SITS - Satellite Image Time Series Analysis for Earth Observation Data Cubes

Overview

The sits R package provides a set of tools for analysis, visualization and classification of satellite image time series. The main aim of SITS is to support land cover and land change classification of image data cubes using machine learning methods. The basic workflow in SITS is:

1. Create a data cube using image collections available in the cloud or in local machines.
2. Extract time series from the data cube which are used as training data.
3. Perform quality control and filtering on the samples.
4. Train a machine learning model using the extracted samples.
5. Classify the data cube using the trained model.
6. Post-process the classified images.

Installation

Pre-Requisites

The sits package relies on sf and rgdal, which in turn, require the installation of the GDAL and PROJ libraries. Please follow the instructions for installing sf and rgdal available at the RSpatial sf github repository.

Obtaining SITS

SITS is currently available on github, as follows:

# Please install the `sits` package from github
devtools::install_github("e-sensing/sits")
library(sits)

AMI Image

For users that have an AWS account, we have prepared a set of AMI (Amazon Machine Images that are optimized for running SITS in the Amazon Elastic Compute Cloud (or EC2). The AMI has the following settings: SITS 0.9.6, Ubuntu 18.04, R 4.0.2, and Rstudio Server 1.3.959. All packages have been updated as of 21 August 2020. The AMI is avaliable for the following regions:

• South America (sa-east-1)
• Frankfurt(eu-central-1)
• US East (us-east-1)
• Asia Pacific Singapore(ap-southeast-1)

When you create an EC2 instance based on this AMI, ensure that your ‘security group’ settings allow incoming HTTP (port 80), HTTPS (port 443) and SSH (port 20) traffic. After the EC2 instance is started, then copy-and-paste the ‘IPv4 Public IP’ address for your running instance to a web browser address bar. That should bring the RStudio server interface in your browser. Use “rstudio” as username and “e-sensing” as password.

Data Cubes

SITS has been designed to work with big satellite image data sets organised as data cubes. Data cubes can be available in the cloud or in a local machine. Currently, SITS supports data cubes available in the following cloud services:

1. Sentinel-2/2A level 2A images in AWS.
2. Collections of Sentinel, Landsat and CBERS images in the Brazil Data Cube (BDC).
3. Collections available in Digital Earth Africa.
4. Data cubes produced by the “gdalcubes” package.
5. Local image collections organized as RasterStacks of RasterBricks.

SITS relies on STAC services provided by these cloud services. The user can define a data cube by selecting a collection in a cloud service and then defining a space-time extent. For example, the following code will define a data cube of Sentinel-2/2A images using AWS.

s2_cube <- sits_cube(
    type = "S2_L2A_AWS",
    name = "T20LKP_2018_2019",
    satellite = "SENTINEL-2",
    sensor = "MSI",
    tiles = "20LKP",
    s2_aws_resolution = "20m",
    start_date = as.Date("2018-07-18"),
    end_date = as.Date("2018-07-23")
)

In the above example, the user has selected the “Sentinel-2 Level 2” collection in the AWS cloud services. The geographical area of the data cube is defined by the tile “20LKP”, and the temporal extent by a start and end date. Access to other cloud services works in similar ways.

Users can derive data cubes from ARD data which have pre-defined temporal resolutions. For example, a user may want to define the best Sentinel-2 pixel in a one month period, as shown below. This can be done in SITS using the “gdalcubes” package. For details in gdalcubes, please see https://github.com/appelmar/gdalcubes.

gc_cube <- sits_cube(type        = "GDALCUBES",
                     name        = "T20LKP_2018_2019_1M",
                     cube        = s2_cube,
                     path_db     = "/my/path/cube.db",
                     path_images = "/my/path/images/",
                     period      = "P1M",
                     agg_method  = "median",
                     resampling  = "bilinear")

Data Access - Individual time series

SITS has been designed to use satellite image time series to derive machine learning models. After the data cube has been created, time series can be retreived individually or by using CSV or SHP files, as in the following example.

