EDNA Plugin: EDPluginControlCharacterisationv10

Name:	EDPluginControlCharacterisationv10
Project:	mxv1
Path:	mxv1/plugins/EDPluginControlCharacterisation-v1.0/plugins/EDPluginControlCharacterisationv10.py
Author:	Olof Svensson, Marie-Francoise Incardona
Date:
Copyright:	European Synchrotron Radiation Facility, Grenoble, France
License:	GPLv3+
Module doc:
Class doc:	The Plugin that controls the whole characterisation.

Datamodels: XSDataCollection

Datamodels: XSDataCollection
targetNamespace "http://www.edna-site.org"

import XSDataCommon.XSData
import XSDataCommon.XSDataAbsorbedDoseRate
import XSDataCommon.XSDataAngle
import XSDataCommon.XSDataAngularSpeed
import XSDataCommon.XSDataBoolean
import XSDataCommon.XSDataDouble
import XSDataCommon.XSDataFile
import XSDataCommon.XSDataFloat
import XSDataCommon.XSDataFlux
import XSDataCommon.XSDataImage
import XSDataCommon.XSDataInput
import XSDataCommon.XSDataInteger
import XSDataCommon.XSDataLength
import XSDataCommon.XSDataMatrixDouble
import XSDataCommon.XSDataResult
import XSDataCommon.XSDataSize
import XSDataCommon.XSDataString
import XSDataCommon.XSDataTime
import XSDataCommon.XSDataVectorDouble
import XSDataCommon.XSDataWavelength
package XSDataMXv1 {
    package MXv1CharacterisationEtc {

        complex type XSDataImageQualityIndicators extends XSData {
            background3D_estimate : XSDataDouble optional
            binPopCutOffMethod2Res : XSDataDouble
            goodBraggCandidates : XSDataInteger
            iceRings : XSDataInteger
            image : XSDataImage
            inResTotal : XSDataInteger
            inResolutionOvrlSpots : XSDataInteger
            maxUnitCell : XSDataDouble optional
            method1Res : XSDataDouble
            method2Res : XSDataDouble optional
            pctSaturationTop50Peaks : XSDataDouble optional
            saturationRangeAverage : XSDataDouble optional
            saturationRangeMax : XSDataDouble optional
            saturationRangeMin : XSDataDouble optional
            selectedIndexingSolution : XSDataIndexingSolutionSelected optional
            signalRangeAverage : XSDataDouble optional
            signalRangeMax : XSDataDouble optional
            signalRangeMin : XSDataDouble optional
            spotTotal : XSDataInteger
            totalIntegratedSignal : XSDataDouble optional
        }

        complex type XSDataInputCharacterisation extends XSDataInput {
            dataCollection : XSDataCollection
        }

        complex type XSDataInputControlISPyB extends XSDataInput {
            characterisationResult : XSDataResultCharacterisation
            dataCollectionId : XSDataInteger optional
            kappa : XSDataAngle optional
            phi : XSDataAngle optional
        }

        complex type XSDataInputControlImageQualityIndicators extends XSDataInput {
            doIndexing : XSDataBoolean optional
            doUploadToIspyb : XSDataBoolean optional
            image : XSDataImage []
        }

        complex type XSDataInputControlXDSGenerateBackgroundImage extends XSDataInput {
            dataCollection : XSDataCollection
        }

        complex type XSDataInputInducedRadiationProcess extends XSDataInput {
            characterisationResult : XSDataResultCharacterisation
        }

        complex type XSDataInputReadImageHeader extends XSDataInput {
            "These two definitions are used by the read image header plugin."
            image : XSDataFile
        }

        complex type XSDataInputSubWedgeAssemble extends XSDataInput {
            "These two definitions are used by the sub wedge assemble plugin."
            file : XSDataFile []
        }

        complex type XSDataInputSubWedgeMerge extends XSDataInput {
            "These two definitions are used by the sub wedge merge plugins."
            subWedge : XSDataSubWedge []
        }

        complex type XSDataResultCharacterisation extends XSDataResult {
            dataCollection : XSDataCollection
            executiveSummary : XSDataString
            imageQualityIndicators : XSDataImageQualityIndicators [] optional
            indexingResult : XSDataIndexingResult optional
            integrationResult : XSDataIntegrationResult optional
            shortSummary : XSDataString
            statusMessage : XSDataString
            strategyResult : XSDataResultStrategy optional
            xdsBackgroundImage : XSDataFile optional
        }

