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adds mockup beamline configured with YAML files
Adding an example of the mockup beamline, where all HWOBJs are configured with YAML files. To start MXCuBE with this version of beamline, use '--repository' command line argument. For example: ./mxcubeweb-server --repository demo.yaml
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‎demo.yaml/aperture.yaml

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%YAML 1.2
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---
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class: ApertureMockup.ApertureMockup
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configuration:
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diameter_size_list: '[10, 20, 50, 100, 150]'

‎demo.yaml/beam.yaml

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%YAML 1.2
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---
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class: BeamMockup.BeamMockup
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configuration:
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beam_divergence_horizontal: 12.0
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beam_divergence_vertical: 12.0
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definer_type: aperture
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username: beam
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objects:
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aperture: aperture.yaml
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slits: slits.yaml

‎demo.yaml/beamline_actions.yaml

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%YAML 1.2
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---
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class: BeamlineActionsMockup.BeamlineActionsMockup
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configuration:
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commands: "
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[
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{'type': 'controller', 'name': 'Centre Beam',
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'command': 'HardwareObjects.mockup.BeamlineActionsMockup.SimulatedAction'},
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{'type': 'controller', 'name': 'Quick Realign',
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'command': 'HardwareObjects.mockup.BeamlineActionsMockup.LongSimulatedAction'},
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{'type': 'controller', 'name': 'Anneal',
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'command': 'HardwareObjects.mockup.BeamlineActionsMockup.SimulatedActionError'},
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{'type': 'annotated',
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'command': 'HardwareObjects.mockup.BeamlineActionsMockup.Anneal2'},
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{'type': 'annotated',
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'command': 'HardwareObjects.mockup.BeamlineActionsMockup.QuickRealign2'},
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{'type': 'annotated',
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'command': 'HardwareObjects.mockup.BeamlineActionsMockup.ComboTest2'},
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]"

‎demo.yaml/beamline_config.yml

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%YAML 1.2
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---
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# The class to initialise, and init parameters
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class:
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mxcubecore.HardwareObjects.Beamline.Beamline
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# objects
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#
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# NBNB some objects that do not currently have their own config files
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# would need those added (e.g. the centring methods)
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#
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objects:
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# The !!omap and the lines starting with '- ' give you an *ordered* dictionary
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# And thus a reproducible loading order
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!!omap
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# The values are the file paths to the configuration file for the
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# object, relative to the configuration file path(s)
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#
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# NB - the order is *NOT* arbitrary, as signal connections are set
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# on one object that require the other to be already loaded.
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#
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# Hardware:
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- session: session.yaml
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- data_publisher: data_publisher.yaml
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- machine_info: machine_info.yaml
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- detector: detector.yaml
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- beam: beam.yaml
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- transmission: transmission.yaml
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- flux: flux.yaml
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- cryo: cryo.yaml
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- energy: energy.yaml
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- resolution: resolution.yaml
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- safety_shutter: safety_shutter.yaml
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- fast_shutter: fast_shutter.yaml
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- sample_changer: sample_changer.yaml
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- sample_changer_maintenance: sample_changer_maint.yaml
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# The 2 lines up have to be used for SC and the 2 line below for the plate manipulator
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# - sample_changer: plate_manipulator.xml
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# - sample_changer_maintenance: plate_manipulator_maint.xml
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# - harvester: harvester.xml
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# - harvester_maintenance: harvester_maintenance.xml
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- diffractometer: minidiff.yaml
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- lims: lims.yaml
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- sample_view: sample_view.yaml
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- queue_manager: queue_manager.yaml
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- queue_model: queue_model.yaml
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# Procedures:
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- beamline_actions: beamline_actions.yaml
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- workflow: ednaparams.yaml
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- collect: mxcollect.yaml
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- xrf_spectrum: xrf.yaml
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- energy_scan: energy_scan.yaml
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- gphl_connection: gphl/gphl-setup.yaml
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- gphl_workflow: gphl/gphl-workflow.yaml
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- xray_centring: xray_centring2.yaml
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- xml_rpc_server: xml_rpc_server.yaml
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# Analysis:
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- offline_processing: auto_processing.yaml
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- online_processing: parallel_processing.yaml
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- characterisation: characterisation.yaml
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configuration:
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advanced_methods:
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- MeshScan
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- XrayCentering
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tunable_wavelength: true
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disable_num_passes: true
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run_processing_parallel: true
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run_number: 1
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click_centring_num_clicks: 3
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mesh_result_format: PNG
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use_native_mesh: true
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enable_2d_points: true
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default_acquisition_parameters:
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default:
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# Default values, also used for standard acquisition.
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# Values not given in other dictionaries are taken from here
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exp_time: 0.02 # exposure time
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osc_start: 0.0 # Only used if no current angle can be found
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osc_range: 0.1
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num_passes: 1
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first_image: 1
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overlap: 0
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num_images: 1
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detector_mode: 1 # Remove as not in practice used ?
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inverse_beam: false
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take_dark_current: true
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skip_existing_images: true
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take_snapshots: true
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sub_wedge_size: 10
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# NB 'compression' not added as apparently never used
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helical:
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# Defaults for helical scan. Missing values are taken from default
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number_of_images: 100
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characterisation:
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# Defaults for characterisation. Missing values are taken from default
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exp_time: 0.05 # exposure time
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osc_range: 1
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overlap: -89
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num_images: 4
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shutterless: false
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mesh:
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# Defaults for 'advanced' acquisition. Missing values are taken from default
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exp_time: 10 # exposure time
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range: 10
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num_images: 100
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cell_counting: zig-zag
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cell_spacing: vertical, horizontal
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mesh_center: top-left
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gphlworkflow:
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{}
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# Apparently this must be here, but we use all values same as default
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acquisition_limit_values:
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exposure_time:
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- 0.02
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- 1000
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osc_range:
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- -10000
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- 10000
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number_of_images:
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- 1
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- 99999
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kappa:
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- -5.0
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- 240.0
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available_methods:
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datacollection: true
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characterisation: true
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helical: true
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xrf_spectrum: true
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energy_scan: true
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mesh: true
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ssx_chip_collection: true
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gphlworkflow: true
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test_collection: true
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undulators:
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- type: PPU35C_GAP
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device_uri: //orion:10000/id/id/30
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- type: PPU35D_GAP
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device_uri: //orion:10000/id/id/30

