SlicerAdaptiveBrush

User Guide

  • Getting Started
    • Prerequisites
    • Tutorial
      • Step 1: Open Sample Data
      • Step 2: Volume Loaded
      • Step 3: Open Segment Editor
      • Step 4: Create Segment
      • Step 5: Select Adaptive Brush
      • Step 6: Configure Settings
      • Step 7: Navigate to Region
      • Step 8: Paint
      • Step 9: Refine Segmentation
      • Step 10: View in 3D
    • Tips for Best Results
      • Keyboard Shortcuts
      • Brush Size
      • Edge Sensitivity
      • Algorithm Selection
      • Presets
    • Next Steps
  • Algorithms
    • Algorithm Comparison
    • Watershed
      • Parameters
      • When to Use
      • Example
    • Connected Threshold
      • Parameters
      • When to Use
      • Limitations
    • Region Growing
      • Parameters
      • When to Use
    • Threshold Brush
      • Parameters
      • When to Use
    • Geodesic Distance
      • Parameters
      • When to Use
    • Level Set
      • Parameters
      • When to Use
      • Limitations
    • Random Walker
      • Parameters
      • When to Use
      • Requirements
    • Algorithm Selection Guide
      • By Structure Type
      • By Priority
      • From Optimization Results
  • Parameter Wizard
    • Starting the Wizard
    • Step 1: Sample Foreground
    • Step 2: Sample Background
    • Step 3: Trace Boundary
    • Step 4: Optional Questions
      • Structure Type
      • Image Modality
      • Priority
    • Step 5: Review Recommendations
      • Algorithm Recommendation
      • Parameter Recommendations
      • Alternative Algorithms
      • Warnings
    • Applying Recommendations
    • Tips for Best Results
      • When Wizard Works Best
      • When to Adjust Manually
      • Re-running the Wizard
    • Behind the Scenes
  • Segmentation Recipes
    • What is a Recipe?
    • Using Recipes
      • Loading a Recipe
      • Replaying a Recipe
      • Comparing to Gold Standard
    • Creating Recipes
      • From the Recorder
      • From Python
      • From Optimization Results
    • Recipe File Format
    • Gold Standards
      • What is a Gold Standard?
      • Gold Standard Structure
      • Creating a Gold Standard
    • Testing Recipes
      • Running Regression Tests
      • In Python
    • Best Practices
      • Recipe Design
      • Gold Standard Quality
      • Version Control

Developer Guide

  • Optimization Tutorial
    • Overview
    • Prerequisites
    • Quick Start
    • Configuration Files
      • Basic Structure
      • Available Configs
    • Running Optimization
      • Command Line Options
      • Examples
    • Understanding Output
      • Directory Structure
      • Lab Notebook
      • Parameter Importance
    • Pruning Behavior
    • Reviewing Results
      • In Slicer
      • Comparing Trials
      • Saving Best Trial as Gold Standard
    • Advanced Usage
      • Custom Objective Functions
      • Multi-Recipe Optimization
      • Algorithm-Specific Spaces
    • Troubleshooting
      • Common Issues
      • Performance Tips
  • Testing and Optimization Workflow
    • Workflow Overview
    • Phase 1: Create Initial Recipe
      • 1.1 Load Sample Data
      • 1.2 Manual Segmentation
      • 1.3 Record Click Locations
      • 1.4 Create Recipe File
    • Phase 2: Create Initial Gold Standard
      • 2.1 Refine Segmentation
      • 2.2 Save Gold Standard
    • Phase 3: Run Optimization
      • 3.1 Create Configuration
      • 3.2 Run Optimization
      • 3.3 Monitor Progress
    • Phase 4: Review Results
      • 4.1 Read Lab Notebook
      • 4.2 Visual Review in Slicer
      • 4.3 Compare Screenshots
    • Phase 5: Update Gold Standard
      • 5.1 Via Reviewer UI
      • 5.2 Via Python
    • Phase 6: Regression Testing
      • 6.1 Update Recipe
      • 6.2 Run Regression Test
    • Continuous Integration
      • GitHub Actions Workflow
    • Best Practices
      • Recipe Design
      • Gold Standard Quality
      • Optimization Strategy
      • Regression Testing
  • Creating Recipes
    • Recipe Formats
    • Python Function Recipes
      • Basic Structure
      • With Parameter Variations
      • With Conditional Logic
    • JSON Action Recipes
      • Basic Structure
      • Action Types
      • Adaptive Brush Parameters
    • Recording Recipes
      • Using the Recorder
      • What Gets Recorded
      • Cleaning Up Recorded Recipes
    • Converting Between Formats
      • Python to JSON
      • JSON to Python
    • Testing Recipes
      • Quick Test
      • With Gold Standard Comparison
    • Best Practices
      • Click Location Selection
      • Parameter Selection
      • Recipe Organization
