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Write a project's ROIs as QuPath GeoJSON

Source: R/io-qupath.R
at_write_qupath.Rd

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; existing UUIDs are kept), and hyperannotatR's own ROI id, layer, source and stored level in properties.metadata. dialect = "legacy" writes the hyperannotatR 0.1 form (object_type, signed colorRGB), which QuPath still reads with a deprecation warning. Publication uses a staged replacement.

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 for the coordinates and the level property. Default 0, as QuPath expects; other levels are for consumers that explicitly support them.

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

Every feature records the pyramid level of its written coordinates as the level property, the ROI's stored level as source_level, and the marker coordinate_schema = "annotatR-pixel-level-v1". QuPath keeps only metadata through its own import and export, so the QuPath dialect repeats the declaration there as annotatr_coordinate_schema and annotatr_coordinate_level; at_read_qupath() restores ROIs at that level.

QuPath keeps one colour per classification name, so a label that has different colours in different layers is written with the first colour found for it.

See also

at_read_qupath(), at_write_geojson()

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

Examples

p <- tempfile(fileext = ".geojson")
at_write_qupath(at_example_project(), p)