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In lbusett/MODIStsp: Find, Download and Process MODIS Land Products Data

MODIStsp 2.1.0

Major changes

• Major product update: remove decommissioned products v6 (thanks @pkautio).
• Changing default version from 006 to 061.

Minor changes

• Remove explicit {rgdal} dependency (https://r-spatial.org/r/2022/12/14/evolution2.html).
• Remove suggested dependency {geojsonlint}.
• Change maintainer's email in order to follow CRAN requirements.

MODIStsp 2.0.10

Minor changes

• Remove explicit {rgdal} dependency (https://r-spatial.org/r/2022/12/14/evolution2.html).
• Remove suggested dependency {geojsonlint}.
• Change maintainer's email in order to follow CRAN requirements.

MODIStsp 2.0.9

Minor changes

• Revise the authenticate type to "any" (default is "basic") to reflect changes on USGS authentication after the maintenance of the U.S. GOVERNMENT COMPUTER.

Bug fixes

• Remove useshinyalert() to avoid warnings.

MODIStsp 2.0.8

Minor changes

• Reducing package size
• State that GDAL with support for HDF4 format is needed (in vignette and package description), and exit gracefully if HDF4 is not supported.

MODIStsp 2.0.7

Minor changes

• Add product version 061 for existing products (#238)
• Closing the support on GitHub issues, due to career change of the maintainer.

Bug fixes

• Fix #245

MODIStsp 2.0.6

Minor changes

• Replace M*D17A3H with M*D17A3HGF and add M*D17A2HGF (#237)
• Avoid errors in case of missing internet connection

Bug fixes

• Patch for bbox loaded from json in case of drawn extent (#228)
• Fix #226
• Fix #232
• Fix #234
• Fix CRAN notes

MODIStsp 2.0.5

Main changes

• Edit documentation related to the change of maintainer (see https://docs.ropensci.org/MODIStsp/articles/lorenzo).

• Add the argument parallel to function MODIStsp() and MODSIStsp_process() to allow running the processing in single core modality.

Minor changes

• Fix Travis tests

• Bug fix (#222)

MODIStsp 2.0.3

Main changes

• This submission should fix errors on Debian CRAN builds, due to improper trigger of an internal function leading to writing in the user's lib folder.

• Fixes a bug leading to crash when using scale_val = TRUE and change_no_data = FALSE

• Fixes a bug leading to the GUI crashing rather than giving info messages in case not all input parameters are specified

• Implements redirection to MODIS products web pages when pressing the corresponding button

• Modifies slightly the Shiny GUI

MODIStsp 2.0.0

Main changes

• Replace the old gWidgets-based GUI with a new one based on Shiny;

• Enhances support for CLI usage. Now all parameters can be passed to the MODIStsp function. If also a opts_file is passed, values specified explicitly in the call override those in the options file;

• Fixes problems in retrieval of corners for MODIS products in 4008 projection (fixes #204);

• Fixes problems/improves support for datasets with multiple NoData values. Now, all NoData values are kept to original values if NoData change is set to FALSE. Also, Scale/Offset are no longer wrongly applied also to NoData values when scaleval = TRUE;

MODIStsp 1.4.0

Main changes

• switch to use of GDAL3/PROJ6 WKTs for projection representation, using sf::gdal_utils to perform gdalwarp/gdaltranslate instead of gdalUtils on external GDAL.

• switch to sf for all internal work on vector data.

• Remove sp, rgdal, rgeos, pacman, gdalUtils dependencies

• Adds support for products MCD19A1 and MCD19A2 products

MODIStsp 1.3.9

Main changes

• 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.

• Updates web links to MODIS products description pages

MODIStsp 1.3.8

Main changes

• Fixed an issue causing incorrect application of scale/offset values on GDAL versions > 2.3 (introduced by change of behaviour of gdal_buildvrt - https://trac.osgeo.org/gdal/ticket/3221#comment:5) - see https://github.com/ropensci/MODIStsp/issues/163

• Added support for the following products: MOD21A1D.006 MOD21A1N.006 MOD21A2.006/

Bug fixing

• Fixed an issue preventing correct processing of some products in offline mode ( https://github.com/ropensci/MODIStsp/issues/142)

MODIStsp 1.3.7

Main changes

• Fixed a bug leading to incorrect computation of custom spectral indices containing "additive" parameters (e.g., (NIR+0.1)/(Red-0.2)) when scale_val == FALSE

