Repository Documentation

Shiver

Main Qt application for shiver

class shiver.shiver.Shiver

Main Shiver window

shiver.shiver.gui()

Main entry point for Qt application

Models

Model for the Sample Parameters dialog

class shiver.models.sample.SampleModel(name=None)

Sample model

connect_error_message(callback)

Set the callback function for error messages

get_lattice_from_ub_matrix(ub_matrix)

check and return lattice parameters using ub matrix

get_lattice_ub()

return oriented lattice object from mtd - if no name provided initialize lattice

get_ub_matrix_from_lattice(params)

check and return ub matrix using lattice parameters

is_nexus_processed(filename)

Return true if the file is NexusProcessed - can be loaded through LoadNexusProcessed, else false

load_isaw_ub(filename)

Mantid LoadIsawUB with Isaw file

load_nexus_processed(filename)

Mantid SetUB with Nexus file

load_nexus_ub(filename)

Mantid SetUB with Nexus file

save_isaw(filename)

Save in Isaw file

set_ub(params)

Mantid SetUB with current workspace

validate_lattice(params)

validate the lattice values

validate_matrix(ub_matrix)

validate the ub matrix values

shiver.models.sample.update_sample_mde_config(name, oriented_lattice)

Update the MDE Config Sample Parameters, if the MDE Config exists

single help module

shiver.models.help.help_function(context)

open a browser with the appropriate help page

Model for the Generate tab

class shiver.models.generate.GenerateMDEObserver(*args: Any, **kwargs: Any)

Observer to handle the execution of GenerateDGSMDE

errorHandle(msg)

Call parent upon error of algorithm

finishHandle()

Call parent upon completion of algorithm

class shiver.models.generate.GenerateModel

Generate model

connect_error_message(callback)

Connect error message

connect_generate_mde_finish_callback(callback)

Connect generate mde finish

finish_generate_mde(obs, error=False, msg='')

Callback from algorithm observer for GenerateDGSMDE

Parameters

obsAlgorithmObserver

Observer of the algorithm

errorbool, optional

Error flag, by default False

msgstr, optional

Error message, by default “”

finish_save_md(obs, error=False, msg='')

Callback from saveMD observer.

Parameters

obsAlgorithmObserver

observer for SaveMD

error: bool

Error flag

msg: str, optional

Error message

generate_mde(config_dict: dict)

Call GenerateDGSMDE algorithm

Parameters

config_dictdict

Configuration dictionary

save_mde_to_disk()

Save the generated MDE workspace to disk.

class shiver.models.generate.SaveMDObserver(*args: Any, **kwargs: Any)

Observer to handle the execution of SaveMD

errorHandle(msg)

Call parent upon error of algorithm

finishHandle()

Call parent upon completion of algorithm

shiver.models.generate.gather_mde_config_dict(workspace_name: str) → dict

Generate a config dictionary for given MDE workspace.

Parameters

workspace_namestr

Name of the MDE workspace

Returns

dict

Dictionary containing the config information

shiver.models.generate.save_mde_config_dict(workspace_name, config_dict)

Save the config dictionary in the given MDE workspace.

The Shiver ConvertDGSToSingleMDE mantid algorithm

class shiver.models.convert_dgs_to_single_mde.ConvertDGSToSingleMDE(*args: Any, **kwargs: Any)

ConvertDGSToSingleMDE algorithm

shiver.models.convert_dgs_to_single_mde.get_Ei_T0(data, data_m, Ei_supplied, T0_supplied, filenames, progress=None)

Determines the Ei and T0 values from the data supplied

The Shiver MakeSlice mantid algorithm

class shiver.models.makeslice.MakeSlice(*args: Any, **kwargs: Any)

MakeSlice algorithm

The Shiver MakeSFCorrectedSlices mantid algorithm

class shiver.models.makeslices.MakeSFCorrectedSlices(*args: Any, **kwargs: Any)

MakeSFCorrectedSlices algorithm

The Shiver GenerateDGSMDE mantid algorithm

class shiver.models.generate_dgs_mde.GenerateDGSMDE(*args: Any, **kwargs: Any)

GenerateDGSMDE algorithm

Model for Corrections tab

class shiver.models.corrections.ApplyDetailedBalanceMDObserver(*args: Any, **kwargs: Any)

Observer for ApplyDetailedBalanceMD algorithm

errorHandle(msg)

Call upon algorithm error

finishHandle()

Call upon algorithm finishing

class shiver.models.corrections.CorrectionsModel

Corrections table model

apply(ws_name: str, detailed_balance: bool, hyspec_polarizer_transmission: bool, temperature: str = '') → None

Apply corrections.

Parameters

ws_namestr

Workspace name

detailed_balancebool

Apply detailed balance

hyspec_polarizer_transmissionbool

Apply HYSPEC polarizer transmission correction

temperaturestr, optional

Temperature value as string or log entry contains temperature, by default “”

Return

None

Note

The applied correction is noted as the suffix of the workspace name

• detailed balance: “_DB”

• HYSPEC polarizer transmission: “_PT”

apply_detailed_balance(ws_name: str, temperature: str, output_ws_name: str) → None

Apply detailed balance to the workspace.

Parameters

ws_namestr

Workspace name

temperaturestr

Temperature value as string or log entry contains temperature

output_ws_namestr

Output workspace name

Returns

None

apply_detailed_balance_finished(ws_name: str, alg: ApplyDetailedBalanceMDObserver, error: bool = False, msg='') → None

Call when ApplyDetailedBalanceMD finishes.

Parameters

ws_namestr

Workspace name

algApplyDetailedBalanceMDObserver

Observer

errorbool, optional

Error flag, by default False

msgstr, optional

Error message, by default “”

Returns

None

apply_scattered_transmission_correction(ws_name: str, output_ws_name: str) → None

Apply DGSScatterTransmissionCorrection to the workspace.

ref: IOP Conf. Series: Journal of Physics: Conf. Series 862 (2017) 012023

Figure 3 Right

Parameters

ws_namestr

Workspace name

output_ws_namestr

Output workspace name

Returns

None

apply_scattered_transmission_correction_finished(ws_name: str, alg: DgsScatteredTransmissionCorrectionMDObserver, error: bool = False, msg='') → None

Call when DgsScatteredTransmissionCorrectionMD finishes.

Parameters

ws_namestr

Workspace name

algDgsScatteredTransmissionCorrectionMDObserver

Observer

errorbool, optional

Error flag, by default False

msgstr, optional

Error message, by default “”

Returns

None

connect_error_message(callback)

Set the callback function for error messages.

Parameters

callbackfunction

Callback function

Returns

None

get_ws_alg_histories(ws_name: str) → list

Get algorithm histories of the workspace.

Parameters

ws_namestr

Workspace name

Returns

list

List of algorithm histories

has_apply_detailed_balance(ws_name: str) → Tuple[bool, str]

Check if the workspace has ApplyDetailedBalanceMD applied.

