Package: pliman 3.0.0

Tiago Olivoto

pliman: Tools for Plant Image Analysis

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.

Authors:Tiago Olivoto [aut, cre]

pliman_3.0.0.tar.gz
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pliman.pdf |pliman.html✨
pliman/json (API)
NEWS

# Install 'pliman' in R:
install.packages('pliman', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/nepem-ufsc/pliman/issues

Pkgdown site:https://nepem-ufsc.github.io

Uses libs:
  • openblas– Optimized BLAS
  • c++– GNU Standard C++ Library v3
  • openmp– GCC OpenMP (GOMP) support library
Datasets:
  • contours - Contour outlines from five leaves

openblascppopenmp

2.78 score 480 scripts 1.3k downloads 228 exports 45 dependencies

Last updated 2 months agofrom:ffab10ab3b. Checks:OK: 2. Indexed: no.

TargetResultDate
Doc / VignettesOKDec 07 2024
R-4.5-linux-x86_64OKDec 07 2024

Exports:%>%analyze_objectsanalyze_objects_iteranalyze_objects_minimalanalyze_objects_shpapply_fun_to_imgsas_imagecalibratecm_to_dpicm_to_pixelscolumn_to_rownamesconv_hullconv_hull_unifiedcustom_palettedist_transformdistancedpidpi_to_cmdraw_circledraw_n_tagondraw_rectangledraw_squaredraw_trian_equidraw_trian_rectefourierefourier_coefsefourier_errorefourier_invefourier_normefourier_powerefourier_shapeellipsefile_dirfile_extensionfile_nameget_biplotget_measuresget_pliman_viewerget_wd_hereggplot_colorimage_alignimage_alphaimage_augmentimage_autocropimage_binaryimage_blurimage_closingimage_combineimage_contrastimage_createimage_cropimage_dilateimage_dimensionimage_erodeimage_expandimage_exportimage_filterimage_horizontalimage_hreflectimage_importimage_indeximage_inputimage_openingimage_paletteimage_plimanimage_prepareimage_resizeimage_rotateimage_segmentimage_segment_iterimage_segment_kmeansimage_segment_manualimage_segment_maskimage_shpimage_skeletonimage_squareimage_thinningimage_thinning_guo_hallimage_to_matimage_trimimage_verticalimage_viewimage_vreflectlandmarkslandmarks_addlandmarks_anglelandmarks_distlandmarks_regradileading_zerosmake_brushmake_maskmanipulate_filesmax_listmean_listmeasure_diseasemeasure_disease_bylmeasure_disease_itermeasure_disease_shpmeasure_injurymin_listmosaic_aggregatemosaic_analyzemosaic_analyze_itermosaic_chmmosaic_chm_extractmosaic_chm_maskmosaic_cropmosaic_drawmosaic_epsgmosaic_exportmosaic_extractmosaic_histmosaic_indexmosaic_index2mosaic_inputmosaic_interpolatemosaic_lonlat2epsgmosaic_plotmosaic_plot_rgbmosaic_preparemosaic_projectmosaic_resamplemosaic_segmentmosaic_segment_pickmosaic_to_plimanmosaic_to_rgbmosaic_vectorizemosaic_viewnpixelsobject_contourobject_coordobject_edgeobject_exportobject_export_shpobject_idobject_isolateobject_labelobject_mapobject_markobject_rgbobject_splitobject_split_shpobject_to_coloropen_wdopen_wd_hereotsupcapick_coordspick_countpick_palettepick_rgbpixel_indexpixels_to_cmpliman_indexespliman_indexes_eqpliman_indexes_ican_computepliman_indexes_mepliman_indexes_rgbplot_contourplot_ellipseplot_idplot_indexplot_index_shpplot_lwplot_massplot_measuresplot_polygonpoly_alignpoly_anglespoly_apex_base_anglepoly_areapoly_caliperpoly_centdistpoly_centdist_masspoly_centerpoly_checkpoly_circularitypoly_circularity_haralickpoly_circularity_normpoly_closepoly_convexitypoly_distptspoly_eccentricitypoly_elongationpoly_flip_xpoly_flip_ypoly_is_closedpoly_jitterpoly_limitspoly_lwpoly_masspoly_measurespoly_pcvpoly_perimeterpoly_rotatepoly_samplepoly_sample_proppoly_slidepoly_smoothpoly_soliditypoly_splinepoly_unclosepoly_width_atprepare_to_shprandom_colorremove_rownamesrgb_to_hsbrgb_to_labrgb_to_srgbround_colsrownames_to_columnsadsd_listsentinel_to_tifseparate_colset_pliman_viewerset_wd_hereshapefile_buildshapefile_editshapefile_exportshapefile_inputshapefile_interpolateshapefile_measuresshapefile_plotshapefile_surfaceshapefile_viewsummary_indexwatershed2

