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Repository Details

An "R" package for automatic download and preprocessing of MODIS Land Products Time Series

MODIStsp

DOI Coverage Status

{MODIStsp} is a R package devoted to automatizing the creation of time series of rasters derived from MODIS Land Products data. {MODIStsp} allows performing several preprocessing steps (e.g., download, mosaicing, reprojection and resize) on MODIS data available within a given time period. Users have the ability to select which specific layers of the original MODIS HDF files they want to process. They also can select which additional Quality Indicators should be extracted from the aggregated MODIS Quality Assurance layers and, in the case of Surface Reflectance products, which Spectral Indexes should be computed from the original reflectance bands. For each output layer, outputs are saved as single-band raster files corresponding to each available acquisition date. Virtual files allowing access to the entire time series as a single file can be also created. All processing parameters can be easily selected with a user-friendly GUI, although non-interactive execution exploiting a previously created Options File is possible. Stand-alone execution outside an โ€œRโ€ environment is also possible, allowing to use scheduled execution of MODIStsp to automatically update time series related to a MODIS product and extent whenever a new image is available.

{MODIStsp} was developed by Lorenzo Busetto and Luigi Ranghetti, Institute of Remote Sensing of Environment - National Research Council - Italy (CNR-IREA). It is dedicated to the memory of Lorenzo.

Citation

To cite {MODIStsp} please use:

L. Busetto, L. Ranghetti (2016) MODIStsp: An R package for automatic preprocessing of MODIS Land Products time series, Computers & Geosciences, Volume 97, Pages 40-48, ISSN 0098-3004, https://doi.org/10.1016/j.cageo.2016.08.020, URL: https://github.com/ropensci/MODIStsp.

Website

For more information, documentation and examples of use, see also the {MODIStsp} website at docs.ropensci.org/MODIStsp.

Important News

  • 29/10/2021 - {MODIStsp} (GitHub version 2.0.6.9000) supports products with version 061. Version 006 will remain the default product version until its decommission will be announced. Version 061 can be specified through the argument prod_version of function MODIStsp() or by selecting it in the GUI.

  • 10/12/2020 - {MODIStsp} was resubmitted to CRAN after the maintainerโ€™s death. Now {MODIStsp} is dedicated to Lorenzo Busetto (https://docs.ropensci.org/MODIStsp/articles/lorenzo).

  • 01/09/2020 - {MODIStsp} 2.0.0 is out. Provides a new GUI interface based on Shiny, getting rid of the archived dependencies on gWidgets/gWidgetsRGtk2. Also provides much easier usage from the CLI, by allowing to set all processing arguments also from the CLI. Note: due to the introduced changes, options files created with previous versions of {MODIStsp} will no longer work. Also, processing scripts using {MODIStsp} may need to be slightly adapted.

  • 09/05/2020 - {MODIStsp} 1.4.0 is out. Switches to use of GDAL3/PROJ6 WKTs for projection representation and usage of {sf} for all internal work on vector data. Adds support for products MCD19A1 and MCD19A2 products.

  • 07/06/2019 - {MODIStsp} 1.3.9 is out. Fixes a bug causing crashes on MOD14A1 product, adds support for product MCD12Q2 and removes support for no longer available version 5 of some products.

  • 05/03/2019 - {MODIStsp} 1.3.8 is out. Fixes an issue causing incorrect application of scale/offset values on GDAL versions > 2.3 (#163) and adds support for products MOD21A1D.006, MOD21A1N.006 and MOD21A2.006.

  • 29/11/2018 - We recently discovered a nasty bug in the computation of some custom spectral indices (those including additions / subtractions on reflectance values, such as in (b1_NIR+0.1) / b2_Red. See here for further details. The bug is fixed as of version 1.3.7.

  • 07/08/2018 - We are glad to report that {MODIStsp} is now included in the rOpenSci packages ecosystem. We thank reviewers Leah Wasser and Jeffrey Hanson for their valuable reviews, which helped us to further improve the package.

  • 10/07/2018 - {MODIStsp} v. 1.3.6 is out (check out the Release Notes for further details).

  • 20/06/2018 - {MODIStsp} v. 1.3.5 is out (check out the Release Notes for further details).

