Getting Started

Starting MxDC

Based on how MxDC is installed in your environment, it can be started either by double-clicking the application icon or by typing mxdc in a terminal.

Only one instance of MxDC can be run on a given subnet at a given moment. If another user is currently using MxDC, the program will terminate after presenting a warning.

Stopping MxDC

MxDC can be stopped either by using the window close button, the Quit menu action in the header bar menu, or the Quit action of the application menu, if applicable. You should avoid closing MxDC by closing the terminal from which MxDC was executed, or by using Ctrl-C.

MxLIVE Integration

The MxDC Application relies on and uses MxLIVE for experiment planning and logging. Although MxDC can operate without MxLIVE, it will be significantly limited in usability.

Typically, users plan their experiment by organising their samples into groups, and giving each sample a unique name. For experiments making use of the Automounter, the samples are then organized into containers. Before the experiment, a shipment consisting of all the relevant groups, samples, and relevant containers is sent to the beamline.

When MxDC starts-up, it fetches sample information from MxLIVE. The information fetched, includes details about exact locations in the Automounter as configured by beamline staff. This information can then be used to mount specific samples, and also to organize data storage in the file system.

Creating Directories

By default, a top-level directory is created for each beamtime session, within which all data will be stored. It is no longer possible to store data out-side of this directory using MxDC, and users are strongly advised not to move data files from their saved locations.

Note

For example: A session directory might look like /users/fodje/CMCFBM-20171018 which includes the beamline acronym and the start date of the session.

MxDC automatically organizes how directories are created for saving datasets and related output files within the session directory. A single configuration parameter Directory Template, accesible through the Application Menu, allows users to configure a preferred directory template. The parameter only needs to be set once but there is no limit on how often it can be changed.

Directory Template

All directories will be created within the top-level session directory according to the specified template. You can use sample variables for substituting context-specific values.

Available variables: {sample}, {group}, {container}, {position}, {port}, {date}, {activity}.

The default template is “/{group}/{sample}/{activity}/” which will produce the following directories structure for a sample named bchi-1 in a group named bchi:

MAD Scan output files: /users/fodje/CMCFBM-20171018/bchi/bchi-1/mad-scan/
Raster Scan files: /users/fodje/CMCFBM-20171018/bchi/bchi-1/raster/
Full Datasets: /users/fodje/CMCFBM-20171018/bchi/bchi-1/data/
Test Images: /users/fodje/CMCFBM-20171018/bchi/bchi-1/test/

Note that additional strings can be used in the template as well, and the sequence of template variables is arbitrary. For example, the template “/CONFIDENTIAL/{activity}/{group}/{sample}/” will produce a directory /users/fodje/CMCFBM-20171018/CONFIDENTIAL/data/bchi/bchi-1/ for the data activity.