graph LR
AnnData_Core_Model["AnnData Core Model"]
Data_Structures_Views["Data Structures & Views"]
I_O_Management["I/O Management"]
Data_Manipulation_Transformation["Data Manipulation & Transformation"]
File_Backing_Lazy_Loading["File Backing & Lazy Loading"]
Indexing_Slicing["Indexing & Slicing"]
Settings_Utilities["Settings & Utilities"]
Experimental_Features["Experimental Features"]
AnnData_Core_Model -- "Manages" --> Data_Structures_Views
AnnData_Core_Model -- "Orchestrates" --> I_O_Management
AnnData_Core_Model -- "uses" --> Data_Structures_Views
Data_Structures_Views -- "relies on" --> Indexing_Slicing
I_O_Management -- "serves" --> AnnData_Core_Model
I_O_Management -- "leverages" --> File_Backing_Lazy_Loading
Data_Manipulation_Transformation -- "operates on" --> AnnData_Core_Model
Data_Manipulation_Transformation -- "utilizes" --> Indexing_Slicing
File_Backing_Lazy_Loading -- "supports" --> AnnData_Core_Model
File_Backing_Lazy_Loading -- "integrates with" --> I_O_Management
Indexing_Slicing -- "provides services to" --> AnnData_Core_Model
Indexing_Slicing -- "supports" --> Data_Structures_Views
Settings_Utilities -- "configures" --> AnnData_Core_Model
Settings_Utilities -- "provides helpers to" --> I_O_Management
Experimental_Features -- "extends" --> AnnData_Core_Model
Experimental_Features -- "leverages" --> I_O_Management
click AnnData_Core_Model href "https://github.com/CodeBoarding/GeneratedOnBoardings/blob/main/anndata/AnnData_Core_Model.md" "Details"
click Data_Structures_Views href "https://github.com/CodeBoarding/GeneratedOnBoardings/blob/main/anndata/Data_Structures_Views.md" "Details"
click I_O_Management href "https://github.com/CodeBoarding/GeneratedOnBoardings/blob/main/anndata/I_O_Management.md" "Details"
click Data_Manipulation_Transformation href "https://github.com/CodeBoarding/GeneratedOnBoardings/blob/main/anndata/Data_Manipulation_Transformation.md" "Details"
click File_Backing_Lazy_Loading href "https://github.com/CodeBoarding/GeneratedOnBoardings/blob/main/anndata/File_Backing_Lazy_Loading.md" "Details"
click Settings_Utilities href "https://github.com/CodeBoarding/GeneratedOnBoardings/blob/main/anndata/Settings_Utilities.md" "Details"
The anndata library is architected as a Scientific Data Management Library, prioritizing a robust, centralized data model with efficient I/O and data manipulation capabilities. The architecture is modular, allowing for extensibility and performance optimization, particularly for large and sparse datasets.
AnnData Core Model [Expand]
The central AnnData object, serving as the primary interface for users to manage and interact with multi-dimensional annotated data. It acts as a facade, simplifying access to complex underlying data structures and orchestrating operations across various components.
Related Classes/Methods:
Data Structures & Views [Expand]
Provides the foundational data structures (e.g., AlignedMappingProperty, Layers, AxisArrays) and efficient storage mechanisms for sparse and dense data within the AnnData object. It also offers read-only views to ensure data integrity and optimize memory usage.
Related Classes/Methods:
I/O Management [Expand]
A comprehensive layer responsible for registering, dispatching, and executing read/write operations for various data formats (H5AD, Zarr, CSV, Loom). It handles data serialization/deserialization and supports lazy loading, acting as the primary interface for data persistence.
Related Classes/Methods:
Data Manipulation & Transformation [Expand]
Provides core functionalities for in-memory data transformations, including combining, merging, and concatenating multiple AnnData objects or their internal components. It ensures proper index alignment and data type unification during these operations.
Related Classes/Methods:
File Backing & Lazy Loading [Expand]
Manages the on-disk representation of AnnData objects, enabling out-of-core computation and lazy loading of data. This component is crucial for efficiently handling datasets that exceed available memory, by providing mechanisms to access data directly from disk.
Related Classes/Methods:
Offers fundamental utilities for normalizing and applying various types of indices (e.g., integer, boolean, label-based) for efficient data access, subsetting, and alignment within AnnData objects and their internal components.
Related Classes/Methods:
Settings & Utilities [Expand]
A collection of general-purpose helper functions, including array conversions, memory usage reporting, deprecation warnings, and I/O-specific helpers. It also manages global configuration settings and provides a compatibility layer for external numerical libraries.
Related Classes/Methods:
utils(1:1)utils(1:1)_settings(1:1)compat(1:1)
A dedicated module for new and experimental functionalities, such as advanced merging strategies, multi-file handling, and integrations with deep learning frameworks. This allows for agile development and testing without impacting the stability of the core library.
Related Classes/Methods: