WVDiagnostics

Produces diagnostics and figures from WVModel output

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Overview

This is a collection of diagnostic tools for analyzing model output

Topics

• Initialization
  • WVDiagnostics Initializes the WVDiagnostics object, loads the wave-vortex transform and diagnostics files.
  • close Close the model-output and diagnostics NetCDF files.
• Diagnostics Generation
  • create1DMirrorFluxes Create 1D mirror flux diagnostics and write them to the diagnostics NetCDF.
  • create2DMirrorFluxes Compute 2D mirror-flux diagnostics and write them to the diagnostics NetCDF.
  • createDiagnosticsFile Create a new diagnostics file and compute diagnostics from WVModel output.
  • createGeostrophicFluxGroup Create a geostrophic flux group in the diagnostics NetCDF and populate it.
  • createReservoirGroup Create a reservoir group in the diagnostics NetCDF and populate it.
• Figures
  • Model Snapshot
    • plotEnergySpectrum Plot the wave/geostrophic energy spectra at a given time.
    • plotEnstrophySpectrum Plot the enstrophy spectrum at a given time.
    • plotFluidDecompositionMultipanel Plot a multipanel decomposition of the fluid state (wave vs geostrophic).
    • plotFluidStateMultipanel Plot multipanel summary of fluid state and spectra
    • plotPotentialEnergySpectrum Plot the potential energy spectrum
  • Energy
    • plotEnergyFluxOverTime Plot energy fluxes as a function of time.
    • plotEnergyFluxTemporalAverage Plot temporally averaged energy flux diagnostics.
    • plotEnergyFluxes1D Plot 1D energy fluxes as a function of pseudo-wavelength / KE-PE / frequency.
    • plotEnergyOverTime Plot energy for each reservoir over time.
    • plotEnergyTriadFluxOverTime Plot inertial flux for each reservoir over time
    • plotSourcesSinksForReservoirGroup Plot sources, sinks, and reservoirs diagram for a reservoir group.
    • plotSourcesSinksReservoirsDiagram Plot sources, sinks, and reservoirs diagram.
    • showDampingFluxVsPseudolength Show Damping Flux Vs Pseudolength.
  • Potential Enstrophy
    • plotEnstrophyFluxOverTime Plot enstrophy fluxes for reservoirs as a function of time.
    • plotEnstrophyFluxTemporalAverage Plot temporally averaged enstrophy flux diagnostics.
    • plotEnstrophyOverTime Plot enstrophy over time
    • plotEnstrophyTriadFluxOverTime Plot enstrophy triad fluxes over time.
  • Ancillary
    • plotMooringRotarySpectrum Plot rotary spectra from mooring velocity time series.
  • Auxiliary functions
    • logWavelengthAxis Produce tick labels and positions for a log-scaled wavelength x-axis.
    • overlayFrequencyContours Overlay contours of nondimensional frequency on the current axes.
    • overlayGeostrophicKineticPotentialFractionContours Overlay contour where geostrophic kinetic fraction equals a given value.
    • overlayGeostrophicKineticPotentialRatioContours Overlay contours of geostrophic kinetic-to-potential energy ratio.
    • plotPoissonFlowOverContours Plot Poisson Flow Over Contours.
    • setLogWavelengthXAxis Configure axis tick labels for a log-scaled wavelength x-axis.
    • showRossbyRadiusYAxis Annotate the axes with a Rossby radius y-axis label.
• Summaries
  • createEnstrophyFluxSummaryTable Create a LaTeX table summarizing enstrophy source/sink fluxes.
  • summarizeSourcesSinksReservoirs Summarize Sources Sinks Reservoirs.
• Diagnostics
  • Energy
    • Time series, [t 1]
      • exactEnergyOverTime Exact Energy Over Time.
      • quadraticEnergyOverTime Compute energy for each reservoir over time.
  • Energy Fluxes
    • General, [j kRadial t]
      • exactEnergyFluxes Return the exact energy flux from the forcing terms, [j kRadial t].
      • quadraticEnergyFluxes Return the energy flux from the forcing terms.
      • quadraticEnergyTriadFluxes Return the energy flux from the inertial terms, specified as triad components.
    • Temporal averages, [j kRadial]
      • exactEnergyFluxesTemporalAverage Temporally averaged exact energy fluxes.
      • quadraticEnergyFluxesTemporalAverage Compute temporally averaged forcing fluxes.
      • quadraticEnergyTriadFluxesTemporalAverage Computes the temporally averaged quadratic triad fluxes.
