mxcubecore.HardwareObjects.abstract.AbstractCharacterisation#
Abstract Characterisation class. Defines: characterise, get_html_report methods, input_from_params, dc_from_output and get_default_characterisation_parameters abstract methods; prepare_input and is_running methods.
Classes
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Abstract Characterisation Class |
- class mxcubecore.HardwareObjects.abstract.AbstractCharacterisation.AbstractCharacterisation(name)[source]#
Bases:
HardwareObjectAbstract Characterisation Class
- abstract characterise(_input)[source]#
Start the characterosation. :param input: :type input: object
- Returns:
(str) The Characterisation result.
- abstract dc_from_output(output)[source]#
Create a data collection from characterisation result :param output: :type output: object
- Returns:
(queue_model_objects.DataCollection)
- abstract get_default_characterisation_parameters(default_input_file)[source]#
- Parameters:
default_input_file (str) – Path to file containing default input.
- Returns:
- object with
default parameters.
- Return type:
(queue_model_objects.CharacterisationsParameters)
- abstract get_html_report(output)[source]#
Get the path to the characterisation html report, generated by the characterisation softare. :param output: Characterisation output object :type output: object
- Returns:
(str) The path to the html result report.
- abstract input_from_params(ref_parameters, char_params, path_str)[source]#
- Parameters:
ref_parameters – (A named tuple or object with following fields): ‘id’, ‘prefix’, ‘run_number’, ‘template’, ‘first_image’, ‘num_images’, ‘osc_start’, ‘osc_range’, ‘overlap’, ‘exp_time’, ‘num_passes’, ‘comments’, ‘path’, ‘centred_positions’, ‘energy’, ‘resolution’, ‘transmission’, ‘shutterless’, ‘inverse_beam’, ‘screening_id’
char_params –
(A named tuple or object with following fields): # Optimisation parameters ‘aimed_resolution’ ‘aimed_multiplicity’ ‘aimed_i_sigma’ ‘aimed_completness’ ‘strategy_complexity’ ‘induce_burn’ ‘use_permitted_rotation’ ‘permitted_phi_start’ ‘permitted_phi_end’
# Crystal ‘max_crystal_vdim’ ‘min_crystal_vdim’ ‘max_crystal_vphi’ ‘min_crystal_vphi’ ‘space_group’
# Characterisation type ‘use_min_dose’ ‘use_min_time’ ‘min_dose’ ‘min_time’ ‘account_rad_damage’ ‘not_use_low_res’ ‘auto_res’ ‘opt_sad’ ‘sad_res’ ‘determine_rad_params’
# Radiation damage model ‘rad_suscept’ ‘beta’ ‘sigma’
path_str (Template string representing path to each image) –
- Returns:
Input for characterisation software