blackfynn 1.7.2

Python client for the Blackfynn Platform

Python client and command line tool for Blackfynn.

Installation

Note: we currently only support Python v2.7.

pip install blackfynn

Credentials Setup

Connection credentials to Blackfynn can sourced from environment variables. In your ~/.bashrc or ~/.bash_profile, set the following variables. Before using the client library or command line tool, ensure these environment variables are set.

export BLACKFYNN_USER=[e-mail]
export BLACKFYNN_PASS=<your-password>

Client Library

Basic Usage: examples

# imports
from blackfynn import Blackfynn

# client
bf = Blackfynn()

# If you belong to more than one organization, explicitly set your context, otherwise, ignore.
bf.set_context('my organization name')

# print your available datasets
datasets = bf.datasets()
print datasets

# grab some dataset (e.g. first one)
ds = datasets[0]

# list items inside dataset (first level)
print ds.items

Upload data

Upload files

You must upload files into a Dataset or Collection.

# upload a file into a dataset (ds)
ds.upload_files('/path/to/my_data.nii.gz')

Retrieve data

Retrieve timeseries data

ts = bf.get('N:package:your-timeseries-id')

# get first minute of data in 1-second chunks
for chunk in ts.get_data_iter(chunk_size='1s', length='1m'):
    # do something with data (pandas Dataframe)
    print "Mean values =", chunk.mean()

# you can do the same thing for a single channel
channel = ts.channels[0]
for chunk in channel.get_data_iter(chunk_size='5s', length='10m'):
    # do something with data (pandas Series)
    print "Max value =", chunk.max()

Command Line Tool

Usage

>> bf --help
Blackfynn Client

Usage:
  bf upload [options] <destination> <file> [<file>...]
  bf append [options] <destination> <file> [<file>...]
  bf search [options] <term> [<term>...]
  bf datasets [options]
  bf dataset [options] <dataset> [<command>] [<action>] [<action-args>...]
  bf create [options] collection <destination> <name>
  bf create [options] dataset <name>
  bf delete [options] <item>
  bf show [options] <item>
  bf orgs [options]
  bf env [options]
  bf version

Options
  -h --help       Show help.
  --user=<user>   Email/username
  --pass=<pass>   Password
  --host=<host>   Blackfynn host
  --org=<org>     Set organization context

Basic examples

Show your setup

bf env

Show your datasets

>> bf datasets --org blackfynn
Datasets:
 - Studies (id: N:dataset:12aba9af-650c-4fd5-b150-ae77a60a92a0)
 - NICU (id: N:dataset:4fb54fdf-aafb-4746-96bc-25b9f6588254)
 - Blackfynn (id: N:dataset:5a6779a4-e3d8-473f-91d0-0a99f144dc44)
 - Streaming (id: N:dataset:79627c2f-cd6c-4095-8f15-4114c80290ec)
 - Patients (id: N:dataset:967ff102-d2d1-4e11-a8c8-a72c99d70b48)
 - Subjects (id: N:dataset:e4189eb0-6e66-47e6-8a23-80d81f4a0095)

Search for things

>> bf search Fred
 * <TimeSeries name='Fred Tugwell' id='N:package:5385f12f-879e-4d9e-a3c2-b7ff798972d8'>
 * <TimeSeries name='Fred Heard' id='N:package:a3e6f016-f9b7-44f3-bb74-0a027935fba6'>

Show specific item

>> bf show 'N:package:1234-1234-1234-1234'

File uploads

Upload a file into a Dataset.

bf upload 'N:dataset:1234-1234-1234-1234' /path/to/my_data.nii.gz

Upload all files and directories into a dataset. This action will create a collection named ‘folder’, and recursively upload all contents into this collection.

bf upload 'N:dataset:1234-1234-1234-1234' /path/to/folder

If your environment variables are not set, you can also enter credentials

bf upload --user=<email> --pass=<pass> 'N:dataset:1234-1234-1234-1234' /path/to/data_i_want_to_upload.mef

Append data into an existing TimeSeries object (note: append process currently only supports timeseries data)

bf append 'N:package:1234-1234-1234-1234' /path/to/data_i_want_to_append.mef