Author: Xavier Laviron
Date: 2020-11-14

# Quick start guide to TheiaR package

#### Xavier Laviron

#### 2020-11-14

# TheiaR: search, download and manage data from Theia

The TheiaR package provides an efficient and clean interface to search, download and manage products from Theia website.

## Overview

The basic functionalities are:

- Search available tiles through Theia API
- Download tiles resulting from a search
- Download tiles contained in a cart (`.meta4` file) obtained from Theia website.
- Read band into `RasterStack` objects (with the `raster` library)
- Read band into `gdalcubes` objects (with the `gdalcubes` library)
- Extract archives (not recommended)

NOTE: To search and download data from Theia, you will need to register to their website.

NOTE: In order to use Landsat or SpotWorldHeritage products, you’ll need to make a first manual download to agree to the license and validate your account.

## Installation

You can install the latest stable version from Github with:

    devtools::install_github('norival/theiaR')

    # or, to install the development version
    devtools::install_github('norival/theiaR', 'devel')

Or, you can install it from CRAN:

    isntall.packages('theiaR')

## Complete example

A workflow to search and download tiles would be something like:

    library(theiaR)

    # create a list containing the query
    myquery <- list(collection = "SENTINEL2",
                    town       = "Grenoble",
                    start.date = "2018-07-01",
                    end.date   = "2018-07-06")

    # create a collection from the query
    mycollection <- TheiaCollection$new(query = myquery, dir.path = ".", check = TRUE)

    # check available tiles fro the query
    mycollection$status

    # download the tiles into 'dir.path'
    mycollection$download(auth = "path/to/auth/file.txt")

## Step-by-step guide

First, load the package.

    library(theiaR)

To search and download data from Theia, you will need to register to their website.

NOTE: In order to use Landsat or SpotWorldHeritage products, you’ll need to make a first manual download to agree to the license and validate your account.

### Create a collection of tiles

The first step is to create a collection of tile(s). This can be done either from a query or from a cart file.

#### Create a collection from a query

A query is simply a named `list` of search terms. For example:

    myquery <- list(collection = "SENTINEL2",
                    town       = "Grenoble",
                    start.date = "2018-07-01",
                    end.date   = "2018-07-06")

will create a query to Theia database, looking for tiles from Sentinel2 satellite around Grenoble, between 2018-07-01 and 2018-07-06.

It accepts the following terms.

- collection: The collection to look for. Accepted values are: `SENTINEL2`, `LANDSAT`, `Landsat57`, `SpotWorldHeritage`, `Snow`. Defaults to `SENTINEL2`.

- platform: The platform to look for. Accepted values are: `LANDSAT5`, `LANDSAT7`, `LANDSAT8`, `SPOT1`, `SPOT2`, `SPOT3`, `SPOT4`, `SPOT5`, `SENTINEL2A`, `SENTINEL2B`.

- level: Processing level of products. Accepted values are: `LEVEL1C`, `LEVEL2A` and `LEVEL3A`, `N2A`. Defaults to `LEVEL2A` (or `N2A` if querying Landsat57 collection).

To specify the location of the tiles, several alternatives are available. You can specify the town around which you want your data with:

- town: The location to look for. Give a not too frequent town name.

You can specify directly the tile ID if you know it:

- tile: The tile identifier to retrieve (e.g. T31TGK)

You can specify a point by giving its x/y coordinates:

- latitude: The x coordinate of a point.

- longitude: The y coordinate of a point.

Or you can specify a rectangle by giving its min/max coordinates:

- latmin: The minimum latitude to search.

- latmax: The maximum latitude to search.

- lonmin: The minimum longitude to search.

- lonmax: The maximum longitude to search.

You can also look for a specific orbit number or relative orbit number:

- orbit.number: The orbit number

- rel.orbit.number: The relative orbit number

Finally, you can filter results by giving the date range and the maximum cloud cover:

- max.clouds: The maximum of cloud cover wanted (0-100).

- start.date: The first date to look for (format: `YYYY-MM-DD`).

- end.date: The last date to look for (format: `YYYY-MM-DD`).

You can then create your collection with:

    mycollection <- TheiaCollection$new(query = myquery, dir.path = ".", check = TRUE)

where `dir.path` is the path you want your tiles to be further downloaded (This only queries Theia’s catalog for available tiles, nothing is downloaded). If tiles are already present in `dir.path`, they will be checked by computing a checksum and comparing it to the hash provided by Theia (only available for Sentinel2 data, no hash is provided for other collections, and files are then assumed to be correct). This ensures that the files have been correctly downloaded. Set `check = FALSE` to skip file’s check.

    print(mycollection)

#### Create a collection from a cart file

Alternatively, you can download a cart from Theia. To create a cart, login to Theia website, make a search for tiles, and add wanted tiles to your cart. Then, download your cart and save the resulting `.meta4` file to your disk.

You can then create your collection using this file:

    cart.path <- system.file("extdata", "cart.meta4", package = "theiaR")

    mycollection <- TheiaCollection$new(cart.path = cart.path,
                                        dir.path  = ".",
                                        check     = TRUE)

    print(mycollection)
    #> An collection of tiles from Theia
    #>
    #> Number of tiles: 2
    #> Directory path : './'
    #>
    #> Obtained from cart file

As above, it will check the hash of files if they are already present in `dir.path`.

### Download your tiles

The next step is to download your collection. You can get the status of your collection by running:

    mycollection$status
    #>                                          tile exists checked correct extracted
    #> 1 SENTINEL2B_20190128-104831-308_L2A_T31TGK_D  FALSE   FALSE   FALSE     FALSE
    #> 2 SENTINEL2A_20190113-104826-809_L2A_T31TGK_D  FALSE   FALSE   FALSE     FALSE

To download all tiles in a collection, simply run:

    mycollection$download(auth = myauth)

where myauth is the path to file storing your Theia credentials. If it does not exist yet, you will be securely prompted for your login and password, and the file will be created.

This will check if files are present, check their hashes, and download them if needed (if files do not exist or checksums are wrong). To overwrite existing files, run:

    mycollection$download(auth = myauth, overwrite = TRUE)

### Read bands from zip files

Alternatively, you can read bands directly from the zip archives (by using the `vsizip` interface provided by GDAL). Use:

    mytile$bands

to get a list of available bands. Then:

    mybands <- mytile$read(bands = c("B5", "B6"))

to load the bands into memory (returns a `RasterStack` object). It performs the necessary corrections on the values.

You can also read bands from a collection by running:

    mybands <- mycollection$read(bands = c("B5", "B6"))

which returns a `list` of `RasterStack` objects.

NOTE: loading several tiles needs a lot of memory (~900MB/tile)

### Create a `gdalcubes` collection

Alternatively, you can use the great gdalcubes package to create a three dimensional representation of the tiles. Simply run:

    library(gdalcubes)

    gdalcubes <- mycollection$as_gdalcube("path/to/gdalcubes.sqlite")

where `path/to/gdalcubes.sqlite` is the path to store the gdalcubes object data.

### Extract tiles

If you want to extract the archives, you can run:

    file.path <- mycollection$extract()

which will extract tiles into the same directory as the archives.

This is not recommended, as this will take a large amount of disk space

## Acknowledgment

Thanks to Olivier Hagolle for his work on `theia_download.py` (github), which has inspired this package.