# Tools for Plant Image Analysis

## Documentation for package ‘pliman’ version 3.1.1

- DESCRIPTION file.
- Package NEWS.

## Help Pages

A C D E F G I L M N O P R S U W misc

## -- A --

analyze_objects | Analyzes objects in an image
analyze_objects_iter | Analyzes objects in an image
analyze_objects_minimal | Analyzes objects in an image
analyze_objects_shp | Analyzes objects using shapefiles
apply_fun_to_imgs | Apply a function to images
as_image | Create an 'Image' object

## -- C --

calibrate | Calibrates distances of landmarks
ccc | Lin's Concordance Correlation Coefficient (CCC)
clear_pliman_cache | Clear cached files created by pliman
cm_to_dpi | Utilities for image resolution
cm_to_pixels | Utilities for image resolution
column_to_rownames | Utilities for handling with rows and columns
contours | Contour outlines from five leaves
conv_hull | Utilities for Polygons
conv_hull_unified | Utilities for Polygons
custom_palette | Generate Custom Color Palette

## -- D --

distance | Utilities for image resolution
dist_transform | Distance map transform
dpi | Utilities for image resolution
dpi_to_cm | Utilities for image resolution
draw_circle | Utilities for drawing coordinates of known shapes
draw_n_tagon | Utilities for drawing coordinates of known shapes
draw_rectangle | Utilities for drawing coordinates of known shapes
draw_square | Utilities for drawing coordinates of known shapes
draw_trian_equi | Utilities for drawing coordinates of known shapes
draw_trian_rect | Utilities for drawing coordinates of known shapes

## -- E --

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
entropy | Compute Shannon Entropy

## -- F --

file_dir | Utilities for file manipulation
file_extension | Utilities for file manipulation
file_name | Utilities for file manipulation

## -- G --

get_biplot | Utilities for Principal Component Axis analysis
get_measures | Utilities for object measures
get_pliman_viewer | Get the value of the pliman_viewer option
get_uuid | Extract UUID from filenames
get_wd_here | Set and get the Working Directory quicky
ggplot_color | ggplot2-like colors generation

## -- I --

image_align | Aligns an 'Image' object by hand
image_alpha | Add Alpha Layer to an RGB Image
image_augment | Augment Images
image_autocrop | Spatial transformations
image_binary | Creates a binary image
image_blur | Spatial transformations
image_canny_edge | Canny Edge Detector
image_closing | Spatial transformations
image_combine | Combines images to a grid
image_contour_line | Smooth Contour Line Detection
image_contrast | Spatial transformations
image_create | Create an 'Image' object of a given color
image_crop | Spatial transformations
image_dilate | Spatial transformations
image_dimension | Spatial transformations
image_erode | Spatial transformations
image_expand | Expands an image
image_export | Import and export images
image_filter | Spatial transformations
image_horizontal | Spatial transformations
image_hreflect | Spatial transformations
image_import | Import and export images
image_index | Image indexes
image_input | Import and export images
image_label | Label Connected Components in a Binary Image
image_line_segment | Line Segment Detection in an Image
image_opening | Spatial transformations
image_palette | Create image palettes
image_pliman | Import and export images
image_prepare | Prepare an image
image_resize | Spatial transformations
image_rotate | Spatial transformations
image_segment | Image segmentation
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_shp | Construct a shape file from an image
image_skeleton | Spatial transformations
image_square | Squares an image
image_thinning | Spatial transformations
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_trim | Spatial transformations
image_vertical | Spatial transformations
image_view | Create an interactive map view of an image
image_vreflect | Spatial transformations

## -- L --

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
leading_zeros | Add leading zeros to a numeric sequence
line_on_halfplot | Extract mid‐lines from half‐plots

## -- M --

make_brush | Makes a brush
make_mask | Makes a mask in an image
manipulate_files | Utilities for file manipulation
max_list | These functions applies common statistics to a list of objects, returning a numeric vector.
mean_list | These functions applies common statistics to a list of objects, returning a numeric vector.
measure_disease | Performs plant disease measurements
measure_disease_byl | Performs plant disease measurements by leaf
measure_disease_iter | Performs plant disease measurements
measure_disease_shp | Measure disease using shapefiles
measure_injury | Measures Injury in Images
min_list | These functions applies common statistics to a list of objects, returning a numeric vector.
mosaic_aggregate | SpatRaster aggregation
mosaic_analyze | Analyze a mosaic of remote sensing data
mosaic_analyze_iter | Analyze mosaics iteratively
mosaic_chm | Calculate Canopy Height Model and Volume
mosaic_chm_extract | Extracts height metrics and plot quality from a Canopy Height Model (CHM)
mosaic_chm_mask | Apply a height mask to CHM data
mosaic_classify | Classify a Mosaic Based on Index Breaks
mosaic_clip | Clip Raster Mosaic by Polygons
mosaic_crop | Crop or Mask a Mosaic Raster
mosaic_draw | Drawing Lines or Polygons with Raster Information
mosaic_epsg | Determine EPSG Code for a Mosaic
mosaic_export | Create and Export mosaics
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 | A wrapper around terra::plot()
mosaic_plot_rgb | A wrapper around terra::plotRGB()
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_rotate | Rotate a mosaic image by specified angles
mosaic_segment | Segment a mosaic
mosaic_segment_pick | Segments a mosaic interactively
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

## -- N --

npixels | Utilities for image resolution

## -- O --

object_bbox | Compute Bounding Boxes from Contours
object_contour | Utilities for working with image objects
object_coord | Utilities for working with image objects
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_id | Utilities for working with image objects
object_isolate | Utilities for working with image objects
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_scatter | Plot object thumbnails at (x, y) coordinates derived from image features
object_split | Splits objects from an image into multiple images
object_split_shp | Splits image objects based on a shape file
object_to_color | Apply color to image objects
open_wd | Set and get the Working Directory quicky
open_wd_here | Set and get the Working Directory quicky
otsu | Calculate Otsu's threshold

