Title: Run local analysis and upload back to Flywheel
Date: 15-Apr-2020
Description:
Find and download input file from flywheel, process locally, create an analysis container and upload local process outputs to it.

Topics that will be covered:

• Find file in Flywheel Acquisition container
• Download file and run analysis locally
• Create Analysis container
• Local outputs are uploaded to the Flywheel Analysis container.

Install and import dependencies

# Install specific packages required for this notebook
!pip install flywheel-sdk nipype

# Import packages
from getpass import getpass
import logging
import os
from pathlib import Path

import flywheel
import nipype
from nipype.interfaces.image import Reorient
from permission import check_user_permission

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

Flywheel API Key and Client

Get a API_KEY. More on this in the Flywheel SDK doc here.

API_KEY = getpass('Enter API_KEY here: ')

Instantiate the Flywheel API client

fw = flywheel.Client(API_KEY if 'API_KEY' in locals() else os.environ.get('FW_KEY'))

Show Flywheel logging information

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

Requirements

Before starting off, we want to check your permission on the Flywheel Instance in order to proceed in this notebook.

min_reqs = {
    "site": "user",
    "group": "ro",
    "project": ['analyses_create_sdk','files_view_contents','files_download','files_create_upload',]
    
}

Tip: Group ID and Project Label can be found on top of the Project page on the Flywheel Instance as shown in the snippet below.

GROUP_ID = input('Please enter the Group ID that you will use in this notebook: ')

PROJECT_LABEL = input('Please enter the Project Labelt that you will use in this notebook: ')

check_user_permission will return True if both the group and project meet the minimum requirement, else a compatible list will be printed.

check_user_permission(fw, min_reqs, group=GROUP_ID, project=PROJECT_LABEL)

Constants

# Flywheel path to the acquistion container with the file we want to process locally
FW_PATH_TO_ACQ = '<you-group>/<your-project>/<subject.label>/<session.label>/<acquisition.label>'
# Filename of the file we want to process locally
FILENAME = '<the-input-filename-here.ext>'
# Path where the input files will be download
DOWNLOAD_PATH = '/tmp'

Main script

Find file

Find the flywheel acquisition container by performing a lookup

acquisition = fw.lookup(FW_PATH_TO_ACQ)

Find the file in that acquisition container by name

file = acquisition.get_file(FILENAME)

Download file locally

dest_path = str(Path(DOWNLOAD_PATH) / FILENAME)

file.download(dest_path)

Process file locally

This is a very simple processing which is just reorienting the nifti image

reorient = Reorient(orientation='LPS')
reorient.inputs.in_file = dest_path
res = reorient.run()
out_file = res.outputs.out_file
log.info('Output file saved to: %s', out_file)

Create analysis container

Create an analysis container attached to the session with reference to the input files

session = fw.get_session(acquisition.parents.session)
analysis = session.add_analysis(label='My Analysis label', inputs=[file.ref()])

Upload the output file to analysis container

analysis.upload_output(out_file)

Check the uploaded file

analysis = analysis.reload()

assert analysis.files[0].name == os.path.basename(out_file)
assert analysis.files[0].size > 0