    • Time series, [t 1]
      • exactEnergyFluxesOverTime Exact energy fluxes over time.
      • quadraticEnergyFluxesOverTime Compute forcing fluxes over time.
    • Spatial-temporal averages, [1 1]
      • exactEnergyFluxesSpatialTemporalAverage Compute spatial-temporal average of the exact forcing fluxes.
      • quadraticEnergyFluxesSpatialTemporalAverage Compute spatial-temporal average of forcing fluxes.
      • quadraticEnergyTriadFluxesSpatialTemporalAverage Compute spatial-temporal average of inertial fluxes.
    • Temporal averages, 1D axes
      • quadraticEnergyMirrorTriadFluxes1D Quadratic Energy Mirror Triad Fluxes1 D.
      • quadraticEnergyMirrorTriadFluxes1D_kepe Quadratic Energy Mirror Triad Fluxes1 D kepe.
      • quadraticEnergyMirrorTriadFluxes1D_omega Quadratic Energy Mirror Triad Fluxes1 D omega.
      • quadraticEnergyPrimaryTriadFluxesTemporalAverage1D Quadratic Energy Primary Triad Fluxes Temporal Average1 D.
      • quadraticEnergyPrimaryTriadFluxesTemporalAverage1D_kepe Quadratic Energy Primary Triad Fluxes Temporal Average1 D kepe.
      • quadraticEnergyPrimaryTriadFluxesTemporalAverage1D_omega Quadratic Energy Primary Triad Fluxes Temporal Average1 D omega.
    • Temporal averages, 2D axes [sparseJWavenumberAxis sparseKRadialAxis]
      • quadraticEnergyMirrorTriadFluxes2D Quadratic Energy Mirror Triad Fluxes2 D.
      • quadraticEnergyPrimaryTriadFluxesTemporalAverage2D outputGrid determines whether or not the fluxes get downsampled to the.
  • Potential Enstrophy
    • Time series, [t 1]
      • exactEnstrophyOverTime Exact Enstrophy Over Time.
      • quadraticEnstrophyOverTime Quadratic Enstrophy Over Time.
  • Potential Enstrophy Fluxes
    • General, [j kRadial t]
      • exactEnstrophyFluxes Return the available potential enstrophy flux from the forcing terms, [j kRadial t].
      • quadraticEnstrophyFluxes Return the enstrophy flux from the forcing terms.
      • quadraticEnstrophyTriadFluxes Return the enstrophy flux from the forcing terms.
    • Temporal averages, [j kRadial]
      • exactEnstrophyFluxesTemporalAverage Compute temporally averaged enstrophy fluxes.
      • quadraticEnstrophyFluxesTemporalAverage Compute temporally averaged enstrophy fluxes.
    • Time series, [t 1]
      • exactEnstrophyFluxesOverTime Compute exact enstrophy fluxes over time.
      • quadraticEnergyTriadFluxesOverTime Compute inertial fluxes over time.
      • quadraticEnstrophyFluxesOverTime Compute enstrophy fluxes over time.
    • Spatial-temporal averages, [1 1]
      • exactEnstrophyFluxesSpatialTemporalAverage Compute spatial-temporal average of the exact enstrophy fluxes.
      • quadraticEnstrophyFluxesSpatialTemporalAverage Compute spatial-temporal average of the qgpv enstrophy fluxes.
  • Flux diagnostics — General
    • Fluxes in space, [sparseJWavenumberAxis sparseKRadialAxis]
      • RescalePoissonFlowFluxForLogSpace Rescale Poisson Flow Flux For Log Space.
  • General — Misc
    • Fluxes in space, [sparseJWavenumberAxis sparseKRadialAxis]
      • cmocean returns perceptually-uniform colormaps created by Kristen Thyng.
      • geostrophicGeostrophicWaveEnergy Note that.
      • waveWaveGeostrophicEnergy Note that.
      • waveWaveGeostrophicEnergyForMode Note that.
    • Fluxes
      • geostrophicFlux Compute the spatial and spectral fluxes for constant stratification
  • Enstrophy fluxes — Triad interactions
    • Fluxes over time, [t 1]
      • quadraticEnstrophyTriadFluxesOverTime Compute enstrophy inertial (aka, triad) fluxes over time.
• Computing Spectra
  • crossSpectrumWithFgTransform Cross Spectrum With Fg Transform.
  • crossSpectrumWithGgTransform Cross Spectrum With Gg Transform.
  • spectrumWithFgTransform Spectrum With Fg Transform.
  • spectrumWithGgTransform Spectrum With Gg Transform.
• Transformations
  • Cosine and Sine
    • CosineTransformBack Fast Discrete Inverse Cosine Transform.
    • CosineTransformForward Fast Discrete Cosine Transform (DCT-I).
    • DCT1 CosineTransformForwardMatrix Discrete Cosine Transform (DCT-I) matrix.
    • DCT2 CosineTransformForwardMatrix_DCT2 Discrete Cosine Transform (DCT-II) matrix.
    • DST1 CosineTransformForwardMatrix Discrete Cosine Transform (DCT-I) matrix.
