testing_mermaid

testing_mermaid.md

%%{ init: {
      'theme':'base',
      'themeVariables': {
        'background': '#a7d2eb',          /* light backdrop */
        'lineColor' : '#09205A',          /* navy outlines / arrows */
        'primaryColor'  : '#005CA9',      /* dark blue */
        'secondaryColor': '#238FD6',      /* light blue */
        'tertiaryColor' : '#F57C00'       /* orange accent */
      }
  } }%%

flowchart TD
    %% ---------- main workflow ----------
    A["Source Data<br/>(SpikeGLX, Intan, TIFF, DeepLabCut, etc)"] 
        --> B["Interface(**source_data)"]
    B --> C["interface.get_metadata()"]
    C --> D["User edits<br/>metadata"]
    D --> E["interface.run_conversion(nwbfile_path,<br/>metadata,<br/>**conversion_options)"]
    E --> F["NWB file"]

    %% ---------- side comments ----------
    A -.-> A_NOTE["Raw acquisition files<br/>on disk"]:::comment
    B -.-> B_NOTE["Instantiate the specific<br/>*DataInterface*.<br/>Only headers parsed;<br/>files remain on disk."]:::comment
    C -.-> C_NOTE["Auto-extract everything<br/>detectable in the source<br/>format (device info,<br/>sampling rate, channel map…)."]:::comment
    D -.-> D_NOTE["User supplies missing<br/>or corrected metadata<br/>(e.g., *session_start_time*)."]:::comment
    E -.-> E_NOTE["Streams data → builds<br/>and writes an *NWBFile*<br/>using PyNWB."]:::comment
    F -.-> F_NOTE["Standardised file ready<br/>for analysis / archive."]:::comment

    %% ---------- styling ----------
    style A fill:#005CA9,color:#ffffff,stroke:#09205A,stroke-width:2,rx:8,ry:8
    style B fill:#238FD6,color:#ffffff,stroke:#09205A,stroke-width:2,rx:8,ry:8
    style C fill:#238FD6,color:#ffffff,stroke:#09205A,stroke-width:2,rx:8,ry:8
    style D fill:#F57C00,color:#ffffff,stroke:#09205A,stroke-width:2,rx:8,ry:8
    style E fill:#F57C00,color:#ffffff,stroke:#09205A,stroke-width:2,rx:8,ry:8
    style F fill:#09205A,color:#ffffff,stroke:#09205A,stroke-width:2,rx:8,ry:8

    classDef comment fill:#ffffff,stroke:#BBBBBB,stroke-dasharray: 5 5,rx:6,ry:6,color:#333;

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