Bug fixing

• Fixed a bug leading to not properly reassigning NoData values when processing full tiles and using change_nodata = TRUE

• Fixed inconsistencies in definition of characteristics of products MOD/MYD13C2/C1 and MOD/MYD13A3 (erroneous layers in xml)

• Fixed a bug leading to help messages in the select layers portion of the GUI to not render

• Updated MOD44B specifications to allow download of v006 version

MODIStsp 1.3.6

Main changes

Maintenance release to solve CRAN build errors on debian, due to the test_resetindexes test. The test is now skipped on CRAN. Additionally, the MODIStsp_addindex function was modified to require explicit permission by the user to write on the MODIStsp_previous.json file

Bug fixing

• Fixed a bug leading to errors if only "Aqua" platform was selected for download #133

MODIStsp 1.3.5

Main changes

Maintenance release to solve CRAN build errors on debian, due to the test_addindex test. The test is now skipped on CRAN. Additionally, the MODIStsp_addindex function was modified to require explicit permission by the user to write on the MODIStsp_previous.json file

Bug fixing

• Fixed bug leading to errors in processing extent when switching products with different Native projection (4008 vs sinusoidal), the projection string was not properly updated. 77f5693e9

• Fixed warnings on check for uniqueness in http addresses

MODIStsp 1.3.4

Main changes

Breaking changes

• Due to improvements and changes in the GUI (see below), MODIStsp .json options files saved with older versions are no longer supported. Users will be informed of this if trying to use an obsolete json file.

• Removed support for FTP download due to switch-off of NASA servers.

Updates in supported products

• Removed all v005 and earlier products, due to discontinuation of their distribution by NASA servers

• Added support for the following products:

MCD64A1; MCD12C1; MCD18A1; MCD18A2; MCD12Q1; MOD44B; MOD44W; MCD12C1; MCD12Q1; MOD12A2; MOD12A3

Improvements in download functions

• Improvements in GUI. It is now possible to set the processing extent interactively using the "Select on Map" button. This opens a browser window allowing to select and extent.

• Use of httr::RETRY to improve behavior while navigating the servers to retrieve available files and while downloading hdf file (when use_aria == FALSE), thus removing dependency to RCurl.

Improvements in processing functions

• Improved functionality for dealing with NoData for products with multiple fill-values. If "Change NoData" is set to "Yes", then in case a layer has multiple Nodata values all those values are set to NA in the output (see github.com/ropensci/MODIStsp#113)

Extensive code refactoring for submission to ropensci.

• Long functions were simplified/split into smaller functions to allow for easier maintenance
• GUI event handlers were moved into dedicated "R" files
• Extensive code linting to abide to ropensci standards
• Switch to jsonlite/xml2 to abide to ropensci standards
• Removal of some less-used dependencies (e.g., hash)

Improvements in documentation and website

• More detailed documentation for the main functions
• Improvements in pkgdown articles to include some "worked examples" (e.g., MODIStsp_Extract)
• New article in pkgdown showing a list of supported products

Improvements in test coverage

• Several new tests added, bringing coverage above 90%

New functions

• Added MODIStsp_resetindexes to remove all custom indexes from a MODIStsp json options file and MODIStsp_reset_options to reset MODIStsp options to default.

Bug fixing

• Fixed bug affecting extent selection when working with non-tiled (MCD) products https://github.com/ropensci/MODIStsp/issues/122

• Fixed bugs affecting the "Seasonal" time series download

MODIStsp 1.3.3.1 Release Notes

This was mostly a maintenance release - fixing a bug in 1.3.3 submission related to a missing import in NAMESPACE

Minor Changes

Improved organization of Virtual Raster files and RData files in the "Time_Series" output subfolder. Now virtual files and RData files are organized by sensor and layer to facilitate access.

