ionique

Getting Started

  • Install
    • Install ionique
    • Installation from Source

User Guide

  • Getting Started
    • Minimal workflow
    • The segment tree
    • What’s next
  • Data Input
    • Supported formats
    • Loading an EDH file
      • Reader parameters
    • Loading an OPT file
    • Creating a TraceFile
    • Voltage protocol
    • SessionFileManager
  • Core Concepts
    • Segments and ranks
    • Segment vs MetaSegment
    • Tree traversal
    • Feature lookup
    • Parsing: creating children
    • Building trees manually
    • Segment statistics
    • Serialization
  • Signal Preprocessing
    • Filtering with Filter
      • Choosing a cutoff frequency
    • Clock-tone removal with ClockFilter
    • Trimming with Trimmer
    • Chaining preprocessors
  • Parsers Guide
    • How parsing works
    • Choosing a parser
    • Chaining parsers
    • Parser output format
    • Saving and loading parsers
      • SpikeParser
        • Parameters
        • Parameter sensitivity
        • Full example
        • Tips
      • SpeedyStatSplit
        • Parameters
        • Parameter sensitivity
        • Full example
        • Additional methods
      • AutoSquareParser
        • Parameters
        • Parameter sensitivity
        • Using rules for post-filtering
        • Full example
        • Per-event features
      • Other Parsers
        • FilterDerivativeSegmenter
        • NoiseFilterParser
        • snakebase_parser
        • ExclusionParser
        • lambda_event_parser
        • IVCurveParser and IVCurveAnalyzer
        • MemoryParse
  • Signal Analysis
    • Segment statistics
    • Extracting features with extract_features
      • Adding constant columns
      • Custom computed columns
      • Combining features from multiple files
    • Scatter plots
    • IV curve analysis
  • Visualization
    • qp_trace — quick plot
      • Parameters
      • Specifying ranks and downsampling
      • Voltage display
      • Styling with ranks_kwargs
      • Downsampling for performance
    • Interactive dashboards
  • Tutorial: End-to-End Nanopore Analysis
    • Step 1: Load the data
    • Step 2: Filter noise
    • Step 3: Trim voltage-step edges
    • Step 4: Detect events
    • Step 5: Extract features
    • Step 6: Visualize results
    • Summary

