mxcubecore.HardwareObjects.Gphl.GphlMessages

Abstract beamline interface message classes

License:

This file is part of MXCuBE.

MXCuBE is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

MXCuBE is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.

You should have received a copy of the GNU Lesser General Public License along with MXCuBE. If not, see <https://www.gnu.org/licenses/>.

Classes

AnomalousScatterer(element, edge)
BcsDetectorSetting(resolution[, id_, orgxy])	Detector position setting with additional (beamline-side) resolution and orgxy
BeamSetting(wavelength[, id_])	Beam setting
BeamlineAbort()	Abort workflow from beamline
BeamstopSetting([id_])	Beamstop position setting
CentringDone(status, timestamp, ...)	Centering-done message
ChooseLattice(indexingSolutions[, ...])	Choose lattice instruction
CollectionDone(proposalId, status[, ...])	Collection Done message
CollectionProposal(relativeImageDir, ...[, id_])	Collection proposal
ConfigurationData(location)	Configuration Data message
DetectorSetting([id_])	Detector position setting
GeometricStrategy(isUserModifiable, ...[, ...])	Geometric strategy
GoniostatRotation([id_])	Goniostat Rotation setting
GoniostatSweepSetting(scanAxis[, id_])	Goniostat Sweep setting
GoniostatTranslation([rotation, ...])	Goniostat Translation setting
IdentifiedElement([id_])	Object with persistent uuid
IndexingSolution(bravaisLattice, cell[, ...])	Indexing solution data
Issue(...)
MessageData()	Topmost superclass for all message data objects
ObtainPriorInformation()	Prior information request
ParsedMessage(message_type, payload, ...)
Payload()	Payload - top level message object
PhasingWavelength(wavelength[, role, id_])	Phasing Wavelength
PositionerSetting([id_])	Positioner Setting object.
PrepareForCentring()	Prior information request
PriorInformation(data_model, image_root)	Prior information to workflow calculation
ReadyForCentring()	Prior information request
RequestCentring(currentSettingNo, ...)	Request for centering
RequestConfiguration()	Configuration request message
SampleCentred(data_model)
Scan(width, exposure, imageStartNum, start, ...)	Collection strategy Scan
ScanExposure(time, transmission[, id_])	Scan Exposure
ScanWidth(imageWidth, numImages[, id_])	Scan Width
SelectedLattice(data_model, solution)	Lattice selected message
SubprocessStarted(name)	Subprocess Started message
SubprocessStopped()	Subprocess Stopped request message
Sweep(goniostatSweepSetting, ...[, ...])	Geometric strategy Sweep
UnitCell(a, b, c, alpha, beta, gamma)	Unit cell data type
UserProvidedInfo(data_model)	User-provided information
WorkflowAborted([issues])
WorkflowCompleted([issues])
WorkflowDone([issues])	End-of-workflow message
WorkflowFailed([reason, issues])

class mxcubecore.HardwareObjects.Gphl.GphlMessages.AnomalousScatterer(element, edge)

Bases: MessageData

class mxcubecore.HardwareObjects.Gphl.GphlMessages.BcsDetectorSetting(resolution, id_=None, orgxy=(), **axisSettings)

Bases: DetectorSetting

Detector position setting with additional (beamline-side) resolution and orgxy

property orgxy

Tuple, empty or of two floats; beam centre on detector

property resolution

Resolution (in A) matching detector distance

class mxcubecore.HardwareObjects.Gphl.GphlMessages.BeamSetting(wavelength, id_=None)

Bases: IdentifiedElement

Beam setting

property wavelength

Wavelength setting for beam

class mxcubecore.HardwareObjects.Gphl.GphlMessages.BeamlineAbort

Bases: Payload

Abort workflow from beamline

class mxcubecore.HardwareObjects.Gphl.GphlMessages.BeamstopSetting(id_=None, **axisSettings)

Bases: PositionerSetting

Beamstop position setting

class mxcubecore.HardwareObjects.Gphl.GphlMessages.CentringDone(status, timestamp, goniostatTranslation)

Bases: Payload

Centering-done message

property timestamp

Time in seconds since the epoch (Jan 1, 1970), as returned by time.time()

class mxcubecore.HardwareObjects.Gphl.GphlMessages.ChooseLattice(indexingSolutions, indexingFormat='IDXREF', indexingHeader=None, priorCrystalClasses=(), priorSpaceGroup=None, priorSpaceGroupString=None, userProvidedCell=None)

