---
title: "Introduction to vol2birdR"
author: Adriaan M. Dokter & Anders Henja
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Introduction to vol2birdR}
  %\VignetteEngine{knitr::rmarkdown}
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---


vol2birdR is an R package for calculating vertical profiles and other biological scatterers from weather radar data. The original **vol2bird** is written as a C-package and has been migrated to also work as an R package.

## Introduction
The vol2birdR package provides necessary functions to process polar volume data of C-band and S-band radars into vertical profiles of biological scatterers. This package also enables libtorch and the MistNet model for segmentation of meteorological and biological signals.

## Calculating vertical profiles
First, define a configuration instance, and modify configuration settings according to needs. 

```
# load the library
library(vol2birdR)

# create a configuration instance
config<-vol2bird_config()

# modify the configuration instance as needed
# in this example we set the maximum range to 25 km:
config$rangeMax <- 25000
```
The configuration object can be modified heavily. Learn more about the available options in the documentation of `vol2bird_config()`

Note that configuration objects are copied by reference by default, and true copies that can be used independently should be assigned using:

```
config <- vol2bird_config()
config_copy <- vol2bird_config(config)
```

Finally, the vertical profile can be calculated using function `vol2bird()`:

```
vol2bird(file="/your/input/pvolfile",config=config, vpfile="/your/output/vpfile")
```

The input pvolfile needs to be in ODIM HDF5 format, IRIS RAW format, or NEXRAD format. The output vpfile containing the profile will be in ODIM HDF5 format.

## MistNet 
### Installation
MistNet is a deep convolution neural net for segmenting out rain in S-band radar data, see the publication at https://besjournals.onlinelibrary.wiley.com/doi/full/10.1111/2041-210X.13280. 
To use MistNet, follow the following additional installation steps:

After installing and loading vol2birdR, run `install_mistnet()` from R. This will download libtorch from the download section of https://pytorch.org as well as a wrapper library from AWS that enables the mistnet functionality:

```
# STEP 1: install mistnet libraries
library(vol2birdR)
install_mistnet()
```

After completing this step, the following command should evaluate to `TRUE`:
```
mistnet_exists()
```

Next, the pytorch mistnet model needs to be downloaded, which is hosted at  http://mistnet.s3.amazonaws.com/mistnet_nexrad.pt. Note that this file is large, over 500Mb. It can be downloaded directly from R using `install_mistnet_model()`:

```
# STEP 2: download mistnet model:
# install mistnet model into vol2birdR package:
install_mistnet_model()
```

`install_mistnet_model()` installs the model by default into the vol2birdR package directory. As a result, when reinstalling vol2birdR the model file will have to be re-downloaded as well.

Alternatively, you can store the model in an alternative location outside the vol2birdR package directory. This has the advantage that you don't have to re-download the model when reinstalling vol2birdR. Simply store the path of the mistnet_nexrad.pt file in the `mistNetPath` element of your configuration object (see `vol2bird_config()`)

vol2birdR will automatically locate the file if it is located at `/opt/vol2bird/etc/mistnet_nexrad.pt`, which can be done as follows:

```
# create the directory
# (in case of a permission-denied error, create the directory manually)
dir.create("/opt/vol2bird/etc", recursive=TRUE)

# download the model
install_mistnet_model(path="/opt/vol2bird/etc/mistnet_nexrad.pt")
```

### Using MistNet
After installing the MistNet libraries and model file, a profile can be calculated as follows:
```
# define configuration object:
config <- vol2bird_config()

# enable MistNet:
config$useMistNet <- TRUE

# calculate the profile:
vol2bird(file="/your/input/pvolfile", config=config, vpfile="/your/output/vpfile")
```
