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Class: PeakDim


    Crosspeak dimension
    Note: There is no attribute 'linewidth', as the term is too ambiguous in practical use to allow a clear definition. Various aspects of line widths are covered by positionError, boxWidth, and decayRate.
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Attribute Methods
Link Attribute Methods
Class Methods
Factory Methods
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Appendix

Inheritance:


Details:

Parent: link peak to class Peak
Main key: dim
Mandatory Attributes: dim
Known Subclasses: None
Children:
link peakDimComponents to class PeakDimComponent
link peakDimContribs to class AbstractPeakDimContrib
Constructor: newObj = PeakDim( peak,dim=value, ... )

Attributes (in package)

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Attribute Type Multiplicity Description
annotation Line 0..1 Descriptive text string, designed for annotation of Xpks on graphics displays. Long annotations should be avoided.  
boxWidth Float 0..1 The full width of the peak footprint in points, i.e. the width of the area that should be considered for integration, fitting, etc. It is not a very precise definition, but this is an input parameter rather than an output parameter.  
decayRate Float 0..1 Fitted decay rate in the time domain (raw-data domain). If the raw data domain unit is seconds, the unit of decayRate is Hz. If an exponential decay is fitted to the function exp(-piRt), the decayrate is R. For a true Lorenzian decayRate is equal to the full-width-half-height.  
decayRateError Float 0..1 Uncertainty (standard deviation) of peak decayRate.  
dim PositiveInt 1..1 Dimension number, from 1 to nuber of dimensions - used as key to get the corresponding DataDim  
lineWidth Float 0..1 Full-width-half-height of peak/multiplet in this dimension. Unit is DataDimRef.unit (typically Hz). Do NOT use this attribute if your data are better described by one of the alternatives : positionError - standard deviation of measured position boxWidth - footprint width of peak for integration limits etc. decayRate - fitted decay rate (in Hz)  
numAliasing Int 1..1 number of aliasings. The real peak position is defined as positionPoints + numAliasing*dataDimRef.dataDim.numPointsOri  
phase Float 0..1 Phase (in degrees) of peak  
phaseError Float 0..1 Uncertainty (standard deviation) of peak phase.  
position Float 0..1 Peak position in *point numbers*. Positions must be between 1.0 and npoints+1. The peak position in the appropriate unit (typically ppm), is given in the derived attribute 'value'.  
positionError Float 0..1 Uncertainty (standard deviation) of peak position (in point numbers).  
realValue Float 0..1 Derived. Peak position in units of ExpDimRef.unit, corresponding to the main DataDimRef. Derived but settable, with special behaviour. If set to an explicit value this will be the value returned later (case 1). If not set / set to None (case 2) self.value will be returned when there are no PeakDimComponents. Ifset to None and there are PeakDimComponents, None is returned. Peak.realValue always gives the best value for the quantity described in the main DataDimRef. The organisation of this parameter lets you store values for the central chemical shift of multiplets (e.g. DQF-COSY), while you still get the peak value in the simple case.  
realValueImpl Float 0..1 Underlying attribute used to store realValue. For technical reasons realValue must be derived, so the value, when set, is stored here instead. It is recommended to read and set realValue and ignore this attribute.  
value Float 0..1 Derived. Real peak position in units of ExpDimRef.unit, after correcting for numAliasing, calculated using the directly linked (main component) DataDimRef. If the DataDimRef is ambiguous or absent, the value is None. If there are PeakDimComponents present the value you get will not reflect the measurement that corresponds to the dataDimRef. If you want either correct values or 'None', use realValue instead. value can be set, provided there is one unique DataDimRef. The effect will be to update position and numAliasing to reflect the value.  
valueError Float 0..1 Derived. Uncertainty (standard deviation) on value, in units of ExpDimRef.unit. Derived from positionError. Depends on the presence of one unambiguous DataDimRef, and returns None if no such is found. valueError can also be set if there is an unambiguous DataDimRef - the effect will be to update positionError.  

