# R Client

Note

You need to become part of the openEO Platform "early adopter" program (opens new window) to access the processing infrastructure.

# Installation

Before you install the R client module into your R environment, please make sure that you have at least R version 3.6. Older versions might also work, but were not tested.

Stable releases can be installed from CRAN:

install.packages("openeo")

Installing the development version

If you want to install the development version, you can install from GitHub. It may contain more features, but may also be unstable.

You need to have the package 'devtools' installed. If it is not installed use install.packages("devtools").

Now you can use install_github from the devtools package to install the development version:

devtools::install_github(repo="Open-EO/openeo-r-client", dependencies=TRUE, ref="develop")

If this gives you an error, something went wrong with the installation so please check the requirements again.

If you have still troubles installing the package, feel free to leave an issue at the GitHub project (opens new window).

Now that the installation was successfully finished, we can load the package and connect to openEO Platform. In the following chapters we quickly walk through the main features of the R client.

# Connect to openEO Platform and explore

First we need to establish a connection to the openEO Platform back-end, which is available at connection URL https://openeo.cloud, or just in short:

library(openeo)
con = connect(host = "https://openeo.cloud")

The object stored as variable con is a connection and resembles the OpenEOClient - an object, that bundles all information and functions to interact with the back-end. It can be used explicitly in all of the functions to determine which connection has to be used (usually parameter con). If only one connection is active, then you can omit the parameter, because the last active connection is always stored in a package environment and used if no specific connection was present (see ?active_connection in the package documentation).

The capabilities of the back-end and the collections are generally publicly available, unless the data collections are proprietary and licensing issues prevent the back-end provider from publishing the collection. For the publicly available information you do not need to have an account on the back-end for reading them.

# Collections

The EO data available at a back-end is organised in so-called collections. For example, a back-end might provide fundamental satellite collections like "Sentinel 1" or "Sentinel 2", or preprocessed collections like "NDVI". Collections are used as input data for your openEO jobs.

Note

More information on how openEO "collections" relate to terminology used in other systems can be found in the openEO glossary (opens new window).

To get the collection list can be indexed by the collections ID to get the more details about the overview information. With the describe_collection function you can get an even more detailed information about the collection.

collections = list_collections()

# print an overview of the available collections (printed as data.frame or tibble)
print(collections)

# to print more of the reduced overview metadata
print(collections$SENTINEL1_GRD)

# Dictionary of the full metadata of the "SENTINEL1_GRD" collection (dict)
s2 = describe_collection("SENTINEL1_GRD") # or use the collection entry from the list, e.g. collections$SENTINEL1_GRD
print(s2)

In general all metadata objects are based on lists, so you can use str() to get the structure of the list and address fields by the $ operator.

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If the package is used with RStudio the metadata can also be nicely rendered as a web page in the viewer panel by running collection_viewer(x="SENTINEL1_GRD").

# Processes

Processes in openEO are operations that can be applied on (EO) data (e.g. calculate the mean of an array, or mask out observations outside a given polygon). The output of one process can be used as the input of another process, and by doing so, multiple processes can be connected that way in a larger "process graph": a new (user-defined) processes that implements a certain algorithm.

Note

Check the openEO glossary (opens new window) for more details on pre-defined, user-defined processes and process graphs.

The following code snippet shows how to get the available processes:

# List of available openEO processes with full metadata
processes = list_processes()

# List of available openEO processes by identifiers (string)
print(names(processes))

# print metadata of the process with ID "load_collection"
print(processes$load_collection)

The list_processes() method returns a list of process metadata objects that the back-end provides. Each process list entry is a more complex list object (called 'ProcessInfo') and contains the process identifier and additional metadata about the process, such as expected arguments and return types.

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As for the collection, processes can also be rendered as a web page in the viewer panel, if RStudio is used. In order to open the viewer use process_viewer() with either a particular process (process_viewer("load_collection")) or you can pass on all processes (process_viewer(processes)). When all processes are chosen, there is also a search bar and a category tree.

# Authentication

In the code snippets above we did not need to log in since we just queried publicly available back-end information. However, to run non-trivial processing queries one has to authenticate so that permissions, resource usage, etc. can be managed properly.

To handle authentication, openEO leverages OpenID Connect (OIDC) (opens new window). It offers some interesting features (e.g. a user can securely reuse an existing account), but is a fairly complex topic, discussed in more depth in the general authentication documentation for openEO Platform.

The following code snippet shows how to log in via OIDC authentication:

Action required

Unfortunately, you need to request a Client ID and a Client Secret for this from the openEO Platform support due to the R client not being officially supported by openEO Platform! Once you have received the Client ID and a Client Secret, you can can continue with the instructions below.

login(login_type = "oidc",
      provider = "egi",
      config = list(
        client_id= "...",
        secret = "...")))