API Reference

  • API Reference
    • ionique.io
      • AbstractFileReader
        • AbstractFileReader.__init__()
        • AbstractFileReader.accepted_keywords
        • AbstractFileReader.current_multiplier
        • AbstractFileReader.ext
        • AbstractFileReader.read()
        • AbstractFileReader.voltage_multiplier
      • EDHReader
        • EDHReader.__init__()
        • EDHReader.accepted_keywords
        • EDHReader.current_multiplier
        • EDHReader.ext
        • EDHReader.voltage_multiplier
      • OPTReader
        • OPTReader.__init__()
        • OPTReader.accepted_keywords
        • OPTReader.current_multiplier
        • OPTReader.ext
        • OPTReader.find_peaks_in_segment()
        • OPTReader.find_peaks_slide_window()
        • OPTReader.process_custom_xml()
    • ionique.core
      • Overview
      • Key Concepts
      • Classes
        • AbstractSegmentTree
        • MetaSegment
        • Segment
      • Working with the Tree Structure
      • Parsing Segments
      • API Reference
        • AbstractSegmentTree
        • MetaSegment
        • Segment
    • ionique.parsers
      • AutoSquareParser
        • AutoSquareParser.__init__()
        • AutoSquareParser.parse()
        • AutoSquareParser.required_parent_attributes
      • ExclusionParser
        • ExclusionParser.__init__()
        • ExclusionParser.parse()
        • ExclusionParser.required_parent_attributes
      • FilterDerivativeSegmenter
        • FilterDerivativeSegmenter.__init__()
        • FilterDerivativeSegmenter.parse()
        • FilterDerivativeSegmenter.set_params()
      • IVCurveAnalyzer
        • IVCurveAnalyzer.__init__()
        • IVCurveAnalyzer.analyze()
      • IVCurveParser
        • IVCurveParser.__init__()
        • IVCurveParser.parse()
      • MemoryParse
        • MemoryParse.__init__()
        • MemoryParse.parse()
      • NoiseFilterParser
        • NoiseFilterParser.__init__()
        • NoiseFilterParser.parse()
      • Parser
        • Parser.__init__()
        • Parser.from_json()
        • Parser.get_init_params()
        • Parser.get_name()
        • Parser.get_process_inputs()
        • Parser.get_process_outputs()
        • Parser.get_required_parent_attributes()
        • Parser.parse()
        • Parser.required_parent_attributes
        • Parser.set_params()
        • Parser.to_dict()
        • Parser.to_json()
      • SpeedyStatSplit
        • SpeedyStatSplit.__init__()
        • SpeedyStatSplit.best_single_split()
        • SpeedyStatSplit.parse()
        • SpeedyStatSplit.parse_meta()
        • SpeedyStatSplit.set_params()
        • SpeedyStatSplit.uiTemplate
      • SpikeParser
        • SpikeParser.__init__()
        • SpikeParser.parse()
        • SpikeParser.required_parent_attributes
      • lambda_event_parser
        • lambda_event_parser.__init__()
        • lambda_event_parser.parse()
        • lambda_event_parser.set_params()
      • pairwise()
      • snakebase_parser
        • snakebase_parser.__init__()
        • snakebase_parser.parse()
        • snakebase_parser.set_params()
    • ionique.utils
      • ClockFilter
        • ClockFilter.__init__()
        • ClockFilter.clock_frequency
        • ClockFilter.sampling_frequency
        • ClockFilter.section_length
      • Filter
        • Filter.sos
        • Filter.__init__()
        • Filter.bidirectional
        • Filter.cutoff_frequency
        • Filter.filter_method
        • Filter.filter_type
        • Filter.order
        • Filter.sampling_frequency
      • Singleton
        • Singleton.__init__()
      • Trimmer
        • Trimmer.__init__()
        • Trimmer.newrank
        • Trimmer.rank
        • Trimmer.samples_to_remove
      • extract_features()
      • si_eval()
      • split_voltage_steps()
    • ionique.datatypes
      • SessionFileManager
        • SessionFileManager.rank
        • SessionFileManager.affector_table
        • SessionFileManager.__init__()
        • SessionFileManager.add_child()
        • SessionFileManager.add_children()
        • SessionFileManager.rank
        • SessionFileManager.register_affector()
        • SessionFileManager.unique_features
      • TraceFile
        • TraceFile.__init__()
        • TraceFile.children
        • TraceFile.delete()
        • TraceFile.end
        • TraceFile.parent
        • TraceFile.plot()
        • TraceFile.rank
        • TraceFile.start
    • ionique.cparsers
      • Modules
      • FastStatSplit
        • FastStatSplit.min_gain
        • FastStatSplit.__init__()
        • FastStatSplit.best_single_split()
        • FastStatSplit.min_gain
        • FastStatSplit.parse()
        • FastStatSplit.parse_meta()
        • FastStatSplit.score_samples()
      • pairwise()
ionique
  • API Reference
  • View page source

API Reference

  • ionique.io
    • AbstractFileReader
    • EDHReader
    • OPTReader
  • ionique.core
    • Overview
    • Key Concepts
    • Classes
    • Working with the Tree Structure
    • Parsing Segments
    • API Reference
  • ionique.parsers
    • AutoSquareParser
    • ExclusionParser
    • FilterDerivativeSegmenter
    • IVCurveAnalyzer
    • IVCurveParser
    • MemoryParse
    • NoiseFilterParser
    • Parser
    • SpeedyStatSplit
    • SpikeParser
    • lambda_event_parser
    • pairwise()
    • snakebase_parser
  • ionique.utils
    • ClockFilter
    • Filter
    • Singleton
    • Trimmer
    • extract_features()
    • si_eval()
    • split_voltage_steps()
  • ionique.datatypes
    • SessionFileManager
    • TraceFile
  • ionique.cparsers
    • Modules
    • FastStatSplit
    • pairwise()
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© Copyright 2025, Ali Fallahi, Dinara Boyko, Wanunu Lab.

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