---
title: "pacu: Precision Agriculture Computational Utilities - Satellite data"
author: "Caio dos Santos & Fernando Miguez"
date: "`r Sys.Date()`"
output: 
  rmarkdown::html_vignette:
    toc: true
vignette: >
  %\VignetteIndexEntry{pacu: Precision Agriculture Computational Utilities - Satellite data}
  %\VignetteEngine{knitr::rmarkdown}
  \usepackage[utf8]{inputenc}
---
  
# Specific vignettes

1.  [Satellite data](pacu_sat.html)

2.  [Weather data](pacu_weather.html)

3.   [Yield monitor data](pacu_ym.html)

4. [Frequently asked questions](pacu_faq.html)

# Satellite data
  
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
library(sf)
library(pacu)
```

## Interacting with the OData API

### Setting up your credentials

The first step is to register the [Data Space](https://dataspace.copernicus.eu/) credentials to the R environment using ***pa_intialize_dataspace()***

```{r initializing-data-space, eval = FALSE}
un <- 'my-username'
pw <- 'my-password'
pa_initialize_dataspace(username = un, password = pw)
```

### Browsing the Data Space catalog

Let us define our area of interest. In this example, we are
interested in a field in Ames, Iowa, U.S.

```{r defining-area-of-interest}
extd.dir <- system.file("extdata", package = "pacu")
area.of.interest <- sf::st_read(file.path(extd.dir, 'cobs_a_aoi.shp'), quiet = TRUE)
```

Now, we can browse the Data Space catalog for images that
meet our requirements. We can specify these requirements in
by passing arguments to the **pa_browse_dataspace()**
function. The function allows us to filter the satellite
image using information such as dates, cloud coverage, and
satellite platform. In this case, we are interested in
images captured by Sentinel 2, with a maximum of 50% of
cloud coverage, and in the year of 2023.

```{r browsing-data-space, eval = FALSE}
available.images <- pa_browse_dataspace(aoi = area.of.interest,
                                        max.cloud.cover = 50,
                                        start.date = '2023-01-01',
                                        end.date = '2023-12-31',
                                        collection.name = 'SENTINEL-2')

```

Each entry in the data frame returned by the function is a
satellite image available to be downloaded from Data Space.
In this case, we can see that there are 68 images the meet
our requirements.

```{r reading-browse-ds, include=FALSE}
available.images <- readRDS(file.path(extd.dir, 'ds-browse-object.rds'))
```

```{r inspecting-browse-ds}
available.images
```

Using the "summary" function, we can extract the number of
available images for every month in the data set.
```{r summary-browse-ds}
summary(available.images)
```


### Downloading satellite images from Data Space

The next step would be to download the images. If we supply
the ***available.images*** object to the function
***download_dataspace()***, the function will download all 68
available images. For this demonstration, we can focus only
on two images. Let's pick the 32nd and 33rd images because
these were captured in mid-July, so there should be maize or
soybeans in the field.

An important consideration is that these images occupy a
considerable amount of storage (about 500 Mb each), this
means that downloading 68 images would take up about 35 Gb
of storage. By providing an ***area of interest (aoi)*** to
the function, it will open the raw file and crop the
images to the relevant extent. This was designed to save storage
space when downloading multiple images.

```{r downloading-an-image, eval=FALSE}
out.dir <- tempdir()
available.images <- available.images[32:33, ]
pa_download_dataspace(x = available.images,
                      dir.path = out.dir,
                      aoi = area.of.interest,
                      verbose = FALSE)
```

```{r out-equal-ext, include=FALSE}
out.dir <- extd.dir
```

### Visualizing downloaded images

Now that we have downloaded the data, we might be interested
in looking at RGB images.

```{r rgb-img, fig.width=7, fig.height=5}
s2.files <- list.files(out.dir, '\\.zip', full.names = TRUE)
rgb.img <- pa_get_rgb(s2.files,
                      aoi = area.of.interest,
                      verbose = FALSE)

pa_plot(rgb.img)
```

Similarly, we might be interested in NDVI or NDRE...
```{r, ndvi-img,  fig.width=7, fig.height=5}
ndvi.img <- pa_compute_vi(s2.files,
                          vi = 'ndvi', 
                          aoi = area.of.interest,
                          verbose = FALSE)

ndre.img <- pa_compute_vi(s2.files, 
                          vi = 'ndre',
                          aoi = area.of.interest,
                          verbose = FALSE)

pa_plot(ndvi.img, main = 'NDVI')
pa_plot(ndre.img, main = 'NDRE')
```

## Areal summary

Often, in precision agriculture applications, we are
interested in a summary value per experimental unit to
evaluate the effect of an applied treatment. This statistic
is commonly the mean or median of the pixels within the
polygon representing the research plot or the area of
interest. To illustrate how that can be achieved within
pacu, we can split our area of interest in four smaller
areas and then compute and visualize summary statistics.