Bases: Payload

Choose lattice instruction

property indexingFormat

Indexing format

property indexingHeader

Indexing header

property indexingSolutions

List of IndexingSolution

property priorCrystalClasses

tuple of crystal class names

property priorSpaceGroup

space group number

property priorSpaceGroupString

space group name

property userProvidedCell

User provided unit cell

class mxcubecore.HardwareObjects.Gphl.GphlMessages.CollectionDone(proposalId, status, procWithLatticeParams=False, imageRoot=None, scanIdMap=None, centrings=None)

Bases: MessageData

Collection Done message

property centrings

set(GoniostatTranslation)

New GoniostatTranslations acquired during acquisition

property imageRoot

Url for directory containing images. Generally an absolute file path.

property procWithLatticeParams

Boolean, whether lattice parameters should be used for processing

property proposalId

uuid of collection proposal that has been executed.

property scanIdMap

GoniostatTranslation.id_

Type:

Dict[str,str] scan.id_

property status

Integer status code for collection result

class mxcubecore.HardwareObjects.Gphl.GphlMessages.CollectionProposal(relativeImageDir, strategy, scans, id_=None)

Bases: IdentifiedElement, Payload

Collection proposal

class mxcubecore.HardwareObjects.Gphl.GphlMessages.ConfigurationData(location)

Bases: Payload

Configuration Data message

property location

Url for directory containing configuration data. Generally an absolute file path.

class mxcubecore.HardwareObjects.Gphl.GphlMessages.DetectorSetting(id_=None, **axisSettings)

Bases: PositionerSetting

Detector position setting

class mxcubecore.HardwareObjects.Gphl.GphlMessages.GeometricStrategy(isUserModifiable, defaultDetectorSetting, defaultBeamSetting, allowedWidths=(), sweepOffset=None, sweepRepeat=None, defaultWidthIdx=None, sweeps=(), id_=None)

Bases: IdentifiedElement, Payload

Geometric strategy

get_ordered_sweeps()

Get sweeps in acquisition order.

Acquisition order is determined by the sweepGroup - to get results deterministic we use a secondary sort on angles, in alphabetical name order as a backup, (in pracite, ‘kappa’, ‘kappa_phi’, ‘phi’) which should match what the workflow does internally. Anyway, it is the sweep

class mxcubecore.HardwareObjects.Gphl.GphlMessages.GoniostatRotation(id_=None, **axisSettings)

Bases: PositionerSetting

Goniostat Rotation setting

get_motor_settings()

Get dictionary of rotation and translation motor setting

property translation

GoniostatTranslation corresponding to self

NB This link can be set only by GoniostatTranslation.__init__

class mxcubecore.HardwareObjects.Gphl.GphlMessages.GoniostatSweepSetting(scanAxis, id_=None, **axisSettings)

Bases: GoniostatRotation

Goniostat Sweep setting

property scanAxis

Scanning axis

class mxcubecore.HardwareObjects.Gphl.GphlMessages.GoniostatTranslation(rotation=None, requestedRotationId=None, id_=None, **axisSettings)

Bases: PositionerSetting

Goniostat Translation setting

NB the reverse GoniostatRotation.translation link is set from here. For this reason the constructor parameters are different from the object attributes. rotation is taken to be newRotation, except that:

if ( rotation is not None and

(requestedRotationId is None or requestedRotationId == rotation.id_):

self.requestedRotationId = rotation.id_ self.newRotation = None

class mxcubecore.HardwareObjects.Gphl.GphlMessages.IdentifiedElement(id_=None)

Bases: MessageData

Object with persistent uuid

property id_

Unique identifier (UUID) for IdentifiedElement. Defaults to new, time-based uuid

class mxcubecore.HardwareObjects.Gphl.GphlMessages.IndexingSolution(bravaisLattice, cell, isConsistent=None, latticeCharacter=None, qualityOfFit=None)

Bases: MessageData

Indexing solution data

property bravaisLattice

One of the 14 Bravais lattices (‘aP’ etc.)

property cell

Unit ce;;

property isConsistent

Is solution consistent with know symmetry?

property latticeCharacter

Integer 1-44

class mxcubecore.HardwareObjects.Gphl.GphlMessages.Issue(status information returned with WorkflowDone messages)

Bases: IdentifiedElement

property code

Part of unique identifier of issue definition

property component

Part of unique identifier of issue definition

property message

Text providing specific details about this issue

class mxcubecore.HardwareObjects.Gphl.GphlMessages.MessageData

Bases: object

Topmost superclass for all message data objects

Later to add e.g. stringification

class mxcubecore.HardwareObjects.Gphl.GphlMessages.ObtainPriorInformation

Bases: Payload

Prior information request

class mxcubecore.HardwareObjects.Gphl.GphlMessages.ParsedMessage(message_type, payload, enactment_id, correlation_id)

