Metadata-Version: 2.4
Name: batplot
Version: 1.8.36
Summary: Interactive plotting tool for material science (1D plot) and electrochemistry (GC, CV, dQ/dV, CPC, operando) with batch processing
Author-email: Tian Dai <tianda@uio.no>
License: MIT License
        
        Copyright (c) 2025 Tian Dai
        
        Permission is hereby granted, free of charge, to any person obtaining a copy
        of this software and associated documentation files (the "Software"), to deal
        in the Software without restriction, including without limitation the rights
        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
        copies of the Software, and to permit persons to whom the Software is
        furnished to do so, subject to the following conditions:
        
        The above copyright notice and this permission notice shall be included in all
        copies or substantial portions of the Software.
        
        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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Project-URL: Homepage, https://github.com/chem-plot/batplot
Project-URL: Repository, https://github.com/chem-plot/batplot
Project-URL: Issues, https://github.com/chem-plot/batplot/issues
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
Classifier: Operating System :: OS Independent
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Visualization
Requires-Python: >=3.9
Description-Content-Type: text/markdown
License-File: LICENSE
License-File: NOTICE
Requires-Dist: numpy>=1.21.0
Requires-Dist: matplotlib>=3.5.0
Requires-Dist: rich>=10.0.0
Requires-Dist: openpyxl>=3.0.0
Dynamic: license-file

# batplot

**Interactive plotting tool for battery and materials characterization data**

`batplot` is a Python CLI tool for visualizing and analyzing electrochemical and structural characterization data with interactive styling and session management. The electrochemistry and operando plots were inspired from Amalie Skurtveit's python scripts (https://github.com/piieceofcake?tab=repositories).

## Features

With a single line of command to easily plot publication-ready plots with customized, intuitive interactive editing features such as:
- **Electrochemistry Plot**: Galvanostatic cycling (GC), cyclic voltammetry (CV), differential capacity (dQdV), capacity per cycle (CPC) with multi-file support
- **1D XY plot**: Designed for XRD, PDF, XAS (XANES/EXAFS) but also support other types
- **Operando Contour plot**: Correlate in-situ characterizations (XRD/PDF/XAS) with electrochemical data
- **Interactive plotting**: Real-time editing customized for each type of plottings
- **Session Persistence**: Save and reload complete plot states with `.pkl` files
- **Style Management**: Import/export plot styles as `.bps`/`.bpsg` files
- **Batch Processing**: Export each file separately with `--all`
- **Column preview**: `--showcol` prints numbered columns, header names when found, and the first 10 values per column (CSV, Excel, text, .mpt, .brml, Bruker .raw, etc.)

## Installation

```bash
pip install batplot
# It is recommended to use separate environment for batplot to aviod compatability issues with dependencies.
```

## Quick Start

- Tutorial: https://drive.google.com/file/d/1NTFJWNBbWW4mgz0H5ZelGjuOBWxoFgkr/view
- Tutorial files: https://github.com/chem-plot/batplot/blob/main/batplot_tutorial.zip
- Manual: https://github.com/chem-plot/batplot/blob/main/batplot_user_manual.pdf

---

## 1D (XY) Mode — XRD, PDF, XAS and much more

In batplot, --xaxis is frequently used to indicate the data type.

### Basic plotting

```bash

# Specify X-axis type (Q, 2theta, r, k, energy, time or any user defined names)
# By defauly, batplot will skip the header lines, plot the first and second columns as x and y
# Q and q are equivalent (case-insensitive)
batplot pattern.xye --xaxis 2theta --i
batplot data.qye --xaxis q --i
batplot data.txt --xaxis whatever --i

# Set X-axis range
batplot pattern.xye --xaxis 2theta --xrange 10 80 --i

# Save to file (default .svg if no extension)
batplot pattern.xye --xaxis 2theta --out figure
batplot pattern.txt --xaxis Energy --out figure.png
```

### Wavelength and Q conversion for XRD data

```bash
# Convert 2θ to Q using wavelength (Å), --xaxis is no longer needed as providing wavelength is implying that user wants to convert and plot the data in Q space
batplot data.raw --wl 1.5406 --i

# Per-file wavelength: file.xye:1.54, in this case --xaxis is also not needed and files will be plotted in Q space
batplot scan1.brml:1.5406 scan2.xye:0.7093 --i

# Convert and export to converted/ subfolder (q and Q equivalent)
batplot data.xye --convert 1.54 q
batplot data.qye --convert q 1.54

# With --readcol for custom column layout (e.g. 2θ in col 3, intensity in col 4)
batplot data.csv --readcol 3 4 --convert 1.54 q
batplot f1.txt --readcol 2 3 f2.txt --readcol 5 6 --convert 1.54 q
```