## -- P --

palettes | Create image palettes
pca | Utilities for Principal Component Axis analysis
pick_coords | Utilities for picking up points in an image
pick_count | Utilities for picking up points in an image
pick_palette | Utilities for picking up points in an image
pick_rgb | Utilities for picking up points in an image
pipe | Forward-pipe operator
pixels_to_cm | Utilities for image resolution
pixel_index | Get the pixel indices for a given row of a binary image
pliman_images | Sample images
pliman_indexes | Utilities for image indexes
pliman_indexes_eq | Utilities for image indexes
pliman_indexes_hs | Utilities for image indexes
pliman_indexes_ican_compute | List Computable Indexes Based on Available Bands
pliman_indexes_me | Utilities for image indexes
pliman_indexes_rgb | Utilities for image indexes
pliman_viewer | Global option for controlling the viewer in pliman package
plot.anal_obj | Analyzes objects in an image
plot.anal_obj_ls | Analyzes objects in an image
plot.anal_obj_ls_minimal | Analyzes objects in an image
plot.anal_obj_minimal | Analyzes objects in an image
plot.image_index | Image indexes
plot.image_shp | S3 method 'plot' for 'image_shp' objects
plot.pca | Utilities for Principal Component Axis analysis
plot_bbox | Add Bounding Boxes to an Existing Plot
plot_contour | Utilities for plotting polygons
plot_ellipse | Utilities for plotting polygons
plot_id | Generate plot IDs with different layouts
plot_index | Plot an image index
plot_index_shp | Plot rectangles colored by a quantitative attribute and overlay on an RGB image
plot_line_segment | Plot Detected Line Segments
plot_lw | Plot length and width lines on objects
plot_mass | Utilities for plotting polygons
plot_measures | Utilities for object measures
plot_polygon | Utilities for plotting polygons
poly_align | Utilities for Polygons
poly_angles | Utilities for Polygons
poly_apex_base_angle | Calculate the apex and base angles of an object
poly_area | Utilities for Polygons
poly_caliper | Utilities for Polygons
poly_centdist | Utilities for Polygons
poly_centdist_mass | Utilities for Polygons
poly_center | Utilities for Polygons
poly_check | Utilities for Polygons
poly_circularity | Utilities for Polygons
poly_circularity_haralick | Utilities for Polygons
poly_circularity_norm | Utilities for Polygons
poly_close | Utilities for Polygons
poly_convexity | Utilities for Polygons
poly_distpts | Utilities for Polygons
poly_eccentricity | Utilities for Polygons
poly_elongation | Utilities for Polygons
poly_flip_x | Utilities for Polygons
poly_flip_y | Utilities for Polygons
poly_is_closed | Utilities for Polygons
poly_jitter | Utilities for Polygons
poly_limits | Utilities for Polygons
poly_lw | Utilities for Polygons
poly_mass | Utilities for Polygons
poly_measures | Utilities for Polygons
poly_pcv | Compute Perimeter Complexity Value (PCV)
poly_perimeter | Utilities for Polygons
poly_rotate | Utilities for Polygons
poly_sample | Utilities for Polygons
poly_sample_prop | Utilities for Polygons
poly_slide | Utilities for Polygons
poly_smooth | Utilities for Polygons
poly_solidity | Utilities for Polygons
poly_spline | Utilities for Polygons
poly_unclose | Utilities for Polygons
poly_width_at | Width at a given height
prepare_to_shp | Prepare images to analyze_objects_shp()

## -- R --

random_color | Random built-in color names
remove_rownames | Utilities for handling with rows and columns
rgb_to_hsb | Convert between colour spaces
rgb_to_lab | Convert between colour spaces
rgb_to_srgb | Convert between colour spaces
round_cols | Utilities for handling with rows and columns
rownames_to_column | Utilities for handling with rows and columns

## -- S --

sad | Produces Santandard Area Diagrams
sd_list | These functions applies common statistics to a list of objects, returning a numeric vector.
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
set_wd_here | Set and get the Working Directory quicky
shapefile_build | Build a shapefile from a mosaic raster
shapefile_crosses | Spatial Operations on Shapefiles
shapefile_difference | Spatial Operations on Shapefiles
shapefile_edit | Edit Features in a Shapefile
shapefile_export | Import/export shapefiles.
shapefile_input | Import/export shapefiles.
shapefile_interpolate | Interpolate values at specific points based on coordinates and a target variable
shapefile_intersection | Spatial Operations on Shapefiles
shapefile_measures | Extract geometric measures from a shapefile object
shapefile_operations | Spatial Operations on Shapefiles
shapefile_outside | Spatial Operations on Shapefiles
shapefile_overlaps | Spatial Operations on Shapefiles
shapefile_plot | A wrapper around terra::plot()
shapefile_surface | Generate a spatial surface plot based on interpolated values
shapefile_touches | Spatial Operations on Shapefiles
shapefile_union | Spatial Operations on Shapefiles
shapefile_view | Import/export shapefiles.
shapefile_within | Spatial Operations on Shapefiles
summary_index | Summary an object index

## -- U --

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 | Utilities for Polygons
utils_polygon_plot | Utilities for plotting 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, returning a numeric vector.
utils_transform | Spatial transformations
utils_wd | Set and get the Working Directory quicky
uuid | Generate Version 7 UUIDs or Random UUIDs

## -- W --

watershed2 | Alternative watershed algorithm

## -- misc --

%>% | Forward-pipe operator