dyco apply-batch

Remove lags listed in an existing tlag_results.csv. Detects nothing — it reads the numbers another run produced and shifts columns by them. Step 2 of the two-step route, after dyco pwb-batch.

Also available as the standalone dyco-apply-batch.

--scalar LABEL:column here reads the lag recorded under LABEL and applies it to column, so one gas’s detected lag can be removed from another gas’s data.

All options

Apply PWB-detected time lags to raw EC files. Alias: uv run dyco-apply-batch

usage: dyco apply-batch [-h] --input-dir INPUT_DIR --output-dir OUTPUT_DIR
                        --results-csv RESULTS_CSV --scalar LABEL:column
                        [--lag-column-template LAG_COLUMN_TEMPLATE] [--hz HZ]
                        [--skiprows SKIPROWS] [--extra-rows EXTRA_ROWS]
                        [--sep SEP] [--lineterm LINETERM]
                        [--na-values NA_VALUES [NA_VALUES ...]]
                        [--na-rep NA_REP] [--period-col PERIOD_COL]
                        [--period-key-regex PERIOD_KEY_REGEX]
                        [--file-key-regex FILE_KEY_REGEX]
                        [--n-workers N_WORKERS] [--strict]

Named Arguments

--input-dir

Directory containing the original EddyPro rotated .txt files.

--output-dir

Output directory for lag-corrected files.

--results-csv

tlag_results.csv produced by dyco-pwb-batch.

--scalar

Gas label and column name, e.g. CH4:ch4. Repeat for each gas.

--lag-column-template

Lag-column template (use {prefix} for lowercased scalar label).

Default: '{prefix}_tlag_final_pf_s'

--hz

Sampling frequency in Hz.

Default: 20

--skiprows

Lines BEFORE the column-name row (EddyPro rotated: 9; raw CSV with header on line 1: 0).

Default: 9

--extra-rows

Extra rows AFTER the header but BEFORE data (e.g. units + instrument-source rows: 2). Each preserved verbatim in the output.

Default: 0

--sep

Field separator. Default: whitespace (regex ‘s+’). Use ‘,’ for CSV, ‘t’ for TSV.

Default: '\s+'

--lineterm

Line terminator written between data rows. Default ‘n’; use ‘rn’ to match Windows-CRLF input.

Default: ' '

--na-values

Strings to treat as NaN on read.

Default: ['-9999', '-9999.0', '-9999.0000000000000']

--na-rep

Value written for NaN on output.

Default: '-9999'

--period-col

Name of the filename column in the results CSV.

Default: 'period'

--period-key-regex

Regex applied to each period value; concatenated capture groups form the key. Pair with –file-key-regex to bridge name mismatches.

--file-key-regex

Regex applied to each filename in –input-dir; concatenated capture groups form the key.

--n-workers

Parallel worker processes (default: os.cpu_count()).

--strict

Re-raise worker exceptions instead of capturing them.

Default: False