```{r  ndvi-img-summary,  fig.width=7, fig.height=5}
split.aoi <- st_make_grid(area.of.interest, n = c(4, 1))
split.aoi <- st_as_sf(split.aoi)
split.aoi <- st_transform(split.aoi, st_crs(ndvi.img))
ndvi.mean <- summary(ndvi.img, by = split.aoi, fun = mean)
pa_plot(ndvi.mean)
```

## Interacting with the Copernicus Statistical API

The Data Space Statistics API allows users to download areal
statistics calculated based on satellite images without
having to download images. The Statistics API uses OAuth2.0
authentication with ***client id*** and ***client secret***.
To use the functions that interact with the Satistics API,
you will need to [register an OAuth client](https://documentation.dataspace.copernicus.eu/APIs/SentinelHub/Overview/Authentication.html).

### Setting up your credentials
 
```{r registering-oauth, eval = FALSE}
cid <- 'my-client-id'
cs <- 'my-client-secret'
pa_initialize_oauth(client_id = cid, client_secret = cs)
```

### Requesting areal statistics

Now that your Oauth client credentials have been registered,
you can request vegetation index statistics using the
Statistics API. Let us request NDVI data for our area of
interest.

```{r requesting-ndvi-statistics, eval = FALSE}
ndvi.statistics <- pa_get_vi_stats(aoi = area.of.interest,
                                   start.date = '2022-01-01',
                                   end.date = '2022-12-31',
                                   vegetation.index = 'ndvi',
                                   agg.time = 'P1D')
```

```{r reading-ndvi-statistics, include = FALSE}
ndvi.statistics <- readRDS(file.path(extd.dir, 'example-ndvi-stats.rds'))
```

The ***pa_plot()*** function helps us visualize the data in
a spatial context. Since we have requested the NDVI
statistics for one polygon, it us to be expected that within
each facet representing a date, there is only one color.

```{r plotting-ndvi-statistics-paplot, fig.width=7, fig.height=5}
pa_plot(ndvi.statistics)
```


Conversely, if we are more interested in examining the data
in a time series format, we can specify the "plot.type".
```{r vis-ndvi-stats, fig.width=7, fig.height = 5}
pa_plot(ndvi.statistics, 
        plot.type = 'timeseries')
```



We might also be interested in comparing the index value
from different regions of the field. Let us split the
previous field in four parts and retrieve NDVI individually
for each section, so we can compare the results.


**note:** it is important to clarify that using the ***by.feature***
argument will send multiple requests to the Statistical API. 
The user should be mindful not to exceed their quota. 
Quotas and limitations can be found [here](https://documentation.dataspace.copernicus.eu/Quotas.html)

```{r requesting-ndre-statistics, eval = FALSE}
ndvi.statistics.2 <- pa_get_vi_stats(aoi = split.aoi,
                                     start.date = '2022-01-01',
                                     end.date = '2022-05-01',
                                     vegetation.index = 'ndvi',
                                     agg.time = 'P1D',
                                     by.feature = TRUE)
```

```{r reading-ndre-statistics, include = FALSE}
ndvi.statistics.2 <- readRDS(file.path(extd.dir, 'example-ndvi-stats-2.rds'))
```


Now, we can visualize the different parts of the field in a spatial and temporal context.
```{r plotting-ndvi-statistics-multiple, fig.width=7, fig.height=5}
pa_plot(ndvi.statistics.2)
```


Similarly to the previous example, we might be interested in examining the data in a time series format. In this case, we can specify the "by" argument and a different series will be plotted for each polygon "id". 
```{r plotting-ndvi-statistics-multiple-timeseries, fig.width=7, fig.height=5}
pa_plot(ndvi.statistics.2, 
        plot.type = 'timeseries',
        by = c('id'),
        legend.outside = TRUE)
```



