# 📊 Diagrams

This project includes a collection of diagrams illustrating the system architecture, data pipelines, and feature extraction workflows. You can view the Mermaid definitions or the rendered diagrams below.

## 📂 System Architecture & Configuration
| Diagram | Mermaid | Image |
|---|---|---|
| **System Architecture** | [assets/system_architecture.mmd](https://github.com/SamoraHunter/pat2vec/blob/main/assets/system_architecture.mmd) | ![System Architecture](https://github.com/SamoraHunter/pat2vec/blob/main/assets/system_architecture.png) |
| **Configuration** | [assets/config.mmd](https://github.com/SamoraHunter/pat2vec/blob/main/assets/config.mmd) | ![Configuration](https://github.com/SamoraHunter/pat2vec/blob/main/assets/config.svg) |

## 🛠️ Data Pipelines
| Diagram | Mermaid | Image |
|---|---|---|
| **Data Pipeline** | [assets/data_pipeline.mmd](https://github.com/SamoraHunter/pat2vec/blob/main/assets/data_pipeline.mmd) | ![Data Pipeline](https://github.com/SamoraHunter/pat2vec/blob/main/assets/data_pipeline.png) |
| **Main Batch Processing** | [assets/main_batch.mmd](https://github.com/SamoraHunter/pat2vec/blob/main/assets/main_batch.mmd) | ![Main Batch](https://github.com/SamoraHunter/pat2vec/blob/main/assets/main_batch.svg) |
| **Example Ingestion** | [assets/example_ingestion.mmd](https://github.com/SamoraHunter/pat2vec/blob/main/assets/example_ingestion.mmd) | <img src="https://github.com/SamoraHunter/pat2vec/blob/main/assets/example_ingestion.png?raw=true" alt="Example Ingestion" height="400"/> |

## 🧩 Methods & Post-Processing
| Diagram | Mermaid | Image |
|---|---|---|
| **Methods Annotation** | [assets/methods_annotation.mmd](https://github.com/SamoraHunter/pat2vec/blob/main/assets/methods_annotation.mmd) | ![Methods Annotation](https://github.com/SamoraHunter/pat2vec/blob/main/assets/methods_annotation.png) |
| **Post-Processing Build Methods** | [assets/post_processing_build_methods.mmd](https://github.com/SamoraHunter/pat2vec/blob/main/assets/post_processing_build_methods.mmd) | ![Post-Processing Build Methods](https://github.com/SamoraHunter/pat2vec/blob/main/assets/post_processing_build_methods.svg) |
| **Post-Processing Anonymisation** | [assets/post_processing_anonymisation_high_level.mmd](https://github.com/SamoraHunter/pat2vec/blob/main/assets/post_processing_anonymisation_high_level.mmd) | ![Post-Processing Anonymisation](https://github.com/SamoraHunter/pat2vec/blob/main/assets/post_processing_anonymisation_high_level.svg) |

## 🔍 Feature Extraction
| Diagram | Mermaid | Image |
|---|---|---|
| **Ethnicity Abstractor** | [assets/ethnicity_abstractor.mmd](https://github.com/SamoraHunter/pat2vec/blob/main/assets/ethnicity_abstractor.mmd) | ![Ethnicity Abstractor](https://github.com/SamoraHunter/pat2vec/blob/main/assets/ethnicity_abstractor.svg) |
| **Get BMI** | [assets/get_bmi.mmd](https://github.com/SamoraHunter/pat2vec/blob/main/assets/get_bmi.mmd) | ![Get BMI](https://github.com/SamoraHunter/pat2vec/blob/main/assets/get_bmi.svg) |
| **Get Demographics** | [assets/get_demographics.mmd](https://github.com/SamoraHunter/pat2vec/blob/main/assets/get_demographics.mmd) | ![Get Demographics](https://github.com/SamoraHunter/pat2vec/blob/main/assets/get_demographics.svg) |
| **Get Diagnostics** | [assets/get_diagnostics.mmd](https://github.com/SamoraHunter/pat2vec/blob/main/assets/get_diagnostics.mmd) | ![Get Diagnostics](https://github.com/SamoraHunter/pat2vec/blob/main/assets/get_diagnostics.svg) |
| **Get Drugs** | [assets/get_drugs.mmd](https://github.com/SamoraHunter/pat2vec/blob/main/assets/get_drugs.mmd) | ![Get Drugs](https://github.com/SamoraHunter/pat2vec/blob/main/assets/get_drugs.svg) |
| **Get Smoking** | [assets/get_smoking.mmd](https://github.com/SamoraHunter/pat2vec/blob/main/assets/get_smoking.mmd) | ![Get Smoking](https://github.com/SamoraHunter/pat2vec/blob/main/assets/get_smoking.svg) |
| **Get News** | [assets/get_news.mmd](https://github.com/SamoraHunter/pat2vec/blob/main/assets/get_news.mmd) | ![Get News](https://github.com/SamoraHunter/pat2vec/blob/main/assets/get_news.svg) |
| **Get Dummy Data Cohort Searcher** | [assets/get_dummy_data_cohort_searcher.mmd](https://github.com/SamoraHunter/pat2vec/blob/main/assets/get_dummy_data_cohort_searcher.mmd) | ![Get Dummy Data Cohort Searcher](https://github.com/SamoraHunter/pat2vec/blob/main/assets/get_dummy_data_cohort_searcher.svg) |
| **Get Method Bloods** | [assets/get_method_bloods.mmd](https://github.com/SamoraHunter/pat2vec/blob/main/assets/get_method_bloods.mmd) | ![Get Method Bloods](https://github.com/SamoraHunter/pat2vec/blob/main/assets/get_method_bloods.svg) |
| **Get Method Patient Annotations** | [assets/get_method_pat_annotations.mmd](https://github.com/SamoraHunter/pat2vec/blob/main/assets/get_method_pat_annotations.mmd) | ![Get Method Patient Annotations](https://github.com/SamoraHunter/pat2vec/blob/main/assets/get_method_pat_annotations.svg) |
| **Get Treatment Docs (No Terms Fuzzy)** | [assets/get_treatment_docs_by_iterative_multi_term_cohort_searcher_no_terms_fuzzy.mmd](https://github.com/SamoraHunter/pat2vec/blob/main/assets/get_treatment_docs_by_iterative_multi_term_cohort_searcher_no_terms_fuzzy.mmd) | ![Get Treatment Docs (No Terms Fuzzy)](https://github.com/SamoraHunter/pat2vec/blob/main/assets/get_treatment_docs_by_iterative_multi_term_cohort_searcher_no_terms_fuzzy.svg) |