      • Version Control
      • Documentation
  • Algorithm Profiles
    • Overview
    • Profile Data Structure
      • Parameter Importance
      • Algorithm Characteristics
      • Modality Recommendations
    • Using Profiles Programmatically
      • Loading Profiles
      • Getting Recommendations
      • Applying Recommendations
    • Generating New Profiles
      • Running Optimization
      • Adding Benchmarks
    • Profile Evolution
      • Adding New Modalities
      • Refining Recommendations
    • Integration with Presets
      • Preset to Algorithm Mapping
    • Future Work
  • API Reference
    • Core Classes
      • Recipe
        • Recipe
        • save()
        • load()
        • optimize()
        • resume()
        • load()
        • list_standards()
        • set_group()
        • save_manifest()
        • hausdorff_95()
      • Running Optimization

API Reference

  • API Reference
    • ActionRecipe
      • Classes
        • RecipeAction
        • ActionRecipe
        • RecordingEffectProxy
      • Functions
        • to_dict()
        • from_dict()
        • paint()
        • erase()
        • set_param()
        • set_algorithm()
        • to_dict()
        • save()
        • load()
        • from_function_recipe()
        • paintAt()
        • eraseAt()
        • slice_to()
        • append_actions()
        • list_action_recipes()
    • ActionRecorder
      • Classes
        • ActionRecorder
      • Functions
        • is_recording()
        • action_count()
        • has_callback()
        • set_action_callback()
        • start()
        • stop()
        • record_paint()
        • record_parameter_change()
        • record_algorithm_change()
        • record_screenshot()
        • record_note()
        • record_pass()
        • record_fail()
    • AlgorithmCharacterizer
      • Classes
        • AlgorithmCharacterizer
      • Functions
        • characterize()
        • characterize_all()
        • create_comparison()
        • save_profiles()
        • load_profiles()
    • AlgorithmProfile
      • Classes
        • PerformanceMetrics
        • OptimalPreset
        • ExampleScreenshot
        • AlgorithmProfile
        • AlgorithmComparison
      • Functions
        • to_dict()
        • to_dict()
        • to_dict()
        • to_dict()
        • from_dict()
        • get_summary()
        • to_dict()
        • from_dict()
        • get_best_for_dice()
        • get_fastest()
        • get_most_efficient()
        • get_display_name()
    • AlgorithmReportGenerator
      • Classes
        • AlgorithmReportGenerator
      • Functions
        • generate_report()
        • save_report()
        • generate_algorithm_report()
    • ComparisonMetrics
      • Classes
        • SegmentationMetrics
        • ComparisonMetrics
      • Functions
        • jaccard()
        • to_dict()
        • compute()
        • compute_slice_metrics()
        • format_summary()
        • last_metrics()
        • compute_metrics_from_nodes()
        • export_seg_to_array()
    • ContourRenderer
      • Classes
        • ContourRenderer
      • Functions
        • get_morphological_outline()
        • find_contours()
        • draw_contours()
        • create_comparison_image()
        • create_error_image()
        • create_combined_image()
        • clear_cache()
    • DICOMLabelMapSegPlugin
      • Classes
        • DICOMLabelMapSegPlugin
      • Functions
        • examineForImport()
        • load()
        • f_inv()
        • gamma()
        • register_plugin()
        • is_labelmap_seg()
    • DependencyManager
      • Classes
        • DependencySpec
        • DependencyManager
      • Functions
        • is_available()
        • ensure_available()
        • clear_session()
        • get_dependency_manager()
    • DicomManager
      • Classes
        • DicomManager
      • Functions
        • database()
        • ensure_database_initialized()
        • generate_uid()
        • create_synthetic_dicom()
        • export_segmentation_as_dicom_seg()
        • load_segmentation_by_uid()
        • get_segmentations_for_volume()
        • get_series_description()
    • EmbeddedWizardUI
      • Classes
        • EmbeddedWizardPanel
      • Functions
        • build_ui()
        • update_sample_count()
        • get_answers()
        • set_recommendation()
        • get_recommendation()
        • current_step()
        • hide()
        • show()
    • GoldStandardManager
      • Classes
        • GoldStandardManager
      • Functions
        • save_as_gold()
        • load_gold()
        • get_dicom_seg_path()
        • list_gold_standards()
