Session 1. DAWN Training - Data Browsing

Session 1. DAWN Training - Data Browsing

This is the first in a series of training sessions to use the DAWN software suite. The aims of this tutorial are :

  • to become familiar with the main DAWN workbench

  • learn what perspectives, editors and views are, and how they can be opened, closed, found and customized

  • use the two data viewing perspectives Data Browsing and DExplore to open files and view data

  • investigate the different methods of viewing multidimensional data

  • perform basic modification of the plotted data, e.g. change the colormap and contrast/brightness of an image or change the axis of a plot to be log....

1. Running DAWN

Diamond Linux Workstations

On a Linux workstation within Diamond, type:

 

[user@workstation ~]$ module load dawn Loading 64-bit Oracle instantclient, version 11.2 Loading 64-bit python, version 2.7.2 Loading 64-bit numpy, version 1.6.1 Loading 64-bit scipy, version 0.10.0 Loading the DLS compute cluster environment. Please report any issues to linux.manager@diamond.ac.uk ***************************************************************** ** DAWN (Data Analysis WorkbeNch) module loaded ** ***************************************************************** To start the application, type "dawn &" For further options, type "dawn --help" **************************************************************** [user@workstation ~]$ dawn &

Anywhere else...

Dawn does not need to be installed, it just needs to be unzipped and run.

Go to: http://www.dawnsci.org/ and head to the download section. Versions for Linux and Windows, x32 and x64 are available. A version for Mac is also available but not supported.

The download is a zip file containing Dawn. Extract the contents of the zip file to a sensible location (for example C:\Dawn). The executable file for Dawn can be found in the extracted folder (DawnDiamond-version number).

 

  • Start DAWN.

2. The Welcome Screen

The first time DAWN is started it opens with the welcome screen showing (if this is not the first time DAWN has started, it will start in the same configuration it was closed in, if this is the case, follow the next set of instructions to return to the welcome screen):

When using DAWN you can return to the welcome screen at any time by pressing the home button.

The Welcome screen contains lots of useful information on how to use DAWN, including links to the web page and youtube channel. DAWN is like a collection of different data analysis programs organised in Perspectives.

  • Click on the perpectives panel now.

This should bring up a list of all the perspectives available in DAWN.

The tools this set of tutorials cover are:

  • Data Browsing

  • DExplore

  • Workflows

  • Python

Exercise 1. Click an icon to open one of the perspectives, then find the home button in the toolbar and click to return to the welcome screen. Click the perspectives panel to return to the list of perspectives.

3. Browsing Data

The goal of the first in this series of training sheets is to use the two generic data viewing perspectives (Data Browsing and DExplore) to visualize different types of data (images, surfaces, traces...) from different types of files (Nexus/hdf5, tiff, img....) and become comfortable with using and changing the versatile interface DAWN provides.

 

  • Click on the icon for the Data Browsing perspective

You will be greeted with a largely blank screen with lots of empty tabs, don't worry about that for now.

Opening A File

Find the Project Explorer tab on the left hand side of the screen (it should be the only one that isn't blank).

  • Expand the data folder to located the example data, double click on the file pow_M99S5_1_0001.cbf (if you do not have this file you may be running with example data from an older version of DAWN. See Appendix I to find out how to get up-to-date example data).

This opens the powder diffraction image for display.

The Project Explorer is like a favorites page for your data, you can link to folders of data on your local computer to this tab without making duplicates of the data.

Make a new data project

  • Go to File -> New..., Project... in the Select Wizard dialog, go to the Data folder and select Data Project

  • Call the project MyData and select a folder containing your data by browsing for the data directory (data can be provided if you don't have your own)

MyData should now be displayed in the Project Explorer

Data can also be opened directly from the file system using the File Navigator tab, or by dragging and dropping directly from a file explorer

Exercise 2. Use the File Navigator to open some data.

Exercise 3. Open some data by directly dragging it into the DAWN plot

Exercise 4. Add a folder to the Data Project by dragging the folder and dropping it in with the example data (choose to link rather than copy)

Editors and views - Plot/Text/Data/Tree

Now lets return to the diffraction image we have displayed.

On double-clicking the file some new tabs appeared and many of the previously blank views now show information. Before we dive in to opening and viewing different types of data lets take a minute to discuss some nomenclature that should make the rest of the tutorial more understandable.

Perspectives

The Data Browsing tool you are currently looking at (and all the other tools mentioned, like DExplore, Workflows....) are technically called Perspectives. In DAWN, a perspective is simply a collection of different tab views designed to help perform a certain task, be it to view and image, or write a python script. Many of these views appear in multiple perspectives and if you see a view in one perspective that looks the same as in another, there is a good chance they will work the same way.

The Editor

Most perspectives show an editor tab, one for each file open. The editor is the tab view that appears when you open a file (it has the name of the file at the top of the tab).  DAWN has different editors for images, nexus files, dat files, python scripts... many different things.  You don't need to worry about which editor you are looking at, DAWN automatically chooses the best editor for the type of file you want to open. (The name "Editor" is a bit odd considering the data files you open cannot be edited. When python source code or a workflow moml file is opened, on the other hand, these also appear in an editor and can be edited).

Views

Pretty much everything that is not an editor is a view. You can identify a view by the name it shows at the top of its tab.

Exercise 5. Locate the Editor and the Meta data, Value, Progress, and Console views in the Data Browsing perspectives, click on the tab to see what each view contains (most will be empty at this stage)

  • Return to the example data project, open MoKedge_1_15.dat

See how a new editor has appeared containing a blank plot and the Meta data view has changed to the Data view. The Data view contains a list of every data set found in the .dat file.

Take another look at the editor.  You should notices some tab pages at the bottom which say Plot, Text, Data and Info. Switch between these tabs to see what they show.

Dat File Editor

  • Plot - shows the currently plotted data (empty if no data selected)

  • Text - a .dat file is just a text file, this tab shows the raw text of the file

  • Data - shows the data which has been selected to plot (or just a warning if no data is selected)

  • Info - shows the name, minimum and maximum values and the type of data each data set holds.