_pkgdown.yml

url: https://cttir.github.io/hyperannotatR/

# Inherit the shared CTTIR house style (Hugo Coder palette, light/dark switch,
# Inter/JetBrains Mono, navbar/footer/sidebar) from the themakR template. The
# default blue accent matches the hyperannotatR hex, so no per-package override is set.
template:
  package: themakR

development:
  mode: auto

reference:
  - title: Images and backends
    desc: Read images and register formats.
    contents:
      - at_read_image
      - at_tile
      - at_dims
      - at_n_levels
      - at_n_bands
      - at_bands
      - at_wavelengths
      - at_is_spectral
      - at_is_pyramidal
      - at_pixel_size
      - at_meta
      - at_backend_list
      - at_backend_get
      - at_backend_detect
      - at_backend_register
      - at_tivita_profile
      - at_cubert_export_envi
      - at_image_capabilities
      - at_close_image
  - title: Hyperspectral metadata
    desc: Band tables, value semantics, display band operations and read accounting.
    contents:
      - at_hsi_meta
      - at_convert_values
      - at_band_operations
      - at_band_view
      - at_read_stats
  - title: Regions of interest
    desc: Construct and measure individual ROIs.
    contents:
      - at_roi_point
      - at_roi_rect
      - at_roi_circle
      - at_roi_ellipse
      - at_roi_polygon
      - at_roi_freehand
      - at_roi_from_sf
      - at_roi_area
      - at_roi_centroid
      - at_roi_bbox
  - title: Geometry
    desc: Transforms, set operations, predicates, and validity.
    contents:
      - at_transform
      - at_roi_rescale
      - at_roi_buffer
      - at_roi_simplify
      - at_flip_y
      - at_snap
      - at_clamp
      - at_roi_union
      - at_roi_intersect
      - at_roi_difference
      - at_roi_symdiff
      - at_roi_ring
      - at_roi_contains
      - at_roi_overlaps
      - at_roi_distance
      - at_rois_overlap
      - at_check_geometry
      - at_fix_geometry
      - at_check_containment
  - title: Layers and projects
    desc: Organise ROIs into layers and projects.
    contents:
      - at_style
      - at_layer
      - at_layer_add
      - at_layer_remove
      - at_layer_rois
      - at_layer_n
      - at_project
      - at_add_layer
      - at_remove_layer
      - at_add_roi
      - at_remove_roi
      - at_layers
      - at_rois
      - at_validate
      - at_summary
  - title: Sessions and batch
    desc: Resumable queues and whole-session operations.
    contents:
      - at_session
      - at_next
      - at_prev
      - at_goto
      - at_current
      - at_set_status
      - at_session_status
      - at_manifest
      - at_resume
      - at_export_all
      - at_summary_table
      - at_batch_apply
      - at_batch_check_geometry
  - title: Masks
    desc: Rasterise annotations and round-trip masks.
    contents:
      - at_mask
      - at_mask_legend
      - at_mask_stats
      - at_mask_boundary
      - at_mask_preview
      - at_mask_stack
      - at_mask_derive
      - at_mask_agreement
      - at_write_mask
      - at_read_mask
      - at_write_masks
      - at_write_npy
      - at_read_npy
  - title: Extraction
    desc: Summarise image and spectral values under ROIs.
    contents:
      - at_extract
      - at_extract_spectrum
      - at_extract_pixels
  - title: Visualisation
    desc: ggplot2 plots.
    contents:
      - at_plot
      - at_plot_image
      - at_plot_project
      - at_plot_overlay
      - at_plot_mask
      - at_plot_spectrum
      - at_plot_summary
  - title: Import and export
    desc: Interchange with GeoJSON, QuPath, CSV, and RDS; inspect and relink saved sources.
    contents:
      - at_write_geojson
      - at_read_geojson
      - at_roi_from_geojson
      - at_write_qupath
      - at_read_qupath
      - at_save_project
      - at_load_project
      - at_save_session
      - at_load_session
      - at_inspect_saved
      - at_inspect_source
      - at_relink_source
      - at_write_rois_csv
      - at_read_rois_csv
  - title: Partner interoperability
    desc: The versioned qupflowR contract - capabilities, manifests, handoffs, staging and commits.
    contents:
      - at_interop_capabilities
      - at_interop_manifest
      - at_annotation_revision
      - at_export_qupflowr
      - at_import_qupflowr
      - at_stage_qupflowr
      - at_commit_qupflowr
  - title: Training datasets
    desc: Leakage-free deep-learning datasets and staged prediction import.
    contents:
      - at_training_export
      - at_training_check
      - at_training_import
  - title: Control service
    desc: The optional loopback annotatr-control-v1 service.
    contents:
      - at_control_capabilities
      - at_control_start
      - at_control_stop
      - at_control_close
      - at_control_connect
      - at_control_state
      - at_control_events
      - at_control_command
      - at_control_request_status
  - title: Shiny application
    desc: The batch annotation app and canvas widget.
    contents:
      - at_app
      - at_annotate
      - at_canvas
      - atCanvasOutput
      - renderAtCanvas
      - at_canvas_proxy
      - at_canvas_set_annotations
      - at_canvas_set_tool
      - at_canvas_set_band
      - at_canvas_set_overlay
      - at_canvas_fit
      - at_canvas_set_selection
      - at_tile_source
  - title: Example data
    desc: Bundled synthetic examples.
    contents:
      - at_example_image
      - at_example_path
      - at_example_project
      - at_example_session
  - title: Concepts
    contents:
      - hyperannotatR-classes
      - hyperannotatR-package

articles:
  - title: Get started
    contents:
      - hyperannotatR
  - title: Concepts
    contents:
      - images-and-backends
      - annotation-model
      - masks
  - title: Workflows
    contents:
      - shiny-workflow
      - interop
      - partner-interop
      - reproducible-analysis