Functions
The CropPhenology package is made up of two functions, PhenoMetrics and MultiPointsPlot.
PhenoMetrics function
The function takes two parameters.
Path parameter which requires the user to enter the file path of the time series of images.
Region Of Interest (ROI) parameter which requires the user to indicate if there is a polygon mask to represent a subset area for which metrics can be calculated. If there is a subset region of interest for metrics calculation, the user has to set the ROI to true and save the polygon boundary of the region in the same folder with the images as a shape file. If the user sets the ROI to FALSE the metrics will be extracted for the whole image.
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Percentage is an optional parameter which requires the user to enter the percentage value of the minimum values above which the Onset and Offset values are defined.
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Given the user’s input with appropriate Path, ROI and percentage values, the PhenoMetrics function then calculates the 15 phenologic metrics; in the order of Onset, OnsetT, MaxV, MaxT, Offset, OffsetT, LengthGS, GreenUpSlope, BrownDownSlope, BeforeMaxT, AfterMaxT, TINDVIBeforeMax, TINDVIAfterMax, TINDVI and Asymmetry. The outputs of the metrics are represented spatially by 13 raster images in the img file format, in the same projection as the input data. The outputs are also provided in a generic ASCII file format, saved in the folder hard codes from the software as “Results”, under the folder specified by the path parameter. The metrics are saved with file names the same as the metrics names; for example Onset.img. The list of all pixels with their NDVI time series is also provided as an output, named as ‘AllPixels.txt’, under the “Results” folder with the pixel number x and y coordinate of the centroid and the consecutive NDVI values extracted from the images with the name ‘AllPixels.txt’.
MultiPointsPlot function
The MultiPointsPlot function provides the ability to visualise the NDVI curve by plotting the temporal sequence of NDVI values of user selected raster pixels. The function provide plots of a maximum of 5 pixels together.
The input parameters are
NumberofPixels- requires the user to specify the number of pixels to be plotted together, and
PixelId parameters - require the user to provide the Pixel number as observed from AllPixels.txt file.
The MultiPointsPlot function takes a variable number of parameters depending on the number of points the user wishes to plot together, which is expressed at Number of Pixels parameter. Visually, the function plots the first pixels as black, red, green, blue and yellow curves in their order of the input. The plotted output allows the user to observe the relative difference in the dynamics of the vegetation index for the selected points. This is useful for assessing the variability in crop growth across a field.