        complex type XSDataResultControlISPyB extends XSDataResult {
            screeningId : XSDataInteger optional
            dataCollectionId : XSDataInteger optional
        }

        complex type XSDataResultControlImageQualityIndicators extends XSDataResult {
            imageQualityIndicators : XSDataImageQualityIndicators [] optional
        }

        complex type XSDataResultControlXDSGenerateBackgroundImage extends XSDataResult {
            xdsBackgroundImage : XSDataFile
        }

        complex type XSDataResultInducedRadiationProcess extends XSDataResult {
            bFactor : XSDataDouble
            crystal : XSDataCrystal
            scale : XSDataDouble
        }

        complex type XSDataResultReadImageHeader extends XSDataResult {
            "These two definitions are used by the read image header plugin."
            subWedge : XSDataSubWedge
        }

        complex type XSDataResultSubWedgeAssemble extends XSDataResult {
            "These two definitions are used by the sub wedge assemble plugin."
            subWedge : XSDataSubWedge []
        }

        complex type XSDataResultSubWedgeMerge extends XSDataResult {
            "These two definitions are used by the sub wedge merge plugins."
            subWedge : XSDataSubWedge []
        }

    }

    package MXv1Crystal {

        complex type XSDataCell extends XSData {
            "Crystallographic properties"
            angle_alpha : XSDataAngle
            angle_beta : XSDataAngle
            angle_gamma : XSDataAngle
            length_a : XSDataLength
            length_b : XSDataLength
            length_c : XSDataLength
        }

        complex type XSDataCrystal extends XSData {
            "Crystallographic properties"
            cell : XSDataCell
            mosaicity : XSDataDouble optional
            spaceGroup : XSDataSpaceGroup
        }

        complex type XSDataSpaceGroup extends XSData {
            "Crystallographic properties"
            ITNumber : XSDataInteger optional
            name : XSDataString
        }

    }

    package MXv1DataCollection {

        complex type XSDataBeam extends XSData {
            "This object contains all the properties related to the beam:\r\n- the exposure time (sec)\r\n- the flux (photons/sec)\r\n- The minimum exposure time permitted by hardware (sec)\r\n- The size of the beam (mm x mm)\r\n- The wavelength (a)\r\n- Transmission in %"
            exposureTime : XSDataTime optional
            flux : XSDataFlux optional
            minExposureTimePerImage : XSDataTime optional
            size : XSDataSize optional
            transmission : XSDataDouble optional
            wavelength : XSDataWavelength optional
        }

        complex type XSDataCollection extends XSData {
            "The data collection carried out or to be carried out with a particular sample with specific user inputs defined by the diffraction plan."
            diffractionPlan : XSDataDiffractionPlan optional
            sample : XSDataSampleCrystalMM optional
            subWedge : XSDataSubWedge []
        }

        complex type XSDataDetector extends XSData {
            "The properties of a detector. "
            beamPositionX : XSDataLength
            beamPositionY : XSDataLength
            bin : XSDataString
            byteOrder : XSDataString
            dataType : XSDataString
            distance : XSDataLength
            gain : XSDataFloat optional
            imageSaturation : XSDataInteger
            name : XSDataString
            numberBytesInHeader : XSDataInteger
            numberPixelX : XSDataInteger
            numberPixelY : XSDataInteger
            pixelSizeX : XSDataLength
            pixelSizeY : XSDataLength
            serialNumber : XSDataString
            twoTheta : XSDataAngle
            ^type : XSDataString
        }

        complex type XSDataExperimentalCondition extends XSData {
            "This object encapsulates all the physical properties of an experiment instrumentation. i.e: Beam, detector, Goniostat."
            beam : XSDataBeam optional
            detector : XSDataDetector optional
            goniostat : XSDataGoniostat optional
        }

        complex type XSDataGoniostat extends XSData {
            "The properties of a goniostat:\r\n- the maximal rotation speed permitted\r\n- the minimal width for an oscillation width of subwedge\r\n- the name of the rotation axis (typically phi)\r\n- the rotation start angle\r\n- the rotation end angle"
            maxOscillationSpeed : XSDataAngularSpeed optional
            minOscillationWidth : XSDataAngle optional
            oscillationWidth : XSDataAngle
            overlap : XSDataAngle optional
            rotationAxis : XSDataString
            rotationAxisEnd : XSDataAngle
            rotationAxisStart : XSDataAngle
            samplePosition : XSDataVectorDouble [] optional
        }

        complex type XSDataSubWedge extends XSData {
            "A subwedge is defined as a list of images that been collected or is to be collected with some particular experimental condition. If the images are to be collected, the image list is empty.\r\nThe subWedgeNumber is an optional number for relating different subwedges, especially for planning data collections."
            action : XSDataString optional
            experimentalCondition : XSDataExperimentalCondition
            image : XSDataImage []
            optional
            subWedgeNumber : XSDataInteger optional
        }