### Stacking and normalization

```bash
# Stack curves vertically (auto-normalizes)
batplot file1.xy file2.xy --stack --i

# Control spacing between stacked curves
batplot file1.xy file2.xy --stack --delta 0.15

# Normalize intensity to 0–1 (without stacking)
batplot file.xy --norm --i
```

### Dual y-axis (right y-axis)

```bash
# Plot selected files on the right y-axis (--ry disables --stack)
batplot file1.xy --ry file2.xy --ry file3.xy file4.xy --ry --i
# Files 1, 2, 4 use right y-axis; file 3 uses left y-axis

# With --txaxis: right y-axis curves use the top x-axis (default: shared bottom x)
batplot file1.xy --ry file2.xy --txaxis --i
```

### Column selection and multi-curve

```bash
# Read columns 2 and 3 as X, Y (1-indexed)
batplot data.xy --readcol 2 3 --wl 1.54 --i

# Per-file columns
batplot file1.xy --readcol 2 3 file2.xy --readcol 4 5 --xaxis r --i

# Multiple curves from same file (cols 1,2 and 1,3)
batplot data.xy --readcol 1 2 1 3 --xaxis 2theta --i

# Range: col 1 as x, cols 2–20 as 19 y-curves
batplot file.txt --readcol 1 2-20 --xaxis Energy --i

# With --convert: use custom columns when converting XRD data
batplot data.csv --readcol 3 4 --convert 1.54 q
```

### Derivatives and EXAFS

```bash
# Plot first derivative (dy/dx)
batplot file.xy --1d --stack --i

# EXAFS k-weighting
batplot data.chik --chik   --i        # χ(k)
batplot data.chik --k2chik        # k²χ(k), most common
batplot data.chik --k3chik --xrange 2 12
```

### Interactive menu

```bash
# Open interactive menu for styling, ranges, export, session save
batplot pattern.xye --i
batplot file1.xy file2.xy --stack --i
batplot allfiles --xaxis 2theta --xrange 15 75 --i
```

---

## Electrochemistry Mode

### Data export requirements from instruments

- **Neware**: Customized report — check all boxes
- **Biologic**: Export all info to .mpt file

### Galvanostatic cycling (GC)

GC mode plots potential vs. capacity for each charge/discharge cycle—the primary visualization for battery cycling data. Batplot automatically detects cycles from Neware `.csv` or Biologic `.mpt` files, assigns each cycle a distinct color, and supports both specific capacity (mAh/g) and raw capacity. For `.mpt` files, pass `--mass` (mg) to compute specific capacity. Discontinuous or paused experiments are handled by splitting data into contiguous charge/discharge segments. Use the interactive menu to customize colors, visibility, and export.

```bash
# From .csv (capacity in file)
batplot battery.csv --gc --i

# From .mpt (requires --mass in mg)
batplot battery.mpt --gc --mass 7.0 --i

```

### Cyclic voltammetry (CV)

```bash
batplot cyclic.mpt --cv --i
batplot cyclic.mpt --cv --i
```

### Differential capacity (dQ/dV)

```bash
batplot battery.csv --dqdv --i
```

### Capacity per cycle (CPC)

```bash
# Single file
batplot stability.csv --cpc --i
batplot stability.mpt --cpc --mass 5.4 --i

# Multiple files with individual colors
batplot file1.csv file2.mpt --cpc --mass 6.0 --i
```

### Time vs potential

```bash
# Plot time (h) vs potential from CSV/MPT
batplot battery.csv --xaxis time --i
```

### Potential window (custom potential–time .mpt)

```bash
# Two columns: potential, time. Use --pw and --cd to plot as GC
batplot custom.mpt --gc --pw 0.01 3 --cd 0.2 --i
```

---

## Operando Mode

Contour plots from a folder of diffraction data, optionally with an electrochemistry side panel.

