89 lines
6.1 KiB
Plaintext
89 lines
6.1 KiB
Plaintext
Photosynthetic, Internal and Stomatal Conductance Analyses of Leaves (PISCAL)
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Instruction for setting up the input file for PISCAL
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-----Mentioning a brand name in this document does not constitute support for the brand-------
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General instruction
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- Variables with labels started with '!' must be provided in order for PISCAL to do any analysis.
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For other variables, fill in with -9999 if unavailable.
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- Each input file must contain only data from a single curve. Separate curves may be stored in
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separate input data files and submitted at the same time.
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- Save data in comma separated value format (.csv)
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Line 1 to Line 10: Space provided for descriptive information about the investigator,
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contact information, the site,the sample leaf and its general environmental condition
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Line 11: Complementary data not used by PISCAL but needed for properly interpreting the A/Ci data and for synthesis
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SiteID - (Dimensionless), Site identifier (do not leave blank between letters)
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Latitude(Degrees) - Site latitude, northern hermisphere positive
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Longitude(Degrees) - Site longitude, east positive
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Elevation - (m), site elevation
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SampleYear - (year), the year when the A/Ci data is taken
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SampleDayOfYear - (day), the day of year (since 1 Jan) when the A/Ci data is taken
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GrowSeasonStart - (day), the approximate start day (since 1 Jan) of growing season
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GrowSeasonEnd - (day), the approximate end day (since 1 Jan) of growing season
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StandAge - (year), stand age since the last disturbance
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CanopyHeight - (m), the height of the canopy
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LeafAreaIndex - (m2/m2), the leaf area index in the middle of growing season
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SpeciesSampled - (dimensionless), the species of the leaf sample (don't leave blank between letters)
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AveTimeResolution - (minutes), the average time interval between two consecutive A/Ci data points
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SampleHeight - (m), the height at which the leaf is located
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LeafAge - (day), the age of the leaf
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SpecificLeafArea - (cm2/g), specific leaf area of the sample
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LfNitrogenContent - (%), dry leaf nitrogen content of the sample
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LfCarbonContent - (%), dry leaf carbon content of the sample
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LfPhosphContent - (%), dry leaf phosphorus content of the sample
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Line 12: The units of corresponding variables in Line 11
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Line 13: The values of corresponding variables in Line 11
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Line 14: The photosysnthetic model parameters you want to keep constant at the values you provide,
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fill in -9999 if you want to let PISCAL decide
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Gamma* - (Pa), chloroplastic CO2 photocompensation point (must be positive if provided)
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Kc - (Pa), Michaelis-Menten constant for RuBP carboxylation (must be positive if provided)
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Ko - (Pa), Michaelis-Menten constant for RuBP oxygenation (must be positive if provided)
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Alpha - (Dimensionless), the fraction of glycolate carbon not returned to the chloroplast (must be between 0~1 if provided)
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Rd - (umol/m2/s), dark respiration (must be positive if provided)
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gi - (umol/m2/s/Pa), internal (also known as mesophyll) conductance
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Line 15: The units of corresponding variables in Line 14
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Line 16: The values of corresponding variables in Line 14
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Line 17: A/Ci data for a variety of analyses, including photosynthesis, stomatal conductance,
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internal conductance, water use efficiency. At this stage, we only provide to users parameters
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from A/Ci curve analysis. Results from other analyses will be provided to users once they are
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thoroughly tested. The format used here represents a typical output from a Licor-6400 except
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for the last two columns (PhiPS2 and OxygenPress). Most variables have the same label as those
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in the Licor-6400 guidebook with the same definition. Not all variables are used by PISCAL.
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By using this format, however, Licor-6400 users don't have to do a lot of data organization
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in order to use PISCAL. Users of other instruments could ignore columns that are not needed
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for A/Ci analyses (fill in those columns with -9999) and just provide the essential variables.
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Again, essential variables have labels started with '!'.
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Obs: (dimensionless), the data point No.
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HHMMSS - (hh:mm:ss), clock time
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FTime - (seconds), number of seconds since file opened
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Photo - (umol/m2/s), photosynthetic rate
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!AdjPhoto - (umol/m2/s), adjusted photosynthetic rate (leakage corrected), must provide
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!StomCond - (mol/m2/s), stomatal conductance, must provide
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!Ci - (umol/mol), intercellular CO2 concentration (umol CO2 / mol moist air), must provide
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!Trmmol - (mmol/m2/s), transpiration rate, must provide
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!VpdL - (KPa), water vapor pressure deficit based on leaf temperature, must provide
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Area - (cm2), leaf area
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StmRat - (NA), estimate of the ratio of stomatal conductances of one side of the leaf to the other
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BLCond - (mol/m2/s), total boundary layer conductance
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Tair - (oC), temperature in sample cell
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!Tleaf - (oC), temperature of leaf thermocouple, must provide
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TBlk - (oC), IRGA Block temperature
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CO2R - (umol/mol), reference CO2 concentration
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CO2S - (umol/mol), Sample CO2 concentration
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H2OR - (mmol/mol), reference cell water vapor concentration
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H2OS - (mmol/mol), sample cell water vapor concentration
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RH_R - (%), Reference cell relative humidity
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RH_S - (%), sample cell relative humidity
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Flow - (umol/s), molar flow rate of air entering the leaf chamber
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!PARi - (umol/m2/s), PAR measured by the in-chamber quantum sensor, must provide
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PARo - (umol/m2/s), PAR measured by the external quantum sensor
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Press - (KPa), atmospheric pressure
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CsMch - (umol/mol), sample CO2 offset
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HsMch - (mmol/mol), sample H2O offset
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StableF - (NA), a stability indicator as a decimal value
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Status -(NA), status flag
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PhiPS2 - (NA), DeltaF/Fm, the fraction of absorbed PSII photons that are used in photochemistry
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OxygenPress - (Pa), atmospheric O2 partial pressure
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Line 18: The units of corresponding variables in Line 17
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Line 19 and below: The actual data body of the A/Ci curve
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