PhysPlot: Advanced Plotting Made Simple

PhysPlot is a scientific plotting and workflow automation application with a spreadsheet-first PyQt6 graphical interface. It supports importing, transforming, plotting, fitting, templating figure appearance, exporting datasets, and replaying saved protocol sequences in headless workflows.

Install on macOS with one command (details in Installation):

curl -fsSL https://raw.githubusercontent.com/MShirazAhmad/PhysPlot/main/scripts/install_macos.sh | bash

Video tutorials

Short live recordings, one per feature, are on YouTube in two playlists: PhysPlot Basics (Simple Mode) and PhysPlot Advanced (protocols, bulk runs, writing file loaders and plotter modules). Every video is listed in Video Tutorials.

Main Features

• Spreadsheet-first data entry and import with explicit column-role dropdowns.

• Instrument exports load directly: Malvern Panalytical .xrdml and CSV, EDAX EDS maps and SmartQuant tables, EMSA .msa spectra, PHI XPS scans, Rigaku .ras scans, TA Instruments TGA/DSC exports, JCAMP-DX spectra, and plain CSV/TXT/Excel tables.

• Replayable protocol sequences: every import, transformation (including plugin functions such as XRD: Baseline Remove), role change, and plot is recorded and can be replayed, exported as Python, and run over whole folders.

• Simple Mode panels for importing data, transforming columns, and generating plots.

• Advanced Mode tabs for building and editing the protocol (Build Protocol) and running it across folders (Run Sequence).

• Figure Editor-based editing for Basic Plotter output.

• Reusable figure templates saved from Figure Editor > PhysPlot > Save as Template and selected from Simple Mode’s Template dropdown.

• Custom fit functions through Figure Editor > Fitting > Add Fit Function, or a least-squares fit from the Plotter Module.

• Backend API and physplot command line for headless use, notebooks, and bulk workflows.

• Native Help menu links for documentation, GitHub, issue reporting, and the About dialog.

Build Modules with an AI Assistant

PhysPlot is extended with small files: a loader for a new instrument, a transformation, a plotter, a sequence, a figure template and more. You do not need to write them yourself. Every kind of module has a guide file written for AI assistants: attach it with a sample of your data to ChatGPT, Claude, Gemini or Copilot, describe what you need, and save the finished file in Documents/PhysPlot/config/<folder>/ (File → Open Config Folder), then choose File → Reload Config Modules.

• Build Modules with an AI Assistant: the steps, which guide to use, and an example request for every kind of module.

• AI Module Examples: the tested example of every kind, with sample data and the resulting plots.

• Extension Guides: each kind of module explained, for writing one by hand.

Project links

• PhysPlot documentation home

• PhysPlot repository

• Feature requests and bug reports

Contents

• Installation
  • Prerequisites
  • macOS: one command
  • Windows: one command
  • Install from source
  • Create and activate a virtual environment
  • Install Python dependencies
  • Run PhysPlot
  • Build a Windows installer
  • Extension and template folders
• PhysPlot GUI Walkthrough
  • 1. Main Window Overview
  • 2. Importing Data
  • 3. Choosing Column Roles
  • 4. Transforming a Column
  • 5. Generating, Editing, and Templating a Plot
  • 6. Adding Fit Functions
  • 7. Building and Replaying the Protocol Sequence
  • 8. File Loaders for Instrument Formats
  • 9. Exporting Processed Data
  • Complete GUI Workflow Summary
  • Notes for Extending PhysPlot
• Video Tutorials
  • Basics (Simple Mode)
  • Advanced
• Sequence Walkthrough: Record, Save, Reuse and Bulk-Run
  • 1. Import the first scan
  • 2. Remove the background
  • 3. Normalise and choose what to plot
  • 4. Plot
  • 5. Review the protocol
  • 6. Save the sequence
  • 7. Open it again later
  • 8. Replay it
  • 9. Use it on a different file
  • 10. Run it over a folder
  • 11. When a file fails
  • 12. Run it without the GUI
  • Quick reference
• UI Reference
  • How the window is organised
  • Keyboard shortcuts
• Data Entry
  • Manual table entry
  • Managing dimensions
  • Delete old entries
• Data Import
  • Supported formats
  • Instrument exports
  • Loader selection
  • XRDML files
  • Import steps
  • Column assignment
• Data Manipulation
  • Transformation panel
  • Controls
  • Available functions
• Protocol Sequences
  • Step status
  • Rerun from a step
  • Editing steps
  • Headless use
• Plot Generation
  • Requirements
  • Generate plot flow
  • Least-squares fitted line
  • Built-in plotter modules
  • Figure Editor
• Curve Fitting
  • Modern Figure Editor fitting
  • Legacy fit models
  • Enable and label legacy fits
• Plot Customization
  • Figure Editor options
  • Reusable templates
  • Marker style options
  • Line style options
  • Color options
• Data Export
  • Export behavior
  • Reproducible runs

Build Modules with AI

• Build Modules with an AI Assistant
• AI Module Examples

Extend and Reference

• Extension Guides
  • Modularity and Auto-Loading Map
  • File-Loader Plugins
  • Function Plugins
  • Plotter Modules and Plot-Type Presets
  • Sequences, Protocol Modules and Pipelines
  • Figure Templates, Fit Styles and Figure Editor Plugins
  • Curve Fitting and Fit-Model Files
• API Reference
  • Application API
  • GUI API (physplot_gui)
  • Utilities API
  • Function Plugin API
  • Curve-Fitting Plugin API
  • File Loader API
  • Configuration API
• Class Reference
  • Core classes
  • Autodoc view
• PhysPlot Project Guide
  • Working Philosophy
  • Project Structure
  • Main User Flows
  • Backend Contracts
  • Workflow Step Pattern
  • Annotated Protocol Drafts
  • Testing Checklist
  • Release Checklist