Write a project's ROIs as QuPath GeoJSON

The default dialect = "qupath" writes what QuPath 0.4 and later read natively (verified with QuPath 0.7.0): objectType, classification with an [r, g, b] colour, isLocked for locked ROIs, a deterministic UUID per ROI as the feature id (QuPath replaces non-UUID ids), and annotatR's own ROI id, layer, source and level in properties.metadata. dialect = "legacy" writes the annotatR 0.1 form (object_type, signed colorRGB), which QuPath still reads with a deprecation warning.

Usage

at_write_qupath(
  project,
  path,
  layer = NULL,
  level = 0L,
  overwrite = FALSE,
  dialect = c("qupath", "legacy"),
  call = rlang::caller_env()
)

Arguments

project

An annot_project.

path

Output file path.

layer

Optional layer filter.

level

Integer pyramid level. Default 0.

overwrite

Logical; overwrite an existing file. Default FALSE.

dialect

"qupath" (default) or "legacy".

call

The calling environment, for error reporting.

Value

The output path, invisibly.

Details

QuPath keeps one colour per classification name, so identical labels with different layer colours collapse to the first colour QuPath sees.

See also

at_read_qupath(), at_write_geojson()

Other io: at_load_project(), at_load_session(), at_read_geojson(), at_read_qupath(), at_read_rois_csv(), at_roi_from_geojson(), at_save_project(), at_save_session(), at_write_geojson(), at_write_rois_csv()

Examples

p <- withr::local_tempfile(fileext = ".geojson")
at_write_qupath(at_example_project(), p)