Parameters

ws_namestr

Workspace name

Returns

Tuple[bool, str]

True if the workspace has ApplyDetailedBalanceMD applied Temperature if the workspace has ApplyDetailedBalanceMD applied

has_scattered_transmission_correction(ws_name: str) → bool

Check if the workspace has DgsScatteredTransmissionCorrectionMD applied.

Parameters

ws_namestr

Workspace name

Returns

bool

True if the workspace has DgsScatteredTransmissionCorrectionMD applied.

class shiver.models.corrections.DgsScatteredTransmissionCorrectionMDObserver(*args: Any, **kwargs: Any)

Observer for DgsScatteredTransmissionCorrectionMD algorithm

errorHandle(msg)

Call upon algorithm error

finishHandle()

Call upon algorithm finishing

Common utility functions

shiver.models.utils.flatten_list(xlst)

Flattens a list of lists list(flatten_list([[[‘test’]],1,2,[3,4,[5,6]]])) will yield [‘test’, 1, 2, 3, 4, 5, 6]

Model for the Histogram tab

class shiver.models.histogram.ADSObserver(*args: Any, **kwargs: Any)

Object to handle interactions with the ADS

addHandle(ws, _)

Callback handle for ADS add

clearHandle()

Callback handle for ADS clear

deleteHandle(ws, _)

Callback handle for ADS delete

register_call_back(callback)

Set the callback function for workspace changes

renameHandle(old, new)

Callback handle for ADS rename

replaceHandle(ws, _)

Callback handle for ADS replace

class shiver.models.histogram.FileLoadingObserver(*args: Any, **kwargs: Any)

Object to handle the execution events of the loading algorithms

errorHandle(msg)

Call parent upon algorithm error

finishHandle()

Call parent upon algorithm finishing

class shiver.models.histogram.HistogramModel

Histogram model

clone(ws_name, ws_clone_name)

Clone the workspace

connect_error_message(callback)

Set the callback function for error messages

connect_makeslice_finish(callback)

Set the callback function for makeslice finish

connect_warning_message(callback)

Set the callback function for error messages

delete(ws_name)

Delete the workspace

do_make_slice(config: dict)

Method to take filename and workspace type and load with correct algorithm

finish_loading(obs, filename, ws_type, ws_name, error=False, msg='')

This is the callback from the algorithm observer

finish_make_slice(obs, ws_names, error=False, msg='')

This is the callback from the algorithm observer

generate_mde(config_dict: dict) → str

Generate MDE workspace from given parameters dictionary.

get_all_valid_workspaces()

Get all existing workspaces

get_ei(ws_name)

Return the Ei for the given workspace

get_make_slice_history(name) → dict

Get the history of the last applied MakeSlice/s algorithm.

Parameters

namestr

The name of the histogram workspace for history retrieval

Returns

dict

A dictionary of the history of the make slice algorithm

get_plot_display_name(ws_name, ndims)

Method retrieve all dimension names, minimum and maximum for displaying in the plot

load(filename, ws_type)

Method to take filename and workspace type and load with correct algorithm

load_dataset(dataset: dict) → Tuple[str, str, str]

Perform dataset loading with given parameters dictionary.

Parameters

datasetdict

Dictionary of parameters for loading the dataset.

Returns

Tuple[str, str, str]

Tuple of workspace names for data, background and normalization.

rename(old_name, new_name)

Rename the workspace from old_name to new_name

save(ws_name, filename)

Save the workspace to Nexus file.

save_history(ws_name, filename)

Save the mantid algorithm history

save_to_ascii(ws_name: str, filename: str, ignore_integrated: bool = False, num_ev_norm: bool = False, format_str: str = '%.6e')

Save an MDHistoToWorkspace to an ascii file (column format).

Parameters

ws_namestr

Name of the workspace to save.

filenamestr

Name of the file to save to.

IgnoreIntegratedbool, optional

If True, the integrated dimensions are ignored (smaller files), but that information is lost (default is False).

NumEvNormbool, optional

Must be set to true if data was converted to MD from a histogram workspace (like NXSPE) and no MDNorm algorithms were used.

format_strstr, optional

Format string for the output (default is “%.6e”).

NOTE

This function is adapted from DGS_SC_scripts/slice_util.py::SaveMDToAscii.

scale(ws_name_in, ws_name_out, scale_factor)

Scale the workspace

symmetry_operations(symmetry)

Validate the symmetry value with mantid

validate_workspace_logs(config: dict)

Method to validate sample logs and flipping ratios of SF and NSF workspaces

ws_change_call_back(callback)

Set the callback function for workspace changes

class shiver.models.histogram.MakeSliceObserver(*args: Any, **kwargs: Any)

Object to handle the execution of MakeSlice algorithms

errorHandle(msg)

Call parent upon algorithm error

finishHandle()

Call parent upon algorithm finishing

shiver.models.histogram.dim2array(dim, center=True) → ndarray

Create a numpy array containing bin centers along the dimension d.

Parameters

dim: IMDDimension center: bool, optional

Returns

from min+st/2 to max-st/2 with step st

shiver.models.histogram.filter_ws(name)

Return the type of workspace

shiver.models.histogram.get_frame(name)

Returns the MDE frame for the given workspace name

shiver.models.histogram.get_num_non_integrated_dims(name)

Returns the number of non-integrated dimensions

Model for the Sample Parameters dialog

class shiver.models.polarized.PolarizedModel(workspace_name=None)

Polarized model

connect_error_message(callback)

Set the callback function for error messages

get_experiment_sample_log(log_name)

Get the sample log with name

get_flipping_ratio()

Method to return the flipping ratio for a workspace

get_polarization_logs()

Get polarization logs from workspace

get_polarization_logs_for_workspace()

Get polarization logs from workspace

get_polarization_state()

Get the polarization state from Sample Log in workspace

save_experiment_sample_log(log_name, log_value)

Add the sample log with log_name and log_value in the workspace with name

save_polarization_logs(polarization_logs)

Save polarization logs in workspace

save_polarization_state(pol_state)

Save the polarization state as Sample Log in workspace

update_polarized_mde_config()

Update the MDE Config Polarized Parameters, if the MDE Config exists

Model for the Refine UB widget

class shiver.models.refine_ub.PeaksTableWorkspaceDisplayModel(*args: Any, **kwargs: Any)

Model for the peaks table

connect_error_message(callback)

Set the callback function for error messages

get_lattice_parameters()

collect and return the lattice parameters from the peaks workspace

get_peaks_from_rows(rows)

Extract a subset of peaks using the row numbers

recenter_rows(rows)

Recenter the selected peaks

refine(rows, lattice_type)

Refine the UB using the selected rows

refine_orientation(rows)

Refine the UB orientation only using the selected rows

set_parent_mde(mde)

set the MDE used for recentering

Drop the DeltaE dimension

set_peak_number_to_rows()

set the peaks numbers to match the rows so that the peaks subset can be match back

set_peaks(peaks)

Replace the peaks workspace in the models

undo()

Set the origonal UB onto the peaks workspace

update_ub(new_ub)

Update the UB of the peaks workspace from the refine workspace

class shiver.models.refine_ub.RefineUBModel(mdh, mde)

Model for the refinement UB tab

connect_error_message(callback)

Set the callback function for error messages

get_mdh()

Return the MDHistoWorkspace

get_peaks_table_model()

get the model for the peaks table

get_perpendicular_slices(peak_row)

Create 3 perpendicular slices center on the peaks corresponding to the given row

predict_peaks()

Run predict peaks, the set new peaks to the peaks table model

update_mde_with_new_ub()

Update the UB in the MDE from the one in the peaks workspace

update_workspaces(mdh, mde)

Set the MD workspace, after the UB has been refined

Presenters

Presenter for the Sample Parameters dialog

class shiver.presenters.sample.SamplePresenter(view, model)

Sample Parameter presenter

error_message(msg)

Pass error message to the view

handle_apply_button(params_dict)

Call SetUB mantid algorithm

handle_isaw_button(filename)

Call LoadIsawUB

handle_lattice_from_ub_matrix(ub_matrix)

Get SetUB matrix

handle_lattice_state(params)

Validate lattices

handle_load_button(filename)

Call LoadNexusProcessed

handle_matrix_state(ub_matrix)

Validate UB matrix

handle_nexus_button(filename)

Call LoadNexusUB

handle_sample_data_init()

Get SetUB matrix

handle_save_isaw_button(filename)

Save file

handle_ub_matrix_from_lattice(params)

Get SetUB matrix

property model

Return the model for this presenter

property view

Return the view for this presenter

shiver.presenters.sample.copy_params_to_dict(oriented_lattice, params)

Copy all oriented lattice and ub matrix to params dictionary

shiver.presenters.sample.get_sample_parameters_from_workspace(oriented_lattice)

Get UB matrix and lattice parameters ina dictionary format

Presenter for the Generate tab

class shiver.presenters.generate.GeneratePresenter(view, model)

Generate Presenter

do_generate_mde()

Slot for Generate button.

Notes

This function will collection configuration information from the view and pass it to the model.

do_save_configuration()

Slot for Save Configuration button.

Notes

This function will collect configuration information from the view and save it to a python file similar to define_dataset.py.

get_config_dict_from_view() → dict

Get configuration dictionary from generate view.

property model

Return the model for this presenter

property view

Return the view for this presenter

shiver.presenters.generate.translate_filelist_to_string(filelist: list) → str

Translate filelist to string.

Parameters

filelistlist

List of files

Returns

str

Comma-separated string of files.

Notes

Mantid’s MultipleFileProperty is expecting a string representation of nested lists, e.g.

For a single layer list, the conversion is simple:

>>> filelist = ['/tmp/file1', '/tmp/file2']
to
>>> filelist = "/tmp/file1, /tmp/file2"

For a nested list, the conversion is slightly more complicated: >>> filelist = [[‘/tmp/file1’, ‘/tmp/file2’], [‘/tmp/file3’]] to >>> filelist = “/tmp/file1+/tmp/file2, /tmp/file3”

Presenter for the Histogram tab

class shiver.presenters.histogram.HistogramPresenter(view, model)

Histogram presenter

build_config_for_make_slice() → dict

Gather parameters from view for MakeSlice.

Returns

configdict

Dictionary of parameters for MakeSlice.

clone_workspace(name, clone_name)

Called by the view to clone a workspace

create_corrections_tab(name)

Create a corrections tab

create_refine_ub_tab()

UB refinement tab

delete_workspace(name)

Called by the view to delete a workspace

do_provenance(workspace_name: str)

Called by the view to show provenance

error_message(msg, **kwargs)

Pass error message to the view

get_polarization_state(name)

get polarization state from polarized model

handle_button(params_dict)

Validate symmetry histogram parameter

load_dataset(dataset: dict)

Call model to perform dataset loading with the given parameters.

load_file(file_type, filename)

Call model to load the filename from the UI file dialog

makeslice_finish(workspace_dimesions, error=False)

Handle the makeslice algorithm finishing

property model

Return the model for this presenter

populate_ui_from_selected_histogram(name)

Populate the UI from the selected histogram

ready_for_histogram()

Check if the view is ready to submit a histogram

refine_ub(ws_name)

Set the histogram parameters needed for UB refinement

remake_slice()

Remake the HKL volume after UB was updated

remove_provenance_tab(workspace_name)

remove provenance tab for a workspace, if it exists

rename_workspace(old_name, new_name)

Called by the view to rename a workspace

save_mde_workspace(name, filepath)

Called by the view to save a workspace

save_polarization_state(name, pol_state)

save polarization state with polarized model

save_workspace(name, filename)

Called by the view to save a workspace

save_workspace_history(name, filename)

Called by the view to rename a workspace

save_workspace_to_ascii(name, filename)

Called by the view to save a workspace to ascii.

scale_workspace(name, output_name, scale_factor)

Called by the view to scale a workspace

submit_histogram_to_make_slice()

Submit the histogram to the model

property view

Return the view for this presenter

warning_message(msg, **kwargs)

Pass warning message to the view

ws_changed(action, name, ws_type, frame=None, ndims=0)

Pass the workspace change to the view

Presenter for the Polarized Options dialog

class shiver.presenters.polarized.PolarizedPresenter(view, model)

Polarized Options presenter

error_message(msg)

Pass error message to the view

get_polarization_logs()

Retrieve the values for the sample logs

handle_apply_button(polarization_logs)

Save the values for the sample logs

property model

Return the model for this presenter

property view

Return the view for this presenter

shiver.presenters.polarized.create_dictionary_polarized_options(sample_log_data)

Create a dictionary from the values for the sample logs

Presenter for the Refine UB widget

class shiver.presenters.refine_ub.PeaksTableWorkspaceDataPresenterStandard(*args: Any, **kwargs: Any)

Peaks table presenter

load_data(table)

load the peaks workspace in the QTable model

update_column_headers()

set the table column headers

class shiver.presenters.refine_ub.PeaksTableWorkspaceDisplay(*args: Any, **kwargs: Any)

Peaks table widget

emit_close()

Handle closing

class shiver.presenters.refine_ub.RefineUB(mdh, mde, model=None, view=None, parent=None)

Refine UB table presenter

peak_selected(peak_row)

called when a peak is selected to create the 3 perpendicular slices

populate(checked)

toggle the peaks overlay in the sliceviewer

predict()

called to predict peaks

recenter()

Recenter the selected rows

refine()

called to refine the UB

refine_orientation()

called to refine the UB orientation only

remake_slice()

called after the UB was changed to remake the HKL slice

undo()

This will return to UB to the origonal state

update_lattice()

called to update the lattice parameters from the model

update_workspaces(mdh, mde)

update the workspaces used

Views

PyQt QGroupBox for the histogram parameters

class shiver.views.histogram_parameters.Dimensions(*args: Any, **kwargs: Any)

Widget for handling the selection of output dimensions

combo_changed(index)

Swap the combo box values when combo boxes are changed

property combo_dimension_boxes

Return a list of combo boxes

property combo_max_boxes

Return a list of combo boxes

property combo_min_boxes

Return a list of combo boxes

combo_step()

