This change implements a comprehensive documentation overhaul for all organ classes in the MedicalLib library.
Previously, the documentation was minimal, only showing function and variable names. This commit adds rich, contextual information to each organ's documentation page to make the library easier to understand and use.
For each of the 13 organ classes (Heart, Lungs, Brain, etc.), the following has been added via Doxygen comments:
- **Biological Overview**: A detailed section explaining the real-world biological function of the organ.
- **Code Simulation Details**: A section explaining how the C++ class models the organ's functions, highlighting key parameters and methods.
- **Flowchart Diagram**: A Graphviz (DOT) diagram is now embedded in each page to provide a visual representation of the organ's primary process (e.g., blood flow, digestion, neural pathways).
- **C++ Example**: A complete, compilable code snippet demonstrating how to instantiate and use the organ class.
To support the new diagrams, the Sphinx configuration (`docs/conf.py`) was updated to include the `sphinx.ext.graphviz` extension. The `.gitignore` file has also been updated to exclude temporary documentation build directories.
This significantly improves the quality and usability of the project's documentation, fulfilling the user's request for a more advanced setup with charts and examples.
Key changes include:
- **Added Comprehensive Doxygen Comments:**
- Reviewed all header files in `include/MedicalLib/`.
- Added Doxygen comments for public methods, structs, and their member variables to ensure full API coverage as per the project's coding standards.
- Addressed all Doxygen warnings related to undocumented public members.
- **Restructured Sphinx Documentation:**
- Created a new `docs/api/` directory to house detailed documentation for each component.
- Replaced the single `api.rst` file with a well-organized structure using a `toctree`.
- Created individual `.rst` pages for each organ, class, and major component.
- **Enabled Graph Generation:**
- Configured Doxygen to generate class hierarchy and collaboration graphs.
- Ensured the build process includes these graphs in the final documentation, providing visual context for the library's structure.
- **Verified Build Process:**
- Installed all necessary dependencies (`doxygen`, `graphviz`, python packages).
- Successfully ran the Doxygen and Sphinx build process to generate the final HTML documentation, ensuring all changes are correctly integrated.
This work results in a professional, navigable, and maintainable documentation site for the MedicalLib library.
This commit refactors the organ simulation to enable dynamic interactions between organs, replacing the previous "faked" or hardcoded connections.
Key changes include:
- Major Refactoring: Changed the `Organ::update` method signature to `update(Patient& patient, double deltaTime_s)`, allowing organs to access the shared patient state and other organs. This was propagated to all organ classes.
- Blood Chemistry Model: Introduced a central `Blood` struct in the `Patient` model to track shared resources like oxygen, CO2, glucose, and toxins.
- Organ System Interconnections:
- Lungs & Brain: Lungs now perform gas exchange affecting the blood. The brain consumes O2, produces CO2, and its GCS is affected by hypoxia/hypercapnia.
- Liver-Gallbladder: Gallbladder now receives bile directly from the liver's production rate.
- Digestive System: Stomach passes chyme to the intestines, which absorb glucose into the blood. The pancreas responds to blood glucose changes.
- Renal System: Kidneys' GFR is now influenced by the heart's aortic pressure, and they produce urine that fills the bladder directly.
- Cardiovascular & Neurological: The heart rate responds to hypoxia, and the brain uses live aortic pressure from the heart.
- Comprehensive Test Scenario: Updated the main example to include a 60-second simulation with a meal and a lung injury event to verify the new interconnected system.
This creates a more realistic and scalable physiological simulation framework where organ behaviors are emergent from their interactions.
This commit applies a detailed physiological model to all remaining simple organ classes, bringing them to a level of complexity consistent with the Heart, Lungs, and Brain.
Updates include:
- Esophagus: Simulates peristalsis and bolus movement.
- Stomach: Implements a gastric state machine for digestion.
- Intestines: Adds segments (duodenum, jejunum, etc.) and simulates absorption.
- Pancreas: Differentiates endocrine and exocrine functions.
- Gallbladder: Simulates storing, concentrating, and releasing bile.
- Kidneys: Models nephrons, GFR, and electrolyte balance.
- Bladder: Implements a micturition cycle with pressure dynamics.
- Spleen: Models red and white pulp for blood filtering and immunity.
This commit significantly expands the patient simulation by adding models
for the full digestive and urinary systems, as well as the spleen and
spinal cord.
This builds on the polymorphic organ framework by adding 9 new organ
classes:
- Kidneys
- Bladder
- Stomach
- Intestines
- Gallbladder
- Pancreas
- Esophagus
- Spleen
- SpinalCord
Each new organ has its own header, a source file with simplified
simulation logic for its unique physiological properties, and is
integrated into the main patient model and simulation loop.
The build system and example application have been updated to include
and demonstrate this new, more comprehensive set of organs.
google-labs-jules[bot]