laue_dials.command_line namespace

Submodules

laue_dials.command_line.compute_rmsds module

This script computes and plots RMSDs for a pair of DIALS experiment/reflection files.

laue_dials.command_line.compute_rmsds.run(args=None, *, phil=<libtbx.phil.scope object>)

Compute and plot RMSDs for a pair of DIALS experiment/reflection files.

Parameters:

• args (list) – Command-line arguments.

• phil – The phil scope for the program.

Returns:

None

laue_dials.command_line.find_spots module

This script performs spotfinding on an imported experiment.

laue_dials.command_line.find_spots.run(args=None, *, phil=<libtbx.phil.scope object>)

Run the spotfinding script with the specified command-line arguments.

Parameters:

• args (list) – Command-line arguments.

• phil – The phil scope for the program.

Returns:

None

laue_dials.command_line.index module

This script performs monochromatic indexing and optional scan-varying refinement.

laue_dials.command_line.index.run(args=None, *, phil=<libtbx.phil.scope object>)

Run the indexing script with the specified command-line arguments.

Parameters:

• args (list) – Command-line arguments.

• phil – The phil scope for the program.

Returns:

None

laue_dials.command_line.integrate module

This script generates integrated MTZ files from refined data with predictions

laue_dials.command_line.integrate.get_refls_image(refls, img_id)

Get the set of reflections lying on a particular image.

Parameters:

• refls (dials.array_family.flex.reflection_table) – Reflection table.

• img_id (int) – Image ID.

Returns:

Reflection table for the specified image.

Return type:

refls (dials.array_family.flex.reflection_table)

laue_dials.command_line.integrate.integrate_image(img_set, refls, isigi_cutoff)

Integrate predicted spots on an image.

Parameters:

• img_set (dxtbx_imageset_ext.Imageset) – Image set.

• refls (dials.array_family.flex.reflection_table) – Reflection table.

• isigi_cutoff (float) – I/SIGI threshold.

Returns:

Updated reflection table.

Return type:

flex.reflection_table

laue_dials.command_line.integrate.run(args=None, *, phil=<libtbx.phil.scope object>)

Run the integration script with the specified command-line arguments.

Parameters:

• args (list) – Command-line arguments.

• phil – The phil scope for the program.

Returns:

None

laue_dials.command_line.optimize_indexing module

This script optimizes Miller indices and wavelengths jointly.

laue_dials.command_line.optimize_indexing.index_image(lam_min, lam_max, d_min, refls, expts, cell=None, n_macrocycles=5, filter_spectrum=True, keep_unindexed=False)

Reindex the given image reflections and update the experiment geometry.

Parameters:

• lam_min (float) – Minimum wavelength of beam spectrum.

• lam_max (float) – Maximum wavelength of beam spectrum.

• d_min (float) – Minimum d-spacing to find reflections for.

• refls (dials.array_family.flex.reflection_table) – Reflection table for a single image.

• expts (dxtbx.model.ExperimentList) – List of experiment objects.

• cell (gemmi.UnitCell) – User-provided unit cell. Default: None.

• n_macrocycles (int) – Number of macrocycles of assignment to run. Default: 5.

• filter_spectrum (bool) – Whether to filter out reflections that optimize out of the wavelength range. Default: True.

• keep_unindexed (bool) – Whether to keep reflections which fail to index. Default: False.

Returns:

The optimized experiment list with updated crystal rotations. refls (dials.array_family.flex.reflection_table): The optimized reflection table with updated wavelengths.

Return type:

expts (dxtbx.model.experiment_list.ExperimentList)

laue_dials.command_line.optimize_indexing.run(args=None, *, phil=<libtbx.phil.scope object>)

Run the script to optimize Miller indices and wavelengths jointly.

Parameters:

• args (list) – Command-line arguments.

• phil – The phil scope for the program.

Returns:

None

laue_dials.command_line.plot_wavelengths module

This script histograms the wavelengths present in a reflection table.

laue_dials.command_line.plot_wavelengths.run(args=None, *, phil=<libtbx.phil.scope object>)

Run the script to histogram the wavelengths present in a reflection table.

Parameters:

• args (list) – Command-line arguments.

• phil – The phil scope for the program.

Returns:

None

laue_dials.command_line.predict module

This script predicts reflections for integration

laue_dials.command_line.predict.predict_spots(lam_min, lam_max, d_min, refls, expts)

Predict spots given a geometry.

Parameters:

• lam_min (float) – Minimum wavelength for the beam spectrum.

• lam_max (float) – Maximum wavelength for the beam spectrum.

• d_min (float) – Minimum d-spacing for reflecting planes.

• refls (dials.array_family.flex.reflection_table) – The reflection table.

• expts (dxtbx.model.experiment_list.ExperimentList) – The experiment list.

Returns:

Predicted reflection table.

Return type:

final_preds (dials.array_family.flex.reflection_table)

laue_dials.command_line.predict.run(args=None, *, phil=<libtbx.phil.scope object>)

Run the prediction script.

Parameters:

• args (list) – Command-line arguments.

• phil – Working phil scope.

laue_dials.command_line.refine module

This script handles polychromatic geometry refinement.

laue_dials.command_line.refine.correct_identifiers(expts, refls)

Correct identifiers in case of skipped images.

Parameters:

• expts (dxtbx.model.ExperimentList) – Experiment list.

• refls (flex.reflection_table) – Reflection table.

Returns:

The corrected experiment list with corrected identifiers. corrected_refls (dials.array_family.flex.reflection_table): The corrected reflection table with updated identifiers.

Return type:

corrected_expts (dxtbx.model.experiment_list.ExperimentList)

laue_dials.command_line.refine.refine_image(params, expts, refls)

Refine image given parameters, experiments, and reflections.

Parameters:

• params (libtbx.phil.scope_extract) – Refinement parameters.

• expts (dxtbx.model.ExperimentList) – Experiment list.

• refls (flex.reflection_table) – Reflection table.

Returns:

The refined experiment list with updated geometry. refined_refls (dials.array_family.flex.reflection_table): The refined reflection table with updated wavelength and centroid data.

Return type:

refined_expts (dxtbx.model.experiment_list.ExperimentList)

laue_dials.command_line.refine.run(args=None, *, phil=<libtbx.phil.scope object>)

Run the refinement script.

Parameters:

• args (list) – Command-line arguments.

• phil – Working phil scope.

laue_dials.command_line.sequence_to_stills module

Split a sequence into a set of stills.

Example

laue.sequence_to_stills monochromatic.expt monochromatic.refl

laue_dials.command_line.sequence_to_stills.run(args=None, phil=<libtbx.phil.scope object>)

Validate the arguments and load experiments/reflections for sequence_to_stills.

Parameters:

• args (list) – Command-line arguments.

• phil – Working phil scope.

Returns:

None

laue_dials.command_line.sequence_to_stills.sequence_to_stills(experiments, reflections, params)

Split a sequence into a set of stills.

This function takes a sequence of experiments and corresponding reflections and splits it into a set of stills. Each still is associated with a specific scan point within the original sequence. The resulting experiments and reflection tables for the stills are returned.

Parameters:

• experiments (List[dxtbx.model.experiment_list]) – The list of experiments representing the sequence.

• reflections (List[dials.array_family.flex.reflection_table]) – The list of reflection tables corresponding to the experiments.

• params (libtbx.phil.scope_extract) – Program parameters.

Returns:

A tuple containing the following: - A list of Experiment objects representing the split stills. - A list of reflection_table objects containing the split reflections for each still.

Return type:

Tuple[List[dxtbx.model.experiment_list.Experiment], List[dials.array_family.flex.reflection_table]]