    }

    package MXv1DiffractionPlan {

        complex type XSDataDiffractionPlan extends XSData {
            "This object contains the main properties a user can parameterize for a crystal characterisation:\r\n\r\n- the aimed* parameters are the parameters that a user would like to reach for a BEST run.\r\n- the required* are not yet used (the idea is to warn the user if these parameters cannot be reached)\r\n- complexity: BEST complexity input, can be either \"none\" (always single wedge strategy). \"min\" (few subwedges) or \"full\" (many subwedges).\r\n- maxExposureTimePerDataCollection is the max total exposure time (shutter open, not including readout time) the crystal can be exposed to the X-ray beam.\r\n- forcedSpaceGroup: option to force the space group of the indexing solution\r\n- strategyOption: extra option for BEST for more advanced strategies like estimating the sensitivity to radiation damage\r\n- anomalousData: Depreccated! Boolean value for enabling anomalous strategy. In the future the strategyOption should be used instead of anomalousData.\r\n- estimateRadiationDamage: Boolean value for enabling or disabling the use of Raddose for estimation of radiation damage. If estimateRadiationDamage is enabled also the flux and beamsize must be provided.\r\n- detectorDistanceMin and detectorDistanceMax: optimal input to BEST for limiting the calculated strategy resolution to be in the range of the detector displacements with respect to the sample.\n- minTransmission: optional input for BEST\r\n- kappaStrategyOption: optional input for kappa strategies\r\n- numberOfPositions: optional input for BEST"
            aimedCompleteness : XSDataDouble optional
            aimedIOverSigmaAtHighestResolution : XSDataDouble optional
            aimedMultiplicity : XSDataDouble optional
            aimedResolution : XSDataDouble optional
            anomalousData : XSDataBoolean optional
            complexity : XSDataString optional
            detectorDistanceMax : XSDataLength
            optional
            detectorDistanceMin : XSDataLength optional
            estimateRadiationDamage : XSDataBoolean optional
            forcedSpaceGroup : XSDataString optional
            goniostatMaxOscillationSpeed : XSDataAngularSpeed optional
            goniostatMinOscillationWidth : XSDataAngle optional
            kappaStrategyOption : XSDataString [] optional
            maxExposureTimePerDataCollection : XSDataTime optional
            minExposureTimePerImage : XSDataTime optional
            minTransmission : XSDataDouble optional
            numberOfPositions : XSDataInteger optional
            requiredCompleteness : XSDataDouble optional
            requiredMultiplicity : XSDataDouble optional
            requiredResolution : XSDataDouble optional
            strategyOption : XSDataString optional
            userDefinedRotationRange : XSDataAngle optional
            userDefinedRotationStart : XSDataAngle optional
        }

    }

    package MXv1Indexing {

        complex type XSDataIndexingInput extends XSDataInput {
            crystal : XSDataCrystal optional
            dataCollection : XSDataCollection
            experimentalCondition : XSDataExperimentalCondition optional
        }

        complex type XSDataIndexingResult extends XSDataResult {
            image : XSDataImage []
            indexingLogFile : XSDataFile optional
            labelitIndexing : XSDataBoolean
            predictionResult : XSDataGeneratePredictionResult optional
            selectedSolution : XSDataIndexingSolutionSelected
            optional
            solution : XSDataIndexingSolution [] optional
        }

        complex type XSDataIndexingSolution extends XSData {
            crystal : XSDataCrystal
            number : XSDataInteger
            penalty : XSDataFloat
        }

        complex type XSDataIndexingSolutionSelected extends XSDataIndexingSolution {
            experimentalConditionRefined : XSDataExperimentalCondition
            mosaicityEstimation : XSDataFloat optional
            orientation : XSDataOrientation
            statistics : XSDataStatisticsIndexing
        }

        complex type XSDataOrientation extends XSData {
            matrixA : XSDataMatrixDouble
            matrixU : XSDataMatrixDouble
        }

        complex type XSDataStatisticsIndexing extends XSData {
            beamPositionShiftX : XSDataLength
            beamPositionShiftY : XSDataLength
            spotDeviationAngular : XSDataAngle
            spotDeviationPositional : XSDataLength
            spotsTotal : XSDataInteger
            spotsUsed : XSDataInteger
        }

