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pliman (version 3.1.0)

Tools for Plant Image Analysis

Description

Tools for both single and batch image manipulation and analysis (Olivoto, 2022 ) and phytopathometry (Olivoto et al., 2022 ). 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) ). 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.

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Version

Install

install.packages('pliman')

Monthly Downloads

959

Version

3.1.0

License

GPL (>= 3)

Issues

Pull Requests

Stars

Forks

Repository

https://github.com/nepem-ufsc/pliman

Homepage

https://nepem-ufsc.github.io/pliman/

Maintainer

Tiago Olivoto

Last Published

August 19th, 2025

Functions in pliman (3.1.0)

apply_fun_to_imgs

Apply a function to images

Lin's Concordance Correlation Coefficient (CCC)

analyze_objects_shp

Analyzes objects using shapefiles

analyze_objects

Analyzes objects in an image

Calibrates distances of landmarks

Contour outlines from five leaves

Create an Image object

Generate Custom Color Palette

Distance map transform

Compute Shannon Entropy

Confidence ellipse

Draw shapes based on Fourier coefficients

ggplot2-like colors generation

Extract UUID from filenames

image_line_segment

Line Segment Detection in an Image

Label Connected Components in a Binary Image

get_pliman_viewer

Get the value of the pliman_viewer option

Normalized Fourier coefficients

Power in Fourier Analysis

image_canny_edge

Canny Edge Detector

Combines images to a grid

Creates a binary image

Prepare an image

Image segmentation

landmarks_regradi

Pseudolandmarks with equally spaced angles

Artificially inflates the number of landmarks

Create image landmarks

Convert an image to a data.frame

Construct a shape file from an image

image_segment_mask

Segment an Image object using a brush mask

mosaic_analyze_iter

Analyze mosaics iteratively

Analyze a mosaic of remote sensing data

Clip Raster Mosaic by Polygons

Create an interactive map view of an image

line_on_halfplot

Extract mid‐lines from half‐plots

Crop or Mask a Mosaic Raster

analyze_objects_minimal

Analyzes objects in an image

Add leading zeros to a numeric sequence

measure_disease_byl

Performs plant disease measurements by leaf

Elliptical Fourier Analysis

Get Fourier coefficients

Aligns an Image object by hand

Erros between the original and reconstructed outline

Create an Image object of a given color

Inverse Elliptical Fourier Analysis

Extract Values from a Raster Mosaic Using a Shapefile

image_contour_line

Smooth Contour Line Detection

measure_disease_shp

Measure disease using shapefiles

A wrapper around terra::hist()

Mosaic Index with GDAL

Splits objects from an image into multiple images

Extract red, green and blue values from objects

image_segment_manual

Image segmentation by hand

Drawing Lines or Polygons with Raster Information

Add Alpha Layer to an RGB Image

image_segment_kmeans

Image segmentation using k-means clustering

Determine EPSG Code for a Mosaic

Expands an image

Makes a mask in an image

landmarks_angle

Angles between landmarks

Distances between landmarks

measure_disease

Performs plant disease measurements

mosaic_resample

A wrapper around terra::resample()

Project a Mosaic to a New Coordinate Reference System (CRS)

mosaic_chm_mask

Apply a height mask to CHM data

Compute Bounding Boxes from Contours

Map Object Distances

Calculate Canopy Height Model and Volume

mosaic_vectorize

Vectorize a SpatRaster mask to an sf object

Squares an image

mosaic_chm_extract

Extracts height metrics and plot quality from a Canopy Height Model (CHM)

Mark Object Points

mosaic_to_pliman

Mosaic to pliman

A wrapper around terra::plot()

mosaic_classify

Classify a Mosaic Based on Index Breaks

mosaic_lonlat2epsg

Project a Mosaic from Lon/Lat to EPSG-based CRS

mosaic_segment_pick

Segments a mosaic interactively

object_export_shp

Export multiple objects from an image to multiple images

image_thinning_guo_hall

Perform Guo-Hall thinning on a binary image or list of binary images

mosaic_plot_rgb

A wrapper around terra::plotRGB()

A wrapper around terra::plot()

poly_apex_base_angle

Calculate the apex and base angles of an object

Compute Perimeter Complexity Value (PCV)

shapefile_surface

Generate a spatial surface plot based on interpolated values

Set and get the Working Directory quicky

utils_transform

Spatial transformations

object_split_shp

Splits image objects based on a shape file

Forward-pipe operator

object_to_color

Apply color to image objects

Measures Injury in Images

pliman_indexes_ican_compute

List Computable Indexes Based on Available Bands

shapefile_interpolate

Interpolate values at specific points based on coordinates and a target variable

Prepare images to analyze_objects_shp()

Edit Features in a Shapefile

Width at a given height

Utilities for working with image objects

Utilities for object measures

Alternative watershed algorithm

Generate Version 7 UUIDs or Random UUIDs

Prepare a mosaic

mosaic_interpolate

Mosaic interpolation

Create and Export mosaics

mosaic_aggregate

SpatRaster aggregation

Rotate a mosaic image by specified angles

Segment a mosaic

Get the pixel indices for a given row of a binary image

set_pliman_viewer

Set the value of the pliman_viewer option

shapefile_build

Build a shapefile from a mosaic raster

Plot an image index

Calculate Otsu's threshold

Random built-in color names

Global option for controlling the viewer in pliman package

S3 method plot for image_shp objects

Create image palettes

shapefile_operations

Spatial Operations on Shapefiles

shapefile_measures

Extract geometric measures from a shapefile object

Produces Santandard Area Diagrams

Export multiple objects from an image to multiple images

Add Bounding Boxes to an Existing Plot

Plot rectangles colored by a quantitative attribute and overlay on an RGB image

Turns a single character column into multiple columns.

sentinel_to_tif

Convert Sentinel data to GeoTIFF format

Summary an object index

plot_line_segment

Plot Detected Line Segments

utils_colorspace

Convert between colour spaces

Utilities for image indexes

Import and export images

Generate plot IDs with different layouts

Utilities for Polygons

Utilities for image resolution

Plot length and width lines on objects

utils_polygon_plot

Utilities for plotting polygons

utils_shapefile

Import/export shapefiles.

utils_rows_cols

Utilities for handling with rows and columns

Utilities for picking up points in an image

Utilities for Principal Component Axis analysis

These functions applies common statistics to a list of objects, returning a numeric vector.

Utilities for drawing coordinates of known shapes

Utilities for file manipulation