NDTS-GUI

Overview

NDTS installations on the spectrometer workstation are comprised of the daemon which runs as a service and the NDTS graphical user interface (NDTS-GUI) which provides status information and allows users to make changes to harvesting status, NAN user, and metadata that will be associated with datasets. NDTS is designed to automatically harvest datasets as they complete when harvesting is set to "on", but datasets can also be manually harvested through the NDTS-GUI.

Mapping NAN users to spectrometer workstation users

Datasets harvested need to be associated with a NAN user to allow the datasets to be visible from the Dataset Browser. This is primarily done through the NDTS-GUI where the NAN user may be changed (if the facility manager settings permit the action). By default the NAN user mapped to the spectrometer workstation is selected. The mapping is controlled by the NMR facility manager through a user management page on the NAN portal facility dashboard.

NDTS harvesting defaults

From the Facility Dashboard facility managers use the Manage Facility Users tool to add NAN users to their facility, map those users to spectrometer workstation accounts, set default harvesting settings, and decide how to handle cases where the spectrometer workstation user is not mapped to a NAN user.

When the NDTS-GUI is launched, or when the NAN user selected within the NDTS-GUI is changed, the default settings defined in the Manage Facility Users tool on the NAN web portal are refreshed to the default settings.

If the NDTS-GUI is not running, than NDTS harvesting falls back to the default settings defined in the Manage Facility Users tool

Launching the NDTS-GUI

As the harvesting settings will default to the settings defined in the Manage Facility Users tool it is important that the NDTS-GUI is running at all times so that the harvesting status is visible, and users have the ability to make changes before data collection to ensure proper harvesting and metadata. For this reason, once started the NDTS-GUI has the close button disabled to avoid accidental closing of the application. Users should also setup the NDTS GUI to launch automatically when logging in graphically to the spectrometer workstation.

Manually launch the NDTS-GUI

While it is better to automatically launch the NAN-GUI upon login, it may be launched manually with the command

/opt/nan-dtdaemon/nan_gui

Automatically Launch the NAN-GUI

The exact procedure will depend on which desktop environment you are using and whether you are setting up automatic launching for a single user account or as a system-wide setting for all users.

Checking which desktop environment you are using

echo $XDG_CURRENT_DESKTOP

or

echo $DESKTOP_SESSION

Creating the launcher script

[Desktop Entry]
Type=Application
Exec=/opt/nan-dtdaemon/nan_gui
Hidden=false
NoDisplay=false
Name=NAN GUI
Comment=NDTS graphical interface
X-GNOME-Autostart-enabled=true

Make it executable:

chmod +x ~/.config/autostart/nan_gui.desktop

Add it to the startup scripts

Desktop environment	Adding through menu bar	Adding directly through command line interface
KDE 3		~/.kde/autostart/nan_gui.desktop
KDE4		~/.kde4/autostart/nan_gui.desktop
KDE Plasma and newer versions	System Settings → Startup & Shutdown → Autostart → Add Program…	~/.config/autostart/nan_gui.desktop
GNOME	Install/launch gnome-tweaks → Startup Applications → ‘+’	~/.config/autostart/nan_gui.desktop
XFCE	Settings Manager → Session & Startup → Application Autostart → Add…	~/.config/autostart/nan_gui.desktop

NDTS-GUI Main Window

NDTS GUI

The NDTS GUI has seven lines and three buttons as described here:

• Top text bar: Shows the status of whether a collected dataset will be harvested or not
  • "Data will be transmitted to NAN"
  • "Data will not be transmitted to NAN"
• Middle text bar: Shows whether harvesting is on or off
  • "NAN Transport is running"
  • "Harvesting is suspended"
• Third text bar: Shows whether TopSpin or VnmrJ is running. Note that if TopSpin / VNMRJ is not running the NAN harvesting setting is irrelevant
  • "Topspin / VNMRJ is running"
  • "Topspin / VNMRJ is not running"
• Ignoring job numbers higher than 19999 - States that any jobs collected in a job number higher than the value shown will not be harvested, regardless of the NAN harvesting setting.
  • This value is defined by the facility manager and can be changed in the daemon configuration file. This allows users to run calibration and other experiments that they do not want to be harvested in job numbers higher than the set value where they will not be harvested and avoids the need to toggle harvesting off for such datasets where it is easy to forget to turn it back on.
• Probe: Lists the probe that the NAN system believes is in the instrument.
  • This is simply informational for users to see so that they may let the facility manager know if it is incorrect and will not affect data harvesting if it is wrong. Note that the facility manager sets the currently installed probe from the Facility Dashboard on the NAN web portal and when they do so they apply a date. Therefore, if a probe was physically changed in the instrument, but the facility manager forgot to make the change on the NAN portal, they can do so retroactively and datasets harvested with the incorrect probe will be corrected.
• NAN user: Shows the NAN user currently selected.
  • If no user is selected than it will read "unselected".
    • Note that if the NAN user is unselected than harvesting will default to whatever the facility managers default harvesting setting for unselected users is on the Manage Facility Users tool on the NAN portal.
  • Having the correct NAN user selected is important as only the NAN user, their PI, and the facility manager will have access to the datasets within the Dataset Browser. Data associated with the incorrect user can be rectified by the NAN User or PI as long as the true NAN user is within the same lab group or by the facility manager who has the ability to reassign the data to any NAN user. Note that non PI NAN users are restricted to reassigning datasets to others in their lab-groups to within three months from harvesting.
• NAN harvesting: Allows the user to toggle harvesting on/off.
  • The ability for a user to toggle this setting is dependent on the whether the facility manager allows it for the given user as is defined on the Manage Facility Users tool. Disallowing harvesting to be turned off can ensure that all data is collected while still allowing users to utilize high job numbers for cases where a calibration or test experiment to not be collected. Likewise, disallowing harvesting to be turned on allows an account where data should never be harvested to not be able to accidently turn it on, such as a commercial entity.
• Enter Experiment Details button: Allows the user to change the selected NAN user and provide additional metadata information and is discussed below
• Manual Harvest button: Allows the user to select a dataset that was inadvertently not harvested to be selected and sent to the NAN archive.