MODIStsp 1.3.3 Release Notes

v1.3.3 was released on 10/08/2017

Major Changes

• Improved speed in computation of spectral indexes, quality indicators and in computation of scaled variables by using raster::calc() and raster::overlay (commits 0f5d76d, 0f5d76d, e462721)

• Added functionality for unit testing using testthat and codecov integration. (commit 0c00fc6 and others)

• Added "testing mode" to allow users to test proper functioning. Now, running MODIStsp(test = X) (with X in (0,6)) runs the processing using default processing parameters (commit 0c00fc6 and others)

Minor Changes

• Suppression of verbose messages and (useless) warning messages while parsing the NASA servers and downloading data using "ftp" ( 3775d60);

Bug fixing

• Fixed a bug preventing the "last" choice (or that present in the json file) from correctly showing in the GUI upon launch/restore of a saved json file (commit 633c2dd)

• Fixed a bug affecting MODIS layers coded as Unsigned Integer - 32 bit (Thanks to Rob Critchlow for signaling this). The bug was due to improper handling of UInt32 data in gdalbuildvrt, causing sometimes an incorrect translation from HDF to output formats (#72).

  M*D09A1 - 500m Reflectance Band Quality (V005 and V006); M*DO9CMG - Coarse Resolution QA (V005 and V006); M*D09CMG - Coarse Resolution Number Mapping (V006); M*D09GA - 500m Reflectance Band Quality (V005 and V006); M*DOCGA - Band quality for MODIS bands 8-15 (V006); M*D11C3 - Days with clear-sky conditions and validated LSTs; Nights with clear-sky conditions and validated LSTs (V005 and V006); MCD43A2 - BRDF_Albedo_Band_Quality (V005 and V006).

• Fixed a bug affecting creation of time series files (RData and virtual rasters) on all MCD products (#77)

• Fixed a bug a error on creation of "burn_date" layers for MCD45A1 product (#77)

• Fixed bugs on specifying spatial extent files on non-interactive execution (#75)

17/04/2017 - MODIStsp is now on CRAN !

MODIStsp was recently accepted on CRAN. From now on, you can install it simply using

install.packages("MODIStsp")

You'll however still be able to install the development version from github, containing the last improvements and bug fixing using:

install_github("ropensci/MODIStsp", ref = "master")

MODIStsp 1.3.2 Release Notes

v1.3.2 was released on 22/03/2017

Major Changes:

• Added functionality to apply scale and offset coefficients on MODIS original values according with the specifications of single MODIS products.

Details:

• MODIS hdf datasets are always stored as integer values, with scales factor and/or offsets to apply in order to convert to the indicated measure units reported in the products' documentation.

• Starting from v1.3.2:

  • Leaving the "Scale output values" option to "No", output files are left as provided by NASA, and additional indices are produced as integer values with a 10000 factor scale;
  • Setting the "Scale output values" option to "Yes", scale factor and offsets are applied if existing (for example, in this case Land Surface Temperature values in the output raster will be in °K), and spectral indices are floating point values (for example, NDVI is between -1 and 1, etc.).

Minor Changes:

• Some product names and output layer names were modified to reduce the length of output file names, homogenize the names of the outputs and correct some errors. For compatibility with already created output files (versions up to 1.3.1), the old "XML" file specifying output files format is still available in inst/ExtData/MODIStsp_ProdOpts_old_v1.3.1.xml. To use the old file naming conventions, users have to:

  1. delete inst/ExtData/MODIStsp_ProdOpts.xml and rename MODIStsp_ProdOpts_old_v1.3.1.xml to MODIStsp_ProdOpts.xml.
  2. delete MODIStsp_ProdOpts.RData from the Previous folder within your_R-library_path/MODIStsp/Previous
  3. Restart MODIStsp

• Timeouts of httr/ftp requests were increased to prevent problems on download on slow connections

Bug fixing:

• Fixed bug on FTP download speed (Issue #65)
• Fixed bug on download of tile 0, preventing download of images with DOY 001 and of all "yearly based" products (e.g., MOD17)(Issue #64)
• Fixed other bugs affecting FTP download (https://github.com/ropensci/MODIStsp/commit/efbf1b469e7518ffc8a7ec6d9922242d6a5c228f, https://github.com/ropensci/MODIStsp/commit/1dc53a5ff5b355965acec86678a3104bd2d27fd9, https://github.com/ropensci/MODIStsp/commit/fa6c7b42eadce516a2f781604c9db28418120f36)

MODIStsp 1.3.1 Release Notes

v1.3.1 was released on 13/02/2017

Major Changes

• Added functionality for processing of Snow Cover datasets: MOD10A1, MOD10A2, MOD10C1, MOD10C2, MOD10CM (Issue #55) on devel

• Added functionality for downloading "partial" years (Issue #54) on devel

• Added functionality for computing vegetation indexes on MCD43A4 (v5-v6), MCD43B4 (v5), MCD43C4 (v5-v6) (Issue #59) on master/devel

