Skip to main content

CLI Tools for Cell Locator

Project description

Cell Locator CLI Tools

Provides some utility CLI tools for dealing with Cell Locator annotation files.

  • cl-export enables converting an annotation file to VTK model or binary labelmap.
  • cl-convert enables upgrading annotation files for compatibility with different versions of Cell Locator.

Quick Start

Installation

$ pip install cell-locator-cli

Sample Usage

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

Export a CCF annotation to labelmap and model

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

Export a 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

CLI Documentation

cl-export

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

Export Cell Locator annotations to VTK model or labelmap.

positional arguments:
  annotation            Input Cell Locator annotation file (JSON).

options:
  -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.

Future Work

  • Add option for different strategies regarding merged/separated model files, or use a multi-valued segmentation format rather than binary labelmap.

cl-convert

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

positional arguments:
  src                   Source JSON file. Use '-' to read from stdin.
  dst                   Destination JSON file. Use '-' to write to stdout.

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

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

options:
  -h, --help  show this help message and exit
usage: cl-convert infer [-h] src

positional arguments:
  src         Source JSON file. Use '-' to read from stdin.

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

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

cell_locator_cli-0.1.0.tar.gz (29.0 kB view details)

Uploaded Source

Built Distribution

cell_locator_cli-0.1.0-py3-none-any.whl (19.4 kB view details)

Uploaded Python 3

File details

Details for the file cell_locator_cli-0.1.0.tar.gz.

File metadata

  • Download URL: cell_locator_cli-0.1.0.tar.gz
  • Upload date:
  • Size: 29.0 kB
  • Tags: Source
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/4.0.1 CPython/3.9.15

File hashes

Hashes for cell_locator_cli-0.1.0.tar.gz
Algorithm Hash digest
SHA256 51e7d818fabedf6fed46e03e498246fe6c0577e8447e625b60a20b457965d195
MD5 cfadb2f42838ff397a42a80261d7f708
BLAKE2b-256 724b7ba24f182b06223efcafb4156385188da17580be38c3c4d65abbf2f6a09f

See more details on using hashes here.

File details

Details for the file cell_locator_cli-0.1.0-py3-none-any.whl.

File metadata

File hashes

Hashes for cell_locator_cli-0.1.0-py3-none-any.whl
Algorithm Hash digest
SHA256 caff46d654df165cc740fd4a9a7ad4d7a3af2b1b7f0a02c382601c9ea3f248b5
MD5 a2625627d22bd5b8f8d7e17c63ec28ad
BLAKE2b-256 6e01e6d6e9d3d4c3ea7732206d92193c6bf8646376925463f8b6f1a0f8e97efd

See more details on using hashes here.

Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page