Label Utils (SCT)

Simple GUI utility to label spinal cord images. This is a subset of all the commands available with the Spinal Cord Toolbox. Spinal Cord Toolbox (SCT) is a comprehensive, free and open-source set of command-line tools dedicated to the processing and analysis of spinal cord MRI data see the GitHub Repo for more information.

For developers: how the service app works

This service is the oSPARC counterpart of the command line tool for labelling images that comes together with SCT. It provides the same GUI that is used when launching this command: sct_label_utils -i <input-image> -o <output-labels> -create-viewer <label_1,label_2,...,label_n>

<input-image> and <label_1,label_2,...,label_n> are mandatory inputs, for this reason a start-up script checks that the appropriate inputs exists before launching the command above.

Basic concept of osparc-ui modules

An osparc-ui module consists of two services, a web proxy web and the actual application app. The web service acts only as a proxy for integration into the osparc platform. The app service consists of the X11 based GUI application that should be accessible via the osparc iframe and some additional supporting programs:

• supervisord: to control the processes in the container
• xtigervnc: VNC client/server application with embedded X-server
• novnc: opensource javascript vnc client
• openbox: Minimal window manager

Usage

Build the module:

$ make build

To run locally at and visit http://127.0.0.1:28080. For the moment this just waits for the input files. For testing better using publish-local

make run-local

To publish in local throw-away registry:

make publish-local

Workflow

1. The application should be installed via modification of the Dockerfile in sct_label_utils/app
2. The [program:app] section in supervisord.conf in sct_label_utils/app/config needs to be modified to accomodate to the correct command line for the program.

Versioning

Service version is updated with make version-*

CI/CD Integration

A template ci config file is created in.github/.yml)

Github

The required CI is already packaged. To build and push to the internal registry you must add it to the oSparc/docker-publisher-osparc-services repository.