        • gold_exists()
        • get_gold_path()
        • update_metadata()
        • update_statistics()
        • delete_gold()
        • save_reference_screenshot()
        • compare_statistics()
        • format_statistics()
        • format_comparison()
    • IntensityAnalyzer
      • Classes
        • IntensityAnalyzer
      • Functions
        • analyze()
    • MetricsCollector
      • Classes
        • TimingResult
        • TimingContext
        • MetricValue
        • MetricsCollector
      • Functions
        • duration_ms()
        • duration_seconds()
        • duration_ms()
        • timing()
        • record_metric()
        • get_metrics()
        • get_timing()
        • get_metric()
        • clear()
    • ModelGrouping
      • Classes
        • ComparisonModel
        • TrialModelMapper
      • Functions
        • best_trial()
        • best_score()
        • trial_count()
        • group_by_algorithm()
        • get_top_n_per_algorithm()
        • group_by_dice_range()
        • group_by_trial_numbers()
        • create_gold_standard_model()
        • get_best_overall()
        • filter_by_algorithm()
        • filter_by_min_dice()
        • quick_compare_algorithms()
        • quick_compare_top_trials()
    • OptimizationConfig
      • Classes
        • ParameterSpec
        • RecipeSpec
        • OptimizationConfig
      • Functions
        • from_dict()
        • load()
        • validate()
        • to_dict()
        • save()
        • create_default_config()
    • OptunaOptimizer
      • Classes
        • OptunaTrialResult
        • OptimizationResults
        • OptunaOptimizer
      • Functions
        • to_dict()
        • to_dict()
        • set_dicom_info()
        • create_study()
        • suggest_params()
        • optimize()
        • wrapped_objective()
        • get_param_importance()
        • report_intermediate()
        • get_best_params()
        • get_best_value()
        • resume()
        • run_optimization_with_recipe()
        • objective()
    • ParameterRecommender
      • Classes
        • ParameterRecommender
      • Functions
        • recommend()
    • ParameterWizard
      • Classes
        • ParameterWizard
      • Functions
        • start()
        • handle_interaction_event()
        • on_foreground_sampled()
        • on_background_sampled()
        • on_boundary_traced()
        • generate_recommendation()
        • apply_recommendation()
        • clear_samples()
    • PerformanceCache
      • Classes
        • PerformanceCache
        • CacheStats
      • Functions
        • computeOrGetCached()
        • getOrComputeGradient()
        • isValidFor()
        • onMouseRelease()
        • invalidate()
        • clear()
        • reset()
        • log_summary()
    • RatingManager
      • Classes
        • ReviewRecord
        • RatingManager
      • Functions
        • label()
        • from_string()
        • to_dict()
        • from_dict()
        • set_reviewer()
        • start_session()
        • rate_trial()
        • get_rating()
        • get_all_ratings()
        • export_csv()
        • export_json()
        • get_summary()
        • clear_session()
    • Recipe
      • Classes
        • Recipe
      • Functions
        • load()
        • execute()
        • list_recipes()
    • RecipeRecorder
      • Classes
        • RecordedStroke
        • RecordedParamChange
        • RecipeRecorder
      • Functions
        • start()
        • stop()
        • record_stroke()
        • record_param_change()
        • save()
        • is_recording()
        • get_global_recorder()
        • start_recording()
        • stop_recording()
        • is_recording()
    • RecipeRunner
      • Classes
        • RecipeResult
        • RecipeRunner
      • Functions
        • run()
        • run_recipe()
    • RecipeTestRunner
      • Classes
        • RecipeTestResult
        • RecipeTestSuiteResult
        • RecipeTestRunner
      • Functions
        • passed()
        • passed_count()
        • total_count()
        • discover_recipes()
        • run_recipe_test()
        • run_all()
        • run_recipe_tests()
    • ReportGenerator
      • Classes
        • ReportGenerator
      • Functions
        • generate_markdown()
        • save_markdown()
        • generate_summary()
        • save_summary()
    • ResultsLoader
      • Classes
        • DicomInfo
        • TrialData
        • OptimizationRun
        • ResultsLoader
      • Functions
        • from_dict()
        • get_trial()
        • get_algorithm_trials()
        • list_runs()
        • load()
        • get_gold_standard_path()
    • ScreenshotCapture