library(sits)
#> SITS - satellite image time series analysis.
#> Loaded sits v0.10.0.
#>         See ?sits for help, citation("sits") for use in publication.
#>         See demo(package = "sits") for examples.
#> Using configuration file: /Users/gilbertocamara/Library/R/4.0/library/sits/extdata/config.yml
#> Users can provide additional configurations in ~/.sits/config.yml
# create a cube from a local file 
file <- c(system.file("extdata/raster/mod13q1/sinop-ndvi-2014.tif",
                      package = "sits"
))
raster_cube <- sits_cube(
  type = "BRICK",
  name = "Sinop-crop",
  satellite = "TERRA",
  sensor = "MODIS",
  timeline = sits::timeline_2013_2014,
  bands = c("ndvi"),
  files = file
)
# obtain a set of locations defined by a CSV file
csv_raster_file <- system.file("extdata/samples/samples_sinop_crop.csv",
                               package = "sits"
)
# retrieve the points from the data cube
points <- sits_get_data(raster_cube, file = csv_raster_file)
#> All points have been retrieved
# show the points
points
#> # A tibble: 12 x 7
#>    longitude latitude start_date end_date   label    cube       time_series     
#>        <dbl>    <dbl> <date>     <date>     <chr>    <chr>      <list>          
#>  1     -55.7    -11.8 2013-09-14 2014-08-29 Pasture  Sinop-crop <tibble [23 × 2…
#>  2     -55.6    -11.8 2013-09-14 2014-08-29 Pasture  Sinop-crop <tibble [23 × 2…
#>  3     -55.7    -11.8 2013-09-14 2014-08-29 Forest   Sinop-crop <tibble [23 × 2…
#>  4     -55.6    -11.8 2013-09-14 2014-08-29 Pasture  Sinop-crop <tibble [23 × 2…
#>  5     -55.7    -11.8 2013-09-14 2014-08-29 Forest   Sinop-crop <tibble [23 × 2…
#>  6     -55.6    -11.7 2013-09-14 2014-08-29 Forest   Sinop-crop <tibble [23 × 2…
#>  7     -55.7    -11.7 2013-09-14 2014-08-29 Soy_Corn Sinop-crop <tibble [23 × 2…
#>  8     -55.7    -11.7 2013-09-14 2014-08-29 Soy_Corn Sinop-crop <tibble [23 × 2…
#>  9     -55.7    -11.7 2013-09-14 2014-08-29 Soy_Corn Sinop-crop <tibble [23 × 2…
#> 10     -55.6    -11.8 2013-09-14 2014-08-29 Soy_Corn Sinop-crop <tibble [23 × 2…
#> 11     -55.6    -11.8 2013-09-14 2014-08-29 Soy_Corn Sinop-crop <tibble [23 × 2…
#> 12     -55.6    -11.8 2013-09-14 2014-08-29 Soy_Corn Sinop-crop <tibble [23 × 2…

After a time series is imported, it is loaded in a tibble. The first six columns contain the metadata: spatial and temporal location, label assigned to the sample, and coverage from where the data has been extracted. The spatial location is given in longitude and latitude coordinates. The first sample has been labelled “Pasture”, at location (-55.65931, -11.76267), and is considered valid for the period (2013-09-14, 2014-08-29). To display the time series, use the plot() function.

plot(points[1,])

For a large number of samples, where the amount of individual plots would be substantial, the default visualisation combines all samples together in a single temporal interval.

# select the "ndvi" band
samples_ndvi <- sits_select(samples_mt_4bands, "NDVI")
# select only the samples with the cerrado label
samples_cerrado <- dplyr::filter(samples_ndvi, 
                  label == "Cerrado")
plot(samples_cerrado)

Samples for NDVI band for Cerrado class

Clustering

Clustering methods in SITS improve the quality of the samples and to remove those that might have been wrongly labeled or that have low discriminatory power. Good samples lead to good classification maps. sits provides support for two clustering methods to test sample quality: (a) Agglomerative Hierarchical Clustering (AHC); (b) Self-organizing Maps (SOM). For more details, please see the vignette “Clustering of Satellite Image Time Series with SITS”

Filtering

Satellite image time series are contaminated by atmospheric influence and directional effects. To make the best use of available satellite data archives, methods for satellite image time series analysis need to deal with data sets that are noisy and non-homogeneous. For data filtering, sits supports Savitzky–Golay (sits_sgolay()), Whittaker (sits_whittaker()), envelope (sits_envelope()) and the “cloud filter” (sits_cloud_filter()). As an example, we show how to apply the Whitakker smoother to a 16-year NDVI time series. For more details, please see the vignette “Satellite Image Time Series Filtering with SITS”