• Added functionality for accelerating download using aria2c (Issue #55) on devel

Bug fixing

• Fixed bug on download with aria, throwing an error on partial download on http download with aria (6fbc875)

• Fixed bug on M*D15A2 processing (Issue #60) on devel/master

• Fixed bug on MCD12Q1 processing (Issue #58) on devel/master

• Fixed bug on MOD13C2 processing (Issue #52) on devel/master

• Fixed bug on insertion of custom projection (Issue #57) on devel/master

• Fixed bug on selection of custom index (Issue #53) on devel/master

MODIStsp 1.3.0 Release Notes

v1.3.0 was released on 11/05/2016

Major Changes

• Added functionality for downloading and preprocessing MODIS collection 006 datasets. For products with both 005 and 006 collections, the user can select the version using a new droplist in the GUI.

• Added functionality for off-line processing. This allows both to i) reprocessing already downloaded data (for example, to create time series for an additional layer) without the need to connect to NASA servers, and ii) process HDF files downloaded outside MODIStsp (e.g., directly from NASA ftp) and stored on the user's PC, without the need of an active internet connection.

• Improved the way in which options are saved. Much more readable. JSON files are now used instead than .RData. User options are no longer saved alongside products characteristics. This will allow to re-use an "old" options file even if changes are made on the XML file describing the products.

• Improved the GUI interface for specifying additional Spectral Indexes. Hints are now showed to the user, and multiple indexes can be added in the same session.

Minor Changes

• General improvements in the GUI interface. Products are now grouped by categories, to allow easier identification and selection.

• Improvements in the README file and vignettes, providing more instructions on package use.

• Improved functionality for checking for "complete" download, by comparing the size of the downloaded files with that of files on the server.

• Added "configure" file for Linux installation.

• Temporary files necessary for processing (e.g., vrt files) are now created (and destroyed) within the "R" temporary folder.

• Miscellaneous bug-fixing

MODIStsp 1.2.1 Release Notes

v1.2.1 was released on 11/05/2016

Major Changes

1. Modified format of "R" output time series from rts objects to RasterStack objects with temporal information added in the "z" attribute via setZ()

2. Major changes/improvements in MODIStsp_extract function:

   • Use of plain RasterStack with "z" attribute instead than rasterstackts
   • Use of gdal_rasterize (gdalUtils) instead of rasterize (rgdal) to improve speed. Temporary shapes and rasters necessary are saved in "R" temporary folder and removed automatically
   • Fixed bugs on functionality for point/lines shapefiles, according to what specified by the "small" and "small_method" parameters
   • Added functionality for retrieving data for small polygons
   • Added out_format selection - xts or plain data.frame
   • Added possibility to use a shp filename as input directly
   • Added conformity checks on inputs
   • Added functionality to run without specifying start and end dates
   • Added id_field parameter for choosing which column of the input SP object should be used for "naming" the columns of the output

3. Removed possibility to use "complex" resampling methods when reprojecting (e.g., bilinear, cubic, etc.) to avoid incorrect resampling on categorical variables and "contamination" of good pixels data.

Minor Changes

• Changed the input method for starting and ending dates selection in the GUI. Now a text field is used
• Added functionality for writing data ignore value on ENVI files
• Removed automatic deletion of XML files created by writeRaster to keep metadata information
• Changed names of products in the GUI for products with both TERRA and AQUA dataset to M*D09A1, M*D13Q1, etc...
• Modified code syntax to satisfy R code styling guidelines
• Modified roxygen parameters so that only required functions are imported from dependent packages
• Updated and corrected the list of dependencies
• Updated required "R" version to 3.2, and minimum versions for dependent packages to current versions.
• Added Welcome message
• Updated links to LPDAAC product description pages
• Changed all "print" and "cat" calls to show messages/warnings to "message" or "warning" to allow easy disabling MODIStsp verbose messages
• Using "R" tempfile/tempdir to save vrt files

Bug Fixes

• Corrected a bug that threw an error in case incorrect bounding box specified

MODIStsp 1.2.0 Release Notes

v1.2.0 was released on 29/07/2015

Major changes

First stable release of advanced implementation of MODIStsp ! We know it should be 1.0.0, but that's it !

lbusett/MODIStsp documentation built on Oct. 16, 2023, 6:59 a.m.