Computational organization
Flywheel supports three types of programming interactions. Gears support stable software tools that many people might use, such as the FSL, FreeSurfer, BIDS, or HCP programs. The [Software Development Kit](Computational-organization#Software Development Kit (SDK)) supports people who are developing specialized analyses; these analyses may be developed for a particular project and experimental design. As the development stabilizes, it might become a Gear. The Command Line Interface is available from the Flywheel instance. This is software that performs various tasks such as uploading and downloading projects and sessions.
Flywheel Gears are a way to share stable and used software. Flywheel has converted many programs into Gears, including some of the FSL, Freesurfer, ANTS and HCP programs. We use Chris Rorden's dcm2niix utility frequently. Nearly any program that runs without user-intervention can be transformed into a Flywheel Gear.
To see the Gears installed at your site click on 'Gears installed' on the left panel of the Flywheel web page. Most sites have added Gears based on their specific interests. These Gears can be based on a compiled program, or they can be based on Python, Matlab or R programs. Read about Gears on this page.
The Flywheel system lets users automatically run a particular Gear when data of a certain type are entered into the database. The system also makes a distinction between Utility Gears and Analysis Gears. The first group includes methods such as conversion between file formats, quality assurance, and data classification. The second group includes more advanced analysis methods, such as atlas alignment, tissue segmentation, and tractography.
To run a Gear the Flywheel system schedules a Job. Flywheel can schedule many Jobs, and depending on the system resources these may run in parallel. For example, you may instruct the Flywheel system to start 100 Jobs with the FreeSurfer Gear. These will be scheduled, and each Gear can be run on a different data set. The Flywheel system will start, monitor, and finish the Jobs based on the available system resources. A FreeSurfer job might take 5 few hours. If you are running on a Cloud platform where many resources can be summoned, running 100 Jobs only takes a little longer than running 1 Job.
The inputs, program parameters, and results of a Job will be stored in the Analysis tab. There is an Analysis tab for each Session, and there is an Analysis tab for each Project. A record of when the Jobs were run and their status (e.g., running or completed) is available in the Provenance Tab.
Many people write their own analysis programs; during this process it may be essential to access Flywheel data and methods. The Flywheel-SDK is a collection of utilities that developers use to interact with Flywheel from their programming environment, either Python, Matlab or R. The scitran methods described here are a wrapper on the Matlab version of the Flywheel-SDK.
Scitran methods use the Flywheel-SDK to interact with data containers, data files, info (metadata), analyses, Gears, and Jobs. The methods are named using a convention of objectAction. For example, suppose you create a scitran object,
st = scitran('stanfordlabs');
Here are examples of methods.
st.containerDownload - downloading one of the several container types
st.containerCreate - create a container on the remote site
st.fileDownload - downloads a data file
st.fileDelete - delete a file
st.analysisUpload - create and upload an analysis structure
If you would like to perform a task involving a data file, and you are wondering what methods are available, use tab-completion (e.g., st.fileTAB) to see the list of File methods. Documentation about a method is available through
doc scitran
doc scitran.containerDownload
doc scitran.<METHOD_NAME>
Examples of the methods are often available you can find them using the stExamplesShow function.
stExamplesShow('scitran.containerDownload');
stExamplesShow('scitran.fileRead');
stExamplesShow('scitran.analysisDownload');
The Flywheel-SDK also includes methods for securely connecting to the site, reading and writing data and metadata, storing analysis results, creating projects, controlling Gears and Jobs, and more.
The command line interface software enables you to perform data upload and download operations, as well as to execute Gears from your command line. The CLI software ('fw') can be downloaded through the user profile page on the Flywheel instance.
The CLI installation instructions are here and the CLI Documentation is here.
After installation, use fw help to see the options
$ fw help
Flywheel command-line interface
Usage:
fw [command]
Available Commands:
batch Start or manage server batch jobs
download Download a remote file or container
export Export data from Flywheel
gear Gear commands (requires Docker)
help Help about any command
import Import data into Flywheel
job Start or manage server jobs
login Login to a Flywheel instance
logout Delete your saved API key
ls Show remote files
status See your current login status
upload Upload a remote file
version Print CLI version
Flags:
-h, --help help for fw
Use "fw [command] --help" for more information about a command.