From a0adff253ee4c872cf7562b8c9f9cdf5c7b3ebe0 Mon Sep 17 00:00:00 2001 From: fabcor Date: Mon, 1 Jul 2024 16:22:58 +0200 Subject: [PATCH] Set 2 characters indentation level for YAML files --- .yamllint.yaml | 3 + .../alba_xaloc13/beamline_config.yml | 177 ++++++++------- .../embl_hh_p14/beamline_config.yml | 182 +++++++-------- .../configuration/esrf_id30a2/gphl-setup.yml | 130 ++++++----- .../lnls_manaca/beamline_config.yml | 210 ++++++++--------- .../lnls_sol/beamline_config.yml | 212 +++++++++--------- .../configuration/mockup/gphl/gphl-setup.yml | 133 ++++++----- .../configuration/mockup/procedure-mockup.yml | 2 +- .../mockup/qt/beamline_config.yml | 191 ++++++++-------- .../mockup/test/beamline_config.yml | 181 ++++++++------- .../mockup/web/beamline_config.yml | 193 ++++++++-------- .../soleil_px1/beamline_config.yml | 195 ++++++++-------- .../soleil_px2/beamline_config.yml | 177 ++++++++------- 13 files changed, 991 insertions(+), 995 deletions(-) diff --git a/.yamllint.yaml b/.yamllint.yaml index 9b74e747e6..0c45561f37 100644 --- a/.yamllint.yaml +++ b/.yamllint.yaml @@ -3,6 +3,9 @@ extends: default rules: + indentation: + spaces: 2 + # Match line length to the one set by `black` the Python formatter line-length: max: 88 diff --git a/mxcubecore/configuration/alba_xaloc13/beamline_config.yml b/mxcubecore/configuration/alba_xaloc13/beamline_config.yml index 0519b38a81..c295a750dc 100644 --- a/mxcubecore/configuration/alba_xaloc13/beamline_config.yml +++ b/mxcubecore/configuration/alba_xaloc13/beamline_config.yml @@ -1,15 +1,12 @@ --- -# yamllint disable rule:comments-indentation -# yamllint disable rule:indentation - # FIRST DRAFT of ALAB xaloc13 configuration. TO BE EDITED # The class to initialise, and init parameters _initialise_class: - class: mxcubecore.HardwareObjects.Beamline.Beamline - # Further key-value pairs here will be passed to the class init -# mode: devel + class: mxcubecore.HardwareObjects.Beamline.Beamline + # Further key-value pairs here will be passed to the class init + # mode: devel # objects # @@ -23,98 +20,100 @@ _objects: # The !!o0map and the lines starting with '- ' give you an *orderd* dictionary # And thus a reproducible loading order !!omap - # The values are the file paths to the configuration file for the - # object, relative to the configuration file path(s) - # - # NB - the order is *NOT* arbitrary, as signal connnections are set - # on one object that require the other to be already loaded. - # - # Hardware: - - session: session.xml - - machine_info: mach-info.xml - - transmission: transmission.xml - - energy: energy.xml - - beam: beam-info.xml - - flux: flux.xml - - detector: pilatus.xml - - resolution: resolution.xml -# - hutch_interlock: door-interlock-mockup.xml -# - safety_shutter: safshut.xml - - fast_shutter: fastshut.xml - - sample_changer: cats.xml - # NBNB TODO remove plate_manipulater and treat as another smaple changer -# - plate_manipulator: plate-manipulator.xml - - diffractometer: mini-diff.xml - - graphics: Qt4_graphics-manager.xml - - lims: dbconnection.xml - - queue_manager: queue.xml - - queue_model: queue-model.xml - # Procedures: - - collect: mxcollect.xml - - xrf_spectrum: xrf-spectrum-mockup.xml - - energy_scan: energyscan-mockup.xml - # - imaging: xray-imaging.xml # Only in EMBL as of 201907 - - gphl_workflow: gphl-workflow.xml - - gphl_connection: gphl-setup.xml - # - centring: centring.xml - # Analysis: - - offline_processing: auto-processing.xml - - online_processing: parallel-processing.xml - - characterisation: data-analysis.xml - # - beam_realign: # Skipped - optional + # The values are the file paths to the configuration file for the + # object, relative to the configuration file path(s) + # + # NB - the order is *NOT* arbitrary, as signal connnections are set + # on one object that require the other to be already loaded. + # + # Hardware: + - session: session.xml + - machine_info: mach-info.xml + - transmission: transmission.xml + - energy: energy.xml + - beam: beam-info.xml + - flux: flux.xml + - detector: pilatus.xml + - resolution: resolution.xml + # - hutch_interlock: door-interlock-mockup.xml + # - safety_shutter: safshut.xml + - fast_shutter: fastshut.xml + - sample_changer: cats.xml + # NBNB TODO remove plate_manipulater and treat as another smaple changer + # - plate_manipulator: plate-manipulator.xml + - diffractometer: mini-diff.xml + - graphics: Qt4_graphics-manager.xml + - lims: dbconnection.xml + - queue_manager: queue.xml + - queue_model: queue-model.xml + # Procedures: + - collect: mxcollect.xml + - xrf_spectrum: xrf-spectrum-mockup.xml + - energy_scan: energyscan-mockup.xml + # - imaging: xray-imaging.xml # Only in EMBL as of 201907 + - gphl_workflow: gphl-workflow.xml + - gphl_connection: gphl-setup.xml + # - centring: centring.xml + # Analysis: + - offline_processing: auto-processing.xml + - online_processing: parallel-processing.xml + - characterisation: data-analysis.xml + # - beam_realign: # Skipped - optional + # Non-object attributes: advanced_methods: - - MeshScan - - XrayCentering + - MeshScan + - XrayCentering + tunable_wavelength: true disable_num_passes: false run_number: 1 default_acquisition_parameters: - default: - # Default values, also used for standard acquisition. - # Values not given in other dictionaries are taken from here - exp_time: 0.3 # (s) exposure time - osc_start: 0.0 # (degrees) Only used if no current angle found - osc_range: 0.1 # (degrees) - num_passes: 1 # (int) - first_image: 1 # (int) - overlap: 0 - num_images: 1 # (int) - detector_binning_mode: 1 # (int) - inverse_beam: false # (bool) - take_dark_current: true # (bool) - skip_existing_images: true # (bool) - take_snapshots: true # (bool) + default: + # Default values, also used for standard acquisition. + # Values not given in other dictionaries are taken from here + exp_time: 0.3 # (s) exposure time + osc_start: 0.0 # (degrees) Only used if no current angle found + osc_range: 0.1 # (degrees) + num_passes: 1 # (int) + first_image: 1 # (int) + overlap: 0 + num_images: 1 # (int) + detector_binning_mode: 1 # (int) + inverse_beam: false # (bool) + take_dark_current: true # (bool) + skip_existing_images: true # (bool) + take_snapshots: true # (bool) - helical: - # Defaults for helical scan. Missing values are taken from default - exp_time: 0.04 # (s) exposure time - num_images: 100 + helical: + # Defaults for helical scan. Missing values are taken from default + exp_time: 0.04 # (s) exposure time + num_images: 100 - characterisation: - # Defaults for chareacterisation. Missing values are taken from default - osc_range: 1.0 + characterisation: + # Defaults for chareacterisation. Missing values are taken from default + osc_range: 1.0 - advanced: - # Defaults for 'advanced' acquisition. Missing values are taken from default - exp_time: 0.04 # (s) exposure time - osc_range: 0.5 - num_images: 100 + advanced: + # Defaults for 'advanced' acquisition. Missing values are taken from default + exp_time: 0.04 # (s) exposure time + osc_range: 0.5 + num_images: 100 acquisition_limit_values: - exposure_time: # (s) - - 0.003 - - 6000.0 - osc_range: # (degrees) - - -2165.0 - - 2165.0 - number_of_images: # (int) - - 1 - - 9999 -# kappa: # (degrees) -# - 0.0 -# - 180.0 -# kappa_phi: # (degrees) -# - 0.0 -# - 360.0 + exposure_time: # (s) + - 0.003 + - 6000.0 + osc_range: # (degrees) + - -2165.0 + - 2165.0 + number_of_images: # (int) + - 1 + - 9999 +# kappa: # (degrees) +# - 0.0 +# - 180.0 +# kappa_phi: # (degrees) +# - 0.0 +# - 360.0 diff --git a/mxcubecore/configuration/embl_hh_p14/beamline_config.yml b/mxcubecore/configuration/embl_hh_p14/beamline_config.yml index d03dd79ba2..533e56f098 100644 --- a/mxcubecore/configuration/embl_hh_p14/beamline_config.yml +++ b/mxcubecore/configuration/embl_hh_p14/beamline_config.yml @@ -4,9 +4,9 @@ # The class to initialise, and init parameters _initialise_class: - class: mxcubecore.HardwareObjects.EMBL.EMBLBeamline.EMBLBeamline - # Further key-value pairs here will be passed to the class init -# mode: devel + class: mxcubecore.HardwareObjects.EMBL.EMBLBeamline.EMBLBeamline + # Further key-value pairs here will be passed to the class init + # mode: devel # objects # @@ -17,104 +17,106 @@ _initialise_class: # would need those added (e.g. the centring methods) # _objects: - # The !!o0map and the lines starting with '- ' give you an *orderd* dictionary - # And thus a reproducible loading order - !!omap - # The values are the file paths to the configuration file for the - # object, relative to the configuration file path(s) - # - # NB - the order is *NOT* arbitrary, as signal connnections are set - # on one object that require the other to be already loaded. - # - # Hardware: - - session: session.xml - - machine_info: mach-info.xml - - transmission: attenuators.xml - - energy: energy.xml - - flux: flux.xml - - detector: eh1/detector.xml - - resolution: eh1/resolution.xml - # EMBL-specific - put before beam as connection is set in beam. - - beam_definer: eh1/beamFocusing.xml - - beam: beam-info.xml - - hutch_interlock: door-interlock.xml - - safety_shutter: safshut.xml - - fast_shutter: fast-shut.xml - - sample_changer: sc-generic.xml - # NBNB TODO remove plate_manipulater and treat as another smaple changer - - plate_manipulator: plate-manipulator.xml - - diffractometer: mini-diff-mockup.xml - - graphics: graphics.xml - - lims: dbconnection.xml - - queue_manager: queue.xml - - queue_model: queue-model.xml - # Procedures: - - collect: mxcollect.xml - - xrf_spectrum: xrf-spectrum.xml - - energy_scan: energyscan.xml - - imaging: xray-imaging.xml - - image_tracking: image-tracking.xml - - gphl_workflow: gphl-workflow.xml - - gphl_connection: gphl-setup.xml - # - centring: centring.xml - # Analysis: - - offline_processing: auto-processing.xml - - online_processing: parallel-processing.xml - - characterisation: data-analysis.xml - # - beam_realign: # Skipped - optional - # EMBL-specific: - - ppu_control: ppu_control.xml + # The !!o0map and the lines starting with '- ' give you an *orderd* dictionary + # And thus a reproducible loading order + !!omap + # The values are the file paths to the configuration file for the + # object, relative to the configuration file path(s) + # + # NB - the order is *NOT* arbitrary, as signal connnections are set + # on one object that require the other to be already loaded. + # + # Hardware: + - session: session.xml + - machine_info: mach-info.xml + - transmission: attenuators.xml + - energy: energy.xml + - flux: flux.xml + - detector: eh1/detector.xml + - resolution: eh1/resolution.xml + # EMBL-specific - put before beam as connection is set in beam. + - beam_definer: eh1/beamFocusing.xml + - beam: beam-info.xml + - hutch_interlock: door-interlock.xml + - safety_shutter: safshut.xml + - fast_shutter: fast-shut.xml + - sample_changer: sc-generic.xml + # NBNB TODO remove plate_manipulater and treat as another smaple changer + - plate_manipulator: plate-manipulator.xml + - diffractometer: mini-diff-mockup.xml + - graphics: graphics.xml + - lims: dbconnection.xml + - queue_manager: queue.xml + - queue_model: queue-model.xml + # Procedures: + - collect: mxcollect.xml + - xrf_spectrum: xrf-spectrum.xml + - energy_scan: energyscan.xml + - imaging: xray-imaging.xml + - image_tracking: image-tracking.xml + - gphl_workflow: gphl-workflow.xml + - gphl_connection: gphl-setup.xml + # - centring: centring.xml + # Analysis: + - offline_processing: auto-processing.xml + - online_processing: parallel-processing.xml + - characterisation: data-analysis.xml + # - beam_realign: # Skipped - optional + # EMBL-specific: + - ppu_control: ppu_control.xml + # Non-object attributes: advanced_methods: - - MeshScan - - XrayCentering + - MeshScan + - XrayCentering + tunable_wavelength: true disable_num_passes: false run_online_processing: true run_number: 1 default_acquisition_parameters: - default: - # Default values, also used for standard acquisition. - # Values not given in other dictionaries are taken from here - exp_time: 0.01 # exposure time - osc_start: 0.0 # Only used if no current angle can be found - osc_range: 0.1 - num_passes: 1 - first_image: 1 - overlap: 0 - num_images: 1 - # detector_binning_mode: 1 # Removed as not in practice used. - inverse_beam: false - take_dark_current: true - skip_existing_images: true - take_snapshots: true - # NB 'compression' not added as apparently never used + default: + # Default values, also used for standard acquisition. + # Values not given in other dictionaries are taken from here + exp_time: 0.01 # exposure time + osc_start: 0.0 # Only used if no current angle can be found + osc_range: 0.1 + num_passes: 1 + first_image: 1 + overlap: 0 + num_images: 1 + # detector_binning_mode: 1 # Removed as not in practice used. + inverse_beam: false + take_dark_current: true + skip_existing_images: true + take_snapshots: true + # NB 'compression' not added as apparently never used - helical: - # Defaults for helical scan. Missing values are taken from default - number_of_images: 100 + helical: + # Defaults for helical scan. Missing values are taken from default + number_of_images: 100 - characterisation: - # Defaults for chareacterisation. Missing values are taken from default - exp_time: 0.04 # exposure time - osc_range: 0.0062 + characterisation: + # Defaults for chareacterisation. Missing values are taken from default + exp_time: 0.04 # exposure time + osc_range: 0.0062 - advanced: - # Defaults for 'advanced' acquisition. Missing values are taken from default - exp_time: 0.0014 # exposure time - range: 0.5 - num_images: 100 + advanced: + # Defaults for 'advanced' acquisition. Missing values are taken from default + exp_time: 0.0014 # exposure time + range: 0.5 + num_images: 100 - imaging: - osc_range: 1.0 - num_images: 360 - # detector_binning_mode: "0" + imaging: + osc_range: 1.0 + num_images: 360 + # detector_binning_mode: "0" acquisition_limit_values: - number_of_images: - - 1 - - 99999 - kappa: - - -5.0 - - 240.0 + number_of_images: + - 1 + - 99999 + kappa: + - -5.0 + - 240.0 diff --git a/mxcubecore/configuration/esrf_id30a2/gphl-setup.yml b/mxcubecore/configuration/esrf_id30a2/gphl-setup.yml index 1d3489370a..7bf606df4d 100644 --- a/mxcubecore/configuration/esrf_id30a2/gphl-setup.yml +++ b/mxcubecore/configuration/esrf_id30a2/gphl-setup.yml @@ -1,93 +1,91 @@ --- -# yamllint disable rule:comments -# yamllint disable rule:comments-indentation -# yamllint disable rule:line-length - _initialise_class: - class: mxcubecore.HardwareObjects.Gphl.GphlWorkflowConnection.GphlWorkflowConnection + class: mxcubecore.HardwareObjects.Gphl.GphlWorkflowConnection.GphlWorkflowConnection directory_locations: - # Directory locations. Can also be used with ${} syntax in this file - GPHL_INSTALLATION: /users/blissadm/applications/GPhL_WorkFlow_beta-academic_20220601 - # GPHL_WRAPPERS: /data/users/p3l-gleb1/gphl/ + # Directory locations. Can also be used with ${} syntax in this file + GPHL_INSTALLATION: /users/blissadm/applications/GPhL_WorkFlow_beta-academic_20220601 + # GPHL_WRAPPERS: /data/users/p3l-gleb1/gphl/ # If set, run workflow through ssh with selected options # and quote parameters as appropriate # NB The Host option is mandatory # ConfigFile is the ssh configuration file, passed to ssh with the -F option -#ssh_options: -# Host: lonsdale -# IdentityFile: /home/rhfogh/.ssh/wf_test_id -# User: rhfogh -# StrictHostKeyChecking: no -# ConfigFile: /path/to/ssh/config/file - -# Directory used for GPhL workflow persistence data and workflow logs: -# Used to set the wdir workflow option -# If relative designates a subdirectory under Session.get_process_directory() -# If absolute taken as it stands +# ssh_options: +# Host: lonsdale +# IdentityFile: /home/rhfogh/.ssh/wf_test_id +# User: rhfogh +# StrictHostKeyChecking: no +# ConfigFile: /path/to/ssh/config/file + +# Directory used for GPhL workflow persistence data and workflow logs: +# Used to set the wdir workflow option +# If relative designates a subdirectory under Session.get_process_directory() +# If absolute taken as it stands gphl_subdir: GPHL -# root name of persistence layer file; suffix'.xml. is added +# root name of persistence layer file; suffix'.xml. is added gphl_persistname: persistence -#Hosts and ports for py4j java-python gateway, all OPTIONAL -#If not set will use py4j default values, which are as given below -#NB python_host is set automatically to localhost or socket.gethostname() -#NB java_host is not needed as all communication is effectively one-way -#connection_parameters: -# python_port: 25334 -# java_port: 25333 +# Hosts and ports for py4j java-python gateway, all OPTIONAL +# If not set will use py4j default values, which are as given below +# NB python_host is set automatically to localhost or socket.gethostname() +# NB java_host is not needed as all communication is effectively one-way +# connection_parameters: +# python_port: 25334 +# java_port: 25333 -#NB Non-absolute file names are interpreted relative to one of the -#HardwareRepository directories on the lookup path +# NB Non-absolute file names are interpreted relative to one of the +# HardwareRepository directories on the lookup path software_paths: - # Mandatory. Directory with workflow config input, e.g. instrumentation.nml - gphl_beamline_config: gphl/config_esrf_id30a1 + # Mandatory. Directory with workflow config input, e.g. instrumentation.nml + gphl_beamline_config: gphl/config_esrf_id30a1 - # MANDATORY for CCP4 => $GPHL_CCP4_PATH/bin/ccp4.setup-sh, - # unless already sourced in environment - GPHL_CCP4_PATH: /opt/pxsoft/ccp4/v7.1/ubuntu20.04-x86_64/ccp4-7.1/bin + # MANDATORY for CCP4 => $GPHL_CCP4_PATH/bin/ccp4.setup-sh, + # unless already sourced in environment + GPHL_CCP4_PATH: /opt/pxsoft/ccp4/v7.1/ubuntu20.04-x86_64/ccp4-7.1/bin - # MANDATORY for XDS => $GPHL_XDS_PATH/xds_par - # unless already sourced in environment - GPHL_XDS_PATH: /opt/pxsoft/bin + # MANDATORY for XDS => $GPHL_XDS_PATH/xds_par + # unless already sourced in environment + GPHL_XDS_PATH: /opt/pxsoft/bin - GPHL_INSTALLATION: /home/opid30/GPhL_WorkFlow_beta-academic + GPHL_INSTALLATION: /home/opid30/GPhL_WorkFlow_beta-academic - # gphl test samples directory - for collection emulation -# gphl_test_samples: gphl/test_samples + # gphl test samples directory - for collection emulation + # gphl_test_samples: gphl/test_samples - #Location of installation used for processing queue (if not reachable from BCS computer. - #Passed as environmental variable GPHL_PROC_INSTALLATION. Optional -# gphl_wf_processing_installation: /users/pkeller/GPhL-ESRF/exe + # Location of installation used for processing queue + # (if not reachable from BCS computer). + # Passed as environmental variable GPHL_PROC_INSTALLATION. Optional + # gphl_wf_processing_installation: /users/pkeller/GPhL-ESRF/exe # Software paths that are passed to global phasing workflow as java properties # Used to specify locations of alternative executables (wrappers) # More (unused) properties are described in the ASTRA workflow documentation software_properties: - #Location of GPhL .license directory - #defaults to GPHL_INSTALLATION - #Only needed if you do NOT use the gphl installation wrapper scripts in .../exe : - # co.gphl.wf.bdg_licence_dir: "{GPHL_RELEASE}/gphl_release/latest" - - # MANDATORY pending change in workflow - co.gphl.wf.stratcal.bin: "{GPHL_INSTALLATION}/exe/run_stratcal_wrap.py" - - # OPTIONAL location of alternative executables (wrappers) supported by the workflow - # Each has an option (rarely used) to specify a specific license directory --> - # co.gphl.wf.process.bin: {GPHL_WRAPPERS}/scripts/aP_wf_process - # co.gphl.wf.process.bdg_licence_dir/fill/me/in - # co.gphl.wf.diffractcal.bin: {GPHL_WRAPPERS}/scripts/aP_wf_rotcal - # co.gphl.wf.diffractcal.bdg_licence_dir/fill/me/in - # co.gphl.wf.simcal_predict.bin: {GPHL_WRAPPERS}/scripts/simcal_predict - # co.gphl.wf.simcal_predict.bdg_licence_dir/fill/me/in - # co.gphl.wf.transcal.bin: {GPHL_WRAPPERS}/scripts/transcal - # co.gphl.wf.transcal.bdg_licence_dir/fill/me/in - # co.gphl.wf.recen.bin: {GPHL_WRAPPERS}/scripts/recen - # co.gphl.wf.recen.bdg_licence_dir/fill/me/in - - # OPTIONAL. simcal *binary* For Mock collection emulation only. Not used by ASTRA workflow -# co.gphl.wf.simcal.bin: "{GPHL_INSTALLATION}/autoPROC/bin/linux64/simcal" + # Location of GPhL .license directory + # defaults to GPHL_INSTALLATION + # Only needed if you do NOT use the gphl installation wrapper scripts in .../exe : + # co.gphl.wf.bdg_licence_dir: "{GPHL_RELEASE}/gphl_release/latest" + + # MANDATORY pending change in workflow + co.gphl.wf.stratcal.bin: "{GPHL_INSTALLATION}/exe/run_stratcal_wrap.py" + + # OPTIONAL location of alternative executables (wrappers) supported by the workflow + # Each has an option (rarely used) to specify a specific license directory --> + # co.gphl.wf.process.bin: {GPHL_WRAPPERS}/scripts/aP_wf_process + # co.gphl.wf.process.bdg_licence_dir/fill/me/in + # co.gphl.wf.diffractcal.bin: {GPHL_WRAPPERS}/scripts/aP_wf_rotcal + # co.gphl.wf.diffractcal.bdg_licence_dir/fill/me/in + # co.gphl.wf.simcal_predict.bin: {GPHL_WRAPPERS}/scripts/simcal_predict + # co.gphl.wf.simcal_predict.bdg_licence_dir/fill/me/in + # co.gphl.wf.transcal.bin: {GPHL_WRAPPERS}/scripts/transcal + # co.gphl.wf.transcal.bdg_licence_dir/fill/me/in + # co.gphl.wf.recen.bin: {GPHL_WRAPPERS}/scripts/recen + # co.gphl.wf.recen.bdg_licence_dir/fill/me/in + + # OPTIONAL. simcal *binary* For Mock collection emulation only. + # Not used by ASTRA workflow. + # co.gphl.wf.simcal.bin: "{GPHL_INSTALLATION}/autoPROC/bin/linux64/simcal" diff --git a/mxcubecore/configuration/lnls_manaca/beamline_config.yml b/mxcubecore/configuration/lnls_manaca/beamline_config.yml index e3bfc50ab5..8bafb3c7b1 100644 --- a/mxcubecore/configuration/lnls_manaca/beamline_config.yml +++ b/mxcubecore/configuration/lnls_manaca/beamline_config.yml @@ -2,9 +2,9 @@ # The class to initialise, and init parameters _initialise_class: - class: mxcubecore.HardwareObjects.Beamline.Beamline - # Further key-value pairs here will be passed to the class init -# mode: devel + class: mxcubecore.HardwareObjects.Beamline.Beamline + # Further key-value pairs here will be passed to the class init + # mode: devel # objects # @@ -15,58 +15,58 @@ _initialise_class: # would need those added (e.g. the centring methods) # _objects: - # The !!o0map and the lines starting with '- ' give you an *orderd* dictionary - # And thus a reproducible loading order - !!omap - # The values are the file paths to the configuration file for the - # object, relative to the configuration file path(s) - # - # NB - the order is *NOT* arbitrary, as signal connnections are set - # on one object that require the other to be already loaded. - # - # Hardware: - - session: session.xml - - machine_info: machine_info.xml - - detector: detector.xml - - beam: beam_info.xml - - energy: energy.xml - - transmission: transmission.xml - - flux: flux.xml - - resolution: resolution.xml - - safety_shutter: safety_shutter.xml - - fast_shutter: fast_shutter.xml - - hutch_interlock: hutchtrigger.xml - - sample_changer: sc.xml - - sample_changer_maintenance: sc_maint.xml - - plate_manipulator: plate_manipulator.xml - - diffractometer: minidiff.xml - - lims: lims.xml - - sample_view: sample_view.xml - - queue_manager: queue.xml - - queue_model: queue_model.xml + # The !!o0map and the lines starting with '- ' give you an *orderd* dictionary + # And thus a reproducible loading order + !!omap + # The values are the file paths to the configuration file for the + # object, relative to the configuration file path(s) + # + # NB - the order is *NOT* arbitrary, as signal connnections are set + # on one object that require the other to be already loaded. + # + # Hardware: + - session: session.xml + - machine_info: machine_info.xml + - detector: detector.xml + - beam: beam_info.xml + - energy: energy.xml + - transmission: transmission.xml + - flux: flux.xml + - resolution: resolution.xml + - safety_shutter: safety_shutter.xml + - fast_shutter: fast_shutter.xml + - hutch_interlock: hutchtrigger.xml + - sample_changer: sc.xml + - sample_changer_maintenance: sc_maint.xml + - plate_manipulator: plate_manipulator.xml + - diffractometer: minidiff.xml + - lims: lims.xml + - sample_view: sample_view.xml + - queue_manager: queue.xml + - queue_model: queue_model.xml - # Procedures: - - xml_rpc_server: xml_rpc_server.xml - - workflow: ednaparams.xml - - collect: mxcollect.xml - - xrf_spectrum: xrf.xml - - energy_scan: energyscan.xml - # - gphl_workflow: gphl-workflow.xml - # - gphl_connection: gphl-setup.xml - # - centring: centring.xml - # Analysis: - - offline_processing: auto_processing.xml - - online_processing: parallel_processing.xml - - characterisation: characterisation.xml - - data_publisher: data_publisher.xml - - scan_mockup: scan_mockup.xml + # Procedures: + - xml_rpc_server: xml_rpc_server.xml + - workflow: ednaparams.xml + - collect: mxcollect.xml + - xrf_spectrum: xrf.xml + - energy_scan: energyscan.xml + # - gphl_workflow: gphl-workflow.xml + # - gphl_connection: gphl-setup.xml + # - centring: centring.xml + # Analysis: + - offline_processing: auto_processing.xml + - online_processing: parallel_processing.xml + - characterisation: characterisation.xml + - data_publisher: data_publisher.xml + - scan_mockup: scan_mockup.xml - # - beam_realign: # Skipped - optional + # - beam_realign: # Skipped - optional # Non-object attributes: advanced_methods: - - MeshScan - - XrayCentering + - MeshScan + - XrayCentering tunable_wavelength: true disable_num_passes: true @@ -75,68 +75,68 @@ run_number: 1 click_centring_num_clicks: 3 default_acquisition_parameters: - default: - # Default values, also used for standard acquisition. - # Values not given in other dictionaries are taken from here - exp_time: 0.02 # exposure time - osc_start: 0.0 # Only used if no current angle can be found - osc_range: 0.1 - num_passes: 1 - first_image: 1 - overlap: 0 - num_images: 1 - detector_mode: 1 # Remove as not in practice used ? - inverse_beam: false - take_dark_current: true - skip_existing_images: true - take_snapshots: true - # NB 'compression' not added as apparently never used + default: + # Default values, also used for standard acquisition. + # Values not given in other dictionaries are taken from here + exp_time: 0.02 # exposure time + osc_start: 0.0 # Only used if no current angle can be found + osc_range: 0.1 + num_passes: 1 + first_image: 1 + overlap: 0 + num_images: 1 + detector_mode: 1 # Remove as not in practice used ? + inverse_beam: false + take_dark_current: true + skip_existing_images: true + take_snapshots: true + # NB 'compression' not added as apparently never used - helical: - # Defaults for helical scan. Missing values are taken from default - number_of_images: 100 + helical: + # Defaults for helical scan. Missing values are taken from default + number_of_images: 100 - characterisation: - # Defaults for chareacterisation. Missing values are taken from default - exp_time: 0.05 # exposure time - osc_range: 1 - overlap: -89 - num_images: 4 + characterisation: + # Defaults for chareacterisation. Missing values are taken from default + exp_time: 0.05 # exposure time + osc_range: 1 + overlap: -89 + num_images: 4 - mesh: - # Defaults for 'advanced' acquisition. Missing values are taken from default - exp_time: 10 # exposure time - range: 10 - num_images: 100 - cell_counting: zig-zag - cell_spacing: vertical, horizontal - mesh_center: top-left + mesh: + # Defaults for 'advanced' acquisition. Missing values are taken from default + exp_time: 10 # exposure time + range: 10 + num_images: 100 + cell_counting: zig-zag + cell_spacing: vertical, horizontal + mesh_center: top-left acquisition_limit_values: - exposure_time: - - 0.02 - - 1000 - osc_range: - - -10000 - - 10000 - number_of_images: - - 1 - - 99999 - kappa: - - -5.0 - - 240.0 + exposure_time: + - 0.02 + - 1000 + osc_range: + - -10000 + - 10000 + number_of_images: + - 1 + - 99999 + kappa: + - -5.0 + - 240.0 available_methods: - datacollection: True # yamllint disable-line rule:truthy - characterisation: True # yamllint disable-line rule:truthy - helical: True # yamllint disable-line rule:truthy - xrf_scan: True # yamllint disable-line rule:truthy - energy_scan: True # yamllint disable-line rule:truthy - mesh_scan: fals + datacollection: True # yamllint disable-line rule:truthy + characterisation: True # yamllint disable-line rule:truthy + helical: True # yamllint disable-line rule:truthy + xrf_scan: True # yamllint disable-line rule:truthy + energy_scan: True # yamllint disable-line rule:truthy + mesh_scan: fals undulators: - - type: PPU35C_GAP - device_uri: //orion:10000/id/id/30 + - type: PPU35C_GAP + device_uri: //orion:10000/id/id/30 - - type: PPU35D_GAP - device_uri: //orion:10000/id/id/30 + - type: PPU35D_GAP + device_uri: //orion:10000/id/id/30 diff --git a/mxcubecore/configuration/lnls_sol/beamline_config.yml b/mxcubecore/configuration/lnls_sol/beamline_config.yml index 425bc3f989..3b0e0734b7 100644 --- a/mxcubecore/configuration/lnls_sol/beamline_config.yml +++ b/mxcubecore/configuration/lnls_sol/beamline_config.yml @@ -1,12 +1,10 @@ --- -# yamllint disable rule:comments-indentation - # The class to initialise, and init parameters _initialise_class: - class: mxcubecore.HardwareObjects.Beamline.Beamline - # Further key-value pairs here will be passed to the class init -# mode: devel + class: mxcubecore.HardwareObjects.Beamline.Beamline + # Further key-value pairs here will be passed to the class init + # mode: devel # objects # @@ -17,58 +15,58 @@ _initialise_class: # would need those added (e.g. the centring methods) # _objects: - # The !!o0map and the lines starting with '- ' give you an *orderd* dictionary - # And thus a reproducible loading order - !!omap - # The values are the file paths to the configuration file for the - # object, relative to the configuration file