pliman3.0.0 package

Tools for Plant Image Analysis

analyze_objects_minimal

Analyzes objects in an image

analyze_objects_shp

Analyzes objects using shapefiles

analyze_objects

Analyzes objects in an image

apply_fun_to_imgs

Apply a function to images

as_image

Create an Image object

calibrate

Calibrates distances of landmarks

custom_palette

Generate Custom Color Palette

dist_transform

Distance map transform

efourier_coefs

Get Fourier coefficients

efourier_error

Erros between the original and reconstructed outline

efourier_inv

Inverse Elliptical Fourier Analysis

efourier_norm

Normalized Fourier coefficients

efourier_power

Power in Fourier Analysis

efourier_shape

Draw shapes based on Fourier coefficients

efourier

Elliptical Fourier Analysis

ellipse

Confidence ellipse

get_pliman_viewer

Get the value of the pliman_viewer option

ggplot_color

ggplot2-like colors generation

image_align

Aligns an Image object by hand

image_alpha

Add Alpha Layer to an RGB Image

image_augment

Augment Images

image_binary

Creates a binary image

image_combine

Combines images to a grid

image_create

Create an Image object of a given color

image_expand

Expands an image

image_index

Image indexes

image_prepare

Prepare an image

image_segment_kmeans

Image segmentation using k-means clustering

image_segment_manual

Image segmentation by hand

image_segment_mask

Segment an Image object using a brush mask

image_segment

Image segmentation

image_shp

Construct a shape file from an image

image_square

Squares an image

image_thinning_guo_hall

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

image_to_mat

Convert an image to a data.frame

image_view

Create an interactive map view of an image

landmarks_add

Artificially inflates the number of landmarks

landmarks_angle

Angles between landmarks

landmarks_dist

Distances between landmarks

landmarks_regradi

Pseudolandmarks with equally spaced angles

landmarks

Create image landmarks

leading_zeros

Add leading zeros to a numeric sequence

make_brush

Makes a brush

make_mask

Makes a mask in an image

measure_disease_byl

Performs plant disease measurements by leaf

measure_disease_shp

Measure disease using shapefiles

measure_disease

Performs plant disease measurements

measure_injury

Measures Injury in Images

mosaic_aggregate

SpatRaster aggregation

mosaic_analyze_iter

Analyze mosaics iteratively

mosaic_analyze

Analyze a mosaic of remote sensing data

mosaic_chm_extract

Extract Canopy Height and Volume

mosaic_chm_mask

Apply a height mask to CHM data

mosaic_chm

Calculate Canopy Height Model and Volume

mosaic_crop

Crop a mosaic

mosaic_draw

Drawing Lines or Polygons with Raster Information

mosaic_epsg

Determine EPSG Code for a Mosaic

mosaic_extract

Extract Values from a Raster Mosaic Using a Shapefile

mosaic_hist

A wrapper around terra::hist()

mosaic_index

Mosaic Index

mosaic_index2

Mosaic Index with GDAL

mosaic_input

Create and Export mosaics

mosaic_interpolate

Mosaic interpolation

mosaic_lonlat2epsg

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

mosaic_plot_rgb

A wrapper around terra::plotRGB()

mosaic_plot

A wrapper around terra::plot()

mosaic_prepare

Prepare a mosaic

mosaic_project

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

mosaic_resample

A wrapper around terra::resample()

mosaic_segment_pick

Segments a mosaic interactively

mosaic_segment

Segment a mosaic

mosaic_to_pliman

Mosaic to pliman

mosaic_to_rgb

Mosaic to RGB

mosaic_vectorize

Vectorize a SpatRaster mask to an sf object

mosaic_view

Mosaic View

object_edge

Object edges

object_export_shp

Export multiple objects from an image to multiple images

object_export

Export multiple objects from an image to multiple images

object_label

Labels objects

object_map

Map Object Distances

object_mark

Mark Object Points

object_rgb

Extract red, green and blue values from objects

object_split_shp

Splits image objects based on a shape file

object_split

Splits objects from an image into multiple images

object_to_color

Apply color to image objects

otsu

Calculate Otsu's threshold

palettes

Create image palettes

pipe

Forward-pipe operator

pixel_index

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

pliman_images

Sample images

pliman_indexes_ican_compute

List Computable Indexes Based on Available Bands

pliman_viewer

Global option for controlling the viewer in pliman package

plot_id

Generate plot IDs with different layouts

plot_index_shp

Plot rectangles colored by a quantitative attribute and overlay on an ...

plot_index

Plot an image index

plot_lw

Plot length and width lines on objects

plot.image_shp

S3 method plot for image_shp objects

poly_apex_base_angle

Calculate the apex and base angles of an object

poly_pcv

Compute Perimeter Complexity Value (PCV)

poly_width_at

Width at a given height

prepare_to_shp

Prepare images to analyze_objects_shp()

random_color

Random built-in color names

sad

Produces Santandard Area Diagrams

sentinel_to_tif

Convert Sentinel data to GeoTIFF format

separate_col

Turns a single character column into multiple columns.

set_pliman_viewer

Set the value of the pliman_viewer option

shapefile_build

Build a shapefile from a mosaic raster

shapefile_edit

Edit Features in a Shapefile

shapefile_interpolate

Interpolate values at specific points based on coordinates and a targe...

shapefile_measures

Extract geometric measures from a shapefile object

shapefile_plot

A wrapper around terra::plot()

shapefile_surface

Generate a spatial surface plot based on interpolated values

summary_index

Summary an object index

utils_colorspace

Convert between colour spaces

utils_dpi

Utilities for image resolution

utils_file

Utilities for file manipulation

utils_image

Import and export images

utils_indexes

Utilities for image indexes

utils_measures

Utilities for object measures

utils_objects

Utilities for working with image objects

utils_pca

Utilities for Principal Component Axis analysis

utils_pick

Utilities for picking up points in an image

utils_polygon_plot

Utilities for plotting polygons

utils_polygon

Utilities for Polygons

utils_rows_cols

Utilities for handling with rows and columns

utils_shapefile

Import/export shapefiles.

utils_shapes

Utilities for drawing coordinates of known shapes

utils_stats

These functions applies common statistics to a list of objects, return...

utils_transform

Spatial transformations

utils_wd

Set and get the Working Directory quicky

watershed2

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.

  • Maintainer: Tiago Olivoto
  • License: GPL (>= 3)
  • Last published: 2024-11-06