sample point and peak

calculate_ellipsoid_surface(coeffs)

calculate_scale_factor(F2s)

calculate_statistics(cutoff)

calculate_structure_amplitudes(params)

Compute complex structure amplitudes Fs (per unique hkl) for given params.

This is identical to the inner part of calculate_structure_factors but returns the complex amplitudes (not squared magnitudes).

calculate_structure_factors(params)

chemical_formula_z_parameter()

cost(params, F2s, I_obs, sig)

detector_bank_scale_factors(params)

ellipsoid_parameters(coeffs)

extinction_correction(param, F2)

Calculate structure factor-dependent extinction correction.

Model	Nature	Parameter
Type I, Gaussian	Secondary	Mosaic [unitless]
Type I, Lorentzian	Secondary	Mosaic [unitless]
Type II	Primary	Block size² [um²]
SHELX	Phenomenological	Crystal size [cm]

[1] P. J. Becker and P. Coppens, Acta Cryst A 30, 2 (1974). [2] P. J. Becker and P. Coppens, Acta Cryst A 30, 2 (1974). [3] A. C. Larson, Crystallographic Computing (1970).

Parameters:

paramfloat

Exinction parameter.

F2array

Structure factors (fm^2).

Returns:

yarray

Extinction (unitless).

extinction_xp(r2, F2, lamda, V)

extinction_xs(g, F2, two_theta, lamda, Tbar, V)

extinction_xx(x, F2, two_theta, lamda, V)

extract_info()

extract_parameters(params, Uiso=0)

generate_parameters()

generate_symmetry_transforms()

initialize_correction(model='type II')

initialize_crystal_structure(sites)

initialize_material()

initialize_unit_cell_atoms(tol=1e-06, rcond=None, enforce_identity=True)

load_hkls(filename)

normalization_correction(params)

objective_correction(params)

Objective for absorption/extinction refinement.

Structure and scale are held fixed; F2s are precomputed for the current structural model.

objective_structure(params)

Objective for structure + scale refinement.

This stage varies positional, occupancy and displacement parameters together with the overall scale, while using the current absorption/extinction parameters as fixed values.

plot_absorption_correction(filename=None)

plot_hkl_families(filename=None)

Create multi-page PDF with one page per hkl family.

plot_result()

plot_sample_shape()

Plot the refined ellipsoidal sample shape with beam directions.

plot_wobble_correction(off, filename=None)

Plot wobble correction scale factors vs rotation angle.

Shows observed data points and model curves for different wavelengths.

prepare_absorption_table(N=100, seed=42, beta=3)

refine(report=True, cutoff=10, n_iter=3, abs_corr=False, off_corr=False, det_corr=False, run_corr=False, norm_corr=False, ext_model='shelx')

Iterative refinement protocol: 7 stages per iteration.

Per iteration:

1. Structure + scale (fixed corrections).

2. Absorption only.

3. Extinction only.

4. Wobble only.

5. Detector scales (optional).

6. Run/orientation scales (optional).

7. Normalization scales (optional).

report(result, det_corr, run_corr)

run_angle_scale_factors(params)

save_corrected_peaks()

Apply absorption corrections to all peaks and save to new file.

save_detector_scales(params)

spherical_absorption()

spherical_absorption_correction(muR, two_theta)

spherical_extinction()

update_sample(parameters)

wobble_correction(off)

Scale model for off-centering/wobble correction.

Based on WobbleCorrection model: accounts for beam displacement and sample misalignment effects on intensity measurements.

Parameters:

offarray-like

[b, c, rx, rz] where: - b: spread (wavelength-dependent scaling) - c: center displacement - rx: in-plane displacement - rz: beam displacement

Returns:

array

Scale factors for each reflection

garnet.utilities.reflections module

class AbsorptionCorrection(peaks, chemical_formula, z_parameter, u_vector=[0, 0, 1], v_vector=[1, 0, 0], params=None, filename=None)

Bases: object

Methods

apply_correction
calculate_correction
save_ellipsoid_stl
set_material
set_orientation
set_shape
verify_chemical_formula
write_absortion_parameters

apply_correction()

calculate_correction()

save_ellipsoid_stl(params, filename='/tmp/ellipsoid.stl')

set_material()

set_orientation()

set_shape()

verify_chemical_formula(formula)

write_absortion_parameters()

class Peaks(peaks, filename, scale=None, point_group=None)

Bases: object

Methods

calculate_statistics
get_cell
load_peaks
load_spectrum
median_absolute_devation
merge_intensities
peak_info
refine_UB
refine_ellipsoids
remove_non_indexed
remove_non_integrated
remove_off_centered
remove_volume_outliers
renormalize_intensities
renumber_peaks
rescale_intensities
reset_satellite
resort_hkl
save_peaks
update_monitor

calculate_statistics(name, filename)

get_cell()

load_peaks()

load_spectrum(filename, instrument)

median_absolute_devation(arr)

merge_intensities(name=None)

peak_info()

refine_UB(peaks)

refine_ellipsoids(peaks)

remove_non_indexed(tol=0.1)

remove_non_integrated()

remove_off_centered()

remove_volume_outliers(n_sigma=5.0)

renormalize_intensities(flux, solid_angle)

renumber_peaks(peaks, k=60, decimals=6, linkage='average')

rescale_intensities()

reset_satellite(peaks=None)

resort_hkl(peaks, filename)

save_peaks(name=None, fit_dict=None)

update_monitor()

main()

garnet.utilities.sliceview module

garnet.utilities.structure module

class StructureAnalysis(config, filename)

Bases: object

Methods

apply_correction
load_peaks
refimenent
save_mtz
save_peaks

apply_correction()

load_peaks()

refimenent(n_iter=10)

save_mtz()

save_peaks()

garnet.utilities.vanadium module

class Vanadium(config)

Bases: object

Methods

apply_absorption_correction
apply_calibration
apply_masks
finalize_and_save
load_instrument
load_runs
process_data
run
set_sample_geometry
subtract_background

apply_absorption_correction()

apply_calibration()

apply_masks()

finalize_and_save()

load_instrument()

load_runs(workspace, ipts, run_nos, time_stop=None)

process_data()

run()

set_sample_geometry(x=0)

subtract_background()

Module contents