‎demo.yaml/beamstop.yaml

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%YAML 1.2
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---
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class: ExporterNStateMockup.ExporterNStateMockup
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configuration:
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use_hwstate: true
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username: beamstop
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values: '{"OUT": "OFF", "IN": "BEAM"}'

‎demo.yaml/beamstop_alignment_x.yaml

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%YAML 1.2
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---
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class: MotorMockup.MotorMockup
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configuration:
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GUIstep: 0.1
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exporter_address: 130.235.94.124:9001
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motor_name: BeamstopAlignmentX
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unit: 0.001
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username: Beamstop Alignemnt X

‎demo.yaml/capillary.yaml

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%YAML 1.2
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---
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class: ExporterNStateMockup.ExporterNStateMockup
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configuration:
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use_hwstate: true
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username: capillary
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values: '{"IN": "BEAM", "OUT": "OFF"}'

‎demo.yaml/characterisation.yaml

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%YAML 1.2
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---
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class: EDNACharacterisationMockup.EDNACharacterisationMockup
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configuration:
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edna_command: /users/blissadm/local/bin/edna_script_bes.py
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edna_default_file: edna_defaults.xml

‎demo.yaml/chip_definition.json

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{
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"current": "SMALL_FOIL",
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"available": {
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"OXFORD_CHIP": {
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"head_type": "CHIP",
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"holder_type": "KNOWN_GEOMETRY",
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"holder_brand": "Oxford Chip",
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"holder_size": [
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30.0,
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30.0
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],
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"sections": [
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{
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"section_offset": [
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0,
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0
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],
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"block_size": [
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30.0,
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30.0
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],
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"block_spacing": [
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15.0,
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15.0
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],
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"block_shape": "RECTANGULAR",
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"number_of_rows": 8,
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"number_of_collumns": 8,
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"row_labels": [
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"1",
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"2",
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"3",
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"4",
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"5",
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"6",
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"7",
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"8"
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],
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"column_lables": [
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"A",
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"B",
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"C",
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"D",
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"E",
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"F",
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"G",
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"H"
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],
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"targets_per_block": [
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20,
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20
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]
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}
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],
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"calibration_data": {
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"top_left": [
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0.0,
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0.0,
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0.0
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],
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"top_right": [
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0.0,
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0.0,
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0.0
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],
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"bottom_left": [
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0.0,
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0.0,
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0.0
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]
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}
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},
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"SMALL_FOIL": {
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"head_type": "CHIP",
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"holder_type": "FREE_GEOMETRY",
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"holder_brand": "FOIL",
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"holder_size": [
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100.0,
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100.0
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],
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"sections": [],
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"calibration_data": {
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"top_left": [
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18.0,
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15.8,
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-0.17
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],
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"top_right": [
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22.0,
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15.8,
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-0.17
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],
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"bottom_left": [
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18.0,
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24.0,
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-0.17
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]
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}
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},
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"BIG_FOIL": {
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"head_type": "CHIP",
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"holder_type": "FREE_GEOMETRY",
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"holder_brand": "FOIL",
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"holder_size": [
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100.0,
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100.0
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],
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"sections": [],
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"calibration_data": {
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"top_left": [
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7.0,
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3.0,
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0.08
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],
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"top_right": [
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32.0,
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3.0,
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0.08
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],
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"bottom_left": [
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7.0,
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28.0,
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0.08
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]
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}
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},
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"CUSTOM_FOIL": {
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"head_type": "CHIP",
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"holder_type": "FREE_GEOMETRY",
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"holder_brand": "FOIL",
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"holder_size": [
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100.0,
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100.0
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],
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"sections": [],
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"calibration_data": {
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"top_left": [
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15.0,
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16.0,
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-0.008
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],
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"top_right": [
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23.0,
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16.0,
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-0.008
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],
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"bottom_left": [
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15.0,
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24.0,
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-0.008
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]
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}
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}
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}
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}

‎demo.yaml/cryo.yaml

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%YAML 1.2
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---
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class: ActuatorMockup.ActuatorMockup
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configuration:
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actuator_name: Cryo
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default_value: 200
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read_only: true
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username: Cryo

‎demo.yaml/data_publisher.yaml

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%YAML 1.2
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---
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class: DataPublisher.DataPublisher
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configuration: {}

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