Bases: tuple

correlation_id

Alias for field number 3

enactment_id

Alias for field number 2

message_type

Alias for field number 0

payload

Alias for field number 1

class mxcubecore.HardwareObjects.Gphl.GphlMessages.Payload

Bases: MessageData

Payload - top level message object

property intent

Message intent - class-level property

class mxcubecore.HardwareObjects.Gphl.GphlMessages.PhasingWavelength(wavelength, role=None, id_=None)

Bases: IdentifiedElement

Phasing Wavelength

property role

Wavelength role

property wavelength

Wavelength setting for beam

class mxcubecore.HardwareObjects.Gphl.GphlMessages.PositionerSetting(id_=None, **axisSettings)

Bases: IdentifiedElement

Positioner Setting object.

Has a uuid and a settings dictionary of axisName:value

property axisSettings

value settings dictionary. NB the returned value is a copy; modifying it does not modify the object internals.

Type:

axisName

class mxcubecore.HardwareObjects.Gphl.GphlMessages.PrepareForCentring

Bases: Payload

Prior information request

class mxcubecore.HardwareObjects.Gphl.GphlMessages.PriorInformation(data_model, image_root)

Bases: Payload

Prior information to workflow calculation

class mxcubecore.HardwareObjects.Gphl.GphlMessages.ReadyForCentring

Bases: Payload

Prior information request

class mxcubecore.HardwareObjects.Gphl.GphlMessages.RequestCentring(currentSettingNo, totalRotations, goniostatRotation)

Bases: Payload

Request for centering

class mxcubecore.HardwareObjects.Gphl.GphlMessages.RequestConfiguration

Bases: Payload

Configuration request message

class mxcubecore.HardwareObjects.Gphl.GphlMessages.SampleCentred(data_model)

Bases: Payload

class mxcubecore.HardwareObjects.Gphl.GphlMessages.Scan(width, exposure, imageStartNum, start, sweep, filenameParams, id_=None)

Bases: IdentifiedElement

Collection strategy Scan

class mxcubecore.HardwareObjects.Gphl.GphlMessages.ScanExposure(time, transmission, id_=None)

Bases: IdentifiedElement

Scan Exposure

property time

Scan exposure transmission

property transmission

Scan exposure transmission

class mxcubecore.HardwareObjects.Gphl.GphlMessages.ScanWidth(imageWidth, numImages, id_=None)

Bases: IdentifiedElement

Scan Width

property imageWidth

Scan image width

property numImages

Number of images

class mxcubecore.HardwareObjects.Gphl.GphlMessages.SelectedLattice(data_model, solution)

Bases: MessageData

Lattice selected message

property solution

Proposed solution

property strategyControl

JSON string of command line options (without prefix) to use for stratcal wrapper call

property strategyDetectorSetting

Detector setting to use for strategy calculation and acquisition

property strategyWavelength

Wavelength to use for strategy calculation and acquisition

property userCrystalClasses

Crystal classes given by user

property userSpaceGroup

Space group (int) given by user

class mxcubecore.HardwareObjects.Gphl.GphlMessages.SubprocessStarted(name)

Bases: Payload

Subprocess Started message

property name

name of subprocess

class mxcubecore.HardwareObjects.Gphl.GphlMessages.SubprocessStopped

Bases: Payload

Subprocess Stopped request message

class mxcubecore.HardwareObjects.Gphl.GphlMessages.Sweep(goniostatSweepSetting, detectorSetting, beamSetting, start, width, beamstopSetting=None, sweepGroup=None, id_=None)

Bases: IdentifiedElement

Geometric strategy Sweep

get_initial_settings()

Get dictionary of rotation and translation motor settings for start of sweep

property scans

Scans that belong to sweeps.

NB this is a two-way link. It is populated when the Scan objects are created

class mxcubecore.HardwareObjects.Gphl.GphlMessages.UnitCell(a, b, c, alpha, beta, gamma)

Bases: MessageData

Unit cell data type

class mxcubecore.HardwareObjects.Gphl.GphlMessages.UserProvidedInfo(data_model)

Bases: MessageData

User-provided information

class mxcubecore.HardwareObjects.Gphl.GphlMessages.WorkflowAborted(issues=None)

Bases: WorkflowDone

class mxcubecore.HardwareObjects.Gphl.GphlMessages.WorkflowCompleted(issues=None)

Bases: WorkflowDone

class mxcubecore.HardwareObjects.Gphl.GphlMessages.WorkflowDone(issues=None)

Bases: Payload

End-of-workflow message

class mxcubecore.HardwareObjects.Gphl.GphlMessages.WorkflowFailed(reason=None, issues=None)

Bases: WorkflowDone