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Build a partner interop manifest

Source: R/interop-manifest.R
at_interop_manifest.Rd

Describe hyperannotatR objects for a partner such as qupflowR without exposing local paths: images are identified by content hash (image_id) and file basename; annotations by string ROI ids and an at_annotation_revision(); masks by type, integer dtype, background, dimensions, level and legend. The coordinate convention, band/wavelength table, HSI value semantics, plane, calibration and transform digests are recorded explicitly. QuPath hierarchy and native ROI shapes, which hyperannotatR does not model, are reported as "unknown" or "approximated", never invented.

Usage

at_interop_manifest(
  x,
  destination = NULL,
  hash_sources = TRUE,
  call = rlang::caller_env()
)

Arguments

x

An annot_project, annot_session, annot_image, annot_layer, annot_roi or annot_mask.

destination

Optional path: an existing directory (the manifest is written as manifest.json inside it) or a .json file path. An existing file is never overwritten.

hash_sources

Logical; hash image source files (needed for a content-derived image_id). Default TRUE.

call

The calling environment, for error reporting.

In a session manifest every ROI and layer record carries the entry_id of its queue entry, so entries that share an image stay separate. An ROI whose review_status attribute is not one of "unreviewed", "reviewed", "rejected" or "staged" is refused (REVIEW_STATUS_INVALID).

Value

The manifest (a list of class at_interop_manifest); invisibly when destination is given.

See also

at_export_qupflowr(), at_interop_capabilities()

Other interop: at_annotation_revision(), at_commit_qupflowr(), at_export_qupflowr(), at_import_qupflowr(), at_interop_capabilities(), at_stage_qupflowr()

Examples

m <- at_interop_manifest(at_example_project())
m$annotations$annotation_revision
#> [1] "sha256:10f56448a98dc069007b9366fb6c4eaf3777abea004593e3f5b7d0fb6fd2d052"
m$images[[1]]$image_id
#> [1] "sha256:3fa00078c93c3a7d"