Function reference • pliman

Image operations

Import, show and export images

as_image(): Create an Image object

image_import() image_export() image_pliman(): Import and export images

image_combine(): Combines images to a grid

image_create(): Create an Image object of a given color

image_expand(): Expands 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 transformation

Performs spatial transformations such as rotation, reflection, and resizing

image_autocrop() image_crop() image_dimension() image_rotate() image_horizontal() image_vertical() image_hreflect() image_vreflect() image_resize() image_trim() image_dilate() image_erode() image_opening() image_closing() image_skeleton() image_thinning() image_filter() image_blur() image_contrast(): Spatial transformations

apply_fun_to_imgs(): Apply a function to images

Utilities for files

Provides utilities for manipulating files

file_extension() file_name() file_dir() manipulate_files(): Utilities for file manipulation

`%>%`: Forward-pipe operator

leading_zeros(): Add leading zeros to a numeric sequence

Utilities for shape files

Provides utilities for creating and analyzing image shape files

analyze_objects_shp(): Analyzes objects using shapefiles

measure_disease_shp(): Measure disease using shapefiles

prepare_to_shp(): Prepare images to analyze_objects_shp()

image_shp(): Construct a shape file from an image

image_align(): Aligns an Image object by hand

object_mark(): Mark Object Points

object_map(): Map Object Distances

plot(<image_shp>): S3 method plot for image_shp objects

Utilities for image resolution and color space

Provides utilities for conversions between size (cm) and resolution (dpi)

dpi_to_cm() cm_to_dpi() pixels_to_cm() cm_to_pixels() npixels() dpi() distance(): Utilities for image resolution

rgb_to_hsb() rgb_to_srgb() rgb_to_lab(): Convert between colour spaces

Utilities for shapes

Provides utilities for construction of know shapes such as circles, squares, triangles, rectangles, and polygons. Several poly_* functions are provided to handle polygons’ coordinates

poly_check() poly_is_closed() poly_close() poly_unclose() poly_angles() poly_limits() conv_hull() conv_hull_unified() poly_area() poly_slide() poly_distpts() poly_centdist() poly_perimeter() poly_rotate() poly_align() poly_center() poly_lw() poly_eccentricity() poly_convexity() poly_caliper() poly_elongation() poly_solidity() poly_flip_y() poly_flip_x() poly_sample() poly_sample_prop() poly_jitter() poly_circularity() poly_circularity_norm() poly_circularity_haralick() poly_mass() poly_spline() poly_smooth() poly_measures(): Utilities for Polygons

plot_contour() plot_polygon() plot_mass() plot_ellipse(): Utilities for plotting polygons

draw_circle() draw_square() draw_rectangle() draw_trian_equi() draw_trian_rect() draw_n_tagon(): Utilities for drawing coordinates of known shapes

plot_lw(): Plot length and width lines on objects

poly_apex_base_angle(): Calculate the apex and base angles of an object

poly_width_at(): Width at a given height

poly_pcv(): Compute Perimeter Complexity Value (PCV)

Utilities for mosaics

Provides utilities for analysis of mosaics class ‘SpatRaster’ containing RGB or multispectral (RGB + RE + NIR) bands.

mosaic_crop(): Crop a mosaic

mosaic_input() mosaic_export(): Create and Export mosaics

mosaic_index(): Mosaic Index

mosaic_prepare(): Prepare a mosaic

mosaic_to_pliman(): Mosaic to pliman

mosaic_to_rgb(): Mosaic to RGB

mosaic_view(): Mosaic View

Utilities for image points

Opens an iterative section to count objects, extract pixel intensity and create image palettes manually.

pick_count() pick_coords() pick_rgb() pick_palette(): Utilities for picking up points in an image

Image segmentation

Performs image segmentation based on indexes such as RGB bands or vegetation indexes

image_augment(): Augment Images

image_binary(): Creates a binary image

image_index() plot(<image_index>): Image indexes

pliman_indexes() pliman_indexes_eq() pliman_indexes_rgb() pliman_indexes_me(): Utilities for image indexes

image_palette(): Create image palettes

dist_transform(): Distance map transform

image_segment() image_segment_iter(): Image segmentation

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_to_mat(): Convert an image to a data.frame

make_brush(): Makes a brush

make_mask(): Makes a mask in an image

otsu(): Calculate Otsu's threshold

plot_index(): Plot an image index

plot_index_shp(): Plot rectangles colored by a quantitative attribute and overlay on an RGB image

pixel_index(): Get the pixel indices for a given row of a binary image

watershed2(): Alternative watershed algorithm

Elliptical Fourier Analysis

Utilities for landmarks extraction and Elliptical Fourier Analysis

efourier(): Elliptical Fourier Analysis

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

ellipse(): Confidence ellipse

landmarks(): Create image landmarks

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

calibrate(): Calibrates distances of landmarks

contours: Contour outlines from five leaves

Analyze objects

Analyze objects in an image

analyze_objects() plot(<anal_obj>) analyze_objects_iter(): Analyzes objects in an image

get_measures() plot_measures(): Utilities for object measures

pliman_images: Sample images

object_coord() object_contour() object_isolate() object_id(): Utilities for working with image objects

object_split_shp(): Splits image objects based on a shape file

object_to_color(): Apply color to image objects

summary_index(): Summary an object index

poly_check() poly_is_closed() poly_close() poly_unclose() poly_angles() poly_limits() conv_hull() conv_hull_unified() poly_area() poly_slide() poly_distpts() poly_centdist() poly_perimeter() poly_rotate() poly_align() poly_center() poly_lw() poly_eccentricity() poly_convexity() poly_caliper() poly_elongation() poly_solidity() poly_flip_y() poly_flip_x() poly_sample() poly_sample_prop() poly_jitter() poly_circularity() poly_circularity_norm() poly_circularity_haralick() poly_mass() poly_spline() poly_smooth() poly_measures(): Utilities for Polygons

object_split(): Splits objects from an image into multiple images

object_edge(): Object edges

object_export(): Export multiple objects from an image to multiple images

object_export_shp(): Export multiple objects from an image to multiple images

object_label(): Labels objects

object_rgb(): Extract red, green and blue values from objects

pixel_index(): Get the pixel indices for a given row of a binary image

Symptomatic area

Calculates the percentage of symptomatic leaf area based in a sample or entire leaf based on provided color palettes samples

measure_disease() measure_disease_iter(): Performs plant disease measurements

measure_disease_byl(): Performs plant disease measurements by leaf

sad(): Produces Santandard Area Diagrams

Misc

Miscellaneous Functions

separate_col(): Turns a single character column into multiple columns.

custom_palette(): Generate Custom Color Palette

pca() get_biplot() plot(<pca>): Utilities for Principal Component Axis analysis

column_to_rownames() rownames_to_column() remove_rownames() round_cols(): Utilities for handling with rows and columns

mean_list() sd_list() max_list() min_list(): These functions applies common statistics to a list of objects, returning a numeric vector.

set_wd_here() get_wd_here() open_wd_here() open_wd(): Set and get the Working Directory quicky

random_color(): Random built-in color names

ggplot_color(): ggplot2-like colors generation

get_pliman_viewer(): Get the value of the pliman_viewer option

set_pliman_viewer(): Set the value of the pliman_viewer option

Iterative visualization

Tools to plot images and create polygons, points, and lines using mapview and mapedit packages.

image_prepare(): Prepare an image

image_view(): Create an interactive map view of an image

pliman_viewer: Global option for controlling the viewer in pliman package