# apply Whitaker filter to a time series sample for the NDVI band from 2000 to 2016
# merge with the original data
# plot the original and the modified series
point_whit <- sits_filter(point_ndvi, sits_whittaker(lambda = 10))
point_whit %>% 
  sits_merge(point_ndvi) %>% 
  plot()

Whitaler filter of NDVI time series

Time Series classification using machine learning

SITS provides support for the classification of both individual time series as well as data cubes. The following machine learning methods are available in SITS:

• Linear discriminant analysis (sits_lda)
• Quadratic discriminant analysis (sits_qda)
• Multinomial logit and its variants ‘lasso’ and ‘ridge’ (sits_mlr)
• Support vector machines (sits_svm)
• Random forests (sits_rfor)
• Extreme gradient boosting (sits_xgboost)
• Deep learning (DL) using multi-layer perceptrons (sits_deeplearning)
• DL with 1D convolutional neural networks (sits_FCN)
• DL combining 1D CNN and multi-layer perceptron networks (sits_TempCNN)
• DL using 1D version of ResNet (sits_ResNet)
• DL using a combination of long-short term memory (LSTM) and 1D CNN (sits_LSTM_FCN)

The following example illustrate how to train a dataset and classify an individual time series. First we use the sits_train function with two parameters: the training dataset (described above) and the chosen machine learning model (in this case, a random forest classifier). The trained model is then used to classify a time series from Mato Grosso Brazilian state, using sits_classify. The results can be shown in text format using the function sits_show_prediction or graphically using plot.

# Train a machine learning model for the mato grosso dataset using SVM
samples_mt_2bands <- sits_select(samples_mt_4bands, bands = c("ndvi", "evi"))
svm_model <- sits_train(data = samples_mt_2bands, 
                         ml_method = sits_svm())

# get a point to be classified with four bands
point_mt_2bands <- sits_select(point_mt_6bands, bands = c("ndvi", "evi"))

# filter the point with a Whittaker smoother
point_filtered <- sits_whittaker(point_mt_2bands, lambda = 0.2, bands_suffix = "") 

# Classify using random forest model and plot the result
class.tb <- sits_classify(point_filtered, svm_model)

# plot the results of the prediction
plot(class.tb, bands = c("ndvi", "evi"))

Time series classification using SVM

The following example shows how to classify a data cube organised as a set of raster bricks. First, we need to build a model based on the the same bands as the data cube.

# estimate a model only for bands "ndvi" and "evi"
samples_mt_2bands <- sits_select_bands(samples_mt_4bands, ndvi, evi)
rfor_model <- sits_train(samples_mt_2bands, ml_method = sits_rfor(num_trees = 300))
# Create a data cube from two raster bricks
evi_file <- system.file("extdata/Sinop", "Sinop_evi_2014.tif", package = "inSitu")
ndvi_file <- system.file("extdata/Sinop", "Sinop_ndvi_2014.tif", package = "inSitu")

# Obtain the associated timeline
time_file <- system.file("extdata/Sinop", "timeline_2014.txt", package = "inSitu")
timeline_2013_2014 <- scan(time_file, character(), quiet = TRUE)

# create a raster metadata file based on the information about the files
raster_cube <- sits_cube(type = "BRICK", name = "Sinop", 
                         satellite = "TERRA", sensor = "MODIS",
                         timeline = timeline_2013_2014, 
                         bands = c("ndvi", "evi"), 
                         files = c(ndvi_file, evi_file))
# Classify the raster cube, generating a probability file
probs_cube <- sits_classify(raster_cube, ml_model = rfor_model)

# label the probability file (by default selecting the class with higher probability)
# apply a bayesian smoothing to remove outliers
bayes_cube <- sits_smooth(probs_cube)

# generate thematic map
label_cube <- sits_label_classification(bayes_cube)

# plot the first raster object with a selected color palette
# make a title, define the colors and the labels)
plot(label_cube, time = 1, title = "SINOP-MT - 2013/2014")

Image classified with XGBoost

Additional information

For more information, please see the vignettes

• “SITS: Data analysis and machine learning for data cubes using satellite image time series”

• “Accessing time series information in SITS”

• “Clustering of satellite image time series with SITS”

• “Satellite image time series filtering with SITS”

• “Time series classification using machine learning”

• “Post classification smoothing using Bayesian techniques in SITS”

How to contribute

The SITS project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.