ccpn.core.lib.PeakPickers package

PeakPickers; user peakPickers are automatically picked up by getPeakPickerTypes

Submodules

ccpn.core.lib.PeakPickers.NmrgluePeakPicker module

Nmrglue-based PeakPicker;

class ccpn.core.lib.PeakPickers.NmrgluePeakPicker.NmrgluePeakPicker(**kwargs)

Bases: ccpn.core.lib.PeakPickers.PeakPickerABC.PeakPickerABC

A peak picker using the Nmrglue peak picking code

findPeaks(data) → list

Find the peaks in the numpy data; return a list with SimplePeak instances; note that SimplePeak.points are ordered z,y,x for nD, in accordance with the numpy data array

Parameters

data – numpy nD array

:return list with SimplePeak instances

onlyFor1D = False

peakPickerType = 'Nmrglue'

ccpn.core.lib.PeakPickers.PeakPicker1D module

Simple 1D PeakPicker; for testing only

class ccpn.core.lib.PeakPickers.PeakPicker1D.PeakPicker1D(**kwargs)

Bases: ccpn.core.lib.PeakPickers.PeakPickerABC.PeakPickerABC

A peak picker based on Eli Billauer, 3.4.05. algorithm (see _findMaxima function).

findPeaks(data)

find the peaks in data (type numpy-array) and return as a list of SimplePeak instances note that SimplePeak.points are ordered z,y,x for nD, in accordance with the numpy nD data array

called from the pickPeaks() method

any required parameters that findPeaks method needs should be initialised/set before using the setParameters() method; i.e.:

myPeakPicker = PeakPicker(spectrum=mySpectrum) myPeakPicker.setParameters(dropFactor=0.2, positiveThreshold=1e6, negativeThreshold=None) corePeaks = myPeakPicker.pickPeaks(axisDict={‘H’:(6.0,11.5),’N’:(102.3,130.0)}, spectrum.peaklists[-1])

Parameters

data – nD numpy array

:return list of SimplePeak instances

To be subclassed

onlyFor1D = True

peakPickerType = 'PeakPicker1D'

ccpn.core.lib.PeakPickers.PeakPickerABC module

PeakPicker abstract base class

class ccpn.core.lib.PeakPickers.PeakPickerABC.PeakPickerABC(**kwargs)

Bases: ccpn.util.traits.CcpNmrJson.CcpNmrJson

ABC for implementation of a peak picker

autoFit

classVersion = 1.0

defaultPointExtension = 1

dimensionCount

dropFactor

findPeaks(data) → list

find the peaks in data (type numpy-array) and return as a list of SimplePeak instances note that SimplePeak.points are ordered z,y,x for nD, in accordance with the numpy nD data array

called from the pickPeaks() method

any required parameters that findPeaks method needs should be initialised/set before using the setParameters() method; i.e.:

myPeakPicker = PeakPicker(spectrum=mySpectrum) myPeakPicker.setParameters(dropFactor=0.2, positiveThreshold=1e6, negativeThreshold=None) corePeaks = myPeakPicker.pickPeaks(axisDict={‘H’:(6.0,11.5),’N’:(102.3,130.0)}, spectrum.peaklists[-1])

Parameters

data – nD numpy array

:return list of SimplePeak instances

To be subclassed

fitMethod

A trait that defines a string object, casts from bytes object and is json serialisable

keysInOrder = True

negativeThreshold

onlyFor1D = False

peakPickerType = None

pickPeaks(sliceTuples, peakList, positiveThreshold=None, negativeThreshold=None) → list

Pick peaks in spectral region defined by sliceTuples=[(start_1,stop_1), (start_2,stop_2), …], sliceTuples are 1-based; sliceTuple stop values are inclusive (i.e. different from the python slice object)

Parameters

• sliceTuples – list of (start,stop) point values per dimension (1-based)

• peakList – peakList instance to add newly pickedPeaks

Returns

list of core.Peak instances

pointExtension

positiveThreshold

saveAllTraitsToJson = True

setDefaultParameters()

Set default values for all parameters

setParameters(**parameters)

Set parameters as attributes of self

Example calling function:

>>> peakPicker.setParameters(**parameters)
>>> peakPicker.setParameters(fitMethod='gaussian', dropFactor=0.1)

The contents of parameters to be defined by the peakPicker class. In the above example, ‘fitMethod’ and ‘dropFactor’ are defined in the baseClass, but their properties and types are to be defined by the subclass.

