ccpn.pipes package

Subpackages

Submodules

ccpn.pipes.APSPipe module

class ccpn.pipes.APSPipe.APSGuiPipe(name='DEMO3 AutoPS', parent=None, project=None, **kw)[source]

Bases: ccpn.ui.gui.widgets.PipelineWidgets.GuiPipe

pipeName = 'DEMO3 AutoPS'
preferredPipe = True
class ccpn.pipes.APSPipe.APSPipe(application=None)[source]

Bases: ccpn.framework.lib.pipeline.PipeBase.SpectraPipe

Apply phasing to all the spectra in the pipeline

guiPipe

alias of ccpn.pipes.APSPipe.APSGuiPipe

pipeCategory = 'Processing'
pipeName = 'DEMO3 AutoPS'
runPipe(spectra)[source]

auto-phase on the imaginaries

ccpn.pipes.AlignSpectra module

class ccpn.pipes.AlignSpectra.AlignSpectra(application=None)[source]

Bases: ccpn.framework.lib.pipeline.PipeBase.SpectraPipe

guiPipe

alias of ccpn.pipes.AlignSpectra.AlignSpectraGuiPipe

pipeCategory = 'Post-Processing'
pipeName = 'Align Spectra'
runPipe(spectra)[source]
Parameters

spectra – inputData

Returns

aligned spectra

class ccpn.pipes.AlignSpectra.AlignSpectraGuiPipe(name='Align Spectra', parent=None, project=None, **kwds)[source]

Bases: ccpn.ui.gui.widgets.PipelineWidgets.GuiPipe

pipeName = 'Align Spectra'
ccpn.pipes.AlignSpectra.addIndividualShiftToSpectra(spectra, shifts, shiftPeaks=True)[source]
ccpn.pipes.AlignSpectra.addShiftToSpectra(spectra, shift, shiftPeaks=True)[source]

ccpn.pipes.AssignMultiplets module

class ccpn.pipes.AssignMultiplets.FindMultipletsGuiPipe(name='Find Multiplets', parent=None, project=None, **kwds)[source]

Bases: ccpn.ui.gui.widgets.PipelineWidgets.GuiPipe

info = 'This Pipe will group existing peaks in Multiplets. Volume, lineWidths, and position will be calculated for new multiplets or derived from the peaks values.'
pipeName = 'Find Multiplets'
preferredPipe = True
class ccpn.pipes.AssignMultiplets.FindMultipletsPipe(application=None)[source]

Bases: ccpn.framework.lib.pipeline.PipeBase.SpectraPipe

guiPipe

alias of ccpn.pipes.AssignMultiplets.FindMultipletsGuiPipe

pipeCategory = 'Analysis'
pipeName = 'Find Multiplets'
runPipe(spectra)[source]
Parameters

data

Returns

ccpn.pipes.AutoAssignmentPipe module

class ccpn.pipes.AutoAssignmentPipe.AutomatedAssignmentGuiPipe(name='Automated Assignment', parent=None, project=None, **kwds)[source]

Bases: ccpn.ui.gui.widgets.PipelineWidgets.GuiPipe

pipeName = 'Automated Assignment'
class ccpn.pipes.AutoAssignmentPipe.AutomatedAssignmentPipe(application=None)[source]

Bases: ccpn.framework.lib.pipeline.PipeBase.SpectraPipe

guiPipe

alias of ccpn.pipes.AutoAssignmentPipe.AutomatedAssignmentGuiPipe

pipeCategory = 'AnalysisAssign'
pipeName = 'Automated Assignment'
runPipe(spectra)[source]

ccpn.pipes.BaselinePipe module

class ccpn.pipes.BaselinePipe.BaselineCorrection1DPipe(application=None)[source]

Bases: ccpn.framework.lib.pipeline.PipeBase.SpectraPipe

Apply phasing to all the spectra in the pipeline

guiPipe

alias of ccpn.pipes.BaselinePipe.BaselineCorrectionGuiPipe

pipeCategory = 'Post-Processing'
pipeName = 'Baseline Correction'
runPipe(spectra)[source]
Parameters

spectra – inputData

Returns

aligned spectra

class ccpn.pipes.BaselinePipe.BaselineCorrectionGuiPipe(name='Baseline Correction', parent=None, project=None, **kw)[source]

