12. Summary of flags and keywords

This chapter is the complete CLI reference for batplot: every --flag, positional keyword, and common file suffix. Interactive menu keys (c, p, u, …) are documented in each mode chapter — see Interactive menus — and are not listed here.

All flags use a double-dash prefix (--). Many also accept a short form (see §12.1).

Worked tutorials: 1D · EC · Operando · Histogram · Batch · Utilities.

Mode-specific terminal help:

batplot --help
batplot --help xy
batplot --help ec
batplot --help op
batplot --help histo

---

12.1 Conventions and short aliases

Form	Notes
--flag	Long form (preferred in docs).
-i, -h, …	Short aliases normalized to long form before parsing.
Keywords	Bare tokens such as allfiles — not flags.
File suffixes	file.xy:1.54, file:q — part of the filename token.
Style files	A positional .bps / .bpsg / .bpsh path applies that style (same idea as interactive i).

Short aliases

Short	Long
-i	--i / --interactive
-h / --h	--help
-v / -V / --v	--version
-m / --m	--manual
-o	--out
-r	--xrange
-d	--delta
-c	--convert
-b	--b (EC potential-window tolerances)

---

12.2 Keywords and filename suffixes

These are not --flags.

Directory expansion keywords

Keyword	What it does	Example
allfiles	Expand to every supported data file in the folder (natural sort). Overlays on one figure (or feeds a mode). Not the same as --all.	batplot allfiles --stack --wl 0.259 --i
all<ext>files	Same, but only that extension (e.g. allxyfiles, allnorfiles, allcsvfiles).	batplot allxyfiles --xaxis 2theta
all	With EC mode only: synonym for batching the cwd (same family as --all). Prefer --all.	batplot --gc all --mass 7

Supported extensions for allfiles include .xy, .xye, .qye, .dat, .csv, .txt, .gr, .nor, .chik, .chir, .mpt, .brml, .raw, .xrdml, .rasx (CIF/session/script files are skipped).

Wavelength / Q suffixes on files

Suffix	What it does	Example
file:λ	Treat X as 2θ at wavelength λ (Å); convert to Q for plotting (data files). On a .cif, sets λ for tick calculation.	batplot scan.xy:1.54 --i
file:λ1:λ2	2θ(λ₁) → Q → 2θ(λ₂) re-projection.	batplot TD_R02.dat:0.259:1.54 --xaxis 2theta --i
file:q	Mark file as already in Q (no conversion).	batplot sim.csv:q --stack --i

Any file:λ or file:q implies Q mode unless --xaxis 2theta wins. Details: 1D — Wavelength Handling.

Positional style / session files

Token	What it does
style.bps / style.bpsg / style.bpsh	Apply exported style (histogram uses .bpsh).
session.pkl	Reload a saved session (--i to edit).
Several *.pkl	Batch interactive edit of same-mode sessions — Ch.9.

---

12.3 Help, version, and documentation

Flag	What it does	Example
--help / --h [topic]	General help, or xy / ec / op / histo.	batplot --help ec
--version / --v	Print version and release notes.	batplot --version
--manual / --m	Open the online user manual in a browser.	batplot --manual

---

12.4 General figure I/O and sessions

Flag	What it does	Example
--i / --interactive	Open the live interactive menu with the figure.	batplot file.xy --i
--out FILE	Save the figure and exit (extension sets format; default .svg if omitted).	batplot file.xy --out plot.png
--savefig FILE	Alternate export path (same role as --out in most modes). Prefer --out in new docs.	batplot file.xy --savefig plot.svg
--save	Write .pkl session(s) without opening --i (prompts for folder/name).	batplot file.xy --xaxis 2theta --save
--format EXT	With --all: image type (svg, png, pdf, jpg, jpeg, eps, tif, tiff). Default svg.	batplot --all --format png
--all [style]	Batch: one output per file under Figures/ (or sessions with --save). Optional style path. See Ch.9.	batplot --all --xaxis 2theta
--canvas	Combine several .pkl sessions into one multi-panel canvas layout.	batplot a.pkl b.pkl --canvas --i
--debug	Extra diagnostic printing (developer / troubleshooting).	batplot file.xy --debug --i

---

12.5 Shared axis and display flags

Used across modes where they make sense.

