Data Model version 2.1.2
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Class: DataSource

The DataSource destructor includes non-standard actions.
    This class describes the stored data matrix from an NMR spectrum.
    It is a general class that may be used to describe data in the time domain, frequency domain a combination of the two, or axes that are neither time nor frequency
    The actual data are kept in a location defined by the dataLocation link. The DataSource attributes contain the information required to extract the data from the source file, but the data model as such does not include the actual data matrix
Attributes
Link Attributes
Attribute Methods
Link Attribute Methods
Class Methods
Factory Methods
Other Methods
Appendix

Inheritance:


Details:

Parent: link experiment to class Experiment
Main key: serial
Mandatory Attributes: dataType, name, numDim
Partitions Children: True
Known Subclasses: None
Children:
link dataDims to class AbstractDataDim
link dataSourceImages to class DataSourceImage
link peakLists to class PeakList
link sparseSamplings to class SparseSampling
Constructor: newObj = DataSource( experiment,dataType=value, name=value, numDim=value, ... )

Attributes (in package)

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Attribute Type Multiplicity Description
dataType DataSourceDataType 1..1 FID, part-processed, processed, other,or whatever.  
details String 0..1 Free text, for notes, explanatory comments, etc.  
isNormalStorage Boolean 1..1 Can this file be read using the normal storage algorithms. Default true. E.g. Kay type P+/-N storage has False for this parameter  
isSimulated Boolean 1..1 Is the DataSource simulated rather than measured?  
name Line 1..1 name of DataSource  
noiseLevel NonNegativeFloat 0..1 Estimated noise level for a spectrum, defined as the estimated standard deviation of the points from the baseplane/line.  
numDim Int 1..1 Number of dimensions - may be different from the numDim of the Experiment to which the DataSource belongs (e.g. projections).  
numShapes NonNegativeInt 1..1 Number of shapes in each matrix decomposition component. If set to zero the data are not decomposed by shape - which is the normal case.  
numSparsePoints NonNegativeInt 1..1 Number of time increments acquired. If nonzero, this signifies that the original data are sparsely sampled - otherwise it can be derived from the size of the grid. Note that this counts the number of time steps, a hypercomplex point counts as one point even if it requires eight real numbers to describe it.  
recordNumber Int 1..1 Number of record (starting at zero) of data record in dataStore. May or may not be relevant, depending on the type of dataStore  
scale Float 1..1 Scaling factor for intensities and volumes in a given datasource, for use when comparing intensities etc. between spectra. Intensities and volumes should be *multiplied* by scale before comparison, so that a scale of e.g. 10.0 means that the intensities are ten times larger than reflected by the numbers stored in the file.  
serial Int 1..1 Serial number of object. Serves as object main key. Serial numbers of deleted objects are not re-used. Serial numbers can only be set by the implementation. Values are in practice always positive, since negative values are interpreted as a signal to set the next free serial  
signalLevel NonNegativeFloat 0..1 'Standard' signal level, estimated according to signalLevelMethod. the snRatio is defined as signalLevel/noiseLevel.  
snRatio NonNegativeFloat 0..1 Derived. S/N ratio, calculated as signalLevel/noiseLevel.  
storageDetails String 0..1 Text description of storage for cases not covered by standard algorithms (isNormalStorage false).  

Inherited Attributes (not in package): applicationDataclassNamefieldNamesinConstructorisDeletedmetaclasspackageNamepackageShortNamequalifiedName

Link Attributes (in package)

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Attribute Type Multiplicity Description
activePeakList PeakList 0..1 Currently active peaklist for DataSource - i.e. PeakList where newly picked peaks will be placed.  
analysisLayouts ccpnmr.api.AnalysisV3.AnalysisLayout 0..* AnalysisLayout referring to DataSources  
analysisPanels ccpnmr.api.AnalysisV3.AnalysisPanel 0..* AnalysisPanels referring to DataSource  
analysisSpectra ccpnmr.api.AnalysisV3.AnalysisSpectrum 0..*  
analysisSpectrum ccpnmr.api.Analysis.AnalysisSpectrum 0..1 AnalysisSpectrum that points to Spectrum  
compressMethod ccp.api.general.Method.Method 0..1 Method used for data compression.  
dataDims AbstractDataDim 0..* (Child link). child link  
dataSourceImages DataSourceImage 0..* (Child link). child link to class DataSourceImage  
dataStore ccp.api.general.DataLocation.NumericMatrix 0..1 Data store where data are located  
experiment Experiment 1..1 (Parent link). parent link  
parent Experiment 1..1 link to parent object - synonym for experiment  
peakLists PeakList 0..* (Child link). child link to class PeakList  
processMethod ccp.api.general.Method.Method 0..1 Method used for processing DataSource.  
processedFrom DataSource 0..1 DataSource used to create the current DataSource. If there are several 'ancestor' DataSources stored, this should link to the most recent ancestor. E.g. the pre-FT data if the current data were Fourier transformed.  
processedTo DataSource 0..* DataSources derived directly from the current DataSource.  
refNmrSpectra ccp.api.lims.RefData.RefNmrSpectrum 0..*  
snMethod ccp.api.general.Method.Method 0..1 Method used to determine S/N ratio  
sparseSamplings SparseSampling 0..* (Child link). child link to class SparseSampling  
trialExperiments ccp.api.nmr.NmrScreen.TrialExperiment 0..*  

