[4.2] Reusable visualization tools for Jupyter.md

Reusable visualization tools for Jupyter

About

This project is to rewrite the widgets in The virtual brain user Interface to become reusable components which can be employed from a Jupyter notebook for use in the Human Brain Project collaboratory, while maintaining compatibility with the existing the virtual brain framework.

**original proposal

As a major feature of The Virtual Brain, anatomical visualization already provides a basic 3D and 2D output. To further employed to a Jupyter notebook for use in the Human Brain Project (HBP) collaboratory, I can use webgl with the help of plotly with is a python library to visualize 3d volumes and glyphs in Jupyter notebook to render it,

Accomplishments

**Reports and discussion

Github Pull Request(PR)

**PR1

**PR2

Prepare and understand a clean TVB working environment

Install Anaconda for python 2.7, and create tvb-run environment Clone tvb-library from Github activate tvb-run env and run "python setup.py develop" in tvb-library cloned folder Jira.

Fix tvb.simulator.plot module in branch neotraits

Based on my inventory in the previous task TVB NOTEBOOKS VISUALIZATION METHODS INVENTORY Jira.

Move all plot related code into tvb.simulator.plot module

I start by moving All plot in Tvb-documentation to tvb.simulator.plot module.

Jira.

3D plots for basic tvb-datatypes

Implement and reuse 3D viewers:

Connectivity Surfaces (cap, cortical, face, etc) Sensors (eeg, meg, seeg) Region mapping Rotate, translate, zoom

Transparency

Jira.

Review the 3D anatomical viewers

Review and plement anatomical viewers Jira.

Improve the phase plane viewer

Fix some errors of the phase plane improve it layout, buttons and some more. Jira.

Work Left

For the last thing that remain is *Interactive Time Series Visualizer with iam working on (Wipp) i will complete it even after the deadline of Google Summer of Code.

Conclusions

I am delighted to say it was a very pleasant one. I think I was really lucky having Lia Domide and Paula Popa as my mentors. they did such a great job in coaching and helping me throughout the project, without their support i can't make it this far. Overall I definitely enjoyed working with them.

I have acquired new skills and knowledge in Jupyter Notebook from ploting up to the writing class, ploting with plotly, Object orientation and alot more all because of Google Summer of code. Also, the entire TVB project is very appealing to me and I intend to continue contributing and maintain all what i have done and even create new features to THE VIRTUAL BRAIN And it Umbrella INCF.