HABIT
0.1.0

Tutorial

  • Installation
    • Windows lightweight installer
    • Source install
  • Demo tutorial
    • Prepare data
    • Run (5 steps)

Web GUI

  • Web GUI (under development)
    • Planned scope
    • Early preview (developers)

How-to guides

  • How-to guides
    • Prepare data
      • Project root
      • Folder layout
      • Data specification
    • Preprocessing
    • Habitat segmentation
    • Feature extraction
    • Traditional radiomics
    • Machine learning
    • Model comparison
    • Auxiliary tools
      • ICC (feature reproducibility)
      • Test-retest habitat mapping
      • DICOM metadata export
      • Merge tables
      • Dice between mask batches

Configuration

  • Configuration Reference
    • Configuration recipe catalog
      • By workflow
      • Starter demos
      • Field reference pages
    • Preprocessing Configuration
      • Preprocessing configuration parameters
      • DICOM sort configuration (habit sort-dicom)
    • DICOM Sort Configuration
      • Top-level fields
      • Notes
    • Habitat Segmentation Configuration
      • Habitat Analysis Configuration Parameters
        • habitat_segmentation.supervoxel — SLIC Superpixel Configuration
        • Habitat Stage-1 Parallelism and Checkpoint Resume (Top-Level Field Reference)
    • Feature Extraction Configuration
    • Traditional Radiomics Configuration
      • paths
      • processing
      • export
      • logging
      • Backward-compatible flat keys
      • PyRadiomics parameter YAML
    • Machine Learning Configuration
      • Machine learning configuration parameters
      • Model comparison (habit compare)
    • Model Comparison Configuration
      • Top-level fields
        • Each files_config item
      • Typical outputs under output_dir
    • Auxiliary Tools and Data Configuration
      • Data configuration parameters
      • ICC analysis configuration (habit icc)
      • Test-Retest configuration (habit retest)
      • Traditional radiomics CLI configuration (habit radiomics)
      • Repository configuration template index
      • Configuration file validation
      • FAQ

Feature reference

  • Feature reference
    • Traditional Radiomics
      • Definition
      • Implementation
      • Output columns
      • Feature definitions
    • Non-radiomics Morphology
      • Output
      • Definition
      • Formula
      • Output columns
      • Implementation
    • Whole / Each Habitat Radiomics
      • whole_habitat
        • Output
        • Definition
        • Output columns
        • Implementation
      • each_habitat
        • Output
        • Definition
        • Output columns
        • Implementation
    • MSI Features
      • Output
      • Definition
      • Formula
      • Output columns
      • Implementation
      • References
    • ITH Score
      • Output
      • Definition
      • Formula
      • Output columns
      • Notes
      • Implementation
      • References

Command reference

  • Command reference
  • Auxiliary commands
    • habit dicom-info
    • habit icc
    • habit retest
    • habit merge-csv
    • habit dice