Dependencies:classclassIntclicodetoolsDBIdigestdoFuturedplyre1071exactextractrfansiforeachfuturefuture.applygenericsglobalsglueiteratorsKernSmoothlatticelifecyclelistenvmagrittrMASSparallellypillarpkgconfigproxypurrrR6rasterRcppRcppArmadillorlangs2sfspterratibbletidyselectunitsutf8vctrswithrwk

Readme and manuals

Help Manual

Help pageTopics
Analyzes objects in an imageanalyze_objects analyze_objects_iter plot.anal_obj plot.anal_obj_ls
Analyzes objects in an imageanalyze_objects_minimal plot.anal_obj_ls_minimal plot.anal_obj_minimal
Analyzes objects using shapefilesanalyze_objects_shp
Apply a function to imagesapply_fun_to_imgs
Create an 'Image' objectas_image
Calibrates distances of landmarkscalibrate
Contour outlines from five leavescontours
Generate Custom Color Palettecustom_palette
Distance map transformdist_transform
Elliptical Fourier Analysisefourier
Get Fourier coefficientsefourier_coefs
Erros between the original and reconstructed outlineefourier_error
Inverse Elliptical Fourier Analysisefourier_inv
Normalized Fourier coefficientsefourier_norm
Power in Fourier Analysisefourier_power
Draw shapes based on Fourier coefficientsefourier_shape
Confidence ellipseellipse
Get the value of the pliman_viewer optionget_pliman_viewer
ggplot2-like colors generationggplot_color
Aligns an 'Image' object by handimage_align
Add Alpha Layer to an RGB Imageimage_alpha
Augment Imagesimage_augment
Creates a binary imageimage_binary
Combines images to a gridimage_combine
Create an 'Image' object of a given colorimage_create
Expands an imageimage_expand
Image indexesimage_index plot.image_index
Prepare an imageimage_prepare
Image segmentationimage_segment image_segment_iter
Image segmentation using k-means clusteringimage_segment_kmeans
Image segmentation by handimage_segment_manual
Segment an 'Image' object using a brush maskimage_segment_mask
Construct a shape file from an imageimage_shp
Squares an imageimage_square
Perform Guo-Hall thinning on a binary image or list of binary imagesimage_thinning_guo_hall
Convert an image to a data.frameimage_to_mat
Create an interactive map view of an imageimage_view
Create image landmarkslandmarks
Artificially inflates the number of landmarkslandmarks_add
Angles between landmarkslandmarks_angle
Distances between landmarkslandmarks_dist
Pseudolandmarks with equally spaced angleslandmarks_regradi
Add leading zeros to a numeric sequenceleading_zeros
Makes a brushmake_brush
Makes a mask in an imagemake_mask
Performs plant disease measurementsmeasure_disease measure_disease_iter
Performs plant disease measurements by leafmeasure_disease_byl
Measure disease using shapefilesmeasure_disease_shp
Measures Injury in Imagesmeasure_injury
SpatRaster aggregationmosaic_aggregate
Analyze a mosaic of remote sensing datamosaic_analyze
Analyze mosaics iterativelymosaic_analyze_iter
Calculate Canopy Height Model and Volumemosaic_chm
Extract Canopy Height and Volumemosaic_chm_extract
Apply a height mask to CHM datamosaic_chm_mask
Crop a mosaicmosaic_crop
Drawing Lines or Polygons with Raster Informationmosaic_draw
Determine EPSG Code for a Mosaicmosaic_epsg
Extract Values from a Raster Mosaic Using a Shapefilemosaic_extract
A wrapper around terra::hist()mosaic_hist
Mosaic Indexmosaic_index
Mosaic Index with GDALmosaic_index2
Create and Export mosaicsmosaic_export mosaic_input
Mosaic interpolationmosaic_interpolate
Project a Mosaic from Lon/Lat to EPSG-based CRSmosaic_lonlat2epsg
A wrapper around terra::plot()mosaic_plot
A wrapper around terra::plotRGB()mosaic_plot_rgb
Prepare a mosaicmosaic_prepare
Project a Mosaic to a New Coordinate Reference System (CRS)mosaic_project
A wrapper around terra::resample()mosaic_resample
Segment a mosaicmosaic_segment
Segments a mosaic interactivelymosaic_segment_pick
Mosaic to plimanmosaic_to_pliman
Mosaic to RGBmosaic_to_rgb
Vectorize a 'SpatRaster' mask to an 'sf' objectmosaic_vectorize
Mosaic Viewmosaic_view
Object edgesobject_edge
Export multiple objects from an image to multiple imagesobject_export
Export multiple objects from an image to multiple imagesobject_export_shp
Labels objectsobject_label
Map Object Distancesobject_map