Parameters

parameters – dict of key, value pairs

class ccpn.core.lib.PeakPickers.PeakPickerABC.PeakPickerTrait(**kwds)

Bases: ccpn.util.traits.CcpNmrTraits.Instance

Specific trait for a PeakPicker instance.

class jsonHandler

Bases: ccpn.util.traits.TraitJsonHandlerBase.CcpNmrJsonClassHandlerABC

klass

alias of ccpn.core.lib.PeakPickers.PeakPickerABC.PeakPickerABC

class ccpn.core.lib.PeakPickers.PeakPickerABC.SimplePeak(points, height, lineWidths=None, volume=None, clusterId=None)

Bases: object

A simple class to hold peak data

currentIndx = 0

ccpn.core.lib.PeakPickers.PeakPickerABC.getPeakPickerTypes() → collections.OrderedDict

Get peakPicker types

Returns

a dictionary of (type-identifier-strings, PeakPicker classes) as (key, value) pairs

ccpn.core.lib.PeakPickers.PeakPickerABC.isRegistered(peakPickerType)

Return True if a PeakPicker class of type peakPickerType is registered

Parameters

peakPickerType – type str; reference to peakPickerType of peakPicker class

Returns

True if class referenced by peakPickerType has been registered else False

ccpn.core.lib.PeakPickers.PeakPickerNd module

Module Documentation here

class ccpn.core.lib.PeakPickers.PeakPickerNd.PeakPickerNd(**kwargs)

Bases: ccpn.core.lib.PeakPickers.PeakPickerABC.PeakPickerABC

A simple Nd peak picker for testing

checkAllAdjacent

findPeaks(data) → list

find the peaks in data (type numpy-array) and return as a list of SimplePeak instances note that SimplePeak.points are ordered z,y,x for nD, in accordance with the numpy nD data array

called from the pickPeaks() method

any required parameters that findPeaks method needs should be initialised/set before using the setParameters() method; i.e.:

myPeakPicker = PeakPicker(spectrum=mySpectrum) myPeakPicker.setParameters(dropFactor=0.2, positiveThreshold=1e6, negativeThreshold=None) corePeaks = myPeakPicker.pickPeaks(axisDict={‘H’:(6.0,11.5),’N’:(102.3,130.0)}, spectrum.peaklists[-1])

Parameters

data – nD numpy array

:return list of SimplePeak instances

fitExistingPeaks(peaks: Sequence[Peak])

Refit the current selected peaks. Must be called with peaks that belong to this peakList

halfBoxFindPeaksWidth

halfBoxFitWidth

halfBoxSearchWidth

minimumLineWidth

Casting list, any iterable

noise

onlyFor1D = False

peakPickerType = 'PeakPickerNd'

pickPeaks(sliceTuples, peakList, positiveThreshold=None, negativeThreshold=None) → list

Set the default functionality for picking simplePeaks from the region defined by axisDict

searchBoxDoFit

searchBoxMode

setLineWidths

singularMode

snapToExtremum(peak) → list

Parameters

• axisDict – Axis limits are passed in as a dict of (axisCode, tupleLimit) key, value pairs with the tupleLimit supplied as (start,stop) axis limits in ppm (lower ppm value first).

• peakList – peakList instance to add newly pickedPeaks

Returns

list of core.Peak instances

ccpn.core.lib.PeakPickers.Simple1DPeakPicker module

Simple 1D PeakPicker; for testing only

class ccpn.core.lib.PeakPickers.Simple1DPeakPicker.Simple1DPeakPicker(**kwargs)

Bases: ccpn.core.lib.PeakPickers.PeakPickerABC.PeakPickerABC

A simple peak picker for testing

findPeaks(data) → list

Find the local (positive) maxima in the numpy data; return a list with SimplePeak instances; note that SimplePeak.points are ordered z,y,x for nD, in accordance with the numpy data array

onlyFor1D = True

peakPickerType = 'Simple1D'