Dear Alison,
This is ok with me. Please include this name and description for SIF for the next update.
Thanks!
-Ranjini
________________________________
From: Alison Pamment - UKRI STFC <alison.pamment at stfc.ac.uk>
Sent: Wednesday, February 6, 2019 12:09:05 PM
To: Ranjini Swaminathan; Martin Juckes - UKRI STFC; cf-metadata at cgd.ucar.edu
Subject: RE: new standard name for solar-induced chlorophyll fluorescence
Dear Ranjini and Martin,
Thanks both for your comments on this name - I think we are close to agreement.
I agree with you both that the name should not say 'photosynthetic' since that is defined as the range 400-700 nm and SIF is clearly outside that.
Ranjini says:
> we'd normally use nm-1 for the spectral part of the units, but I think this may not be allowed.
In fact it would be fine to have units of W m-2 sr-1 nm-1 in your data files, even though the canonical unit would be stated as W m-2 sr-1 m-1 in the standard name table. Units in the CF conventions are required to be compatible with the UDunits software package (
https://www.unidata.ucar.edu/software/udunits/#documentation). In practice, this means that the units in your file don't have to be identical to the canonical unit provided UDunits can convert between them. If your units have the correct physical dimensions there shouldn't be a problem.
The only remaining question is whether the name itself should include 'chlorophyll'. We would of course continue to mention it in the definition. The abbreviation 'SIF' would tend to suggest that the name should be solar_induced_fluorescence and indeed a quick internet search for
'solar induced fluorescence' produced links to quite a number of articles. Thus it appears to be widely used in the literature and seems unlikely to be confused with fluorescence from any other molecule. Based on this, and unless there are strong reasons for keeping 'chlorophyll' in the name, I would tend to go with Martin's suggestion of
toa_outgoing_radiance_per_unit_wavelength_due_to_solar_induced_fluorescence (Canonical units: W m-2 sr-1 m-1)
'The abbreviation "toa" means top of atmosphere. Radiance is the radiative flux in a particular direction, per unit of solid angle. The direction towards which it is going must be specified, for instance with a coordinate of zenith_angle. A coordinate variable for radiation wavelength should be given the standard name radiation_wavelength. The specification of a physical process by the phrase "due_to_" process means that the quantity named is a single term in a sum of terms which together compose the general quantity named by omitting the phrase. Some of the solar energy absorbed by pigment systems of plant leaves during photosynthesis is re-emitted as fluorescence. This is called solar-induced (chlorophyll) fluorescence (SIF). It is a radiance that can be measured on a global scale at various wavelengths and by multiple space borne instruments. SIF is considered a measurement of the photosynthetic machinery in plants and can provide a direct approach for the diagnosis of the actual functional status of vege
tation. It is therefore considered a functional proxy of terrestrial gross primary productivity which has the standard name gross_primary_productivity_of_biomass_expressed_as_carbon. SIF spans the wavelength range 600-800nm.'
Ranjini, would this be okay? If so, then I think this standard name could be accepted (I have just completed the February update, but the next one is scheduled for 4th March).
Best wishes,
Alison
------
Alison Pamment Tel: +44 1235 778065
NCAS/Centre for Environmental Data Archival Email: alison.pamment at stfc.ac.uk
STFC Rutherford Appleton Laboratory
R25, 2.22
Harwell Oxford, Didcot, OX11 0QX, U.K.
From: Ranjini Swaminathan <r.swaminathan at reading.ac.uk>
Sent: 05 February 2019 15:20
To: Juckes, Martin (STFC,RAL,RALSP) <martin.juckes at stfc.ac.uk>; Pamment, Alison (STFC,RAL,RALSP) <alison.pamment at stfc.ac.uk>; cf-metadata at cgd.ucar.edu
Subject: Re: new standard name for solar-induced chlorophyll fluorescence
Dear Martin, Alison,
I am including some feedback from colleagues on this:
Would the following name be suited?
------
toa_outgoing_radiance_per_unit_wavelength_due_to_solar_induced_chlorophyll_fluorescence (Canonical units: W m-2 sr-1 m-1)
because the outgoing radiance is not necessarily in the PAR domain.
Also we'd normally use nm-1 for the spectral part of the units, but I think this may not be allowed.
-------
I am aware of SIF data used at the following wavelengths : 755,757,771,772nm.
Thanks!
