Tools for Plant Image Analysis
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Documentation for package ‘pliman’ version 3.0.0
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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 |
| 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 |
-- 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_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_closing | Spatial transformations |
| image_combine | Combines images to a grid |
| 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_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 |
-- 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 | Extract Canopy Height and Volume |
| mosaic_chm_mask | Apply a height mask to CHM data |
| mosaic_crop | Crop a mosaic |
| 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_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_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_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_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_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_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_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_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 |
| shapefile_view | Import/export 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 |
-- W --
| watershed2 | Alternative watershed algorithm |
-- misc --
| %>% | Forward-pipe operator |