Flag	What it does	Example
--xaxis TYPE	X-axis kind or label: Q/q, 2theta, d, r, k, energy, rft, time, or a custom string. Optional for plain X/Y.	batplot file.xy --xaxis 2theta
--xrange MIN MAX	Display X limits.	batplot file.xy --xrange 10 80
--wl λ	Wavelength in Å (2θ↔Q and related conversions for all listed files).	batplot file.xy --wl 1.54
--ro	Swap X and Y before plotting.	batplot file.csv --xaxis time --ro
--norm	Normalize Y to 0–1 (1D).	batplot a.xy b.xy --norm --i
--1d / --2d	First derivative dy/dx (1D curves, or each operando scan). --2d is an alias of --1d in operando help.	batplot R03_Se.nor --1d --xaxis energy
--errors	Plot error bars when a third column is available.	batplot file.xye --errors --i
--autoscale	With --stack / --delta: scale vertical spacing relative to each curve’s Y range.	batplot a.xy b.xy --stack --delta 0.2 --autoscale

---

12.6 1D / XY mode

Default mode (no --gc / --operando / --histo / …).

Flag	What it does	Example
--stack	Stack curves vertically (implies intensity normalization for stacking).	batplot a.xy b.xy --stack --i
--delta N	Stack spacing (default depends on --stack).	batplot a.xy b.xy --stack --delta 0.15
--ry	Plot the preceding file(s) on the right Y-axis (disables --stack). Repeatable pattern.	batplot left.xy --ry right.xy --i
--txaxis	With --ry: right-Y curves use the top X-axis (default: shared bottom X).	batplot a.xy --ry b.xy --txaxis --i
--chik	EXAFS χ(k) labeling / weighting mode.	batplot data.chik --chik --i
--kchik	Plot k·χ(k).	batplot data.chik --kchik --i
--k2chik	Plot k²·χ(k).	batplot data.chik --k2chik --i
--k3chik	Plot k³·χ(k).	batplot data.chik --k3chik --i
--fullprof XSTART XEND XSTEP [λ]	FullProf-style row-wise .dat overlay (start, end, step; optional wavelength).	batplot pattern.dat --fullprof 10 80 0.02 1.54 --i

CIF reference ticks: pass .cif paths (optionally phase.cif:λ) together with data files — see 1D — CIF.

---

12.7 Column selection (--readcol…)

Default 1D plotting uses columns 1 and 2 (1-indexed).

Flag	What it does	Example
--readcol X Y …	Global or per-file X/Y (repeat pairs for multi-curve; Y1-Y2 range shorthand in help).	batplot f.dat --readcol 1 3 --i
--readcolxy X Y	Only for .xy files.	batplot a.xy --readcolxy 1 2
--readcolxye X Y	Only for .xye.
--readcolqye X Y	Only for .qye.
--readcolnor X Y	Only for .nor.
--readcoldat X Y	Only for .dat.
--readcolcsv X Y	Only for .csv.
--readcol<ext> X Y	Any custom extension (e.g. --readcolafes 2 3 for .afes).	batplot f.afes --readcolafes 2 3
--readcolc X Y	Operando contour scan columns.	batplot --operando --readcolc 1 2 --i
--readcols X Y	Operando EC side-panel columns.	batplot --operando --readcols 1 2 --i

Per-file placement: put --readcol after the file it applies to when mixing files. Details: 1D — readcol · Utilities.

---

12.8 Utilities: preview, strip, convert, Bruker extract

Full walkthroughs: Ch.11 Utilities.

Flag	What it does	Example
--showcol	Print column names / first values; then exit.	batplot --showcol demo_cols.txt
--strip-header N	Copy files with first N lines removed → stripped/ (originals untouched).	batplot demo_cols.txt --strip-header 2
--convert FROM TO	Convert XRD X among 2θ / Q / d (or λ₁→λ₂); write converted/.	batplot clean.xy --convert 1.54 q
--convert-ext EXT	Force output extension for --convert (default .qye for Q, else .xy).	batplot f.xy --convert 1.54 q --convert-ext .qye
--ext EXT[,EXT…]	With folder + --convert / --strip-header: only these extensions.	batplot folder --ext .xy --convert 0.26 q
--extract-brml-scans [OUT_DIR]	Split a Bruker .brml into per-scan .xy files.	batplot run.brml --extract-brml-scans

--convert tokens: a number means 2θ at that λ (Å); units q/d/2theta (aliases 2th, tth, …). Matrix: Convert XRD files.

