RasterTools

RasterTools is a set of small Java programs to conduct common tasks in preparing data for species distribution modeling. The programs need to be run from the command-line, using a command like java -jar nameOfProgram.jar. When run like this, the program will print out the flags that can be used to specify input files and control the program.

The applymask.jar program applies a landmask to an environmental raster. We have used this to homogenize the landmask between rasters in Bio-ORACLE. It adds no-data-values where data is available in pixels that are not supposed to have data and interpolates from surrounding pixels if a pixel that is supposed to have data doesn't have data.

The extractDataForCoordinates.jar program extracts data from a set of rasters in a folder for a file with species occurrence records (geographic coordinates). We use this to generate SWD files for Maxent runs.

The moveCoordinatesToClosestDataPixel.jar program reads a set of occurrence records. For every record that is situated in a no-data-pixel, the record is moved to the closest pixel that has data. The new coordinates are provided in csv format suitable for Maxent runs.

Downloads

applymask.jar v.1.01 download jar file
extractDataForCoordinates.jar v.1.04 download jar file
moveCoordinatesToClosestDataPixel.jar v.1.04 download jar file

Citation

If you find these tools useful, please cite them in your work. I recommend citing them as follows:
Verbruggen H. (2017) RasterTools: moveCoordinatesToClosestDataPixel.jar version 1.04. http://www.phycoweb.net/software
(or similar citation for the other scripts).

Notes and disclaimer

The RasterTools are in development and have not been tested extensively. It is quite plausible that incorrectly formatted input could lead to nonsensical output.

The RasterTools are provided "as is" without warranty of any kind, either expressed or implied. The entire risk as to the quality and performance of the programs is with you. Should the programs prove defective, you assume the cost of all necessary servicing, repair or correction. The author will not be liable to you for damages, including any general, special, incidental or consequential damages arising out of the use or inability to use the programs (including but not limited to loss of data or data being rendered inaccurate or losses sustained by you or third parties or a failure of the program to operate with any other programs).