directory_structure.txt

Bachelor Thesis: Directory Structure of Machine-Learning-BSC-Thesis-2024
==============================
machine-learning-bsc-thesis-2024/
│
├── grobid_client_python/                                   # GROBID client for extracting XML data from PDF files
│
├── project_submission/                                     # Project submission files
│   ├── 00_project/                                         # Project files
│   │   ├── annotation_data/
│   │   │   └── annotation_data_raw.xlsx                    # Raw annotation data 
│   │   | 
│   │   ├── annotation_guide_and_scheme/                    # Annotation guide and scheme files
│   │   │   ├── annotation_guide_details.pdf
│   │   │   ├── annotation_images.pdf
│   │   │   └── annotation_scheme_and_guide.xlsx 
│   │   |
│   │   └── notebooks/  # Project notebooks
|   |       |
│   │       ├── 00MICCAI_total_outputs/                                     # Total outputs of the project 
|   |       |    ├── 01MICCAI_all_outputs/                                  # All outputs of the project notebook 01
|   |       |    |    └── 01MICCAI_2023_notebook_database_miccai2023.csv
|   |       |    |
|   |       |    ├── 03MICCAI_all_outputs/                                  # All outputs of the project notebook 03
|   |       |    |    ├── 03MICCAI_notebook_cleaned_dataframes/             # Cleaned dataframes    
|   |       |    |    ├── 03MICCAI_2023_notebook_GROBID_dataframes/         # GROBID dataframes
|   |       |    |    └── 03MICCAI_2023_notebook_GROBID_processed_volumes/  # GROBID processed volumes
|   |       |    |    |    
|   |       |    |    ├── 03MICCAI_2023_notebook_100_randomly_selected_papers.csv    
|   |       |    |    ├── 03MICCAI_2023_notebook_df_paper_extractions_all_cleaned.csv
|   |       |    |    ├── 03MICCAI_2023_notebook_df_paper_extractions_cancer_csv
|   |       |    |    └── 03MICCAI_2023_notebook_df_paper_extractions_patients_and_cancer.csv
|   |       |    |
|   |       |    ├── 04MICCAI_all_outputs/                                  # All outputs of the project notebook 04
|   |       |    |    ├── 04MICCAI_notebook_extracted_keywords/
|   |       |    |    └── 04MICCAI_notebook_extracted_sentences/
|   |       |    |    
|   |       |    └── 05MICCAI_all_outputs/                                  # All outputs of the project notebook 05
|   |       |        ├── 05MICCAI_notebook_data_visualization/
|   |       |        ├── 05MICCAI_notebook_summary_statistics/
|   |       |        |
|   |       |        ├── 05MICCAI_notebook_dataset_counts.csv
|   |       |        ├── 05MICCAI_notebook_normalized_datasets.csv
|   |       |        ├── 05MICCAI_notebook_preprocessed_annotation_data.csv
|   |       |        ├── 05MICCAI_notebook_unique_image_types.csv
|   |       |        └── 05MICCAI_notebook_unique_organs.csv
|   |       |    
│   │       ├── 01MICCAI_2023_HTML_Data_Extraction.ipynb                            # HTML data extraction notebook
│   │       ├── 02MICCAI_2023_PDF_Segmentation.ipynb                                # PDF segmentation notebook
│   │       ├── 03MICCAI_2023_XML_Data_Extraction_and_Paper_Selection.ipynb         # XML data extraction and paper selection notebook
│   │       ├── 04MICCAI_2023_Keyword_Sentence_Extraction.ipynb                     # Keyword and sentence extraction notebook
│   │       └── 05MICCAI_2023_Annotation_Analysis.ipynb                             # Annotation analysis notebook
│   │                 
│   ├── 01_experiment                   # Experiment files
│   ├── 02_old_notebooks                # Old notebooks
│   └── 03_archive                      # Archive files
│
│
├── directory_structure.txt/            # Directory structure text file                      
├── meeting_w_theo.md                   # Meeting notes with Theo
├── README.md                           # Instructions and descriptions
├── requirements.txt                    # Python packages requirements overview
└── weekly-meetings-yasmin.md           # Weekly meetings notes