Read ROIs from a QuPath GeoJSON file

Reads QuPath 0.4+ exports (a native feature array, a FeatureCollection or a single Feature) and the legacy hyperannotatR 0.1 dialect. classification.name (or the joined names of a derived class, e.g. "Tumor: Positive") becomes the ROI label, the classification colour (a current color RGB array or a legacy colorRGB integer) the layer style colour, and features without a classification are labelled "unclassified". Everything else QuPath carries is kept, never invented, under each ROI's attributes$qupath: the object id and type, name, measurements (with explicit value_state), the image plane (zero-based c, z, t; c = NA for all channels), metadata, a nucleus geometry, and roi_native = "ellipse" with geometry_fidelity = "approximated" for polygonised ellipses. A hyperannotatR id stored in metadata.annotatr_roi_id is restored as the ROI id; ordinary external ids are kept unchanged.

Usage

at_read_qupath(
  path,
  layer_name = "qupath",
  level = 0L,
  call = rlang::caller_env(),
  coordinate_level = NULL,
  legacy_levels = c("error", "recorded")
)

Arguments

path

Path to a QuPath GeoJSON file.

layer_name

Layer name for the imported ROIs. Default "qupath".

level

Integer fallback level for features without level metadata. Default 0 (standard full-resolution QuPath coordinates).

call

The calling environment, for error reporting.

coordinate_level

Optional integer overriding every recorded level without scaling coordinates. Use only when the actual coordinate level is known, for example 0L for legacy hyperannotatR exports that wrote level-0 coordinates beside a nonzero source level. NULL (default) uses the schema and legacy_levels policy. Coordinates are never automatically repaired.

legacy_levels

How to interpret files without the coordinate schema marker: "error" (default) rejects ambiguous nonzero recorded levels; "recorded" explicitly trusts those levels. Level-0 files remain unambiguous.

Value

An annot_layer.

Details

Input is validated strictly and keys are matched exactly: malformed structure, contradictory duplicate fields (identical duplicates, which QuPath 0.7.0 emits, are accepted), conflicting colours or object types for a feature, conflicting colours for one label, and repeated ROI ids are refused with an at_validation_error of code INVALID_GEOJSON.

See also

Other io: at_inspect_saved(), at_inspect_source(), at_load_project(), at_load_session(), at_read_geojson(), at_read_rois_csv(), at_relink_source(), at_roi_from_geojson(), at_save_project(), at_save_session(), at_write_geojson(), at_write_qupath(), at_write_rois_csv()