Step border color and histogram button update

property combo_step_boxes

Return a list of combo boxes

compare_numbers(minnum, maxnum)

Check Minimum and Maximum value pairs are: float numbers, Minimum < Maximum

min_max_checked(cmin, cmax)

Ensure Minimum and Maximum value pairs are: float numbers, Minimum < Maximum and both exist at the same time

min_max_compare(cmin, cmax)

Ensure Minimum and Maximum value pairs are: float numbers, Minimum < Maximum if both exist at the same time

set_field_invalid_state(item)

if parent exists then call the corresponding function and update the color

set_field_valid_state(item)

remove the item from the field_error list and its invalid style, if it was previously invalid and enable the corresponding button

steps_valid_state()

Check whether required steps are filled in

update_combo()

Update combo box dimension values

update_dimension_names(basis)

Update the combo box dimension selection items based on the projection values

validate_min_max_checked(cmin, cmax, sender_flag)

Validate Minimum and Maximum value pairs are: float numbers, Minimum < Maximum and both exist at the same time and update their state if sender_flag ==1 sender =cmin else sender =cmax

validate_step(step)

Step border color and histogram button update

class shiver.views.histogram_parameters.HistogramParameter(*args: Any, **kwargs: Any)

Histogram parameters widget

property combo_dimx

Returns the combo boxes for the dimensions

property combo_maxx

Returns the max spin boxes for the dimensions

property combo_minx

Returns the min spin boxes for the dimensions

property combo_stepx

Returns the step spin boxes for the dimensions

connect_histogram_submit(callback)

callback for the histogram submit button

gather_histogram_parameters() → dict

Gathers the histogram parameters

Returns

dict – histogram parameters

initialize_default()

initialize default values

property is_valid: bool

Checks if the histogram parameters are valid

Returns

bool – True if valid, False otherwise

populate_histogram_parameters(parameters: dict)

Populates the histogram parameters from given dictionary.

projection_to_hkl(projection: str) → str

Converts the projection to H,K,L

Arguments:

projection {str} – projection

Returns:

str – H,K,L

projection_updated()

Validate the projection values

set_dimension(btn)

Update parameter table based on mode.

Based on the radio button step, allow the corresponding step values to be filled in; the rest become read-only

Parameters

btnQRadioButton

radio button for the step

set_field_invalid_state(item)

if parent exists then call the corresponding function and update the color

set_field_valid_state(item)

remove the item from the field_error list and its invalid style, if it was previously invalid and enable the corresponding button

update_plot_num()

Updates the plot number if name_checkbox is unchecked

validate_projection_values()

Validate the projection values on co-linear

validate_symmentry_once()

validate symmetry once the current invalid text is updated. Note: the actual validation happens in models

class shiver.views.histogram_parameters.V3DValidator(*args: Any, **kwargs: Any)

Validates the projection values

validate(teststring, pos)

Validates the projections 3-digit array format: [1,0,0]

shiver.views.histogram_parameters.return_valid(validity, teststring, pos)

Returns state during validation

shiver.views.histogram_parameters.translation(number, character)

Used in projection

PyQt QDialog for Sample Parameters

class shiver.views.sample.LatticeParametersWidget(*args: Any, **kwargs: Any)

Lattice Parameters widget

changed

alias of dict

check_and_update_matrix()

Validate parameters and updates the UB matrix

get_lattice_parameters()

Return all values of lattice parameters in a dictionary

lattice_state()

Check all lattice parameters; returns true if they are all in acceptable state

set_field_invalid_state(item)

if parent exists then call the corresponding function and update the color

set_field_valid_state(item)

remove the item from the field_error list and its invalid style, if it was previously invalid and enable the corresponding button

set_lattice_parameters(params)

Set values in lattice parameters

trigger_update_matrix(ub_matrix)

Emit the signal for changed

update_all_background_color(valid)

Update the background color of all lattice parameters fields

class shiver.views.sample.SampleDialog(*args: Any, **kwargs: Any)

Histogram parameters widget

btn_apply_submit()

Check everything is valid and then call the ub mandit algorithm

btn_cancel_action()

Cancel the sample dialog

btn_help_action()

Show the help for the sample dialog

btn_isaw_submit()

Open the file dialog and update the fields using the Mat file

btn_load_submit()

Open the file dialog and update the fields using the Nexus file

btn_nexus_submit()

Open the file dialog and update the fields using the Nexus file

btn_save_isaw_submit()

Open the file dialog to select file location and name

changed

alias of dict

check_items_and_update_lattice()

Check whether ub matrix cell items are in valid state and update lattice values

get_matrix_values_as_2d_list()

Retrieve the UB matrix cell values into a 2d list

get_matrix_values_as_string()

‘Serialize’ the ub matrix cell values into a comma-separated string

get_sample_parameters()

Return all parameters in a dictionary returned format {‘a’:5.12484,’b’:5.33161,’c’:7.31103, ‘alpha’:90,’beta’:90,’gamma’:90, ‘u’:’-0.0493617,4.27279,-4.37293’, ‘v’:’-0.0706905,-3.18894,-5.85775’, ‘matrix_ub’:’-0.00000,-0.00000,7.00000,-0.00000,-0.00000,7.00000,-0.00000,-0.00000,7.00000’}

initialize_matrix()

initialize ub matrix cells

matrix_update_all_background_color(valid)

Update the background color of all ub matrix cells

populate_sample_parameters()

Set the default values for lattice and UB matrix

populate_sample_parameters_from_dict(param_dict)

Set the values for lattice from the dictionary and use them to calculate UB matrix expected format: {‘a’:5.12484,’b’:5.33161,’c’:7.31103, ‘alpha’:90,’beta’:90,’gamma’:90, ‘u’:’-0.0493617,4.27279,-4.37293’, ‘v’:’-0.0706905,-3.18894,-5.85775’}

set_field_invalid_state(item)

include the item in the field_error list and disable the corresponding button

set_field_valid_state(item)

remove the item from the field_error list and enable the corresponding button

show_error_message(msg)

Will show a error dialog with the given message

trigger_update_lattice(lattice)

Emit the signal for changed

ub_matrix_state()

Check whether the ub matrix cells are all in a valid state

update_all_background_color(valid)

Update the background color of all fields

update_matrix(dict_ub_matrix)

Update the value of each ub matrix cell from the dictionary

validate_cell_value()

Check whether the ub matrix cell is in a valid state

class shiver.views.sample.SampleView(*args: Any, **kwargs: Any)

View for Sample Parameters

connect_apply_submit(callback)

callback for the apply submit button

connect_btn_save_isaw_callback(callback)

callback for the isaw save button

connect_isaw_submit(callback)

callback for the isaw submit button

connect_lattice_from_ub_matrix(callback)

callback for the matrix data

connect_lattice_state(callback)

callback for the matrix data

connect_load_submit(callback)

callback for the loaf submit button

connect_matrix_state(callback)

callback for the matrix data

connect_nexus_submit(callback)

callback for the nexus submit button

connect_sample_data(callback)

callback for the matrix data

connect_ub_matrix_from_lattice(callback)

callback for the matrix data

get_error_message(msg)

received the error message from model

get_sample_parameters_dict()

Get all sample parameters as a dictionary

set_sample_parameters_dict()

Set all sample parameters as a dictionary

start_dialog()

initialize and start dialog

CSS styles invalid fields

PyQt widget for the OnCat widget in General tab.

class shiver.views.oncat.OnCatAgent(use_notes=False)

Agent to interface with OnCat

get_agent_instance()

Get OnCat agent instance

get_datasets(facility: str, instrument: str, ipts: int) → list

Get datasets for given facility, instrument, and IPTS.

