Flyhweel Software Developer Kit (SDK) Basics and Helpful Hints

Date modified: 28-July-2022 Authors: Amy Hegarty, Lena Sherbakov, Intermountain Neuroimaging Consortium

Description: The following includes a set of basic SDK commands for Flywheel. Examples included below:

Basic Flywheel Heirarchy (finding a session)

Links

Flywheel SDK documentation here
Flywheel python SDK examples here

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print("Welcome to Intermountain Neuroimaging Consortium!")

Welcome to Intermountain Neuroimaging Consortium!

Import Python Dependencies

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import os
import logging
import flywheel

Define Supporting Functions

Flywheel API Key and Client

An API Key is required to interact with the datasets on flywheel db. More on this in the Flywheel SDK doc here. Here we pull the API key directly from the user’s os enviornment, set within the flywheel command line interface.

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# Instantiate a logger
logging.basicConfig(level=logging.INFO, format='%(asctime)s %(levelname)s %(message)s')
log = logging.getLogger('root')

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# Create client, using CLI credentials
fw = flywheel.Client()

# who am I logged in as?
log.info('You are now logged in as %s to %s', fw.get_current_user()['email'], fw.get_config()['site']['api_url'])

Viewing a Flywheel Project

The fw.lookup function can be used to find any container in flywheel by path. This is an easy way to find projects, subjects, or sessions. Lets view a Flywheel project and list all sessions and their scan date.

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project = fw.lookup('<group>/<project>')

# lookup function pulls a lite version of the project object. Get the actual project object...
project = fw.get(project.id)

# loop through all project sessions
for session in project.sessions.find():

    # Loop through all sessions in the project container.
    dt = session.timestamp
    if not dt:
        dt = "NAN"
    else:
        dt = dt.strftime(" %x %X")
    print('%s: Subject: %s Session: %s\tScanning Date: %s' % (session.id, session.subject.label, session.label, dt))

Viewing a Flywheel Analysis

Similarly, we can view analyses that have been either uploaded to Flywheel or generated by running flywheel gears. Here, lets look for all analyses attached to a single session.

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# start by finding a session of interest
session = fw.lookup('<group>/<project>/<subject>/<session>')

# we need to take an extra step to get the full session object, not just basic info
session_object = fw.get_session(session.id)

# print all the analyses for this session
for analysis in session_object.analyses:
    if hasattr(analysis.job,'state'):
        print('%s: %s %s' % (analysis.id, analysis.label, analysis.job.state))
    else:
        print('%s: %s' % (analysis.id, analysis.label))

Update Metadata In Flywheel

In this example, lets rename an acquisition to add an “include-BIDS” suffix used to indicate to skip BIDS curation for that acquisition.

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for acq in session_object.acquisitions():
    # get the full acquisition object
    acq = fw.get(acq.id)
    acq.update({'label':acq.label+"_ignore-BIDS"})

Looking for more? Check out our github repository with some commonly used SDK examples! (here)<>