path(s) - # - # NB - the order is *NOT* arbitrary, as signal connnections are set - # on one object that require the other to be already loaded. - # - # Hardware: - - session: session.xml - - machine_info: machine_info.xml - - detector: detector.xml - - beam: beam_info.xml - - transmission: transmission.xml - - flux: flux.xml - - energy: energy.xml - - resolution: resolution.xml - - safety_shutter: safety_shutter.xml - - fast_shutter: fast_shutter.xml - - hutch_interlock: hutchtrigger.xml - - sample_changer: sc.xml - - sample_changer_maintenance: sc_maint.xml - - plate_manipulator: plate_manipulator.xml - - diffractometer: minidiff.xml - - lims: lims.xml - - sample_view: sample_view.xml - - queue_manager: queue.xml - - queue_model: queue_model.xml + # The !!o0map and the lines starting with '- ' give you an *orderd* dictionary + # And thus a reproducible loading order + !!omap + # The values are the file paths to the configuration file for the + # object, relative to the configuration file path(s) + # + # NB - the order is *NOT* arbitrary, as signal connnections are set + # on one object that require the other to be already loaded. + # + # Hardware: + - session: session.xml + - machine_info: machine_info.xml + - detector: detector.xml + - beam: beam_info.xml + - transmission: transmission.xml + - flux: flux.xml + - energy: energy.xml + - resolution: resolution.xml + - safety_shutter: safety_shutter.xml + - fast_shutter: fast_shutter.xml + - hutch_interlock: hutchtrigger.xml + - sample_changer: sc.xml + - sample_changer_maintenance: sc_maint.xml + - plate_manipulator: plate_manipulator.xml + - diffractometer: minidiff.xml + - lims: lims.xml + - sample_view: sample_view.xml + - queue_manager: queue.xml + - queue_model: queue_model.xml - # Procedures: - - xml_rpc_server: xml_rpc_server.xml - - workflow: ednaparams.xml - - collect: mxcollect.xml - - xrf_spectrum: xrf.xml - - energy_scan: energyscan.xml -# - gphl_workflow: gphl-workflow.xml -# - gphl_connection: gphl-setup.xml -# - centring: centring.xml - # Analysis: - - offline_processing: auto_processing.xml - - online_processing: parallel_processing.xml - - characterisation: characterisation.xml - - data_publisher: data_publisher.xml - - scan_mockup: scan_mockup.xml + # Procedures: + - xml_rpc_server: xml_rpc_server.xml + - workflow: ednaparams.xml + - collect: mxcollect.xml + - xrf_spectrum: xrf.xml + - energy_scan: energyscan.xml + # - gphl_workflow: gphl-workflow.xml + # - gphl_connection: gphl-setup.xml + # - centring: centring.xml + # Analysis: + - offline_processing: auto_processing.xml + - online_processing: parallel_processing.xml + - characterisation: characterisation.xml + - data_publisher: data_publisher.xml + - scan_mockup: scan_mockup.xml - # - beam_realign: # Skipped - optional + # - beam_realign: # Skipped - optional # Non-object attributes: advanced_methods: - - MeshScan - - XrayCentering + - MeshScan + - XrayCentering tunable_wavelength: true disable_num_passes: true @@ -77,68 +75,68 @@ run_number: 1 click_centring_num_clicks: 3 default_acquisition_parameters: - default: - # Default values, also used for standard acquisition. - # Values not given in other dictionaries are taken from here - exp_time: 0.02 # exposure time - osc_start: 0.0 # Only used if no current angle can be found - osc_range: 0.1 - num_passes: 1 - first_image: 1 - overlap: 0 - num_images: 1 - detector_mode: 1 # Remove as not in practice used ? - inverse_beam: false - take_dark_current: true - skip_existing_images: true - take_snapshots: true - # NB 'compression' not added as apparently never used + default: + # Default values, also used for standard acquisition. + # Values not given in other dictionaries are taken from here + exp_time: 0.02 # exposure time + osc_start: 0.0 # Only used if no current angle can be found + osc_range: 0.1 + num_passes: 1 + first_image: 1 + overlap: 0 + num_images: 1 + detector_mode: 1 # Remove as not in practice used ? + inverse_beam: false + take_dark_current: true + skip_existing_images: true + take_snapshots: true + # NB 'compression' not added as apparently never used - helical: - # Defaults for helical scan. Missing values are taken from default - number_of_images: 100 + helical: + # Defaults for helical scan. Missing values are taken from default + number_of_images: 100 - characterisation: - # Defaults for chareacterisation. Missing values are taken from default - exp_time: 0.05 # exposure time - osc_range: 1 - overlap: -89 - num_images: 4 + characterisation: + # Defaults for chareacterisation. Missing values are taken from default + exp_time: 0.05 # exposure time + osc_range: 1 + overlap: -89 + num_images: 4 - mesh: - # Defaults for 'advanced' acquisition. Missing values are taken from default - exp_time: 10 # exposure time - range: 10 - num_images: 100 - cell_counting: zig-zag - cell_spacing: vertical, horizontal - mesh_center: top-left + mesh: + # Defaults for 'advanced' acquisition. Missing values are taken from default + exp_time: 10 # exposure time + range: 10 + num_images: 100 + cell_counting: zig-zag + cell_spacing: vertical, horizontal + mesh_center: top-left acquisition_limit_values: - exposure_time: - - 0.02 - - 1000 - osc_range: - - -10000 - - 10000 - number_of_images: - - 1 - - 99999 - kappa: - - -5.0 - - 240.0 + exposure_time: + - 0.02 + - 1000 + osc_range: + - -10000 + - 10000 + number_of_images: + - 1 + - 99999 + kappa: + - -5.0 + - 240.0 available_methods: - datacollection: True # yamllint disable-line rule:truthy - characterisation: True # yamllint disable-line rule:truthy - helical: True # yamllint disable-line rule:truthy - xrf_scan: True # yamllint disable-line rule:truthy - energy_scan: True # yamllint disable-line rule:truthy - mesh_scan: fals + datacollection: True # yamllint disable-line rule:truthy + characterisation: True # yamllint disable-line rule:truthy + helical: True # yamllint disable-line rule:truthy + xrf_scan: True # yamllint disable-line rule:truthy + energy_scan: True # yamllint disable-line rule:truthy + mesh_scan: fals undulators: - - type: PPU35C_GAP - device_uri: //orion:10000/id/id/30 + - type: PPU35C_GAP + device_uri: //orion:10000/id/id/30 - - type: PPU35D_GAP - device_uri: //orion:10000/id/id/30 + - type: PPU35D_GAP + device_uri: //orion:10000/id/id/30 diff --git a/mxcubecore/configuration/mockup/gphl/gphl-setup.yml b/mxcubecore/configuration/mockup/gphl/gphl-setup.yml index 99c742cebb..2cf291bf8f 100644 --- a/mxcubecore/configuration/mockup/gphl/gphl-setup.yml +++ b/mxcubecore/configuration/mockup/gphl/gphl-setup.yml @@ -1,95 +1,94 @@ --- -# yamllint disable rule:comments # yamllint disable rule:line-length _initialise_class: - class: mxcubecore.HardwareObjects.Gphl.GphlWorkflowConnection.GphlWorkflowConnection + class: mxcubecore.HardwareObjects.Gphl.GphlWorkflowConnection.GphlWorkflowConnection directory_locations: - # Directory locations. Can also be used with ${} syntax in this file - GPHL_INSTALLATION: /alt/rhfogh/Software/GPhL/gphl_release - # GPHL_INSTALLATION: /alt/rhfogh/Software/GPhL/nightly_20230823/Files_workflow_TRUNK_alpha-bdg - # GPHL_INSTALLATION: /alt/rhfogh/Software/GPhL/nightly_20230602/Files_workflow_BETA_beta-academic + # Directory locations. Can also be used with ${} syntax in this file + GPHL_INSTALLATION: /alt/rhfogh/Software/GPhL/gphl_release + # GPHL_INSTALLATION: /alt/rhfogh/Software/GPhL/nightly_20230823/Files_workflow_TRUNK_alpha-bdg + # GPHL_INSTALLATION: /alt/rhfogh/Software/GPhL/nightly_20230602/Files_workflow_BETA_beta-academic # If set, run workflow through ssh with selected options # and quote parameters as appropriate # NB The Host option is mandatory # ConfigFile is the ssh configuration file, passed to ssh with the -F option -#ssh_options: -# Host: lonsdale -# IdentityFile: /home/rhfogh/.ssh/wf_test_id -# User: rhfogh -# StrictHostKeyChecking: no -# ConfigFile: /path/to/ssh/config/file - -# Directory used for GPhL workflow persistence data and workflow logs: -# Used to set the wdir workflow option -# If relative designates a subdirectory under Session.get_process_directory() -# If absolute taken as it stands +# ssh_options: +# Host: lonsdale +# IdentityFile: /home/rhfogh/.ssh/wf_test_id +# User: rhfogh +# StrictHostKeyChecking: no +# ConfigFile: /path/to/ssh/config/file + +# Directory used for GPhL workflow persistence data and workflow logs: +# Used to set the wdir workflow option +# If relative designates a subdirectory under Session.get_process_directory() +# If absolute taken as it stands gphl_subdir: GPHL -# root name of persistence layer file; suffix'.xml. is added +# root name of persistence layer file; suffix'.xml. is added gphl_persistname: persistence -#Hosts and ports for py4j java-python gateway, all OPTIONAL -#If not set will use py4j default values, which are as given below -#NB python_host is set automatically to localhost or socket.gethostname() -#NB java_host is not needed as all communication is effectively one-way -#connection_parameters: -# python_port: 25334 -# java_port: 25333 +# Hosts and ports for py4j java-python gateway, all OPTIONAL +# If not set will use py4j default values, which are as given below +# NB python_host is set automatically to localhost or socket.gethostname() +# NB java_host is not needed as all communication is effectively one-way +# connection_parameters: +# python_port: 25334 +# java_port: 25333 -#NB Non-absolute file names are interpreted relative to one of the -#HardwareRepository directories on the lookup path +# NB Non-absolute file names are interpreted relative to one of the +# HardwareRepository directories on the lookup path software_paths: - # Mandatory. Directory with workflow config input, e.g. instrumentation.nml - gphl_beamline_config: gphl_beamline_config + # Mandatory. Directory with workflow config input, e.g. instrumentation.nml + gphl_beamline_config: gphl_beamline_config - # MANDATORY for CCP4 => $GPHL_CCP4_PATH/bin/ccp4.setup-sh, - # unless already sourced in environment - GPHL_CCP4_PATH: /alt/rhfogh/Software/CCP4/latest/bin/ + # MANDATORY for CCP4 => $GPHL_CCP4_PATH/bin/ccp4.setup-sh, + # unless already sourced in environment + GPHL_CCP4_PATH: /alt/rhfogh/Software/CCP4/latest/bin/ - # MANDATORY for XDS => $GPHL_XDS_PATH/xds_par - # unless already sourced in environment - GPHL_XDS_PATH: /alt/rhfogh/Software/XDS/latest/ + # MANDATORY for XDS => $GPHL_XDS_PATH/xds_par + # unless already sourced in environment + GPHL_XDS_PATH: /alt/rhfogh/Software/XDS/latest/ - # gphl test samples directory - for collection emulation - gphl_test_samples: gphl/test_samples + # gphl test samples directory - for collection emulation + gphl_test_samples: gphl/test_samples - #Location of installation used for processing queue (if not reachable from BCS computer. - #Passed as environmental variable GPHL_PROC_INSTALLATION. Optional -# gphl_wf_processing_installation: /users/pkeller/GPhL-ESRF/exe + # Location of installation used for processing queue (if not reachable from BCS computer. + # Passed as environmental variable GPHL_PROC_INSTALLATION. Optional + # gphl_wf_processing_installation: /users/pkeller/GPhL-ESRF/exe # Software paths that are passed to global phasing workflow as java properties # Used to specify locations of alternative executables (wrappers) # More (unused) properties are described in the ASTRA workflow documentation software_properties: - #Location of GPhL .license directory - #defaults to GPHL_INSTALLATION - #Only needed if you do NOT use the gphl installation wrapper scripts in .../exe : - # co.gphl.wf.bdg_licence_dir: "{GPHL_RELEASE}/gphl_release/latest" - - # MANDATORY pending change in workflow - co.gphl.wf.stratcal.bin: "{GPHL_INSTALLATION}/exe/run_stratcal_wrap.py" - - # OPTIONAL location of alternative executables (wrappers) supported by the workflow - # Each has an option (rarely used) to specify a specific license directory --> - # co.gphl.wf.process.bin: {GPHL_WRAPPERS}/scripts/aP_wf_process - # co.gphl.wf.process.bdg_licence_dir/fill/me/in - # co.gphl.wf.diffractcal.bin: {GPHL_WRAPPERS}/scripts/aP_wf_rotcal - # co.gphl.wf.diffractcal.bdg_licence_dir/fill/me/in - # co.gphl.wf.simcal_predict.bin: {GPHL_WRAPPERS}/scripts/simcal_predict - # co.gphl.wf.simcal_predict.bdg_licence_dir/fill/me/in - # co.gphl.wf.transcal.bin: {GPHL_WRAPPERS}/scripts/transcal - # co.gphl.wf.transcal.bdg_licence_dir/fill/me/in - # co.gphl.wf.recen.bin: {GPHL_WRAPPERS}/scripts/recen - # co.gphl.wf.recen.bdg_licence_dir/fill/me/in - - # OPTIONAL. simcal *binary* For Mock collection emulation only. Not used by ASTRA workflow - co.gphl.wf.simcal.bin: /alt/rhfogh/Software/GPhL/nightly_20240311/Files_workflow_TRUNK_alpha-bdg/autoPROC/bin/linux64/simcal - co.gphl.wf.simcal.bdg_licence_dir: /alt/rhfogh/Software/GPhL/nightly_20240311/Files_workflow_TRUNK_alpha-bdg -# co.gphl.wf.simcal.bin: /alt/rhfogh/Software/GPhL/gphl_release/autoPROC/bin/linux64/simcal -# co.gphl.wf.simcal.bdg_licence_dir: /alt/rhfogh/Software/GPhL/gphl_release -# co.gphl.wf.simcal.bin: "{GPHL_INSTALLATION}/autoPROC/bin/linux64/simcal"/alt/rhfogh/Software/GPhL/gphl_release + # Location of GPhL .license directory + # defaults to GPHL_INSTALLATION + # Only needed if you do NOT use the gphl installation wrapper scripts in .../exe : + # co.gphl.wf.bdg_licence_dir: "{GPHL_RELEASE}/gphl_release/latest" + + # MANDATORY pending change in workflow + co.gphl.wf.stratcal.bin: "{GPHL_INSTALLATION}/exe/run_stratcal_wrap.py" + + # OPTIONAL location of alternative executables (wrappers) supported by the workflow + # Each has an option (rarely used) to specify a specific license directory --> + # co.gphl.wf.process.bin: {GPHL_WRAPPERS}/scripts/aP_wf_process + # co.gphl.wf.process.bdg_licence_dir/fill/me/in + # co.gphl.wf.diffractcal.bin: {GPHL_WRAPPERS}/scripts/aP_wf_rotcal + # co.gphl.wf.diffractcal.bdg_licence_dir/fill/me/in + # co.gphl.wf.simcal_predict.bin: {GPHL_WRAPPERS}/scripts/simcal_predict + # co.gphl.wf.simcal_predict.bdg_licence_dir/fill/me/in + # co.gphl.wf.transcal.bin: {GPHL_WRAPPERS}/scripts/transcal + # co.gphl.wf.transcal.bdg_licence_dir/fill/me/in + # co.gphl.wf.recen.bin: {GPHL_WRAPPERS}/scripts/recen + # co.gphl.wf.recen.bdg_licence_dir/fill/me/in + + # OPTIONAL. simcal *binary* For Mock collection emulation only. Not used by ASTRA workflow + co.gphl.wf.simcal.bin: /alt/rhfogh/Software/GPhL/nightly_20240311/Files_workflow_TRUNK_alpha-bdg/autoPROC/bin/linux64/simcal + co.gphl.wf.simcal.bdg_licence_dir: /alt/rhfogh/Software/GPhL/nightly_20240311/Files_workflow_TRUNK_alpha-bdg + # co.gphl.wf.simcal.bin: /alt/rhfogh/Software/GPhL/gphl_release/autoPROC/bin/linux64/simcal + # co.gphl.wf.simcal.bdg_licence_dir: /alt/rhfogh/Software/GPhL/gphl_release + # co.gphl.wf.simcal.bin: "{GPHL_INSTALLATION}/autoPROC/bin/linux64/simcal"/alt/rhfogh/Software/GPhL/gphl_release diff --git a/mxcubecore/configuration/mockup/procedure-mockup.yml b/mxcubecore/configuration/mockup/procedure-mockup.yml index 0ce7fdd407..42025fe712 100644 --- a/mxcubecore/configuration/mockup/procedure-mockup.yml +++ b/mxcubecore/configuration/mockup/procedure-mockup.yml @@ -2,4 +2,4 @@ # The class to initialise, and init parameters _initialise_class: - class: mxcubecore.HardwareObjects.mockup.ProcedureMockup.ProcedureMockup + class: mxcubecore.HardwareObjects.mockup.ProcedureMockup.ProcedureMockup diff --git a/mxcubecore/configuration/mockup/qt/beamline_config.yml b/mxcubecore/configuration/mockup/qt/beamline_config.yml index 940f589432..cfd9a5cfe0 100644 --- a/mxcubecore/configuration/mockup/qt/beamline_config.yml +++ b/mxcubecore/configuration/mockup/qt/beamline_config.yml @@ -1,13 +1,10 @@ --- -# yamllint disable rule:comments-indentation -# yamllint disable rule:indentation - # The class to initialise, and init parameters _initialise_class: - class: mxcubecore.HardwareObjects.Beamline.Beamline - # Further key-value pairs here will be passed to the class init -# mode: devel + class: mxcubecore.HardwareObjects.Beamline.Beamline + # Further key-value pairs here will be passed to the class init + # mode: devel # objects # @@ -18,108 +15,110 @@ _initialise_class: # would need those added (e.g. the centring methods) # _objects: - # The !!o0map and the lines starting with '- ' give you an *ordered* dictionary - # And thus a reproducible loading order - !!omap - # The values are the file paths to the configuration file for the - # object, relative to the configuration file path(s) - # - # NB - the order is *NOT* arbitrary, as signal connnections are set - # on one object that require the other to be already loaded. - # - # Hardware: - - session: session.xml - - machine_info: mach-info-mockup.xml - - transmission: transmission-mockup.xml - - energy: energy-mockup.xml - - beam: beam-mockup.xml - - flux: flux-mockup.xml - - detector: detector-mockup.xml - - resolution: resolution-mockup.xml - - hutch_interlock: door-interlock-mockup.xml - - safety_shutter: safety-shutter-mockup.xml - - fast_shutter: fast-shutter-mockup.xml - - sample_changer: sample-changer-mockup.xml - # NBNB TODO remove plate_manipulater and treat as another sample changer - - plate_manipulator: plate-manipulator-mockup.xml - - diffractometer: diffractometer-mockup.xml - - sample_view: sample-view.xml - - lims: lims-client-mockup.xml - - queue_manager: queue.xml - - queue_model: queue-model.xml - # Procedures: - - collect: collect-mockup.xml - - xrf_spectrum: xrf-spectrum-mockup.xml - - energy_scan: energyscan-mockup.xml -# - imaging: xray-imaging.xml # Only in EMBL as of 201907 - - gphl_connection: gphl-setup.yml - - gphl_workflow: gphl-workflow.yml - - xray_centring: xray_centring2.yml - # - centring: centring.xml - # Analysis: - - offline_processing: offline-processing-mockup.xml - - online_processing: online-processing-mockup.xml - - characterisation: characterisation-mockup.xml - # - beam_realign: # Skipped - optional + # The !!o0map and the lines starting with '- ' give you an *ordered* dictionary + # And thus a reproducible loading order + !!omap + # The values are the file paths to the configuration file for the + # object, relative to the configuration file path(s) + # + # NB - the order is *NOT* arbitrary, as signal connnections are set + # on one object that require the other to be already loaded. + # + # Hardware: + - session: session.xml + - machine_info: mach-info-mockup.xml + - transmission: transmission-mockup.xml + - energy: energy-mockup.xml + - beam: beam-mockup.xml + - flux: flux-mockup.xml + - detector: detector-mockup.xml + - resolution: resolution-mockup.xml + - hutch_interlock: door-interlock-mockup.xml + - safety_shutter: safety-shutter-mockup.xml + - fast_shutter: fast-shutter-mockup.xml + - sample_changer: sample-changer-mockup.xml + # NBNB TODO remove plate_manipulater and treat as another sample changer + - plate_manipulator: plate-manipulator-mockup.xml + - diffractometer: diffractometer-mockup.xml + - sample_view: sample-view.xml + - lims: lims-client-mockup.xml + - queue_manager: queue.xml + - queue_model: queue-model.xml + # Procedures: + - collect: collect-mockup.xml + - xrf_spectrum: xrf-spectrum-mockup.xml + - energy_scan: energyscan-mockup.xml + # - imaging: xray-imaging.xml # Only in EMBL as of 201907 + - gphl_connection: gphl-setup.yml + - gphl_workflow: gphl-workflow.yml + - xray_centring: xray_centring2.yml + # - centring: centring.xml + # Analysis: + - offline_processing: offline-processing-mockup.xml + - online_processing: online-processing-mockup.xml + - characterisation: characterisation-mockup.xml + # - beam_realign: # Skipped - optional + # Non-object attributes: advanced_methods: - MeshScan - XrayCentering + tunable_wavelength: true disable_num_passes: false run_online_processing: false run_number: 1 default_acquisition_parameters: - default: - # Default values, also used for standard acquisition. - # Values not given in other dictionaries are taken from here - exp_time: 0.04 # (s) exposure time - osc_start: 0.0 # (degrees) Only used if no current angle found - osc_range: 0.1 # (degrees) - num_passes: 1 # (int) - first_image: 1 # (int) - overlap: 0 - num_images: 1 # (int) - # detector_binning_mode: 1 # Removed as not in practice used. - inverse_beam: false # (bool) - take_dark_current: true # (bool) - skip_existing_images: true # (bool) - take_snapshots: true # (bool) + default: + # Default values, also used for standard acquisition. + # Values not given in other dictionaries are taken from here + exp_time: 0.04 # (s) exposure time + osc_start: 0.0 # (degrees) Only used if no current angle found + osc_range: 0.1 # (degrees) + num_passes: 1 # (int) + first_image: 1 # (int) + overlap: 0 + num_images: 1 # (int) + # detector_binning_mode: 1 # Removed as not in practice used. + inverse_beam: false # (bool) + take_dark_current: true # (bool) + skip_existing_images: true # (bool) + take_snapshots: true # (bool) - helical: - # Defaults for helical scan. Missing values are taken from default - num_images: 100 + helical: + # Defaults for helical scan. Missing values are taken from default + num_images: 100 - characterisation: - # Defaults for chareacterisation. Missing values are taken from default - osc_range: 1 - opt_sad: False # yamllint disable-line rule:truthy - account_rad_damage: True # yamllint disable-line rule:truthy - strategy_complexity: 0 - max_crystal_vdim: 1.0 - min_crystal_vdim: 1.0 - max_crystal_vphi: 1.0 - min_crystal_vphi: 1.0 + characterisation: + # Defaults for chareacterisation. Missing values are taken from default + osc_range: 1 + opt_sad: False # yamllint disable-line rule:truthy + account_rad_damage: True # yamllint disable-line rule:truthy + strategy_complexity: 0 + max_crystal_vdim: 1.0 + min_crystal_vdim: 1.0 + max_crystal_vphi: 1.0 + min_crystal_vphi: 1.0 - advanced: - # Defaults for 'advanced' acquisition. Missing values are taken from default - osc_range: 0.5 - num_images: 100 + advanced: + # Defaults for 'advanced' acquisition. Missing values are taken from default + osc_range: 0.5 + num_images: 100 acquisition_limit_values: - exposure_time: # (s) - - 0.04 - - 6000.0 - osc_range: # (degrees) - - -1000.0 - - 10000.0 - number_of_images: # (int) - - 1 - - 99999 - kappa: # (degrees) - - 0.0 - - 180.0 -# kappa_phi: # (degrees) -# - 0.0 -# - 360.0 + exposure_time: # (s) + - 0.04 + - 6000.0 + osc_range: # (degrees) + - -1000.0 + - 10000.0 + number_of_images: # (int) + - 1 + - 99999 + kappa: # (degrees) + - 0.0 + - 180.0 +# kappa_phi: # (degrees) +# - 0.0 +# - 360.0 diff --git a/mxcubecore/configuration/mockup/test/beamline_config.yml b/mxcubecore/configuration/mockup/test/beamline_config.yml index f1aa7dfd08..1b7182260b 100644 --- a/mxcubecore/configuration/mockup/test/beamline_config.yml +++ b/mxcubecore/configuration/mockup/test/beamline_config.yml @@ -1,13 +1,10 @@ --- -# yamllint disable rule:comments -# yamllint disable rule:comments-indentation - # The class to initialise, and init parameters _initialise_class: - class: mxcubecore.HardwareObjects.Beamline.Beamline - # Further key-value pairs here will be passed to the class init -# mode: devel + class: mxcubecore.HardwareObjects.Beamline.Beamline + # Further key-value pairs here will be passed to the class init + # mode: devel # objects # @@ -18,101 +15,103 @@ _initialise_class: # would need those added (e.g. the centring methods) # _objects: - # The !!o0map and the lines starting with '- ' give you an *ordered* dictionary - # And thus a reproducible loading order - !!omap - # The values are the file paths to the configuration file for the - # object, relative to the configuration file path(s) - # - # NB - the order is *NOT* arbitrary, as signal connnections are set - # on one object that require the other to be already loaded. - # - # Hardware: - - session: session.xml - - machine_info: mach-info-mockup.xml - - transmission: transmission-mockup.xml - - energy: energy-mockup.xml - - beam: beam-mockup.xml - - flux: flux-mockup.xml - - detector: detector-mockup.xml - - resolution: resolution-mockup.xml - #- hutch_interlock: door-interlock-mockup.xml - - safety_shutter: safety-shutter-mockup.xml - #- fast_shutter: shutter-mockup.xml - - sample_changer: sample-changer-mockup.xml - # NBNB TODO remove plate_manipulater and treat as another smaple changer - #- plate_manipulator: plate-manipulator.xml - - diffractometer: diffractometer-mockup.xml - - sample_view: sample-view-mockup.xml - - lims: lims-client-mockup.xml - #- queue_manager: queue.xml - #- queue_model: queue-model.xml - # Procedures: - #- collect: mxcollect.xml - - xrf_spectrum: xrf-spectrum-mockup.xml - #- energy_scan: energyscan-mockup.xml -# - imaging: xray-imaging.xml # Only in EMBL as of 201907 - #- gphl_workflow: gphl-workflow.xml - #- gphl_connection: gphl-setup.xml - # - centring: centring.xml - # Analysis: - #- offline_processing: auto-processing-mockup.xml - #- online_processing: parallel-processing.xml - #- characterisation: data-analysis.xml - # - beam_realign: # Skipped - optional - - mock_procedure: procedure-mockup.yml + # The !!o0map and the lines starting with '- ' give you an *ordered* dictionary + # And thus a reproducible loading order + !!omap + # The values are the file paths to the configuration file for the + # object, relative to the configuration file path(s) + # + # NB - the order is *NOT* arbitrary, as signal connnections are set + # on one object that require the other to be already loaded. + # + # Hardware: + - session: session.xml + - machine_info: mach-info-mockup.xml + - transmission: transmission-mockup.xml + - energy: energy-mockup.xml + - beam: beam-mockup.xml + - flux: flux-mockup.xml + - detector: detector-mockup.xml + - resolution: resolution-mockup.xml + # - hutch_interlock: door-interlock-mockup.xml + - safety_shutter: safety-shutter-mockup.xml + # - fast_shutter: shutter-mockup.xml + - sample_changer: sample-changer-mockup.xml + # NBNB TODO remove plate_manipulater and treat as another smaple changer + # - plate_manipulator: plate-manipulator.xml + - diffractometer: diffractometer-mockup.xml + - sample_view: sample-view-mockup.xml + - lims: lims-client-mockup.xml + # - queue_manager: queue.xml + # - queue_model: queue-model.xml + # Procedures: + # - collect: mxcollect.xml + - xrf_spectrum: xrf-spectrum-mockup.xml + # - energy_scan: energyscan-mockup.xml + # - imaging: xray-imaging.xml # Only in EMBL as of 201907 + # - gphl_workflow: gphl-workflow.xml + # - gphl_connection: gphl-setup.xml + # - centring: centring.xml + # Analysis: + # - offline_processing: auto-processing-mockup.xml + # - online_processing: parallel-processing.xml + # - characterisation: data-analysis.xml + # - beam_realign: # Skipped - optional + - mock_procedure: procedure-mockup.yml + # Non-object attributes: advanced_methods: - - MeshScan - - XrayCentering + - MeshScan + - XrayCentering + tunable_wavelength: true disable_num_passes: false run_online_processing: false run_number: 1 default_acquisition_parameters: - default: - # Default values, also used for standard acquisition. - # Values not given in other dictionaries are taken from here - exp_time: 0.04 # (s) exposure time - osc_start: 0.0 # (degrees) Only used if no current angle found - osc_range: 0.1 # (degrees) - num_passes: 1 # (int) - first_image: 1 # (int) - overlap: 0 - num_images: 1 # (int) - # detector_binning_mode: 1 # Removed as not in practice used. - inverse_beam: false # (bool) - take_dark_current: true # (bool) - skip_existing_images: true # (bool) - take_snapshots: true # (bool) + default: + # Default values, also used for standard acquisition. + # Values not given in other dictionaries are taken from here + exp_time: 0.04 # (s) exposure time + osc_start: 0.0 # (degrees) Only used if no current angle found + osc_range: 0.1 # (degrees) + num_passes: 1 # (int) + first_image: 1 # (int) + overlap: 0 + num_images: 1 # (int) + # detector_binning_mode: 1 # Removed as not in practice used. + inverse_beam: false # (bool) + take_dark_current: true # (bool) + skip_existing_images: true # (bool) + take_snapshots: true # (bool) - helical: - # Defaults for helical scan. Missing values are taken from default - num_images: 100 + helical: + # Defaults for helical scan. Missing values are taken from default + num_images: 100 - characterisation: - # Defaults for chareacterisation. Missing values are taken from default - osc_range: 1 + characterisation: + # Defaults for chareacterisation. Missing values are taken from default + osc_range: 1 - advanced: - # Defaults for 'advanced' acquisition. Missing values are taken from default - osc_range: 0.5 - num_images: 100 + advanced: + # Defaults for 'advanced' acquisition. Missing values are taken from default + osc_range: 0.5 + num_images: 100 acquisition_limit_values: - exposure_time: # (s) - - 0.04 - - 6000.0 - osc_range: # (degrees) - - -1000.0 - - 10000.0 - number_of_images: # (int) - - 1 - - 99999 - kappa: # (degrees) - - 0.0 - - 180.0 -# kappa_phi: # (degrees) -# - 0.0 -# - 360.0 + exposure_time: # (s) + - 0.04 + - 6000.0 + osc_range: # (degrees) + - -1000.0 + - 10000.0 + number_of_images: # (int) + - 1 + - 99999 + kappa: # (degrees) + - 0.0 + - 180.0 +# kappa_phi: # (degrees) +# - 0.0 +# - 360.0 diff --git a/mxcubecore/configuration/mockup/web/beamline_config.yml b/mxcubecore/configuration/mockup/web/beamline_config.yml index 0e88617861..274f3958c3 100644 --- a/mxcubecore/configuration/mockup/web/beamline_config.yml +++ b/mxcubecore/configuration/mockup/web/beamline_config.yml @@ -1,11 +1,10 @@ --- - # The class to initialise, and init parameters _initialise_class: - class: mxcubecore.HardwareObjects.Beamline.Beamline - # Further key-value pairs here will be passed to the class init -# mode: devel + class: mxcubecore.HardwareObjects.Beamline.Beamline + # Further key-value pairs here will be passed to the class init + # mode: devel # objects # @@ -16,108 +15,110 @@ _initialise_class: # would need those added (e.g. the centring methods) # _objects: - # The !!o0map and the lines starting with '- ' give you an *ordered* dictionary - # And thus a reproducible