---

12.9 Electrochemistry (GC / CV / dQ/dV / CPC / EPC)

Flag	What it does	Example
--gc	Galvanostatic cycling (potential vs capacity).	batplot B443.csv --gc --i
--cv	Cyclic voltammetry (potential vs current).	batplot file.mpt --cv --i
--dqdv	Differential capacity dQ/dV vs potential.	batplot B443.csv --dqdv --i
--cpc	Capacity per cycle + coulombic efficiency.	batplot B443.csv --cpc --i
--epc	Energy per cycle (when supported by the file).	batplot file.csv --epc --i
--mass M	Active mass in mg (or grams with a g suffix, e.g. 0.0065g). Repeatable for per-file mass. Required for many .mpt workflows.	batplot a.mpt --mass 6.5 --gc --i
--cum	With --gc: cumulative (throughput) capacity — charge/discharge laid end-to-end.	batplot file.csv --gc --cum --i
--pw VMIN VMAX	Potential-window custom GC from potential–time data (use with --cd).	batplot cell.mpt --gc --pw 0.01 3 --cd 0.2 --i
--cd RATE	Current density (mA/g) for --pw capacity calculation.	(with --pw)
--b TOL_UP TOL_LO	Boundary tolerances (V) for --pw edge detection (defaults ~0.05 / 0.005).	batplot cell.mpt --gc --pw 0.01 3 --cd 0.2 --b 0.05 0.005
--anode / --cathode	Select anode- vs cathode-oriented parsing for indexed voltage–time custom GC.	batplot cell.mpt --gc --anode --pw … --cd …
--xaxis time	Time (h) vs potential from Neware CSV / Biologic MPT (no --gc required).	batplot B443.csv --xaxis time --i

Batch EC: batplot --all --gc --mass 7 — Ch.9.

---

12.10 Operando / contour mode

Flag	What it does	Example
--operando	Contour map from a folder of sequential scans (+ optional EC side panel).	batplot --operando --i
--contour	Alias for --operando.	batplot --contour --wl 1.54 --i
--wl λ	Convert scan X from 2θ to Q.	batplot --operando --wl 1.54 --i
--xaxis …	Force axis type (e.g. 2theta, Q).	batplot --operando --xaxis 2theta --i
--1d / --2d	Contour of dy/dx for each scan.	batplot --operando --1d --i
--average N	Average every N consecutive scans before contouring.	batplot --operando --average 2 --i
--sum N	Sum every N consecutive scans (not both with --average).	batplot --operando --sum 2 --i
--readcolc X Y	Columns for contour scans.	batplot --operando --readcolc 1 2 --i
--readcols X Y	Columns for EC side panel.	batplot --operando --readcols 1 2 --i

Pass a folder path and/or .cif files on the command line as needed.

---

12.11 Histogram mode

Flag	What it does	Example
--histo	Histogram mode (tabular .csv / .txt).	batplot sizes.csv --histo --i
--histocol N	Column to bin (1-indexed). With --i and no column, a wizard lists columns.	batplot sizes.csv --histo --histocol 2 --bins 10
--binwidth W	Bin width.	batplot sizes.csv --histo --histocol 2 --binwidth 0.5
--bins N	Number of equal-width bins (alternative to --binwidth).	batplot sizes.csv --histo --histocol 2 --bins 40
--xrange A B	Histogram display / data window.	batplot sizes.csv --histo --histocol 2 --xrange 0 16

Batch: batplot --all --histo --histocol 2 (requires --histocol). Style files use .bpsh.

---

12.12 Alphabetical flag index

Flag	Section
--1d / --2d	12.5, 12.10
--all	12.4
--anode / --cathode	12.9
--autoscale	12.5
--average	12.10
--b	12.9
--bins / --binwidth	12.11
--canvas	12.4
--cd	12.9
--chik / --kchik / --k2chik / --k3chik	12.6
--contour	12.10
--convert / --convert-ext	12.8
--cpc / --cv / --cum	12.9
--debug	12.4
--delta	12.6
--dqdv	12.9
--epc	12.9
--errors	12.5
--ext	12.8
--extract-brml-scans	12.8
--format	12.4
--fullprof	12.6
--gc	12.9
--help / --h	12.3
--histo / --histocol	12.11
--i / --interactive	12.4
--manual / --m	12.3
--mass	12.9
--norm	12.5
--operando	12.10
--out	12.4
--pw	12.9
--readcol…	12.7
--ro	12.5
--ry / --txaxis	12.6
--save / --savefig	12.4
--showcol	12.8
--stack	12.6
--strip-header	12.8
--sum	12.10
--version / --v	12.3
--wl	12.5
--xaxis / --xrange	12.5

Keywords / suffixes: §12.2 (allfiles, all<ext>files, file:λ, file:λ1:λ2, file:q, style/session paths).