graph LR
ConfigurationManager["ConfigurationManager"]
GUIManager["GUIManager"]
DataLoader["DataLoader"]
SignalProcessor["SignalProcessor"]
NetworkConstructor["NetworkConstructor"]
NetworkAnalyzer["NetworkAnalyzer"]
StatisticalAnalyzer["StatisticalAnalyzer"]
ResultVisualizer["ResultVisualizer"]
GUIManager -- "reads from" --> ConfigurationManager
GUIManager -- "updates" --> ConfigurationManager
ConfigurationManager -- "provides parameters to" --> DataLoader
ConfigurationManager -- "provides parameters to" --> SignalProcessor
ConfigurationManager -- "provides parameters to" --> NetworkConstructor
ConfigurationManager -- "provides parameters to" --> NetworkAnalyzer
ConfigurationManager -- "provides parameters to" --> StatisticalAnalyzer
ConfigurationManager -- "provides parameters to" --> ResultVisualizer
The analysis provides an abstract overview of the MEA-NAP pipeline components and their relationships. Due to limitations in tool calls and the inability to identify correct package structures, concrete links to specific classes or methods in the codebase could not be established. The 'Related Classes/Methods' sections serve as placeholders, acknowledging the absence of verifiable source file references.
The core of the configuration management subsystem. It is responsible for centralizing, managing, and persisting all configurable parameters for the entire MEA-NAP pipeline. This includes file paths, processing thresholds, analysis algorithms, and visualization settings. It ensures consistent behavior across different pipeline stages and provides a centralized mechanism for parameter control, persistence, and retrieval.
Related Classes/Methods:
ConfigurationManager(1:100)ConfigurationManager(1:100)ConfigurationManager(1:100)
Manages the graphical user interface, providing the user with controls to view and modify application parameters. It acts as the primary interface for users to interact with and update the settings stored within the ConfigurationManager.
Related Classes/Methods:
GUIManager(1:100)GUIManager(1:100)GUIManager(1:100)
The initial stage of the data analysis pipeline, responsible for ingesting raw experimental data from various sources (e.g., Axion Biosystems, MCS). It retrieves necessary operational parameters, such as file paths, data formats, or specific loading configurations, directly from the ConfigurationManager.
Related Classes/Methods:
DataLoader(1:100)DataLoader(1:100)DataLoader(1:100)
Processes the raw loaded data, performing operations suchs as spike detection, filtering, or noise reduction. It relies on specific processing thresholds, algorithms, and other parameters provided by the ConfigurationManager to ensure consistent and reproducible signal conditioning.
Related Classes/Methods:
SignalProcessor(1:100)SignalProcessor(1:100)SignalProcessor(1:100)
Builds network representations (e.g., connectivity matrices, graphs) from the processed signal data, potentially utilizing modules like the Spike Time Tiling Coefficient (STTC) or the Brain Connectivity Toolbox (BCT). The specific methods and parameters for network construction are obtained from the ConfigurationManager.
Related Classes/Methods:
NetworkConstructor(1:100)NetworkConstructor(1:100)NetworkConstructor(1:100)
Applies various graph theory and network science algorithms to the constructed networks to extract meaningful metrics and insights. The specific analysis algorithms, parameters (e.g., for centrality measures, community detection), and output formats are configured through the ConfigurationManager.
Related Classes/Methods:
NetworkAnalyzer(1:100)NetworkAnalyzer(1:100)NetworkAnalyzer(1:100)
Performs statistical tests and comparisons on the results obtained from network analysis, allowing for quantitative assessment and hypothesis testing. Statistical parameters, significance thresholds, and chosen test methods are retrieved from the ConfigurationManager.
Related Classes/Methods:
StatisticalAnalyzer(1:100)StatisticalAnalyzer(1:100)StatisticalAnalyzer(1:100)
Generates visual representations (e.g., plots, graphs, heatmaps, reports) of the analysis outcomes for interpretation and presentation. Visualization settings, such as plot types, color schemes, axis labels, and output file formats, are dynamically configured by the ConfigurationManager.
Related Classes/Methods:
ResultVisualizer(1:100)ResultVisualizer(1:100)ResultVisualizer(1:100)