      • Classes
        • ScreenshotInfo
        • ScreenshotGroup
        • ScreenshotCapture
      • Functions
        • to_dict()
        • next_number()
        • set_base_folder()
        • set_group()
        • new_group()
        • current_group()
        • screenshot()
        • capture_layout()
        • capture_slice_view()
        • capture_layout_with_3d()
        • capture_3d_view()
        • capture_widget()
        • save_manifest()
        • update_description()
        • get_all_screenshots()
        • get_group_screenshots()
        • get_screenshots_by_tags()
        • get_doc_screenshots()
    • ScreenshotViewer
      • Classes
        • ScreenshotInfo
        • ScreenshotViewer
      • Functions
        • set_screenshots()
        • load_from_directory()
        • select()
        • get_selected()
        • select_next()
        • select_previous()
        • view_full_size()
        • copy_path_to_clipboard()
        • get_count()
        • clear()
    • SegmentEditorEffect
      • Classes
        • BrushOutlinePipeline
      • Functions
        • setSliceWidget()
        • updateOutline()
        • setCrosshairSettings()
        • updatePreview()
        • hidePreview()
        • hide()
        • cleanup()
        • register()
        • clone()
        • icon()
        • helpText()
        • setupOptionsFrame()
        • onCrosshairColorPicker()
        • onCrosshairSettingsChanged()
        • onPresetChanged()
        • onResetPreset()
        • applyPreset()
        • paintAt()
        • brushRadiusMm()
        • brushRadiusMm()
        • edgeSensitivityValue()
        • edgeSensitivityValue()
        • onRadiusChanged()
        • onSensitivityChanged()
        • onZoneChanged()
        • onSamplingMethodChanged()
        • onAdvancedParamChanged()
        • onSphereModeChanged()
        • onPreviewModeChanged()
        • onModeChanged()
        • onWizardClicked()
        • setAlgorithm()
        • setRadiusMm()
        • setEdgeSensitivity()
        • setThresholdRange()
        • onAlgorithmChanged()
        • onThresholdChanged()
        • onAutoThresholdChanged()
        • onThresholdMethodChanged()
        • onSetFromSeedClicked()
        • onCachingChanged()
        • onBackendChanged()
        • activate()
        • deactivate()
        • setMRMLDefaults()
        • updateGUIFromMRML()
        • updateMRMLFromGUI()
        • interactionNodeModified()
        • layoutChanged()
        • processViewNodeEvents()
        • cleanup()
        • sourceVolumeNodeChanged()
        • masterVolumeNodeChanged()
        • referenceGeometryChanged()
        • processInteractionEvents()
        • processPoint()
        • computeAdaptiveMask()
        • applyMaskToSegment()
    • SegmentationMetrics
      • Classes
        • MetricsResult
        • SegmentationMetrics
        • StrokeRecord
        • StrokeMetricsTracker
      • Functions
        • to_dict()
        • compute()
        • compute_dice_only()
        • to_dict()
        • record_stroke()
        • get_summary()
        • reset()
    • SequenceRecorder
      • Classes
        • SequenceRecorder
        • ViewGroupManager
        • SceneViewBookmarks
      • Functions
        • step_count()
        • is_recording()
        • start_recording()
        • record_step()
        • add_note()
        • goto_step()
        • get_note_at_step()
        • stop_recording()
        • cleanup()
        • get_browser_node()
        • get_sequence()
        • is_linked()
        • enable_linking()
        • disable_linking()
        • set_linked()
        • setup_slice_observer()
        • get_slice_offset()
        • get_slice_range()
        • set_slice_offset()
        • cleanup()
        • count()
        • add_bookmark()
        • restore_bookmark()
        • list_bookmarks()
        • get_bookmark_name()
        • remove_bookmark()
        • clear_all()
        • cleanup()
    • SteppingRecipeRunner
      • Classes
        • SegmentationCheckpoint
        • SteppingRecipeRunner
      • Functions
        • size_bytes()
        • total_steps()
        • is_at_start()
        • is_at_end()
        • is_branching()
        • set_step_callback()
        • set_checkpoint_callback()
        • setup()
        • step_forward()
        • step_backward()
        • goto_step()
        • run_to_end()
        • get_current_action()
        • get_next_action()
        • start_branch()
        • stop_branch()
        • add_manual_action()
        • save_branch()
        • get_checkpoint_stats()
        • cleanup()
    • TestCase
      • Classes
        • Assertion
        • TestResult
