mxcubecore.HardwareObjects.abstract.AbstractCharacterisation#

Abstract hardware object class for characterisation.

Classes

AbstractCharacterisation(name)

Abstract hardware object class for characterisation.
class mxcubecore.HardwareObjects.abstract.AbstractCharacterisation.AbstractCharacterisation(name)[source]#

Bases: HardwareObject

Abstract hardware object class for characterisation.

abstract characterise(_input)[source]#

Start the characterosation.

Parameters:

input (object) – Characterisation input object.

Returns:

(str) The Characterisation result.

abstract dc_from_output(output)[source]#

Create a data collection from characterisation result

Parameters:

output (object) – Characterisation result 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.

Parameters:

output (object) – Characterisation 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.

is_running() → bool[source]#
Returns:

True if process is running otherwise False.

Return type:

bool

prepare_input(_input)[source]#

Called by characterise before characterisation starts.

Can be used to manipulate edna_input object before characterisation starts. Example: to set a site specific output directory

Parameters:

_input (object) – Characterisation input object.