gen_vi 2.1

Generate Vegetation Index (VI) in GTiff Format from Landsat SR Stack

gen_vi(imgFile,outFile,VI,redBand,nirBand,fmaskBand,maskValue,bluBand)  
batch_gen_vi(VI,path,pattern)  
gen_vi.sh VI path pattern
gen_vi_njob.sh VI path pattern njob

About

The R script generates vegetation index (VI) such as NDVI (Normalized Difference Vegetation Index) and EVI (Enhanced Vegetation Index) layer based on Landsat surface reflectance data. The Landsat SR data need to be single stack in ENVI format including an additional cloud masking band. The output of the script is a single band raster in GeoTiff format. The resulting NDVI value is multiplied by 10000.

The batch function allows generating VI images for all existing Landsat images in a specific directory. The function searches the input directory and it's sub-directories for ENVI header file (.hdr) with a specific pattern ('*stack' by default). The newly created NDVI image will be named as the original image file appended with '_ndvi(/evi)', and it will be saved in the same directory as the original image.

The new version 2.1 added support for submitting multiple bash jobs for the VI generating process. Input images will be divided evenly accross all jobs. The number of jobs must be less than the total number of images to be processed. The maximum number of jobs that can be submitted depends on the server that you are working on.

Instruction

For single images, call gen_vi() with correct inputs.

Input Arguments:

• imgFile (String) - path and file name of the image file that the NDVI is generated from.
• outFile (String) - path and file name of the output file (include extension .tif).
• VI (String) - the vegetation index to calculate (support ndvi (default) and evi right now).
• redBand (Integer) - sequence of the red band within the stack (default is 3 for Landsat).
• nirBand (Integer) - sequence of the NIR band within the stack (default is 4 for Landsat).
• fmaskBand (Integer) - sequence of the fmask band within the stack (default is 8).
• maskValue (Vector, Integer) - a set of value to be masked in the fmask band (default is [255 2 3 4]).
• bluBand (Integer) - sequence of the blue band within the stack for EVI calculation (default is 1 for Landsat).

Returns 0 indicates successful completion.

For batch processing, call batch_gen_vi() with correct inputs.

Input Arguments:

• VI (String) - the vegetation index to calculate (supports ndvi (default) and evi right now).
• path (String) - path of where the program seek for Landsat images.
• pattern (String) - pattern based on which the program searches for Landsat images (default is '*stack').
• njob (Vector) - [1]:total number of jobs that was submitted; [2]:current job number that is being executed. ([1,1] means single job processing)

Return 0 indicates successful completion.

For submitting single qsub jobs, submit gen_vi.sh with correct inputs.

Input Arguments:

• VI (String) - the vegetation index to calculate (supports ndvi (default) and evi right now).
• path (String) - path of where the program seek for Landsat images.
• pattern (String) - pattern based on which the program searches for Landsat images (default is '*stack').

For submitting multiple qsub jobs, use gen_vi_njob.sh with correct inputs.

Input Arguments:

• VI (String) - the vegetation index to calculate (supports ndvi (default) and evi right now).
• path (String) - path of where the program seek for Landsat images.
• pattern (String) - pattern based on which the program searches for Landsat images (default is '*stack').
• njob (Integer) - number of jobs to be submitted (must be less than total number of images to be processed).

Example

gen_vi('C:/LND1999123EDC00stack','C:/LND1999123EDC00.ndvi.tif','evi',3,4,8,c(255,2,3,4),1)  
gen_vi('C:/LND1999123EDC00stack','C:/LND1999123EDC00.ndvi.tif','ndvi')

batch_gen_vi('ndvi','C:/','*landsat')  
batch_gen_vi('evi','C:/')  

qsh gen_vi.sh 'ndvi' 'C:/' '*stack'  

gen_vi_njob.sh 'evi' 'C:/' '*stack' 20  

Dependencies:

R (2.15.2 or higher)
sp package (1.0-8 or higher)
raster package (2.1-16 or higher)
rgdal package (0.8-6 or higher)

To run as a shell job:
bash (4.1.2 or higher)
RCurl Package (1.95-4.3 or higher)