Tools for Plant Image Analysis
Analyzes objects in an image
Analyzes objects using shapefiles
Analyzes objects in an image
Apply a function to images
Create an Image
object
Calibrates distances of landmarks
Generate Custom Color Palette
Distance map transform
Get Fourier coefficients
Erros between the original and reconstructed outline
Inverse Elliptical Fourier Analysis
Normalized Fourier coefficients
Power in Fourier Analysis
Draw shapes based on Fourier coefficients
Elliptical Fourier Analysis
Confidence ellipse
Get the value of the pliman_viewer option
ggplot2-like colors generation
Aligns an Image
object by hand
Add Alpha Layer to an RGB Image
Augment Images
Creates a binary image
Combines images to a grid
Create an Image
object of a given color
Expands an image
Image indexes
Prepare an image
Image segmentation using k-means clustering
Image segmentation by hand
Segment an Image
object using a brush mask
Image segmentation
Construct a shape file from an image
Squares an image
Perform Guo-Hall thinning on a binary image or list of binary images
Convert an image to a data.frame
Create an interactive map view of an image
Artificially inflates the number of landmarks
Angles between landmarks
Distances between landmarks
Pseudolandmarks with equally spaced angles
Create image landmarks
Add leading zeros to a numeric sequence
Makes a brush
Makes a mask in an image
Performs plant disease measurements by leaf
Measure disease using shapefiles
Performs plant disease measurements
Measures Injury in Images
SpatRaster aggregation
Analyze mosaics iteratively
Analyze a mosaic of remote sensing data
Extract Canopy Height and Volume
Apply a height mask to CHM data
Calculate Canopy Height Model and Volume
Crop a mosaic
Drawing Lines or Polygons with Raster Information
Determine EPSG Code for a Mosaic
Extract Values from a Raster Mosaic Using a Shapefile
A wrapper around terra::hist()
Mosaic Index
Mosaic Index with GDAL
Create and Export mosaics
Mosaic interpolation
Project a Mosaic from Lon/Lat to EPSG-based CRS
A wrapper around terra::plotRGB()
A wrapper around terra::plot()
Prepare a mosaic
Project a Mosaic to a New Coordinate Reference System (CRS)
A wrapper around terra::resample()
Segments a mosaic interactively
Segment a mosaic
Mosaic to pliman
Mosaic to RGB
Vectorize a SpatRaster
mask to an sf
object
Mosaic View
Object edges
Export multiple objects from an image to multiple images
Export multiple objects from an image to multiple images
Labels objects
Map Object Distances
Mark Object Points
Extract red, green and blue values from objects
Splits image objects based on a shape file
Splits objects from an image into multiple images
Apply color to image objects
Calculate Otsu's threshold
Create image palettes
Forward-pipe operator
Get the pixel indices for a given row of a binary image
Sample images
List Computable Indexes Based on Available Bands
Global option for controlling the viewer in pliman package
Generate plot IDs with different layouts
Plot rectangles colored by a quantitative attribute and overlay on an ...
Plot an image index
Plot length and width lines on objects
S3 method plot
for image_shp
objects
Calculate the apex and base angles of an object
Compute Perimeter Complexity Value (PCV)
Width at a given height
Prepare images to analyze_objects_shp()
Random built-in color names
Produces Santandard Area Diagrams
Convert Sentinel data to GeoTIFF format
Turns a single character column into multiple columns.
Set the value of the pliman_viewer option
Build a shapefile from a mosaic raster
Edit Features in a Shapefile
Interpolate values at specific points based on coordinates and a targe...
Extract geometric measures from a shapefile object
A wrapper around terra::plot()
Generate a spatial surface plot based on interpolated values
Summary an object index
Convert between colour spaces
Utilities for image resolution
Utilities for file manipulation
Import and export images
Utilities for image indexes
Utilities for object measures
Utilities for working with image objects
Utilities for Principal Component Axis analysis
Utilities for picking up points in an image
Utilities for plotting polygons
Utilities for Polygons
Utilities for handling with rows and columns
Import/export shapefiles.
Utilities for drawing coordinates of known shapes
These functions applies common statistics to a list of objects, return...
Spatial transformations
Set and get the Working Directory quicky
Alternative watershed algorithm
Tools for both single and batch image manipulation and analysis (Olivoto, 2022 <doi:10.1111/2041-210X.13803>) and phytopathometry (Olivoto et al., 2022 <doi:10.1007/S40858-021-00487-5>). The tools can be used for the quantification of leaf area, object counting, extraction of image indexes, shape measurement, object landmark identification, and Elliptical Fourier Analysis of object outlines (Claude (2008) <doi:10.1007/978-0-387-77789-4>). The package also provides a comprehensive pipeline for generating shapefiles with complex layouts and supports high-throughput phenotyping of RGB, multispectral, and hyperspectral orthomosaics. This functionality facilitates field phenotyping using UAV- or satellite-based imagery.
Useful links