Calling this method opens your system web browser, with which you can authenticate yourself on the back-end authentication system. After that the website will give you the instructions to go back to the R client, where your connection has logged your account in. This means, that every call that comes after that via the connection variable is executed by your user account.

As OpenID Connect authentication is a bit more complex and depends on the environment your are using it in, please refer to the general Authentication documentation for openEO Platform for more information.

# Creating a (user-defined) process

Now that we know how to discover the back-end and how to authenticate, lets continue by creating a new batch job to process some data.

First we need to create a process builder object that carries all the available predefined openEO processes of the connected back-end as attached R functions with the parameters stated in the process metadata.

p = processes()

The functions of the builder return process nodes, which represent a particular result in the workflow. As one of the first steps we need to select the source data collection.

datacube = p$load_collection(
  id = "SENTINEL1_GRD",
  spatial_extent=list(west = 16.06, south = 48.06, east = 16.65, north = 48.35),
  temporal_extent=c("2017-03-01", "2017-04-01"),
  bands=c("VV", "VH")
)

This results in a process node that represents a datacube (opens new window) and contains the "SENTINEL1_GRD" data restricted to the given spatial extent, the given temporal extent and the given bands .

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You can also filter the datacube at a later stage by using the following filter methods:

datacube = p$load_collection(id = "SENTINEL1_GRD")
datacube = p$filter_bbox(data = datacube, extent=list(west=16.06, south=48.06, east=16.65, north=48.35))
datacube = p$filter_temporal(data=datacube,extent=c("2017-03-01","2017-04-01"))
datacube = p$filter_bands(data = datacube, bands=c("VV", "VH"))

Still, it is recommended to always use the filters in load_collection to avoid loading too much data upfront.

Having the input data ready, we want to apply a process on the datacube. Therefore, we can call the process directly on the datacube object, which then returns a datacube with the process applied.

min_reducer = function(data,context) { 
  return(p$min(data = data))
}

reduced = p$reduce_dimension(data = datacube, reducer = min_reducer, dimension="t")

The datacube is now reduced by the time dimension named t, by taking the minimum value of the timeseries values. Now the datacube has no time dimension left. Other so called "reducer" processes exist, e.g. for computing maximum and mean values.

Note

Everything applied to the datacube at this point is neither executed locally on your machine nor executed on the back-end. It just defines the input data and process chain the back-end needs to apply when it sends the datacube to the back-end and executes it there. How this can be done is the topic of the next chapter.

After applying all processes you want to execute, we need to tell the back-end to export the datacube, for example as GeoTiff:

formats = list_file_formats()

result = p$save_result(data = reduced, format = formats$output$GTIFF)

The first line retrieves the back-ends offered input and output formats. The second line creates the result node, which stores the data as a zipped GeoTiff.

# Batch Job Management

After you have finished working on your (user-defined) process, we can now send it to the back-end and start the execution. In openEO, an execution of a (user-defined) process is called a (batch) job (opens new window). Therefore, we need to create a job at the back-end using our datacube, giving it the title Example Title.

job = create_job(graph=result, title = "Example Title")

The create_job method sends all necessary information to the back-end and creates a new job, which gets returned. After this, the job is just created, but has not started the execution at the back-end yet. It needs to be queued for processing explicitly:

start_job(job = job)

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It can be annoying to manage and monitor batch jobs via code. If you want to use an interface for your batch jobs (or other resources) that is easier to use, you can also open the openEO Platform Editor (opens new window). After login, you'll be able to manage and monitor your batch jobs in a near-realtime interactive environment; Look out for the "Data Processing" tab.

After the job was executed, status updates can be fetched by using the list_jobs() function. This function returns a list of job descriptions, which can be indexed with the jobs ID to limit the search results. But remember that only list_jobs() refreshes this list. So, to monitor a job you have to iteratively call the job (describe_job()) or the job list list_jobs().

jobs = list_jobs()
jobs # printed as a tibble or data.frame, but the object is a list

# or use the job id (in this example 'cZ2ND0Z5nhBFNQFq') as index to get a particular job overview
jobs$cZ2ND0Z5nhBFNQFq

# alternatively request detailed information about the job
describe_job(job = job)

When the job is finished, calling download_results() will download the results of a job. Using list_results() will return an overview about the created files and their download link or it states the error message, in case of an error.

# list the processed results
list_results(job = job)

# download all the files into a folder on the file system
download_results(job = job, folder = "/some/folder/on/filesystem")

Note

The printing behavior and the actual data structure might differ!

# Additional Information

Last Updated: 11/24/2021, 4:49:05 PM