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pliman (version 2.1.0)

Tools for Plant Image Analysis

Description

Tools for single or batch image manipulation and analysis as described by Olivoto (2022) that can be used to quantify plant leaf area, assess disease severity, count objects, obtain shape measures, object landmarks, and compute Elliptical Fourier Analysis of the object outline, as described by Claude (2008) . Additionally, the package includes tools for analyzing grids, which enables high throughput field phenotyping using RGB imagery captured by unmanned aerial vehicles.

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Install

install.packages('pliman')

Monthly Downloads

1,070

Version

2.1.0

License

GPL (>= 3)

Issues

3

Pull Requests

0

Stars

52

Forks

9

Maintainer

Tiago Olivoto

Last Published

October 14th, 2023

Functions in pliman (2.1.0)

custom_palette

Generate Custom Color Palette
contours

Contour outlines from five leaves
apply_fun_to_imgs

Apply a function to images
dist_transform

Distance map transform
as_image

Create an Image object
efourier

Elliptical Fourier Analysis
analyze_objects_shp

Analyzes objects using shapefiles
calibrate

Calibrates distances of landmarks
efourier_coefs

Get Fourier coefficients
analyze_objects

Analyzes objects in an image
image_align

Aligns an Image object by hand
efourier_error

Erros between the original and reconstructed outline
efourier_norm

Normalized Fourier coefficients
ggplot_color

ggplot2-like colors generation
image_augment

Augment Images
efourier_power

Power in Fourier Analysis
efourier_shape

Draw shapes based on Fourier coefficients
efourier_inv

Inverse Elliptical Fourier Analysis
get_pliman_viewer

Get the value of the pliman_viewer option
ellipse

Confidence ellipse
image_create

Create an Image object of a given color
image_segment_kmeans

Image segmentation using k-means clustering
image_binary

Creates a binary image
image_segment_manual

Image segmentation by hand
image_combine

Combines images to a grid
image_segment_mask

Segment an Image object using a brush mask
image_prepare

Prepare an image
image_segment

Image segmentation
image_index

Image indexes
image_expand

Expands an image
image_thinning_guo_hall

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

Angles between landmarks
image_square

Squares an image
image_view

Create an interactive map view of an image
landmarks_regradi

Pseudolandmarks with equally spaced angles
image_to_mat

Convert an image to a data.frame
landmarks_add

Artificially inflates the number of landmarks
image_shp

Construct a shape file from an image
landmarks

Create image landmarks
landmarks_dist

Distances between landmarks
mosaic_crop

Crop a mosaic
make_mask

Makes a mask in an image
make_brush

Makes a brush
mosaic_index

Mosaic Index
mosaic_input

Create and Export mosaics
measure_disease_byl

Performs plant disease measurements by leaf
measure_disease

Performs plant disease measurements
leading_zeros

Add leading zeros to a numeric sequence
measure_disease_shp

Measure disease using shapefiles
mosaic_prepare

Prepare a mosaic
mosaic_view

Mosaic View
object_map

Map Object Distances
object_label

Labels objects
mosaic_to_pliman

Mosaic to pliman
mosaic_to_rgb

Mosaic to RGB
object_export

Export multiple objects from an image to multiple images
object_edge

Object edges
object_mark

Mark Object Points
object_export_shp

Export multiple objects from an image to multiple images
object_rgb

Extract red, green and blue values from objects
pixel_index

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

Create image palettes
object_to_color

Apply color to image objects
object_split_shp

Splits image objects based on a shape file
pliman_images

Sample images
otsu

Calculate Otsu's threshold
object_split

Splits objects from an image into multiple images
plot.image_shp

S3 method plot for image_shp objects
pipe

Forward-pipe operator
pliman_viewer

Global option for controlling the viewer in pliman package
plot_lw

Plot length and width lines on objects
plot_index

Plot an image index
poly_apex_base_angle

Calculate the apex and base angles of an object
sad

Produces Santandard Area Diagrams
separate_col

Turns a single character column into multiple columns.
poly_pcv

Compute Perimeter Complexity Value (PCV)
poly_width_at

Width at a given height
plot_index_shp

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

Prepare images to analyze_objects_shp()
random_color

Random built-in color names
utils_colorspace

Convert between colour spaces
set_pliman_viewer

Set the value of the pliman_viewer option
utils_file

Utilities for file manipulation
summary_index

Summary an object index
utils_image

Import and export images
utils_dpi

Utilities for image resolution
utils_measures

Utilities for object measures
utils_objects

Utilities for working with image objects
utils_pick

Utilities for picking up points in an image
utils_pca

Utilities for Principal Component Axis analysis
utils_transform

Spatial transformations
utils_polygon

Utilities for Polygons
utils_polygon_plot

Utilities for plotting polygons
utils_shapes

Utilities for drawing coordinates of known shapes
utils_stats

These functions applies common statistics to a list of objects, returning a numeric vector.
watershed2

Alternative watershed algorithm
utils_wd

Set and get the Working Directory quicky
utils_rows_cols

Utilities for handling with rows and columns