Package index • annotatR

Images and backends

Read images and register formats.

at_read_image(): Read an image
at_tile(): Read a tile from an image
at_dims(): Image dimensions at a pyramid level
at_n_levels(): Number of pyramid levels
at_n_bands(): Number of bands (channels)
at_bands(): Band (channel) table
at_wavelengths(): Band centre wavelengths
at_is_spectral(): Is the image a spectral cube?
at_is_pyramidal(): Is the image pyramidal?
at_pixel_size(): Physical pixel size
at_meta(): Image metadata
at_backend_list(): List registered image backends
at_backend_get(): Get a registered backend
at_backend_detect(): Detect the backend for a file
at_backend_register(): Register an image backend

Regions of interest

Construct and measure individual ROIs.

at_roi_point(): Create a point ROI
at_roi_rect(): Create a rectangular ROI
at_roi_circle(): Create a circular ROI
at_roi_ellipse(): Create an elliptical ROI
at_roi_polygon(): Create a polygon ROI
at_roi_freehand(): Create a freehand ROI
at_roi_from_sf(): Create an ROI from an existing sf geometry
at_roi_area(): ROI area
at_roi_centroid(): ROI centroid
at_roi_bbox(): ROI bounding box

Geometry

Transforms, set operations, predicates, and validity.

at_transform(): Transform an ROI between pyramid levels using real image dimensions
at_roi_rescale(): Rescale an ROI between pyramid levels
at_roi_buffer(): Buffer an ROI
at_roi_simplify(): Simplify an ROI
at_flip_y(): Flip an ROI's y-axis
at_snap(): Snap ROI vertices to a grid
at_clamp(): Clip an ROI to image bounds
at_roi_union() at_roi_intersect() at_roi_difference() at_roi_symdiff(): Set operations on ROIs
at_roi_ring(): Ring (annulus) along an ROI margin
at_roi_contains(): Test whether points fall inside an ROI
at_roi_overlaps(): Test whether two ROIs intersect
at_roi_distance(): Distance between two ROIs
at_rois_overlap(): Pairwise ROI overlaps within a layer
at_check_geometry(): Check the geometry of every ROI in a project
at_fix_geometry(): Repair the geometry of a project
at_check_containment(): Check cross-layer containment

Layers and projects

Organise ROIs into layers and projects.

at_style(): Layer style
at_layer(): Create a layer
at_layer_add(): Add an ROI to a layer
at_layer_remove(): Remove an ROI from a layer
at_layer_rois(): Layer ROI table
at_layer_n(): Number of ROIs in a layer
at_project(): Create an annotation project
at_add_layer(): Add a layer to a project
at_remove_layer(): Remove a layer from a project
at_add_roi(): Add an ROI to a project layer
at_remove_roi(): Remove an ROI from a project
at_layers(): Layer summary table
at_rois(): Query the ROIs of a project
at_validate(): Validate a project's invariants
at_summary(): Summarise a project

Sessions and batch

Resumable queues and whole-session operations.

at_session(): Create a batch annotation session
at_next(): Advance to the next image
at_prev(): Step back to the previous image
at_goto(): Jump to a specific image
at_current(): The current project
at_set_status(): Set the status of a queued image
at_session_status(): The session manifest
at_manifest(): Session progress manifest with per-label counts
at_resume(): Resume a saved session
at_export_all(): Export a whole session
at_summary_table(): Session summary statistics
at_batch_apply(): Apply a function to every project in a session
at_batch_check_geometry(): Check geometry across a whole session

Masks

Rasterise annotations and round-trip masks.

at_mask(): Rasterise ROIs to a mask ("Schablone")
at_mask_legend(): Legend of a mask
at_mask_stats(): Per-value statistics of a mask
at_mask_boundary(): Object boundaries of a mask
at_mask_preview(): Downsampled preview of a mask
at_mask_stack(): Stack per-layer masks into a 3D array
at_mask_derive(): Derive a training mask from layer masks
at_mask_agreement(): Agreement between two masks
at_write_mask(): Write a mask to disk
at_read_mask(): Read a mask into editable ROIs
at_write_masks(): Batch-write the masks of a project
at_write_npy(): Write a mask to a NumPy .npy file
at_read_npy(): Read a NumPy .npy integer mask

Extraction

Summarise image and spectral values under ROIs.

at_extract(): Extract summary statistics under ROIs
at_extract_spectrum(): Extract mean/median spectra for a spectral cube
at_extract_pixels(): Extract per-pixel values under ROIs

Visualisation

ggplot2 plots.

at_plot(): Plot generic for annotatR objects
at_plot_image(): Plot an image
at_plot_project(): Plot a project's ROIs
at_plot_overlay(): Plot ROIs overlaid on the image
at_plot_mask(): Plot a mask
at_plot_spectrum(): Plot spectra
at_plot_summary(): Plot a project summary

Import and export

Interchange with GeoJSON, QuPath, CSV, and RDS.

at_write_geojson(): Write a project's ROIs to GeoJSON
at_read_geojson(): Read ROIs from a GeoJSON file
at_roi_from_geojson(): Convert a GeoJSON feature to an ROI
at_write_qupath(): Write a project's ROIs as QuPath GeoJSON
at_read_qupath(): Read ROIs from a QuPath GeoJSON file
at_save_project(): Save a project
at_load_project(): Load a project
at_save_session(): Save a session
at_load_session(): Load a session
at_write_rois_csv(): Write a project's ROIs to CSV
at_read_rois_csv(): Read ROIs from a CSV with WKT geometry

Shiny application

The batch annotation app and canvas widget.

at_annotate(): Launch the batch annotation application
at_canvas(): An annotation canvas widget
atCanvasOutput(): Shiny output for the annotation canvas
renderAtCanvas(): Render an annotation canvas in Shiny
at_canvas_proxy(): A proxy for an existing annotation canvas
at_canvas_set_annotations(): Replace the annotations on a canvas
at_canvas_set_tool(): Set the active drawing tool
at_canvas_set_band(): Set the displayed band or RGB triple
at_canvas_set_overlay(): Overlay a mask on the canvas
at_canvas_fit(): Zoom the canvas to a bounding box
at_tile_source(): Build a tile-source descriptor for the canvas

Example data

Bundled synthetic examples.

at_example_image(): Read a bundled example image
at_example_path(): Path to a bundled example file
at_example_project(): A populated example project
at_example_session(): An example batch session

Concepts

annotatR-classes annot_image annot_roi annot_layer annot_project annot_session annot_mask annot_style annot_summary: annotatR S3 classes
annotatR annotatR-package: annotatR: Multi-Layer Region-of-Interest Annotation for Images and Spectral Cubes