Bases: ccpn.ui.gui.widgets.PipelineWidgets.GuiPipe

pipeName = 'Baseline Correction'
preferredPipe = True

ccpn.pipes.DIPipe module

class ccpn.pipes.DIPipe.DIGuiPipe(name='DEMO4 DI', parent=None, project=None, **kw)[source]

Bases: ccpn.ui.gui.widgets.PipelineWidgets.GuiPipe

pipeName = 'DEMO4 DI'
preferredPipe = True
class ccpn.pipes.DIPipe.DIPipe(application=None)[source]

Bases: ccpn.framework.lib.pipeline.PipeBase.SpectraPipe

Apply phasing to all the spectra in the pipeline

guiPipe

alias of ccpn.pipes.DIPipe.DIGuiPipe

pipeCategory = 'Processing'
pipeName = 'DEMO4 DI'
runPipe(spectra)[source]

Discard the imaginaries

ccpn.pipes.DuplicateSpectraPipe module

class ccpn.pipes.DuplicateSpectraPipe.DuplicateSpectrumGuiPipe(name='Duplicate Spectra', parent=None, project=None, **kwds)[source]

Bases: ccpn.ui.gui.widgets.PipelineWidgets.GuiPipe

pipeName = 'Duplicate Spectra'
preferredPipe = True
class ccpn.pipes.DuplicateSpectraPipe.DuplicateSpectrumPipe(application=None)[source]

Bases: ccpn.framework.lib.pipeline.PipeBase.SpectraPipe

guiPipe

alias of ccpn.pipes.DuplicateSpectraPipe.DuplicateSpectrumGuiPipe

pipeCategory = 'Generic'
pipeName = 'Duplicate Spectra'
runPipe(spectra)[source]
Parameters

spectra – inputData

Returns

new spectra

ccpn.pipes.ExcludeRegionsFromSpectrum module

class ccpn.pipes.ExcludeRegionsFromSpectrum.ExcludeRegionsGuiPipe(name='Exclude Regions', parent=None, project=None, **kwds)[source]

Bases: ccpn.ui.gui.widgets.PipelineWidgets.GuiPipe

pipeName = 'Exclude Regions'
preferredPipe = True
restoreWidgetsState(**widgetsState)[source]

Restore the gui params. overide the default function first to recreate the correct number of boxes. Then call the super to restore values.

class ccpn.pipes.ExcludeRegionsFromSpectrum.ExcludeRegionsPipe(application=None)[source]

Bases: ccpn.framework.lib.pipeline.PipeBase.SpectraPipe

guiPipe

alias of ccpn.pipes.ExcludeRegionsFromSpectrum.ExcludeRegionsGuiPipe

pipeCategory = 'Generic'
pipeName = 'Exclude Regions'
runPipe(spectra)[source]

get excluded region of the spectrum and add to the pipeline kwargs. Spectra is not really needed for this pipe. But is essential for the base class pipe.

ccpn.pipes.ExcludeSolventRegions module

class ccpn.pipes.ExcludeSolventRegions.ExcludeRegionsGuiPipe(name='Exclude Solvent Regions', parent=None, project=None, **kwds)[source]

Bases: ccpn.ui.gui.widgets.PipelineWidgets.GuiPipe

pipeName = 'Exclude Solvent Regions'
preferredPipe = False
class ccpn.pipes.ExcludeSolventRegions.ExcludeRegionsPipe(application=None)[source]

Bases: ccpn.framework.lib.pipeline.PipeBase.SpectraPipe

guiPipe

alias of ccpn.pipes.ExcludeSolventRegions.ExcludeRegionsGuiPipe

pipeCategory = 'Generic'
pipeName = 'Exclude Solvent Regions'
runPipe(spectra)[source]

:get excluded region of the spectrum and add to the pipeline kwargs. Spectra is not really needed for this pipe. But is essential for the base class pipe.

