Upload an Image

In this example, we will show you how to use the BQAPI to upload one of the over 100+ supported Biological formats from a Jupyter Notebook.

The API call goes as follows:

  1. Instantiate a BisQue session
  2. Login using USERNAME and PASSWORD
  3. Upload the Image

STEP 0. Import Dependencies

Before we can even attempt anything cool with the API, we need to import the necessary packages. In this case, we need the following packages:

import os
from bqapi.comm import BQSession

Place these at the top of your Jupyter notebook or Python script to ensure these run first. If you have not installed the BQAPI via pip, then install the BQAPI here.

STEP 1. Instantiate a BisQue session

This instantiation enables the user to effectively communicate with BisQue. Without this, you will not be able to login and interact with the API.

bq = BQSession()

STEP 2. Login using BisQue Credentials

Here is where we will login into our BisQue account to upload the data to our account. We show an alternative chained version (line 2) of the commands here to instantiate the BQSession and login at the same time.

bq.init_local(user, pwd, bisque_root=root)
# bq = BQSession().init_local(user, pwd, bisque_root=root)

Inputs

If you do not have an account on BisQue, make an account here.

Example.

bq.init_local(user=amil_khan, pass=bisque1234,
              bisque_root="https://bisque.ece.ucsb.edu")

STEP 3. Upload the Image

The final step is to upload the image on your local system to BisQue. To do this, we will use the instantiated session bq along with the postblob function to upload the NIFTI image below.

# Post image to BisQue and get the response
image_path = '/PATH/TO/IMAGE/supercoolscientificimage.DICOM'
img_upload = bq.postblob(image_path)

Example. If your image is in the current directory of your Jupyter Notebook, then simply input the filename. Otherwise, specify the full path /home/amil/Documents/T1_brain.nii.gz or ~/Documents/T1_brain.nii.gz.

img_upload = bq.postblob('T1_brain.nii.gz')