### Bruker operando (.brml)

For Bruker operando XRD (multi-scan .brml files named cyc1, cyc2, cyc3, etc.):

```bash
# Place .brml files (e.g. RA_O5_cyc1.brml, RA_O5_cyc2.brml) in the folder
# Use --wl for Q conversion (e.g. synchrotron λ=0.709 Å)
batplot RA_O5 --operando --wl 0.709 --i

# EC side panel: .mpt or Biologic DataLogger CSV (*--DataLogger.csv), sorted by cyc
# Time vs potential is concatenated across files (continuous time axis)
```

### Standard XY files

```bash
# Contour from folder of .xy/.xye/.qye/.dat
batplot --operando --wl 1.54 --i

# With folder path
batplot /path/to/data --operando --xaxis 2theta --i

# Q conversion from 2θ
batplot --operando --wl 0.25995 --i

# Column selection: --readcolc for contour, --readcols for side panel (.mpt)
batplot --operando --readcolc 2 3 --readcols 1 2 --i

# Derivative contour
batplot --operando --1d --i

# With CIF tick labels
batplot folder phase.cif:1.54 --operando --i
```

Operando column selection:
- `--readcolc <x> <y>`: columns for the contour plot (from .xy/.xye/.qye/.dat files)
- `--readcols <x> <y>`: columns for the side panel (from .mpt file)

---

## Plotting multiple files

```bash
# All XY files in current directory on same figure
batplot allfiles
batplot allfiles --stack --i

# Only specific extension (natural-sorted)
batplot allxyfiles
batplot "/path/to/data" allnorfiles --i

# Explicit file list
batplot file1.xye file2.qye structure.cif:1.54 --stack --i
```

---

## Batch export (--all)

Export each file as a separate figure to `Figures/`:

```bash
batplot --all
batplot --all --format png
batplot --all --xaxis 2theta --xrange 10 80
batplot --all style.bps --gc --mass 7

# With --readcol for custom columns (put --readcol before style file)
batplot --all --readcol 2 3 --xaxis 2theta
batplot --all --readcol 2 3 style.bps --xaxis 2theta
```

---

## Supported File Formats

| Type | Formats |
|------|---------|
| **Electrochemistry** | `.csv` (Neware, Biologic DataLogger), `.mpt` (Biologic), `.xlsx` (Landt/Lanhe CPC) |
| **XRD / PDF** | `.xye`, `.xy`, `.qye`, `.dat`, `.csv`, `.txt`; Bruker `.brml`, `.raw` |
| **Operando** | `.xy`, `.xye`, `.qye`, `.dat`; Bruker `.brml` (cyc1/cyc2/cyc3); EC: `.mpt` or DataLogger `.csv` |
| **XAS** | `.nor`, `.chik`, `.chir` |
| **Generic** | Use `--readcol` and `--xaxis` for custom formats |

---

## Interactive Features

With `--interactive`:
- **Cycle/Scan Control**: Toggle visibility, change colors
- **Multi-file palette (EC/CV/dQdV)**: Press `c`, then type `fall viridis` (all files), `f1-5 viridis` (files 1–5), or `f1 f3 f5 4` (each file gets one color)
- **CPC file palette**: In `ly`/`ry` color submenu, apply palette to file range: `1-5 viridis`, `1 3 5 4`
- **Styling**: Line widths, markers, fonts
- **Axes**: Labels, limits, ticks, spine styles
- **Export**: Sessions (`.pkl`), styles (`.bps`/`.bpsg`), high-res images. Colors persist via `p` (print style), `i` (import), `s` (save session), `b` (undo)
- **Live Preview**: All changes update in real-time

---

## Help & Documentation

```bash
batplot --help              # General help
batplot --help xy           # XY mode guide
batplot --help ec           # Electrochemistry guide
batplot --help op           # Operando guide
batplot --version           # Version and release notes
batplot --manual            # Open illustrated manual
```

- [USER_MANUAL.md](USER_MANUAL.md) — Detailed usage and workflows
- [FLAGS_REFERENCE.md](FLAGS_REFERENCE.md) — Complete flag reference by mode

---

## Requirements

- Python ≥ 3.9
- numpy
- matplotlib

## License

See [LICENSE](LICENSE)

## Author & Contact

Tian Dai  
tianda@uio.no  
University of Oslo  
https://www.mn.uio.no/kjemi/english/people/aca/tianda/  
https://github.com/chem-plot/

**Subscribe for Updates**: Join batplot-lab@kjemi.uio.no for updates. If not from UiO, email sympa@kjemi.uio.no with subject: "subscribe batplot-lab@kjemi.uio.no your-name"