FAQ

  • FAQ
    • Installation
    • Runtime
    • GUI (under development)
    • Data

Background

  • Habitats and clustering
    • Clustering strategies

Developer

  • Developer Guide
    • Design Philosophy
      • Research constraints
      • Five design pillars
      • Trade-offs
      • See also
    • Core Concepts and Mental Model
      • Global mental model
      • Domain concepts
      • Engineering roles
      • Workflow and Runner
      • Configuration to execution
    • Architecture
      • Design principles
      • Layered architecture
      • Configuration-to-execution chain
      • Key components
      • Subsystems
      • CLI-to-core mapping
    • Complete Request Lifecycle
      • Seven stages
      • Stage 1: CLI entry
      • Stage 2: command layer
      • Stage 3: loading and validation
      • Stage 4: core API
      • Stage 5: assembly
      • Stage 6: execution
      • Stage 7: artifacts
    • Code Map
      • Repository root
      • habit/ package structure
      • Top-level package responsibilities
      • Shared utilities: habit/utils/
      • Cross-subsystem contract files
      • Where to start when changing X
    • Configuration System
      • Overview
      • Loading and path resolution
      • Schema layers
      • Parameter registry and validation
      • Domain configurators
      • Summary
    • Subsystems
      • Habitat analysis
        • Clustering strategies
        • Training and prediction
      • Machine learning
        • Execution flow
    • Extension and Plugin Guide
      • Core extension contracts
      • Example 1: Custom preprocessing step (ClassRegistry)
      • Example 2: Custom feature selector (CallableRegistry)
      • Example 3: Custom machine-learning model (ModelFactory)
      • Extension point reference
    • Invariants and Architecture Contracts
      • Scientific correctness
      • Configuration rules
      • Registry contracts
      • Orchestrator contracts
      • Engineering conventions
      • See also
    • Contributor Workflow
      • Environment setup
      • Code conventions
      • Testing
        • Architecture contract tests
        • Demo data flow
      • Scenario 1: Add a CLI command
      • Scenario 2: Add a configuration-step schema
      • Scenario 3: Web GUI and bridge
    • Contributing
      • How to contribute
        • Report bugs
        • Submit code
      • Code style
      • Documentation
      • Development setup
      • Pull requests
      • Code of conduct
    • Recommended reading order
  • Customization and Extension Guide
    • Overview
    • Extension principles
    • Custom preprocessors
    • Custom feature extractors
    • Custom clustering algorithms
    • Custom models
    • Custom feature selectors
    • Best practices
    • FAQ
    • Next steps
  • API Reference
    • Python API
      • Migration from deep imports
      • Recommended object API
      • Preprocessing
      • In-memory configuration
      • DICOM sort
      • Habitat segmentation
      • Feature extraction
      • Traditional radiomics
      • Machine learning
      • sklearn-compatible estimators
      • Model comparison
      • ICC analysis
      • Test-retest analysis
      • Image I/O and geometry
      • Low-level radiomics extraction
      • Plugins, provenance, and errors
      • Top-level package exports
    • Image and geometry API
      • Module reference
    • Low-level radiomics API
      • Module reference
    • habitat_analysis module
      • Core analysis
      • Configuration
      • Pipeline and steps
      • Domain services
      • Analyzers and extractors
    • machine_learning module
      • Developer entry point
      • Core contracts
      • Workflows
      • Runners
      • Reporting components
      • Model factory
      • Evaluation
      • Visualization
    • preprocessing module
      • Core pipeline
      • Correction
      • Normalization
      • Spatial transform
      • Format conversion
      • Base and factory
        • BasePreprocessor
    • habit.core.dicom_sort
      • API exports
      • Implementation modules
    • Plugin discovery API
      • Module reference
    • API contracts, provenance, and errors
      • Workflow results
      • Provenance
      • Exceptions
      • Module reference
    • common module
      • Configuration system
      • Data utilities
    • utils module
      • I/O
      • DICOM
      • Parallel processing
      • Logging and progress
        • LoggerManager
        • setup_logger()
        • get_module_logger()
        • disable_external_loggers()
        • resolve_radiomics_logging_level()
        • radiomics_feature_class_logging()
        • restore_logging_in_subprocess()
        • shutdown_subprocess_logging()
        • stop_queue_listener()
        • setup_output_logger()
      • Visualization
      • Math and metrics
    • CLI Commands API
      • Command Line Interface
      • Main Commands
    • Command-oriented API notes
      • Prepare data
        • Project root
        • Folder layout
        • Data specification
      • Preprocessing
      • Habitat segmentation
      • Feature extraction
      • Machine learning
      • Model comparison
  • Upstream Dependencies and Documentation Links
    • Image preprocessing (habit preprocess)
    • Habitat segmentation (habit get-habitat)
    • Habitat features and traditional radiomics (habit extract / habit radiomics)
    • Machine learning (habit model / habit cv)
    • Model comparison (habit compare)
    • ICC / Test–retest / other
    • ROI delineation (external tools)
  • Changelog
    • Version 2.0 (2026-01-25)
      • Metrics Module Major Optimization
      • Bug Fixes
      • Configuration Improvements
      • Workflow Enhancements
    • Version 1.x
    • Future Roadmap
    • See Also
  • Acknowledgments
    • Core developers
    • Future developers
    • Clinical collaborators
    • Special thanks
    • Open source community
    • How to contribute
    • Contact
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