Command reference

Everything is reachable through one command:

dyco                    # list the workflows
dyco <command> --help   # options for one of them

Command	Does	When
dyco tui	detect-remove behind a form, with live validation and a preflight check.	Start here.
dyco detect-remove	The main command. Split long raw files into averaging-period chunks, rotate, detect the lag per chunk, then remove it. One pass, one output folder.	Almost always. Scripting, or when you prefer a command line.
dyco pwb-batch	Detect only, on files that are already split into averaging periods. Writes tlag_results.csv and stops.	Step 1 of the two-step route.
dyco apply-batch	Remove lags listed in an existing tlag_results.csv. Detects nothing.	Step 2 of the two-step route.

Each also exists standalone: dyco-detect-remove, dyco-detect-remove-tui, dyco-pwb-batch, dyco-apply-batch.

Everything else in dyco is a library API with no command of its own: the file splitter, the flux detection limit, the covariance-maximization estimator.

Note

The pages below are generated from the argparse parsers themselves, so they always match what --help prints.

• dyco detect-remove
• dyco pwb-batch
• dyco apply-batch
• dyco tui

Taking a gas’s lag from another gas

A trace gas can be too noisy to locate its own lag. When that happens PWBOPT rejects the detections, and the last resort is the median of those same rejected numbers, which on real data is often a negative lag no tube can produce. A reference gas travelling the same tube is a better answer.

Say so per gas, with @lagfrom= (Lag from in the TUI):

dyco detect-remove ... --scalar "CO2:CO2_DRY_[IRGA72-A]" --scalar "N2O:N2O_DRY_[QCL-C2]@lagfrom=CO2"

N₂O keeps every lag it detects and PWBOPT accepts (S1 or S2), and it keeps its own lag carried forward from an earlier period for as long as that lag is allowed to travel — see the carry limit below. Only past that does it take the CO₂ lag, for that same period, so a donor lag that drifts is followed rather than flattened into a constant. The summary records the choice for every period in {gas}_lag_source (own, from:CO2, median), so a borrowed lag is never mistaken for a detected one.

The gas’s own lag comes first at both tiers on purpose. Two gases down one tube still have different delays — a systematic 0.35 s between CH₄ and N₂O is ordinary — so borrowing swaps a stale number for a biased one. It is worth doing once the gas’s own lag is old enough that staleness is the bigger error, and that is a judgement the carry limit expresses.

Pick a donor that behaves like the recipient. H₂O is not interchangeable with the dry gases. It sticks to the tube wall and comes off again, so its lag is longer than the travel time through the tube, and it shifts with humidity and tube age. CO₂, CH₄ and N₂O move with the flow. H₂O is also, in most runs, the gas that detects most reliably, which is what makes it the tempting donor and the wrong one: giving its lag to an inert gas adds a wall effect that gas does not have, and biases the flux. Let inert gases donate to inert gases, and keep a sticky donor for a sticky recipient.

Chains work (CH4 from N2O from CO2); circular ones are rejected.

Limiting how far a lag may be carried

PWBOPT’s S3 rule gives a period with no usable detection the nearest earlier optimal lag, with no limit on the distance — one good half hour can supply the rest of a week. --max-carry N (Max carry in the TUI) caps it at N averaging periods. Beyond that the lag expires ({gas}_flag_* = S3_expired) and the period falls through to the donor gas, or to the median.

{gas}_carry_periods reports the distance for every period: 0 where the lag was detected in that very period, n where it travelled n periods, empty where it came from somewhere else entirely.

The default is unlimited, which is the published behaviour. It also means a donor is nearly idle: with no limit the gas carries its own lag forever and only the periods before its first detection are left to borrow. @lagfrom= and --max-carry are meant to be set together, and dyco warns when a donor is named without one.

The two-step route

pwb-batch to detect, then apply-batch, where --scalar LABEL:column reads the lag of one gas and shifts the column of another. It applies when your files are already split into averaging periods by other software, leaving nothing for detect-remove to chunk.

Important

PWB detection needs wind-rotation-corrected high-frequency data. dyco detect-remove handles this itself. Files fed to dyco pwb-batch must already be rotated (double rotation or planar fit, e.g. EddyPro “Advanced” rotated output). A non-zero mean W corrupts the cross-correlation.

Input file formats

Flag	Handles
--sep	Field separator. , by default; \t for TSV, \s+ for whitespace-aligned.
--skiprows	Metadata lines before the column-name row. 0 for a plain CSV with names on line 1; 9 for EddyPro rotated output.
--extra-rows	Rows after the header but before the data, such as units and instrument tags. Default 2. They are preserved byte-for-byte in the output.
--na-values / --na-rep	What counts as missing on the way in, what is written for it on the way out.
--lineterm	auto reproduces the input’s CRLF or LF. Force it with \r\n or \n.
--file-pattern	Which files to read. Compression is transparent: .gz, .bz2, .xz and .zip are read as the text they contain.
--output-suffix	The extension the written chunks carry, dot included. Give the whole thing (.csv, .csv.gz, .dat.zip), just the text format (.csv, which writes plain text and drops any compression), or just the compression (.zip, which keeps the input’s text format, so file1.csv gives file1.csv.zip). auto (default) reuses the input’s own extension. A suffix without the leading dot is refused, so .csv is written the same way as .csv.gz.

Two limits worth knowing. This path reads delimited text only; Parquet is read by dyco.files.read_raw_data, which serves the file splitter, not this pipeline. And it needs no data-timestamp column: chunking is driven by --hz and record count, and the wall-clock time comes from the filename via --start-time-regex.