The Jupyter Lab Interface ========================= .. Should we add a note about why we use jupyter lab interface or perhaps link to our blog explaining why. Add a note about the different levels of user experience we have developed. 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". .. Do we need to discuss the password here? Could the system be locked? Once logged in and loaded, the following will be displayed. .. figure:: /images/workspace_edited.png :width: 100% :alt: left sidebar and main workspace in jupyter lab Jupyter Lab Interface .. Insert image of the interface. 1. **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. 2. **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 ------------ .. figure:: /images/sidebar_icons.png :width: 100% :alt: sidebar icons numbered from 1 to 4 Left Sidebar Icons .. Create list with the tab pictures as the bullet points. need to look up how to format this There are four tabs in the left sidebar which can be used to access the *ilumr* content and experiments. 1. File Browser 2. List of Active Terminals and Kernels 3. *ilumr* Dashboards Apps 4. 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. .. figure:: /images/file_browser_edit.png :width: 100% :alt: file browser and open file showing saved shim values 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. .. figure:: /images/kernels_edit.png :width: 100% :alt: tab showing two open tabs and five running kernels 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. .. figure:: /images/dashboard.png :width: 100% :alt: tab showing dashboard apps and FID dashboard 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: 1. System Setup * Admin * Noise Check * Temperature * Find Frequency * Wobble * Pulse Calibration 2. NMR Dashboards * FID * CPMG 3. 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 :ref:`dashboards:Dashboard Apps` section. Notebook Table of Contents ^^^^^^^^^^^^^^^^^^^^^^^^^^ Click the list icon to open the Notebook table of contents tab. .. figure:: /images/contentsbar_edit.png :width: 100% :alt: tab showing different sections of a lab notebook 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. .. figure:: /images/layout.png :width: 100% :alt: subdivided workspce with three dashboards open Workspace Layout