FIELDimagePy: A tool to estimate zonal statistics from an image, bounded by one or multiple polygons

Abstract

Vegetation indices have become an indispensable tool in remote sensing-based agricultural research. A recent area of advancement in agricultural remote sensing research is in high-throughput phenotyping, often conducted on a plot by plot basis. FIELDimageR is a tool used extensively in high-throughput phenotyping that estimates zonal statistics of vegetation indices per plot. However, being written in R language, FIELDimageR requires high computing time. As a high-resolution image over a large area means a large number of pixels, FIELDimageR is incapable of using high-resolution orthomosaicked images without reducing image resolution by aggregating digital numbers of several pixels and treating them as one pixel. This research tool implements FIELDimageR in the Python language as FIELDimagePy. FIELDimagePy follows similar workflows as FIELDimageR and generates equivalent results for zonal statistics of vegetation indices per plot. FIELDimagePy is significantly and substantially faster than FIELDimageR. Computing time by FIELDimagePy are three to four times lower than computing times by FIELDimageR, even when using raw images with 16 times denser pixels. Moreover, FIELDimagePy is useful beyond plot by plot research in agriculture and capable of estimating zonal statistics of any raster bounded by any polygons. With slight modifications, FIELDimagePy can be useful for other disciplines of science, such as geophysics, geography, economics, medical sciences, among others. FIELDimagePy can be accessed from the GitHub repository: https://github.com/SumantraChatterjee/FIELDimagePy.