Inherited Attributes (not in package): accessactiveAccessroottopObject

Attribute Methods (in package)

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Attribute Method Return Parameters Comment
dataType
getDataType DataSourceDataType -
setDataType - DataSourceDataType
details
getDetails String -
setDetails - String
isNormalStorage
getIsNormalStorage Boolean -
setIsNormalStorage - Boolean
isSimulated
getIsSimulated Boolean -
setIsSimulated - Boolean
name
getName Line -
setName - Line
noiseLevel
getNoiseLevel NonNegativeFloat -
setNoiseLevel - NonNegativeFloat
numDim
getNumDim Int -
setNumDim - Int
numShapes
getNumShapes NonNegativeInt -
setNumShapes - NonNegativeInt
numSparsePoints
getNumSparsePoints NonNegativeInt -
setNumSparsePoints - NonNegativeInt
recordNumber
getRecordNumber Int -
setRecordNumber - Int
scale
getScale Float -
setScale - Float
serial
getSerial Int -
setSerial - Int
signalLevel
getSignalLevel NonNegativeFloat -
setSignalLevel - NonNegativeFloat
snRatio
getSnRatio NonNegativeFloat - non-std.
storageDetails
getStorageDetails String -
setStorageDetails - String

Link Attribute Methods (in package)

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Attribute Method Return Parameters Comment
activePeakList
getActivePeakList PeakList -
setActivePeakList - PeakList
analysisLayouts
getAnalysisLayouts ccpnmr.api.AnalysisV3.AnalysisLayout Set -
setAnalysisLayouts - ccpnmr.api.AnalysisV3.AnalysisLayout Set
sortedAnalysisLayouts ccpnmr.api.AnalysisV3.AnalysisLayout List -
addAnalysisLayout - ccpnmr.api.AnalysisV3.AnalysisLayout
removeAnalysisLayout - ccpnmr.api.AnalysisV3.AnalysisLayout
findFirstAnalysisLayout ccpnmr.api.AnalysisV3.AnalysisLayout keyword=value pairs
findAllAnalysisLayouts ccpnmr.api.AnalysisV3.AnalysisLayout Set keyword=value pairs
analysisPanels
getAnalysisPanels ccpnmr.api.AnalysisV3.AnalysisPanel Set -
setAnalysisPanels - ccpnmr.api.AnalysisV3.AnalysisPanel Set
sortedAnalysisPanels ccpnmr.api.AnalysisV3.AnalysisPanel List -
addAnalysisPanel - ccpnmr.api.AnalysisV3.AnalysisPanel
removeAnalysisPanel - ccpnmr.api.AnalysisV3.AnalysisPanel
findFirstAnalysisPanel ccpnmr.api.AnalysisV3.AnalysisPanel keyword=value pairs
findAllAnalysisPanels ccpnmr.api.AnalysisV3.AnalysisPanel Set keyword=value pairs
analysisSpectra
getAnalysisSpectra ccpnmr.api.AnalysisV3.AnalysisSpectrum Set -
setAnalysisSpectra - ccpnmr.api.AnalysisV3.AnalysisSpectrum Set
sortedAnalysisSpectra ccpnmr.api.AnalysisV3.AnalysisSpectrum List -
findFirstAnalysisSpectrum ccpnmr.api.AnalysisV3.AnalysisSpectrum keyword=value pairs
findAllAnalysisSpectra ccpnmr.api.AnalysisV3.AnalysisSpectrum Set keyword=value pairs
analysisSpectrum
getAnalysisSpectrum ccpnmr.api.Analysis.AnalysisSpectrum -
setAnalysisSpectrum - ccpnmr.api.Analysis.AnalysisSpectrum
compressMethod
getCompressMethod ccp.api.general.Method.Method -
setCompressMethod - ccp.api.general.Method.Method
dataDims
getDataDims AbstractDataDim Set -
sortedDataDims AbstractDataDim List -
findFirstDataDim AbstractDataDim keyword=value pairs
findAllDataDims AbstractDataDim Set keyword=value pairs
dataSourceImages
getDataSourceImages DataSourceImage Set -
sortedDataSourceImages DataSourceImage List -
findFirstDataSourceImage DataSourceImage keyword=value pairs
findAllDataSourceImages DataSourceImage Set keyword=value pairs
dataStore
getDataStore ccp.api.general.DataLocation.NumericMatrix -
setDataStore - ccp.api.general.DataLocation.NumericMatrix
experiment
getExperiment Experiment -
parent
getParent Experiment -
peakLists
getPeakLists PeakList Set -
sortedPeakLists PeakList List -
