New NPQ photosynthesis functions #1981

Is your feature request related to a problem? Please describe.
There are several photosynthetic parameters that can be calculated with the data in the photosynthesis subpackage for other components of NPQ. New functions can provide these calculations after the photosynthesis subpackage has been refactored.

This is only for PAM Time (PMT) file types.

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• analyze.npqcomponents Analyze npq components #1995

qP = Fraction of open reaction centers (based on puddle mode)/ Photochemical quenching =(Fm'-Fs')/(Fm'-F0') There will be one vaue for each timepoint in the light adapted portion of PAM time. In plantCV import language, this = (Fmp-Fp)/(Fmp-F0p)

qN = Term for quantifying non-photochemical quenching, requires measurement of Fo (minimum fluorescence in darkness). Values are between 0 and 1. One value per object. = 1-(Fm’-Fo’)/(Fm-Fo) In plantCV import language, this = 1-(Fmp-F0p)/(Fm-F0)

qL = Fraction of open reaction centers (based on lake mode)/ Photochemical quenching. There will be one vaue for each timepoint in the light adapted portion of PAM time = qP*Fo'/Fs' In plantCV import language, this = qP*F0p/Fp

qI = Slow relaxing component of non-photochemical quenching. There will be one vaue for each timepoint in the second dark adaptation of PAM time = (Fm-Fm")/Fm" In plantCV import language, this = (Fm-Fmpp)/Fmpp

qE = Fast relaxing component of non-photochemical quenching There will be one vaue for each timepoint in the second dark adaptation of PAM time = Fm*(Fm"-Fm')/(Fm"*Fm') In plantCV import language, this = Fm*(Fmpp-Fmp)/(Fmpp*Fmp)

phiNO = Quantum yield of non-regulated energy dissipation ՓNO+ՓNPQ+Fq’/Fm’=1 . There will be one vaue for each timepoint in the second dark adaptation of PAM time, since qI has one value for each timepoint in the second dark adaptation of PAM time. = 1/(NPQ+1+ql*Fm/Fo) In plantCV import language, this = 1/(NPQ+1+ql*Fm/F0)

phiNPQ = Quantum yield of non-photochemical quenching (regulated energy dissipation). There will be one vaue for each timepoint in the second dark adaptation of PAM time, since phiNO has one value for each timepoint in the second dark adaptation of PAM time. ՓNO+ՓNPQ+Fq’/Fm’=1 . = 1-Fq’/Fm’-phiNO In plantCV import language, this = 1-Fqp/Fmp-phiNO

• This function works withPAM time frames only.

• Here, Fs' refers to minimal fluorescence level under light at each timepoint prior to the endpoint of light, so will have the time dimension. We use Fp to refer to Fsp in PlantCV for consistent naming.

• Here, Fo’= fluorescence level after illumination with only far-red light that is measured in PAM Time.

Second function

• analyze.npqfast Analyze npq fast #1996
  NPQ(t) = Fast NPQ measurement (no measurements in dark-adapted plants is needed). There will be one vaue for each timepoint in the light adapted portion of PAM time = 4.88/(Fm’/Fo’-1)-1 In plantCV import language, this = 4.88/(Fmp/F0p-1)-1
• This function works with OJIP light, NPQ, PAM light, or PAM time.