mxcubecore.HardwareObjects.abstract.AbstractCollect#

Abstract hardware object for data collection.

Classes

`AbstractCollect`(name)	Abstract hardware object for data collection.
`BeamlineConfig`(synchrotron_name, ...)

class mxcubecore.HardwareObjects.abstract.AbstractCollect.AbstractCollect(name)[source]#

Bases: HardwareObject, object

Abstract hardware object for data collection.

Define a sequence in which data collection is executed.

Emits:

collectReady (bool)
collectOscillationStarted (dict)
progressInit (tuple[str, int, bool]) – For example: ("Collection", progress, bool).
collectOscillationFailed (dict)
collectOscillationFinished (dict)
progressStop

close_detector_cover()[source]#: Close detector cover.

close_fast_shutter()[source]#: Close fast shutter.

close_safety_shutter()[source]#: Close safety shutter.

collect(owner, dc_parameters_list)[source]#

Main collection method.

It spawns “do_collect” as well as ready event handling.

Parameters:

owner (str) – Owner instance.
dc_parameters_list (list[dict]) – List of dictionary containing all collection parameters.

collection_failed(failed_msg=None)[source]#: Collection failed method

collection_finished()[source]#: Collection finished behaviour

collection_stopped()[source]#: Collection stopped method

create_directories(*args)[source]#

Creates folders on disk.

Parameters:: args (list(str)) – List of directories to create.

create_file_directories()[source]#

Method to create directories for raw and processing files.

Directory names for xds, mosflm and hkl are created.

data_collection_cleanup()[source]#: Method called when at end of data collection, successful or not.

abstract data_collection_hook()[source]#: Descript. :

do_collect(owner)[source]#

Actually collect the sequence.

Parameters:: owner (str) – owner instance

get_beam_size() → tuple[source]#

Get beam size.

Returns:: Beam width, and beam height.
Return type:: tuple

get_cryo_temperature() → float[source]#

Get cryogenic temperature.

Returns:: Current cryo temperature [K].
Return type:: float

get_detector_distance() → float[source]#

Get current detector distance.

Returns:: Current detector distance position [mm].
Return type:: float

get_machine_current() → float[source]#

Get machine current.

Returns:: Machine current [mA].
Return type:: float

get_machine_fill_mode() → str[source]#

Get machine fill mode.

Returns:: Machine filling mode.
Return type:: str

get_machine_message() → str[source]#

Get machine message.

Returns:: Current machine message if any.
Return type:: str

get_measured_intensity() → float[source]#

Get beam intensity.

Returns:: Beam intensity.
Return type:: float

get_resolution() → float[source]#

Get current resolution.

Returns:: Current resolution [Å].
Return type:: float

get_sample_info() → None[source]#

Get current sample information in LIMS database.

Information is stored in the internal “current_dc_parameters” dictionary.

Return type:: None

get_slit_gaps() → tuple[source]#

Get slit gap distance.

Returns:: Horizontal gap, and vertical gap.
Return type:: tuple

get_transmission() → float[source]#

Get current beamline transmission.

Returns:: Current transmission.
Return type:: float

get_undulators_gaps() → dict[source]#

Get undulator gaps.

Returns:: Undulator gaps.
Return type:: dict

get_wavelength() → float[source]#

Get current wavelength.

Returns:: Current beamline wavelength [Ä].
Return type:: float

init()[source]#

‘public’ post-initialization method. Override as needed.

For ConfiguredObjects called after loading contained objects.

move_to_centered_position() → None[source]#

Move motors to the centered position.

Move motors to the centered position as stored in “current_dc_parameters” dictionary.

Return type:: None

open_detector_cover()[source]#: Open detector cover.

open_fast_shutter()[source]#: Open fast shutter.

open_safety_shutter()[source]#: Open safety shutter.

prepare_input_files() → tuple[str | None, str | None, str | None][source]#

Prepare input files for xds, mosflm and hkl2000.

Return type:: tuple[str | None, str | None, str | None]

setCentringStatus(status)[source]#: Descript. :

set_beamline_configuration(**configuration_parameters) → None[source]#

Sets beamline configuration

Parameters:: configuration_parameters (dict) – Configuration parameters.
Return type:: None

set_energy(value: float)[source]#

Set energy.

Parameters:: value (float) – Energy value to set.

set_fast_characterisation(arg)[source]#: Descript. :

set_helical(arg)[source]#: Descript. :

set_helical_pos(arg)[source]#: Descript. :

set_mesh_scan_parameters(num_lines: int, total_nb_frames: int, mesh_center_param: tuple, mesh_range_param: tuple) → None[source]#

Set the mesh scan parameters.

Parameters:

num_lines (int) –
total_nb_frames (int) –
mesh_center_param (tuple) –
mesh_range_param (tuple) –

Return type:

None

set_resolution(value: float)[source]#

Set resolution.

Parameters:: value (float) – Resolution value to set.

set_transmission(value: float)[source]#

Set transmission.

Parameters:: value (float) – Transmission value to set.

set_wavelength(value: float)[source]#

Set wavelength.

Parameters:: value (float) – Wavelength value to set.

stop_collect()[source]#: Stop data collection.

store_data_collection_in_lims()[source]#: Store current data collection information in LIMS database.

store_image_in_lims(frame_number: int, motor_position_id: int | None = None)[source]#

Store image information in LIMS database.

Parameters:

frame_number (int) – Frame number of the image within the data collection.
motor_position_id (int | None) – Motor position ID.

store_sample_info_in_lims()[source]#: Store current sample information in LIMS database.

take_crystal_snapshots() → None[source]#

Take crystal snapshots of the currently loaded sample.

Return type:: None

abstract trigger_auto_processing(process_event, frame_number)[source]#: Descript. :

update_data_collection_in_lims() → None[source]#

Update current data collection information in LIMS database.

Return type:: None

update_lims_with_workflow(workflow_id: int, grid_snapshot_filename: str) → None[source]#

Update collection with information about workflow.

Parameters:

workflow_id (int) – Workflow ID.
grid_snapshot_filename (str) – Grid snapshot file path.

Return type:

None

class mxcubecore.HardwareObjects.abstract.AbstractCollect.BeamlineConfig(synchrotron_name, directory_prefix, default_exposure_time, minimum_exposure_time, detector_fileext, detector_type, detector_manufacturer, detector_model, detector_px, detector_py, detector_binning_mode, undulators, focusing_optic, monochromator_type, beam_divergence_vertical, beam_divergence_horizontal, polarisation, input_files_server)#

Bases: tuple

beam_divergence_horizontal#: Alias for field number 15

beam_divergence_vertical#: Alias for field number 14

default_exposure_time#: Alias for field number 2

detector_binning_mode#: Alias for field number 10

detector_fileext#: Alias for field number 4

detector_manufacturer#: Alias for field number 6

detector_model#: Alias for field number 7

detector_px#: Alias for field number 8

detector_py#: Alias for field number 9

detector_type#: Alias for field number 5

directory_prefix#: Alias for field number 1

focusing_optic#: Alias for field number 12

input_files_server#: Alias for field number 17

minimum_exposure_time#: Alias for field number 3

monochromator_type#: Alias for field number 13

polarisation#: Alias for field number 16

synchrotron_name#: Alias for field number 0

undulators#: Alias for field number 11