findFirstPeakList PeakList keyword=value pairs
findAllPeakLists PeakList Set keyword=value pairs
processMethod
getProcessMethod ccp.api.general.Method.Method -
setProcessMethod - ccp.api.general.Method.Method
processedFrom
getProcessedFrom DataSource -
setProcessedFrom - DataSource
processedTo
getProcessedTo DataSource Set -
setProcessedTo - DataSource Set
sortedProcessedTo DataSource List -
addProcessedTo - DataSource
removeProcessedTo - DataSource
findFirstProcessedTo DataSource keyword=value pairs
findAllProcessedTo DataSource Set keyword=value pairs
refNmrSpectra
getRefNmrSpectra ccp.api.lims.RefData.RefNmrSpectrum Set -
setRefNmrSpectra - ccp.api.lims.RefData.RefNmrSpectrum Set
sortedRefNmrSpectra ccp.api.lims.RefData.RefNmrSpectrum List -
addRefNmrSpectrum - ccp.api.lims.RefData.RefNmrSpectrum
removeRefNmrSpectrum - ccp.api.lims.RefData.RefNmrSpectrum
findFirstRefNmrSpectrum ccp.api.lims.RefData.RefNmrSpectrum keyword=value pairs
findAllRefNmrSpectra ccp.api.lims.RefData.RefNmrSpectrum Set keyword=value pairs
snMethod
getSnMethod ccp.api.general.Method.Method -
setSnMethod - ccp.api.general.Method.Method
sparseSamplings
getSparseSamplings SparseSampling Set -
sortedSparseSamplings SparseSampling List -
findFirstSparseSampling SparseSampling keyword=value pairs
findAllSparseSamplings SparseSampling Set keyword=value pairs
trialExperiments
getTrialExperiments ccp.api.nmr.NmrScreen.TrialExperiment Set -
setTrialExperiments - ccp.api.nmr.NmrScreen.TrialExperiment Set
sortedTrialExperiments ccp.api.nmr.NmrScreen.TrialExperiment List -
addTrialExperiment - ccp.api.nmr.NmrScreen.TrialExperiment
removeTrialExperiment - ccp.api.nmr.NmrScreen.TrialExperiment
findFirstTrialExperiment ccp.api.nmr.NmrScreen.TrialExperiment keyword=value pairs
findAllTrialExperiments ccp.api.nmr.NmrScreen.TrialExperiment Set keyword=value pairs

Class Methods (in package)

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Method Return Parameters Comment
checkValid - Boolean
checkAllValid - Boolean
getByKey DataSource memops.api.Implementation.MemopsObject, Any List static
getFullKey Any List Boolean
getLocalKey Any -
get Any String
set - String, Any

Factory Methods (in package)

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Method Return Parameters
newDataSourceImage DataSourceImage dataStore, ...
newFidDataDim FidDataDim dim, isComplex, numPoints, numPointsValid, valuePerPoint, expDim, ...
newFreqDataDim FreqDataDim dim, isComplex, numPoints, numPointsOrig, valuePerPoint, expDim, ...
newPeakList PeakList ...
newSampledDataDim SampledDataDim dim, isComplex, numPoints, expDim, ...
newSparseSampling SparseSampling dim, ...

Other Methods (in package)

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Method Return Parameters Comment
None

Appendix

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guid:

www.ccpn.ac.uk_Fogh_2006-08-16-14:22:46_00020

isImplicit:

False

Tag

Value
repositoryId $Id: $

Tag

Value
repositoryTag $Name: $

Special constructor code:

None

Special destructor code:

if self is self.experiment.rawData:
  self.experiment.rawData = None

Special postDestructor code:

None

Constraints:

None
Known inward one-way links: ccp.api.nmr.Nmr.Experiment.rawDataccp.api.nmr.NmrCalc.PeakListData.dataSourceccp.api.nmr.NmrCalc.SpectrumData.dataSource
  Data Model Version 2.1.2
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  Autogenerated by  PyApiDocGen  revision 1.3   on  Thu Oct 2 16:09:34 2014    from data model package  ccp.api.nmr.Nmr.DataSource   revision ?  
  Work done by the CCPN team.
www.ccpn.ac.uk