        • TestCaseInfo
      • Functions
        • failed_assertions()
        • setup()
        • run()
        • verify()
        • teardown()
    • TestContext
      • Classes
        • TestContext
      • Functions
        • output_folder()
        • assertions()
        • screenshots()
        • metrics()
        • set_screenshot_context()
        • screenshot()
        • screenshot_slice_view()
        • screenshot_3d_view()
        • timing()
        • record_metric()
        • metric()
        • log()
        • assert_true()
        • assert_false()
        • assert_equal()
        • assert_not_equal()
        • assert_greater()
        • assert_greater_equal()
        • assert_less()
        • assert_less_equal()
        • assert_is_not_none()
        • assert_is_none()
        • assert_almost_equal()
    • TestRegistry
      • Classes
        • TestRegistry
      • Functions
        • register()
        • unregister()
        • get()
        • list_tests()
        • list_categories()
        • clear()
        • register_test()
        • decorator()
    • TestRunFolder
      • Classes
        • TestRunFolder
      • Functions
        • create()
        • path()
        • screenshots_folder()
        • logs_folder()
        • save_metadata()
        • save_results()
        • save_screenshot_manifest()
        • copy_slicer_log()
        • append_manual_action()
    • TestRunner
      • Classes
        • TestSuiteResult
        • TestRunner
      • Functions
        • passed()
        • passed_count()
        • failed_count()
        • total_count()
        • list_tests()
        • list_categories()
        • run_test()
        • run_suite()
        • discover_tests()
    • VisualizationController
      • Classes
        • VisualizationController
      • Functions
        • load_gold_segmentation()
        • load_gold_from_dicom_cache()
        • load_test_segmentation_from_dicom()
        • set_view_mode()
        • toggle_gold()
        • toggle_test()
        • cleanup()
        • get_gold_node()
        • get_test_node()
    • WizardAnalyzer
      • Classes
        • WizardAnalyzer
      • Functions
        • analyze_intensities()
        • analyze_shape()
        • estimate_boundary_roughness()
    • WizardDataStructures
      • Classes
        • WizardSamples
        • IntensityAnalysisResult
        • ShapeAnalysisResult
        • WizardRecommendation
      • Functions
        • has_foreground()
        • has_background()
        • has_boundary()
        • foreground_count()
        • background_count()
        • clear_foreground()
        • clear_background()
        • clear_boundary()
        • clear_all()
        • threshold_range()
        • is_well_separated()
        • is_small_structure()
        • is_large_structure()
        • has_smooth_boundary()
        • is_high_confidence()
        • has_warnings()
        • has_threshold_suggestion()
    • WizardSampler
      • Classes
        • WizardSampler
      • Functions
        • is_active()
        • activate()
        • deactivate()
        • process_event()
        • get_samples()
        • clear()
        • sample_count()
    • WizardUI
      • Classes
      • Functions
        • update_sample_count()
        • isComplete()
        • update_sample_count()
        • isComplete()
        • update_sample_count()
        • isComplete()
        • get_answers()
        • isComplete()
        • set_recommendation()
        • get_recommendation()
        • get_questions_answers()
        • set_recommendation()
        • was_applied()

Algorithm Reference

  • Algorithms
    • Algorithm Comparison
      • When to Use Each Algorithm
        • For Speed
        • For Precision
        • For Noisy Images
        • For General Use
    • Connected Threshold
      • Overview
      • Parameters
      • Strengths
      • Limitations
      • Screenshots
    • Geodesic Distance
      • Overview
      • Parameters
      • Strengths
      • Limitations
      • Screenshots
    • Level Set
      • Overview
      • Parameters
      • Strengths
      • Limitations
      • Screenshots
    • Random Walker
      • Overview
      • Parameters
      • Strengths
      • Limitations
      • Screenshots
    • Region Growing
      • Overview
      • Parameters
      • Strengths
      • Limitations
      • Screenshots
    • Threshold Brush
      • Overview
      • Parameters
      • Strengths
      • Limitations
      • Screenshots
    • Watershed
      • Overview
      • Parameters
      • Strengths
      • Limitations
      • Screenshots
SlicerAdaptiveBrush
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