    }

    package MXv1PredictionAndIntegration {

        complex type XSDataGeneratePredictionInput extends XSDataInput {
            "This generalisation is not very logical in terms of names, it should be fixed after the prototype (see bug #49)."
            dataCollection : XSDataCollection
            selectedIndexingSolution : XSDataIndexingSolutionSelected
        }

        complex type XSDataGeneratePredictionResult extends XSDataResult {
            predictionImage : XSDataImage []
        }

        complex type XSDataIntegrationInput extends XSDataGeneratePredictionInput {
            "This generalisation is not very logical in terms of names, it should be fixed after the prototype (see bug #49)."
            crystalRefined : XSDataCrystal optional
            experimentalConditionRefined : XSDataExperimentalCondition optional
        }

        complex type XSDataIntegrationResult extends XSDataResult {
            integrationSubWedgeResult : XSDataIntegrationSubWedgeResult [] optional
        }

        complex type XSDataIntegrationSubWedgeResult extends XSData {
            bestfileDat : XSDataString
            bestfileHKL : XSDataString
            bestfilePar : XSDataString
            experimentalConditionRefined : XSDataExperimentalCondition
            generatedMTZFile : XSDataFile
            integrationLogFile : XSDataFile
            statistics : XSDataStatisticsIntegration
            statisticsPerResolutionBin : XSDataStatisticsIntegrationPerResolutionBin []
            subWedgeNumber : XSDataInteger
        }

        complex type XSDataStatisticsIntegration extends XSData {
            RMSSpotDeviation : XSDataLength
            iOverSigmaAtHighestResolution : XSDataDouble
            iOverSigmaOverall : XSDataDouble
            numberOfBadReflections : XSDataInteger
            numberOfFullyRecordedReflections : XSDataInteger
            numberOfNegativeReflections : XSDataInteger
            numberOfOverlappedReflections : XSDataInteger
            numberOfPartialReflections : XSDataInteger
            numberOfReflectionsGenerated : XSDataInteger
        }

        complex type XSDataStatisticsIntegrationAverageAndNumberOfReflections {
            averageIOverSigma : XSDataDouble
            averageIntensity : XSDataDouble
            averageSigma : XSDataDouble
            numberOfReflections : XSDataInteger
        }

        complex type XSDataStatisticsIntegrationPerReflectionType extends XSData {
            fullyRecorded : XSDataStatisticsIntegrationAverageAndNumberOfReflections
            partials : XSDataStatisticsIntegrationAverageAndNumberOfReflections
        }

        complex type XSDataStatisticsIntegrationPerResolutionBin extends XSData {
            maxResolution : XSDataDouble
            minResolution : XSDataDouble
            profileFitted : XSDataStatisticsIntegrationPerReflectionType
            summation : XSDataStatisticsIntegrationPerReflectionType
        }

    }

    package MXv1Sample {

        complex type XSDataAtom extends XSData {
            "This object describes a single atom content (of type \'symbol\' i.e \'S\') that could be either expressed in concentration if dilute in a solvent (mM) or in number in a structure"
            concentration : XSDataDouble optional
            numberOf : XSDataDouble optional
            symbol : XSDataString
        }

        complex type XSDataAtomicComposition extends XSData {
            atom : XSDataAtom [] optional
        }

        complex type XSDataChain extends XSData {
            "A polymer chain of type \'protein\', \'dna\' or \'rna\' that contains monomers (which number is defined by numberOfMonomers) and a list of heavy atoms. The number of this is particular chain in the whole polymer is defined by numberOfCopies."
            heavyAtoms : XSDataAtomicComposition
            numberOfCopies : XSDataDouble
            "number of identical chain within the structure"
            numberOfMonomers : XSDataDouble
            "should be the number of amino-acid, ribonuclotides or desoxyribonucleotides depending on the type"
            ^type : XSDataString "should be either: \'protein\', \'dna\'or \'rna\'"
        }

        complex type XSDataChemicalCompositionMM extends XSData {
            "This is the composition of a crystal sample of a Macro Molecule (MM stand for Macro Molecule)"
            solvent : XSDataSolvent
            structure : XSDataStructure
        }

        complex type XSDataLigand extends XSData {
            "A polymer ligand that contains a set of heavy atoms, the number of all the light atoms (weight <= Oxygen) and the number of copies of this particular ligand in the polymer."
            heavyAtoms : XSDataAtomicComposition
            numberOfCopies : XSDataDouble
            "should be the number of chemically identical ligands in the structure"
            numberOfLightAtoms : XSDataDouble
            "Should be the total of the number of atoms of C, O, N\r\nH is negligible"
        }