-Ranjini
________________________________________
From: Martin Juckes - UKRI STFC
Sent: Wednesday, January 23, 2019 1:41:05 PM
To: Alison Pamment - UKRI STFC; Ranjini Swaminathan; mailto:cf-metadata at cgd.ucar.edu
Subject: Re: new standard name for solar-induced chlorophyll fluorescence
Dear Ranjini, Alison,
I'd like to propose a further modification to Alison's suggestion. Firstly, after reading a little about SIF (this is a useful description:
http://terraluma.net/applications-2/uas-spectrometry-for-sun-induced-chlorophyll-fluorescence-retrieval/ ) I feel that the "photosynthetic" in "_photosynthetic_radiance_" is inappropriate here: the SIF is a small fraction (around 1%) of the incident photosynthetic radiation (less than the reflected component) and it has a different wavelength distribution. It is also redundant in this term, so "photosynthetic" can be left out. Secondly, SIF is often defined as "Solar Induced Flourescence", since adding chlorophyll is redundant. Hence, a shorter name could be used:
toa_outgoing_radiance_per_unit_wavelength_due_to_solar_induced_fluorescence (Canonical units: W m-2 sr-1 m-1)
'The abbreviation "toa" means top of atmosphere. Radiance is the radiative flux in a particular direction, per unit of solid angle. The direction towards which it is going must be specified, for instance with a coordinate of zenith_angle. A coordinate variable for radiation wavelength should be given the standard name radiation_wavelength. The specification of a physical process by the phrase "due_to_" process means that the quantity named is a single term in a sum of terms which together compose the general quantity named by omitting the phrase. Some of the solar energy absorbed by pigment systems of plant leaves during photosynthesis is re-emitted as fluorescence. This is called solar-induced (chlorophyll) fluorescence (SIF). It is a radiance that can be measured on a global scale at various wavelengths and by multiple space borne instruments. SIF is considered a measurement of the photosynthetic machinery in plants and can provide a direct approach for the diagnosis of the actual functional status of vege
tation. It is therefore considered a functional proxy of terrestrial gross primary productivity which has the standard name gross_primary_productivity_of_biomass_expressed_as_carbon. SIF spans the wavelength range 600-800nm.'
Is there a standard wavelength that SIF is retrieved at?
It may be worth checking our definitions of "albedo". I think we have, in the past, assumed that "outgoing shortwave" was equivalent to "reflected". Hence, we have planetary_albedo defined in terms of the ratio of outgoing to incoming shortwave radiation: it should perhaps be the ratio of reflected to incoming shortwave radiation, which would exclude the contribution of fluorescence.
We also have a "bioluminescent_photon_rate_in_sea_water" name ... but I don't think that is closely related.
regards,
Martin
________________________________
From: CF-metadata on behalf of Alison Pamment - UKRI STFC
Sent: 06 December 2018 16:49
To: 'Ranjini Swaminathan'; mailto:cf-metadata at cgd.ucar.edu
Subject: Re: [CF-metadata] new standard name for solar-induced chlorophyll fluorescence
Dear Ranjini,
Thank you for proposing this new standard name and apologies for the delay in getting back to you.
> Name : solar_induced_chlorophyll_fluorescence
> Canonical Units : W/m^2/sr/micron
>
> Description: Some of the solar energy absorbed by pigment systems of plant leaves are reemitted as fluorescent photons. This signal is called solar-induced cholorophyll fluorescence (SIF) , is a radiance and can be measured on a global scale at various
> wavelengths and by multiple space borne instruments. SIF is considered a measurement of the the photosynthetic machinery in plants and can provide a direct approach for the diagnosis of the actual functional status of vegetation. It is therefore also
> considered a functional proxy of terrestrial Gross Primary Productivity.
Certainly we don't currently have a standard name for this quantity, so we will need to introduce a new one.
Where possible, we try to make new names consistent with existing ones and I found a few examples that may be helpful as templates for the quantity you are proposing .
Firstly, we have some existing names related to photosynthetic fluxes, for example:
fraction_of_surface_downwelling_photosynthetic_radiative_flux_absorbed_by_vegetation (Canonical Units: 1)
' Downwelling radiation is radiation from above. It does not mean "net downward". The sign convention is that "upwelling" is positive upwards and "downwelling" is positive downwards. The surface called "surface" means the lower boundary of the atmosphere. The quantity with standard name fraction_of_surface_downwelling_photosynthetic_radiative_flux_absorbed_by_vegetation, often called Fraction of Absorbed Photosynthetically Active Radiation (FAPAR), is the fraction of incoming solar radiation in the photosynthetically active radiation spectral region that is absorbed by a vegetation canopy. "Photosynthetic" radiation is the part of the spectrum which is used in photosynthesis e.g. 400-700 nm. The range of wavelengths could be specified precisely by the bounds of a coordinate of "radiation_wavelength". When thought of as being incident on a surface, a radiative flux is sometimes called "irradiance". In addition, it is identical with the quantity measured by a cosine-collector light-meter and sometimes called "
vector irradiance". In accordance with common usage in geophysical disciplines, "flux" implies per unit area, called "flux density" in physics. "Vegetation" means any plants e.g. trees, shrubs, grass. The term "plants" refers to the kingdom of plants in the modern classification which excludes fungi. Plants are autotrophs i.e. "producers" of biomass using carbon obtained from carbon dioxide.'
We also have existing radiance names, for example:
surface_downwelling_radiance_in_sea_water (Canonical units: W m-2 sr-1)
'The surface called "surface" means the lower boundary of the atmosphere. Downwelling radiation is radiation from above. It does not mean "net downward". The sign convention is that "upwelling" is positive upwards and "downwelling" is positive downwards. Radiance is the radiative flux in a particular direction, per unit of solid angle. The direction from which it is coming must be specified, for instance with a coordinate of zenith_angle. If the radiation does not depend on direction, a standard name of isotropic radiance should be chosen instead.'