Mark Object Pointsobject_mark
Extract red, green and blue values from objectsobject_rgb
Splits objects from an image into multiple imagesobject_split
Splits image objects based on a shape fileobject_split_shp
Apply color to image objectsobject_to_color
Calculate Otsu's thresholdotsu
Create image palettesimage_palette palettes
Forward-pipe operator%>% pipe
Get the pixel indices for a given row of a binary imagepixel_index
Sample imagespliman_images
List Computable Indexes Based on Available Bandspliman_indexes_ican_compute
Global option for controlling the viewer in pliman packagepliman_viewer
Generate plot IDs with different layoutsplot_id
Plot an image indexplot_index
Plot rectangles colored by a quantitative attribute and overlay on an RGB imageplot_index_shp
Plot length and width lines on objectsplot_lw
S3 method 'plot' for 'image_shp' objectsplot.image_shp
Calculate the apex and base angles of an objectpoly_apex_base_angle
Compute Perimeter Complexity Value (PCV)poly_pcv
Width at a given heightpoly_width_at
Prepare images to analyze_objects_shp()prepare_to_shp
Random built-in color namesrandom_color
Produces Santandard Area Diagramssad
Convert Sentinel data to GeoTIFF formatsentinel_to_tif
Turns a single character column into multiple columns.separate_col
Set the value of the pliman_viewer optionset_pliman_viewer
Build a shapefile from a mosaic rastershapefile_build
Edit Features in a Shapefileshapefile_edit
Interpolate values at specific points based on coordinates and a target variableshapefile_interpolate
Extract geometric measures from a shapefile objectshapefile_measures
A wrapper around terra::plot()shapefile_plot
Generate a spatial surface plot based on interpolated valuesshapefile_surface
Summary an object indexsummary_index
Convert between colour spacesrgb_to_hsb rgb_to_lab rgb_to_srgb utils_colorspace
Utilities for image resolutioncm_to_dpi cm_to_pixels distance dpi dpi_to_cm npixels pixels_to_cm utils_dpi
Utilities for file manipulationfile_dir file_extension file_name manipulate_files utils_file
Import and export imagesimage_export image_import image_input image_pliman utils_image
Utilities for image indexespliman_indexes pliman_indexes_eq pliman_indexes_me pliman_indexes_rgb utils_indexes
Utilities for object measuresget_measures plot_measures utils_measures
Utilities for working with image objectsobject_contour object_coord object_id object_isolate utils_objects
Utilities for Principal Component Axis analysisget_biplot pca plot.pca utils_pca
Utilities for picking up points in an imagepick_coords pick_count pick_palette pick_rgb utils_pick
Utilities for Polygonsconv_hull conv_hull_unified poly_align poly_angles poly_area poly_caliper poly_centdist poly_centdist_mass poly_center poly_check poly_circularity poly_circularity_haralick poly_circularity_norm poly_close poly_convexity poly_distpts poly_eccentricity poly_elongation poly_flip_x poly_flip_y poly_is_closed poly_jitter poly_limits poly_lw poly_mass poly_measures poly_perimeter poly_rotate poly_sample poly_sample_prop poly_slide poly_smooth poly_solidity poly_spline poly_unclose utils_polygon
Utilities for plotting polygonsplot_contour plot_ellipse plot_mass plot_polygon utils_polygon_plot
Utilities for handling with rows and columnscolumn_to_rownames remove_rownames round_cols rownames_to_column utils_rows_cols
Import/export shapefiles.shapefile_export shapefile_input shapefile_view utils_shapefile
Utilities for drawing coordinates of known shapesdraw_circle draw_n_tagon draw_rectangle draw_square draw_trian_equi draw_trian_rect utils_shapes
These functions applies common statistics to a list of objects, returning a numeric vector.max_list mean_list min_list sd_list utils_stats
Spatial transformationsimage_autocrop image_blur image_closing image_contrast image_crop image_dilate image_dimension image_erode image_filter image_horizontal image_hreflect image_opening image_resize image_rotate image_skeleton image_thinning image_trim image_vertical image_vreflect utils_transform
Set and get the Working Directory quickyget_wd_here open_wd open_wd_here set_wd_here utils_wd
Alternative watershed algorithmwatershed2