mxcubecore.HardwareObjects.DESY.P11EDNACharacterisation#

Classes

P11EDNACharacterisation(name)

class mxcubecore.HardwareObjects.DESY.P11EDNACharacterisation.P11EDNACharacterisation(name)[source]#

Bases: EDNACharacterisation

dc_from_output(edna_result, reference_image_collection)[source]#

Create a data collection from characterisation result

Parameters:

output (object) – Characterisation result object

Returns:

(queue_model_objects.DataCollection)

edna_maxwell(process_directory, inputxml, outputxml)[source]#

Executes a command on a remote cluster using SSH and SBATCH for EDNA processing.

Parameters:

  • process_directory – Directory where the processing will take place.

  • inputxml – Path to the input XML file.

  • outputxml – Path to the output XML file that will be generated.

get_html_report(edna_result)[source]#
Parameters:

output (EDNAResult) –

Returns:

(str) The path to the html result report generated by the characterisation software

input_from_params(data_collection, char_params)[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.

mkdir_with_mode(directory, mode)[source]#

The function creates a directory with a specified mode if it does not already exist.

Parameters:

directory – The “directory” parameter is the path of the directory that you want to

create. It can be an absolute path or a relative path :param mode: The “mode” parameter in the above code refers to the permissions that will be set for the newly created directory. It is an optional parameter that specifies the access mode for the directory. The access mode is a numeric value that represents the permissions for the directory