Merge pull request #26 from radionets-project/update_readme

Update readme

README.md

@@ -1,16 +1,40 @@
-# pyvisgen [![Actions Status](https://github.com/radionets-project/pyvisgen/workflows/CI/badge.svg)](https://github.com/radionets-project/pyvisgen/actions) [![codecov](https://codecov.io/gh/radionets-project/pyvisgen/branch/main/graph/badge.svg?token=84ATCQQAMN)](https://codecov.io/gh/radionets-project/pyvisgen)
-
-Possible names:
-* pyvisgen
-* pyvs
-* vsim
-* visim
-* vissim
-
-Python implementation of the VISGEN tool developed at [Haystack Observatory](https://www.haystack.mit.edu/astronomy/).
-
-Todo:
-* find more infos about MAPS packet on the website
-* explain usage
-* implement polarization
-* 
+# pyvisgen [![Actions Status](https://github.com/radionets-project/pyvisgen/workflows/CI/badge.svg)](https://github.com/radionets-project/pyvisgen/actions)
+
+Python implementation of the VISGEN tool developed at [Haystack Observatory](https://www.haystack.mit.edu/astronomy/). It uses the Radio Interferometer Measurement Equation (RIME) to simulate the measurement process of a radio interferometer. A gridder is also implemented to process the resulting visibilities and convert them to images suitable as input for the neural networks developed in the [radionets repository](https://github.com/radionets-project/radionets).
+
+## Installation
+You can install the necessary packages in a conda environment of your choice by executing
+```
+$ pip install -e .
+```
+
+## Usage
+There are 3 possible modes at the moment:  `simulate` (default), `slurm`, and `gridding`. `simulate` and `slurm` both utilize the RIME formalism for creating visibilities data. With the option `gridding`, these visibilities get gridded and prepared as input images for training a neural network from the radionets framework. The necessary options and variables are set with a `toml` file. An exemplary file can be found in `config/data_set.toml`.
+```
+$ pyvisgen_create_dataset --mode=simulate some_file.toml
+```
+In the examples directory, you can find introductory jupyter notebooks which can be used as an entry point.
+
+## Input images
+As input images for the RIME formalism, we use GAN-generated radio galaxies created by [Rustige et. al.](https://doi.org/10.1093/rasti/rzad016) and [Kummer et. al.](https://doi.org/10.18420/inf2022_38).
+Below, you can see four example images consisting of FRI and FRII sources.
+
+![sources](https://github.com/radionets-project/pyvisgen/assets/23259659/285e36f6-74e7-45f1-9976-896a38217880)
+
+Any image can be used as input for the formalism, as long as they are stored in the h5 format, generated with [`h5py`](https://www.h5py.org/).
+
+## RIME
+Currently, we use the following expression for the simulation process:
+$$\mathbf{V}_{\mathrm{pq}}(l, m) = \sum\_{l, m} \mathbf{E}\_{\mathrm{p}}(l, m) \mathbf{K}\_{\mathrm{p}}(l, m) \mathbf{B}(l, m) \mathbf{K}^{H}\_{\mathrm{q}}(l, m) \mathbf{E}^{H}\_{\mathrm{q}}(l, m) $$
+Here, $\mathbf{B}(l, m)$ corresponds to the source distribution, $\mathbf{K}(l, m) = \exp(-2\pi\cdot i\cdot (ul + vm))$ represents the phase delay and $\mathbf{E}(l, m) = \mathrm{jinc}\left(\frac{2\pi}{\lambda}d\cdot \theta\_{lm}\right)$ the telescope properties, with $\mathrm{jinc(x)}=\frac{J_1(x}{x}$ and $J_1(x)$ as the first Bessel function.
+An exemplary result can be found below.
+
+![visibilities](https://github.com/radionets-project/pyvisgen/assets/23259659/858a5d4b-893a-4216-8d33-41d33981354c)
+
+## Visualization of Jones matrices
+In this section, you can see visualizations of the matrices $\mathbf{E}(l, m)$  and $\mathbf{K}(l, m)$.
+### Visualization of the E matrix
+![visualize_E](https://github.com/radionets-project/pyvisgen/assets/23259659/194a321b-77cd-423b-9d01-c18c0741d6c5)
+
+### Visualization of the K matrix
+![visualize_K](https://github.com/radionets-project/pyvisgen/assets/23259659/501f487a-498b-4143-b54a-eb0e2f28e417)

docs/changes/26.maintenance.rst

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+- update readme