TomoGUI

User Guide

  • Installation
    • Requirements
      • Python Version
      • Core Dependencies
      • External Tools
      • AI Reco
    • Installation Methods
      • From Source (recommended)
      • Using Conda Environment
    • Verifying Installation
    • Troubleshooting
      • Qt Platform Plugin Issues
      • PyQt5 Import Errors
      • CUDA Issues
      • AI Reco model not found
  • Getting Started
    • Launching TomoGUI
    • Basic Workflow
    • Your First Reconstruction
    • Understanding the Interface
      • Main Layout
      • Log Output
    • Next Steps
  • Interface Overview
    • Main Window Layout
    • Top tab bar
    • Left Panel
      • Data Selection
      • Tab System
        • Main Tab
        • Reconstruction Parameters Tabs
        • Advanced Config Tab
        • Batch table (on the Main tab)
        • HDF5 Viewer
    • Right Panel
      • Image display
      • Log Output
  • Reconstruction Workflow
    • Quick reference
    • Try vs Full
      • Try Reconstruction
      • Full Reconstruction
    • Reconstruction Methods
    • Centre of Rotation
    • Output folders
    • Per-dataset parameters
  • AI Reconstruction
    • How it works
    • Single-file AI Reco
    • Batch AI Reco
    • Fix COR Outliers
      • Algorithm
    • Series tinting and auto-skip
    • TomoLog auto-contrast
  • Batch Processing Guide
    • Overview
    • Quick start
    • Per-file and top-bar COR
    • Series-aware operations
      • Series grouping
      • Series tinting
      • Auto-skip undersized files
      • Fix COR Outliers (also fills missing CORs)
    • Deleting files from the list
    • Remote / multi-GPU
  • Themes
    • Toggling
    • Customising

Features

  • Main Tab
    • Layout
    • Reconstruction parameter tabs
    • Right-hand visualisation
      • Auto-contrast
    • Log output
  • Reconstruction Parameters
    • Recon tab
    • Hardening tab
    • Phase tab
    • Rings tab
    • Geometry tab
    • Data tab
    • Performance tab
    • Per-dataset persistence
  • Batch Processing Tab
    • Features
    • File table
      • Selection
    • Batch Try / Full
    • Batch AI Reco
    • Fix COR Outliers (also fills missing CORs)
    • Auto-skip undersized files
    • Delete Selected
    • Remote execution
  • HDF5 Data Viewer
    • Opening a file
    • Image tab
    • Metadata tab
    • Expected structure
    • Common failures
    • See Also
  • Advanced Configuration
    • Fields
    • Persistence
    • Config file editing
  • TomoLog Integration
    • Launching TomoLog
    • Dialog fields
    • Per-file auto-contrast

Advanced Topics

  • SSH Setup for Remote Machines
    • Requirements
    • Configuring TomoGUI
    • Non-interactive shell env
    • Shared storage
    • Troubleshooting
  • GPU Management
    • Single-file mode
    • Batch mode (unified queue)
      • Per-phase subprocesses
    • Monitoring
    • Remote GPUs
  • COR Management
    • Sources of COR
    • Resolution order (batch)
    • Storage
    • Fix COR Outliers
      • Why series grouping?
    • Auto-skip undersized files
  • Troubleshooting
    • GUI / launch
    • Reconstruction
    • AI Reco
    • TomoLog

Developer Guide

  • Architecture
    • Packages
    • Layering
    • Key subsystems
      • Unified batch queue
      • AI Reco pipeline
      • Fix COR Outliers
      • Per-dataset parameter persistence
  • API Reference
    • Main classes
    • Entry points
    • Inference pipeline
    • Internal helpers (TomoGUI methods)
  • Contributing
    • Development Setup
    • Code Style
    • Testing
TomoGUI
  • Search

© Copyright 2024, Xiaoyang Liu, Alberto Mittone.

Built with Sphinx using a theme provided by Read the Docs.