Parameters

facilitystr

Facility name

instrumentstr

Instrument name

iptsint

IPTS number

Returns

list

List of datasets

get_ipts(facility: str, instrument: str) → list

Get IPTS numbers for given facility and instrument.

Parameters

facilitystr

Facility name

instrumentstr

Instrument name

Returns

list

List of IPTS numbers in string format (IPTS-XXXXX)

property has_token

Check if token exists

property is_connected

Check if connected to OnCat

login(username: str, password: str)

Connect to OnCat with given username and password.

Parameters

usernamestr

Username for OnCat

passwordstr

Password for OnCat

class shiver.views.oncat.OnCatLogin(*args: Any, **kwargs: Any)

OnCat login dialog

accept()

Accept

class shiver.views.oncat.Oncat(*args: Any, **kwargs: Any)

ONCat widget

as_dict() → dict

Return widget state as dictionary

connect_error_callback(callback)

Connect error message callback

connect_to_oncat()

Connect to OnCat

property connected_to_oncat: bool

Check if connected to OnCat

get_angle_integration()

Get angle integration target

get_dataset()

Get dataset

get_facility()

Get facility based on instrument

get_instrument()

Get instrument

get_ipts()

Get IPTS

get_ipts_number()

Get IPTS number

get_suggested_path() → str

Return a suggested path based on current selection.

get_suggested_selected_files() → list

Return a list of suggested files to be selected based on dataset selection.

populate_from_dict(state: dict)

Populate widget from dictionary

set_dataset_to_custom()

Set dataset to custom

sync_with_remote(refresh=False)

Update all items within OnCat widget.

update_connection_status()

Update connection status

update_datasets()

Update dataset list

update_ipts()

Update IPTS list

class shiver.views.oncat.OncatToken(token_path: str)

Class to hold OnCat token

read_token()

Read token from file

write_token(token)

Write token to file

shiver.views.oncat.get_data_from_oncat(login: ONCat, projection: list, ipts_number: int, instrument: str, facility: str = 'SNS', tags: str = 'type/raw') → dict

Get data according to a projection from oncat

Parameters:

loginpyoncat.ONCat

An object that contains login information to oncat database.

projectionlist

A list of paths in the oncat datafile to extract the relevant information.

ipts_numberint,str

The experiment identifier number (IPTS)

instrumentstr

The instrument associated with the datafiles

facilitystr, optional

The facility associated with the datafiles (Default = ‘SNS’)

tagsstr, optional

The type of files to look for in the OnCat database (Default = ‘type/raw’)

Returns:

datafiles: dict

A dictionary containing information requested from the OnCat database

shiver.views.oncat.get_dataset_info(*, login, ipts_number, instrument, dataset_name=None, use_notes=False, facility='SNS', group_by_angle=False, angle_pv='omega', angle_bin=0.5, include_runs=None, exclude_runs=None)

A function to return a list of runs in a dataset, optionally grouped by angle. Grouping by angle is from the lowest value, within angle_bin.

Parameters:

loginpyoncat.ONCat

An object that contains login information to oncat database.

ipts_numberint,str

The experiment identifier number (IPTS)

instrumentstr

The instrument associated with the datafiles

dataset_namestr, optional

The name of a dataset to look for in the database. It can be None.

use_notesbool, optional

A flag to indicate that the names of the datasets are stored in the Notes/Comments (as opposed to sequence name)

facilitystr, optional

The facility associated with the datafiles (Default = ‘SNS’)

group_by_anglebool, optional

A flag to indicate if the runs should be grouped by angle

angle_pvstr, optional

The name of the angle process variable. The value read from this variable will be used for grouping files together.Default is ‘omega’

angle_binfloat, optional

The maximum difference (in degrees) between angles in the same group. Default is 0.5

include_runsarray_like, optional

A list or array of additional runs to be added to the same dataset. The default is None

exclude_runsarray_like, optional

A list or array of runs to be excluded from the dataset. The default is None

Returns:

file_nameslist

List of runs in the dataset, or list of list of runs at the same angle

Raises:

ValueError

If any of the include_runs is not in the OnCat database for this IPTS If any of the include_runs is already in the dataset If any of the exclude_runs is not already accounted for If no runs were found to match the criteria (for example, dataset_name=None and include_runs=None)

shiver.views.oncat.get_dataset_names(login: ONCat, ipts_number: int, instrument: str, use_notes: bool = False, facility: str = 'SNS') → list

A function to return the names of the datasets, either from sequence names or from comments

Parameters:

loginpyoncat.ONCat

An object that contains login information to oncat database.

ipts_numberint,str

The experiment identifier number (IPTS)

instrumentstr

The instrument associated with the datafiles

use_notesbool, optional

A flag to indicate that the names of the datasets are stored in the Notes/Comments (as opposed to sequence name)

facilitystr, optional

The facility associated with the datafiles (Default = ‘SNS’)

Returns:

dsn: set of strings

A set containing strings with the dataset names, as tored in the OnCat database

PyQt widget for the histogram tab

class shiver.views.generate.Buttons(*args: Any, **kwargs: Any)

Processing buttons

class shiver.views.generate.Generate(*args: Any, **kwargs: Any)

Generate widget

as_dict() → dict

Return the widget as a dict.

Returns

dict

The widget as a dict.

connect_generate_mde_callback(callback)

Connect the callback for generating the MDE

connect_save_configuration_callback(callback)

Connect the callback for saving the configuration

do_generate_mde()

Generate the MDE

do_save_configuration()

Save the configuration

error_message_signal

alias of str

generate_mde_finish_callback(activate)

Toggle the generate button disabled state

get_save_configuration_filepath(default_filename: str, default_output_dir: str) → str

Return the filename and output directory to save the configuration.

Parameters:

default_filename: str

The default filename to save the configuration.

default_output_dir: str

The default output directory to save the configuration.

Returns:

str:

The full path to save the configuration.

populate_from_dict(data: dict)

Populate all child widgets with the given dict.

Parameters

datadict

The data to populate the widgets with.

set_dataset_to_custom()

Set the dataset in the oncat widget to “custom”.

set_field_invalid_state(item)

include the item in the field_error list and disable the corresponding button/s

set_field_valid_state(item)

remove the item from the field_error list and enable the corresponding button/s

show_error_message(msg)

Will show a error dialog with the given message

This will emit a signal so that other threads can call this but have the GUI thread execute

update_raw_data_widget_path()

Update the path in the raw data widget

update_raw_data_widget_selection()

Update the selection in the raw data widget

update_workspace_in_reduction_params()

Update the workspace name from mde to reduction parameters

class shiver.views.generate.MDEType(*args: Any, **kwargs: Any)

MDE type widget

as_dict() → dict

Return the MDE type widget as a dictionary.

check_mde_name() → bool

Check if the mde name is valid.