Inherited Attributes (not in package): applicationDataclassNamefieldNamesinConstructorisDeletedmetaclasspackageNamepackageShortNamequalifiedName

Link Attributes (in package)

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Attribute Type Multiplicity Description
dataDerivations AbstractDataDerivation 0..* DataDerivations calculated using PeakDim  
dataDim AbstractDataDim 1..1 Derived. DataDim corresponding to PeakDim  
dataDimRef DataDimRef 0..1 DataDimRef relevant to PeakDim - As there may be several alternative dataDimRefs for a given dimension, assigning this link may involve a measure of assignment.  
mainPeakDimContribs AbstractPeakDimContrib 0..* Derived. AbstractPeakDimContribs that refer to the main assignment component of the peakDim, rather than to any explicit PeakDimComponent.  
measurements AbstractMeasurement 0..* Measurements deriving from PeakDim.  
parent Peak 1..1 link to parent object - synonym for peak  
peak Peak 1..1 (Parent link). parent link  
peakDimComponents PeakDimComponent 0..* (Child link). child link to class PeakDimComponent  
peakDimContribs AbstractPeakDimContrib 0..* (Child link). child link to class AbstractPeakDimContrib  

Inherited Attributes (not in package): accessactiveAccessroottopObject

Attribute Methods (in package)

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Attribute Method Return Parameters Comment
annotation
getAnnotation Line -
setAnnotation - Line
boxWidth
getBoxWidth Float -
setBoxWidth - Float
decayRate
getDecayRate Float -
setDecayRate - Float
decayRateError
getDecayRateError Float -
setDecayRateError - Float
dim
getDim PositiveInt -
setDim - PositiveInt
lineWidth
getLineWidth Float -
setLineWidth - Float
numAliasing
getNumAliasing Int -
setNumAliasing - Int
phase
getPhase Float -
setPhase - Float
phaseError
getPhaseError Float -
setPhaseError - Float
position
getPosition Float -
setPosition - Float
positionError
getPositionError Float -
setPositionError - Float
realValue
getRealValue Float - non-std.
setRealValue - Float non-std.
realValueImpl
getRealValueImpl Float -
setRealValueImpl - Float
value
getValue Float - non-std.
setValue - Float non-std.
valueError
getValueError Float - non-std.
setValueError - Float non-std.

Link Attribute Methods (in package)

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Attribute Method Return Parameters Comment
dataDerivations
getDataDerivations AbstractDataDerivation Set -
setDataDerivations - AbstractDataDerivation Set
sortedDataDerivations AbstractDataDerivation List -
addDataDerivation - AbstractDataDerivation
removeDataDerivation - AbstractDataDerivation
findFirstDataDerivation AbstractDataDerivation keyword=value pairs
findAllDataDerivations AbstractDataDerivation Set keyword=value pairs
dataDim
getDataDim AbstractDataDim - non-std.
dataDimRef
getDataDimRef DataDimRef -
setDataDimRef - DataDimRef
mainPeakDimContribs
getMainPeakDimContribs AbstractPeakDimContrib Set - non-std.
sortedMainPeakDimContribs AbstractPeakDimContrib List -
findFirstMainPeakDimContrib AbstractPeakDimContrib keyword=value pairs
findAllMainPeakDimContribs AbstractPeakDimContrib Set keyword=value pairs
measurements
getMeasurements AbstractMeasurement Set -
setMeasurements - AbstractMeasurement Set
sortedMeasurements AbstractMeasurement List -
addMeasurement - AbstractMeasurement
removeMeasurement - AbstractMeasurement
findFirstMeasurement AbstractMeasurement keyword=value pairs
findAllMeasurements AbstractMeasurement Set keyword=value pairs
parent
getParent Peak -
peak
getPeak Peak -
peakDimComponents
getPeakDimComponents PeakDimComponent Set -
sortedPeakDimComponents PeakDimComponent List -
findFirstPeakDimComponent PeakDimComponent keyword=value pairs
findAllPeakDimComponents PeakDimComponent Set keyword=value pairs
peakDimContribs
getPeakDimContribs AbstractPeakDimContrib Set -
sortedPeakDimContribs AbstractPeakDimContrib List -
findFirstPeakDimContrib AbstractPeakDimContrib keyword=value pairs
findAllPeakDimContribs AbstractPeakDimContrib Set keyword=value pairs

Class Methods (in package)

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Method Return Parameters Comment
checkValid - Boolean
checkAllValid - Boolean
getByKey PeakDim 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
newPeakDimComponent PeakDimComponent ...
newPeakDimContrib PeakDimContrib peakContribs, resonance, ...
newPeakDimContribN PeakDimContribN peakContribs, resonances, ...

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_00013

isImplicit:

False

Tag

Value
repositoryId $Id: PeakDim.xml,v 1.68 2011-01-13 14:40:35 rhfogh Exp $

Tag

Value
repositoryTag $Name: not supported by cvs2svn $

Special constructor code:

None

Special destructor code:

None

Constraints:

None
Known inward one-way links: None
  Data Model Version 2.0.6
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  Autogenerated by  PyApiDocGen  revision 1.3   on  Wed Aug 7 15:06:46 2013    from data model package  ccp.api.nmr.Nmr.PeakDim   revision 1.68  
  Work done by the CCPN team.
www.ccpn.ac.uk