Set body annotations for fish2 via Clio

Set one or more Clio body annotations for the fish2 dataset.

Usage

fish_annotate(
  x,
  test = TRUE,
  version = NULL,
  write_empty_fields = FALSE,
  allow_new_fields = FALSE,
  designated_user = NULL,
  protect = c("user"),
  chunksize = 50,
  ...
)

Arguments

x

Annotation data usually as a data.frame containing a bodyid column. Please see malevnc::manc_annotate_body for other options.

test

Whether to use the clio test sore

version

Optional clio version to associate with this annotation. The default NULL uses the current version returned by the API.

write_empty_fields

When x is a data.frame, this controls whether empty fields in x (i.e. NA or "") overwrite fields in the clio-store database (when they are not protected by the protect argument). The (conservative) default write_empty_fields=FALSE does not overwrite. If you do want to set fields to an empty value (usually the empty string) then you must set write_empty_fields=TRUE.

allow_new_fields

Whether to allow creation of new clio fields. Default FALSE will produce an error encouraging you to check the field names.

designated_user

Optional email address when one person is uploading annotations on behalf of another user. See Users section for details.

protect

Vector of fields that will not be overwritten if they already have a value in clio store. Set to TRUE to protect all fields and to FALSE to overwrite all fields for which you provide data. See details for the rationale behind the default value of "user"

chunksize

When you have many bodies to annotate the request will by default be sent 50 records at a time to avoid any issue with timeouts. Set to Inf to insist that all records are sent in a single request. NB only applies when x is a data.frame.

...

Additional parameters passed to pbapply::pbsapply

Value

The result returned by manc_annotate_body.

Details

This function sets annotations for one or more bodyids. Logically these annotations move with the bodyid (rather than a point location on the object). The rules for annotation merges/transfers seem to work well in practice but in general detailed annotations should be reserved for large/mature bodies.

The function wraps malevnc::manc_annotate_body for the fish2 dataset. The default test=TRUE is retained for safety, but there does not currently appear to be a separate fish2 annotation test server. Please inspect the returned metadata carefully before assuming the result matches what you intended to write.

See also

Other live-annotations: fish_dvid_annotations()

Examples

if (FALSE) { # \dontrun{
fish_annotate(data.frame(bodyid = 100003384, group = 100003384), test = TRUE)
} # }