Returns:

bool: True if the mde name is valid, False otherwise.

check_output_dir() → bool

Check if the output directory is valid.

Returns:

bool:

True if the output directory is not empty and does not contains any special char, False otherwise.

connect_error_callback(callback)

Connect the error callback.

Parameters:

callback: callable

The error callback.

connect_update_title_callback(callback)

Connect the update title callback.

Parameters:

callback: callable

The update title callback.

property is_valid: bool

Check if the MDE type widget is valid.

populate_from_dict(param_dict: dict) → bool

Populate the MDE type widget from a dictionary.

Parameters:

param_dict: dict

The dictionary containing the MDE type widget parameters.

Returns:

bool:

True if the MDE type widget is populated successfully, False otherwise.

re_init_widget()

Re-initialize the widget.

set_field_invalid_state(item)

if parent exists then call the corresponding function

set_field_valid_state(item)

remove the item from the field_error list and its invalid style, if it was previously invalid and enable the corresponding button

shiver.views.generate.has_special_char(var_name: str) → bool

Check if the variable name contains special characters.

Parameters:

var_name: str

The variable name to check.

Returns:

bool:

True if the variable name contains special characters, False otherwise.

shiver.views.generate.is_valid_name(var_name: str) → bool

Check if the variable name is valid.

Parameters:

var_name: str

The variable name to check.

Returns:

bool:

True if the variable name is valid, False otherwise.

NOTE:

The variable name must follow the following rules: - must not be empty - must start with a letter or underscore - must only contain letters, numbers, and underscores

PyQt QDialog for Sample Parameters

class shiver.views.advanced_options.ADValidator(*args: Any, **kwargs: Any)

Validates the additional dimensions value

validate(teststring, pos)

Validates the 3-element values

validate_cell(teststring, start, end, pos)

Validates in 3-element comma-separated format: <string>,<min_number>,<max_number>

class shiver.views.advanced_options.AdvancedDialog(*args: Any, **kwargs: Any)

Advanced Options widget

adt_dim_update()

Validate the additional dimension values

btn_add_row()

Add a new row

btn_apply_submit()

Check everything is valid and close dialog

btn_cancel_action()

Cancel the sample dialog

btn_delete_row()

Delete selected row

btn_help_action()

Show the help for the sample dialog

check_num_input(min_value, max_value)

Ensure numbers are: float, Minimum < Maximum and both exist at the same time

get_advanced_options_dict()

Return advanced options as a dictionary

get_clicked_row()

Allow for one selected row to be return for possible deletion

get_table_values_dict()

Return table cells as a dictionary

initialize_cells()

Initialize table cells

lcutoff_color_update()

Update LowerCutoff valid state based on the input

lcutoff_update()

Enable/Disable LowerCutoff based on the filter check box

min_max_checked(min_input, max_input, required)

Ensure Minimum and Maximum value pairs are valid and whether they are required

populate_advanced_options_from_dict(params)

Populate all fields from dictionary

set_cell_invalid_state(item)

include the item in the invalid_cells and field_error list and disable the corresponding button

set_cell_valid_state(item)

remove the item from the invalid_cells and field_error list and enable the corresponding button

set_field_invalid_state(item)

include the item in the field_error list and disable the corresponding button

set_field_valid_state(item)

remove the item from the field_error list and enable the corresponding button

set_table_values(maskinputs)

Populate all table rows from list of rows

show_error_message(msg)

Will show a error dialog with the given message

tib_update()

Enable/Disable TIB min and max based on the apply tib radio buttons

validate_cell()

Validates the cells using the IntArrayProperty-based format: <num1>,<num2>, .., <range1>-<range2>, <range1>:<range2> <range1>:<range2>:<step>

shiver.views.advanced_options.return_valid(validity, teststring, pos)

Returns state during validation

PyQt widget for the raw data selection

class shiver.views.data.RawData(*args: Any, **kwargs: Any)

Raw data selection widget

as_dict(use_grouped=False)

Return a dictionary of the current state

check_file_input()

check whether any files are selected

get_selected(use_grouped=False)

Return a list of the full path of the files selected

populate_from_dict(config_dict: dict)

Populate the widget from a dictionary

set_field_invalid_state(item)

if parent exists then call the corresponding function

set_field_valid_state(item)

remove the item from the field_error list and its invalid style, if it was previously invalid and enable the corresponding button

set_selected(filenames: list)

Set the selected files.

Parameters

filenameslist

list of filenames with full path.

Notes

1. Expects a list of full file paths

2. This makes the assumption that all the files for in the same directory.

shiver.views.data.filename_str_to_list(filenames_str)

Convert a string of filenames to a list.

Parameters

filenames_strstr

String of filenames separated by a comma. Grouped filenames are connected with “+”, i.e. “file1.nxs.h5,file2.nxs.h5+file3.nxs.h5,file4.nxs.h5” to [“file1.nxs.h5”, [“file2.nxs.h5”, “file3.nxs.h5”], “file4.nxs.h5”]

PyQt widget for the histogram tab

class shiver.views.loading_buttons.LoadingButtons(*args: Any, **kwargs: Any)

Buttons for Loading

connect_error_msg(callback)

connect a function to the error message.

Parameters

callbackfunction

the function to be called when an error message is needed.

connect_load_dataset(callback)

connect a function to the selection of a dataset.

Parameters

callbackfunction

the function to be called when a dataset is selected.

connect_load_file(callback)

connect a function to the selection of a filename

extract_dataset_list(filename)

extract the dataset list from the given file.

Parameters

filenamestr

the file name of the Python file that defines the dataset.

Returns

data_set_listlist

a list of data set.

PyQt widget for the histogram tab input workspaces

class shiver.views.workspace_tables.ADSList(*args: Any, **kwargs: Any)

List widget that will add and remove items from the ADS

add_ws(name, ws_type, frame, ndims)

Adds a workspace to the list if it is of the correct type

del_ws(name)

Removes a workspace from the list if it is of the correct type

set_selected(name)

method to set the selected workspace as selected

Parameters

namestr

Name of the workspace to select

class shiver.views.workspace_tables.Frame(value)

An enumeration.

class shiver.views.workspace_tables.HistogramWorkspaces(*args: Any, **kwargs: Any)

Histogram workspaces widget

add_ws(name, ws_type, frame, ndims)

Adds a workspace to the list if it is of the correct type

clear_ws()

Clears all workspaces from the lists

del_ws(name)

Removes a workspace from the list if it is of the correct type

histogram_selected_signal

alias of str

on_item_clicked(item)

method to emit a signal when a workspace is selected

class shiver.views.workspace_tables.InputWorkspaces(*args: Any, **kwargs: Any)