    • DST2 SineTransformForwardMatrix_DST2 Discrete Sine Transform (DST-II) matrix.
    • SineTransformBack Fast Discrete Inverse Sine Transform.
    • iDCT1 CosineTransformBackMatrix Discrete Cosine Transform (DCT-I) matrix.
    • iDCT2 InverseCosineTransformMatrix_DCT2 Inverse of forward DCT-II matrix.
    • iDST1 CosineTransformBackMatrix Discrete Cosine Transform (DCT-I) matrix.
    • iDST2 InverseSineTransformMatrix_DST2 Inverse of forward DST-II matrix.
    • General
      • SineTransformForward Fast Discrete Sine Transform (DST-I).
  • Axes
    • sparseJKAxisBinMatrices Bin matrices for sparseKRadialAxis and sparseJWavenumberAxis
    • sparseJWavenumberAxis Sparse JWavenumber Axis.
    • sparseKRadialAxis Sparse KRadial Axis.
    • sparseKePeAxis Sparse kenetic-potential energy ratio Axis.
    • sparseOmegaAxis Sparse Omega Axis.
    • sparsePseudoRadialAxis Create Sparse Pseudo-Radial Wavenumber Axis and Bin Assignments.
    • transformToKePeAxis Transform To Ke Pe Axis.
    • transformToOmegaAxis transforms in the from (j,kRadial) to omegaAxis.
    • transformToPseudoRadialWavenumber transforms in the from (j,kRadial) to kPseudoRadial.
    • transformToPseudoRadialWavenumberA0 transforms in the from (j,kRadial) to kPseudoRadial.
    • transformToPseudoRadialWavenumberApm transforms Ap/Am modes in the from (j,kRadial) to kPseudoRadial.
• Utilities
  • crameri returns perceptually-uniform scientific colormaps created.
• Internal
  • Support functions for createReservoirGroup
    • addTriadFluxesForReservoirGroupAtTime Add Triad Fluxes For Reservoir Group At Time.
    • filterEnergyForSourcesSinksReservoirs This function returns values assuming three reservoirs: geo, wave, and.
    • fluxesForReservoirGroup Fluxes For Reservoir Group.
    • variablesForReservoirGroup Variables For Reservoir Group.
• Developer
  • classDefinedPropertyAnnotations return array of WVPropertyAnnotation initialized by default
• Units
  • escale energy scaling (numeric value)
  • escale_units energy units (string value)
  • flux_scale energy flux scaling (numeric value)
  • flux_scale_units energy flux units (string value)
  • setEnergyUnits Set the time and energy scaling and units for plotting and output.
  • tscale time axis scaling (numeric value)
  • tscale_units time axis units (string value)
  • z_flux_scale potential enstrophy flux scaling (numeric value)
  • z_flux_scale_units potential enstrophy flux units (string value)
  • zscale potential enstrophy scaling (numeric value)
  • zscale_units potential enstrophy units (string value)
• Dependent property getter
  • t_diag Get time vector from the diagnostics file
• Other
  • Lr2
  • Lr2_pm
  • PoissonFlowFromFlux We will treat the first dimension as `x’ and the second
  • PoissonFlowFromFluxDCTI We will treat the first dimension as `x’ and the second
  • PoissonFlowFromFluxType1 We will treat the first dimension as `x’ and the second
  • PoissonFlowFromFluxWithAxes We will treat the first dimension as `x’ and the second
  • areEnergyReservoirsComplete
  • areTriadComponentsComplete
  • diagfile NetCDFFile instance for the diagnostics file
  • diagnosticsHasExplicitAntialiasing
  • diagpath path to the diagnostics file
  • fancyNameForName
  • filterFluxesForReservoir
  • forcingNames
  • geo_hke_jk
  • geo_pe_jk
  • iTime
  • iTimeChanged
  • j
  • jWavenumber
  • kPseudoRadial
  • kRadial
  • kePeAxis
  • omegaAxis
  • omega_jk
  • plotPoissonFlowOverPcolor
  • pseudoRadialBinning choose an algorithm for pseudoRadialBinning
  • symmetricTintMap Colormap going from color -> tinted white -> color
  • t_wv
  • version Locate folder containing this class file
  • wvaapath path to a WVTransform with explicit anti-aliasing
  • wvfile NetCDFFile instance for the WaveVortexModel output
  • wvpath path to the WaveVortexModel output
  • wvt WVTransform instance, set to the current iTime
  • wvt_aa

Developer Topics

These items document internal implementation details and are not part of the primary public API.

• Initialization
  • delete Release owned NetCDF files when a WVDiagnostics instance is deleted.

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