Changelog

Source: NEWS.md

annotatR 0.0.1

Initial development release.

Images and backends

• at_read_image() reads an image into a lightweight annot_image handle, auto-detecting the backend. at_tile() is the universal [y, x, band] tile accessor. Six backends ship (raster, tiff, ometiff, cuvis, tivita, envi); register more with at_backend_register().
• The tivita backend reads bare Diaspective Vision TIVITA *_SpecCube.dat cubes directly (big-endian float32, 640x480x100, 500-995 nm), in addition to ENVI-conformant exports; such cubes also auto-detect.
• Accessors: at_dims(), at_n_levels(), at_n_bands(), at_bands(), at_wavelengths(), at_is_spectral(), at_is_pyramidal(), at_pixel_size(), at_meta().

Regions of interest and geometry

• Constructors at_roi_point(), at_roi_rect(), at_roi_circle(), at_roi_ellipse(), at_roi_polygon(), at_roi_freehand(), at_roi_from_sf(), storing validated sf geometry in image pixel coordinates.
• Measures and transforms: at_roi_area(), at_roi_centroid(), at_roi_bbox(), at_roi_buffer(), at_roi_simplify(), at_roi_rescale(), at_transform(), at_flip_y(), at_snap(), at_clamp().
• Set operations at_roi_union()/intersect()/difference()/symdiff(), at_roi_ring() (an annulus straddling an ROI margin, e.g. a penumbra band), predicates at_roi_contains()/overlaps()/distance()/at_rois_overlap(), and validation at_check_geometry() / at_fix_geometry().
• at_check_containment() reports ROIs that fall outside a container region declared by a layer’s within metadata (e.g. state painted only inside the anatomy wound), enforcing the annotation guideline’s containment rule.

Layers, projects, and sessions

• at_layer(), at_style(), at_project(), and their pure mutators (at_add_layer(), at_add_roi(), at_remove_layer(), at_remove_roi()), with the at_rois() query contract, at_layers(), at_validate(), and at_summary().
• Resumable sessions: at_session(), at_next()/at_prev()/at_goto(), at_current(), at_set_status(), at_manifest(), at_resume().

Masks

• at_mask() produces binary, labelled, or multi-class integer masks with a documented pixel-coverage contract, six overlap policies, and a self-describing legend. A values argument pins labels to explicit integer codes, and the "bitor" overlap policy bitwise-ORs overlapping values to build bitfield masks (e.g. an artefact layer where a pixel is specular | blood). Helpers: at_mask_stats(), at_mask_boundary(), at_mask_preview(), at_mask_stack().
• at_mask_derive() combines layer masks into a derived training mask (state WHERE anatomy == keep AND artefact == 0 AND state != background).
• at_mask_agreement() scores two masks with per-class Dice / IoU and an overall accuracy and Cohen’s kappa (e.g. against a .npy ground truth).
• at_write_mask() writes TIFF/PNG/RDS with a sidecar JSON legend; at_read_mask() polygonises a mask back into editable ROIs. at_write_npy() / at_read_npy() losslessly interchange integer masks (incl. bitfields) with NumPy .npy, the format used by external HSI annotation tools.

Extraction, plots, interchange, and batch

• Tile-wise at_extract(), at_extract_spectrum(), at_extract_pixels().
• ggplot2 plots at_plot_image(), at_plot_project(), at_plot_overlay(), at_plot_mask(), at_plot_spectrum(), at_plot_summary().
• Round-tripping I/O: at_write_geojson()/at_read_geojson(), at_write_qupath()/at_read_qupath(), at_write_rois_csv()/ at_read_rois_csv(), project/session RDS.
• Whole-session at_export_all(), at_summary_table(), at_batch_apply(), at_batch_check_geometry().

Application

• at_annotate() launches a resumable, keyboard-first batch annotation app with live mask preview, built on shiny and a deep-zoom canvas widget.