The command line

fluxatlas INPUT --list
fluxatlas INPUT -o atlas.html --vars TA,PREC
fluxatlas INPUT -o atlas.html --var TA=air_temp --qc TA=TA_FLAG

python -m fluxatlas is the same entry point.

The command line is a thin wrapper over fluxatlas.atlas. Nothing is computed in it that a caller using the library would have to write again.

Naming the variables

There are two ways to say which variables to build, and one call can use both.

--vars KEY[,KEY...]

Names canonical keys and lets the registry find the columns. Use it where the file uses FLUXNET names (TA_F, P_F, SW_IN_F, and so on). Repeatable, and comma-separated lists work.

--var KEY=COLUMN

Names the column outright, which is what a file with its own naming needs. --qc KEY=COLUMN adds the quality flag beside it (0 measured, above 0 modelled). --factor KEY=NUMBER converts the column onto the canonical unit. Both refine a --var mapping and are an error without one.

--list prints what the registry can find in a file. Run it first to see whether --vars will do.

Naming nothing builds every registry variable the file can supply.

Examples

# What does this file carry? Read from the header, so it is quick on a large file.
fluxatlas record.csv --list

# Everything the registry finds, written beside the input as <SITE>_atlas.html
fluxatlas record.csv

# Two variables, named by canonical key
fluxatlas record.csv -o atlas.html --vars TA,PREC

# A file with its own column names
fluxatlas record.parquet -o atlas.html --var TA=air_temp --qc TA=TA_FLAG

# A column published in Pa, converted onto the canonical kPa
fluxatlas record.parquet -o atlas.html --var VPD=vpd_pa --factor VPD=0.001

# Two half-years instead of four seasons, and a smaller file
fluxatlas record.csv -o atlas.html --seasons DJFMAM --no-hourly

File size

--no-hourly drops the hourly arrays behind the day panel’s diurnal charts. They are most of the output: a twenty-one-year FULLSET page with them runs to about 6 MB. Dropping them costs the diurnal composites and nothing else.

Every option

Build an atlas page from a half-hourly FLUXNET-standardized file.

usage: fluxatlas [-h] [-o OUT] [--vars KEY[,KEY...]] [--var KEY=COLUMN]
                 [--qc KEY=COLUMN] [--factor KEY=NUMBER] [--seasons MONTHS]
                 [--site SITE] [--site-long SITE_LONG]
                 [--first-year FIRST_YEAR] [--last-year LAST_YEAR]
                 [--no-hourly] [--title TITLE] [--list] [--open] [-q]
                 input

Positional Arguments

input

the half-hourly input file (.csv or .parquet)

Named Arguments

-o, --out

output HTML file; the default is <SITE>_atlas.html beside the input

--vars

canonical variables to build, with their columns found by the registry (TA, PREC, SW_IN, VPD, RH, SWC, NEE, GPP, RECO, LE, H). Repeatable.

--var

name the column that supplies a variable, for a file that does not use FLUXNET names. Repeatable.

--qc

the quality flag beside a –var column: 0 measured, above 0 modelled. Repeatable.

--factor

multiply a –var column onto the canonical unit, e.g. –factor VPD=0.001 for Pa to kPa. Repeatable.

--seasons

the first season, as month initials (DJF, JJA) or numbers (12,1,2). The rest of the year is divided into seasons of the same length, so DJF gives the usual four and DJFMAM gives two half-years. Use ‘none’ for a site whose year has no seasons. Default: DJF

Default: 'DJF'

--site

site identifier; the default is read from the file name

--site-long

longer site description for the page

Default: ''

--first-year

first year to include

--last-year

last year to include

--no-hourly

leave out the hourly arrays behind the day panel’s diurnal charts, which are most of the file size

Default: False

--title

page title; the default names the site and the span

--list

print the variables the registry can find in the file, and exit

Default: False

--open

open the finished page in the default browser

Default: False

-q, --quiet

print nothing but errors

Default: False

examples:

fluxatlas record.csv –list fluxatlas record.csv -o atlas.html fluxatlas record.csv -o atlas.html –vars TA,PREC fluxatlas record.parquet -o atlas.html –var TA=air_temp –qc TA=TA_FLAG fluxatlas record.parquet -o atlas.html –var VPD=vpd_pa –factor VPD=0.001

Errors

An argument error, an unknown canonical key, a --qc or --factor that refines nothing, a missing input file, or an invalid --seasons value: each exits with a message and a non-zero status. The season value is checked before the file is opened, so a typo does not first cost a read of several hundred megabytes.