MDE and Normalization workspace widget

add_ws(name, ws_type, frame, ndims)

Adds a workspace to the list if it is of the correct type

clear_ws()

Clears all workspaces from the lists

del_ws(name)

Removes a workspace from the list if it is of the correct type

initialize_default()

initialize invalid style color due to absence of data

set_field_invalid_state(item)

if parent exists then call the corresponding function to disable the button

set_field_valid_state(item)

if parent exists then call the corresponding function to enable the button

class shiver.views.workspace_tables.MDEList(*args: Any, **kwargs: Any)

Special workspace list widget so that we can add a menu to each item

add_ws(name, ws_type, frame, ndims)

Adds a workspace to the list if it is of the correct type

all_data()

return all the selected data workspace names

property background

return the workspace name set as background (optional, may be None)

clone_ws(name)

method to clone the selected workspace

connect_get_polarization_logs(callback)

connect a function to get the sample logs for workspace

connect_get_polarization_state_workspace(callback)

connect a function to get the polariation state for workspace

connect_save_mde_workspace_callback(callback)

connect a function to save the mde workspace

connect_save_polarization_state_workspace(callback)

connect a function to save the polarization state for workspace

property data

return unpolarized data

property data_nsf

return the workspace name set as polarized no spinflip data

property data_sf

return the workspace name set as polarized spinflip data

property data_u

return the workspace name set as unpolarized data

delete_ws(name)

method to delete the currently selected workspace

do_provenance(workspace_name: str)

Method to open the provenance window

Parameters

workspace_namestr

Name of the workspace to open the provenance window for.

get_data_workspaces_not_allowed(pol_state)

method to return unallowed data workspaces based on the polarization state

initialize_default()

initialize invalid style color due to absence of data

mousePressEvent(event)

mouse click event handler

refine_ub(name)

method to set refinement UB histogram and open refine ub tab

rename_ws(name)

method to rename the currently selected workspace

save_mde_ws(name)

method to save workspace data in file

scale_ws(name)

method to scale the workspace data, creating a new workspace

set_background(name)

method to set the selected workspace as ‘background’ and update border color

set_corrections(name)

method to open the correction tab to apply correction for given workspace

set_data(name, pol_state)

method to set the selected workspace as data pol_state and update border color

set_field_invalid_state(item)

if parent exists then call the corresponding function and update the color

set_field_valid_state(item)

remove the item from the field_error list and its invalid style, if it was previously invalid and enable the corresponding button

set_pol_options(name)

Open the dialog to set polarization options in the selected workspace

set_sample(name)

method to set sample parameters in the selected workspace

unset_all()

reset the list and update border color

unset_background(name)

method to unset the selected workspace as ‘background’

unset_selected_data(data_workspaces)

method to unset the selected workspaces in field defined by data_workspaces

unset_selected_states_with_name(name)

method to unselect the workspace with name

validate_data_workspace_state()

method to check whether there is at least one selected data workspace and update boarder color-valid state

class shiver.views.workspace_tables.MDHList(*args: Any, **kwargs: Any)

List widget that will add and remove items from the ADS

add_ws(name, ws_type, frame, ndims)

Adds a workspace to the list if it is of the correct type

contextMenu(pos)

right-click event handler

delete_ws(name)

Method to delete the currently selected workspace.

get_display_name_and_intensity_limits(selected_ws, ndims)

get the display name and intensity limits

plot_1d(name, display_name, intensity_limits, log_scale, errors, overplot)

method to do 1D plots

plot_2d(name, display_name, intensity_limits, log_scale)

method to do 2D plots

plot_slice_viewer(name, intensity_limits, log_scale)

method to open sliceviewer

save_script(name)

method to handle the saving of script

save_ws(name: str)

Method to handle the saving data to NeXus file.

Parameters

name

name of the workspace to be saved

save_ws_to_ascii(name: str)

Method to handle the saving data to ASCII file.

Parameters

name

name of the workspace to be saved

class shiver.views.workspace_tables.NormList(*args: Any, **kwargs: Any)

List widget that will add and remove items from the ADS

contextMenu(pos)

right-click event handler

delete_ws(name)

method to delete the currently selected workspace

deselect_all()

reset the list

get_selected()

method to get the selected workspace

Returns

str

Name of the selected workspace

rename_ws(name)

method to rename the currently selected workspace

PyQt widget for the workspace icons

class shiver.views.workspace_icons.IconLegend(*args: Any, **kwargs: Any)

Legend for the icons in the MDE table

shiver.views.workspace_icons.get_icon(name: str) → qtpy.QtGui.QIcon

return a icon for the given name

Functions to plot histograms

shiver.views.plots.do_1d_plot(workspaces, display_name, intensity_limits=None, log_scale=False, errors=False, overplot=False)

Create an 1D plot for the provided workspace

shiver.views.plots.do_colorfill_plot(workspaces, display_name=None, intensity_limits=None, log_scale=False)

Create a colormesh plot for the provided workspace

shiver.views.plots.do_default_plot(workspace, ndims, display_name=None, intensity_limits=None)

Create the default plot for the workspace and number of dimensions

shiver.views.plots.do_slice_viewer(workspaces, parent=None, intensity_limits=None, log_scale=False)

Open sliceviewer for the provided workspace

PyQt QDialog for Sample Parameters

class shiver.views.polarized_options.PolarizedDialog(*args: Any, **kwargs: Any)

Polarized Options widget

btn_apply_submit()

Check everything is valid and close dialog

btn_cancel_action()

Cancel the sample dialog

btn_help_action()

Show the help for the sample dialog

dir_update()

Remove direction from invalid_fields

disable_params()

Disable/hide direction, ratio and log parameters

enable_params()

Enable/show direction, ratio and log parameters

get_polarized_direction()

Return polarized direction

get_polarized_options_dict()

Return polarized options as a dictionary

get_polarized_state()

Return polarized state

log_update()

Check sample log and update ratio validation status

log_validate()

Check whether sample log is in valid state

populate_pol_options_from_dict(params)

Populate all fields from dictionary

populate_polarized_options()

Populate all fields from workspace

psda_update()

Validate the psda value

ratio_update()

Validate the ratio value

set_field_invalid_state(item)

include the item in the field_error list and disable the corresponding button

set_field_valid_state(item)

remove the item from the field_error list and enable the corresponding button

set_polarized_state_dir(params)

Set state and direction from polarized state

show_error_message(msg)

Will show a error dialog with the given message

class shiver.views.polarized_options.PolarizedView(*args: Any, **kwargs: Any)

View for Sample Parameters

connect_apply_submit(callback)

connect to save the polarization logs for workspace

connect_populate_polarized_options(callback)

connect to get the polarization logs for workspace

get_error_message(msg)

received the error message from model

set_parameter_dict()

Set all polarized parameters as a dictionary in current and parent view

start_dialog(disable_psda=False)

initialize and start dialog

class shiver.views.polarized_options.RatioValidator(*args: Any, **kwargs: Any)

Validates the additional dimensions value

validate(teststring, pos)