ccpn.pipes.FFTPipe module

class ccpn.pipes.FFTPipe.FFT1DPipe(application=None)[source]

Bases: ccpn.framework.lib.pipeline.PipeBase.SpectraPipe

Apply phasing to all the spectra in the pipeline

guiPipe

alias of ccpn.pipes.FFTPipe.FFTGuiPipe

pipeCategory = 'Processing'
pipeName = 'DEMO2 FFT'
runPipe(spectra)[source]

FFT

class ccpn.pipes.FFTPipe.FFTGuiPipe(name='DEMO2 FFT', parent=None, project=None, **kw)[source]

Bases: ccpn.ui.gui.widgets.PipelineWidgets.GuiPipe

pipeName = 'DEMO2 FFT'
preferredPipe = True

ccpn.pipes.IntegrationPipe module

class ccpn.pipes.IntegrationPipe.CalculateAreaGuiPipe(name='Calculate Integrals 1D (experimental)', parent=None, project=None, **kwds)[source]

Bases: ccpn.ui.gui.widgets.PipelineWidgets.GuiPipe

pipeName = 'Calculate Integrals 1D (experimental)'
preferredPipe = True
class ccpn.pipes.IntegrationPipe.CalculateAreaPipe(application=None)[source]

Bases: ccpn.framework.lib.pipeline.PipeBase.SpectraPipe

guiPipe

alias of ccpn.pipes.IntegrationPipe.CalculateAreaGuiPipe

pipeCategory = 'Analysis'
pipeName = 'Calculate Integrals 1D (experimental)'
runPipe(spectra)[source]
Parameters

data

Returns

ccpn.pipes.NoiseThresholdPipe module

class ccpn.pipes.NoiseThresholdPipe.NoiseThresholdGuiPipe(name='Noise Threshold', parent=None, project=None, **kwds)[source]

Bases: ccpn.ui.gui.widgets.PipelineWidgets.GuiPipe

pipeName = 'Noise Threshold'
preferredPipe = True
class ccpn.pipes.NoiseThresholdPipe.NoiseThresholdPipe(application=None)[source]

Bases: ccpn.framework.lib.pipeline.PipeBase.SpectraPipe

guiPipe

alias of ccpn.pipes.NoiseThresholdPipe.NoiseThresholdGuiPipe

pipeCategory = 'Generic'
pipeName = 'Noise Threshold'
runPipe(spectra)[source]

For Now this pipe is a special case because it doesn’t return a new inputData for the next pipe, but set _kwargs in the pipeline and will be available for the next pipes they might need more then once. If this is run twice, the pipeline will use only the last set. Spectra is not really needed for this pipe. But is essential for the base class pipe.

ccpn.pipes.OLD_PeakPicker1DPipe module

class ccpn.pipes.OLD_PeakPicker1DPipe.PeakPicker1DGuiPipe(name='OLD Peak Picker 1D', parent=None, project=None, **kwds)[source]

Bases: ccpn.ui.gui.widgets.PipelineWidgets.GuiPipe

pipeName = 'OLD Peak Picker 1D'
preferredPipe = True
class ccpn.pipes.OLD_PeakPicker1DPipe.PeakPicker1DPipe(application=None)[source]

Bases: ccpn.framework.lib.pipeline.PipeBase.SpectraPipe

guiPipe

alias of ccpn.pipes.OLD_PeakPicker1DPipe.PeakPicker1DGuiPipe

pipeCategory = 'Analysis'
pipeName = 'OLD Peak Picker 1D'
runPipe(spectra)[source]
Parameters

data

Returns

ccpn.pipes.OutputPipeline module

class ccpn.pipes.OutputPipeline.OutputPipelineGuiPipe(name='Output Pipeline', parent=None, project=None, **kwds)[source]

Bases: ccpn.ui.gui.widgets.PipelineWidgets.GuiPipe

pipeName = 'Output Pipeline'
preferredPipe = True
class ccpn.pipes.OutputPipeline.OutputSpectraPipe(application=None)[source]

