diff --git a/README.md b/README.md index 97a008f..06799b4 100644 --- a/README.md +++ b/README.md @@ -5,45 +5,51 @@ The implementation is based on Ben-Eliezer et al. 2015 (https://doi.org/10.1002/ ## Install -Recommended and tested is to clone git repository. -From the repository root, run with a name of your choice: +Recommended and tested is to clone the git repository. +From the repository root, create a conda environment with an `env_name` of your choice by running: -`conda env create -f environment.yml -n ` +```shell +conda env create -f environment.yml -n env_name -`conda activate ` +conda activate env_name +``` + +If you don't have a conda installation, +we recommend using [Miniforge](https://conda-forge.org/miniforge/). +You should also consider calling `mamba` instead of `conda` for a faster resolution of dependencies. ## Usage The Package contains simulation of dictionary databases as well as the fitting of data to such databases. + #### Simulation -To simulate with configuration found in the "example/simulate" folder run: -`python simulate.py` +To simulate with the configuration found in the `example/simulate` folder run: +```shell +python simulate.py +``` To see all options run -`python simulate.py --help` - +```shell +python simulate.py --help +``` The simulation needs information about Gradients and RF events. -The basic inputs can be seen in the "example/simulate/emc_params.json" file. -Default configuration will create a database and some plots within the "example/simulate/" folder. - +The basic inputs can be seen in the `example/simulate/emc_params.json` file. +The default configuration will create a database and plots within the `example/simulate/` folder. #### Fit -To fit with a configuration found in the "example/fit" folder run: -`python fit.py` +To fit with the configuration found in the `example/fit` folder run: +`python fit.py` To see all options run `python fit.py --help` - The fit can take additional input files and needs specification of data and database. -The basic inputs can be seen in the "example/fit/fit_config.json" file. -Default configuration will use the data within the "examples/fit" folder and b1 regularization. - - +The basic inputs can be seen in the `example/fit/fit_config.json` file. +The default configuration will use the data within the `examples/fit` folder and b1 regularization. diff --git a/environment.yml b/environment.yml index 133eab5..c01e629 100644 --- a/environment.yml +++ b/environment.yml @@ -1,7 +1,6 @@ name: emc_env channels: - conda-forge - - defaults dependencies: - python=3.10 - pandas=2.0.3 @@ -13,4 +12,5 @@ dependencies: - plotly=5.16.1 - simple-parsing - tqdm - - nibabel \ No newline at end of file + - nibabel + - wandb