Running FlatmapMaker¶

Generate a flatmap from its source manifest.

usage: mapmaker [-h] [-v] [--log LOG_FILE] [--silent] [--verbose]
                [--background-tiles] [--clean-connectivity]
                [--disconnected-paths] [--force] [--id ID] [--ignore-git]
                [--ignore-sckan] [--invalid-neurons] [--path-arrows]
                [--path-layout] [--no-path-layout] [--publish SPARC_DATASET]
                [--sckan-version {production,staging}] [--authoring] [--debug]
                [--only-networks] [--save-drawml] [--save-geojson]
                [--tippecanoe] [--initial-zoom N] [--max-zoom N]
                [--max-raster-zoom N] [--commit GIT_COMMIT]
                [--export-bondgraphs] [--export-features EXPORT_FILE]
                [--export-neurons EXPORT_FILE] [--export-svg EXPORT_FILE]
                [--manifest MANIFEST_PATH] [--single-file {celldl,svg}]
                --output OUTPUT --source SOURCE

Named Arguments¶

-v, --version: show program’s version number and exit

Logging¶

--log

Append messages to a log file as JSON

--silent

Suppress all messages to screen

Default: False

--verbose

Show progress bars

Default: False

Map generation¶

--background-tiles

Generate image tiles of map’s layers (may take a while…)

Default: False

--clean-connectivity

Refresh local connectivity knowledge from SciCrunch

Default: False

--disconnected-paths

Include paths that are disconnected in the map

Default: False

--force

Generate the map even if it already exists

Default: False

--id

Set explicit ID for flatmap, overriding manifest

--ignore-git

Don’t check that sources are committed into git

Default: False

--ignore-sckan

Don’t check if functional connectivity neurons are known in SCKAN. Sets –invalid-neurons option

Default: False

--invalid-neurons

Include functional connectivity neurons that aren’t known in SCKAN

Default: False

--path-arrows

Render arrows at the terminal nodes of paths

Default: False

--path-layout

Do TransitMap optimisation of paths

Default: False

--no-path-layout

Don’t do TransitMap optimisation of paths

Default: False

--publish

Create a SPARC Dataset containing the map’s sources and the generated map

--sckan-version

Possible choices: production, staging

Overide version of SCKAN specified by map’s manifest

Diagnostics¶

--authoring

For use when checking a new map: highlight incomplete features; show centreline network; no image tiles; no neuron paths; etc

Default: False

--debug

See log.debug() messages in log

Default: False

--only-networks

Only output features that are part of a centreline network

Default: False

--save-drawml

Save a slide’s DrawML for debugging

Default: False

--save-geojson

Save GeoJSON files for each layer

Default: False

--tippecanoe

Show command used to run Tippecanoe

Default: False

Zoom level¶

--initial-zoom

Initial zoom level (defaults to 4)

Default: 4

--max-zoom

Maximum zoom level (defaults to 10)

Default: 10

--max-raster-zoom

Maximum zoom level of rasterised tiles (defaults to maximum zoom level)

Miscellaneous¶

--commit

The branch/tag/commit to use when the source is a Git repository

--export-bondgraphs

Export functional modelling components as CellDL bondgraphs

Default: False

--export-features

Export identifiers and anatomical terms of labelled features as JSON

--export-neurons

Export details of functional connectivity neurons as JSON

--export-svg

Export Powerpoint sources as SVG

--manifest

The relative path of the manifest when the source is a Git repository

--single-file

Possible choices: celldl, svg

Source is a single file of the designated type, not a flatmap manifest

Required arguments¶

--output

Base directory for generated flatmaps

--source

Path of a flatmap manifest or the URL of a Git repository: containing a manifest. The –manifest option is required if the source is a Git repository