Command Line Tools

Utility CLI tools for processing Cell Locator annotation files.

For information on extending cl-convert, see the Converter API Documentation

Installation

$ pip install cell-locator-cli

Tools

cl-export

Export Cell Locator annotations to VTK model or labelmap.

usage: cl-export [-h] [-m MODEL_PATH] [-l LABELMAP_PATH] [-a ATLAS_PATH]
                 [--pir]
                 annotation

annotation: Input Cell Locator annotation file (JSON).

-h, --help: show this help message and exit

-m <model_path>, --model <model_path>: Output path for annotation model. If not provided, model generation is skipped.

-l <labelmap_path>, --labelmap <labelmap_path>: Output path for annotation labelmap. If not provided, labelmap generation is skipped. Requires –atlas for spacing information.

-a <atlas_path>, --atlas <atlas_path>: Atlas volume or labelmap. Used to set spacing/direction on the output labelmap.

--pir: If set, read the annotation in PIR format rather than RAS. This should only be necessary for old-style CCF annotations.

cl-convert

A tool used to upgrade annotation .json files through breaking changes to the file format. The converter can also downgrade file formats, but this is not as thoroughly tested.

usage: cl-convert [-h] {convert,versions,infer} ...

-h, --help: show this help message and exit

cl-convert convert

usage: cl-convert convert [-h] -v VERSION [-t TARGET] [--no-indent] src dst

src: Source JSON file. Use ‘-’ to read from stdin.

dst: Destination JSON file. Use ‘-’ to write to stdout.

-h, --help: show this help message and exit

-v <version>, --version <version>: Source file version. Use ‘-v?’ to infer the version.

-t <target>, --target <target>: Target file version. Defaults to the latest version.

--no-indent: Do not indent output JSON.

cl-convert infer

usage: cl-convert infer [-h] src

src: Source JSON file. Use ‘-’ to read from stdin.

-h, --help: show this help message and exit

cl-convert versions

usage: cl-convert versions [-h] [target]

target: Show versions matching this target. If empty, show all versions.

-h, --help: show this help message and exit

Sample Usage

Export an MNI annotation to labelmap and model

$ cl-export \
   mni-annotation.json \
  -m mni-annotation.vtk \
  -l mni-annotation.label.nrrd \
  -a mni_annotation_contiguous.nrrd
$ f3d mni-annotation.vtk
$ f3d -v mni-annotation.label.nrrd

Export a CCF annotation to labelmap only

$ cl-export \
  ccf-annotation.json \
  -l ccf-annotation.label.nrrd \
  -a ccf_annotation_25_contiguous.nrrd \
  --pir
$ f3d ccf-annotation.vtk
$ f3d -v ccf-annotation.label.nrrd

Update an old annotation file

$ cl-convert convert -v'?' -t v0.2 older.json newer.json
Inferred version 'v0.0.0+2020.08.26'
$ cl-convert infer newer.json                           
v0.2.1+2022.03.04

Version Identifiers

cl_convert.converters.match(target)

Find the most-recent versions matching the target.

Prefix with d to interpret as a date. Prefix with v, or no prefix, to interpret as a literal version.

Example Versions	`v1.1`	`v1.1.`	`d2020.`
`1.1.0+2019.02.01`	yes	yes	no
`1.1.1+2020.02.07`	yes	yes	yes
`1.2.0+2020.05.01`	no	no	yes
`1.10.1+2021.03.01`	yes	no	no

Parameters:: target – String describing target versions.
Returns:: Matching versions, in order of precedence (most-recent first)