        complex type XSDataSample extends XSData {
            "This defines the main properties of a sample:\r\n- absorbed dose rate in Gray/sec\r\n- shape: the factor that is related to the sample and the beam size (1 if crystal smaller than beam size or = to the ratio of crystal size to the beam size if the beam is smaller then crystal).\r\n- sample size\r\n- the susceptibility of the sample to radiation damage."
            absorbedDoseRate : XSDataAbsorbedDoseRate optional
            radiationDamageModelBeta : XSDataDouble optional
            radiationDamageModelGamma : XSDataDouble optional
            shape : XSDataDouble optional
            size : XSDataSize optional
            susceptibility : XSDataDouble optional
        }

        complex type XSDataSampleCrystal extends XSDataSample {
            "A crystal sample. Inherites of all the XSDataSample attributes (inheritance relationship). In addition has the crystallographic properties (cell, mosaicity, space, group)"
            crystal : XSDataCrystal
        }

        complex type XSDataSampleCrystalMM extends XSDataSampleCrystal {
            "A particular crystal sample that contains a macro molecule defined by its chemical composition."
            chemicalComposition : XSDataChemicalCompositionMM
        }

        complex type XSDataSolvent extends XSData {
            "Defines the content of the solvent by defining the concentration of elements in millimoles/litre. Note that this atom composition should not include oxygen and lighter atoms."
            atoms : XSDataAtomicComposition
        }

        complex type XSDataStructure extends XSData {
            "This is the polymer structure composed by a list of chains and a list of ligands.\r\nThis structure is also defined by its number in the asymmetric unit."
            chain : XSDataChain [] optional
            ligand : XSDataLigand [] optional
            numberOfCopiesInAsymmetricUnit : XSDataDouble
        }

    }

    package MXv1Strategy {

        complex type XSDataCollectionPlan extends XSData {
            "The comment can be used for describing exotic data collections, for example without collecting any images."
            collectionPlanNumber : XSDataInteger
            collectionStrategy : XSDataCollection
            comment : XSDataString optional
            statistics : XSDataStatisticsStrategy
            strategySummary : XSDataStrategySummary
        }

        complex type XSDataInputStrategy extends XSDataInput {
            bestFileContentDat : XSDataString
            bestFileContentHKL : XSDataString []
            bestFileContentPar : XSDataString
            crystalRefined : XSDataCrystal
            dataCollection : XSDataCollection optional
            diffractionPlan : XSDataDiffractionPlan
            experimentalCondition : XSDataExperimentalCondition
            sample : XSDataSampleCrystalMM
            xdsBackgroundImage : XSDataFile optional
        }

        complex type XSDataResolutionBin extends XSData {
            IOverSigma : XSDataDouble
            IOverSigmaChi : XSDataDouble optional
            averageIntensity : XSDataDouble
            averageIntensityOverAverageSigma : XSDataDouble optional
            averageSigma : XSDataDouble
            chi2 : XSDataDouble
            optional
            completeness : XSDataDouble
            maxResolution : XSDataDouble
            minResolution : XSDataDouble
            percentageOverload : XSDataDouble
            rFactor : XSDataDouble
            rFriedel : XSDataDouble optional
            redundancy : XSDataDouble
        }

        complex type XSDataResultStrategy extends XSDataResult {
            "Several collection plans could be present in case of multi-sweep strategy"
            bestGraphFile : XSDataFile []
            optional
            bestLogFile : XSDataFile optional
            collectionPlan : XSDataCollectionPlan [] optional
            raddoseLogFile : XSDataFile optional
            sample : XSDataSampleCrystalMM optional
        }

        complex type XSDataStatisticsStrategy extends XSData {
            resolutionBin : XSDataResolutionBin [] optional
        }

        complex type XSDataStrategySummary extends XSData {
            "OBS! The attribute \"attenuation\" in XSDataStrategySummary is deprecated, see bug #379. Please use instead \"transmission\" in XSDataBeam."
            attenuation : XSDataDouble optional
            completeness : XSDataDouble
            iSigma : XSDataDouble
            rankingResolution : XSDataDouble
            redundancy : XSDataDouble
            resolution : XSDataDouble
            resolutionReasoning : XSDataString
            totalDataCollectionTime : XSDataTime
            totalExposureTime : XSDataTime
        }

    }

}

Datamodels: XSDataCollection