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A semi-automatic R script for the determination of crop height and lodging from point clouds or DEMs.

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DOCHAL (determination of crop height and lodging)

This is an R script that can be used to derive crop heights and lodging areas from point clouds or digital elevation models of agricultural plots.

 

Required input datasets are:

  • terrain height information (as point cloud (.laz) or DTM (.tif))
  • crop surface information (as point cloud (.laz) or DSM (.tif))
  • Shapefile with plot boundaries
  • (optional) Shapefile with region of interest

The output generated by this script is:

  • a table (.xlsx) with crop height statistics and lodging percentages per plot
  • the input plot boundary Shapefile with added plot attributes (crop heights and lodging percentages)
  • a crop height model (.tif) of the plot areas
  • a raster (.tif) with a lodging/no-ldging classification of the plot areas

 

Several processing parameters can be set by the user:

  • type of input datasets (point cloud or raster)
  • desired resolution of generated DTM and DSM (if input datasets are point clouds)
  • export of generated raster datasets
  • buffer width of plot boundaries

 

The meaning of the columns in the output table is as follows (height values in meters):

Column Meaning
ID plot ID
Parzelle plot index
mean_height mean height
median_height median height
SD_height standard deviation of heights
MAD_height median absolute deviation of heights
percentile.90. 90th percentile of height
most_likely_lodging_% percentage of plot area that is most likely lodging
probably_lodging_% percentage of plot area that is probably lodging
probably_not_lodging_% percentage of plot area that is probably not lodging
most_likely_not_lodging_% percentage of plot area that is most likely not lodging
threshold height threshold between lodging and not-lodging classes
lower height threshold between the classes "most likely lodging" and "probably lodging"
upper height threshold between the classes "probably not lodging" and "most likely not lodging"
min_angle minimum lodging angle that leads to classification as lodging

 

The lodging/no-lodging classes are represented by the following values in the output classification raster:

Class Raster value
most likely lodging 1
probably lodging 2
probably not lodging 3
most likely not lodging 4

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A semi-automatic R script for the determination of crop height and lodging from point clouds or DEMs.

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