NDTS Experimental Details Window

Experiment Details Window

The Experimental Details window allows the NAN user to be changed and metadata to be entered which will then be associated with collected datasets

• NAN user: Allows the operator to select from a list of NAN users.
  • The list of users are those defined by the facility manager from the Manage Facility Users tool and the ability of a workstation user to change the NAN user is also controlled from the Manage Facility Users tool
• Project / Study / Sample: The Projects, Studies, and Samples for the selected NAN user are provided as pull-down lists.
  • This allows users to associate datasets with Projects and Studies and assign Samples at the time of data collection. These assignments can be done later in the dataset browser as well.
• Refresh button: The NAN user lists along with users projects, studies, and samples are pulled automatically every 10 minutes so that changes on the NAN portal are reflected in the NAN GUI in a reasonable time frame. However, in the event that a user is entering data at the same time of setting up data collection (e.g. creating a sample), than they may force a refresh of the user, project, study, and sample lists immediately.
• Solution / Solid toggle: Selects whether the dataset is a solution or solids dataset. In addition to adding that metadata to the datasets it also changes the additional metadata fields available on the screen
• Magic angle spinning: Toggle to indicate that the dataset is collected with magic angle spinning
• MAS rate (kHz): Allows the MAS spinning rate to be entered for cases where the rate is not properly stored in the experimental parameter sets
• Z0drift correction: Allows the Z0 drift rate, if known, to be entered allowing that metadata to be captured with the datasets
• Multi-receiver and time sharing checkboxes: can be checked if either apply
• Notes: User defined text that can be associated with datasets

Overview

An NDTS installation on a spectrometer workstation has two parts:

• NDTS daemon – background service that harvests datasets.
• NDTS-GUI – shows harvesting status and lets users set the NAN user, toggle harvesting, and add metadata.

With harvesting On, datasets are captured automatically at experiment completion; with harvesting Off, users can still harvest manually.

Mapping NAN users to workstation accounts

Harvested datasets must belong to a NAN user to appear in the Dataset Browser. Mappings between workstation logins and NAN users are set by the facility manager in Facility Dashboard → Manage Facility Users. A user can change the selected NAN user in the GUI only if the manager permits it.

NDTS harvesting defaults

Default behaviour—harvesting state, job-number cutoff, handling of unmapped users—is defined in Manage Facility Users. These settings refresh whenever the GUI starts or the selected NAN user changes. If the GUI is not running, the daemon uses those defaults unchanged.

Launching the NDTS-GUI

Because harvesting status should always be visible, configure the GUI to autostart on login. The window’s close button is disabled to prevent accidental exit.

Manual start

/opt/nan-dtdaemon/nan_gui

Automatic start

Identify the desktop environment:

echo $XDG_CURRENT_DESKTOP    # or   echo $DESKTOP_SESSION

Create the launcher file and make it executable:

[Desktop Entry]
Type=Application
Exec=/opt/nan-dtdaemon/nan_gui
Hidden=false
NoDisplay=false
Name=NAN GUI
Comment=NDTS graphical interface
X-GNOME-Autostart-enabled=true

chmod +x ~/.config/autostart/nan_gui.desktop

Desktop environment	Menu method	File method
KDE 3	–	~/.kde/autostart/nan_gui.desktop
KDE 4	–	~/.kde4/autostart/nan_gui.desktop
KDE Plasma (5 +)	System Settings → Startup & Shutdown → Autostart → Add Program…	~/.config/autostart/nan_gui.desktop
GNOME	gnome-tweaks → Startup Applications → ‘+’	~/.config/autostart/nan_gui.desktop
XFCE	Settings Manager → Session & Startup → Application Autostart → Add…	~/.config/autostart/nan_gui.desktop

NDTS-GUI Main Window

NDTS GUI

GUI element	Purpose	Typical states / notes
Status 1	Will the next dataset be harvested?	Data will be transmitted to NAN / Data will not be transmitted to NAN
Status 2	Harvesting state.	NAN Transport is running / Harvesting is suspended
Status 3	Whether TopSpin / VNMRJ is running.	TopSpin / VNMRJ is running / not running
Job-number cutoff	Jobs above this number are ignored.	Value set by facility manager
Probe	Probe recorded for instrument.	Informational; manager can correct retroactively
NAN user	Current user or unselected.	Determines dataset visibility
Harvesting toggle	Turn harvesting On/Off.	User access controlled in Manage Facility Users
Enter Experiment Details…	Opens the Experiment Details window.
Manual Harvest…	Harvest a missed dataset.

Experiment Details Window

Experiment Details Window

Field / control	Function / options
NAN user	Select from users allowed on this workstation (defined in Manage Facility Users).
Project / Study / Sample	Pulldown lists let users link datasets to projects, studies, and samples at acquisition time.
Solution / Solid	Toggle sets sample state and reveals relevant fields.
Magic Angle Spinning	Checkbox.
MAS rate (kHz)	Enter spinning rate if not in parameters.
Z0 drift correction	Enter drift rate (if known).
Multi-receiver	Checkbox.
Time-sharing	Checkbox.
Notes	Free-text notes saved with each dataset.
Refresh	Refresh user, project, study, and sample lists immediately (auto-refresh every 10 min).