Toolboxes class

Creating and uploading an FTM file

The toolboxes object (in this case called tbx) contains two types of information. One is a command that can be executed to test whether the toolbox is on the path (testcmd). The second is a structure that contains enough information to download a git repository.

disp(tbx)
  toolboxes with properties:

    testcmd: 'dtiError'
    gitrepo: [1×1 struct]

The gitrepo structure contains this information

>> disp(tbx.gitrepo)
       user: 'scitran-apps'
    project: 'dti-error'
     commit: 'master'

scitran data directory includes several examples and a script s_tbxSave, that writes out toolbox files. They are written out as JSON files with the git repo projection and a .json extension.

tbx = toolboxes('');
tbx.testcmd     = 'dtiError';
tbx.gitrepo.user    = 'scitran-apps'; 
tbx.gitrepo.project = 'dti-error'; 
tbx.saveinfo;

Toolboxes can be combined into a single file and uploaded to a Flywheel project page. In this example, the stToolbox() function reads a JSON file for two repositories. These are placed in an array, and written out to a new JSON file.

tbx(1) = stToolbox('dtiError.json');
tbx(2) = stToolbox('vistasoft.json');
tbxWrite('aldit-toolboxes.json',tbx);
% Subsequently, your could read the combined file
% tbx = stToolbox('aldit-toolboxes.json');

% upload to the project page
project = st.search('project','project label exact','ALDIT');
st.upload('aldit-toolboxes.json','project',project{1}.project.x_id);

Toolboxes methods

The key toolboxes methods are saveinfo, install and clone. These methods add a github repository with your project's toolbox onto your Matlab path. The scitran method, 'runFunction', downloads and executes a function stored on the Flywheel site, typically on a project page, that relies on these toolboxes.

We suggest that you include the toolboxes.install or toolboxes.clone within the function you are sharing and that will be executed by scitran.runFunction. The toolboxes command first check whether the toolbox is on your path, and the function only downloads if the toolbox is not present.

saveinfo

install

Read a toolbox.json file and get a zip archive, put it on path

clone

Clone a a git repository and add it to your path. cloneDepth allowed.

Creating and uploading a toolbox.json file

Examples

Single unit physiology (Newsome)

FMRI example (Logothetis)

ECoG example (Hermes)