Also:
surface_downwelling_radiance_per_unit_wavelength_in_sea_water (Canonical units: W m-2 m-1 sr-1)
'The surface called "surface" means the lower boundary of the atmosphere. Downwelling radiation is radiation from above. It does not mean "net downward". The sign convention is that "upwelling" is positive upwards and "downwelling" is positive downwards. Radiance is the radiative flux in a particular direction, per unit of solid angle. The direction from which it is coming must be specified, for instance with a coordinate of zenith_angle. If the radiation does not depend on direction, a standard name of isotropic radiance should be chosen instead. A coordinate variable for radiation wavelength should be given the standard name radiation_wavelength.'
toa_outgoing_radiance_per_unit_wavelength (Canonical units: W m-2 sr-1 m-1)
'The abbreviation "toa" means top of atmosphere. The TOA outgoing radiance is the upwelling radiance, i.e., toward outer space. Radiance is the radiative flux in a particular direction, per unit of solid angle. In accordance with common usage in geophysical disciplines, "flux" implies per unit area, called "flux density" in physics.
Your description says the proposed quantity is a radiance, so we should state that in the name itself. Also we need to state a direction (upwelling/downwelling in air or incoming/outgoing at toa). Since this is radiation originating from vegetation on the earth's surface I assume we want to call it an upwelling or outgoing flux. It is being measured from space, which would suggest a toa quantity. You are proposing canonical units of W/m^2/sr/micron. In the standard name table we should write this as W m-2 sr-1 m-1, as in the existing names. It is fine to use microns in your data files, because the Udunits package, which is used as the basis for units in the CF conventions, would be able to convert to the canonical unit. The name should reflect the fact that you are measuring at multiple wavelengths (m-1 / micron-1) so it should start with toa_outgoing_radiance_per_unit_wavelength.
The radiation is being emitted by vegetation due to the process of solar induced chlorophyll fluorescence. In standard names we often use the pattern 'due_to_process', hence I suggest the name should end in _due_to_solar_induced_chlorophyll_fluorescence.
Looking at your description, perhaps it would also make sense to call this as a 'photosynthetic' quantity.
We have standard pieces of text that should go into the definition of the name (based on the phrases it is built from) and of course we should add to this the text you have provided in the proposal. So, pulling everything together, we'd have the following.
toa_outgoing_photosynthetic_radiance_per_unit_wavelength_due_to_solar_induced_chlorophyll_fluorescence (Canonical units: W m-2 sr-1 m-1)
'The abbreviation "toa" means top of atmosphere. Radiance is the radiative flux in a particular direction, per unit of solid angle. The direction towards which it is going must be specified, for instance with a coordinate of zenith_angle. "Photosynthetic" radiation is the part of the spectrum which is used in photosynthesis e.g. 400-700 nm. A coordinate variable for radiation wavelength should be given the standard name radiation_wavelength. The specification of a physical process by the phrase "due_to_" process means that the quantity named is a single term in a sum of terms which together compose the general quantity named by omitting the phrase. Some of the solar energy absorbed by pigment systems of plant leaves are re-emitted as fluorescent photons. This is called solar-induced chlorophyll fluorescence (SIF). It is a radiance that can be measured on a global scale at various wavelengths and by multiple space borne instruments. SIF is considered a measurement of the photosynthetic machinery in plants and
can provide a direct approach for the diagnosis of the actual functional status of vegetation. It is therefore considered a functional proxy of terrestrial gross primary productivity which has the standard name gross_primary_productivity_of_biomass_expressed_as_carbon.'
Does that sound okay?
Best wishes,
Alison
------
Alison Pamment Tel: +44 1235 778065
NCAS/Centre for Environmental Data Archival Email: mailto:alison.pamment at stfc.ac.uk
STFC Rutherford Appleton Laboratory
R25, 2.22
Harwell Oxford, Didcot, OX11 0QX, U.K.
From: CF-metadata On Behalf Of Ranjini Swaminathan
Sent: 14 November 2018 09:13
To: mailto:cf-metadata at cgd.ucar.edu
Subject: [CF-metadata] new standard name for solar-induced chlorophyll fluorescence
Dear All,
I'd like to request an addition to the standard name list for the variable solar-induced chlorophyll fluorescence. This variable is derived from satellite measurements and is available as a product from GOSAT and OCO-2 satellite missions at this time. Here is relevant information regarding this variable :
---------------------------------------------
Proposal for a new standard variable name
Name : solar_induced_chlorophyll_fluorescence
Canonical Units : W/m^2/sr/micron
Description: Some of the solar energy absorbed by pigment systems of plant leaves are reemitted as fluorescent photons. This signal is called solar-induced cholorophyll fluorescence (SIF) , is a radiance and can be measured on a global scale at various wavelengths and by multiple space borne instruments. SIF is considered a measurement of the the photosynthetic machinery in plants and can provide a direct approach for the diagnosis of the actual functional status of vegetation. It is therefore also considered a functional proxy of terrestrial Gross Primary Productivity.
----------------------------------------------
Thanks!
-Ranjini
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