loading order - !!omap - # The values are the file paths to the configuration file for the - # object, relative to the configuration file path(s) - # - # NB - the order is *NOT* arbitrary, as signal connnections are set - # on one object that require the other to be already loaded. - # - # Hardware: - - session: session.xml - - machine_info: mach-info-mockup.xml - - transmission: transmission-mockup.xml - - energy: energy-mockup.xml - - beam: beam-mockup.xml - - flux: flux-mockup.xml - - detector: detector-mockup.xml - - resolution: resolution-mockup.xml - - hutch_interlock: door-interlock-mockup.xml - - safety_shutter: safety-shutter-mockup.xml - - fast_shutter: fast-shutter-mockup.xml - - sample_changer: sample-changer-mockup.xml - # NBNB TODO remove plate_manipulater and treat as another smaple changer - - plate_manipulator: plate-manipulator-mockup.xml - - diffractometer: diffractometer-mockup.xml - - sample_view: sample-view.xml - - lims: lims-client-mockup.xml - - queue_manager: queue.xml - - queue_model: queue-model.xml - # Procedures: - - collect: collect-mockup.xml - - xrf_spectrum: xrf-spectrum-mockup.xml - - energy_scan: energyscan-mockup.xml - # - imaging: xray-imaging.xml # Only in EMBL as of 201907 - - gphl_connection: gphl-setup.yml - - gphl_workflow: gphl-workflow.yml - # - centring: centring.xml - # Analysis: - - offline_processing: offline-processing-mockup.xml - - online_processing: online-processing-mockup.xml - - characterisation: characterisation-mockup.xml - # - beam_realign: # Skipped - optional + # The !!o0map and the lines starting with '- ' give you an *ordered* dictionary + # And thus a reproducible loading order + !!omap + # The values are the file paths to the configuration file for the + # object, relative to the configuration file path(s) + # + # NB - the order is *NOT* arbitrary, as signal connnections are set + # on one object that require the other to be already loaded. + # + # Hardware: + - session: session.xml + - machine_info: mach-info-mockup.xml + - transmission: transmission-mockup.xml + - energy: energy-mockup.xml + - beam: beam-mockup.xml + - flux: flux-mockup.xml + - detector: detector-mockup.xml + - resolution: resolution-mockup.xml + - hutch_interlock: door-interlock-mockup.xml + - safety_shutter: safety-shutter-mockup.xml + - fast_shutter: fast-shutter-mockup.xml + - sample_changer: sample-changer-mockup.xml + # NBNB TODO remove plate_manipulater and treat as another smaple changer + - plate_manipulator: plate-manipulator-mockup.xml + - diffractometer: diffractometer-mockup.xml + - sample_view: sample-view.xml + - lims: lims-client-mockup.xml + - queue_manager: queue.xml + - queue_model: queue-model.xml + # Procedures: + - collect: collect-mockup.xml + - xrf_spectrum: xrf-spectrum-mockup.xml + - energy_scan: energyscan-mockup.xml + # - imaging: xray-imaging.xml # Only in EMBL as of 201907 + - gphl_connection: gphl-setup.yml + - gphl_workflow: gphl-workflow.yml + # - centring: centring.xml + # Analysis: + - offline_processing: offline-processing-mockup.xml + - online_processing: online-processing-mockup.xml + - characterisation: characterisation-mockup.xml + # - beam_realign: # Skipped - optional + # Non-object attributes: advanced_methods: - - MeshScan - - XrayCentering + - MeshScan + - XrayCentering + tunable_wavelength: true disable_num_passes: false run_online_processing: false run_number: 1 default_acquisition_parameters: - default: - # Default values, also used for standard acquisition. - # Values not given in other dictionaries are taken from here - exp_time: 0.04 # (s) exposure time - osc_start: 0.0 # (degrees) Only used if no current angle found - osc_range: 0.1 # (degrees) - num_passes: 1 # (int) - first_image: 1 # (int) - overlap: 0 - num_images: 1 # (int) - # detector_binning_mode: 1 # Removed as not in practice used. - inverse_beam: false # (bool) - take_dark_current: true # (bool) - skip_existing_images: true # (bool) - take_snapshots: true # (bool) + default: + # Default values, also used for standard acquisition. + # Values not given in other dictionaries are taken from here + exp_time: 0.04 # (s) exposure time + osc_start: 0.0 # (degrees) Only used if no current angle found + osc_range: 0.1 # (degrees) + num_passes: 1 # (int) + first_image: 1 # (int) + overlap: 0 + num_images: 1 # (int) + # detector_binning_mode: 1 # Removed as not in practice used. + inverse_beam: false # (bool) + take_dark_current: true # (bool) + skip_existing_images: true # (bool) + take_snapshots: true # (bool) - helical: - # Defaults for helical scan. Missing values are taken from default - num_images: 100 + helical: + # Defaults for helical scan. Missing values are taken from default + num_images: 100 - characterisation: - # Defaults for chareacterisation. Missing values are taken from default - osc_range: 1 - opt_sad: False # yamllint disable-line rule:truthy - account_rad_damage: True # yamllint disable-line rule:truthy - strategy_complexity: 0 - strategy_program: Optimal - max_crystal_vdim: 1.0 - min_crystal_vdim: 1.0 - max_crystal_vphi: 1.0 - min_crystal_vphi: 1.0 + characterisation: + # Defaults for chareacterisation. Missing values are taken from default + osc_range: 1 + opt_sad: False # yamllint disable-line rule:truthy + account_rad_damage: True # yamllint disable-line rule:truthy + strategy_complexity: 0 + strategy_program: Optimal + max_crystal_vdim: 1.0 + min_crystal_vdim: 1.0 + max_crystal_vphi: 1.0 + min_crystal_vphi: 1.0 - advanced: - # Defaults for 'advanced' acquisition. Missing values are taken from default - osc_range: 0.5 - num_images: 100 + advanced: + # Defaults for 'advanced' acquisition. Missing values are taken from default + osc_range: 0.5 + num_images: 100 acquisition_limit_values: - exposure_time: # (s) - - 0.04 - - 6000.0 - osc_range: # (degrees) - - -1000.0 - - 10000.0 - number_of_images: # (int) - - 1 - - 99999 - kappa: # (degrees) - - 0.0 - - 180.0 -# kappa_phi: # (degrees) -# - 0.0 -# - 360.0 + exposure_time: # (s) + - 0.04 + - 6000.0 + osc_range: # (degrees) + - -1000.0 + - 10000.0 + number_of_images: # (int) + - 1 + - 99999 + kappa: # (degrees) + - 0.0 + - 180.0 +# kappa_phi: # (degrees) +# - 0.0 +# - 360.0 diff --git a/mxcubecore/configuration/soleil_px1/beamline_config.yml b/mxcubecore/configuration/soleil_px1/beamline_config.yml index 7021007343..227f132b66 100644 --- a/mxcubecore/configuration/soleil_px1/beamline_config.yml +++ b/mxcubecore/configuration/soleil_px1/beamline_config.yml @@ -1,14 +1,12 @@ --- -# yamllint disable rule:comments-indentation - # FIRST DRAFT of SOLEIL px1 configuration. TO BE EDITED # The class to initialise, and init parameters _initialise_class: - class: mxcubecore.HardwareObjects.Beamline.Beamline - # Further key-value pairs here will be passed to the class init -# mode: devel + class: mxcubecore.HardwareObjects.Beamline.Beamline + # Further key-value pairs here will be passed to the class init + # mode: devel # objects # @@ -21,110 +19,111 @@ _initialise_class: _objects: # The !!o0map and the lines starting with '- ' give you an *orderd* dictionary # And thus a reproducible loading order - # yamllint disable-line rule:indentation !!omap - # The values are the file paths to the configuration file for the - # object, relative to the configuration file path(s) - # - # NB - the order is *NOT* arbitrary, as signal connnections are set - # on one object that require the other to be already loaded. - # - # Hardware: - - session: session.xml - - machine_info: mach.xml - - transmission: attenuators_pslits.xml - - energy: energy.xml - - beam: beam-info.xml - - flux: flux.xml - - detector: pilatus.xml - - resolution: resolution.xml -# - hutch_interlock: door-interlock-mockup.xml - - safety_shutter: safety_shutter.xml - - fast_shutter: fastshut.xml - - sample_changer: cryotong.xml - # NBNB TODO remove plate_manipulater and treat as another smaple changer -# - plate_manipulator: plate-manipulator.xml - - diffractometer: minidiff.xml - - graphics: Qt4_graphics-manager.xml - - lims: dbconnection.xml - - queue_manager: queue.xml - - queue_model: queue-model.xml - # Procedures: - - collect: mxcollect.xml - - xrf_spectrum: xrf-spectrum-mockup.xml - - energy_scan: energyscan.xml - # - imaging: xray-imaging.xml # Only in EMBL as of 201907 - - gphl_workflow: gphl-workflow.xml - - gphl_connection: gphl-setup.xml - # - centring: centring.xml - # Analysis: -# - offline_processing: auto-processing.xml -# - online_processing: parallel-processing.xml - - characterisation: data-analysis.xml - # - beam_realign: # Skipped - optional + # The values are the file paths to the configuration file for the + # object, relative to the configuration file path(s) + # + # NB - the order is *NOT* arbitrary, as signal connnections are set + # on one object that require the other to be already loaded. + # + # Hardware: + - session: session.xml + - machine_info: mach.xml + - transmission: attenuators_pslits.xml + - energy: energy.xml + - beam: beam-info.xml + - flux: flux.xml + - detector: pilatus.xml + - resolution: resolution.xml + # - hutch_interlock: door-interlock-mockup.xml + - safety_shutter: safety_shutter.xml + - fast_shutter: fastshut.xml + - sample_changer: cryotong.xml + # NBNB TODO remove plate_manipulater and treat as another smaple changer + # - plate_manipulator: plate-manipulator.xml + - diffractometer: minidiff.xml + - graphics: Qt4_graphics-manager.xml + - lims: dbconnection.xml + - queue_manager: queue.xml + - queue_model: queue-model.xml + # Procedures: + - collect: mxcollect.xml + - xrf_spectrum: xrf-spectrum-mockup.xml + - energy_scan: energyscan.xml + # - imaging: xray-imaging.xml # Only in EMBL as of 201907 + - gphl_workflow: gphl-workflow.xml + - gphl_connection: gphl-setup.xml + # - centring: centring.xml + # Analysis: + # - offline_processing: auto-processing.xml + # - online_processing: parallel-processing.xml + - characterisation: data-analysis.xml + # - beam_realign: # Skipped - optional + # Non-object attributes: # advanced_methods: -# - MeshScan -# - XrayCentering +# - MeshScan +# - XrayCentering + tunable_wavelength: true disable_num_passes: false run_number: 1 default_acquisition_parameters: - default: - # Default values, also used for standard acquisition. - # Values not given in other dictionaries are taken from here - exp_time: 0.1 # (s) exposure time - osc_start: 0.0 # (degrees) Only used if no current angle found - osc_range: 0.1 # (degrees) - num_passes: 1 # (int) - first_image: 1 # (int) - overlap: 0 - num_images: 1 # (int) - # detector_binning_mode: 1 # Removed as not in practice used. - inverse_beam: false # (bool) - take_dark_current: true # (bool) - skip_existing_images: true # (bool) - take_snapshots: true # (bool) + default: + # Default values, also used for standard acquisition. + # Values not given in other dictionaries are taken from here + exp_time: 0.1 # (s) exposure time + osc_start: 0.0 # (degrees) Only used if no current angle found + osc_range: 0.1 # (degrees) + num_passes: 1 # (int) + first_image: 1 # (int) + overlap: 0 + num_images: 1 # (int) + # detector_binning_mode: 1 # Removed as not in practice used. + inverse_beam: false # (bool) + take_dark_current: true # (bool) + skip_existing_images: true # (bool) + take_snapshots: true # (bool) -# helical: -# # Defaults for helical scan. Missing values are taken from default -# exp_time: 0.04 # (s) exposure time -# num_images: 100 + # helical: + # # Defaults for helical scan. Missing values are taken from default + # exp_time: 0.04 # (s) exposure time + # num_images: 100 - characterisation: - # Defaults for chareacterisation. Missing values are taken from default - exp_time: 1.0 # (s) exposure time - osc_range: 1.0 + characterisation: + # Defaults for chareacterisation. Missing values are taken from default + exp_time: 1.0 # (s) exposure time + osc_range: 1.0 - mesh: - # Defaults for 'advanced' acquisition. Missing values are taken from default - exp_time: 10.0 # (s) exposure time - osc_range: 10.0 - num_images: 100 - cell_counting: inverse-zig-zag - cell_spacing: vertical,horizontal - mesh_center: top-left + mesh: + # Defaults for 'advanced' acquisition. Missing values are taken from default + exp_time: 10.0 # (s) exposure time + osc_range: 10.0 + num_images: 100 + cell_counting: inverse-zig-zag + cell_spacing: vertical,horizontal + mesh_center: top-left -# advanced: -# # Defaults for 'advanced' acquisition. Missing values are taken from default -# exp_time: 0.04 # (s) exposure time -# osc_range: 0.5 -# num_images: 100 +# advanced: +# # Defaults for 'advanced' acquisition. Missing values are taken from default +# exp_time: 0.04 # (s) exposure time +# osc_range: 0.5 +# num_images: 100 acquisition_limit_values: - exposure_time: # (s) - - 0.01 - - 10.0 - osc_range: # (degrees) - - -0.0 - - 760.0 - number_of_images: # (int) - - 1 - - 10000 -# kappa: # (degrees) -# - 0.0 -# - 180.0 -# kappa_phi: # (degrees) -# - 0.0 -# - 360.0 + exposure_time: # (s) + - 0.01 + - 10.0 + osc_range: # (degrees) + - -0.0 + - 760.0 + number_of_images: # (int) + - 1 + - 10000 +# kappa: # (degrees) +# - 0.0 +# - 180.0 +# kappa_phi: # (degrees) +# - 0.0 +# - 360.0 diff --git a/mxcubecore/configuration/soleil_px2/beamline_config.yml b/mxcubecore/configuration/soleil_px2/beamline_config.yml index c781a949d9..7606024945 100644 --- a/mxcubecore/configuration/soleil_px2/beamline_config.yml +++ b/mxcubecore/configuration/soleil_px2/beamline_config.yml @@ -1,14 +1,12 @@ --- -# yamllint disable rule:comments-indentation - # FIRST DRAFT of SOLEIL px2 configuration. TO BE EDITED # The class to initialise, and init parameters _initialise_class: - class: mxcubecore.HardwareObjects.Beamline.Beamline - # Further key-value pairs here will be passed to the class init -# mode: devel + class: mxcubecore.HardwareObjects.Beamline.Beamline + # Further key-value pairs here will be passed to the class init + # mode: devel # objects # @@ -21,100 +19,101 @@ _initialise_class: _objects: # The !!o0map and the lines starting with '- ' give you an *orderd* dictionary # And thus a reproducible loading order - # yamllint disable-line rule:indentation !!omap - # The values are the file paths to the configuration file for the - # object, relative to the configuration file path(s) - # - # NB - the order is *NOT* arbitrary, as signal connnections are set - # on one object that require the other to be already loaded. - # - # Hardware: - - session: singleton_objects/session.xml -# - machine_info: mach.xml - - transmission: singleton_motors/transmission.xml - - energy: singleton_motors/photon_energy.xml - - beam: singleton_objects/beaminfo_exporter.xml -# - flux: flux.xml - - detector: mockups/detector-mockup.xml - - resolution: singleton_motors/resolution.xml -# - hutch_interlock: door-interlock-mockup.xml -# - safety_shutter: safety_shutter.xml -# - fast_shutter: fastshut.xml - - sample_changer: singleton_objects/cats.xml - # NBNB TODO remove plate_manipulater and treat as another smaple changer -# - plate_manipulator: plate-manipulator.xml - - diffractometer: diffractometer/diffractometer.xml - - graphics: singleton_objects/Qt4_graphics-manager.xml - - lims: singleton_objects/dbconnection.xml -# - queue_manager: queue.xml -# - queue_model: queue-model.xml - # Procedures: - - collect: experimental_methods/diffraction_methods.xml - - xrf_spectrum: mockups/xrf-spectrum-mockup.xml - - energy_scan: mockups/energyscan-mockup.xml - # - imaging: xray-imaging.xml # Only in EMBL as of 201907 - - gphl_workflow: gphl-workflow.xml - - gphl_connection: gphl-setup.xml - # - centring: centring.xml - # Analysis: -# - offline_processing: auto-processing.xml -# - online_processing: parallel-processing.xml - - characterisation: singleton_objects/data-analysis.xml - # - beam_realign: # Skipped - optional + # The values are the file paths to the configuration file for the + # object, relative to the configuration file path(s) + # + # NB - the order is *NOT* arbitrary, as signal connnections are set + # on one object that require the other to be already loaded. + # + # Hardware: + - session: singleton_objects/session.xml + # - machine_info: mach.xml + - transmission: singleton_motors/transmission.xml + - energy: singleton_motors/photon_energy.xml + - beam: singleton_objects/beaminfo_exporter.xml + # - flux: flux.xml + - detector: mockups/detector-mockup.xml + - resolution: singleton_motors/resolution.xml + # - hutch_interlock: door-interlock-mockup.xml + # - safety_shutter: safety_shutter.xml + # - fast_shutter: fastshut.xml + - sample_changer: singleton_objects/cats.xml + # NBNB TODO remove plate_manipulater and treat as another smaple changer + # - plate_manipulator: plate-manipulator.xml + - diffractometer: diffractometer/diffractometer.xml + - graphics: singleton_objects/Qt4_graphics-manager.xml + - lims: singleton_objects/dbconnection.xml + # - queue_manager: queue.xml + # - queue_model: queue-model.xml + # Procedures: + - collect: experimental_methods/diffraction_methods.xml + - xrf_spectrum: mockups/xrf-spectrum-mockup.xml + - energy_scan: mockups/energyscan-mockup.xml + # - imaging: xray-imaging.xml # Only in EMBL as of 201907 + - gphl_workflow: gphl-workflow.xml + - gphl_connection: gphl-setup.xml + # - centring: centring.xml + # Analysis: + # - offline_processing: auto-processing.xml + # - online_processing: parallel-processing.xml + - characterisation: singleton_objects/data-analysis.xml + # - beam_realign: # Skipped - optional + # Non-object attributes: advanced_methods: - - MeshScan - - XrayCentering - - LineScsn + - MeshScan + - XrayCentering + - LineScsn + tunable_wavelength: true disable_num_passes: false run_number: 1 default_acquisition_parameters: - default: - # Default values, also used for standard acquisition. - # Values not given in other dictionaries are taken from here - exp_time: 0.025 # (s) exposure time - osc_start: 0.0 # (degrees) Only used if no current angle found - osc_range: 0.1 # (degrees) - num_passes: 1 # (int) - first_image: 1 # (int) - overlap: 0 - num_images: 1800 # (int) - # detector_binning_mode: 1 # Removed as not in practice used. - inverse_beam: false # (bool) - take_dark_current: true # (bool) - skip_existing_images: true # (bool) - take_snapshots: true # (bool) + default: + # Default values, also used for standard acquisition. + # Values not given in other dictionaries are taken from here + exp_time: 0.025 # (s) exposure time + osc_start: 0.0 # (degrees) Only used if no current angle found + osc_range: 0.1 # (degrees) + num_passes: 1 # (int) + first_image: 1 # (int) + overlap: 0 + num_images: 1800 # (int) + # detector_binning_mode: 1 # Removed as not in practice used. + inverse_beam: false # (bool) + take_dark_current: true # (bool) + skip_existing_images: true # (bool) + take_snapshots: true # (bool) -# helical: -# # Defaults for helical scan. Missing values are taken from default -# num_images: 100 + # helical: + # # Defaults for helical scan. Missing values are taken from default + # num_images: 100 - characterisation: - # Defaults for chareacterisation. Missing values are taken from default - overlap: -89 - wedge_size: 10 # (int) + characterisation: + # Defaults for chareacterisation. Missing values are taken from default + overlap: -89 + wedge_size: 10 # (int) - advanced: - # Defaults for 'advanced' acquisition. Missing values are taken from default - osc_range: 0.5 - num_images: 100 + advanced: + # Defaults for 'advanced' acquisition. Missing values are taken from default + osc_range: 0.5 + num_images: 100 acquisition_limit_values: - exposure_time: # (s) - - 0.00134 - - 6000.0 - osc_range: # (degrees) - - -1000.0 - - 10000.0 - number_of_images: # (int) - - 1 - - 99999 - kappa: # (degrees) - - -9.0 - - 240.0 -# kappa_phi: # (degrees) -# - 0.0 -# - 360.0 + exposure_time: # (s) + - 0.00134 + - 6000.0 + osc_range: # (degrees) + - -1000.0 + - 10000.0 + number_of_images: # (int) + - 1 + - 99999 + kappa: # (degrees) + - -9.0 + - 240.0 +# kappa_phi: # (degrees) +# - 0.0 +# - 360.0