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Use a local snapshot of the Aedes synapse table

Source: R/synapse-snapshot.R
aedes_use_snapshot.Rd

Selects a downloaded snapshot of the Aedes synapse table so that aedes_partner_summary() and aedes_synapse_data() can answer queries locally, without contacting CAVE for synapses. Each snapshot records the root id of both partners of every synapse at one moment in time.

Usage

aedes_use_snapshot(
  snapshot = NULL,
  version = NULL,
  timestamp = NULL,
  root = aedes_snapshot_root(),
  set = TRUE
)

Arguments

snapshot

The snapshot tag, or "latest" for the most recent snapshot in root. The default (NULL) chooses one to match version, timestamp or the aedes.version option.

version, timestamp

A CAVE materialisation version or a timestamp (including "now") to choose the snapshot for. Either one also sets the aedes.version option.

root

The snapshot folder. Defaults to aedes_snapshot_root().

set

Whether to make this the default snapshot for the session.

Value

When set = TRUE, the previous option values (invisibly, suitable for passing to options()). Otherwise a list with the snapshot tag, timestamp and root.

Details

A snapshot folder contains static.parquet (one row per synapse, with its supervoxels, positions and size) and one sub-folder per snapshot tag. A tag folder has a meta.json with the snapshot timestamp and either the full root id table (by_pre.parquet, sorted by presynaptic root, plus an optional by_post.parquet sorted by postsynaptic root) or, for a checkpoint, a log.parquet with the synapses whose root ids changed since its parent snapshot. A checkpoint is read as its full base snapshot plus the logs of every checkpoint between them, so it is only used when all of those are present. Queries use DuckDB (from the suggested packages duckdb, DBI and dbplyr) and only read the parts of the parquet files that they need. DuckDB uses every core; set the aedes.duckdb_threads option before the first query to use fewer, e.g. on a shared machine.

When no snapshot is given, the newest one at or before the requested time is used: timestamp or the time of version when given, otherwise the aedes.version option (see aedes_set_version()). So by default ("now") this is the newest snapshot, while for "latest" it is the snapshot of the newest materialisation version. aedes_partner_summary() answers queries for later times by fetching the edits made since the snapshot from CAVE (see its details).

The aedes.version option is only changed when you give version or timestamp, so that metadata and root ids from other aedes functions match the synapse data.

If there is no snapshot in root, you are asked whether to download one with aedes_download_snapshot() (in an interactive session) or get an error saying how to.

Every few hours (the aedes.snapshot_check_hours option, default 6; Inf turns this off) it also downloads any new checkpoints that have been published. A new full snapshot is only announced, since it is larger: fetch it with aedes_download_snapshot().

See also

aedes_partner_summary(), aedes_synapse_data()

Examples

if (FALSE) { # \dontrun{
options(aedes.synapse_snapshot_root = "~/data/aedes/syn_snapshot")
aedes_use_snapshot()
# answered locally at the time of the latest materialisation
aedes_partner_summary("class:DNa")
} # }