The Jupyter Lab Interface
The Jupyter Lab interface may initally take some time to load. If a pop up appears while it is loading that reads “Loading… This loading screen is taking a long time. Would you like to clear the workspace or keep waiting”, click “Continue Waiting”.
Once logged in and loaded, the following will be displayed.
Jupyter Lab Interface
Left Sidebar: The left sidebar contains a number of tabs that open additional sidebars. These sidebars provide access to various features. Each sidebar can be collapsed or expanded by simply clicking on the active tab.
Main Workspace: The main workspace is a customisable space where all active windows are displayed. Dashboards, terminals, notebooks, and text editors can be laid out in this space.
Left Sidebar
Left Sidebar Icons
There are four tabs in the left sidebar which can be used to access the ilumr content and experiments.
File Browser
List of Active Terminals and Kernels
ilumr Dashboards Apps
Notebook Table of Contents
Note
Note that the dashboard app sidebar (with the ilumr icon) is an extension unique to ilumr, and not a part of the standard jupyterlab environment.
File Browser
Click the file icon. The following sidebar will appear.
Jupyter Lab File Browser
The file browser is a folder structure containing directories for system parameter files, custom jupyter notebooks, data saving, and user guides.
System - Read-only folder containing Python code for system dashboard apps and pulse programs.
Notebooks - Directory for storing notebooks, these are powerful, customisable workflows capable of data acquisition, processing, and visualisation. Some example notebooks are provided.
Globals - Files containing system related global parameters.
Data - Directory for data files saved by dashboard apps and Notebooks.
Active Terminals and Kernels
Click the icon that looks like a stop button. This will open the active terminals and kernels tab.
Active Tabs and Kernels
The active tab shows you which notebooks are open and which kernels are running.
Having many notebooks open at once can use a lot of system memory and slow ilumr down. If you notice any issues, you can use this tab to shutdown the running kernels or unused notebooks and free up system resources.
ilumr Dashboard Apps
Click the ilumr icon to open up the dashboard apps menu.
Dashboard Apps
The dashboard apps provide the user with a simple way of both setting up the instrument for use and running some standard experiments.
The 3 main categories for these apps are as follows:
- System Setup
Admin
Noise Check
Temperature
Find Frequency
Wobble
Pulse Calibration
- NMR Dashboards
FID
CPMG
- MRI Dashboards
1D SE
2D RARE
2D RARE Advanced
3D RARE
3D RARE Advanced
3D FISP
Slice Viewer
You can learn more about using these dashboards in the Dashboard Apps section.
Notebook Table of Contents
Click the list icon to open the Notebook table of contents tab.
Notebook Contents
This tab helps you navigate quickly through long Jupyter Notebooks. If you are viewing a dashboard or a Notebook without headings, this tab will be empty. If you are viewing a Notebook with headings, you will see a hierarchical heading list as shown above. Click each heading to skip to that section in the Notebook.
Main Workspace
This area allows you to arrange dashboards and other activities into panels of tabs that can be resized or subdivided. To try, click a few of the dashboards to open them up. When clicked, they will by default open on the currently active panel.
Try dragging a tab around the work area and see how options for subdividing the work area are highlighted using pale blue boxes. Release the tab into an area and then resize it as required.
The work area can have a single interactive activity and this is marked with a blue border on the top of the active tab. However, dashboards that do not require interaction will continue to receive data even if they are not selected as the active tab, for example, the temperate monitoring dashboard updates continuously.
Workspace Layout