Validates number or formula

shiver.views.polarized_options.return_valid(validity, teststring, pos)

Returns state during validation

Main Qt window for shiver

class shiver.views.mainwindow.MainWindow(*args: Any, **kwargs: Any)

Main shiver widget

handle_help()

get current tab type and open the corresponding help page

Widget for background minimization options

class shiver.views.minimize_background.MinimizeBackgroundOptions(*args: Any, **kwargs: Any)

Background minimization options

as_dict()

Return the background minimization widget as a dictionary.

check_grouping_file()

Check that the grouping filename has been set

check_num_input(min_value, max_value)

Ensure numbers are: float, Minimum < Maximum, between 0 and 100 and both exist at the same time

min_max_checked()

Ensure Minimum and Maximum value pairs are valid

populate_from_dict(param_dict)

Populate this widget from a dictionary

set_enabled(enabled)

Set this widget as enabled or not, and set correct valid state

set_field_invalid_state(item)

include the item in the field_error list and disable the corresponding button

set_field_valid_state(item)

remove the item from the field_error list and enable the corresponding button

PyQt widget for the Reduction Parameters section

class shiver.views.reduction_parameters.ReductionParameters(*args: Any, **kwargs: Any)

Generate reduction parameter widget

get_reduction_params_dict()

Return all reduction parameters as a dictionary

populate_red_params_from_dict(params)

Populate all fields and inner dialogs from dictionary

set_adv_btn()

Open the dialog to set advanced options

set_field_invalid_state(item)

if parent exists then call the corresponding function

set_field_valid_state(item)

remove the item from the field_error list and its invalid style, if it was previously invalid and enable the corresponding button

set_pol_btn()

Open the dialog to set polarization options

set_sample_btn()

Open the dialog to set sample parameters

update_polarization_label()

It updates the label with the plarization state and direction

validate_t0()

validate t0 input

View for the Refine UB widget

class shiver.views.refine_ub.PeaksTableModel(*args: Any, **kwargs: Any)

A QAbstractTableModel for use with a QTableView

columnCount(_)

Returns the number of columns

data(index, role=qtpy.QtCore.Qt.DisplayRole)

Returns the data stored under the given role for the item referred to by the index.

deselect_all()

Deselect all refine/recenter checkboxes

flags(index)

Returns the item flags for the given index.

headerData(section, orientation, role)

Returns the data for the given role and section in the header with the specified orientation.

load_data(data_model)

update the data used in this model

recenter_rows()

Return a list of row number where “Recenter” box is checked

refine_rows()

Return a list of row number where “Refine” box is checked

round_hkl()

Round all HKL values to integer

rowCount(_)

Returns the number of rows

select_all()

Select all refine/recenter checkboxes

setData(index, value, role)

Sets the role data for the item at index to value.

setHorizontalHeaderLabels(labels)

Update the attribute storing the header labels

class shiver.views.refine_ub.RefineUBView(*args: Any, **kwargs: Any)

The view for the Refine UB widget

connect_peak_selection(callback)

Connect the peak selection callback

connect_populate_peaks(callback)

connect the “populate peaks” button callback

connect_predict_peaks(callback)

connect the “predict peaks” button callback

connect_recenter_peaks(callback)

connect the recenter button callback

connect_refine(callback)

connect the refine button callback

connect_refine_orientation(callback)

connect the refine orientation button callback

connect_undo(callback)

connect the undo button callback

get_lattice_type()

return the lattice type from the combobox

plot_perpendicular_slice(centers, *slices)

Update the 3 plots with the workspace slices and draw peak positions

refine_call()

call when refine button pressed

refine_orientation_call()

call when “refine orientation” button pressed

remove_sliceviewer()

remove the current sliceviewer

this will prevent issues when the workspace is updated

select_row(row)

Set which peaks is currently selected

selected_rows()

return the currently selected rows in peak table

set_lattice(parameters)

Update the lattice parameters widget from the parameters dict

set_sliceviewer(sliceviewer)

insert the new sliceviewer into the layout

undo_call()

call when Undo button pressed

PyQt widget for the correction tab

class shiver.views.corrections.Corrections(*args: Any, **kwargs: Any)

Correction widget

balance_temp_validate()

Validate balance: validate balance and temperature combination

set_field_invalid_state(item, invalid_style)

include the item in the field_error list and disable the corresponding button

set_field_valid_state(item)

remove the item from the field_error list and enable the corresponding button

PyQt widget for the histogram tab

class shiver.views.histogram.Histogram(*args: Any, **kwargs: Any)

Histogram widget

add_ws(name, ws_type, frame=None, ndims=0)

Adds a workspace to the list if it is of the correct type

clear_ws()

Clears all workspaces from the lists

connect_clone_workspace(callback)

connect a function to clone a workspace

connect_corrections_tab(callback)

connect a function to the creation of a corrections tab

connect_delete_workspace(callback)

connect a function to the selection of a filename

connect_do_provenance_callback(callback)

connect a function to the creation of a corrections tab.

Parameters

callbackfunction

The function to call when the provenance button is clicked.

connect_plot_display_name_callback(callback)

callback for the display name-description for the plot

connect_refine_ub(callback)

connect a function to the Refine sample parameters button

connect_refine_ub_tab(callback)

connect a function to the creation of a Refine UB tab

connect_rename_workspace(callback)

connect a function to the selection of a filename

connect_save_script_workspace(callback)

connect a function to the save script for workspace

connect_save_workspace(callback)

connect a function to the save a workspace

connect_save_workspace_to_ascii(callback)

connect a function to the save a workspace to ascii

connect_scale_workspace(callback)

connect a function to scale the workspace

del_ws(name)

Removes a workspace from the list if it is of the correct type

disable_while_running(disable)

This will disable the UI elements for histgramming while MakeSlice is running

error_message_signal

alias of str

gather_workspace_background()

Return the name of background workspace.

gather_workspace_data() → list

Return the name of data workspace unpolarized.

gather_workspace_normalization()

Return the name of normalization workspace.

get_plot_data(ws_name, ndims)

Get display name and intensities data for plotting.

get_selected_normalization()

Return the selected normalization workspace.

is_valid()

return whether the field_errors is empty

make_slice_finish(ws_name, ndims)

Handle the UI updates for when MakeSlice has finished.

This will emit a signal so that other threads can call this but have the GUI thread execute it.

makeslice_finish_signal

alias of str

select_normalization(normalization)

Select the normalization workspace.

set_background(background)

Set the background workspace.

set_data(data, pol_state)

Set the data unpolarized workspace and update its valid state.

set_field_invalid_state(item)

include the item in the field_error list and disable the corresponding button

set_field_valid_state(item)

remove the item from the field_error list and enable the corresponding button

show_error_message(msg, accumulate=False)

Will show a error dialog with the given message.

This will emit a signal so that other threads can call this but have the GUI thread execute it.

Parameters

msgstr

The message to show

accumulatebool, optional

If True, the error message will be accumulated and shown when accumulate is False

show_warning_message(msg)

Will show a warning dialog with the given message and return button click as True/False

unset_all()

Unset all workspaces.