add details to readme

README.md

@@ -20,44 +20,32 @@ tags:
 
 ## Description
 
-TODO
+This repository contains the models and training pipeline for my master thesis. The main repository is hosted on [GitHub](https://github.com/13hannes11/master_thesis_code).
 
-## How to run
-
-TODO
+The project structure is based on the template by [ashleve](https://github.com/ashleve/lightning-hydra-template).
 
-Install dependencies
+The metadata is stored in `data/focus150/`. The relevant files are `test_metadata.csv`, `train_metadata.csv` and `validation_metadata.csv`. Image data (of 150 x 150 px images) is not published together with this repository therefore training runs are not possible to do without it. The layout of the metadata files is as follows
 
-```bash
-# clone project
-git clone https://github.com/YourGithubName/your-repo-name
-cd your-repo-name
-
-# [OPTIONAL] create conda environment
-conda create -n myenv python=3.8
-conda activate myenv
+```csv
+,image_path,scan_uuid,study_id,focus_height,original_filename,stack_id,obj_name
+0,31/b0d4005e-57d0-4516-a239-abe02a8d0a67/I02413_X009_Y014_Z5107_750_300.jpg,b0d4005e-57d0-4516-a239-abe02a8d0a67,31,-0.013672000000000017,I02413_X009_Y014_Z5107.jpg,1811661,schistosoma
+1,31/274d8969-aa7c-4ac0-be60-e753579393ad/I01981_X019_Y014_Z4931_450_0.jpg,274d8969-aa7c-4ac0-be60-e753579393ad,31,-0.029296999999999962,I01981_X019_Y014_Z4931.jpg,1661371,schistosoma
+...
+```
 
-# install pytorch according to instructions
-# https://pytorch.org/get-started/
 
-# install requirements
-pip install -r requirements.txt
-```
+## How to run
 
-Train model with default configuration
+Train model with chosen experiment configuration from `configs/experiment/`
 
 ```bash
-# train on CPU
-python train.py trainer.gpus=0
-
-# train on GPU
-python train.py trainer.gpus=1
+python train.py experiment=focusResNet_150
 ```
 
-Train model with chosen experiment configuration from [configs/experiment/](configs/experiment/)
+Train with hyperparameter search from `configs/hparams_search/`
 
 ```bash
-python train.py experiment=experiment_name.yaml
+python train.py -m hparams_search=focusResNetMSE_150
 ```
 
 You can override any parameter from command line like this
@@ -65,3 +53,7 @@ You can override any parameter from command line like this
 ```bash
 python train.py trainer.max_epochs=20 datamodule.batch_size=64
 ```
+
+## Jupyter notebooks
+
+Figures and other evaluation code was run in Jupyter notebooks. These are available at `notebooks/`