Bases: ccpn.framework.lib.pipeline.PipeBase.SpectraPipe

guiPipe

alias of ccpn.pipes.OutputPipeline.OutputPipelineGuiPipe

pipeCategory = 'Outputs'
pipeName = 'Output Pipeline'
runPipe(spectra)[source]

ccpn.pipes.PeakFilterNdPipe module

class ccpn.pipes.PeakFilterNdPipe.PeakFilterNdGuiPipe(name='Peak Filter ND', parent=None, project=None, **kwds)[source]

Bases: ccpn.ui.gui.widgets.PipelineWidgets.GuiPipe

pipeName = 'Peak Filter ND'
preferredPipe = True
class ccpn.pipes.PeakFilterNdPipe.PeakFilterNdPipe(application=None)[source]

Bases: ccpn.framework.lib.pipeline.PipeBase.SpectraPipe

guiPipe

alias of ccpn.pipes.PeakFilterNdPipe.PeakFilterNdGuiPipe

pipeCategory = 'Analysis'
pipeName = 'Peak Filter ND'
runPipe(spectra)[source]

ccpn.pipes.PeakPicker1DPipe module

class ccpn.pipes.PeakPicker1DPipe.PeakDetector1DGuiPipe(name='Peak Picker 1D', parent=None, project=None, **kwds)[source]

Bases: ccpn.ui.gui.widgets.PipelineWidgets.GuiPipe

pipeName = 'Peak Picker 1D'
preferredPipe = True
class ccpn.pipes.PeakPicker1DPipe.PeakPicker1DPipe(application=None)[source]

Bases: ccpn.framework.lib.pipeline.PipeBase.SpectraPipe

guiPipe

alias of ccpn.pipes.PeakPicker1DPipe.PeakDetector1DGuiPipe

pipeCategory = 'Analysis'
pipeName = 'Peak Picker 1D'
runPipe(spectra)[source]
Parameters

data

Returns

ccpn.pipes.PeakPickerNdPipe module

class ccpn.pipes.PeakPickerNdPipe.PeakPickerNdGuiPipe(name='Peak Picker ND', parent=None, project=None, **kwds)[source]

Bases: ccpn.ui.gui.widgets.PipelineWidgets.GuiPipe

pipeName = 'Peak Picker ND'
preferredPipe = True
class ccpn.pipes.PeakPickerNdPipe.PeakPickerNdPipe(application=None)[source]

Bases: ccpn.framework.lib.pipeline.PipeBase.SpectraPipe

guiPipe

alias of ccpn.pipes.PeakPickerNdPipe.PeakPickerNdGuiPipe

pipeCategory = 'Analysis'
pipeName = 'Peak Picker ND'
runPipe(spectra)[source]
Parameters

data

Returns

ccpn.pipes.PhasingPipe module

class ccpn.pipes.PhasingPipe.Phasing1DPipe(application=None)[source]

Bases: ccpn.framework.lib.pipeline.PipeBase.SpectraPipe

Apply phasing to all the spectra in the pipeline

guiPipe

alias of ccpn.pipes.PhasingPipe.PhasingSpectraGuiPipe

pipeCategory = 'Post-Processing'
pipeName = 'Phasing Spectra'
runPipe(spectra)[source]
Parameters

spectra – inputData

Returns

aligned spectra

class ccpn.pipes.PhasingPipe.PhasingSpectraGuiPipe(name='Phasing Spectra', parent=None, project=None, **kw)[source]

Bases: ccpn.ui.gui.widgets.PipelineWidgets.GuiPipe

pipeName = 'Phasing Spectra'
preferredPipe = True
ccpn.pipes.PhasingPipe.autoPhasing(spectrum, engine='peak_minima')[source]
ccpn.pipes.PhasingPipe.phasing1D(spectrum, ph0, ph1, pivot)[source]
Parameters
  • spectrum

  • ph0 – degrees

  • ph1

  • pivot – in points

Returns

intensities

ccpn.pipes.ReferencingSpectra1Dpipe module

class ccpn.pipes.ReferencingSpectra1Dpipe.ReferencingSpectra(application=None)[source]

