The file system structure
The image format
Download a sample dataset (300kB)

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The file system structure

The Gui saves an experiment (i.e. a data collection) into file system following a hierarchy of folders and files. In this structure, an experiment is a folder, and beamline data, ccd data, leem data, scan data, comments, and images are represented by files. The figure 1 shows this kind of structure.

The user only defines the location of the data root folder; the system automatically defines the other file names according to the following schemes:

Experiment folder name
<experiment date>_<progressive number>
where <experiment date> = YYYY_MM_DD and <progressive number>= NNN
examples: 2001_09_21_001, 2001_09_21_002, 2001_09_21_003, ...

Beamline data file name
<experiment folder name>_beam#<progressive number>.txt
examples: 2001_09_21_018_beam#000.txt, 2001_09_21_018_beam#001.txt, ...

CCD data file name
<experiment folder name>_ccd#<progressive number>.txt
examples: 2001_09_21_018_ccd#000.txt, 2001_09_21_018_ccd#001.txt, ...

LEEM data file name
<experiment folder name>_leem#<progressive number>.txt
examples: 2001_09_21_018_leem#000.txt, 2001_09_21_018_leem#001.txt, ...

Image file name
<experiment folder name>#<progressive number>.png
examples: 2001_09_18_001#000.png, 2001_09_18_001#001.png, ....

Comments file
from the Acquire Single Image panel the user can write a comment. In this case the Gui saves a text file with the following syntax: <experiment foldername>_comment#<progressive number>.txt.
From a jython script, the user can write one (or more) text file containing any kind of things such as image array values, comments, parameters value, etc. This user file can be saved by the jython script both with a standard nameor with a custom name

The format of the standard experiment files is a list of comma separated pairs <parameter_name>, <parameter_value> but from a jython script you can write your custom format.

 

Image format

Images acquired from the ccd detector have up to 16 bits per pixel so the ideal would be to save the images in a 16 bit GRAY-SCALE format. Unfortunately, to our knowledge with Java it is not possible to save 16 bit images. However, it is possible to save a 16 bit image using two channels of 8 bit RGB. Figure 2 explains this concept.

Now, if you display an image of this kind with joint G and B channels, you will see a blue-green palette image with much more shades than the simple 8 bit gray scale image you can see on your computer screen (the computer screen visualizes images always with 8 bit per channel, that means also a 16 bit gray-scale image is displayed as an 8 bit gray-scale image on a computer screen). Therefore the Gui saves also a 8-bit gray scale image (the result of a 16-bit to 8-bit fitting process) into the R channel. To recover the 16 bit values acquired by the ccd detector you must do a transformation of this kind: Image = (G*256)+B.
If you want just to see the gray scale image you have simply to recover thered channel of the png image.
Figure 3 shows the fit image concept:

A fitted image is obtained by a transformation like this: ((PIXVAL - MINPIX)*255)/(MAXPIX-MINPIX)