  • 11/04/2018 - Due to new NASA Policies the MODIS FTP servers were shut down starting, April 2, 2018. FTP download is therefore no longer working and will be removed in the next MODIStsp version.

  • 11/04/2018 - Decommissioning of MODIS Version 5 Land Data Products. As per NASA notice above, MODIS v005 products are going to be decommissioned, and will soon be no longer available for download. Support for those products will be removed in the next MODIStsp version.

  • 11/08/2017 - {MODIStsp} 1.3.3 was released today. It provides improvements in processing speed, as well as the usual bug fixes (thanks to all the users that signaled problems). Check the Release Notes for further details.

  • 25/07/2017 - As of today, **most of the content related to {MODIStsp} has been moved to our new website at docs.ropensci.org/MODIStsp **, which provides a much better user interface and ease of access to MODIStsp-related information. From now on, please consult the new website for detailed and updated information on the package.

  • Also our previous FAQ page on GitHub containing info for solving common installation, downloading and processing problems and issues was discontinued and migrated at docs.ropensci.org/MODIStsp/articles/faq.html.

Problems and Issues

System Requirements

{MODIStsp} requires R v >= 3.6.3.


Installation Instructions

Installing on Windows

You can install the stable version of {MODIStsp} from CRAN:

install.packages("MODIStsp")

, or the development version (containing the latest improvements and bug fixes) from GitHub:

install.packages("remotes")
library(remotes)
install_github("ropensci/MODIStsp")

Installing on Linux Systems

To install {MODIStsp} on Linux, you need to be able to install the {sf} package, which requires several dependencies. See here if you have trouble installing {sf}.

Then, you can install the stable version of MODIStsp from CRAN:

install.packages("MODIStsp")

, or the development version (containing the latest improvements and bug fixes) from GitHub:

library(devtools)
install_github("ropensci/MODIStsp")

Installing on Mac

To install {MODIStsp} on Mac, you need to be able to install the {sf} package, which requires several dependencies. See here if you have trouble installing {sf}.

Then, you can install the stable version of {MODIStsp} from CRAN:

install.packages("MODIStsp")

, or the development version (containing the latest improvements and bug fixes) from GitHub:

library(devtools)
install_github("ropensci/MODIStsp")

Usage

The easiest way to use {MODIStsp} is to use its powerful GUI (Graphical User Interface) for selection of processing options, and then run the processing.

To open the GUI, load the package and launch the MODIStsp function, with no parameters:

library(MODIStsp)
MODIStsp()

This opens a Shiny GUI from which processing options can be specified (and eventually saved or loaded). After specifying all required parameters, clicking on โ€œStartโ€ will start the processing (see here for more detailed instructions).

{MODIStsp} can also be launched in non-interactive mode within an R session or script by setting the optional GUI parameter to FALSE, and the opts_file parameter to the path of a previously saved JSON Options file. This allows to exploit {MODIStsp} functionalities within generic โ€œRโ€ processing scripts.

library(MODIStsp) 
# --> Specify the path to a valid options file saved in advance from MODIStsp GUI 
opts_file <- "X:/yourpath/youroptions.json" 
  
# --> Launch the processing
MODIStsp(gui = FALSE, opts_file = opts_file)

Finally, {MODIStsp} can be run by manually specifying all processing arguments, or by overwriting some of the arguments contained in a saved json file in the call to the package, such as in:

library(MODIStsp) 
# --> Specify the path to a valid options file saved in advance from MODIStsp GUI 
opts_file <- "X:/yourpath/youroptions.json" 
  
# --> Launch the processing
MODIStsp(gui        = FALSE, 
         opts_file  = opts_file, 
         start_date = "2020.05.01", 
         end_date   = "2020.08.01", 
         spatmeth   = "file", 
         spafile    = "X:/path_to/spatial_extent_file.gpkg")

, where we are overwriting the options related to spatial and temporal extent contained in the options file with new values. This allows easily running processing based on the same main options (e.g., product layers, output format, etc.) but changing on the fly the desired ones.

See here for more detailed instructions and examples.

Code of Conduct

Please note that this package is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.

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