Bases: ccpn.framework.lib.pipeline.PipeBase.SpectraPipe

Add a shift value to all the spectra in the pipeline

guiPipe

alias of ccpn.pipes.ReferencingSpectra1Dpipe.ReferencingSpectraGuiPipe

pipeCategory = 'Post-Processing'
pipeName = 'Referencing Spectra'
runPipe(spectra)[source]
Parameters

spectra – inputData

Returns

aligned spectra

class ccpn.pipes.ReferencingSpectra1Dpipe.ReferencingSpectraGuiPipe(name='Referencing Spectra', parent=None, project=None, **kwds)[source]

Bases: ccpn.ui.gui.widgets.PipelineWidgets.GuiPipe

pipeName = 'Referencing Spectra'
preferredPipe = True
ccpn.pipes.ReferencingSpectra1Dpipe.addShiftToSpectra(spectra, shift)[source]

ccpn.pipes.RefitPeaks module

class ccpn.pipes.RefitPeaks.RefitPeaksGuiPipe(name='Refit Peaks', parent=None, project=None, **kw)[source]

Bases: ccpn.ui.gui.widgets.PipelineWidgets.GuiPipe

pipeName = 'Refit Peaks'
class ccpn.pipes.RefitPeaks.RefitPeaksPipe(application=None)[source]

Bases: ccpn.framework.lib.pipeline.PipeBase.SpectraPipe

Apply phasing to all the spectra in the pipeline

guiPipe

alias of ccpn.pipes.RefitPeaks.RefitPeaksGuiPipe

pipeCategory = 'Analysis'
pipeName = 'Refit Peaks'
runPipe(spectra)[source]
Parameters

spectra – inputData

Returns

spectra

ccpn.pipes.RevPipe module

class ccpn.pipes.RevPipe.RevGuiPipe(name='DEMO5 Rev', parent=None, project=None, **kw)[source]

Bases: ccpn.ui.gui.widgets.PipelineWidgets.GuiPipe

pipeName = 'DEMO5 Rev'
preferredPipe = True
class ccpn.pipes.RevPipe.RevPipe(application=None)[source]

Bases: ccpn.framework.lib.pipeline.PipeBase.SpectraPipe

Apply phasing to all the spectra in the pipeline

guiPipe

alias of ccpn.pipes.RevPipe.RevGuiPipe

pipeCategory = 'Processing'
pipeName = 'DEMO5 Rev'
runPipe(spectra)[source]

Discard the imaginaries

ccpn.pipes.Scale1D module

class ccpn.pipes.Scale1D.Scale1DGuiPipe(name='Scale spectra', parent=None, project=None, **kw)[source]

Bases: ccpn.ui.gui.widgets.PipelineWidgets.GuiPipe

pipeName = 'Scale spectra'
preferredPipe = True
class ccpn.pipes.Scale1D.Scale1DPipe(application=None)[source]

Bases: ccpn.framework.lib.pipeline.PipeBase.SpectraPipe

Apply phasing to all the spectra in the pipeline

guiPipe

alias of ccpn.pipes.Scale1D.Scale1DGuiPipe

pipeCategory = 'Post-Processing'
pipeName = 'Scale spectra'
runPipe(spectra)[source]
Parameters

spectra – inputData

Returns

scaled spectra

ccpn.pipes.ZfPipe module

class ccpn.pipes.ZfPipe.ZFGuiPipe(name='DEMO1 ZF', parent=None, project=None, **kw)[source]

Bases: ccpn.ui.gui.widgets.PipelineWidgets.GuiPipe

pipeName = 'DEMO1 ZF'
preferredPipe = True
class ccpn.pipes.ZfPipe.ZFPipe(application=None)[source]

Bases: ccpn.framework.lib.pipeline.PipeBase.SpectraPipe

Apply phasing to all the spectra in the pipeline

guiPipe

alias of ccpn.pipes.ZfPipe.ZFGuiPipe

pipeCategory = 'Processing'
pipeName = 'DEMO1 ZF'
runPipe(spectra)[source]

Zero filling